Center vortices, magnetic condensate and confinement in a simple gauge system

The confining mechanisms of 't Hooft and Mandelstam have a simple microscopic realization in 3D Z2 gauge theory: the center vortex and the magnetic monopole condensation are associated, in the set of configurations contributing to the confining phase, to the presence of two kinds of infinite clusters. These generate the area law of the large Wilson loops and the universal finite size effects produced by the quantum fluctuations of the bosonic string describing the infrared behavior of the flux tube.Comment: 8 pages, 4 eps figures. Contributed to NATO Advanced Research Workshop on Confinement, Topology, and other Nonperturbative Aspects of QCD, Stara Lesna, Slovakia, 21-27 Jan 200

Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes

Gene regulation in eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational method to identify regulatory elements in the upstream region of eukaryotic genes. The genes are grouped in sets sharing an overrepresented short motif in their upstream sequence. For each set, the average expression level from a microarray experiment is determined: If this level is significantly higher or lower than the average taken over the whole genome, then the overerpresented motif shared by the genes in the set is likely to play a role in their regulation. The method was tested by applying it to the genome of Saccharomyces cerevisiae, using the publicly available results of a DNA microarray experiment, in which expression levels for virtually all the genes were measured during the diauxic shift from fermentation to respiration. Several known motifs were correctly identified, and a new candidate regulatory sequence was determined.Comment: Published version available from http://www.biomedcentral.com/1471-2105/3/