Welcome iGEM team 2007

1. Welcome iGEM team 2007 Research at the Interface Biology Engineering Chemistry Economics Physics Computer Science

2. Programming Cells Goal: Can we Program cells in a manner analogous to how we now program computers? #include <iostream> main() { int input; cout << “Please Enter 0 or 1”; cin >> input; if (input = = 1) cout << “Hello iGEM"; else cout << “Goodbye”; return 0; }

3. Programming Cells Goal: Can we Program cells in a manner analogous to how we now program computers? Cellular Pseudocode { read in input; //light, chemical, etc if (input is equal to “Chemical A”) “Turn on Gene 1”; else “Gene 1 remains off”; }

4. Programming Cells Goal: Can we Program cells in a manner analogous to how we now program computers? Cellular Pseudocode { read in input; //light, chemical, etc if (input is equal to “Chemical A”) “Turn on Gene 1”; else “Gene 1 remains off”; } Chemical A Activator Gene Promoter Region

5. Programming Cells Goal: Can we Program cells in a manner analogous to how we now program computers? Cellular Pseudocode { read in input; //light, chemical, etc if (input is equal to “Chemical A”) “Turn on Gene 1”; else “Gene 1 remains off”; } Chemical A Activator Gene Promoter Region

6. Programming Cells Goal: Can we Program cells in a manner analogous to how we now program computers? Cellular Pseudocode { read in input; //light, chemical, etc if (input is equal to “Chemical A”) “Turn on Gene 1”; else “Gene 1 remains off”; } Chemical A Activator Gene Promoter Region mRNA Protein

7. Programming Cells Goal: Can we Program cells in a manner analogous to how we now program computers? Cellular Pseudocode { read in input; //light, chemical, etc if (input is equal to “Chemical A”) “Turn on Gene 1”; else “Gene 1 remains off”; } Repressor Promoter Region

8. Programming Cells Goal: Can we Program cells in a manner analogous to how we now program computers? Cellular Pseudocode { read in input; //light, chemical, etc if (input is equal to “Chemical A”) “Turn on Gene 1”; else “Gene 1 remains off”; } Chemical A Repressor Promoter Region

9. Programming Cells Goal: Can we Program cells in a manner analogous to how we now program computers? Cellular Pseudocode { read in input; //light, chemical, etc if (input is equal to “Chemical A”) “Turn on Gene 1”; else “Gene 1 remains off”; } Chemical A Repressor Promoter Region

10. Programming Cells Goal: Can we Program cells in a manner analogous to how we now program computers? Cellular Pseudocode { read in input; //light, chemical, etc if (input is equal to “Chemical A”) “Turn on Gene 1”; else “Gene 1 remains off”; } Chemical A Repressor Promoter Region mRNA Protein

11. Programming Cells But Really We would like to “write more complex cellular programs” dozens of lines of code (or even 100s) Multiple input types Multiple output types Crosstalk Loops Counters Perform a Variety of Activities

12. Engineering Biology Engineering -Framework for Design We would like a toolbox of Modular Genetic Parts -Standardized Parts (BioBricks) -Swap components- Put together in new ways to perform new function -Portability - Transfer into new organisms or strains -Ability to program Hierarchy: Parts Devices Systems Library of Parts http://parts.mit.edu Build Devices With the Parts Link Devices Together

13. http://parts.mit.edu

14. BioBrick Parts Assembly Strategy

15. The Cell is a Complex System Dynamic System Although we do know the complete set of genes for many organisms We don’t know exactly how everything works together (Goal of Systems Biology) Schematic of an E. coli cell, by D. Goodsell, Scripps

16. Synthetic Biology Research at the Interface What can we do with reprogrammed cells: 1. Harness for production (metabolic engineering) -Introduce New Pathways -Malarial Drug (artemisinin) 2. Coordinate Behavior of Cells Target cells to tissues or other cell types Respond to disease states or disease cells (biosensor, target cell death) 2-D Patterns 3. Bacteria to Build or Fabricate Systems

17. Sensors Sensors -respond to external commands -Can be used to turn genes on and off -Control motility, etc 1. Cytoplasmic Regulatory Proteins 2. Two-Component Systems 3. Environment Responsive Promoter 4. Regulatory RNAs

18. Sensors Cytoplasmic Regulatory Proteins - Inducers – Usually a small molecule – pass through cell membrane binds to a cytoplasmic regulatory protein 1. Turn on an activator 2. Turns off a repressor Maximal Induced State Graded population induction (All cells behave similar) Basal activity Intermediate Induction Difficult Dynamic Range of Induction

19. Sensors Sensor Domain NarX Two Component Systems -Membrane Bound Sensor with Kinase Domain -Responds to different stimuli (light, temp, chemicals) -Phosphorylates a Response Regulator(Triggers Transcription, binds promoter) Kinase Domain tar P

20. Sensors Sensor Domain NarX Environmental Response Promoters - pH, temp, Oxygen, UV light -might not know the protein elements involved (but know result) Kinase Domain tar P Degrade cI repressor UV light Promoter Region System used in “Tumor Killing Bacteria” -Anaerobic Inducible Promoter

21. Sensors Regulatory RNAs RNA aptamers – Change Conformation when bound to small molecule, protein, or peptide Potentially can be used to regulate any gene Off conformation (ligand not bound) On conformation (ligand bound) On Conformation Binds to target transcript And inhibits transcription (Antisense) Schematic by C. Smolke

22. Genetic Circuits Genetic Circuits Enable Cells to - Process Input Signals - Make Logical Decisions - Cell-Cell Comunication Switch -Used to turn on Gene Expression (once input is above a threshold) Forms: Transcriptional Activators or Repressors Pre-transcription

23. Genetic Circuits Inverter – a switch that produces a reciprocal response (logic gate) on off repressor Toggle Switch – can exist in two states -where one or the other repressor is fully expressed -switch can be flipped between states

24. Genetic Circuits Dynamic Circuits - Oscillator – Cascade - 3 Repressors GFP in a single cell over time (Elowitz and Leibler)

25. Genetic Circuits Cell – Cell Communication Sender Cell Receiver Cell Chemical Signal acyl-homoserine lactone (AHL) Figure from Basu … Weiss

26. Actuators Actuators-To control the output Mechanical Device for Moving a System Invasion of Malignant Cells (hypoxic environment triggers invasion of cells) Y. pseudotuberculosis invasin

27. In Conclusion We now have the tools to build new and exciting devices within biological cells Where we can construct new parts, new devices, and new systems We can build on previous work in Synthetic Biology Develop novel uses for this technology (Medical applications) Share with others through iGEM Thanks!