Summary The homeodomain (HD) protein Bicoid (Bcd) is thought to function as a gradient morphogen that positions boundaries of target genes via threshold-dependent activation mechanisms. Here we analyze 66 Bcd-dependent regulatory elements, and show that their boundaries are positioned primarily by repressive gradients that antagonize Bcd-mediated activation. A major repressor is the pair-rule protein Runt, which is expressed in an opposing gradient, and is necessary and sufficient for limiting Bcd-dependent activation. Evidence is presented that Runt functions with the maternal repressor Capicua and the gap protein Kruppel as the principal components of a repression system that correctly orders boundaries throughout the anterior half of the embryo. These results put conceptual limits on the Bcd morphogen hypothesis, and demonstrate how the Bcd gradient functions within the gene network that patterns the embryo.

Adsorption is one of the widely used processes in the chemical industry environmental application. As compared to mathematical models proposed to describe batch adsorption in terms of isotherm and kinetic behavior, insufficient models are available to describe and predict fixed-bed or column adsorption, though the latter one is the main option in practical application. The present review first provides a brief summary on basic concepts and mathematic models to describe the mass transfer and isotherm behavior of batch adsorption, which dominate the column adsorption behavior in nature. Afterwards, the widely used models developed to predict the breakthrough curve, i.e., the general rate models, linear driving force (LDF) model, wave propagation theory model, constant pattern model, Clark model, Thomas model, Bohart-Adams model, Yoon-Nelson model, Wang model, Wolborska model, and modified dose-response model, are briefly introduced from the mechanism and mathematical viewpoint. Their basic characteristics, including the advantages and inherit shortcomings, are also discussed. This review could help those interested in column adsorption to reasonably choose or develop an accurate and convenient model for their study and practical application.

In vivo cross-linking studies suggest that the Drosophila transcription factor Bicoid (Bcd) binds to several thousand sites during early embryogenesis, but it is not clear how many of these binding events are functionally important. In contrast, reporter gene studies have identified >60 Bcd-dependent enhancers, all of which contain clusters of the consensus binding sequence TAATCC. These studies also identified clusters of TAATCC motifs (inactive fragments) that failed to drive Bcd-dependent activation. In general, active fragments showed higher levels of Bcd binding in vivo and were enriched in predicted binding sites for the ubiquitous maternal protein Zelda (Zld). Here we tested the role of Zld in Bcd-mediated binding and transcription. Removal of Zld function and mutations in Zld sites caused significant reductions in Bcd binding to known enhancers and variable effects on the activation and spatial positioning of Bcd-dependent expression patterns. Also, insertion of Zld sites converted one of six inactive fragments into a Bcd-responsive enhancer. Genome-wide binding experiments in zld mutants showed variable effects on Bcd-binding peaks, ranging from strong reductions to significantly enhanced levels of binding. Increases in Bcd binding caused the precocious Bcd-dependent activation of genes that are normally not expressed in early embryos, suggesting that Zld controls the genome-wide binding profile of Bcd at the qualitative level and is critical for selecting target genes for activation in the early embryo. These results underscore the importance of combinatorial binding in enhancer function and provide data that will help predict regulatory activities based on DNA sequence.

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