Biology subjects

Boni, E.

Publications and source records attributed to Boni, E..

3 recordsLinked to original sources

bioRxiv2026

Harnessing Escherichia coli motility to engineer bacterial Voronoi patterns

Cell motility drives spatial pattern formation across diverse biological systems. Here, we engineer Escherichia coli motility in semi-solid agar to control Voronoi patterns in two and three dimensions, partitioning space into regions closest to their respective inoculation seeds. Consistent with our reaction-diffusion model, we observed that collisions between expansion fronts generate either biomass depletion (''gaps'') or accumulation (''anti-gaps''), governed by the relative diffusion rates of bacteria and nutrients. By engineering strains with distinct expansion rates and tuneable motility, and by integrating these experimental data into a dynamic Voronoi model, we achieved precise control over pattern geometry. This enabled the generation of gaps with varying widths, curved boundaries, asymmetric structures, seedless regions, and complex composite patterns. Together, these findings establish bacterial Voronoi patterns as a programmable platform for engineering multicellular spatial organization, with potential applications in synthetic biology and materials science.

synthetic biology↗

bioRxiv2025

An engineered multi-step differentiation program in Escherichia coli for self-organized spatial patterning

In nature, complex multicellular structures originate from individual cells containing all essential information for differentiation, patterning and morphogenesis. Synthetic biology enables a bottom-up approach to study these processes by engineering and combining individual modules to progressively increase the systems complexity. Here, we engineered a multi-step program mimicking cell differentiation in the model prokaryote Escherichia coli. Starting from genetically identical cells and without providing any external positional information, we generated autonomous spatial patterns of colonies on a solid surface. We first employed a toggle switch to break population homogeneity (symmetry breaking), stochastically differentiating cells into two subpopulations: senders and receivers. Next, we activated expression of a third reporter in receiver colonies located in close proximity to sender colonies via quorum-sensing based communication (paracrine signaling). Finally, we mimic maturation of the newly emerged population by expressing a fourth reporter via an orthogonal, self-activating, quorum sensing signal (autocrine signaling). The diversity of spatial patterns generated by this multi-step program was accurately captured by simulations of a corresponding mathematical model. Together, these results demonstrate that multi-step differentiation programs can be engineered in unicellular bacteria to drive fully self-organized spatial pattern formation.

synthetic biology↗

bioRxiv2024

GRN modeler: An Intuitive Tool for Constructing and Evaluating Gene Regulatory Networks and its Applications to Oscillators and a Light Biosensor

Modeling and simulating gene regulatory networks (GRNs) is crucial for understanding biological processes, predicting system behavior, guiding the design of synthetic biological systems, and interpreting experimental data. In synthetic biology, GRNs play a pivotal role in enabling the design and control of complex systems for a wide range of applications. However, GRN simulations can be time-consuming and often require specialized expertise. To make this process more accessible, we developed a user-friendly application with a graphical user interface (GUI), allowing users to create simple phenomenological models without requiring prior programming experience. We demonstrate the versatility of our tool through several examples, including the design of novel oscillator families capable of robust oscillation with an even number of nodes. These complement the well-known repressilator family, which only oscillates with odd-numbered nodes. Furthermore, we showcase how GRN modeler allowed us to develop a light-detecting biosensor in Escherichia coli that can track light intensity over several days, leaving a record in the form of ring patterns in bacterial colonies. In summary, our work empowers biologists to model their systems of interest even without programming expertise.

synthetic biology↗