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This Week in PLOS: Dec 29, 2014

In PLOS One, Belgian researchers describe bacterial communities found at three freshwater reservoirs with varying alkalinity levels and carbon contents. Based on 16S ribosomal RNA gene sequencing information and other data generated from samples collected at freshwater reservoir sites in Belgium over several time points over a year, the team considered bacterial community composition patterns in the context of physical and chemical features found at each reservoir during these sampling events. "Our results evidence that the retrieved [bacterial community composition] in the analyzed reservoirs was strongly influenced by pH, alkalinity, and organic carbon content," the researchers write, "whereas comparatively little change was observed among layers in stratified conditions."

An Uppsala University-led team took a look at the transcriptomic and proteomic patterns in bone marrow and related lymphohematopoietic samples representing spleen, appendix, and lymph node tissues for another PLOS One paper. Based on RNA sequence data for more than 20,000 genes in 95 lymphohematopoietic tissue samples, the researchers identified nearly 700 genes showing higher-than-usual expression in at least one of the tissue types. Together with proteomic profiles generated using in situ affinity-based methods, the transcriptomic signatures offered hints to understanding tissue-specific expression features in the lymphohematopoietic system.

A 233-gene signature seems to coincide with the risk of late recurrence in individuals treated for hepatocellular carcinoma, according to a study by researchers from the US and Korea in PLOS Medicine. Starting with matched tumor and normal samples from 72 individuals with hepatocellular carcinoma, the team used array-based expression profiling to narrow in on genes showing altered expression in patients with late recurrence — a signature it subsequently validated in hundreds more individuals treated for the disease. The study's authors also did further analyses on a 65-gene signature implicated in early recurrence in hepatocellular carcinoma, concluding that the "[t]wo independently developed predictors reflected well the differences between early and late recurrence of [hepatocellular carcinoma] at the molecular level and provided new biomarkers for risk stratification."

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.