Gene expression regulation in microbial organisms occurs at multiple steps involving both the transcriptional and translational levels. Codon usage bias is a major determinant of gene expression and acts on several regulatory points of this process. Theoretical methods are used to predict protein expression levels based on codon usage bias for 30 bacterial and archaeal genomes. I describe strong correlations of the predicted expression values to other regulatory elements that are known to affect gene expression: the Shine-Dalgarno (SD) sequence, the start and stop codons, and the potential of a transcript to form secondary structures. These data provide important insights into the evolution of the Shine-Dalgarno sequence and its interaction with the anti-SD motif in the 3' end of the 16S rRNA gene.; Using oligonucleotide microarrays, transcriptomes of diverse maize tissues are profiled across three genetic backgrounds. Biological stage markers are identified by genetic ablation and enrichment of tissue types with male sterile mutants; similarly genes that may play important roles in cell type specification and determination are enumerated. Reproductive tissues, including the anther and mature pollen, display a more congruent profile than a strictly vegetative tissue, the leaf, in comparisons across diverse lines. The anther transcriptome is estimated to comprise about half of the total maize transcripts, indicating complex genetic regulations during the development of this male reproductive organ.
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