ROADBLOCK: Towards Programmable Defensive Bacterial Coatings & Skins

Lead Research Organisation: University of Sheffield
Department Name: Computer Science

Abstract

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.
 
Description We have developed a coherent methodology, integrated into a computational tool, for using formal verification tools for verifying the behaviour of Synthetic Biology models.
We have also characterised the production of salycylic acid by specific bacteria and the type of biofilms that it produces
Exploitation Route The verification methodology can be used together with the IBW tool. In order to make it accessible to non-specialists, a set of natural language patterns are made available with the tool.
Sectors Education,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

 
Description When the IBW tool will be complete, by the end of 2015, this might be used by any systems and synthetic biology communities interested in modelling, simulation and verification of their systems, using stochastic approaches. An initial version of the tool should be available by the end of this year. Cited within academic publications
First Year Of Impact 2014
Impact Types Economic

 
Description Using a synthetic biology approach to engineer urban water system biofilms
Amount £246,458 (GBP)
Funding ID EP/M017680/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Academic/University
Country United Kingdom
Start 01/2015 
End 12/2016
 
Description Research Seminar - overview of activities 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Invited research seminar to School of Engineering, Newcastle University, where I gave an overview of my research activities with the aim of future collaborations
Year(s) Of Engagement Activity 2018