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'''<br>All cells, wokers and idlers, have ''the same'' genetic circuit. Workers expresses RFP; while, idlers GFP.]]
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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. ]]
==Workers (State A)==
==Workers (State A)==
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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.
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.
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)'''<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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<br><br><br><br>
==Idlers (State B)==
==Idlers (State B)==
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'''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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<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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As shown in '''Fig 4''', if A-state cells are removed, B-state cells sense the absense of A-cells.  Responding to the decrease of AHL, cells stop producing repressor Rb. Now that repressions of Pa by Rb as well as that of Pb by Ra are declined, either states cannot be clearly expressed, as if the cells were 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.  
<!--<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？
<!--<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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[[Image:B status.JPG|thumb|350px| '''Fig.3: Idlers (State B)'''<br>In the presence of enough AHL, an idler, 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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[[Image:OnlyB.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: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.]]
==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.
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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<!--==他の遺伝子回路の案==
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==Other ideas of genetic circuit==
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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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In addition, we thought of other ideas of genetic circuits, which perform the same function.
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その案を以下に示す。-->
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==== cf. Other suggestions on the genetic circuit on the A side====
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The ideas are [[Tokyo/Genetic circuit/other|here]].
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As to genetic circuits to realize our Concept & Model, there were some other suggestions as fololows:
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== ==
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'''Suggestion 1.'''
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<br>[[Image:suggestion1.jpg|'''Fig. 1 Suggestion 1''']]
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<br>Merit:
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<br>The repressor R1 can be inserted after constructing the other part.
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<br>'''Suggestion 2.'''
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<br>[[Image:suggestion2.jpg|'''Fig. 2 Suggestion 2''']]
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<br>Merit:
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<br>A ribosome binding site here is easily exchangeable; therefore, the expression level can be modulated without changing the promoter and regulators.
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<br>'''Suggestion 3.'''
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<br>[[Image:suggestion3.jpg|'''Fig. 3 Suggestion 3''']]
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<br>Merit:
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<br>Promoters can be easily exchanged, and the expression level can be modulated at promoter level.
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<br>'''Suggestion 4.'''
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<br>[[Image:suggestion4.jpg|'''Fig. 4 Suggestion 4''']]
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<br>Merit:
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<br>The precursor of this part was constructed for the functional check of BioBrick parts and available; <br>therefore, this construction can be done in much shorter time.
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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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