Biology subjects

Tripathy, R.

Publications and source records attributed to Tripathy, R..

9 recordsLinked to original sources

bioRxiv2026

A ribosome exit tunnel component is required for robust expression of the Drosophila hox gene, abdominal A

Ribosomes, the molecular machines responsible for protein synthesis, are fundamental to all cellular life. Although the higher-level architecture of ribosomes is conserved, a small subunit acting as the mRNA decoding site and a large subunit that catalyses peptide bond formation, there are differences in the numbers of components of each of the subunits between the 3 domains of life. Despite their well-established role in translating genetic information into functional proteins, many complexities in ribosome biology and functionality are only just being revealed. Defects in ribosomal components contribute to a class of disorders termed ribosomopathies that come with a range of symptoms and severities. Here we show that a mutation in the Drosophila ribosomal protein RpL39 causes an anterior-posterior embryonic patterning defect through impaired accumulation of the hox protein Abdominal-A (abdA). Deletions uncovering subunits of the Nascent peptide-Associated Complex (NAC) and Ribosome-Associated Complex (RAC) act as genetic enhancers of the RpL39 mutation leading us to speculate that RpL39 forms a relay between the nascent peptide in the exit tunnel and the exterior surface of the ribosome, modulating the interaction with these ribosomally-associated complexes. This work enhances our knowledge of the roles played by individual ribosome components and feeds into our understanding of the mechanisms of ribosome quality control.

cell biology↗

bioRxiv2026

Mechanism of spike opening in a mammalian gammacoronavirus

Coronavirus spike proteins mediate receptor binding and fusion and are key determinants of viral host range. To bind protein receptors, some CoV spikes undergo conformational changes termed opening, which expose the receptor-binding surface. Yet, the prerequisites and mechanism of spike opening remain poorly understood, especially outside of beta-CoVs, and many CoV spikes have been observed only in the closed conformation. The receptor specificities of gamma-CoVs, for which birds are natural hosts, await in-depth characterisation and their spikes have not been observed to open. Here, we report structures of the spike from an unusual mammalian gamma-CoV isolated from a beluga whale (BwCoV), in closed and open conformations, the latter with two S1B domains erect. BwCoV spike opening is associated with changes throughout S1 that resemble those observed in beta-CoV spikes and similarly propagate into destabilisation of the fusogenic S2 core. Furthermore, the BwCoV-S structure contains an additional density likely corresponding to a fatty acid, consistent with lipid binding stabilising the closed conformation through a pocket distinct from that identified for beta-CoVs. These structural insights reveal conserved principles regulating spike dynamics across coronavirus genera and support lipid binding as a potential modulatory mechanism of spike opening.

biochemistry↗

bioRxiv2026

A stable subgenomic reporter coronavirus enables transcriptional profiling of bystander cells.

Insertion of fluorescent reporter genes into viral genomes is a powerful tool for monitoring infection. In coronaviruses, this is commonly achieved by replacing accessory open reading frames, thereby deleting endogenous gene functions. An alternative strategy is to manipulate viral RNA synthesis by inserting copies of the viral transcription regulatory sequence (TRS) which drive the transcription of viral subgenomic RNAs. However, coronavirus transcription is tightly regulated, and these modifications frequently disrupt native subgenomic RNA synthesis and attenuate viral growth. Here, we describe a reporter coronavirus that overcomes these limitations. Using human coronavirus (HCoV)-OC43 as a model system, we inserted an mNeonGreen reporter between the Spike and ORF5 coding regions, engineering the TRS and surrounding sequence to minimise off-target effects to transcription. This virus is genetically stable, with wildtype growth kinetics and unaltered subgenomic RNA transcriptional ratios. We developed a flexible reverse genetics system, which allows rapid cloning and virus recovery, supported by optimised HCoV-OC43 culture conditions, for high-titre stock generation, and validated analytical reagents. Our reporter virus enabled sensitive detection and isolation of infected cells, facilitating transcriptomic analyses that distinguish host responses in infected and bystander populations. We found that transcriptional responses to infection of cells in culture were predominantly inflammatory, rather than interferon-mediated, and that bystander cells upregulated pathways associated with cytokine response signalling and cell-cell contact sensing. Together, these tools expand the experimental utility of HCoV-OC43, an important seasonal respiratory pathogen and low containment model for betacoronavirus biology.

microbiology↗

bioRxiv2025

A complex of MAST1 and 14-3-3 regulates Tau phosphorylation in the developing cortex

The MAST family of serine/threonine kinases has been implicated in a spectrum of human neurodevelopmental disorders. However, little is known about their biological function or regulation. Seeking to fill these gaps in our knowledge, we have identified upstream and downstream partners of MAST1. 14-3-3, a neuronal 14-3-3 paralog, specifically interacts with MAST1 at two regulatory serines, S90 and S161. PAK, a neuronal regulator of the actin cytoskeleton, phosphorylates MAST1 to regulate its interaction with 14-3-3. Exploiting mouse models of human Mega Corpus Callosum Syndrome (MCC) and whole brain phosphoproteomics, we identify the microtubule-associated protein Tau as a substrate of MAST1. We show that pathogenic MAST1 mutations perturb protein function either through misfolding or attenuation of kinase activity. Our data is consistent with a model in which the MAST kinases couple PAK, a neuronal regulator of the actin cytoskeleton, to microtubule remodeling during the differentiation and specification of cortical neurons.

molecular biology↗

bioRxiv2021

Designing Interpretable Convolution-Based Hybrid Networks for Genomics

Hybrid networks that build upon convolutional layers with attention mechanisms have demon-strated improved performance relative to pure convolutional networks across many regulatory genome analysis tasks. Their inductive bias to learn long-range interactions provides an avenue to identify learned motif-motif interactions. For attention maps to be interpretable, the convolutional layer(s) must learn identifiable motifs. Here we systematically investigate the extent that architectural choices in convolution-based hybrid networks influence learned motif representations in first layer filters, as well as the reliability of their attribution maps generated by saliency analysis. We find that design principles previously identified in standard convolutional networks also generalize to hybrid networks. This work provides an avenue to narrow the spectrum of architectural choices when designing hybrid networks such that they are amenable to commonly used interpretability methods in genomics.

bioinformatics↗

bioRxiv2021

Exploiting marker genes for robust classification and characterization of single-cell chromatin accessibility

MotivationSingle-cell Assay for Transposase Accessible Chromatin using sequencing (scATAC-seq) is a valuable resource to learn cis-regulatory elements such as cell-type specific enhancers and transcription factor binding sites. However, cell-type identification of scATAC-seq data is known to be challenging due to the heterogeneity derived from different protocols and the high dropout rate. ResultsIn this study, we perform a systematic comparison of 7 scATAC-seq datasets of mouse brain to benchmark the efficacy of neuronal cell-type annotation from gene sets. We find that redundant marker genes give a dramatic improvement for a sparse scATAC-seq annotation across the data collected from different studies. Interestingly, simple aggregation of such marker genes achieves performance comparable or higher than that of machine-learning classifiers, suggesting its potential for downstream applications. Based on our results, we reannotated all scATAC-seq data for detailed cell types using robust marker genes. Their meta scATAC-seq profiles are publicly available at https://gillisweb.cshl.edu/Meta_scATAC. Furthermore, we trained a deep neural network to predict chromatin accessibility from only DNA sequence and identified key motifs enriched for each neuronal subtype. Those predicted profiles are visualized together in our database as a valuable resource to explore cell-type specific epigenetic regulation in a sequence-dependent and -independent manner. Contactjesse.gillis@utoronto.ca Supplementary informationSupplementary data are available at xxxxxx online. Key pointsO_LI7 scATAC-seq datasets of mouse brain are systematically compared to benchmark the efficacy of neuronal cell-type annotation from gene sets. C_LIO_LIRedundant marker genes give a dramatic improvement for a sparse scATAC-seq annotation beyond the heterogeneity of scATAC-seq data. C_LIO_LIWe reannotated all scATAC-seq data for detailed cell types using robust marker genes and their meta scATAC-seq profiles are publicly available at a new Meta scATAC-seq server. C_LIO_LIPredicted profiles from only DNA sequence using a deep neural network are visualized together to explore sequence-dependent and -independent epigenetic regulation. C_LI

bioinformatics↗

bioRxiv2017

A 23bp Indel Polymorphism in TLR2 Gene Enhances Inflammation and Disease Severity in Dengue

BackgroundDengue is the most rapidly spreading viral disease transmitted by the bite of infected Aedes mosquitos. Pathogenesis of dengue is still unclear; although host genetic factors, immune responses and virus serotypes have been proposed to contribute to disease severity. The development of high-throughput methods have allowed to scale up capabilities of identifying the key markers of inflammation. Since NS1 protein of dengue virus has been reported to activate immune cells towards enhanced inflammation through TLR2, we examined the role of a polymorphism, a 23bp deletion in 5UTR region of TLR2 gene in patients with dengue (with and without warning signs) and correlated with plasma levels of inflammatory mediators with disease severity and viral serotypes.\n\nMethodsEighty nine patients classified as per WHO 2009 criteria during dengue outbreak in Odisha, India in 2016 were included in the current study. Presence of dengue virus (DENV) was demonstrated by detecting NS1 antigen, IgM capture ELISA and serotypes in circulation were discriminated by type-specific RT-PCR and/or sequencing. Sixty-one confirmed dengue cases were typed for TLR2 indel polymorphism and compared with 485 disease free controls. Plasma samples were assayed for 41-plex cytokine/ chemokines using Luminex bead based immunoassay.\n\nResultsPresence of 23bp deletion allele of TLR2 gene was significantly more in patients with severe dengue in comparison to dengue fever cases (p= 0.03; Odds ratio 4.05) although the frequency of insertion (Ins) allele of TLR2 was comparable in healthy controls and dengue cases (82.4 and 87.9 % respectively). Seventy-three (82%) samples were found to be positive by NS1/IgM capture ELISA/ RT-PCR. DENV-2 was predominant (58%) during the outbreak. Among the host inflammatory biomarkers 9 molecules were significantly altered in dengue patients when compared to healthy controls. The increased levels of IFN-{gamma}, GM-CSF, IL-10, IL-1R and MIP-1{beta} correlated significantly with severe dengue.\n\nConclusionsThe frequency of 23bp Indel mutation of TLR2 was comparable between healthy controls and dengue fever (with and without warning signs), suggesting that this indel mutation does not contribute significantly to susceptibility/ resistance to dengue; however, del allele of TLR2 gene was significantly more associated in patients with severe dengue symptoms when compared to dengue fever cases.

microbiology↗

bioRxiv2017

A primate specific loss of function polymorphism in TLR2 gene decreases inflammation and protects humans from organ dysfunction in Malaria

Polymorphisms of TLR genes could regulate and contribute functionally to innate immunity and inflammation. TLR2, a promiscous receptor recognizes Pathogen Associated Molecular Patterns from several microbes, bacterial, viral, protozoan and helminths. We demonstrate that monocytes of humans with deletion polymorphism in TLR2 gene (a 23 bp deletion in 5 UTR region) respond more vigorously in vitro to several TLR2 ligands in comparison to those with insertion allele. Lower primates such as Rhesus monkeys and Baboon display deletion genotype while insertion is found in higher primates viz., Orangutan, Chimpanzees and Gorilla. Enhanced inflammation is a hallmark of pathogenesis in human severe malaria leading to bad prognosis and odds ratio of patients prone to develop severe malaira such as multi organ failure with del/del genotype was found to be very high. Based on induction of inflammatory cytokines by normal human PBMCs in vitro and circulating cytokine levels in cohorts of patients with severe P. falciparum malaria, we propose that insertion of a 23bp sequence in 5UTR region of TLR2 gene could have led to moderated TLR2 induced inflammation thus offering survival advantage to higher primates by rendering them relatively refractory to multi-organ dysfunction in severe malaria.\n\nOne Sentence SummaryA 23bp deletion in TLR2 gene is associated with high inflammation and susceptibility to organ dysfunction in Plasmodium falciparum malaria.

immunology↗

bioRxiv2017

Sepsis: Partial least squares structural equation modelling (PLS-SEM) suggests a critical role for anti-inflammatory responses in clinical severity

BackgorundDespite major advances in medicine, Sepsis remains one of the major killers in critical care wards around the world. For several years it was widely believed that an early pro-inflammatory host response is followed by an overwhelming anti-inflammatory phase. The hypo-inflammatory status, termed as Compensatory anti-inflammatory response syndrome (CARS), was proposed to be the primary cause of sepsis-associated mortality. However, this paradiam changed in recent years since there was little evidence to support the linear model of host response and pathogenesis in sepsis. Currently held view is that both inflammatory and anti-inflammatory host responses are stimulated in an overlapping manner. In this study a robust statistical model to study the complex interplay of host cytokines in human sepsis has been developed to evaluate host responses in sepsis that contribute significantly to clinical pathology.\n\nMethodsTwentyseven cytokines/ chemokines were quantified in 139 sepsis patients and multivariate analysis of variance (MANOVA) was performed to assess differences in host responses in different categories of clinical severity. Partial least squares regression based structural equation modelling (PLS-SEM) was used to assess interactions between different groups of cytokines and their contribution to clinical pathology. An array of 23 cytokines was analysed in a mouse model of endotoxemia and a similar mathematical model was constructed.\n\nResultsThe results of MANOVA demonstrated the ability of combined cytokine response to discriminate sepsis patients according to clinical severity or outcome. Structural equation modelling revealed strong positive association between inflammatory and anti-inflammatory cytokines. In human sepsis, anti-inflammatory cytokines emerged as a significant entity associated with clinical severity as assessed by APACHE II scores.\n\nConclusionPLS-SEM modeling of cytokine responses and APACHE II score in human sepsis revealed that anti-inflammatory molecules contribute significantly towards clinical severity. More critically, the model offers emperical evidence for failures of clinical trials conducted during the last two decades in which antagonists of inflammatory host responses for human Sepsis were used for sepsis. The model also provides credence to the notion that inflammatory and anti-inflammatory host responses occur concurrently in both experimental endotoxemia and in human sepsis.

immunology↗