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Team:UNIPV-Pavia/Project
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|To mimic an OR gate in Mux, we need a biological function which can be activated (or repressed) alternatively by two distinct upstream signals or by both. Thus, we combine the outputs of the upstream AND gates to assemble directly an OR reporter function, by simply repeating the reporter gene (GFP) under two different promoters (Plux and Plas). It’s sufficient to activate one of the two promoters (or both) to recover the GFP signal from engineered bacteria. | |To mimic an OR gate in Mux, we need a biological function which can be activated (or repressed) alternatively by two distinct upstream signals or by both. Thus, we combine the outputs of the upstream AND gates to assemble directly an OR reporter function, by simply repeating the reporter gene (GFP) under two different promoters (Plux and Plas). It’s sufficient to activate one of the two promoters (or both) to recover the GFP signal from engineered bacteria. | ||
There should not be an over-expression problem for GFP, in fact, in Mux device, only one of Plux or Plas promoters can be active. | There should not be an over-expression problem for GFP, in fact, in Mux device, only one of Plux or Plas promoters can be active. | ||
| - | |[[Image: | + | |[[Image:pv_proj_OR.png|thumb|340px|left|Genetic OR]] |
|} | |} | ||
| - | <br><br> | + | <br><br><br><br><br><br><br> |
=== NOT === | === NOT === | ||
| - | + | {|align="left" | |
| + | |To mimic a NOT gate, we need an efficient and regulated repressor of a specific downstream promoter: in this case, we choose cI repression on Pl, which should be specific and, upon cI activation, quick and efficient. | ||
| + | |[[Image:pv_proj_NOT.png|thumb|340px|left|Genetic NOT]] | ||
| + | |} | ||
== The Experiments == | == The Experiments == | ||
== Results == | == Results == | ||
Revision as of 12:52, 24 June 2008
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Contents |
Overall project
We are trying to mimic Multiplexer (Mux) and Demultiplexer (Demux) logic functions in E. coli.
In the following paragraphs project details will be described from both digital electronic and genetic points of view.
Electronic Implementation
What kind of components are Mux and Demux?
Mux is a component which conveys one of the two input channels values into a single output channel. The choice of the input channel is made by a selector.
Demux is a component which conveys the only input channel value into one of the two output channels. The choice of the output channel is made by a selector.
The following pictures show data flow in Mux and Demux:
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What kind of signals do we process?
In this project we consider Boolean logic signals, thus every input/output value can assume only the values: 0 and 1. A function that processes Boolean values is called logic function.
Mux and Demux can be considered by now as black boxes which implement a logic function that can process input signals to output signals. Here you can see examples of Boolean data flow in Mux and Demux:
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In the following documentation we will see what is inside this black boxes.
How can we formalize Mux and Demux logic behavior?
Logic functions can be formalized writing a truth table; a truth table is a mathematical table in which every row represents a combination of input values and its respective output values. The table has to be filled with every input combination.
Here you can see Mux and Demux truth tables (output columns are gray):
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Building a logic circuit from a truth table
Our goal in this section is to project two logic gates networks which behave like Mux and Demux truth tables. A very useful tool to transform a truth table into a logic network is Karnaugh map.
It is possible to read about Karnaugh maps at: [1]
Following Karnaugh maps method, we can write these two logic networks for Mux and Demux:
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Genetic Implementation
Our goal is to mimic Mux and Demux logic networks into a biological device, such as E. coli. To perform this, we use protein/DNA and protein/protein interactions to build up biological logic gates.
Mux and Demux logic circuits are composed by three fundamental logic gates, AND, OR, NOT: in the next paragraphs genetic implementation of these logic gates will be provided.
AND
| To mimic an AND gate, we need a biological function, such as a promoter activation, which is directly turned on by the interaction between two upstream genes. In this view, we use the luxR/luxI system: luxR can activate Plux promoter only upon 3-oxo-hexanoyl-homoserine lactone (HSL) binding; luxI generates HSL; so, only the contemporary expression of LuxR and luxI proteins can activate the downstream Plux-dependent gene expression. Another AND gate we use is the lasR/lasI system, which works in a very similar way but through another chemical intermediate, N-(3-oxododecanoyl) homoserine lactone (PAI-1). |  |
OR
| To mimic an OR gate in Mux, we need a biological function which can be activated (or repressed) alternatively by two distinct upstream signals or by both. Thus, we combine the outputs of the upstream AND gates to assemble directly an OR reporter function, by simply repeating the reporter gene (GFP) under two different promoters (Plux and Plas). It’s sufficient to activate one of the two promoters (or both) to recover the GFP signal from engineered bacteria.
There should not be an over-expression problem for GFP, in fact, in Mux device, only one of Plux or Plas promoters can be active. |  |
NOT
| To mimic a NOT gate, we need an efficient and regulated repressor of a specific downstream promoter: in this case, we choose cI repression on Pl, which should be specific and, upon cI activation, quick and efficient. |  |
