In vivo integral feedback control for robust synthetic biology

生物技术公司使用单个细胞(细菌、酵母或哺乳动物)作为“细胞工厂”，生产用于许多不同行业的分子，如制药、酶、生物燃料、化妆品或香水。在某些情况下，这意味着以前从不可再生资源(石油)中生产的化合物可以从可再生资源中生产。在其他情况下，细胞工厂生产有用的化合物，这些化合物是不可能的、太难的或太昂贵的，无法用其他方式生产(例如使用化学方法)。到目前为止，生物技术过程的创新一直集中在最大化产量上，但现在的挑战是通过减少所需的能量和营养投入来更有效地利用细胞工厂。此外，随着我们对如何设计和控制活细胞有了更多的了解，我们可以开始设想这些‘活机器’的新的令人兴奋的潜在用途，特别是在医疗保健领域。为了做到这一点，我们需要能够设计出在不断变化的条件下可控的活细胞。这就是这个项目要达到的目标。在电子、机械和化学工程中，鲁棒控制通常是通过使用“积分反馈控制”来实现的，这是一种确保对阶跃扰动和不确定性具有鲁棒性的有效策略。这需要一个积分器。简而言之，集成商积累有关系统过去行为的信息，并在获得更多信息时使用这些信息来调整和改进其活动。例如，集成反馈控制允许巡航控制系统保持汽车的恒速，而不考虑道路的坡度或乘客的综合重量；或者自动扶梯的速度保持恒定，而不考虑使用它的人数。在这个项目中，我们将设计、建模、建造和测试一个生物集成器，以实现在体内的稳健控制。一个完全(重新)可编程和可控的细胞是蓬勃发展的合成生物学领域的核心长期目标之一。然而，目前还不存在生物积分器。为了填补这一空白，我们将设计出第一个体内可为不同应用定制的“即插即用”生物集成器设备。为了展示我们的生物积分器设备的功能，我们将使用它来创建工程细胞，该细胞可以牢固地将选定的小分子的浓度维持在指定值附近。要做到这一点，细胞将具备感知细胞外分子浓度的能力，以及合成和分泌分子本身的能力。严格的控制设计将允许分泌率动态变化，以抵消分子胞外浓度的阶梯式扰动。这将为将来将这项研究扩展到活体环境奠定必要的理论和实验基础。例如，生物整合装置将使设计出与其他生物共生或在其中生存的微生物成为可能，这些微生物能够感知和自我调节不断变化和不确定的外部条件。我们预计，这反过来可能导致一种革命性的新医学形式的出现，我们将其称为‘体内活性药物’，即植入患者体内并监测与疾病相关的生物分子(如胰岛素)浓度的细胞，根据患者的需要调节这些分子的产生。为了研究体内活性药物如何在现实世界条件下实施，我们在这个项目中纳入了一个关于‘负责任的研究和创新’的工作计划，旨在将广泛相关各方的观点纳入到活性体内药物的任何未来发展中，包括：生物医学研究人员、临床医生、患者团体、监管机构、制药公司和生物伦理学家。

Biotechnology companies use single cells (bacteria, yeast, or mammalian) as 'cell factories' to produce molecules of use in many different sectors, such as pharmaceuticals, enzymes, biofuels, cosmetics or fragrances. In some cases this means that compounds that were previously produced from non-renewable sources (petroleum) can be produced from renewable sources. In other cases cell factories produce useful compounds that would be impossible, too difficult, or too expensive to produce in other ways (e.g. using chemistry). To date, innovation for biotechnological processes has focused on maximising output, but now the challenge is to use cell factories more efficiently by reducing the required input of energy and nutrients. Moreover, as we learn more about how to design and control living cells, we can begin to envision new exciting potential uses for these 'living machines', especially in the healthcare sector.In order to do this, we need to be able to engineer living cells that behave controllably in the face of changing conditions. This is what this project aims to achieve. In electronic, mechanical and chemical engineering, robust control is typically accomplished through the use of 'Integral Feedback Control', which is an effective strategy to guarantee robustness to step-like perturbations and uncertainties. This requires an integrator. In a nutshell, the integrator accumulates information about the system's past behaviour and uses it to adjust and improve its activity as more information becomes available. Integral Feedback Control allows, for example, cruise control systems to maintain a car at constant speed irrespective of the slope of the road or the combined weight of the passengers; or the speed of an escalator to remain constant regardless of the number of people using it. In this project, we will design, model, construct and test a biological integrator to implement 'in-vivo robust control'.A fully (re-)programmable and controllable cell is one of the core long-term objectives of the blossoming field of synthetic biology. However, no biological integrator currently exists. To fill this gap, we will engineer the first in vivo 'plug-and-play' bio-integrator device that can be customised for different applications. To demonstrate the functionality of our bio-integrator device, we will use it to create engineered cells that can robustly maintain the concentration of a chosen small molecule around a specified value. To accomplish this, the cell will be equipped with both the ability to sense the extracellular concentration of the molecule and to synthesise and secrete the molecule itself. A rigorous control design will allow for the secretion rate to change dynamically so as to counteract step-like perturbations in the extracellular concentration of the molecule. This will establish the necessary theoretical and experimental basis for future extension of this research into in vivo environments.For example, a biological integrator device would make it possible to engineer microbes that reside symbiotically with or within other organisms, and that are able to sense and self-adjust to changing and uncertain external conditions. We anticipate that this in turn could lead to the emergence of a revolutionary new form of medicine that we are calling 'active in vivo medicine', i.e. cells that are implanted in patients and monitor the concentration of disease-related biomolecules (e.g. insulin), modulating their production of these molecules in response to patient need.In order to investigate how active in vivo medicine might be implemented in real-world conditions, we have integrated into this project a programme of work on 'Responsible Research and Innovation' designed to incorporate the perspectives of a wide range of interested parties into any future development of active in vivo medicine, including: biomedical researchers, clinicians, patient groups, regulators, pharmaceutical firms, and bioethicists.