Davidson 2006

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| <center>[[Image:logo.gif]]<br>http://www.davidson.edu<br><br><big>'''[[#overview|Project Overview]]'''<br><br>'''[http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006&group=Davidson Davidson Parts]'''<br><br>'''[[#members|Team Members]]'''<br><br>'''[[#tools|Tools and Resources]]'''<br><br>Check out our [http://www.bio.davidson.edu/courses/synthetic/photos/FlapJack_HotCakes.html Official Team Photo]<br><br>
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<br>
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<font color = red>NEW</font> [[Davidson's Awards]] and [[Photo Gallery]] from iGEM Jamboree 2006</big></center>
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| [[Image:igem_team_web.jpg|thumb|450px|Left to Right: Lance, Erin, Samantha, Sabriya, Karmella, Laurie, Malcolm]]
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[http://www.bio.davidson.edu/courses/synthetic/photos/FlapJack_HotCakes.html '''Official Team Photo (rollover image)''']<br><br>
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|}
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[[Image:DC_team.JPG|429px|]] [[Image:Ehop.jpg|Logo]] </center>
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:::::::Malcolm, Laurie, Sabriya, Erin, Lance
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----
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{| width="900px"
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|<font size=4><div id="overview">Solving the Pancake Problem with an ''E. coli'' Computer</div></font>
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[http://2006.igem.org/Image:IGEM2006T_Davidson.ppt PowerPoint Presentation] and [http://2006.igem.org/Image:IGEM2006_Davidson_poster.ppt Poster]
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|-
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|Our goal is to genetically engineer a biological system that can compute solutions to a puzzle called the burnt pancake problem. The '''E.HOP computer''' is a proof of concept for computing ''in vivo,'' with implications for future data storage devices and transgenic systems. Our work was done in collaboration with the [http://2006.igem.org/wiki/index.php/Missouri_Western_State_University_2006 Missouri Western iGEM Team] and an undergraduate research fellow from [http://www.hamptonu.edu/ Hampton University].
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|[[image:EHOP.gif|250px]]
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|}
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==<font color='green'>Project</font color>==
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====The Burnt Pancake Problem====
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{| width="900px"
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|The [http://en.wikipedia.org/wiki/Pancake_sorting pancake problem] is a puzzle in which a scrambled series of units (or stack of pancakes) must be shuffled into the correct order and orientation. You can try solving [http://www.cut-the-knot.org/SimpleGames/Flipper.shtml a simple version of the pancake problem] yourself.<br><br>In the burnt pancake problem, each pancake is given an orientation by burning one side. To solve the problem, every unit, or pancake, must be placed in the proper order (largest on bottom, smallest on top) and in the proper orientation (burnt side down, golden side up).  The pancakes are flipped with two spatulas: one to lift pancakes off the top of the stack, the other to flip part (or all) of the remaining stack of pancakes.  The pancakes lifted by the first spatula are returned to the top of the stack without being flipped.  Figure 1 illustrates how the puzzle is solved. 
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|-
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|[[Image:solving4cakes.jpg|thumb|600px|center|'''Figure 1.'''  A scrambled stack of four burnt pancakes, sorted into correct order and orientation in 3 flips. Proper orientation is indicated by solid color, improper orientation by hatched color. ]]
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Who: The Mammoths, and FlapJack and the Pancakes
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==== Approach ====
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{| width="900px"
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|- valign="top"
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| Trial and error is one approach to solving the burnt pancake problem, but how could one compute the quickest solution?  Our idea is to let E. coli do the work, using each cell as a tiny processor in a massively parallel machine.  A mathematical model of the flipping process helps us design the system and interpret the output of our EHOP computer.
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|- valign="top"
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|[[Image:Jmol_Hin_tetrad_DNA.gif|thumb|250px|left|'''Figure 2.''' 3-D structure of a Hin protein complex bound to DNA. View the [http://www.rcsb.org/pdb/explore/explore.do?structureId=1ZR4 interactive 3-D Jmol image].]]'''Biological System:''' The biological representation of a pancake is a functional unit of DNA such as a promoter or coding region. To flip these units of DNA, we have reconstituted the Hin/ Hix invertase system (Figure 2) from ''Salmonella typhimurium'' as a BioBrick compatible system in ''E. coli''. '''Hin invertase''' (<partinfo>J31001</partinfo>) was cloned from ''S. typhimurium'', Ames strain TA100 and tagged with LVA. We built the recombinational enhancer (RE) and Hin invertase recognition sequence HixC using the publicly available genomic sequence of ''S. typhimurium'' and [http://gcat.davidson.edu/IGEM06/oligo.html a dsDNA assembly program we created] for gene synthesis from overlapping oligos.
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What: Our goal is to solve the Pancake problem[http://www.cut-the-knot.org/SimpleGames/Flipper.shtml] in a biological system.
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Every segment of DNA flanked by a pair of HixC sites is a "pancake" capable of being inverted. Hin invertase recognizes pairs of HixC sites and inverts the DNA fragment in between the two HixC sites with the help of the Fis protein bound to the RE. In our system, selectable phenotypes (including antibiotic resistance and RFP expression), depend upon the proper arrangement of a series of HixC-flanked DNA segments in a plasmid. This allows us to select for cells that have successfully solved the puzzle. An example of a sorted stack of two pancakes is shown in Figure 3.  There are 7 other configurations of 2 pancakes.  If we increase the number of pancakes to 4, there are 384 configurations.  In general, there are 2<sup>n</sup> n! configurations of ''n'' pancakes, a combinatorial explosion of possibilities.  How many should we build and test?  Which ones are most informative?  We need a mathematical model to help answer this question.
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When: Summer and Fall '06
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|[[Image:biocake.jpg|thumb|400px|right|'''Figure 3.''' A sorted stack of two biological "pancakes"]]
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Where: Missouri Western State University and Davidson College
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'''Mathematical Model:''' Our mathematical representation of a stack of pancakes is a '''signed permutation''', in which each numerical value represents the pancake size and the sign of the number represents the orientation. For example, (1, 2, 3, 4) is a sorted stack of four pancakes, all in the proper order and orientation, and (-2, 4, -1, 3) is the scrambled stack of four pancakes shown on the far left of Figure 1. Note that pancakes 1 and 2 are negative, indicating that these two pancakes are in the wrong orientation (burnt side up).
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Why: Because we love breakfast... well most of us.
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[[Image:two_pancake_families.jpg|thumb|400px|right|'''Figure 4.''' Simulation results for two pancakes]]  We simulated the flipping process by assuming that each segment of DNA flanked by Hix sites is equally likely to be flipped by Hin invertase. In an ''n''-pancake stack, there are <sub>n+1</sub>C<sub>2</sub> ways to choose a segment: two spatula locations must be chosen from among the ''n'' + 1 potential locations.  For example, there are <sub>5</sub>C<sub>2</sub>  = 5! 3! / 2! = 10 different ways to perform a single flip in a stack of 4 pancakes.  The random flipping process continues until the stack is sorted in the correct order and orientation, or until we artificially stop the random flipping process.  Figure 4 shows the percent of plasmids that we expect to be sorted after 1 flip, 2 flips, and so on, up to 20 flips, for each of the eight initial configurations.  
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How: Trying to invert antibiotic resistance genes using the Hin/Hix inversion method found in ''Salmonella typhimurium''.
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From these simulations, and similar results for stacks of 3 and 4 pancakes, we discovered that the probability of a plasmid being sorted after ''k'' flips was determined by how many ways the solution could be obtained.  Several initial configurations had essentially the same graph in our simulations because they had the same number of ways of being sorted.  Only '''one''' representative from each of these "families" of initial configurations needs to be built and tested.  
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<br>
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{| width="900px" cellpadding="5" border="1" border-style="solid" border-color="blue"
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* Our overall goal was to see if we could use synthetic methods to construct an ''E. coli'' computer. If we grew 10<sup>15</sup> cells, and each cell was attempting to solve the problem, then even rare events might be solvable by ''E. coli'' computers.
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|-
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| align="center" colspan="4"| <big>'''Methods and Results'''</big><br>The following is an outline of what the Davidson team will present at iGEM 2006
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|- valign="top"
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| width="300px" | <big>'''Basic parts'''</big><br><br>
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Parts used in this project were designed by two iGEM Teams
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*[http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006&group=Davidson Davidson]
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*[http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006&group=Missouri Missouri Western]<br><br>
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<big>'''Modeling'''</big><br><br>
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*[[Modeling pancake flipping]]: deducing kinetics and size biases
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*[[Choosing constructs]]: deciding which unsorted pancake stacks to start with
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*[[The effect of plasmid copy number]]
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| width="300px" | <big>'''Building the Biological System'''</big><br><br>
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* [[DNA Pancake|Defining a DNA pancake]] - what parts are flippable?
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* [[Read Through Transcription Problem|Read-through from the carrier vector backbone]] leads to uncontrolled Tet expression and uncontrolled flipping
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* [[pSB1A7| New vector insulates parts from read-through]], but is not compatible with parts carrying double terminator B0015
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* [[pSB1A7 Cloning Solution| Cloning solution]] - design pancake constructs without double terminator B0015
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* [[Biological Equivalence Problem|Dealing with biological equivalence]] - distinguishing 1,2 from -2,-1 using an RFP reporter
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* [[Two Pancake Stacks|Two-pancake stacks]] - final design
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| width="300px" | <big>'''Conclusions'''</big><br><br>
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*'''[[Consequences of devices]]'''
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** Practical: proof-of-concept for bacterial computers, data storage
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** Basic research: transgene rearrangement in vivo, insights into evolution that has occurred via DNA rearrangements
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*'''[[Next steps]]''': can solve problem but need control over kinetics
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*'''[[Lessons learned]]''':
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**Troubleshooting, communication, teamwork, publicity
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**Math and Biology meshed really well and even uncovered a new proof
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**Multiple campuses can increase capacity through communication and cooperation
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**Size of school is not a limiting factor
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**We had a blast and learned heaps!!!
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|}
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* 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  <font color='red'>XX (need to insert name)</font color>, and Hin from ''S. typhimurium'', strain TA100 .
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----
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<font size=4><div id="members">TEAM MEMBERS</div></font>
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* 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<sup>R</sup> resistance gene isolated from a plasmid in the Registry. For higher stacks of pancakes, we will also use chloramphenicol<sup>R</sup> and cycloheximide<sup>R</sup>.
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'''Students'''
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* [mailto:fizzle6821@yahoo.com|  Sabriya Rosemond] is a junior biology major at Hampton University.
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== <font face="chalkboard"><font color='blue'> Students</font color> ==
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* [mailto:erzwack@davidson.edu| Erin Zwack] is a junior biology major at Davidson College.
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* [mailto:laharden@davidson.edu| Lance Harden] is a sophomore math major at Davidson College.
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<font face="chalkboard">
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* [mailto:sasimpson@davidson.edu| Samantha Simpson] is a sophomore at Davidson College who might design a major in genomics.
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* [mailto:fizzle6821@yahoo.com|  Sabriya Rosemond] is a rising junior biology major at Hampton University.
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* [mailto:erzwack@davidson.edu| Erin Zwack] is a rising junior biology major at Davidson College.
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* [mailto:laharden@davidson.edu| Lance Harden] is a rising sophomore math major at Davidson College.
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* [mailto:sasimpson@davidson.edu| Samantha Simpson] is a rising sophomore at Davidson College who might design a major in genomics.</font face>
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==<font face="chalkboard"> <font color='magenta'>Faculty</font color> ==
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'''Faculty'''
* [mailto:macampbell@davidson.edu| A. Malcolm Campbell] [http://www.bio.davidson.edu/campbell Department of Biology]
* [mailto:macampbell@davidson.edu| A. Malcolm Campbell] [http://www.bio.davidson.edu/campbell Department of Biology]
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* [mailto:laheyer@davidson.edu| Laurie J. Heyer] [http://www.davidson.edu/math/heyer/ Department of Mathematics]
* [mailto:laheyer@davidson.edu| Laurie J. Heyer] [http://www.davidson.edu/math/heyer/ Department of Mathematics]
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* [mailto:kahaynes@davidson.edu| Karmella Haynes] [http://www.bio.davidson.edu/ Department of Biology - teaching postdoc and visiting assistant professor]
* [mailto:kahaynes@davidson.edu| Karmella Haynes] [http://www.bio.davidson.edu/ Department of Biology - teaching postdoc and visiting assistant professor]
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== <font face="chalkboard"><font color='lime'>[[Papers of Interest]]</font color> ==
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==<font face="chalkboard"><font color='orange'>Parts Created</font color></font face>==
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<font size=4><div id="tools">Tools and Resources</div></font>
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<font face="chalkboard">[[Pancake Parts]]</font face>
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{| width="840px" cellpadding="5" border="0"
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|- valign="top"
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==<font color='purple'><font face="chalkboard">Questions</font color></font face> ==
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| width="210px" | <big>'''iGEM 2006 Jamboree'''</big><br><br>
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<div style="padding: 3px; color:white; background-color: white; width: 1000px">
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*[[Presentation Outline]]
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*[http://2006.igem.org/Image:IGEM2006T_Davidson.ppt PowerPoint Presentation]
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* <font face= "chalkboard">[[General Questions]]</font face>&nbsp;&nbsp;&nbsp;
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*[http://2006.igem.org/Image:IGEM2006_Davidson_poster.ppt Poster] - ppt file
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* <font face= "chalkboard">[[Math Questions]]</font face>&nbsp;&nbsp;&nbsp;
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| width="210px" | <big>'''White Board'''</big><br><br>
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* <font face= "chalkboard">[[Biology Questions]]</font face>
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* [[General Questions]]  
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</div>
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* [[Math Questions]]
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* [[Biology Questions]]
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==<font face="chalkboard"><font color= 'tan'>Assembly</font color></font face><font outline color> ==
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| width="210px" | <big>'''Assembly Plans'''</big><br><br>
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*[[Assembly powerpoint]]
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* <font face="chalkboard">[[The How's and the What's]]</font face>
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* <font face="chalkboard"> [[Assembly powerpoint]]</font face>
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*[[Assembly plan]]
*[[Assembly plan]]
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*<font color='black'>Final Assembly plans:</font color>
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*[[Western Assembly Plan]]
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**[[Western Assembly Plan]]
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*[[Davidson Assembly Plan]]
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**[[Davidson Assembly Plan]]
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*[[pLac Tet Pancake Plan]] (new)
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| width="210px" | <big>'''Progress'''</big><br><br>
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== <font color='cyan'><font face="chalkboard">Progress</font face></font color>==
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*[[Plasmids and Bacteria]]
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*[[Hix and RE]]
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*[[Hin and Antibiotic Pancakes]]
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<font face="chalkboard">[[Plasmids and Bacteria]] &nbsp;&nbsp;&nbsp;
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*[[Ligations]]
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[[Hix and RE]]&nbsp;&nbsp;&nbsp;
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|-  valign="top"
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[[Hin and Antibiotic Pancakes]]&nbsp;&nbsp;&nbsp;
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| width="210px" | <big>'''Wet Lab Tools'''</big><br><br>
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[[Ligations]]
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*[http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006&group=Davidson Davidson Parts]
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</font face>
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*[http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006&group=Missouri Missouri Western Parts]
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*Summer 2006 [[Pancake Parts]]
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==<font face="chalkboard">Pancake Simulators aka <font color='red'>T</font color><font color='blue'>h</font color><font color='orange'>e</font color><font color='silver'> L</font color><font color='sky blue'>a</font color><font color='magenta'>n</font color><font color= 'orange'>c</font color><font color='green'>e</font color><font color=cyan>l</font color><font color='red'>a</font color><font color='brown'>t</font color><font color='blue'>o</font color><font color='violet'>r</font color> (MATLAB Code)==
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*[[The What's and How's| Davidson Protocols]]
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*[http://gcat.davidson.edu/IGEM06/oligo.html Oligo Cuts Optimization]: by Lance Harden
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===The Original Flipping Simulators===
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*[[Papers of Interest]]
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[http://gcat.davidson.edu/IGEM06/randompancakeflipper.m User-Friendly Version]<br>
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*[[Freezer Stocks]]
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[http://gcat.davidson.edu/IGEM06/powerflipper.m Power-User Version]<br>
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| width="210px" | <big>'''Simulators'''</big><br><br>
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[http://gcat.davidson.edu/IGEM06/powerflipperplus.m Power-User Update]<br>
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*<font color='red'>T</font color><font color='blue'>h</font color><font color='orange'>e</font color><font color='silver'> L</font color><font color='sky blue'>a</font color><font color='magenta'>n</font color><font color= 'orange'>c</font color><font color='green'>e</font color><font color=cyan>l</font color><font color='red'>a</font color><font color='brown'>t</font color><font color='blue'>o</font color><font color='violet'>r</font color> Pancake Flipping Simulator(MATLAB Code)
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[http://gcat.davidson.edu/IGEM06/findmin.m Findmin]<br>
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* Other Flipping Simulators
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[http://gcat.davidson.edu/IGEM06/bigtrial.m Bigtrial]<br>
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**[http://gcat.davidson.edu/IGEM06/randompancakeflipper.m User-Friendly Version]
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**[http://gcat.davidson.edu/IGEM06/powerflipper.m Power-User Version]
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===Graphing Tools===
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**[http://gcat.davidson.edu/IGEM06/powerflipperplus.m Power-User Update]
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[http://gcat.davidson.edu/IGEM06/pancakeplotter.m Pancakeplotter]<br>
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**[http://gcat.davidson.edu/IGEM06/findmin.m Findmin]
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[http://gcat.davidson.edu/IGEM06/permplotter.m Permplotter]<br>
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**[http://gcat.davidson.edu/IGEM06/bigtrial.m Bigtrial]
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[http://gcat.davidson.edu/IGEM06/adjmat.m Adjmat - creates adjacency matrices]<br>
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| width="210px" | <big>'''Graphing Tools'''</big><br><br>
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[http://gcat.davidson.edu/IGEM06/bioadjmat.m Bioadjmat - Adjmat with biological equivalence]<br>
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*[http://gcat.davidson.edu/IGEM06/pancakeplotter.m Pancakeplotter]
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[http://gcat.davidson.edu/IGEM06/make_radial.m Make_radial - creates a radially-embedded graph]<br>
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*[http://gcat.davidson.edu/IGEM06/permplotter.m Permplotter]
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[http://gcat.davidson.edu/IGEM06/find_diam.m Find_diam - finds the diameter of a pancake graph]<br>
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*[http://gcat.davidson.edu/IGEM06/adjmat.m Adjmat - creates adjacency matrices]
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*[http://gcat.davidson.edu/IGEM06/bioadjmat.m Bioadjmat - Adjmat with biological equivalence]
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===Miscellaneous===
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*[http://gcat.davidson.edu/IGEM06/make_radial.m Make_radial - creates a radially-embedded graph]
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[http://gcat.davidson.edu/IGEM06/signedperms.m Signedperms - lists all signed permutations for a stack of k pancakes]<br>
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*[http://gcat.davidson.edu/IGEM06/find_diam.m Find_diam - finds the diameter of a pancake graph]
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[http://gcat.davidson.edu/IGEM06/bioperms.m Bioperms - Signedperms with biological equivalence]<br>
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| width="210px" | <big>'''Miscellaneous Computation Tools'''</big><br><br>
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[http://gcat.davidson.edu/IGEM06/oligo.html Oligo Cuts Optimization]<br>
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*[http://gcat.davidson.edu/IGEM06/signedperms.m Signedperms - lists all signed permutations for a stack of k pancakes]
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</font face>
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*[http://gcat.davidson.edu/IGEM06/bioperms.m Bioperms - Signedperms with biological equivalence]
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|}

Latest revision as of 19:12, 19 February 2007

Logo.gif
http://www.davidson.edu

Project Overview

[http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006&group=Davidson Davidson Parts]

Team Members

Tools and Resources

Check out our [http://www.bio.davidson.edu/courses/synthetic/photos/FlapJack_HotCakes.html Official Team Photo]

NEW Davidson's Awards and Photo Gallery from iGEM Jamboree 2006
Left to Right: Lance, Erin, Samantha, Sabriya, Karmella, Laurie, Malcolm
Solving the Pancake Problem with an E. coli Computer

[http://2006.igem.org/Image:IGEM2006T_Davidson.ppt PowerPoint Presentation] and [http://2006.igem.org/Image:IGEM2006_Davidson_poster.ppt Poster]

Our goal is to genetically engineer a biological system that can compute solutions to a puzzle called the burnt pancake problem. The E.HOP computer is a proof of concept for computing in vivo, with implications for future data storage devices and transgenic systems. Our work was done in collaboration with the [http://2006.igem.org/wiki/index.php/Missouri_Western_State_University_2006 Missouri Western iGEM Team] and an undergraduate research fellow from [http://www.hamptonu.edu/ Hampton University]. EHOP.gif

The Burnt Pancake Problem

The [http://en.wikipedia.org/wiki/Pancake_sorting pancake problem] is a puzzle in which a scrambled series of units (or stack of pancakes) must be shuffled into the correct order and orientation. You can try solving [http://www.cut-the-knot.org/SimpleGames/Flipper.shtml a simple version of the pancake problem] yourself.

In the burnt pancake problem, each pancake is given an orientation by burning one side. To solve the problem, every unit, or pancake, must be placed in the proper order (largest on bottom, smallest on top) and in the proper orientation (burnt side down, golden side up). The pancakes are flipped with two spatulas: one to lift pancakes off the top of the stack, the other to flip part (or all) of the remaining stack of pancakes. The pancakes lifted by the first spatula are returned to the top of the stack without being flipped. Figure 1 illustrates how the puzzle is solved.
Figure 1. A scrambled stack of four burnt pancakes, sorted into correct order and orientation in 3 flips. Proper orientation is indicated by solid color, improper orientation by hatched color.

Approach

Trial and error is one approach to solving the burnt pancake problem, but how could one compute the quickest solution? Our idea is to let E. coli do the work, using each cell as a tiny processor in a massively parallel machine. A mathematical model of the flipping process helps us design the system and interpret the output of our EHOP computer.
Figure 2. 3-D structure of a Hin protein complex bound to DNA. View the [http://www.rcsb.org/pdb/explore/explore.do?structureId=1ZR4 interactive 3-D Jmol image].
Biological System: The biological representation of a pancake is a functional unit of DNA such as a promoter or coding region. To flip these units of DNA, we have reconstituted the Hin/ Hix invertase system (Figure 2) from Salmonella typhimurium as a BioBrick compatible system in E. coli. Hin invertase () was cloned from S. typhimurium, Ames strain TA100 and tagged with LVA. We built the recombinational enhancer (RE) and Hin invertase recognition sequence HixC using the publicly available genomic sequence of S. typhimurium and [http://gcat.davidson.edu/IGEM06/oligo.html a dsDNA assembly program we created] for gene synthesis from overlapping oligos.

Every segment of DNA flanked by a pair of HixC sites is a "pancake" capable of being inverted. Hin invertase recognizes pairs of HixC sites and inverts the DNA fragment in between the two HixC sites with the help of the Fis protein bound to the RE. In our system, selectable phenotypes (including antibiotic resistance and RFP expression), depend upon the proper arrangement of a series of HixC-flanked DNA segments in a plasmid. This allows us to select for cells that have successfully solved the puzzle. An example of a sorted stack of two pancakes is shown in Figure 3. There are 7 other configurations of 2 pancakes. If we increase the number of pancakes to 4, there are 384 configurations. In general, there are 2n n! configurations of n pancakes, a combinatorial explosion of possibilities. How many should we build and test? Which ones are most informative? We need a mathematical model to help answer this question.

Figure 3. A sorted stack of two biological "pancakes"

Mathematical Model: Our mathematical representation of a stack of pancakes is a signed permutation, in which each numerical value represents the pancake size and the sign of the number represents the orientation. For example, (1, 2, 3, 4) is a sorted stack of four pancakes, all in the proper order and orientation, and (-2, 4, -1, 3) is the scrambled stack of four pancakes shown on the far left of Figure 1. Note that pancakes 1 and 2 are negative, indicating that these two pancakes are in the wrong orientation (burnt side up).

Figure 4. Simulation results for two pancakes
We simulated the flipping process by assuming that each segment of DNA flanked by Hix sites is equally likely to be flipped by Hin invertase. In an n-pancake stack, there are n+1C2 ways to choose a segment: two spatula locations must be chosen from among the n + 1 potential locations. For example, there are 5C2 = 5! 3! / 2! = 10 different ways to perform a single flip in a stack of 4 pancakes. The random flipping process continues until the stack is sorted in the correct order and orientation, or until we artificially stop the random flipping process. Figure 4 shows the percent of plasmids that we expect to be sorted after 1 flip, 2 flips, and so on, up to 20 flips, for each of the eight initial configurations.

From these simulations, and similar results for stacks of 3 and 4 pancakes, we discovered that the probability of a plasmid being sorted after k flips was determined by how many ways the solution could be obtained. Several initial configurations had essentially the same graph in our simulations because they had the same number of ways of being sorted. Only one representative from each of these "families" of initial configurations needs to be built and tested.

Methods and Results
The following is an outline of what the Davidson team will present at iGEM 2006
Basic parts

Parts used in this project were designed by two iGEM Teams

  • [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006&group=Davidson Davidson]
  • [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006&group=Missouri Missouri Western]

Modeling

 Building the Biological System

 Conclusions

  • Consequences of devices
    • Practical: proof-of-concept for bacterial computers, data storage
    • Basic research: transgene rearrangement in vivo, insights into evolution that has occurred via DNA rearrangements
  • Next steps: can solve problem but need control over kinetics
  • Lessons learned:
    • Troubleshooting, communication, teamwork, publicity
    • Math and Biology meshed really well and even uncovered a new proof
    • Multiple campuses can increase capacity through communication and cooperation
    • Size of school is not a limiting factor
    • We had a blast and learned heaps!!!
TEAM MEMBERS

Students

  • Sabriya Rosemond is a junior biology major at Hampton University.
  • Erin Zwack is a junior biology major at Davidson College.
  • Lance Harden is a sophomore math major at Davidson College.
  • Samantha Simpson is a sophomore at Davidson College who might design a major in genomics.

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]
Tools and Resources
iGEM 2006 Jamboree

  • Presentation Outline
  • [http://2006.igem.org/Image:IGEM2006T_Davidson.ppt PowerPoint Presentation]
  • [http://2006.igem.org/Image:IGEM2006_Davidson_poster.ppt Poster] - ppt file
White Board

 Assembly Plans

 Progress

Wet Lab Tools

  • [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006&group=Davidson Davidson Parts]
  • [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006&group=Missouri Missouri Western Parts]
  • Summer 2006 Pancake Parts
  • Davidson Protocols
  • [http://gcat.davidson.edu/IGEM06/oligo.html Oligo Cuts Optimization]: by Lance Harden
  • Papers of Interest
  • Freezer Stocks
Simulators

  • The Lancelator Pancake Flipping Simulator(MATLAB Code)
  • Other Flipping Simulators
    • [http://gcat.davidson.edu/IGEM06/randompancakeflipper.m User-Friendly Version]
    • [http://gcat.davidson.edu/IGEM06/powerflipper.m Power-User Version]
    • [http://gcat.davidson.edu/IGEM06/powerflipperplus.m Power-User Update]
    • [http://gcat.davidson.edu/IGEM06/findmin.m Findmin]
    • [http://gcat.davidson.edu/IGEM06/bigtrial.m Bigtrial]
Graphing Tools

  • [http://gcat.davidson.edu/IGEM06/pancakeplotter.m Pancakeplotter]
  • [http://gcat.davidson.edu/IGEM06/permplotter.m Permplotter]
  • [http://gcat.davidson.edu/IGEM06/adjmat.m Adjmat - creates adjacency matrices]
  • [http://gcat.davidson.edu/IGEM06/bioadjmat.m Bioadjmat - Adjmat with biological equivalence]
  • [http://gcat.davidson.edu/IGEM06/make_radial.m Make_radial - creates a radially-embedded graph]
  • [http://gcat.davidson.edu/IGEM06/find_diam.m Find_diam - finds the diameter of a pancake graph]
Miscellaneous Computation Tools

  • [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]
Retrieved from "http://2006.igem.org/wiki/index.php/Davidson_2006"
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