Biology subjects

Gupta, V. K.

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

At least 19 recordsLinked to original sources

bioRxiv2026

Tobacco Carcinogen Induces Persistent DNA Damage and Homologous Recombination Dysregulation in Pancreatic Ductal Carcinogenesis

Cigarette smoking is a well-established risk factor for the development of pancreatic ductal adenocarcinoma (PDAC), yet the mechanisms by which tobacco carcinogens, such as Nicotine-Derived Nitrosamine Ketone (NNK), drive pancreatic carcinogenesis remain incompletely understood. We investigated the impact of NNK on pancreatic epithelium by treating human pancreatic ductal epithelial cells (HPDE6-E6E7; H6c7) with NNK for 5 or 50 days followed by genome-wide RNA sequencing, qRT-PCR, immunofluorescence, comet assay, and {gamma}H2AX ELISA. We assessed {gamma}H2AX by immunohistochemistry in human PDAC tissue microarrays and in TCGA-PAAD datasets to identify clinical correlates. Acute NNK exposure (5 days) induced DNA double-strand breaks and activated ATM-{gamma}H2AX signaling, accompanied by increased RAD51 and BRCA2 recruitment, consistent with activation of homologous recombination (HR)-mediated DNA repair. In contrast, chronic NNK exposure (50 days) resulted in persistent DNA damage signaling and transcriptional upregulation of HR-associated genes, including RAD51, BRCA1, BRCA2, FANCD2, and PLK1. Despite sustained accumulation of RAD51- and BRCA2-positive repair foci, chronic NNK exposure was associated with altered RAD51 localization, persistent DNA damage, and chromosomal instability, suggesting dysregulation of HR repair fidelity during prolonged genotoxic stress. {gamma}H2AX expression was significantly elevated in NNK-treated cells, KRAS-driven premalignant pancreatic lesions, and pancreatic tissues from smokers. Increased {gamma}H2AX expression correlated with tumor progression and poor overall survival, while elevated RAD51 expression was associated with adverse outcomes in patients with PDAC. Collectively, these findings reveal a biphasic DNA damage response to NNK characterized by early activation of ATM-{gamma}H2AX-dependent DNA repair followed by persistent DNA damage signaling, dysregulated HR repair, and genomic instability during chronic exposure. Tobacco-induced disruption of DNA repair homeostasis may represent a key mechanism driving pancreatic carcinogenesis and supports {gamma}H2AX as a clinically relevant prognostic biomarker in tobacco-associated PDAC.

cancer biology↗

bioRxiv2026

A Disease-Agnostic Nasal Microbiome Wellness Index for Standardized Assessment of Upper-Airway Respiratory Health

BackgroundUpper-airway and respiratory conditions impose a large and growing global burden, yet there is no standardized way to assess whether a nasal microbiome is "healthy". Currently, monitoring remains reactive, beginning only after symptoms manifest. The nasal cavity is well suited to proactive monitoring: it shapes respiratory health and pathogen colonization resistance, and can be sampled non-invasively and repeatedly. To address this gap, we introduce the Nasal Microbiome Wellness Index (NMWI), a disease-agnostic, continuous score of nasal microbiome health derived from LASSO-penalized logistic regression. Rather than counting taxa, it learns which taxa (and in what balance) characterize a healthy nose and returns the predicted log-odds that a profile resembles a healthy state. The index was trained on 1654 nasal 16S rRNA gene amplicon sequencing samples (589 healthy, 1065 non-healthy) pooled from 27 publicly available studies, uniformly reprocessed through a single computational pipeline. ResultsThe NMWI comprises an interpretable signature of 24 taxa whose combined relative abundances determine the health-associated log-odds. Health-associated genera such as Corynebacterium and Cutibacterium raised the score, while dysbiosis-associated genera such as Pseudomonas and Escherichia-Shigella lowered it. The NMWI substantially outperformed the Shannon, Simpson, and Chao1 diversity indices, which showed negligible, directionally inconsistent separation between healthy and non-healthy samples (|Cliffs{delta} | = 0.01-0.20), whereas the NMWI produced large, consistent separation ({delta} = 0.65). It achieved a balanced accuracy of 74.37% on the training data (resubstitution estimate), and 73.43% under repeated 10-times 10-fold cross-validation. Performance remained stable at mean balanced accuracy of 73.82% under a leave-one-study-out framework, reflecting cross-study generalizability. In independent external cohorts, the balanced accuracy was 71.49%, and leave-one-disease-out analysis (in which each disease condition was withheld from training) showed a mean balanced accuracy of 63.92% across unseen conditions, consistent with a disease-agnostic design. The index also generalized across heterogeneous datasets spanning multiple 16S rRNA gene hypervariable regions--to our knowledge the first demonstration of such cross-study, cross-region transferability for the nasal cavity. ConclusionsThe NMWI distills a complex nasal microbial profile into a single interpretable score computed directly from the 16S rRNA gene data that dominate existing nasal research, making it immediately applicable to published and future datasets without re-sequencing. By replacing descriptive, diversity-based comparison with a quantitative standard, it offers a reproducible, open-source foundation for cross-study benchmarking, individual-level phenotyping, and longitudinal respiratory wellness monitoring.

bioinformatics↗

bioRxiv2026

Synergistic retinal UCHL1 dysregulation and synaptic vulnerability reflect Alzheimer's disease severity

Synaptic failure predicts cognitive decline in Alzheimers disease (AD), yet its impact and molecular drivers in the human retina remain unclear. Leveraging the retina as an accessible central nervous system (CNS) proxy, we integrated spatially resolved histopathology of retinal cross-sections with ultrastructural, proteomic, and biochemical profiling across independent postmortem cohorts spanning normal cognition, mild cognitive impairment due to AD (MCI), and AD dementia. We uncover early, progressive degeneration of excitatory glutamatergic synapses, evidenced by losses of presynaptic vesicular glutamate transporter 1 (VGLUT1) and synaptophysin, and postsynaptic density protein 95 (PSD95) and N-methyl-D-aspartate receptor subunit 2A (NMDAR2A), accompanied by disruption of synaptic ultrastructure. Retinal synaptic loss tightly associates with local accumulation of amyloid-{beta} 42 (A{beta}42) and immature tau species, heightened oxidative stress, and upregulation of the A{beta}-binding death receptor p75 neurotrophin receptor (p75NTR). Notably, the synapse-enriched deubiquitinase ubiquitin C-terminal hydrolase L1 (UCHL1) is profoundly dysregulated, correlates with synaptic integrity and cognition, and emerges as the strongest retinal predictor of Braak stage and cognitive status in multivariable machine-learning models. Together, these findings position retinal A{beta}/p75NTR-mediated UCHL1 imbalance as a proteostasis-synapse mechanistic hub and candidate biomarker reflecting AD severity.

neuroscience↗

bioRxiv2026

Bidirectional fibrogenic cross-talk revealed in a human iPSC-derived epithelial-mesenchymal co-culture model of pulmonary fibrosis

Pulmonary fibrosis (PF) can arise from mutations in alveolar epithelial type 2 (AT2) cell-specific genes, but manifests in fibrotic activation of mesenchymal cells, thus involving fibrogenic epithelial-mesenchymal crosstalk. The ligand-receptor interactions underlying the onset and early progression of PF remain poorly understood. Induced pluripotent stem cell (iPSC)-derived models are powerful tools to study respiratory diseases, yet are currently limited to reductionist single lineage epithelial models or multi-lineage systems that lack purity and lung-specificity of the mesenchyme. Here we generate a human iPSC line carrying both a lung mesenchyme-specific reporter (TBX4-LERtdTomato) and a reporter for mesenchymal activation/differentiation (ACTA2GFP). Applying this line, we develop a directed differentiation protocol capable of generating cells that express key molecular and functional features of primary human developing lung mesenchyme across multiple iPSC genetic backgrounds. We then establish co-cultures of these iPSC-derived lung mesenchymal cells (iLM) with patient-specific iPSC-derived alveolar epithelial type 2 cells (iAT2s) carrying an SFTPCI73T mutation as a model for PF. We find increased expression of fibrotic markers in co-cultures with mutant iAT2s as compared to co-cultures with gene-corrected iAT2s. Moreover, mutant iAT2s express markers of alveolar-basal intermediate (ABI) cells only in the presence of iLM, suggesting that bidirectional crosstalk promotes this aberrant cell state. We identify ligand-receptor pairs enriched in co-cultures with mutant iAT2s, including TGF{beta}, multiple integrins, and additional genes that have not been previously linked to PF. Finally, we show that small molecule-mediated inhibition of TGF{beta} or integrins V{beta}1/V{beta}6 attenuates both fibrotic mesenchymal activation and the presence of ABI cells in iLM/iAT2 co-cultures. Thus, we have established a human iPSC-derived co-culture system that recapitulates key molecular hallmarks of bidirectional fibrogenic epithelial-mesenchymal crosstalk in pulmonary fibrosis, and enables the identification and study of potentially druggable pathways involved in disease initiation and progression.

molecular biology↗

bioRxiv2025

Targeting CREB remodels the immune microenvironment to enhance immunotherapy responses in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) remains a challenging disease in need of improved treatments. Cyclic adenosine monophosphate response element binding protein 1 (CREB) is an emerging therapeutic target whose oncogenic effects in PDAC have been largely attributed to a key molecular interplay between oncogenic KrasG12D/+ (Kras*) and chronic inflammation driving irreversible acinar to ductal reprogramming. Here, we demonstrate that CREB activation fosters tumor associated macrophage (TAM) mediated immunosuppression and promotes PDAC growth in an aggressive LSL-KrasG12D/+;Trp53R172H/+;Pdx1Cre/+(KPC) genetically engineered mouse model. Selective deletion of CREB (Crebfl/fl) in KPC(KPCC-/-) mice attenuates primary disease burden. Unbiased transcriptomic analysis and validation using diverse molecular, genetic and pharmacological approaches in vitro and in vivo identify CREB-mediated transcriptional regulation of leukemia inhibitory factor (Lif) as one of the potential mediators of tumor cell-macrophage crosstalk promoting a pro-tumor polarization of TAMs, thereby attenuating the infiltration of effector T cells. Mechanistically, cancer cell derived LIF facilitates an immunosuppressive, pro-tumorigenic state. Importantly, pharmacological targeting of the CREB-LIF signaling axis between cancer cells and macrophages, using a CREB-specific inhibitor (CREBi), significantly suppresses tumor growth and sensitizes PDAC to immunotherapy, highlighting the therapeutic potential of this treatment combination to improve outcomes in this aggressive disease.

cancer biology↗

bioRxiv2025

Identification of Chlamydia pneumoniae and NLRP3 inflammasome activation in Alzheimer's disease retina

Chlamydia pneumoniae (Cp), an obligate intracellular bacterium, has been implicated in Alzheimers disease (AD), yet its role in retinal pathology remains unexplored. We analyzed postmortem tissues from 95 human donors and found 2.9-4.1-fold increases in Cp inclusions in AD retinas and brains, with no significant elevation in mild cognitive impairment (MCI). Proteomics revealed dysregulation of retinal and brain bacterial infection-related proteins and NLRP3 inflammasome pathways. NLRP3 expression was markedly elevated in MCI and AD retinas, and its activation was evident by increased N-terminal gasdermin D (NGSDMD) and mature interleukin-1{beta}. Retinal Cp strongly correlated with A{beta}42 and NLRP3 inflammasome components, which tightly linked to cleaved caspase-3-apoptotic and NGSDMD-pyroptotic cell death. Although retinal microgliosis was elevated in AD, Cp-associated microglia were reduced by 62%, suggesting impaired Cp phagocytosis. Higher retinal Cp burden correlated with APOE{varepsilon}4, Braak stage, and cognitive deficit. Machine learning identified retinal Cp or NLRP3 combined with A{beta}42 as strong predictors of AD diagnosis, staging, and cognitive impairment. Our findings suggest that Cp infection contributes to AD dementia but not initiating pathology, whereas early NLRP3 activation may promote disease development, warranting studies on Cps role in AD pathogenesis and early antibiotic or inflammasome-targeted therapies.

neuroscience↗

bioRxiv2024

Epigenetic derepression of H3K9me3 mitigates Alzheimer-related pathology and improves cognition via immunomodulation and Vgf induction

We investigated the role of histone 3 lysine 9 trimethylation (H3K9me3), an epigenetic mechanism involved in the repression of synaptic plasticity and memory-related genes, within aging and Alzheimers disease (AD). Our study reveals that elevated cortical H3K9me3 strongly correlates with cognitive dysfunction in individuals with mild cognitive impairment (MCI) and AD. In old (18 months) and younger (14 months) APPSWE/PS1{Delta}E9 and 3xTg AD mouse models, inhibiting SUV39H1 methyltransferase with ETP69, substantially reduces cerebral H3K9me3 levels and attenuates amyloid-{beta} burden, tau pathology, and gliosis. Administration of ETP69 further promotes dendritic spine formation, leading to rapid and sustained improvements in cognitive function. Proteomics analysis indicates that a significant proportion of dysregulated proteins in the brains of AD-model mice are reversed by ETP69. These proteins are enriched for synaptic plasticity and learning-related pathways. ETP69 exerts its effects through multiple neuroprotective mechanisms, including regulation of neuroinflammation, induction of both blood and cerebral-infiltrating monocytes involved in cerebral A{beta} clearance. Moreover, ETP69 activates brain-derived neurotrophic factor (Bdnf) network, and particularly its downstream effector neurosecretory protein Vgf. These findings support the pharmacological inhibition of H3K9me3-mediated gene silencing to reverse AD-related pathology and cognitive decline.

neuroscience↗

bioRxiv2023

Gut Microbiome Wellness Index 2 for Enhanced Health Status Prediction from Gut Microbiome Taxonomic Profiles

Recent advancements in human gut microbiome research have revealed its crucial role in shaping innovative predictive healthcare applications. We introduce Gut Microbiome Wellness Index 2 (GMWI2), an advanced iteration of our original GMWI prototype, designed as a robust, disease-agnostic health status indicator based on gut microbiome taxonomic profiles. Our analysis involved pooling existing 8069 stool shotgun metagenome data across a global demographic landscape to effectively capture biological signals linking gut taxonomies to health. GMWI2 achieves a cross-validation balanced accuracy of 80% in distinguishing healthy (no disease) from non-healthy (diseased) individuals and surpasses 90% accuracy for samples with higher confidence (i.e., outside the "reject option"). The enhanced classification accuracy of GMWI2 outperforms both the original GMWI model and traditional species-level -diversity indices, suggesting a more reliable tool for differentiating between healthy and non-healthy phenotypes using gut microbiome data. Furthermore, by reevaluating and reinterpreting previously published data, GMWI2 provides fresh insights into the established understanding of how diet, antibiotic exposure, and fecal microbiota transplantation influence gut health. Looking ahead, GMWI2 represents a timely pivotal tool for evaluating health based on an individuals unique gut microbial composition, paving the way for the early screening of adverse gut health shifts. GMWI2 is offered as an open-source command-line tool, ensuring it is both accessible to and adaptable for researchers interested in the translational applications of human gut microbiome science.

bioinformatics↗

bioRxiv2023

Characterization of B646L (p72) gene and the resistance pattern of African swine fever Virus tolerant to indigenous Doom Pig breeds of India

African Swine Fever (ASF) has affected all pig breeds in North-East India since 2020, except Doom pigs, a unique indigenous breed from Assam and the closest progenitor to Indian wild pigs, resulting in significant economic losses for pig farmers in the region. Based on the complete sequences of the B646L (p72) gene, it has been determined that the virus responsible for the outbreak is ASFV genotype II. The further characterization of three complete sequences of the B646L (p72) gene established 100% identical with other existing sequences of different parts of the world as well as confirmed that there is no co-circulation of different genotypes of ASFV in India except genotype II. Present studies also corroborate that MYD88, LDHB and IFIT1 were important genes of the immune system involved in the pathogenesis of ASFV. The differential expression patterns of these genes in ASFV-infected survived, and healthy Doom breed pigs, compared to healthy control pigs, were studied to distinguish the expression pattern at different stages. The hardiness and ability of the Doom pig to withstand common pig diseases, along with its genetic resemblance to wild pigs, make it an ideal candidate for studying tolerance to ASFV infection. So, the present study investigates the natural resistance to ASF in Doom pigs from an endemic area in North-East India to support the proposition that Doom pigs can co-exist with virulent ASFVs recently break in North-East India. The results of this study also provide important molecular insights into the regulation of the ASFV-tolerant gene. ImportanceStudying the natural resistance to African Swine Fever (ASF) in Doom pigs from North-East India holds crucial importance. ASF has inflicted significant economic losses on pig farmers in the region, necessitating the identification and comprehension of factors contributing to resistance and tolerance in specific pig breeds such as Doom pigs. Understanding the molecular mechanisms and genetic factors associated with ASFV tolerance could help in breeding programs and the selection of resilient pig breeds, ultimately aiding in disease control efforts.

microbiology↗

bioRxiv2023

Incidences of Helicobacter infection in pigs and tracing occupational hazard in pig farmers

Helicobacter species (H. sp.) is a gram-negative spiral-shaped motile bacteria that causes gastritis in pigs and also colonizes the human stomach. The current study seeks to assess the prevalence of various H. sp. in the gastric mucosa of slaughtered and dead pigs, as well as the prevalence of Helicobacter infection among pig farmers. A total of 403 stomach samples from various pig slaughter points, 74 necropsy samples from various pig farms and 97 stool samples from pig farmers were collected from Assam, India. Among 477 pig stomach samples tested, 214 samples with gastritis (20.09%) showed Gram negative, spiral-shaped organisms in brush cytology from the mucosal surface, and the rest of the 263 stomach samples without any gastric lesion showed only 3.04% Gram negative, spiral-shaped organisms. In ultrastructure investigation, Scanning Electron Microscopy (SEM) of the four urease positive stomach samples revealed a tightly coiled Helicobacter bacterium (spiral-shaped) found in the mucous lining of the stomach. In histopathological examination of pars esophagia, cardiac and fundic mucosa showed chronic gastritis associated with hemorrhagic necrosis, leucocytic infiltration with neutrophils and macrophages, and lymphoid aggregates (lymphoid follicles) etc. PCR confirmed 16S rRNA genes of Helicobacter suis (H. suis) where a total of 42 (19.63%) out of 214 pig stomach samples and 2 (2.08%) out of 96 stool samples of pig farmers were found positive for H. suis. of these 96 stool samples of pig farmers 3 (3.12%) were confirmed positive for Helicobacter pylori (H. pylori) Phosphoglucosamine mutase gene in PCR. Phylogenic analysis of the 16S rRNA gene of H. suis showed distinct clusters with other H. sp. In conclusion, this study provides evidence for the prevalence of Helicobacter both in pig gastric mucosa and human stool. The findings highlight the need for improved sanitation and hygiene practices among pig farmers to minimize the risk of Helicobacter infection in humans.

microbiology↗

bioRxiv2023

Mass spectrometric analysis and biostimulatory effects of boar seminal gel, saliva and semen in pigs

The present study aimed to identify novel biostimulatory compounds in boar seminal gel (SG), saliva and semen using Gas chromatography-mass spectrometry (GC-MS). SG alone and its combined application with saliva (SG+saliva) and semen (SG+semen) also studied to train young boars. SG alone and SG+Saliva investigated for estrus induction in gilts and sows. Distilled water (DW) exposure was kept as control. SG, saliva and semen screened for total 105, 96 and 89 compounds. The highest concentration was of alkanes followed by sugar alcohols, then hydrocarbons, amino acids and fatty acids. Elaidic acid is the novel compound identified in pigs. Other compounds were tridecenol, undecane, hexadecone, eicosane, tetracosane etc. Further, young males (64.86%) were able to get trained. Significant higher (p<0.05) number of males got trained in exposure to SG (80%), SG+saliva (75%) and SG+semen (75%) than control. The time (hrs) taken by young boars to get trained on exposure to combination of SG+saliva (244{+/-}22.19) and SG+semen (216{+/-}13.14) was lesser (p<0.05) than SG (356{+/-}61.85) alone. Interval (hrs) for exhibition of different sexual behaviour by males on exposure to SG, saliva and semen was lesser (p<0.05) than control. Estrus was induced in 61.25% of females. Significant (p<0.05) higher number of females showed estrus response to exposure of SG (72.72%) and SG+saliva (69.23%) than control. Interval taken to exhibit estrus was lesser (p<0.05) in females exposed to SG+saliva (201.88{+/-}12.66) than SG (262.14{+/-}20.06) alone. Interval (hrs) for exhibition of different sexual behaviour by females on exposure to SG+saliva was lesser (p<0.05) than control. In conclusion, novel compounds with biostimulatory properties have been identified in boar SG, saliva and semen. The combined exposure of SG with saliva and semen have more intense biostimulation effect than SG alone. Such compounds and biostimulatory effects can be exploited for augmenting reproductive efficiency in pigs.

animal behavior and cognition↗

bioRxiv2023

Hormonal Interventions for optimizing reproductive efficiency in pigs at Farmers field

ObjectiveOptimizing reproductive efficiency in terms of estrus induction and production performance using simplified hormonal intervention using GnRH, gonadotropins and progesterone at farmers field conditions to bred animals with superior quality semen and also to reduce the maintenance cost. MethodThe present study was planned for optimizing reproductive efficiency using four different easily available hormonal agents with simplified protocols at farmers field. A total of 126 females were used in the study. Hormonal protocols I, II, III and IV using GnRH + (PMSG+ hCG), (PMSG+ hCG), PMSG alone and prepared progesterone gel respectively were used for estrus induction in gilts and sows. ResultsThe estrus induction/rate was (77.77%, 81.36%, 78.57% and 50% respectively. The corresponding figures for interval (hrs) of heat exhibition from hormonal administration (121.33{+/-}4.93, 121.54{+/-}3.60, 78.52{+/-}4.52 and 192{+/-}24), conception rate (%) (72.22%, 81.25%, 68.18% and 33.33%) farrowing rate (55.55%, 68.29%, 68.18% and 33.33 %), total litter size at birth (7.2{+/-}0.64, 7.90{+/-}0.47, 8.90{+/-}0.47 and 7.00{+/-}0) and hormonal cost (Rs.) per animal (570, 335, 280 and 250 Rs.) were respectively. The easier to use protocol was III followed by II, I and IV. ConclusionIt was found that protocol II and III are effective and easier so can be used for optimizing reproductive efficiency in pigs at farmers field.

physiology↗

bioRxiv2023

Metagenomic analysis of Pigs' faecal microbiome and its functional response associated with dietary fibre

Pig husbandry is the most valued and economically sustainable husbandry in the livestock farming system. The performance and productivity of the pig are chiefly dependent on the nutritional factor steered by gut beneficial bacteria. The swine gut microbiome has a direct relationship with feed efficiency. As a consequence, identifying microbial taxonomy and functional capacity is critical for proper nutrient digestion. In the present investigation, eighteen grower pigs aged 3 months and weighing 30{+/-}0.55 kg were allocated into three different groups using a randomized block layout and supplemented with QPM maize fodder of 0, 5, and 10% to the basal diet by substituting (wt/wt on DM) the maize grains, and named as T0, T1, and T2 to probe the increase in gut beneficial bacteria found in the faecal contents. For comparison with T0, T1, and T2, a random faecal sample designated R was collected from six grower pigs of the same age group and bodyweight fed a maize-soya bean-based diet. The experiment is being carried out to investigate the effect of various maize fodder levels on the metagenomic profiles of pig gut microbiota using the 16S rRNA gene. All of the experimental diets were iso-nitrogenous, with protein content ranging from 18.37 to 18.63 per cent. The data generated by 16S rRNA amplicon analysis was 68, 56, 61, and 39 Mb in R, T0, T1, and T2 samples, respectively. From taxonomic distribution, bacterial phyla namely Firmicutes, Bacteroidetes, Proteobacteria, and Spirochetes are found in descending order of relative abundance in the R, T0, and T1 groups, respectively, while Spirochaetes, Proteobacteria, Fibrobacteres, Bacteroidetes, and Firmicutesare found in descending order of relative abundance in the T2 group. The relative profusion of Fibrobacter succinogenes is 0.89% and 16.84% in the T1 and T2 groups. According to the findings, a higher level of maize fodder in the diet of grower pigs promotes the growth of fibre-degrading bacteria in the gut microbiota, particularly Fibrobacter succinogenes. Moreover, feeding green maize has decreased the population of methanobacteria in the gut of pigs, which in turn has limited the production of methane.

genomics↗

bioRxiv2022

Detection and Whole Genome of Japanese Encephalitis Virus Genotype III strains isolated from Indian Pig and Mosquito vector

Japanese encephalitis virus(JEV) are globally prevalent as deadly pathogens in human and animals including pig, horse and cattle. Japanese encephalitis (JE) still remains as an important cause of epidemic encephalitis worldwide and exists in a zoonotic transmission cycle. Assam is one of the highly endemic state for JE in India. In the present study, to understand the epidemiological status of JE circulating in pigs and mosquito particularly in Assam, India, molecular detection of JEV and the complete genome sequencing of the JEV isolates from pig and mosquito were done. The complete genome analysis of two JEV isolates from pig and mosquito were revealed7 and 21 numbers of unique points polymorphism of nucleotide during alignment of the sequences with other available sequences, respectively. Phylogenetic analysis revealed that the isolates of present investigation were belongs to genotype III and closely related with the strains of neighbouring country China. This study represents the transboundary nature of the JEV genotype III circulation and maintained the same genotype through mosquito-swine transmission cycles.

genomics↗

bioRxiv2022

Whole-Genome Sequence of African Swine Fever Virus isolate from India provides insights into diversity and evolution

African swine fever (ASF) was first reported in 1921, and since then has posed a major threat to the world pig industry and still remains a major challenge as there is no vaccine or therapy available. In May 2020, the first incidence of ASF was recorded in India, followed by a number of outbreaks in the north eastern part of India. In this study, we report the first whole genome of an Indian isolate of ASF virus (ASF/IND/20/CAD/543) using next generation sequencing and compared with the other ASFV complete genome. On phylogenetic analysis, the virus was assigned to genotype II on the basis of p72 genotyping. However, the whole genome based phylogeny distinguished it from other genotype II isolates of clade 1.1.1. This study adds to our understanding of ASFVs genetic diversity and molecular evolution.

microbiology↗

bioRxiv2022

Systemic infection of SARS-CoV-2 in free ranging Leopard (Panthera pardus fusca) in India

We report patho-morphological and virological characterization of SARS-CoV-2 in naturally infected, free ranging Indian Leopard (Panthera pardus fusca). Whole genome sequence analysis confirmed infection of Delta variant of SARS-CoV-2, possibly spill over from humans, but the case was detected when infection level had dropped significantly in human population. This report underlines the need for intensive screening of wild animals for keeping track of the virus evolution and development of carrier status of SARS-CoV-2 among wildlife species.

microbiology↗

bioRxiv2021

Cationic inhalable particles for enhanced drug delivery to M. tuberculosis infected macrophages

Inhalable microparticle-based drug delivery platforms are being investigated extensively for Tuberculosis (TB) treatment as they offer efficient deposition in lungs and improved pharmacokinetics of the encapsulated cargo. However, the effect of physical parameters of microcarriers on interaction with Mycobacterium tuberculosis (Mtb) infected mammalian cells is underexplored. In this study, we report that Mtb-infected macrophages are highly phagocytic and microparticle surface charge plays a major role in particle internalization by infected cells. Microparticles of different sizes (0.5 - 2 m) were internalized in large numbers by Mtb-infected THP-1 macrophages and murine primary Bone Marrow Derived Macrophages in vitro. Drastic improvement in particle uptake was observed with cationic particles in vitro and in mice lungs. Rapid uptake of rifampicin-loaded cationic microparticles allowed high intracellular accumulation of the drug and lead to enhanced anti-bacterial function when compared to non-modified rifampicin-loaded microparticles. Cytocompatibility assay and histological analysis in vivo confirmed that the formulations were safe and did not elicit any adverse reaction. Additionally, pulmonary delivery of cationic particles in mice resulted in two-fold higher uptake in resident alveolar macrophages compared to non-modified particles. This study provides a framework for future design of drug carriers to improve delivery of anti-TB drugs inside Mtb-infected cells.

bioengineering↗

bioRxiv2021

TaxiBGC: a Taxonomy-guided Approach for the Identification of Experimentally Verified Microbial Biosynthetic Gene Clusters in Shotgun Metagenomic Data

Biosynthetic gene clusters (BGCs) in microbial genomes encode for bioactive secondary metabolites (SMs), which can play important roles in microbe-microbe and host-microbe interactions. Given the biological significance of SMs and the current profound interest in the metabolic functions of microbiomes, the unbiased identification of BGCs from high-throughput metagenomic data could offer novel insights into the complex chemical ecology of microbial communities. Currently available tools for predicting BGCs from shotgun metagenomes have several limitations, including the need for computationally demanding read-assembly; predicting a narrow breadth of BGC classes; and not providing the SM product. To overcome these limitations, we developed TaxiBGC (Taxonomy-guided Identification of Biosynthetic Gene Clusters), a command-line tool for predicting experimentally characterized BGCs (and inferring their known SMs) in metagenomes by first pinpointing the microbial species likely to harbor them. We benchmarked TaxiBGC on various simulated metagenomes, showing that our taxonomy-guided approach could predict BGCs with much-improved performance (mean F1 score: 0.56, mean PPV score: 0.80) compared to directly identifying BGCs by mapping sequencing reads onto the BGC genes (mean F1 score: 0.49, mean PPV score: 0.41). Next, by applying TaxiBGC on 2,650 metagenomes from the Human Microbiome Project and various case-control gut microbiome studies, we were able to associate BGCs (and their SMs) with different human body sites and with multiple gastrointestinal diseases, including Crohns disease and liver cirrhosis. In all, TaxiBGC provides an in silico platform to predict experimentally characterized BGCs and their SM production potential in metagenomic data while demonstrating important advantages over existing techniques. IMPORTANCECurrently available bioinformatics tools to identify BGCs from metagenomic sequencing data are limited in their predictive capability or ease of use to even computationally-oriented researchers. We present an automated computational pipeline called TaxiBGC, which predicts experimentally characterized BGCs (and infers their known SMs) in shotgun metagenomes by first considering the microbial species source. Through rigorous benchmarking techniques on simulated metagenomes, we show that TaxiBGC provides a significant advantage over existing methods. When demonstrating TaxiBGC on thousands of human microbiome samples, we associate BGCs encoding for bacteriocins with different human body sites and diseases, thereby elucidating a possible novel role of this antibiotic class in maintaining the stability of microbial ecosystems throughout the human body. Furthermore, we report for the first time gut microbial BGC associations shared amongst multiple pathologies. Ultimately, we expect our tool to facilitate future investigations into the chemical ecology of microbial communities across diverse niches and pathologies.

bioinformatics↗