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This Week in PNAS: Nov 21, 2017

In the early, online edition of the Proceedings of the National Academy of Sciences, researchers from Stanford University and the Chan Zuckerberg Biohub describe results from a T cell receptor beta-chain sequencing and immune profiling analysis of blood, tumor, and matched normal breast tissue samples from more than a dozen individuals with early-stage breast cancer. Based on results for 16 breast cancer patients, they saw enhanced T cell density and distinct clonal patterns relative to the blood and normal breast tissue. As some T cell sequences overlapped in each individual's tumor, blood, and normal tissue, the authors note that they also uncovered a "subset of 'enriched' [T cell receptor beta] sequences with high abundance in each tumor and absent or low abundance in normal breast." 

A team from the US and Japan take a look at the consequences of transposable element bursts in Oryza sativa rice. Using whole-genome sequencing and comparative genomics, the researchers profiled transposable element patterns in two rice strain pairs — sets of inbred rice that diverged from a common ancestor within the past few decades. In both cases, insertions involving a type of class 2 transposable elements called mPing elements were about twice as common as new SNPs in each rice strain pair. There was a dearth of insertions by other transposable element families, the authors note, suggesting mPing insertion bursts can dodge host detection for decades after strains start diverging.

University of California, Riverside, researchers report on a transgenic CRISPR/Cas9 approach for editing the genome of the Aedes aegypti mosquito, a common vector for dengue virus, Zika virus, and several other disease-causing arboviruses. In the hopes of accomplishing more effective genome engineering in the mosquito species, the team established transgenic mosquito strains that carry and express Cas9 in their genomes. Paired with improve homology-directed repair in this genome engineering system, the authors saw a boost in the ability to upend selected Ae. aegypti mosquito genes. "Given their high editing efficiencies, the Cas9 strains we developed can be used to quickly generate genome modifications, allowing for high-throughput gene targeting, and can possibly facilitate the development of gene drives," they write.