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  Director : Coppée Jean-Yves (jycoppee@pasteur.fr)


  abstract

 

The aim of the platform is to develop biochip technology for the study of model microorganisms and infectious diseases (comparative genomics and gene expression profiling). We have the expertise in the making and the analysis of microarrays (glass slides hybridized with fluorescent probes) and macroarrays (nylon membranes hybridized with radioactive probes).



  report

cale

The availability of the complete genome sequences of a growing number of microorganisms and the emergence of new technologies for the study of gene expression lead the Pasteur Institute to set up a platform dedicated to the fabrication and analysis of biochips for the study of model microorganisms and infectious diseases. These studies involve both the agents responsible for these pathologies (comparative genomics and gene expression profiling) and the response of the host (gene expression profiling). The platform has at its disposal robotic stations for the arraying of nylon membranes and glass slides. It has the expertise in the labeling and hybridization of the probes (fluorescent and radioactive), in the analysis of hybridization signals and in the interpretation of the data. The platform is in charge of projects selected by internal calls for proposals. Most of the selected projects have national or european frameworks.

Projects of the year 2000-2001

Following the first call for proposals, 5 projects have been completed and two others are in progress:

Project

Density / number of macroarrays

Collaboration

 

Study of global regulations in the model microorganism Escherichia coli.

300 PCR / 90 membranes

P. Bertin

Analysis of the distribution of non ubiquitous ORFs in Helicobacter pylori.

388 PCR / 200 membranes

A. Labigne

Study of the sulfur metabolism in the model microorganism Bacillus subtilis.

130 PCR / 12 membranes

P. Bertin

Identification in Photorhabdus luminescens of genes encoding biopesticides and of regulatory genes controlling virulence .

200 PCR / 60 membranes

P. Bertin

Global gene expression analyses of the pathogen bacterium Listeria monocytogenes. Analysis of the transcription of the model strain EGDe and comparison of strains from different origins

2840 PCR / 300 membranes

P. Glaser

P. Cossart

Global gene expression analyses of pre-erythrocytic stages in Plasmodium berghei.

In progress

R. Menard

Nylon macroarrays for the analysis of the gene expression profile of Aspergillus nidulans.

In progress

C. d'Enfert

For all these projects based on the macroarray technology (arraying of PCR products on nylon membranes and hybridization with radioactive probes), the platform performed the PCR amplifications (primers design, amplification reactions, PCR controls by agarose electrophoresis, random sequencing of 10 % of the PCR products), the arraying and the quality controls of the macroarrays (hybridization with control probes). These macroarrays are now in use by the teams of the Pasteur Institute involved in the projects.

Developments of the microarray technology

Important developments of the microarray technology have also been performed.

These include :

  • Glass slides chemistry (three types of slides are used : polylysines, amines, aldehydes)
  • Labeling of the probes (direct and indirect labeling of RNA and DNA)
  • Arraying of the slides (PCR products and oligonucleotides)
  • Quality controls (RNA, labeling efficiency, arraying quality)
  • Reproducibilty of the so obtained gene expression profiles

Most of these improvements have been obtained in the frame of a project aiming at the global gene expression analysis in Plasmodium falciparum (collaboration with Peter H. David, Unité d'Immunologie Moléculaire des Parasites). A complete set of 6000 oligonucleotides (70mer) covering most of the P. falciparum identified genes has been spotted on polylysine glass slides. These slides are now in use for the comparison of the gene expression profiles associated with the different development stages of the parasite.

 

 

 



  web site

puce More informations on our web site


  publications

puce Publications of the unit on Pasteur's references database


  personnel

  Office staff Researchers Scientific trainees Other personnel
     

Maitournam Aboubakar

Coppée, Jean-Yves, jycoppee@pasteur.fr

Lacroix Céline, clacroix@pasteur.fr

Schiavo Angèle, angsch@pasteur.fr

Sismeiro Odile, osisme@pasteur.fr


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