Modeling Development: Spikes of the Sea Urchin

Clemens Kühn[1] (
Alexander Kühn[1] (
Albert J. Poustka{1] (
Edda Klipp[1][2] (

[1]Max-Planck-Institute for Molecular Genetics, Ihnestr 63-73, 14195 Berlin, Germany
[2]Humboldt Universität zu Berlin, Institute for Biology, Invalidenstr 42, 10115 Berlin, Germany


Modeling of specification events during development poses new challenges to biochemical modeling. These include data limitations and a notorious absence of homeostasis in developing systems. The sea urchin is one of the best studied model organisms concerning development and a network, the Endomesoderm Network, has been proposed that is presumed to control endoderm and mesoderm specification in the embryo of Strongylocentrotus purpuratus. We have constructed a dynamic model of a subnetwork of the Endomesoderm Network. In constructing the model, we had to resolve the following issues: choice of appropriate subsystem, assignment of embryonic data to cellular model, choice of appropriate kinetics. Although the resulting model is capable of reproducing fractions of the experimental data, it falls short of reproducing specification of cell types. These findings can facilitate the refinement of the Endomesoderm Network.

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Japanese Society for Bioinformatics