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.
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
Liyanagedera SBW
(2022)
SpyPhage: A Cell-Free TXTL Platform for Rapid Engineering of Targeted Phage Therapies.
in ACS synthetic biology
| 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 |