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This Week in Nucleic Acids Research: May 30, 2013

Researchers from DSM Nutritional Products in Switzerland and the University of Oslo's Natural History Museum present a mapping-based scheme for deciphering mitochondrial genome sequence data in silico from next-generation sequencing data, even in the absence of an existing reference sequence. The group's mitochondrial baiting and iterative mapping, or MITObim, approach proved useful for putting together mitochondrial genomes for Gyrodactylus thymalli and G. derjavinoides, fish parasites that live on the surface of European grayling and rainbow trout, respectively. In their subsequent experiments, the researchers gleaned mitochondrial sequence and/or barcode information about the fish hosts, too. And their simulations suggest MITObim could be applicable to metagenomic or pooled sequence data.

An Argentina-led team has come up with a web server to spell out co-evolution patterns in proteins with multiple sequence alignment data represented as circos plots. The investigators outline the method — known as the mutual information server to infer co-evolution, or MISTIC — in an early, online study in Nucleic Acids Research. "[T]he MISTIC server allows [the user] to integrate sequence and structure information contained in [a multiple sequence alignment] in a comprehensive, compact, visually rich manner that enables the user to extract essential information in terms of networks, conservation and structure for any subset of residues of interest guiding the identification of functionally important residues in a protein," study authors say.

A study by researchers based in the US, Ireland, and Russia looks at evolutionarily conserved reading frame transitions present in prokaryotic genomes. The team brought together data from more than 1,100 existing prokaryotic genomes, using a frameshift prediction program called GeneTack to see such transitions in hundreds of thousands of genes. Genes within that set were further classified by folding in information on frameshift conservation and predicted protein similarity to one another. From there, researchers narrowed in on 4,730 frameshift transition-containing genes that have apparently undergone recoding — a collection of genes they mined further for additional functional experiments.

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.