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This Week in Genome Biology: Dec 2, 2009

Based on a systematic analysis of the mitochondrial genome, Radek Szklarczyk and Martijn Huynen at Radboud University Medical Center in The Netherlands were able to estimate that "the mitochondrial proteome expanded at least 50% since the common ancestor of human and yeast." The authors' work, which appears this week in Genome Biology, found that gene duplications led to the expansion in humans, and that the most common of these are intra-mitochondrial and inter-compartmental.

Researchers led by Ben Langmead and Steven Salzberg at the University of Maryland have combined Bowtie and SOAPsnp to create Crossbow, an aligner and SNP caller that runs off of the cloud. "Executing in parallel using Hadoop," they say, "Crossbow analyzes data comprising 38-fold coverage of the human genome in three hours using a 320-CPU cluster rented from a cloud computing service for about $85." In a methods paper, scientists at Boston College present the Coding Motif Identification Tool, or COMIT, algorithm, which detects functional noncoding motifs in coding regions "using sequence conservation, explicitly separating nucleotide from amino acid effects," they write in the abstract.

Anna De Grassi and Francesca Ciccarelli from the European Institute of Oncology in Milan show that internal tandem repeats within human primate-specific paralogs alter the structure of the gene. They found that about 7 percent of primate paralogous genes in the human genome contain variable tandem repeats and that half of these repeats are within coding exons. When these repeats are inside exons, they say, "they encode variable amino acid repeats. When located at exon-intron boundaries, ITRs can generate alternative splicing pattern through the formation of novel introns."

Plant biologists at CNRS and INRA in France have studied miRNAs and their patterns of expression in a paper appearing this week. Performing a comparative genomic analysis in rice, poplar, and Arabidopsis, they identified miRNA clusters encoding miRNAs of the same family and clusters expressing miRNAs with unrelated sequences that are typically not evolutionarily conserved. "Strikingly, non-homologous miRNAs from the same cluster were predicted to target transcripts encoding related proteins," they write, and they predict being able to use this knowledge as a tool to "simultaneously control the expression of different genes."

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.