Synthetic Portabolomics: Leading the way at the crossroads of the Digital and the Bio Economies

合成代谢组学：在数字经济和生物经济的十字路口引领潮流

• 批准号: EP/N031962/1
• 负责人: Natalio Krasnogor
• 金额: $ 554.77万
• 依托单位: Newcastle University
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2016
• 资助国家: 英国
• 起止时间: 2016 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=EP%2FN031962%2F1
• 关键词: Synthetic; Portabolomics; Leading; way; crossroads

Synthetic biology involves the design and development of novel, useful biological systems, or the redesign of those systems that exist already. This approach promises to be of major value to society. Potential applications include the production of high-value materials, such as fine chemicals and pharmaceuticals, bio-remediation, sustainable energy, medical diagnostics, and agriculture. In Synthetic Biology novel biological genetic circuits are developed using engineering principles in order to add the new properties to a given organism - called a host or chassis. The type of chassis used will vary according to the application and the circuit. For example, for food and agriculture it is highly desirable to use organisms that have been shown to be safe for human consumption. However, currently, most circuits are designed for, and tested in, a single organism such as the commonly used bacterium Escherichia coli. Moving these circuits to another organism requires the circuit to be re-engineered and retested in the new organism, a process which is very time consuming and costly. This process of 'refactoring' slows down research and costs industry a huge amount of time, effort and money. A major problem is that the connections between the designed genetic circuit and the chassis organism are specific to a given species of chassis. So the genetic circuit ends up being redesigned to meet the new connections required for a different species. In our project we will standardise the connection between a given genetic circuit and the chassis organism. We will develop a set of academically and industrially useful organisms where the plug-in points for the genetic circuit will be the same for each of our organisms, allowing the genetic circuit to be moved from one organism to another with changes. We refer to this standardised plug-in system as a 'bio-adaptor'.This programme grant will initiate a new field in Synthetic Biology, called 'Portabolomics'. This is a highly novel approach that has not been achieved by any other groups to-date. The key to the success of the project is to understand the networks of molecular processes that occur in a cell, since it is these networks that will need to be modified to make the bio-adaptor. We will apply a range of the state-of-the-art computing approaches to this task including many techniques from Computing Science, including network analysis, formal methods and data mining, for which our group has a wide range of world-leading expertise.The results of the Portabolomics project will not only be a new system of major value to UK synthetic biology research and industry, but will enhance the field of computing science as new computational techniques will need to be developed to achieve our goals.

合成生物学涉及设计和开发新的，有用的生物系统，或重新设计已经存在的系统。这一方法有望对社会产生重大价值。潜在的应用包括高价值材料的生产，如精细化学品和药物，生物修复，可持续能源，医疗诊断和农业。在合成生物学中，新的生物遗传电路是使用工程原理开发的，以便将新的特性添加到给定的生物体-称为宿主或底盘。使用的底盘类型将根据应用和电路而变化。例如，对于粮食和农业，非常希望使用已被证明对人类消费安全的生物体。然而，目前，大多数电路都是为单一生物体设计和测试的，例如常用的细菌大肠杆菌。将这些电路转移到另一个生物体需要在新的生物体中重新设计和重新测试电路，这是一个非常耗时和昂贵的过程。这种“重构”的过程减慢了研究的速度，并花费了大量的时间、精力和金钱。一个主要的问题是，设计的遗传电路和底盘生物体之间的连接是特定于特定物种的底盘。因此，基因电路最终被重新设计，以满足不同物种所需的新连接。在我们的项目中，我们将讨论给定的遗传电路和底盘有机体之间的联系。我们将开发一套在学术和工业上有用的生物体，其中基因回路的插入点对于我们每个生物体来说都是相同的，允许基因回路从一个生物体移动到另一个生物体并发生变化。我们把这种标准化的插件系统称为“生物适配器”。这项计划资助将开创合成生物学的一个新领域，称为“便携生物学”。这是一种非常新颖的方法，迄今为止还没有任何其他团体实现过。该项目成功的关键是了解细胞中发生的分子过程网络，因为正是这些网络需要进行修改以制造生物适配器。我们将应用一系列最先进的计算方法来完成这项任务，包括来自计算科学的许多技术，包括网络分析，形式化方法和数据挖掘，我们的团队在这方面拥有广泛的世界领先的专业知识。Portabolomics项目的结果不仅将成为对英国合成生物学研究和工业具有重大价值的新系统，而且将增强计算科学领域，因为需要开发新的计算技术来实现我们的目标。

项目成果

Expression, Localization, and Protein Interactions of the Partitioning Proteins in the Gonococcal Type IV Secretion System.

• DOI: 10.3389/fmicb.2021.784483
• 发表时间: 2021
• 期刊: Frontiers in microbiology
• 影响因子: 5.2
• 作者: Callaghan MM;Koch B;Hackett KT;Klimowicz AK;Schaub RE;Krasnogor N;Dillard JP
• 通讯作者: Dillard JP

Automatic recognition of feeding and foraging behaviour in pigs using deep learning

• DOI: 10.1016/j.biosystemseng.2020.06.013
• 发表时间: 2020-09-01
• 期刊: BIOSYSTEMS ENGINEERING
• 影响因子: 5.1
• 作者: Alameer, Ali;Kyriazakis, Ilias;Bacardit, Jaume
• 通讯作者: Bacardit, Jaume

The Synthetic Biology Open Language Supports Integration of the Engineering Life-Cycle for Synthetic Biologists

合成生物学开放语言支持合成生物学家工程生命周期的整合

• 发表时间: 2018
• 作者: Bartley B

Communicating Structure and Function in Synthetic Biology Diagrams.

• DOI: 10.1021/acssynbio.9b00139
• 发表时间: 2019-08-16
• 期刊: ACS synthetic biology
• 影响因子: 4.7
• 作者: Beal J;Nguyen T;Gorochowski TE;Goñi-Moreno A;Scott-Brown J;McLaughlin JA;Madsen C;Aleritsch B;Bartley B;Bhakta S;Bissell M;Castillo Hair S;Clancy K;Luna A;Le Novère N;Palchick Z;Pocock M;Sauro H;Sexton JT;Tabor JJ;Voigt CA;Zundel Z;Myers C;Wipat A
• 通讯作者: Wipat A

BioDynaMo: a modular platform for high-performance agent-based simulation.

• DOI: 10.1093/bioinformatics/btab649
• 发表时间: 2022-01-03
• 期刊: Bioinformatics (Oxford, England)
• 作者: Breitwieser L;Hesam A;de Montigny J;Vavourakis V;Iosif A;Jennings J;Kaiser M;Manca M;Di Meglio A;Al-Ars Z;Rademakers F;Mutlu O;Bauer R
• 通讯作者: Bauer R