COST Action 853 Agricultural Biomarkers for ArrayTechnology

1
COST Action 853Agricultural Biomarkers for
Array-Technology
Chairman Jürg E. Frey(a)
Vice-Chairman Günter Adam
Scientific Secretary John Williams
(a)Swiss Federal Research Station for Fruit
Growing, Viticulture and Horticulture, P.O. Box
185, CH-8820 Wädenswil, Switzerland
France Germany Greece Hungary
Signatories
Cyprus Czech Republik Denmark Finland
Italy Lithuania TheNetherlands Norway
Poland Portugal Slovenia Spain
Switzerland United Kingdom
Austria Belgium Bulgaria
Objectives
Working Groups
The main objective of COST Action 853 is to
establish and support Microarray technology - in
the form of nucleic acid- and protein-based
arrays - as a new tool for breeding, diagnosis,
and high throughput screening in the field of
agriculture.  The need for a flexible system
that allows molecular diagnostics of large sample
sizes of many species has long been recognised.
However, current technology generally requires
focusing on narrow taxonomic groups. Microarray
technology, being based on highly parallel
simultaneous analysis, has shown its potential
for large-scale genome analysis. The technology
would allow for simultaneous querying of hundreds
of species specific markers and will thus enable
the production of microarray chips that can be
used for larger taxonomic groups such as the
entire bacteria or, in higher eukaryotes, for
example the entire class of insecta. The Action
that was launched in March 2002 and to date
involves 21 participating countries. Information
can be obtained on our website under
http//www.COST853.ch
WG1 Nucleic Acid Based Microarrays
WG2 Protein Based Microarrays
WG3.1 Internet Office
WG3 Bioinformatics and Information Dissemination
WG4 Chip Production and Analysis
WG5 Microarray Technology forEnwironmental
Monitoring
Large diversity of target organisms
Photographs mactode
Microarray-Technology Evaluation and development
of nucleic acid and protein arrays
Example 2 Genome marker approach
Example 1 Sequence specific approach
Sequence information
Probe- and oligonucleotide design
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1
In silicio designed primers and probes
(inverse of primer) with random sequence
Organism 1
3-AACTTGTGCAGCACG-5
Organism 2
3-AACTGTTCACCCC-5
3-GGACTACCAGACC-5
Probe Design of specific oligonucleotide
sequences
2
Spotting
of random probes onto microarray slide
2
3-TGCCCAC-5
3-CCTTCAT-5
AACTTGTGCAGCACG
Spotting
of designed probes onto microarray slide
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GGACTACCAGACC
AACTGTTCACCCC
TGCCCAC
Labeling of random primers with a match on the
genome by
single-base-extension of primers
CCTTCAT
3
Labeling of target DNA using labeled primers or
dNTPs
Labeling by single-base extension of target
matching primers
DNA Extraction
4
DNA Extraction
PCR-amplification and labeling
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3
TTGACAAGTGGGGT
Organism 3
ddNTP
5
GGAAGTA
3
AACTGTTCACCCCA
5
3
Organism 1
5
3
GGAAGTA
Hybridization, reading and identification
4
Hybridization, reading and identification
5
GGAAGTA
TTGACAAGTGGGGT
Organism specific pattern
Sequence-specific detection of
CCTTCAT
AACTGTTCACCCC
Organism 1
Fluorescence detection
Fluorescence detection
TGCCCAC
Contents by J. E. Frey M. Pfunder
http//www.COST853.ch