An engineering platform for rapid prototyping synthetic genetic networks

用于快速构建合成遗传网络原型的工程平台

• 批准号: EP/P017401/1
• 负责人: Yizhi Cai
• 金额: $ 12.84万
• 依托单位: University of Manchester
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2017
• 资助国家: 英国
• 起止时间: 2017 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=EP%2FP017401%2F1
• 关键词: engineering; platform; rapid; prototyping; synthetic

Synthetic biology is an exciting new discipline which offers the potential to bring many benefits to human health and welfare. One near-market example is the use of engineered genetic networks to make biological sensors, or biosensors, which can rapidly detect toxins and harmful microorganisms. However, most synthetic biology systems are based on living genetically modified cells, and due to safety concerns and regulatory issues, they can not be used outside of a specially approved laboratory, whereas the greatest unmet need for biosensors is in the field, for 'point-of-use' and 'point-of-care' tests for health hazards. The laboratory of Professor James Collins recently reported a remarkable breakthrough, using non-living biological systems based on genetic components dried onto strips of paper. These systems can be prepared very cheaply, can be stored stably for long periods, and, since they are not alive and can not replicate, they pose no risks to the environment. This technology is therefore ideal for further development of sensors for human health. In addition, these cell-free systems can be prepared in large numbers very rapidly, in a matter of hours, and tested rapidly, in a matter of minutes, whereas living cell based systems may take weeks to prepare and days to test. This makes the new technology ideal for 'rapid prototyping' of genetic circuits. Many designs can be rapidly generated and tested, and the most successful can then be used to generate cell-based systems for applications where this is required, such as engineered metabolic pathways for manufacturing pharmaceuticals and other valuable compounds. In this project, we will further develop these remarkable systems and create new tools which will make it even easier to design and develop them. Firstly, we will create new computational tools which can be used to design genetic circuits for many applications. These will be made available on-line for the benefit of the research community. Secondly, we will establish methods for rapid automated assembly and testing of new circuits, allowing many thousands of variants to be generated and tested in a very short time with minimal human effort. Thirdly, we will seek to improve the basic technology, to improve the performance of the cell-free devices, and also develop low cost open-source electronic readers which can easily be used in the field along with the sensors we develop. Fourthly, we will demonstrate the usefulness of the technology by generating sensors which can rapidly and sensitively detect various external inputs. All of our new inventions will be made available to the research community. In addition to the other advantages mentioned above, this technology also makes it easy for users to develop their own assays simply by adding appropriate DNA components to a basic mixture, using standard protocols. Such devices can be manufactured and distributed cheaply on a very large scale. In conjunction with low-cost readers, ubiquitous mobile devices equipped with GPS and time data, and cloud-computing, this will offer the possibility to detect health hazards with unprecedented levels of speed and detail, with potentially huge effects on human health and welfare. Furthermore, these devices are ideal for use in education, allowing users to design and test their own genetic circuits without the issues inherent in using living cells. For these reasons, our proposal offers tremendous benefits and represents a step change in the real-word applicability of synthetic biology.

合成生物学是一门令人兴奋的新学科，它有可能为人类健康和福祉带来许多好处。一个近乎市场化的例子是利用工程遗传网络来制造生物传感器，或生物传感器，它可以快速检测毒素和有害微生物。然而，大多数合成生物学系统都是基于活的转基因细胞，并且由于安全问题和监管问题，它们不能在专门批准的实验室之外使用，而生物传感器最大的未满足需求是在现场，因为“点”针对健康危害的“使用”和“护理点”测试。詹姆斯·柯林斯教授的实验室最近报告了一项显着的突破，他们使用了基于干燥在纸条上的遗传成分的非生命生物系统。这些系统的制备成本非常低，可以长期稳定存储，并且由于它们不具有生命力且无法复制，因此不会对环境造成风险。因此，该技术非常适合进一步开发人类健康传感器。此外，这些无细胞系统可以在几小时内非常快速地大量制备，并在几分钟内快速测试，而基于活细胞的系统可能需要数周的准备时间和数天的测试时间。这使得新技术成为遗传电路“快速原型制作”的理想选择。许多设计可以快速生成和测试，最成功的设计可以用于生成基于细胞的系统，用于需要的应用，例如用于制造药物和其他有价值化合物的工程代谢途径。在这个项目中，我们将进一步开发这些卓越的系统并创建新的工具，使设计和开发它们变得更加容易。首先，我们将创建新的计算工具，可用于设计许多应用的遗传电路。这些内容将在线提供，以造福研究界。其次，我们将建立新电路的快速自动化组装和测试方法，允许在很短的时间内以最少的人力生成和测试数千种变体。第三，我们将寻求改进基础技术，提高无细胞设备的性能，并开发低成本的开源电子阅读器，与我们开发的传感器一起可以轻松地在现场使用。第四，我们将通过生成能够快速、灵敏地检测各种外部输入的传感器来展示该技术的实用性。我们所有的新发明都将提供给研究界。除了上述其他优点之外，该技术还使用户可以轻松开发自己的检测方法，只需使用标准方案将适当的 DNA 成分添加到基本混合物中即可。此类设备可以廉价地大规模制造和分销。与低成本阅读器、配备 GPS 和时间数据的无处不在的移动设备以及云计算相结合，这将提供以前所未有的速度和细节检测健康危害的可能性，对人类健康和福祉可能产生巨大影响。此外，这些设备非常适合用于教育，允许用户设计和测试自己的遗传电路，而不会出现使用活细胞固有的问题。由于这些原因，我们的建议提供了巨大的好处，并代表了合成生物学的实际应用性的一步变化。

项目成果

Synthetic genomics: a new venture to dissect genome fundamentals and engineer new functions.

• DOI: 10.1016/j.cbpa.2018.04.002
• 发表时间: 2018-10
• 期刊: Current opinion in chemical biology
• 影响因子: 7.8
• 作者: Schindler D;Dai J;Cai Y
• 通讯作者: Cai Y

Genetic Constructor: An Online DNA Design Platform.

Genetic Constructor：在线 DNA 设计平台。

• DOI: 10.1021/acssynbio.7b00236
• 发表时间: 2017
• 期刊: ACS synthetic biology
• 影响因子: 4.7
• 作者: Bates M

EMMA assembly explained: A step-by-step guide to assemble synthetic mammalian vectors.

EMMA 组装说明：组装合成哺乳动物载体的分步指南。

• DOI: 10.1016/bs.mie.2018.12.017
• 发表时间: 2019
• 期刊: Methods in enzymology
• 作者: Jones S

Designing with living systems in the synthetic yeast project.

• DOI: 10.1038/s41467-018-05332-z
• 发表时间: 2018-07-27
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Szymanski E;Calvert J
• 通讯作者: Calvert J

Rapid pathway prototyping and engineering using in vitro and in vivo synthetic genome SCRaMbLE-in methods.

使用体外和体内合成基因组 SCRaMbLE-in 方法进行快速途径原型设计和工程设计

• DOI: 10.1038/s41467-018-04254-0
• 发表时间: 2018-05-22
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Liu W;Luo Z;Wang Y;Pham NT;Tuck L;Pérez-Pi I;Liu L;Shen Y;French C;Auer M;Marles-Wright J;Dai J;Cai Y
• 通讯作者: Cai Y