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Meeting COST 853
Agricultural Biomarkers for Array-Technology

WG 4 Chip production and analysis
and
WG 5 Environmental monitoring

Meeting site:
Villeurbanne, Campus scientifique de La Doua
INSA Bâtiment La Rotonde

Tuesday, November 29

13:30 Registration
14:00 Welcome address: Philippe Normand

Working Group 5 "Environmental Monitoring"
Introduction Xavier Nesme

Genomic diversity

14:30 O-01 Alice Guidot, Stéphane Genin, Philippe Prior, Christian Boucher
DNA chips and comparative genomics reveal evolution of the plant pathogenic bacterium Ralstonia solanacearum.

15:00 O-02 Philippe Marullo, Gaël Yvert, Denis Dubourdieu,Michel Aigle
Use of CGH with microarray to analyze functional QTL in wild Saccharomyces cerevisiae.

15:30 – 16:00 Coffee Break

16:00 O-03 Xavier Bailly, Gilles Béna, Vanina Lenief, Philippe de Lajudie, Jean-Christophe Avarre
“Lab-made” macroarrays for genotype analysis of bacterial populations of Sinorhizobium.

16:15 O-04 Zewdu Terefework, Petri Penttinen, Dario Greco, Lars Paulin, Petri Auvinen, Kristina Lindström
CGH on Sinorhizobium meliloti microarrays to show inter- and intra-specific genetic variation

16:30 O-05 Denis Costechareyre, Perrine Portier, David Chapulliot, Catherine Lerondelle, Vincent Daubin, Tim Vogel, Xavier Nesme
AFLP, MLSA and pangenomic microarrays to study the genome divergence between and within species in Agrobacterium spp.

16:45 O-06 Christian Oste
CGS: a two-step approach to characterizing genomic variability in prokaryots

17:15 – 18:30 Discussion & Poster session

20:00 Dinner. A taste of Lyonnaise specialities

Wednesday, November 30
Working Group 5 "Environmental Monitoring"
(continued)

Meta-genome fingerprinting, marker functions and metagenomics

8:30 O-07 Alexander Loy
Isotopic labeling and PhyloChips: Exploring ecophysiology of microbial communities.

9:00 O-08 Benoît Remenant, Hervé Sanguin, Timothy M. Vogel, Geneviève L. Grundmann
Use of a taxonomic microarray for bacterial diversity assessment in soil at the microscale.

9:15 O-09 Nina Silkenbeumer, Kristina Kappel and Dietmar Blohm
The fish-chip as a first step for measuring fish biodiversity in the marine environment

9:30 O-10 Nancy Stralis-Pavese, Angela Sessitsch, Andrea Watzinger, Thomas Reichenauer, Alexandra Weilharter, LeventeBodrossy
High-throughput analysis of methanotroph diversity and community structure using a microbial diagnostic microarray.

9:45 O-11 Arjen Speksnijder
Recovery and real time analysis of functional genes in antagonistic soils.

10:00 O-12 Angela van Hoek
Detection of antibiotic resistance genes by oligonucleotide microarray analysis

10:15 – 10:45 Coffee Break

10:45 O-13 Cyrille Jarrin, Aurélien Ginolhac, Renaud Nalin
Development of molecular markers for the identification of novel biosynthetic pathways by HTS of metagenomic libraries.

Bio-marker expression

11:05 O-14 Aurélie Darchis, Arnaud Lagorce, Fabien Munier, Jean-Benoit Morel, Rick De Rose, Roland Beffa, Marc-Henri Lebrun
Transcriptional Analysis of genes from the Pathogenic Fungus Magnaporthe grisea during rice infection using genome wide DNA arrays.

11:25 O-15 Gaël Le Trionnaire, Beatriz Sabater-Muñoz, Fabrice Legeai, Alessandra Benedetto, Joël Bonhomme, Jean-Pierre
Gauthier, Stéphanie Jaubert, Nathalie Leterme, Carole Dossat, Patrick Wincker, Jean-Christophe Simon, Denis Tagu
A pea aphid cDNA array to study phenotypic plasticity

11:45 O-16 Hubert Charles, Federica Calevro, José Viñuelas
Transcriptional responses of Buchnera aphidicola to combined amino acid and osmotic stress in the diet of its symbiotic partner, Acyrthosiphon pisum.

12:05 – 12:30 Discussion

12:30 – 14:00 Lunch

Working Group 4 "DNA Chip technology"

14:00 O-17 Dietmar Blohm
A worldwide microarray co-operation network offered by the CAG of the University of Bremen

14:30 O-18 Georg Nies, Diethard Tautz
Implementation of a DNA-Taxonomy concept on Microarrays

15:00 O-19 Catherine Hänni
Identification of vertebrate species using microarrays

15:20 O-20 Carole Vachon
AQUAGEN project: a full process for controlling microbiological quality of drinking water using a high-density microarray

15:40 – 16:10 Coffee Break

16:15 O-21 Florence Hommais , Sabrina Pereira, Cécile Acquaviva, Patricia Escobar-Páramo, and Erick Denamur
Single Nucleotide Polymorphism Phylotyping in bacteria

16:30 O-22 Richard Thwaites, Christine Henry
Advantages and disadvantages of using microarrays for specific sequence detection.

16:45 O-23 Mojca Milavec, Katja Cankar, Drago Kuzman, Peter Juvan, Kristina Gruden
How to prepare custom potato microarray.

17:00 O-24 Ingrid H. Franke-Whittle, Susanne H. Klammer, Sabine Mayrhofer, Heribert Insam
Comparison of different labeling methods for the production of labeled target DNA for microarray hybridisation.

17:15 O-25 Sascha Todt, Dietmar Blohm
Considering hybridisation efficiency as a necessity for quantifying of microarray analyses

17:30 O-26 Marianna Szemes, Ronald van Doorn, Els Nijhuis, Annette Dullemans, Peter Bonants, Marjanne de Weerdt, Cor D. Schoen
Diagnostic application of padlock probes - multiplex detection of plant pathogens using universal microarrays.

17:45 – 18:00 Discussion

18:00 Closing

Posters (WG4 & WG5)

P-01 Arjen Speksnijder
Metagenomics of antagonistic soils

P-02 Martine Maes, Baeyen S., Van Bost M.A., Cottyn B.
Influence of soil treatments on the bacterial community structure of strawberry rhizosphere.

P-03 B. Scherm, M.A. Demontis, S. Ghignone, M. Schmoll, C. P. Kubicek, Quirico Migheli
A rapid substraction hybridization approach for identifying and cloning differentially expressed genes during the interaction between Trichoderma harzianum and Rhizoctonia solani.

P-04 Quarta A., Felis G., Dellaglio F., Morea M., Palmiro Poltronieri
Comparison between tuf and recA-based primers for Identification of Lactobacillus communities using oligonucleotide arrays

P-05 Hervé Sanguin , Benoit Remenant, Arnaud Dechesne , Pascal Simonet, Tim M. Vogel, Philippe Normand, Xavier Nesme, Yvan Moënne-Loccoz Y, Geneviève L. Grundmann
Application of a 16S taxonomic microarray to assess bacterial community diversity in the environment.

P-06 Aleksandra Trzewik, Kasia Wiejacha, L.B. Orlikowski
An occurrence of Phytophthora spp. in natural stands of Alnus spp. in Poland

P-07 José Viñuelas, Federica Calevro, Jacques Bernillon,Yvan Rahbe, Gérard Febvay, Jean-Michel Fayard, Hubert Charles
Genomic DNA: an attractive candidate for microarray data normalization

P-08 Dietmar Blohm, Doris Meyerdierks
The EU-project “Gensensor-Nanoparts”

P-09 Nina Silkenbeumer, Mark Kochzius, Dietmar Blohm
The EU-project “Fish-and-Chips”

P-10 Almira Ramanaviciene, Irena Vitkauskien, Arunas Ramanavicius
Immobilization methods for electrochemical DNA chip technology.

P-11 Arunas Ramanavicius, Jurgita Kapciunaite, Almira Ramanaviciene
Alternative DNA detection methods.

P-12 C. Schoen, Arjen Speksnijder, A. Dullemans, E. Nijhuis, M. Szemes, R. van Doorn, P. Bonants.
Padlock probe technology, vision of a universal, multiplex diagnostic system for versatile applications.

P-13 Emmanuel Prestat, Christine Oger-Desfeux, Benoît Remenant, Hervé Sanguin, Geneviève Grundmann, Timothy M. Vogel, Christian Gautier
Interactive Microarray Data Management System : A tool to help with the design and analysis of phylogenetic microarrays for the study of bacterial communitie.