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，它为人类健康和福利带来许多好处提供了潜力。一个接近市场的例子是使用工程的遗传网络来制造生物传感器或生物传感器，该传感器可以快速检测毒素和有害的微生物。但是，大多数合成生物学系统都是基于生命的基因修饰细胞，由于安全问题和调节问题，无法在特殊批准的实验室之外使用它们，而对生物传感器的最大未满足生物传感器的需求是在现场，用于“使用点”和“对健康危害的服务点”测试。詹姆斯·柯林斯（James Collins）教授的实验室最近报告了基于基于遗传成分干燥到纸条的遗传成分的非生物生物系统的突破。这些系统可以非常便宜地制备，可以长期稳定存储，并且由于它们还没有活力并且无法复制，因此它们对环境没有任何风险。因此，该技术是进一步开发人类健康传感器的理想选择。此外，这些无细胞的系统可以在几小时内非常迅速地大量制备，并在几分钟内迅速测试，而基于活细胞的系统可能需要数周的时间准备和几天进行测试。这使得新技术是遗传回路“快速原型制作”的理想选择。可以快速生成和测试许多设计，然后最成功的设计可用于为需要的应用程序生成基于细胞的系统，例如用于制造药品的工程代谢途径和其他有价值的化合物。在这个项目中，我们将进一步开发这些出色的系统并创建新工具，从而使设计和开发它们更加容易。首先，我们将创建新的计算工具，可用于为许多应用设计遗传电路。这些将在线提供，以使研究界受益。其次，我们将建立快速自动组装和测试新电路的方法，从而在很短的时间内以最少的人力努力在很短的时间内生成和测试数千种变体。第三，我们将寻求改进基本技术，以提高无单元设备的性能，并开发低成本的开源电子读取器，这些读取器可以与我们开发的传感器一起在现场轻松使用。第四，我们将通过生成可以快速而灵敏地检测各种外部输入的传感器来证明技术的实用性。我们所有的新发明都将提供给研究社区。除了上述其他优点外，该技术还可以轻松地使用标准协议向基本混合物中添加适当的DNA组件来简单地开发自己的测定法。这样的设备可以廉价地制造和分发。与低成本的读者结合使用，配备了GPS和时间数据以及云计算的无处不在的移动设备，这将为检测具有前所未有的速度和细节水平的健康危害的可能性，并可能对人类健康和福利产生巨大影响。此外，这些设备非常适合在教育中使用，使用户可以设计和测试自己的遗传回路，而无需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现实词适用性的步骤变化。

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

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

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

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