1. WP Molecular diagnostics of microorganisms Annual Report 2008, Perugia January 2009 EUROBIOTECH – European Biotechnology Agr. n° 2007-2566 / 001-001 project n° 134310-LLP-1-2007-1-IT-ERASMUS-ENW project n° 134310-LLP-1-2007-1-IT-ERASMUS-ENW Juraj Krajčovič Faculty of Natural Sciences, Comenius University 842 15 Bratislava, Slovakia E-mail: krajcovic@fns.uniba.sk With the support of the Lifelong Learning Programme of the European Union EUROBIOTECH – European Biotechnology Agr. n° 2007-2566 / 001-001 project n° 134310-LLP-1-2007-1-IT-ERASMUS-ENW This project has been funded with support from the European Commission. This publication reflects the views only of the author, and the Commission cannot be held responsible for any use which may be made of the information contained therein

2. Effective DNA identification of microorganisms in clinical, food and environmental isolates several workgroups in a close interconnection of research, education and innovation Partner numberCountryShort-nameApproximate number of staff days Category 1 Category 2 Category 3 Category 4 Lead partner Pnr 35 SlovakiaKrajcovic, J. Univ. Bratislava 40 P(nr) 23LatviaZilevica, A., Univ. Riga12 P(nr) 21ItalyD’Agaro, E., Univ. Udine 12 P(nr) 27PolandJafra, S., Univ. Gdansk12 P(nr) 20ItalyMaffia, M., Univ. Salento 6 P(nr) 20ItalyStorelli, C., Univ. Salento 6 All partners88 Original proposal

3. workpackage Molecular diagnostics of microorganisms Extension of working groups and Workpackage schedule during the Kickoff meeting in Perugia (January 2008) Workpackage schedule proposal prepared together with Prof. Algimantas Paulauskas (Kaunas, Lithuania) (a.paulauskas@gmf.vdu.lt) a.paulauskas@gmf.vdu.lt Dr. Andrej Susek (Maribor, Slovenia) (andrej.susek@uni-mb.si) andrej.susek@uni-mb.si Prof. Ján Turňa (Bratislava, Slovakia) (turna@fns.uniba.sk) turna@fns.uniba.sk

4. Extension, modification/replacement of partners within the workpackage around the workpackage meeting in Bratislava (September 2008): extensions: (i) Univ. Udine (Italy): M. Manzano (marisa.manzano@uniud.it), G. Comi (giuseppe.comi@uniud.it), L. Iacumin (lucilla.Iacumin@uniud.it ) – DNA identification of microorganisms in food and food industry facilities marisa.manzano@uniud.itgiuseppe.comi@uniud.itmarisa.manzano@uniud.itgiuseppe.comi@uniud.it (ii) Univ. Bratislava (Slovakia): H. Drahovská (drahovská@fns.uniba.sk), R. Dušinský (dusinsky@fns.uniba.sk) – DNA identification of microorganisms in food and food industry facilities drahovská@fns.uniba.skdusinsky@fns.uniba.skdrahovská@fns.uniba.skdusinsky@fns.uniba.sk modification: Univ. Gdansk, (Poland): S. Jafra (jafra@biotech.ug.gda.pl) (a mediator), W. Sledz (sledz@biotech.ug.gda.pl) (active person) – molecular diagnostic of plant pathogenic bacteria jafra@biotech.ug.gda.plsledz@biotech.ug.gda.pljafra@biotech.ug.gda.plsledz@biotech.ug.gda.pl replacement: Univ. Maribor (Slovenia): A. Susek replaced by T. Langerholc (tomaz.langerholc@uni-mb.si ) tomaz.langerholc@uni-mb.si

5. Outcomes and users Molecular diagnostics of microorganisms A higher education training course in Molecular diagnostics of microorganisms designed to develop skills in the participants. Training materials and manuals for university students and SME partners which operate in the field of microbe identification DNA identification of bacteria in food Special accent will be based on techniques developed for DNA identification of bacteria in food, i.e. pathogenic bacteria – genus Salmonella, Listeria, Enterococcus and Escherichia and probiotic bacteria – genus Lactococcus, Lactobacillus, Enterococcus and Bifidobacterium

6. Genomics and Bioinformatics Training Course, May 20-22, 2008 Department of Molecular Biology and Center of Genomics Faculty of Natural Sciences,Comenius University Bratislava Participants: 30 PhD students and researchers from universities and scientiffic institutions from Slovak republic

7. Training Course in Genomics and Bioinformatics, Faculty of Natural Sciences, Comenius University Bratislava, May 20-22, 2008; Program of the course: * Methods of DNA manipulation – DNA isolation, recombinant DNA methods, PCR and its modifications, separation and detection of DNA molecules * Real Time PCR – qualitative and quantitative detection of specific DNA molecules (types of probes, reaction mixtures, evaluation of results, MCA) * Fragment analysis (separation and detection of DNA fragments based on high resolution capillary electrophoresis – detection of PCR products, SNaPShot, SNPlex, MLPA * DNA sequencing (principle, methods, technical equipments used, future perspectives) * Methods and instruments for searching of DNA polymorphism (HRM, dHPLC) * Microarray instruments and applications (DNA chips, expression profiles, comparative genomic hybridization, sequencing on chip) * Bioinformatics methods in genomics (public bioinformatics databases and applications, processing of sequencing data, analysis of non-sequencing data) * Automation and high-throughput methods in molecular-genetic laboratory (types of biorobots used in laboratories and possible applications);

8. Training Course in Genomics and Bioinformatics, Faculty of Natural Sciences, Comenius University Bratislava, May 20-22, 2008; Texbooks used: * Kuchta T., Drahovská H., Pangallo D., Siekel P.: Application of Polymerase Chain Reaction to Food Analysis, Food Research Institute, Bratislava (2006); * Turňa J., Stuchlík S., Drahovská H., Gálová Z., Timko J.: Techniques of the recombinant DNA (in Slovak), Bratislava, Veda (2004); * Valková D., Turňa J., Timko J.: Introduction to molecular biotechnology (in Slovak), Bratislava, Veda (2005); * Drahovská H., Minárik G., Ficek A., Szemeš T., Šoltýsová A., Baldovič M., Vlková B.: Genomics and Bioinformatics (in Slovak), Bratislava, Veda (2007) plus preliminary protocols prepared within the workpackage (and still under continuous preparation).

9. Invitation Molecular diagnostics of microorganisms A higher education training courses in Molecular diagnostics of microorganisms designed to develop skills in the participants (university students and SME partners) Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia – June 2009 and 2010 – three to five days courses, please contact us: organized by the Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia – June 2009 and 2010 – three to five days courses, please contact us: turna@fns.uniba.sk; krajcovic@fns.uniba.sk

10. Intercollegiate Faculty of Biotechnology of University of Gdansk & Medical University of Gdansk Dr S. Jafra – jafra@biotech.ug.gda.pl jafra@biotech.ug.gda.pl Dr W. Sledz – sledz@biotech.ug.gda.pl sledz@biotech.ug.gda.pl Work performed Training in molecular diagnostic of plant pathogenic bacteria (PCR, PCR-RFLP) for diploma students and staff of Voivodship Inspectorate Protection of Plants and Seeds in Gdansk Training in molecular diagnostic of plant pathogenic bacteria (PCR, PCR-RFLP) for diploma students and staff of Voivodship Inspectorate Protection of Plants and Seeds in Gdansk Modification of the Microbiological Diagnostic course curriculum (human pathogenic bacteria) with cooperation with MSc. M. Grinholc Modification of the Microbiological Diagnostic course curriculum (human pathogenic bacteria) with cooperation with MSc. M. Grinholc detection and differentiation of Staphylococcus aureus strains detection and differentiation of Staphylococcus aureus strains biochemical, immunological and molecular diagnostic of others bacterial species biochemical, immunological and molecular diagnostic of others bacterial species The research project on diagnostic of plant pathogens – life/dead bacterial cells staining combined with species specific PCR ( Pectobacterium The research project on diagnostic of plant pathogens – life/dead bacterial cells staining combined with species specific PCR ( PectobacteriumFuture Preparation of ODL and booklet: Detection and identification of pathogenic bacteria (human and plant) : Salmonella, Shigella and Pectobacterium

11. Correction of the study curricula of Biotechnology “Biotechnology” courses (both, i.e. First Level Degree „Bacalar“ and Master Degree „Magister“) at the Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia (March 2008) main topics: Fermentation Biotechnology Processes in Biotechnology Agrobiotechnology Enwironmental biotechnology Farmaceutical Biotechnology Medical Biotechnology

12. Constitution a Centre of Excellency in this field at Comenius University, located primarily at the Faculty of Natural Sciences in Bratislava a mega-project has been prepared and submitted (August 2008) to be supported by EU Structural funds (2009-2010): accepted for financing (December 2008) “Centre of Excellency to use bioinformatic macromolecules to improve quality of life and for health” top equipment and the latest modern techniques for molecular diagnostics

13. Meeting of the workpackage Molecular diagnostics of microorganisms the “EUROPEAN BIOTECHNOLOGY” PROJECT* Bratislava, September 4, 2008 AGENDA 15:00 – 15:20 Workpackage Molecular diagnostics of microorganisms – the state of the art. Juraj Krajčovič, Institute of Cell Biology, Faculty of Natural Sciences Comenius University, Bratislava, Slovakia 15:20 – 15:40 Identification of Lactic Acid Bacteria in the Slovak sheep cheese Bryndza., Institute of Cell Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia 15:20 – 15:40 Identification of Lactic Acid Bacteria in the Slovak sheep cheese Bryndza.Roman Dušinský, Institute of Cell Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia 15:40 – 16:00 Research and projects at the Department of Molecular Biology in Bratislava; Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia 15:40 – 16:00 Research and projects at the Department of Molecular Biology in Bratislava; Ján Turňa, Hana Drahovská, Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia 16:00 – 16:20 Genomics and Bioinformatics – Training Courses in Bratislava;, Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia 16:00 – 16:20 Genomics and Bioinformatics – Training Courses in Bratislava; Hana Drahovská, Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia 16:20 – 16:40 Research and projects in the Microbiological section of the Deparment of Food Science in Udine. Deparment of Food Science, University of Udine, Italy 16:20 – 16:40 Research and projects in the Microbiological section of the Deparment of Food Science in Udine. Marisa Manzano, Deparment of Food Science, University of Udine, Italy *EUROBIOTECH – European Biotechnology Agr. n° 2007-2566 / 001-001 project n° 134310-LLP-1-2007-1- IT-ERASMUS-ENW; This project has been funded with support from the European Commission.

14. * organization of the Meeting of the "EUROPEAN BIOTECHNOLOGY" project n° 134310-LLP-1- 2007-1-IT-ERASMUS-ENW (4-6, September 2008, Bratislava, Slovakia) * active participation at the NATO ADVANCED RESEARCH WORKSHOP “Detection of bacteria, viruses, parasites and fungi” (18-21, November 2008, Perugia, Italy)

15. the NATO ADVANCED RESEARCH WORKSHOP “Detection of bacteria, viruses, parasites and fungi” since the topic of the NATO ARW meeting is very closely related to the main activity of the workpackage (Molecular Diagnostics of Microorganisms) several partners from the workpackage (Univ. Bratislava, Univ. Udine, Univ. Maribor) were: * deeply interested and engaged in preparation of the meeting (primarily contacting some keynote speakers), * presented their contributions there, * prepared manuscripts for the book (Springer) from the meeting * are keeping contacts and extending their collaborations with some other participants of the Perugia NATO ARW meeting

16. the NATO ADVANCED RESEARCH WORKSHOP “Detection of bacteria, viruses, parasites and fungi” (18-21, November 2008, Perugia, Italy) Contributions of the workpackage partners (Molecular Diagnostics of Microorganisms): Univ. Udine (Italy) – Marisa Manzano: Molecular methods to detect Bacillus cereus and B. thuringiensis in foods Univ. Bratislava (Slovakia) – Juraj Krajčovič: Genetic diversity of Enterococcus faecium isolated from Bryndza cheese Univ. Maribor (Slovenia) – Walter Chinguaru, Avrelija Cencic: HEV (an emerging pathogen) interactions with the intestinal tract

17. Thank you! once more an invitation A higher education training courses in Molecular diagnostics of microorganisms designed to develop skills in the participants (university students and SME partners) organized by the Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia – June 2009 and 2010 – three to five days courses, please contact us: krajcovic@fns.uniba.sk; turna@fns.uniba.sk