NSF/MCB-BSF: Quantitative analysis and modeling of Notch signaling using in vivo synthetic biology

动物在其一生中如何形成复杂的组织类型是一个重要而基本的问题。许多细胞信号需要一起工作，所以这个过程完美无缺。本项目将系统地建立果蝇胚胎发育过程中细胞信号通路的理论认识。与动物发育所需的许多遗传途径一样，这种信号通路最初是在果蝇中发现的，后来被证明对正常的人类发育和健康至关重要。这个项目将促进美国和以色列之间的科学合作。来自生物学、工程学和物理学的学生将研究如何使用实验和计算方法将外部信号转换为特定的输出。研究生和本科生将由一个多学科研究团队进行培训，该团队在实验室和理论方法方面具有广泛的专业知识。生物医学和计算机工程专业的本科生将获得动手实验经验，并与高级学生作为一个团队合作，实现共同的目标。这将有助于他们与同学交流想法和结果，并促进跨学科培训。这个合作研究项目的中心目标是了解不同的细胞类型如何在动物发育过程中将相同的细胞信号通路转化为不同的反应。定义一个信号如何引起适当的细胞反应是至关重要的，因为信号通路确保在生物体的整个生命周期中产生必要的细胞类型。在整个动物发育过程中，果蝇的Notch信号通路被反复地用于调用不同细胞类型的不同反应。该项目的具体目标是利用体内合成生物学方法和数学建模，对Notch信号如何转化为细胞特异性输出进行系统、定量的理解。携带一组报告基因的果蝇将被创造出来，这些报告基因系统地改变了notch调节的DNA结合位点的数量和结构。定量表达分析和转录因子占用数据将通过高分辨率成像固定和活组织获得。实验数据将用于建立数学模型和计算模拟。模型将基于转录的统计力学描述来描述关键参数（DNA结合位点，效应蛋白的比率，结合亲和力和蛋白质降解）如何改变Notch输出。这些模型的预测将经过实验检验，并将用于改进数学模型。对核心Notch转录模块的定量描述将为系统地探索其他生物因子在Notch介导转录中的作用提供一个框架。这个美国/以色列合作项目由美国国家科学基金会和以色列两国科学基金会支持。

How an animal develops complex tissue types during its lifetime is an important and fundamental question. Many cell signals are required to work together so this process works flawlessly. This project will systematically build a theoretical understanding of a cell signaling pathway in developing fruit fly embryos. Like many genetic pathways required for animal development, this signaling pathway was initially discovered using fruit flies and later shown to be essential for normal human development and health. This project will foster scientific collaborations between the U.S and Israel. Students from biology, engineering, and physics will examine how an external signal is converted into specific outputs using experimental and computational approaches. Both graduate and undergraduate students will be trained by a multidisciplinary research team that has wide-ranging expertise in laboratory and theoretical methods. Undergraduate students in Biomedical and Computer engineering will gain hands-on laboratory experiences and work with advanced students as a team, to achieve a common goal. This will help them to communicate ideas and results to fellow students and will promote interdisciplinary training.The central aim of this collaborative research project is to understand how different cell types convert the same cell signaling pathway into distinct responses during animal development. Defining how a signal invokes appropriate cell responses is of fundamental importance because signaling pathways ensure essential cell types are generated throughout an organism's lifespan. The Notch signaling pathway in Drosophila is iteratively used to invoke distinct responses in different cell types throughout animal development. The specific goals of this project are to develop a systematic, quantitative understanding of how the Notch signal is converted into cell-specific outputs using an in vivo synthetic biology approach and mathematical modeling. Drosophila carrying a set of reporters that systematically vary in number and architecture of Notch-regulated DNA binding sites will be created. Quantitative expression analysis and transcription factor occupancy data will be obtained using high resolution imaging of fixed and live tissues. Experimental data will be used to build mathematical models and computational simulations. Models will be based on a statistical mechanics description of transcription to describe how key parameters (DNA binding sites, ratios of effector proteins, binding affinities, and protein degradation) alter Notch output. Predictions from these models will be tested experimentally and will be used to improve the mathematical models. A quantitative description for the core Notch transcription module will provide a framework to systematically explore the role of additional biological factors on Notch-mediated transcription.This collaborative US/Israel project is supported by the US National Science Foundation and the Israeli Binational Science Foundation.