Working Group 1: Nucleic-Acid Based Microarrays

Working Group Leader: Peter BONANTS, Plant Research International, Business Unit Biointeractions and Plant Health, P. O. Box 16, NL - 6700 AA WAGENINGEN, (+ 31 317 476213, Fax+ 31 317 418094, Email peter.bonants@wur.nl

• Subgroup 1: Viral Diagnostics
• Subgroup 2: Prokaryotic Diagnostics
• Subgroup 3: Eukaryotic Diagnostics

The objective of this WG is to collect all available information on suitable DNA and RNA markers (i.e., sequences) for phytodiagnostic purposes. As this task requires in-depth knowledge of different fields, such as virology and phytopathology, the WG is divided into three Subgroups. Each Subgroup focuses on one large field with its peculiarities.
For example, many viruses are RNA based and thus require the corresponding markers, and this will be one of the main activities of Subgroup 1. Subgroup 2 will be mainly involved in bacterial diagnostics. Quite a number of bacterial genomes are now fully sequenced, which allows for database search of the most suitable genomic regions for species-level identification. One marker system, the 16S rDNA, is already widely and successfully used for species identification in bacteria and a corresponding chip already exists. Therefore, this marker sequence is a good candidate to be used in microarray based prokaryotic identification. Consequently, one focus of this Subgroup will be to assess the suitability of such a chip on a broad scale in phytodiagnostics and to evaluate potential alternatives. The focus of Subgroup 3 will be the genomes of higher eukaryotes, mainly fungi, nematodes, and arthropods. The large size of each of these three taxa may require splitting this Subgroup further.

Working Group 2: Protein Based Microarrays

Working Group Leader: Neil BOONHAM, Central Science Laboratory, Sand Hutton, York, YO41 1LZ Tel: +44 (0)1904 462000 Fax: +44 (0)1904 462111 Email: n.boonham@csl.gov.uk

In principle, this WG will have the same tasks as WG 1, i.e., to collect all available information on suitable protein markers for phytodiagnostic purposes. As this technology is even more recent than the DNA-based microarray technology, potential Subgroups will be established within the first year, if necessary.


Working Group 3: Bio-informatics and Information Dissemination

Working Group Leader: Ulrich WAGNER, Transcriptome Bioinformatics, Functional Genomics Center Zurich, Uni ETH Zurich, Winterthurerstrasse 190, 8057 Zürich Tel: ++41 (0) 1 635 3923, Fax: ++41 (0) 1 635 3922, Email ulrich.wagner@fgcz.ethz.ch; ulrich.wagner@fgcz.unizh.ch

Subgroup 3.1: Internet Office

This WG will provide the expertise in bio-informatics required for completion of this Action, and it will provide a platform for co-ordination and dissemination of the accumulated information. The main tasks will be: 1) To search public databases, e.g., Genebank, for potential probes; 2) to establish a database with all potential probes, i.e, those from the database search and those communicated by WG 1 and WG 2; 3) to adjust probe design to optimal reaction conditions; and 4) to perform microarray data analysis (in collaboration with WG 4). These tasks may eventually be organised in several Subgroups, yet one specific Subgroup 1 will be formed at the onset of the Action, and its task will be to create an interactive internet homepage for information dissemination. This Subgroup will obtain reports, summaries and discussion contributions from all WG's to be placed on the web-page.

Working Group 4: Chip Production and Analysis

Working Group Leader: Dietmar BLOHM, Universität Bremen, Leobener Strasse, 28359 BREMEN, (+ 49 - 421 218 4780, Fax+ 49 - 421 218 7578 , Email dhb@biotec.uni-bremen.de

Microarray production requires sophisticated equipment that to date is not available in many laboratories. Essentially, a robotic spotting device is needed that allows the probes to be spotted onto the surface of choice for the desired microarray. Alternatively, methods exist for production of short oligonucleotides directly on the chip. These methods, however, are covered by patents and are not easily accessible. In addition to the spotter a microarray reader is required. The members of WG 4 either have this equipment in their own laboratories or they have access to such devices. The main task of this WG will be: 1) microarray spotting and distribution (in collaboration with WG 1 and 2), and 2) microarray scanning and data analysis (in collaboration with WG 3). Close contacts to companies involved in microarray technology will be established to ensure that optimal technology is used and to enable potential collaboration.


Working Group 5: Micro-Array Technology for Environmental Monitoring

Working Group Leader: Xavier NESME, Université Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, 43, boulevard du 11 novembre 1918, 69622 VILLEURBANNE Cedex, (+ 32 4 72 44 82 89, Fax+ 32 4 72 43 12 23, Email nesme@univ-lyon1.fr

The objective of this new Working Group is to collect information to develop MT for environmental monitoring in agro-ecosystems as required for instance to evaluate the impact of phytosanitary or other pollutant input, of agricultural practices or of other relevant ecological factors. For this purpose, MT may be used to measure the effect on three environmental indicators:

• community diversity (meta-genome fingerprinting)
• key gene expression of functional communities (marker function)
• whole genome expression of selected strains (bio-marker expression).