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This Week in PNAS: Feb 18, 2014

In the early, online edition of the Proceedings of the National Academy of Sciences, researchers from China, Sweden, and the Netherlands present a gene co-expression-based method for classifying glioma tumors. By looking for genes with expression profiles resembling those of the known glioma contributors EGFR and PDGFRA, the team tracked down 29 genes showing EGFR-like, or "EM," expression and another 40 with "PM" patterns that resembled expression characteristics of PDGFRA in the cancer. Those co-expression signatures, in turn, proved useful for clustering almost 1,400 glioma tumors into three sub-types with different diagnostic and prognostic patterns.

A Swiss and American team takes a look at the genotypes and gene expression patterns at play during interactions between the trypanosome parasite Crithidia bombi and its bumblebee host, Bombus terrestris. By sequencing the transcriptomes of bees from four colonies infected with three genotypes of C. bombi parasites, the researchers saw that different genes were dialed up and down in the host bees depending on the C. bombi genotype involved in the infection. Likewise, this host gene expression response varied somewhat with the host bee's genotype, the study's authors report. "[T]he expression of a number of genes depends on the host genotype and the parasite genotype and the interaction between both host and parasite genotypes," they add.

The Lawrence Berkeley National Laboratory's Adam Arkin and collaborators from the US and China used a GeoChip functional gene array to track microbial community succession in groundwater ecosystem over time, before and after adding emulsified vegetable oil as a bioremediation method for immobilizing uranium. Based on data for seven groundwater wells affected by this vegetable oil amendment and one "up-gradient" control well over nine months, the team concluded that dynamic, stochastic events likely make more pronounced contributions to this process than static, deterministic features of the environment. In addition, the study's authors noted that "[w]hereas both deterministic and stochastic processes played roles in controlling community assembly, their relative importance was time dependent."