Tokyo Tech

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__NOTOC__
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==[[Tokyo_Tech|Abstract]]&nbsp;&nbsp;&nbsp;[[Tokyo/Model|Concept & Model]]&nbsp;&nbsp;&nbsp;[[Tokyo/Requirements |Requirements]]&nbsp;&nbsp;&nbsp;[[Tokyo/Genetic circuit|Genetic_circuit]]&nbsp;&nbsp;&nbsp;[[Tokyo/Works|Works]]&nbsp;&nbsp;&nbsp;[[Tokyo/About our team|About_our_team]]==
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<h1> ''' Abstract''' </h1>
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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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==1. [[Tokyo/Model|Concept & Model]]==
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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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'''The goal of our project is to make a bacterial society that follows Pareto's principle as an [[Tokyo/Concepts|ant society]] does.
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<br>[[Image:Tokyo_simulation_s2.jpg|350px]]
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'''On the other word, we try to construct a bacterial system which takes "balanced differentiation".([[Tokyo/Model|See more.]])'''
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<br>[[Image:our goal.JPG|350px]]
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<br>[[Image:Defferentiation4.JPG|450px]]
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<br>'''1. Differentiation => 2. Worker Removal '''
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<br>　'''3. Dedifferentiation => 4.Redifferentiation'''
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<h1>'''2,Works'''</h1>
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==2. [[Tokyo/Requirements |Requirements]]==
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<!--<h1> ''' [[Tokyo/Experiments |Experiments]]''' </h1>-->
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'''Bistability and cell-cell communication are necessary to realize our model of "Balanced differentiation". ([[Tokyo/Requirements|See more.]])'''
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<br><br><br>
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'''1．Differentiation generated by mutual-inhibition circuit.'''
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<!-- '''1．Bistability generated by one genetic circuit.''' -->
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<br>'''2．Cell-cell communication .'''
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<br>[[Image:Cellcell.JPG|450px]]
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===[[Tokyo/Approach |Approach]]===
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==3. [[Tokyo/Genetic circuit|Genetic circuit]]==
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====Combination of Wet & Dry trials====
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'''The genetic circuit in this project consisted of [[Tokyo/Genetic circuit/the new parts|the new parts]] as well as BioBrick parts. ([[Tokyo/Genetic circuit|See more.]])'''
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We have alternated/combined Wet and Dry experiments to achieve our goal
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<!--（木賀）biobrickがdeliverされたのは当然なのでこの単語を消去-->
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<!--ここで言いたいことはgenetic circuitの大きさと自分達が作った新しいパーツを使っているということ-->
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<br>[[Image:Geneticcurcuit.JPG|290px|left]]
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[[Image:This is the new part.JPG|150px|none]]
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<br><br>'''The new parts of this year are [[Tokyo/Genetic circuit/the new parts|here]]!!'''
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===0.<span style="color:#ff33cc;">Wet </span>:　[[Tokyo/Hybrid promoter|Hybrid promoter]]===
 
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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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[[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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==4. [[Tokyo/Works|Works]]==
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We wrote the Formulation
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'''Our model has been sophisticated through successive combinations of wet and dry approaches. ([[Tokyo/Works|See more.]])'''
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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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'''<span style="color:#ff33cc;">Wet assay </span>'''
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<br>[[Image:hill AHL.JPG|200px]][[Image:hill IPTG.JPG|200px]]
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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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[[Image:hill AHL.JPG|190px]]|[[Image:hill IPTG.JPG|190px]]
 
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===3.<span style="color:#0066ff;">Dry </span>: 　[[Tokyo/Simulation |Simulation]]===
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'''<span style="color:#0066ff;">Dry simulation </span>'''
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'''<br>Using the data from wet experiments,the guideline for the design of the model was established'''
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<br>[[Image:Defferentiation result.JPG|450px]]
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<!--<br>[[Image:Tokyo_simulation_s4.jpg|300px]]-->
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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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== 5. [[Tokyo/About our team |About our team]] ==
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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>
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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。
 
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<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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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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Continueing these processes, if time permits, would further sophisticate our model.
 
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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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<h1> '''3,[[Tokyo/About our team |About our team ]][[Image:TeamLogo.jpg]]'''</h1>
 
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'''Students'''
'''Students'''
<br>[[Tokyo/Satoru Akama |Satoru Akama ]] | [[Tokyo/Kenichiro Iwasaki |Kenichiro Iwasaki]] | [[Tokyo/Hiroki Kawahara |Hiroki Kawahara ]] | [[Tokyo/Hajime Nakatani|Hajime Nakatani]]
<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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<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]
<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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[[Tokyo/sunaba |sunaba ]]
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<br>[[Tokyo/sunaba2 |sunaba2 ]]4分割表紙バージョン
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<br>[[Tokyo/alternative|alternative]]こんな表紙はいかが？
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== ==
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<br>[[Tokyo/alternative2|alternative2]]
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'''[[Tokyo/Reference|Reference]]'''

Latest revision as of 04:30, 27 October 2007

Tokyotech4.JPG


Abstract   Concept & Model   Requirements   Genetic_circuit   Works   About_our_team

Abstract

1. Concept & Model

The goal of our project is to make a bacterial society that follows Pareto's principle as an ant society does. On the other word, we try to construct a bacterial system which takes "balanced differentiation".(See more.)
Defferentiation4.JPG
1. Differentiation => 2. Worker Removal
　3. Dedifferentiation => 4.Redifferentiation

2. Requirements

Bistability and cell-cell communication are necessary to realize our model of "Balanced differentiation". (See more.)


1．Differentiation generated by mutual-inhibition circuit.
2．Cell-cell communication .
Cellcell.JPG

3. Genetic circuit

The genetic circuit in this project consisted of the new parts as well as BioBrick parts. (See more.)


Geneticcurcuit.JPG
This is the new part.JPG



The new parts of this year are here!!


4. Works

Our model has been sophisticated through successive combinations of wet and dry approaches. (See more.)

Wet assay
Hill AHL.JPGHill IPTG.JPG


Dry simulation
Using the data from wet experiments,the guideline for the design of the model was established
Defferentiation result.JPG

5. About our team

Students
Satoru Akama | Kenichiro Iwasaki | Hiroki Kawahara | Hajime Nakatani

Advisors: Last year's member
Shotaro Ayukawa | Akio Kobayashi

Instructors
[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]




Reference

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