Engineering and safeguarding synthetic genomes

该提案的总体目标是开发一个综合技术平台，用于在基因组规模上有效和安全地工程化生物学。我建议通过三个相辅相成的工作包来实现这一雄心勃勃的目标。一揽子工作是实质性和重要的，但相互补充。这一愿景的成功实现需要所有三个工作包的协调共同发展。首先，我将开发一个下一代计算机辅助设计师，能够将高层次的，基于语义的功能纳入高等真核基因组设计。CAD软件将提供序列筛选功能，以识别潜在有害序列。这项序列筛选开发将与核威胁倡议（NTI）、联合国（UN）和世界经济论坛（WEF）支持的国际财团协调。为了提高基因组合成和组装的效率，我将应用最先进的机器人技术实现基因组合成的自动化，并使用工艺工程原理来监控和安排基因组组装管道。我还将开发一种新的并行基因组组装方法来并行构建。将合成基因组从酵母移植到其他生物体是一项重大挑战。我将通过开发一种新的标准化模块化组装工具包来有效组装大型合成染色体来解决这个障碍。然后，我将探索和优化三种不同的基因组转移方法，以在王国之间穿梭这些合成染色体。为了追踪潜在危险的合成基因组，我们将开发基因组隐写术，在合成基因组中嵌入可追踪的水印，这些水印是防篡改的，不会干扰正常的细胞生理学。最后，为了最大限度地减少合成基因组技术引起的生物恐怖主义和生物错误的风险，我将开发SafeGuard技术，将遗传密码改变和转录，重组，和蛋白质稳定性开关以包含合成菌株。我将在允许和限制的条件下评估他们各自的表现。总之，我提出了一个高度创新和集成的基因组设计，制造，转移和保护工程平台。

The overarching goal of this proposal is the development of an integrated technological platform for efficiently and safely engineering biology at the genome scale. I propose tackling this ambitious goal with three complementary work packages. Work packages are substantial and significant, but complementary to each other. The successful delivery of this vision will require the coordinated co-developments of all three work packages.First, I will develop a next-generation computer- assisted designer, capable of incorporating high- level, semantics-based features within higher eukaryotic genome design. The CAD software will provide sequence screening functionality to identify potentially harmful sequences. This sequence screening development will be coordinated with an international consortium backed by the Nuclear Threat Initiative (NTI), United Nations (UN) and World Economic Forum (WEF).To improve the efficacy of genome synthesis and assembly, I will apply state-of-the-art robotics for the automation of genome synthesis and use process engineering principles to monitor and schedule genome assembly pipelines. I will also develop a new concurrent genome assembly method to parallelise construction. Transplanting synthetic genomes from yeast to other organisms is a significant challenge. I will tackle this obstacle by developing a new standardised modular assembly kit to efficiently assemble large synthetic chromosomes. I will then exploring and optimising three distinct genome transfer methods to shuttle these synthetic chromosomes across kingdoms. To trace potentially dangerous synthetic genomes, we will develop genomic steganography to embed traceable watermarks, which are tamper-resistant and do not interfere with normal cellular physiology, across synthesised genomes.Finally, to minimise the risk of bioterrorism and bio-error arising from synthetic genome technology, I will develop SafeGuard technologies incorparating genetic code alterations and transcriptional, recom- binational, and protein stability switches to contain synthetic strains. I will characterise their respective performances under permissible and restrictive conditions. In summary, I propose a highly innovative and integrated engineering platform for genome design, manufacture, transfer and safeguarding.