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This Week in Science: Aug 15, 2008

In this news story, Steven Salzberg discusses TIGR's involvement in the Bruce Ivins anthrax case. Instead of using standard sequencing, investigators grew up the spores from the envelopes into colonies and looked for ones that differed from the majority. Those odd-looking colonies then had their genomes sequenced, work partially done at TIGR, and compared to the Ames strain to look for mutations. The mutations found were then used to develop a test to find those mutations in other anthrax samples.

Francis Collins penned a retrospective on Victor McKusick's work that established the field of medical genetics. "While the influence of some scientific leaders wanes with their passing, McKusick's will only grow with time," writes Collins.

Researchers led by John van der Oost report how prokaryotes use fragments of viral nucleic acids to become resistant to viruses. The viral fragments are stored as clusters of regularly interspaced short palindromic repeats and, after these CRISPRs are transcribed, a complex of CRISPR-associated proteins, called Cascade, cleaves the CRISPR RNA precursors. The mature RNA, along with helicase Cas3, helps Cascade halt viral proliferation.

Max Planck researchers made a high-throughput sequence of the human transcriptome from a human embryonic kidney and a B-cell line. Of the randomly distributed reads they generated through shotgun sequencing, half mapped to unique genomic regions and 80 percent to known exons. They also found that RNA-seq could detect 25 percent more genes than microarrays and that the most common form of alternative splicing is exon skipping.

Like viruses, this article says, bacteria have evolved to suppress RNA silencing to cause disease. To see how miRNA affects innate immunity in plants, the researchers studied miRNA-deficient mutants of Arabidopsis. In this plant mutant, two strains of Pseudomonas and E. coli were able grow. "We show here that the miRNA pathway plays a major role in antibacterial basal defense," write the researchers.


The Scan

Genetic Tests Lead to Potential Prognostic Variants in Dutch Children With Dilated Cardiomyopathy

Researchers in Circulation: Genomic and Precision Medicine found that the presence of pathogenic or likely pathogenic variants was linked to increased risk of death and poorer outcomes in children with pediatric dilated cardiomyopathy.

Fragile X Syndrome Mutations Found With Comprehensive Testing Method

Researchers in Clinical Chemistry found fragile X syndrome expansions and other FMR1 mutations with ties to the intellectual disability condition using a long-range PCR and long-read sequencing approach.

Team Presents Strategy for Speedy Species Detection in Metagenomic Sequence Data

A computational approach presented in PLOS Computational Biology produced fewer false-positive species identifications in simulated and authentic metagenomic sequences.

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.