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This Week in PNAS: Apr 14, 2009

In this week's issue of PNAS, Belgian scientists looked at duplication events in flowering plants to find that the majority of the independent genome duplications coincide in time with the Cretaceous-Tertiary extinction event, which is thought to have wiped out the dinosaurs as well as many species of plants. Those with double genomes, they argue, had a better chance to survive. "Due to advantages such as altered gene expression leading to hybrid vigor and an increased set of genes and alleles available for selection," polyploid plants may have been more adaptable to a changing environment, they write in the abstract.

Work led by WashU's Jeffrey Gordon looked at how the two main bacterial phyla, the Firmicutes and the Bacteroidetes, work together in the human gut in vivo. Comparing sequences from two species from one of the most common gut Firmicute clades to five other gut Firmicutes and Bacteroidetes, the scientists found that Firmicutes have smaller genomes and a smaller number of glycan-degrading enzymes. When they colonized mice with the Firmicute Eubacterium rectale and the Bacteroidete Bacteroides thetaiotaomicron, and then followed it with whole-genome transcriptional profiling, high-resolution proteomic analysis, and biochemical assays of microbe-microbe and microbe-host interactions, they showed that each specifically adapted to the other, suggesting a certain level of "niche specialization and functional redundancy."

Published early online last week, scientists reported that 21-nt nontargeted siRNAs suppress growth of blood and lymphatic vessels in mouse models as efficiently as 21-nt siRNAs targeting vascular endothelial growth factor-A. In effect, the non-targeted molecules are activating TLR3, a double-stranded RNA immune receptor, rather than having a silencing effect. Our sister publication, RNAi News, has the full scoop here.

Scientists took a genome-wide look at structural variation related to disease progression in colorectal cancer. Performing statistical analysis of 299 expression and 130 SNP arrays profiled at different stages of the disease, they found broad duplications and deletions. Combining with gene expression data, they show that deletions of 8p, 4p, and 15q are associated with survival and disease progression, and that "simultaneous deletions" in 18q, 8p, 4p, and 15q have a "particularly poor prognosis."