DevoWorm: differentiation waves and computation in C. elegans embryogenesis

Abstract

Development is a complex process that, under normal circumstances, proceeds in a stable and patterned fashion. Developmental morphogenesis (called embryogenesis) can tell us a great deal about the function and structure of an adult organism. One of the most important aspects of development to understand is the progression of cell division and differentiation in what will become an adult worm. This is where the DevoWorm project can both address multiple outstanding theoretical issues and provide graphical clarity to the embryogenetic process. As a representative of mosaic development, C. elegans embryogenesis is both tractable in terms of cell number and relatively well-characterized. In this paper, we will lay out a theoretical re-interpretation of embryogenesis in addition to developing an RDF-based computational framework for visualizing the results of this theoretical effort. Our theoretical efforts will ultimately involve the construction of a differentiation tree and data analyses that support the concept of differentiation waves acting to coordinate cellular differentiation and embryonic form. The differentiation tree will also feature a means to perturb development in a manner that mimics phenotypic mutagenesis. This will allow us to understand the selective variability that is inherent in biological development, but that remains so poorly understood. In tandem, these developments will allow us to construct a conceptual and computational framework which can be applied to both mosaic and regulative development.