David W. Knowles*, Soile Keranen+, Suman Dasgupta*, Mark D. Biggin+, Damir Sudar*
Departments of Cell and Molecular Biology* and Genome Sciences+, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720

The first 14 mitotic cycles in Drosophila result in a single layer of nuclei surrounding a yolk sac in the pregastrula embryo. Despite this morphological simplicity, the transcriptional network controlling pregastrula development is complex and little is know about what aberrations occur or the responses they evoke. To understand the role of biological variability during development, we are producing novel optical imaging techniques to map the relative position and gene expression of every nucleus within the embryo. Total DNA and specific gene products are imaged in 3D using confocal fluorescence microscopy. Innovative algorithms allow automatic segmentation of the DNA-image and produce an enumerated mask defining individual nuclear boundaries. The developmental stage of each embryo is classed by mitotic division number and determined from the total nuclei number; then the morphological mask is used to quantify gene-product on a per nuclei basis. What results is a map of pregastrular development showing the variability of nuclear number, relative nuclear packing density, and the expression pattern of specific gene products. This work illustrates the power of quantitative optical imaging and is an initial step towards uncovering the rules determining how patterns of gene expression are generated.