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通信，并且这些信号需要指示细胞在胚胎发育期间形成复杂的组织和器官。因此，确定细胞如何将特定信号转化为准确的细胞反应对于理解动物和人类发育至关重要。该项目的目标是系统地建立一个理论模型，用于研究保守的信号通路Notch如何在发育中的果蝇组织和哺乳动物细胞中转化为准确的细胞反应。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信号转换为特定输出。多学科研究团队还将纳入代表性不足的高中生，学生们将通过将实践实验室经验与理论计算方法相结合，共同努力实现一个共同的目标。这种方法将有助于他们与同学交流想法和结果，并将促进跨学科的培训。信号通路提供了一种细胞间通讯的手段，以调节发育过程中的细胞特异性反应。细胞信号传导通常通过膜上的受体-配体相互作用激活，并通过级联传递到细胞核中，该级联聚集在激活和/或抑制靶基因的效应转录因子（TF）上。相同的核心途径如何在不同组织中诱导可重复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建立和测试预测模型，以了解Notch信号如何使用体内合成生物学方法转化为特定的转录反应，该方法将定量数据与数学建模相结合。含有不同类型的DNA结合位点的合成Notch报告基因用于破译Notch转录应答的规则。果蝇遗传学、基因组工程和生物化学用于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。细胞培养被用来开发新的成像工具，以评估Notch信号动力学在真实的时间，和计算模拟被开发来描述关键参数（DNA结合位点的组成，效应蛋白的比例，蛋白结合动力学，和蛋白质降解）如何改变TF复合物的浓度，增强子占用，和转录输出。总的来说，这些模型将被用于开发一个全面的定量理解Notch信号使用基于细胞和整个生物体的assays.This奖项反映了NSF的法定使命，并已被认为是值得的支持，通过评估使用基金会的智力价值和更广泛的影响审查标准。

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.