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This Week in Nucleic Acids Research: Feb 6, 2013

Imperial College researchers Leandro Castellano and Justin Stebbing report on microRNAs and small interfering RNAs in mammalian tissues. The researchers sifted through hundreds of millions of mouse RNA sequences representing a range of somatic tissues and cell types. The search led to more than five dozen new miRNA coding loci in the mouse genome, including sites producing so-called "mirtrons," or pre-miRNA hairpins produced through intron splicing. The study's authors also tracked down previously unappreciated endogenous siRNAs as well as already annotated miRNAs that weren't processed via conventional miRNA pathways, prompting them to argue that "the current miRNA miRBase database list should be refined and re-defined."

Francis Collins and company discuss a scheme for tracking transgene activity in another Nucleic Acids Research study. The National Human Genome Research Institute researchers demonstrate that they could successfully see transgene insertion sites and related structural rearrangements in a transgenic mouse line using a combination of microarray-based hybrid capture and high-throughput sequencing. With that data in hand, the group went on to develop a PCR assay for discerning wild-type animals from those heterozygous or homozygous for the transgene in question. "Although we worked with a bacterial artificial chromosome transgenic mouse line," authors of the study say, "this method can be used to analyze the integration site and configuration of any foreign DNA in a sequenced genome."

Finally, Paul Freemont and co-authors from the Imperial College London report on an in vitro strategy for assessing regulatory elements — information that's useful in a synthetic biology setting. The investigators plopped a plasmid library into Escherichia coli. Because the plasmids contained DNA regulatory elements upstream of a green fluorescent protein reporter, the team was ultimately able to gauge the activity of the regulatory elements based on fluorescence levels in cell-free extract from the transformed bugs. "This in vitro approach is significantly quicker than current characterization methods," the researchers say, "and is amenable to high-throughput techniques, providing a valuable tool for rapidly prototyping libraries of DNA regulatory elements for synthetic biology."

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.