1. HKUSTers Jean and Winnie
iGEM 2009 Tutorial 2
Good afternoon, everyone! We are from Hong Kong University of Science and Technology.
We are very excited to have this opportunity to talk about a big topic with you. Even Einstein didn’t think of it. The topic is, does God play dice with the cell.
HKUSTers
Jean and Winnie

2. Review Quiz
What is central dogma?

3. Central Dogma Central Dogma
Central Dogma establishes the fundamental rationale that by manipulating DNA, we could generate RNA, and protein, which are used to reshape the cellular behavior and function.
E.coli, as a result of its simplicity as well as its extensive research, works as a good model organism for our project.
E.coli, its simplicity and extensive previous study makes it a good model organism 3

4. Central Dogma (cont.) Pol Pol Transcription regulation: (DNA->RNA)
Promoter
Terminator
Repressor/Activator
Translation regulation:
(RNA->Protein)
RBS
Before going into very detailed design, first I wanna have a brief introduction about transcription and translation.
Promoter and terminator where RNA polymerase bind and release, the area between them will be transcribed as mRNA.
Repressor and/or Activator could bind to regulatory sequence to repress or activate transcription
When mRNA is formed, RBS on the RNA( thus on DNA) is needed for Ribosome to bind to mRNA and start translation (mRNA protein)
Standard symbols for several parts.
RBS
Promoter RBS coding gene reporter terminator 4

6. Application To generate true randomness:
Statistical sampling & analysis
Gambling
Biological Process ….
Besides helping you select a candidate to vote for. There are many other applications of randomness.
In statistical sampling & analysis, random numbers are needed as sampling inputs to analyze the process result.
When simulating real and complex process, such as temperature turbulation in biology experiment simulation, we need random numbers to act as noise.

7. A Switch
….with randomness
[1]
[0]
either right [0], ………

8. A Switch
….with randomness
[1]
[0]
…..or left [1].

9. Devices in our design

10. Genetic circuit START Transcription blocked
Lamda promoter has problem for integration, so the modified version, using overlapped T7 promoter pair + cI434 and TerR repressor binding site, to generate mutually repression.
T7 polymerase could be generated as pulses.
T7 polymerase
Promoter
Terminator
Ribosome binding site
TetR repressor
Green/Red fluorescence protein 10

11. Genetic circuit START Transcription blocked
Lamda promoter has problem for integration, so the modified version, using overlapped T7 promoter pair + cI434 and TerR repressor binding site, to generate mutually repression.
T7 polymerase could be generated as pulses.
T7 polymerase
Promoter
Terminator
Ribosome binding site
cI434 repressor
Green/Red fluorescence protein 11

12. Add Memorizer + Reporter
Further extension
Add Memorizer + Reporter
Same outcome 
No response
Start A B A B
Randomizer
Memorizer
Another extension is to further add a memorizer and a reporter. The output of the Randomizer can be read by a Memorizer so that it will store this random signal. And then after another random signal is generated, the Reporter will compare these two signals and reports nothing when they are the same or reports a jackpot hit when they are different. The content of the memorizer should change to the last generated signal.
Jackpot signal! 12 12

13. Further extension If it works successfully,
we can generate random binary numbers
within a single bacterial cell.
If our randomizer works successfully, we can generate larger random numbers in binary format in a single bacterial cell. Then we will achieve the true randomness. 13

14. Proposals Randomizer Pattern Formation Chemo-runner

15. Hurdles Time Management Simulation Difficulties in Wetlab
Organizational Structure
So….

16. Let’s start EARLY this year! & show your COMMITMENT!!!

17. End Products Team wiki: http://2008.igem.org/Team:HKUSTers
Parts to Registry
Poster
Presentation:

19. End Products Team wiki: http://2008.igem.org/Team:HKUSTers
Parts to Registry
Poster
Presentation:

20. Projects Categories Food or Energy Project Environment Project
Health or Medicine Project
Manufacturing Project
New Application Area
Foundational Advance
Software Tool Track
Judging Criteria:

21. How to start? Registration Deadline: March 31 2009
OpenWetWare:
Lab Tour
DNA Engineering
especially the day1-5 handouts
Systems Engineering
especially the day1-3 handouts

22. Homework

23. Q & A
If you have any question you may ask now. 23

24. & Small group discussion
Time to know each other!!!
& Small group discussion

25. How to Assemble?
Standard Assembly