Davidson 2006

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Project Overview

Davidson Parts

Team Members

Tools and Resources

Check out our [http://www.bio.davidson.edu/courses/synthetic/photos/FlapJack_HotCakes.html Official Team Photo]
Left to Right: Malcolm, Laurie, Sabriya, Erin and Lance

PROJECT OVERVIEW Logo

Goal
Our goal is to mathematically model and genetically engineer a biological system that can compute the solution to a puzzle called the 'pancake problem'. Our work was done in collaboration with the Missouri Western iGEM Team and an undergraduate research fellow from Hampton University.

Approach


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 .
  • 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 (smaller) in one case, and the coding region (bigger) in another case. The coding region is TetR resistance gene isolated from a plasmid in the Registry. For higher stacks of pancakes, we will also use chloramphenicolR and cycloheximideR.


Contents

Students

  • Erin Zwack is a rising junior biology major at Davidson College.
  • Lance Harden is a rising sophomore math major at Davidson College.
  • Samantha Simpson is a rising sophomore at Davidson College who might design a major in genomics.

Faculty

  • 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

Presentation Outline

Presentation Outline

Parts Created

Pancake Parts

Questions

Assembly

Progress

Plasmids and Bacteria     Hix and RE    Hin and Antibiotic Pancakes    Ligations

Pancake Simulators aka The Lancelator (MATLAB Code)

The Original Flipping Simulators

[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]

Graphing Tools

[http://gcat.davidson.edu/IGEM06/pancakeplotter.m Pancakeplotter]
[http://gcat.davidson.edu/IGEM06/permplotter.m Permplotter]
[http://gcat.davidson.edu/IGEM06/adjmat.m Adjmat - creates adjacency matrices]
[http://gcat.davidson.edu/IGEM06/bioadjmat.m Bioadjmat - Adjmat with biological equivalence]
[http://gcat.davidson.edu/IGEM06/make_radial.m Make_radial - creates a radially-embedded graph]
[http://gcat.davidson.edu/IGEM06/find_diam.m Find_diam - finds the diameter of a pancake graph]

Miscellaneous

[http://gcat.davidson.edu/IGEM06/signedperms.m Signedperms - lists all signed permutations for a stack of k pancakes]
[http://gcat.davidson.edu/IGEM06/bioperms.m Bioperms - Signedperms with biological equivalence]
[http://gcat.davidson.edu/IGEM06/oligo.html Oligo Cuts Optimization]

Personal tools
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