Projects / Programmes
Biotechnology and Plant Systems Biology
January 1, 2015
- December 31, 2021
| Code |
Science |
Field |
Subfield |
| 4.06.00 |
Biotechnical sciences |
Biotechnology |
|
| 1.03.00 |
Natural sciences and mathematics |
Biology |
|
| Code |
Science |
Field |
| T490 |
Technological sciences |
Biotechnology |
| Code |
Science |
Field |
| 4.04 |
Agricultural and Veterinary Sciences |
Agricultural biotechnology |
Plant systems biology, stress, microbial plant pathogens, biological variability, biotechnological and biological plant protection, genetically modified organisms, technological platform, quantitative and qualitative detection of nucleic acids, bioinformatics, metrology
Researchers (50)
Organisations (1)
| no. |
Code |
Research organisation |
City |
Registration number |
No. of publicationsNo. of publications |
| 1. |
0105 |
National Institute of Biology |
Ljubljana |
5055784 |
13,498 |
Abstract
The proposed research program supports both excellence in science and excellence in teaching at all levels of higher education in the field of biotechnology and food safety. It is also strongly connected to the professional work for Slovene governmental organizations and different companies related to the agriculture, environment, food safety, and biotechnological and pharmaceutical industry.
In the program we will continue our study of plant stress responses with the application of the systems biology tools, which generate a tremendous amount of data on biological systems. In order to integrate those data of dynamic interactions between genes, RNA molecules, proteins and metabolites into a multi-level model, new approaches and tools for data analysis and interpretation are required. Because in our research the main stressors are microorganisms, the study of their biology is needed. Based on the obtained knowledge we will continue developing new sustainable plant protection strategies and methods for ensuring food and water safety.
The main goals of the proposed research program are therefore:
(1) to gain better understanding of plant stress (mainly biotic) responses using systems biology approaches;
(2) to gain a better insight into the biology of microbes in order to understand their diversity, pathogenicity and epidemiology, and to elucidate their role in plant host and on the basis of obtained results develop efficient and sustainable biotechnological and biological control methods;
(3) to develop new plant protection strategies and strategies for food and water safety;
(4) to upgrade the technological platform to support the systems biology research and todevelop new metrologically sound technological support, more efficient identification and detection methods for microbes and GMOs which may be applicable in fields of pharmacy, human health and environment.
To achieve these goals we will apply state-of-the-art approaches and methodologies, specifically metagenomic studies, next generation sequencing (NGS), quantitative analysis of nucleic acids, isothermal amplification nucleic acids (e.g. LAMP), digital PCR, life cell imaging and bioinformatic and bioststistic approaches.
The research program has achieved excellent results in the past due to the interdisciplinary of the team that covered diverse fields of molecular biology, biology, microbiology, biochemistry, biotechnology, mathematics, biostatistics and computational science. In addition, it had established strong international collaboration with researchers in EU and Slovenia.The program team members participated in several EU projects. The research program represented small but very important part of the research support to the Department of Biotechnology and Systems Biology. Due to the the fast growing fields of systems biology, biotechnology and food safety, which are our main directions, the department doubled its budget and the number of employees from 20 to 43 in the last 10 years.
Significance for science
Mechanisms of host responses to different disease agents are still poorly understood; e. g. in the case of phytoplasma the lack of knowledge is due to impossibility for their culturing in vitro environment and in the case of viruses due to their constantly evolving genome which influence interaction with target cells. The aims of the proposed work are, therefore, to gain better knowledge about the interaction between different hosts and their pathogens. Special emphasis will be given to the analysis of multitrofic challenges including metagenomics to better understand the complex network of interactions in the ecosystem. The novelty will also be the complexity of research approach and introduction of different spatial and temporal levels where we will combine a set of non-invasive techniques to monitor selected components of plant defense and standard omics techniques that will be downscaled to allow for analysis of small tissue sections. In our study we will focus on the genes, proteins and final metabolic products to feed the dynamical models. The results of the program will have a great impact on the new knowledge about the biology of both, host and pathogen. The proposed hypotheses obtained by modeling will be evaluated using reverse genetics - through use of transgenic plants. 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. The results of this research, therefore, will be of great importance to develop new plant protection strategies for plant protection, food and water safety. The recognition of gene determinants and on the other hand the knowledge on biodiversity will help in the development of new molecular diagnostic tools. Our goals will be reached using the approaches of genomics, transcriptomics, proteomics, metabolomics and applying the advanced tools of bioinformatics and biostatistics. Members of the proposed program team are highly specialized for genomic studies using microarray, real-time polymerase chain reaction (qPCR), digital PCR, isothermal amplification technologies and next generation sequencing, as well as microscopy observations for all of which they also develop new innovative approaches and applications. New approaches including next generation sequencing coupled with concentration of viruses from environmental waters will enable new insight in epidemiology and population of viruses which are of plant and human health importance and will bring new possibilities for microbe elimination.
During the course of the program we will continue our well established collaboration with the leading Slovene and international partner laboratories, through the participation in European and other international projects and the mobility of researchers. By development and validation of methods for pathogen and GMOs detection we are one of leading partners in the European network for GMO laboratories (headquarter in Joint Research Center Ispra, Italy) and the European plant protection organization (EPPO) as well as members in their professional bodies. Through the development of new strategies for the identification of new GMOs, including unauthorized GMOs and cis-genic plants, we will gain a new scientific knowledge and develop new tools with their potential use in other related fields. Methods allowing absolute quantification are opening new era in more accurate and simpler preparation of reference materials. Our involvement in European platforms for systems biology and bioinformatics (ELIXIR and ISBE) will contribute to interexchange of knowledge and resources in the field of systems biology.
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 harmoniz
Significance for the country
Taking into account the geographic position of Slovenia and current agro-economic trends, we will investigate harmful plant pathogens that have been already present in Slovenia or we anticipate 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. Our concerns are both economic and environmental. We aim 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 appointed by the Ministry of Agriculture and the Environment and accredited by the Slovenian accreditation, Reg No. LP-28 (standard ISO/IEC 17025:2005) 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 are also authorized for measuring and counting molecules since 2009, when the metrology Institute of the Republic of Slovenia (MIRS) appointed our Department of Biotechnology and Systems Biology as a holder of national measurement standard for the amount of substance in food of plant origin (NNE) in the food safety area.
Additionally, we offer professional support and diagnosis for the Administration of the Republic of Slovenia for Food Safety, Veterinary Sector and Plant Protection at the Ministry of Agriculture and Environment of the Republic of Slovenia. For the Administration we provide diagnostics for several quarantine microorganisms, e. g. bacterium Erwinia amylovora, a causal agent of the pear blight, phytoplasmas that cause diseases on stone fruit trees, grapevine and other plants and new emerging diseases like Xylella fastidiosa, Pseudomonas syringae actinidiae, Potato spindle tuber viroid and others. Up till now we 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, implemented in joint projects and publications, 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 tightly cooperate 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 organize practical hands-on international workshops on molecular biology (qPCR) and developed software for automated molecular biology work. Together with company Omega we 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. An example of s
Most important scientific results
Annual report
2015,
interim report
Most important socioeconomically and culturally relevant results
Annual report
2015,
interim report
