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This Week in Nature: Jan 8, 2015

In Nature Genetics this week, an international team of researchers report on the use of a transposon mutagenesis screen in mice to identify genes and evolutionary forces driving the progression of colorectal cancer. They also discovered a set of genes that appear to be important for malignant tumor progression and a new human colorectal cancer suppressor gene that could potentially be involved in other cancers.

Over in Nature Methods, University of Washington investigators described a new single-volume, site-directed mutagenesis approach based on microarray-programmed oligonucleotides. The approach — called programmed allelic series, or PALS — combines low-cost, microarray-based DNA synthesis with overlap-extension mutagenesis to introduce only a single mutation per cDNA template in a massively parallel fashion. Using the approach, the group generated libraries including nearly all missense mutations as singleton events for the yeast transcription factor Gal4 and the human tumor suppressor gene p53. GenomeWeb also covers this study here.

In the new Nature Plants, a research group led by University of Denmark researchers describes using an analysis of DNA sequences of ancient and modern maize samples to determine that the plant was originally introduced into the US from Mexico where it was domesticated via a highland route over the Sierra Madre Mountains. The findings settle a long-standing archaeological debate and show the potential of paleogenomics to uncover the details of domestication. GenomeWeb has more on this study, here.

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.