Biology subjects

Subedi, A.

Publications and source records attributed to Subedi, A..

8 recordsLinked to original sources

bioRxiv2026

Benchmarking Large Language Models for Transcriptomic Data Analysis and Visualization: Multi-Model Workflow Evaluation

This study presents a comprehensive benchmarking evaluation of large language models(LLMs) and agentic coding systems for automated analysis and visualization workflows for transcriptomic data, in particular human responses to COVID-19 infection. Multiple models, including ChatGPT 5.5, Claude Sonnet 4.6, Gemini 3.1, and Llama4-Scout, were assessed across a series of scientific prompts designed to test their ability to reproduce workflow components such as dimensionality reduction, clustering, outlier detection, reproducibility, and code generation. The benchmark protocol involved varying prompt specificity and examined both quantitative metrics such as clustering scores and outlier counts as well as qualitative aspects such as code quality and reproducibility. Results indicate that prompt specificity improves code structure and methodological correctness, but quantitative performance depends heavily on preprocessing choices and execution environment. While some models produced strong code and reproducible outputs, alignment with scientific targets like label-based clustering was inconsistent. The findings highlight the promise and limitations of current LLMs for automating scientific data analysis and visualization and suggest directions for future benchmarking and workflow standardization.

bioinformatics↗

bioRxiv2026

Cell-state-dependent responses to PLK1 inhibition reveal a non-canonical microtubule-endolysosomal vulnerability in quiescent leukemia stem cells

Relapse in cancer is frequently driven by therapy-resistant quiescent cancer stem cells. Conventional chemotherapy has been designed to target proliferating tumor cells and is generally presumed to be ineffective against non-cycling cancer stem cells. Using acute myeloid leukemia (AML) as a model, we challenge this prevailing view by showing that inhibition of the mitotic master regulator Polo-like kinase 1 (PLK1), a kinase extensively pursued for antiproliferative cancer therapy, unexpectedly eradicates quiescent leukemia stem cells (LSC) through a mechanism distinct from its canonical mitotic function. In proliferating AML cells, PLK1 inhibition (PLK1i) induced G2/M arrest and mitotic catastrophe. In contrast, quiescent LSC underwent apoptosis independent of mitotic arrest, revealing a cell-state-dependent mode of drug action. Mechanistically, PLK1i initiated a multi-step process through disruption of a previously unrecognized, stem cell-specific interaction between PLK1 and MAP1A, resulting in perturbed vesicle trafficking and endolysosomal homeostasis characterized by altered receptor internalization, vesicle accumulation and lysosomal dysfunction, ultimately culminating in apoptotic cell death. Combinatorial pharmacologic perturbation studies established microtubule regulation as a critical determinant of quiescent LSC survival, while ex vivo and in vivo assays demonstrated depletion of functionally-defined LSC following PLK1i. These findings identify a previously unrecognized role for PLK1 in intracellular trafficking and establish MAP1A-dependent control of vesicle homeostasis as a mechanistic determinant of cancer stem cell survival. More broadly, this study demonstrates that classical antimitotic compounds, including microtubule-targeting agents and PLK1 inhibitors, can eradicate both cycling leukemic blasts and quiescent LSC through distinct, cell state-dependent mechanisms, challenging proliferation-centric models of chemotherapy action.

cancer biology↗

bioRxiv2026

Allelic Diversity and Core Conservation of Type III Effectors Across Xanthomonads Causing Bacterial Spot of Pepper and Tomato

Bacterial spot of tomato and pepper (BST/P) is an economically devastating disease caused by four distinct Xanthomonas pathogens: X. euvesicatoria pv. euvesicatoria (Xe), X. euvesicatoria pv. perforans (Xp), X. hortorum pv. gardneri (Xg), and X. vesicatoria (Xv). A key component of virulence in these pathogens is the type III secretion system (T3SS), which delivers type III effector (T3E) proteins into host plant cells. To comprehensively characterize T3E repertoires and assess the stability of core effectors at a population scale, we evaluated a global dataset comprising 1,037 quality-filtered genomes, including 585 Xp, 350 Xe, 69 Xg, and 33 Xv strains. Across this collection, genes for six effectors were present in 100% of the examined genomes (XopK, XopL, XopM, XopN, XopX, and XopZ1) and an additional four effectors in [≥]95% of genomes (XopK, XopL, XopM, XopN, XopX, and XopZ1). Xp and Xe populations maintained large total effector repertoires with extensive allelic variation, displaying exceptional polymorphism within XopD and XopAD. In contrast, Xg and Xv exhibited highly stable effector profiles with markedly reduced allelic diversification across geographic regions and decades. Disruptive mutations, including early stop codons and frameshifts mutations, in genes for XopAZ, XopAF, and XopAR were prevalent across specific pathogens pointing to ongoing pseudogenization and targeted gene loss. These findings provide a high-resolution characterization of the conserved and variable components of the BST/P pathogen effector arsenal and serve as a foundation for monitoring population evolution and breeding durable disease resistance to multiple pathogens.

genomics↗

bioRxiv2025

Rapid population flux in bacterial spot xanthomonads during a transition in dominance between two genotypes in consecutive tomato production seasons and identification of a new species Xanthomonas oklahomensis sp. nov.

In the bacterial spot of tomato disease complex, Xanthomonas euvesicatoria pv. perforans (Xep) is known to outcompete X. euvesicatoria pv. euvesicatoria (Xee). The result, over time in tomato production systems where both pathogens are present, is the anticipated displacement of Xee by Xep. In this study, we characterized the population of recovered strains from grower fields in response to a bacterial spot of tomato outbreak in east and central Oklahoma in 2018 and 2019. Tomato and pepper strains sampled in earlier years were included to provide additional context. Phenotypic and genome-based analyses showed marked differences in race and species composition in recovered strains. All pre-2018 (2001-2014) tomato bacterial spot strains were Xep race T3, except one T4 strain. Tomato bacterial spot strains in 2018 consisted of Xee race T1 and Xep T3, while strains recovered in 2019 from the same locations were exclusively Xep T4 strains. The 2019 Xep T4 strains form the same cluster with the 2014 Xep T4 strain on the phylogenetic tree, suggesting the same population. Only the Xep race T4 strains showed an expanded host range to pepper. The recovered strains were also variable in copper sensitivity and effector content. We additionally recovered non-bacterial spot xanthomonads, one of which belongs to the new species, Xanthomonas oklahomensis sp. nov. These results contributes to novel insights in understanding genomic heterogeneity and seasonal population flux between competing bacterial genotypes during disease outbreaks and can be considered when developing disease management strategies.

plant biology↗

bioRxiv2024

Intercontinental dissemination and diversification of Xanthomonas perforans in tomato production

Emerging and re-emerging plant diseases continue to present multifarious threats to global food security. Considerable recent efforts are therefore being channeled towards understanding the nature of pathogen emergence, their spread and evolution. Xanthomonas euvesicatoria pv. perforans (Xep), one of the causal agents of bacterial spot of tomato, rapidly emerged and displaced other bacterial spot xanthomonads in tomato production regions around the world. In less than three decades, it has become a dominant xanthomonad pathogen in tomato production systems across the world and presents a model for understanding diversification of recently emerged bacterial plant pathogens. Although Xep has been continuously monitored in Florida since its discovery, the global population structure and evolution at the genome-scale is yet to be fully explored. The objectives of this work were to determine genetic diversity globally to ascertain if different tomato production regions contain genetically distinct Xep populations, to examine genetic relatedness of strains collected in tomato seed production areas in East Asia and other production regions, and to evaluate variation in type III effectors, which are critical pathogenicity and virulence factors, in relationship to population structure. We used genome data from 270 strains from 13 countries for phylogenetic analysis and characterization of Xop effector gene diversity among strains. Our results showed notable genetic diversity in the pathogen. We found genetically similar strains in distant tomato production regions, including seed production regions, and diversification over the past 100 years, which is consistent with intercontinental dissemination of the pathogen in hybrid tomato production chains. Evolution of the Xep pangenome, including the acquisition and loss of type III secreted effectors, is apparent within and among phylogenetic lineages. The apparent long-distance movement of the pathogen, together with variants that may not yet be widely distributed, poses risks of emergence of new variants in tomato production.

microbiology↗

bioRxiv2024

Nerve injury downregulates δ-opioid and cannabinoid CB1 receptor genes through REST in primary sensory neurons

The transcription repressor REST in the dorsal root ganglion (DRG) is upregulated by peripheral nerve injury and promotes the development of chronic pain. However, the genes targeted by REST in neuropathic pain development remain unclear. The expression levels of 4 opioid receptor (Oprm1, Oprd1, Oprl1, Oprk1) and the cannabinoid CB1 receptor (Cnr1) genes in the DRG regulate nociception. In this study, we determined the role of REST in the control of their expression in the DRG induced by spared nerve injury (SNI) in both male and female mice. Transcriptomic analyses of male mouse DRGs followed by quantitative reverse transcription polymerase chain reaction analyses of both male and female mouse DRGs showed that SNI upregulated expression of Rest and downregulated mRNA levels of all 4 opioid receptor and Cnr1 genes, but Oprm1 was upregulated in female mice. Analysis of publicly available bioinformatic data suggested that REST binds to the promoter regions of Oprm1 and Cnr1. Chromatin immunoprecipitation analyses indicated differing levels of REST at these promoters in male and female mice. Full-length Rest conditional knockout in primary sensory neurons reduced SNI-induced pain hypersensitivity and rescued the SNI-induced reduction in the expression of Oprd1 and Cnr1 in the DRG in both male and female mice. Our results suggest that nerve injury represses the transcription of Oprd1 and Cnr1 via REST in primary sensory neurons and that REST is a potential therapeutic target for neuropathic pain.

neuroscience↗

bioRxiv2022

Genetically defined nucleus incertus neurons differ in connectivity and function

The nucleus incertus (NI), a conserved hindbrain structure implicated in the stress response, arousal, and memory, is a major site for production of the neuropeptide relaxin-3. On the basis of goosecoid homeobox 2 (gsc2) expression, we identified a neuronal cluster that lies adjacent to relaxin 3a (rln3a) neurons in the zebrafish analogue of the NI. To delineate the characteristics of the gsc2 and rln3a NI neurons, we used CRISPR/Cas9 targeted integration to drive gene expression specifically in each neuronal group, and found that they differ in their efferent and afferent connectivity, spontaneous activity, and functional properties. gsc2 and rln3a NI neurons have widely divergent projection patterns and innervate distinct subregions of the midbrain interpeduncular nucleus (IPN). Whereas gsc2 neurons are activated by electric shock, rln3a neurons exhibit spontaneous fluctuations in calcium signaling and regulate locomotor activity. Our findings define heterogeneous neurons in the NI and provide new tools to probe its diverse functions.

neuroscience↗

bioRxiv2018

Brain-wide cellular resolution imaging of Cre transgenic zebrafish lines for functional circuit-mapping

Decoding the functional connectivity of the nervous system is facilitated by transgenic methods that express a genetically encoded reporter or effector in specific neurons; however, most transgenic lines show broad spatiotemporal and cell-type expression. Increased specificity can be achieved using intersectional genetic methods which restrict reporter expression to cells that co-express multiple drivers, such as Gal4 and Cre. To facilitate intersectional targeting in zebrafish, we have generated more than 50 new Cre lines, and co-registered brain expression images with the Zebrafish Brain Browser, a cellular resolution atlas of 264 transgenic lines. Lines labeling neurons of interest can be identified using a web-browser to perform a 3D spatial search (zbbrowser.com). This resource facilitates the design of intersectional genetic experiments and will advance a wide range of precision circuit-mapping studies.

neuroscience↗