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PNAS Studies on Belgian Neanderthals, Great Dane Genome, HIV Latency-Promoting Agent Screen

A University of Oxford-led team presents evidence suggesting Neanderthals may have vanished from northwestern Europe much earlier than estimated from prior radiocarbon dating analyses on collagen samples in Belgium, which put Neanderthal disappearance there at around 23,880 years ago. With the help of a compound-specific radiocarbon analysis (CSRA) to remove soil contaminants, the investigators re-dated samples from four of the nine Belgian caves where relatively young Neanderthal samples have been reported in the past. Together with mitochondrial DNA genome sequence data from a femur sample at the Fonds-de-Forêt cave, the CSRA data suggested that Neanderthals persisted at the Belgian caves until around 40,600 to 44,200 years ago. "Our data contribute significantly to refining models for Neanderthal disappearance in Europe and, more broadly, show that chronometric models regarding the appearance or disappearance of animal or hominin groups should be based on radiocarbon dates obtained using robust pre-treatment methods," the authors report.

Researchers at the University of Michigan, Bowling Green State University, and other centers in the US and France outline findings from a new genome assembly for the Great Dane. Using a combination of Pacific Biosciences long-read and Illumina short-read sequencing technologies, the team put together a 2.3-gigabase pair genome assembly for a female Great Dane, identifying almost 22,200 predicted protein-coding genes and more than 7,000 long non-coding RNAs in the new pooch genome. When they compared the assembly to a reference genome called CanFam, developed using sequences from a dog in the Boxer breed, the authors filled in sequence gaps in the CanFam3.1, tracked down tens of thousands of small insertions and deletions, and continued to characterize mobile element and other patterns in the broader dog genome. "Our analysis provides a more complete view of the canine genome," they argue, "and demonstrates that the distribution of extremely GC-rich sequences and the activity of mobile elements are major factors affecting the content of canine genomes."

A team from the University of Illinois at Urbana-Champaign shares findings from a drug screen focused on finding potential HIV treatments that promote latency in infected T cells. The researchers used time lapse microscopy to screen for gene expression shifts in a cell line infected with a fluorescently tagged HIV-containing vector, which was independently exposed to more than 1,800 drug compounds. From there, they focused in on a handful of apparent latency-promoting agents (LPAs) for further analysis, uncovering two more LPAs with functional analog experiments. "The LPAs presented here may provide new strategies to complement antiretroviral treatments," the authors write, adding that similar gene expression noise-based screening "holds the potential for drug discovery in other diseases."

The Scan

Gone, But Now Reconstructed SARS-CoV-2 Genomes

In a preprint, a researcher describes his recovery of viral sequences that had been removed from a common database.

Rare Heart Inflammation Warning

The Food and Drug Administration is adding a warning about links between a rare inflammatory heart condition and two SARS-CoV-2 vaccines, Reuters reports.

Sandwich Sampling

The New York Times sent tuna sandwiches for PCR analysis.

Nature Papers Describe Gut Viruses, New Format for Storing Quantitative Genomic Data, More

In Nature this week: catalog of DNA viruses of the human gut microbiome, new dense depth data dump format to store quantitative genomic data, and more.