Microarrays Research Today is a free monthly online journal that collates and summarizes the latest research about Microarrays, including details on experiments, designs, statistics, analysis, software.

Evaluation of the Premi(R)Test Salmonella, a commercial low-density DNA microarray system intended for routine identification and typing of Salmonella enterica.

Wattiau P, Weijers T, Andreoli P, Schliker C, Veken HV, Maas HM, Verbruggen AJ, Heck ME, Wannet WJ, Imberechts H, Vos P

VAR (Veterinary and Agrochemical Research Centre) Department of Bacteriology and Immunology, Groeselenberg 99, B-1180 Brussels, Belgium.

A new commercial system based on genetic profiling and aimed at identifying Salmonella enterica serovars was evaluated by comparing its performance with classical serotyping on 443 strains. Within 62 serovars represented, 60 gave unique genetic profiles while 2 were undistinguishable. Results were obtained within 8 h, were reproducible and clear-cut. The system allowed single-tube processing of the samples and required no peculiar technical skill. It showed interesting potential for routine laboratory testing.

Published 29 April 2008 in Int J Food Microbiol, 123(3): 293-8.
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Articles on Microarrays published 29 April 2008:

CoPub: a literature-based keyword enrichment tool for microarray data analysis.   Nucleic Acids Res.

Medline is a rich information source, from which links between genes and keywords describing biological processes, pathways, drugs, pathologies and diseases can be extracted. We developed a publicly available tool called CoPub that uses the information in the Medline database for the biological interpretation of microarray data. CoPub allows batch input of multiple human, mouse or rat genes and produces lists of keywords from several biomedical thesauri that are significantly correlated with ... [Abstract] [Full-text]

A software framework for microarray and gene expression object model (MAGE-OM) array design annotation.   BMC Genomics, 9: 133.

BACKGROUND: The MIAME and MAGE-OM standards defined by the MGED society provide a specification and implementation of a software infrastructure to facilitate the submission and sharing of data from microarray studies via public repositories. However, although the MAGE object model is flexible enough to support different annotation strategies, the annotation of array descriptions can be complex. RESULTS: We have developed a graphical Java-based application (Adamant) to assist with submission of ... [Abstract] [Full-text]

Screening Autoantibody Profiles in Systemic Rheumatic Disease with a Diagnostic Protein Microarray That Uses a Filtration-Assisted Nanodot Array Luminometric Immunoassay (NALIA).   Clin Chem, 54(5): 883-90.

BACKGROUND: We developed a cost-efficient modular system for multiplex analysis of the multiple autoantibodies that characterize systemic rheumatoid diseases. METHODS: The nanodot array luminometric immunoassay (NALIA) system consists of conventional 96-well membrane-bottomed plates in which antigens or antibodies are adsorbed onto the underside of the membrane. Current arrays use a 5 x 5 format (25 dots/well), which allows 10 analytes to be measured in duplicate: double-stranded DNA (dsDNA), ... [Abstract] [Full-text]

Normalization for triple-target microarray experiments.   BMC Bioinformatics, 9(1): 216.

ABSTRACT: BACKGROUND: Most microarray studies are made using labelling with one or two dyes which allows the hybridization of one or two samples on the same slide. In such experiments, the most frequently used dyes are Cy3 and Cy5. Recent improvements in the technology (dye-labelling, scanner and, image analysis) allow hybridization up to four samples simultaneously. The two additional dyes are Alexa 488 and Alexa 494. The triple-target or four-target technology is very promising, since it ... [Abstract] [Full-text]

Heterologous microarray experiments allow the identification of the early events associated with potato tuber cold sweetening.   BMC Genomics, 9: 176.

BACKGROUND: Since its discovery more than 100 years ago, potato (Solanum tuberosum) tuber cold-induced sweetening (CIS) has been extensively investigated. Several carbohydrate-associated genes would seem to be involved in the process. However, many uncertainties still exist, as the relative contribution of each gene to the process is often unclear, possibly as the consequence of the heterogeneity of experimental systems. Some enzymes associated with CIS, such as beta-amylases and invertases, ... [Abstract] [Full-text]

Microarray analysis of transcriptional responses to infection by herpes simplex virus types 1 and 2 and their US3-deficient mutants.   Microbes Infect, 10(4): 405-413.

Herpes simplex virus types 1 (HSV-1) and 2 (HSV-2) induce similar responses in infected cells and animals but differ in several significant respects. Previous studies have shown that defects in the US3-encoded protein kinase greatly affect both viruses in their interactions with cells and hosts. To investigate the impact of infection with HSV-1, HSV-2 and their US3-deficient mutants (DeltaUS3) on cellular transcriptional responses, we performed a global microarray analysis on human epithelial ... [Abstract] [Full-text]

Articles on Microarrays published 28 April 2008:

Molecular Characterization of Neisseria meningitidis Isolates Using a Resequencing DNA Microarray.   J Mol Diagn, 10(3): 265-71.

Neisseria meningitidis is a major cause of both meningitis and septicemia. Typically, isolates are characterized by using a combination of immunological phenotyping, using monoclonal and polyclonal antisera, and Sanger nucleotide sequencing of epitope-encoding variable regions, although these methods can be both time-consuming and limited by reagent availability. Herein, we describe and evaluate a novel microarray to define the porB and porA serotypes of N. meningitidis by the resequencing of ... [Abstract] [Full-text]

Unequal group variances in microarray data analyses.   Bioinformatics, 24(9): 1168-74.

MOTIVATION: In searching for differentially expressed (DE) genes in microarray data, we often observe a fraction of the genes to have unequal variability between groups. This is not an issue in large samples, where a valid test exists that uses individual variances separately. The problem arises in the small-sample setting, where the approximately valid Welch test lacks sensitivity, while the more sensitive moderated t-test assumes equal variance. METHODS: We introduce a moderated Welch test ... [Abstract] [Full-text]

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