NSF/MCB-BSF: Modeling the mechanisms that define Notch signal strength using in-vivo synthetic and quantitative biology

动物体内的许多不同类型的细胞使用信号进行交流，这些信号是在胚胎发育期间指导细胞形成复杂组织和器官所必需的。因此，确定细胞如何将特定信号转化为准确的细胞反应是理解动物和人类发育的基础。这个项目的目标是系统地建立一个理论模型，说明在发育中的果蝇组织和哺乳动物细胞中，一个被称为Notch的保守信号通路是如何转化为精确的细胞反应的。通过美国和以色列之间的科学合作，来自生物学、工程学、数学和物理学的本科生和研究生将研究如何使用实验和计算方法将Notch信号转换为特定的输出。多学科研究团队还将包括代表性不足的高中学生，学生们将通过将实践实验室经验与理论计算方法相结合，共同朝着一个共同的目标努力。这种方法将有助于他们与同学交流想法和结果，并将促进跨学科培训。在发育过程中，信号通路提供了一种细胞间通讯的手段来调节细胞特异性反应。细胞信号通常通过细胞膜上的受体-配体相互作用激活，并通过级联传递到细胞核，该级联聚集在激活和/或抑制靶基因的效应转录因子（TF）上。相同的核心通路如何在不同组织中诱导可复制的细胞特异性结果仍然是生物学中的一个主要问题。该项目的中心目标是利用结合定量数据和数学建模的体内合成生物学方法，建立和测试Notch信号如何转化为特定转录反应的预测模型。含有不同类型DNA结合位点的合成Notch报告子被用来破译Notch转录反应的规则。果蝇遗传学、基因组工程和生物化学被用来评估蛋白质稳定性和基因剂量的变化如何影响细胞特异性输出。细胞培养用于开发新的成像工具来实时评估Notch信号动力学，并开发了计算模拟来描述关键参数（DNA结合位点组成，效应蛋白比例，蛋白质结合动力学和蛋白质降解）如何改变TF复合物浓度，增强子占用和转录输出。总的来说，这些模型将用于使用基于细胞和整个生物体的分析来开发对Notch信号的全面定量理解。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

The many different cell types within an animal body use signals to communicate, and such signals are required to instruct cells to form complex tissues and organs during embryonic development. Determining how cells convert specific signals into accurate cellular responses is therefore fundamental to understanding both animal and human development. The goal of this project is to systematically build a theoretical model for how a conserved signaling pathway, called Notch, is converted into accurate cellular responses in both developing fruit fly tissues and mammalian cells. Through a scientific collaboration between the U.S and Israel, undergraduate and graduate students from biology, engineering, mathematics, and physics will examine how the Notch signal is converted into specific outputs using experimental and computational approaches. The multidisciplinary research team will also incorporate under-represented high school students, and collectively students will work towards a common goal as a team by combining hands-on laboratory experiences with theoretical computational methods. This approach will help them to communicate ideas and results to fellow students and will promote interdisciplinary training.Signaling pathways provide a means of cell-to-cell communication to regulate cell-specific responses during development. Cell signaling is typically activated via receptor-ligand interactions at the membrane and relayed into the nucleus via a cascade that converges on an effector transcription factor (TF) that activates and/or represses target genes. How the same core pathway induces reproducible cell-specific outcomes in different tissues remains a major question in biology. The central goal of this project is to build and test predictive models for how the Notch signal is converted into specific transcription responses using an in-vivo synthetic biology approach that incorporates quantitative data with mathematical modeling. Synthetic Notch reporters containing distinct types of DNA binding sites are used to decipher the rules of the Notch transcriptional response. Drosophila genetics, genome engineering, and biochemistry are used to assess how changes in protein stability and gene dose impact cell-specific outputs. Cell culture is used to develop new imaging tools to assess Notch signaling dynamics in real time, and computational simulations are developed to describe how key parameters (DNA binding site composition, ratios of effector proteins, protein binding dynamics, and protein degradation) alter TF complex concentration, enhancer occupancy, and transcriptional output. Collectively, these models will be used to develop a thorough quantitative understanding of Notch signaling using both cell based and whole organism assays.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.