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This Week in PNAS: Sep 18, 2012

Using the 18S ribosomal DNA gene as a barcode when looking at environmental samples may miss some members of the communities being tested, according to a study in the early, online edition of the Proceedings of the National Academy of Sciences this week by researchers based in the UK, Italy, Germany, and the US. In particular, authors of the study argue that the 18S marker underestimates the diversity of so-called meiofauna — microscopic invertebrate animals. In contrast, they say, cytochrome C oxidase subunit I, or COI, gene sequences would serve as a better marker for these creatures. In their analyses, for instance, the COI marker bumped up the detectable meiofauna diversity by a factor of more than seven-fold. "We conclude that taxonomic entities estimated from analyses using 18S are not reliable proxies for diversity and very likely underestimate true species richness," the team wrote.

A research team from Massachusetts and Maryland used array-based transcriptome profiling to explore the genetic basis of a progressive neuromuscular condition called facioscapulohumeral muscular dystrophy, or FSHD. By testing bicep and deltoid muscle biopsy samples from dozens of individuals with FSHD and almost as many unaffected relatives of those subjects, the team tracked down hundreds of genes showing expression shifts in those with FSHD. Of those, 29 genes were differentially expressed in both bicep and deltoid muscle samples, the researchers report. And, they found expression levels at 15 genes could distinguish between bicep samples from those with or without the disease around 90 percent of the time in follow-up experiments. The accuracy was closer to 80 percent when classifying deltoid tissue based on expression of these genes. Those involved in the study say such a 'molecular signature' of FSHD could help in understanding the disease and in testing new treatments for it.

In another study slated to appear online this week in PNAS, Indiana University researchers describe the whole-genome sequencing strategy that they used to not only estimate the spontaneous mutation rate in Escherichia coli, but also to assess the nature of these mutations. The investigators tested wild type E. coli grown over hundreds of thousands of generations. They also evaluated an E. coli mutant with defects to its functional mismatch repair pathway. In the absence of a fully functional MMR pathway — the system usually used to fix errors that crop up during replication — mutation rates in E. coli were elevated more than 100 times and frequently involved swaps from adenine and thymine nucleotides to guanine and cytosine residues, the team found. In contrast, wild type bugs were more prone to G-C to A-T changes and had a somewhat lower-than-anticipated mutation rate.

The Scan

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Arranged Killing, Fraud Alleged by Prosecutors

The Wall Street Journal reports that prosecutors allege that the co-founder of a biotech arranged to have a business associate who threatened to expose him as a fraud killed.

Whirlwind Decade of CRISPR

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PNAS Papers on Blue Cone Monochromacy Structural Variants, HIV-1 Mutant, T-ALL

In PNAS this week: structural variants linked to blue cone monochromacy, HIV-1 variants affecting the matrix protein p17, and more.