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Science Papers on Approach to Isolate DNA from Sediment, Algorithm to Construct Signaling Networks

A team led by scientists from the Max Planck Institute report in Science this week a new technique for obtaining and studying nuclear DNA from sediment, enabling the use of trace amounts of ancient DNA for research. Although mitochondrial DNA from archaic humans is often retrieved from cave sediments, it has little value for studying population relationships since it only carries information about the maternal lineage. Nuclear DNA is far more informative, but its retrieval in sufficient quantities from sediment is challenging. To address this, the researchers developed a method to retrieve, enrich, and study nuclear DNA from cave sediment that involves using hybridization capture to target regions in the nuclear genome with high mammalian sequencing diversity. They demonstrate the method by applying it to cave deposits from western Europe and southern Siberia that are between 200,000 years and 500,000 years old. GenomeWeb has more on this here.

An algorithm that enables the de novo construction of cell type-specific signaling networks using single-cell transcriptomic data is described in Science Advances this week. Called CytoTalk, the algorithm creates an integrated network consisting of intracellular and intercellular functional gene interactions from which candidate pathways are identified using the prize-collecting Steiner forest algorithm. CytoTalk's developers benchmark the algorithm's performance using high-throughput spatial transcriptomic data and single-cell RNA sequencing data with receptor gene perturbation and use it to perform a comparative analysis of signaling networks between macrophages and endothelial cells across human adult and fetal tissues.

The Scan

J&J Booster Support

A US Food and Drug Administration advisory panel has voted to support a booster dose of Johnson & Johnson's SARS-CoV-2 vaccine, according to the Los Angeles Times.

To Keep the Cases Moving

The president of the UK Royal College of Pathologists tells the Financial Times that more investment is needed to tackle a backlog of cases.

NAS Expels Archaeologist

Science reports Luis Jaime Castillo Butters' expulsion is the first of an international member from the US National Academy of Sciences.

PLOS Papers on Angelman Syndrome-Like Cases, Salmonella Paratyphi A, SARS-CoV-2 in Brazil

In PLOS this week: exome sequencing analysis of Angelman syndrome-like cases, genetic epidemiology of Salmonella Paratyphi A, and more.