21EngBio: Engineering Bioprogrammable Materials Using Hydrogel-Based Cell-Free Gene Expression and Spatiotemporal Modelling

生命系统拥有许多不同的分子和生物化学手段来检测和响应广泛的内部和外部刺激。这包括识别竞争对手、捕食者或猎物，以及识别可能造成伤害的食物或化学品的来源。在细胞水平上，这些刺激经常通过化学物质与蛋白质伴侣的结合来检测。这可能直接改变基因表达或可能触发细胞内的进一步信号传导途径。利用这些机制，细胞不断监测导致一系列结果的多种输入。这些变化可能是生物化学变化（例如，产生酶来解毒物质或开发新的食物来源），也可能是允许生长向更有利条件的变化。从发育的角度来看，内部和外部信号的整合对于生物体的身体计划的发展至关重要。然而，看起来复杂的反应通常来自简单的局部分子相互作用以及信号分子的扩散。能够在材料中复制生命系统的某些细胞方面-而不使用活细胞-可能对一系列应用具有变革性。这可能允许开发能够检测特定病原体的材料，并随后生产靶向抗菌剂，警告用户有毒化学物质存在的材料，甚至在分子水平上自我组织多种功能。例如，少量化学信号的扩散及其对基因表达的影响，可以解释味觉受体在舌头上的位置和伪装图案的发展。然而，在材料中使用生命系统是有问题的。它需要维持一个良性的环境和了解现有的细胞调节机制，而释放转基因生物在许多地区是不可取的。我们的目标是在不受活细胞限制的材料中使用细胞分子和生物化学网络。我们最近展示了具有不同物理性质和最终用户应用的水凝胶内的无细胞基因表达，并且我们使用无细胞蛋白质合成反应来改变材料本身的性质。此外，使用细胞外的分子生物学和生物化学组分允许与不可能在活生物体内发生的非活化学物质整合。例如，我们目前正在将酶活性与无细胞基因表达相结合，以创建用于病毒和病毒载体被动监测的材料（BB/V017209/1，BB/V017551/1）。在这里，我们将产生基本的实验数据和数学模型，描述三维水凝胶基质中的扩散和基因表达之间的关系。我们将使用这种理解来设计基因网络，可以均匀分布，但导致异构功能。此外，我们将利用这个机会来研究一些更广泛的考虑，围绕生物可编程物质的概念，并利用这种对话，为未来的研究计划。

Living systems possess many and varied molecular and biochemical means to detect and respond to a wide range of internal and external stimuli. This includes identifying competitors, predators or prey, and the identification of sources of food or chemicals that may cause harm. At a cellular level, these stimuli are frequently detected through the binding of a chemical with a protein partner. This may directly alter gene expression or may trigger further signalling pathways within the cell. Using these mechanisms, cells continually monitor multiple inputs leading to a range of outcomes. These may be biochemical changes (for example, producing enzymes to detoxify substances or exploit new sources of food) or they may be changes that permit growth towards more favourable conditions. From a developmental perspective, the integration of internal and external signalling is crucial for the development of an organism's body plan. What appear as complex responses however, frequently emerge from simple, local molecular interactions coupled with the diffusion of signal molecules. Being able to replicate some of these cellular aspects of living systems in materials - without using living cells - could be transformative to a range of applications. This may permit the development of materials capable of detecting specific pathogens and the subsequent production of targeted antimicrobials, materials that alert the user to the presence of noxious chemicals, or even self-organisation of multiple functions at a molecular level. The diffusion of a small number of chemical signals and their impact on gene expression for example, may explain the placement of taste receptors on the tongue and the development of camouflage patterns. Using living systems within materials however, is problematic. It requires the maintenance of a benign environment and an understanding of existing cellular regulatory mechanisms, while the release of genetically modified organisms is not desirable in many regions. Our goal is to use cellular molecular and biochemical networks in materials free from the constraints of living cells. We have recently demonstrated cell-free gene expression inside hydrogels with different physical properties and end-user applications and we have used cell-free protein synthesis reactions to alter the properties of the materials themselves. Further, the use of molecular biology and biochemical components outside of a cell allows integration with non-living chemistries that is not possible to enact within a living organism. For example, we are currently combining enzymatic activities with cell-free gene expression to create materials for passive surveillance of viruses and vectors of viruses (BB/V017209/1, BB/V017551/1). Here we will generate the foundational experimental data and mathematical models that describe the relationship between diffusion and gene expression in three dimensional hydrogel matrices. We will use this understanding to design gene networks that can be homogeneously distributed but result in heterogeneous functionality. In addition, we will use this opportunity to examine some of the broader considerations around the concept of bioprogrammable matter, and use this dialogue to inform future research programmes.