et al., 2010) and bind to CArG-boxes, which are small 8–10 bp DNA sequences composed of 6–8 A or Ts flanked by C and G bases (de Folter and Angenent, 2006). The Arabidopsis genome contains an estimated 340,000 potential MADS binding sites (de Folter and Angenent, 2006), leading to the intriguing question: What is the biological significance of the large number of potential MADS binding sites, a...

Members of the MADS-box transcription factor family play essential roles in almost every developmental process in plants. Many MADS-box genes have conserved functions across the flowering plants, but some have acquired novel functions in specific species during evolution. The analyses of MADS-domain protein interactions and target genes have provided new insights into their molecular functions....

In this article, we tackle the automatic algorithm configuration problem (ACP), finding the best configuration of an algorithm such that some measure of its performance is optimized. We study the mesh adaptive direct search (MADS) method for the ACP. MADS is an iterative algorithm for global optimization. It does not require any infomation of the evaluation function, therefore the ACP can be re...

Changes in genes encoding transcriptional regulators can alter development and are important components of the molecular mechanisms of morphological evolution. MADS-box genes encode transcriptional regulators of diverse and important biological functions. In plants, MADS-box genes regulate flower, fruit, leaf, and root development. Recent sequencing efforts in Arabidopsis have allowed a nearly ...

Floral organs are specified by the combinatorial action of MADS-domain transcription factors, yet the mechanisms by which MADS-domain proteins activate or repress the expression of their target genes and the nature of their cofactors are still largely unknown. Here, we show using affinity purification and mass spectrometry that five major floral homeotic MADS-domain proteins (AP1, AP3, PI, AG, ...

Over the last decade, the yeast two-hybrid system has become the tool to use for the identification of protein-protein interactions and recently, even complete interactomes were elucidated by this method. Nevertheless, it is an artificial system that is sensitive to errors resulting in the identification of false-positive and false-negative interactions. In this study, plant MADS box transcript...

MADS (Minichromosome Maintenance1 Agamous Deficiens Serum response factor) box genes encode transcription factors and they play a key role in growth and development of flowering plants. There are two types of MADS box genes- Type I (serum response factor (SRF)-like) and Type II (myocyte enhancer factor 2 (MEF2)-like). Type II MADS box genes have a conserved MIKC domain (MADS DNA-binding domain,...

The Arabidopsis MADS domain proteins AP1, AP3, PI, and AG specify floral organ identity. All of these proteins contain a MADS domain required for DNA binding and dimerization; a region termed L (linker between MADS domain and K domain), which plays an important role in dimerization specificity; the K domain, named for its similarity to the coiled-coil domain of keratin; and a C-terminal region ...

The context of this research is multiobjective optimization where conflicting objectives are present. In work, these only available as the outputs a blackbox for which no derivative information available. This work proposes new extension mesh adaptive direct search (MADS) algorithm to derivative-free with bound constraints. method does not aggregate and keeps list non dominated points converges...