Characterization of the Drosophila segment determination morphome

Abstract

Here we characterize the expression of the full system of genes which control the segmentation morphogenetic field of Drosophila at the protein level in one dimension. The data used for this characterization are quantitative with cellular resolution in space and about 6 min in time. We present the full quantitative profiles of all 14 segmentation genes which act before the onset of gastrulation. The expression patterns of these genes are first characterized in terms of their average or typical behavior. At this level, the expression of all of the genes has been integrated into a single atlas of gene expression in which the expression levels of all genes in each cell are specified. We show that expression domains do not arise synchronously, but rather each domain has its own specific dynamics of formation. Moreover, we show that the expression domains shift position in the direction of the cephalic furrow, such that domains in the anlage of the segmented germ band shift anteriorly while those in the presumptive head shift posteriorly. The expression atlas of integrated data is very close to the expression profiles of individual embryos during the latter part of the blastoderm stage. At earlier times gap gene domains show considerable variation in amplitude, and significant positional variability. Nevertheless, an average early gap domain is close to that of a median individual. In contrast, we show that there is a diversity of developmental trajectories among pair-rule genes at a variety of levels, including the order of domain formation and positional accuracy. We further show that this variation is dynamically reduced, or canalized, over time. As the first quantitatively characterized morphogenetic field, this system and its behavior constitute an extraordinarily rich set of materials for the study of canalization and embryonic regulation at the molecular level.

Determining the scale of the Bicoid morphogen gradient

“…This is also shown in Fig. 2D, where we plot the Bicoid concentration along the AP axis at cycle 12 for different flow velocities along with an experimental profile obtained from the FlyEx database (25)(26)(27)(28). Again, the profile for v f low ϭ 0 exhibits a length scale that is much smaller than the experimentally observed one.…”

“…Other cases, such as stronger binding in the nuclei or stronger nuclear degradation, may result in slower diffusion and, therefore, in a smaller length scale. To compare the profile obtained from our simple diffusion model with experiments, we have also plotted a profile obtained from the FlyEx database (25)(26)(27)(28). This comparison shows that the length scale obtained using the simple diffusion and degradation model is much smaller than the experimentally observed one.…”

Properties of developmental gene regulatory networks

“…This results in mesoderm-specific expression of the Delta ligand, with the consequence that Notch signaling is constrained to the adjacent cells where it activates sim and other genes required for the specification of the ventral midline of the neurogenic ectoderm (2, 5). Although not explicitly described, the entire anterior-posterior patterning network of the Drosophila embryo is also composed of a series of double-negative gates, in which broadly distributed gap gene repressors establish domains of pair-rule gene expression by crossrepressive interactions among themselves (6).…”

A software for parameter optimization with Differential Evolution Entirely Parallel method

“…A model provides a dynamical description of gap gene regulatory system, using detailed DNA-based information, as well as spatial TF concentration data at varying time points. The gap gene regulatory network controls segment determination in the early Drosophila embryo (Akam, 1987;Jaeger, 2011;Surkova et al, 2008).…”