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This Week in Nature: Mar 21, 2014

In Nature this week, researchers from the Lawrence Berkeley National Laboratory report data showing that the fruit fly transcriptome is far more complex than previously thought. They examined various Drosophila cultured cell lines at different developmental stages and dissected organ systems, revealing new genes, proteins, and transcripts, including hundreds of previously unidentified long non-coding RNAs. Notably, transcripts and expression patterns were found to be similar to those in other animals, suggesting that some mechanisms are conserved in metazoans.

Meanwhile, in Nature Biotechnology, a team from the University of California, Berkeley, publish details of an automated process for genome annotation that integrates RNA-seq and gene-boundary datasets. Dubbed Generalized RNA Integration Tool, or GRIT, the approach was applied to Drosophila short-read RNA-seq, cap analysis of gene expression, and poly(A)-site-seq data collected for the modENCODE Project, allowing the researchers to recover the vast majority of previously annotated transcripts while doubling the total number of transcripts cataloged. Overall, GRIT showed 30 percent higher precision and recall than popular transcript assembly tools.

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.