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

该项目的目标是合成定制的基因电路和无细胞蛋白表达技术，以创建与生物膜发育相关的小分子生物传感器。该项目的目标之一是一类检测水系统和医疗设备中生物膜形成的传感器和报告器电路。这些传感器不仅更可靠，在生物防护之外发挥作用，而且还可以帮助医务人员识别和消除可能藏匿致病细菌的生物膜，并帮助水质监测专家识别基础设施中的微生物污染。该项目建议开发使用转录翻译（TX-TL）无细胞技术来实现这一目标。在这些系统中使用无细胞提取物不仅可以提高系统的速度和可靠性，而且如果不需要活生物体或蛋白质提取方法，还可以降低成本。此外，无细胞技术对系统的每个部分提供了更多的控制，使其具有更高的准确性和稳定性。如果这些产品比现有技术更可靠，并可在实地使用，许多利益攸关方将受益，这将是一项重要成就。一系列的原型电路和TX-TL协议将在这个项目中合成，专门为最终用户应用的需求量身定制。对于这一应用，马尔文光学是沃里克大学的现有合作者。马尔文将参与确保论文工作的成功。暂定的时间轴如下：1.第一年：使用来自生物物理学和系统理论的原理和技术合成基本感测和响应TX-TL电路并优化TX-TL协议。目标出版物：一份会议论文和一份期刊投稿。出版地点：国际生物设计与自动化研讨会（IWBDA），ACS合成生物学。第二年：合成更先进的感测和响应TX-TL电路并优化TX-TL协议。与Malvern合作表征生物膜形成。目标出版物：一份会议论文和一份期刊论文。出版地点：IWBDA，ACS Synthetic Biology。3.第3年：优化启动子，并进一步优化TX-TL方案。a.目标出版物：一份会议论文和一份期刊论文。出版地点：IWBDA，ACS Synthetic Biology。4.最后6个月：完成案例研究和博士论文的工作。提交并答辩博士论文。目标出版物：一份会议文件、一份期刊文件、软件包b。出版地点：IWBDA，PNAS。

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.