Research topics in Slovenia related to PathoGenoMics

1. Research topics in Slovenia related to PathoGenoMics Dr. Livija Tušar Ministry of Higher Education, Science and Technology Dr. Roman Jerala National Institute of Chemistry Bonn, 7.–8. April 2005

2. Resarch activity financing related to PathoGenoMics Research programms (5 years) 13 programms from 2004-2008 In year 2004 the budget was 2.9 MEUR Basic and applied research projects (2-3 years) 15 projects financed from 2004 (0.3 MEUR/2004) Young researchers (up to 4 years) 22 young researchers financed in 2004 (0.4 MEUR) Research infrastructure 0.46 MEUR for research instruments in 2004 International cooperation 5 bilateral projects 2004/2005 (travel, subsistence costs) Participation in 5th and 6th FW projects

3. Main areas of research of participating groups Microbiology Immunology Biochemistry and molecular biology Genetics Veterinary medicine Pharmacy

4. Affiliation of participating groups University of Ljubljana medical faculty biotechnical faculty University of Maribor medical faculty National institute of chemistry

5. Research Program: Coexsistence of parasites Prof. Dr. Tatjana AvsicZupanc,avsic@mf.uni-lj.si Development and introduction of quick diagnostic methods for discrimination of bacterial and fungal infections Study of emerging microogranisms in the area of Slovenia,establishment of the best possible methodology for their discovery Study of natural resistance and immune response of host defence against microorganisms. (Examination of apoptosis, clonal selection, cytokine dependent poliferation and differentiation of cells of the immune system. Importance of cytokines in regulation of immune system.) Study of immunopathologic changes in inflammatory tissue and testing of mechanisms of invasion and defenceon animal models Study of ecology and epidemiology of some microorganisms important for Slovenian territory. Investigation on genetic markers significant to host-carrier-parasite relationship. Study of improvements in diagnostic procedures, genetic variability and spread of Hepatitis C in Slovenia

6. Research Program: Coexsistence of parasites Prof.Dr. Tatjana AvsicZupanc,avsic@mf.uni-lj.si Microorganisms studied: -Bacteria:Staphylococcus aureus, Streptococcus pyogenes, Streptococcus pneumoniae, Listeria monocytogenes, Escherichia, Pseudomonas, Haemophilus influenzae, Helicobacter pylori, Borrelia burgdorferi… -Eucariotic organisms: Toxoplasma sp., Cryptosporidium parvum, Blastocystis hominis, Diroflaria repens, Dermatobia homini -Viruses:Caliciviruses, herpes virus 6, tick borne meningoencephalitis, hepatitis B, C, cytomegalovirus…

7. Research Program: Comparative genomics and genome biodiversity Prof.Dr. Peter Dovc, peter.dovc@bfro.uni-lj.si Study of immune response to natural and experimental infections in animal models; signal pathwayfor triggering the immune response, Identification of abnormalities in the genome with cytogenetic molecular methods and bioinformatic approachwith the goal to establish novel diagnostic methods, identification of mutations, which affect reproductive performance, Microorganisms studied: -Mycoplasma spec., Chlamydia spec....

8. Research Program: Biology of microorganisms Prof.Dr. Miklavz Grabnar, miklavz.grabnar@uni-lj.si Study of microbial virulence factors; expression of colicins andbiotechnological production for therapeutic purposes, regulation of virulence determinants in a population of bacterial cells, Study of bacterial resistance mechanisms to antimicrobial compounds; resistance against the peptide antibiotic bacitracin Microorganisms studied: -Bacteria: Bacillus spec., Clostridiumspec, Escherichia spec, Klebsiella spec.

9. Research Program: Molecular biology: from the dynamics of biological systems to applications Prof.Dr. Roman Jerala, roman.jerala@ki.si Molecular basis of the recognition of pathogen associated molecular patterns by Toll-like receptors Structure-based design of antimicrobial agents (peptides) which neutralize endotoxin; Identification of structural motif for efficient neutralization of endotoxin by small peptides Microorganisms studied: -Gram-negative bacteria: Escherichia coli, Pseudomonas aeruginosa, Brucella abortus, Helicobacter pylori -Gram-positive bacteria: Staphilococcus aureus, Staphylococcus epidermidis, -Fungi: Aspergillus niger

10. Research Program: Pharmaceutical chemistry: designing, synthesys and analysis of drugs Prof.Dr. Danijel Kikelj, danijel.kikelj@ffa.uni-lj.si Rational design, synthesis, characterization and biological testing of new active compounds of pure synthetic or natural origin; peptidomimetics(e.g. thrombin inhibitors, fibrinogen receptor antagonists, analogs of N-acetylmuramyl-L-alanine-D-isoglutamine) Investigation of new diagnostic markers for specific detection, diagnosis and monitoring of different pathological states.

11. Research Program: Microbiology and biotechnology of food and environment Prof.Dr. Peter Raspor, peter.raspor@bf.uni-lj.si Study of the effect of biological factors and their interactions,physical and chemical stress parameters on microorganisms in laboratory model systems; nutrients supply, temperature, humidity, concentrations of salts, metal ions and different anti-microbial agents..., Study of the ecology of microbial populations and communities in complex model and natural systems (soil, water) and bioprocess environments (grapes/must and other foods; anti-microbial agents production), Development of classical and molecular-biological methods for detection, identification and tipization of microorganisms in food and environmentfor detection and monitoring of microorganisms in natural and industrial environments. Microorganisms studied: -Bacteria: Listeria monocytogenes, Bacillus sp., Shigella sp., Vibrio cholerae, Campylobacter jejuni, Acetobacter sp., Lactobacillus sp., ... -Fungi: Yeasts; Saccharomyces sp, Candida sp....

12. Research Program: Nutrition and ecology of gastrointestinal tract Dr. Irena Rogelj, irena.rogelj@bfro.uni-lj.si Study of interactions of microorganismsin the human and/or animal gastrointestinal tract ecosystems usingin vitro, ex vivo and in vivo methods and animal models, Nutrition studies in domestic and laboratory animals;monitoring of metabolic parameters and investigation of nutritional factors by different biological markers, microbial activity in particular parts of the intestinal tract..., Study of mechanisms and new approaches in feeding, enabling the production of functional foodof animal origin, finding out the effects of selected probiotics and prebiotics on the composition of microbial population in the gut of domestic animals or humans... Selection of markers for measurement of influences of feed, nutrients, probiotics and other bioactive substances in organism and development of toxicological, genotoxicological and immunological methods for tracing of their positive and negative effects. Microorganisms studied: -Bacteria:Lactobacillus sp....

13. Research Program: Diseases in Slovenia caused by arthropods Prof.Dr. Franc Strle, franc.strle@mf.uni-lj.si Antigenic and genetic characterization of tick-borne diseases;Lyme boreliosis, Human granulocytic ehrlichiosis (HGE) and meningoecephalitis, Development of diagnostic techniques for tick-borne diseases detection Microorganisms studied: -Bacteria: Borrelia burgdorferi, Rickettsia sp. -Virus: tick borne meningoencephalitis

14. Topics of research proposals from Slovenia regarding to Pathogenomics proposed research agenda • A: The microbes (1) • Screening of epithelial cells for probiotic bacteria • B: Host-microbe interractions (6) • Host recognition of pathogenic microorganisms • Screening of epithelial cells for probiotic bacteria • Invasive growth mechanisms and diagnostical methods • New methods for detection, prediction and antimicrobial treatment of pathogens on ephitelial cells • Inhibitors of microbial growth in food • Emerging risk zoonosis control • C: Development and improvement of tools (7) • Development of novel principles for anti-microbial treatment for replacingor supplementing anti-microbial treatment • Host recognition of pathogenic microorganisms • Cytokines as adjuvants and bioassays for immune response • Development of new diagnostical tools for autoimmune diseases • Invasive growth mechanisms and diagnostical methods • Emerging risk zoonosis control • Diagnostical tools for transfer of virulence factors

15. Proposed future research topics in PathoGenoMics 1. Development of novel principles for anti-microbial treatment for replacingor supplementing anti-microbial treatments 2. Host recognition of pathogenic microorganisms 3. Cytokines as adjuvants and bioassays for immune response 4. Screening of epithelial cells for probiotic bacteria 5. New methods for detection, prediction and antimicrobial treatment of pathogens on ephitelial cells

16. Proposed future research topics in PathoGenoMics 6. Development of new diagnostical tools for autoimmune diseases 7. Invasive growth mechanisms and diagnostical methods 8. Inhibitors of microbial growth in food 9. Emerging risk zoonosis control 10.Diagnostical tools for transfer of virulence factors

17. 1. Development of novel principles for anti-microbial treatment for replacingor supplementing current anti-microbial treatment. Novel therapeutic priciples to overcome resistance to current antimicrobials. Innovative approaches toexploit knowledge of host/pathogen interactions and microbial and host genome for thedevelopment of new anti-bacterial and/or antifungal treatment and/orprophilaxis against micro-organisms resistant to existing antimicrobials. 2. Host recognition of pathogenic microorganisms. Molecular mechanism ofrecognition of pathogenic microbes, microbial strategiesto evade detection by the host, identification of potential targets fortherapeutic intervention, potential for development of novel targets ortherapies to boost immune response or prevent excessive stimulation.Genetic susceptibility to microbial infection, correlation to atherosclerosis orautoimmune diseases, identification of risk factors.

18. 3. Cytokines as adjuvants and bioassays for immune response Development of alternative strategies to manage infectious diseases in animals by development and application of new vaccines, based on alternative adjuvants providing long-term andsafe protection, without side-effects. Use of innovative approaches exploiting knowledge on cytokines to study theimmune response during vaccination. The development of use of different cytokines as vaccine as well as probiotics adjuvants is encouraged. Development of different types of biological assays for interferonsbased on: antiinvasive, immunomodulatory, antiproliferative, antitumor activity. Particularly encouraged is the development of different new cell systems specifically sensitive to such kind of biological activities in comparison to ELISA.

19. 4. Screening of epithelial cells for probiotic bacteria Research on the probiotic microbial flora composition in the intestinal tract.Studies on the bacterial adhesion mechanismson the epithelial cells of the intestinuum.The isolation and cultivation of intestinal epithelial cells of different animal species, such chicken, pig, bovine, human as well as their screening for probiotic bacteriain vitro should be included into the research. 5. New methods for detection, prediction and antimicrobial treatment of pathogens of ephitelial cells. Development of molecular biology based methods for detection and prediction of the occurrence and virulence of pathogens and host-pathogen interaction. Development of principles and methods that can reduce the viability and virulence/infectivity of pathogens on epithelial cells. Innovative approach to exploit knowledge of cross-talk between pathogen-epithelium-immune system in cell functional models.

20. 6. Development of new diagnostical tools for autoimmune diseases Microbial antigenes have the potential to initiate autoreactivity through molecular mimicry, polyclonal activation, or the release of previously sequestered antigens. Development of innovative approaches, exploiting knowledge of different DC subsets in peripheral blood and development of in vitro system is proposed. Innovative approaches, exploiting knowledge of peripheral B-lymphocyte subpopulations in infections with such organisms and in patients with autoimmune diseases (SLE). Development of diagnostically valuable tools for monitoring progress of disease in patients with SLE.

21. 7. Invasive growth mechanisms and diagnostical methods The problem of new food borne pathogenes in immunocompromised human population. Understanding mechanisms of invasive growth of pathogen microorganisms. Development of methods (in vitro, in vivo) and determination of parameters for invasive growth monitoring is encouraged. 8. Inhibitors of microbial growth in food Screening of new pathogen microbial growth inhibitors in traditional food matrices. Development of (in vitro, in vivo) methods to study mechanisms of inhibition of pathogen microorganism growth in host (gastrointestinal tract).

22. 9. Emerging risk zoonosis control Regulation mechanisms of host invasion of pathogenic microorganisms representing major emerging risk zoonosis; viable but not culturable microorganisms Campylobacter sp., Mycobacterium paratuberculosis. Development of early warning diagnostic tools for microorganisms in animals and human capable to switch-on pathogen activity based on the knowledge of virulence genetic information. Determination of selective molecular markers. 10.Diagnostical tools fortransfer of virulence factors Development of early warning systems; diagnostic tools for microorganisms in animals and human capable of intra (inter) species transfer of virulence factors based on the genetic information of virulence transfer mechanisms.