In the period 1999-2003 research in the Department of Plant Physiology and Biotechnology was concentrated mainly on the following areas: 1. Mechanisms of host plant-pathogen and -pest interactions 2. Breeding of pathogen resistant plants (obtained by genetic transformation) 3. Research on plant pathogens and development of phytodiagnostic methods 4. Tissue culture for producing pharmaceutical substances 5. Jasmonic acid in the regulation of plant growth The mechanism of host plant-pathogen interaction was studied in potato plants (Solanum tuberosum L.) infected with the very aggressive potato virus YNTN, which causes the severe potato tuber necrotic ring disease. Development of the disease was studied using cytological, biochemical and molecular approaches. The results of physiological studies of potato cysteine proteinases indicate their involvement in synthesis and transport of metabolites and in processes leading to organogenesis. It was suggested that the constitutive protein with molecular weight 43000, which was detected in significantly higher amounts in the leaves of a resistant potato variety than in a susceptible one, has a role in potato resistance to virus infection. We also investigated the effect of virus infection on plant peroxidases and photosynthetic pigments. It was demonstrated that viral induced senescence is not the same as natural senescence. Virus infection also induced changes in chloroplast ultrastructure. We introduced methods for determining jasmonic and salicylic acid, important signal molecules in the plant response to pathogen infection. The adaptation of insects to potato defence proteins was studied using microarrays developed for studies on insects and plants. Coat protein of PVYNTNT was introduced in potato plants of the susceptible variety Igor. With this method we obtained different transgenic lines, of which some were resistant to virus infection. The total genome nucleotide sequence of virus PVYNTN, Slovenian strain, was also determined. Research is supported by the development of modern methods for detecting pathogens like viruses, bacteria, and phytoplasmas. In the context of virus research, we described for the first time the morphology of a virus connected with stem pitting of grape vine (RuSPaV), using recombinant antibodies for immuno electron microscopy. We detected the first infection with Tospovirus on Allium in the surroundings of Nova Gorica. It was identified as the Iris yellow spot virus and the spectrum of its host plants was described. In the context of bacterial research, we investigated the molecular methods for detecting the quarantine bacterium Erwinia amylovora, which causes fire blight disease and Ralstonia solanacearum, which causes brown potato rot disease. The production of pharmaceutically important substances in tissue culture was studied on pharmaceutical plants: Primula veris, containing high amount of saponins, Solanum laciniatum, containing glycoalcaloid solasonin, and Taxus x media Rhed. containing cytostatic taxanes. Chrysanthemum cinerariefolim, which produces insecticides pyrethrines, was also introduced in tissue culture. The involvement of jasmonic acid (JA) in the growth and development of plants has been further investigated, contributing to a basic understanding of the role of this not so long ago discovered plant hormone. We demonstrated that the fern Platycerium bifurcatum is a very good model plant for investigating the effect of JA on morphogenesis.