Tokyo/Genetic circuit

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==[[Tokyo_Tech|Abstract]]　　[[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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==[[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]]==
==Genetic Circuit==
==Genetic Circuit==
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'''Fig.1''' is an outline of the genetic circuit in our model, designed to realize our Concept & Model.
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[[Image:genetic1.JPG|thumb|450px| '''Fig.1: Genetic Circuit'''<br>All cells, workers and idlers, have ''the same'' genetic circuit. Workers express RFP; while, idlers GFP.]]
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<br><br><br>'''Fig.1''' is an outline of the genetic circuit in our model, designed to realize our Concept & Model.
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All cells, workers and idlers, have '''THE SAME''' genetic circuit (just as 'society' members have practically the same genetic backgrounds).
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All cells, wokers and idlers, have '''THE SAME''' genetic circuit (just as 'society' members have practically ''the same'' genetic backgrounds).
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<br><br><br>
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[[Image:Genetic Circuit.JPG|thumb|350px| '''Fig.1: '''Genetic Circuit]]
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[[Image:genetic2.JPG|thumb|350px| '''Fig.2: Workers (State A)'''<br>A worker, an A-state cell expresses the Pa’s downstream genes including the repressor Ra, LuxI, and RFP. The Pb and its downstream genes for idlers are positively repressed. ]]
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==Workers (State-A)==
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==Workers (State A)==
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('''Fig2''')
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As shown in '''Fig. 2''',
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In the A-state cell, promoter Pa is "on", and the cell expresses repressor Ra, luxI, and RFP. Repressor Ra put the promoter Pb into "off", and prohibits to change the state.
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an A-state cell, in which the promoter Pa is "on," expresses the repressor Ra, LuxI, and RFP. The repressor Ra "turns off" the promoter Pb and inhibits the cell-state change.
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This cell also expresses luxI, which makes AHL (cell-cell communication molecule). And in the downstream of these genes, there is an RFP gene. Therefore we can detect state A cell with FACS.
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This cell also expresses LuxI, which makes AHL, cell-cell communication molecules. Downstream of these genes, there is an RFP gene; therefore, we would be able to detect A-state cell using flow cytometer.
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[[Image:A status.JPG|thumb|350px| '''Fig.2: '''Workers (State-A)]]
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<br><br><br><br>
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==Idlers (State-B)==
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==Idlers (State B)==
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('''Fig3''') In the B-state cell, with the exsistence of AHL, promoter Pb is "on". And repressor Rb and GFP are expressed. Repressor Rb inhibits the expression of promoter Pa, and GFP is used to detect state-B cells.
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<br>'''Fig. 3''' shows a B-state cell, in which promoter Pb is "turned on" in the presence of AHL, and repressor Rb and GFP are expressed. Repressor Rb represses the expression of promoter Pa and thereby RFP; therefore, fluorescence of GFP is used to detect B-state cells.
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[[Image:genetic3.JPG|thumb|350px| '''Fig.3: Idlers (State B)'''<br>In the presence of enough AHL, an idler or a B-state cell expresses the Pb’s downstream genes including the repressor Rb and GFP. The Pa and its downstream genes for workers are positively repressed. ]]
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<br><br><br><br><br><br>
==If Workers are removed...==
==If Workers are removed...==
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('''Fig 4''')If A-state cells are removed, B-state cells recognizes the absense of A-cells. That is, they respond to the decrease of AHL, not to produce repressor Rb. In this condition, repressions of Pa by Rb, and Pb by Ra are declined. This puts the toggle-like circuit into "reset".  
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As shown in '''Fig 4''', if A-state cells are removed, B-state cells sense the absence of A-state cells. Responding to the decrease of AHL, cells stop producing repressor Rb. Now that repression of Pa by Rb as well as that of Pb by Ra are declined, either state cannot be clearly expressed, as if the cells were reset.  
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<br>(鮎川)toggle-likeという言葉はうちのgenetic circuitには当てはまらないと思います。そもそもtoggle switchにAでもBでもないresetという状態はないのでは？
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<!--<br>(鮎川)toggle-likeという言葉はうちのgenetic circuitには当てはまらないと思います。そもそもtoggle switchにAでもBでもないresetという状態はないのでは？<上のようなのはどうですか？
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-->
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[[Image:B status.JPG|thumb|350px| '''Fig.3: '''Idlers (State-B)]]
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[[Image:genetic4.JPG|thumb|350px| '''Fig.4: If Workers are removed...'''<br>If workers are removed, AHL concentration decreases, which declines activation of promoter Pb. With less gene expression downstream of Pb, the B-state becomes unstable.]]
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[[Image:OnlyB.JPG|thumb|350px| '''Fig.4: '''If Workers are removed...]]
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==Hybrid promoter==
==Hybrid promoter==
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これを実装するためにPbはハイブリッドプロモータである必要がある。
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<!--これを実装するためにPbはハイブリッドプロモータである必要がある。
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⇒ハイブリッドプロモーターとは？Workのページへ[[Tokyo/Works/Hybrid promoter|Hybrid promoter]]
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⇒ハイブリッドプロモーターとは？Workのページへ[[Tokyo/Works/Hybrid promoter|hybrid promoter]]-->
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To realize such a genetic circuit, Pb should be "'''[[Tokyo/Works/Hybrid promoter|Hybrid promoter]]'''" regulated by AHL and LacI as shown in the figures.
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==Other ideas of genetic circuit==
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In addition, we thought of other ideas of genetic circuits, which perform the same function.
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The ideas are [[Tokyo/Genetic circuit/other|here]].
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==他の遺伝子回路の案==
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== ==
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コンセプトモデルを遺伝子回路にする上で、他にもいくつか方法が考えられた。
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その案を以下に示す。
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Latest revision as of 05:05, 27 October 2007


Abstract   Concept & Model   Requirements   Genetic_circuit   Works   About_our_team

Genetic Circuit

Fig.1: Genetic Circuit
All cells, workers and idlers, have the same genetic circuit. Workers express RFP; while, idlers GFP.




Fig.1 is an outline of the genetic circuit in our model, designed to realize our Concept & Model. All cells, workers and idlers, have THE SAME genetic circuit (just as 'society' members have practically the same genetic backgrounds).




Fig.2: Workers (State A)
A worker, an A-state cell expresses the Pa’s downstream genes including the repressor Ra, LuxI, and RFP. The Pb and its downstream genes for idlers are positively repressed.

Workers (State A)

As shown in Fig. 2, an A-state cell, in which the promoter Pa is "on," expresses the repressor Ra, LuxI, and RFP. The repressor Ra "turns off" the promoter Pb and inhibits the cell-state change. This cell also expresses LuxI, which makes AHL, cell-cell communication molecules. Downstream of these genes, there is an RFP gene; therefore, we would be able to detect A-state cell using flow cytometer.



Idlers (State B)


Fig. 3 shows a B-state cell, in which promoter Pb is "turned on" in the presence of AHL, and repressor Rb and GFP are expressed. Repressor Rb represses the expression of promoter Pa and thereby RFP; therefore, fluorescence of GFP is used to detect B-state cells.

Fig.3: Idlers (State B)
In the presence of enough AHL, an idler or a B-state cell expresses the Pb’s downstream genes including the repressor Rb and GFP. The Pa and its downstream genes for workers are positively repressed.







If Workers are removed...

As shown in Fig 4, if A-state cells are removed, B-state cells sense the absence of A-state cells. Responding to the decrease of AHL, cells stop producing repressor Rb. Now that repression of Pa by Rb as well as that of Pb by Ra are declined, either state cannot be clearly expressed, as if the cells were reset.

Fig.4: If Workers are removed...
If workers are removed, AHL concentration decreases, which declines activation of promoter Pb. With less gene expression downstream of Pb, the B-state becomes unstable.

Hybrid promoter

To realize such a genetic circuit, Pb should be "Hybrid promoter" regulated by AHL and LacI as shown in the figures.


Other ideas of genetic circuit

In addition, we thought of other ideas of genetic circuits, which perform the same function.

The ideas are here.

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