Biology subjects

Vasudevan, S.

Publications and source records attributed to Vasudevan, S..

At least 19 recordsLinked to original sources

bioRxiv2025

CAcnesDB: A database of Cutibacterium acnes with Integrated Functional Insights derived from Multi-modal Genome Annotation

Cutibacterium acnes is a predominant member of the human skin microbiome, generally as a beneficial or a benign inhabitant, which under specific conditions transforms into a pathogen, causing acne and associated inflammatory responses. While there is a wealth of data on the microbiology and genomics of the microbe, there is a lack of comprehensive annotation of the proteins coded by the genome, slowing progress in understanding its unique metabolic versatility and survival in host hypoxic sebaceous niches. We configured an integrated pipeline for functional annotation of the C. acnes genome, combining gene calling, domain and ontology mapping, KEGG pathways assignment, proteome-scale structural modeling, predicting Pockets and associating the small-molecule metabolites based on binding site similarity to facilitate structure-to-function annotation. Structural predictions using ColabFold covered nearly the full proteome, with 67.4% of models showing high confidence. To infer protein function, ligand-binding sites in the C. acnes modeled proteome were predicted using a consensus of three independent algorithms, PocketDepth, SiteHound, and FPocket. The resulting pockets were matched with known small-molecule binding sites in PDB to map potential ligands, resulting in the C. acnes predicted metabolome (CApM) comprising 1,954 ligands across 1,865 proteins. CAcnesDB is a comprehensive up-to-date database of the C. acnes genome, hosting functional annotation from multiple levels of input and analyses, covering 2297 protein-coding genes. Impact StatementCutibacterium acnes (C. acnes) is implicated in acne vulgaris, a common skin condition affecting millions of people worldwide, yet the absence of a unified genomic resource limits comprehensive understanding of the underlying biology. In this work, we introduce CAcnesDB, a genome-wide annotation resource built through multi-modal integration of sequence- and structure-based analyses, structural proteome models, predicted binding sites associated with small-molecule metabolites, functional classes, protein-protein interactions, and pathways. This resource consolidates enriched annotations to enable systematic exploration of C. acnes biology and pathogenic mechanisms. We showcase its utility through detailed analyses of membrane transporters and hypothetical proteins, highlighting novel functional insights into this skin microbe. Given the clinical relevance of C. acnes in skin health and its role in skincare product development, CAcnesDB represents a valuable platform for both basic research and translational applications.

bioinformatics↗

bioRxiv2025

The Green Band: Using Production and Catch to Judge Distortive Pressure on an Ecosystem

Ecosystem based fisheries management is an increasingly accepted approach for many fisheries management agencies. Indicators and methods that can usefully support the aspiration of making ecosystem based fisheries management decisions on tactical time frames are slowly accumulating, but have primarily focused on biomass status and trends. We first verify that fishing can distort the cumulative distribution of connections within an ecosystem, and then show (via theoretical testing and application to four contrasting case study locations) how relating catch with production by defining an acceptable band of exploitation pressure - the "Green Band" - can help inform fisheries decision makers as to whether an ecosystem is under distortive patterns of fishing pressure that will ultimately undermine the structure of the ecosystem.

ecology↗

bioRxiv2025

Modulating populational variance of methyl-guanine methyl transferase expression through miR-181d degradation: a novel mechanism of temozolomide resistance

Intratumoral heterogeneity plays a pivotal role in cancer evolution, providing the substrate for adaptation to selective pressures, including treatment with chemotherapy. Here, we show that micro-RNA regulation of variance in the expression of the DNA repair protein methyl-guanine methyl transferase (MGMT) contributes to this heterogeneity and acquired therapeutic resistance. In cell lines derived from glioblastomas, the most common form of primary brain tumor, treatment with standard-of-care temozolomide chemotherapy triggers a feed-forward loop between polyribonucleotide nucleotidyltransferase 1 (PNPT1) and miR-181d, an MGMT regulating miRNA, expediting miR-181d degradation. This degradation requires the activation of Ataxia Telangiectasia and Rad3-related (ATR) kinase. The degradation of miR-181d in glioblastoma cells increased both the mean and the variance of MGMT expression in the cell population. Subclone reconstituted cell populations with similar populational mean MGMT levels but with differences in the variance of MGMT expression exhibited differential temozolomide sensitivity, with the higher MGMT variance population showing increased resistance. This resistance is suppressed by exogenously transfected miR-181d. These findings suggest a key role for miRNA in regulating intra-tumoral heterogeneity through modulation of key DNA repair enzymes and provide a compelling rationale for miRNA delivery as a platform for glioblastoma therapy. Significance StatementThis study demonstrates a mechanistic link between a feed-forward loop mediating microRNA degradation and cell-to-cell variance in gene expression, and the contribution of this mechanism to intratumoral heterogeneity and therapeutic resistance. We show that when glioblastoma, the most common form of adult primary brain tumor, is treated with standard-of-care chemotherapy, temozolomide, a feed-forward loop between miR-181d and PNPT1 is initiated, causing rapid degradation of miR-181d. This degradation increases the cell-to-cell variability in methyl-guanine methyl transferase (MGMT) expression, expanding intra-tumoral heterogeneity and contributing to acquired temozolomide resistance. This process can be suppressed by therapeutic delivery of microRNA, providing compelling considerations for clinical translation.

cancer biology↗

bioRxiv2025

Aggregation of the constitutively active K296E rhodopsin mutant contributes to retinal degeneration

A K296E mutation in rhodopsin causes autosomal dominant retinitis pigmentosa, a progressive retinal degenerative disease. Early in vitro characterizations of this mutation studied on a bovine rhodopsin background indicated that the mutation causes the receptor to be constitutively active. This molecular defect has been the primary focus when considering the pathogenic mechanism of the mutation. Knockin mice expressing the K296E rhodopsin mutant were generated and characterized to better understand the pathogenic mechanism of the mutation. Knockin mice exhibited progressive retinal degeneration characteristic of retinitis pigmentosa. The K296E rhodopsin mutant mislocalized in photoreceptor cells and, surprisingly, appeared to aggregate, as indicated by the dye PROTEOSTAT, which binds protein aggregates. The propensity of the K296E rhodopsin mutant to aggregate was tested and confirmed in vitro but was dependent on the species background of rhodopsin. The K296E mutation on either murine or human rhodopsin backgrounds exhibited similar propensities to aggregate. The same mutation on a bovine rhodopsin background, however, exhibited a lower propensity to aggregate, indicating this species background does not adequately model the effects of the K296E mutation. In contrast to previous expectations, we demonstrate here that aggregation of the K296E rhodopsin mutant can promote photoreceptor cell loss.

neuroscience↗

bioRxiv2024

Increased 5-HT2A receptor signalling efficacy differentiates serotonergic psychedelics from non-psychedelics

Background and PurposeSerotonergic psychedelic drugs are under renewed investigation for the potential treatment of several psychiatric disorders. While all serotonergic psychedelics have 5-HT2A receptor activity, the explanation for why some 5-HT2A receptor agonists are not psychedelic is unknown. To address this question, we investigated the 5-HT2A receptor signalling bias and efficacy of a panel of psychedelics and non-psychedelics. Experimental ApproachG -coupled (Ca2+ and IP) and {beta}-arrestin2 signalling effects of eight chemically diverse psychedelics (psilocin, 5-MeO-DMT, LSD, mescaline, 25B-NBOMe and DOI) and non-psychedelics (lisuride and TBG) were characterised using SH-SY5Y cells expressing recombinant human 5-HT2A receptors. Measurements of signalling efficacy and bias were derived from dose-responses curves for each agonist, compared to 5-HT. Follow-up experiments sought to confirm the generality of findings using rat C6 cells expressing endogenous 5-HT2A receptors. Key ResultsIn SH-SY5Y cells, all psychedelics were partial agonists at both 5-HT2A receptor signalling pathways and none showed significant signalling bias. In comparison, in SH-SY5Y cells the non-psychedelics lisuride and TBG were not distinguishable from psychedelics in terms of biased agonist properties, but both exhibited the lowest 5-HT2A receptor signalling efficacy of all drugs tested, a result confirmed in C6 cells. Conclusion and ImplicationsIn summary, all psychedelics tested were unbiased, partial 5-HT2A receptor agonists. Importantly, the non-psychedelics lisuride and TBG were discriminated from psychedelics, not through biased signalling but rather by relatively low efficacy. Thus, 5-HT2A receptor signalling efficacy and not bias provides a possible explanation for why some 5-HT2A receptor agonists are not psychedelic.

pharmacology and toxicology↗

bioRxiv2024

The transition from a non-westernized to westernized gut microbiome in Indian-Immigrants and Indo-Canadians is associated with dietary acculturation

Indian immigration to westernized countries has recently surged, increasing their risk of Inflammatory Bowel Disease (IBD) post-migration. While crucial for understanding IBD risk, the gut microbiome remains understudied in Indians. This cross-sectional study examines the gut microbiomes of Indians residing in India, Indo-Immigrants, and Indo-Canadians in comparison to Euro-Canadian and Euro-Immigrant controls to understand the impact of westernization on their gut. Stool samples for 16S rRNA and shotgun sequencing assessed microbial taxa and functional profiles, complemented by dietary and demographic data to evaluate lifestyle patterns. Results revealed distinct microbiotas in Indians and Indo-Immigrants compared to control groups, with high abundances of Prevotella spp. and CAZymes reflecting their high complex carbohydrate diet. Indo-Canadians exhibited a transitional microbiome towards westernization, mirroring increasing dietary acculturation. Considering 44% of Canadians are first- and second-generation immigrants and the global adoption of westernized practices, future research should investigate the health implications of such microbiome transitions in immigrant populations and newly industrialized nations.

microbiology↗

bioRxiv2024

BAMBI: Integrative biostatistical and artificial-intelligence method discover coding and non-coding RNA genes as biomarkers

Accurate disease diagnosis and prognosis are crucial for effective treatment management and improving patient outcomes. However, accurately detecting early signs of certain diseases or recurrence remains challenging. Existing machine-learning methods for identifying gene expression biomarkers have several limitations, including poor performance on independent test datasets, inability to directly process omics data, and difficulty in identifying noncoding RNA genes as biomarkers. Additionally, these methods may not provide sufficient biological interpretation of their results, and the panel biomarkers they identify may not be suitable for clinical application. To address these limitations, we have developed a new computational method called BAMBI, which integrates multiple machine-learning algorithms and statistical approaches to identify putative coding and noncoding genes as biomarkers for disease diagnosis and prognosis. We evaluated BAMBI ability to identify diagnostic and prognostic biomarkers by analyzing multiple RNA-seq datasets from cancerous and non-cancerous diseases at population levels. The results from BAMBI demonstrate significant biological interpretability and state-of-the-art prediction performance. When the singular gene identified by BAMBI is used as a diagnostic biomarker, it achieves a balance accuracy exceeding 95% in studies of both breast cancer and psoriasis. Additionally, the prognostic biomarkers that BAMBI identifies from RNA-seq data of Acute Myeloid Leukemia (AML) patients significantly correlate with the survival rates in an independent AML patient cohort. Additionally, BAMBI outperforms existing methods by delivering more robust results, identifying biomarkers with fewer genes, and simultaneously achieving superior prediction accuracy. We have implemented BAMBI into user-friendly software for the research community. In summary, BAMBI serves as a more reliable pipeline for identifying both coding and noncoding genes as biosignature markers, enhancing the accuracy of disease diagnosis and prognosis. BAMBI is available via https://github.com/CZhouLab/BAMBI.

bioinformatics↗

bioRxiv2023

Adenosine Kinase regulates Sleep Timing and the Homeostatic Sleep Response through Distinct Molecular Pathways

Sleep behaviour is broadly regulated by two drives, the circadian (Process C), which is orchestrated by the suprachiasmatic nuclei (SCN), and controls sleep timing, and the homeostatic (Process S), which controls sleep amount and the response to sleep deprivation (Borbely et al., 2016). However, the molecular pathways that mediate their independent effects, and their interactions remain unclear. Adenosine is an important integrator of both processes (Bjorness & Greene, 2009; Jagannath et al., 2021, 2022), such that adenosine levels track and modulate wakefulness, whilst adenosine signalling inhibits the circadian response to light. Therefore, we studied the sleep/circadian behaviour, and cortical and SCN transcriptomic profiles of a mouse model overexpressing Adenosine Kinase (Adk-Tg) (Fedele et al., 2005), (Palchykova et al., 2010). We found that overall, the Adk-Tg mouse slept less and showed lower amplitude circadian rhythms with an altered sleep/wake distribution across the 24h day, which correlated with changes in transcription of synaptic signalling genes that would shift the excitatory/inhibitory balance. In addition, the Adk-Tg mouse showed a reduced level of ERK phosphorylation, and attenuation of DNA repair related pathways. After sleep deprivation, however, the Adk-Tg mouse significantly increased relative to wildtype, immediate early gene expression levels including of Arc, but paradoxically reduced ERK phosphorylation. Thus, baseline sleep levels and timing are regulated by ERK signalling, whereas the response to sleep loss is mediated by the alteration of the transcriptomic landscape independently of ERK.

molecular biology↗

bioRxiv2023

Regulation of RNA methylation by therapy treatment, promotes tumor survival

Our data previously revealed that chemosurviving cancer cells translate specific genes. Here, we find that the m6A-RNA-methyltransferase, METTL3, increases transiently in chemotherapy-treated breast cancer and leukemic cells in vitro and in vivo. Consistently, m6A increases on RNA from chemo-treated cells, and is needed for chemosurvival. This is regulated by eIF2 phosphorylation and mTOR inhibition upon therapy treatment. METTL3 mRNA purification reveals that eIF3 promotes METTL3 translation that is reduced by mutating a 5'UTR m6A-motif or depleting METTL3. METTL3 increase is transient after therapy treatment, as metabolic enzymes that control methylation and thus m6A levels on METTL3 RNA, are altered over time after therapy. Increased METTL3 reduces proliferation and anti-viral immune response genes, and enhances invasion genes, which promote tumor survival. Consistently, overriding phospho-eIF2 prevents METTL3 elevation, and reduces chemosurvival and immune-cell migration. These data reveal that therapy-induced stress signals transiently upregulate METTL3 translation, to alter gene expression for tumor survival. One sentence summarym6A enzyme translation upon therapy stress, promotes tumor survival

molecular biology↗

bioRxiv2022

Circadian regulation of human immunodeficiency virus type 1 replication

Human immunodeficiency virus 1 (HIV-1) is a life-threatening pathogen that still lacks curative therapies or vaccines. Circadian rhythms are endogenous daily oscillations that coordinate an organisms response to its environment and invading pathogens. Recent reports of diurnal variation in peripheral viral load in HIV-1 infected subjects highlights the need for mechanistic studies. Here, we demonstrate rhythmic HIV-1 replication in circadian-synchronised model systems and show the circadian transcription factors, BMAL1 and REV-ERB, bind conserved motifs in the HIV-1 promoter. REV-ERB competes with ROR for binding to the same regulatory motif, and we uncover a role for ROR inhibitors to perturb rhythmic HIV-1 replication and host gene expression. We demonstrate that many HIV-1 host factors are circadian regulated and likely to define rhythmic viral replication. In summary, this study increases our understanding of the mechanisms underlying the circadian regulation of HIV that can inform HIV therapy and management.

microbiology↗

bioRxiv2022

NF-κB inhibitor alpha has a cross-variant role during SARS-CoV-2 infection in ACE2-overexpressing human airway organoids

As SARS-CoV-2 continues to spread worldwide, tractable primary airway cell models that accurately recapitulate the cell-intrinsic response to arising viral variants are needed. Here we describe an adult stem cell-derived human airway organoid model overexpressing the ACE2 receptor that supports robust viral replication while maintaining 3D architecture and cellular diversity of the airway epithelium. ACE2-OE organoids were infected with SARS-CoV-2 variants and subjected to single-cell RNA-sequencing. NF-{kappa}B inhibitor alpha was consistently upregulated in infected epithelial cells, and its mRNA expression positively correlated with infection levels. Confocal microscopy showed more I{kappa}B expression in infected than bystander cells, but found concurrent nuclear translocation of NF-{kappa}B that I{kappa}B usually prevents. Overexpressing a nondegradable I{kappa}B mutant reduced NF-{kappa}B translocation and increased viral infection. These data demonstrate the functionality of ACE2-OE organoids in SARS-CoV-2 research and identify an incomplete NF-{kappa}B feedback loop as a rheostat of viral infection that may promote inflammation and severe disease.

microbiology↗

bioRxiv2022

Sleep and circadian rhythm disruption alters the lung transcriptome to predispose to viral infection

Sleep and circadian rhythm disruption (SCRD), as encountered during shift work, increases the risk of respiratory viral infection including SARS-CoV-2. However, the mechanism(s) underpinning higher rates of respiratory viral infection following SCRD remain poorly characterised. To address this, we investigated the effects of acute sleep deprivation on the mouse lung transcriptome. Here we show that sleep deprivation profoundly alters the transcriptional landscape of the lung, causing the suppression of both innate and adaptive immune systems, disrupting the circadian clock, and activating genes implicated in SARS-CoV-2 replication, thereby generating a lung environment that promotes viral infection and associated disease pathogenesis. Our study provides a mechanistic explanation of how SCRD increases the risk of respiratory viral infections including SARS-CoV-2 and highlights therapeutic avenues for the prevention and treatment of COVID-19.

neuroscience↗

bioRxiv2021

Ribosome changes elicit non-canonical translation for chemosurvival in G0 leukemic cells

Quiescent leukemic cells survive chemotherapy, with translation changes. Our data reveal that FXR1, a protein amplified in several aggressive cancers, increases in quiescent and chemo- treated leukemic cells, and promotes chemosurvival. This suggests undiscovered roles for this RNA- and ribosome-associated protein in chemosurvival. FXR1 depletion decreases translation and ribosome subunits, with altered rRNAs, snoRNAs, and ribosomal proteins (RPs). We find that FXR1 binds factors that promote ribosome gene transcription and bind snoRNAs. Ribosome changes increased in FXR1-overexpressing cells, including increased snoRNAs and RPLP0/uL10, activate eIF2 kinases. Accordingly, phospho-eIF2 increases, enabling non- canonical translation of survival and immune regulators in FXR1-overexpressing cells. Overriding these with inhibitors reduces chemosurvival. Thus, increased FXR1 in quiescent or chemo-treated leukemic cells, alters ribosomes that trigger stress signals to re-direct translation for chemosurvival. One Sentence SummaryFXR1 alters ribosomes in G0, which induce stress signals to elicit noncanonical translation for AML drug and immune survival.

molecular biology↗

bioRxiv2021

The Transcriptome Architecture of Polyomaviruses

Polyomaviruses (PyV) are ubiquitous pathogens that can cause devastating human diseases. Due to the small size of their genomes, PyV utilize complex patterns of RNA splicing to maximize their coding capacity. Despite the importance of PyV to human disease, their transcriptome architecture is poorly characterized. Here, we compare short- and long-read RNA sequencing data from eight human and non-human PyV. We provide a detailed transcriptome atlas for BK polyomavirus (BKPyV), an important human pathogen, and the prototype PyV, simian virus 40 (SV40). We identify pervasive wraparound transcription in PyV, wherein transcription runs through the polyA site and circles the genome multiple times. Comparative analyses identify novel, conserved transcripts that increase PyV coding capacity. One of these conserved transcripts encodes superT, a T antigen containing two RB-binding LxCxE motifs. We find that superT-encoding transcripts are abundant in PyV-associated human cancers. Together, we show that comparative transcriptomic approaches can greatly expand known transcript and coding capacity in one of the simplest and most well-studied viral families.

microbiology↗

bioRxiv2021

Light-regulated SIK1 remodels the synaptic phosphoproteome to induce sleep

The sleep and circadian systems act in concert to regulate sleep-wake timing, yet the molecular mechanisms that underpin their interaction to induce sleep remain unknown. Synaptic protein phosphorylation, driven by the kinase SIK3, correlates with sleep pressure, however it is unclear whether these phosphoproteome changes are causally responsible for inducing sleep. Here we show that the light-dependent activity of SIK1 controls the phosphorylation of a subset of the brain phosphoproteome to induce sleep in a manner that is independent of sleep pressure. By uncoupling phosphorylation and sleep induction from sleep pressure, we establish that synaptic protein phosphorylation provides a causal mechanism for the induction of sleep under different environmental contexts. Furthermore, we propose a framework that details how the salt-inducible kinases regulate the synaptic phosphoproteome to integrate exogenous and endogenous stimuli, thereby providing the molecular basis upon which the sleep and circadian systems interact to control the sleep-wake cycle.

neuroscience↗

bioRxiv2021

Controlling Staphylococcus aureus by 2-phenol (2-MAMP) in a co-culture moderates the biofilm and virulence of Pseudomonas aeruginosa

Staphylococcus aureus and Pseudomonas aeruginosa are the most encountered organisms in a polymicrobial chronic wound infection. Production of multiple virulence factors by this duo delays wound healing process. Notably, P. aeruginosa displays enhanced virulence in the presence of S. aureus by a peptidoglycan sensing mechanism. Thus, novel therapies are imperative to address polymicrobial infections effectively. Previously, it has been suggested that targeting S. aureus might be a possible approach to reduce the severity of P. aeruginosa in a polymicrobial infection. In this aspect, we have used 2-[(Methylamino)methyl]phenol (2-MAMP), our previously reported QS inhibitor to target S. aureus and phenotypically determine the virulence factors of P. aeruginosa under this condition. Analysis of major virulence factors of Pseudomonas viz. biofilm, pyocyanin and pyoveridine showed a significant reduction. The competitive index (CI) and relative increase ratio (RIR) were determined to understand the organisms interaction in co-culture. Results indicated competitiveness among the strains and on increasing ratios of S. aureus cells, co-existence was noticed. Further, as a sensible approach antibiotic - antivirulence drug combinations were tested on co-culture. Significant improvement in the growth inhibition was observed. Our preliminary results presented here would enable further research to address polymicrobial infection in a novel way.

microbiology↗

bioRxiv2021

Design of a novel DNA Gyrase B inhibitor with a rhodanine scaffold: in silico and in vitro approaches

Methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin intermediate-resistant Staphylococcus aureus (VRSA) is one among the WHO high priority pathogens. Among these two, MRSA is the most globally documented pathogen that necessitates the pressing demand for new classes of anti-MRSA drugs. Bacterial gyrase targeted therapeutics are unique strategies to overcome cross-resistance as they are present only in bacteria and absent in higher eukaryotes. The GyrB subunit is essential for the catalytic functions of the bacterial enzyme DNA Gyrase, thereby constituting a promising druggable target. The current study performed a structure-based virtual screening to designing GyrB target-specific candidate molecules. The de novo ligand design of novel hit molecules was performed using a rhodanine scaffold. Through a systematic in silico screening process, the hit molecules were screened for their synthetic accessibility, drug likeliness and pharmacokinetics properties in addition to its target specific interactions. Of the total 374 hit molecules obtained through de novo ligand design, qsl-304 emerged as the most promising ligand. qsl-304 was synthesized through a one-step chemical synthesis procedure, and the in vitro activity was proven, with an IC50 of 31.23 g/mL against the novobiocin resistant clinical isolate of Staphylococcus aureus sa-P2003. Further studies on time-kill kinetics showed the bacteriostatic nature with the diminished recurrence of resistance.

microbiology↗

bioRxiv2021

Mapping cellular subpopulations within triple negative breast cancer tumors provides a tool for cancer sensitization to radiotherapy

Triple negative breast cancer (TNBC) is an aggressive type of cancer that is known to be resistant to radiotherapy (RT). Evidence is accumulating that is indicative of the plasticity of TNBC, where one cancer subtype switches to another in response to various treatments, including RT. In this study we aim to overcome tumor resistance by designing TNBC-sensitizing targeted therapies that exploit the plasticity occurring due to radiation exposure. Using single cell analysis of molecular changes occurring in irradiated TNBC tumors, we identified two initially undetected distinct subpopulations, represented by overexpressed Her2 and cMet, expanding post-RT and persisting in surviving tumors. Using murine cancer models and patient-derived TNBC tumors, we showed that only simultaneous targeting of Her2 and cMet was successful in sensitizing TNBC to RT and preventing its regrowth. The strategy presented herein holds the potential to be broadly applicable in clinical use. HighlightsO_LISensitization of TNBC to radiotherapy (RT) is a clinically unmet need C_LIO_LISingle cell strategy creates a precise map of subpopulations expanding post-RT C_LIO_LIEvolution of intra-tumor heterogeneity is turned into a therapeutic advantage C_LIO_LISimultaneous targeting of expanding subpopulations sensitizes TNBC to radiotherapy C_LI

cancer biology↗