Biology subjects

Gunasekaran, D.

Publications and source records attributed to Gunasekaran, D..

4 recordsLinked to original sources

bioRxiv2025

An optimized protocol for Candida albicans infection in Schmidtea mediterranea to study fungal pathogenesis and host defense

Candida albicans is a common opportunistic fungal pathogen that asymptomatically colonizes most humans. Although typically a benign commensal, dysbiosis caused by antibiotic use, immune dysfunction, or epithelial barrier disruption can trigger fungal overgrowth and infection, ranging from superficial mucosal disease to life-threatening systemic candidiasis. New preclinical infection models are needed to dissect C. albicans pathogenesis in vivo across distinct stages of infection and with different measurable host outcomes. We previously established the planarian Schmidtea mediterranea as an invertebrate host for studying host-pathogen interactions during C. albicans infection. S. mediterranea relies entirely on conserved innate immune mechanisms capable of overcoming infection with pathogenic microorganisms, including bacteria and fungi. Planarians remarkable regenerative capacity and accessible stem cell populations make this organism a tractable model to analyze early immune responses, tissue repair, and pathogen clearance in vivo. This model supports simultaneous analysis of fungal virulence and host transcriptional responses, providing valuable insights into infection dynamics. Here, we present an updated protocol with detailed modifications, standardized procedures, and optimized steps for infecting S. mediterranea with C. albicans, designed to enhance reproducibility and enable systematic studies of fungal pathogenesis and host defense. SUMMARYWe present an optimized and detailed protocol for using the planarian Schmidtea mediterranea as a model system to study host-pathogen interactions during fungal infection. This method builds on our previous procedure for infecting planarians with the human fungal pathogen Candida albicans, providing detailed guidance to enhance reproducibility and experimental consistency. The system enables comprehensive, parallel analysis of both host and pathogen responses throughout infection - from initial colonization and disease progression to diverse host outcomes, including clearance or mortality.

microbiology↗

bioRxiv2022

Hybran: Hybrid Reference Transfer and ab initio Prokaryotic Genome Annotation

De novo assembly has become commonplace for microbial organisms, increasing the demand for reliable genome annotation. Ab initio annotation is not an ideal approach for closely related strains due to suboptimal matching of the short or hypervariable genomic features that reference-based annotation transfer can overcome through identification of conserved synteny. At the same time, reference-based annotation methods leave gaps in the annotation where structural variations introduce unique sequence. We present Hybran, a hybrid reference-based and ab initio prokaryotic genome annotation pipeline that transfers features from a curated reference annotation and supplements unannotated regions with ab initio predictions. It builds on existing tools to create initial annotations using both approaches, then compares and resolves them to produce the hybrid annotation. With this pipeline, full advantage is taken of the communitys experimental efforts on reference strains to propagate as many known features as possible without sacrificing best-effort ab initio predictions for the remaining unannotated loci. Genome annotation performed in this way can facilitate comparative genomics and the investigation of evolutionary dynamics in microbial populations. Hybran is freely available at https://lpcdrp.gitlab.io/hybran

bioinformatics↗

bioRxiv2018

Resolving the hypotheticome: annotating M. tuberculosis gene function through bibliomic reconciliation and structural modeling

Accurate and timely functional genome annotation is essential for translating basic pathogen research into clinically impactful advances. Here, through literature curation and structure-function inference, we systematically update the functional genome annotation of Mycobacterium tuberculosis virulent type strain H37Rv. First, we systematically curated annotations for 589 genes from 662 publications, including 282 gene products absent from leading databases. Second, we modeled 1,711 under-annotated proteins and developed a semi-automated pipeline that captured shared function between 400 protein models and structural matches of known function on protein data bank, including drug efflux proteins, metabolic enzymes, and virulence factors. In aggregate, these structure- and literature-derived annotations update 940/1,725 under-annotated H37Rv genes and generate hundreds of functional hypotheses. Retrospectively applying the annotation to a recent whole-genome transposon mutant screen provided missing function for 48% (13/27) of under-annotated genes altering antibiotic efficacy and 33% (23/69) required for persistence during mouse TB infection. Prospective application of the protein models enabled us to functionally interpret novel laboratory generated Pyrazinamide-resistant (PZA) mutants of unknown function, which implicated the emerging Coenzyme A depletion model of PZA action in the mutants PZA resistance. Our findings demonstrate the functional insight gained by integrating structural modeling and systematic literature curation, even for widely studied microorganisms. Functional annotations and protein structure models are available at https://tuberculosis.sdsu.edu/H37Rv in human- and machine-readable formats. IMPORTANCEMycobacterium tuberculosis, the primary causative agent of tuberculosis, kills more humans than any other infectious bacteria. Yet 40% of its genome is functionally uncharacterized, leaving much about the genetic basis of its resistance to antibiotics, capacity to withstand host immunity, and basic metabolism yet undiscovered. Irregular literature curation for functional annotation contributes to this gap. We systematically curated functions from literature and structural similarity for over half of poorly characterized genes, expanding the functionally annotated Mycobacterium tuberculosis proteome. Applying this updated annotation to recent in vivo functional screens added functional information to dozens of clinically pertinent proteins described as having unknown function. Integrating the annotations with a prospective functional screen identified new mutants resistant to a first-line TB drug supporting an emerging hypothesis for its mode of action. These improvements in functional interpretation of clinically informative studies underscores the translational value of this functional knowledge. Structure-derived annotations identify hundreds of high-confidence candidates for mechanisms of antibiotic resistance, virulence factors, and basic metabolism; other functions key in clinical and basic tuberculosis research. More broadly, it provides a systematic framework for improving prokaryotic reference annotations.

genomics↗

bioRxiv2018

Developing A Programmable, Self-Assembling Squash Leaf Curl China Virus (SLCCNV) Capsid Proteins Into \"Nano-Cargo\"-Like Architecture: A Next-Generation \"Nanotool\" For Biomedical Applications

A new era has begun in which pathogens have become useful scaffolds for nanotechnology applications. In this research/study, an attempt has been made to generate an empty cargo-like architecture from a high-profile plant pathogen of Squash leaf curl China virus (SLCCNV). In this approach, SLCCNV coat protein monomers are obtained efficiently by using a yeast Pichia pastoris expression system. Further, dialysis of purified SLCCNV-CP monomers against various pH strengthenened (5-10) disassembly and assembly buffers produced a self-assembled \"Nanocargo\"-like architecture, which also exhibited an ability to encapsulate the magnetic nanoparticles at in vitro. Bioinformatics tools were also utilized to predict the possible self-assembly kinetics and bioconjugation sites as well. The biocompatibility of \"SLCNNV-CP-Nanocargo\" particles was also evaluated by in vitro cancer cells, which eventually proved the particles to be versatile material for the next generation \"nanotool\" capable of housing various therapeutic or imaging agents.

systems biology↗