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This Week in PLoS: Aug 10, 2009

Harvard's Stuart Shieber has penned an article for PLoS Biology this week arguing for leveling the playing field for open access journals. He says that this "inequity" can be remedied with a simple, cost-effective system. He writes: "To mitigate this problem – to place open-access processing-fee journals on a more equal competitive footing with subscription-fee journals – requires those underwriting the publisher's services for subscription-fee journals to commit to a simple 'compact' guaranteeing their willingness to underwrite them for processing-fee journals as well."

In PLoS Genetics, Cornell's Carlos Bustamante and Andrew Clark led a study that looked at polymorphisms in the noncoding genome in order to see how these affect the evolution of gene regulation. They resequenced candidate cis-regulatory regions spanning more than 15,000 genes in 15 African Americans and 20 European Americans and aligned them back to the chimp genome, finding that there is a "general pattern of selective constraint on conserved non-coding sites in the flanking regions of genes," they say. "Overall we find that natural selection has played an important role in the evolution of candidate cis-regulatory regions throughout hominid evolution."

Texas A&M University's Huijie Hou was first author on a paper published this week in PLoS One that developed a microbial fuel cell array, which is a "compact and user-friendly platform for the identification and characterization of electrochemically active microbes." The array houses 24 chambers that act as 24 independent fuel cells. Using the array to screen environmental microbes, they were able to test their system by identifying an isolate that was related to Shewanella putrefaciens IR-1 and Shewanella sp. MR-7.

Finally, computational biologists from GSK, Guanghui Hu and Pankaj Agarwal, have created a human disease-drug network from gene expression profiles. From the approximately 7,000 public transcriptomic profiles, they developed a network of 170,027 "significant interactions," including 645 disease-disease, 5,008 disease-drug, and 164,374 drug-drug relationships. Among the disease-drug links, they say, "connections with negative scores suggest new indications for existing drugs ... while the positive scoring connections can aid in drug side effect identification." Their paper was published in PLoS One.

The Scan

Gone, But Now Reconstructed SARS-CoV-2 Genomes

In a preprint, a researcher describes his recovery of viral sequences that had been removed from a common database.

Rare Heart Inflammation Warning

The Food and Drug Administration is adding a warning about links between a rare inflammatory heart condition and two SARS-CoV-2 vaccines, Reuters reports.

Sandwich Sampling

The New York Times sent tuna sandwiches for PCR analysis.

Nature Papers Describe Gut Viruses, New Format for Storing Quantitative Genomic Data, More

In Nature this week: catalog of DNA viruses of the human gut microbiome, new dense depth data dump format to store quantitative genomic data, and more.