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In Print: Last Week's Microarray Papers of Note: Nov 27, 2012


APOA5 Q97x Mutation Identified through homozygosity mapping causes severe hypertriglyceridemia in a Chilean consanguineous family.
BMC Med Genet. 2012 Nov 15;13(1):106.
Dussaillant C, Serrano V, Maiz A, et al.

Very high triglyceride plasma levels were found in two sisters of a Chilean consanguineous family, which is strongly suggestive of a recessive highly penetrant mutation. The aim of this study was to determine the genetic locus responsible for the severe HTG in this family. The authors carried out a genome-wide linkage study using the Illumina Human CytoSNP-12 panel. Using the homozygosity mapping strategy, they searched for chromosome regions with excess of homozygous genotypes in the affected cases compared to non-affected relatives. A large homozygous segment was found in the long arm of chromosome 11, with more than 2,500 consecutive homozygous SNP shared by the proband with her affected sister, and containing the APOA5/A4/C3/A1 cluster. Direct sequencing of the APOA5 gene revealed a known homozygous nonsense Q97X mutation found in both affected sisters but not in non-affected relatives nor in a sample of unrelated controls.

A high density recombination map of the pig reveals a correlation between sex-specific recombination and GC content.
BMC Genomics. 2012 Nov 15;13:586.
Tortereau F, Servin B, Frantz L, et al.

Four different pig pedigrees were genotyped using the Illumina PorcineSNP60 BeadChip. Recombination maps for the autosomes were computed for each individual pedigree using a common set of markers. The resulting genetic maps comprised 38,599 SNPs, including 928 SNPs not positioned on a chromosome in the current assembly of the pig genome.

A gene expression atlas of the domestic pig.
BMC Biol. 2012 Nov 15;10:90.
Freeman T, Ivens A, Baillie J, et al.

This paper describes the first genome-wide analysis of the transcriptional landscape of the pig. A new porcine Affymetrix expression array was designed in order to provide comprehensive coverage of the known pig transcriptome. The new array was used to generate a genome-wide expression atlas of pig tissues derived from 62 tissue and cell types. These data were subjected to network correlation analysis and clustering.

RNA-seq and microarray complement each other in transcriptome profiling.
BMC Genomics. 2012 Nov 15;13(1):629.
Kogenaru S, Qing Y, Guo Y, et al.

The authors compared the performance of RNA-seq and microarray in their ability to detect known HrpX target genes by profiling the transcriptome from the wild-type and the hrpX mutant strains of gamma-proteobacterium Xanthomonas citri subsp. citri. Their comparative analysis indicated that gene expression levels quantified by RNA-seq and microarray were well correlated both at absolute as well as relative levels. Further, the expression levels quantified by RNA-seq and microarray for the significantly differentially expressed genes were also well correlated with qRT-PCR-based quantification. Finally, in addition to the 55 newly identified DEGs, 72 percent of the already known HrpX target genes were detected by both RNA-seq and microarray, while the remaining 28 percent could only be detected by either one of the methods.

Versatile high resolution oligosaccharide microarrays for plant glycobiology and cell wall research.
J Biol Chem. 2012 Nov 16;287(47): 39429-38.
Pedersen H, Fangel J, McCleary B, et al.

The authors report the assembly of a library of well-characterized plant oligosaccharides produced either by partial hydrolysis from polysaccharides or by de novo chemical synthesis. Once coupled to protein, these neoglycoconjugates are versatile reagents that can be printed as microarrays onto a variety of slide types and membranes, they claim. In this paper, they report that these microarrays are suitable for the high-throughput characterization of the recognition capabilities of monoclonal antibodies, carbohydrate-binding modules, and other oligosaccharide-binding proteins of biological significance and also that they have potential for the characterization of carbohydrate-active enzymes.

Embryos whose polar bodies contain isolated reciprocal chromosome aneuploidy are almost always euploid.
Hum Reprod. 2012 Nov 20. [Epub ahead of print]
Forman E, Treff N, Stevens J, et al.

The authors used SNP arrays to analyze previously diagnosed aneuploid embryos that had reciprocal polar body aneuploidy. Among 34 embryos with evaluable results, 31 were euploid on re-analysis. Of 43 chromosomes that had reciprocal aneuploidy in the polar bodies, 41 were disomic in the embryo, indicating that premature separation of sister chromatids was likely to have occurred 95 percent of the time. The log-2-ratio signal intensity from the chromosomes that underwent non-disjunction, resulting in unbalanced embryos, were outliers when compared with those that underwent PSSC.

High-throughput profiling of peptide-RNA interactions using peptide microarrays.
J Am Chem Soc. 2012 Nov 21;134(46):19287-96.
Pai J, Yoon T, Kim N, et al.

This paper describes the development of a quantitative method to evaluate binding properties of hairpin RNAs to peptides using peptide microarrays. The microarray was shown to be a powerful tool for high-throughput analysis of RNA-peptide interactions by its application to profiling interactions between 111 peptides and six hairpin RNAs. The peptide microarrays were also employed to measure hundreds of dissociation constants of RNA-peptide complexes.

Transcriptome analysis reveals unique metabolic features in the Cryptosporidium parvum oocysts associated with environmental survival and stresses.
BMC Genomics. 2012 Nov 21;13(1):647.
Zhang H, Guo F, Zhou H, et al.

Cryptosporidium parvum is a globally distributed zoonotic parasite and an important opportunistic pathogen in immunocompromised patients. Little is known on the metabolic dynamics of the parasite, and study is hampered by the lack of molecular and genetic tools. Here the authors report the development of an Agilent microarray for C. parvum, called the CpArray15K, that covers all predicted ORFs in the parasite genome. They also report that global transcriptome analysis using CpArray15K coupled with real-time qRT-PCR uncovered a number of unique metabolic features in oocysts, the infectious and environmental stage of the parasite.

The Scan

Pfizer-BioNTech Seek Full Vaccine Approval

According to the New York Times, Pfizer and BioNTech are seeking full US Food and Drug Administration approval for their SARS-CoV-2 vaccine.

Viral Integration Study Critiqued

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Giraffe Species Debate

The Scientist reports that a new analysis aiming to end the discussion of how many giraffe species there are has only continued it.

Science Papers Examine Factors Shaping SARS-CoV-2 Spread, Give Insight Into Bacterial Evolution

In Science this week: genomic analysis points to role of human behavior in SARS-CoV-2 spread, and more.