Multiplex analysis of boundary formation in the Drosophila embryo

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This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).In this proposal, the investigators propose to automate the acquisition of gene expression data from individual cell nuclei in Drosophila embryos and use this new quantitative tool to analyze the formation of a sharp straight border between two domains of cells. Their goal in these studies is to create computational tools that will permit the automated acquisition and analysis of multiple fluorescent signals from single cells in the Drosophila embryo. These advances should allow for the quantitative analysis of 10-20 gene expression patterns at single nucleus resolution using a multi-probe based approach to in situ hybridization. The proposed automated multiplex methods should contribute substantially to enabling the creation of comprehensive gene expression atlases such as the Brain Atlases created by the Allen Institute, which are important for understanding basic biological processes such as organization of tissues and organs and changes in these structures during the evolution of developmental patterns. These methods should also make it possible to determine the exact relative expression patterns of different genes expressed in similar regions, which currently is not possible. Such refined gene expression maps will therefore make it possible to reconstruct transcription profiles for multiple genes simultaneously in individual cell types within an embryo. The software and protocols will be made available to the scientific community, and this project will include a graduate student and several undergraduates. Thus, it will also have important educational benefits for society.