Two-Exponential Models of Gene Expression Patterns for Noisy Experimental Data

Quantification reveals early dynamics in Drosophila maternal gradients

The Bicoid (Bcd) protein is a primary determinant of early anterior-posterior (AP) axis specification in Drosophila embryogenesis. This morphogen is spatially distributed in an anterior-high gradient, and affects particular AP cell fates in a concentration-dependent manner. The early distribution and dynamics of the bicoid (bcd) mRNA, the source for the Bcd protein gradient, is not well understood, leaving a number of open questions for how Bcd positional information develops and is regulated. Confocal microscope images of whole early embryos, stained for bcd mRNA or the Staufen (Stau) protein involved in its transport, were processed to extract quantitative AP intensity profiles at two depths (apical-under the embryo surface but above the nuclear layer; and basal-below the nuclei). Each profile was quantified by a two- (or three-) exponential equation. The parameters of these equations were used to analyze the early developmental dynamics of bcd. Analysis of 1D profiles was compared with 2D intensity surfaces from the same images. This approach reveals strong early changes in bcd and Stau, which appear to be coordinated. We can unambiguously discriminate three stages in early development using the exponential parameters: pre-blastoderm (1-9 cleavage cycle, cc), syncytial blastoderm (10-13 cc) and cellularization (from 14A cc). Key features which differ in this period are how fast the first exponential (anterior component) of the apical profile drops with distance and whether it is higher or lower than the basal first exponential. We can further discriminate early and late embryos within the pre-blastoderm stage, depending on how quickly the anterior exponential drops. This relates to the posterior-wards spread of bcd in the first hour of development. Both bcd and Stau show several redistributions in the head cytoplasm, quite probably related to nuclear activity: first shifting inwards towards the core plasm, forming either protrusions (early pre-blastoderm) or round aggregations (early nuclear cleavage cycles, cc, 13 and 14), then moving to the embryo surface and spreading posteriorly. These movements are seen both with the 2D surface study and the 1D profile analysis. The continued spreading of bcd can be tracked from the time of nuclear layer formation (later pre-blastoderm) to the later syncytial blastoderm stages by the progressive loss of steepness of the apical anterior exponential (for both bcd and Stau). Finally, at the beginning of cc14 (cellularization stage) we see a distinctive flip from the basal anterior gradient being higher to the apical gradient being higher (for both bcd and Stau). Quantitative analysis reveals substantial (and correlated) bcd and Stau redistributions during early development, supporting that the distribution and dynamics of bcd mRNA are key factors in the formation and maintenance of the Bcd protein morphogenetic gradient. This analysis reveals the complex and dynamic nature of bcd redistribution, particularly in the head cytoplasm. These resemble observations in oogenesis; their role and significance have yet to be clarified. The observed co-localization during redistribution of bcd and Stau may indicate the involvement of active transport.

Quantitative Analysis of the Dynamics of Maternal Gradients in the Early Drosophila Embryo

Predetermination, formation, and maintenance of the primary morphogenetic gradient (bicoid, bcd) of the early Drosophila embryo involves many interrelated processes. Here we focus on the biological systems analysis of the bcd mRNA redistribution in an early embryo. The results of the quantitative analysis of experimental data, together with the results of their dynamic modeling, substantiate the role of active transport in the redistribution of the bcd mRNA. The role of the nonlinearity of degradation mechanisms in the mRNA pattern robustness is discussed.

Protein Network Analysis of the Fifth Chromosome of Zebrafish

In the past 20 years, zebrafish has gradually become an important animal model for studying the function of human genes. At the same time, identification of zebrafish reference genome sequences and >10,000 protein-coding genes indicates that they are at least 75% homologous to human genes, further validating its utility as a research model for growth and developments (GDs). However, the molecular mechanism of zebrafish GDs has almost no molecular interactions, so a protein-protein interaction (PPI) network is highly desirable. The project extracted 58 genes on the fifth chromosome of the model organism, and studied and modeled its GDs mechanisms, which encompassed 296 interactions between the 58 proteins involved in GDs. This includes not only accurate predictions of PPI but also those molecular interactions collected from the literature and experimentally derived. These molecules then interact, modularize, look for central genes, analyze, and predict their GDs processes, and hope to help scholars study the process of GDs, providing hypotheses and help.