Biology subjects

Rose, E.

Publications and source records attributed to Rose, E..

5 recordsLinked to original sources

bioRxiv2026

Season-long head acceleration exposure, prior contact-sport history, and cognitive performance in British amateur American football players

Background: Head acceleration events (HAEs) are common in contact sports, but season-long exposure and its relationship with cognitive performance in amateur British American football remain poorly characterised. Methods: Thirty male players were recruited from three British American football teams. Cognitive performance was assessed pre-season, mid-season, and post-season using the Sport Concussion Assessment Tool 6 and computerised Stroop, 2-back, Go/No-go, and visual-search tasks. Seasonal cognitive analyses included 23 participants with available data. HAEs were quantified using helmet-mounted accelerometers; exposure-linked analyses were restricted to 19 participants who provided sufficiently complete sensor recordings across contact training sessions and competitive matches. Seasonal cognitive changes were assessed using mixed-effects models. Associations of in-season HAE metrics and previous contact-sport seasons with global cognitive change were examined using simple linear regression and elastic-net regression. Results: In the 19-participant exposure-linked cohort, prior contact-sport exposure showed the strongest nominal univariate association with worse global cognitive change (r squared = 0.337, p = 0.009), although this did not remain significant after correction for multiple comparisons (Benjamini-Hochberg-adjusted p = 0.055). Corrected nested cross-validation indicated little out-of-sample performance for the multivariable elastic-net model (r = 0.144, predictive R squared = -0.008). Although previous contact-sport seasons had the largest standardised coefficient in the final full-cohort fit, predictor retention varied substantially across resamples. Conclusion: Prior contact-sport exposure showed the strongest exploratory association with relatively worse global cognitive change, whereas in-season HAE metrics showed weaker associations. However, the multivariable model did not demonstrate useful out-of-sample predictive performance, and the small exposure-linked cohort precludes firm conclusions regarding the relative importance of individual predictors.

neuroscience↗

bioRxiv2023

High-throughput single-nucleus hybrid sequencing reveals genome-transcriptome correlations in cancer

To deepen our understanding of cancer heterogeneity and uncover the dynamic interactions of tumor and host cells, we introduce hybrid BAG-seq: a high-throughput, multi-omic method that simultaneously captures DNA and RNA from tens of thousands of individual single nuclei. This method provides dual molecular layer information: DNA to distinguish tumor from stroma, identify tumor subclones, and detect mutant stromal sub-populations; and RNA to characterize distinct cell types, cell states, and signatures of aberrant expression. Additionally, we developed a suite of analysis tools to illuminate cluster phylogeny and connections between DNA identity and RNA expression. We applied this hybrid protocol to 65,499 single nuclei from samples of five uterine cancer patients, and validated the clustering using RNA-only and DNA-only protocols on 34,651 and 21,432 nuclei, respectively, from the same tissues. Multiple tumor genome or expression clusters were often present within a patient, with different tumor clones projecting into distinct or shared expression states, demonstrating nearly all possible genome-transcriptome correlations across the cohort. While tumor expression profiles were highly unique to each patient, the stromal cell types generally recurred across samples, but certain patients and tissues exhibited unique stromal sub-types characterized by aberrant expression. Moreover, we identified mutant stroma in various cell types from several patients with a significant loss of the X-chromosome. This study reveals the complex landscape of genome and transcriptome interactions at the resolution of single nuclei, providing new insights into mutant stroma and tumor heterogeneity.

genomics↗

bioRxiv2021

Frugivore gut passage increases seed germination: an updated meta-analysis

Many plants rely on animal mutualists for reproduction. Quantifying how animal mutualists impact plant performance provides a foundation for modelling how change in animal communities affects the composition and functioning of plant communities. We performed a meta-analysis of 2539 experiments, 6 times more than the last comprehensive meta-analysis, examining how gut passage by frugivores influences seed germination. We simultaneously analyzed multiple predictor variables related to study methodology, location, and frugivore identity to disentangle methodological from ecological impacts on effect sizes. We found that gut passage by birds, fish, reptiles, bats, primates, and other mammals on average increased seed germination, but that the magnitude varied across vertebrate groups. The positive effects of gut passage were largely explained by the de-inhibitory effects of pulp removal rather than by the scarification of seed tissues. Some previous studies and meta-analyses that found no effect of gut passage only tested scarification or did not distinguish between these tests of scarification and pulp removal. We found that, for a typical fleshy-fruited plant species, the lack of gut passage reduces germination by 60%. From an evolutionary perspective, this indicates a large risk associated with reliance on animal mutualists that is balanced against the benefits of animal-mediated seed dispersal. From a conservation perspective, this highlights the potential for large demographic consequences of frugivore declines on plant populations. Our database and findings advance quantitative predictions for the role of fruit-frugivore interactions in shaping plant communities in the Anthropocene.

ecology↗

bioRxiv2019

Absolute measurement of the tissue origins of cell-free DNA in the healthy state and following paracetamol overdose

BackgroundDespite the emergence of cell-free DNA (cfDNA) as a clinical biomarker in cancer, the tissue origins of cfDNA in healthy individuals have to date been inferred only by indirect and relative measurement methods, such as tissue-specific methylation and nucleosomal profiling.\n\nMethodsWe performed the first direct, absolute measurement of the tissue origins of cfDNA, using tissue-specific knockout mouse strains, in both healthy mice and following paracetamol (APAP) overdose. We then investigated the utility of total cfDNA and the percentage of liver-specific cfDNA as clinical biomarkers in patients presenting with APAP overdose.\n\nResultsAnalysis of cfDNA from healthy tissue-specific knockout mice showed that cfDNA originates predominantly from white and red blood cell lineages, with minor contribution from hepatocytes, and no detectable contribution from skeletal and cardiac muscle. Following APAP overdose in mice, total plasma cfDNA and the percentage fraction originating from hepatocytes increased by ~100 and ~19-fold respectively. Total cfDNA increased by an average of more than 236-fold in clinical samples from APAP overdose patients with biochemical evidence of liver injury, and 18-fold in patients without biochemically apparent liver injury. Measurement of liver-specific cfDNA, using droplet digital PCR and methylation analysis, revealed that the contribution of liver to cfDNA was increased by an average of 175-fold in APAP overdose patients with biochemically apparent liver injury compared to healthy subjects, but was not increased in overdose patients with normal liver function tests.\n\nConclusionsWe present a novel method for measurement of the tissue origins of cfDNA in healthy and disease states and demonstrate the potential of cfDNA as a clinical biomarker in APAP overdose.

pharmacology and toxicology↗

bioRxiv2018

Cold shock as a screen for genes involved in cold acclimatization in Neurospora crassa

When subjected to rapid drops of temperature (cold shock), Neurospora responds with a dramatic, but temporary shift in its branching pattern. While the cold shock response has been described morphologically, it has yet to be examined genetically. This project aims to begin the genetic characterization of the cold shock response and the associated acclimatization to cold environments. We report here the results of a screen of mutants from the Neurospora knockout library for alterations in their morphological response to cold shock and thus, their ability to acclimatize to the cold. Three groups of knockouts were selected to be subject to this screen: genes previously suspected to be involved in hyphal development as well as knockouts resulting in morphological changes; transcription factors; and genes homologous to E. coli genes known to alter their expression in response to cold shock. Several strains were identified with altered responses. The genes impacted in these mutants are listed and discussed. A significant percentage (81%) of the knockouts of genes homologous to those previously identified in E. coli showed altered cold shock responses in Neurospora - suggesting that the response in these two organisms is largely shared in common.

cell biology↗