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This Week in Nature: Dec 31, 2009

In the advance, online edition of Nature Biotechnology this week, researchers from Germany and Singapore examined the how gene expression shifts when the malarial parasite Plasmodium falciparum is exposed to 20 compounds that inhibit an early stage of the parasite's development in blood cells. The team found at least three-fold changes in the expression of roughly 59 percent of P. falciparum coding genes after treatment with one or more of the chemicals. By combining these expression patterns with sequence, domain, two-hybrid and other data, the team came up with an interaction network that they say "may facilitate identification of novel antimalarial drugs and vaccines."

Mark Gerstein and his colleagues used a method called BreakSeq to find previously overlooked structural variants in genomes sequenced using short read methods. To do this, researchers compared short read-sequenced genomes with a breakpoint library they developed by integrating and standardizing data on some 2,000 known structural variants and then characterizing these variants. "As new data become available, we expect our BreakSeq approach will become more sensitive and facilitate rapid [structural variant] genotyping of personal genomes," Gerstein and his co-authors write.

The online edition of Nature Genetics this week has a paper on genetic variants affecting human metabolism. For that study, German, Austrian, and British researchers did a genome-wide association study of 163 metabolic traits in blood samples taken from more than 1,800 individuals. In the process, the team found nine loci associated with metabolic traits and replicated in 422 additional study participants. Of these, eight appear to involve variants in or around genes coding for enzymes or solute carriers involved in metabolic function.

In the print issue of the journal, University of Washington researchers Jay Shendure and Michael Bamshad report on the use of exome sequencing to find the mutations behind a single gene disease called Miller syndrome. By sequencing the exomes of four individuals from three families and comparing them with SNP databases and previously sequenced exomes, the team honed in on the pyrimidine biosynthesis enzyme-coding gene DHODH as the Miller syndrome culprit. Our sister publication GenomeWeb Daily News previously reported on the paper's online publication.

The Scan

Tens of Millions Saved

The Associated Press writes that vaccines against COVID-19 saved an estimated 20 million lives in their first year.

Supersized Bacterium

NPR reports that researchers have found and characterized a bacterium that is visible to the naked eye.

Also Subvariants

Moderna says its bivalent SARS-CoV-2 vaccine leads to a strong immune response against Omicron subvariants, the Wall Street Journal reports.

Science Papers Present Gene-Edited Mouse Models of Liver Cancer, Hürthle Cell Carcinoma Analysis

In Science this week: a collection of mouse models of primary liver cancer, and more.