Difference between revisions of "Davidson Missouri W"

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<center>[[Davidson Missouri W| <span style="color:black">Home</span>]] | [[Davidson Missouri W/Background Information| <span style="color:red">Background Information</span>]] | [[Davidson Missouri W/Solving the HPP in vivo| <span style="color:red">Current Project: Solving the Hamiltonian Path Problem ''in vivo''</span>]] | [[Davidson Missouri W/Mathematical Modeling| <span style="color:red">Mathematical Modeling</span>]] | [[Davidson Missouri W/Gene splitting| <span style="color:red"> Gene Splitting </span>]] | [[Davidson Missouri W/Controlling Expression| <span style="color:red"> Controlling Expression </span>]] | [[Davidson Missouri W/Traveling Salesperson Problem| <span style="color:red">Traveling Salesperson Problem</span> ]] | [[Davidson Missouri W/Backwards promotion and read-through transcription| <span style="color:red">Backwards Promotion and Read-Through Transcription</span>]] | [[Davidson Missouri W/Software|<span style="color:red">Software</span>]] | [[Davidson Missouri W/Resources and Citations|<span style="color:red">Resources and Citations</span>]]</center>
  
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<hr>
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|+'''The Team'''
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<br>
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[[Image:DMW-1.jpg|300px|center]]
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<center>
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=The Team=
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</center>
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{| border="1" cellpadding="5" cellspacing="0" align="center" width="100%"
 
|-
 
|-
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! style="color: yellow; background-color: red;"| The Team
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! style="color: white; background-color: black;"| The Team
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! colspan="2" style="color: yellow; background-color: red;" | The Faculty
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! style="color: white; background-color: black;" | The Faculty
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! style="color: white; background-color: black;" | Team Logos
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! style="color: white; background-color: black;" | Group Photo
 
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|style="color: red; background-color: black;" align="center"| '''Davidson''' <br> [[Oyinade Adefuye]]  <br> [[Will DeLoache]]  <br> [[Jim Dickinson]]  <br> [[Andrew Martens]]  <br> [[ Amber Shoecraft]]  <br> [[Mike Waters]]
 
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|style="color: red; background-color: black;" align="center"| [[A. Malcolm Campbell ]] <br> [[Karmella Haynes]] <br> [[Laurie Heyer]]
 
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|-
 
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|style="color: yellow; background-color: black;" align="center"|'''Missouri Western'''<br>Jordan Baumgardner <br> Tom Crowley <br> Lane H. Heard <br> Nickolaus Morton <br> Michelle Ritter <br> Jessica Treece <br> Matthew Unzicker <br> Amanda Valencia
 
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|style="color: yellow; background-color: black;" align="center"|Todd Eckdahl <br> Jeff Poet
 
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|}
 
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<br><br>
 
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{| border="1" cellpadding="5" cellspacing="0" align="center" width="90%"
 
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|+'''The Problem'''
 
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|-
 
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! style="color: black; background-color: red;" width="20%"| In Depth
 
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! colspan="3" style="color: black; background-color: red;" width="60%"| Overview
 
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|-
 
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|style="color: black; background-color: white;" align="center"|  [[Probability and Statistics]] <br><br><br> [[Gene splitting]] <br><br><br> [[Controlling Expression]] <br><br><br> [[Hix Insertion]] <br><br><br>[[Possible Constructs]]<br><br><br> [[History]] <br><br><br>
 
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|align="center"|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.
 
  
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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. <br>  
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|style="color: black; background-color: red;" align="center"| '''Davidson'''
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<b>
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[[Davidson Missouri W/Oyinade Adefuye|<span style="color:black">Oyinade Adefuye</span>]]
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<br>
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[[Davidson Missouri W/Will DeLoache|<span style="color:black">Will DeLoache</span>]]
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<br>
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[[Davidson Missouri W/Jim Dickson|<span style="color:black">Jim Dickson</span>]]
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<br>
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[[Davidson Missouri W/Andrew Martens|<span style="color:black">Andrew Martens</span>]]
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<br>
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[[Davidson Missouri W/Amber Shoecraft|<span style="color:black">Amber Shoecraft</span>]]
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<br>
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[[Davidson Missouri W/Mike Waters|<span style="color:black">Mike Waters</span>]]
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</b>
  
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[[Image:AdelmanGraph.JPG|thumb|300px|center| ]]  
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|style="color: black; background-color: red;" align="center"|
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<b>
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[[Davidson Missouri W/A. Malcolm Campbell|<span style="color:black">A. Malcom Campbell</span>]]
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<br>
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[[Davidson Missouri W/Karmella Haynes|<span style="color:black">Karmella Haynes</span>]]
 
<br>
 
<br>
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[[Image:HamiltonianGraph.PNG|thumb|700px|center|]]
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[[Davidson Missouri W/Laurie Heyer|<span style="color:black">Laurie Heyer</span>]]
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|}
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</b>
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<br><br>
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{| border="1" cellpadding="5" cellspacing="0" align="center" width="80%"
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|style="color: black; background-color: white;" align="center"|
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|+'''Secondary Projects'''
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[[Image:DavidsonLogo.gif]]
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|style="color: black; background-color: white;" align="center"|
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[[Image:Team1.jpg|thumb|300px]]
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|-
 
|-
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! style="color: red; background-color: black;"| Project
 
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! colspan="2" style="color: red; background-color: black;" | Short Description
 
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|-
 
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|align="center"|[[Burnt Pancake Problem]]
 
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|align="center"|Flipping DNA "Pancakes" with hix "spatualas" until the pancakes are in the correct order and orientation
 
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|-
 
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|align="center"|[[Traveling Salesman Problem and Anti-terminators]]
 
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|align="center"|Solving the Hamiltonian Path problem AND minimizing distance traveled
 
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|-
 
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|align="center"|[http://gcat.davidson.edu/iGEM07/genesplitter.html Spliting Genes Web Tool]
 
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|align="center"|A Davidson iGEM 2007-designed primer sequencer for gene splitting
 
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|-
 
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|align="center"|[[Backwards promotion and read-though transcription]]
 
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|align="center"|Davidson's investigation into control of "leaky" gene expression
 
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|}
 
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<br><br><br>
 
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== '''Resources / Citations'''==
 
  
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[http://parts.mit.edu/wiki/index.php/The_What%27s_and_How%27s Davidson's Wet Lab Protocols]
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|style="color: black; background-color: gold;" align="center"|'''Missouri Western'''
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<b>
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[[Davidson Missouri W/Jordan Baumgardner|<span style="color:black;">Jordan Baumgardner</span>]]
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<br>
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[[Davidson Missouri W/Tom Crowley|<span style="color:black;">Tom Crowley</span>]]
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<br>
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[[Davidson Missouri W/Lane H. Heard|<span style="color:black;">Lane H. Heard</span>]]
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<br>
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[[Davidson Missouri W/Nickolaus Morton|<span style="color:black;">Nickolaus Morton</span>]]
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<br>
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[[Davidson Missouri W/Michelle Ritter|<span style="color:black;">Michelle Ritter</span>]]
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<br>
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[[Davidson Missouri W/Jessica Treece|<span style="color:black;">Jessica Treece</span>]]
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<br>
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[[Davidson Missouri W/Matthew Unzicker|<span style="color:black;">Matthew Unzicker</span>]]
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<br>
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[[Davidson Missouri W/Amanda Valencia|<span style="color:black;">Amanda Valencia</span>]]
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</b>
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|style="color: black; background-color: gold;" align="center"|
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<b>
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[[Davidson Missouri W/Todd Eckdahl|<span style="color:black;">Todd Eckdahl</span>]]
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<br>
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[[Davidson Missouri W/Jeff Poet|<span style="color:black;">Jeff Poet</span>]]
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</b>
  
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[http://parts.mit.edu/igem07/index.php/Davidson_Missouri_W/MWSU_protocols Missouri Western's Wet Lab Protocols]
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|style="color: black; background-color: white;" align="center"|[[Image:MWLogo.gif]]
  
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[http://gcat.davidson.edu/iGEM07/genesplitter.html Spliting Genes Web Tool]
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|style="color: black; background-color: white;" align="center"|
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|-
  
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[http://www.bio.davidson.edu/courses/Molbio/Protocols/ORIs.html '''Compatibility of Plasmids''']
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|}
  
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#'''DMW Part Numbers for 2007 are BBa_I715000 to BBa_I715999.'''
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<br>
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#[http://parts.mit.edu/registry/index.php/Help:BioBrick_Part_Names How to Name a New Part]
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[[Image:Team_graph.jpg|center|thumb|500px|A Human Representation of Adleman's Graph (see below)]]
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#[http://parts.mit.edu/registry/index.php/Add_a_Part_to_the_Registry Entering the Part to the Registry]
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<br><br>
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#[http://parts.mit.edu/registry/index.php/Help:Part_Features How to Annotate a Part]
 
  
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Cool site for Breakfast
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<center>
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[http://www.cut-the-knot.org/SimpleGames/Flipper.shtml]
 
  
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Karen Acker's paper describing GFP and TetA(c) with Hix insertions
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=Our Project=
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[http://www.bio.davidson.edu/Courses/Immunology/Students/spring2006/Acker/Acker_finalpaperGFP.doc]
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</center>
  
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Bruce Henschen's paper describing one-time flippable Hix sites
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{| border="1" cellpadding="5" cellspacing="0" align="center" width="90%"
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[http://www.bio.davidson.edu/Courses/genomics/2006/henschen/Bruce_Finalpaper.doc]
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|-
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! style="color: black; background-color: red;" width="20%"| <font size="+1">In Depth</font>
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! colspan="3" style="color: black; background-color: red;" width="60%"| <font size="+1">Overview</font>
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|-
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|style="color: black; background-color: black;" align="center"|
 +
[[Davidson Missouri W/Background Information|<span style="color:red">Background Information</span>]]
 +
<br><br><br>
 +
[[Davidson Missouri W/Solving the HPP in vivo|<span style="color:red">Current Project: Solving the Hamiltonian Path Problem ''in vivo''</span>]]
 +
<br><br><br>
 +
[[Davidson Missouri W/Mathematical Modeling|<span style="color:red">Mathematical Modeling</span>]]
 +
<br><br><br>
 +
[[Davidson Missouri W/Gene splitting|<span style="color:red">Gene Splitting</span>]]
 +
<br><br><br>
 +
[[Davidson Missouri W/Controlling Expression|<span style="color:red">Controlling Expression</span>]]
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<br><br><br>
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[[Davidson Missouri W/Traveling Salesperson Problem|<span style="color:red">Traveling Salesperson Problem</span>]]
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<br><br><br>
 +
[[Davidson Missouri W/Backwards Promotion and read-through transcription|<span style="color:red">Backwards Promotion and Read-Through Transcription</span>]]
 +
<br><br><br>
 +
[[Davidson Missouri W/Resources and Citations|<span style="color:red">Resources and Citations</span>]]
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<br><br><Br>
 +
|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.
  
−
Intro to Hamiltonian Path Problem and DNA
+
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.
−
[http://www.ams.org/featurecolumn/archive/dna-abc2.html]
 
  
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Adleman, LM. Molecular Computation of Solutions To Combinatorial Problems. Science.  11 November 1994. Vol. 266. no. 5187, pp. 1021 - 1024
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<br>
  
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Ptashne, Mark.  A Genetic Switch: Phage Lambda Revisited, Third Edition. New York. Cold Spring Harbor Laboratory Press: 2004.
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[[Image:AdelmanGraph.JPG|thumb|300px|center|The Adleman graph.]] 
 +
<br>
 +
[[Image:HamiltonianGraph.PNG|thumb|700px|center|A graph implemented on a plasmid.]]
  
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Sambrook and Russell. 2001. Molecular Cloning A Laboratory Manual. Cold Spring Harbor Laboratry Press. Cold Spring Harbor, New York pg. 1.145. 2007 June.
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|}

Latest revision as of 15:22, 9 August 2007

Home | Background Information | Current Project: Solving the Hamiltonian Path Problem in vivo | Mathematical Modeling | Gene Splitting | Controlling Expression | Traveling Salesperson Problem | Backwards Promotion and Read-Through Transcription | Software | Resources and Citations


DMW-1.jpg

The Team

The Team The Faculty Team Logos Group Photo
Davidson

Oyinade Adefuye
Will DeLoache
Jim Dickson
Andrew Martens
Amber Shoecraft
Mike Waters

A. Malcom Campbell
Karmella Haynes
Laurie Heyer

DavidsonLogo.gif

Team1.jpg
Missouri Western

Jordan Baumgardner
Tom Crowley
Lane H. Heard
Nickolaus Morton
Michelle Ritter
Jessica Treece
Matthew Unzicker
Amanda Valencia

Todd Eckdahl
Jeff Poet

MWLogo.gif


A Human Representation of Adleman's Graph (see below)



Our Project

In Depth Overview

Background Information


Current Project: Solving the Hamiltonian Path Problem in vivo


Mathematical Modeling


Gene Splitting


Controlling Expression


Traveling Salesperson Problem


Backwards Promotion and Read-Through Transcription


Resources and Citations


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.


The Adleman graph.


A graph implemented on a plasmid.
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