- Modularity of biological parts and devices.
A key concept in synthetic biology is the composition of predictable systems from a set of reusable, well characterized parts. This paradigm has been successful in all the fields of engineering and, similarly, it could enable the design of customized biological systems without following trial-and-error approaches. However, modularity is required to accomplish this task, as only in a modular framework parts can be individually characterized and assembled in a complex system in a predictable way. Towards this goal, we are now investigating the predictability boundaries of biological components to disclose the modularity limits of several parts and devices when tested in different conditions (e.g. chassis, copy number, media) and assembled in increasingly complex circuits in prokaryotes.
The foundational research studies on biological parts are exploited to optimize a recombinant metabolic pathway, including a pyruvate decarboxylase and an alcohol dehydrogenase, for ethanol production from lactose fermentation in E. coli. Lactose is an abundant sugar in dairy industry waste (cheese whey and whey permeate) that can be considered as a free raw material for biofuel production. The expression of recombinant genes is optimized, in terms of product yield and phenotype stability, via orthogonal well-characterized regulatory parts and codon optimization. The engineered microbes are a starting point for the development of a cost-effective industrial valorization process of whey and also for the production of other fuels with synthetic biology.
- Quorum sensing re-engineering
Quorum sensing elements are used to engineer a genetic circuit that implements a closed-loop control system. Mathematical models are used to predict the static and dynamic behaviour of the designed circuit and its variants. The final system must be able to mimic in a predictable fashion the key features of a traditional closed-loop regulated engineering device, e.g. steady state regulation, noise rejection and robustness. We intend to carry out these goals by following a rigorous bottom-up procedure where sub-circuits are quantitatively characterized to identify the main model parameters, the whole system behaviour is tested in silico and finally it is experimentally validated to compare real vs simulated results.
- Genetic and computational tools for synthetic biology.
Physical and measurement standards are some of the key concepts introduced by engineers to facilitate the rational design and construction of biological systems in synthetic biology. We aim to develop 1) user-friendly genetic tools to solve recurrent problems in the generation of engineered strains, e.g. a BioBrick integrative vector for E. coli (BBa_K300000) that can be specialized to target the desired genomic locus or the construction of orthogonal inducible systems for gene expression that respond to different stimuli; 2) detailed datasheets of industrially-attractive biological parts/devices, e.g. a synthetic bacterial self-destruction device; 3) mathematical studies that support the design of complex systems in a predictable way, e.g. mathematical models that are able to predict the effects of copy number variations of promoters and transcription factors.