Oscillator based
From 2006.igem.org
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)
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Contents |
Scope
This group is focussing on Ideas related to Counters and Oscillators.
People
People currently working on these Ideas:
Please feel free to add your name.
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.
Module Tree
---------------- -----------
| | | | |
|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 socillator. 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
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
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:
--- ---- ---
\ / \ /
\ / \ /
---------------- ----------------
toggle switch
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
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