Optimization of Cell-Free Circuits and Protocols 1=Engineering 2=Biomaterials and Tissue Engineering

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The goal of this project is to synthesize custom genetic circuits and cell-free protein expression technology to create biosensors of small molecules associated with biofilm development. One of the products of this project aims will be a class of sense-and-reporter circuits which detect biofilm formation in water systems and medical equipment. Not only will these sensors be more reliable and function outside of biological containment but these can also help medical personnel to identify and eradicate biofilms which can harbour pathogenic bacteria, and water quality monitoring specialists to identify microbial contamination in infrastructures. The project proposes to develop the use of transcription translation (TX-TL) cell free techniques to achieve this goal. Use of cell-free extract in these systems will not only increase the speed and reliability of the systems, it can also reduce the costs if the need for live organisms or protein extraction methods is removed. Furthermore, cell-free technology offers much more control over each part of the system, giving it a much higher accuracy and stability. If the products are more reliable than existing techniques and can be used in the field, many stakeholders will benefit and this will be an important achievement. A range of prototype circuits and TX-TL protocols will be synthesized in this project, specifically tailored for the needs of the end-user application. For this application, Malvern Optical is an existing collaborator for the University of Warwick. Malvern will participate in ensuring the success of the thesis work. A tentative timeline is as follows:1. Year 1: Synthesis of elementary sense-and-respond TX-TL circuits and optimization of the TX-TL protocols using principles and techniques from biophysics and systems theory.a. Target Publications: One conference paper and one journal submission.b. Publication Venues: International Workshop on Biodesign and Automation (IWBDA), ACS Synthetic Biology.2. Year 2: Synthesis of more advanced sense-and-respond TX-TL circuits and optimization of the TX-TL protocols. Characterization biofilm formation in collaboration with Malvern.a. Target Publications: One conference paper and one journal paper.b. Publication Venues: IWBDA, ACS Synthetic Biology.3. Year 3: Optimisation of the promoters and further work on the optimization of the TX-TL protocols. a. Target Publications: One conference paper and one journal paper.b. Publication Venues: IWBDA, ACS Synthetic Biology.4. Final 6 Months: Finish the work on the case studies and the PhD thesis. Submit and defend the PhD thesis.a. Target Publications: One conference paper, one journal paper, software packageb. Publication Venues: IWBDA, PNAS.