Sandpit: The Programmable Rhizosphere

沙坑：可编程根际

基本信息

批准号：
EP/H019162/1
负责人：
James Haseloff
金额：
$ 123.97万
依托单位：
University of Cambridge
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2009
资助国家：
英国
起止时间：
2009 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=EP%2FH019162%2F1
关键词：
Sandpit Programmable Rhizosphere

项目摘要

Humans have striven for centuries to control and exploit living organisms for their own purposes. Agricultural practices have been developed to maximise the yield of plants and animals. More recently, microbial systems have been manipulated to increase their utility in the food, biotech and brewing industries. Many of these changes have been achieved through breeding and chance selection for improved agronomic characters. Recent developments in genetic engineering have allowed scientists to apply precise perturbations that lead to beneficial changes in an organism. However, the complexity of biological systems makes it difficult to manually design and implement large changes that predictably produce an intended phenotype using conventional genetic engineering techniques. Our ability to synthesise DNA far outstrips our ability to design new genetic systems. Synthetic Biology holds the promise of rational design and reproducible fabrication of biological circuits that can be used to introduce a desired function in an organism. One of the main premises of this approach is that engineering principles should be applied to the design of modular circuits from well-characterized parts and components, using defined composition rules. A framework that enables this approach to the engineering of biology has, to date, been lacking. In this project, we propose to develop such a framework, and a unique library of new DNA parts. Specifically, we propose to tackle the problem of how cellular circuits in organisms (such as microbes and plants) can be designed in to self-organise and interact with other organisms in a predictable and robust fashion. To this end we will develop novel mathematical and computational approaches that automatically transform a quantitative description of a desired function into a circuit design that implements this function in bacteria. In addition we will generate a collection of DNA parts that will allow the construction of new channels of communication between different cell populations or organisms, and the pathways for symbiotic exchange of nutrients. There are many situations where improvements in the ability to regulate cells, and to form stable new ecologies, would be of benefit to humans. These range from applications in tissue engineering through to bioremediation, biotechnology and bioenergy. In this project we have chosen to focus on the relationship between plants and soil bacteria that normally live alongside the root system. We wish to engineer communication between a model bacterium and model plant, to allow negotiation and establishment of a new symbiotic relationship. The system would have many applications for improvements in sustainable agriculture, bioproduction and food security, such as improvements in soil use, pest resistance, weed suppression and creation of new crop plants capable of nitrogen fixation.

人类已经为自己的目的而努力控制和利用生物。已经开发出农业实践来最大化动植物的产量。最近，已经操纵微生物系统以提高其在食品，生物技术和酿造行业中的效用。通过繁殖和机会选择改善农艺特征，已经实现了许多这些变化。基因工程的最新发展使科学家能够采用精确的扰动，从而导致有机体有益变化。但是，生物系统的复杂性使得难以手动设计和实施大型变化，可以预见，使用常规的基因工程技术产生预期的表型。我们合成DNA的能力远远超过了设计新遗传系统的能力。合成生物学具有理性设计和可再现的生物回路制造的希望，这些电路可用于在生物体中引入所需功能。这种方法的主要前提之一是，使用定义的组成规则，应将工程原理应用于来自特征良好的零件和组件的模块化电路的设计。迄今为止，已经缺乏这种实现这种生物学工程方法的框架。在这个项目中，我们建议开发这样的框架，以及一个独特的新DNA零件库。具体而言，我们建议解决生物体中的细胞回路（例如微生物和植物）如何以可预测且强大的方式与其他生物相互作用的问题。为此，我们将开发新型的数学和计算方法，这些方法会自动将所需函数的定量描述转换为在细菌中实现此功能的电路设计。此外，我们将生成一系列DNA零件，这些零件将允许在不同的细胞群体或生物之间建立新的通信渠道，以及养分共生交换的途径。在许多情况下，调节细胞的能力并形成稳定的新生态的能力会对人类有益。这些范围从组织工程的应用到生物修复，生物技术和生物能源。在这个项目中，我们选择着眼于通常与根系一起生活的植物和土壤细菌之间的关系。我们希望在模型细菌和模型工厂之间进行沟通，以允许谈判和建立新的共生关系。该系统将有许多应用程序来改善可持续农业，生物生产和粮食安全，例如改善土壤使用，耐药性，抑制杂草以及能够固定氮的新作物植物的创造。

项目成果

期刊论文数量（10）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

BacillusRegNet: a transcriptional regulation database and analysis platform for Bacillus species.

BacillusRegNet：芽孢杆菌属转录调控数据库和分析平台。

DOI：
10.2390/biecoll-jib-2014-244
发表时间：
2014
期刊：
Journal of integrative bioinformatics
影响因子：
1.9
作者：
Misirli G
通讯作者：
Misirli G

Computational modeling of synthetic microbial biofilms

合成微生物生物膜的计算模型

DOI：
10.1021/sb30003
发表时间：
2012
期刊：
ACS Synthetic Biology
影响因子：
4.7
作者：
Rudge T.J.
通讯作者：
Rudge T.J.

Orthogonal intercellular signaling for programmed spatial behavior.

DOI：
10.15252/msb.20156590
发表时间：
2016-01-25
期刊：
Molecular systems biology
影响因子：
9.9
作者：
Grant PK;Dalchau N;Brown JR;Federici F;Rudge TJ;Yordanov B;Patange O;Phillips A;Haseloff J
通讯作者：
Haseloff J

Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization.

DOI：
10.1093/bioinformatics/btv660
发表时间：
2016-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
0
作者：
Misirli G;Cavaliere M;Waites W;Pocock M;Madsen C;Gilfellon O;Honorato-Zimmer R;Zuliani P;Danos V;Wipat A
通讯作者：
Wipat A

Synthetic Biology: opportunities for Chilean bioindustry and education.

合成生物学：智利生物工业和教育的机会。