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[iGEM Workshop] Coming up with a Project
[iGEM Workshop] Coming up with a Project
[iGEM Workshop] Coming up with a Project
[iGEM Workshop] Coming up with a Project
[iGEM Workshop] Coming up with a Project
[iGEM Workshop] Coming up with a Project
[iGEM Workshop] Coming up with a Project
[iGEM Workshop] Coming up with a Project
[iGEM Workshop] Coming up with a Project
[iGEM Workshop] Coming up with a Project
[iGEM Workshop] Coming up with a Project
[iGEM Workshop] Coming up with a Project
[iGEM Workshop] Coming up with a Project
[iGEM Workshop] Coming up with a Project
[iGEM Workshop] Coming up with a Project
[iGEM Workshop] Coming up with a Project
[iGEM Workshop] Coming up with a Project
[iGEM Workshop] Coming up with a Project
[iGEM Workshop] Coming up with a Project
[iGEM Workshop] Coming up with a Project
[iGEM Workshop] Coming up with a Project
[iGEM Workshop] Coming up with a Project
[iGEM Workshop] Coming up with a Project
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[iGEM Workshop] Coming up with a Project

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iGEM Works

iGEM Works

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  • 1. Coming up with a project Teach the Teachers Workshop 2010Sunday, May 23, 2010
  • 2. Talk to peopleSunday, May 23, 2010
  • 3. Previous iGEM projects igem.orgSunday, May 23, 2010
  • 4. New organismsSunday, May 23, 2010
  • 5. New parts and tools for future teams Most commonly used parts: B0015 - a terminator F2620 - an inducible promoter B0034 - a RBS R0011 - lac promoter Plasmid backbonesSunday, May 23, 2010
  • 6. BBa_F2620 BBa_F2620 3OC6HSL PoPS Receiver Mechanism & Function Component Parts A transcription factor (LuxR) that is active in the presence of a cell-cell signaling molecule (3OC6HSL) is controlled by a regulated operator (PLtetO-1). Device input is 3OC6HSL. Device output is PoPS from a LuxR-regulated operator. If R0040 B0034 C0062 B0015 R0062 used in a cell containing TetR then a second input such as PLtetO-1 RBS luxR Term. Plux,R aTc can be used to produce a Boolean AND function. Static Performance* Dynamic Performance* http://parts.mit.edu/registry/index.php/Part:BBa_F2620 600 8 600 8 GFP synthesis rate (molecules cell!1 s!1) GFP synthesis rate (molecules cell!1 s!1) Population Mean Colony Range 7 + 3OC6HSL 7 500 Hill Equation 500 6 6 400 400 5 5 PoPS cell!1 PoPS cell!1 300 4 300 4 Reuse and 3 3 200 200 GFP synthesis rate (Low Input) 2 GFP synthesis rate (High Input) 2 100 100 Polynomial Fit (High Input) 1 PoPS (High Input) 1 0 0 0 0 0E+00 1E!10 1E!09 1E!08 1E!07 1E!06 1E!05 1E!04 !10 0 10 20 30 40 50 [3OC6HSL] (M) Time (min) Pmax [3OC6HSL]n Pmax: 6.6 PoPS cell-1 BBa_F2620 Response Time: <1 min existing parts Pout = K: 1.5E-09 M 3OC6HSL BBa_T9002 Response Time: 6±1 min K n + [3OC6HSL]n n: 1.6 Inputs: 0 M (Low), 1E-07 M (High) 3OC6HSL Input Compatibility* Reliability** 600 8 GFP synthesis rate (molecules cell!1 s!1) C4HSL C6HSL 7 500 3OC6HSL 6 C7HSL 92 400 5 74 C8HSL gs PoPS cell!1 56 lin 3OC8HSL 300 38 92 ub 4 1E0 Signaling Devices GFP 1E1 Do C10HSL 20 (arb1E2 1E3 74 gs C12HSL 3 itrar 1E4 56 y un lin 200 its) ub 38 2 Low Input GFP1E0 1E1 Do (0 M 3OC6HSL) (arb 1E2 1E3 20 100 itrar 1 y un 1E4 its) High Input 0 0 (1E -7 M 3OC6HSL) 0E+00 1E!10 1E!09 1E!08 1E!07 1E!06 1E!05 1E!04 [AHL] (M) Genetic: >92/>56 culture doublings Part Compatibility (qualitative) Performance: >92/>56 culture doublings (low/high input during propagation) Chassis: MC4100, MG1655, and DH5 Plasmids: pSB3K3 and pSB1A2 Conditions (abridged) Devices: E0240, E0430 and E0434 Output: PoPS measured via BBa_E0240 Culture: Supplemented M9, 37ºC Transcriptional Output Demand (low/high input) Plasmid: pSB3K3 Nucleotides: 0 / 6xNt nucleotides cell-1 s-1 Chassis: MG1655 Polymerases: 0 / 1.5E-1xNt RNAP cell-1 *Equipment: PE Victor3 multi-well fluorimeter (Nt = downstream transcript length) **Equipment: BD FACScan cytometerAuthors: Barry Canton Ania Labno Registry of Standard Biological Parts License: PublicUpdated: March 2008 making life better, one part at a timeSunday, May 23, 2010
  • 7. Let the students chooseSunday, May 23, 2010
  • 8. Help them make smart choices • Figure out what’s practical: How many assembly stages could the team possibly do over the course of the summer? That sets an upper limit to the size of the system. • Design the project so that different modules can be done in parallel. • It doesn’t have to be a brand new idea.Sunday, May 23, 2010
  • 9. Describe your project on your team wiki Teach the Teachers Workshop 2010Sunday, May 23, 2010
  • 10. Sunday, May 23, 2010
  • 11. Measurement • Only some parts in the Registry have characterization data • It can be hard to compare the measurements we do have • Registry tour: BBa_F2620 and Anderson families • Controls • Where to put the data: on the RegistrySunday, May 23, 2010
  • 12. Sunday, May 23, 2010
  • 13. Standard assembly Teach the Teachers Workshop 2010Sunday, May 23, 2010
  • 14. BioBrick standard parts EcoRI XbaI BioBrick part SpeI PstI Knight, 2003Sunday, May 23, 2010
  • 15. BioBrick standard assembly E X BioBrick part 1 S P E X BioBrick part 2 S P Digest with Digest with EcoRI and SpeI XbaI and PstI E X BioBrick part 1 S E X BioBrick part 2 S P Ligate E X BioBrick part 1 Mixed BioBrick part 2 S PSunday, May 23, 2010
  • 16. A AB B ABCD C CD D E EF F EFGH G GH HSunday, May 23, 2010
  • 17. Why use the BioBrick standard? • It is faster to build multi-part systems • Assembling every two parts is the same • You can reuse parts from the Registry • Other people can reuse your parts • It is required to win a prize at iGEM!Sunday, May 23, 2010
  • 18. Get the enzymes cheaperSunday, May 23, 2010
  • 19. Sunday, May 23, 2010
  • 20. Sunday, May 23, 2010
  • 21. Sunday, May 23, 2010
  • 22. Plasmid backbones Teach the Teachers Workshop 2010Sunday, May 23, 2010
  • 23. Sunday, May 23, 2010

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