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This Week in PNAS: Sep 22, 2009

This week in the Proceedings of the National Academy of Sciences, scientists at the Ludwig Institute for Cancer Research in Sao Paulo have used bioinformatics to build the human cell surfaceome. From this catalog of 3,702 cell surface transmembrane proteins, they were able to look at gene expression differences to find surfaceome genes that could be possible tumor targets, 593 of which they validated using qPCR. They identified several candidates as potential diagnostic and therapeutic targets for colorectal tumors and glioblastoma.

Boston University researchers led work that cataloged all triplet repeats in genic regions in the human genome, showing a bias in noncoding DNA repeat lengths. Among other things, they found that for short repeats, there is a low rate of repeat-length polymorphisms in exons and "somewhat surprisingly, in introns," they say, adding that their repeat assay "could someday complement SNP arrays for producing tests that assess the risk of an individual to develop a disease, or become part of personalized genomic strategy that provides therapeutic guidance with respect to drug response."

In work out of Jonathan Eisen's lab at the University of California, Davis, scientists looked at how the human gut microbiome changes after small bowel transplantation. Using qPCR on the bacteria from the small bowel lumen of 17 small bowel transplant patients, they found that the microbial community shifts from being dominated by the anaerobic Bacteroides and Clostridia bacteria to Lactobacilli and Enterobacteria, which can be either anaerobic or aerobic.

Finally, an editorial from NIH's Alan Guttmacher, Elizabeth Nabel, and Francis Collins makes the case for data-sharing policies. "The model of the investigator owning data has been increasingly replaced by one in which society owns data," they write. While access to data is beneficial to research as a whole, policies should be improved upon and policed in order to protect the rights of researchers and participants. They highlight NIH's Policy for Sharing of Data Obtained in NIH Supported or Conducted Genome-Wide Association Studies.

The Scan

Alzheimer's Risk Gene Among Women

CNN reports that researchers have found that variants in MGMT contribute to Alzheimer's disease risk among women but not men.

Still Hanging Around

The Guardian writes that persistent pockets of SARS-CoV-2 in the body could contribute to long COVID.

Through a Little Spit

Enteric viruses like norovirus may also be transmitted through saliva, not just the fecal-oral route, according to New Scientist.

Nature Papers Present Method to Detect Full Transcriptome, Viruses Infecting Asgard Archaea, More

In Nature this week: VASA-seq approach to detect full transcriptome, analysis of viruses infecting Asgard archaea, and more.