Davidson 2006

From 2006.igem.org

Revision as of 01:40, 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 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.

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.</font face>

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]

TEAM RESOURCES White Board

• General Questions
• Math Questions
• Biology Questions

Lab Work

• Pancake Parts</font face>

General

• Papers of Interest
• Presentation Outline

Assembly

[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]