Biology subjects

Bonte, T.

Publications and source records attributed to Bonte, T..

3 recordsLinked to original sources

bioRxiv2025

Cut-Detector: A Tool for Automated Temporal Analysis of Late Cytokinetic Events

Cytokinesis is the final step of cell division, resulting in the physical separation of the two daughter cells. Despite its fundamental importance in cell biology, biologists currently lack automatic tools for large-scale profiling of cytokinesis dynamics. In particular, the timing of the first microtubule cut in the intercellular bridge connecting the daughter cells is crucial, as it marks a critical step preceding abscission. Here, we introduce Cut-Detector, an open-source tool for the automatic analysis of late cytokinesis timing from time-lapse microscopy movies. Cut-Detector employs an AI approach to carry out the multiple tasks required to monitor cytokinesis: cell segmentation and tracking, detection of cell division events, localization of the intercellular bridge, and detection of the microtubule cuts. Cut-Detector will facilitate large-scale analyses to uncover new cytokinetic genes, a task that would be impractical without automation.

bioinformatics↗

bioRxiv2025

A Deep Learning approach for time-consistent cell cycle phase prediction from microscopy data

The cell cycle consists of four phases and impacts most cellular processes. In imaging assays, the cycle phase can be identified using dedicated cell-cycle markers. However, such markers occupy fluorescent channels that may be needed for other reporters. Here, we propose to address this limitation by inferring the phase from a widely used fluorescent reporter: SiR-DNA. Our method is based on a variational auto-encoder, enhanced with two auxiliary tasks: predicting the intensity of phase-specific markers and enforcing the latent space temporal consistency. Our model is freely available, along with a new dataset comprising over 600,000 annotated HeLa Kyoto nuclear images.

bioinformatics↗

bioRxiv2024

Cell cycle-dependent mRNA localization in P-bodies

Understanding the dynamics of RNA targeting to membraneless organelles is essential to disentangle their functions. Here, we investigate how P-bodies (PBs) evolve during cell cycle progression. PB purification across the cell cycle uncovers widespread changes in their RNA content, which are partly uncoupled from cell cycle-dependent changes in RNA expression. Single molecule FISH shows various mRNA localization patterns in PBs peaking in G1, S, or G2, with examples illustrating the timely capture of mRNAs in PBs when their encoded protein becomes dispensable. Yet, rather than directly reflecting absence of translation, cyclic mRNA localization in PBs can be controlled by RBPs, such as HuR in G2, and by RNA features. Indeed, while PB mRNAs are AU-rich at all cell cycle phases, they are specifically longer in G1, possibly related to post-mitotic PB reassembly. Altogether, our study supports a model where PBs are more than a default location for excess untranslated mRNAs.

cell biology↗