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In Print: Mar 8, 2011

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Microarrays Papers of Note Published February 2011

Journal: Animal Genetics. 2011 Feb;42(1):75-82.

Title: Characterization of a 6K oligonucleotide turkey skeletal muscle microarray.

Authors: Sporer K, et al.

The authors constructed this 6,000-probe array with the aim of developing a new tool for the study of turkey growth and development at the muscle transcriptome level. The turkey skeletal muscle long oligo microarray contains oligos designed from sequences obtained from skeletal muscle cDNA libraries from several developmental stages. According to the authors, qquality control hybridizations were completed, confirming the validity and repeatability of the array.


Journal: Applied and Environmental Microbiology. 2011 Feb 18. [Epub ahead of print]

Title: Development of an enterococcal DNA microarray for species, virulence and antibiotic resistance gene determination among poultry isolates.

Authors: Champagne J, et al.

A DNA microarray was designed with probes targeting four species-specific taxonomic identifiers to discriminate among 18 different enterococcal species while other probes were designed to identify 18 virulence factors and 174 antibiotic resistance genes. In total, 262 genes were used for rapid species identification of enterococcal isolates while characterizing their virulence potential through the simultaneous identification of endogenous antibiotic resistance and virulence genes. The new so-called enteroarray should prove to be a useful tool to accurately genotype strains of enterococci and assess their virulence potential, according to the authors.


Journal: BMC Genomics. 2011 Feb 16;12(1):115. [Epub ahead of print]

Title: The living microarray: a high-throughput platform for measuring transcription dynamics in single cells.

Authors: Rajan S, et al.

The authors describe a high-throughput platform for measuring transcriptional changes in real time in single mammalian cells. By using reverse transfection microarrays, they were able to transfect fluorescent reporter plasmids into 600 independent clusters of cells plated on a single microscope slide and image the clusters every 20 minutes. The authors claim their method is scalable and readily adaptable to studying complex systems, including cell proliferation, differentiation and apoptosis. BioArray News spoke with the authors about the study last month (BAN 2/22/2011).


Journal: BMC Genomics. 2011 Feb 28;12(1):134. [Epub ahead of print]

Title: ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis.

Authors: Ho J, et al.

The authors performed a systematic analysis of a modENCODE dataset consisting of 31 pairs of ChIP-chip/ChIP-seq profiles of the coactivator CBP, RNA polymerase II, and six histone modifications across four developmental stages of Drosophila melanogaster. The authors found that both technologies produced highly reproducible profiles within each platform, but said that ChIP-seq generally produces profiles with a better signal-to-noise ratio, and allows detection of more peaks and narrower peaks.


Journal: Haematologica. 2011 Feb;96(2):221-30.

Title: Evaluation of gene expression signatures predictive of cytogenetic and molecular subtypes of pediatric acute myeloid leukemia.

Authors: Balgobind B, et al.

The authors examined the potential of gene expression profiles to classify pediatric acute myeloid leukemia. Gene expression microarray data of 237 children with acute myeloid leukemia were collected and a double-loop cross validation approach was used to generate a subtype-predictive gene expression profile in the discovery cohort which was then tested for its true predictive value in the independent validation cohort. The authors concluded that gene expression profiling correctly predicted the most prevalent cytogenetic subtypes of pediatric acute myeloid leukemia with high accuracy.

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Journal: IEEE Transactions on Nanobioscience. 2011 Feb 22. [Epub ahead of print]

Title: Statistical design of position-encoded microsphere arrays.

Authors: Sarder P, et al.

The authors designed a microsphere array device that includes microspheres with controllable positions for error-free target identification. They conducted a statistical design analysis to select the optimal distance between the microspheres as well as the optimal temperature. Potential applications for the array include molecular recognition, specificity of targeting molecules, protein-protein dimerization, high throughput screening assays for enzyme inhibitors, drug discovery, and gene sequencing, according to the authors.


Journal: International Journal of Oncology. 2011 Feb;38(2):427-35.

Title: Reverse-phase protein microarrays (RPPA) as a diagnostic and therapeutic guide in multidrug resistant leukemia.

Authors: Maraldi T, et al.

In this study, lysates from parental and multidrug resistant CEM leukemia cells were spotted onto reverse-phase protein microarrays and probed with a panel of phospho-antibodies to ERK, PCK and Akt pathways. They found that while total Akt1 protein level is higher in parental CEM cells, the activated isoform content, p-Akt1, increases in doxorubicin-selected CEM cells. This was confirmed later by Western blot analysis.


Journal: Journal of Human Genetics. 2011 Feb;56(2):110-24.

Title: Clinical application of array-based comparative genomic hybridization by two-stage screening for 536 patients with mental retardation and multiple congenital anomalies.

Authors: Hayashi S, et al.

To apply the array comparative genomic hybridization technique to the diagnosis as well as investigation of multiple congenital anomalies and mental retardation, the authors organized a consortium with 23 medical institutes and hospitals in Japan, and recruited 536 patients with clinically uncharacterized MCA/MR, whose karyotypes were normal according to conventional cytogenetics, for two-stage screening using two types of microarrays. The first screening using a targeted array detected pathogenic CNVs in 54 of 536 cases, while the second screening of the 349 cases negative in the first screening using a genome-wide high-density array detected pathogenic CNVs in 48 cases, including CNVs relevant to recently established microdeletion or microduplication syndromes, CNVs containing pathogenic genes and recurrent CNVs containing the same region among different patients.


Journal: Journal of Immunological Methods. 2011 Feb 1;364(1-2):21-32.

Title: Multiple protein extract microarray for profiling human food-specific immunoglobulins A, M, G and E.

Authors: Renault N, et al.

The authors describe a microarray test based on protein extracts of food components. Their approach relies on using arrayed food samples sequentially extracted with detergent and chaotropic agents, measuring four different immunoglobulin classes simultaneously, and analyzing the generated data via a suitable bioinformatics interface. The test prototype contains extracts of approximately 350 food ingredients that cover most of the food products found in the UK.


Journal: Lab on Chip. 2011 Feb 7;11(3):528-34.

Title: Hydrogel droplet microarrays with trapped antibody-functionalized beads for multiplexed protein analysis.

Authors: Li H, et al.

The authors present a three-dimensional antibody microarray format based on the entrapment of antibody-coated microbeads within alginate droplets that were spotted onto a glass slide using an inkjet. As a proof of concept, six proteins including cytokines, breast cancer biomarkers, and one cancer-related protein were profiled in multiplex using sandwich assays. The authors argue that the beads-in-gel microarrays can be used for multiplexed protein analysis.


Journal: Langmuir. 2011 Feb 15;27(4):1536-42.

Title: Patterning of peptide nucleic acids using reactive microcontact printing.

Authors: Calabretta A, et al.

According to the authors of this study, peptide nucleic acids were immobilized onto surfaces using reactive microcontact printing. The surfaces were first modified with aldehyde groups to react with the amino end of the synthesized PNAs. When patterning fluorescent-labeled PNAs by reactive microcontact printing using oxygen-oxidized polydimethylsiloxane stamps, homogeneous arrays were fabricated and characterized using optical methods. The PNA-patterned surfaces were then hybridized with complementary and mismatched dye-labeled oligonucleotides to test their ability to recognize DNA sequences.

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Journal: Langmuir.. 2011 Feb 1;27(3):882-6.

Title: Aldehyde-functionalized benzenediazonium cation for multiprobe immobilization on microelectrode array surfaces.

Authors: Haque, et al.

The authors discuss in situ generation of aldehyde-functionalized benzenediazonium cation and its use as a suitable linker molecule for fast and selective immobilization of biomolecules on indium-tin-oxide electrode surfaces. They also showed that successive electrodeposition of ABD and probe molecules on individually addressable microarray electrode surfaces can provide a platform for the detection of multianalyte. In the paper, the usage of ABD is demonstrated by the patterning of three different probe molecules on a single substrate and the simultaneous detection of two target molecules.


Journal: Nucleic Acids Research. 2011 Feb 8. [Epub ahead of print]

Title: QDMR: a quantitative method for identification of differentially methylated regions by entropy.

Authors: Zhang Y, et al.

The authors present a quantitative approach, called quantitative differentially methylated regions, to quantify methylation difference and identify DMRs from genome-wide methylation profiles. QDMR was applied to synthetic methylation patterns and methylation profiles detected by methylated DNA immunoprecipitation microarray in human tissues and cells. The authors claim their approach can give a reasonable quantitative measure of methylation difference across multiple samples.


Journal: PLoS One. 2011 Feb 11;6(2):e17167.

Title: Systematic evaluation of three microRNA profiling platforms: microarray, beads array, and quantitative real-time PCR array.

Authors: Wang B, et al.

In this study, the authors systematically analyzed three representative microRNA profiling platforms: a locked nucleic acid microarray, a bead array, and a TaqMan quantitative real-time PCR low density array. The miRNA profiles of 40 human osteosarcoma xenograft samples were generated by all three platforms. The results showed that each of the three platforms performed similarly regarding intra-platform reproducibility or reproducibility of data within one platform, while the LNA array and TaqMan array had the best inter-platform reproducibility or reproducibility of data across platforms.


Journal: PLoS One. 2011 Feb 9;6(2):e16486.

Title: Performance of microarray and liquid based capture methods for target enrichment for massively parallel sequencing and SNP discovery.

Authors: Kiialainen A, et al.

In this study, the authors compared two hybridization methods for target enrichment for massively parallel sequencing and SNP discovery, namely the Roche NimbleGen sequence capture arrays and the Agilent Technologies SureSelect liquid-based hybrid capture system. They prepared sequencing libraries from three HapMap samples using both methods, sequenced the libraries on the Illumina Genome Analyzer, mapped the sequencing reads back to the genome, and called variants in the sequences. They determined that the Roche NimbleGen method gave better results when judged by the number of SNPs called, but said this came at the cost of more over-sampling.


Journal: The Analyst. 2011 Feb 7;136(3):560-9.

Title: Multiplex suspension array for human anti-carbohydrate antibody profiling.

Authors: Pochechueva T, et al.

In this study, a microsphere-based flow-cytometric immunoassay was applied for multiplexed detection of glycan-binding antibodies in human serum. The array design was based on coupling of end-biotinylated glycopolymers, and the resulting glyco-microspheres were used for detection of IgM and IgG antibodies directed against ABO blood group antigens.


Journal: The Plant Journal. 2011 Feb 1. [Epub ahead of print]

Title: Improved protein-binding microarrays for the identification of DNA-binding specificities of transcription factors.

Authors: Godoy, et al.

The authors report on the development of a protein binding microarray containing all possible double-stranded 11-mers for the determination of DNA-binding specificities of transcription factors. They applied this tool to determine binding site specificities of two Arabidopsis TFs, MYC2 and ERF1, rendering the G-box and the GCC-box respectively as their highest affinity binding sites. Analysis of transcriptomic data revealed that high- and medium-affinity binding sites have biological significance, likely representing relevant cis-acting elements in vivo.


Journal: The Plant Journal. 2011 Feb 7. [Epub ahead of print]

Title: Genome-wide atlas of transcription through maize development.

Authors: Sekhon R, et al.

The authors present atlas of global transcription profiles across developmental stages and plant organs in maize. They used a Roche NimbleGen microarray containing 80,301 probe sets to profile transcription patterns in 60 distinct tissues representing 11 major organ systems of the inbred line B73. Of the 30,892 probe sets representing the filtered B73 gene models, 91.4 percent were expressed in at least one tissue. Clustering of maize tissues based on global gene expression profiles lead to formation of 19groups of biologically related tissues.

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For Better Odds

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Snipping HIV Out

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PLOS Papers on Cancer Risk Scores, Typhoid Fever in Colombia, Streptococcus Protection

In PLOS this week: application of cancer polygenic risk scores across ancestries, genetic diversity of typhoid fever-causing Salmonella, and more.