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This Week in PNAS: Dec 16, 2014

In the early, online edition of the Proceedings of the National Academy of Sciences, a team from China and the US describe the proteogenomic approach it used to profile prokaryotic post-translational modifications and gene expression in a unicellular plant model organism. For their proof-of-principle study, the researchers applied the liquid chromatography and mass spectrometry-based proteomic pipeline to the cyanobacterium species Synechococcus sp. PCC 7002. There, they defined more than 20 types of post-translational modifications and tracked down nearly 3,000 gene products, representing roughly 92 percent of the organism's predicted protein-coding repertoire. The team also improved on the cyanobacterium's existing annotation, identifying new protein-coding genes and adjusting the definition of dozens more.

An exome, genome, and RNA sequencing study by a Boston-led group has uncovered a recurrent role for the PI3 kinase/mTOR pathway in the bone cancer osteosarcoma. The researchers did whole-exome sequencing on matched tumor and normal samples from 59 individuals with osteosarcoma. They also assessed 35 of the cases RNA sequencing and subjected 13 sample sets to whole-genome sequencing. Although TP53 was the only gene that popped out as being recurrently mutated in the team's initial analysis, a closer look at mutation-affected pathways and further experimentation in mice uncovered a role for PI3K/mTOR signaling in the disease.

Finally, a group led by investigators at the University of Copenhagen did genome sequencing on two ancient horse samples as a means of comparing and contrasting the features found in horse lineages before and after domestication. Sequences from the 16,000- and 43,000-year old horse samples clustered with one another phylogenetically, it turned out, in a lineage distinct from domesticated horses and from existing wild horses in the Przewalski's horse lineage. Still, the ancient lineage appears to have intermixed with the domestic horse lineage in the past, the study's authors explain. And by comparing the genomes of horses in all three lineages, they were able to look for selection signals associated with domestication. GenomeWeb has more on the study, here.

The Scan

Purnell Choppin Dies

Purnell Choppin, a virologist who led the Howard Hughes Medical Institute, has died at 91, according to the Washington Post.

Effectiveness May Decline, Data From Israel Suggests

The New York Times reports that new Israeli data suggests a decline in Pfizer-BioNTech SARS-CoV-2 vaccine effectiveness against Delta variant infection, though protection against severe disease remains high.

To See Future Risk

Slate looks into the use of polygenic risk scores in embryo screening.

PLOS Papers on Methicillin-Resistant Staphylococcus, Bone Marrow Smear Sequencing, More

In PLOS this week: genomic analysis of methicillin-resistant Staphylococcus pseudintermedius, archived bone marrow sequencing, and more.