Canalization of gene expression and domain shifts in the Drosophila blastoderm by dynamical attractors.

The variation in the expression patterns of the gap genes in the blastoderm of the fruit fly Drosophila melanogaster reduces over time as a result of cross regulation between these genes, a fact that we have demonstrated in an accompanying article in PLoS Biology (see Manu et al., doi:10.1371/journal.

Characterization of the Drosophila segment determination morphome.

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.

Analysis of pattern precision shows that Drosophila segmentation develops substantial independence from gradients of maternal gene products.

We analyze the relation between maternal gradients and segmentation in Drosophila, by quantifying spatial precision in protein patterns. Segmentation is first seen in the striped expression patterns of the pair-rule genes, such as even-skipped (eve). We compare positional precision between Eve and the maternal gradients of Bicoid (Bcd) and Caudal (Cad) proteins, showing that Eve position could be initially specified by the maternal protein concentrations but that these do not have the precision to specify the mature striped pattern of Eve.

Bicoid cooperative DNA binding is critical for embryonic patterning in Drosophila.

Cooperative interactions by DNA-binding proteins have been implicated in cell-fate decisions in a variety of organisms. To date, however, there are few examples in which the importance of such interactions has been explicitly tested in vivo. Here, we tested the importance of cooperative DNA binding by the Bicoid protein in establishing a pattern along the anterior-posterior axis of the early Drosophila embryo.

A kinetic mechanism for Drosophila bicoid cooperative binding.

The Bicoid (Bcd) protein is a concentration-dependent transcriptional activator in the embryo of Drosophila melanogaster. Bcd regulates the expression of the maternal and zygotic gene hunchback (hb) that shows a step-like-function expression pattern, in the anterior half of the egg. The regulatory region of hb contains six major binding sites for the Bcd protein, named A1, A2, A3 (strong sites), and X1, X2, X3 (weak sites).

A high-throughput method for quantifying gene expression data from early Drosophila embryos.

We describe an automated high-throughput method to measure protein levels in single nuclei in blastoderm embryos of Drosophila melanogaster by means of immunofluorescence. The method consists of a chain of specific algorithms assembled into an image processing pipeline. This pipeline transforms a confocal scan of an embryo stained with fluorescently tagged antibodies into a text file.

Dynamical analysis of regulatory interactions in the gap gene system of Drosophila melanogaster.

Genetic studies have revealed that segment determination in Drosophila melanogaster is based on hierarchical regulatory interactions among maternal coordinate and zygotic segmentation genes. The gap gene system constitutes the most upstream zygotic layer of this regulatory hierarchy, responsible for the initial interpretation of positional information encoded by maternal gradients. We present a detailed analysis of regulatory interactions involved in gap gene regulation based on gap gene circuits, which are mathematical gene network models used to infer regulatory interactions from quantitative gene expression data.

Dynamic control of positional information in the early Drosophila embryo.

Morphogen gradients contribute to pattern formation by determining positional information in morphogenetic fields. Interpretation of positional information is thought to rely on direct, concentration-threshold-dependent mechanisms for establishing multiple differential domains of target gene expression. In Drosophila, maternal gradients establish the initial position of boundaries for zygotic gap gene expression, which in turn convey positional information to pair-rule and segment-polarity genes, the latter forming a segmental pre-pattern by the onset of gastrulation.

Sharp borders from fuzzy gradients.

Critical boundaries in the early Drosophila embryo are set by morphogenetic gradients. A new quantitative study shows that the placement of one such boundary is more accurate than the gradient thought to set it. Genetic analysis of the accuracy of the process implicates a gene not previously thought to be involved.