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综合网络图谱揭示图灵模式普遍存在但不稳健。

A Comprehensive Network Atlas Reveals That Turing Patterns Are Common but Not Robust.

机构信息

Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.

Department of Life Sciences, Imperial College London, London SW7 2AZ, UK; Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK.

出版信息

Cell Syst. 2019 Sep 25;9(3):243-257.e4. doi: 10.1016/j.cels.2019.07.007. Epub 2019 Sep 18.

Abstract

Turing patterns (TPs) underlie many fundamental developmental processes, but they operate over narrow parameter ranges, raising the conundrum of how evolution can ever discover them. Here we explore TP design space to address this question and to distill design rules. We exhaustively analyze 2- and 3-node biological candidate Turing systems, amounting to 7,625 networks and more than 3 × 10 analyzed scenarios. We find that network structure alone neither implies nor guarantees emergent TPs. A large fraction (>61%) of network design space can produce TPs, but these are sensitive to even subtle changes in parameters, network structure, and regulatory mechanisms. This implies that TP networks are more common than previously thought, and evolution might regularly encounter prototypic solutions. We deduce compositional rules for TP systems that are almost necessary and sufficient (96% of TP networks contain them, and 92% of networks implementing them produce TPs). This comprehensive network atlas provides the blueprints for identifying natural TPs and for engineering synthetic systems.

摘要

图灵模式(TPs)是许多基本发育过程的基础,但它们的运作范围很窄,这就提出了一个难题,即进化如何能发现它们。在这里,我们探索 TP 的设计空间来解决这个问题,并提炼设计规则。我们详尽地分析了 2 节点和 3 节点的生物候选图灵系统,共计 7625 个网络和超过 3000 个分析场景。我们发现,仅网络结构既不暗示也不保证出现新兴的 TP。很大一部分(>61%)的网络设计空间可以产生 TP,但这些 TP 对参数、网络结构和调控机制的细微变化非常敏感。这意味着 TP 网络比以前想象的更为普遍,进化可能会经常遇到典型的解决方案。我们推导出 TP 系统的组合规则,这些规则几乎是必要和充分的(96%的 TP 网络包含它们,而实现它们的 92%的网络产生 TP)。这个全面的网络图谱为识别自然 TP 和设计合成系统提供了蓝图。

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