Davidson 2006

From 2006.igem.org

Revision as of 02:33, 18 October 2006

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

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 [http://2006.igem.org/wiki/index.php/Missouri_Western_State_University_2006 Missouri Western iGEM Team] and an undergraduate research fellow from Hampton University.

The Pancake Problem: at the Interface of Math and Biology
Our project integrates math and biology using the pancake problem, a puzzle in which a disordered series of units (or stack of pancakes) must be shuffled into the correct order. Every unit, or pancake, must be placed in the proper order (largest on bottom, smallest on top) and in the proper orientation (burnt side down, golden side up). Try this puzzle out for yourself [http://www.cut-the-knot.org/SimpleGames/Flipper.shtml here].

Trial and error is one approach to solving the problem, but how could one compute the quickest solution? A stack of pancakes can be represented mathematically as well as biologically. Mathematically, signed permutations can be used to represent pancake stacks. "1, 2, 3" is a stack of three pancakes all in the proper order and orientation. "2, 3, -1" is the same stack, but here pancake 1 is out of order and in the wrong orientation (burnt side up).

Approach

What: Our goal is to solve the Pancake problem in a biological system.

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 Tet^R resistance gene isolated from a plasmid in the Registry. For higher stacks of pancakes, we will also use chloramphenicol^R and cycloheximide^R.

TEAM MEMBERS

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 math major at Davidson College.
• 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]

TOOLS AND RESOURCES

iGEM 2006 Jamboree

• Presentation Outline

White Board

• General Questions
• Math Questions
• Biology Questions

Biology Tools (Wet Bench)

• Pancake Parts
• The What's and How's: Davidson Protocols
• [http://gcat.davidson.edu/IGEM06/oligo.html Oligo Cuts Optimization]: by Lance Harden
• Papers of Interest

Math Tools

• Pancake Simulators, aka The Lancelator (MATLAB Code)
• Other 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]

Bio-Math Tools

• [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]

Assembly Plans

• Assembly powerpoint
• Assembly plan
• Western Assembly Plan
• Davidson Assembly Plan

Progress

• Plasmids and Bacteria
• Hix and RE
• Hin and Antibiotic Pancakes
• Ligations