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In Print: Last Week's Microarray Papers of Note: Feb 12, 2013

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Bacterial communities in commercial aircraft high-efficiency particulate air (HEPA) filters assessed by PhyloChip analysis.

Indoor Air. 2013 Feb;23(1):50-61.

Korves T, Piceno Y, Tom L, et al.

To aid in the design of biosensors for infectious organisms in commercial aircraft, the authors characterized bacterial diversity in aircraft air. Samples from 61 aircraft high-efficiency particulate air filters were analyzed with the PhyloChip, a custom microarray of 16S rRNA gene sequences representing bacterial lineages and a total of 606 subfamilies from 41 phyla were detected. The most abundant bacterial subfamilies included bacteria associated with humans, especially skin, gastrointestinal and respiratory tracts, and with water and soil habitats.

BioArray News recently spoke with the authors of this study.


SNP genotyping in melons: genetic variation, population structure, and linkage disequilibrium.

Theor Appl Genet. 2013 Feb 5. [Epub ahead of print]

Esteras C, Formisano G, Roig C, et al.

The authors present a validated design for a genotyping array with 768 SNPs that are evenly distributed throughout the melon genome. The customized Illumina GoldenGate assay was used to genotype a collection of 74 accessions, representing most of the botanical groups of the species. Since many of the genotyped accessions are being used as the parents of breeding populations in various programs, the authors believe the set of mapped markers could be used for future mapping and breeding efforts.


Stallion sperm transcriptome comprises functionally coherent coding and regulatory RNAs as revealed by microarray analysis and RNA-seq

PLoS One. 2013 Feb 11. [Epub ahead of print]

Das P, McCarthy F, Vishnoi M, et al.

The authors report the first characterization of the global transcriptome of the sperm of fertile stallions. Using 21,000-marker equine whole-genome arrays and RNA-seq, they interrogated the stallion sperm transcriptome. Based on their analysis, the authors suggest that the "rich repertoire" of coding and non-coding RNAs in stallion sperm is not a random remnant from spermatogenesis in testes, but a selectively retained and functionally coherent collection of RNAs.


Functional gene differences in soil microbial communities from conventional, low-input, and organic farmlands.

Appl Environ Microbiol. 2013 Feb;79(4):1284-92.

Xue K, Wu L, Deng Y, et al.

The authors used the GeoChip, a high-throughput microarray containing approximately 28,000 probes for genes involved in nitrogen, carbon, sulfur, phosphorus cycles, and other processes, to evaluate the potential functions of soil microbial communities under conventional, low-input, and organic management systems at an agricultural research site in Michigan.

The Scan

Missed Early Cases

A retrospective analysis of blood samples suggests early SARS-CoV-2 infections may have been missed in the US, the New York Times reports.

Limited Journal Editor Diversity

A survey finds low diversity among scientific and medical journal editors, according to The Scientist.

How Much of a Threat?

Science writes that need for a provision aimed at shoring up genomic data security within a new US bill is being questioned.

PNAS Papers on Historic Helicobacter Spread, Brain Development, C. difficile RNAs

In PNAS this week: Helicobacter genetic diversity gives insight into human migrations, gene expression patterns of brain development, and more.