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This Week in Nucleic Acids Research: Jun 27, 2013

The University of California, Irvine's Ana Tereza Ribeiro de Vasconcelos and colleagues from the US and Brazil report on results from a genome sequencing study of Anopheles darlingi, a mosquito known for transmitting malaria in neotropical regions such as the Amazon. Within the A. darlingi genome, the team identified almost 10,500 predicted protein-coding sequences, including many that resemble genes found in A. gambiae, another mosquito that can transmit malaria. The investigators also considered A. darlingi's SNP set, insertion and deletion patterns, transposable element repertoire, and other genome features in the hopes of better understanding the mosquito's history and propensity for malaria transmission.

Two researchers from India's National Centre for Biological Sciences tallied up predicted DNA binding proteins in the plant model organism Arabidopsis thaliana. Drawing from structure and sequence patterns in protein databases, the duo came up with a list of almost 4,500 A. thaliana proteins from hundreds of protein families that appear to be capable of binding DNA. A more detailed analysis of this protein set provided clues about the distribution and functional capabilities of these potential DNA-binding proteins in A. thaliana, the study author say, which included some proteins previously classified as hypothetical and/or as having an unknown function.

Taking microRNA and messenger RNA expression data into account can bolster the ability to find targets for the miRNAs, according to a study by investigators in the Netherlands. The team attempted to predict miRNA targets with the help of in silico prediction tools developed to look not only at sequence information but also at interrelationships between miRNA and mRNA expression. After validating their approach using data for differentiating muscle precursor cells, the researchers took a crack at applying it to prostate cancer cells, too, identifying new and known miRNA targets in each of the cell types.

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.