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In Print: Last Week's Microarray Papers of Note: Oct 28, 2014


Generation of a neuro-specific microarray reveals novel differentially expressed noncoding RNAs in mouse models for neurodegenerative diseases.
RNA. 2014 Oct 24. [Epub ahead of print]
Gstir R, et al.

The authors developed a neuro-specific non-coding RNA microarray, covering 1,472 ncRNA species, to investigate their expression in different mouse models for central nervous system diseases. They analyzed ncRNA expression in two mouse models with impaired calcium channel activity, implicated in Epilepsy or Parkinson's disease, respectively, as well as in a mouse model mimicking pathophysiological aspects of Alzheimer's disease. In the Alzheimer mouse model, they identified two small nucleolar RNAs, whose expression was deregulated prior to amyloid plaque formation. In addition to known ncRNAs species, the authors also identified 63 differentially expressed ncRNA candidates, located in intronic or intergenic regions of the mouse genome.

Combination of an unbiased amplification method and a resequencing microarray for detecting and genotyping equine arteritis virus.
J Clin Microbiol. 2014 Oct 22. pii: JCM.01935-14. [Epub ahead of print]
Hans A, et al.

The authors applied an unbiased amplification method to equine arteritis virus RNA in order to improve the sensitivity of the RT-qPCR assay recommended by the World Organisation for Animal Health. Twelve viral RNA amplified using this method were then hybridized on a high-density resequencing microarray for viral characterization.

MicroRNA polymorphisms and risk of colorectal cancer.
Cancer Epidemiol Biomarkers Prev. 2014 Oct 23. [Epub ahead of print]
Schmit S, et al.

This study expanded the search for miRNA-related polymorphisms contributing to the etiology of colorectal cancer across the genome using the Axiom miRNA Target Site Genotyping Array. After quality control, the study included 596 cases and 429 controls from the Molecular Epidemiology of Colorectal Cancer study, a population-based case-control study of colorectal cancer in northern Israel. The authors claim their study is the first to examine associations between genetic variation in miRNA target sites and colorectal cancer using a genome-wide approach.

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.