The Molecular Nose

哺乳动物细胞使用更多的基因来调节生物过程，而不是执行这些过程。这些包括所有基本的过程，如细胞生长、分化、生存、代谢以及感知和产生正确的生物分子补体以与环境沟通的能力。生物过程的网络组织进一步提高了复杂性。理解这种复杂网络的行为和反应将是解决生物学中突出问题的关键。为了满足这一需求，我们将建立一个多路传感器平台，可以评估和量化哺乳动物细胞中生化网络功能状态的动态变化，并使用这些数据在系统范围内重建细胞网络相互作用及其动态行为。支撑该平台的概念与生物科学中用于评估细胞功能的现有方法有根本不同，与电子鼻相似，电子鼻首先用单个刺激训练一系列传感器，以建立响应模式库，随后用于反卷积复杂输入。分子鼻将使用人工转录报告器同时监测细胞群或单细胞中数百个网络组件的输出，并设计用于其功能分析的软件框架和算法。分子鼻子将分为三个版本。其中一个将使用分子生物学工具构建，并将允许使用大型阵列（多达1000个）传感器。然而，由于检测器在细胞外，它需要被裂解的细胞进行测量。这个版本对于训练系统和建立一个大型的响应模式库特别有用。第二个版本将把单独的传感器和相应的探测器集成到条形码纳米颗粒上，这些纳米颗粒将被引入细胞，并使用表面增强共振拉曼散射光谱进行读取。这种装置将使用较少数量的传感器（最多30个），但可以用来实时监测活细胞的反应。同时，我们将开发将这些粒子库引入细胞的方法。第三个版本是将基于质粒的传感器库稳定整合到胚胎小鼠干细胞中，目的是产生转基因传感器小鼠。干细胞也可用于器官型培养和体外分化系统。分子鼻将使系统测试和合理解释蜂窝网络的行为成为可能。该技术是通用的，在单细胞和细胞群中都有广泛的应用，包括突出的生物学问题，如药物作用的分析和副作用的预测；干细胞分化，以期最终控制分化；细胞命运规范以支持组织工程；通过合成工程途径生产所需蛋白质和代谢物的遗传和生化网络；以及适应性网络反应和进化的研究。目前，我们缺乏有效的实验工具来分析这些复杂的相互作用。

THE MOLECULAR NOSEMammalian cells use more genes to regulate biological processes than to carry them out. These include all fundamental processes such as cell growth, differentiation, survival, metabolism and the ability to sense and produce the correct complement of biomolecules to communicate with the environment. Complexity is further enhanced by the organization of biological processes as networks. Understanding the behaviour and responses of such complex networks will be crucial to solve eminent questions in biology. To address this need we will build a multiplexed sensor platform that can assess and quantify dynamic changes in the functional state of biochemical networks in mammalian cells, and use these data to reconstruct cell network interactions and their dynamic behaviour on a systems wide level. The concept underpinning this platform is fundamentally different from existing methods used in the biological sciences to assess cell function, and similar to the Electronic Nose , where an array of sensors is first trained with individual stimuli to establish a library of response patterns which subsequently are used to deconvolute complex inputs. The Molecular Nose will monitor the outputs of several hundred network components simultaneously in cell populations or single cells using artificial transcriptional reporters, and design a software framework and algorithms for their functional analysis. The Molecular Nose will be built in three versions. One will be constructed using molecular biology tools, and will permit to use a large array (up to 1000) of sensors. However, it requires the cell being lysed for the measurement as the detector is outside of the cell. This version will be particularly useful for training the system and establishing a large library of response patterns. The second version will be built by integrating both individual sensors and their corresponding detectors onto bar-coded nanoparticles which will be introduced into cells and read using surface enhanced resonance Raman scattering spectroscopy. This setup will use a smaller number of sensors (up to 30), but can be used to monitor responses in living cells in real time. In parallel we will develop methods for the controlled introduction of these particle libraries into cells. The third version is the stable integration of a plasmid based sensor library into the embryonic mouse stem cells with the aim to generate a transgenic sensor mouse. The stem cells also can be used for organotypic cultures and in vitro differentiation systems.The Molecular Nose will enable the systematic testing and rational interpretation of the behaviour of cellular networks. The technique is generic with a wide range of applications in both single cells and cell populations, including eminent biological problems such as the analysis of drug effects and prediction of side effects; stem cell differentiation with a view to eventually control differentiation; cell fate specification in order to support tissue engineering; genetic and biochemical networks for the production of desired proteins and metabolites by synthetically engineered pathways; and the investigation of adaptive network responses and evolution. Currently, we are lacking efficient experimental tools to analyse these complex interactions.