Team:UT-Tokyo/Sudoku abstract

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= '''Sudoku''' =
= '''Sudoku''' =
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<html>
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Introduction   
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<div>
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[https://2010.igem.org/Team:UT-Tokyo/Sudoku_construct System]   
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        <ul id="inpagemenu">
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[https://2010.igem.org/Team:UT-Tokyo/Sudoku_lab_note  Lab note]       
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                <li><span>Introduction</span></li>
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[https://2010.igem.org/Team:UT-Tokyo/Sudoku_result  Result]
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                <li><a href="/Team:UT-Tokyo/Sudoku_construct" id="construct">System</a></li>
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                <li><a href="/Team:UT-Tokyo/Sudoku_modeling" id="modeling">Modeling</a></li>
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                <li><a href="/Team:UT-Tokyo/Sudoku_experiments" id="experiment">Experiments</a></li>
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                <li><a href="/Team:UT-Tokyo/Sudoku_perspective" id="perspective">Perspective</a></li>
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            <li><a href="/Team:UT-Tokyo/Sudoku_reference" id="reference">Reference</a></li>
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            </ul>
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</div>
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<div id="clear"></div>
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</html>
== '''Introduction''' ==
== '''Introduction''' ==
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We're trying to make ''E.coli'' solve Sudoku puzzle. Human and Computers can solve Sudoku, of course. But ''E.coli'', which is lower animal, solves sudoku in our project. It is very very interesting!
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==='''Background'''===
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The ability to integrate and process information is indispensable for biological devices that operate autonomously in intricate environments, such as in "smart drugs", which sense and respond to the patient's health state appropriately.
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Therefore, the design and construction of such genetic circuits has long been pursued in the field of synthetic biology since its inauguration. Accomplishments include the toggle switch, logic gate, counter, and flip-flop switch.
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However, the function of most of these circuits is either limited to relatively simple form, such as Boolean logic element, or not robust enough to work correctly. A universal means of communication between individual elements is also generally lacking. As part of the solution, here we propose a new information processing unit which receives multiple inputs, memorizes the inputs stably, and makes a decision based on the combination of the inputs. In addition, we have devised a means of communication between individual bacterial-based elements. Importantly, this system allows destination-specific delivery of information even when the number of possible destinations is immensely large. As proof-on-principle of the above systems, we have created bacteria that solve "Sudoku", a world famous puzzle game.
==='''What is Sudoku?'''===
==='''What is Sudoku?'''===
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[[Image:What_Sudoku_99.png|200px|thumb|What's Sudoku?]]
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[[Image:9x9.png|200px|thumb|The example of Sudoku (9x9)]]
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Sudoku is a puzzle game with the objective of filling a 9x9 grid of cells with the numbers 1~9 without entering the same number in a column, row or “block (see figure).” A player is given a grid in which some of the cells are filled in from the beginning and must complete filling in the grid by entering the remaining numbers. The rules are simple, but some puzzles can get very difficult, and it attracts fans from all over the world. For simplicity, here we solve a 4x4 grid version. However, expanding on the same principles, our E. coli can theoretically solve larger grids, for example 9x9 grids.
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==='''Solving Sudoku with our E. coli'''===
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[[Image:Parallel_computing.png|200px|thumb|16 kinds E. coli corresponding to each cell]]
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[[Image:Differenciation-model.png|200px|thumb|Every cells can "differentiate"]]
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Now, we explain how to make E. coli solve Sudoku. First, we make 16 kinds E. coli corresponding to each cell.
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Our E. coli are in one of two states, which we designate “differentiated” or “undifferentiated.” There are four differentiated states corresponding to the numbers one to four.
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Differentiated E. coli have the ability to inform other bacteria what number they are, so that relevant bacteria do not differentiate into that number. Some E. coli are differentiated from the beginning. These bacteria set in action a chain of transmission events that result in the differentiation of bacteria corresponding to all 16 cells.
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These events take place in a flask which contains a co-culture of the 16 types of bacteria. Each of these 16 types interacts with detection bacteria on a plate which in turn inform the viewer the number the 16 cells have differentiated into with the use of fluorescent proteins.
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=='''Reference'''==
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==='''cre recombinase'''===
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==='''as RNA'''===
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1.Artificial antisense RNAs silence lacZ in E. coli by decreasing target mRNA concentration
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Stefan Alessandra, Tonelli Alessandro, Schwarz Flavio and Hochkoeppler Alejandro, BMB reports, 568-74 (2008)
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2.Kill the messenger: bacterial antisense RNA promotes mRNA decay
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E Gerhart H Wagner, nature structural & molecular biology, 16, 804-6 (2009)
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3.Distance between RBS and AUG plays an important role in overexpression of recombinant proteins
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Sunil K. Berwal, R.K. Sreejith and Jayanta K. Pal, Analytical Biochemistry, 405, 275-7 (2010)
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4.Antisense RNA Control of Plasmid R1 Replication
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Charlotta Malmgren, E. Gerhart H. Wagner, Chantal Ehresmann, Bernard Ehresmann and Pascale Romby, The Journal of Biologycal Chemistry, 272, 12508-12 (1997)
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5.Paired termini stabilize antisense RNAs and enhance conditional gene silencing in Escherichia coli
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Nobutaka Nakashima, Tomohiro Tamura and Liam Good, Nucleic Acids Research, 34, e138 (2006)
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6.The Influence of Antisense Oligonucleotide-induced RNA Structure on Escherichia coli RNase H1 Activity
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Walt F. Lima, Venkatraman Mohan and Stanley T. Crooke, The Journal of Biological Chemistry, 272, 18191-8 (2010)
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==='''MS2 phage'''===
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1.Studies on Sex Pili: Mutants of the Sex Factor F in Escherichia coli Defective in Bacteriophage-Adsorbing Function of F Pili
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Munemitsu Tomoeda, Akemi Shuta and Manabu Inuzuka, Journal of Bacteriology, 112, 1358-63 (1972)
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2.Crystal structure of an RNA bacteriophage coat protein-operator complex
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Karin Valegard, James B. Murray, Peter G. Stockley, Nicola J. Stonehouse and Lars Liljas, Nature, 371, 626 (1994)
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3.Ribonucleoprotein Complexes of R17 Coat Protein and a Translational Operator Analog
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Dorothy Beckett and Olke C. Uhlenbeck, Journal of Molecular Biology, 204, 927-38 (1988)
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4.A unique mechanism regulating gene expression: Translational inhibition by a complementary RNA transcript (micRNA)
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Takeshi Mizuno, Mei-Yin Chou and Masayori Inoue, Proc. Nail. Acad. Sci. USA, 81, 1966-70 (1984)
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5微生物学講義録  前国立感染症研究所長 吉倉　廣 著 第14章 　RNAファージ<br />
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Sudoku is a puzzle game with the objective of filling a 9x9 grid of cells with the numbers 1~9 without entering the same number in a column, row or “block (see figure).” A player is given a grid in which some of the cells are filled in from the beginning and must complete filling in the grid by entering the remaining numbers. The rules are simple, but some puzzles can get very difficult, and it attracts fans from all over the world. For simplicity, here we solve a 4x4 grid version. However, expanding on the same principles, our ''E. coli'' can theoretically solve larger grids, for example 9x9 grids.
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http://jsv.umin.jp/microbiology/main_014.htm
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==='''To write introduction'''===
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==='''Solving Sudoku with our ''E. coli'''''===
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[[Image:E.coli corresponding.png|200px|thumb|16 kinds of ''E. coli'' corresponding to each cell]]
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[[Image:Differentiation-model.png|200px|thumb|Every cells can "differentiate"]]
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1.Purnick, P.E., and Weiss, R.
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Now, we explain how to make ''E. coli'' solve Sudoku. First, we make 16 kinds of ''E. coli'' corresponding to each cell.
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The second wave of synthetic biology: from modules to systems. Nat. Rev. Mol. Cell. Biol. 10, 410?422.(2009).
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2.Gardner, T. S., Cantor, C. R. & Collins, J. J.
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Our E. coli are in one of two states, which we designate “differentiated” or “undifferentiated.” There are four differentiated states corresponding to the numbers from one to four.
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Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339?342 (2000).
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3.Anderson, J. C., Clarke, E. J., Arkin, A. P. & Voigt, C. A.
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Differentiated ''E. coli'' have the ability to inform other bacteria what number they are, so that relevant bacteria do not differentiate into that number. Some ''E. coli'' are differentiated from the beginning. These bacteria set in action a chain of transmission events that result in the differentiation of bacteria corresponding to all 16 cells.
-
Environmentally controlled invasion of cancer cells by engineered bacteria. J. Mol. Biol. 355, 619?627 (2006).
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These events take place in a flask which contains a co-culture of the 16 types of bacteria. Each of these 16 types interacts with detection bacteria on a plate which in turn inform the viewer the number which the 16 cells have differentiated into with the use of fluorescent proteins.
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4.Anderson, J.C., Voigt, C.A. & Arkin, A.P.
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If you'd like to know how our ''E.coli'' solves SUDOKU particularly, please see the [https://2010.igem.org/Team:UT-Tokyo/Sudoku_construct  System] page.
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Environmental signal integration by a modular AND gate. Mol. Syst. Biol. 3, 133 (2007).
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5.Win, M. N. & Smolke, C. D.
 
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Higher-order cellular information processing with synthetic RNA devices. Science 322, 456?460 (2008).
 
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6.Ham, T. S., Lee, S. K., Keasling, J. D. & Arkin, A. P.
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<html>
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Design and construction of a double inversion recombination switch for heritable sequential genetic memory. PLoS ONE 3, e2815 (2008).
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<object width="640" height="385"><param name="movie" value="http://www.youtube.com/v/wzcryKryME8?fs=1&amp;hl=ja_JP"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/wzcryKryME8?fs=1&amp;hl=ja_JP" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="640" height="385"></embed></object>
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</html>
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7.Friedland, A. et al. Synthetic gene networks that
 
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count. Science 324, 1199?1202 (2009).
 
{{UT-Tokyo_Foot}}
{{UT-Tokyo_Foot}}

Latest revision as of 03:57, 28 October 2010

UT-Tokyo

Sudoku

Introduction

Background

The ability to integrate and process information is indispensable for biological devices that operate autonomously in intricate environments, such as in "smart drugs", which sense and respond to the patient's health state appropriately. Therefore, the design and construction of such genetic circuits has long been pursued in the field of synthetic biology since its inauguration. Accomplishments include the toggle switch, logic gate, counter, and flip-flop switch.

However, the function of most of these circuits is either limited to relatively simple form, such as Boolean logic element, or not robust enough to work correctly. A universal means of communication between individual elements is also generally lacking. As part of the solution, here we propose a new information processing unit which receives multiple inputs, memorizes the inputs stably, and makes a decision based on the combination of the inputs. In addition, we have devised a means of communication between individual bacterial-based elements. Importantly, this system allows destination-specific delivery of information even when the number of possible destinations is immensely large. As proof-on-principle of the above systems, we have created bacteria that solve "Sudoku", a world famous puzzle game.

What is Sudoku?

The example of Sudoku (9x9)

Sudoku is a puzzle game with the objective of filling a 9x9 grid of cells with the numbers 1~9 without entering the same number in a column, row or “block (see figure).” A player is given a grid in which some of the cells are filled in from the beginning and must complete filling in the grid by entering the remaining numbers. The rules are simple, but some puzzles can get very difficult, and it attracts fans from all over the world. For simplicity, here we solve a 4x4 grid version. However, expanding on the same principles, our E. coli can theoretically solve larger grids, for example 9x9 grids.

Solving Sudoku with our E. coli

16 kinds of E. coli corresponding to each cell
Every cells can "differentiate"

Now, we explain how to make E. coli solve Sudoku. First, we make 16 kinds of E. coli corresponding to each cell.

Our E. coli are in one of two states, which we designate “differentiated” or “undifferentiated.” There are four differentiated states corresponding to the numbers from one to four.

Differentiated E. coli have the ability to inform other bacteria what number they are, so that relevant bacteria do not differentiate into that number. Some E. coli are differentiated from the beginning. These bacteria set in action a chain of transmission events that result in the differentiation of bacteria corresponding to all 16 cells. These events take place in a flask which contains a co-culture of the 16 types of bacteria. Each of these 16 types interacts with detection bacteria on a plate which in turn inform the viewer the number which the 16 cells have differentiated into with the use of fluorescent proteins.

If you'd like to know how our E.coli solves SUDOKU particularly, please see the System page.



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