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Nature Papers Present Genomic Analysis of Bronze Age Mummies, Approach to Study Host-Pathogen Interactions

A genome-wide analysis of Bronze Age mummies discovered in Xinjiang, China appears in Nature, highlighting their local origin. The Tarim Basin mummies were discovered in the early 20th century and their unique appearance has led to debate over where they originated. To solve the question, a team led by researchers from Seoul National University analyzed genomic DNA of 13 of the mummies, dating to around 2100 to 1700 BC, as well as five mummies dating to around 3000 to 2800 BC from the nearby northern Dzungarian Basin. They find that the Dzungarian mummies' ancestry was largely from populations in southern Siberia with some local genetic influences, while the Tarim mummies only had local ancestry. Milk proteins found within deposits on the teeth of seven of the Tarim mummies also suggests that this population relied on dairy farming. The findings, the scientists write, suggests that the Tarim mummies belonged to a genetically isolated local population, although one that maintained ties with neighboring herder and farmer populations. GenomeWeb has more on this, here.

A new technique for studying the genomics of host-pathogen interactions at the single-cell level is reported in Nature Biotechnology this week. Called Perturb-seq, the scalable approach combines CRISPR-based genetic perturbations with rich phenotypic profiling by single-cell transcriptomics. The University of California, San Francisco, scientists who developed the method use it to examine the functional contributions of individual viral and host factors involved in human cytomegalovirus infection in primary human fibroblasts, recording the transcriptomes of tens of thousands of CRISPR-modified single cells. They identify host restriction factors and dependency factors critical for viral entry and for progression from early to late stages of infection. They also show that targeting key viral factors derails the viral gene expression program in specific ways. "Taken together, our findings reveal a dichotomy between the roles of host and viral factors, with the set of viral factors solely defining the trajectory of infection and host factors creating the environment permitting the execution of that program," the researchers write. "More generally, we envision that our approach of single-cell functional genomics can serve as a blueprint for studying other viruses and can define their vulnerabilities to genetic or pharmacological intervention." GenomeWeb also covers this, here.

The Scan

Looking for Omicron

NPR reports that SARS-CoV-2 testing in the US has gotten better but also that some experts say more needs to be done to better track the Omicron variant.

Holmes Alleges Abuse

The Associated Press reports that Theranos' Elizabeth Holmes has testified at her wire fraud trial that her business and romantic partner abused her.

Bit More Diverse, But More to Do

While Black and Hispanic patients are more likely to participate in cancer clinical trials than previously, they are still underrepresented, according to US News & World Report.

PNAS Papers on Yeast Gene Silencing, Zika Virus Inhibition, Immunoglobulin Hypermutation

In PNAS this week: gene silencing in Saccharomyces cerevisiae, possible neuroprotective role for SHFL in a mouse model of Zika virus infection, and more.