In vivo integral feedback control for robust synthetic biology

生物技术公司使用单细胞（细菌、酵母或哺乳动物）作为“细胞工厂”，生产用于许多不同领域的分子，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）中产生的化合物可以从可再生资源中产生。在其他情况下，细胞工厂生产有用的化合物，这些化合物用其他方法（如化学）是不可能、太难或太昂贵的。迄今为止，生物技术过程的创新主要集中在最大化产出上，但现在的挑战是通过减少所需的能量和营养物质的投入来更有效地利用细胞工厂。此外，随着我们更多地了解如何设计和控制活细胞，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，我们需要能够设计活细胞，使其在面对变化的条件时能够控制行为。这就是这个项目的目标。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，这是一种有效的策略，可以保证对阶跃扰动和不确定性的鲁棒性。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它来调整和改进其活动。例如，积分反馈控制允许巡航控制系统使汽车保持恒定速度，而不管道路的坡度或乘客的总重量；或者自动扶梯的速度保持不变，不管有多少人使用它。在这个项目中，我们将设计、建模、构建和测试一个生物集成器，以实现“体内鲁棒控制”。一个完全（重新）可编程和可控的细胞是合成生物学蓬勃发展的领域的核心长期目标之一。然而，目前还没有生物整合器存在。为了填补这一空白，我们将设计第一个体内“即插即用”生物集成器设备，可以针对不同的应用进行定制。为了演示我们的生物整合器装置的功能，我们将使用它来创建工程细胞，这些细胞可以稳定地将选定的小分子的浓度维持在指定值附近。为了实现这一目标，细胞将同时具备感知细胞外分子浓度的能力，以及自身合成和分泌分子的能力。严格的控制设计将允许分泌速率动态变化，以抵消细胞外分子浓度的阶梯状扰动。这将为今后将该研究扩展到体内环境奠定必要的理论和实验基础。例如，一种生物整合器装置将使设计与其他生物体共生或共生的微生物成为可能，这些微生物能够感知和自我调整，以适应不断变化和不确定的外部条件。我们预计，这反过来可能会导致一种革命性的新型药物的出现，我们称之为“活体活性药物”，即植入患者体内的细胞，监测与疾病相关的生物分子（如胰岛素）的浓度，根据患者的需要调节这些分子的产生。为了研究活体活性药物如何在现实条件下实施，我们将“负责任的研究和创新”工作计划整合到该项目中，旨在将广泛感兴趣的各方的观点纳入活体活性药物的未来发展，包括：生物医学研究人员、临床医生、患者群体、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.