|HEAD||Coppee Jean-Yves, PhD / firstname.lastname@example.org|
|MEMBERS||Dr Coppee, Jean-Yves / Dr Barthelemy, Matthieu / Dr Dillies, Marie-Agnès / Dr Jacquelin, Béatrice / Proux, Caroline / Regnault, Béatrice / Sismeiro, Odile / Soubigou, Guillaume
The DNA microarrays platform (PF2) is dedicated to the development of microarrays for gene expression profiling and comparative genomics of model microorganisms and pathogens. The platform also deals with studies centered on higher eukaryotes (host responses to infection and developmental biology). Various technologies are available at the PF : home made spotted arrays and commercial arrays (Agilent, Nimblegen and Affymetrix arrays). In 2007, the platform has been involved in more than 20 projects. These projects are mainly long-term collaborations with Pasteurian research units. The platform is also collaborating with teams from the International Network of Pasteur Institutes and has established collaborations with several non-Pasteurian teams.
The complete list of all these projects is available on the website of the platform. The projects centered on model microorganisms and pathogens notably concern Legionella pneumophila, Entamoeba histolytica, Plasmodium falciparum, Streptomyces lividans and Mycobacterium. The projects dedicated to higher eukaroytes mainly concern human, mouse drosophila and zebrafish.
These projects aim at answering the following biological questions:
- study of virulence factors
- inter-species transcriptome comparisons
- study of host-pathogen interactions
- study of the effects of environmental pressures (stress, immune pressure, drug pressure...) on the pathogen
- identification of regulator targets (virulence, motility...)
The platform is in charge of the preparation of the arrays (probes design, spotting if needed) as well as of training for the use of the chips and analysis of results. For the projects based on the Affymetrix technology, the PF is also in charge of labelling and hybridization reactions. Data analysis and handling represent 50% of the activities of the platform. Several tools allowing normalization of the data and their statistical analysis are developped and installed at the platform. We are essentially working with the R environment (Bioconductor) and with several commercial softwares for data mining and interpretation (Arrayminer, S-Plus-ArrayAnalyzer, Ingenuity, Genomatix...)
All equipments and softwares needed for the use and the analysis of the chips are freely accessible for the whole campus. This functioning mode allows the development of strong interactions between the PF and the teams with which we are collaborating.
The platform also has some training activities. In 2007, we have participated to several Pasteur Courses (Molecular and Cellular Genetics, Mouse Molecular Genetics, Proteins Biochemistry)
The PF also exerts a bibliographical and technical survey activity (wet and dry lab) so to rapidly integrate all the technological improvements and new applications of this technology.
Santi-Rocca J, Weber C, Guigon G, Sismeiro O, Coppee JY, Guillen N. The lysine- and glutamic acid-rich protein KERP1 plays a role in Entamoeba histolytica liver abscess pathogenesis. Cell Microbiol. 2008, 10 (1) : 202-217.
Crameri A, Marfurt J, Mugittu K, Maire N, Regös A, Coppee JY, Sismeiro O, Burki R, Huber E, Laubscher D, Puijalon O, Genton B, Felger I, Beck HP. Rapid microarray-based method for monitoring of all currently known single-nucleotide polymorphisms associated with parasite resistance to antimalaria drugs.J Clin Microbiol. 2007, 45(11):3685-91
Hamon MA, Batsche E, Regnault B, Tham TN, Seveau S, Muchardt C, Cossart P. Histone modifications induced by a family of bacterial toxins. Proc Natl Acad Sci U S A. 2007, 104(33):13467-72
Jacquelin B, Mayau V, Brysbaert G, Regnault B, Diop OM, Arenzana-Seisdedos F, Rogge L, Coppee JY, Barre-Sinoussi F, Benecke A, Muller-Trutwin MC. Long oligonucleotide microarrays for African green monkey gene expression profile analysis. FASEB J. 2007, 21(12) : 3262-3271
Weber C, Guigon G, Bouchier C, Frangeul L, Moreira S, Sismeiro O, Gouyette C, Mirelman D, Coppee JY, Guillen N. Stress by heat shock induces massive down regulation of genes and allows differential allelic expression of the Gal/GalNAc lectin in Entamoeba histolytica.Eukaryot Cell. 2006, 5(5):871-5
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Activity Reports 2007 - Institut Pasteur
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