From 2007.igem.org

(Difference between revisions)

Revision as of 18:01, 22 October 2007

1,Abstruct

2,Works

Approach

Combination of Wet & Dry trials

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

2.Wet : 　Assay

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

|

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.

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

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
alternativeこんな表紙はいかが？
alternative2

2,Works

2-0.Wet : Hybrid promoter

2-1.Dry : Formulation

2-2.Wet : Assay

2-3.Dry : Simulation

2-4.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。

2-5.Future works

2,Works

2-0.Wet : Hybrid promoter

2-1.Dry : Formulation

2-2.Wet : Assay

2-3.Dry : Simulation

2-4.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。

2-5.Future works

3,About our team

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

Advisors: Last year's member
Syotarou 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

@@ Line 1: / Line 1: @@
-砂場2
 <!--[[Image:homepage1.JPG]]-->
 [[Image:tokyotech3.JPG|700px]]
 __NOTOC__
-<h1> ''' 1,[[Tokyo/Project |Project]]''' </h1>
 {| cellspacing="5"
-|width="550px" valign="top" |
-===[[Tokyo/Concept |Concept & Model]]===
-====We made bacterial society that follows Pareto's principle,for example ,[[Tokyo/Ant society|Ant society]]====
+|width="550px" valign="top" |
-<br>[[Image:TOP.JPG|350px]]
+<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]]
 ===[[Tokyo/Requirements |Requirements]]===
-====Our requirements for construction this model are two things,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]]-->
 ===[[Tokyo/Genetic circuit|Genetic circuit]]===
-====We constructed the genetic circuit to fill its requirements. Therefore we made [[Tokyo/new parts |new parts]] ====
+====We designed the genetic circuit to satisfy its requirements and developed necessary [[Tokyo/new parts |new parts]]. ====
-<br>[[Image:Tokyo_genetic circuit_s.jpg|350px]]
+<br>[[Image:Tokyo_genetic circuit_s.jpg|100px]]
-====　　　　　　　　　　　　　　　Our construction parts are [[Tokyo/construction|Here]]!!! ====
+====　　　　　　　　　　　　　　　Our constructed parts are [[Tokyo/construction|Here]]!!! ====
 ===[[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.====
 <br>[[Image:Tokyo_simulation_s2.jpg|350px]]
+<br>[[Image:our goal.JPG|350px]]
 |width="400px" valign="top" |
-|width="400px" valign="top" |
+<h1>'''2,Works'''</h1>
-|width="400px" valign="top" |
+<!--<h1> ''' [[Tokyo/Experiments |Experiments]]''' </h1>-->
-====We indicated [[Tokyo/simulation|our goal]] of the project by the simulation!! The simulation proved that our genetic circuit have existence of solution.====
+<!--[[Image:homepage4.jpg]]-->
+===[[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]]===
+{| cellspacing="5"
+|width="350px" valign="top" |
+====We need to develop the promoter that can receive two input, AHL & reperssor. We tried to create and [[Tokyo/Hybrid promoter|succeeded]]!! ====
+<!--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
+<br>図　概念図、配列とグラフ図
+-->
+|width="150px" valign="top" |
+[[Image:Hybridgraph.JPG|200px|]]
+|}
+===1.<span style="color:#0066ff;">Dry </span>:　 [[Tokyo/Formulation |Formulation]]===
+We wrote the 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]]===
+====We decided the parameter of hill coefficients by the assay of AHL & IPTG====
+ <!--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]]===
+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.
+ <!--最終日に動画と差し替え？？-->
+<br>
 <br>[[Image:Tokyo_simulation_s2.jpg|350px]]
+===4.<span style="color:#ff33cc;">Wet </span>: 　[[Tokyo/Assay |Assay]]===
+ <!--====We determined the feasibility test of this ====-->
+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>
+. 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.
+<br>
+. 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.
+<!--
+<h1> '''3,[[Tokyo/Achievements |Achievements ]]'''</h1>
+<br>[[Tokyo/Hybrid promoter |Hybrid promoter ]]
+<br>[[Tokyo/Bistability analisis|Bistability analysis]]
+<br>[[Tokyo/Others |Others ]]
+-->
+<h1> '''3,[[Tokyo/About our team |About our team ]][[Image:TeamLogo.jpg]]'''</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 ]]
+<br>[[Tokyo/alternative|alternative]]こんな表紙はいかが？
+<br>[[Tokyo/alternative2|alternative2]]
 <h1>'''2,[[Tokyo/Works |Works]]'''</h1>
 <!--<h1> ''' [[Tokyo/Experiments |Experiments]]''' </h1>-->

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Tokyo/sunaba2

From 2007.igem.org

Revision as of 18:01, 22 October 2007

1,Abstruct

Concept & Model

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

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.

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.

2,Works

Approach

Combination of Wet & Dry trials

0.Wet : Hybrid promoter

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

1.Dry : Formulation

2.Wet : Assay

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

3.Dry : Simulation

4.Wet : Assay

5.Future works

3,About our team

2,Works

2-0.Wet : Hybrid promoter

2-1.Dry : Formulation

2-2.Wet : Assay

2-3.Dry : Simulation

2-4.Wet : Assay

2-5.Future works

2,Works

2-0.Wet : Hybrid promoter

2-1.Dry : Formulation

2-2.Wet : Assay

2-3.Dry : Simulation

2-4.Wet : Assay

2-5.Future works

3,About our team

　　　　　　　　　　　　　　　Our constructed parts are Here!!!

0.Wet :　Hybrid promoter

1.Dry :　 Formulation

2.Wet : 　Assay

3.Dry : 　Simulation

4.Wet : 　Assay