Modeling morphological movements prior to gastrulation in Drosophila

work with the BDTNP Imaging Group at LBL


To accurately describe gene expression and computationally model animal transcriptional networks, it is essential to determine the changing locations of cells in developing embryos.

Using automated image analysis methods, we provide the first quantitative description of temporal changes in morphology and gene expression with cellular resolution in whole embryos, using the Drosophila blastoderm as a model. Analyses based on both fixed and live embryos reveal complex, previously undetected three-dimensional changes in nuclear density patterns caused by nuclear movements prior to gastrulation. Gene expression patterns move in part with these changes in morphology, but additional spatial shifts in expression patterns are also seen, supporting a previously proposed model of pattern dynamics based on the induction and inhibition of gene expression. We show that mutations that disrupt either the anterior/posterior (a/p) or the dorsal/ventral (d/v) transcriptional cascades alter morphology and gene expression along both the a/p and d/v axes in a way suggesting that these two patterning systems interact via both transcriptional and morphological mechanisms.

Our work establishes a new strategy for measuring temporal changes in the locations of cells and gene expression patterns that uses fixed cell material and computational modeling. It also provides a coordinate framework for the blastoderm embryo that will allow increasingly accurate spatio-temporal modeling of both the transcriptional control network and morphogenesis.


  • S. Keränen, C. Fowlkes, C. Luengo Hendriks, D. Sudar, D. Knowles, J. Malik, M. Biggin, ``3D Morphology and Gene Expression in the Drosophila Blastoderm at Cellular Resolution II: Dynamics'', Genome Biology, [pdf]

  • C. Fowlkes, J. Malik. "Inferring nuclear movements from fixed material", Technical Report EECS-2006-142, EECS Department, University of California, Berkeley, (November 2006). [pdf]

  • C. Fowlkes, C. Luengo Hendriks, S. Keränen, A. DePace, G. Weber, O. Rübel, M-Y Huang, L. Simirenko, B. Hamann, M. Eisen, D. Sudar, D. Knowles, M. Biggin, J. Malik, "Complex Interactions Between D/V and A/P Patterning Systems Before Gastrulation Revealed by a 3-D Atlas of Gene Expression Patterns." 47th Drosophila Research Conference, Houston, TX, (April 2006). [pdf]