Talk:Tokyo Tech

From 2007.igem.org

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<br>
<br>
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<!--[[Image:homepage1.JPG]]-->
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[[Image:tokyotech3.JPG|700px]]
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[[Image:Title.JPG|700px]]
__NOTOC__
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{| cellspacing="5"
{| cellspacing="5"
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<h1> ''' 1. [[Tokyo/Project |Abstruct]]''' </h1>
<h1> ''' 1. [[Tokyo/Project |Abstruct]]''' </h1>
===[[Tokyo/Model|Concept & Model]]===
===[[Tokyo/Model|Concept & Model]]===
-
We made a bacterial society that follows Pareto's principle as an [[Tokyo/Concept|Ant society]] does.
+
A bacterial society designed in this project follows Pareto's principle as an [[Tokyo/Concept|Ant society]] does.
 +
<br>
 +
To realize this model, the behaviors of the model '''- bistability of each individual and the system's stability under the coexsistence of the two types - '''have been confirmed ''in silico'' and ''in virto''.
 +
<br>[[Image:Tokyo_simulation_s2.jpg|350px]]
 +
<br>[[Image:our goal.JPG|350px]]
 +
 
 +
===[[Tokyo/Requirements |Requirements]]===
 +
Bistability
 +
<br>Coexistence by cell-cell communication.
 +
<!--<br>[[Image:Bistability.JPG|200px]][[Image:Coexistence.JPG|250px]]-->
 +
 
 +
 
 +
|width="400px" valign="top" |
 +
 
 +
<h1>'''2. [[Tokyo/Works |Works]]'''</h1>
 +
<!--<h1> ''' [[Tokyo/Experiments |Experiments]]''' </h1>-->
 +
<!--[[Image:homepage4.jpg]]-->
 +
 
 +
===2-a. [[Tokyo/Genetic circuit|Genetic circuits]] ===
 +
 
 +
===2-b. [[Tokyo/Approach |Combinational Wet & Dry Approaches]]===
 +
 
 +
===0. <span style="color:#ff33cc;">Wet </span>:　[[Tokyo/Hybrid promoter|Hybrid promoter]]===
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{| cellspacing="5"
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|width="350px" valign="top" |
 +
 
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[[Tokyo/Hybrid promoter|The newly deviced hybrid promoter regulated by two inputs.]]
 +
<!--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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|}
 +
 
 +
===1. <span style="color:#0066ff;">Dry </span>:　 [[Tokyo/Formulation |Formulation]]===
 +
<!--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
 +
<br>図　3つの式
 +
-->
 +
 
 +
===2. <span style="color:#ff33cc;">Wet </span>: 　[[Tokyo/Assay |Assay]]===
 +
 
 +
For the parameters of Hill coefficients by AHL and IPTG assays
 +
<!--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。
 +
<br>図大腸菌の絵、FLAの絵、フィッティングのグラフ
 +
-->
 +
[[Image:hill AHL.JPG|190px]]|[[Image:hill IPTG.JPG|190px]]
 +
 
 +
===3. <span style="color:#0066ff;">Dry </span>: 　[[Tokyo/Simulation |Simulation]]===
 +
 
 +
===4. <span style="color:#ff33cc;">Wet </span>: 　[[Tokyo/Assay |Assay]]===
 +
We tested whether our plasmids gave the other parameters to satisfy the simulation by the experiments using ''E. coli''.
 +
 
 +
===5. Future works===
 +
 
 +
Continue this combinational approaches to sophisticate our model.
 +
[[See more.]]
 +
 
 +
 
 +
<!--
 +
<h1> '''3,[[Tokyo/Achievements |Achievements ]]'''</h1>
 +
 
 +
<br>[[Tokyo/Hybrid promoter |Hybrid promoter ]]
 +
<br>[[Tokyo/Bistability analisis|Bistability analysis]]
 +
<br>[[Tokyo/Others |Others ]]
 +
-->
 +
 
 +
<h1> '''3. About our team'''</h1>
 +
<!--[[Image:team photo.jpg]] -->
 +
'''Students'''
 +
<br>[[Tokyo/Satoru Akama |Satoru Akama ]] | [[Tokyo/Kenichiro Iwasaki |Kenichiro Iwasaki]] | [[Tokyo/Hiroki Kawahara |Hiroki Kawahara ]] | [[Tokyo/Hajime Nakatani|Hajime Nakatani]]
 +
 
 +
'''Advisors: Last year's member '''
 +
<br>[[Tokyo/Shotaro Ayukawa |Shotaro Ayukawa ]] | [[Tokyo/Akio Kobayashi|Akio Kobayashi ]]
 +
 
 +
'''Instructors'''
 +
<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]
 +
 
 +
'''Links'''
 +
[[Tokyo/sunaba |sunaba ]]
 +
 
 +
----
 +
----
 +
<!--[[Image:homepage1.JPG]]-->
 +
[[Image:tokyotech3.JPG|700px]]
 +
__NOTOC__
 +
{| cellspacing="5"
 +
 
 +
 
 +
 
 +
|width="550px" valign="top" |
 +
<h1> ''' 1,Abstruct''' </h1>
 +
===[[Tokyo/Model|Concept & Model]]===
 +
====We made a bacterial society that follows Pareto's principle as an [[Tokyo/Concept|Ant society]] does.====
<br>[[Image:TOP.JPG|250px]]
<br>[[Image:TOP.JPG|250px]]
===[[Tokyo/Requirements |Requirements]]===
===[[Tokyo/Requirements |Requirements]]===
-
====Bistability and coexistence by cell-cell communication.====
+
====Our requirements to construct this model are two things, bistability and coexistence by cell-cell communication.====
  <!--<br>[[Image:Bistability.JPG|200px]][[Image:Coexistence.JPG|250px]]-->
  <!--<br>[[Image:Bistability.JPG|200px]][[Image:Coexistence.JPG|250px]]-->
-
===[[Tokyo/Genetic circuit|Genetic circuit]] [[Image:Tokyo_genetic circuit_s.jpg|100px]]===
+
===[[Tokyo/Genetic circuit|Genetic circuit]]===
 +
====We designed the genetic circuit to satisfy its requirements and developed necessary [[Tokyo/new parts |new parts]]. ====
 +
<br>[[Image:Tokyo_genetic circuit_s.jpg|100px]]
-
[[Tokyo/Genetic circuit|Genetic circuit construction]]
+
====　　　　　　　　　　　　　　　Our constructed parts are [[Tokyo/construction|Here]]!!! ====
-
<br>[[Tokyo/new parts |new parts]]
+
-
===[[Tokyo/simulation|GOAL]]===
+
===[[Tokyo/simulation|Our GOAL]]===
-
We indicated [[Tokyo/simulation|our goal]] of the project by the simulation!! The simulation proved that our genetic circuit have existence of solution.
+
====We indicated [[Tokyo/simulation|our goal]] of the project by the simulation!! The simulation proved that our genetic circuit have existence of solution.====
<br>[[Image:Tokyo_simulation_s2.jpg|350px]]
<br>[[Image:Tokyo_simulation_s2.jpg|350px]]
<br>[[Image:our goal.JPG|350px]]
<br>[[Image:our goal.JPG|350px]]
|width="400px" valign="top" |
|width="400px" valign="top" |
-
<h1>'''2. [[Tokyo/Works |Works]]'''</h1>
+
<h1>'''2,Works'''</h1>
<!--<h1> ''' [[Tokyo/Experiments |Experiments]]''' </h1>-->
<!--<h1> ''' [[Tokyo/Experiments |Experiments]]''' </h1>-->
<!--[[Image:homepage4.jpg]]-->
<!--[[Image:homepage4.jpg]]-->
-
===[[Tokyo/Approach |Combinational Wet & Dry Approaches]]===
+
===[[Tokyo/Approach |Approach]]===
 +
====Combination of Wet & Dry trials====
 +
We have alternated/combined Wet and Dry experiments to achieve our goal
===0.<span style="color:#ff33cc;">Wet </span>:　[[Tokyo/Hybrid promoter|Hybrid promoter]]===
===0.<span style="color:#ff33cc;">Wet </span>:　[[Tokyo/Hybrid promoter|Hybrid promoter]]===
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'''Links'''
'''Links'''
[[Tokyo/sunaba |sunaba ]]
[[Tokyo/sunaba |sunaba ]]
 +
<br>[[Tokyo/sunaba2 |sunaba2 ]]4分割表紙バージョン
 +
<br>[[Tokyo/alternative|alternative]]こんな表紙はいかが？
 +
<br>[[Tokyo/alternative2|alternative2]]

Latest revision as of 14:40, 23 October 2007

how about arranging this page like this? --Hiroki 22:33, 16 October 2007 (EDT)

Homepage design.jpg


Previous homepage design--Hiroki 12:25, 17 October 2007 (EDT) Tokyo alliance header.JPG


Project

Concept

Works

Parts

Wet

Dry


Information

Team

Members

Advisors

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]

Links

Cycle.jpg


Title.JPG

1. Abstruct

Concept & Model

A bacterial society designed in this project follows Pareto's principle as an Ant society does.
To realize this model, the behaviors of the model - bistability of each individual and the system's stability under the coexsistence of the two types - have been confirmed in silico and in virto.
Tokyo simulation s2.jpg
Our goal.JPG

Requirements

Bistability
Coexistence by cell-cell communication.


2. Works

2-a. Genetic circuits

2-b. Combinational Wet & Dry Approaches

0. Wet :　Hybrid promoter

The newly deviced hybrid promoter regulated by two inputs.

Hybridgraph.JPG

1. Dry :　 Formulation

2. Wet : 　Assay

For the parameters of Hill coefficients by AHL and IPTG assays Hill AHL.JPG|Hill IPTG.JPG

3. Dry : 　Simulation

4. Wet : 　Assay

We tested whether our plasmids gave the other parameters to satisfy the simulation by the experiments using E. coli.

5. Future works

Continue this combinational approaches to sophisticate our model. See more.


3. 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]

Links sunaba

Tokyotech3.JPG

1,Abstruct

Concept & Model

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


TOP.JPG

Requirements

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

Genetic circuit

We designed the genetic circuit to satisfy its requirements and developed necessary new parts.


Tokyo genetic circuit s.jpg

　　　　　　　　　　　　　　　Our constructed parts are Here!!!

Our GOAL

We indicated our goal of the project by the simulation!! The simulation proved that our genetic circuit have existence of solution.


Tokyo simulation s2.jpg
Our goal.JPG

2,Works

Approach

Combination of Wet & Dry trials

We have alternated/combined Wet and Dry experiments to achieve our goal

0.Wet :　Hybrid promoter

We need to develop the promoter that can receive two input, AHL & reperssor. We tried to create and succeeded!!

Hybridgraph.JPG

1.Dry :　 Formulation

We wrote the Formulation

2.Wet : 　Assay

We decided the parameter of hill coefficients by the assay of AHL & IPTG

Hill AHL.JPG|Hill IPTG.JPG

3.Dry : 　Simulation

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。 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.

Tokyo simulation s2.jpg

4.Wet : 　Assay

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。
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.
2. We tested whether our plasmids gave the other parameters to satisfy the simulation by the experiments using E. coli.

5.Future works

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. Continueing these processes, if time permits, would further sophisticate our model.


3,About our team TeamLogo.jpg


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]

Links sunaba
sunaba2 4分割表紙バージョン
alternativeこんな表紙はいかが？
alternative2

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