Biology subjects

Ruparelia, A. A.

Publications and source records attributed to Ruparelia, A. A..

4 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↗

bioRxiv2026

Observing concurrent subcellular dynamics in large living tissues

An outstanding question in eukaryotic biology is the mechanistic connection between events occurring at (sub)cellular levels (time scales of milliseconds to minutes) to those at the tissue levels (tens of minutes to months). Deciphering such mechanisms requires imaging approaches capable of simultaneously achieving high spatial and temporal resolutions for large samples over long periods of time. Here, we demonstrate Airy beam-based light sheet microscopy of organelles in tens to hundreds of cells in a few hundred micrometre-wide tissue environments. We achieve a typical resolution of 320 nm over 266 x 266 x 100 m3 volumes at a temporal rate of 0.05 Hz, typically with generally used fluorophores such as Green Fluorescent Protein, over extended periods of time that allow tracking of organelle and protein dynamics. We validated our approach across different length and time scales by imaging mitochondria and endosome dynamics in very large fields of view in zebrafish tissue, molecular assemblies of myosin as gastrulation proceeds in Drosophila embryos, 3D mitochondrial streaming in mouse oocytes, pressure-driven motility and protrusions in amoebae, mitochondrial dynamics in cancer spheroids, 5 -colour fast imaging in iBlastoids, and endosomal dynamics in single cells. Through these model systems, we demonstrate the versatility of Airy beam light sheet microscopy to image large tissues at unprecedented high resolution; to capture dynamics in photosensitive, delicate samples; and to screen 3D samples. We anticipate that our Airy beam-based approach will represent a pivotal advance in cellular biology--especially developmental biology--as it provides, for the first time, true subcellular resolution over large imaging volumes with high temporal resolution.

developmental biology↗

bioRxiv2019

Metformin rescues muscle function in BAG3 myofibrillar myopathy models

Dominant de novo mutations in the co-chaperone BAG3 cause a severe form of myofibrillar myopathy, exhibiting progressive muscle weakness, muscle structural failure, and protein aggregation.\n\nTo identify therapies we generated two zebrafish models, one conditionally expressing BAG3P209L and one with a nonsense mutation in bag3. Whilst transgenic BAG3P209L expressing fish display protein aggregation, modelling the early phase of the disease, bag3-/- fish demonstrate impaired autophagic activity, exercise dependent fibre disintegration, and reduced swimming activity, consistent with later stages.\n\nWe confirmed the presence of impaired autophagy in patient samples and screened autophagy promoting compounds for their effectiveness at removing protein aggregates, identifying nine including Metformin. Further evaluation demonstrated Metformin is not only able to remove the protein aggregates in zebrafish and human myoblasts but is also able to rescue the fibre disintegration and swimming deficit observed in the bag3-/- fish. Therefore, repurposing Metformin provides a promising therapy for BAG3 myopathy.

genetics↗