04
Dec
qPCR plant pathology workshop 2011
The first international workshop on high technology research and the molecular diagnostics of pathogens using real-time PCR was held in Ljubljana from 29th November to 2nd December 2011. This international workshop was co-organized by the Slovenian National Institute of Biology (NIB) and BioSistemika d.o.o., in collaboration with the European projects COST Action 873 and q-detect.
Researchers and diagnosticians from many European countries attended the workshop and benefited from the exchange of knowledge: The Netherlands, Finland, Spain, Italy, Estonia, Norway, France, Poland, Serbia and Slovenia.
Participants had an opportunity to share and discuss their experience with the qPCR experts of the Department of Biotechnology and Systems Biology, under the supervision of Professor Maja Ravnikar, and BioSistemika d.o.o. A guest lecturer, Neil Boonham, team leader at FERA (The Food and Environment Research Agency, York, United Kingdom) gave further insights into the use of real-time PCR and other molecular-biology based methods set to significantly contribute to plant pathogen diagnostics in the future years.
During the practical work, participants used real-time PCR assays for detection and quantification of fire blight and grapevine yellows, both Flavescence Dorée and Bois Noir, in plant material. All of these diseases are of particular concern for the European region.
The real-time PCR assays that were used during the workshop were all developed by the lecturers’ themselves. The lecturers have extensive experience in designing real-time PCR assays, their validations and their application in routine analyses and are able to address them in a practical, straightforward way. This has resulted in a very positive response of the participants to the content and executions of the workshop. You can find more information on our lecturers below the photo of participants of the workshop.
Prof. Dr. Maja Ravnikar, NIB, is the head of the Department of Biotechnology and Systems Biology Together with the research team she has established the research work on plant biotechnology and pathology and developed many new diagnostic methods and systems biology tools. She leads an authorized diagnostic laboratory for determination of micro-organisms for the Phytosanitary Administration (MAFF), phytosanitary inspection and closely cooperate with many companies. Research is focused on the biology of plant pathogenic viruses, bacteria and phytoplasmas including biodiversity and development of new tools in diagnostic and biotechnology. She is a member of the Panel of diagnostics and quality assurance in the European and Mediterranean Plant Protection Organization (EPPO).
Dr. Tanja Dreo, NIB, is an excellent phytobacteriologist with extensive knowledge on the biology of plant pathogenic bacteria, their detection and identification methods based on different biological principles and method validation. She shares her more than 10 year experience in the plant health and its relation to a wider society through collaborations at the national and international levels, as a lecturer in workshops and as an advisor. Real-time PCR that she developed for detection of a slow-growing grapevine pathogen, Xylophilus ampelinus (Dreo et al., 2007), is the first real-time PCR based method included in the EPPO standard diagnostic protocol (PM 7/96 (1)).
Mag. Nataša Mehle, NIB, is a top reasercher in the field of viral and phytoplasmal plant diseases. She has more than 10 year experience in development of novel methods for detection of new emergent plant pathogens (viruses, phytoplasmas and viroids) and research of the pathogens’ biology and their interactions with host plants. She excels in diagnostic process optimization and has significantly reduced the time required for Flavescence Dorée and Bois Noire phytoplasma diagnosis while at the same time increasing sensitivity and reliability of real-time PCR assays.
Dr. Manca Pirc is a biologist with specialized knowledge in molecular biology based detection methods of phytopathogenic bacteria, method development and their evaluation for reaserach and diagnostic use. In the frame of her PhD thesis she developed a real-time PCR method for Erwinia amylovora, a causative agent of fire blight (Pirc et al., 2009), that was one of the examples with which participants worked during the workshop.
Dr. Špela Baebler, NIB, is a biologist, specialized in gene expression studies in plant pathogen interactions, namely interaction of potato and potato virus Y (Baebler et al, 2009). She is involved in development and establishment of transcriptomic laboratory and data analysis/integration/interpretation methods in plant biology, and pharmaceutical research. At BioSistemika she is a product manager, responsible for organization of qPCR workshops.
Dr. Urška Čepin, BioSistemika d.o.o., is a biologist specialized in virology and real-time PCR technology. During her PhD she developed and validated real-time PCR method for Grapevine fanleaf virus (GFLV) detection and quantification which was also the case study for practical relative quantification session during the workshop (Čepin et al., 2010). She is a research and development assistant at BioSistemika developing applications for automation of diagnostic procedures based on real-time PCR methodology.
Dr. Matjaž Hren, BioSistemika d.o.o., is a biologist specialized in modern approaches in transcriptomics, which was together with introduction of novel real-time PCR based diagnostic methods his main subject during PhD at NIB. He is also experienced in quality assurance in laboratories and laboratory workflow optimization. He leads research and development department in BioSistemika.
Researchers and diagnosticians from many European countries attended the workshop and benefited from the exchange of knowledge: The Netherlands, Finland, Spain, Italy, Estonia, Norway, France, Poland, Serbia and Slovenia.
Participants had an opportunity to share and discuss their experience with the qPCR experts of the Department of Biotechnology and Systems Biology, under the supervision of Professor Maja Ravnikar, and BioSistemika d.o.o. A guest lecturer, Neil Boonham, team leader at FERA (The Food and Environment Research Agency, York, United Kingdom) gave further insights into the use of real-time PCR and other molecular-biology based methods set to significantly contribute to plant pathogen diagnostics in the future years.
During the practical work, participants used real-time PCR assays for detection and quantification of fire blight and grapevine yellows, both Flavescence Dorée and Bois Noir, in plant material. All of these diseases are of particular concern for the European region.
The real-time PCR assays that were used during the workshop were all developed by the lecturers’ themselves. The lecturers have extensive experience in designing real-time PCR assays, their validations and their application in routine analyses and are able to address them in a practical, straightforward way. This has resulted in a very positive response of the participants to the content and executions of the workshop. You can find more information on our lecturers below the photo of participants of the workshop.
Prof. Dr. Maja Ravnikar, NIB, is the head of the Department of Biotechnology and Systems Biology Together with the research team she has established the research work on plant biotechnology and pathology and developed many new diagnostic methods and systems biology tools. She leads an authorized diagnostic laboratory for determination of micro-organisms for the Phytosanitary Administration (MAFF), phytosanitary inspection and closely cooperate with many companies. Research is focused on the biology of plant pathogenic viruses, bacteria and phytoplasmas including biodiversity and development of new tools in diagnostic and biotechnology. She is a member of the Panel of diagnostics and quality assurance in the European and Mediterranean Plant Protection Organization (EPPO).
Dr. Tanja Dreo, NIB, is an excellent phytobacteriologist with extensive knowledge on the biology of plant pathogenic bacteria, their detection and identification methods based on different biological principles and method validation. She shares her more than 10 year experience in the plant health and its relation to a wider society through collaborations at the national and international levels, as a lecturer in workshops and as an advisor. Real-time PCR that she developed for detection of a slow-growing grapevine pathogen, Xylophilus ampelinus (Dreo et al., 2007), is the first real-time PCR based method included in the EPPO standard diagnostic protocol (PM 7/96 (1)).
Mag. Nataša Mehle, NIB, is a top reasercher in the field of viral and phytoplasmal plant diseases. She has more than 10 year experience in development of novel methods for detection of new emergent plant pathogens (viruses, phytoplasmas and viroids) and research of the pathogens’ biology and their interactions with host plants. She excels in diagnostic process optimization and has significantly reduced the time required for Flavescence Dorée and Bois Noire phytoplasma diagnosis while at the same time increasing sensitivity and reliability of real-time PCR assays.
Dr. Manca Pirc is a biologist with specialized knowledge in molecular biology based detection methods of phytopathogenic bacteria, method development and their evaluation for reaserach and diagnostic use. In the frame of her PhD thesis she developed a real-time PCR method for Erwinia amylovora, a causative agent of fire blight (Pirc et al., 2009), that was one of the examples with which participants worked during the workshop.
Dr. Špela Baebler, NIB, is a biologist, specialized in gene expression studies in plant pathogen interactions, namely interaction of potato and potato virus Y (Baebler et al, 2009). She is involved in development and establishment of transcriptomic laboratory and data analysis/integration/interpretation methods in plant biology, and pharmaceutical research. At BioSistemika she is a product manager, responsible for organization of qPCR workshops.
Dr. Urška Čepin, BioSistemika d.o.o., is a biologist specialized in virology and real-time PCR technology. During her PhD she developed and validated real-time PCR method for Grapevine fanleaf virus (GFLV) detection and quantification which was also the case study for practical relative quantification session during the workshop (Čepin et al., 2010). She is a research and development assistant at BioSistemika developing applications for automation of diagnostic procedures based on real-time PCR methodology.
Dr. Matjaž Hren, BioSistemika d.o.o., is a biologist specialized in modern approaches in transcriptomics, which was together with introduction of novel real-time PCR based diagnostic methods his main subject during PhD at NIB. He is also experienced in quality assurance in laboratories and laboratory workflow optimization. He leads research and development department in BioSistemika.
