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This Week in PNAS: Apr 10, 2018

In the early, online edition of the Proceedings of the National Academy of Sciences, researchers from the University of Oregon, Hunter College, Harvard University, and elsewhere explore potential ties between immunity and growth patterns in children from the Shuar tribe, an indigenous forager-horticulturalist population in Amazonian regions of Ecuador. The team considered blood immune biomarker and anthropometric growth profiles for 261 Shuar children between the ages of 4 years and 11 years old for a prospective analysis looking at the interplay between energy allotted to immune function that may impact growth. The results revealed significant growth reduction in children when immune function was high, the authors note, "highlighting the energy constraint of childhood and the characteristic ability of our species to respond sensitively to dynamic environmental conditions." 

A New York University- and University College London-led team digs into gene regulation in the nematode worm Acrobeloides nanus to get a better look at developmental evolution. The researchers began by sequencing and assembling a 248 million base A. nanus genome and accompanying transcriptome, comparing the gene regulatory program and expression patterns present in A. nanus relative to that in another nematode worm (the model organism Caenorhabditis elegans). "The gene regulatory programs of these two species show many differences early in development, but significantly converge at the mid-developmental transition," they report, noting that "variation is not evenly distributed but, rather, that developmental and evolutionary constraints act to shape gene regulatory programs."

Researchers in China and the US report on results from a CRISPR-Cas9 screen on a human immune T lymphocyte cell line. For the genome-wide loss-of-function screen, the team systematically edited out genes using hundreds of thousands of single-guide RNAs for CRISPR-based editing. Following stimulating the edited immune T cells through the T cell receptor, the investigators used deep sequencing to narrow in on immune regulators, including known immune regulators and novel candidates such as FAM49B — a gene that appears to contribute to both T cell activation and actin dynamics.

The Scan

Machine Learning Helps ID Molecular Mechanisms of Pancreatic Islet Beta Cell Subtypes in Type 2 Diabetes

The approach helps overcome limitations of previous studies that had investigated the molecular mechanisms of pancreatic islet beta cells, the authors write in their Nature Genetics paper.

Culture-Based Methods, Shotgun Sequencing Reveal Transmission of Bifidobacterium Strains From Mothers to Infants

In a Nature Communications study, culture-based approaches along with shotgun sequencing give a better picture of the microbial strains transmitted from mothers to infants.

Microbial Communities Can Help Trees Adapt to Changing Climates

Tree seedlings that were inoculated with microbes from dry, warm, or cold sites could better survive drought, heat, and cold stress, according to a study in Science.

A Combination of Genetics and Environment Causes Cleft Lip

In a study published in Nature Communications, researchers investigate what combination of genetic and environmental factors come into play to cause cleft lip/palate.