Team:HKUSTers/Initial Proposal/Memorizer

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==Bi-stable Switch==
 +
Yeast Two Hybrid is a well-known system that have been developed for many years. However, similar scenario also exists in E.coli, there have already been multiple two hybrid systems in E.coli. So we can adapt two hybrid system into our design to generate a bi-stable switch. The scheme is as followed.
[[Image:Two-Hybrid.png]]
[[Image:Two-Hybrid.png]]
 +
 +
*Advantages:
 +
#first adopt two hybrid system to build up bistable switch,
 +
#AD and BD can have synergistic effect, a natural AND gate
 +
#AD and BD form reporting system directly, which reduces intermediate steps.
 +
 +
*Disadvantages: Promoter and AD/BD needs to be constructed or designed.
 +
#If two hybrid alone can’t perform bistable switch, we may need to find two pairs of repressor and inducer to construct bistable switch, in that case, to have self synthesized inducer is really a problem, since it seems that AHL can be self-produced, but it will also diffuse out, which is undesirable in our model.
 +
#For the AD-BD detailed design, I am still searching for past papers, I will come up with concrete molecules before June 30th.
 +
 +
==Reporter System==
 +
XOR gate is a digital logic gate. The X in the XOR gate stands for "exclusive."  This means that the output from this gate will be a 1 ONLY when one or the other of the inputs is a 1. In other words, this is an either-or gate.
 +
 +
Since AD and BD functions by nature as an AND gate, which means they activate promoter only two both exist. Looking back at the bistable switch, we can observe that, when a new AD comes, for example AD1 comes, if BD2 originally exists in the cell, there will be no effect, and AD1 and BD2 can coexist, but if BD1 originally exists, there will be a switch, cell will switch from BD1 to BD2, and vice versa for a symmetric system.
 +
 +
So BD2 (BD1) works as memory molecule of AD1 (AD2), and if AD1 induces BD1 to switch to BD2 and stabilize the state, then it also induces BD1 at the reporting XOR gate circuits, which turns on the promoter, since BD1 will not sustain, so a self-induction (positive feedback) is needed to stabilize reporter gene. By the same analogy, the bistable switch needs also be on without AD-BD activation
 +
 +
[[Image:Memorizer.png]]
 +
 +
 +
*Advantages
 +
AD-BD are naturally exist AND gate components, and two AD-BD pairs can form an OR gate and no interference would happen.
 +
 +
*Additional attention
 +
AD-BD self-activator needs to be unique to BD1 BD2 binding, thus won’t interfere with Bistable switch.

Latest revision as of 04:39, 30 October 2008

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Bi-stable Switch

Yeast Two Hybrid is a well-known system that have been developed for many years. However, similar scenario also exists in E.coli, there have already been multiple two hybrid systems in E.coli. So we can adapt two hybrid system into our design to generate a bi-stable switch. The scheme is as followed. Two-Hybrid.png

  • Advantages:
  1. first adopt two hybrid system to build up bistable switch,
  2. AD and BD can have synergistic effect, a natural AND gate
  3. AD and BD form reporting system directly, which reduces intermediate steps.
  • Disadvantages: Promoter and AD/BD needs to be constructed or designed.
  1. If two hybrid alone can’t perform bistable switch, we may need to find two pairs of repressor and inducer to construct bistable switch, in that case, to have self synthesized inducer is really a problem, since it seems that AHL can be self-produced, but it will also diffuse out, which is undesirable in our model.
  2. For the AD-BD detailed design, I am still searching for past papers, I will come up with concrete molecules before June 30th.

Reporter System

XOR gate is a digital logic gate. The X in the XOR gate stands for "exclusive." This means that the output from this gate will be a 1 ONLY when one or the other of the inputs is a 1. In other words, this is an either-or gate.

Since AD and BD functions by nature as an AND gate, which means they activate promoter only two both exist. Looking back at the bistable switch, we can observe that, when a new AD comes, for example AD1 comes, if BD2 originally exists in the cell, there will be no effect, and AD1 and BD2 can coexist, but if BD1 originally exists, there will be a switch, cell will switch from BD1 to BD2, and vice versa for a symmetric system.

So BD2 (BD1) works as memory molecule of AD1 (AD2), and if AD1 induces BD1 to switch to BD2 and stabilize the state, then it also induces BD1 at the reporting XOR gate circuits, which turns on the promoter, since BD1 will not sustain, so a self-induction (positive feedback) is needed to stabilize reporter gene. By the same analogy, the bistable switch needs also be on without AD-BD activation

Memorizer.png


  • Advantages

AD-BD are naturally exist AND gate components, and two AD-BD pairs can form an OR gate and no interference would happen.

  • Additional attention

AD-BD self-activator needs to be unique to BD1 BD2 binding, thus won’t interfere with Bistable switch.

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