Biology subjects

Hughes, C. E.

Publications and source records attributed to Hughes, C. E..

6 recordsLinked to original sources

bioRxiv2026

Droplet microfluidics reports digital and tuneable single-platelet ADP secretion describing primed, active and hyper-active states

New platelet function assays that provide an accurate assessment of platelet reactivity as a surrogate for thrombosis risk could change the paradigm for acute myocardial infarction and stroke prevention. Considering ADP secretion as a hallmark of platelet activation, we developed a method for encapsulating single platelets with a fluorescent reporter for extracellular ADP in picolitre droplets. The method, termed the Droplet ADP Secretion Assay (DASA), robustly detected dose-dependent ADP secretion responses to agonists. Digital ADP secretion heterogeneity was observed with the major fraction of platelets responding and the remaining fraction being non-responders. Primed platelets had elevated responses to agonists, with increased ADP secretion and an increased fraction of secreting platelets, demonstrating that priming can convert otherwise inactive platelets to a reactive state. Uniquely, the method detected ADP secretion from primed platelets in the absence of agonists. In contrast, primed platelets were not detected by flow cytometry involving CD63 and CD62P endpoints. In a preliminary clinical study, some patients had platelets with a priming-like ADP secretion signature, suggesting treatment with P2Y12 inhibitors may be warranted. In vitro aspirin and ticagrelor treatments reduced ADP secretion responses to agonists. In summary, DASA offers a novel approach to assess platelet reactivity and holds promise for assessing thrombotic tendency and personalised therapeutics.

pathology↗

bioRxiv2026

Vacuole pH loss triggers ESCRT-dependent plasma membrane remodeling to prevent amino acid toxicity

Loss of lysosomal or vacuolar acidity is a hallmark of aging, metabolic dysfunction, and cellular stress, yet how cells adapt to this condition remains poorly understood. In budding yeast, where the vacuole serves as a major reservoir for intracellular amino acids, impaired vacuolar acidification disrupts amino acid homeostasis. Here we performed a genome-wide screen in budding yeast to identify pathways required for survival during vacuole pH stress. We found that endocytic trafficking and ESCRT/MVB components become essential when vacuolar acidification is disrupted. Vacuole deacidification triggered ESCRT-dependent rerouting and degradation of plasma membrane amino acid transporters, thereby limiting nutrient influx. Blocking this response stabilized transporters at the cell surface and caused synthetic lethality under vacuole stress. This growth defect was suppressed by lowering amino acid availability or reducing transporter expression, whereas amino acid supplementation restored toxicity. Nitrogen starvation prevented transporter internalization, indicating that nutrient status gates this adaptive response. Together, these findings reveal a vacuole-plasma membrane communication pathway that protects cells from amino acid toxicity by matching nutrient influx to vacuolar function.

cell biology↗

bioRxiv2022

Phosphate Starvation Signaling Increases Mitochondrial Membrane Potential through Respiration-independent Mechanisms

Mitochondrial membrane potential directly powers many critical functions of mitochondria, including ATP production, mitochondrial protein import, and metabolite transport. Its loss is a cardinal feature of aging and mitochondrial diseases, and cells closely monitor membrane potential as an indicator of mitochondrial health. Given its central importance, it is logical that cells would modulate mitochondrial membrane potential in response to demand and environmental cues, but there has been little exploration of this question. We report that loss of the Sit4 protein phosphatase in yeast increases mitochondrial membrane potential, both through inducing the electron transport chain and the phosphate starvation response. Indeed, a similarly elevated mitochondrial membrane potential is also elicited simply by phosphate starvation or by abrogation of the Pho85-dependent phosphate sensing pathway. This enhanced membrane potential is primarily driven by an unexpected activity of the ADP/ATP carrier. We also demonstrate that this connection between phosphate limitation and enhancement of the mitochondrial membrane potential is also observed in primary and immortalized mammalian cells as well as in Drosophila. These data suggest that mitochondrial membrane potential is subject to environmental stimuli and intracellular signaling regulation and raise the possibility for therapeutic enhancement of mitochondrial functions even with defective mitochondria.

cell biology↗

bioRxiv2022

Precipitation is the main axis of tropical phylogenetic turnover across space and time

Early natural historians - Compte de Buffon, von Humboldt and De Candolle - established ecology and geography as two principal axes determining the distribution of groups of organisms, laying the foundations for biogeography over the subsequent 200 years, yet the relative importance of these two axes remains unresolved. Leveraging phylogenomic and global species distribution data for Mimosoid legumes, an pantropical plant clade of 3,400 species, we show that the water availability gradient from deserts to rainforests dictates turnover of lineages within continents across the tropics. We demonstrate that 95% of speciation occurs within a precipitation niche, showing profound phylogenetic niche conservatism, and that lineage turnover boundaries coincide with isohyets of precipitation. We reveal similar patterns on different continents, implying that evolution and dispersal follow universal processes.

evolutionary biology↗

bioRxiv2022

The innovation of the symbiosome has enhanced the evolutionary stability of nitrogen fixation in legumes

O_LINitrogen-fixing symbiosis is globally important in ecosystem functioning and agriculture, yet the evolutionary history of nodulation remains the focus of considerable debate. Recent evidence suggesting a single origin of nodulation followed by massive parallel evolutionary losses raises questions about why a few lineages in the N2-fixing clade retained nodulation and diversified as stable nodulators while most did not. Within legumes, nodulation is restricted to the two most diverse subfamilies, Papilionoideae and Caesalpinioideae, which show stable retention of nodulation across their core clades. C_LIO_LIWe characterize two nodule anatomy types across 128 species in 56 of the 150 genera of the legume subfamily Caesalpinioideae: 1) fixation thread nodules (FTs), where nitrogen-fixing bacteroids are retained within the apoplast in modified infection threads and 2) symbiosomes, where rhizobia are symplastically internalized in the host cell cytoplasm within membrane-bound symbiosomes. C_LIO_LIUsing a robust phylogenomic tree based on 997 genes from 146 caesalpinioid genera, we show that losses of nodulation are more prevalent in lineages with FTs. C_LIO_LIWe propose that evolution of the symbiosome allows for a more intimate and enduring symbiosis through greater compartmentalisation of their rhizobial microsymbionts, resulting in greater evolutionary stability of nodulation across this species-rich pantropical clade of legumes. C_LI

evolutionary biology↗

bioRxiv2019

Diversification in evolutionary arenas -- assessment and synthesis

Understanding how and why rates of evolutionary diversification vary is a key issue in evolutionary biology, ecology, and biogeography, and the metaphorical concepts of adaptive radiation and evolutionary stasis describe two opposing aspects causing variation in diversification rates. Here we review the central concepts in the evolutionary diversification literature and synthesize these into a simple, general framework for studying rates of diversification and quantifying their underlying dynamics, which can be applied across clades and regions and across spatial and temporal scales. Our framework describes the diversification rate (d) as a function of the abiotic environment (a), the biotic environment (b) and clade-specific phenotypes or traits (c); thus d[~]a,b,c. We refer to the four components (a-d) and their interactions collectively as the Evolutionary Arena. We outline analytical approaches to this framework and present a case study on conifers, for which we parameterise the general model. We also discuss three conceptual examples: the Lupinus radiation in the Andes in the context of emerging ecological opportunity and fluctuating connectivity due to climatic oscillations; oceanic island radiations in the context of island formation and erosion; and biotically driven radiations of the Mediterranean orchid genus Ophrys. The results of the conifer case study are consistent with the long-standing scenario that low competition and high rates of niche evolution promote diversification. The conceptual examples illustrate how using the synthetic Evolutionary Arena framework helps to identify and structure future directions for research on evolutionary radiations. In this way, the Evolutionary Arena framework promotes a more general understanding of variation in evolutionary rates by making quantitative results comparable between case studies, thereby allowing new syntheses of evolutionary and ecological processes to emerge.

evolutionary biology↗