Coming up with a                           project                         Teach the Teachers Workshop                    ...
Talk to peopleSunday, May 23, 2010
Previous iGEM projects                        igem.orgSunday, May 23, 2010
New organismsSunday, May 23, 2010
New parts and tools                        for future teams                          Most commonly used parts:            ...
BBa_F2620                                                                                                                 ...
Let the students                            chooseSunday, May 23, 2010
Help them make smart                         choices                       • Figure out what’s practical: How many        ...
Describe your project                        on your team wiki                           Teach the Teachers Workshop      ...
Sunday, May 23, 2010
Measurement                       • Only some parts in the Registry have                         characterization data    ...
Sunday, May 23, 2010
Standard assembly                         Teach the Teachers Workshop                                     2010Sunday, May ...
BioBrick standard parts                        EcoRI   XbaI   BioBrick part   SpeI   PstI                                 ...
BioBrick standard assembly          E      X         BioBrick part 1       S    P           E   X        BioBrick part 2  ...
A                           AB                       B                                ABCD                       C        ...
Why use the BioBrick                            standard?                       • It is faster to build multi-part systems...
Get the                       enzymes                       cheaperSunday, May 23, 2010
Sunday, May 23, 2010
Sunday, May 23, 2010
Sunday, May 23, 2010
Plasmid backbones                         Teach the Teachers Workshop                                     2010Sunday, May ...
Sunday, May 23, 2010
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[iGEM Workshop] Coming up with a Project

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[iGEM Workshop] Coming up with a Project

  1. 1. Coming up with a project Teach the Teachers Workshop 2010Sunday, May 23, 2010
  2. 2. Talk to peopleSunday, May 23, 2010
  3. 3. Previous iGEM projects igem.orgSunday, May 23, 2010
  4. 4. New organismsSunday, May 23, 2010
  5. 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. 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. 7. Let the students chooseSunday, May 23, 2010
  8. 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. 9. Describe your project on your team wiki Teach the Teachers Workshop 2010Sunday, May 23, 2010
  10. 10. Sunday, May 23, 2010
  11. 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. 12. Sunday, May 23, 2010
  13. 13. Standard assembly Teach the Teachers Workshop 2010Sunday, May 23, 2010
  14. 14. BioBrick standard parts EcoRI XbaI BioBrick part SpeI PstI Knight, 2003Sunday, May 23, 2010
  15. 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. 16. A AB B ABCD C CD D E EF F EFGH G GH HSunday, May 23, 2010
  17. 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. 18. Get the enzymes cheaperSunday, May 23, 2010
  19. 19. Sunday, May 23, 2010
  20. 20. Sunday, May 23, 2010
  21. 21. Sunday, May 23, 2010
  22. 22. Plasmid backbones Teach the Teachers Workshop 2010Sunday, May 23, 2010
  23. 23. Sunday, May 23, 2010

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