新技术：全新生物细胞操作系统

　　

生物通报道：来自英国诺丁汉大学的研究人员发表了题为“A computational study of liposome logic: towards cellular computing from the bottom up”的文章，研发出了一种新型的体内生物细胞计算机操作系统——AUdACiOuS，这种系统能在不改动硬件的条件下重编程细胞，将可以应用到药物研发，病患移植等方面，这一研究成果公布在《Systems and Synthetic Biology》杂志上。

领导这项研究的是诺丁汉大学Natalio Krasnogor教授，他表示，修改细胞DNA改变行为不是一件轻而易举的事情，他希望在五年内能在计算机中编程细菌细胞，编译和储存程序，然后在新细胞中执行。

这项研究是计算机科学与生命科学的合作成果，研究人员试图创造一种生物细胞，使其同计算机操作系统有一定的等价性，比如可以对一组给定的细胞可以进行无缝再编程，于是可在不需要改动硬件的情况下执行任何功能。他们希望能获得一项根本性的突破，最终实现合成全新的、不存在于自然界的生物实体，用于全新的应用领域。

Krasnogor教授说，“目前每次我们需要一个能执行一定新功能的细胞的时候，都不得不从零开始创建它；这是个漫长与艰苦的过程。大多数人认为要想改变细胞行为，而我们所要做的只是修改细胞的DNA。但其实这并不简单——我们常常发现实验是错误的，那时又不得不回到起点”，“如果AUdACiOuS项目成功的话，那么一年之内，我们将能通过计算机对细菌细胞进行编辑，并将程序存储在这些新的细胞中，使之执行。就像是对一台计算机一样，我们正试图创造一个生物细胞的基本操作系统。”

原文摘要：

A computational study of liposome logic: towards cellular computing from the bottom up

In this paper we propose a new bottom-up approach to cellular computing, in which computational chemical processes are encapsulated within liposomes. This “liposome logic” approach (also called vesicle computing) makes use of supra-molecular chemistry constructs, e.g. protocells, chells, etc. as minimal cellular platforms to which logical functionality can be added. Modeling and simulations feature prominently in “top-down” synthetic biology, particularly in the specification, design and implementation of logic circuits through bacterial genome reengineering. The second contribution in this paper is the demonstration of a novel set of tools for the specification, modelling and analysis of “bottom-up” liposome logic. In particular, simulation and modelling techniques are used to analyse some example liposome logic designs, ranging from relatively simple NOT gates and NAND gates to SR-Latches, D Flip-Flops all the way to 3 bit ripple counters. The approach we propose consists of specifying, by means of P systems, gene regulatory network-like systems operating inside proto-membranes. This P systems specification can be automatically translated and executed through a multiscaled pipeline composed of dissipative particle dynamics (DPD) simulator and Gillespie’s stochastic simulation algorithm (SSA). Finally, model selection and analysis can be performed through a model checking phase. This is the first paper we are aware of that brings to bear formal specifications, DPD, SSA and model checking to the problem of modeling target computational functionality in protocells. Potential chemical routes for the laboratory implementation of these simulations are also discussed thus for the first time suggesting a potentially realistic physiochemical implementation for membrane computing from the bottom-up.