iGEM Public Debrecen2010

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This is a description of the results of the iGEM Debrecen 2010 team.

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iGEM Public Debrecen2010

  1. 1. Synthetic Biology Based on Interchangeble Parts Bálint L. Bálint - a tool for building genetically engineered machines-
  2. 2. Maxwell / Darwin Physics / Biology 1900’s / 2000’s Science ~ 1870 Electrical engr. ~ 1905 Major ideas: modularity, hierarchy, information, black box behavior, feedback, design & synthesis, control of materials, technological substrate Science ~ 1960 Synthetic biology ~ 2000 Major ideas: modularity, hierarchy, information, black box behavior, feedback, design & synthesis, control of materials, technological substrate Tom Knight
  3. 3. Powerful tools of engineering design <ul><li>abstraction </li></ul><ul><li>hierarchy </li></ul><ul><li>modularity </li></ul><ul><li>standardization </li></ul><ul><li>isolation, separation of concerns </li></ul><ul><li>flexibility </li></ul>Tom Knight
  4. 4. Science and Engineering Natural organisms Engineered organisms, modular tools Knowledge & understanding Excellent models Science Systems Biology Engineering Synthetic Biology Tom Knight NO DISCOVERY BUT BUILDING FUNCTIONAL TOOLS Biology is the nanotechnology which works
  5. 5. “ In this country, no organized attempt has yet been made to establish any system, each manufacturer having adopted whatever his judgment may have dictated as best, or as most convenient for himself.” Williams Sellers “On a Uniform System of Screw Threads” Franklin Institute April 21, 1864 Tom Knight
  6. 6. Standards enable variability
  7. 7. Standard file formats in Biology
  8. 8. Standardized experimental descriptions Dealing with complexity needs standardization
  9. 9. Modular building is seen on several hierarchical levels - standardized connection are needed to build up hierarchical devices-
  10. 10. Complex engeneering requires modular building and standard assembly procedures
  11. 11. Abstraction levels in Synthetic Biology
  12. 12. iGEM Workflow Synthetize parts + test your hypothesis Predesigned parts + published knowledge Extract knowledge + redesign published sequences Draw conclusions + present your work Share knowledge + newly designed parts
  13. 13. Synthetic biology based on interchangeable parts iGEM = International Genetically Engineered Machine competition 2004: 6 teams, 2010: 133 teams, MIT Boston, MA Jamboree, November 6-8, 1300 participants Grand prix: Slovenia BioBrick Foundation, Parts Registry, Open Wetware
  14. 14. Standard Component Form gca GAATTC gcggccgc t TCTAGA g cgt CTTAAG cgccggcg a AGATCT c EcoRI XbaI t ACTAGT a GCGGCCG CTGCAG gct a TGATCA t cgccggc GACGTC cga SpeI PstI E X S P No internal sequences of the form EcoRI: GAATTC XbaI: TCTAGA SpeI: ACTAGT PstI: CTGCAG Tom Knight BBF_RFC_10
  15. 15. Assembly 3-Way E P E X S t A CTAGA a a TGATC T t SpeI XbaI t ACTAGA a a TGATCT t mixed E X S P X S P vector origin antibiotic resistance Tom Knight
  16. 16. Classical plasmid representation Eugene plasmid representation
  17. 17. <ul><li>iGEM main benefit: </li></ul><ul><li>Expert education </li></ul><ul><li>Project type thinking </li></ul><ul><li>Interdisciplinarity (bio+info+math+biotech) </li></ul><ul><li>Team work skills </li></ul><ul><li>Rigurous protocoll following </li></ul><ul><li>International very cooperative community </li></ul><ul><li>Open source tools for biology </li></ul><ul><li>Focus on deadlines and results </li></ul><ul><li>What is needed: </li></ul><ul><li>Tutors and students </li></ul><ul><li>Interdisciplinary support groups </li></ul><ul><li>Lab infrastructure </li></ul><ul><li>Funds </li></ul>
  18. 18. 4th Molecular Cell and Immune Biology Winter School 14th January 2011 Presenting students: Endre Károly Kristóf, Bence Dániel, Katalin Sándor, Erika Berényi, Tímea Beregi Department of Biochemistry and Molecular Biology Instructors: Dr. Bálint László Bálint Dr. Gábor Zahuczky Dr. Máté Demény Péter Brázda University of Debrecen, MHSC
  19. 19. Modular tools and team work: results of the Debrecen-Hungary team at the MIT in Boston The Lipid Sensing Eukaryotic Toolkit
  20. 22. Team: Debrecen-Hungary 2010
  21. 23. http://2010.igem.org/Team:Debrecen-Hungary/meetteam
  22. 24. http://2010.igem.org/Team:Debrecen-Hungary
  23. 25. http://partsregistry.org/Main_Page
  24. 26. Video Project: “Film in Lab” http://www.youtube.com/user/debrecenigem2010 Debrecen Team 2010
  25. 27. On the Media Science!!!
  26. 28. Objective <ul><li>Creating a toolkit containing </li></ul><ul><ul><li>Lipid sensors which may be activated by extracellular </li></ul></ul><ul><ul><li>lipids and deliver a gene expression output </li></ul></ul><ul><ul><li>Expanding the possibilities of the eukaryote system in </li></ul></ul><ul><ul><li>synthetic biology by adding DNA binding domains, chimeric </li></ul></ul><ul><ul><li>receptors, expression vectors as well as other parts to the </li></ul></ul><ul><ul><li>parts registry </li></ul></ul>
  27. 29. Function and structural organization of nuclear receptors <ul><li>a. Function </li></ul><ul><li>Metabolism </li></ul><ul><li>Development </li></ul><ul><li>Homeostasis </li></ul>b. Structure Nat Struct Mol Biol. 2008 Sep;15(9):924-31. Itoh et al.
  28. 30. Nuclear receptors in C. elegans Robinson et al. J Mol Evol (2005) 60:577–586 <ul><li>Drosophila 21 </li></ul><ul><li>Human 48 </li></ul><ul><li>C. Elegans 284 </li></ul>
  29. 31. Cloning I. II. III. IV. LBD LBD LBD pMAT GAL4 pSB1C3 pSB1C3 GAL4 LBD pSB1C3 LBD GAL4 pCDNA3.1 MCS
  30. 32. Mammalian Two-Hybrid System b. Ligand testing Detected luciferase activity correlates with ligand binding or strength of interaction a. Interaction experiment LUCIFERASE ENZYME
  31. 33. Testing receptors in action 1. Activity
  32. 34. Testing receptors in action
  33. 35. Testing receptors in action 2. Dimer formation
  34. 36. Testing receptors in action 2. Dimer formation
  35. 37. Dimer formation of receptors Dimer formation of PXR (with RXR) Classical approach
  36. 38. Arsenic side project Importance: 10 μg per liter is the WHO threshold for arsenic in drinking water Background: Team Edinburgh, 2006 made an arsenic biosensor, which can be a useful tool for on site arsenic detection Our aim: We tested the system on real samples from South-East Hungary, and the results are the followings
  37. 39. In a Nutshell <ul><li>Eleven different lipid sensors were designed cloned, </li></ul><ul><li>tested and added to the parts registry </li></ul><ul><li>Two new eukaryotic expression vectors were generated. </li></ul>
  38. 40. a. Remote control of gene therapy or smart cells b. Synthetic organisms with an environmental “sixth sense” for pollutants Possible application
  39. 41. Medals in the iGEM competition a. Addition of new synthetic parts to the parts registry - Bronze b. Showing (through results) that the new parts work- Silver c. Helping other teams characterize their parts, improving pre existing parts or developing a NEW Standard (e.g. RFC_64)– Gold
  40. 42. Medals in the iGEM competition a. Addition of new synthetic parts to the parts registry - Bronze b. Showing (through results) that the new parts work- Silver c. Helping other teams characterize their parts or improving pre existing parts – Gold
  41. 43. Debrecen-Hungary Team Sponsors: Video protocols: http://2010.igem.org/Team:Debrecen-Hungary/protocols <ul><li>and: </li></ul><ul><li>Department of Biochemistry and Molecular Biology </li></ul><ul><li>Department of Biochemistry and Molecular Biology-Apoptosis Phagocytosis Research Group </li></ul><ul><li>University of Debrecen, International Educational Center </li></ul><ul><li>University of Debrecen, TEK, Department of Biotechnology </li></ul><ul><li>DOTE Apoptozis Kutatási Alapítvány </li></ul>
  42. 44. Thanks for your attention!

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