Event Processing Device
From 2006.igem.org
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^ | ^ | ||
¦ | ¦ | ||
| - | high ¦ | + | high ¦ PoPS_out2 _______ _________ PoPS_out1 |
¦ \ / | ¦ \ / | ||
¦ \ / | ¦ \ / | ||
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¦ / \ | ¦ / \ | ||
¦ / \ | ¦ / \ | ||
| - | low ¦ | + | low ¦ PoPS_out1 _______/ \_________ PoPS_out2 |
¦--------------------------------------------------> PoPS_in, t | ¦--------------------------------------------------> PoPS_in, t | ||
| - | 0 1 | + | 0 1 |
| - | + | ||
==Input-module Schematic== | ==Input-module Schematic== | ||
Revision as of 13:27, 19 August 2005
Contents |
Organisational
Group Members
- Christophe, Dominic (coordinator), Giorgia, Herve, Kristian, Zlatko
Group Meeting History
log 2005-08-17: Wednesday, ~13:00 @ polyterasse: Discussion of module, next steps, task distrib.
Input-module Development
Module Description
In a nutshell, this module has 2 system boundaries, both of which are characterized by PoPS. Its purpose is to take a single input PoPS and output 2 different PoPS. One of the outputs should be high and the other low when S is high and vice versa when S is low.
PoPS_outn
^
¦
high ¦ PoPS_out2 _______ _________ PoPS_out1
¦ \ /
¦ \ /
¦ \ /
¦ \ /
¦ \ /
¦ X
¦ / \
¦ / \
¦ / \
¦ / \
low ¦ PoPS_out1 _______/ \_________ PoPS_out2
¦--------------------------------------------------> PoPS_in, t
0 1
Input-module Schematic
Below a preliminary parts-view of the module, i.e. encapsulation of biological specific implementations into a functional box with general PoPS interfaces.
-----------------------
¦ ¦
¦ ,--- a ---. ¦
¦ / ¦ ¦
-------- ¦------- act V ¦
¦ ¦ ¦¦ ¦ -- P_a -- PoPS_out1 --> to R_1,R_3
I -> ¦ P_in ¦-- PoPS_in -->¦¦ Reg ¦ ¦
¦ ¦ ¦¦ ¦ -- P_r -- PoPS_out2 --> to R_2,R_4
-------- ¦------- rep --- ¦
¦ \ ¦ ¦
¦ `--- r ---' ¦
¦ ¦
----------------------¦
legend: I: input signal that will bind to the promotor P_in, e.g. heat shock dependent etc. P_in: promotor that allows the signal of choice I to bind. PoPS_in: polymerase per second dependent on promotor and concentration of I Reg: regulation genes. there are different solutions possible, see below. r: repressing signal. highly dependent on Reg, P_r and of course speed and binding considerations a: activating signal. highly dependent on Reg, P_a and of course speed and binding considerations rep: repression, indicated by horizontal bar act: activation, indicated by arrow P_r: promotor region to be repressed and/or "roadblock" region. constitutively active P_a: promotor region to be activated and/or "roadblock" region. not constitutively active PoPS_out1: polymerase per second dependent on P_r and r. PoPS_out2: polymerase per second dependent on P_a and a. R_n: toggle switch gene(s)
Possible Implementations
Check the following page for lists of transcriptional regulators in E.Coli: [http://www.weizmann.ac.il/mcb/UriAlon/Network_motifs_in_coli/ColiNet-1.1/regInterFullFiltered.html] [http://biocyc.org/ECOLI/new-image?object=BC-3.1.2.3]
Two Regulators (a,r)
In the strategies below, the input PoPS regulates two proteins, an activator and a repressor. That has the advantage of being very simple, but requires that both proteins have roughly similar production and degradation speed.
"Basic" (Giorgia)
Antisense (Giorgia)
One Regulator (ar)
In the implementations below, the input PoPs regulate the production of a sole protein that somehow acts as activator and repressor. With only one regulator, production and degradation are perfectly uniform, which is good, but in some cases, it might be harder to obtain a symmetrical activity, which is bad.
AraC (Giorgia)
"Lunatic Activator" (Christophe)
The "Lunatic Activator" is an activator because it is required for the transcription of gene 1 and 3, but is lunatic because it can also acts as a roadblock on genes 2 and 4. Send me an email if you know such protein.
Zinc Finger YY1 (Hervé)
Secondary Metabolism (Christophe)
The idea here would be to use an existing regulator that both activates and represses genes required in the secondary metabolism (e.g. Amino-acid production). To minimize interference with E.Coli, it would be wise to try a system from a very different bacteria (e.g. B. Subtilis).
