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This Week in PLoS: Feb 15, 2011

The Netherlands Cancer Institute's Laura Van't Veer and her colleagues used whole-genome cDNA-mediated annealing, selection, extension, and ligation — or DASL — on 20 matched tissue samples to show in this week's PLoS One that "gene expression profiles from formalin fixed paraffin embedded breast cancer tissue are largely comparable to fresh frozen matched tissue." When properly processed, Van't Veer et al. write, FFPE breast cancer samples "are comparable to data extracted from the FF counterpart," which in effect "opens up the possibility of using both ... in gene expression analyses, leading to a vast increase in the potential resources available for cancer research," they add.

In PLoS Biology this week, Michael Eisen and his colleagues at the University of California, Berkeley, report that a system of early zygotic dosage compensation in Drosophila causes "nearly identical transcript levels for key X-linked developmental regulators," such as giant, brinker, buttonhead, and short gastrulation in both male and female fly embryos. By characterizing Drosophila embryo transcriptomes according to stage and sex and measuring genome-wide mRNA abundance, the team found "limited sex-specific zygotic transcription, with a weak tendency for genes on the X to be expressed at higher levels in females," and, overall, "widespread dosage compensation prior to the activation of the canonical MSL [protein]-mediated dosage compensation system."

Over in PLoS Genetics, a team led by investigators at Tufts University shows that, beyond its role in sister chromatid cohesion, Ctf-RFC functions to preserve genome stability through "lesion bypass by replication forks and post-replication repair," among other mechanisms in a yeast model. The team first performed single-cell analyses on Ctf18-RFC Saccharomyces cerevisiae mutants and found that Ctf18-RFC acts to preserve genome stability.

A team led by researchers at the University of Wisconsin-Madison reports its use of 454 sequencing to map the leaf-cutter ant, Atta cephalotes, genome, which it says "reveals insights into its obligate symbiotic lifestyle." For example, it may have "undergone genetic modifications that reflect its obligate dependence on [a specialized, mutalistic] fungus for nutrients." Our sister publication GenomeWeb Daily News has more on the leaf-cutter ant genome, here.

The Scan

Self-Reported Hearing Loss in Older Adults Begins Very Early in Life, Study Says

A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.

Genome-Wide Analysis Sheds Light on Genetics of ADHD

A genome-wide association study meta-analysis of attention-deficit hyperactivity disorder appearing in Nature Genetics links 76 genes to risk of having the disorder.

MicroRNA Cotargeting Linked to Lupus

A mouse-based study appearing in BMC Biology implicates two microRNAs with overlapping target sites in lupus.

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.