Tokyo/sunaba2

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[[Image:tokyotech3.JPG|700px]]
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__NOTOC__
__NOTOC__
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{| cellspacing="5"
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==[[Tokyo_Tech|Abstruct]]　　[[Tokyo/Model|Concept & Model]]　　[[Tokyo/Requirements |Requirements]]　　[[Tokyo/Genetic circuit|Genetic_circuit]]　　[[Tokyo/Works|Works]]　　[[Tokyo/about our team|About_our_team]]==
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|width="550px" valign="top" |  
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<h1> ''' 1,Abstruct''' </h1>
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===[[Tokyo/Model|Concept & Model]]===
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====We made a bacterial society that follows Pareto's principle as an [[Tokyo/Concept|Ant society]] does.====
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<br>[[Image:TOP.JPG|250px]]
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===[[Tokyo/Requirements |Requirements]]===
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====Our requirements to construct this model are two things, bistability and coexistence by cell-cell communication.====
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<!--<br>[[Image:Bistability.JPG|200px]][[Image:Coexistence.JPG|250px]]-->
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===[[Tokyo/Genetic circuit|Genetic circuit]]===
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====We designed the genetic circuit to satisfy its requirements and developed necessary [[Tokyo/new parts |new parts]]. ====
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<br>[[Image:Tokyo_genetic circuit_s.jpg|100px]]
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====　　　　　　　　　　　　　　　Our constructed parts are [[Tokyo/construction|Here]]!!! ====
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===[[Tokyo/simulation|Our GOAL]]===
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====We indicated [[Tokyo/simulation|our goal]] of the project by the simulation!! The simulation proved that our genetic circuit have existence of solution.====
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<br>[[Image:Tokyo_simulation_s2.jpg|350px]]
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<br>[[Image:our goal.JPG|350px]]
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|width="400px" valign="top" |
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<h1>'''2,Works'''</h1>
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<!--<h1> ''' [[Tokyo/Experiments |Experiments]]''' </h1>-->
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<!--[[Image:homepage4.jpg]]-->
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===[[Tokyo/Approach |Approach]]===
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<h1> '''Abstruct''' </h1>
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====Combination of Wet & Dry trials====
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We have alternated/combined Wet and Dry experiments to achieve our goal
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===0.<span style="color:#ff33cc;">Wet </span>:　[[Tokyo/Hybrid promoter|Hybrid promoter]]===
 
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|width="350px" valign="top" |
 
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====We need to develop the promoter that can receive two input, AHL & reperssor. We tried to create and [[Tokyo/Hybrid promoter|succeeded]]!! ====
 
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<!--New part development:Hybrid promoterPBとして、2つの入力を受けるプロモータを開発する必要があった
 
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<br>図　概念図、配列とグラフ図
 
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-->
 
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|width="150px" valign="top" |
 
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[[Image:Hybridgraph.JPG|200px|]]
 
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|}
 
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===1.<span style="color:#0066ff;">Dry </span>:　 [[Tokyo/Formulation |Formulation]]===
 
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We wrote the Formulation
 
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<!--リプレッサーＡ，Ｂ，シグナル分子Ｓの時間変化を式として表し、安定性解析を行った結果、Hill係数が大切であることがわかった
 
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<br>図　3つの式
 
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-->
 
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===2.<span style="color:#ff33cc;">Wet </span>: 　[[Tokyo/Assay |Assay]]===
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====We decided the parameter of hill coefficients by the assay of AHL & IPTG====
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==1.[[Tokyo/Model|Concept & Model]]==
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<!--新しいパーツであるハイブリッドプロモータに関して、大腸菌を用いた実験から、2つの入力それぞれに対するHill係数を求めた。
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====We made a bacterial society that follows Pareto's principle as an [[Tokyo/Concepts|Ant society]] does.([[Tokyo/Model|more…]])====
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<br>図大腸菌の絵、FLAの絵、フィッティングのグラフ
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<br>[[Image:TOP.JPG|350px]]
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-->
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====1.coexistence====
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[[Image:hill AHL.JPG|190px]]|[[Image:hill IPTG.JPG|190px]]
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====2.Removal of Worker====
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====3.coexistence again====
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===3.<span style="color:#0066ff;">Dry </span>: 　[[Tokyo/Simulation |Simulation]]===
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wet実験で求められたパラメータを用いて、集団が怠け者の細胞のみとなった場合に、一度不安定化して、続いて働き者と怠け者になれることをStocastic Simulationで確認した。このシステムの挙動に必要な他のパラメータ範囲が判明した。
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Based on stochastic simulation using parameters obtained from our wet experiments, we have confirmed that the whole system becomes unstable when there are only idlers left, and then, they become either of workers and idlers. Also we have determined other parameters necessary for the desired behavior of this system.
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<!--最終日に動画と差し替え？？-->
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<br>
<br>
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<br>[[Image:Tokyo_simulation_s2.jpg|350px]]
 
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===4.<span style="color:#ff33cc;">Wet </span>: 　[[Tokyo/Assay |Assay]]===
 
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<!--====We determined the feasibility test of this ====-->
 
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Simulationを満たすための他のパラメータが現在のプラスミドで可能であるかを、大腸菌を用いた実験で確認した。
 
<br>
<br>
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1. By the wet experiments using ''E. coli'', we testified whether our current plasmids could satisfy the other required conditions (for the desired behavior of the system) estimated by the simulation.
 
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<br>
 
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2. We tested whether our plasmids gave the other parameters to satisfy the simulation by the experiments using ''E. coli''.
 
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===5.Future works===
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==2.[[Tokyo/Requirements |Requirements]]==
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====Our requirements to construct this model are two things, bistability and coexistence by cell-cell communication.([[Tokyo/Requirements|more…]])====
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<br>[[Image:Bistability.JPG|200px]][[Image:Coexistence.JPG|250px]]
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Based on the results from the wet experiments in the step 4, the next dry approach - analysis and simulation - should be performed, which will in turn be testified and confirmed by wet experiments.
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<!--メニュー-->
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Continueing these processes, if time permits, would further sophisticate our model.
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__NOTOC__
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<!--
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==3.[[Tokyo/Genetic circuit|Genetic circuit]]==
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<h1> '''3,[[Tokyo/Achievements |Achievements ]]'''</h1>
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====We designed the genetic circuit to satisfy its requirements and developed [[Tokyo/new parts |new parts]] required ([[Tokyo/Genetic circuit|more…]]). ====
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<br>[[Image:Tokyo_genetic circuit_s.jpg|250px]]
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<br>[[Tokyo/Hybrid promoter |Hybrid promoter ]]
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====　　　　　　　　　　Our constructed parts are [[Tokyo/construction|Here]]!!! ====
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<br>[[Tokyo/Bistability analisis|Bistability analysis]]
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<br>[[Tokyo/Others |Others ]]
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-->
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<h1> '''3,[[Tokyo/About our team |About our team ]][[Image:TeamLogo.jpg]]'''</h1>
 
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<!--[[Image:team photo.jpg]] -->
 
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|width="500px" valign="top" |
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'''Students'''
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==4.[[Tokyo/Works|Works]]==
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<br>[[Tokyo/Satoru Akama |Satoru Akama ]] | [[Tokyo/Kenichiro Iwasaki |Kenichiro Iwasaki]] | [[Tokyo/Hiroki Kawahara |Hiroki Kawahara ]] | [[Tokyo/Hajime Nakatani|Hajime Nakatani]]
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====The simulation using parameters obtained from wet experiments for our brand-new part indicated that the whole system becomes unstable when there are only idlers left, and then, they can differentiate into either of workers and idlers. ([[Tokyo/Works|more…]])====
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'''Advisors: Last year's member '''
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====<span style="color:#ff33cc;">Wet assay </span>====
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<br>[[Tokyo/Shotaro Ayukawa |Shotaro Ayukawa ]] | [[Tokyo/Akio Kobayashi|Akio Kobayashi ]]
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<br>[[Image:hill AHL.JPG|190px]]|[[Image:hill IPTG.JPG|190px]]
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====<span style="color:#0066ff;">Dry simulation </span>====
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<br>[[Image:Tokyo_simulation_s2.jpg|350px]]
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'''Instructors'''
 
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<br>[http://www.sb.dis.titech.ac.jp/ Daisuke Kiga] | [http://www.es.dis.titech.ac.jp/ Masayuki Yamamura] | [http://nicosia.is.s.u-tokyo.ac.jp/~hagiya/ Masami Hagiya] | [http://www.sb.dis.titech.ac.jp/ Masahiko Uchiyama]
 
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'''Links'''
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|}
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[[Tokyo/sunaba |sunaba ]]
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<br>[[Tokyo/alternative|alternative]]こんな表紙はいかが？
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<br>[[Tokyo/alternative2|alternative2]]
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<h1>'''2,[[Tokyo/Works |Works]]'''</h1>
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<!--<h1> ''' [[Tokyo/Experiments |Experiments]]''' </h1>-->
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<!--[[Image:homepage4.jpg]]-->
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===2-0.Wet : [[Tokyo/Hybrid promoter|Hybrid promoter]]===
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[[Image:Hybridgraph.JPG|200px|]]
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===2-1.Dry : [[Tokyo/Formulation |Formulation]]===
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[[Image:Expression4-1.jpg|300px]]
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===2-2.Wet : [[Tokyo/Assay |Assay]]===
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<!--====We decided the parameter of hill coefficients by the assay of AHL & IPTG====-->
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<!--新しいパーツであるハイブリッドプロモータに関して、大腸菌を用いた実験から、2つの入力それぞれに対するHill係数を求めた。
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<br>図大腸菌の絵、FLAの絵、フィッティングのグラフ
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-->
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[[Image:hill AHL.JPG|180px]][[Image:hill IPTG.JPG|180px]]
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===2-3.Dry : [[Tokyo/Simulation |Simulation]]===
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===2-4.Wet : [[Tokyo/Assay |Assay]]===
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<!--====We determined the feasibility test of this ====-->
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Simulationを満たすための他のパラメータが現在のプラスミドで可能であるかを、大腸菌を用いた実験で確認した。
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<br>
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===2-5.Future works===
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<!--
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<h1> '''3,[[Tokyo/Achievements |Achievements ]]'''</h1>
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<br>[[Tokyo/Hybrid promoter |Hybrid promoter ]]
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<br>[[Tokyo/Bistability analisis|Bistability analysis]]
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<br>[[Tokyo/Others |Others ]]
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-->
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<h1>'''2,[[Tokyo/Works |Works]]'''</h1>
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<!--<h1> ''' [[Tokyo/Experiments |Experiments]]''' </h1>-->
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<!--[[Image:homepage4.jpg]]-->
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===2-0.Wet : [[Tokyo/Hybrid promoter|Hybrid promoter]]===
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[[Image:Hybridgraph.JPG|200px|]]
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===2-1.Dry : [[Tokyo/Formulation |Formulation]]===
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[[Image:Expression4-1.jpg|300px]]
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===2-2.Wet : [[Tokyo/Assay |Assay]]===
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<!--====We decided the parameter of hill coefficients by the assay of AHL & IPTG====-->
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<!--新しいパーツであるハイブリッドプロモータに関して、大腸菌を用いた実験から、2つの入力それぞれに対するHill係数を求めた。
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<br>図大腸菌の絵、FLAの絵、フィッティングのグラフ
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-->
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[[Image:hill AHL.JPG|180px]][[Image:hill IPTG.JPG|180px]]
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===2-3.Dry : [[Tokyo/Simulation |Simulation]]===
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===2-4.Wet : [[Tokyo/Assay |Assay]]===
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<!--====We determined the feasibility test of this ====-->
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Simulationを満たすための他のパラメータが現在のプラスミドで可能であるかを、大腸菌を用いた実験で確認した。
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<br>
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===2-5.Future works===
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<!--
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<h1> '''3,[[Tokyo/Achievements |Achievements ]]'''</h1>
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<br>[[Tokyo/Hybrid promoter |Hybrid promoter ]]
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<br>[[Tokyo/Bistability analisis|Bistability analysis]]
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<br>[[Tokyo/Others |Others ]]
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-->
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<h1> '''3,[[Tokyo/About our team |About our team ]]'''</h1>
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<!--[[Image:team photo.jpg]] -->
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'''Students'''
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<br>[[Tokyo/Satoru Akama |Satoru Akama ]] | [[Tokyo/Kenichiro Iwasaki |Kenichiro Iwasaki]] | [[Tokyo/Hiroki Kawahara |Hiroki Kawahara ]] | [[Tokyo/Hajime Nakatani|Hajime Nakatani]]
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'''Advisors: Last year's member '''
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<br>[[Tokyo/Syotarou Ayukawa |Syotarou Ayukawa ]] | [[Tokyo/Akio Kobayashi|Akio Kobayashi ]]
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'''Instructors'''
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<br>[http://www.sb.dis.titech.ac.jp/ Daisuke Kiga] | [http://www.es.dis.titech.ac.jp/ Masayuki Yamamura] | [http://nicosia.is.s.u-tokyo.ac.jp/~hagiya/ Masami Hagiya] | [http://www.sb.dis.titech.ac.jp/ Masahiko Uchiyama]
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'''Links'''
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<h1> ''' ''' </h1>
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[[Tokyo/sunaba |sunaba ]]
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==⇒[[Tokyo/No click version|"No click version"]]==

Latest revision as of 11:27, 23 October 2007

Tokyotech3.JPG

Abstruct　　Concept & Model　　Requirements　　Genetic_circuit　　Works　　About_our_team

Abstruct

1.Concept & Model

We made a bacterial society that follows Pareto's principle as an Ant society does.(more…)


TOP.JPG

1.coexistence

2.Removal of Worker

3.coexistence again



2.Requirements

Our requirements to construct this model are two things, bistability and coexistence by cell-cell communication.(more…)


Bistability.JPGCoexistence.JPG



3.Genetic circuit

We designed the genetic circuit to satisfy its requirements and developed new parts required (more…).


Tokyo genetic circuit s.jpg

　　　　　　　　　　Our constructed parts are Here!!!

4.Works

The simulation using parameters obtained from wet experiments for our brand-new part indicated that the whole system becomes unstable when there are only idlers left, and then, they can differentiate into either of workers and idlers. (more…)

Wet assay


Hill AHL.JPG|Hill IPTG.JPG

Dry simulation


Tokyo simulation s2.jpg


⇒"No click version"

Retrieved from "http://2007.igem.org/wiki/index.php/Tokyo/sunaba2"