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This Week in PNAS: Feb 6, 2018

Researchers from China, the UK, and the US search for genetic contributors to Alzheimer's disease in China using whole-genome sequence data. For the analysis, collaborators at Novogene began by doing low-coverage genome sequencing on samples from 1,222 individuals in China, including 489 Alzheimer's disease cases, 260 individuals with mild cognitive impairment, and 473 unaffected controls. After folding in additional Chinese population whole-genome sequence data, the investigators compared variant patterns in 477 Alzheimer's disease cases and 442 controls that passed their quality control steps in a two-stage association analysis. Along with a known risk locus at APOE, their hunt led to more subtle associations between Alzheimer's disease and variants in and around GCH1 and KCNJ15 genes that appeared to influence immune pathway activity.

An international team led by investigators in Brunei, the US, China, and Malaysia provide a classification framework for tropical plants from around the world, informed by phylogenetic relationships, evolutionary distance between plants, and biogeography. "To determine the phylogenetic distance between locations," the authors say, "we constructed a dated phylogenetic tree that was resolved to genus level and contained all taxa used for our classification analyses." Based on phylogenetic clues gleaned from angiosperm trees in old-growth tropical forests at hundreds of locations, they identified five main tropical forest regions, with further clustering between sites that were once connected on the Gondwana supercontinent.

Finally, Swiss, German, and French researchers take a look at the post-transcriptional regulatory features governing transcript dynamics over the span of a day in the mouse liver. Using a mathematical model designed to track and quantify messenger RNA (mRNA) and pre-mRNA cycles, the team analyzed available RNA sequence data for mouse liver samples collected every two hours over several days. In the process, they identified transcripts with transcriptional or post-transcriptional regulation, including a subset of mRNAs with rhythmic representation stemming from post-transcriptional regulatory events that appeared to be under circadian clock control. "Such regulation is only partially dependent on the circadian clock," they write, "showing that systemic pathways and feeding patterns contribute important post-transcriptional control of gene expression in liver."