Biology subjects

Kaur, J.

Publications and source records attributed to Kaur, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Conformational plasticity of LptC regulates lipopolysaccharide transportby the LptB2FGC complex

The outer membrane of Gram-negative bacteria is coated with lipopolysaccharide (LPS). The Lpt system maintains membrane asymmetry by transporting LPS from the inner to the outer membrane. Transport begins with the LptB2FGC complex, where the ABC transporter LptB2FG associates with LptC to extract LPS. LPS is then passed via LptA to the LptDE translocon. While LptB2FGC structures suggest an extrusion mechanism, the role of LptC remains unclear. Here, we reconstituted the complex in vitro from purified LptB2FG and LptC, and demonstrate that LptC stabilizes the complex and modulates ATPase activity. Using differential isotope labeling and solid-state NMR including dynamic nuclear polarization, we observed that the LptC transmembrane helix LptCTMH is tightly associated with the transporter in the apo state. Upon LPS or ATP binding, LptCTMH becomes dynamic, favoring cavity collapse and substrate-coupled ATPase activity. Our data support a model in which LptC acts as a mechanical transducer linking transport and energy consumption.

biophysics↗

bioRxiv2025

Electrocorticographic Detection of Speech Networks in Glioma-infiltrated Cortex

Direct cortical stimulation (DCS) is the clinical gold standard for identifying functional cortex in the human brain, which is essential for the safe removal of brain lesions. Defining the electro-physiological properties of DCS- positive cortical regions may facilitate the identification of critical language regions, thereby permitting safe glioma resections in communities without access. Leveraging a multicenter electrophysiologic dataset of DCS- positive language regions spatially matched with subdural arrays, we analyzed regions identified as functionally critical (DCS+) versus functionally non-critical (DCS-) during intraoperative language mapping. In IDH-mutant gliomas, DCS+ regions exhibited significantly greater speech-related neural activity and enhanced encoding and decoding of linguistic and semantic features. We demonstrate that resting-state classifiers distinguish DCS+ from DCS- regions in IDH-mutant tumors. Task-based and resting-state electrophysiologic distinctions were pathology-specific and not present in IDH-wildtype glioblastomas. These findings may accelerate DCS mapping by guiding surgeons to priority regions, improving efficiency, and patient outcomes.

neuroscience↗

bioRxiv2025

Aperiodic neural dynamics define a novel signature of glioma-induced excitation-inhibition dysregulation

Diffuse gliomas remodel neuronal circuits with prognostic and therapeutic significance for patients. Electrophysiologic measures of cortical excitability hold promise for monitoring disease progression and evaluating therapeutic responses. The power law exponent (aperiodic slope) reflects the balance between excitatory and inhibitory activity within neuronal networks, a critical aspect of normal brain function often disrupted in neurological conditions. Despite its potential, the significance of the aperiodic slope in glioma-infiltrated tissue and its underlying cellular processes has not been fully investigated. Here, we integrate multi-modal electrophysiological analysis with transcriptomic profiling to analyze the aperiodic slope in both normal and glioma-infiltrated cortex. We determine that glioma infiltration induces a flattening of the aperiodic slope, indicating a shift toward excitation dominance that varies according to tumor subtype and correlates with impairments in semantic naming. Single-nucleus RNA sequencing revealed that cortical regions with flat aperiodic slope exhibit transcriptional programs enriched in glutamatergic signaling, membrane depolarization, and excitatory synaptic transmission. The aperiodic slope responds to pharmacologically induced changes in cortical inhibition during propofol administration, a GABAA agonist. Our results establish the aperiodic slope as a robust biomarker of glioma-associated excitation-inhibition imbalance, with potential applications in tumor classification and treatment monitoring.

cancer biology↗

bioRxiv2025

Clinical and Genomic Characterization of Recalcitrant Enterococcal Bacteremia: A Multicenter Prospective Cohort Study (VENOUS)

BackgroundPatients with recalcitrant enterococcal bloodstream infections are at greater risk of adverse outcomes. We identified patients in the 2016-2022 Vancomycin-Resistant Enterococcal Bacteremia Outcomes Study (VENOUS) cohort experiencing recalcitrant bloodstream infections for further clinical and genomic characterization. MethodsBacteremia episodes were considered "persistent" if there was a lack of clearance on day four while receiving [≥] 48 hours of active therapy and recurrent if there was clearance during hospitalization with a subsequent positive culture (collectively, "recalcitrant" bacteremia). A matched comparison group of non-recalcitrant bacteremia patients was chosen in a 2:1 control:case ratio. Isolates were subjected to short- and long-read whole-genome sequencing. Hybrid assemblies were created using a custom pipeline. Findings. A total of 46 recalcitrant infections from 41 patients were identified. Patients with persistent bacteremia were more often admitted to the ICU upon admission relative to controls. E. faecalis strains causing persistent infections had a significantly higher proportion of genes associated with carbohydrate utilization relative to controls. Representation of functional groups associated with mutated genes was disparate between E. faecium and E. faecalis index and persistent isolates, suggesting species-specific adaptation. DiscussionEnterococcal isolates causing recalcitrant bacteremia were genomically diverse, indicating that strain-specific signatures are not drivers of persistence. However, comparisons of index vs. persistent isolates revealed that E. faecium may be genetically pre-adapted to cause persistent infection, and site-specific structural variation during infection suggests the role of differential gene expression in adaptation and persistence. This data lays groundwork for future studies to define signatures of enterococcal adaptation during bacteremia.

genomics↗

bioRxiv2025

Common and distinct neural mechanisms of aversive and appetitive pain-related learning

Appetitive and aversive conditioning are both fundamental to adaptive behaviour, yet there remains limited understanding of how they differ on the behavioural and neural level. We investigated the two processes during acquisition and extinction using functional magnetic resonance imaging and behavioural measures. In a within-subject differential conditioning paradigm (preregistration DRKS00027448), aversive learning was induced by pairing visual cues with a temperature increase (pain rise), while appetitive learning involved a temperature decrease (pain reduction). Valence and contingency ratings confirmed successful learning for both types of learning, though only the appetitive condition showed a return to baseline ratings during extinction, suggesting incomplete extinction in the aversive condition. On the neural level, both engaged the visual cortex during acquisition (with increased functional connectivity with the right frontal operculum) and the ventromedial prefrontal cortex (vmPFC) during extinction. However, aversive learning showed a stronger activation increase in the mediodorsal thalamus with heightened connectivity with the locus coeruleus during acquisition, as well as sustained parahippocampal activity during extinction. Moreover, incomplete extinction in the aversive condition (as indicated by contingency ratings) was associated with sustained activity in the visual cortex during pain anticipation. These results suggest that while appetitive and aversive learning share activation in regions involved in sensory processing (occipital lobe) and learning (vmPFC), aversive learning uniquely engages areas promoting rapid acquisition (mediodorsal thalamus and locus coeruleus) and cautious unlearning, in line with the notion of a better-safe-than-sorry strategy.

neuroscience↗

bioRxiv2025

Feeding niches drive specialist herbivore responses of conspecific insects to plant defenses in biocontrol

O_LIBiological invasions threaten global ecosystems and economies, prompting the need for sustainable management approaches such as releasing natural enemies from the native range (i.e., classical biological control; CBC). While the release of multiple natural enemies can enhance the effectiveness of CBC, interactions between these agents and their host plants defenses are poorly understood. C_LIO_LIThis study explored the interactions between two congeneric specialist herbivores introduced for the control of Dioscorea bulbifera (air potato) in Florida, USA: Lilioceris cheni (Coleoptera: Chrysomelidae), which feeds primarily on leaves and L. egena, which feeds primarily on the aerial reproductive structures (i.e., bulbils). Specifically, we investigated whether foliar herbivory by L. cheni or induced defenses by jasmonic acid (JA) or salicylic acid (SA) influenced L. egenas feeding behavior and performance on bulbils. C_LIO_LIWe conducted feeding assays to measure bulbil consumption and its relationship to pupal mass and adult eclosion as indicators of beetle performance. Additionally, we performed dose-dependent feeding assays to test how varying concentrations of saponins, a key defense compound in air potato, influenced feeding and survival of L. cheni and L. egena. C_LIO_LIOur results indicated no significant differences in bulbil feeding by L. egena across treatments; however, SA-treated plants produced significantly heavier pupae and adults compared to controls. Dose-response assays revealed non-linear, hump-shaped, feeding and survival patterns in L. cheni, while L. egena experienced reduced feeding and survival with increasing saponin concentrations. C_LIO_LIThese findings suggest that the two beetles respond differently to plant defenses while occupying distinct feeding niches, likely allowing for additive impacts on D. bulbifera. This study provides insights into the role of plant defenses in CBC and informs strategies to optimize biocontrol programs for invasive species management. C_LI

ecology↗

bioRxiv2025

Epigenetic Modulation of Host Immunity related genes in Pulmonary Tuberculosis: A Comprehensive Analysis of DNA Methylation Profiles in Peripheral Blood Mononuclear Cells

BackgroundIn the last few years, there has been increasing evidence in the literature for promoter hypermethylation of various host genes following infection with various pathogens. Therefore, in the present study, the role of epigenetic reprogramming of host cells through DNA methylation was evaluated which indicates that the disease progression takes place through changes in host immune response related genes. ObjectiveTo elucidate the differential genome-wide DNA methylation profile of peripheral blood mononuclear cells in pulmonary tuberculosis (PTB) patients. Materials and methodsTo decipher the methylation profile of PBMCs in PTB patients whole genome bisulphite sequencing was performed using 4 DNA samples from each study group i.e. PTB, healthy controls and diseased controls. Briefly, the samples were subjected to bisulphite conversion followed by library preparation and whole genome bisulphite sequencing. The data then were analysed for differential methylation analysis followed by gene set enrichment analysis to select DMRs for validation by sanger sequencing. Further the GEOR2 online server was used to investigate the mRNA expression of selected genes associated with hypermethylated DMRs in promoter region. ResultsDifferential methylation region analysis was performed for the following comparisons. TB v/s Diseased (Hypermethylated=1756; Hypomethylated=1886), TB v/s Healthy( Hypermethylated=2203; Hypomethylated=2466), Diseased v/s Healthy ( Hypermethylated=1656; Hypomethylated=3936). Further gene set enrichment analysis showed that the hypermetylated regions belonged to genes that are involved in immune responses mainly T cell functioning and T cell mediated immune processes. There were 8 DMR belonging to TAF8,FZD5, HLA-DRB, MIR483, PVRIG, SH2B2, ZAP70, TNFRSF13C simultaneously (n=10 from each study group). mRNA expression analysis with GEOR2 (Datasets used n= 12) revealed significant downregulation of TNFRSF13C, ZAP70, PVRIG Among the selected genes associated with hypermethylated DMRs in promoter region. (e) ConclusionThe altered differential methylation profile of PBMCs from TB patients shows that on onset the active disease there occurs aberrant methylation of expression regulating regions that in turn results in decreased T cell functions and hence suboptimal immune responses in TB

molecular biology↗

bioRxiv2024

Synovial fluid transcriptome dynamics in osteoarthritis progression: Implications in pathogenesis

BackgroundOsteoarthritis, a degenerative joint disease associated with various pathological manifestations in the joint including cartilage loss, alterations in subchondral bone and synovial inflammation. ObjectiveThis study aimed to elucidate the transcriptional and molecular changes in synovial fluid associated with OA progression, focusing on differential gene expression and pathway enrichment across OA grades. MethodologyPatients with different OA grades were recruited from PGIMER, Chandigarh, following the KL classification. Microarray analysis was conducted to study the transcriptional profiles in different OA grades using a fold-change (FC) cutoff of 2 and a p-value cutoff of 0.05, followed by pathway analysis performed using GSEA and STRING database. Selected genes from microarray and pathway analysis were validated using qRT-PCR. ResultsMicroarray analysis reveals distinct gene expression patterns corresponding to different OA stages (KL grade 2 to KL grade 4). Notably, the upregulation of AMTN and DKK2, alongside the downregulation of MSLN, highlighted their roles in pathological mineralization and disrupted bone remodeling in OA. Pathway enrichment analysis revealed significant changes in immune response, inflammation related pathways and cellular processes such as autophagy and programmed cell death, indicating their involvement in disease progression. Furthermore, mitochondrial dysfunction and impaired autophagy were linked to increased inflammation in advanced OA. ConclusionThese findings suggest that targeting mineralization and inflammatory pathways could offer novel therapeutic avenues for OA management.

pathology↗

bioRxiv2024

Replay of procedural experience is independent of the hippocampus

Sleep is critical for consolidating all forms of memory1-3, from episodic experience to the development of motor skills4-6. A core feature of the consolidation process is offline replay of neuronal firing patterns that occur during experience7,8. This replay is thought to originate in the hippocampus and trigger the reactivation of ensembles of cortical and subcortical neurons1,3,9-18. However, non-declarative memories do not require the hippocampus for learning or for sleep-dependent consolidation19-26 meaning what drives their consolidation is unknown. Here we show, using an unsupervised method, that replay occurs in the dorsal striatum of mice during offline consolidation of a non-declarative, procedural, memory and that this replay is generated independently of the hippocampus. Replay occurred at both real-world and time-compressed speeds and was also prioritised both at the level of the individual neurons and the type of neural sequence. Complete bilateral lesions of the hippocampus had no effect on any feature of this replay. Our results demonstrate that procedural replay during consolidation of a non-declarative memory is independent of the hippocampus. These results support the view that replay drives active consolidation of all types of memory during sleep but challenges the idea that the hippocampus is the source of this replay.

neuroscience↗

bioRxiv2024

Integrative spatial omics reveals distinct tumor-promoting multicellular niches and immunosuppressive mechanisms in African American and European American patients with TNBC

Racial disparities in the clinical outcomes of triple-negative breast cancer (TNBC) have been well-documented, but the underlying biological mechanisms remain poorly understood. To investigate these disparities, we employed a multi-omic approach integrating imaging mass cytometry and spatial transcriptomics to characterize the tumor microenvironment (TME) in self-identified Black American (BA) and White American (WA) TNBC patients. Our analysis revealed that the TME in BA patients is marked by a network of endothelial cells, macrophages, and mesenchymal-like cells, which correlates with reduced patient survival. In contrast, the WA TNBC microenvironment is enriched in T-cells and neutrophils, indicative of T-cell exhaustion and suppressed immune responses. Ligand-receptor and pathway analyses further demonstrated that BA TNBC tumors exhibit a relatively "immune-cold" profile, while WA TNBC tumors display features of an "inflamed" TME, suggesting the evolution of a unique immunosuppressive mechanism. These findings provide insight into racially distinct tumor-promoting and immunosuppressive microenvironments, which may contribute to the observed differences in clinical outcomes among BA and WA TNBC patients. Statement of SignificanceThis study identifies distinct tumor microenvironment (TME) profiles in Black and White American TNBC patients, providing new insights into the biological mechanisms driving outcome disparities. Our findings highlight the role of the tumor-endothelial-macrophage niche in these disparities, offering a potential therapeutic target for race-inclusive strategies aimed at improving clinical outcomes. By revealing racial differences in treatment response profiles, this work underscores the necessity for tailored therapies in TNBC. These insights lay the groundwork for the development of inclusive, precision-driven treatment approaches that may help mitigate racial disparities and enhance patient outcomes.

cancer biology↗

bioRxiv2023

SARS-CoV-2 antibodies cross-react and enhance dengue infection

The presence of non-neutralizing antibodies of any dengue serotype, increase the severity of subsequent infection by other dengue serotypes. During SARS-CoV-2 pandemic, the number of symptomatic dengue cases increased in India. We describe that antibodies isolated from convalescent plasma from COVID-19 patients enhances DENV2 infection in vitro. CR3022, one antibody against SARS-CoV-2 spike protein, also showed elevated DENV2 infection in vitro. In silico protein-protein interactions between the spike antibodies and the DENV2 E-protein revealed significant interactions. Likewise, few monoclonal/polyclonal antibodies against SARS-CoV-2 showed increased dengue infection in vitro. Importantly, the AG129 mice infected with SARS-CoV-2 three-weeks prior to DENV2 infection, showed elevated dengue pathogenesis. Thus, highlighting the possibilities of elevated infection and symptomatic dengue disease in COVID-19 survivors.

immunology↗

bioRxiv2023

Arrest of movement induced by Pedunculopontine-stimulation obstructs hippocampal theta rhythm

Complete movement arrest has recently been reported to be induced in rodents by optogenetic stimulation of a subpopulation within the pedunculopontine nucleus (PPN). This evoked arrest appears conspicuously similar to freezing behavior often seen as a fear response in prey animals but could also be akin to the freezing of gait, which is a symptom of Parkinsons disease. This introduces two perspectives on the functional roles of this sub-region: A hub for orchestrating fear-related responses or an omnipotent halting mechanism devoid of emotional components. To better understand this phenomenon and its cognitive component, we engage the distinct electrical brain activity, the hippocampal theta rhythm. This rhythm has a well-described contextual association between various aspects of cognition and behavior. It is prominent during locomotor activity in rodents and immobile yet aroused states like behavioral freezing. We recorded the electrical activity in the hippocampus of rats while walking and being arrested by PPN stimulation. A clear obstruction of the ongoing theta activity was associated with the motor arrest. The timescale of movement arrest was less than 200 ms, similar to the obstruction of the theta rhythm. Since, anxiety, fear, and behavioral freezing are associated with hippocampal theta rhythm, which we did not see during PPN stimulation, we suggest the induced motor arrest occurs without an associated emotional component.

neuroscience↗

bioRxiv2023

cTBS Over the Left Supplementary Motor Area (lSMA) Does Not Modulate Rhythmic Bimanual Coordination in the Presence and Absence of Visual Cues

Bimanual coordination modes, namely in-phase and anti-phase, represent two distinct movement patterns characterized by simultaneous & symmetrical movements of both hands and alternating complementary actions, respectively. These coordination modes are integral in various activities, such as playing musical instruments, typing, and participating in sports that demand precise hand-eye coordination. The objective of the present experiment was to investigate the impact of continuous theta burst stimulation (cTBS) targeting the left supplementary motor area (lSMA) on bimanual coordination during in/anti-phase coordination modes. To explore this, we utilized a steady-state system of coordination dynamics and evaluated the continuous relative phase ({phi}) and variability of relative phase (SD{phi}) during cued and non-cued trials in both pre- and post-transcranial magnetic stimulation (TMS) conditions. The results revealed that visual cues (cued trials) significantly enhanced bimanual coordination performance in both in/anti-phase coordination modes. However, contrary to expectations, the downregulation of lSMA through cTBS did not lead to significant disruptions in movement during in/anti-phase bimanual coordination in pre- and post-TMS stimulation. Potential factors for the lack of observed effects include methodological limitations, individual differences, and functional redundancy within the motor system. Further research is needed to optimize stimulation parameters, increase sample sizes, and explore the interactions between the lSMA, and other brain regions involved in motor control to gain a comprehensive understanding of the contributions of the lSMA in bimanual coordination.

neuroscience↗

bioRxiv2023

Development of Fully Human, Bispecific Antibodies that Effectively Block Omicron Variant Pseudovirus Infections

The emergence of highly immune invasive and transmissible variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has decreased the effectiveness of existing vaccines. It is, therefore, critical to develop effective and safe therapeutics for SARS-CoV-2 infections, especially for the most vulnerable and immunocompromised patients. Neutralizing antibodies have been shown to be successful at preventing severe disease from early SARS-CoV-2 strains, although their efficacy has diminished with the emergence of new variants. Here, we aim to develop fully human and broadly neutralizing monoclonal (mAb) and bispecific (BsAb) antibodies against SARS-CoV-2 and its variants. Specifically, we first identified two antibodies from human transgenic mice that bind to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein and are capable of neutralizing SARS-CoV-2 and variants of concern with high to moderate affinity. Two non-competing clones with the highest affinity and functional blocking of ACE2 binding were then selected to be engineered into two BsAbs, which were then demonstrated to have relatively improved affinity, ACE2 blocking ability, and pseudovirus inhibition against several variants, including Omicron (B.1.1.529). Our findings provide one mAb candidate and two bsAb candidates for consideration of further clinical development and suggest that the bispecific format may be more effective than mAbs for SARS-CoV-2 treatment.

biochemistry↗

bioRxiv2023

In vitro and in vivo effects of zoledronate on senescence and senescence-associated secretory phenotype markers

In addition to reducing fracture risk, zoledronate has been found in some studies to decrease mortality in humans and extend lifespan and healthspan in animals. Because senescent cells accumulate with aging and contribute to multiple co-morbidities, the non-skeletal actions of zoledronate could be due to senolytic (killing of senescent cells) or senomorphic (inhibition of the secretion of the senescence-associated secretory phenotype [SASP]) actions. To test this, we first performed in vitro senescence assays using human lung fibroblasts and DNA repair-deficient mouse embryonic fibroblasts, which demonstrated that zoledronate killed senescent cells with minimal effects on non-senescent cells. Next, in aged mice treated with zoledronate or vehicle for 8 weeks, zoledronate significantly reduced circulating SASP factors, including CCL7, IL-1{beta}, TNFRSF1A, and TGF{beta}1 and improved grip strength. Analysis of publicly available RNAseq data from CD115+ (CSF1R/c-fms+) pre-osteoclastic cells isolated from mice treated with zoledronate demonstrated a significant downregulation of senescence/SASP genes (SenMayo). To establish that these cells are potential senolytic/senomorphic targets of zoledronate, we used single cell proteomic analysis (cytometry by time of flight [CyTOF]) and demonstrated that zoledronate significantly reduced the number of pre-osteoclastic (CD115+/CD3e-/Ly6G-/CD45R-) cells and decreased protein levels of p16, p21, and SASP markers in these cells without affecting other immune cell populations. Collectively, our findings demonstrate that zoledronate has senolytic effects in vitro and modulates senescence/SASP biomarkers in vivo. These data point to the need for additional studies testing zoledronate and/or other bisphosphonate derivatives for senotherapeutic efficacy.

physiology↗

bioRxiv2023

CVD-associated SNPs with regulatory potential drive pathologic non-coding RNA expression

BackgroundCardiovascular diseases (CVDs) are the leading cause of death worldwide. Genome-wide association studies (GWAS) have identified many single nucleotide polymorphisms (SNPs) appearing in non-coding genomic regions in CVDs. The SNPs may alter gene expression by modifying transcription factor (TF) binding sites and lead to functional consequences in cardiovascular traits or diseases. To understand the underlying molecular mechanisms, it is crucial to identify which variations are involved and how they affect TF binding. MethodsThe SNEEP (SNP exploration and analysis using epigenomics data) pipeline was used to identify regulatory SNPs, which alter the binding behavior of TFs and link GWAS SNPs to their potential target genes for six CVDs. The human induced pluripotent stem cells derived cardiomyocytes (hiPSC-CMs), monoculture cardiac organoids (MCOs) and self-organized cardiac organoids (SCOs) were used in the study. Gene expression, cardiomyocyte size and cardiac contractility were assessed. ResultsBy using our integrative computational pipeline, we identified 1905 regulatory SNPs in CVD GWAS data. These were associated with hundreds of genes, half of them non-coding RNAs (ncRNAs), suggesting novel CVD genes. We experimentally tested 40 CVD-associated non-coding RNAs, among them RP11-98F14.11, RPL23AP92, IGBP1P1, and CTD-2383I20.1, which were upregulated in hiPSC-CMs, MCOs and SCOs under hypoxic conditions. Further experiments showed that IGBP1P1 depletion rescued expression of hypertrophic marker genes, reduced hypoxia-induced cardiomyocyte size and improved hypoxia-reduced cardiac contractility in hiPSC-CMs and MCOs. ConclusionsIGBP1P1 is a novel ncRNA with key regulatory functions in modulating cardiomyocyte size and cardiac function in our disease models. Our data suggest ncRNA IGBP1P1 as a potential therapeutic target to improve cardiac function in CVDs.

genomics↗

bioRxiv2023

Multiparametric senescent cell phenotyping reveals CD24 osteolineage cells as targets of senolytic therapy in the aged murine skeleton

Senescence drives organismal aging, yet the deep characterization of senescent cells in vivo remains incomplete. Here, we applied mass cytometry by time-of-flight (CyTOF) using carefully validated antibodies to analyze senescent cells at single-cell resolution. We used multiple criteria to identify senescent mesenchymal cells that were growth arrested and resistant to apoptosis (p16+/Ki67-/BCL-2+; "p16KB" cells). These cells were highly enriched for senescence-associated secretory phenotype (SASP) and DNA damage markers and were strongly associated with age. p16KB cell percentages were also increased in CD24+ osteolineage cells, which exhibited an inflammatory SASP in aged mice and were robustly cleared by both genetic and pharmacologic senolytic therapies. Following isolation, CD24+ skeletal cells exhibited growth arrest, SA-{beta}gal positivity, and impaired osteogenesis in vitro. These studies thus provide a new approach using multiplexed protein profiling by CyTOF to define senescent mesenchymal cells in vivo and identify a highly inflammatory, senescent CD24+ osteolineage population cleared by senolytics.

cell biology↗

bioRxiv2022

Comparative genomics and integrated system biology approach unveiled undirected phylogeny patterns, mutational hot spots, functional patterns and molecule repurposing for monkey pox virus

Monkeypox is a viral zoonosis with symptoms that are reminiscent to those experienced in previous smallpox cases. GSAID databases (Global Initiative on Sharing Avian Influenza Data) was used to assess 630 genomes of MPXV. Six primary clades were inferred from the phylogenetic study, coupled with a lesser percentage in radiating clades. Individual clades that make up various nationalities may have formed as a result of a particular SNP hotspot type, which may have mutated in a particular population type. The most significant mutation, based on a mutational hotspot analysis, was found at G3729A and G5143A. The gene ORF138, which encodes the Ankyrin repeat (ANK) protein, was found to have the most mutations. This protein is known to mediate molecular recognition via protein-protein interactions. It was shown that 243 host proteins interacted with 10 monkeypox proteins identified as the hub proteins E3, SPI2, C5, K7, E8, G6, N2, B14, CRMB, and A41 through 262 direct connections. The interaction with chemokine system-related proteins provides further evidence that the human protein is being suppressed by the monkey pox virus in order to facilitate its survival against innate immunity. A few FDA-approved molecules were likely used as possible inhibitors after being researched for blocking F13, a significant envelope protein on the membrane of extracellular versions of virus. A total of 2500 putative ligands were docked individually with the F13 protein. The F13 protein and these molecules interaction may help prevent the monkey pox virus from spreading. As a result, after being confirmed by experiments, these putative inhibitors might have an impact on the activity of these proteins and be utilised in monkeypox treatments.

genomics↗