Cost-meetings Eden Roc, esp may 2007

E. Meeting Comments and Final Discussion

This final combined COST 853 WG and ARRAY meeting was the extraordinary highlight of a highly successful COST Action. We had a tight schedule and, despite the extremely pleasant environment, all sessions attracted virtually all attendants so that the speakers could present their results in a full house. Many excellent talks were held by members of COST Action 853 as well as of members of the other participating COST Actions. These high-quality presentations were accompanied by extraordinary presentations of invited experts that gave a up-to-date keynote lectures of the cutting-edge topics in the field. Finally, the contributions of the representatives of several companies working in the field of microarray technology contributed important input in their talks as well as in the discussions. The summaries of all talks have been included in this report. As described in the MCM report, the MC-members decided to assemble short presentations on the activities and achievements of this COST Action 853 that will be published as a book to be printed by COST. Furthermore, the chairman will continue hosting the webpage to allow COST members access to the achievement of this action for the foreseeable future.

Final Discussion Summary
Several topics to be addressed were initially collected and are outlined in Fig. 1. They included 1) collaboration, 2) PCR free amplification systems and microfluidics, 3) improvement of Tm calculations, 4) database establishment, 5) quantification of multiple targets, and 6) usability of results.

On point 1, P. Bonants suggested that if we collaborate more closely we may be much more successful because we have access to much larger sample sizes and we may be able to much more thoroughly test our methods. This suggestion was agreed upon by all attendants and likely will be realized by several laboratories. With respect to point 2, C. Schoen mentioned that it would be important if we could have some influence on the nanotechnology development which is where this research is conducted. G. Adam proposed to contact the nanotechnology group in Hamburg and to establish a link between C. Schoen and this group. A. Ramanavicius mentioned that he disposes of a variety of nanoparticles for a range of uses and offers them to colla-borators. Points 3 and 4 were discussed together. M. Sip and J.E. Frey mentioned that if we could include probes and their sequences that did not perform well in the database this would eventually allow to develop better algorithms for Tm calculations. However, the descriptions should be very detailed as the conditions for the different techniques (Taqman, regular hybridisation, regular PCR, single base extension labelling, etc.) are very different. P. Bonants finally suggested to just add references into the database, together with the contact addresses, in order to keep the workload to a minimum. G. Adam suggested to try a wikipedia-like interface, in which each contributor would enter his/her data him/herself. Point 5 was raised by P. Bonants who is looking for collaboration in the project using the high-density quantitative real-time PCR chip of BioTrove. The last point was raised by X. Nesme and G. Adam. Nesme raised the point that to date, many different microarray platforms exist which leads to a problem of marked acceptance. He asks how, under these conditions, a wide use of microarrays may be promoted. In the following discussion several problems were analysed and it was concluded that the market will solve the problem. No individual method will be able to survive unless there is a market. Also, with current methods and equipment, microarray technology does not yet lend itself to mass-screening. Furthermore, cheap fluorescent readers are not yet in sight, however, this problem may be solved by using electronic detection instead. The discussion eventually was very fruitfully extended by two company representatives, J. Clough of OGT and Chr. Oste of Nimblegen, who explained the market side of the problems. The discussion ended with the conclusion of J.E. Frey that some of the members of this action have reached a very high state of development that would render collaborative projects with companies a very promising strategy.

Finally, we would like to emphasize the general regret of most MCmembers about the fact that this extremely active and fruitful COST Action 853 came to an end. Many of us have the feeling that we are just now beginning to earn on the exceptional efforts to establish a solid basis for microarray based agricultural diagnostics and other implementations of this technology. We feel that the great potential for synergism in our collaboration is only now about to appear. Thus, we would expect that if we could continue this very fruitful collaboration under a new COST Action with a similar technology focus, there would be an even greater outcome than the already highly impressive results that could be elaborated under this extremely successful COST Action 853.
The discussed topics are summarised in the Mindmap below:

F. Participant list



Abell Guy

[e-mail]

[phone]

Austrian Research Centers GmbH - ARC

Seibersdorf,

Austria
Adam Günther

[e-mail]

[phone]

Biozentrum Klein Flottbek

Hamburg

Germany
Adams Ian

[e-mail]

[phone]

Central Science Laboratory

York

United kingdom

Agha Saif

 [e-mail]

+ 34 973 00 34 34

IRTA

Lleida

Spain
Aharoni Asaph

[e-mail]

+972 - 8 - 9343643

Weizmann Institute of Science

Rehovot

Israel
Beckmann Christiane

[e-mail]

[phone]

Kantonales Laboratorium Basel-Stadt

Basel

Switzerland

Bendixen Christian

[e-mail]

[phone]/ [phone]

University of Aarhus

Tjele

Danemark
Bergervoet Jan

[e-mail]

[phone]

Plant Research International

Wageningen

the Netherlands
Blank Livia

[e-mail]

49-6722-502-646

Forschungsanstalt Geisenheim

Geisenheim

Germany
Bonants Peter

[e-mail]

+31.317.476213

Plant Research International BV

Wageningen

The Netherlands
Boonham Neil

[e-mail]

[phone]

Central Science Laboratory

York

United kingdom

Budroni Marilena

[e-mail]

[phone]

Sezione di Microbiologia Dip. Scienze Ambientali Agrarie Biotecnologie Agroalimentari

Sassari

Italy
Buncek Martin

[e-mail]

[phone]

GENERI BIOTECH s.r.o.

Hradec Kralove

Czech Republic
Camps Céline

PhD student

[e-mail]

[phone]

ISVV / INRA Bordeaux

Villenave d’Ornon

France
Canovas Angela

 [e-mail]

[phone]

IRTA

Lleida

Spain
Carbone Fabrizio

[e-mail]

[phone]

ENEA

Rotondella

Italy
Claes Loes

[e-mail]

[phone]

Scientia Terrae Research Institute

Sint-Katelijne-Waver

Belgium
Clough James

[e-mail]

44 1865 856359

Oxford Gene Technology

Yarnton Oxford

United kingdom
Duffy Brion

[e-mail]

[phone]

Agroscope Changins-Wädenswil

Wädenswil

Switzerland

Ferrarini Alberto

[e-mail]

[phone]

Universita di Verona

Verona

Italy
Förster Frank

[e-mail]

[phone]

University Hamburg, Biocenter Klein Flottbek

Hamburg

Germany
Frey Jürg

[e-mail]

[phone]

Agroscope Changins-Wädenswil

Wädenswil

Switzerland

Glissant David

[e-mail]

[phone]

Universita di Verona

Verona

Italy
Glover Rachel

 [e-mail]

[phone] (x 3215)

Central Science Laboratory

York

United kingdom
Grinholc Mariusz

[e-mail]

[phone]

Intercollegiate Faculty of Biotechnology University of Gdansk

Gdansk

Poland
Hatey François

[e-mail]

[phone]

INRA, Laboratoire de Genetique Cellulaire

Castanet-Tolosan

France
Hoheisel Jörg

[e-mail]

Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum

Heidelberg

Germany
Huber Elisabeth

[e-mail]

[phone]

ARK-Genomics

Roslin

United kingdom

Justé Annelies

[e-mail]

0032 15 30 55 90

Scientia Terrae Research Institute

Sint-Katelijne-Waver

Belgium
Kochzius Mark

[e-mail]

[phone]

Universität Bremen

Bremen

Germany
Kogovšek Polona

[e-mail]

[phone]

National Institute of Biology

Ljubljana

Slovenia

Korkeala Hannu

[e-mail]

[phone] [phone]

University of Helsinki, Department of Food and Environmental Hygiene

Helsinki

Finland
Kostic Tanja

[e-mail]

 ARC

Seibesdorf

Austria
Lenz Ondrej

[e-mail]

[phone]

Biology centre ASCR

Ceske Budejovice

Czech Republic
Leppäranta Outi

[e-mail]

[phone]

Finnish Food Safety Authority Evira

Helsinki

Finland
Lindström Miia

[e-mail]

[phone]

Department of Food and Environmental Hygiene, University of Helsinki

Helsinki

Finland
Maghuly Fatemeh

[e-mail]

[phone]

Institut of applied Microbiology

Vienna

Austria
Malinowski Tadeusz

[e-mail]

++48 46 8345335

Research Institute of Pomology and Floriculture

Skierniewice

Poland
Marais-Colombel Armelle

[e-mail]

[phone]

INRA, UMR GDPP, Virology group

Villenave d’Ornon

France
Martinez Giner Maria

[e-mail]

[phone]

IRTA

Lleida

Spain
Mendes Marta

[e-mail]

[phone]

Institute for Molecular and Cell Biology

Porto

Portugal

Moenne loccoz Yvan

[e-mail]

+ 33 4 72 43 13 49

UMR CNRS 5557 Ecologie Microbienne, Université Lyon 1

Lyon

France
Nesme Xavier

[e-mail]

[phone]

University of Lyon

Lyon

France
Nicolaisen Mogens

[e-mail]

[phone]

University of Aarhus, Faculty of Agricultural Sciences

Slagelse

Danemark

Oger Christine

[e-mail]

33 4 26 23 44 70

PRABI Univ. Lyon1

Lyon

France
Oste Christian

[e-mail]

Nimblegen

Pasquer Frederique

[e-mail]

[phone]

Agroscope Changins-Wädenswil

Wädenswil

Switzerland

Pena Romi

[e-mail]

[phone]

IRTA

Lleida

Spain
Perriere Guy

[e-mail]

[phone]

Laboratoire de Biométrie et Biologie Évolutive Université Claude Bernard Lyon 1

Lyon

France
Perrotta Gaetano

[e-mail]

[phone]

ENEA

Rotondella

Italy
Poltronieri Palmiro

[e-mail]

+ 39 0832422609

ISPA-CNR

Lecce

Italy
Pompe-Novak Marusa

[e-mail]

[phone]

National Institute of Biology

Ljubljana

Slovenia

PortilloBocanegra Mary Esperanza

[e-mail]

+34.925. 26.57.52

Universitad de Castilla

Toledo

Spain
Primiceri Elisabetta

[e-mail]

0832-298338

ISPA-CNR

Lecce

Italy
Prins Theo

[e-mail]

+31.317.475606

Rikilt

Wageningen

The Netherlands

Ramanaviciene Almira

[e-mail]

[phone]

Institute of Immunology of Vilnius University

Vilnius

Lithuania

Ramanavicius Arunas

[e-mail]

[phone]

Vilnius University

Vilnius

Lithuania

Romanowski Tomasz

[e-mail]

0048 58 301 28 07

Intercollegiate Faculty of Biotechnology University of Gdansk

Gdansk

Poland
Sanz-Alférez Soledad

[e-mail]

[phone]

Universidad autonoma de Madrid

Madrid

Spain
Schäfer Wilhelm

[e-mail]

[phone]

University Hamburg

Hamburg

Germany
Schauzu Marianna

[e-mail]

[phone]

Federal Institute for Risk Assessment

Berlin

Germany
Schoen Cornelis

[e-mail]

[phone]

Plant Research International

Wageningen

The Netherlands

Sip Miroslav

[e-mail]

[phone]

University of South Bohemia

Ceske Budejovice

Czech Republic

Slawiak Monika

 [e-mail]

(48) 58 523 63 31

Intercollegiate Faculty of Biotechnology University of Gdansk

Gdansk

Poland
Somervuo Panu

[e-mail]

[phone]

University of Helsinki, Department of Applied Biology

Helsinki

Finland
Suproniene Skaidre

[e-mail]

[phone]

University of Aarhus,

Faculty of Agricultural Sciences

Slagelse

Danemark
Tomlinson Jenny

 [e-mail]

[phone] (x 3215)

Central Science Laboratory

York

United kingdom

Trainotti Livio

[e-mail]

[phone]

Department of Biology, University of Padua

Padua

Italy
Valkonen Jari

[e-mail]

[phone] / [phone]

University of Helsinki, Department of Applied Biology

Helsinki

Finland
Varga Gabriella

[e-mail]

+36 76/494888

Research Institute for Viticulture and Enology

Kecskemét-Miklóstelep

Hungary
Wagner Ulrich

[e-mail]

FGCZ

Zurich

Switzerland

Willians John

[e-mail]

[phone]

COST Office

Brussels

Belgium
Winter Stephan

[e-mail]

[phone]

DSMZ Plant Virus Department

Braunschweig

Germany

	REPORT COST 853 ~ page