Biotechnology and Plant Systems Biology

The main strength of the research program which moves the borders of knowledge was in making connections between diverse disciplines (microbiology and plant biology, molecular biology, bioinformatics, biostatistics, computer sciences) in order to solve biological questions. Special emphasis was given to the analysis of multitrofic challenges including metagenomics to better understand the complex network of interactions in the ecosystem. The novelty was also the complexity of research approaches and introduction of different spatial and temporal levels in which we combined a set of non-invasive techniques to monitor selected components of plant defense and standard omics techniques that were downscaled to allow for analysis of small tissue sections. In our study we focused on the genes, proteins and final metabolic products to feed the dynamical models. Some genes recognized to be involved in the process of pathogen infection and plant recovery might prove to be useful markers for early detection of the disease, markers for resistance and recovery, and possible targets for biological control of the disease. Through the development of new strategies for the identification of new GMOs we have gained a new scientific knowledge and develop new tools with their potential use in other related fields. Methods allowing absolute quantification have opened a new era in more accurate and simpler preparation of reference materials. Metrological aspects of the research will provide a sound basis for reliable quantification and qualification of nucleic acids and cells. In particular, metrological approaches will be first implemented to harmonize international approaches of detection and identification of GMOs and human pathogens. Results of the program have been already published in the most prestigious scientific journals. They will be of great importance to develop new strategies for plant protection, food and water safety, as well as for developing new tools in molecular biology and molecular diagnostics.

Taking into account the geographic position of Slovenia and current agro-economic trends, we investigated harmful plant pathogens that have been already present in Slovenia or we anticipated their occurrence in near future. The understanding of pathogen biology and mechanisms of disease development is a prerequisite for the development of appropriate strategies for their control and risk assessment for introduced technologies to the agronomical practice. We aimed to develop efficient and sustainable biotechnological and biological control methods and new strategies for food and water safety, without an extensive use of pesticides and keeping in mind conservation of great biodiversity in Slovenia. We are a National reference laboratory for determination of GMOs in food, feed and seeds accredited by the Slovenian accreditation for detection of genetically modified organisms and microorganisms – plant pathogens. We are also involved in development of standards for GMOs detection, both authorized and unauthorized, and microorganisms at CEN and ISO level. Our knowledge about genetic modification of plants has already supported implementation of Slovene and European legislation on food safety, plant and environment protection and GMOs. We have been authorized for measuring and counting molecules since 2009, when the metrology institute MIRS appointed our department as a holder of national measurement standard for the amount of substance in food of plant origin in the food safety area. Additionally, we have offered professional support and diagnosis for the Administration of the Republic of Slovenia for Food Safety, Veterinary and Plant Protection. For the Administration we have provided diagnostics for several quarantine microorganisms that cause diseases on stone fruit trees, grapevine and other plants and new emerging diseases. Up till now we have found for the first time more than 20 plant pathogens, most of them with quarantine status in Slovenia and EU, some of them were one of the first finding in Europe. Strong and ongoing collaborations with research groups at the national and worldwide level have been implemented in joint projects and publications and have resulted in access to the international know-how as well as to promotion of Slovenia in the international scientific community. Our involvement in the EU platforms for systems biology and bioinformatics (ISBE and ELIXIR) is an opportunity for Slovenia to have wider access to research as well as to computing infrastructure. Our research and expertise is of high relevance for industry. We have tightly cooperated with many companies working in agriculture, biotechnology and pharmacy. Our knowledge on systems biology and bioinformatics has qualified us to perform contract research with pharmaceutical company Lek d.d. Sandoz for many years. With a high-tech biotechnological company BiaSeparations we developed new biotechnological applications for concentration and purification of viruses, which have opened a whole new area in detection and elimination of water borne pathogens. Together with our spin-off company BioSistemika we have organized practical hands-on international workshops on molecular biology (qPCR) and developed software for automated molecular biology work. Together with company Omega we have built next generation sequencing platform. Our technological platforms for studies of human and plant pathogens are applicable in fields related to pharmacy, human and animal health, and environment. Six program researchers are actively involved in the undergraduate and graduate studies at the University of Ljubljana, University of Nova Gorica and International Postgraduate School Jožef Stefan and are mentors to many MSc and PhD students and thus the transfer of knowledge is guaranteed.