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This Week in PNAS: Nov 22, 2016

In the early, online edition of the Proceedings of the National Academy of Sciences, Swedish researchers explore ties between somatic structural variants and gene expression effects in a wide range of human cancer types profiled for the Cancer Genome Atlas Project. With genome sequencing data for more than 600 tumors representing 18 cancer types assessed for TCGA, the team scrutinized somatic rearrangement, gene fusion, and other structural variants in the tumors, looking at their relationship to copy number and expression patterns. "At a global level," the authors say, "we find that such events often contribute to altered gene expression in human cancer, and also highlight specific events that may have functional roles during tumor development."

An international team led by investigators in Norway and the UK describe findings from a population genomics study of Mycobacterium tuberculosis isolates from the L2 sub-lineage, which were involved an outbreak in western Europe that affected Norwegians and Afghan nationals. From variant patterns and phylogenetic features found in 85 M. tuberculosis isolates, the researchers tracked dispersal and resistance patterns in the clade, estimating that it arrived in Afghanistan between 1979 and the late 1980s during the Soviet-Afghan war, before expanding to other parts of the world after American forces arrived in the country in 2001. "Our results indicate that the fall of the Soviet Union and the ensuing collapse of public health systems led to a rise in M. tuberculosis drug resistance," they write. "We also show that armed conflict and population displacement is likely to have aided the export of this clade from central Asia to war-torn Afghanistan and beyond."

Austrian researchers present findings from proteomic, genomic, and comparative genomic analyses of Nitrososphaera viennensis EN76, an archaea species that contributes to global nitrogen and carbon cycles by oxidizing ammonia. The team put together a more than 2.5 million base genome for an N. viennensis EN76, comparing it with sequences from seven related archaea from the same ammonia-oxidizing archaea (AOA) phylum. The genome housed an estimated 3,123 protein-coding genes and the group saw evidence for translation of almost half of those predicted genes through mass spectrometry-based proteomic profiling on forms of N. viennensis grown in the laboratory environment. "This comparative analysis allows us to narrow down the minimal active gene set of AOA, reconstruct central metabolic pathways, including possible regulatory mechanisms, and identify candidates for potential missing steps in the core energy metabolism of AOA," the authors note.