Transcript Faculty of Natural Sciences, Comenius

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
Juraj Krajčovič
Faculty of Natural Sciences, Comenius University
842 15 Bratislava, Slovakia
E-mail: [email protected]
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
Effective DNA identification of microorganisms in
clinical, food and environmental isolates
several workgroups in a close interconnection of research,
education and innovation
Original proposal
Partner number
Country
Short-name
Approximate number of staff days
Category
1
Lead
partner
Pnr
35
Category
2
Slovakia
Krajcovic, J. Univ.
Bratislava
40
P(nr) 23
Latvia
Zilevica, A., Univ. Riga
12
P(nr) 21
Italy
D’Agaro, E., Univ.
Udine
12
P(nr) 27
Poland
Jafra, S., Univ. Gdansk
12
P(nr) 20
Italy
Maffia, M., Univ.
Salento
6
P(nr) 20
Italy
Storelli, C., Univ.
6
Category
3
Category
4
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) ([email protected])
Dr. Andrej Susek (Maribor, Slovenia) ([email protected])
Prof. Ján Turňa (Bratislava, Slovakia) ([email protected])
Extension, modification/replacement of partners within
the workpackage around
the workpackage meeting in Bratislava (September 2008):
extensions: (i) Univ. Udine (Italy): M. Manzano ([email protected]),
G. Comi ([email protected]), L. Iacumin ([email protected] ) – DNA
identification of microorganisms in food and food industry facilities
(ii) Univ. Bratislava (Slovakia): H. Drahovská (drahovská@fns.uniba.sk), R.
Dušinský ([email protected]) – DNA identification of microorganisms in
food and food industry facilities
modification: Univ. Gdansk, (Poland): S. Jafra ([email protected]) (a
mediator),W. Sledz ([email protected]) (active person) – molecular diagnostic
of plant pathogenic bacteria
replacement: Univ. Maribor (Slovenia): A. Susek replaced by T.
Langerholc ([email protected] )
Outcomes and users
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
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
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
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);
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).
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:
[email protected]; [email protected]
Intercollegiate Faculty of Biotechnology of University of Gdansk & Medical
University of Gdansk
Dr S. Jafra – [email protected]
Dr W. Sledz – [email protected]
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

Modification of the Microbiological Diagnostic course
curriculum (human pathogenic bacteria) with cooperation with MSc. M.
Grinholc
 detection and differentiation of Staphylococcus aureus strains
 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
Future
Preparation of ODL and booklet: Detection and identification of pathogenic
bacteria (human and plant) : Salmonella, Shigella and Pectobacterium
–
Correction of the study curricula of
“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
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
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.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; 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; 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. Marisa Manzano, Deparment of Food Science, University of Udine,
Italy
*EUROBIOTECH – European Biotechnology Agr. n° 2007-2566 / 001-001 project n° 134310-LLP-1-2007-1IT-ERASMUS-ENW; This project has been funded with support from the European Commission.
* organization of the Meeting of the "EUROPEAN
BIOTECHNOLOGY" project n° 134310-LLP-12007-1-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)
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
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
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: [email protected]; [email protected]