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PNAS Papers on Metagenomic Pathogen Monitoring, Iberian Lynx, Epigenetic MRI

Editor's Note: Some of the articles described below are not yet available at the PNAS site but are scheduled to be posted this week.

Researchers at the National Institute of Allergy and Infectious Diseases and other centers in the US and Cambodia describe a metagenomics-based pathogen monitoring system used to find fever-causing pathogens in Cambodia. Using metagenomic RNA sequencing, along with an open-source bioinformatics method called IDseq on the CZID cloud-based platform, the team screened 489 blood serum samples from 464 individuals treated for fever at hospitals or community sites from the spring of 2019 to the fall of 2020, identifying pathogens in 203 cases. Along with dengue virus, which was detected in 138 samples, the authors saw pathogens ranging from Plasmodium knowlesi to chikungunya virus. "This study is a 'real world' example of the use of [metagenomic next-generation sequencing] surveillance of febrile individuals, executed in-country, to identify outbreaks of vector-borne, zoonotic, and other emerging pathogens in a resource-scarce setting," they write.

A team from Spain, Russia, Poland, and France compare deleterious mutation burdens in the highly endangered Iberian lynx (Lynx pardinus) and its more common sister species, the Eurasian lynx (Lynx lynx). Based on whole-genome sequences of 20 Iberian lynx and 28 Eurasian lynx, the investigators saw signs of "genetic purging" in both Iberian lynx populations considered, as evidenced by lower-than-usual deleterious allele burdens stemming from selection against recessive deleterious variants. That selection seemed to be less pronounced in certain parts of the Iberian lynx genome, including centromeres and the X chromosome. "Beyond adding to the ongoing debate on the relationship between deleterious burden and population size, and on the impact of genetic factors in endangered species variability," they write, "this work contributes a whole-genome catalog of deleterious variants, which may become a valuable resource for future conservation efforts."

University of Illinois at Urbana-Champaign researchers report on a non-invasive DNA methylation imaging approach called epigenetic MRI (eMRI), which combines magnetic resonance spectroscopic imaging with diet-based DNA methylation labeling. For its proof-of-principle analyses, the team used eMRI to map DNA methylation in the brain hemispheres of pigs fed a 13C-methionine-rich diet. "Significant eMRI signal differences were observed in animals fed with enriched diet for different numbers of days, demonstrating the dynamic nature of this signal," the authors note. "Given the non-invasiveness of our method, these results provide a path toward a global DNA methylation brain imaging paradigm for humans."

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