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This Week in PNAS: Nov 18, 2014

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 the early edition of the Proceedings of the National Academy of Sciences, researchers from the Salk Institute for Biological Studies, Stanford University, and elsewhere compare and contrast transcriptional patterns in dozens of mouse and human tissue samples. Using deep RNA sequence data generated for up to 15 mouse and human tissues, the team saw some examples of tissue-specific expression profiles that were shared between corresponding tissues from mice and humans. For the most part, though, the transcriptional patterns in tissues from mice tended to cluster together, while human tissues formed their own group. GenomeWeb has more on the study here.

Researchers from China, the US, and Germany present evidence for proteome-wide shifts in the face of changes to the genetic code in the bacterial species Methanosarcina acetivorans. To understand the potential consequences of reducing the number of amino acids an organism can encode, the team developed an M. acetivorans deletion strain that was unable to read the stop codon UAG as pyrrolysine — a coding reassignment and amino acid expansion achieved by an operon present in a miniscule fraction of genomes sequenced so far. The genetic change led to a pronounced shift in the bug's proteome, the study's authors say, and hints that its genetic code has been expanded to offer more carbon source and metabolic options for the organism.

Finally, a group led by investigators at the La Jolla Institute for Allergy and Immunology describe its approach for tracking oxidized methylcytosine (oxi-mCs) marks such as 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine in the genome using a method called diglucosylation, coupled with single-molecule, real-time sequencing. The researchers demonstrated the feasibility of this approach to profile epigenetic patterns and regulation in the fungal species Coprinopsis cinerea. "Our study describes a method to map three species of oxi-mC simultaneously and reveals the colocation of [5-methylcytosine] and oxi-mC at functional elements throughout the C. cinerea genome," they note.

The Scan

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.

DNA Storage Method Taps Into Gene Editing Technology

With a dual-plasmid system informed by gene editing, researchers re-wrote DNA sequences in E. coli to store Charles Dickens prose over hundreds of generations, as they recount in Science Advances.

Researchers Model Microbiome Dynamics in Effort to Understand Chronic Human Conditions

Investigators demonstrate in PLOS Computational Biology a computational method for following microbiome dynamics in the absence of longitudinally collected samples.

New Study Highlights Role of Genetics in ADHD

Researchers report in Nature Genetics on differences in genetic architecture between ADHD affecting children versus ADHD that persists into adulthood or is diagnosed in adults.