Towards a Universal Biological-Cell Operating System (AUdACiOuS)

迈向通用生物细胞操作系统（AUdACiOuS）

• 批准号: EP/J004111/2
• 负责人: Natalio Krasnogor
• 金额: $ 88.13万
• 依托单位: Newcastle University
• 依托单位国家: 英国
• 项目类别: Fellowship
• 财政年份: 2014
• 资助国家: 英国
• 起止时间: 2014 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=EP%2FJ004111%2F2
• 关键词: Towards; Universal; Biological; Cell; Operating

A living cell, e.g. a bacterium, is an information-processing machine. It is composed of a series of sub-systems that work in concert by sensing external stimuli, assessing its own internal states and making decisions through a network of complex and interlinked biological regulatory networks (BRN) motifs that act as the bacterium neural network. A bacterium's decision making processes often result in a variety of outputs, e.g. the creation of more cells, chemotaxis, bio-film formation, etc. It was recently shown that cells not only react to their environment but that they can even predict environmental changes. The emerging discipline of Synthetic Biology (SB), considers the cell to be a machine that can be built -from parts- in a manner similar to, e.g., electronic circuits, airplanes, etc. SB has sought to co-opt cells for nano-computation and nano-manufacturing purposes. During this leadership fellowship programme of research I will aim at making E.coli bacteria much more easily to program and hence harness for useful purposes. In order to achieve this, I plan to use the tools, methodologies and resources that computer science created for writing computer programs and find ways of making them useful in the microbiology laboratory.

活细胞，如细菌，是一个信息处理机器。它由一系列子系统组成，这些子系统通过感知外部刺激，评估自身内部状态并通过复杂且相互关联的生物调节网络（BRN）基序网络做出决策，这些子系统协同工作，充当细菌神经网络。细菌的决策过程通常会产生各种各样的结果，例如产生更多的细胞、趋化性、生物膜的形成等。最近的研究表明，细胞不仅会对环境做出反应，而且还能预测环境的变化。合成生物学（Synthetic Biology，简称SB）这一新兴学科认为细胞是一种机器，可以用类似于电子电路、飞机等的方式由部件组装而成。SB已经寻求将细胞用于纳米计算和纳米制造目的。在这个领导研究项目中，我的目标是使大肠杆菌更容易编程，从而更容易利用。为了实现这一目标，我计划使用计算机科学为编写计算机程序创造的工具、方法和资源，并找到使它们在微生物实验室中有用的方法。

项目成果

Photochromic molecular implementations of universal computation.

通用计算的光致变色分子实现。

• DOI: 10.1016/j.biosystems.2014.09.004
• 发表时间: 2014
• 期刊: Bio Systems
• 作者: Chaplin JC

Transcriptomic Responses to Coaggregation between Streptococcus gordonii and Streptococcus oralis.

• DOI: 10.1128/aem.01558-21
• 发表时间: 2021-10-28
• 期刊: Applied and environmental microbiology
• 影响因子: 4.4
• 作者: Choo SW;Mohammed WK;Mutha NVR;Rostami N;Ahmed H;Krasnogor N;Tan GYA;Jakubovics NS
• 通讯作者: Jakubovics NS

Automatic selection of verification tools for efficient analysis of biochemical models.

• DOI: 10.1093/bioinformatics/bty282
• 发表时间: 2018-09-15
• 期刊: Bioinformatics (Oxford, England)
• 作者: Bakir ME;Konur S;Gheorghe M;Krasnogor N;Stannett M
• 通讯作者: Stannett M

Blind optimisation problem instance classification via enhanced universal similarity metric

• DOI: 10.1007/s12293-014-0145-7
• 发表时间: 2014-12-01
• 期刊: MEMETIC COMPUTING
• 影响因子: 4.7
• 作者: Contreras, Ivan;Arnaldo, Ignacio;Ignacio Hidalgo, J.
• 通讯作者: Ignacio Hidalgo, J.

Synthesis and cell-free cloning of DNA libraries using programmable microfluidics.

• DOI: 10.1093/nar/gkv1087
• 发表时间: 2016-02-29
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Ben Yehezkel T;Rival A;Raz O;Cohen R;Marx Z;Camara M;Dubern JF;Koch B;Heeb S;Krasnogor N;Delattre C;Shapiro E
• 通讯作者: Shapiro E