Discovery of diseases and their causes in the field is performed with visual inspection. To confirme the presence, the laboratory diagnostics is often required. This is specially unavoidable in the case of plant pathogens, where use of serological, molecular or other laboratory methods is needed. To shorten the time of first plant pest recognition, fast, serological and later molecular on-site detection methods were developed. The major progress was reached with the development of fast, molecular method LAMP, which can be performed under constant temperature, therefore simple fluorimeter is used for detection of LAMP product. The method is less prone to inhibitors; therefore the sample preparation could be faster and simple. The tests are developed in the frame of two European projects Vitisens and Qdetect. Developed test could be adapted for easy use in the laboratory, at the production site, warehouses, airports, ports and country borders.
B.03 Paper at an international scientific conference
COBISS.SI-ID: 2891855In plant virology several studies have been carried out using NGS technologies for the detection of new pathogens. One of the most important current focuses in the field is the one dealing with sample preparation. The enrichment for viral nucleic acids during sample preparation could greatly facilitate the analytical step and reduce the cost of the entire process. Different approaches can be adopted, such as: subtractive hybridization, enrichment for double stranded RNA, small RNA sequencing and purification of viral particles. However, their evaluation and comparison are still missing. We tested the utility of total RNA and small RNA deep sequencing on the SOLiD sequencing platform for the detection of Potato virus Y (PVY) in potato plants. Both approaches yielded sufficient amount of information for reliable PVY detection. Results were disseminated in the Slovenian biochemical society conference.
F.01 Acquisition of new practical knowledge, information and skills
COBISS.SI-ID: 30821081In the frame of the Department of Biotechnology and Systems Biology, Maja Ravnikar is leading the laboratory for official detection of quarantine and other plant pathogens. The laboratory performs diagnostics and scientific support for Phytosanitary Administration of the Republic of Slovenia, Phytosanitary Inspection Service and commercially. The laboratory takes part in expert support to state administration, education of inspectors and public relations in the case of epidemics. In 2010, Dany Morisset and Maja Ravnikar started their activities within the new 7th framework project Qdetect.
D.08 Management and development of research activities
COBISS.SI-ID: 29518809The laboratory is accredited since 2003 by Slovenian Accreditation (Reg. no. LP028) for the domain of genetically modified organisms. In 2012, the laboratory accreditation also managed to expand the domain of accreditation to microorganisms. For both areas, the scope of accreditation is partially flexible, allowing the laboratory to introduce, if necessary, new methods and add them to the list of accredited methods. Granted accreditation further enhances the visibility of the laboratory in the world and the possibilities of cooperation at the international level.
D.05 Laboratory accreditation
The last international workshop on high technology research and the molecular diagnostics of pathogens using real-time PCR was held in Ljubljana from 3rd to 6th December 2013. This international workshop was co-organized by the Slovenian National Institute of Biology (NIB) and BioSistemika d.o.o., in collaboration with the European project Bicopoll (http://www.coreorganic2.org/). qPCR Workshops integrate excellent technical knowledge with vast practical experience in design, validation and use of real-time PCR in official diagnostics and research in plant pathology. Up to date news from the field are part of the course as well as a special section of troubleshooting tailord to participants. Also this time researchers and diagnosticians from many European countries attended the workshop and benefited from the exchange of knowledge and holiday spirit in the capital of Slovenia: Austria, Great Britain, France, Poland, Finland, Lithuania, Latvia, Montenegro and Slovenia.
B.01 Organiser of a scientific meeting