Biology subjects

Belpaire, T. E. R.

Publications and source records attributed to Belpaire, T. E. R..

6 recordsLinked to original sources

bioRxiv2026

Matrix-controlled emergence of biofilm architecture shapes antimicrobial survival

Biofilms are structured microbial communities whose extracellular matrix is widely regarded as a basis of their protection against antimicrobial compounds. Yet how matrix production by individual bacteria gives rise to collective architecture and antimicrobial protection remains poorly understood. Here, we systematically varied expression of the master biofilm regulator csgD in Salmonella enterica and found that increasing matrix production reorganizes biofilms from dense, isotropic packings into sparse, nematically aligned communities by altering cell-cell interactions. By combining experimentally measured biofilm architectures with reaction-diffusion modeling, we show that these structural changes produce distinct patterns of antimicrobial killing, ranging from preferential killing near the liquid-biofilm interface to more uniform killing throughout the community. Consequently, increasing matrix production unexpectedly reduces antimicrobial survival by shifting the biofilm into different transport regimes, while strain-specific physiological differences further modulate antimicrobial depletion. Rather than acting as a passive barrier, EPS therefore shapes antimicrobial susceptibility by reorganizing biofilm architecture and its transport properties. EPS thus provides a physical link between molecular regulation, collective architecture and antimicrobial survival, providing a quantitative framework for understanding how cellular matrix production generates emergent biofilm function.

microbiology↗

bioRxiv2026

Cellular timing heterogeneity regulates phase transitions in living matter

Rigidity transitions govern tissue organization in ways reminiscent of inert materials. Yet, living tissues are composed of active units with autonomous timing mechanisms, raising the question whether microscopic cellular timing distribution influences collective mechanical states. Here we identify heterogeneity in cellular timescales as a heritable parameter, regulating rigidity transitions in embryonic tissues. Lineage tracking and quantitative mechanical analysis reveal that zebrafish morphogenesis starts with a tissue rigidity collapse occurring at maximal cell cycle length heterogeneity. This heterogeneity arises from size-dependent stochastic differences in resource allocation, with resource availability defining the cell cycle length. Such differences are inherited across generations, amplifying and structuring tissue-wide cell cycle length heterogeneity. Experiments and large-scale 3D simulations identify an optimum level of cellular timing variability at which cell-cell contact remodelling is spatially coordinated driving timely and robustly the rigidity transition. These findings demonstrate that embryos exploit microscopic temporal disorder for timing and tuning tissue morphogenesis.

biophysics↗

bioRxiv2025

Cell-substrate friction controls biofilm development

Bacteria often live in biofilms, surface-attached communities that can form on nearly any surface, from coarse sands to smooth glass. It is often hypothesized that cell-substrate friction can impact biofilm growth and development on these disparate surfaces. However, the experimental difficulty in measuring the friction between a biofilm and its surface has limited our understanding of how friction forces impact emergent colony-level behaviors and morphologies. Here, we demonstrate that increasing cell-substrate friction increases the biofilm contact angle, which, in turn, decreases the horizontal biofilm range expansion rate. We first used individual-based simulations to isolate the impact of friction. In this simple model, we found that increasing friction increases biofilm contact angle, and, in turn, that the contact angle emerges from a simple dynamic force balance between cell-substrate friction, cell-cell steric forces, and cell-cell adhesion, reminiscent of Youngs equation for sessile liquid drops. We developed an approach to directly measure the friction between bacterial colonies and agar surfaces, and found that the friction between the substrate and the biofilm is higher on substrates made with higher agar weight percentage. Additionally, we observed that biofilm contact angles increase with friction, following a Young-equation-like balance. Finally, we found that contact angle increases with agar percentage for a wide range of bacteria, suggesting that the biophysical impact of friction may play a role for a wide array of microbes.

biophysics↗

bioRxiv2024

Active foam dynamics of tissue spheroid fusion

Three-dimensional tissue spheroids are a key building block in biofabrication, yet the link between their material properties and active mechanics of individual cells is not fully understood. We study the material properties of small spheroids of human periosteum-derived cells as they effect spheroid fusion, an elementary operation for constructing large tissue structures. We use two-photon confocal microscopy to measure cell-cell tension and individual cell motility throughout fusion. Cytoskeletal inhibition through Y-27632 (ROCKi) results in more granular tissues with decreased cell rearrangements, but accelerated fusion. Further reducing cell contractility with blebbistatin and ROCKi increases tissue granularity, decreases rearrangements, and slows down fusion. In all conditions, complete fusion is associated with frequent cellular rearrangements. Using a novel computational model that represents tissue material as an active cellular foam, with cells depicted as viscous shells with interfacial tension and persistent, random motility, we construct a phase diagram of spheroid fusion in function of relative cell-cell tension and cell motility. Our results reveal a close relationship between microscopic tissue fluidity and the visco-elastic properties of spheroid fusion. Additionally, we find that cell-cell friction promotes arrested fusion by inducing jamming through a distinct physical mechanism. Combined, our findings offer a framework for understanding spheroid fusion dynamics that can aid in the robust generation of large tissue constructs for regenerative medicine.

biophysics↗

bioRxiv2022

Spatial distribution of bacteria and extracellular polymeric substances impacts nanoparticle penetration in biofilms

Extracellular polymeric substances (EPS) in bacterial biofilms complicate treatment by inactivating drugs and slowing down diffusion. Through enhanced penetration and resistance to degradation in bacterial biofilms, nanoparticle (NP) carriers can help improve biofilm treatment. However, the way in which biofilm architecture influences the diffusive properties and penetration of NPs in biofilms is still poorly understood. In this work, we combined single particle tracking (SPT) and confocal laser scanning microscopy (CLSM) in Salmonella biofilms with simulations of a Brownian dynamics model to quantify how macro- (spatial organization of the bacteria) and micro- (EPS dependent) structure of the biofilm affects NP penetration. In CLSM images we observed immobilization of NPs in the EPS, which allows shielding of bacteria from the NPs, an effect that was more pronounced in dispersed biofilms, grown in nutrient-rich conditions, than in compacted biofilms, grown in nutrient-poor conditions. SPT experiments revealed anomalous diffusion, with an increased probability for small displacements near clusters of bacteria. Simulations of a Brownian dynamics model revealed that EPS reinforces shielding by affecting the pore structure of the biofilm. Finally, in virtual biofilms with varying spatial distribution of bacteria, we found that even for the same number of bacteria, dispersed biofilm structures provide more shielding than biofilms organized in dense, compacted clusters, even when accounting for decreased NP diffusivity.

microbiology↗

bioRxiv2021

Permissive aggregative group formation favors coexistence in yeast

In Saccharomyces cerevisiae, the FLO1 gene encodes flocculins that lead to formation of multicellular flocs, that offer protection to the constituent cells. Flo1p was found to preferentially bind to fellow cooperators compared to defectors lacking FLO1 expression, resulting in enrichment of cooperators within the flocs. Given this dual function in cooperation and kin recognition, FLO1 has been termed a green beard gene. Because of the heterophilic nature of Flo1p binding however, we hypothesize that kin recognition is permissive and depends on the relative stability of FLO1+/flo1- versus FLO1+/FLO1+ bonds, which itself can be dependent on environmental conditions and intrinsic cell properties. We combine single cell measurements of adhesion strengths, individual cell-based simulations of cluster formation and evolution, and in vitro flocculation experiments to study the impact of relative bond stability on defector exclusion as well as benefit and stability of cooperation. We hereto vary the relative bond stability by changing the shear flow rate and the inherent bond strength. We identify a marked trade-off between both aspects of the green beard mechanism, with reduced relative bond stability leading to increased kin recognition, but at the expense of decreased cluster sizes and benefit of cooperation. Most notably, we show that the selection of FLO1 cooperators is negative-frequency dependent, which we directly attribute to the permissive character of the Flo1p bond. Taking into account the costs associated to FLO1 expression, this asymmetric selection results in a broad range of ecological conditions where coexistence between cooperators and defectors is stable. Although the kin recognition aspect of the FLO1 green beard gene is thus limited and condition dependent, the negative-frequency dependency of selection can conserve the diversity of flocculent and non-flocculent phenotypes ensuring flexibility towards variable selective pressures.

evolutionary biology↗