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This Week in PLoS: May 10, 2010

In PLoS Genetics this week, a trio of researchers from the University of California, San Diego, report that post-replication repair "prevents replication damage from becoming double strand breaks and/or regulates the activity of HR [homologous recombination] on DSBs." Namely, by investigating RAD6 and RAD18-dependent post-replication repair, the team found that "the RAD5-, MMS2-, [and] UBC13-dependent error-free PRR branch acted in concert with the replication stress checkpoint to suppress duplication-mediated GCRs formed by homologous recombination," they write, adding that "the extreme sensitivity of our assay to post-replication repair defects reveals substantial complexity in the interaction of PRR defects, suggesting the presence of many alternative PRR pathways."

In PLoS One, researchers in Tokyo present their program, MuSICA 2, which "assembles millions of short (36-nucleotide) reads collected from a single flow cell lane of Illumina Genome Analyzer to shotgun-sequence ~800 human full-length cDNA clones." The authors write that using their method, researchers can perform the sequencing and shotgun assembly in less than a week, at a cost of about three dollars per clone. "MuSICA 2 performs a hybrid assembly in which an external de novo assembler is run first and the result is then improved by reference alignment of shotgun reads," the authors write, adding that when comparing MuSICA 2 assemblies with "200 pooled full-length cDNA clones finished independently by the conventional primer-walking using Sanger sequencers," the nucleotide-level accuracy of coding sequences was more than 99.99 percent.

Also in PLoS One, investigators in the US and Canada report their analysis of the "evolution of the sex-related locus and genomic features shared in microsporidia and fungi." In inspecting whole genomes, the authors found RPS9-RPL21, a "unique syntenic gene pair," was present in fungal and microsporidian genomes, but not in other eukaryotic lineages. "The sex/sex-related loci appear to have been subject to frequent gene conversion and translocations in microsporidia and zygomycetes," the team writes, adding that their study highlights that the genomic hallmarks between microsporidia and fungi "are independent of sequence-based phylogenetic comparisons."

An international research team identifies three new loci for human eye color of genome-wide significance. They elucidated the regions, 1q42.3, 17q25.3, and 21q22.13, by performing a genome-wide association study on 5,951 individuals from the Rotterdam Study. The team replicated the latter two loci in cohorts from the UK and Australia, and suggest that "the LYST gene at 1q42.3 and the DSCR9 gene at 21q22.13 serve as promising functional candidates." They write that their data "exemplify that fine phenotyping is a useful strategy for finding genes involved in human complex traits."

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.