Biology subjects

Bonazzi, D.

Publications and source records attributed to Bonazzi, D..

5 recordsLinked to original sources

bioRxiv2026

Apical adhesion of meningococci controls host cell basal traction force through Ancreopodia formation

Extracellular bacterial pathogens remodel the apical surface of host cells, but whether these local interactions are mechanically transmitted across the cell to the basal extracellular matrix remains unclear. Using a combination of in vitro infection models, high-resolution imaging, traction force microscopy and bacterial genetics, we show that Neisseria meningitidis (Nm) adhesion to endothelial cells triggers a rapid increase in traction forces and localized, colony-associated traction-force hotspots on the extracellular matrix. Formation of these hotspots is associated with a novel actin-rich structure, which we term ancreopodia, that links apical bacterial colonies to the basal substrate. Super-resolution microscopy revealed ancreopodia spanning the cell thickness, connecting apical cortical plaques to reorganized basal stress fibers and focal-adhesion components. Dynamic imaging demonstrated coordinated movements of bacterial colonies and basal mechanosensitive proteins, while analysis of pili mutants showed that pilus retraction is required to focus traction forces beneath colonies. Disruption of branched actin assembly or myosin-II activity likewise impaired apico-basal organization and vinculin recruitment. Functionally, Nm infection enhanced local anchoring while restricting single-cell migration and collective endothelial dynamics. Together, these findings identify ancreopodia as a vertical mechanotransduction structure through which an extracellular pathogen couples apical adhesion to basal force transmission and reshapes host-cell mechanics.

cell biology↗

bioRxiv2026

Automated Optimization of Bacterial Tracking Pipelines with TrackMate 8

Quantitative analysis of bacterial dynamics in time-lapse microscopy requires robust tracking pipelines, yet selecting and optimizing algorithms for specific experiments remains challenging. Indeed, Microbiologists are confronted with numerous algorithms that must be carefully chosen and parameterized to achieve optimal tracking for their experiments. We present an automated methodology to determine optimal tracking configurations for microbiological applications. It is based on TrackMate 8, a novel version of the TrackMate Fiji plugin extended with microbiology-specific tools. Our approach systematically evaluates algorithm-parameter combinations optimizing biologically relevant metrics (e.g., cell-cycle accuracy, bacteria morphology) and includes: (1) integration of deep-learning algorithms (Omnipose, YOLO, Trackastra) adequate for bacteria images in TrackMate, (2) a TrackMate-Helper extension for parameter optimization, and (3) a tracking and segmentation editor for tracking ground-truth generation. We demonstrate the effectiveness of the methodology on two use cases showing its adaptability to diverse experimental conditions. This methodology enables microbiologists with a widely applicable, automated framework to optimize tracking pipelines, facilitating quantitative analysis in bacterial imaging.

microbiology↗

bioRxiv2024

Bacterial growth under confinement requires transcriptional adaptation to resist metabolite-induced turgor pressure build-up

Bacterial proliferation often occurs in confined spaces, during biofilm formation, within host cells, or in specific niches during infection, creating mechanical constraints. We investigated how spatial confinement and growth-induced mechanical pressure affect bacterial physiology. Here, we found that, when proliferating in a confining microfluidic-based device with access to nutrients, Escherichia coli cells generate forces in the hundreds of kPa range. This pressure decouples growth and division, producing shorter bacteria with higher protein concentrations. This leads to cytoplasmic crowding, which ultimately arrests division and stalls protein synthesis. In this arrested state, the pressure produced by bacteria keeps increasing. A minimal theoretical model of bacterial growth predicts this novel regime of steady pressure increase in the absence of protein production, that we named overpressurization. In this regime, the Rcs pathway is activated and that abnormal shapes appear in rcs mutant populations only when they reach the overpressurized state. A uropathogenic strain of E. coli displayed the same confined growth phenotypes in vitro and requirement for Rcs in a mice model of urinary tract infection, suggesting that these pressurized regimes are relevant to understand the physiopathology of bacterial infections.

microbiology↗

bioRxiv2021

Bringing TrackMate in the era of machine-learning and deep-learning.

TrackMate is an automated tracking software used to analyze bioimages and distributed as a Fiji plugin. Here we introduce a new version of TrackMate rewritten to improve performance and usability, and integrating several popular machine and deep learning algorithms to improve versatility. We illustrate how these new components can be used to efficiently track objects from brightfield and fluorescence microscopy images across a wide range of bio-imaging experiments.

bioinformatics↗

bioRxiv2018

Adhesion to nanofibers drives cell membrane remodeling through 1D wetting

The shape of cellular membranes is highly regulated by a set of conserved mechanisms. These mechanisms can be manipulated by bacterial pathogens to infect cells. Human endothelial cell plasma membrane remodeling by the bacterium Neisseria meningitidis is thought to be essential during the blood phase of meningococcal infection, but the underlying mechanisms are unknown. Here we show that plasma membrane remodeling occurs independently of F-actin, along meningococcal type IV pili fibers, by a novel physical mechanism we term \" onedimensional\" membrane wetting. We provide a theoretical model that gives the physical basis of 1D wetting and show that this mechanism occurs in model membranes interacting with model nanofibers, and in human cells interacting with model extracellular matrices. It is thus a new general principle driving the interaction of cells with their environment at the nanoscale that is diverted by meningococcus during infection.

cell biology↗