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This Week in PLOS: Jan 14, 2013

A pair of PLOS One studies led by investigators at Duke University describes gene expression signatures in host blood that correspond with specific viral or bacterial infections. For the first of these, researchers tracked down similar, but slightly different, blood gene expression patterns associated with those with symptomatic H1N1 and H3N2 influenza A infection. These gene expression patterns arose prior to the first signs of infection, they say, hinting that such signatures might ultimately prove useful for diagnosing, tracking, or treating infections. In the second paper, meanwhile, members of the same team describe distinct gene expression profiles in humans and mice that differ in Staphylococcus aureus-infected individuals compared to uninfected individuals or individuals infected with another bacterial species.

For more on these studies, check out a related story in our sister publication GenomeWeb Daily News.

Lymphoma samples are more likely to show intermediate levels of cytosine methylation across the genome than the normal B-cells from which these cancers arise, a new PLOS Genetics study suggests. An international team profiled DNA methylation patterns in two common types of lymphoma — follicular lymphoma and diffuse large B-cell lymphomas — and in normal B-cell populations. The comparison uncovered a number of unusual DNA methylation characteristics in the lymphoma samples. For example, researchers report, the lymphomas generally had more heterogeneous methylation levels than the normal B-cell samples. And that was particularly true of the advanced or aggressive lymphoma cases examined.

GWDN also has more on the study here.

Finally, the University of Glasgow's Massimo Palmarini and colleagues from the UK, Italy, and Germany delve into genetic features contributing to virulence in Schmallenberg virus, or SBV. The Orthobunyavirus genus virus, first detected in Germany in 2011, can infect pregnant ruminant animals, leading to congenital malformations in their spontaneously aborted, stillborn, or newborn offspring. The team relied on reverse genetics for the study, looking for sections of the viral RNA genome capable of restoring typical replication and infections patterns in mutated forms of the virus. "This work provides the experimental tools to understand how this newly emerged virus causes disease in ruminants," the authors say in the PLOS Pathogens study. For instance, the approach led investigators to non-structural proteins contributing to SBV virulence in cell lines and mouse models of SBV infection.

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.