Scientists have performed a comparative functional analysis of the C. elegans and D. melanogaster proteomes. Their work was published this week in PLoS Biology. Using shotgun proteomics, they identified more than half of all predicted C. elegans proteins. When comparing the proteome to the fruit fly's, they found that protein abundance is highly conserved between the two. "So, although worms and flies look very different, they need similar amounts of each conserved, orthologous protein," they write in the author summary.
In work in PLoS Genetics, Ohio State researchers used ChIP-chip to study what genes are involved in the differentiation of Arabidopsis epidermal cells into trichomes. They identified about 20 genes to be targets of the transcription factors GL3 and GL1, including SIM (SIAMESE), which encodes a cyclin-dependent kinase inhibitor, and RBR1 (RETINOBLASTOMA RELATED1), which corresponds to a negative regulator of the cell cycle transcription factor E2F.
Scientists at Genomic Health have developed a real-time PCR-based assay to identify SNPs in tumors. The method is based on TaqMan real-time PCR and combines Allele-Specific PCR with a Blocking reagent (ASB-PCR) to suppress amplification of the wild-type allele. It can be used to detect germ line or somatic mutations in either DNA or RNA from any type of tissue, including FFPE tumor specimens.
In an article in PLoS Medicine, scientists summarize how best to perform systematic reviews and meta-analyses of GWAS, based on standards from the Human Genome Epidemiology Network (HuGENet). Systematic reviews, they say, are less subjective than narrative ones and should include more than one bibliographic database, as well as online data. It is important to assess the validity of each included study and also to perform a meta-analysis of effect sizes, for example, odds ratios, whenever possible.