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

1. Synthetic Biology Based on Interchangeble Parts Bálint L. Bálint - a tool for building genetically engineered machines-

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

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. “ 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. Standards enable variability

7. Standard file formats in Biology

8. Standardized experimental descriptions Dealing with complexity needs standardization

9. Modular building is seen on several hierarchical levels - standardized connection are needed to build up hierarchical devices-

10. Complex engeneering requires modular building and standard assembly procedures

11. Abstraction levels in Synthetic Biology

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. 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. 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. 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. Classical plasmid representation Eugene plasmid representation

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. Modular tools and team work: results of the Debrecen-Hungary team at the MIT in Boston The Lipid Sensing Eukaryotic Toolkit

22. Team: Debrecen-Hungary 2010

23. http://2010.igem.org/Team:Debrecen-Hungary/meetteam

24. http://2010.igem.org/Team:Debrecen-Hungary

25. http://partsregistry.org/Main_Page

26. Video Project: “Film in Lab” http://www.youtube.com/user/debrecenigem2010 Debrecen Team 2010

27. On the Media Science!!!

31. Cloning I. II. III. IV. LBD LBD LBD pMAT GAL4 pSB1C3 pSB1C3 GAL4 LBD pSB1C3 LBD GAL4 pCDNA3.1 MCS

32. Mammalian Two-Hybrid System b. Ligand testing Detected luciferase activity correlates with ligand binding or strength of interaction a. Interaction experiment LUCIFERASE ENZYME

33. Testing receptors in action 1. Activity

34. Testing receptors in action

35. Testing receptors in action 2. Dimer formation

36. Testing receptors in action 2. Dimer formation

37. Dimer formation of receptors Dimer formation of PXR (with RXR) Classical approach

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

40. a. Remote control of gene therapy or smart cells b. Synthetic organisms with an environmental “sixth sense” for pollutants Possible application

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

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

44. Thanks for your attention!