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This Week in Science: Oct 9, 2015

In this week's Science, a multi-institute team of researchers reports the successful sequencing of the full genome of an ancient African, revealing new details about the origin of current African populations. By sequencing DNA obtained a bone from a skeleton of a man discovered in the Southern Ethiopian highlands who lived about 4,500 years ago, prior to a wave of Eurasian backflow into Africa. Using this ancient Ethiopian genome as a reference, the researchers found that this Eurasian backflow came from a population closely related to Early Neolithic farmers who colonized Europe about 4,000 before. The researchers also determined that the backflow extended into Central, Western, and Southern Africa, affecting populations that were previously thought to be relatively unadmixed. GenomeWeb has more on this study here.

Also in Science, a group of European investigators publishes data showing that alterations in histone methylation during sperm formation in a single generation can result in developmental abnormalities and reduced survival in offspring up to three generations later. The scientists altered mice to overexpress a human protein that removes methyl groups from the histone H3K4me2. A significant portion of the offspring whose fathers overexpressed the protein had higher than normal rates of birth defects, neonatal mortality, and altered gene expression — effects that were observed for three generations even when subsequent generations bred with animals with normal histone methylation, while an RNA analysis revealed widespread RNA misregulation.

And in Science Translational Medicine, a group of industry and academic researchers present details about the use of high-throughout genomic sequencing to diagnose cutaneous T cell lymphoma (CTCL), a blood cancer that causes skin tumors but also rashes that are commonly misdiagnosed as benign inflammation. The scientists used high-throughput sequencing to analyze T cell receptor genes from blood and skin tissue samples of 46 CTCL patients, as well as skin samples from healthy individuals and patients with psoriasis, eczema, and other non-cancerous inflammatory skin diseases. The technique was able to distinguish the cancer CTCL from the other conditions in all of the cancer patients, while a PCR approach was only able to make the correct diagnosis in about 70 percent of cases and often missed early-stage tumors. In a related editorial, two Yale scientists discuss the promise and challenges of using high-throughput sequencing as a clinical diagnostic. GenomeWeb has more on this 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.