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This Week in Nature: Dec 12, 2013

In this week's Nature, researchers from Washington University report on the discovery of a new genetic risk variant for Alzheimer's disease. The team conducted whole-exome sequencing on DNA from 29 affected individuals and 11 unaffected people, from 14 families with histories of late-onset Alzheimer's disease. It discovered a rare variant in the phospholipase D3, or PLD3, gene that was associated with a significantly greater risk of the disease. Cell culture testing showed that higher levels of the PLD3 protein reduced amyloid-beta, which accumulates in the brains of Alzheimer's disease patients, whereas lower levels of PLD3 increased amyloid-beta.

GenomeWeb Daily News has more on this study here.

Meanwhile, in Nature Methods, investigators from the University of Toronto highlight the presence of DNase I cleavage bias in transcription factor footprint identification. The sequencing of DNase I hypersensitive sites, or DNase-seq, is widely used to identify cis-regulatory elements across the genome. In an analysis of genome-wide binding sites of 36 transcription factors, the group found that footprinting data from DNase-seq was informative for some of them, but uninformative for many others. The researchers determined that "intrinsic DNase I cutting biases, a factor that had not been adequately accounted for in previous footprinting studies, can be incorrectly interpreted as patterns induced by TF binding."

The Scan

Dropped Charges

The US Justice Department has dropped visa fraud charges against five Chinese researchers, according to the Wall Street Journal.

More Kids

The Associated Press says Moderna is expanding its SARS-CoV-2 vaccine study to included additional children and may include even younger children.

PNAS Papers on Rat Clues to Human Migration, Thyroid Cancer, PolyG-DS

In PNAS this week: ancient rat genome analysis gives hints to human migrations, WDR77 gene mutations in thyroid cancer, and more.

Purnell Choppin Dies

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