Biology subjects

Locop, J.

Publications and source records attributed to Locop, J..

3 recordsLinked to original sources

bioRxiv2026

fishROI: A specialized workflow for semi-automated muscle morphometry analysis in teleosts

Quantitative histological analysis of skeletal muscle morphometry provides critical insights into muscle physiology but remains labor-intensive and technically demanding. While recent developments in machine-learning-based image segmentation techniques have facilitated large-scale tissue analysis, existing tools that automate muscle morphometry analysis are largely tailored to mammalian models, with limited applicability to teleosts. Moreover, there is a lack of effective tools for visualizing spatial organization and morphometric variability of teleost muscle fibers, a feature that is important for understanding hyperplastic muscle growth dynamics in teleosts. In this study, we show that cytoplasmic staining combined with deep learning-based cell segmentation offers a robust and accurate approach for automated muscle morphometry analysis in developing zebrafish. We also introduce a FIJI2 plugin, implemented in Jython, that streamlines both morphometric analysis and visualization. This tool accommodates shallow and deep learning-based segmentation techniques and incorporates novel quantification and visualization methods suited to teleost-specific muscle features, including mosaic hyperplasia dynamics. The plugin features an intuitive graphical user interface and is designed for flexibility, with minimal constraints regarding species, image quality, or staining protocol. Its modular architecture allows it to be used as a baseline for automated muscle morphometry analysis, while permitting integration with other tools and workflows.

cell biology↗

bioRxiv2026

Divergence in skeletal muscle growth by differential spatial hyperplastic patterning in teleost fishes

Skeletal muscle plays important locomotive and metabolic functions, yet its formation and maintenance are processes remaining largely unclear mechanistically in any animal. Teleost fishes display extraordinary muscle growth due to their ability to undergo both hyperplasia and hypertrophy throughout life. These phenomena vary greatly even between closely related species, providing opportunities to elucidate growth dynamics and underlying mechanisms through cross-species comparisons. Using histological and genetic approaches, we compared muscle growth dynamics in three closely related danionin species with distinct growth capacities: the giant danio (Devario malabaricus), the zebrafish (Danio rerio), and Danionella cerebrum, as well as the more distantly related African turquoise killifish (Nothobranchius furzeri). Our study reveals alterations in spatial patterning of muscle hyperplasia and developmental timing to be major contributors to observed differences in muscle growth between examined species. Single-cell RNA profiling, in situ hybridization chain reaction and cell type-specific mutagenesis revealed muscle stem cell-specific expression of extracellular matrix genes that mediate stem cell activity, which in turn may drive growth differences between species. Taken together, our findings highlight autonomous regulation of muscle stem cells as a conserved but adaptable mechanism governing muscle patterning and diversification.

evolutionary biology↗

bioRxiv2023

An obligate aerobe adapts to hypoxia by hybridising fermentation with carbon storage

In soil ecosystems, obligately aerobic bacteria survive oxygen deprivation (hypoxia) by entering non-replicative persistent states. Little is known about how these bacteria rewire their metabolism to stay viable in these states. The model obligate aerobe Mycobacterium smegmatis maintains redox homeostasis during hypoxia by mediating fermentative hydrogen production. However, the fate of organic carbon during fermentation, and the associated remodeling of carbon metabolism, is unresolved. Here we systematically profiled the metabolism of M. smegmatis during aerobic growth, hypoxic persistence, and the transition between these states. Using differential isotope labelling, and paired metabolomics and proteomics, we observed rerouting of central carbon metabolism through the pentose phosphate pathway and Entner-Doudoroff pathway during hypoxia. We show that M. smegmatis excretes high levels of hydrogen concurrently with upregulating triacylglyceride synthases and accumulating glycerides as carbon stores. Using electron cryotomography (cryo-ET), we observed the presence of large spheroid structures consistent with the appearance of lipid droplets. Thus, in contrast to obligately and facultative anaerobic fermentative bacteria, M. smegmatis stores rather than excretes organic carbon during hypoxia. This novel hybrid metabolism likely provides a competitive advantage in resource-variable environments by allowing M. smegmatis to simultaneously dispose excess reductant during hypoxia and maintain carbon stores to rapidly resume growth upon reoxygenation.

microbiology↗