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PNAS Studies Describe Adipocyte Subtypes, Plant Expressome Analysis, More

Researchers from the University of Massachusetts and the University of Copenhagen describe four human adipocyte fat cell subtypes, along with the corresponding mesenchymal progenitor cells giving rise to them. Using RNA sequencing, the team profiled gene expression patterns in mesenchymal progenitor cells generated at different stages of differentiation in the lab, uncovering four specialized adipocyte subtypes that showed distinct tissue functions in follow-up experiments. "Recognizing the existence of these different adipocyte subtypes and their progenitors will allow us to elucidate mechanisms that control their abundance and properties," they say, "and to better understand how dysregulation of these mechanisms can lead to metabolic disease." 

A team from the University of Minnesota presents a computational approach for improving plant genome annotation, distinguishing expressed transcripts, or the "expressome," from pseudogenes or gene fragments shuttled around the genome by transposable elements. After using available transcriptome and proteome profiles to train their random forest algorithm — based on machine learning on epigenetic marks in the genome — they demonstrated that gene body cytosine methylation marks or histone changes could accurately sort genes with messenger RNA expression, protein expression, or both in the maize reference genome and other inbred maize lines. "Our new method uses only epigenomic patterns to classify the expression potential of annotated genes and identifies pseudogenes that are difficult to classify based solely on sequence," they write. 

Researchers at the Georgia Institute of Technology and elsewhere profile the genes that appear to be essential for the Aggregatibacter actinomycetemcomitans oral pathogen when it infects mice in combination with other oral microbes or with microbes not normally found in that environment. The team's transposon sequencing experiments suggest A. actinomycetemcomitans relies on roughly one-third of its genome — and dozens of core genes — to maintain fitness when growing in mouse abscesses that contain other microbes. Other genes appeared to be essential for A. actinomycetemcomitans bugs found during co-infection, particularly in the presence of "sympatric" microbes from the same natural environment. On the other hand, presence of "allopatric" microbes not typical to the oral environment appeared to ease the need for other A. actinomycetemcomitans genes during coinfection, the authors note, hinting that "some allopatric microbes can drastically alleviate gene essentialities" for the oral pathogen.