Davidson Missouri W

From 2007.igem.org

Revision as of 13:16, 19 June 2007

===Davidson & Missouri Western Team Logos, iGEM2006===

Team Meeting Notes

Western Meeting Notes 051407 to Present [1]

Math Related Notes

Notes 051407 to Present [2]

Students

• Will DeLoache, Junior Biology Major, [3]

• Oyinade Adefuye, Senior Biology Major, [4]

• Jim Dickson, Junior Math and Economics Major, [5]

• Amber Shoecraft, Math Major, [6]

• Andrew Martens, Senior Biology Major, [7]

• Michael Waters, Sophomore Biology Major, [8]

• Jordan Baumgardner, Junior Biology, Biochemistry/Molecular Biology Major, [9]

• Ryan Chilcoat, Junior Biology Major (Health Sciences), [10]

• Tom Crowley, Senior Biochemisty/Molecular Biology Major, [11]

• Lane H. Heard, Central High School graduate, [12]

• Nickolaus Morton, Junior Chemistry Major, [13]

• Michelle Ritter, Junior Mathematics Major, [14]

• Jessica Treece, Junior Biology Major (Health Sciences), [15]

• Matthew Unzicker, Senior Biochemistry/Molecular Biology Major, [16]

• Amanda Valencia, Senior Biochem/Molecular Biology Major, [17]

Faculty

• Malcolm Campbell [http://www.bio.davidson.edu/people/macampbell/macampbell.html], Professor, Department of Biology, [18]

• [http://www.bio.davidson.edu/people/kahaynes/kahaynes.html Karmella Haynes], Visiting Assistant Professor, Department of Biology, [19]

• Laurie Heyer [http://www.davidson.edu/math/heyer/], Associate Professor, Department of Mathematics, [20]

Shipping Address: Malcolm Campbell, Biology Dept. Davidson College, 209 Ridge Road, Davidson, NC 28036 [(704) 894-2692]

• Todd Eckdahl [http://staff.missouriwestern.edu/~eckdahl/], Professor, Department of Biology, [21]

• Jeff Poet [http://staff.missouriwestern.edu/~poet/], Assistant Professor, Department of Computer Science, Mathematics, and Physics, [22]

Shipping Address: Todd Eckdahl, Biology Department, Missouri Western State University, 4525 Downs Drive, Saint Joseph, MO, 64507 [(816) 271-5873]

Project Overview

Hamiltonian Path Problem As a part of iGEM2006, a combined team from Davidson College and Missouri Western State University reconstituted a hin/hix DNA recombination mechanism which exists in nature in Salmonella as standard biobricks for use in E. coli. The purpose of the 2006 combined team was to provide a proof of concept for a bacterial computer in using this mechanism to solve a variation of The Pancake Problem from Computer Science. This task utilized both biology and mathematics students and faculty from the two institutions.

For 2007, we continue our collaboration and our efforts to manipulate E. coli into mathematics problem solvers as we refine our efforts with the hin/hix mechanism to explore another mathematics problem, the Hamiltonian Path Problem. This problem was the subject of a groundbreaking paper by Adelman in 1994 (citation below) where a unique Hamiltonian path was found in vitro for a particular directed graph on seven nodes. We propose to make progress toward solving the particular problem in vivo.

Splitting Genes for HPP

Resources / Citations

Davidson's Wet Lab Protocols

Missouri Western's Wet Lab Protocols

[http://gcat.davidson.edu/iGEM07/genesplitter.html Spliting Genes Web Tool]

1. DMW Part Numbers for 2007 are BBa_I715000 to BBa_I715999.
2. [http://partsregistry.org/Help:BioBrick_Part_Names How to Name a New Part]
3. [http://partsregistry.org/Add_a_Part_to_the_Registry Entering the Part to the Registry]
4. [http://partsregistry.org/Help:Part_Features How to Annotate a Part]

Cool site for Breakfast [http://www.cut-the-knot.org/SimpleGames/Flipper.shtml]

Karen Acker's paper describing GFP and TetA(c) with Hix insertions [http://www.bio.davidson.edu/Courses/Immunology/Students/spring2006/Acker/Acker_finalpaperGFP.doc]

Bruce Henschen's paper describing one-time flippable Hix sites [http://www.bio.davidson.edu/Courses/genomics/2006/henschen/Bruce_Finalpaper.doc]

Intro to Hamiltonian Path Problem and DNA [http://www.ams.org/featurecolumn/archive/dna-abc2.html]

Adelman, LM. Molecular Computation of Solutions To Combinatorial Problems. Science. 11 November 1994. Vol. 266. no. 5187, pp. 1021 - 1024

Ptashne, Mark. A Genetic Switch: Phage Lambda Revisited, Third Edition. New York. Cold Spring Harbor Laboratory Press: 2004.

Sambrook and Russell. 2001. Molecular Cloning A Laboratory Manual. Cold Spring Harbor Laboratry Press. Cold Spring Harbor, New York pg. 1.145. 2007 June.

Literature and Registry Research

Registry Search for Possible Promoters:

BBa_J24669 --- arabinose induced

BBa_R0082 --- Is upstream of the ompC porin gene

BBa_R0074 --- Penl regulated

BBa_I14017 --- P(Rhl)

BBa_I14018 --- P (Bla) --> amp resistance

BBa_J3902 --- Pr Fe (Pl + Pll rus operon)

BBa_R0077 --- CinR --> thought to have own terminator

BBa_R0078 --- CinR (no RBS)

BBa_R0062 --- luxR & HSL regulated -- luxpR

Possibly the use of Constitutive Promoter Family Members to strengthen other promoters.

Literature Search for Polycistronic Genes on Plasmids

Sol Operon http://www.jstage.jst.go.jp/article/bbb/71/1/58/_pdf

Transfer (tra) Operon http://www.pubmedcentral.nig.gov/picrender.fcgi?artid=1347297&blobtype=pdf

Oligopeptide Permease (opp) http://www.pubmedcentral.nig.gov/picrender.fcgi?artid=1087318&blobtype=pdf