Biology subjects

Demontis, F.

Publications and source records attributed to Demontis, F..

4 recordsLinked to original sources

bioRxiv2026

MakeMyFigure: An Interactive Platform for Reproducible Quantitative Data Visualization, Analysis, and Scientific Figure Construction

Reproducible data analysis and visualization are essential for reliable biological and biomedical research, yet creating high-quality, publication-ready figures often requires moving data and results between multiple analysis, visualization, and graphics tools. This fragmented, multi-layered process can make it difficult to trace how individual figure panels were generated, preserve the underlying analytical decisions, and reproduce them later. Here, we introduce MakeMyFigure, a free and open-source platform for data visualization, analysis, and creation of multi-panel scientific figures. MakeMyFigure integrates data processing, statistical analysis, visualization, and figure assembly within a single workflow. It supports a range of quantitative data formats and structures, including feature-by-sample matrices and precomputed statistical results, and provides data-aware visualization recommendations to help users select appropriate plots from a library of 38 visualization types. These capabilities allow researchers to move directly from experimental measurements to commonly used statistical analyses and graphical representations without requiring programming expertise. Eighteen statistical procedures are implemented, and their results are drawn directly onto the plot families that support statistical annotation, keeping analytical results linked to the panels they generate. Importantly, MakeMyFigure uses machine-readable JSON specifications to record the identity and checksum of the source data, the processing steps, visualization settings, and statistical parameters used to generate each figure panel. It can also save a figure as a portable package, freezing the specifications together with the data. This allows figures to be regenerated from their recorded specifications and source data, or from the package alone on another computer, rather than relying on manually reconstructed workflows. Using published datasets from several biological fields, independent statistical validation in R, and a comparison with 15 representative analysis, visualization, and figure-generation tools, we show that MakeMyFigure combines accessible, code-free figure creation with panel-level computational reproducibility. Overall, MakeMyFigure provides a unified approach for creating, documenting, and reproducing scientific figures. Source code and documentation are available at https://github.com/surPoudel/make-my-figure, https://github.com/surPoudel/make-my-figure/releases/tag/v1.1.0.

bioinformatics↗

bioRxiv2025

Uniaxial tensile tests and Digital Image Correlation analysis for the mechanical characterization of human Fascia Lata under different decellularization treatments

Fascia Lata (FL) is frequently employed as a graft source in reconstructive surgery. To minimize unwanted responses from the host immune system, several decellularization treatments have been proposed. Effective treatments should aim at avoiding the deterioration of the physical and mechanical properties of the implanted tissue. In this work, we carried out a mechanical characterization of FL specimens from human dead donors, both in their native-physiological condition and upon decellularization with three commonly used detergents, t-octyl-phenoxypolyethoxyethanol (Triton X-100), sodium dodecyl sulfate (SDS), and tri-n-butyl phosphate (TnBP). Uniaxial tensile tests were used to characterize the elastic stiffness and ultimate stresses of the tissue, and Digital Image Correlation (DIC) was applied to monitor the strain evolutions and meso-mechanical deformation responses. None of the investigated decellularization protocols was found to lead to a significant deterioration of the FL mechanical properties, suggesting the applicability of these chemical treatments for graft preparation and usage in the clinical practice. The application of DIC also allowed us to get a first estimate of the FL Poisson ratio as well as to draw the attention on the inhomogeneity of strain distributions, suggesting that the use of average engineering strains can lead to an oversimplification of the actual deformation field.

bioengineering↗

bioRxiv2024

Linear ubiquitin chains remodel the proteome and influence the levels of hundreds of regulators in Drosophila

Ubiquitin controls many cellular processes via its post-translational conjugation onto substrates. Its use is highly variable due to its ability to form poly-ubiquitin with various topologies. Among them, linear chains have emerged as important regulators of immune responses and protein degradation. Previous studies in Drosophila melanogaster found that expression of linear poly-ubiquitin that cannot be dismantled into single moieties leads to their own ubiquitination and degradation or, alternatively, to their conjugation onto proteins. However, it remains largely unknown which proteins are sensitive to linear poly-ubiquitin. To address this question, here we expanded the toolkit to modulate linear chains and conducted ultra-deep coverage proteomics from flies that express non-cleavable, linear chains comprising 2, 4, or 6 moieties. We found that these chains regulate shared and distinct cellular processes in Drosophila by impacting hundreds of proteins. Our results provide key insight into the proteome subsets and cellular pathways that are influenced by linear poly-ubiquitin with distinct lengths and suggest that the ubiquitin system is exceedingly pliable.

cell biology↗

bioRxiv2023

The ubiquitin-conjugating enzyme UBE2D/eff maintains a youthful proteome and ensures protein quality control during aging

Ubiquitin-conjugating enzymes (E2s) are key for regulating protein function and turnover via ubiquitination but it remains undetermined which E2s maintain proteostasis during aging. Here, we find that E2s have diverse roles in handling a model aggregation-prone protein (huntingtin-polyQ) in the Drosophila retina: while some E2s mediate aggregate assembly, UBE2D/effete (eff) and other E2s are required for huntingtin-polyQ degradation. UBE2D/eff is key for proteostasis also in skeletal muscle: eff protein levels decline with aging, and muscle-specific eff knockdown causes an accelerated buildup in insoluble poly-ubiquitinated proteins (which progressively accumulate with aging) and shortens lifespan. Transgenic expression of human UBE2D2, homologous to eff, partially rescues the lifespan and proteostasis deficits caused by muscle-specific effRNAi by re-establishing the physiological levels of effRNAi-regulated proteins, which include several regulators of proteostasis. Interestingly, UBE2D/eff knockdown in young age reproduces part of the proteomic changes that normally occur in old muscles, suggesting that the decrease in UBE2D/eff protein levels that occurs with aging contributes to reshaping the composition of the muscle proteome. Altogether, these findings indicate that UBE2D/eff is a key E2 ubiquitin-conjugating enzyme that ensures protein quality control and helps maintain a youthful proteome composition during aging.

cell biology↗