Biology subjects

Murgia, M.

Publications and source records attributed to Murgia, M..

9 recordsLinked to original sources

bioRxiv2026

AutoWrinkleID: a machine learning pipeline for biofilm wrinkle identification and quantitative analysis

Biofilms are widely distributed in both natural and engineered systems and play a fundamental role in microbial ecology and biotechnological applications. When grown on agar substrates, biofilms often exhibit macroscopic structural features due to mechanical instabilities driven by matrix production. These wrinkles encode relevant information about biofilm growth and structural development and have even been shown to possess some functional roles. Despite their relevance, currently available approaches for wrinkle detection from images rely on manual annotation, which is time-consuming, not scalable, and strongly dependent on the annotator. In the present study, we developed an end-to-end machine learning pipeline, named AutoWrinkleID, that starts from bright field images of biofilms and performs wrinkle identification, characterisation, and quantification across multiple bacterial species and strains. The name reflects the automated identification and subsequent characterisation and quantification of biofilm wrinkles. The annotations used to generate the masks, namely images containing only the wrinkle structures, were obtained both through manual labelling and using constitutive fluorescence and motility fluorescence. Interestingly, we found that models trained using only manual annotations perform worse than those trained using motility fluorescence markers. A comparison between motility and constitutive fluorescence masks further indicates that motility based annotations consistently outperform constitutive fluorescence across all strains, strongly suggesting that motile phenotypes are tightly associated with wrinkle structures. Additional computational analysis is conducted on the same dataset to assess the robustness and limitations of the results as a function of training dataset. We also observed that Sholl analysis, originally developed for the study of neuronal dendrites and later applied to wrinkle analysis, can effectively characterize wrinkle patterns, although its applicability is strongly limited by wrinkle shape and by the quality of the masks.

biophysics↗

bioRxiv2026

Multi-platform plasma proteomics reveals orthogonal metabolic signatures distinguishing elite athletic phenotypes

Exercise confers profound health benefits, yet the molecular mechanisms linking physical activity to health and longevity are incompletely known. Here we applied three mass spectrometry (MS)-based and one aptamer-based proteomics workflows to elite athletes with contrasting metabolic phenotypes, sampled before and after maximal exhaustive exercise. MS detected larger effect sizes and resolved isoforms; aptamers extended proteome coverage but with unannotated proteoform biases. Acute exercise induced coordinated platelet degranulation, neutrophil activation, and extracellular matrix turnover, with peptide topology analysis providing direct evidence for vesicular release. Chronic adaptations organized along two orthogonal axes: a muscle mass gradient marked by hypertrophy signaling and attenuated systemic inflammation, and an oxidative capacity gradient characterized by metabolic health-associated proteins (APOA4, IGFBP2, ITLN1) and dampened IGF-I signaling. Exploratory biological age analysis suggested younger adipose age in athletes. The plasma proteome provides an integrated readout of exercise adaptation, linking cardiorespiratory fitness to metabolic health and healthy aging.

biochemistry↗

bioRxiv2025

Spatiotemporal multi-omics atlas of the aging neuromuscular junction

The demographic shift toward a global aging population, coupled with rising prevalence of neurodegenerative diseases, poses major public health challenges. Aging is the primary risk factor for most neurodegenerative conditions, making the elucidation of its molecular mechanisms critical for developing effective interventions. Dysfunction of the neuromuscular junction (NMJ), the specialized synapse essential for motor function, is an early hallmark of aging and several neurodegenerative disorders, yet its molecular determinants remain incompletely understood. To shed light on potential common underlying mechanisms, we performed a spatiotemporal multi-omics analysis of the murine NMJ during aging, uncovering several genes showing decoupling between transcript and protein trajectories that may drive the related progressive motor decline. NMJs of soleus (SOL) and extensor digitorum longus (EDL) muscles, differing in fiber composition and vulnerability to aging and disease, displayed distinct spatiotemporal dynamics: fast-twitch EDL, more susceptible to degeneration, exhibited stronger mRNA-protein decoupling than aged slow-twitch SOL or younger SOL and EDL muscles. Elevated expression of miRNAs and RNA-binding proteins in aged EDL highlights the key role of post-transcriptional regulation in NMJ aging. This study provides new insights into the physiopathology of neuromuscular aging and offers a resource for investigating mechanisms shared between aging and neurodegenerative diseases. Additionally, it opens avenues for AI-driven discovery of drug targets and early biomarkers, potentially accelerating the development of therapeutic strategies.

neuroscience↗

bioRxiv2025

MCUR1-CCDC90B complex is a conserved regulator of metabolic homeostasis

The mitochondrial calcium uniporter regulator 1 (MCUR1) is an evolutionarily conserved protein of the inner mitochondrial membrane1, yet its physiological role has remained elusive. Although initially proposed to function as a subunit of the mitochondrial calcium uniporter complex (MCUC)2-4, emerging evidence suggests that MCUR1 has a broader functional spectrum5-7. Here, we identify a biallelic loss-of-function MCUR1 variant (c.802C>T; p.R268X) in a patient with a progressive neurological phenotype. This mutation leads to loss of MCUR1 protein and exerts a dominant-negative effect on its paralog, CCDC90B. We show that MCUR1 and CCDC90B form a hetero-oligomeric complex whose stability depends on MCUR1. Deletion of MCUR1 and CCDC90B in the fission yeast Schizosaccharomyces pombe, which lacks the MCUC, impairs lipid and amino acid metabolism and causes nitrogen source-dependent growth defects that are rescued by expression of human MCUR1. Patient serum metabolomics confirms an imbalance in the amino acid pool, while MCUR1 deficiency in patient-derived skin fibroblasts upregulates autophagy, perturbs non-essential amino acid metabolism, and limits biosynthetic capacity, resulting in delayed proliferation and migration. These findings redefine the MCUR1-CCDC90B coiled-coil complex as a transmembrane scaffold critical for the integrity of mitochondrial protein complexes and the maintenance of metabolic homeostasis, suggesting a potential link between MCUR1 deficiency and human neurometabolic disease.

cell biology↗

bioRxiv2025

A Solid-Phase Extraction Capture (SPEC) workflow in nanoliter volumes for fast, robust and ultrasensitive proteomics

Sample preparation remains a critical bottleneck in mass spectrometry (MS)-based proteomics, particularly for limited sample amounts where surface adsorption and dilution cause substantial losses. Here, we present Solid-Phase Extraction Capture (SPEC), a workflow that confines protein processing to nanoliter volumes within ion-exchange or C18 matrix inside a pipette tip. This achieves near-complete proteolysis within 5 minutes instead of hours and maintains full compatibility with strong detergents without cleanup steps, enabling effective lysis of challenging samples. From 200 ng FFPE tissue, SPEC achieves proteome depth and reproducibility exceeding conventional bulk protocols using 100 {micro}g, critical when sample is irreplaceable. The modular two-tip configuration enables on-tip chemical modifications for mTRAQ labeling and fractionation, while integration with enrichment workflows yields 2-fold improved glycopeptide identifications from plasma and 3-fold enhanced ubiquitin remnant identification at low amounts. SPEC enables nanoPhos for cell-type resolved tissue phosphoproteomics and provides a universal platform for proteomics sample preparation.

systems biology↗

bioRxiv2025

Antioxidant supplementation blunts the proteome response to three weeks of sprint interval training preferentially in human type 2 muscle fibres

Sprint interval training (SIT) is a time-efficient type of endurance training that involves large type 2 muscle fibre recruitment. Effiective antioxidant supplementation may mitigate positive training adaptations by limiting the oxidant challenge. Our aim was to test whether SIT affiects type 2 more than type 1 muscle fibres, and whether the training response is mitigated by antioxidant treatment. Young men performed three SIT sessions (6 x 30 s all-out cycling) per week for three weeks while treated with antioxidants (vitamin C, 1 g/day; vitamin E, 235 mg/day) or placebo. Vastus lateralis biopsies were taken to measure (i) activation of genes for reactive oxygen/nitrogen species (ROS) sensors and inflammatory mediators with quantitative RT PCR and (ii) fibre type-specific proteome adaptations using mass spectrometry-based proteomics. Vitamin treatment decreased the upregulation of genes for ROS sensors and inflammatory regulators during the first SIT session. The three weeks of SIT caused generally larger proteome adaptations in type 2 than in type 1 fibres, and this included larger increases in abundance of proteins involved in mitochondrial energy production. Vitamin treatment blunted the SIT-induced proteome adaptations, whereas it did not affiect the training-induced improvement in maximal cycling performance. In conclusion, (i) the large type 2 fibre recruitment and resulting proteome adaptations are instrumental to the effiectiveness of SIT, and (ii) antioxidant supplementation counteracts positive muscular adaptations to SIT, which would blunt any improvement in submaximal endurance performance, whereas it does not affiect the improvement in maximal cycling performance, where O2 delivery to muscle would be limiting.

physiology↗

bioRxiv2024

Systematic mapping of MCU-mediated mitochondrial calcium signaling networks

The Mitochondrial Ca2+ Uniporter Channel (MCUC) allows calcium entry into the mitochondrial matrix to regulate energy metabolism but also cell death. Although, several MCUC components have been identified, the molecular basis of mitochondrial Ca2+ signaling networks and their remodeling upon changes in uniporter activity have not been systematically assessed. Using an unbiased and quantitative proteomic approach, we map the MCUC interactome in HEK293 cells under physiological conditions and upon chronic loss or gain of mitochondrial Ca2+ uptake. Besides all previously known subunits of the uniporter, we identify 89 high-confidence interactors linking MCUC to several mitochondrial complexes and pathways, half of which are currently linked to metabolic, neurological, and immunological diseases. As a proof-of-concept, we validate EFHD1 as a binding partner of MCU, EMRE and MCUB with a MICU1-dependent inhibitory effect on Ca2+ uptake. To investigate compensatory mechanisms and functional consequences of mitochondrial Ca2+ dyshomeostasis, we systematically survey the MCU interactome upon silencing of EMRE, MCUB, MICU1 or MICU2. We observe profound changes in the MCU interconnectivity, whereby downregulation of EMRE reduces the number of MCU interactors of over 10-fold, while silencing of MCUB leads to a wider functional network linking MCU to mitochondrial stress response pathways and cell death. Altogether our study provides a comprehensive map of MCUC protein-protein interactions and a rich, high-confidence resource that can be explored to gain insights into the players and mechanisms involved in calcium signal transduction cascades and their relevance in human diseases.

cell biology↗

bioRxiv2023

Acyl-CoA thioesterase-2 facilitates beta-oxidation in glycolytic skeletal muscle in a lipid supply dependent manner

Acyl-Coenzyme A (acyl-CoA) thioesters are compartmentalized intermediates that participate in in multiple metabolic reactions within the mitochondrial matrix. The limited availability of free CoA (CoASH) in the matrix raises the question of how the local acyl-CoA concentration is regulated to prevent trapping of CoASH from overload of any specific substrate. Acyl-CoA thioesterase-2 (ACOT2) hydrolyzes long-chain acyl-CoAs to their constituent fatty acids and CoASH, and is the only mitochondrial matrix ACOT refractory to inhibition by CoASH. Thus, we reasoned that ACOT2 may constitutively regulate matrix acyl-CoA levels. Acot2 deletion in murine skeletal muscle (SM) resulted in acyl-CoA build-up when lipid supply and energy demands were modest. When energy demand and pyruvate availability were elevated, lack of ACOT2 activity promoted glucose oxidation. This preference for glucose over fatty acid oxidation was recapitulated in C2C12 myotubes with acute depletion of Acot2, and overt inhibition of {beta}-oxidation was demonstrated in isolated mitochondria from Acot2-depleted glycolytic SM. In mice fed a high fat diet, ACOT2 enabled the accretion of acyl-CoAs and ceramide derivatives in glycolytic SM, and this was associated with worse glucose homeostasis compared to when ACOT2 was absent. These observations suggest that ACOT2 supports CoASH availability to facilitate {beta}-oxidation in glycolytic SM when lipid supply is modest. However, when lipid supply is high, ACOT2 enables acyl-CoA and lipid accumulation, CoASH sequestration, and poor glucose homeostasis. Thus, ACOT2 regulates matrix acyl-CoA concentration in glycolytic muscle, and its impact depends on lipid supply.

biochemistry↗

bioRxiv2018

Single fiber proteomics of respiratory chain defects in mitochondrial disorders

Mitochondrial DNA mutations progressively compromise the respiratory chain of skeletal muscle, resulting in a mosaic of metabolically healthy and defective fibers. The single fiber investigation of this important diagnostic feature has been beyond the capability of large-scale technologies so far. We used laser capture microdissection (LCM) to excise thin sections of individual muscle fibers from frozen biopsies of patients suffering from chronic progressive external ophthalmoplegia. We then applied a highly sensitive mass spectrometry (MS)-based proteomics workflow to analyze healthy and defective muscle fibers within the same biopsy. We quantified more than 4000 proteins in each patient, covering 75% of all respiratory chain subunits, and compared their expression in metabolically healthy and defective muscle fibers. Our findings show that mitochondrial disease causes extensive proteomic rearrangements, affecting the OPA1-dependent cristae remodeling pathway and mitochondrial translation. We provide fiber type-specific information showing that increased expression of fatty acid oxidation enzymes occurs in defective slow but not fast muscle fibers. Our findings shed light on compensatory mechanisms in muscle fibers that struggle with energy shortage and metabolic stress.

pathology↗