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 equipqment and the expertise for making and using microarrays (glass slides hybridized with fluorescent targets) and macroarrays (nylon membranes hybridized with radioactive targets). We are also developing the bioinformatical and statistical tools necessary for the analysis of the results and for their handling.

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 targets (fluorescent and radioactive), in the analysis of hybridization signals and 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. The selected projects receive fundings from the Genopole.

Following the second call for proposals (October 2001), 5 projects have been started in 2002.

For the projects based on the macroarray technology (arraying of PCR products on nylon membranes and hybridization with radioactive targets), 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 targets). These macroarrays are now in use by the teams of the Pasteur Institute involved in the projects.

The activities of the platform are centered on microbiology (model and pathogen microorganisms). Nevertheless, part of our activities have also been oriented in 2002 to the development of chips dedicated to higher eukaryotes (human). There is indeed an important demand on the campus for developing arrays aiming at the analysis of the response of the host to the infection. A first array containing 1000 human genes involved in the response at the infection by Shigella flexneri has been developed. This array will be developed and upgraded to be usable by other teams interested in these questions.

In 2002, we have continued the development of the microarrays technology. This concerns among others the spotting of long oligos instead of PCR products and has been done in the frame of a project aiming at the global gene expression analysis in Plasmodium falciparum. This project is part of a global project (starting in February 2003) which involves 20 laboratories from France and from the International Network of the Pasteur Institutes. This global project aims at the analysis of the transcriptome during the cellular cell cycle of the parasite and in response to various immune, environmental or drugs pressures. A first batch of more than 300 microarrays containing 6000 oligos has been spotted. It has been used for establishing all the experimental settings (growth conditions, nucleic acids preparations, synchronizations…) of this project and for time course experiments. Several statistical tools (normalisation, identification of differentially expressed genes, clustering) have also been tested on the data obtained in the frame of this project. We have also started in collaboration with the annotation platfrom the building of a database for the handling and storage of microrrays results. This database will be available in March 2003.

The DNA chips platform has also some service activity. This activity consists in a limited particpation according to the availability of the equipment and of the people of the platform. The platform has also been involved in the practical courses of two Pasteur Courses (Genomes Analysis, Molecular and Cellular Genetics).

Keywords: Transcriptome analysis, comparative genomics, microarrays, macroarrays, microbiology, infectious diseases