ROADBLOCK: Towards Programmable Defensive Bacterial Coatings & Skins

This project fits the EPSRC Synthetic Biology Signpost.This application-driven research project will seek to integrate the creation of new computational algorithms, tools and theories for synthetic biology (SB) with well-established wet lab techniques to develop an integrated and validated software suite (i.e. an in silico workbench) for SB. This project will focus on synthetic biology (SB) routes for creating engineered coatings, based on modified bacteria, that will act as bio-programmable shields against colonisation. The target application in this proposal is healthcare, using SB to develop biological based tools to tackle infection, however it is envisaged that ROADBLOCK constructs could be applicable in other medical, environmental or industrial applications in which bacterial colonisation or biofilm formation should be avoided. It will also consider the major social and ethical issues raised by this technology. The new computational tools will permit rapid bio-model prototyping and specification, simulation, verification, analysis and optimisation. Moreover, it will create ROADBLOCK biological parts, devices and systems. Previous SB projects had mainly mathematical (e.g. control theory, bifurcation analysis, differential equations, etc) components as auxiliary tools. In this project, Computer Science (CS) takes centre stage as we look to push its boundaries in the context of ROADBLOCK bio-devices. To the best of our knowledge, this is the first wet SB project that will directly drive the development of cutting-edge computer science (CS) activities.

This application is at the crossroad of executable biology, an emergent computational approach to biological problems, and synthetic biology, a growing discipline in its own right. A successful outcome to this project will impart momentum to the computational sciences behind synthetic biology and would, for the first time, demonstrate conclusively that executable biology/algorithmic systems biology are not mere academic curiosities applicable to small and well know biological systems but rather practical and useful tools for designing, analyzing and verifying large and complex biological systems. From the biological applications viewpoint, ROADBLOCK could extend its scope beyond clinical settings into different industrial sectors. In industry (e.g. drinking water distribution systems, dental water unit lines, food processing), distribution pipes get colonised by pathogenic bacteria that form biofilms, which may have health implications if not treated appropriately. Those pipes could be coated or treated with the bacterial skins reducing the use of environmentally unfriendly chemicals. In agriculture bacterial spy bullets could be used to spray plant and protect them against bacterial diseases. The public at large (see impact statement )will also benefit from a very intensive activity of engagement whereby they will not only have the opportunity to learn about synthetic biology and its potential impacts (health, environment, etc) but also inform the workings of this consortium. Thus, we believe, this proposal to be highly relevant, timely and may well have a wide impact (for more details please see impact statement).