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This Week in PNAS: Oct 31, 2017

In the early, online version of the Proceedings of the National Academy of Sciences, researchers from Michigan State University and Virginia Tech take a look at the evolutionary history of the cultivated potato, Solanum tuberosum L., by sequencing dozens of S. tuberosum related cultivars, cultivated landraces, and wild, tuber-bearing Solanum species. Along with extensive sequence and genomic diversity in cultivated potato and its wild counterparts, the team identified thousands of genes that appear to have been subject to selection in domesticated plants adapted to distinct geographic contexts. In addition, the study's authors say, the results point to "a historic role of wild Solanum species in the diversification of long-day-adapted tetraploid potatoes, showing that extant natural populations represent an essential source of untapped adaptive potential."

A team from the University of California, San Diego, describes SISSOR ("single-stranded sequencing using microfluidics reactors," a method for doing sequencing and haplotyping analyses on individual, diploid cells. The approach involves separating Watson and Crick DNA strands using a microfluidic processor, the researchers explain, followed by multiple displacement amplification and library construction on DNA strands spanning millions of bases that are randomly allocated into multiple compartments. "The separation and partitioning of large single-stranded DNA fragments of the homologous chromosome pairs allows for the independent sequencing of each of the complementary and homologous strands," they write, leading to "long haplotypes and reduction of sequence errors by using the redundant sequence information and haplotype-based error removal."

A National Cancer Institute-led team considers the consequences of pro-inflammatory enzyme expression in estrogen receptor-negative breast cancer. Using immunohistochemistry, the researchers profiled nearly 250 surgically resected tumor samples, tracking co-expression of nitric oxide synthase 2 and cyclooxygenase 2 — inflammation-associated enzymes that appeared to be linked to shorter-than-usual survival times in individuals with ER-negative breast cancer. Results from their follow-up analyses also suggested that interactions between the NOS2 and COX2 pathways contribute to ER-negative breast cancer progression and aggressiveness.