At lab de tecnología libre we are investigating how chemical coupling between bistable genetic networks modulates the emergence of ordered, disordered, and scale-free patterns of gene expression in bacteria that resemble systems operating in the proximity of critical points of continuous phase transitions (Simpson, K. et al). The project leverages insights from statistical physics and employs synthetic biology alongside microfabrication technology for the study of phase transitions in gene networks. These approaches permit the dynamical study of coupled and bistable synthetic gene networks (CB-SGNs) from single-cells to microcolonies of Escherichia coli at different chemical coupling strength conditions. This experimental setup allows us to study the dynamics of CB-SGNs’ induced pattern formation under precisely controlled and steady growth conditions at a single-cell resolution, as opposed to observing metabolically-drained bacterial colonies growing on a surface of solid agar. The main objectives of this work are (1) to characterize the spatial behavior of CB-SGNs, (2) to examine the effect of chemical coupling strength, and (3) to evaluate the existence of a continuous phase transition in the system.

The research intends to provide insights into the principles of spatial self-organization in biological systems and its implications for biotechnological applications, highlighting the role of chemical coupling as a pivotal control parameter in the dynamics of spatial patterns of gene networks.

For more details please check out the resulting research article.

The Swarm is a decentralized and diverse research group that study microbes, not in an ordinary way, but through building open-source hardware (e.g. HomeScope, an open-source robotic microscope) and playing My Swarm, a (biotic) game that operates on the biological process of adaptation and computation of swarming bacteria living in complex habitats.

In the gamified context of the project, The Swarm is a group of researchers-players who build their HomeScope, a microscope turned into a game console, along with the game cartridges (simple microfluidic devices) where soil bacteria grow, develop and expand over its surface. In these cell-ecosystem machines, computer vision and machine learning algorithms abstract living biological structures and map them into game elements that make up My Swarm, which creates a virtual ecology where real bacterial cultures living in different HomeScope consoles can compete and play, providing an ecological context for the directed evolution of game-winner strains.

Our vision is deeply motivated by the idea of making science accessible for everyone and decentralized, which is why we are learning how to run My Swarm on a blockchain’s virtual machine and tokenize observations of natural history (strain’s data) made by people.

Homemade RaspiCam/Arduino-based digital microscope system capable of recording video and image capture (time-lapse microscopy) while robotically scanning a sample. The HomeScope as a whole package is not only a DIY biologist solution for developing robotic microscopy capabilities for the home laboratory but also a means to learn (and teach) subjects across disciplines.

This open-source project was developed collectively by biotexturas and collaborators.