Biology subjects

Ryan, P.

Publications and source records attributed to Ryan, P..

7 recordsLinked to original sources

bioRxiv2026

Detection of Candidate Circular RNAs to Monitor Anti-Hormonal Response in the Mammary Gland

Anti-hormonal therapies such as selective estrogen receptor modulators like tamoxifen or aromatase inhibitors like letrozole represent a cornerstone for breast cancer prevention and therapy of estrogen receptor-positive breast cancer. Therapeutic monitoring can include blood tests and imaging; however, genetically-based approaches are not yet in practice. Ideally, a test would be able to detect a positive molecular response across different estrogen pathway-suppressive approaches. Circular RNAs are a species of non-coding RNAs detectable in plasma that have been proposed as non-invasive therapeutic biomarkers. To determine whether a set of specific circular RNAs is altered across estrogen-suppressive pathway approaches, we analyzed mammary gland-specific total RNA sequencing data from two individual genetically engineered mouse models (GEMMs) of estrogen pathway-induced breast cancer, with or without exposure to tamoxifen or letrozole. The nf-core/circrna pipeline was used to identify circRNAs that were differentially expressed in response to either tamoxifen or letrozole. We then screened for circRNAs that were differentially regulated by both anti-hormonals. Four up-regulated and 31 down-regulated circRNAs with host genes known to be expressed in human breast epithelial cells were identified as showing reproducible differential regulation in response to anti-hormonal treatment.

cancer biology↗

bioRxiv2025

Phylogenetics, evolution and biogeography of four Digitaria food crop lineages across West Africa, India, and Europe

Background and AimsMillet crops in the grass genus Digitaria include white and black fonio (D. exilis and D. iburua), raishan (D. compacta) and Polish millet (D. sanguinalis), cultivated across West Africa, India, and Europe. Fonio and raishan crops are important to supporting food security and subsistence agricultural systems in rural communities, while D. sanguinalis is no longer cultivated. These crops are resilient to challenging climates. We aim to produce an integrated study of these crops: a phylogeny of the Digitaria genus including all four food species, to identify key crop wild relatives (CWRs); time-calibrated biogeographic analysis, to investigate the history and evolution of Digitaria; and morphological study to assess the transition between wild and domesticated species. MethodsWe use the Angiosperm 353 target-enrichment sequencing approach to produce maximum likelihood and coalescent model nuclear phylogenies for 46 Digitaria species, including ploidy estimations, and bayesian methods to propose an evolutionary and biogeographic history for the genus. Morphology of wild and cultivated species is investigated for spikelets and growth habits using microscopy and SEM imaging techniques. Key ResultsFour distinct lineages are proposed for the evolution of Digitaria crops, and close CWRs D. fuscescens, D. atrofusca, D. setigera and D. radicosa, and D. ciliaris are identified. South and eastern Africa is proposed as the origin of early Digitaria divergence, with crop lineages diverging from wild relatives around 2-6mya. Incomplete domestication traits are observed, including the loss of trichomes, but no significant difference in spikelet or abscission zone morphology. ConclusionsDigitaria crops have important climate-resilient traits and hold strong potential for stabilising vulnerable food systems against the challenges of future climate change. The knowledge produced in this study about CWRs will be useful in improving crop traits through targeted breeding and indigenous crop conservation programmes.

genetics↗

bioRxiv2025

Impacts of climate change on fonio millet: in-vitro seed germination and suitability modelling of an important indigenous West African crop

Seed germination is highly temperature sensitive. Climate change factors such as increasing temperatures are likely to have a harmful effect on agriculture, particularly after crop sowing. Better utilisation of indigenous, arid-resilient crops like fonio (Digitaria exilis) are a commonly proposed solution to improving food security. This study develops knowledge of fonio germination requirements and how these correspond to future climate conditions across West Africa. We use a combined approach; integrating seed germination experiments under a range of temperatures, and niche suitability modelling to investigate how cultivation of fonio will be impacted by climate change. We find that from 37 seed accessions collected across Guinea, Togo, Mali, and Burkina Faso, the ceiling temperature for germination is around 42{degrees}C, with an optimum temperature of 30-35{degrees}C - also noted from phenotypic observations. Drought trials show successful germination to beyond -1MPa. There is no obvious difference in response by accessions originating from either hotter or cooler climates. By comparing these temperature thresholds with future climate predictions, alongside a suitability modelling approach, we predict an average decline of 10% in the suitable area for fonio cultivation, especially affecting Senegal, Mali, and Burkina Faso. Newly suitable area is predicted to increase in Guinea, Ghana, Cote dIvoire, and Nigeria by around 5%. These findings provide valuable insight for developing future dryland agriculture policies and prioritisation of resilient crops.

plant biology↗

bioRxiv2024

Differentiating wild and domesticated enset (Musaceae) using phytolith analysis

Enset (Ensete ventricosum, Musaceae) is an important economic crop from Ethiopia which accounts for 20% of the staple diet in Ethiopia today. However, its evolutionary history and spread is poorly understood. Archaeology could provide evidence of past use and contribute to our understanding of its early history, but so far, this has not transpired. Cultivated enset is clonally reproduced and seed production rarely occurs, therefore, looking for seed remains is futile and instead archaeobotanical research should focus on microfossils such as phytoliths. Phytoliths have been shown to be diagnostic for the presence of banana (Musa) and are expected to be similarly useful for identifying enset, but we need a better understanding of phytolith production and variability, and the extent to which this may be used to track domestication. The current study provides a fundamental baseline for the identification of Ensete phytoliths through the examination of phytoliths from leaves and other plant parts based on their size and shape. We consider the differentiation of phytoliths across a single plant, based on location in the leaf, the age of the leaf, and different organs of the plant. We also compare phytoliths in the Musaceae Family, and between the enset cultivar and wild samples. HIGHLIGHTSWe provide the first identification baseline to differentiate wild from domesticated enset by looking at variation across an individual enset plant and comparing these results to phytoliths from wild plants.

plant biology↗

bioRxiv2022

Introduced crops supplement rather than replace indigenous crops in an African center of agrobiodiversity

O_LICrop diversity plays a major role in underpinning food security. It is especially important to smallholder and subsistence farmers, who often rely on crop diversity for stable and resilient production. Despite this, global expansion of a small pool of major crops and the associated homogenisation of global agricultural systems may decrease on-farm crop diversity. C_LIO_LIWe surveyed 1,369 subsistence farms stratified across climate gradients in the Ethiopian Highlands, to characterise the richness and cultivated area of the 83 edible crops they contained. We further categorise these crops by their period of introduction to Ethiopia. We apply non-metric multidimensional scaling and mixed effects modelling to characterise agrisystem composition and test the impact of crop introductions. C_LIO_LIWe find a significant positive relationship between introduced and indigenous crop richness, suggesting that crop introductions have tended to supplement rather than replace or reduce indigenous crop diversity. Geographically matched farms with higher proportions of introduced crops, had significantly higher overall crop richness. Analysis of socio-economic drivers indicates that both poverty and low accessibility are associated with reduced cultivation of modern introductions. C_LIO_LIWe conclude that global patterns of major crop expansion do not necessarily result in agrobiodiversity loss for subsistence farmers, in our Ethiopian case study. Importantly, socioeconomic factors may strongly influence the farmers propensity to adopt novel species, suggesting targets for agricultural extension policies. Given the rapid climatic, economic and demographic changes impacting global food systems and the threats to food security these entail, robust indigenous agricultural systems supplemented with diverse introduced crops may enhance resilience. C_LI

ecology↗

bioRxiv2020

Archaeogenomics of a ~2,100-year-old Egyptian leaf provides a new timestamp on date palm domestication

O_LIThe date palm (Phoenix dactylifera) has been a cornerstone of Middle Eastern and North African agriculture for millennia. It is presumed that date palms were first domesticated in the Persian Gulf and subsequently introduced into North Africa, where their evolution in the latter region appears to have been influenced by gene flow from the wild relative P. theophrasti, which is restricted to Crete and Turkey. However, the timing of gene flow from P. theophrasti to P. dactylifera remains unknown due to the limited archaeobotanical evidence of P. theophrasti and their exclusion from population genomic studies. C_LIO_LIWe addressed this issue by investigating the relatedness and ancestry of a ~2,100-year-old P. dactylifera leaf from Saqqara (Egypt), combining genome sequencing of this ancient specimen with a broad sample of date palm cultivars and closely related species. C_LIO_LIThe ancient Saqqara date palm shares close genetic ancestry with North African date palm populations. We find clear genomic admixture between the Saqqara date palm, P. theophrasti and the closest known relative P. sylvestris. C_LIO_LIOur study highlights that gene flow from P. theophrasti and P. sylvestris to North African date palms had already occurred at least ~2,100 years ago, providing a minimum timestamp for hybridisation between species. C_LI

evolutionary biology↗

bioRxiv2019

Drug related and psychopathological symptoms in HIV-positive men who have sex with men who inject drugs during sex (Slamsex): Data from the U-SEX GESIDA 9416 Study.

ObjectivesIntravenous sexualized drug use also known as slamsex seems to be increasing among HIV-positive men who have sex with men (MSM). This practice may entail severe consequences for physical and mental health in this population. Research on the subject is scarce. The aim of our study was to describe the psychopathological background of a sample of HIV positive MSM who practiced slamsex during the previous year and compare the physical and psychological symptoms between these participants and those who practiced sexualized drug use (SDU) or chemsex without slamsex.\n\nDesign and MethodsParticipants (HIV-positive MSM) were recruited from the U-Sex study in 22 HIV clinics in Madrid during 2016-17. All participants completed an anonymous cross-sectional survey on sexual behaviour and recreational drug use. The present analysis is based on HIV-positive MSM who had practiced SDU.\n\nResultsThe survey sample comprised 742 participants. Of all the participants who completed the survey, 216 (29.1%) practiced chemsex, and of these, 34 (15.7%) had practiced slamsex. Participants who practiced slamsex were more likely to have current psychopathology (depression, anxiety and drug related disorders) than chemsex users. In addition, participants who practiced slamsex had more high-risk sexual behaviours, polydrug use and were more often diagnosed with sexually transmitted infections (STIs) and hepatitis C than those who did not inject drugs. Compared with patients who did not inject drugs, patients who engaged in slamsex showed more severe drug related symptoms (withdrawal and dependence), symptoms of severe intoxication (loss of consciousness), and severe psychopathological symptoms related to SDU, such as paranoid thoughts and suicidal behaviour.\n\nConclusionSlamsex (intravenous SDU) is closely associated with current psychiatric disorders and severe drug-related and psychiatric symptoms.

scientific communication and education↗