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The research work of the Department of Biotechnology and Systems Biology is concentrated on tree topics: omics, microorganisms and genetically modified organisms. In the field of microorganism’s research, we study plant – microorganism interections and we are constantly developing and validating new laboratory methods for diagnostic of viruses, bacteria and phytoplasmas. Beside molecular methods we study possibilities for concentration of microorganisms from extremely diluted samples like waters and air. The research is mostly, but not exclusively, focused on phytopathogenes.
Viruses
We investigate grapevine viruses, especially the Grapevine fan leaf virus (GFLV) and the Ruperstris stem pitting associated virus (RSPaV), where we study the genetic diversity of those viruses and its biological significance. In RSPaV infected plants we also study the distribution of the virus and the morphological changes caused by the infection by means of electron microscopy.
The development of real-time PCR for diagnosis of potato and tomato viruses is directed into the detection of the Potato virus Y (PVY) and the Pepino mosaic virus (PepMV) and their isolates (Pepeira). Among the Tospoviruses on Chrysanthemum plants, we identified the stem necrotic virus (CSNV, Chrysanthemum stem necrotic virus) and developed real-time PCR which enabled the separation of the virus from the kindred Tomato Spotted Wilt Virus (TSWV) and detection of virus in low concentrations.
Potato – PVY interactions
From the omics point of view we are investigating the mechanism of the response of potato plants (Solanum tuberosum L.) to the infection with the PVY, which causes the disease called potato tuber necrotic ringspot disease. The plant response is studied at biochemical, cytological and molecular level. In the research variously aggressive variants of the virus, PVYN and PVYNTN, and variously sensitive potato varieties are included. Hybridization of cDNA microarrays enables the monitoring of the response of a very susceptible cultivar Igor in comparison with the responses of variously resistant varieties, i.e. the cultivar Sante, to the infection with PVYNTN. For more specific needs, real time PCR method is used for monitoring the changes in the expression of the selected genes.
Bacteria
We ascertain the diversity of disease causing bacteria Pseudomonas syringae on the fruit trees. We investigate growth enhancement of the tomato plant by using various bacteria isolated from rhyzosphere, where some bacteria, which successfully encouraged growth, especially in low nutrient substrates, were identified.
We were ascertaining antibacterial effects of fungus extracts on the growth of phytopathogen fungi, their multiplication and pathogenesis in co-operation with the Jožef Štefan Institute.
We developed the real-time PCR method for detection of grapevine bacteria Xylophilus ampelinus, where diagnostics with classical methods is extremely difficult and time consuming. The detection and identification of the Erwinia amylovora, the causing agent of the fire blight was also improved by the development of real-time PCR, where we interested also in quantification of the bacteria in plant samples.
We developed the real time PCR method for detection of the phytoplasma of Flavescence dorée and phytoplasma of black wood (Bois noir), and compared it with the existent methods of detecting Flavescence dorée (PCR and nested PCR). The method is also suitable for testing carriers of Flavescence dorée and other plants infected with phytoplasmas. Due to its greater sensitivity and reliability, we successfully introduced it into the analysis procedure.
Selected publications
- M. Hren, J. Boben, A. Rotter, P. Kralj, K. Gruden, M. Ravnikar. Real-time PCR detection systems for Flavescence dorée and Bois noir phytoplasmas in grapevine: comparison with conventional PCR detection and application in diagnostics. 2007. Plant Pathology 56 (5), 785–796.
- M. Pompe Novak, I. Gutierrez-Aguirre, J. Vojvoda, M. Blas, I. Tomažič, E. Vigne, M. Fuchs, M. Ravnikar, N. Petrovič. Genetic variability within RNA2 of grapevine fanleaf virus. 2007. European Journal of Plant Pathology 117, 307-312.
- J. Boben, P. Kramberger, N. Petrovič, K. Cankar, M. Peterka, A. Štrancar, M. Ravnikar. Detection and quantification of Tomato mosaic virus in irrigation waters. 2007. European Journal of Plant Pathology, 118, 59-71
- T. Dreo, K. Gruden, C. Manceau, J.D. Janse, M. Ravnikar. Development of real-time PCR based method for Xylophilus ampelinus detection. 2007. Plant Pathology, 56, 9-16.
- M. Pompe Novak, K. Gruden, Š. Baebler, H. Krečič-Stres, M. Kovač, M.A. Jongsma, M. Ravnikar. Potato virus Y induced changes in the gene expression of potato (Solanum tuberosum L.). 2006. Physiological and Molecular Plant Pathology, 67, 237-247.
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Polona Kogovšek (phD)
polona.kogovsek()nib.si
Dr Maruša Pompe-Novak
marusa.pompe.novak()nib.si
Dr Maja Ravnikar
maja.ravnikar()nib.si
National Institute of Biology
Department of biotechnology and systems biology
Vecna pot 111, SI-1000 Ljubljana, Slovenia
Ph. (386) 1 423 33 88 ext. 28Fax. (386) 1 257 38 47
http://www.nib.s
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