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This Week in PLoS: Jan 30, 2012

An international team led by investigators at the University of Bristol reports in PLoS Genetics this week on its effort to "efficiently capture information on population structure provided by patterns of haplotype similarity." The researchers' approach is based on a coancestry matrix that can be summarized as "chromosome painting," as they call it, in which "each individual in a sample is considered in turn as a recipient, whose chromosomes are reconstructed using chunks of DNA donated by the other individuals." Analyzing Human Genome Diversity Panel data for 938 people and 641,000 markers with its approach, the team identified "226 populations reflecting differences on continental, regional, local, and family scales," it says. Overall, the team adds that such information on more subtle population structure in human populations "is only captured by the haplotype-based approach."

In the same journal, a team led by investigators at the US National Cancer Institute presents an approach for studying gene-environment interaction "based on a Bayesian model that uses a latent genetic profile variable to capture all of the genetic variation in the entire targeted region and allows the environment effect to vary across different genetic profile categories."

Elsewhere in PLoS Genetics, researchers at the University of Rochester Medical Center, along with their collaborators at the University of California, San Diego, show that "heterochromatin formation promotes longevity and represses ribosomal RNA synthesis." More specifically, the team shows that, in Drosophila, "animals with decreased heterochromatin levels exhibit a dramatic shortening of lifespan, whereas increasing heterochromatin prolongs lifespan."

Finally, researchers in Austria this week present what they call a "novel and cost-effective approach for estimating population frequencies of TE [transposable element] insertions using paired-end Illumina reads from a pooled population sample," which "treats insertions present in and absent from the reference genome identically, allowing unbiased TE population frequency estimates." Using its Pool-seq approach, the group analyzed data from a natural Drosophila melanogaster population, finding that, consistent with previous reports, "low recombining genomic regions harbor more TE insertions and maintain insertions at higher frequencies than do high recombining regions," it says.

The Scan

Vaccine Update Recommended

A US Food and Drug Administration panel recommends booster vaccines be updated to target Omicron, CNBC reports.

US to Make More Vaccines for Monkeypox Available

The US is to make nearly 300,000 vaccine doses available in the coming weeks to stem the spread of human monkeypox virus, according to NPR.

Sentence Appealed

The Associated Press reports that Swedish prosecutors are appealing the sentence given to a surgeon once lauded for transplanting synthetic tracheas but then convicted of causing bodily harm.

Genome Biology Papers on COVID-19 Effector Genes, Virtual ChIP-seq, scDART

In Genome Biology this week: proposed COVID-19 effector genes, method to predict transcription factor binding patterns, and more.