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This Week in Nucleic Acids Research: Jul 25, 2013

Researchers from the US, France, and Russia report on efforts to dial back the set of amino acids encoded by the Mycoplasma genitalium genome as a means of reducing the minimal genome size for the bacterial species. Using computational methods, the team looked at the possibility of reining in or completely replacing cysteine, the rarest amino acid residue in that microbe. Based on their results so far, the study's authors concluded that "drastic reduction of the content of the rarest amino acid in a minimal proteome appears to be possible, but its complete elimination is challenging."

A new computational framework can help those interested in searching an organism's genome for conserved non-genic elements, even when sequences from closely related organisms aren't available, according to a study in Nucleic Acids Research by Stanford University researchers. The group demonstrated the utility of its comparative genomics alignment framework using genome sequences from the zebrafish, a commonly used but phylogenetically isolated model organism. Using the computational approach, the investigators identified 54,533 predicted conserved non-genic elements in the zebrafish genome, including nearly 12,000 that appear to be conserved in other animals such as mice or humans.

A team from Icahn School of Medicine at Mount Sinai presents new software for calling variants from deep sequence datasets. When the researchers tested their algorithm, known as MiST, for calling variants in whole-exome sequence data, they found that it compared favorably with genotyping-based variant calling or with the Broad Institute's GATK software, uncovering SNPs found in the dbSNP database and producing variant profiles that could be confirmed by Sanger sequencing more than 90 percent of the time.

The Scan

Machine Learning Helps ID Molecular Mechanisms of Pancreatic Islet Beta Cell Subtypes in Type 2 Diabetes

The approach helps overcome limitations of previous studies that had investigated the molecular mechanisms of pancreatic islet beta cells, the authors write in their Nature Genetics paper.

Culture-Based Methods, Shotgun Sequencing Reveal Transmission of Bifidobacterium Strains From Mothers to Infants

In a Nature Communications study, culture-based approaches along with shotgun sequencing give a better picture of the microbial strains transmitted from mothers to infants.

Microbial Communities Can Help Trees Adapt to Changing Climates

Tree seedlings that were inoculated with microbes from dry, warm, or cold sites could better survive drought, heat, and cold stress, according to a study in Science.

A Combination of Genetics and Environment Causes Cleft Lip

In a study published in Nature Communications, researchers investigate what combination of genetic and environmental factors come into play to cause cleft lip/palate.