%0 Journal Article
%T Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development
%A S¨¦bastien Terrat
%A Eric Peyretaillade
%A Olivier Gon£¿alves
%A Eric Dugat-Bony
%A Fabrice Gravelat
%A Anne Mon¨¦
%A Corinne Biderre-Petit
%A Delphine Boucher
%A Julien Troquet
%A Pierre Peyret
%J BMC Bioinformatics
%D 2010
%I BioMed Central
%R 10.1186/1471-2105-11-478
%X First we have validated our approach by studying eight enzymes involved in the degradation of polycyclic aromatic hydrocarbons from the model strain Sphingomonas paucimobilis sp. EPA505 using a designed microarray of 8,048 probes. As expected, microarray assays identified the targeted set of genes induced during biodegradation kinetics experiments with various pollutants. We have then confirmed the identity of these new genes by sequencing, and corroborated the quantitative discrimination of our microarray by quantitative real-time PCR. Finally, we have assessed metabolic capacities of microbial communities in soil contaminated with aromatic hydrocarbons. Results show that our probe design (sensitivity and explorative quality) can be used to study a complex environment efficiently.We successfully use our microarray to detect gene expression encoding enzymes involved in polycyclic aromatic hydrocarbon degradation for the model strain. In addition, DNA microarray experiments performed on soil polluted by organic pollutants without prior sequence assumptions demonstrate high specificity and sensitivity for gene detection. Metabolic Design is thus a powerful, efficient tool that can be used to design explorative probes and monitor metabolic pathways in complex environments, and it may also be used to study any group of genes. The Metabolic Design software is freely available from the authors and can be downloaded and modified under general public license.Assessing the metabolic potential of microorganisms in variable ecosystems is a novel and stimulating challenge in biology. Microorganisms are present in all environmental habitats, even the most extreme, yet despite their ubiquity, we know relatively little about these communities. Microorganisms display vast diversity, each one having its own set of genes, cell components and metabolic reactions [1]. Thus 1 g of soil may contain up to 109 bacteria cells, which may represent between 1,000 and 10,000 different species [
%U http://www.biomedcentral.com/1471-2105/11/478