Distributed biological circuits

To circumvent the size-limit on scaling up of genetic circuits in single cells, several research teams have proposed multicellular approaches for building distributed biological circuits. However, most examples of distributed circuits have so far been limited to using a small set of molecular signals, repurposed from nature, as external wires for intercellular communication. In this research theme, we are constructing bacteriophage-derived synthetic orthogonal signals for cell-to-cell communication in bacterial communities, and using them to build larger and more complex multicellular circuits.

Cross-species design strategies

Incompatibility between the host chassis and the target product currently limits us from leveraging the full potential of the biotechnological process. Engineering the most compatible chassis organism for the target molecule of interest, rather than relying on a model host organism, can help address this problem. Yet, non-model organisms are often less tractable and considerable effort is required to identify and characterise new genetic parts before they can be used for engineering. In this research theme, we develop cross-species compatible genetic tools and expression systems that can be ported between species, to enable rapid prototyping of genetic circuits and metabolic pathways in non-model organisms.

Cell-free systems for information processing and diagnostics

Lysate-based cell-free expression systems are made up of cellular contents re-energized to execute several molecular functions. They can be used to deploy genetic and metabolic circuits for many medical, industrial, and environmental applications. Our research in cell-free systems aims to: (1) improve the cell-free technology to make it more simple, efficient, and cost-effective, and (2) use cell-free systems to build biosensors for different molecules for multiplex detection and complex information processing. In this research theme, we have combined genetic knockouts of the chassis strain with buffer-optimization to increase the stability of linear DNA templates in the cell-free system. We have also implemented in cell-free systems sense and antisense riboregulators, CRISPR-based sensors of endogenous RNAs, toehold switches for rosewood detection, and combined detection of several small molecules in the form of a metabolic perceptron.

Expression costs of synthetic genetic circuits

As the size and complexity of synthetic genetic circuits increase, they progressively become too burdensome for a single cell. Consequently, many genetic circuits are easily lost to negative selection when the engineered organisms are exposed to more stressful environments. In contrast, natural systems are able to carry much larger programmes by using complex regulatory mechanisms to keep the costs of expression under check. In this research theme, we aim to develop experimental and theoretical methods to measure the cost of maintaining and executing synthetic genetic circuits in cells. The quantitative models will be used to choose the most economical design architectures for implementing a genetic circuit with a specified function. The circuit designs will be studied under different growth and stress conditions to assess the relationship between the estimated costs and circuit performance.