Biology subjects

Gupta, M. K.

Publications and source records attributed to Gupta, M. K..

At least 19 recordsLinked to original sources

bioRxiv2026

Species Distribution, Antifungal Susceptibility, and Machine Learning-Based Prediction of Optimal Therapies Against Candida Species

Invasive candidiasis has become more common in recent decades, particularly within ICUs. Identifying specific Candida spp., and testing their sensitivity to antifungal drugs is crucial for effective treatment that helps healthcare providers to detect potential treatment challenges early. This study aimed to identify Candida spp. at their spp. level present in blood, assess their susceptibility to antifungal agents, and apply a random forest classifier to predict the best antifungal drug for a given species. The isolates were classified at the species complex level through MALDI-TOF MS. The strains' susceptibility to antifungal agents such as AMB, FLZ, VOZ, ITZ, POZ, CAS, MFN, and ANF was assessed using CLSI guidelines. Out of the 354 Candida spp. isolated from blood, C. utilis was found to be the predominant species, followed by C. tropicalis, and C. albicans. This study demonstrated that MFN and ANF exhibited high potency, with an impressive MIC90 of 0.12 {micro}g/mL against all isolates, surpassing CAS, which had a slightly higher overall MIC90 of 0.25 {micro}g/mL. FLZ exhibited the highest MIC90 value among the azoles at 16 {micro}g/mL, while VOZ, ITZ, and POZ all had MIC90 values of 0.5 {micro}g/mL. AMB MIC90 values were 2 {micro}g/mL against all isolated Candida species. The Random Forest AI/ML model showed perfect overall prediction, with the actual and predicted best antifungal drugs matching for all fungal species. This study is particularly essential because rare Candida spp. becoming more common and exhibiting higher MICs to AMB and FLZ and required suitable remedies for controlling the infection.

microbiology↗

bioRxiv2026

HR-FRGS: A Novel Biomarker Discovery Protocol using Dual Layer Hypergraph Learning for NGS RNA Sequence Data

Biomarker discovery from high-dimensional RNA sequencing data remains challenging. Conventional methods such as differential expression analysis, pairwise protein-protein interaction networks, and weighted gene co-expression network analysis suffer from false-positive interactions, transitivity-driven noise, and arbitrary thresholds for feature selection. Addressing these limitations, this study proposed a novel framework, Hypergraph Regularised Fuzzy Rough Gene Selection (HR-FRGS), for knowledge-driven biomarker discovery. This pipeline integrates information-rich protein clustering with entropy filtering and PPI-pruned co-expression interactions to form a dual-layer hypergraph. A hypergraph-based scoring method that combines Random Walk with Restart diffusion and Hypergraph Betweenness Centrality is used to identify genes that are central in the biological network. Furthermore an autonomous fuzzy rough set selection eliminates arbitrary threshold dependency for gene selection. HR-FRGS was applied to four TCGA cancer cohorts: Lung Adenocarcinoma, Head and Neck Cancer, Kidney Clear Cell Carcinoma, and Colon Cancer, which reduced over 60,000 transcripts to compact biomarker panels. Validation using classical Machine Learning algorithms with cross-validation demonstrated that biomarker panels matched or exceeded the classification performance of the full transcriptome (AUC > 0.99, MCC > 0.94) and confirmed generalizability (MCC $\geq$ 0.893). Benchmarking against baseline methods and an ablation study showed the contribution of major parts of the algorithm. Functional enrichment analysis captures established pan-cancer hallmarks and cohort-specific oncogenic mechanisms, confirming the biological relevance of the identified genes.

bioinformatics↗

bioRxiv2026

In Vitro and Computational Evaluation of Thrombolytic Activity of Kinemakinase of Kinema, an Indigenous Fermented Food of Eastern Nepal

Kinema is a traditional fermented soybean food indigenous to the eastern Himalayan regions of Nepal and India. The fermentation process is primarily mediated by the bacterium Bacillus subtilis, which produces several bioactive compounds and enzymes with potential therapeutic applications. Considering the growing burden of cardiovascular diseases and the need for effective fibrinolytic agents for thrombolytic therapy, this study aimed to extract, partially purify, and evaluate the thrombolytic potential of kinemakinase derived from kinema prepared from white soybeans. Partial purification of the enzyme was achieved using ammonium sulfate precipitation. Thrombolytic activity was assessed in vitro using human blood clots, where three enzyme dilutions demonstrated clot lysis ranging from 66% to 68%, indicating considerable fibrinolytic potential. In silico analyses were also performed to investigate the structural and functional characteristics of the enzyme. The tertiary structure obtained from UniProt was modeled using the Robetta server and refined with GalaxyRefine. Docking with fibrin using ClusPro 2.0 and molecular dynamics simulations using iMODS confirmed favorable interaction and structural stability, while disulfide engineering enhanced protein stability. The findings suggest that kinema-derived kinemakinase may serve as a promising alternative thrombolytic agent, warranting further biochemical characterization and dosage optimization. Keywords: Kinema, Kinemakinase, Thrombolytic activity, Bacillus subtilis, Fermentation

microbiology↗

bioRxiv2026

Decoupling T Cell Cytotoxicity: A CCL21+ICAM1-Based Synthetic Immune Niche Enhances Tumor Elimination by Accelerating Lytic Hit Delivery

Preserving T cell cytotoxic function during ex vivo expansion remains a major challenge for adoptive cancer immunotherapy. A synthetic immune niche (SIN) composed of immobilized CCL21 and ICAM1 was shown to improve T cell expansion while preserving cytotoxicity; however, it remains unclear which specific step of the T cell killing process is enhanced by the SIN stimulation. Here, we combined advanced imaging based on time-lapse microscopy with a mean-field model to analyze the distinct stages in killing of B16 melanoma cells by CD8+ T cells. This framework enabled us to resolve the tumor cell killing process into discrete steps throughout target cell engagement with SIN-treated T cells and lytic hit delivery. We found that tumor cell death is best explained by a multi-hit process, requiring approximately four discrete hits to trigger cell death. Model-based analysis identified an increase in the lytic hit delivery as the parameter that best accounts for the enhanced cytotoxicity of SIN-treated T cells, a difference not explained by changes in target encounter frequency or conjugate stability. Global sensitivity analysis further showed that tumor control is more strongly improved by enhancing lytic hit delivery than by increasing target encounter rates. These findings fundamentally reorient our understanding of optimized T cell manufacturing, suggesting that the lytic execution step may be the primary rate-limiting bottleneck in this in-vitro system, and that engineering strategies targeting granule polarization or discharge warrant prioritization alongside affinity-enhancement approaches.

immunology↗

bioRxiv2024

Enhancing HBV-specific T cell responses through a combination of epigenetic modulation and immune checkpoint inhibition

ObjectiveChronic hepatitis B virus (HBV) infection results in the exhaustion of HBV-specific T cells and the development of epigenetic imprints that impair immune responses and limit the effectiveness of immune checkpoint inhibitor (ICI) monotherapy, such as PD-L1. This study aimed to determine whether the DNA methyltransferase inhibitor decitabine (DAC) can reverse these epigenetic imprints and enhance the efficacy of ICI in restoring HBV-specific T cell responses. MethodsWe investigated HBV-specific CD4+ and CD8+ T cell responses by 10-day in vitro stimulation of peripheral blood mononuclear cells (PBMCs) from patients with chronic HBV infection. PBMCs were stimulated with HBV core-specific overlapping peptide pools and HLA-A*02-restricted peptides, including core18 and pol455. The immunomodulatory effect of the combination of DAC/PD-L1 was assessed via flow cytometry. Responder stratification was investigated by comparison of clinical characteristics, ex vivo DNA methylation analysis of PBMCs, and determination of IFN{gamma} plasma levels. ResultsTreatment with DAC and PD-L1 enhanced HBV-specific CD4+ T cell responses in a significant proportion of 53 patients, albeit with variability. The effect was independent of the HBcrAg level. Ex vivo DNA methylation revealed hypermethylation of key genes like IFNG among DAC-responders versus non-responders, supported by altered ex vivo IFN{gamma} plasma levels. Further analysis of HBV-specific CD8+ T cell responses in 22 HLA-A*02-positive patients indicated distinct response patterns between HBV-core18- and HBV-pol455-specific T cells, with pol455-specific CD8+ T cells showing increased susceptibility to DAC/PD-L1, surpassing PD-L1 monotherapy response. ConclusionsThe combination of DAC and PD-L1 shows promising effects in improving HBV-specific T cell responses in vitro. Our study highlights the potential of remodeling exhaustion-associated epigenetic signatures to enhance HBV-specific T cell restoration, suggesting a novel immunotherapeutic avenue for chronic HBV infections. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=129 SRC="FIGDIR/small/611632v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@156d0fborg.highwire.dtl.DTLVardef@b22d2corg.highwire.dtl.DTLVardef@1b3c4e2org.highwire.dtl.DTLVardef@1430bbf_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIRemodeling epigenetic signatures with a DNA methyltransferase inhibitor enhances the effectiveness of immune checkpoint inhibition in restoring HBV-specific T cell responses. C_LIO_LIResponsiveness is associated with specific IFN{gamma} DNA methylation patterns and plasma levels. C_LIO_LIEpigenetic remodeling had distinct effects on two CD8 T cell epitopes, with more pronounced effects on HBV-pol455-specific CD8+ T cell responses. C_LI

immunology↗

bioRxiv2024

Polymeric Micellar Nanoparticles Enable Image-guided Drug Delivery in Solid Tumors

We report the development of a nanotechnology to co-deliver chemocoxib A with a reactive oxygen species (ROS)-activatable and COX-2 targeted pro-fluorescent probe, fluorocoxib Q (FQ) enabling real time visualization of COX-2 and CA drug delivery into solid cancers, using a di-block PPS135-b-POEGA17 copolymer, selected for its intrinsic responsiveness to elevated reactive oxygen species (ROS), a key trait of the tumor microenvironment. FQ and CA were synthesized independently, then co-encapsulated within micellar PPS135-b-POEGA17 co-polymeric nanoparticles (FQ-CA-NPs), and were assessed for cargo concentration, hydrodynamic diameter, zeta potential, and ROS-dependent cargo release. The uptake of FQ-CA-NPs in mouse mammary cancer cells and cargo release was assessed by fluorescence microscopy. Intravenous delivery of FQ-CA-NPs to mice harboring orthotopic mammary tumors, followed by vital optimal imaging, was used to assess delivery to tumors in vivo. The CA-FQ-NPs exhibited a hydrodynamic diameter of 109.2 {+/-} 4.1 nm and a zeta potential ({zeta}) of -1.59 {+/-} 0.3 mV. Fluorescence microscopy showed ROS-dependent cargo release by FQ-CA-NPs in 4T1 cells, decreasing growth of 4T1 breast cancer cells, but not affecting growth of primary human mammary epithelial cells (HMECs). NP-derived fluorescence was detected in mammary tumors, but not in healthy organs. Tumor LC-MS/MS analysis identified both CA (2.38 nmol/g tumor tissue) and FQ (0.115 nmol/g tumor tissue), confirming the FQ-mediated image guidance of CA delivery in solid tumors. Thus, co-encapsulation of FQ and CA into micellar nanoparticles (FQ-CA-NPs) enabled ROS-sensitive drug release and COX-2-targeted visualization of solid tumors.

bioengineering↗

bioRxiv2023

Cell-Free Protein Expression in Polymer Materials

While synthetic biology has advanced complex capabilities like sensing and molecule synthesis in aqueous solutions, important applications may also be pursued for biological systems in solid materials. Harsh processing conditions used to produce many synthetic materials such as plastics makes incorporation of biological functionality challenging. One technology that shows promise in circumventing these issues is cell-free protein synthesis (CFPS), where core cellular functionality is reconstituted outside the cell. CFPS enables genetic functions to be implemented without the complications of membrane transport or concerns over cellular viability or release of genetically modified organisms. Here we demonstrate that dried CFPS reactions have remarkable tolerance to heat and organic solvent exposure during the casting processes for polymer materials. We demonstrate the utility of this observation by creating plastics that have spatially patterned genetic functionality, produce antimicrobials in situ, and perform sensing reactions. The resulting materials unlock the potential to deliver DNA-programmable bio-functionality in a ubiquitous class of synthetic materials.

synthetic biology↗

bioRxiv2022

Evaluation of the safety, immunogenicity and efficacy of a new live-attenuated lumpy skin disease vaccine in India

Lumpy skin disease (LSD) was reported for the first time in India in 2019 and since then, it has become endemic. Since a homologous (LSD-virus based) vaccine was not available in the country, goatpox virus (GPV)-based heterologous vaccine was authorized for mass immunization against LSD in cattle. This study describes the evaluation of safety, immunogenicity and efficacy of a new live-attenuated LSD vaccine developed using an Indian field strain (LSDV/India/2019/Ranchi). The virus was attenuated by continuous passage (P=50) in Vero cells. The vaccine (50th LSDV passage in Vero cells, named as Lumpi-ProVacInd) did not induce any local or systemic reaction upon its experimental inoculation in calves (n=10). At day 30 post-vaccination (pv), the vaccinated animals were shown to develop antibody- and cell-mediated immune response and exhibited complete protection upon virulent LSDV challenge. We observed a minimum Neethling response (0.018% animals; 5 out of 26940 animals) of the vaccine in field trials among 26940 animals. There was no significant reduction in the milk yield in lactating animals (n=10108), besides there was no abortion or any other reproductive disorder in the pregnant animals (n=2889). Sero-conversion was observed in 85.18% animals in the field by day 30 pv.

microbiology↗

bioRxiv2022

A Bioinformatics Approach To Reveal Common Genes And Molecular Pathways Shared By Cutaneous Melanoma and Uveal Melanoma.

BackgroundMelanomas are highly aggressive in nature and are known for metastasis and death. Melanocytes that give rise to melanomas are neural crest progenitor-cells. Our research is primarily concerned with Uveal Melanoma (UM) and Cutaneous Melanoma (CM). Although they both share same melanocytic origin, but the biology of their respective is different. AimThe aim of our study is to recognize the common differentially expressed genes (DEGs) between UM and CM. MethodologyThe gene expression profile was downloaded from the GEO and analyzed by GEO2R for identification of DEGs. By applying DAVID, GO and KEGG, pathway enrichment analysis was performed. PPI of these DEGs was analyzed using STRING and visualized through Cytoscape and MCODE. Further, we utilized HPA and GEPIA to obtain Kaplan-Meier Graph for survival analysis in order to assess the prognostic value of hub genes. ResultsWe examined the UM and CM datasets and discovered three common upregulated and eight common downregulated DEGs for both the melanomas based on computational analysis. HMGCS1 and ELOVL5 were shown to be enriched in a variety of altered molecular pathways and pathways in cancer. Overexpression of HMGCS1 and ELOVL5 were linked to poor prognosis in CM. ConclusionOn computational evaluation, we found that HMGCS1 and ELOVL5 were upregulated in both of these melanomas. Enrichment analysis showed that these genes are involved in cancer metabolism pathway and associated with poor prognosis in CM. However, the molecular study of these genes in UM is limited. Therefore, a better understanding of the cancer metabolism pathways should be carried to pave the way for clinical benefits.

bioinformatics↗

bioRxiv2022

Protein-protein interaction map in pre-eclampsia through the interaction of hub genes, transcription factors and microRNAs

Pre-eclampsia causes complications in pregnancy and characterized by uremia, proteinuria and hypertension in unattended cases. Blood biomarkers for pre-eclampsia are lacking. In this study, microarray gene expression data from peripheral blood of pre-eclampsia women was analyzed. In our study we developed a combined network approach for hub node prediction regulated by transcription factors and microRNAs corresponding to pre-eclampsia. Differentially expressed genes (DEGs) interaction map was constructed using STRING database. JUN, RPL35, NDUFB2, ATP5I, UQCRQ, COX7C, and FN1 were predicted as potential novel hub genes. Pathway analysis showed metabolic pathways, cytokine signaling in the immune system, Wnt, and MAPK signaling pathways involvement in pre-eclampsia. Regulatory network analysis showed that transcription factors JUN and STAT1 were connected with hub nodes, and microRNAs (miRNAs) like hsa-miR-26b-5p and hsa-miR-155-5p. In conclusion, the expression pattern of hub genes, analyzed deciphers a molecular signature for understanding the pathophysiology of pre-eclampsia and prediction of biomarkers for diagnosis.

bioinformatics↗

bioRxiv2022

NaCl Triggers the Sessile-to-Motile Transition of Bacillus subtilis

Various chemical cues are known to alter the motile and sessile states of bacteria differentially and, in turn, the formation of biofilms. However, the underlying mechanisms at the cellular and molecular level remain less understood, which severely limits our ability to control biofilms. Here, we systematically studied the effects of NaCl on the dynamics of biofilm formation across various length scales and the associated changes in the regulation of gene expression in an undomesticated natural isolate of Bacillus subtilis. Interestingly, NaCl induced significant changes in the architecture of pellicles and yielded systematic increase in lateral expansion rates of biofilms when grown on an agar surface. At the microscopic level, both in the presence and absence of NaCl, bacteria displayed super-diffusive motion at times lesser than a second. However, at larger delay times, we observed an intriguing NaCl-induced transition from sub-diffusion behavior of individual bacterial cells to rapid diffusion behavior. In addition, NaCl reduced the dynamical heterogeneity of the bacterial cells within the biofilm. The reduced heterogeneity and the increased flagellation in a subpopulation of cells in the presence of NaCl corroborates well with the observed higher motility of the cells. Further, the cellular uptake of NaCl resulted in the downregulation of several genes underlying the formation of biofilms, revealing the role of chemical cues like NaCl in controlling the gene regulatory circuit underlying the sessile to motile transition. Our study opens a new avenue to decipher the competitive advantage provided to the subcellular populations by NaCl due to lifestyle switch in Bacillus subtilis.

microbiology↗

bioRxiv2021

Prediction of molecular markers of bovine mastitis by meta-analysis of differentially expressed genes using combined p-value and robust rank aggregation

Bovine mastitis causes significant economic loss to the dairy industry by affecting milk quality and quantity. E.coli and S.aureus are the two common mastitis-causing bacteria among the consortia of mastitis pathogens, wherein E.coli is an opportunistic environmental pathogen, and S.aureus is a contagious pathogen. This study was designed to predict molecular markers of bovine mastitis by meta-analysis of differentially expressed genes (DEG) in E.coli or S.aureus infected mammary epithelial cells (MECs) using p-value combination and robust rank aggregation (RRA) methods. High throughput transcriptome of bovine (MECs, infected with E.coli or S.aureus, were analyzed, and correlation of z-scores were computed for the expression datasets to identify the lineage profile and functional ontology of DEGs. Key pathways enriched in infected MECs were deciphered by Gene Set Enrichment Analysis (GSEA), following which combined p-value and RRA were used to perform DEG meta-analysis to limit type I error in the analysis. The miRNA-Gene networks were then built to uncover potential molecular markers of mastitis. Lineage profiling of MECs showed that the gene expression levels were associated with mammary tissue lineage. The up-regulated genes were enriched in immune-related pathways whereas down-regulated genes influenced the cellular processes. GSEA analysis of DEGs deciphered the involvement of Toll-like receptor (TLR), and NF- Kappa B signalling pathway during infection. Comparison after meta-analysis yielded with genes ZC3H12A, RND1 and MAP3K8 having significant expression levels in both E.coli and S.aureus dataset and on evaluating miRNA-Gene network 7 pairs were common to both sets identifying them as potential molecular markers.

molecular biology↗

bioRxiv2021

Stromal-cell deletion of STAT3 protects mice from kidney fibrosis by inhibiting pericytes trans-differentiation and migration

Signal transducer and activator of transcription 3 (STAT3) is a key transcription factor implicated in the pathogenesis of kidney fibrosis. Although tubular Stat3 deletion in tubular epithelial cells is known to protect mice from kidney fibrosis, the exact function of STAT3 in stromal cells remains unknown. We utilized stromal-cell Stat3 knock-out (KO) mice, CRISPR and pharmacologic activators and inhibitors of STAT3 to investigate its function in pericyte-like cells. STAT3 is phosphorylated in tubular epithelial cells in acute kidney injury whereas its activation expanded to interstitial cells in chronic kidney disease in mice and humans. Stromal cell-specific deletion of Stat3 protects mice from folic acid- and aristolochic acid-induced kidney fibrosis. Mechanistically, STAT3 directly regulates the inflammatory pathway, differentiation of pericytes into myofibroblasts. Specifically, STAT3 activation leads to an increase in migration and profibrotic signaling in genome-edited pericyte-like cells, 10T1/2. Conversely, Stat3 KO or blocking STAT3 function inhibits detachment, spreading, migration, and profibrotic signaling. Furthermore, STAT3 binds to Collagen1a1 promoter of fibrotic mouse kidneys and in pericyte-like cells. Together, our study identifies a previously unknown function of STAT3 in stromal cells that promotes kidney fibrosis and may have therapeutic value in fibrotic kidney disease. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=73 SRC="FIGDIR/small/456872v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@35dcbforg.highwire.dtl.DTLVardef@2fc055org.highwire.dtl.DTLVardef@fc0d92org.highwire.dtl.DTLVardef@1def2e6_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2021

ROS-Degradable Polythioketal Urethane Foam Dressings to Promote Porcine Skin Wound Repair

Impaired skin healing and progression into chronic wounds is a prevalent and growing medical problem. Porous, resorbable biomaterials can be used as temporary substrates placed into skin defects to support cell infiltration, neo-tissue formation, and remodeling of nonhealing wounds. Naturally-derived biomaterials have promising healing benefits, but their low mechanical properties and exuberant costs limit their performance and use. Synthetic materials can be affordably manufactured and tuned across a broader range of physiochemical properties, but opportunities remain for tailoring them for ideal host immune and regenerative responses. Polyesters are the most clinically-tested class of synthetic biomaterials, but their hydrolysis releases acidic degradation products that can cause autocatalytic degradation processes that are poorly controlled and are not tied to cellular or other biologic activities. Here, we systemically explored a series of ROS-degradable polythioketal (PTK) urethane (UR) foams with varied hydrophilicity as an alternative class of synthetic biomaterials for wound healing. It was found that the most hydrophilic PTK- UR variant, which had 7 ethylene glycol (EG7) repeats flanking each side of each thioketal bond, had the highest ROS reactivity of the PTK-URs tested. In an in vivo porcine excisional skin wound healing model, hydrophilic EG7 PTK-UR foams more effectively promoted tissue integration, ECM deposition, and re- epithelialization of full-thickness skin wound compared to more hydrophobic PTK-UR variants. Resolution of type 1 inflammation and lower foreign body response to scaffold remnants was also observed for EG7 versus more hydrophobic PTK-UR scaffolds. Finally, porcine wound healing studies showed that EG7 PTK-UR foams had similar wound healing response to a collagen-based clinical gold standard product, Integra Bilayer Wound Matrix (BWM), while outperforming polyester UR foam-based NovoSorb Biodegradable Temporizing Matrix (BTM) with respect to increased ECM production, vascularization, and biomaterial-associated immune phenotype. In sum, PTK-UR foams warrant further development toward a new class of synthetic biomaterial foams for skin wound healing applications.

bioengineering↗

bioRxiv2021

Engineering Gelation Kinetics in Living Silk Hydrogels by Differential Dynamic Microscopy Microrheology and Machine Learning

Microbes embedded in hydrogels comprise one form of living material. Discovering formulations that balance potentially competing mechanical and biological properties in living hydrogels--for example gel time of the hydrogel formulation and viability of the embedded organisms--can be challenging. In this work, a pipeline is developed to automate characterization of the gel time of hydrogel formulations. Using this pipeline, living materials comprised of enzymatically crosslinked silk and embedded E. coli--formulated from within a 4D parameter space--are engineered to gel within a pre-selected timeframe. Gelation time is estimated using a novel adaptation of microrheology analysis using differential dynamic microscopy (DDM). In order to expedite the discovery of gelation regime boundaries, Bayesian machine learning models are deployed with optimal decision-making under uncertainty. The rate of learning is observed to vary between AI-assisted planning and human planning, with the fastest rate occurring during AI-assisted planning following a round of human planning. For a subset of formulations gelling within a targeted timeframe of 5-15 minutes, fluorophore production within the embedded cells is substantially similar across treatments, evidencing that gel time can be tuned independent of other material properties--at least over a finite range--while maintaining biological activity.

bioengineering↗

bioRxiv2020

Isolation and characterization of lumpy skin disease virus from cattle in India

Lumpy skin disease (LSD) has devastating economic impact. During the last decade, LSD had spread to climatically new and previously disease-free countries, which also includes its recent emergence in the Indian subcontinent (2019). This study deals with the LSD outbreak(s) from cattle in Ranchi (India). Virus was isolated from the scabs (skin lesions) in the primary goat kidney cells. Phylogenetic analysis based on nucleotide sequencing of LSD virus (LSDV) ORF011, ORF012 and ORF036 suggested that the isolated virus (LSDV/Bos taurus-tc/India/2019/Ranchi) is closely related to Kenyan LSDV strains. Further, we adapted the isolated virus in Vero cells, an alternative cell line that was found suitable for LSDV propagation. In addition, kinetics of viral DNA synthesis and one-step growth curve analysis suggested that LSDV initiates synthesizing its genome at [~]24 hours post-infection (hpi) with a peak level at [~]96 hpi whereas evidence of progeny virus particles was observed at 36-48 hours (h) with a peak titre at [~]120 h. This study reports the first successful isolation of LSDV in India, besides describing alternative cells for virus isolation (primary goat kidney cells) and in vitro propagation (Vero cells) as well as providing some insights on LSDV life cycle. Author SummaryThis study describes the first successful isolation of LSDV in India. Nucleotide sequencing of LSDV ORF011, ORF012 and ORF036 suggested that the isolated virus is closely related to Kenyan LSDV strains. This is in accordance with the previous (only) study, thereby suggesting that a single LSDV strain is circulating in India. For the first time, we employed primary goat kidney (PGK) cells for the isolation of LSDV, where PGK cells were found more sensitive for LSDV isolation as compared to the primary lamb testicle (PLT) and primary goat testicle (PGT) cells. We also adapted the isolated virus in Vero cells and demonstrated that Vero cells are also suitable for in vitro propagation of LSDV. Besides, we also provide some insights on the LSDV life cycle.

microbiology↗

bioRxiv2020

Cardiac overexpression of microRNA-7 is associated with adverse cardiac remodeling

Role of microRNA-7 (miRNA-7) in targeting Epidermal growth factor receptor (EGFR/ERBB) family is known in dividing cancer cells while less is known about its role in terminally differentiated cardiac cells. We generated transgenic (Tg) mice with cardiomyocyte-specific overexpression of miRNA-7 to determine its role in regulating cardiac function. Despite similar survival, expression of miRNA-7 results in cardiac dilation as measured by echocardiography, instead of age-based cardiac hypertrophy observed in littermate controls. In contrast to the classical adaptive hypertrophy in response to TAC, miRNA-7 Tg mice directly undergo cardiac dilation post-TAC that is associated with increased fibrosis. Interestingly, significant loss in ERBB2 expression was observed in cardiomyocytes with no changes in ERBB1 (EGFR). Gene ontology and cellular component analysis using the cardiac proteomics data showed significant reduction in mitochondrial membrane integrity reflecting the differential enrichment/loss of proteins in miRNA-7 Tg mice compared to littermate controls. Consistently, electron microscopy showed that miRNA-7 Tg hearts had disorganized and rounded mitochondrial morphology indicating mitochondrial dysfunction. These findings show that expression of miRNA-7 uniquely results in cardiac dilation instead of adaptive hypertrophic response to cardiac stress providing insights on adverse remodeling in physiology and pathology.

physiology↗

bioRxiv2020

Chemotherapeutic cardiotoxicity is associated with elevated β1-adrenergic receptor density

ObjectiveTo understand the underlying pathways that promote cardiotoxicity following chemotherapy. BackgroundAnthracyclines are associated with cardiotoxicity which could be potentiated with use of complementary agents (like anti-ERBB2 inhibitors) which together afford robust anti-neoplastic effects. Anthracyclines lead to oxidative stress and thought to induce cardiotoxicity. However, interventions reducing oxidative stress in patients have been unsuccessful suggesting mechanisms beyond oxidative stress. Despite {beta}-adrenergic receptors ({beta}ARs) being key regulators of cardiac function, nothing is known about their role in chemotherapy-mediated cardiotoxicity. Methods{beta}1 and/or {beta}2-AR density was assessed in end-stage human heart failure patient samples either due to anthracycline cardiotoxicity or non-anthracycline dilated cardiomyopathy (DCM). Since ERBB2 inhibition is integral to overall chemotherapeutic arsenal, we assessed {beta}1- and/or {beta}2-AR density, cardiac function by echocardiography and immunohistochemistry in mice following ERBB2-specific inhibitor AG825. ResultsSelective increase in cardiac {beta}1AR density is observed in end-stage human heart failure patient samples due to anthracycline cardiotoxicity as well as in ERBB2 inhibitor-treated mice. ConclusionsElevated {beta}1AR density may be the key common underlying mechanism which is altered in response to chemotherapy promoting cardiac dilation of otherwise healthy hearts. HighlightsIn contrast to downregulation of {beta}1-adrenergic receptors ({beta}1AR) in end-stage human heart failure, anthracycline cardiotoxicity-mediated failure is associated with selective increase in {beta}1AR density. ERBB2 inhibitor (AG825) treatment in mice results in cardiac dilation and selective rise in {beta}1AR density showing that increased {beta}1AR density in the heart could be a common mechanism underlying cardiotoxicity.

pharmacology and toxicology↗