Davidson Missouri W

From 2007.igem.org

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===Davidson & Missouri Western Team Logo, iGEM2007=== <br>
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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/Results| <span style="color:red">Results</span>]] |  [[Davidson Missouri W/Traveling Salesperson Problem| <span style="color:red">Traveling Salesperson Problem</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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[[Image:DMW.jpg|thumb|300px|center| ]]
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<br>
<br>
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[[Image:dmw_logo2.png|center]]
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==[[Davidson Missouri W/Project Description|Project Description]]==
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[[Image:Computer.png|center]]
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The 2007 Davidson/Missouri Western iGEM team is building an E. coli computer capable of solving the Hamiltonian Path Problem. E. coli provide the massive parallel processing power required to solve this computationally intense problem from Graph Theory. We use a Hin/hixC DNA recombination mechanism to randomly generate possible paths through the graph. We then use gene expression and fragment length to screen for a Hamiltonian Path.
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To construct our computer, we have inserted hixC sites into reporter genes in a location that destroys the gene’s function when the split segments are not united but allows for normal gene expression when the two segments are contiguous. So far we have successfully split GFP and RFP in this manner. Our method demands that the Hin/hixC system be able to rearrange multiple DNA elements into every possible ordering. Therefore, we have tested and confirmed that Hin/hixC can rearrange 2 DNA elements into all 8 signed permutations. Our math modeling shows that it will be feasible to detect true Hamiltonian Paths even in complex graphs.
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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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|-
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! style="color: white; background-color: black;"| The Team
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! style="color: white; background-color: black;" | The Faculty
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! style="color: white; background-color: black;" | School Logos
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! style="color: white; background-color: black;" | Group Photo
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|-
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== '''Team Meeting Notes''' ==
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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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Western Meeting Notes 051407 to Present
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|style="color: black; background-color: red;" align="center"|
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[https://2007.igem.org/Davidson_Missouri_W/WesternMeetingNotes]
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<b>
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[[Davidson Missouri W/A. Malcolm Campbell|<span style="color:black">A. Malcolm Campbell</span>]]
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<br>
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[[Davidson Missouri W/Karmella Haynes|<span style="color:black">Karmella Haynes</span>]]
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<br>
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[[Davidson Missouri W/Laurie Heyer|<span style="color:black">Laurie Heyer</span>]]
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</b>
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== '''Math Related Notes''' ==
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|style="color: black; background-color: white;" align="center"|
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[[Image:DavidsonLogo.gif]]
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Notes 051407 to Present
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|style="color: black; background-color: white;" align="center"|
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[https://2007.igem.org/Davidson_Missouri_W/MathMeetingNotes]
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[[Image:Team1.jpg|thumb|center|300px]]
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[https://2007.igem.org/Davidson_Missouri_W/FalsePositiveProgram False Positives]
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|-
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[https://2007.igem.org/Davidson_Missouri_W/ProjectsCompleted Projects Completed]
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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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[https://2007.igem.org/Davidson_Missouri_W/Graphs Graphs]
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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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== '''Students''' ==
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|style="color: black; background-color: white;" align="center"|[[Image:MWLogo.gif]]
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[[Image:Logo.gif]]
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|style="color: black; background-color: white;" align="center"|[[Image:MWSUteam.jpeg|thumb|center|300px]]
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|-
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• Will DeLoache, Junior Biology Major,  [mailto:wideloache@davidson.edu]
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|}
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• Oyinade Adefuye, Senior Biology Major,  [mailto:oyinadeadefuye@yahoo.com]
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• Jim Dickson, Junior Math and Economics Major,    [mailto:jidickson@davidson.edu]
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• Amber Shoecraft, Math Major,  [mailto:amshoecraft@davidson.edu]
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• Andrew Martens, Senior Biology Major,  [mailto:anmartens@davidson.edu]
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• Michael Waters, Sophomore Biology Major,  [mailto:miwaters@davidson.edu]
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<br>
<br>
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[[Image:Team1.jpg|200px|]] [[Image:Team_graph.jpg|200px|]]
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<center>
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-----
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=Our Successful Project=
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</center>
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[[Image:Header_01.gif]]
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{| border="1" cellpadding="5" cellspacing="0" align="center" width="90%"
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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"|
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[[Davidson Missouri W/Background Information|<span style="color:red">Background Information</span>]]
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<br><br><br>
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[[Davidson Missouri W/Solving the HPP in vivo|<span style="color:red">Current Project: Solving the Hamiltonian Path Problem ''in vivo''</span>]]
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<br><br><br>
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[[Davidson Missouri W/Mathematical Modeling|<span style="color:red">Mathematical Modeling</span>]]
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<br><br><br>
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[[Davidson Missouri W/Gene splitting|<span style="color:red">Gene Splitting</span>]]
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<br><br><br>
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[[Davidson Missouri W/Results|<span style="color:red">Results</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>
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[[Davidson Missouri W/Software|<span style="color:red">Software</span>]]
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<br><br><br>
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[[Davidson Missouri W/Resources and Citations|<span style="color:red">Resources and Citations</span>]]
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<br><br><Br>
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|Hamiltonian Path Problem
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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 successfully continued 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 Adleman in 1994 (see [[Davidson_Missouri_W/Resources_and_Citations | citations]]) where a unique Hamiltonian path was found ''in vitro'' for a particular directed graph on seven nodes. We were able to use bacterial computers to solve the Hamiltonian path problem ''in vivo''. ([[Davidson Missouri W/Background Information#Why Use Bacteria?|Why use a bacterial computer?]])
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• Jordan Baumgardner, Junior Biology, Biochemistry/Molecular Biology Major,  [mailto:jbaumgardner@missouriwestern.edu]
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<br>
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[[Image:Adelman.png|thumb|300px|center|The Adleman graph.]]  
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• Tom Crowley, Senior Biochemisty/Molecular Biology Major,  [mailto:stc8033@missouriwestern.edu]
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<center> For the graph used in Adleman's paper (shown above), the Hamiltonian Path Problem would ask: can you find a path along the directed edges that travels from node 1 (green) to node 5 (red) and visits each node on the graph exactly once? <br>
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[https://static.igem.org/mediawiki/2007/6/6f/Adelmansolution.png Click here] for the solution.
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</center>
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|}
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• Lane H. Heard, Central High School graduate,  [mailto:axenmoon@hotmail.com]
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<br>
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<center> '''A Human Representation of the Adleman Graph. (mouse over to see the full effect)'''
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• Nickolaus Morton, Junior Chemistry Major,  [mailto:nmorton@missouriwestern.edu]
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<html>
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<head>
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<link rel="stylesheet" href="https://2007.igem.org/wiki/index.php?title=User:Wideloache/igem2007.css&action=raw&ctype=text/css" type="text/css" />
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</style>
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</head>
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<body>
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• Michelle Ritter, Junior Mathematics Major,  [mailto:mrr5418@missouriwestern.edu]
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<div class="rollover">
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<center>
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<a href="#"></a>
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</center>
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</div>
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</body>
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</html>
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• Jessica Treece, Junior Biology Major (Health Sciences),  [mailto:jtreece@missouriwestern.edu]
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<br>
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<br>
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• Matthew Unzicker, Senior Biochemistry/Molecular Biology Major,  [mailto:mru8487@missouriwestern.edu]
 
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• Amanda Valencia, Senior Biochem/Molecular Biology Major,  [mailto:avalencia@missouriwestern.edu]
 
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== '''Faculty''' ==
 
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[[Image:Logo.gif]]
 
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• A. Malcolm Campbell [http://www.bio.davidson.edu/people/macampbell/macampbell.html], Professor, Department of Biology, [mailto:macampbell@davidson.edu]
 
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• [https://2007.igem.org/User:Kahaynes Karmella Haynes], Visiting Assistant Professor, Department of Biology, [mailto:kahaynes@davidson.edu]
 
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• [http://www.davidson.edu/math/heyer/ Laurie Heyer], Associate Professor, Department of Mathematics, [mailto:laheyer@davidson.edu]
 
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Shipping Address: Malcolm Campbell, Biology Dept. Davidson College, 209 Ridge Road, Davidson, NC 28036 [(704) 894-2692]
 
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[[Image:Header_01.gif]]
 
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• Todd Eckdahl [http://staff.missouriwestern.edu/~eckdahl/], Professor, Department of Biology, [mailto:eckdahl@missouriwestern.edu]
 
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• Jeff Poet [http://staff.missouriwestern.edu/~poet/], Assistant Professor, Department of Computer Science, Mathematics, and Physics, [mailto:poet@missouriwestern.edu]
 
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Shipping Address: Todd Eckdahl, Biology Department, Missouri Western State University, 4525 Downs Drive, Saint Joseph, MO, 64507 [(816) 271-5873]
 
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== '''Project Overview'''==
 
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<font color="blue">Hamiltonian Path Problem</font color>
 
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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.
 
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[[Image:AdlemanGraph.jpg|thumb|300px|center| ]] 
 
<br>
<br>
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[[Image:Sample_graph.png|thumb|700px|center|]]
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<hr>
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==[[Splitting Genes for HPP]]==
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==[[Davidson's First HPP Construct]]==
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==[[Missouri Western's First HPP Construct]]==
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==[[Assembly Plan]]==
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[[Image:HPPAssemblyPlan72007.jpg|thumb|600px|center| ]]
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==[[Traveling Salesperson Problem?]]==
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==[[Synthesis of First Bacterial Computer]]==
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== '''Resources / Citations'''==
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[https://2006.igem.org/wiki/index.php/The_What%27s_and_How%27s Davidson's Wet Lab Protocols]
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[https://2007.igem.org/Davidson_Missouri_W/MWSU_protocols Missouri Western's Wet Lab Protocols]
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[http://gcat.davidson.edu/iGEM07/genesplitter.html Spliting Genes Web Tool]
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[http://www.bio.davidson.edu/courses/Molbio/Protocols/ORIs.html '''Compatibility of Plasmids''']
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[https://2006.igem.org/wiki/index.php/Freezer_Stocks Freezer Stocks - iGEM 2006 Project]
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[http://spreadsheets.google.com/pub?key=pw-NamR_FPJOfhl6mDrkZcw Davidson Freezer Stocks - iGEM 2007 Project]
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#'''DMW Part Numbers for 2007 are BBa_I715000 to BBa_I715999.'''
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#[http://partsregistry.org/Help:BioBrick_Part_Names How to Name a New Part]
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#[http://partsregistry.org/Add_a_Part_to_the_Registry Entering the Part to the Registry]
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#[http://partsregistry.org/Help:Part_Features How to Annotate a Part]
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Cool site for Breakfast
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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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[http://www.bio.davidson.edu/Courses/Immunology/Students/spring2006/Acker/Acker_finalpaperGFP.doc]
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Bruce Henschen's paper describing one-time flippable Hix sites
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[http://www.bio.davidson.edu/Courses/genomics/2006/henschen/Bruce_Finalpaper.doc]
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Intro to Hamiltonian Path Problem and DNA
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[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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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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==[[Literature Research]]==
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<Previous Section | [[Davidson Missouri W/Background Information | Next Section>]]
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</center>

Latest revision as of 04:32, 27 October 2007

Home | Background Information | Current Project: Solving the Hamiltonian Path Problem in vivo | Mathematical Modeling | Gene Splitting | Results | Traveling Salesperson Problem | Software | Resources and Citations


Dmw logo2.png
Computer.png

The Team

The Team The Faculty School Logos Group Photo
Davidson

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

A. Malcolm 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
MWSUteam.jpeg


Our Successful Project

In Depth Overview

Background Information


Current Project: Solving the Hamiltonian Path Problem in vivo


Mathematical Modeling


Gene Splitting


Results


Traveling Salesperson Problem


Software


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 successfully continued 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 Adleman in 1994 (see citations) where a unique Hamiltonian path was found in vitro for a particular directed graph on seven nodes. We were able to use bacterial computers to solve the Hamiltonian path problem in vivo. (Why use a bacterial computer?)


The Adleman graph.
For the graph used in Adleman's paper (shown above), the Hamiltonian Path Problem would ask: can you find a path along the directed edges that travels from node 1 (green) to node 5 (red) and visits each node on the graph exactly once?

Click here for the solution.


A Human Representation of the Adleman Graph. (mouse over to see the full effect)




<Previous Section | Next Section>

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