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This Week in PLOS: Dec 8, 2014

In PLOS Genetics, researchers from the US Department of Agriculture Forest Service and elsewhere report on findings from their effort to characterize the genome, transcriptome, and secretome of Phlebiopsis gigantea, a white-rot fungus from the Agaricomycetes fungal class that can successfully set up shop in conifer material containing compounds that deter most other fungal species. Using a combination of sequencing and mass spectrometry, the team took a look at the fungus' genome sequence, expressed transcripts, and secreted compounds, comparing them to related species and considering the effects of pine extract on the pathogen's gene expression patterns.

A PLOS Neglected Tropical Disease study outlines improvements and upgrades to the original draft genome assemblies for Paracoccidioides, dimorphic fungal pathogen species that cause a South American tropical disease known as paracoccidioidomycosis. A team from Colombia and the US did deep Illumina genome re-sequencing on three strains of Paracoccidioides fungus, representing two different species. By incorporating this data into existing Sanger assemblies, the researchers were able to re-annotate the genomes and establish improved predictions about the pathogens' genes and transcripts, including those suspected of contributing to virulence.

Genetic patterns in a population of non-migratory humpback whales found in the Arabian Sea suggests the animals have low genetic diversity and high levels of isolation from other humpback whales. As they say in PLOS One, researchers from the US, Portugal, Oman, and elsewhere profiled microsatellite and mitochondrial sequences in tissue samples from 67 humpback whales in the Arabian Sea. Through comparisons with existing data on humpback whales in the Southern Hemisphere and North Pacific, the team estimates that the Arabian Sea population shares ancestry with humpback whales in the Southern Ocean, though it appears to have been isolated for up to 70,000 years. Based on the low levels of genetic diversity, limited population size, and potential environmental threats, the study's authors argue in favor of classifying the population as critically endangered rather than endangered (its current designation on the International Union for Conservation of Nature Red List).

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.