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This Week in Genome Biology: Apr 22, 2015

Using arrays and 16S ribosomal RNA gene sequencing, researchers from the US and Canada investigated host gene expression and microbial community members present in individuals with ulcerative colitis who developed a form of intestinal inflammation called pouchitis after surgery for their condition. From 255 samples collected from more than 200 individual treated for ulcerative colitis, the team found that transcripts expressed in host intestinal tissue tended to coincide with inflammation status, the site biopsied, and the presence or absence of microbes from a handful of groups. On the other hand, the microbial species present appeared to be more strongly influenced by antibiotic use.

Researchers from the University of Liverpool and elsewhere describe findings from a genome sequencing study of the liver fluke, Fasciola hepatica, a damaging livestock pathogen that also infections humans in some parts of the world. The new draft genome assembly — coming in at around 1.3 billion bases — contained an estimated 22,676 protein-coding genes and did not show signs of widespread duplications or repeat expansions. Through resequencing, transcriptome sequencing, and so on, the team got a glimpse at the liver fluke's genetic diversity and biology, including the gene expression changes that mark its progression from an infected host gut to the liver.

A Japanese team used single-cell RNA sequencing to follow drug response patterns in cells from various lung adenocarcinoma cell lines before and after treatment with a tysosine kinase inhibiting drug called vandetanib. When they sequenced transcripts in more than 300 individual cells from seven lung cancer cell lines, the researchers found that vandetanib treatment typically led to more uniform expression of housekeeping genes from one cell to the next. In contrast, the expression patterns for genes targeted by the drug, such as EGFR, appeared more apt to remain diverse between cells.