Biology subjects

Soria, M.

Publications and source records attributed to Soria, M..

10 recordsLinked to original sources

bioRxiv2026

Molecular responsiveness to testosterone is uncoupled from skeletal muscle mass and strength in males aged 18 - 80 years

Objective Testosterone exerts wide-ranging physiological effects, including the regulation of anabolic processes in skeletal muscle. However, its role in skeletal muscle ageing remains unclear. This study aimed to establish the association between endogenous testosterone levels and skeletal muscle phenotype across the adult lifespan and determine whether ageing modulates this relationship. Methods Eighty-one healthy males aged 18-80 underwent comprehensive phenotypic assessment. Body composition and muscle morphology were assessed using dual-energy X-ray absorptiometry (DEXA) and peripheral quantitative computed tomography (pQCT). Muscle strength was estimated leg press one-repetition maximum (e1RM). Vastus lateralis biopsies were used to assess fibre type, sequence the transcriptome and establish primary myocytes. Cell lines from young (n=5) and older (n=7) donors were cultured and compared under control and testosterone-treated conditions for cellular phenotype. Results Ageing was associated with lower free testosterone, muscle mass and strength, altered type IIa fibre characteristics, and widespread transcriptional changes in skeletal muscle. Free, but not total, testosterone was strongly associated with the muscle transcriptome, although neither fraction was associated with muscle mass or strength. In primary myocytes, testosterone increased androgen receptor abundance and nuclear localisation and enriched pathways involved in protein translation. Conclusion Testosterone is biologically active in male skeletal muscle, with its free fraction strongly associated with the transcriptome; however, these molecular effects do not translate into differences in muscle mass or strength. Testosterone may therefore play a primary role in establishing the male muscle phenotype during puberty, before transitioning to a more ancillary role in adult skeletal muscle.

physiology↗

bioRxiv2026

MetAR: A semi-automated meta-analysis of skeletal muscle androgen receptors association with age

BackgroundThe maintenance of skeletal muscle health plays a pivotal role in prolonging both the lifespan and healthspan. However, muscle mass and strength exhibit significant declines with age. Ageing is associated with a reduced muscle protein synthesis response to key anabolic stimuli, including the androgen hormone testosterone, termed anabolic resistance. Testosterone enacts its anabolic effects in muscle through androgen receptor (AR) mediated pathways. Emerging evidence suggests that AR availability may represent a rate-limiting factor in androgen signalling, with AR saturation occurring below physiological testosterone levels in some tissues. Prior research in rodents has reported age-related reductions in AR expression, suggesting changes in AR protein content may constitute a key component of anabolic resistance. However, reports of the effects of age on the human skeletal muscle AR are inconclusive and limited by small sample sizes. Therefore, this study aimed to characterise age-related changes in expression of the AR, its regulators and downstream target genes in human skeletal muscle. MethodsWe developed and used a novel R-based pipeline, MetAR, to perform reproducible meta-analyses of publicly available bulk RNA-Seq datasets from NCBI GEO and investigate associations between target gene expression and variables of interest without the need for high-performance computing. Eligible datasets included skeletal muscle samples from healthy adult males aged [≥]18 years, with an age range of [≥] 10 years and sample size [≥] 6. Raw counts data were downloaded, appraised and TMM normalised. Dataset-level associations between age and target gene expression were assessed using linear and generalised additive models (GAMs). Random-effects meta-analyses were performed, and heterogeneity, publication bias and leave-one-out sensitivity assessed. ResultsSixteen skeletal muscle bulk RNA-seq datasets (n = 364; age 18-92 years) were eligible for inclusion in the meta-analyses. AR expression was negatively associated with age ({beta} = -0.006 log2 TMM-CPM per year, p < 0.001) corresponding to a 4.4% decrease in expression per decade. Age was also associated with a significant reduction in expression of various regulators of AR stability, transcriptional activity and nuclear transport. Additionally, steroidogenic enzymes and key downstream targets of the AR, including genes encoding for key structural proteins and mitochondrial function were negatively associated with age. ConclusionsCollectively, these findings suggest a multi-faceted age-associated remodelling of AR expression, signalling and nuclear transport that may contribute to the development of anabolic resistance and consequent age-associated muscle loss.

physiology↗

bioRxiv2025

On-site microbial community analysis in rivers: integrating autonomous sampling with a portable sequencing workflow

Studies focused on bacterial diversity in rivers often face significant limitations. Traditional sampling approaches frequently overlook spatial and temporal variability at the reach scale. Molecular techniques, such as metabarcoding and metagenomics, can partially address this issue by providing deeper insights. However, this approach usually involves highly specialized laboratories and high costs, making large-scale and long-term monitoring of river networks unfeasible in most cases. Thus, we developed a methodology based on remote-controlled boats, allowing the collection of integrated samples in freshwater ecosystems. Combined with a portable laboratory, this approach enabled the development of new surface water monitoring strategies. Here, we describe the operational application of this system for in situ monitoring of bacterioplankton communities across 8 sections of the Ter River (Catalonia, Spain). [To explore its potential, we applied both 16S rRNA gene sequencing using Nanopore technology (MinION) in the field, and shotgun metagenomics using Illumina technology in the laboratory, acknowledging the intrinsic differences between sequencing targets, platforms, and analysis pipelinesMinIONMinION sequencing enabled microbiome characterization and identification of the main bacterial taxa just 72 h after sampling, offering significantly lower costs and reduced manpower requirements. Furthermore, amplification facilitated the full characterization of bacterioplankton diversity along the river, preventing the exclusion of uncommon taxa. While shotgun metagenomics is still necessary for understanding the functional activity of these organisms, our approach provides a cost-effective framework for developing efficient follow-up sampling methodologies.

microbiology↗

bioRxiv2025

Drying halves decomposition rates in river networks by disrupting structure-function linkages

River drying is intensifying worldwide due to climate change and water abstraction, with major consequences for biodiversity and ecosystem functioning. In river networks, drying not only alters local environmental conditions but also disrupts hydrological connectivity, reshaping the movement of organisms and resources at the network scale. Leaf litter decomposition--a key ecosystem function in freshwater systems--is particularly sensitive to changes in the structure of decomposer communities. We hypothesized that spatiotemporal patterns of drying regulate decomposition by altering the diversity and composition of detritivore macroinvertebrates, bacteria and fungi. We combined data from six European drying river networks (DRNs) spanning a wide latitudinal gradient to assess how local drying intensity and regional hydrological connectivity affect decomposition through changes in these decomposer groups. We found that short drying events ([≤] six dry days) reduced decomposition rates by up to 50% by shifting the control of decomposition from a balanced contribution of fungi, bacteria, and detritivores to one dominated by dry-tolerant but less efficient bacteria. These community shifts persisted after flow resumption, leading to sustained reductions in decomposition even under flowing conditions. Regional connectivity alleviated these negative effects of local drying by facilitating the recovery of more efficient aquatic decomposers through dispersal. However, this effect depended on DRN context. In particular, in southern, more arid DRNs, stronger fragmentation hindered the recovery of decomposer communities after flow resumption. Overall, our results provide mechanistic evidence that spatiotemporal patterns of drying can regulate the linkages between community structure and ecosystem functioning in river networks. As drying events become more frequent and prolonged, increasing disruption of these linkages will impact carbon cycling and energy fluxes in freshwater ecosystems under global change.

ecology↗

bioRxiv2024

The transcriptomic signature of age and sex is not conserved in human primary myocytes

BackgroundHuman primary muscle cell (HPMC) lines derived from skeletal muscle biopsies are potentially powerful tools to interrogate the molecular pathways underlying fundamental muscle mechanisms. HPMCs retain their genome in culture, but many endogenous circulating factors are not present in the in vitro environment, or at concentrations that do not mirror physiological levels. To address the assumption that HPMCs are valid models of age and sex-specificity in human muscle research, we examined to what extent HPMC lines retain their source phenotype in culture. MethodsBiopsies from the vastus lateralis muscle were collected from ten males aged 18-30, ten females aged 18-30 and ten males aged 60-75 recruited from a general, healthy population. A portion of the muscle was used for the establishment of 30 individual HMPC lines. The remaining sample was immediately snap frozen and stored for further analysis. RNA was extracted from muscle tissue samples and their corresponding, fully differentiated HMPCs and analysed using RNA Sequencing. To compare their transcriptomic signature, principal component analysis (PCA), differential expression analysis, single-cell deconvolution and pathway enrichment analysis were conducted in R. ResultsA comparison of the transcriptomic signature of 30 human muscle biopsies and their corresponding HPMCs indicated a near-complete lack of retention of the genes and pathways differentially regulated in vivo when compared to their in vitro equivalent, with the exception of several genes encoded on the Y-chromosome. ConclusionsThe diversity of resident cell populations in muscle tissue and the lack of sex- and age-dependent circulating factors in the cellular milieu likely contribute to these observations, which call for caution when using HPMCs as an experimental model of human muscle sex or age.

cell biology↗

bioRxiv2024

Mitochondria isolated from male skeletal muscle contain a distinct 1 population of miRNA that are differentially expressed following acute exercise

Initially thought to localise at the cytosol and nucleus only, emerging evidence indicates that miRNAs also localise within the mitochondria where they could regulate diverse pathological and physiological processes. Therefore, the aim of the current study was to use small RNA sequencing to profile and compare the entire population of miRNAs in human skeletal muscle of healthy males in whole-tissue and in isolated mitochondria at rest and in response to acute endurance exercise. Twelve healthy males (age 26 {+/-} 4 years, mean {+/-} SD) cycled for 60 min at 70% VO2peak and muscle biopsies were collected at rest, immediately after and 3 h after exercise. The mitochondria were isolated by immunoprecipitation, further purified, then the resident RNA was sequenced to assess the mitochondrial transcriptome. Small RNA sequencing revealed that mitochondria isolated from male skeletal muscle tissue contain a small and distinct population of miRNAs. Of the approximately 110 mature miRNAs detected in skeletal muscle mitochondria at each time-point, the canonical myo-miRs miR-1, miR-133 and miR-206 families constituted on average 45% of total mitochondria miRNA reads. However, none of these canonical myo-miRs were differentially expressed in mitochondria following endurance exercise. One miRNA, hsa-miR-146b-3p, was differentially expressed in both whole muscle tissue and mitochondria when adjusted for multiple testing (FDR <0.05). Future research is now required to investigate miRNA-mRNA interactions in the mitochondria of skeletal muscle tissue. KEY POINTS SUMMARYO_LIEmerging evidence suggests microRNA are localised in the mitochondria of skeletal muscle cells and may play a role in regulating mitochondrial function. C_LIO_LIWe recently optimised an approach to isolate RNA from mitochondria of human skeletal muscle that is free from contaminating cytosolic RNA and suitable for RNA sequencing. C_LIO_LIIn this study we examined the microRNA population from male skeletal muscle mitochondria before and in the hours following 60 minutes of moderate intensity cycling exercise. C_LIO_LIWe detected around 110 microRNAs in skeletal muscle mitochondria, with the muscle enriched myo-miR such as miR-1, miR-133 and miR-206 families constituting almost half of the reads. However, only one microRNA, hsa-miR-146b-3p, was differentially expressed whereby it increased [~] 10-fold following exercise. C_LIO_LIThe results provide new knowledge into how mitochondria might be regulated at the subcellular level and in response to physiological stressors such as exercise. C_LI

cell biology↗

bioRxiv2024

Natural disturbances and connectivity shape the seasonal variability of aquatic macroinvertebrate communities across Europe

Understanding the joint influence of natural disturbance, spatial connectivity and biogeography on biodiversity is essential to forecast its responses to climate change. Macroinvertebrate communities in drying river networks constitute an ideal study system to understand the interplay of these ecological processes. We analyze the taxonomic and functional structure of macroinvertebrate communities sampled across 126 reaches with perennial and intermittent streamflow, surveyed in six drying river networks (DRN) across Europe, six times over one year. Drying frequency decreased community richness and functional diversity of communities, whereas spatio-temporal connectivity increased community richness in intermittent reaches. Communities experiencing a high drying frequency increased the proportion of taxa with K-strategies and drying resistance traits. Communities experiencing a long drying duration compensated by high spatio-temporal connectivity had more taxa with a r-strategy and high dispersal ability. Perennial communities varied from taxa-poor communities of r-strategists in spring and autumn and taxa-rich communities of K-strategists in summer and had a constant functional diversity throughout the year. When drying frequency increased, communities showed a similar pattern except in autumn when they shifted towards species-poor communities of K-strategists. Functional diversity then peaked in summer. Community trait structure and in particular optimal drying resistance traits changed across biogeographical scales. It opposed communities from mountainous DRN (with more r-strategies and high dispersal ability) to non-mountainous DRN (with more K-strategies). Drying frequency, drying duration, and spatio-temporal connectivity drive divergent community structures, suggesting the presence of an ecological threshold that explains the variability of disturbed ecosystems across broad spatial scales. These factors also shaped seasonal community variations, particularly after summer, with intermittent communities influenced by stochastic recolonization events in spring and autumn. Spatial-temporal connectivity proved crucial for maintaining diversity in communities subjected to intense drying. Lastly, the effectiveness of drying resistance traits was dependent on the biogeographical and environmental conditions of drying river networks.

ecology↗

bioRxiv2024

Both environmental conditions and intra- and interspecific interactions influence the movements of a marine predator

Animal movements are typically influenced by multiple environmental factors simultaneously and individuals vary in their response to this environmental heterogeneity. Therefore, understanding how environmental aspects, including biotic, abiotic and anthropogenic factors, influence the movements of wild animals is an important focus of wildlife research and conservation. We apply Exponential Random Graph Models (ERGMs) to analyse movement networks of a bull shark population in a network of acoustic receivers and identify the effects of environmental, social or other types of covariates on their movements. We found that intra- and interspecific factors often had stronger effects on movements than environmental variables. ERGMs proved to be a potentially useful tool for studying animal movement network data especially in the context of spatial attribute heterogeneity.

ecology↗

bioRxiv2024

The interactive effect of sustained sleep restriction and resistance exercise on skeletal muscle transcriptomics in young females

IntroductionBoth sleep loss and exercise regulate gene expression in skeletal muscle, yet little is known about how the interaction of these stressors affects the transcriptome. The aim of this study was to investigate the effect of nine nights of sleep restriction, with repeated resistance exercise (REx) sessions, on the skeletal muscle transcriptome of young, trained females. MethodsTen healthy females aged 18-35 years undertook a randomised cross-over study of nine nights sleep restriction (SR; 5-h time in bed) and normal sleep (NS; [≥]7 h time in bed) with a minimum 6-week washout. Participants completed four REx sessions per condition (day 3, 5, 7 and 9). Muscle biopsies were collected both pre- and post-REx on days 3 and 9. Gene and protein expression were assessed by RNA sequencing and Western Blot, respectively. ResultsThree or nine nights of sleep restriction had no effect on the muscle transcriptome independently of exercise. However, close to 3000 transcripts were differentially regulated (FDR < 0.05) 48 h post the completion of three resistance exercise sessions in both NS and SR conditions. Only 39% of downregulated and 18% of upregulated genes were common between both conditions, indicating a moderating effect of sleep restriction on the response to exercise. ConclusionSleep restriction and resistance exercise interacted to alter the enrichment of skeletal muscle transcriptomic pathways in young, resistance-trained females. Performing exercise when sleep restricted may not provide the same adaptive response for individuals as if they were fully rested.

genomics↗

bioRxiv2021

Gene name errors: lessons not learned

Erroneous conversion of gene names into other dates and other data types has been a frustration for computational biologists for years. We hypothesized that such errors in supplementary files might diminish after a report in 2016 highlighting the extent of the problem. To assess this, we performed a scan of supplementary files published in PubMed Central from 2014 to 2020. Overall, gene name errors continued to accumulate unabated in the period after 2016. An improved scanning software we developed identified gene name errors in 30.9% of articles with supplementary Excel gene lists; a figure significantly higher than previously estimated. This is due to gene names being converted not just to dates and floating-point numbers, but also to internal date format (five-digit numbers). These findings further reinforce that spreadsheets are ill-suited to use with large genomic data.

genomics↗