Editor's Note: Some of the articles described below are not yet available at the PNAS site, but they are scheduled to be posted some time this week.
In a study slated to appear in the early, online edition of the Proceedings of the National Academy of Sciences this week, researchers from the US and Egypt report on findings from a metabolism-centered study of previously sequenced Escherichia coli strains. Using existing genome sequence data for dozens of E. coli and Shigella strains, the team came up with genome-level metabolic models that subsequently offered clues to understanding E. coli growth capabilities in hundreds of different conditions. Using a dozen of the genome-scale models, for instance, the study authors predicted growth in six nutritional regimens in ways that corresponded to experimental outcomes around 80 percent of the time.
A team led by investigators at the Salk Institute for Biological Studies and the J. Craig Venter Institute describe a scheme for sequencing RNA from individual nuclei. Using single nuclei originating from either mouse neural progenitor stem cell lines or mouse hippocampal tissue, the investigators showed that it was possible sequence low levels of messenger RNA and pick up transcripts coinciding with more than 16,000 genes. They also saw gene expression patterns that appeared to jibe with those found in mouse cells. Based on their results to date, the study's authors argue that the single nucleus approach to transcriptome sequencing "will be useful for analysis of processes occurring in the nucleus and for gene expression studies of highly interconnected cells such as neurons."
Finally, University of Michigan researchers highlight methylation shifts and changes in methylation-related gene expression in so-called Müller glia cells from zebrafish regenerating retinal tissue after injury. In particular, their analysis points to enhanced demethylation during early stages of Müller glia reprogramming to a progenitor cell state, followed by a rise in new methylation events in subsequent stages of the process. "Our data identify a dynamic DNA methylation landscape as zebrafish [Müller glia] transition to an [Müller glia progenitor cells]," they write, "and suggest that DNA methylation changes will complement other regulatory mechanisms to ensure gene expression programs controlling [Müller glia] reprogramming are appropriately activated during retina regeneration."