Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Rapid Identification of Bacterial Pathogens using a PCR- and Microarray-Based Assay

ABSTRACT: A method based on a modified broad-range PCR and an oligonucleotide microarray for the simultaneous detection and identification of 12 bacterial pathogens at the species level. The feasibility of this assay in routine diagnostic testing was evaluated using 146 blood culture positive and 40 blood culture negative samples. The processed data are composed of ORGANISM NAME or NEGATIVE answer depending if the pathogen is detected in the sample or not. See supplementary file linked below.

ORGANISM(S): Homo sapiens

SUBMITTER: Minna Maki

PROVIDER: E-GEOD-17221 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Rapid identification of bacterial pathogens using a PCR- and microarray-based assay.

Järvinen Anna-Kaarina AK Laakso Sanna S Piiparinen Pasi P Aittakorpi Anne A Lindfors Merja M Huopaniemi Laura L Piiparinen Heli H Mäki Minna M

BMC microbiology 20090810

<h4>Background</h4>During the course of a bacterial infection, the rapid identification of the causative agent(s) is necessary for the determination of effective treatment options. We have developed a method based on a modified broad-range PCR and an oligonucleotide microarray for the simultaneous detection and identification of 12 bacterial pathogens at the species level. The broad-range PCR primer mixture was designed using conserved regions of the bacterial topoisomerase genes gyrB and parE. ...[more]

PMID: 19664269

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Project description:Studying the salivary glands potential role during intestinal infections,using advantage from the ingenious GAL4/UAS-system available in the fly Epithelial immunity is a very simple but nevertheless indispensable type of immune response. Amongst all epithelial tissues, the intestine and the airways are outstanding, because they provide huge surface areas, where colonization or invasion of potential pathogens has to be obviated. The intestine is of special interest, because it has to hold the balance between tolerance and immunity, to protect the own microbial flora. An essential part of the intestinal tract has been completely overlooked, the salivary glands. They are the gatekeepers of the intestinal system, being essential for various aspects of the intestineâs immunity. Using the bipartite Gal4/UAS expression system, it is possible to activate the immune system ectopically in different organs of the fly. Activation of the IMD-pathway in the salivary glands is possible; because a very specific driver line is available that directs expression of any gene of interest into the salivary glands only. Flies, where the IMD-pathway in the salivary glands has been activated have a very distinct phenotype. They show a smaller body length as well as a smaller salivary gland length than the parental animals Microarray data analysis showed that 457 genes were upregulated and 578 genes downregulated. Interestingly, the sets of regulated genes show only a very small overlap with the canonical set of Drosophila immune genes. Other physiological scenarios such as autophagic cell death are apparently also not activated upon IMD-pathway activation. Among the regulated genes, those that code for signaling associated protease activity are significantly modulated. This holds especially true for presenilin and the signal peptide peptidase. The comparison of the transcriptional events induced following IMD-activation in the trachea and the salivary glands shows also only a small overlap, indicating that the general IMD-activated core transcriptome is rather small. In conclusion, the salivary glands may a very good tool to study the physiological role of selected genes that are of importance for human health such as the Alzheimerâs disease related presenilin gene in a functional environment. Ectopic activiation of the Immune deficiency pathway in the larval salivary glands using the Gal4/UAS-system of Brand and Perrimon. The activation was induced by the overexpression of the pattern recognition receptor PGRP-LCx using a driver line which was specific for the salivary glands.In general four replicates were performed including dye-swaps in two-colour arrays.

Dataset Information

Rapid Identification of Bacterial Pathogens using a PCR- and Microarray-Based Assay

Publications

Rapid identification of bacterial pathogens using a PCR- and microarray-based assay.

Similar Datasets

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