Davidson 2006
From 2006.igem.org
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How: Trying to invert antibiotic resistance genes using the Hin/Hix inversion method found in ''Salmonella typhimurium''. | How: Trying to invert antibiotic resistance genes using the Hin/Hix inversion method found in ''Salmonella typhimurium''. | ||
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| + | * Our overall goal was to see if we could use synthetic methods to construct an ''E. coli'' computer. If we grew 10<sup>15</sup> cells, and each cell was attempting to solve the problem, then even rare events might be solvable by ''E. coli'' computers. | ||
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| + | * We decided to tackle the burnt pancake problem since DNA, like burnt pancakes, has a directionality. We needed a way to flip the DNA and chose the Hin/Hix system. We had to isolate RE, HixC from ''S. typhimurium'' strain <font color='red'>XX (need to insert name)</font color>, and Hin from ''S. typhimurium'', strain <font color='red'>TA100 (is this right?)</font color>. | ||
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| + | * We decided to test the size constraints first, so we are building stacks of pancakes only one high at first. We will try to flip the promoter in one case, and the coding region in another case. The coding region is Tet<sup>R</sup> resistance gene isolated from plasmids in the Registry. For higher stacks of pancakes, we will also use Chloramphenicol<sup>R</sup> and cycloheximide<sup>R</sup>. | ||
== '''Assembly Plan'''== | == '''Assembly Plan'''== | ||
Revision as of 19:52, 31 July 2006
[http://www.bio.davidson.edu/courses/synthetic/photos/FlapJack_HotCakes.html Official Team Photo (rollover image)]
- Malcolm, Laurie, Sabriya, Erin, Lance
Contents |
Project
Who: The Mammoths, and FlapJack and the Pancakes
What: Our goal is to solve the Pancake problem[http://www.cut-the-knot.org/SimpleGames/Flipper.shtml] in a biological system.
When: Summer and Fall '06
Where: Missouri Western State University and Davidson College
Why: Because we love breakfast... well most of us.
How: Trying to invert antibiotic resistance genes using the Hin/Hix inversion method found in Salmonella typhimurium.
- Our overall goal was to see if we could use synthetic methods to construct an E. coli computer. If we grew 1015 cells, and each cell was attempting to solve the problem, then even rare events might be solvable by E. coli computers.
- We decided to tackle the burnt pancake problem since DNA, like burnt pancakes, has a directionality. We needed a way to flip the DNA and chose the Hin/Hix system. We had to isolate RE, HixC from S. typhimurium strain XX (need to insert name), and Hin from S. typhimurium, strain TA100 (is this right?).
- We decided to test the size constraints first, so we are building stacks of pancakes only one high at first. We will try to flip the promoter in one case, and the coding region in another case. The coding region is TetR resistance gene isolated from plasmids in the Registry. For higher stacks of pancakes, we will also use ChloramphenicolR and cycloheximideR.
Assembly Plan
Students
- Sabriya Rosemond is a rising junior biology major at Hampton University.
- Erin Zwack is a rising junior biology major at Davidson College.
- Lance Harden is a rising sophomore at Davidson College who will probably major in math.
- Samantha Simpson is a rising sophomore at Davidson College who might design a major in genomics.
Faculty
- A. Malcolm Campbell [http://www.bio.davidson.edu/campbell Department of Biology]
- Laurie J. Heyer [http://www.davidson.edu/math/heyer/ Department of Mathematics]
- Karmella Haynes [http://www.bio.davidson.edu/ Department of Biology - teaching postdoc and visiting assistant professor]
Papers of Interest
Parts Created
Questions
Assembly Issues
Current Course of Action
Plasmids and Bacteria Hix and RE Hin and Antibiotic Pancakes Things That we Have Done
Pancake Simulators aka The Lancelator
MATLAB Code
[http://gcat.davidson.edu/IGEM06/randompancakeflipper.m User-Friendly Version]
[http://gcat.davidson.edu/IGEM06/powerflipper.m Power-User Version]
[http://gcat.davidson.edu/IGEM06/powerflipperplus.m Power-User Update]
[http://gcat.davidson.edu/IGEM06/findmin.m Findmin]
[http://gcat.davidson.edu/IGEM06/bigtrial.m Bigtrial]
[http://gcat.davidson.edu/IGEM06/pancakeplotter.m Pancakeplotter]
[http://gcat.davidson.edu/IGEM06/permplotter.m Permplotter]
[http://gcat.davidson.edu/IGEM06/bioperms.m Bioperms]
[http://gcat.davidson.edu/IGEM06/signedperms.m Signedperms]
[http://gcat.davidson.edu/IGEM06/adjmat.m Adjmat]
[http://gcat.davidson.edu/IGEM06/make_radial.m Make_radial]
[http://gcat.davidson.edu/IGEM06/find_diam.m Find_diam]
