Projects / Programmes source: ARIS

Biotechnology and Plant Systems Biology

Research activity

Code Science Field Subfield
4.06.00  Biotechnical sciences  Biotechnology   

Code Science Field
4.04  Agricultural and Veterinary Sciences  Agricultural biotechnology 
plant systems biology, stress, pathogens, epidemiology, biotechnological and biological plant protection methods, GMO, technological platform, quantitative determination of nucleic acids, bioinformatics, metrology, network modeling, detection, mechanistic modelling, drought, synthetic biology
Evaluation (rules)
source: COBISS
Data for the last 5 years (citations for the last 10 years) on April 18, 2024; A3 for period 2018-2022
Data for ARIS tenders ( 04.04.2019 – Programme tender , archive )
Database Linked records Citations Pure citations Average pure citations
WoS  549  13,122  11,207  20.41 
Scopus  611  15,284  13,070  21.39 
Researchers (33)
no. Code Name and surname Research area Role Period No. of publicationsNo. of publications
1.  36320  PhD Špela Alič  Biology  Researcher  2022 - 2024  82 
2.  50563  PhD Katarina Bačnik  Biotechnology  Researcher  2022 - 2024  132 
3.  19116  PhD Špela Baebler  Biotechnology  Researcher  2022 - 2024  313 
4.  52760  Aleksander Benčič  Biotechnology  Junior researcher  2022 - 2024  26 
5.  54569  PhD Carissa Robyn Bleker  Biotechnology  Researcher  2022 - 2024  15 
6.  37410  PhD Alexandra Bogožalec Košir  Biology  Researcher  2022 - 2024  93 
7.  34130  PhD Anna Coll Rius  Biochemistry and molecular biology  Researcher  2022 - 2024  163 
8.  08280  PhD Marina Dermastia  Biology  Researcher  2022 - 2024  872 
9.  23611  PhD Tanja Dreo  Biotechnology  Researcher  2022 - 2024  507 
10.  12688  PhD Kristina Gruden  Biotechnology  Head  2022 - 2024  985 
11.  55807  Vladimir Grujić  Biotechnology  Junior researcher  2022 - 2024 
12.  51987  PhD Mojca Juteršek  Biotechnology  Researcher  2022 - 2024  42 
13.  52584  Zala Kogej Zwitter  Biotechnology  Junior researcher  2022 - 2024  104 
14.  37409  PhD Maja Križnik  Biotechnology  Researcher  2022 - 2024  42 
15.  54678  Valentina Levak  Biotechnology  Junior researcher  2022 - 2024  16 
16.  36323  PhD Tjaša Lukan  Biology  Researcher  2022 - 2024  125 
17.  53968  Nastja Marondini  Biotechnology  Technical associate  2022 - 2024  11 
18.  23610  PhD Nataša Mehle  Biotechnology  Researcher  2022 - 2024  542 
19.  19119  PhD Mojca Milavec  Biotechnology  Researcher  2022 - 2024  318 
20.  54306  Karmen Pogačar  Biotechnology  Junior researcher  2022 - 2024  20 
21.  18467  PhD Maruša Pompe Novak  Biotechnology  Researcher  2022 - 2024  291 
22.  34502  PhD Živa Ramšak  Biology  Researcher  2022 - 2024  118 
23.  05229  PhD Maja Ravnikar  Biotechnology  Researcher  2022 - 2024  1,369 
24.  29635  Katja Stare  Biology  Technical associate  2022 - 2024  86 
25.  50566  PhD Špela Tomaž  Biotechnology  Junior researcher  2022  28 
26.  36377  PhD Miha Tome  Biotechnology  Researcher  2022 - 2024  31 
27.  50578  PhD Eva Turk  Biology  Researcher  2022 - 2024  22 
28.  34129  Neža Turnšek    Technical associate  2022 - 2024  35 
29.  56878  Anže Vozelj  Biochemistry and molecular biology  Junior researcher  2022 - 2024  13 
30.  54287  PhD Ana Vučurović  Plant production  Researcher  2022 - 2024  221 
31.  39320  PhD Maja Zagorščak  Interdisciplinary research  Researcher  2022 - 2024  57 
32.  32446  PhD Jan Zrimec  Biochemistry and molecular biology  Researcher  2022 - 2024  97 
33.  27522  PhD Anže Županič  Systems and cybernetics  Researcher  2022 - 2024  179 
Organisations (1)
no. Code Research organisation City Registration number No. of publicationsNo. of publications
1.  0105  National Institute of Biology  Ljubljana  5055784  13,251 
In the coming decades, it will no longer be environmentally sustainable to increase agricultural land to provide food for a growing world population. Instead, it will be necessary to improve crop yields as well as to reduce losses in food distribution chain and processing. The proposed research program focuses on understanding of responses of plants to abiotic and biotic stress which cause major losses in crop yield with the goal to provide tools and knowledge for sustainable agriculture of the future. The originality of the proposal lies in its multidisciplinary approach, including sensitive and generic microorganisms detection approaches, quantitative molecular biology tools, bioinformatics, population genetics and multiomics analysis and mathematical modeling. This will enable us to follow the spread of microorganisms, and smart surveillance and forecasting of related disease risks. With the proposed approach we will, for the first time, enable insights into dynamics of the response using a combination of synthetic and systems biology. Altogether the results will represent a breakthrough towards an understanding of the signaling mechanisms in complex stress conditions, resembling the natural environment. Specific objectives of the research: o to study plant responses in complex environments using a combination of systems, synthetic and cell biology, considering multiple molecular levels at high spatiotemporal resolution o to study the biology, diversity, epidemiology, evolution and distribution of pathogenic and non-pathogenic microorganisms associated with plants, and develop reliable cutting edge assays for their detection and characterization o to develop new plant protection strategies and strategies for food safety based on sustainable biotechnological methods o to upgrade the technological platform to support new developments in systems and quantitative molecular biology research and to develop new metrologically sound technological support for cutting edge identification and quantification methods, which may all be applicable in fields of pharmacology, human health and environment The proposed state of the art technological platform provides means for innovations. We were allready successful in tehnology transfer in the previous period and will continue to transfer methodological innovations to different biotechnological fields and support its industry. The generated knowledge will also be transferred to students and early stage researchers from Slovenia and abroad. We will continue our well established collaborations with the international science in european scientific infrastructure community as well as with the European network for genetically modified organisms laboratories and as a partner of European Union reference laboratories in the field of plant health.
Significance for science
With agriculture being an ecological threat to quality of groundwater on one hand and the growing world population requiring increased food production on the other, major changes in agricultural practices are required. Understanding the fundamental principles of crop interactions with their environment is critical for the protection of food security worldwide. However, the mechanisms of plant responses to the environment are still not well understood. Studies of plant immune signalling have in the past often led to contradictory conclusions. One example is the interaction between JA and SA signalling, with the majority of results showing antagonism while in some studies synergism was reported. Also, the same components of immune signalling were found to respond both in interaction with beneficial microbes, or pathogens and pests, albeit with different timing and intensity. Even more, the immune signalling network strongly overlaps with the abiotic stress signaling network. This shows that the network properties, and not single signalling components, are important for efficient stress response. With the proposed workplan we will, for the first time, enable insights into the dynamics of the response using a combination of synthetic and systems biology. The results will represent a breakthrough towards an understanding of the signalling mechanisms in complex stress conditions, resembling the natural environment of the crops. Furthermore, downscaling of multi-omics analysis to single cell and tissue levels will allow us to increase our understanding of cell heterogeneity and their communication and organization within tissues, which is still at its infancy in plant sciences. Expanding the research of microbial composition of crop plants and other related samples of interest will help establish a basic catalogue of detrimental and non-detrimental pathogens, which will increase our understanding of the detrimental role pathogens have in culture crops and allow the design of accurate diagnostics methods and prevention tool against future outbreaks and epidemics. Finally, experimental research on virus evolution will enable us to better understand the factors responsible for virus adaptation and (re)emergence, which are amongst key points for achievement of optimal plant protection strategies, and will ultimately contribute to the reduction of economic losses generated by plant pathogens and pests and helping ensure "crop to fork" sustainability. Some genes recognized to be involved in the stress signalling 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. The results of this research, therefore, will be of great importance to develop new plant protection strategies for plant protection, food and water safety. Last but not least the proposed state of the art technological platform coupled with the advanced experimental designs provide means for innovations not only in agriculture but can also be implemented in other areas of biotechnology, pharmacy among others.
Significance for the country
It has now become globally recognized that human survival on Earth depends not only on our health, but also on the health of our biotic and abiotic environment. The One Health concept, to which our research is tightly connected, therefore includes not only public health, but also food and environmental safety. Our research will provide tools for production of safe foods for consumers, for decreasing the environmental footprint of agriculture and for improving the health and economic conditions for the farmers. Our research is also in line with EU initiative Healthy Soils, part of the Biodiversity strategy, which will be improved through the use of novel crop protection strategies. Taking into account the geographic position of Slovenia and current agro­economic trends, we will investigate harmful plant pathogens that have been already present in Slovenia or we anticipate their occurrence in near future. Both abiotic and biotic stressors cause major losses in crop yield which represents a major socio-economic problem for farmers in Slovenia and globally and has a significant impact on the price of food, which affects the purchasing power of the population and especially endangers the socially weakest groups. The generated knowledge will be further used to design new innovative strategies for crop protection. We will be able to develop knowledge informed breeding markers, which is a prerequisite for precision breeding of the future. Using this approach, plants resilient to different environmental stresses in long term can be designed. Microorganisms are undeniably one of the most important factors in ecosystems health. Our microorganisms based research designed crop protection products are considered as one of the promising strategies to improve food sustainability and food security. The importance and potential of microbiome innovations was recognised by the United Nations and the EU and were, therefore, implemented in the Bioeconomy strategy and Green Deal. Understanding of epidemiology of disease and susceptibility of the crop in different environmental settings will help in design of improved agricultural management practices. The proposed technological platform, involving state of the art technologies, expertise and bioinformatics tools, provides and will continue providing means for innovations. The newly designed synthetic biology tools will contribute both to developments in plant synthetic biology as well as in different biotechnological applications. The developed packages, pipelines and tools will allow for broader adoption of mechanistic modelling in plant sciences and broader. 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 and plant pathogens. We will be able to transfer methodological innovations to different biotechnological fields and support its industry. In the previous period we were members of Slovenian centers of excellence COBIK and KC-Brin and have participated in public-private partnership consortia for production of biologics and vaccines Biopharm.si. We are and will continue offering innovative technological solutions for Slovenian and global companies (e.g. BIA doo, Lek-Novartis, BIA Separations-Sartorius, Agdia, Promega, Dechra, AciesBio, HZPC). Such an approach has already resulted in the spin off of two companies from our group, the highly successful Biosistemika (https://biosistemika.com/), and the Niba Labs founded in 2021. In the field of development and validation of methods for GMOs detection we are one of leading partners in the European network of GMO laboratories (ENGL). All results from the proposed Program related to plant health protection are continuously transferred to National and European plant protection authorities. Several members of the research group are active members in European plant protection organization's (EPPO) panels, as well as partners in two out of five European Union reference laboratories in the field of plant health: EURL for bacteria and EURL for viruses, viroids and phytoplasmas. Timely identification of potential new pathogens and tracking of their spread is vital to prevent and reduce economic damage to agriculture. We are also actively participating in European infrastructures; we are co-leading the Plant Science community in infrastructure for bioinformatics ELIXIR and also actively promoting systems biology within the same infrastructure. Department of Biotechnology and Systems Biology is also a holder of national measurement standard for the amount of substance in food of plant origin (NNE) in the food safety area. The generated knowledge is rapidly and fluently transferred to students and early stage researchers from Slovenia and abroad, through inclusion of program members in under and postgraduated studies of different universities and through coordination and participation in Marie Curie ITN networks, such as the INEXTVIR MSCA ITN, which is coordinated by NIB (Maja Ravnikar). Our graduates often continue their careers in industry, thus we are contributing to regional development of human resources. Due to the participation and leadership of researchers from the program in several international projects (described in chapter D32), the program will be strongly involved in international research trends, allowing efficient dissemination of programme results and ensure availability of the state of the art knowledge in Slovenia. The members of the research group are also regularly communicating their results to wider audiences and participate in public debate related to the programme topics as guests of TV and radio shows or organizers of science communication events (e.g. Researcher's Night, Fascination of Plants Day).
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