Shanghai University

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Lecture to the sophomore students of Pr Dabing Zhang, Shanghai Jiao Tong University. October 2008

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Shanghai University

  1. 1. Research: thoughts on a personal experience. Dany Morisset [email_address] http://www.nib.si/en/
  2. 2. <ul><li>Contents: </li></ul><ul><li>Slovenia </li></ul><ul><li>The National Institute of Biology </li></ul><ul><li>The Department of Biotechnology and Systems Biology </li></ul><ul><ul><li>Introduction </li></ul></ul><ul><ul><li>GMO (Genetically Modified Organism) </li></ul></ul><ul><li>Personal career and some thoughts </li></ul>
  3. 3. Where is Slovenia? Shanghai Slovenia
  4. 4. Slovenia
  5. 5. Italy Germany Venezzia (Venice)
  6. 6. Slovenia (Slovenija) GENERAL INFORMATION Area: ............. ............. 20,273 km2 (80km x 260 km) 7,037km2 for Shanghai (city) Forest: .......... ............. 10,124 km2 (49.9%) Vineyards: ......... ......... 216 km2 Length of coast:..........46.6 km Capital: ........... ........... Ljubljana Population: ........ ... .....2 ,023,000 (2008) 18,450,000 in Shanghai (2007) Language: ........ ........ .Slovene Currency: ....... ....... ....Euro, 1 January 2007 Education: ........... ...... Universities in Ljubljana , Nova Gorica and Maribor cca 90,000 students
  7. 7. Triglav, the highest Slovenian mountain Bled, jewel of the Julian Alps Ljubljana, the capital city Rafting on the Soča River
  8. 8. Piran, Tartini’s coastal town Piran bay Julian Alps
  9. 9. Postojna Cave Lipica horses Proteus anguinus or human fish Karstic land in Škocjan park
  10. 10. Vineyard from Štajerska Region Slovenian specialities Slovenian wine producing
  11. 11. National Institute of Biology at the Biological Centre in Ljubljana Italy Germany Venezzia (Venice)
  12. 12. NIB is the leading institution for basic and applied research in biological sciences in Slovenia… and… the third largest institution in the field of natural sciences in Slovenia!
  13. 13. Mission NIB is a public research institute, established by the Republic of Slovenia with the mission: - to create new (basic) knowledge on the field of biology and related natural sciences; - to transfer new knowledge into use for improvement of the quality of life (to enrich the life on Earth).
  14. 14. Staff
  15. 17. National Institute of Biology <ul><li>Departments </li></ul><ul><ul><li>Department of Biotechnology and Systems Biology </li></ul></ul><ul><ul><li>Department of Freshwater and Terrestrial Ecosystems Research </li></ul></ul><ul><ul><li>Department of Entomology </li></ul></ul><ul><ul><li>Marine Biology Station </li></ul></ul><ul><ul><li>Department of Genetic Toxicology and Cancer Biology </li></ul></ul>
  16. 18. Department of Biotechnology and Systems Biology <ul><ul><li>37 employees </li></ul></ul><ul><ul><li>8 senior researchers, 6 postdocs, 8 technical assistants, 5 research assistants, </li></ul></ul><ul><ul><li>8 PhD students, </li></ul></ul><ul><ul><li>2 administrative assistants </li></ul></ul>Pr. Dr Maja Ravnikar
  17. 19. - Horizontal project organisation: - OMICS (Kristina Gruden) - MICROBIOLOGY (Maja Ravnikar) - GENETICALY MODIFIED ORGANISMS (Jana Žel) - Infrastructure (Maruša Pompe Novak) - Quality Assurance and lab safety issues (Marjana Camloh) - Human resources and pedagogical activities (Maja Kovač, Marina Dermastia) - Bio-security (Mojca Milavec) Activities
  18. 20. Projects <ul><li>Cca 55 project per year on 1,2 or 3 years basis </li></ul><ul><li>Ratio between basic and applied research: 60% / 40 % </li></ul><ul><li>Applied research: </li></ul><ul><ul><li>Research for companies (LEK, BIA Separations, Krka...) </li></ul></ul><ul><ul><li>Detection of pathogens (bacteria, phytoplasma, viruses) </li></ul></ul><ul><ul><li>Detection of genetically modified plants in food, feed and seed </li></ul></ul><ul><li>Every year, application for 30 – 40 projects </li></ul>
  19. 21. International cooperation <ul><li>4 EU projects </li></ul><ul><li>13 bilateral projects </li></ul><ul><li>5 COST </li></ul><ul><li>2 Twining </li></ul><ul><li>2 ERA-NET </li></ul><ul><li>2 Technology Platforms </li></ul>
  20. 22. OMICS: Systems biology approaches Methodologies <ul><li>Transcriptomics: DNA microarrays and quantitative real time PCR </li></ul><ul><li>Proteomics </li></ul><ul><li>In-situ hybridization </li></ul><ul><li>Biochemical and cytological research </li></ul><ul><li>Bioinformatics and biostatistics </li></ul>
  21. 23. OMICS: Systems biology approaches <ul><li>Plant-pathogen/pest interactions </li></ul><ul><ul><li>Potato – Virus PVY </li></ul></ul><ul><ul><li>Potato – Colorado Potato Beetle </li></ul></ul><ul><ul><li>Grapevine – Phytoplasma </li></ul></ul><ul><li>Cell therapy of cancer </li></ul><ul><li>Projects with pharmaceutical industry: </li></ul><ul><ul><li>Drug discovery , drug production </li></ul></ul>Biological problems :
  22. 24. MICROBIOLOGY <ul><li>New f i ndings of plant pathogens, emerging diseases, biosecurity </li></ul><ul><li>Study of biology of plant pathogens – biodiversity </li></ul><ul><li>Development of diagnostic methods </li></ul>
  23. 25. Real time RT- PCR: PVY NTN - distinction of strains CSNV, TSWV, INSV ToMV (CIM), CaMV (CIM), PePMV - distinction of strains, Rotaviruses – water samples Xylophyllus ampelinus , Eam, Phytoplasmas Microarray technology, ring trial New Methods: Development of sensitive methods for plant pathogen detection
  24. 26. Concentration and purification of plant viruses <ul><li>Using CIM ® chromatographic supports, quick and efficient method for virus concentration in irrigation water was elaborated </li></ul><ul><li>Studies of virus purification: purification step for ToMV is finished in one day </li></ul>
  25. 27. <ul><li>- Transgenic plants: Development and research of plants resistant to pathogens and pests </li></ul><ul><li>- Research and development, projects </li></ul><ul><li>Development of methods for routine detection of GMOs </li></ul><ul><li>Policy advisors, quality system, Working Groups </li></ul>Genetically Modified Organisms (GMOs):
  26. 28. <ul><li>Selection of promising genes from transient expression </li></ul><ul><li>“ omics” studies for stable transformation </li></ul>Transgenic plants
  27. 29. <ul><li>Co-Extra EU project </li></ul><ul><ul><li>Traceability and coexistence of GMOs </li></ul></ul><ul><ul><li>Integrated project, 54 partners, 24Mo Euros </li></ul></ul><ul><ul><li>Objectives: </li></ul></ul><ul><ul><ul><li>Fill-in the gap between the set legal framework and its practical implementation </li></ul></ul></ul><ul><ul><li>Works: </li></ul></ul><ul><ul><ul><li>Critical point of GMO quantification (extraction, DNA quantification…) </li></ul></ul></ul><ul><ul><ul><li>Automation set-up, machine robustness </li></ul></ul></ul><ul><ul><ul><li>Gene variability, new reference genes and materials, new chemicals </li></ul></ul></ul><ul><ul><ul><li>New detection methods (microarray, real-time detection) </li></ul></ul></ul>Research and development, projects
  28. 30. GMOs diagnostics <ul><li>Development and validation of analytical methods in GMO-testing </li></ul><ul><li>Introduction and validation of analytical methods </li></ul><ul><li>Routine diagnostics (private, inspectorate...) </li></ul><ul><li>Follow-up of results in proficiency tests </li></ul><ul><li>Participation to international studies </li></ul><ul><li>Respect of QA (ISO 17025) </li></ul>
  29. 31. National Reference laboratory <ul><li>Cooperation with different ministries in Slovenia </li></ul><ul><ul><li>Routine analysis </li></ul></ul><ul><ul><li>Sc. and Tec. experts, Slovenian representative </li></ul></ul><ul><ul><li>Training </li></ul></ul><ul><ul><li>Communication </li></ul></ul><ul><li>Cooperation with standardization bodies (CEN, Slo) </li></ul><ul><li>Cooperation with CRL (JRC, Ispra, Italy) </li></ul><ul><ul><li>Validations of methods </li></ul></ul><ul><ul><li>Consultant </li></ul></ul><ul><li>Cooperation with ENGL </li></ul><ul><ul><li>Member of Steering Committee </li></ul></ul><ul><ul><li>Cooperation in WG </li></ul></ul>
  30. 32. Studies, PhD
  31. 33. Studies, PhD <ul><li>B . sc . Biochemistry </li></ul><ul><li>M . sc . Biochemistry </li></ul><ul><li>Pre-PhD Biotechnology, opt. Biochemistry </li></ul><ul><li>PhD microbiology & Biochemistry </li></ul><ul><li>Postdoc microbiology & Biochemistry </li></ul>Poitiers University, France
  32. 34. <ul><li>“ Structure/function relationships of an anti-listerial bacteriocin, mesentericin Y105” </li></ul><ul><ul><li>Microbiology, Biochemistry and Molecular biology. Food safety orientated </li></ul></ul><ul><ul><li>Purely fundamental research but partially financed by private company (Danisco, ex Rhodia Food, Lactic ferment company) </li></ul></ul><ul><li>Opportunity to give lectures in University (Freshmen, Sophomores, Juniors): Biophysics, Biochemistry, Microbiology and molecular Biology </li></ul>
  33. 35. First postdoc
  34. 36. First postdoc Postdoctoral studies in University Laval and Hospital Laval, Quebec city, Qc, Canada <ul><li>“ Role of the new WAP protein, HE4” </li></ul><ul><li>Use of previous knowledge: cloning, biochemistry, microbiology </li></ul><ul><li>New knowledge: cell biology, enzymology, yeast, cancer/inflammation processes </li></ul><ul><li>Purely fundamental, public funding </li></ul><ul><li>University + hospital </li></ul><ul><li>First experience abroad </li></ul><ul><ul><ul><li>New experience in different domain, flexibility, living abroad </li></ul></ul></ul><ul><ul><ul><li>Loss of contact with France, less opportunities to come back, need for more applied research </li></ul></ul></ul>Neutrophil inhibitors PDE4 inhibitors Alveolar repair Mucoregulators Immunosuppressants? Protease inhibitors AAT, SLPI, pre-elafin, TIMPs Mediator antagonists LTB 4 inhibitors Chemokine antagonists Quit smoking Emphysema Mucus hypersecretion PROTEASES Neutrophil elastase Cathepsins MMPs Neutrophil Alveolar macrophage CD8 + lymphocyte Chemotactic mediators (IL-8, LTB 4 ) MCP-1 ?
  35. 37. Actual work <ul><li>Started 2005. </li></ul><ul><li>“ Development of alternative DNA-amplification system to PCR technology” </li></ul><ul><ul><li>Within CoExtra project </li></ul></ul><ul><ul><li>Broad view on different DNA-amplification systems </li></ul></ul><ul><ul><li>Adapt ideas to GMO context </li></ul></ul><ul><ul><li>First “real” applied project (milestones, deliverables, deadlines): project manager </li></ul></ul><ul><ul><li>Wild card for the development </li></ul></ul><ul><ul><ul><ul><li>Real motivation </li></ul></ul></ul></ul>
  36. 38. Traceability issues <ul><ul><li>Alternative real-time DNA amplifications, real-time NAIMA </li></ul></ul><ul><ul><li>Improving microarrays in GMO detection: Target amplification using NAIMA, signal amplification dendrimers </li></ul></ul><ul><li>Morisset et al. , Nucl. Acids Res. August 2008. </li></ul><ul><li>Morisset et al ., 2008. Eur. Food Res. Tech.. 227: 1287-1297 </li></ul>
  37. 39. <ul><li>Added new responsibilities: “responsible analyst for routine GMO detection” </li></ul><ul><ul><li>Work in a Quality system (ISO 9001/17025) </li></ul></ul><ul><ul><li>Few research per se </li></ul></ul><ul><ul><li>Developing new methods (new markers) </li></ul></ul><ul><ul><li>Introduction methods validated in ring-trial </li></ul></ul><ul><ul><li>Prepare and control in-house validation </li></ul></ul><ul><ul><li>Follow-up lab’s performances (studies, PT) </li></ul></ul><ul><ul><li>Follow-up of GMO’s novelty </li></ul></ul><ul><ul><li>Advise authorities </li></ul></ul>Actual work
  38. 40. Relation with authorities <ul><ul><li>Opinions for legislation purposes </li></ul></ul><ul><ul><li>Official control support (recommendations, opinions..) </li></ul></ul><ul><ul><li>Public presentations on GMOs (like for Farmers Unions...) </li></ul></ul><ul><ul><li>Scientific and technical assistance to the competent authorities </li></ul></ul>NATIONAL INSTITUTE OF BIOLOGY Ministry of Health Ministry of Environment and Spatial Planning Ministry of Agriculture, Forestry and Food Inspectorate for Agriculture, Forestry and Food Inspectorate for the Environment and Spatial Planning Health Inspectorate Ministry of Defence and Slovenian Research Agency
  39. 41. <ul><li>Development of novel approaches to GMO field </li></ul><ul><ul><li>How to simplify routine analysis (automation, mixes, procedure) </li></ul></ul><ul><ul><li>How to decrease cost (screening, GMO track) </li></ul></ul><ul><ul><li>How to handle unapproved GMOs </li></ul></ul><ul><li>Participation to several WG/works </li></ul><ul><ul><li>ENGL </li></ul></ul><ul><ul><li>JRC </li></ul></ul><ul><ul><li>CEN </li></ul></ul><ul><ul><li>CoExtra </li></ul></ul><ul><li>Participation to congresses/lectures/(review) </li></ul>Actual work
  40. 42. National Reference laboratory <ul><li>Cooperation with CRL (JRC, Ispra, Italy) </li></ul><ul><ul><li>Validations of methods (17 until now) </li></ul></ul><ul><ul><li>Other (Working Groups for quality assurance of laboratories coop. in validations…) </li></ul></ul><ul><li>NIB is ENGL member since 2004 </li></ul><ul><ul><li>Member of Steering Committee </li></ul></ul><ul><ul><li>Cooperation in WG: </li></ul></ul><ul><ul><ul><li>Working group on GMO analytes </li></ul></ul></ul><ul><ul><ul><li>Working group of unknown GMOs </li></ul></ul></ul>
  41. 43. Conclusion <ul><li>Free choice of career: </li></ul><ul><ul><li>There is no intelligent design (!) </li></ul></ul><ul><ul><li>Use previous knowledge for new topics </li></ul></ul><ul><ul><li>Possibility to quit “wet” science </li></ul></ul><ul><li>Applied/fundamental: make your choice </li></ul><ul><ul><li>Pressure is different </li></ul></ul><ul><ul><li>Length/aim are different </li></ul></ul><ul><li>Need for motivation: </li></ul><ul><ul><li>short/long projects </li></ul></ul><ul><ul><li>are you made for science? </li></ul></ul>
  42. 44. Conclusion <ul><li>Industry/public: </li></ul><ul><ul><li>Applied research also in public/ Commercial aspects (patents/ commercialisation/spin-off) </li></ul></ul><ul><ul><li>Industry’s choice vs search for funding (but SME also look for funding) </li></ul></ul><ul><ul><li>One project/ work on different projects at one time </li></ul></ul><ul><li>Network: extremely important </li></ul><ul><ul><li>Collaboration on papers (better success) </li></ul></ul><ul><ul><li>Ease application for projects </li></ul></ul><ul><ul><li>Trust </li></ul></ul><ul><ul><li>Career opportunities </li></ul></ul><ul><li>Salary/perception: don’t dream! </li></ul>

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