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基于三进制逻辑的工程化多层计算基因网络。

Multi-layered computational gene networks by engineered tristate logics.

机构信息

Department of Pharmacy, Center for Regenerative and Aging Medicine, the Fourth Affiliated Hospital of School of Medicine and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, Zhejiang 322000, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Medicine and School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China.

Department of Biology and Chemistry, College of Science, National University of Defense Technology, Changsha, Hunan 410073, China; College of Computer Science and Technology, National University of Defense Technology, Changsha, Hunan 410073, China.

出版信息

Cell. 2024 Sep 5;187(18):5064-5080.e14. doi: 10.1016/j.cell.2024.07.001. Epub 2024 Jul 31.

Abstract

So far, biocomputation strictly follows traditional design principles of digital electronics, which could reach their limits when assembling gene circuits of higher complexity. Here, by creating genetic variants of tristate buffers instead of using conventional logic gates as basic signal processing units, we introduce a tristate-based logic synthesis (TriLoS) framework for resource-efficient design of multi-layered gene networks capable of performing complex Boolean calculus within single-cell populations. This sets the stage for simple, modular, and low-interference mapping of various arithmetic logics of interest and an effectively enlarged engineering space within single cells. We not only construct computational gene networks running full adder and full subtractor operations at a cellular level but also describe a treatment paradigm building on programmable cell-based therapeutics, allowing for adjustable and disease-specific drug secretion logics in vivo. This work could foster the evolution of modern biocomputers to progress toward unexplored applications in precision medicine.

摘要

到目前为止,生物计算严格遵循数字电子学的传统设计原则,而在组装更复杂的基因电路时,这些原则可能会达到极限。在这里,我们通过创建三态缓冲器的遗传变体而不是使用传统逻辑门作为基本信号处理单元,引入了一种基于三态的逻辑综合(TriLoS)框架,用于资源高效设计能够在单细胞群体中执行复杂布尔计算的多层基因网络。这为简单、模块化和低干扰映射各种感兴趣的算术逻辑以及在单个细胞内有效扩大工程空间奠定了基础。我们不仅构建了在细胞水平上运行全加器和全减器操作的计算基因网络,还描述了一种基于可编程基于细胞的治疗方法的治疗范例,允许在体内进行可调节和针对特定疾病的药物分泌逻辑。这项工作可以促进现代生物计算机的发展,探索在精准医学中的应用。

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