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This Week in Genome Biology: Oct 12, 2011

In a paper published online in advance in Genome Biology this week, researchers at the University of Würzburg in Germany report their use of a differential RNA-seq approach with specific enrichment of primary transcripts to define the "transcriptome of purified elementary bodies and reticulate bodies of C.[Chlamydia] pneumoniae strain CWL-029." The Würzburg team mapped 565 transcriptional start sites of annotated genes and novel transcripts, and identified "a distinct transcription start site or an affiliation to an operon" for 862 out of 1074 annotated protein-coding genes. Overall, the researchers suggest that "the precise transcriptional landscape as a complement to the genome sequence will provide new insights into the organization, control and function of genes" in this human pathogen.

Lawrence Berkeley National Laboratory's Aindrila Mukhopadhyay and her colleagues report in Genome Biology this week their "systematic mapping of the genes regulated by all transcriptionally acting response regulators in a single bacterium," Desulfovibrio vulgaris. In its study, the Mukhopadhyay group predicted new genes and regulatory networks, "which found corroboration in a compendium of transcriptome data available for D. vulgaris." Mukhopadhyay et al. add that their "in vitro array-based method … is generally applicable for the study of such systems in all organisms."

The Scan

Researchers Compare WGS, Exome Sequencing-Based Mendelian Disease Diagnosis

Investigators find a diagnostic edge for whole-genome sequencing, while highlighting the cost advantages and improving diagnostic rate of exome sequencing in EJHG.

Researchers Retrace Key Mutations in Reassorted H1N1 Swine Flu Virus With Avian-Like Features

Mutations in the acidic polymerase-coding gene boost the pathogenicity and transmissibility of Eurasian avian-like H1N1 swine influenza viruses, a PNAS paper finds.

Genome Sequences Reveal Evolutionary History of South America's Canids

An analysis in PNAS of South American canid species' genomes offers a look at their evolutionary history, as well as their relationships and adaptations.

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.