Team:DTU-Denmark/Project

From 2010.igem.org

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<li><a href="http://2010.igem.org/Team:DTU-Denmark/Background">Background</a></li><br>
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<li><a href="http://2010.igem.org/Team:DTU-Denmark/Background">Synthetic Biology</a></li><br>
<li><a href="http://2010.igem.org/Team:DTU-Denmark/Regulatory_sytems">Regulatory Systems</a></li>
<li><a href="http://2010.igem.org/Team:DTU-Denmark/Regulatory_sytems">Regulatory Systems</a></li>
<ul><font size="2">
<ul><font size="2">
<li><a href="http://2010.igem.org/Team:DTU-Denmark/Regulatory_sytems#lambda">Lambda Phage</a></li>
<li><a href="http://2010.igem.org/Team:DTU-Denmark/Regulatory_sytems#lambda">Lambda Phage</a></li>
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<li><a href="http://2010.igem.org/Team:DTU-Denmark/Regulatory_sytems#gifsy">Gifsy Phage</a></li>
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<li><a href="http://2010.igem.org/Team:DTU-Denmark/Regulatory_sytems#gifsy">Gifsy Phages</a></li>
</font></ul>
</font></ul>
<br>
<br>
<li><a href="http://2010.igem.org/Team:DTU-Denmark/Switch">The Switch</a></li>
<li><a href="http://2010.igem.org/Team:DTU-Denmark/Switch">The Switch</a></li>
<ul><font size="2">
<ul><font size="2">
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<li><a href="http://2010.igem.org/Team:DTU-Denmark/Switch#Biological_Switch">What is a biological switch?</a></li>
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<li><a href="http://2010.igem.org/Team:DTU-Denmark/Switch#Biological_Switch">Biological Switches</a></li>
 +
<li><a href="http://2010.igem.org/Team:DTU-Denmark/Switch#Bistable_Switches">Bistable Switches</a></li>
<li><a href="http://2010.igem.org/Team:DTU-Denmark/Switch#Design">Design of our Bi[o]stable Switch</a></li>
<li><a href="http://2010.igem.org/Team:DTU-Denmark/Switch#Design">Design of our Bi[o]stable Switch</a></li>
<li><a href="http://2010.igem.org/Team:DTU-Denmark/Switch#Engineering">Step-wise Engineering of the Switch</a></li>
<li><a href="http://2010.igem.org/Team:DTU-Denmark/Switch#Engineering">Step-wise Engineering of the Switch</a></li>
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<li><a href="http://2010.igem.org/Team:DTU-Denmark/Switch#Applications_of_our_Bi[o]stable_switch">Applications of our Bi[o]stable switch</a></li>
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<li><a href="http://2010.igem.org/Team:DTU-Denmark/Switch#Applications">Applications</a></li>
</font></ul>
</font></ul>
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<br><li><a href="http://2010.igem.org/Team:DTU-Denmark/SPL">Synthetic Promoter Library</a></li><br>
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<br><li><a href="http://2010.igem.org/Team:DTU-Denmark/SPL">Synthetic Promoter Library</a>
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<li ><a href="http://2010.igem.org/Team:DTU-Denmark/Modelling">Modelling</a>
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<ul><font size="2">
<ul><font size="2">
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<li><a href="http://2010.igem.org/Team:DTU-Denmark/Modelling#Introduction">Introduction</a></li>
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<li><a href="http://2010.igem.org/Team:DTU-Denmark/SPL#standard">The DTU SPL Standard</a>
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<li><a href="http://2010.igem.org/Team:DTU-Denmark/Modelling#Approach">Modelling Approach</a></li>
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<ul>
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<li><a href="http://2010.igem.org/Team:DTU-Denmark/Modelling#SPL">Modelling SPL</a></li>
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<li><a href="http://2010.igem.org/Team:DTU-Denmark/SPL#strategy">Strategy</a></li>
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<li><a href="http://2010.igem.org/Team:DTU-Denmark/Modelling#AntiRepressors">Modelling Anti-Repressors</a></li>
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<li><a href="http://2010.igem.org/Team:DTU-Denmark/SPL#design">Primer Design</a></li>
 +
<li><a href="http://2010.igem.org/Team:DTU-Denmark/SPL#protocol">Protocol</a></li>
 +
</ul>
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</li>
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<li><a href="http://2010.igem.org/Team:DTU-Denmark/SPL#advantages">Advantages</a></li>
 +
</ul></font>
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</li><br>
 +
<li ><a href="http://2010.igem.org/Team:DTU-Denmark/Modelling">Modeling</a>
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<ul><font size="2">
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<li><a href="http://2010.igem.org/Team:DTU-Denmark/Modelling#Approach">Modeling Approach</a></li>
</ul></font>
</ul></font>
</li><br>
</li><br>
</ul>
</ul>
</td>
</td>
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<td>
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  <td width="556px" height="100%" valign="top">
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<h1>Introduction</h1>
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  <font color="#990000" face="arial" size="5">
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<h3>Aim</h3>
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<br>  
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<p align="justify">The goal of our project is to enable colonies of <i>E. coli</i> bacteria to transition between production of two different reporter proteins. In our system, switching between states will be induced by two different inputs. Each of the states will have a specific input associated with it. There are multiple potential applications for biologicals "switches" such as these, this includes the improved control of production of additives in industrial biotechnological processes.</p>
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<b>Project Concept</b><br><br>
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<h3>Project Concept</h3>
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  </font>
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<p align="justify">As previously stated, the main goal of our project is to design a bistable switch. The switching between the two states will be controlled by the introduction of two different inputs, each input responsible for the induction of a different state. As a proof of concept, we’re using fluorescent proteins as reporter genes which makes it easy to observe and characterise the system. In principle, however, any reporter gene can be used.</p>
+
<p align="justify">As previously stated, the main goal of our project is to design a bistable switch. We want to enable bacteria to transition between two stable states. In our system, switching between states will be induced by two different inputs and each of the states will have a specific output associated with it.</p>
 +
-
<p align="justify">Our original project concept revolved around using light-receptors to instigate the switch between the two stable state. It was thought that the production of the first reporter protein would be induced by red light (660 nm). At the same time, production of the other reporter will be suppressed by a coexpressed repressor. Conversely, production of the second reporter would be induced by blue light (470 nm). Bistability of the system is achieved by using two repressors which negatively regulate each other’s expression. This enables the system to sustain state without continuous input, i. e. once production of a reporter protein is initiated, it will persist until the system is forced into the other state.</p>
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<p align="justify">Our original project concept evolved around building a switch that we could turn on and off continuously. Not only did we want the switch to be able to switch states, but we also wanted it to be able to stay in a certain state without having to induce it constantly. Several designs were discussed, for example using light at different wavelengths to induce the system.</p>
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<table class="http://2010.igem.org/wiki/images/f/ff/DTU_Project_illustration_1.png" align="center">
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-
  <caption align="bottom"><p align="justify"><b>Figure 1</b>: Simple bistable switch.</p></caption>
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<p align="justify">During the last couple of years several attempts have been made to construct bistable switches. One switch design is a one input, two outputs stable switch. It has a stable output but it looses the switching ability and 90% of the individuals in the population are killed when the switch is induced by UV-light (Lou, C. et al.,2010). Another mechanism tested has been a flipases system where the DNA is inverted by specific recognition sites. The system was found to function but was limited by the robustness of the flipase systems and knowledge about their function (Ham, T.S. et al.,2008). Another general problem with the construction of synthetic switches is the loss of function over time (Canton, B. et al.,2008). The limited function and stability of existing switches also limit the application to short time spans. Based on these problems we saw the untapped potential in designing a novel biological switch.</p>
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<tr><td><img src="http://2010.igem.org/wiki/images/f/ff/DTU_Project_illustration_1.png"  width="400px"></td></tr>
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 +
<p align="justify">Our switch design is a complex regulatory system, which is induced with the help of input plasmids carrying inducible promoters.  However due to the complexity of the design of the bistable switch it was out of the scope of this project to construct the entire switch. Therefore focus was put on characterizing the key regulatory subparts needed for successful switch function. Characterizing subparts also enable future teams to use them in other contexts.</p>
 +
 
 +
<table class="http://2010.igem.org/wiki/images/9/9a/Intro_switch.png" align="center">
 +
  <caption align="bottom"><p align="justify"><b>Figure 1</b>: A simplified illustration of our bistable switch.</p></caption>
 +
<tr><td><img src="http://2010.igem.org/wiki/images/9/9a/Intro_switch.png"  width="400px"></td></tr>
</table><br>
</table><br>
-
<p align="justify">Our project concept has since changed to concentrating on the different composite parts of the switch and leave the assembling of the entire switch as an option for next years DTU team.</p>
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-
<h1>Applications</h1>
+
<font color="#990000" face="arial" size="5">
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<p align="justify"> If successfully engineered this new technological tool could advance methods used with in many different fields of biological science as environmental engineering, food applications and medico technology, a few suggestions are listed below. Further description of applications see the Switch section under <a href="http://2010.igem.org/Team:DTU-Denmark/Switch#Applications_of_our_Bi[o]stable_switch" target="_blank">applications</a>.</p>
+
<br>  
-
<ul>
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<b>Design of our switch</b><br><br>
-
<li>In manufacturing it could be applied as a cheap proof reading or control mechanism in production plants, if the product is exposed to the right or wrong treatment, or an un wanted biological infection or compound, it will change color.</li>
+
  </font>
-
<li>In manufacturing or environmental technology it could be used for error  tracking  or leakage tracking in process plants or in the environment. If the compound to be tracked cannot be measured, or measurements are difficult to obtain, if a biological sensor exists it is possible to track the organism or the reporter downstream of the inducer signal.</li>
+
 
-
<li> In food control it could be used as a small piece of tape, containing the modified organism, on the package. It will then be possible to track if the product have been exposed to high temperatures, or unwanted compounds and the consumer can see it directly on the package.</li>
+
<p align="justify"> We have set up the complete design for a bistable switch. The main design criteria has been that the switch should be able to toggle  back and forth between states, stay in its induced state until it receives another input and remain stable through subsequent generations. These criteria imply that:
-
<li>A medical application could be to ingest the modified organism. It can then be tested if the organism experience a certain drug, or condition on the way through the intestinal track.</li>
+
-
<li> In molecular or medical science it could be used for investigations on chemotaxis and biofilm formation experiments, by exposing the biological matrix with, for an example, different light sources, there will be developed layers in the matrix and movements and development can be tracked, in relation to the two different exposures and the time between them.</li>
+
-
</ul>
+
-
<p align="justify"> Our original project idea was developed around the last example, where light (red light at 660nm and blue light at 470nm) would be used as input to induce switching between the two stable states. The initial ideas behind this was to use the bacteria to create artistic drawing or to track movement in biofilm.</p>
+
-
<p align="justify"> Based on this idea, as well as research of biological switches and the regulatory mechanisms found in phages, we discovered untapped potential in designing a biological switch.</p>
+
-
<h1>Design of our switch</h1>
+
-
<p align="justify"> We have set up the complete design for a bistable switch. The main design criteria has been that is should remain stable through subsequent generations, which implies that:
+
<ul>
<ul>
-
<li>It should be designed with out induction by UV-light, and not be based on essential native regulatory mechanisms.</li>
+
<li>It should be designed without induction by UV-light.</li>
 +
<li>It should not be based on essential native regulatory mechanisms.</li>
<li>It should be possible to incorporate into the genome for stable replication, and function in subsequent generations.</li>
<li>It should be possible to incorporate into the genome for stable replication, and function in subsequent generations.</li>
</ul>
</ul>
-
<p align="justify">A simplified version of our switch design can be illustrated using two logical NOR-gates typically used when representing electronic circuits. The NOR-gates are integrated within a SR flip-flop switch as illustrated in Figure 1. This switch has two different, mutually exclusive outputs, induced by two different inputs. The last set output will stay on even when the input signal ceases. For further description on the logical behavior and requirements of switches see the <a href="http://2010.igem.org/Team:DTU-Denmark/Modelling" target="_blank">modeling section</a></p>.
+
<p align="justify">A simplified version of our switch design can be illustrated using a basic  SR (Set-Reset) flip flop circuit used when representing electronic circuits. It provides feedback from its outputs to its inputs and is commonly used in memory circuits to store data bits. The term flip-flop relates to the actual operation of the device, as it can be "Flipped" into one logic state or "Flopped" back into another <a href="http://www.electronics-tutorials.ws/sequential/seq_1.html" target="_blank"> (reference)</a>. For further description on the logical behavior and requirements of switches see the <a href="http://2010.igem.org/Team:DTU-Denmark/Modelling" target="_blank">modeling section</a>.</p>
<table class="http://2010.igem.org/wiki/images/5/53/SRflipflop.png" align="center">
<table class="http://2010.igem.org/wiki/images/5/53/SRflipflop.png" align="center">
  <caption align="bottom"><p align="justify"><b>Figure 2</b>: SR flip-flop switch.</p></caption>
  <caption align="bottom"><p align="justify"><b>Figure 2</b>: SR flip-flop switch.</p></caption>
<tr><td><img src="http://2010.igem.org/wiki/images/5/53/SRflipflop.png"  width="200px"></td></tr>
<tr><td><img src="http://2010.igem.org/wiki/images/5/53/SRflipflop.png"  width="200px"></td></tr>
</table><br>
</table><br>
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<p align="justify">The switch is constructed based on phage regulatory mechanisms, that function when inserted into the chromosome (prophages). Furthermore, we used the Gifsy phage repressor - anti-represor system to circumnavigate the use of UV-light. The switch has three levels of regulatory mechanisms to ensure a stable expression and tight control and thereby creating a robust bistable switch (see Figure 3):</p>
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<p align="justify">The switch design is based on phage regulatory systems. We used the repressor/anti-represor system from the Gifsy phages and an anti-termination system from the lambda-phage.</p>
 +
<p align="justify"> The switch has three levels of regulatory mechanisms to ensure a stable expression and tight control and thereby creating a robust bistable switch (see Figure 3):
<ol>
<ol>
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<li>The first level is negative feed back control, repressing the other side of the switch.</li>
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<li>The first level is negative feed back control - repression of the uninduced state of the switch.</li>
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<li>The second mechanism is a positive feed back mechanism that has a threshold level that when triggered will induce the third level of regulation.</li>
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<li>The second level is a positive feed back mechanism with a threshold level that when triggered will induce the third level of regulation - antitermination allows third level to be induced.</li>
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<li>The third regulatory level is a positive feed back mechanism increasing the expression of the winning side by, repression of the opposite sites repression, in step one.</li>
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<li>The third regulatory level is a positive feed back mechanism stabilizing the expression of the winning state by, anti-repression of the repression from the loosing states.</li>
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</ol>
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</ol></p>
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<table class="http://2010.igem.org/wiki/images/e/e1/DTU-background_im1.png" align="center">
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 +
<table class="http://2010.igem.org/wiki/images/1/14/Threestages.png" align="center">
  <caption align="bottom"><p align="justify"><b>Figure 3</b>: Simplified representation of the regulatory mechanisms: [<b>1</b>] negative feed back control of opposite side. [<b>2</b>] positive feed back trigger mechanism for side commitment. [<b>3</b>] positive feed back mechanism, by canceling the opposite sides repressor.</p></caption>
  <caption align="bottom"><p align="justify"><b>Figure 3</b>: Simplified representation of the regulatory mechanisms: [<b>1</b>] negative feed back control of opposite side. [<b>2</b>] positive feed back trigger mechanism for side commitment. [<b>3</b>] positive feed back mechanism, by canceling the opposite sides repressor.</p></caption>
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<tr><td><img src="http://2010.igem.org/wiki/images/e/e1/DTU-background_im1.png"  width="400px"></td></tr>
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<tr><td><img src="http://2010.igem.org/wiki/images/1/14/Threestages.png"  width="400px"></td></tr>
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</table><br>
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<p align="justify">For an in depth description of the function and origin of the regulatory parts see the switch section.</p>
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<h1>Characterizing phage regulatory mechanisms</h1>
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<p align="justify"> Due to the complexity of the regulatory circuit design, it was out of the scope of this project to construct the entire switch so focus was put on characterizing the key regulatory subparts needed for successful system function.</p>
+
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<p align="justify">The main regulatory parts are the anti-terminator function from lambda phage, and the repressor system from Gifsy phages, see Figure 4 and Figure 5.</p>
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-
<table class="http://2010.igem.org/wiki/images/a/a4/DTU_repressorsystem.png" align="center">
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<caption align="bottom"><p align="justify"><b>Figure 4</b>: Graphical presentation of the anti-terminator part of our regulatory system from the lambda phage.</p></caption>
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<tr><td><img src="http://2010.igem.org/wiki/images/a/a4/DTU_repressorsystem.png"  width="200px"></td></tr>
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</table><br>
</table><br>
 +
<p align="justify">For an in depth description of the function and origin of the regulatory parts have a look into the <a href=" http://2010.igem.org/Team:DTU-Denmark/Switch" target="_blank">switch</a> section.</p>
 +
<p align="justify">One important feature of the switch is the strength of the promoters. For the switch to work properly we need promoters of equal strength. To solve this problem we utilized a <a href=" http://2010.igem.org/Team:DTU-Denmark/SPL" target="_blank">synthetic promoter library</a>, enabling us to generate a library of promoters with a wide variety of different strengths.</p>
 +
 +
<font color="#990000" face="arial" size="5">
 +
<br> 
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<b>Characterizing phage regulatory mechanisms</b><br><br>
 +
  </font>
 +
 +
 +
<p align="justify">The main regulatory parts of the switch are the repressor/antirepressor system from the Gifsy phages and the anti-terminator system from lambda phage, see Figure 4, Figure 5 and Figure 6.</p>
 +
<table class="http://2010.igem.org/wiki/images/c/c8/DTU_anitsystem.png" align="center">
<table class="http://2010.igem.org/wiki/images/c/c8/DTU_anitsystem.png" align="center">
-
  <caption align="bottom"><p align="justify"><b>Figure 5</b>: Graphical presentation of the repressor part of our regulatory system from the Gifsy phages.</p></caption>
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  <caption align="bottom"><p align="justify"><b>Figure 4</b>: Graphical presentation of the repressor part of our regulatory system from the Gifsy phages.</p></caption>
-
<tr><td><img src="http://2010.igem.org/wiki/images/c/c8/DTU_anitsystem.png"  width="200px"></td></tr>
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<tr><td><img src="http://2010.igem.org/wiki/images/c/c8/DTU_anitsystem.png"  width="225px"></td></tr>
</table><br>
</table><br>
 +
 +
<table class="http://2010.igem.org/wiki/images/2/26/Repressor_antirepressor.png" align="center">
 +
<caption align="bottom"><p align="justify"><b>Figure 5</b>: Graphical presentation of the anti-repressor part of our regulatory system from the Gifsy phages.</p></caption>
 +
<tr><td><img src="http://2010.igem.org/wiki/images/2/26/Repressor_antirepressor.png"  width="350px"></td></tr>
 +
</table><br>
 +
 +
<table class="http://2010.igem.org/wiki/images/a/a4/DTU_repressorsystem.png" align="center">
 +
<caption align="bottom"><p align="justify"><b>Figure 6</b>: Graphical presentation of the anti-terminator part of our regulatory system from the lambda phage.</p></caption>
 +
<tr><td><img src="http://2010.igem.org/wiki/images/a/a4/DTU_repressorsystem.png"  width="180px"></td></tr>
 +
</table><br>
 +
 +
 +
<p align="justify">As a proof of concept for the regulatory mechanisms, we constructed plasmids that were able to test the regulatory mechanism and strength of the two systems. We used low copy number plasmids and fluorescent proteins as reporters. For more information about the experimental setup and characterization results of the Repressor - Anti-Repressor system please click <a href="http://2010.igem.org/Team:DTU-Denmark/Repressor_Section" target="_blank">here</a> and for the Terminator - Anti-Terminator system please click <a href="http://2010.igem.org/Team:DTU-Denmark/AntiTermination_Section" target="_blank">here</a>.</p>
<p align="justify">As a proof of concept for the regulatory mechanisms, we constructed plasmids that were able to test the regulatory mechanism and strength of the two systems. We used low copy number plasmids and fluorescent proteins as reporters. For more information about the experimental setup and characterization results of the Repressor - Anti-Repressor system please click <a href="http://2010.igem.org/Team:DTU-Denmark/Repressor_Section" target="_blank">here</a> and for the Terminator - Anti-Terminator system please click <a href="http://2010.igem.org/Team:DTU-Denmark/AntiTermination_Section" target="_blank">here</a>.</p>
-
<p align="justify">The key parts of the regulatory systems have been testes and are available as biobricks through the parts registry. See the parts page for a list of the parts available. </p>
+
<p align="justify">The key parts of the regulatory systems have been tested and are available as BioBricks through the parts registry. See the <a href=" http://2010.igem.org/Team:DTU-Denmark/Parts" target="_blank">parts</a> page for a list of available parts. </p>
-
<h1>Conclusion</h1>
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<p align="justify">We have shown that the gifsy repressor system have a sufficient tight expression and control to be used in the future construction of biological switches.</p>
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<font color="#990000" face="arial" size="5">
 +
<br> 
 +
<b>Conclusion</b><br><br>
 +
  </font>
 +
 
 +
<p align="justify">We have shown that the Gifsy repressor system has a sufficient tight expression and control to be used in the future construction of biological switches.</p>
<p align="justify">We have set up the frame work for testing anti-terminator function, but further characterization is needed before it can be applied in standard regulatory systems.</p>
<p align="justify">We have set up the frame work for testing anti-terminator function, but further characterization is needed before it can be applied in standard regulatory systems.</p>
-
<p align="justify">Further we have developed and demonstrated the functionality of a synthetic promoter library, compatible with the biobrick standard, that can find multiple applications and be used for characterization of biobricks.</p>
+
<p align="justify">Furthermore we have designed and demonstrated the functionality of a Synthetic Promoter Library, compatible with the BioBrick standard. We have also developed a standard for integrating a BioBrick compatible Synthetic Promoter Library in bacteria in order to fine-tune the expression of BioBrick parts and devices.</p>
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<p align="justify">We hope from this work to inspire and give ideas about a possible construction of a genetic switch and hope that it will be possible for next year’s teams to build on our work, benefit from the Synthetic promoter standard, investigate missing functionality of our switch and be able to assemble the entire regulatory system.</p>
+
<p align="justify">We hope that this work will inspire future teams to take up the challenge of constructing a genetic bistable switch. They can easily benefit from the new DTU Synthetic Promoter Library standard and our submitted BioBricks.</p>
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== References ==
== References ==
-
* (Gottesman et.al. 2002) Gottesman. Max E, Nudler. Evgeny, 2002  ”Transcription termination and anti-termination in E.coli”  Genes to cells.  (a good introduction review to termination function)
+
* Canton, B. et al. Refinement and standardization of synthetic biological parts and devices. Nature Biotechnology 26, 787-793, (2008)
-
 
+
* Ham, T.S. et al. Design and construction of a double inversion recombination Switch for Heritable Sequential Genetic Memory. PloS ONE 3(7),(2008)
-
* (Franklin et.al. 1989) NC Franklin, JH Doelling - Am Soc Microbiol "Overexpression of N antitermination proteins of bacteriophages lambda, 21, and P22: loss of N protein specificity." - Journal of bacteriology, 1989
+
* Lou, C. et al. Synthesizing a novel genetic sequential logic circuit: a push-on push-off switch. Mol Syst Biol 6, (2010)
-
 
+
-
* (Jensen 2004) Ole Nørregaard Jensen, “Modification-specific proteomics: characterization of post-translational modifications by mass spectrometry,” Current Opinion in Chemical Biology 8, no. 1 (February 2004): 33-41.
+
* [1] http://syntheticbiology.org/FAQ.html
* [1] http://syntheticbiology.org/FAQ.html
* [2]http://www.nature.com.globalproxy.cvt.dk/nrg/journal/v6/n7/execsumm/nrg1637.html
* [2]http://www.nature.com.globalproxy.cvt.dk/nrg/journal/v6/n7/execsumm/nrg1637.html
* [3]http://www.nature.com.globalproxy.cvt.dk/msb/journal/v2/n1/full/msb4100073.html
* [3]http://www.nature.com.globalproxy.cvt.dk/msb/journal/v2/n1/full/msb4100073.html
* [4]www.partsregistry.org
* [4]www.partsregistry.org

Latest revision as of 03:58, 28 October 2010

Welcome to the DTU iGEM wiki!


Project Concept

As previously stated, the main goal of our project is to design a bistable switch. We want to enable bacteria to transition between two stable states. In our system, switching between states will be induced by two different inputs and each of the states will have a specific output associated with it.

Our original project concept evolved around building a switch that we could turn on and off continuously. Not only did we want the switch to be able to switch states, but we also wanted it to be able to stay in a certain state without having to induce it constantly. Several designs were discussed, for example using light at different wavelengths to induce the system.

During the last couple of years several attempts have been made to construct bistable switches. One switch design is a one input, two outputs stable switch. It has a stable output but it looses the switching ability and 90% of the individuals in the population are killed when the switch is induced by UV-light (Lou, C. et al.,2010). Another mechanism tested has been a flipases system where the DNA is inverted by specific recognition sites. The system was found to function but was limited by the robustness of the flipase systems and knowledge about their function (Ham, T.S. et al.,2008). Another general problem with the construction of synthetic switches is the loss of function over time (Canton, B. et al.,2008). The limited function and stability of existing switches also limit the application to short time spans. Based on these problems we saw the untapped potential in designing a novel biological switch.

Our switch design is a complex regulatory system, which is induced with the help of input plasmids carrying inducible promoters. However due to the complexity of the design of the bistable switch it was out of the scope of this project to construct the entire switch. Therefore focus was put on characterizing the key regulatory subparts needed for successful switch function. Characterizing subparts also enable future teams to use them in other contexts.

Figure 1: A simplified illustration of our bistable switch.



Design of our switch

We have set up the complete design for a bistable switch. The main design criteria has been that the switch should be able to toggle back and forth between states, stay in its induced state until it receives another input and remain stable through subsequent generations. These criteria imply that:

  • It should be designed without induction by UV-light.
  • It should not be based on essential native regulatory mechanisms.
  • It should be possible to incorporate into the genome for stable replication, and function in subsequent generations.

A simplified version of our switch design can be illustrated using a basic SR (Set-Reset) flip flop circuit used when representing electronic circuits. It provides feedback from its outputs to its inputs and is commonly used in memory circuits to store data bits. The term flip-flop relates to the actual operation of the device, as it can be "Flipped" into one logic state or "Flopped" back into another (reference). For further description on the logical behavior and requirements of switches see the modeling section.

Figure 2: SR flip-flop switch.


The switch design is based on phage regulatory systems. We used the repressor/anti-represor system from the Gifsy phages and an anti-termination system from the lambda-phage.

The switch has three levels of regulatory mechanisms to ensure a stable expression and tight control and thereby creating a robust bistable switch (see Figure 3):

  1. The first level is negative feed back control - repression of the uninduced state of the switch.
  2. The second level is a positive feed back mechanism with a threshold level that when triggered will induce the third level of regulation - antitermination allows third level to be induced.
  3. The third regulatory level is a positive feed back mechanism stabilizing the expression of the winning state by, anti-repression of the repression from the loosing states.

Figure 3: Simplified representation of the regulatory mechanisms: [1] negative feed back control of opposite side. [2] positive feed back trigger mechanism for side commitment. [3] positive feed back mechanism, by canceling the opposite sides repressor.


For an in depth description of the function and origin of the regulatory parts have a look into the switch section.

One important feature of the switch is the strength of the promoters. For the switch to work properly we need promoters of equal strength. To solve this problem we utilized a synthetic promoter library, enabling us to generate a library of promoters with a wide variety of different strengths.


Characterizing phage regulatory mechanisms

The main regulatory parts of the switch are the repressor/antirepressor system from the Gifsy phages and the anti-terminator system from lambda phage, see Figure 4, Figure 5 and Figure 6.

Figure 4: Graphical presentation of the repressor part of our regulatory system from the Gifsy phages.


Figure 5: Graphical presentation of the anti-repressor part of our regulatory system from the Gifsy phages.


Figure 6: Graphical presentation of the anti-terminator part of our regulatory system from the lambda phage.


As a proof of concept for the regulatory mechanisms, we constructed plasmids that were able to test the regulatory mechanism and strength of the two systems. We used low copy number plasmids and fluorescent proteins as reporters. For more information about the experimental setup and characterization results of the Repressor - Anti-Repressor system please click here and for the Terminator - Anti-Terminator system please click here.

The key parts of the regulatory systems have been tested and are available as BioBricks through the parts registry. See the parts page for a list of available parts.


Conclusion

We have shown that the Gifsy repressor system has a sufficient tight expression and control to be used in the future construction of biological switches.

We have set up the frame work for testing anti-terminator function, but further characterization is needed before it can be applied in standard regulatory systems.

Furthermore we have designed and demonstrated the functionality of a Synthetic Promoter Library, compatible with the BioBrick standard. We have also developed a standard for integrating a BioBrick compatible Synthetic Promoter Library in bacteria in order to fine-tune the expression of BioBrick parts and devices.

We hope that this work will inspire future teams to take up the challenge of constructing a genetic bistable switch. They can easily benefit from the new DTU Synthetic Promoter Library standard and our submitted BioBricks.

References