Biology subjects

Tracy, S.

Publications and source records attributed to Tracy, S..

5 recordsLinked to original sources

bioRxiv2026

Quantifying the effects of arbuscular mycorrhizal fungi and potato cyst nematodes on root system architecture using X-ray computed tomography

Crop root systems develop in biologically complex soils where beneficial symbionts and pathogenic organisms can jointly influence root architecture and, consequently, belowground function. In this work, we used X-ray computed tomography (CT) to assess how colonisation by the arbuscular mycorrhizal fungus Rhizophagus irregularis (AMF) and infection by the potato cyst nematode Globodera pallida (PCN) influence root system architecture in soil-grown tomato and potato plants. Root architectural traits, including root volume and root surface area, were quantified non-destructively from intact root systems to evaluate the individual and combined effects of AMF colonisation and PCN infection over time. AMF inoculation increased root volume and surface area, whereas PCN infection caused pronounced reductions in these traits, particularly during early development. AMF-associated increases in root system size were maintained in both PCN-free and PCN-infected plants, indicating largely additive effects of beneficial and pathogenic soil biota on root architectural outcomes. These findings show that soil organisms can independently reshape crop root development in ways likely to influence soil exploration and resource acquisition under biologically complex conditions. More broadly, the study highlights the value of X-ray CT as a non-destructive approach for linking belowground biotic interactions with functionally relevant root traits in sustainable agroecosystems.

plant biology↗

bioRxiv2024

Leukemia escapes immunity by imposing a Type-1 regulatory program on neoantigen-specific CD4+ T cells.

The significance of endogenous immune surveillance in acute lymphoblastic leukemia (ALL) remains controversial. Using clinical B-ALL samples and a novel mouse model, we show that neoantigen-specific CD4+ T cells are induced to adopt type-1 regulatory (Tr1) function in the leukemia microenvironment. Tr1s then inhibit cytotoxic CD8+ T cells, preventing effective leukemia clearance. Leukemic cells induce Tr1s by phenocopying hematopoietic stem cells, which normally are subject to effective surveillance by this CD4+ subset. This mechanism effectively redirects Tr1 cells from a role in preventing cancer to maladaptively promoting clinical relapse. In mouse models, inhibition of Tr1 expansion with IL10 receptor (IL10R) blockade is insufficient to improve leukemia control. In contrast, combined therapy with a cytotoxic agent and anti-PDL1 blockade eradicated measurable residual disease. This correlates with polarization of the neoantigen-specific CD4+ T-cell population from Tr1 towards Th1 states. Our findings uncover a mechanism that enables leukemic relapse and resolves existing controversies on the role of immune surveillance towards this cancer type. Therapeutic polarization of neoantigen-specific CD4+ T cells towards Th1 states may improve contemporary immune therapies by reshaping the immune microenvironment towards states permissive for cytotoxic attack of residual leukemia. Key PointsO_LIB-ALL induces neoantigen-specific CD4+ T cells to adopt Type-1 regulatory states, which protect leukemic cells from immune pressure. C_LIO_LIRepolarizing neoantigen-specific CD4+ T-cells towards Th1 states eradicates measurable residual disease. C_LI

cancer biology↗

bioRxiv2024

The use of X-ray Computed Tomography revolutionises soil pathogen detection

Potato cyst nematodes (PCN), namely Globodera pallida, pose a significant threat to potato production worldwide. Accurately quantifying nematode population densities is crucial for effective management strategies. However, traditional detection methods are time-consuming and often imprecise. X-ray computed tomography (CT) offers high-resolution, non-destructive and three-dimensional (3D) imaging frequently used to visualise internal structures of objects, materials or biological tissues, allowing for detailed analysis of their composition, defects, and morphology. Here, we demonstrate the effectiveness of X-ray CT in detecting and quantifying PCN cysts in different soil types. The ability to achieve 3D imaging and volume quantification of PCN cysts from soils allows accurate enumeration of their egg content. To explore future potential, we propose that when integrated with AI-led quantification of X-ray CT-generated cyst counts, this method could evolve into a next-generation technology to accurately and rapidly quantify these damaging pests in agricultural soils. Combined with the potential to co-analyse other organisms within the same sample, we propose X-ray CT as a fundamental tool for comprehensive soil health assessments and sustainable pest management in agriculture. Author SummaryPotato cyst nematodes are a major threat causing significant crop losses worldwide. Traditionally, detecting this pathogen in soil is challenging, often requiring time-consuming and imprecise. Our study explores a new approach using X-ray computed tomography (CT), a powerful imaging tool that creates detailed 3D images in situ. We observed that X-ray CT can effectively detect and measure the cysts nematodes, even within different soil types. This detailed analysis allows us to determine the cyst structures and estimate the eggs contained. In the future, combining X-ray CT with artificial intelligence could make detecting and quantifying these nematodes even faster and more accurate. This method could also be expanded to study other soil organisms, making it a valuable tool for monitoring soil health and improving agricultural pest management.

plant biology↗

bioRxiv2021

Rvb1/Rvb2 proteins couple transcription and translation during glucose starvation

During times of unpredictable stress, organisms must adapt their gene expression to maximize survival. Along with changes in transcription, one conserved means of gene regulation during conditions that quickly represses translation is the formation of cytoplasmic phase-separated mRNP granules such as P-bodies and stress granules. Previously, we identified that distinct steps in gene expression can be coupled during glucose starvation as promoter sequences in the nucleus are able to direct the subcellular localization and translatability of mRNAs in the cytosol. Here, we report that Rvb1 and Rvb2, conserved ATPase proteins implicated as protein assembly chaperones and chromatin remodelers, were enriched at the promoters and mRNAs of genes involved in alternative glucose metabolism pathways that we previously found to be transcriptionally upregulated but translationally downregulated during glucose starvation in yeast. Engineered Rvb1/Rvb2-binding on mRNAs was sufficient to sequester the mRNAs into phase-separated granules and repress their translation. Additionally, this Rvb-tethering to the mRNA drove further transcriptional upregulation of the target genes. Overall, our results point to Rvb1/Rvb2 coupling transcription, mRNA granular localization, and translatability of mRNAs during glucose starvation. This Rvb-mediated rapid gene regulation could potentially serve as an efficient recovery plan for cells after stress removal.

molecular biology↗

bioRxiv2017

Rare Variant Burden in Known Dystonia Genes in Population Controls and Sporadic Dystonia Patients

BackgroundRare mutations in genes associated with Mendelian forms of disease are a potential mechanism for sporadic disease. The need to assess the clinical significance of such variants is increasing as personalized medicine and genome sequencing increases.\n\nObjectiveTo evaluate the rate of rare, functional variants in dystonia genes in the general population to improve interpretation of the clinical relevance of potentially pathogenic variants in dystonia cases.\n\nMethodsWe performed an \"aggregated\" collapsing analysis of exome sequence that considered rare coding variants in genes previously associated with dystonia, a rare neurological movement disorder, on 2,372 population controls of European ethnicity. We then performed a pilot study in sporadic dystonia to assess whether there was a substantially greater incidence of individuals with rare variation in dystonia genes.\n\nResultsNearly half of population controls had a rare coding variant when 148 genes associated with a dystonia phenotype were considered. When the subset of genes causing isolated dystonia (14 genes) was evaluated, 3-4% of controls harbored rare qualifying variants. Our pilot study of case exomes was powered to identify a five-fold higher or greater rate of qualifying variants in isolated dystonia genes in sporadic dystonia cases compared to population controls; we did not find such an enrichment.\n\nConclusionsWe provide the first systematic analysis of rare variation in dystonia genes considered collectively. Our findings emphasize the need to consider the overall frequency of variants in rare disease-related genes in the general population when considering their potential role in clinical presentations.

genomics↗