Revision as of 19:13, 10 June 2009

This space will be used starting April, 2009 for brainstorming and a shared whiteboard space.

Davidson Lab Protocols
MWSU Lab Protocols
BioMath Connections Page
GCAT-alog Freezer Stocks

iGEM 2009 Project

We need to learn more about these topics:

1. How do signal sequences/peptides work in bacteria, and how can we use them?
2. Plasmid Creation
3. What is msDNA?
4. How is msDNA normally produced? Olivia/Alyndria
5. How many copies are carried per cell? Alyndria
6. What would we need to do to turn this into a BioBrick device? Romina
7. How could we swap out msDNA sequences? Shamita
8. What role can physical modeling of protein structure play in our project?
9. What role can physical modeling of proteins play in our project? Eric Sawyer
10. What other cool reporters are there? (Discrete On/Off or Continuous) Bryce Szczepanik
11. Can we use promoter strength/opposite directions to subtract? Clif Davis
12. Can we use suppressor tRNAs to encode logical operators (suppressor suppressor logic, SSL)?
13. How is msDNA stored in E. coli? Olivia
14. What is the sequence of bacterial reverse transcriptase and can we clone that gene? Shamita
15. Can we redesign the normal msDNA pathway to produce new segments of DNA of our choosing? All
16. What are other available reverse transcriptases? Leland
17. What other math problems (e.g. NP- complete) are accessible to us? Annie Siya Sun
18. What is the relationship between 3-SAT and map coloring? Ashley Schnoor
19. What activators are there that turn on a promoter without any help?
20. Can we use protein interactions to compute? (Post-translation, proteases, quaternary structure) Will Vernon
21. Could we do something with clocks/counting?
22. Could we have/use multiple synthetic organelles in a cell?
23. What ideas from previous iGEM teams are useful to us?
24. Examples of Metabolic Pathways in E.coli

1. Can we get bacteria to solve a problem large enough to challenge a person?
2. What interesting challenges or problems does origami offer?
3. Can we produce a series of increasingly difficult goals that might be possible to produce in the lab?
4. What has been done before and how can we improve upon that?
5. We can perform some pilot experiments using synthesized DNA and later switch to msDNA (maybe).
6. Can we address the Boolean Satisfiability (SAT) problem with a bacterial computer?
7. How has 3SAT been addressed with a DNA computer? Can we use those methods?

1. Can we get bacteria to solve a problem large enough to challenge a computer (probably not, but it is fun to think about)?
2. What are some linear algebra applications for DNA origami?
3. How can we use origami to solve 3-SAT problems?

1. What constructs are we testing?
2. What school districts do we have access to?
3. Where is the Synthetic Biology page we want high school teachers to use after the survey?
4. Do you need any more input from the veterans before the survey is ready?

1. Can we solve a 3-SAT problem with supressor logic?

Here is a link to the animation of the Hin/Hix system created by the "E. HOP living computer project folks. Hin/Hix Animation