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化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来源。在细胞水平上，这些刺激经常通过化学物质与蛋白质伙伴的结合而被检测到。这可能会直接改变基因的表达，或者可能触发细胞内更多的信号通路。使用这些机制，细胞持续监测多个输入，从而产生一系列结果。这些可能是生化变化(例如，产生酶来解毒物质或开发新的食物来源)，或者它们可能是允许生长朝着更有利的条件生长的变化。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，看起来复杂的反应往往来自简单的局部分子相互作用，再加上信号分子的扩散。能够在材料中复制生命系统的一些细胞方面--而不使用活细胞--可能会对一系列应用产生变革。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、警告用户存在有毒化学物质的材料，或者甚至在分子水平上自组织多种功能。例如，少量化学信号的扩散及其对基因表达的影响，可能解释了味觉受体在舌头上的位置和伪装模式的发展。然而，在材料中使用生命系统是有问题的。它需要维持一个良好的环境，并了解现有的细胞调控机制，而在许多地区，释放转基因生物是不可取的。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化网络。我们最近展示了具有不同物理性质和终端用户应用的水凝胶中的无细胞基因表达，我们还利用无细胞蛋白质合成反应来改变材料本身的性质。此外，在细胞外使用分子生物学和生化成分允许与非生物化学物质整合，这在活的有机体内是不可能实现的。例如，我们目前正在将酶活性与无细胞基因表达相结合，以创建被动监测病毒和病毒载体的材料(BB/V017209/1，BB/V017551/1)。在这里，我们将生成描述三维水凝胶基质中扩散和基因表达之间关系的基本实验数据和数学模型。我们将利用这一理解来设计可以均匀分布但功能不同的基因网络。此外，我们将利用这一机会审查围绕生物可编程物质概念的一些更广泛的考虑，并利用这一对话为未来的研究方案提供信息。

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.