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Revision as of 10:03, 9 August 2005

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Scope

This group is focussing on Ideas related to Counters and Oscillators.

Motto

ASCII is an art form!

Organisation

People

People currently working on these Ideas:

• Urs A. Müller
• Jonas Nart
• Christophe Dessimoz

Please feel free to add your name.

Meetings

Friday, 5. August, 09:00 @ Christophe's bureau (CAB F61.2) Summary of the meeting
Monday, 8. August, 15:00 @ Christophe's bureau (CAB F61.2)
Tuesday, 9. August, 09:00 @ Christophe's bureau (CAB F61.2)Summary of the meeting
Wednesday, 10. August, 09:15 @ Christophe's bureau (CAB F61.2)

Modules

We try to divide all the Ideas related to our scope in some 5 or 6 Modules. Our Goal on the one hand is to define the modules in a way that allows one to design, implement and test the individual modules independently. On the other hand, we also want to ensure that it is possible to connect them to build bigger components with more functionality.

----------------       ----------- 
|              |       |    |    |
|cell division |-----> |    |    |
|              |       |    |    |
----------------       |    |    | 
                       |----|    |     ---------------------
----------------       |    |    |     |                   |      ------------
|              |       |    |    |     |                   |      |          |
|  oscillator  |-----> |    |    |---->|  divisor/counter  |----->| reporter |
|              |       |    |    |     |                   |      |          |
----------------       |    |    |     |                   |      ------------
                       |----|    |     ---------------------
----------------       |    |    |
|  triggering  |       |    |    |
|   by hand    |-----> |    |    |
|              |       |    |    |
----------------       -----------
                        Interface

cell division

oscillator

Bad news! I raed the paper about oscillatory behavior in E coli (atkinson03) and if I did get it right then they didn't completely succed to develop a stable oscillator. Their design enabled them to achieve 4 different behaviors of the circuit by changing the promoters, repressors, copy numbers and cooperativity. Due to theire simulations the circuit should have been able to act as a toggle switch, a damped oscillator and a stable oscillator (with different frequencies and peak concentrations). They succeded in establishing reproducibly a damped oscillation. But by shifting the system parameters into the region of stable oscillation the damping didn't disappear. Pushing it further could possibly help but I don't know if it's worth it and if we have enough time for this.

Furthermore they didn't include all the genes into peptides but a part also in the DNA of the E coli itself. I don't know if this would be a problem but I wanted to mention it anyway.

triggering by hand

Interface

The interface represents the link between the different triggering methods (cell division, oscillator or triggering by hand) and the divisor/counter. A possible goal could be to have only one interface accepting all three triggering methods as an input and only one output which matches the input of the divisor/counter.

divisor / counter

This module will get an input concentration from the interface module and will count, due to the changing input, to 4. Also a reporter (for example different colors) will be produced which could serve as an indicater for the state the circuit is currently occupiing.

'4 genes' counter

Idea and Implementation

During our discussion about the divisor implementation we noticed that the previous one wasn't quite stable. Talking about toggle switches we suddenly had the idea of combining the base structur of the toggle switch we learned to know during the crash course with the allready existing design. The follwing drawings show this new design which is basically a combination of two such toggle switches.

All substances which are involved should be produced and decomposed quickly
S = concentration signal from the interface
R1 is produced by gene (1) and represses gene (0) and (3)
R2 is produced by gene (2) and represses gene (0) and (1)
R3 is produced by gene (3) and represses gene (1) and (2)
R0 is produced by gene (0) and represses gene (2) and (3)

                 
                     ---S---                         
     R1             /       \              R3              R3 R0         R1 R2
      \             |       |             /                 | |           | |
       \/|____      |       |      ____|\/          /|___   | |           | |  ____|\ 
    ___/  (1) |_____v__   __v_____| (3)  \___   ___/  (2) |_=_=____   ____=_=_|(0=4) \___
       \  ____| = =           = = |____  /         \  ____|     =       =     |____  /
        \|      | |           | |      |/          /\|          |       |          |/\
                | |           | |                 /             |       |             \
               R2 R3         R0 R1               R2             \       /              R0
                                                                 ---S---

The following time lines should be the result of this gene circuit:
S:
    -----       -----       -----       -----          Let's assume that the counter is in state 0 
   |     |     |     |     |     |     |     |         (expressing R0). As soon as the concentration
   |     |     |     |     |     |     |     |         of S goes up (0) and (2) are repressed
---       -----       -----       -----       ----     (no further expressing of R0). Now R1 can be
R1:                                                    expressed while (3) is still repressed 
     ----                    ----                      by R0. The production of R1 ensures that (3) 
    /    \                  /    \                     won'tbe active when R0 is totally decomposed.
   /      \                /      \                    -> We are in state (1).
---        ----------------        ---------------     When the S goes down again R1 can't be
R2:                                                    expressed anymore. Now R2 can be 
           ----                    ----                expressed while (0) is still repressed by R1. 
          /    \                  /    \               The production of R2 ensures that (0) won't 
         /      \                /      \              be active when R1 is totally decomposed.
---------        ----------------        ---------     -> We are in state (2)
R3:                                                    And so on...
                 ----                    ----
                /    \                  /    \
               /      \                /      \
---------------        ----------------        ---
R0:
---                    ----                    ---
   \                  /    \                  /
    \                /      \                /
     ----------------        ----------------

Challanges

• The combination of promoters, repressing and activating substances will be quite a challange. They should change the state rather quick. Therefore most of the substances have to be expressed and decomposed quickly. But on the other hand the repression at certain points should stay long enough to ensure that there is only one state the system can fall in.
• I think the repression by the input signal S will affect the expression of R2 and R0 quickly. But will the decreasing concentration of S have the same affect on R1 and R3 in comparable time? Or is a second input needed with the reverse effect of S?

reporter

This will probably be one or more colors to indicate the current state of the counter.

Discussions

We invite anyone to make comments and participate in discussions here

Attic

Have a look at Oscillator_based_Attic for old toggle stuff.

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