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This Week in PNAS: Mar 17, 2009

In early online publication this week, scientists used microfluidic cards to profile miRNA expression in kidney transplants. They profiled seven renal allograft biopsies against 365 miRNAs and performed control expression analysis on 26 other transplants, finding a strong association between intragraft expression of both miRNAs and mRNAs and that acute rejection "could be predicted with a high level of precision using intragraft levels of miRNAs," they write in the abstract. "miRNA expression patterns may serve as biomarkers of human renal allograft status."

Australian researchers have characterized cytochrome P450 genes in the fruit fly. Looking at P450 expression patters in D. melanogaster embryos and two stages of third instar larvae, they identified many expressed in the fat body, Malpighian tubules, and in regions of the midgut, and other P450s expressed in organs such as the gonads, corpora allata, oenocytes, hindgut, and brain. When they combined this expression data with RNAi screens, they were able to distinguish candidate P450s that play a role in developmental processes from those that take part in detoxification.

Published last week, Italian and French scientists developed a computational method for the genome-wide identification of transcription factor binding sites based on positional weight matrices, comparative genomics, and gene expression profiling. When they applied the method to Stat3 and validated using chIP, they found 12 of the 14 tested sites bound by Stat3 in vivo, and in the end identified nine Stat3 transcriptional targets.

Work led by Scripps' Gary Siuzdak that was published online in February but appeared in print last week used metabolomics to study the effects of the gut microbiome on blood metabolites in mammals. Comparing germ-free mice with normal, they found the microbiomes differed significantly. Using various MS-based methods, they found amino acid metabolites to be especially affected. "A broad, drug-like phase II metabolic response of the host to metabolites generated by the microbiome was observed, suggesting that the gut microflora has a direct impact on the drug metabolism capacity of the host," they write in the abstract.

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.