In PLoS Genetics, a paper links genetic and fossil data. Robert Meredith from the University of California, Riverside, is first author on work that sequenced most of the protein-coding region of the enamelin gene in four different orders of placental mammals that lack teeth or have teeth without enamel. In all cases, they found frameshift mutations and/or stop codons that result in a mutated, dysfunctional form of the enamelin protein. The work, they say, "provides manifest evidence for the predictive power of Darwin's theory." Bloggers chime in here and here.
Steve Hoffmann at the University of Leipzig led a study appearing in PLoS Computational Biology that developed a computational approach to fast map short-read sequences that can handle mismatches, insertions, and deletions. The authors say their method makes use of enhanced suffix arrays and it maps more reads and achieves higher recall rates than previous methods, including for 454 and Illumina reads. The software can be found here.
DNA2.0 scientists have led work that found enhanced design parameters to optimize protein expression from synthetic genes. To find sequences that affect protein expression, they synthesized two sets of 40 genes encoding two commercially valuable proteins and expressed them in E. coli. "The amount of protein produced in E. coli was strongly dependent on the codons used to encode a subset of amino acids," they write in the abstract, and that this dependency has a biochemical base. Their work appears in PLoS One today.
Finally, an article from the editors of PLoS Medicine breaches the subject of ghostwriting, and what can be done about it. "It's time to get serious about tackling ghostwriting," they write. While preventing the practice is ultimately the goal, journals should set down strict rules if a case does come up. "For example, if nothing is declared on submission but inappropriate involvement of a medical writer subsequently comes to light, any papers where this breach is substantiated should be immediately retracted and those authors found to have not declared such interest should be banned from any subsequent publication in the journal and their misconduct reported to their institutions," they write.