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This Week in PNAS: Oct 21, 2014

In the early edition of the Proceedings of the National Academy of Sciences, investigators from the US and Pakistan present findings from their transcriptome sequencing study of metastatic breast cancer cells that had or had not been treated with the chemotherapeutic drug paclitaxel. Using single-cell and bulk RNA sequencing, the team characterized gene expression profiles in untreated cells, cells that have become resistant to paclitaxel, and cells that are stressed by paclitaxel exposure. For instance, their findings revealed widespread transcriptional variability between individual cells that had become paclitaxel tolerant, though resistant cells tended to contain microtubule-related variants not found in other cells.

A University of California at Santa Barbara-led team presents evidence for parallel transcriptome evolution in the bioluminescent organs of two squid species that evolved photophores independently of one another via convergent evolution. Through transcriptome sequencing on photophores from three Hawaiian bobtail squid (Euprymna scolopes) and three Uroteuthis edulis squid — followed by phylogenetic and other analyses — the researchers saw signs of predictable transcriptome evolution over time, as the organs adopted convergent features. From these findings, the study's authors speculate that "predictable solutions may drive not only the evolution of novel, complex organs but also the evolution of overall gene expression levels that underlie them."

Researchers from Taiwan and the US used genome and transcriptome sequencing to study Antrodia cinnamomea, a Taiwanese mushroom that's been touted for its apparent medicinal qualities. Within the more than 32 million-base draft genome, for example, the team annotated some 9,254 predicted protein-coding genes. By folding in gene expression data from different stages of A. cinnamomea development and performing pathway analyses, meanwhile, the group got a glimpse at metabolic and developmental features of the mushroom, which has been employed as a remedy for everything from high blood pressure and hangovers to cancer.