In PNAS this week, Steven Gygi at Harvard led work that used stable-isotope dilution and high-resolution mass spec to measure kinase activity. His multiplexed assay was able to measure up to 90 site-specific peptide phosphorylation rates at the same time, and he could apply it to a variety of cells and cellular processes, including mitogen stimulation, cell cycle, pharmacological inhibition of pathways, and to a panel of breast cancer cell lines.
A team of researchers led by Marc Friedländer and including Martin Hirst, Marco Marra, and Chad Nusbaum performed the first comprehensive small RNA analysis in animals belonging to the third animal superphylum, the Lophotrochozoa, they say in the abstract. Cloning and sequencing of small RNAs from the planarian Schmidtea mediterranea gave millions of unique small RNAs, including 61 novel miRNA genes and 10 miRNAs enriched in the flatworm's stem cells.
University of Washington scientists teamed up with those at the Benaroya Research Institute in Seattle to study the structure of the vertebrate genome. In this paper, they found that the genome of the sea lamprey, Petromyzon marinus, loses hundreds of millions of base pairs from many somatic cell types during embryonic development. Their study, they say, is "the first example of broad-scale programmed rearrangement of a definitively vertebrate genome."
Finally, Georgia Institute of Technology's Navin Elango was first author on a paper appearing this week that took a look at patterns of DNA methylation in the honeybee, Apis mellifera. The scientists show that genes in A. mellifera can be divided into two classes, one with low-CpG dinucleotide content and another with high-CpG dinucleotide content. "High-CpG genes, which are predicted to be hypomethylated in germlines, are enriched with functions associated with developmental processes, whereas low-CpG genes, predicted to be hypermethylated in germlines, are enriched with functions associated with basic biological processes," they write.