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This Week in Genome Biology: Oct 8, 2009

In Genome Biology this week, joint senior authors Dieter Ebert at the University of Basel and Patrick Keeling at the University of British Columbia have sequenced the genome of Octosporea bayeri, a large microsporidian pathogen, and compared it to the more popular, and smaller, genome of Encephalitozoon cuniculi. Using Illumina sequencing, they generated 898 Mb of sequence data and annotated 2,174 genes, 893 of which encode proteins with assigned function. From this, they conclude that this species "might be less bio-chemically dependent on its host for its metabolism than its more reduced relatives."

Max Planck Institute for Informatics scientists have led work developing a new software to help analyze DNA methylation across multiple samples for biomarker studies. MethMarker, as it's called, can be used "for transforming disease-specific differentially methylated genomic regions into robust clinical biomarkers." And, in a methods paper, scientists led by the Broad Institute's David Jaffe show that their assembler, ALLPATHS2, was more successful in generating accurate assemblies from short paired end sequencing reads than two other popular algorithms, Velvet and EULER-SR.

Brendan Wren at the London School of Hygiene and Tropical Medicine is senior author on work that studied the evolution of Clostridium difficile virulence, considering the emergence of a highly virulent clone, PCR-ribotype 027. Comparing the genomes of non-epidemic 027 C. difficile (CD196), a recent epidemic and hypervirulent 027 (R20291), and a previously sequenced PCR-ribotype 012 strain (630), they found that the virulent genome has 234 additional genes, which they think may play a role in enhancing its motility, antibiotic resistance, and toxicity.

A short video announces a call to nominate research articles for BioMed Central's 4th Annual Research Awards for 2010. The award will help celebrate "ten years of excellence in open access publishing," says BioMed Central's editorial director. Nominations must be for a groundbreaking piece of research that has been published in Genome Biology in 2009 and can be submitted via forms on the web site up till the end of the year. Judges will be announced soon.

Finally, a study used transcriptome profiling to look into the spatio-temporal regulation of gene expression in the developing cortex of mice. Using SAGE libraries from different developmental stages, the scientists found 561 differentially expressed transcripts, 70 of which they validated. Genomic clustering of these 70 revealed two highly transcribed loci, Sox4 and Sox11, with "unusual overlapping sense and antisense transcripts," they say in the abstract. "The Sox4 and Sox11 antisense transcripts were highly expressed in the brain as compared to other mouse organs and are differentially expressed in both the proliferating and differentiating neural stem/progenitor cells and P19 (embryonal carcinoma) cells," suggesting these transcripts are important in cerebral corticogenesis and neuronal/glial cell differentiation.

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.