title: The effect of reactions on the formation and readout of the gradient of Bicoid.
abstract: During early development, the establishment of gradients of transcriptional factors determines the patterning of cell fates. The case of Bicoid (Bcd) in Drosophila melanogaster embryos is well documented and studied. There are still controversies as to whether SDD models in which Bcd is Synthesized at one end, then Diffuses and is Degraded can explain the gradient formation within the timescale observed experimentally. The Bcd gradient is observed in embryos that express a Bicoid-eGFP fusion protein (Bcd-GFP) which cannot differentiate if Bcd is freely diffusing or bound to immobile sites. In this work we analyze an SDID model that includes the Interaction of Bcd with binding sites. We simulate numerically the resulting full reaction-diffusion system in a cylindrical domain using previously determined biophysical parameters and a simplified version of the Bcd source. In this way we obtain solutions that depend on the spatial location approximately as observed experimentally and that reach such dependence at a time that is also compatible with the experimental observations. Analyzing the differences between the free and bound Bcd distributions we observe that the latter spans over a longer lengthscale. We conclude that deriving the lengthscale from the distribution of Bcd-GFP can lead to an overestimation of the gradient lengthscale and of the Hill coefficient that relates the concentrations of Bcd and of the protein, Hunchback, whose production is regulated by Bcd.
authors.affiliation: Departamento de Física, FCEN-UBA, and IFIBA, CONICET, Ciudad Universitaria, Pabellón I, (1428) Buenos Aires, Argentina. Laboratoire J. A. Dieudonné Université de Nice Sophia Antipolis, UMR 7351 CNRS, Parc Valrose, F-06108 Nice Cedex 02, France. Author to whom any correspondence should be addressed.
authors.forename: Emiliano Perez
authors.initials: EP
authors.lastname: Ipiña
authors.forename: Silvina Ponce
authors.initials: SP
authors.lastname: Dawson
mesh_terms: D000818:Animals; D003198:Computer Simulation; D004058:Diffusion; D029721:Drosophila Proteins; D004331:Drosophila melanogaster / Q000196:embryology* / Q000378:metabolism; D018398:Homeodomain Proteins / Q000032:analysis / Q000378:metabolism*; D008954:Models, Biological; D015534:Trans-Activators / Q000032:analysis / Q000378:metabolism*
chemical_list: D029721:Drosophila Proteins; D018398:Homeodomain Proteins; D015534:Trans-Activators; C056478:bcd protein, Drosophila