The fruit fly Drosophila is a premier system for investigating how animal embryos self-organize their body plan. The blueprint for the fly's body is created by networks of genes operating in an ellipsoidal shell of cell nuclei called the blastoderm. We create predictive models of this process using systems of ordinary or partial differential equations fit to gene expression data by simulated annealing and/or Lagrangian methods. In this talk I will discuss the entire pattern formation project, from colorful fluorescently stained embryos to image processing, new optimization algorithms, and finally to new biological results. Also, although the notion of 'cis-regulatory modules' central to modern molecular biology, I will show that our understanding of the function and organization of these entities is fundamentally insufficient for understanding developmental biology. I will propose a solution to this problem through a new theoretical approach in concert with quantitative data from promoter-reporter constructs.
References
J. Jaeger, S. Surkova, M. Blagov, H. Janssens, D. Kosman, K. N. Kozlov, M. and E. Myasnikova, C. E. Vanario-Alonso, M. Samsonova, D. H. Sharp and J. Reinitz, 2004, Dynamic control of positional information in the early Drosophila embryo, Nature, 430:368-371.
E. Myasnikova, A. Samsonova, K. Kozlov, M. Samsonova and J. Reinitz, 2001, Registration of the Expression Patterns of Drosophila Segmentation Genes by Two Independent Methods, Bioinformatics, 17:3-12.
K.-W. Chu, Y. Deng and J. Reinitz, 1999, Parallel Simulated Annealing by Mixing of States, Journal of Computational Physics, 148:646-662.
E. Mjolsness, D. H. Sharp and J. Reinitz, 1991, A Connectionist Model of Development, Journal of Theoretical Biology, 152:429-453.