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This Week in PLoS: Jan 28, 2009

A study published today in PLoS Biology looked at increased evolutionary rates in genes, and found, among alignments of 10,238 human genes to their orthologues in chimpanzee and macaque, exons evolving at a fast rate in humans have a tendency to contain clusters of AT-to-GC (weak-to-strong) biased substitutions. These exons are found in regions with increased male recombination rates and exhibit an increase in nonsynonymous substitutions relative to the genomic average, the authors write.

Computational biologists used the Joint Evolutionary Trees method on families of homologous sequences to provide proof of concept work that JET is a reliable method for detecting protein interactions. They applied the method to a database of 62 heterodimer, homodimer, and transient complexes and on 265 interfaces belonging to signal transduction proteins, enzymes, inhibitors, antibodies, antigens, and others. Their work was published in PLoS Computational Biology.

In PLoS Genetics, there's a paper studying the genetic changes among species of E. coli. Scientists re-annotated the genomes of 20 E. coli strains and one strain of E. fergusonii and found that within the approximately 18,000 families of orthologous genes, about 2,000 were common to all strains. Genome flux in E. coli is confined to a small number of conserved positions in the chromosome, they write, such that "overall, despite a very high gene flow, genes co-exist in an organized genome."

Finally, a paper in PLoS One used NMR metabolomic profiling to study the unexpected antileukemic effects of bezafibrate and medroxyprogesterone acetate on three acute myeloid leukemia cell lines. They found that the early changes in cells were less noticeable than the constitutive metabolic differences between cell types, suggesting that metabolic profiling is a good tool for drug discovery.

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.