WORKINGGROUP 1
  • Participants:

    Participant
    Organization
    E-mail
    Phone number
    Fax
    Ake LUNDKVIST  Sweden  ake.lundkvist@smi.se  -  - 
    Anders ALDERBORN  Sweden  anders.alderborn@genpat.uu.se  +46 18 471 44 32  +46 18 471 48 08 
    DAVEY Hazel  UK  hlr@aber.ac.uk  +44 1970 621829  - 
    Dimitrios FRANGOULIDIS  Germany  DimitriosFrangoulidis@Bundeswehr.org  +49 89 3168 3869  +49 89 3168 3292 
    Erhan PISKIN  Turkey  erhanpiskin@biyomedtek.com  +90 312 2363577  +90 312 2363657 
    FRANCOIS Patrice  Switzerland  patrice.francois@hcuge.ch  +41 (0) 22 372 93 38  +41 (0) 22 372 98 30 
    Garteth Wyn GRIFFITH  UK  gwg@aber.ac.uk  +44 (0) 1970 622325  +44 (0) 1970 622350 
    HUYGHE Antoine  Switzerland  antoine.huyghe@genomic.ch  +41 (0) 22 372 93 38  +41 (0) 22 372 98 30 
    Jacques SCHRENZEL, Chair  Geneva University Hospitals; Switzerland  jacques.schrenzel@genomic.ch  +41 (0) 22 372 73 01  + 41 (0) 22 372 73 08 
    Jasper KIEBOOM  The Netherlands  jasper.kieboom@tno.nl  +31 15 284 3011  +31 15 284 3963 
    Jean-Luc GALA  UCL; Belgium  gala@lbcm.ucl.ac.be  +32 2 764 3165  +32 2 764 3166 
    Joachim FREY  Switzerland  joachim.frey@vbi.unibe.ch  +41 (0) 31 631 24 14  +41 (0) 31 631 26 34 
    Karl WALRAVENS  CODA-CERVA-VAR; Belgium  kawal@var.fgov.be  +32 (0) 2 379 13 03  +32 2 379 13 36 
    Levente BODROSSY  ARCS Seibersdorf; Austria  levente.bodrossy@arcs.ac.at  +43 50550 3548  +43 50550 3444 
    Martien P. BROEKHUIJSEN, M. Sc.  TNO Defence, Security and Safety  martien.broekhuijsen@tno.nl  +31 15 284 3491  +31 15 284 3963 
    Michael MULVEY  Canada  Michael_mulvey@phac-aspc.gc.ca  +1 204 789 2133  +1 204 789 5020 
    Paola PILO  Switzerland  paola.pilo@vbi.unibe.ch  +41 (0) 31 631 23 69  +41 (0) 31 631 26 34 
    SCHOEN Cornelis  Plant Research International The Netherlands  cor.schoen@wur.nl  0031 317 47 6026/480601  0031 317 41 8094 
    Tanja KOSTIC  ARCS Seibersdorf; Austria  Tanja.Kostic@arcs.ac.at  +43 50 550 3635  +43 50 550 3666 
    Ulrich NUBEL  Germany  nuebelu@rki.de  +49 3943 679 338  +49 3943 679 317 


  • Description:
    WG1 Technology platform
    • Flowcytometric method with cytometric beads.
      • Objective:
        Development of a multiplexed flow array for the simultaneous detection of different pathogenic agents and/or pathogens products.
      • Description:
        Suspension arrays of microspheres analyzed using flow cytometry offer a new approach to multiplexed assays for large-scale screening applications. By optically encoding micron-sized polymer particles, suspension microarrays can be created to enable highly multiplexed analysis of complex samples. Each element in the array is comprised of a subpopulation of particles with distinct optical properties and each array element bears a different surface receptor; these may be oligonucleotides, antigens or antibodies. These multiply fluorescent microspheres, conjugated to different probes, constitute the solid phase for detecting the presence of a biological agent?s gene or antigen in samples. These assays have proven to have at least the same sensitivity as traditional immunoassays, in addition, they have a high throughput capacity, and provide a wide analytical dynamic range. Additionally, they have multiplexing ability and can be used simultaneously with different types of probes (DNA, Lipid, proteins etc.).
        Therefore, a major advantage for the diagnosis of biological threat agents would be to detect the presence of specific DNA sequences, antigens and/or toxins simultaneously in a suspect sample. The project contains two approaches that will be developed simultaneously: a DNA microarray and an antibody microarray. A suspension microarray based on the detection of specific nucleic acid sequences will be developed using nucleic captured/revelation probes. This will be compared to a suspension microarray using antibodies directed against antigens specific for the different biological agents. Changing the nature of targets by using antibodies as probes, will allow us to detect a wider range of agents? products such as toxins.
    • Micro-array.
      • Objective:
        To use DNA microarray technology for characterisation of microorganisms and to evaluate a new diagnostic test for the broad-range diagnosis/detection and characterisation of specific pathogens.
      • Description:
        Genomic sequencing, although very popular for the genome-wide analysis of microorganisms and very successful in terms of generated knowledge, is not suitable for the study of large quantities of strains. To discover and use new and suitable genetic markers for broad-range diagnostics of microorganisms, many strains need to be examined by comparative genomics (DNA-DNA hybridisation experiments). Microarray technology is very suitable for a genome-wide analysis of many strains in parallel. It will also define unique fragments within these organisms that will allow the mircoorganisms under investigation to be fully characterised in all aspects of their genome. These fragments may encode virulence, which upon further investigations may lead to targets for vaccines and antimicrobial compounds. They can also be important for immunological investigations.
        Microarray technology is technically very demanding and requires specialised and skilled staff. Moreover, it is a substantial investment for a laboratory.
        High-throughput-PCR will be applied on genomic libraries from the micro-organisms under investigation, or alternatively, oligo-probes will be designed of strains that have been fully sequenced, whereafter the PCR products or oligo-probes will be spotted onto a solid phase. DNA from comparative strains will be labelled and hybridised to the probes on the slide.
        Microarray technology relies heavily on bio-informatics. There is a great need for specialised software methods for the design of microarrays, normalisation of array data, analysis of array data, and handling of the huge resulting databases. This will involve a significant part of the effort. Array design has been a neglected area. However, with designed arrays data quality control will be much more efficient than today and in addition array design has the potential to improve analysis methods and in particular normalization methods. We will focus on developing strategies for array design and developing analysis methods that take full advantage of the design. In particular three areas will be considered: data quality methods, normalization methods and methods for estimating distributions of test statistics. In addition, the ambition is to develop a general statistical model that can describe DNA microarray data.
        To convert the data into a common standard for transforming the existing data from participants, so that the synergies coming from common representation of data may be obtained, shall require a lot of effort. A User Manual will be specifically designed for the members of the Network. Courses for the users will be organized in order to create a common expertise for mining expression data.
  • Actions:

    Action
    Description
    download
    Booklet on microarray technology NOTE that the chapters are to be sent to jacques.schrenzel@genomic.ch by April 1st, 2007


  • Publications:

    Name
    Year
    Title
    Periodical
    Volume
    Page
    Pubmed
    A.Loy and L.Bodrossy 2006 Highly parallel microbial diagnostics using oligonucleotide microarrays Clinical Chimica Acta 363(1-2) 106-119 link to pubmed
    L.Bodrossy and A.Loy 2006 Oligonucleotide microarrays in microbial diagnostics Encyclopedia of Medical Genomics and Proteomics (Editors: J. Fuchs and M. Podda) Online edition. DOI: 10.1081/E-EDGP-120041475.Taylor & Francis - - link to pubmed
    L.Bodrossy, N.Stralis-Pavese, M.Konrad-K?szler, A.Weilharter, T.Reichenauer, D.Sch?fer, and A.Sessitsch 2006 mRNA-based parallel detection of active methanotroph populations using a diagnostic microarray Applied and Environmental Microbiology 72 (2) 1672-1676 link to pubmed
    A.Loy, M.W. Taylor, L.Bodrossy and M.Wagner 2006 Applications of Nucleic Acid Microarrays in Soil Microbial Ecology Molecular Techniques for Soil and Rhizosphere Microorganisms (Editors: JE Cooper, JR Rao). CABI Publishing, Wallingford, Oxfordshire, UK - 18-41 link to pubmed
    A. Sessitsch, E. Hackl, P. Wenzl, A. Kilian, T. Kostic, N. Stralis-Pavese, B. Tankouo Sandjong and L. Bodrossy 2006 Diagnostic microbial microarrays in soil ecology New Phytologist 171 719-736 link to pubmed
    T.Kostić, A.Weilharter, S.Rubino, G.Delogou, S.Uzzau, K.Rudi, A.Sessitsch and L.Bodrossy 2006 A microbial diagnostic microarray technique for the sensitive detection and identification of pathogenic bacteria in a background of non-pathogens Analytical Biochemistry In Press - link to pubmed
    Assun?ao, P., Antunes, N.T., de la Fe, C., Rosales, R.S., Poveda J.B and Davey, H.M. 2006 Flow cytometric determination of the effect of antibacterial agents on M. agalactiae, M. putrefaciens, M. capricolum subsp. capricolum and M. mycoides subsp. mycoides large colony-type Antimicrobial Agents and Chemotherapy 50 2845-2849 link to pubmed
    Stratilo CW, C. Lewis, L. Bryden, M. R. Mulvey, D. Bader 2006 Identification of Bacillus anthracis isolates using single nucleotide repeat analysis (SNRA) Journal of Clinical Microbiology 44 777-782 link to pubmed
    Gustafsdottir SM, Nordengrahn A, Fredriksson S, Wallgren P, Rivera E, Schallmeiner E, Merza M, Landegren U. 2006 Detection of individual microbial pathogens by proximity ligation Clinical Chemistry 52 1152-1160 link to pubmed
    T.Kostić, A.Weilharter, A.Sessitsch and L.Bodrossy 2005 High sensitivity, PCR-free detection of microorganisms and their functional genes using 70mer oligonucleotide diagnostic microarray Analytical Biochemistry 346 333-335 link to pubmed
    F. Lecouvet, L.M. Irenge, B. Vandercam, A. Nzeusseu, S. Hamels, J.L. Gala* 2004 The etiologic diagnosis of infectious discitis is improved by amplification-based DNA analysis Arthritis & Rheumatism 9 2985-94 link to pubmed
    S. Hamels, J.L. Gala, S. Dufour, P. Vannuffel, N. Zammateo, J. Remacle 2001 Consensus PCR and microarray for diagnosis of the genus Staphylococcus, species, and methicillin resistance Biotechniques 31 1364-1366,1368,1370-1372. link to pubmed
    Antwerpen et al. 0 DNA microarray for detection of antibiotic resistance determinants in Bacillus anthracis and closely related Bacillus cereus Mol. Cell. Probes In Press - link to pubmed