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

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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.