Sandpit: The Programmable Rhizosphere

几个世纪以来，人类一直在努力控制和利用生物体以达到自己的目的。农业实践已经发展到最大限度地提高动植物产量。最近，微生物系统已被操纵，以增加其在食品，生物技术和酿造工业中的效用。这些变化中有许多是通过育种和机会选择来改善农艺性状的。基因工程的最新发展使科学家能够应用精确的扰动，导致生物体的有益变化。然而，生物系统的复杂性使得很难使用传统的基因工程技术手动设计和实施可预测地产生预期表型的大变化。我们合成DNA的能力远远超过我们设计新遗传系统的能力。合成生物学有望实现生物电路的合理设计和可重复制造，这些生物电路可用于在生物体中引入所需的功能。这种方法的主要前提之一是，工程原理应适用于模块化电路的设计，从良好的特征部分和组件，使用定义的组成规则。迄今为止，还缺乏一个框架，使这种方法能够用于生物工程。在这个项目中，我们建议开发这样一个框架，以及一个独特的新DNA部分库。具体来说，我们建议解决生物体（如微生物和植物）中的细胞回路如何设计成以可预测和稳健的方式自组织并与其他生物体相互作用的问题。为此，我们将开发新的数学和计算方法，自动将所需功能的定量描述转换为在细菌中实现此功能的电路设计。此外，我们将产生一系列DNA部分，这些部分将允许在不同细胞群体或生物体之间构建新的通信渠道，以及营养物质共生交换的途径。在许多情况下，调节细胞和形成稳定的新生态的能力的改善将对人类有益。这些应用范围从组织工程到生物修复、生物技术和生物能源。在这个项目中，我们选择专注于植物和土壤细菌之间的关系，这些细菌通常与根系一起生活。我们希望设计模式细菌和模式植物之间的通信，以允许谈判和建立新的共生关系。该系统将在改善可持续农业、生物生产和粮食安全方面有许多应用，例如改善土壤利用、抗虫害、抑制杂草和创造能够固氮的新作物。

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.