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This Week in PLoS: Dec 2, 2008

This week in PLoS, researchers led by Judith Campisi used antibody arrays to analyze proteins secreted by senescent cells. They found that this secretory phenotype includes inflammatory and tumorigenic elements that are induced by genotoxic stress. They also identified two malignant phenotypes, epithelial–mesenchyme transition and invasiveness, promoted by senescent cells and found that oncogenic RAS or the loss of p53 function amplifies the senescent phenotype. Abel Pharmboy posts an interview with one of the researchers, Chris Patil, on his blog. There, Patil says, "For me, these results have really driven home the intimate connection between cancer and aging."

European Bioinformatics Institute's Joern Toedling and Wolfgang Huber have an educational piece in PLoS Computational Biology, walking readers through how to use Bioconductor to analyze ChIP-chip data including determining data quality, how to visualize the data, and finding ChIP-enriched regions. "As with any high-throughput technology, there are aspects of ChIP-chip experiments that need close attention, such as specificity and sensitivity of the antibodies, and potential cross-hybridization of the microarray reporters," Toedling and Huber write.

A review by Australian researchers discusses the challenges in differentiating protein-coding and noncoding RNA. They go through a variety of strategies such as comparing open reading frame length or conservation, as well as structural and experimental approaches. They also wonder if this is a false dichotomy. "Looking ahead, we must also be prepared to cast off our historical biases toward what appears now to be an increasingly false dichotomy, and instead embrace the likelihood that RNA is a molecular multi-tasker," they write.

Cedric Chauve and Eric Tannier developed a model-free computational method for paleogenomics studies that determines ancestral genome structure based on physical mapping techniques. They applied their framework to mammalian genome datasets and their results coincide with cytogenetic studies.

A paper in PLoS Genetics reports on a genome-wide association study of 363 metabolites found in human serum from 284 men. The researchers saw that SNPs are associated with many of the differences seen in metabolic homeostasis, accounting for up to 12 percent of the variance. They also found four variants in enzyme genes and traced the pathway their corresponding metabotype affected. "Metabolomics delivers its promise of providing access to functionally relevant endpoints in the framework of GWA studies, and thereby opens new avenues for a functional investigation of the role of gene-environment interactions in the etiology of complex diseases," the authors write.

 

The Scan

NFTs for Genome Sharing

Nature News writes that non-fungible tokens could be a way for people to profit from sharing genomic data.

Wastewater Warning System

Time magazine writes that cities and college campuses are monitoring sewage for SARS-CoV-2, an approach officials hope lasts beyond COVID-19.

Networks to Boost Surveillance

Scientific American writes that new organizations and networks aim to improve the ability of developing countries to conduct SARS-CoV-2 genomic surveillance.

Genome Biology Papers on Gastric Cancer Epimutations, BUTTERFLY, GUNC Tool

In Genome Biology this week: recurrent epigenetic mutations in gastric cancer, correction tool for unique molecular identifier-based assays, and more.