Davidson Missouri W/Background Information - Revision history

Amshoecraft at 15:16, 9 August 2007

2007-08-09T15:16:49Z

Synthetic Students: make images thumbnails

2007-07-27T00:53:15Z

make images thumbnails

Synthetic Students at 19:39, 11 July 2007

2007-07-11T19:39:09Z

Synthetic Students: Background Information moved to Davidson Missouri W/Background Information

2007-07-11T19:33:46Z

Background Information moved to Davidson Missouri W/Background Information

Synthetic Students at 19:28, 11 July 2007

2007-07-11T19:28:39Z

Synthetic Students at 18:18, 9 July 2007

2007-07-09T18:18:38Z

Synthetic Students at 18:18, 9 July 2007

2007-07-09T18:18:20Z

Synthetic Students at 18:12, 9 July 2007

2007-07-09T18:12:48Z

WikiSysop: /* Flipping Pancakes */

2007-07-09T17:41:17Z

‎Flipping Pancakes

WikiSysop: /* The Hin Recombinase/''HixC'' System Revisited */ captions

2007-07-08T03:25:50Z

‎The Hin Recombinase/''HixC'' System Revisited: captions

← Older revision		Revision as of 15:16, 9 August 2007
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−	<center>[[Davidson Missouri W\| <span style="color:red">Home</span>]] \| [[Davidson Missouri W/Background Information\| <span style="color:black">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/~~Probability and Statistics~~\| <span style="color:red">~~Probability and Statistics~~</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/Resources and Citations\|<span style="color:red">Resources and Citations</span>]]</center>	+	<center>[[Davidson Missouri W\| <span style="color:red">Home</span>]] \| [[Davidson Missouri W/Background Information\| <span style="color:black">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/Resources and Citations\|<span style="color:red">Resources and Citations</span>]]</center>

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 ''Salmonella typhimurium'' is a bacterium which moves using flagella.  Depending on its environment, it expresses different sets of surface proteins on its flagella.  It is able to change this expression through the use of Hin Recombinase and ''HixC'' sites.  The Hin Recombinase enzyme catalyzes the inversion of DNA that lies between a pair of ''HixC'' sites.  By flipping DNA segments between ''HixC'' sites ''S. typhimurium'' can express alternate flagellar surface proteins.
-# Given a segment of DNA, flanked by ''HixC'' sites (blue arrow):<br>[[Image:hinhix1.png|frame|none|Figure 1.]]
+# Given a segment of DNA, flanked by ''HixC'' sites (blue arrow):<br>[[Image:hinhix1.png|thumb|none|800px|Figure 1.]]
-# Two dimers of Hin Recombinase protein attach to a pair of ''HixC'' sites around the DNA segment.<br>[[Image:hinhix2.png|frame|none|Figure 2.]]
+# Two dimers of Hin Recombinase protein attach to a pair of ''HixC'' sites around the DNA segment.<br>[[Image:hinhix2.png|thumb|none|800px|Figure 2.]]
-# The DNA segment between the pair of ''HixC'' sites is inverted.  Note that the green arrow is unaffected.<br>[[Image:hinhix3.png|frame|none|Figure 3.]]
+# The DNA segment between the pair of ''HixC'' sites is inverted.  Note that the green arrow is unaffected.<br>[[Image:hinhix3.png|thumb|none|800px|Figure 3.]]
 =Flipping Pancakes=

← Older revision		Revision as of 19:39, 11 July 2007
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−	<center>[[Davidson/Missouri W\| <span style="color:red">Home</span>]] \| [[Background Information\| <span style="color:black">Background Information</span>]] \| [[Solving the HPP in vivo\| <span style="color:red">Current Project: Solving the Hamiltonian Path Problem ''in vivo''</span>]] \| [[Probability and Statistics\| <span style="color:red">Probability and Statistics</span>]] \| [[Gene splitting\| <span style="color:red"> Gene Splitting </span>]] \| [[Controlling Expression\| <span style="color:red"> Controlling Expression </span>]] \| [[Traveling Salesperson Problem\| <span style="color:red">Traveling Salesperson Problem</span> ]] \| [[Backwards promotion and read-through transcription\| <span style="color:red">Backwards ~~promotion~~ and Read-Through Transcription</span>]] \| [[Resources and Citations\|<span style="color:red">Resources and Citations</span>]]</center>	+	<center>[[Davidson Missouri W\| <span style="color:red">Home</span>]] \| [[Davidson Missouri W/Background Information\| <span style="color:black">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/Probability and Statistics\| <span style="color:red">Probability and Statistics</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/Resources and Citations\|<span style="color:red">Resources and Citations</span>]]</center>

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← Older revision		Revision as of 19:28, 11 July 2007
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−	<center>[[Davidson/Missouri ~~Western iGEM 2007~~\| <span style="color:red">Home</span>]] \| [[Background Information\| <span style="color:black">Background Information</span>]] \| [[Solving the HPP in vivo\| <span style="color:red">Current Project: Solving the Hamiltonian Path Problem ''in vivo''</span>]] \| [[Probability and Statistics\| <span style="color:red">Probability and Statistics</span>]] \| [[Gene splitting\| <span style="color:red"> Gene Splitting </span>]] \| [[Controlling Expression\| <span style="color:red"> Controlling Expression </span>]] \| [[Traveling Salesperson Problem\| <span style="color:red">Traveling Salesperson Problem</span> ]] \| [[Backwards promotion and read-through transcription\| <span style="color:red">Backwards promotion and Read-Through Transcription</span>]] \| [[Resources and Citations\|<span style="color:red">Resources and Citations</span>]]</center>	+	<center>[[Davidson/Missouri W\| <span style="color:red">Home</span>]] \| [[Background Information\| <span style="color:black">Background Information</span>]] \| [[Solving the HPP in vivo\| <span style="color:red">Current Project: Solving the Hamiltonian Path Problem ''in vivo''</span>]] \| [[Probability and Statistics\| <span style="color:red">Probability and Statistics</span>]] \| [[Gene splitting\| <span style="color:red"> Gene Splitting </span>]] \| [[Controlling Expression\| <span style="color:red"> Controlling Expression </span>]] \| [[Traveling Salesperson Problem\| <span style="color:red">Traveling Salesperson Problem</span> ]] \| [[Backwards promotion and read-through transcription\| <span style="color:red">Backwards promotion and Read-Through Transcription</span>]] \| [[Resources and Citations\|<span style="color:red">Resources and Citations</span>]]</center>

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← Older revision		Revision as of 18:18, 9 July 2007
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−	<center>[[Davidson/Missouri Western iGEM 2007\| <span style="color:red">Home</span>]] \| [[Background Information\| <span style="color:~~gold~~">Background Information</span>]] \| [[Solving the HPP in vivo\| <span style="color:red">Current Project: Solving the Hamiltonian Path Problem ''in vivo''</span>]] \| [[Probability and Statistics\| <span style="color:red">Probability and Statistics</span>]] \| [[Gene splitting\| <span style="color:red"> Gene Splitting </span>]] \| [[Controlling Expression\| <span style="color:red"> Controlling Expression </span>]] \| [[Traveling Salesperson Problem\| <span style="color:red">Traveling Salesperson Problem</span> ]] \| [[Backwards promotion and read-through transcription\| <span style="color:red">Backwards promotion and Read-Through Transcription</span>]] \| [[Resources and Citations\|<span style="color:red">Resources and Citations</span>]]</center>	+	<center>[[Davidson/Missouri Western iGEM 2007\| <span style="color:red">Home</span>]] \| [[Background Information\| <span style="color:black">Background Information</span>]] \| [[Solving the HPP in vivo\| <span style="color:red">Current Project: Solving the Hamiltonian Path Problem ''in vivo''</span>]] \| [[Probability and Statistics\| <span style="color:red">Probability and Statistics</span>]] \| [[Gene splitting\| <span style="color:red"> Gene Splitting </span>]] \| [[Controlling Expression\| <span style="color:red"> Controlling Expression </span>]] \| [[Traveling Salesperson Problem\| <span style="color:red">Traveling Salesperson Problem</span> ]] \| [[Backwards promotion and read-through transcription\| <span style="color:red">Backwards promotion and Read-Through Transcription</span>]] \| [[Resources and Citations\|<span style="color:red">Resources and Citations</span>]]</center>

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← Older revision	Revision as of 19:33, 11 July 2007
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← Older revision		Revision as of 18:12, 9 July 2007
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		+	<center>[[Davidson/Missouri Western iGEM 2007\| <span style="color:red">Home</span>]] \| [[Background Information\| <span style="color:red">Background Information</span>]] \| [[Solving the HPP in vivo\| <span style="color:red">Current Project: Solving the Hamiltonian Path Problem ''in vivo''</span>]] \| [[Probability and Statistics\| <span style="color:red">Probability and Statistics</span>]] \| [[Gene splitting\| <span style="color:red"> Gene Splitting </span>]] \| [[Controlling Expression\| <span style="color:red"> Controlling Expression </span>]] \| [[Traveling Salesperson Problem\| <span style="color:red">Traveling Salesperson Problem</span> ]] \| [[Backwards promotion and read-through transcription\| <span style="color:red">Backwards promotion and Read-Through Transcription</span>]] \| [[Resources and Citations\|<span style="color:red">Resources and Citations</span>]]</center>
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	In 1994 Adleman developed a system to solve the Hamiltonian Path problem using DNA ''in vitro''. We have implemented a bacterial system to solve Hamiltonian Path problems ''in vivo''. Our bacterial computer works by taking advantage of the Hin Recombinase protein and ''HixC'' sites to perform a "flipping" operation. By strategically placing ''HixC'' sites on a plasmid, along with reporter genes, we can simulate paths on a graph through flipping.		In 1994 Adleman developed a system to solve the Hamiltonian Path problem using DNA ''in vitro''. We have implemented a bacterial system to solve Hamiltonian Path problems ''in vivo''. Our bacterial computer works by taking advantage of the Hin Recombinase protein and ''HixC'' sites to perform a "flipping" operation. By strategically placing ''HixC'' sites on a plasmid, along with reporter genes, we can simulate paths on a graph through flipping.

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 [[Image:pancake_sorting.gif|frame|none|How many flips does this take?]]
-Using mathematical models it is possible to compute these estimates for small stacks.  However, adding pancakes to a stack increasing the number of possible permutations non-linearly.  The number of possible stacks of ''n'' pancakes is equal to: 2^n (n!).  Thus traditional computers are not well-suited for computations involving large pancake stacks.
+Using mathematical models it is possible to compute these estimates for small stacks.  However, adding pancakes to a stack increases the number of possible permutations non-linearly.  The number of possible stacks of ''n'' pancakes is equal to: 2^n (n!).  Thus traditional computers are not well-suited for computations involving large pancake stacks.
 However, it is possible to model pancake flipping using bacteria.  If each pancake is given an identification number, along with a sign designating its orientation, then this can be stated equivalently using genes.  Thus the following images show equivalent notations for pancake stacks: