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

Lead Research Organisation: University of Warwick
Department Name: Sch of Engineering

Abstract

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 package
b. Publication Venues: IWBDA, PNAS.

Publications

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Studentship Projects

Project Reference Relationship Related To Start End Student Name
EP/N509796/1 01/10/2016 30/09/2021
1917070 Studentship EP/N509796/1 02/10/2017 15/09/2021 Sahan Bandara LIYANAGEDERA
 
Description - Cell Free System Developed
- Cell Free System Incorporated into hydrogel based materials through the construction of Synthetic Cells
Exploitation Route Following the completion of this PhD project, the resulting publications will outline simple fabrication methods for the creation of sense and respond materials. The design principles and strategies that will be established will allow for the creation of novel antimicrobial materials which could be deployed in healthcare and industrial settings.
Sectors Aerospace, Defence and Marine,Environment,Healthcare,Pharmaceuticals and Medical Biotechnology

 
Description CRISPR Selection for Bacteriophage Engineering 
Organisation Hungarian Academy of Sciences (MTA)
Department Biological Research Centre (BRC)
Country Hungary 
Sector Academic/University 
PI Contribution We created genetic sequence designs for the editing of K1F bacteriophages, to enable their immobilisation onto a hydrogel based material. These sequences were ordered and sent to the lab of Dr Tamas Feher to be used to engineer K1F bacteriophages.
Collaborator Contribution The lab of Dr Tamas Feher constructed a library of engineered K1F bacteriphages using the genetic designs and constructs provided by our lab. Our lab is currently working with these new engineered bacteriophages to create novel smart biomaterials.
Impact No significant outcomes have yet resulted from this collaboration. The only outcomes thus far have been the creation of a library of engineered K1F bacteriophages.
Start Year 2019
 
Description Hydrogel Synthesis 
Organisation University of Warwick
Department Department of Chemistry
Country United Kingdom 
Sector Academic/University 
PI Contribution Our lab has developed a method for the facile immobilisation of biological entities on to a hydrogel synthesised in the lab of Dr Paul Wilson in the Department of Chemistry at the University of Warwick.
Collaborator Contribution Dr Paul Wilson's lab has helped in the synthesis of various polymers and molecules for the construction of hydrogels and synthetic cells. Dr Paul Wilson's lab has also provided expert advice on hydrogel formulations for smart materials and bioprinting.
Impact No significant outcomes to date.
Start Year 2017
 
Description UK - China Smart Materials Collaboration 
Organisation Shanghai Jiao Tong University
Country China 
Sector Academic/University 
PI Contribution Our group has helped in the writing of a Review Paper on Smart Materials to be published this year.
Collaborator Contribution The lab of Professor Xiao Xia hosted me during a 6 month placement funded by the UK-China Newton Fund Fellowship. Professor Xia continues to provide expert advice on hydrogel formulations.
Impact No significant outcomes to date.
Start Year 2018