Biology subjects

Tiwari, S. K.

Publications and source records attributed to Tiwari, S. K..

9 recordsLinked to original sources

bioRxiv2026

Cell-type specific impact of opioid use disorder and HIV on the human forebrain and cerebellum

Opioid use disorder (OUD), which frequently co-occurs with HIV infection, causes long-term neurological disease, yet the epigenetic and transcriptomic effects of OUD and HIV on specific cell types and regions of the brain are poorly understood. To assess the cell-type specific impacts of OUD and HIV across the human brain, we measured single cell transcriptomes and epigenomes of 580,353 cells in the prefrontal cortex, amygdala and cerebellum of 44 donors. We cataloged over 750k candidate cis-regulatory elements (cCREs) and identified gene regulatory networks (GRNs) of transcription factor activity across 35 neuronal and non-neuronal cell types. We identified specific neuronal and glial populations whose cCREs were significantly enriched for genetic risk of addiction-related traits. In OUD donors, we found evidence for reduced metabolic function in neurons in the PFC and cerebellum as well as increased gene expression related to voltage-gated calcium channel activity in the cerebellum. Using a cerebellar organoid model, fentanyl treatment reduced metabolic activity while increasing neuronal activity. Across brain regions, HIV activated immune-related pathways in glial populations, while comorbid OUD and HIV exacerbated metabolic changes in cortical glial cells. Cerebellum-specific Bergmann glia, in addition to forebrain microglia and astrocytes, showed expansion of reactive state identity in HIV. These results highlight shared and specific changes to immune, synaptic, and metabolic processes in OUD and HIV across brain regions and reveal that cerebellar cell types are distinctly affected by opioid abuse.

genomics↗

bioRxiv2026

A Systematic Benchmark of Antibiotic Resistance Gene Detection Tools for Shotgun Metagenomic Datasets

1.Accurate detection of antimicrobial resistance genes (ARGs) from metagenomic data is essential for understanding resistance dissemination within microbial communities, yet tool performance remains influenced by sequencing coverage, community complexity, and dataset variability. In this study, we systematically benchmarked five widely used read-based ARG detection tools (ARGprofiler, KARGA, ARIBA, GROOT, and SRST2) across simulated metagenomic datasets representing varying sequencing coverages, microbial complexities, and approximate realistic metagenomic dataset. The results demonstrated that sequencing coverage is a major determinant of ARG detection accuracy, with reliable detection achieved at 10x coverage and performance stabilizing between 20x and 30x. ARGprofiler exhibited the highest overall F1-score (0.891 at [≥]10x), whereas KARGA showed higher recall at low coverage levels, but lower precision compared to ARGprofiler. Increasing community complexity led to a decline in accuracy across all tools, and under realistic uneven coverage, performance variability increased substantially, with KARGA achieving the highest mean F1- score (0.122 {+/-} 0.067). Runtime evaluation further revealed substantial differences in computational efficiency, with ARGprofiler, SRST2, and GROOT being the most resource-efficient, while KARGA imposed the highest computational burden. Collectively, these findings highlight that both sequencing coverage and community complexity profoundly shape ARG detection outcomes and that tool selection should balance accuracy with computational efficiency. The study also emphasizes the need for standardized benchmarking datasets that reflect true metagenomic complexity to ensure robust and comparable ARG surveillance across analytical pipelines.

bioinformatics↗

bioRxiv2026

Identifying Fundamental Gaps in Functional Metagenomics: A StepTowards Unlocking Microbiome Research Potential

Incomplete functional annotation systematically limits biological interpretation in microbiome studies and their translational potential. Poor annotation arises from multiple causes1 with incomplete gene-protein-reaction mapping being one tractable yet under-examined contributor. We address this gap by developing a comprehensive hierarchical framework that systematically integrates gene families in UniRef1 proteins in UniProt1 and metabolic reactions in BioCyc1 mapping 76% of reactions (432,510 of 562,1869 reactions in BioCyc across 211244 organisms) to the encoding gene families using EC and Pfam domain-based strategies. To demonstrate how database mapping choices impact metagenomics studies1 we applied our framework to human gut metagenome dataset using HMP Unified Metabolic Analysis Network (HUMAnN) and compared outcomes with HUMAnNs default database mapping approach. Our GPR mapping increased detectable metabolic reactions by 28-fold and significantly increased the data prevalence across samples (from 35% to 80% core reactions). This directly addresses the problem of data sparsity1 a critical barrier to statistical and machine learning applications. These gains derive from systematic database integration alone1 without predictive algorithms1 demonstrating that substantial functional dark matter and data sparsity problems in microbiome studies arises from methodological artifacts that are directly addressable.

bioinformatics↗

bioRxiv2025

Investigation of CNS damage following HIV infection and methamphetamine exposure using human iPSC-derived microglia and 3D cerebral assembloid models

HIV-associated neurocognitive disorder (HAND) is characterized by glial activation and neuroinflammation emerging from HIV infection. Moreover, methamphetamine (METH) is a highly addictive psychostimulant whose use is linked to high HIV prevalence, significantly worsening clinical outcomes for people living with HIV and hastening onset of systemic illness. Overall, pathologies associated with HIV infection/METH use comorbidity include neuroinflammation, neurotoxicity, synaptodendritic damage, and resulting cognitive dysfunction. However, mechanisms underlying this neuropathogenesis remain elusive due to the scarcity of human brain-specific experimental model systems. Therefore, we created a next-generation three-dimensional (3D) human brain model derived from human induced pluripotent stem cells (hiPSCs). Specifically, this 3D in vitro cerebral assembloid model integrates functional microglia derived from hiPSCs with cerebral organoids. Microglia are key contributors to HAND symptoms associated with HIV/METH comorbidity. We show that the presence of microglia in this assembloid model allows productive infection with HIV, which is enhanced by METH exposure, resulting in increased glial activation, inflammatory responses (namely IL-1{beta} and IL-6 release), and neurotoxicity marked by neuronal cell death and synaptic protein loss. Importantly, in this model, we observed markedly decreased levels of the microglial receptor TREM2, which is implicated in microglial functions including phagocytosis, apoptosis and inflammatory responses following HIV infection and METH treatment. Analysis of our model showed that decreased TREM2 function may lead to HIV- and METH-associated pathological changes. Overall, our assembloid model could be a valuable tool for future analyses of HIV/METH/CNS interactions and mechanisms underlying HAND, which could lead to novel therapeutic approaches to decreasing the CNS viral reservoir.

neuroscience↗

bioRxiv2024

Interferon-Inducible Guanylate-Binding Protein 5 Inhibits Replication of Multiple Viruses by Binding to the Oligosaccharyltransferase Complex and Inhibiting Glycoprotein Maturation

Viral infection induces production of type I interferons and expression of interferon-stimulated genes (ISGs) that play key roles in inhibiting viral infection. Here, we show that the ISG guanylate-binding protein 5 (GBP5) inhibits N-linked glycosylation of key proteins in multiple viruses, including SARS-CoV-2 spike protein. GBP5 binds to accessory subunits of the host oligosaccharyltransferase (OST) complex and blocks its interaction with the spike protein, which results in misfolding and retention of spike protein in the endoplasmic reticulum likely due to decreased N-glycan transfer, and reduces the assembly and release of infectious virions. Consistent with these observations, pharmacological inhibition of the OST complex with NGI-1 potently inhibits glycosylation of other viral proteins, including MERS-CoV spike protein, HIV-1 gp160, and IAV hemagglutinin, and prevents the production of infectious virions. Our results identify a novel strategy by which ISGs restrict virus infection and provide a rationale for targeting glycosylation as a broad antiviral therapeutic strategy. HighlightsO_LIThe interferon-stimulated gene GBP5 is induced by SARS-CoV-2 infection in vitro and in vivo. C_LIO_LIER-localized GBP5 restricts N-linked glycosylation of SARS-CoV-2 spike protein, leading to protein misfolding and preventing transport to the Golgi apparatus. C_LIO_LIGBP5 binds to OST complex accessory proteins and potentially blocks access of the catalytic subunit to the spike protein. C_LIO_LIGBP5 inhibits N-glycosylation of key proteins in multiple viruses, including SARS-CoV-2 C_LIO_LIPharmacological inhibition of OST blocks host cell infection by SARS-CoV-2, variants of concern, HIV-1, and IAV. C_LI SignificanceViral infection induces production of type I interferons and expression of interferon-stimulated genes (ISGs) that play key roles in inhibiting viral infection. We found that the interferon-stimulated gene GBP5 is induced by SARS-CoV-2 infection in vitro and in vivo. GBP5 inhibits N-glycosylation of key proteins in multiple viruses, including SARS-CoV-2. Importantly, pharmacological inhibition of Oligosaccharyltransferase (OST) Complex blocks host cell infection by SARS-CoV-2, variants of concern, HIV-1, and IAV, indicating future translational application of our findings.

microbiology↗

bioRxiv2023

A hybrid and poly-polish workflow for the complete and accurate assembly of phage genomes: a case study of ten przondoviruses

Bacteriophages (phages) within the Przondovirus genus are T7-like podoviruses belonging to the Studiervirinae subfamily, within the Autographiviridae family and have a highly conserved genome organisation. The genome size of these phages ranges from 37 kb to 42 kb, encode 50-60 genes and are characterised by the presence of direct terminal repeats (DTRs) flanking the linear chromosome. These DTRs are often deleted during short-read-only and hybrid assemblies. Moreover, long-read-only assemblies are often littered with sequencing and/or assembly errors and require additional curation. Here, we present the isolation and characterisation of ten novel przondoviruses targeting Klebsiella spp. We describe HYPPA - a HYbrid and Poly-polish Phage Assembly workflow, which utilises long-read assemblies in combination with short-read sequencing to resolve phage DTRs and correcting errors, negating the need for laborious primer walking and Sanger sequencing validation. Our data demonstrate the importance of careful curation of phage assemblies before publication, and prior to using them for comparative genomics. IMPACT STATEMENTThe current workflows employed for phage genome assembly are often error-prone and can lead to many incomplete phage genomes being deposited within databases. This can create challenges when performing comparative genomics, and may also lead to incorrect taxonomic assignment. To overcome these challenges we proposed HYPPA, a workflow that can produce complete and high-quality phage genomes without the need for laborious lab-based validation. DATA SUMMARYPhage raw reads are available from the National Centre for Biotechnology Information Sequence Read Archive (NCBI-SRA) under the BioProject number PRJNA914245. Phage annotated genomes have been deposited at GenBank under the accessions OQ579023-OQ579032 (Table 1). Bacterial WGS data for clinical preterm infant samples have been deposited at GenBank under BioProject accession PRJNA471164 (Table S1). Bacterial raw reads for food samples are available from NCBI-SRA with individual accessions (SAMN33593347-SAMN33593351), and can be found under the BioProject number PRJNA941224 (Table S1). Strain-specific details for bacteria and publicly-available phages used in these analyses, along with accessions for the latter can be found in Table S1 and Table S6, respectively. The CL1-CL8 clinical Klebsiella strains (Table S1) were under a Materials Transfer Agreement, for which sequencing data and strain information is not available. O_TBL View this table: org.highwire.dtl.DTLVardef@8cae53org.highwire.dtl.DTLVardef@8e512org.highwire.dtl.DTLVardef@1f71a67org.highwire.dtl.DTLVardef@1e6947dorg.highwire.dtl.DTLVardef@11ebc58_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1.C_FLOATNO O_TABLECAPTIONPrzondoviruses within the collection to date and data relating to the closest database relative. C_TABLECAPTION C_TBL

microbiology↗

bioRxiv2022

Induction of neutralizing antibodies against SARS-CoV-2 variants by a multivalent mRNA-lipid nanoparticle vaccine encoding SARS-CoV-2/SARS-CoV Spike protein receptor-binding domains

To address the need for multivalent vaccines against Coronaviridae that can be rapidly developed and manufactured, we compared antibody responses against SARS-CoV, SARS-CoV-2, and several variants of concern in mice immunized with mRNA-lipid nanoparticle vaccines encoding homodimers or heterodimers of SARS-CoV/SARS-CoV-2 receptor-binding domains. All vaccine constructs induced robust anti-viral antibody responses, and the heterodimeric vaccine elicited an IgG response capable of cross-neutralizing SARS-CoV, SARS-CoV-2 Wuhan-Hu-1, B.1.351 (beta), and B.1.617.2 (delta) variants.

immunology↗

bioRxiv2022

Genome-wide association reveals host-specific genomic traits in Escherichia coli

Escherichia coli is an opportunistic pathogen that can colonize or infect various host species. There is a significant gap in our understanding to what extent genetic lineages of E. coli are adapted or restricted to specific hosts. In addition, genomic determinants underlying such host specificity are unknown.By analyzing a randomly sampled collection of 1198 whole-genome sequenced E. coli isolates from four countries (Germany, UK, Spain, and Vietnam), obtained from five host species (human, pig, cattle, chicken, and wild boar) over 16 years, from both healthy and diseased hosts, we demonstrate that certain lineages of E. coli are frequently detected in specific hosts. We report a novel nan gene cluster, designated nan-9, putatively encoding acetylesterases and determinants of uptake and metabolism of sialic acid, to be associated with the human host as identified through genome wide association studies. In silico characterization predicts nan-9 to be involved in sialic acid (Sia) metabolism. In vitro growth experiments with a representative {Delta}nan E. coli mutant strain, using sialic acids 5-N-acetyl neuraminic acid (Neu5Ac) and N-glycolyl neuraminic acid (Neu5Gc) as the sole carbon source, indicate an impaired growth behaviour compared to the wild-type. In addition, we identified several additional E. coli genes that are potentially associated with adaptation to human, cattle and chicken hosts, but not for the pig host. Collectively, this study provides an extensive overview of genetic determinants which may mediate host specificity in E. coli. Our findings should inform risk analysis and epidemiological monitoring of (antimicrobial resistant) E. coli.

genomics↗

bioRxiv2019

Development and validation of microsatellite markers from de novo transcriptome assembly of eggplant (Solanum melongena L.) and its putative progenitor S. incanum L. cultivars

An elite cultivar of eggplant, Ramnagar Giant (Solanum melongena L.) and W-4 (S. incanum L.) with contrasting horticultural traits were used as parental lines to develop a mapping population of RILs. To accelerate breeding programs and to develop large scale SSR markers to be used in QTL mapping, RNASeq libraries from different tissues of both the parental plants were deep sequenced and assembled into representation of a high quality de novo transcriptome using Illumina-based Next Generation Sequencing technology. 99.99% of high quality bases were obtained from all the tissues and deposited in TSA database at the NCBI link. Total 3, 156 and 3, 196 SNVs were detected in S. melongena and S. incanum, respectively. In S. melongena, 11, 262 SSR while in S. incanum 11, 829 SSR containing regions were identified. Based on functional annotation, 21, 914 unique genes could be identified for S. melongena, 21,706 unique genes for S. incanum and overall, 60 different transcription factors were identified in both the lines. Further, a total of 536 SSR markers were designed and screened for polymorphism of which, 157 markers produced polymorphism between the parental lines. The polymorphic SSRs shall be used for genotyping of RILs to map QTLs for various horticultural traits in eggplant and identification of candidate genes in response to biotic and abiotic stress.

genomics↗