ETHZ

From 2007.igem.org

(Difference between revisions)
('''.:: Acknowledgements ::.''')
(Multipurpose Cell Lines)
 
(121 intermediate revisions not shown)
Line 1: Line 1:
-
<center>[[Image:Eth_zh_logo_4.png|830px]]</center>
+
[[Image:ETHZ_banner.png|830px]]
 +
<!--
 +
<center>[[ETHZ | Main Page]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Model | System Modeling]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Simulation | Simulations]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Biology | System Implementation]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Biology/Lab| Lab Notes]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Meet_the_team | Meet the Team]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Internal | Team Notes]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Pictures | Pictures!]]</center><br>
 +
-->
 +
__NOTOC__
 +
<html>
 +
<script type="text/javascript" src="http://christos.bergeles.net/eth_dropdowntabs.js">
 +
 
 +
/***********************************************
 +
* Drop Down Tabs Menu- (c) Dynamic Drive DHTML code library (www.dynamicdrive.com)
 +
* This notice MUST stay intact for legal use
 +
* Visit Dynamic Drive at http://www.dynamicdrive.com/ for full source code
 +
***********************************************/
 +
 
 +
</script>
 +
 
 +
<!-- CSS for Drop Down Tabs Menu #1 -->
 +
<link rel="stylesheet" type="text/css" href="http://christos.bergeles.net/eth_ddcolortabs.css" />
 +
<div id="colortab" class="ddcolortabs">
 +
<ul>
 +
<li><a href="https://2007.igem.org/wiki/index.php?title=ETHZ" title="Home" rel="dropmenu_home"><span>Home</span></a></li>
 +
<li><a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Model" title="Modeling" rel="dropmenu_modeling"><span>System Modeling</span></a></li>
 +
<li><a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Simulation" title="Simulations" rel="dropmenu_simulation"><span>Simulations</span></a></li>
 +
<li><a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Biology" title="System Implementation" rel="dropmenu_biology"><span>System Implementation</span></a></li>
 +
<li><a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Meet_the_team" title="Meet the team" rel="dropmenu_meettheteam"><span>Meet the team</span></a></li>
 +
<li><a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Pictures" title="Pictures!" rel="dropmenu_pictures"><span>Pictures!</span></a></li>
 +
</ul>
 +
</div>
 +
<div class="ddcolortabsline">&nbsp;</div>
 +
 
 +
 
 +
<!--1st drop down menu -->
 +
<div id="dropmenu_home" class="dropmenudiv_a">
 +
<a href="https://2007.igem.org/wiki/index.php?title=ETHZ#Introduction">Introduction</a>
 +
<a href="https://2007.igem.org/wiki/index.php?title=ETHZ#Team_Members">Team Members</a>
 +
<a href="https://2007.igem.org/wiki/index.php?title=ETHZ#Acknowledgments">Acknowledgments</a>
 +
<a href="https://2007.igem.org/wiki/index.php?title=ETHZ#Site_Map">Site map</a>
 +
</div>
 +
 
 +
 
 +
<!--2nd drop down menu -->
 +
<div id="dropmenu_modeling" class="dropmenudiv_a" style="width: 150px;">
 +
<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Model#Introduction">Introduction</a>
 +
<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Model#Model_Overview">Model Overview</a>
 +
<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Model#Detailed_Model">Detailed Model</a>
 +
<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Model#Final_Model">Final Model</a>
 +
<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Modeling_Basics">Modeling Basics Page</a>
 +
<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Model#Mathematical_Model">Mathematical Model</a>
 +
<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/FSM">FSM View Page</a>
 +
<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/FlipFlop">Flip-Flop View Page</a>
 +
<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Parameters">Parameters Page</a>
 +
</div>
 +
 
 +
<!--3rd drop down menu -->
 +
<div id="dropmenu_simulation" class="dropmenudiv_a" style="width: 150px;">
 +
<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Simulation#Introduction">Introduction</a>
 +
<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Simulation#Simulation_of_Test_Cases">Test Cases</a>
 +
<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Simulation#Sensitivity_Analysis">Sensitivity Analysis</a>
 +
</div>
 +
 
 +
<!--4th drop down menu -->
 +
<div id="dropmenu_biology" class="dropmenudiv_a" style="width: 150px;">
 +
<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Biology#Introduction">Introduction</a>
 +
<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Biology#The_Complete_System">The Complete System</a>
 +
<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Biology#System_Phases">System Phases</a>
 +
<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Biology#Current_Cloning_Status">Current Cloning Status</a>
 +
<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Biology/parts">System Parts Page</a>
 +
<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Biology/Lab">Lab Notes Page</a>
 +
</div>
 +
 
 +
<!--5th drop down menu -->
 +
<div id="dropmenu_meettheteam" class="dropmenudiv_a" style="width: 150px;">
 +
<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Meet_the_team#The_ETH_Zurich_07_Team">The ETH Zurich 07 Team</a>
 +
<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Meet_the_team#Team_Description">Team Description</a>
 +
<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Internal">Brainstorming Page</a>
 +
</div>
-
<center>[[ETHZ | Main Page]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Model | System Modeling]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Simulation | Simulations]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Biology | System Implementation]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Biology/Lab | Lab Notes]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Meet_the_team | Meet the Team]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Internal | Team Notes]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Pictures | Pictures!]]</center><br>
+
<script type="text/javascript">
 +
//SYNTAX: tabdropdown.init("menu_id", [integer OR "auto"])
 +
tabdropdown.init("colortab", 3)
 +
</script>
 +
</html>
__NOTOC__
__NOTOC__
-
<center><font size = '+2'><b> .:: ETH Zurich - educatETH ''E.coli'' ::. </b></font></center><br>
+
<html>
 +
<p align="center"><font size="6"><b>ETH Zurich - educatETH <i>E.coli</i> System</b></font></p>
 +
</body>
 +
</html>
-
==='''.:: Introduction ::.'''===
+
=Introduction=
-
<blockquote>"ALL ANIMALS ARE EQUAL BUT SOME ANIMALS ARE MORE EQUAL THAN OTHERS" ''(Animal Farm by George Orwell)''</blockquote>   
+
<blockquote>"All <i>E.coli</i> 's are equal, but some <i>E.coli</i> 's are more equal than others..." ''(freely adapted from "Animal Farm" by George Orwell)''</blockquote>   
-
In this year's iGEM, the ETH team is interested in quite small but well known animals, ''E.coli'' 's. And even for these, Orwell's remark holds (although in a somewhat more positive way): We have been working on teaching ''E.coli'' 's in order to make them capable of deliberately recognizing their environment.
+
... this is what George Orwell would have written, were he a synthetic biologist. In the <i>E.coli</i> colonies on petri dishes, all bacteria are equal; except for some special ones. Our project is about designing such special <i>E.coli</i> that are "more equal" than the rest: they have the ability to be trained in order to memorize and recognize their environment in the future. Their  story will be presented through this wiki ...
-
In detail, our combined team of biologists and engineers was working on the ''E.coli'' 's ability, first, to recognize two different inputs (here we used two different chemicals), second, to remember which input was presented to them, and third, when confronted with a new input to recognize if it is the same as before. Thereby, the educatETH ''E.coli'' 's provide a first step towards the development of biological equivalents to complex engineering building blocks like, e.g. , [[ETHZ/FlipFlop | flip-flops]] and other logical circuits. The concept of learning and recognition plays a major role in different high-level applications like, e.g., recognition of handwriting on a [http://en.wikipedia.org/wiki/Personal_digital_assistant PDA]. On the other hand, learning plays a major role for living organisms, as well: it enables them to survive by adapting to an ever-changing environment. Therefore, engineering a simple biological system which exhibits learning behavior (e.g. epigenetics) is of great interest as it can support our understanding of this procedure by comparison with natural systems.
+
==Motivation==
-
In the following, we would like to present you a detailed description of the proposed system: starting with the [[ETHZ/Model | modeling of the system]], we describe both, [[ETHZ/Simulation | simulations and theoretical considerations]] of the system, as well as the actual [[ETHZ/Biology | implementation using bio-bricks]] accompanied by our [[ETHZ/Biology/Lab | lab notes]]. Additionally, you find some further [[ETHZ/Meet_the_team | information on the team]], some more details about [[ETHZ/Internal | ideas we developed]] before we came up with the system we finally implemented, and some [[ETHZ/Pictures | pictures]] documenting our work.
+
[[Image:ethz_main_pic.jpg|right|thumb|<b>Fig. 1</b>: Artist's approach to the different stages of the development. We started by modeling and simulating the system. We continued by specifying the DNA strands for its implementation. Finally in the end, our system should report with different fluorescent proteins (image edited)|600px]]
-
==='''.:: Team Members ::.'''===
+
Our combined team of biologists and engineers is coping with the problem of implementing memory capabilities in bacterial colonies. First, ''E.coli'' are able to respond differently (with distinct fluorescent proteins) to two different inputs (we used chemicals). Second, they remember which input was presented to them. Finally, when confronted with a new input, they are able to recognize whether it is the one that they were trained with or not.
-
[[Image:ETHZ_Group_photo_4.png|center|thumb|ETHZ iGEM2007 Team|500px]]
+
In other words, in this project '''we are educating the <i>E.coli</i>'''!
-
The ETH Zurich team consists of good mixture between biologists and engineering students, we are:
+
===Multipurpose Cell Lines===
 +
 
 +
Our system has the ability to behave in different ways according to an internal toggle inside it switching states based on the chemical substances that the system is exposed to. The toggle states could generally be used to trigger events such as enzyme synthesis, transcriptional regulation, virion production, or even cell death. Therefore, one may view the bacterial cell line containing this system as a multipurpose cell line. By adding a certain chemical to a cell line, the latter may be trained to exhibit a desired behavior, and then it is not necessary any more to construct two independent cell lines.
 +
 
 +
This means that one applies an “input engineering” instead of a “DNA engineering” approach. If one extends this idea to several multi-inducible toggle switches being harbored in the same cell line, the number of possible phenotypes increases to 2<i><sup>n</sup></i>, where <i>n</i> equals the number of toggle switches. For example, if one would have 5 such toggle switches inside a cell line, 32 different behavior patterns would be possible.
 +
 
 +
For the purpose of creating a toggle switch that is activated in a specific phase only and not always (a multi-inducible toggle switch), as is required for stable biological automatons, we introduced the concept of [https://2007.igem.org/ETHZ/Biology/parts#double_promoters double promoters] to the [http://partsregistry.org/Main_Page Registry of Standard Biological Parts], which can be helpful for engineering systems which exhibit a desired behavior only at specific times.
 +
 
 +
===Link to Epigenetics===
 +
Epigenetics refers to features like chromatin or DNA modifications that do not involve changes in the underlying DNA sequence and are stable over many cell divisions [1],[2]. If one has a closer look at our proposed system, one can also view it as a model-system for epigenetics: Although the DNA sequence itself stays the same, two different subpopulations of cells with different phenotypes can develop from it. Put simply, depending in which state (subpopulation) the toggle switch is, the cells will produce different fluorescent proteins upon addition of two different inducer molecules. Therefore, the epigenetic feature here is the binding of specific repressor proteins whose production is dependent on the toggle switch state.
 +
 
 +
===Intelligent Biosensors and Self-Adaptation===
 +
 
 +
The system is capable of sensing different chemicals and producing different fluorescent proteins. Since the cells can be trained to produce one of several specific fluorescent protein types when a certain chemical is present, one can also view those cells as intelligent biosensors which recognize chemical substances according to a training phase. The intelligent biosensors are not limited to detect chemicals; temperature, pH, light, pressure could be detected with an appropriate system as well. Such an application could be especially of interest when the environment to be probed is harmful for humans, for example due to high toxicity.
 +
 
 +
==Team Members==
 +
[[Image:ETHZ_Group_photo_6.png|right|thumb|The ETH Zurich iGEM2007 Team|270px]]
 +
 
 +
The ETH Zurich team consists of a good mixture between biologists and engineering students.
 +
We are:
<ul>  
<ul>  
-
<li><i>Undergraduate students</i>:  
+
<li><i>Undergraduate students</i>: <br>
-
[https://2007.igem.org/User:brutsche Martin Brutsche], [https://2007.igem.org/User:kdikaiou Katerina Dikaiou], [https://2007.igem.org/User:Raphael Raphael Guebeli], [https://2007.igem.org/User:hoehnels Sylke Hoehnel],  
+
[https://2007.igem.org/User:brutsche Martin Brutsche], [https://2007.igem.org/User:kdikaiou Katerina Dikaiou], <br>[https://2007.igem.org/User:Raphael Raphael Guebeli], [https://2007.igem.org/User:hoehnels Sylke Hoehnel], <br>
[https://2007.igem.org/Nan_Li Nan Li],  
[https://2007.igem.org/Nan_Li Nan Li],  
[https://2007.igem.org/User:Stefan Stefan Luzi]
[https://2007.igem.org/User:Stefan Stefan Luzi]
-
<li><i>Graduate students</i>:  
+
<li><i>Graduate students</i>: <br>
[http://christos.bergeles.net Christos Bergeles],  
[http://christos.bergeles.net Christos Bergeles],  
-
[http://www.tik.ee.ethz.ch/~sop/people/thohm/ Tim Hohm], [http://www.fussenegger.ethz.ch/people/kemmerc Christian Kemmer],  
+
[http://www.tik.ee.ethz.ch/~sop/people/thohm/ Tim Hohm], <br>
-
[https://2007.igem.org/User:JoeKnight Joseph Knight],  
+
[http://www.fussenegger.ethz.ch/people/kemmerc Christian Kemmer],  
-
[http://csb.inf.ethz.ch/people/uhr.html Markus Uhr],
+
[https://2007.igem.org/User:JoeKnight Joseph Knight], <br>
-
[http://www.ricomoeckel.de Rico Möckel]
+
[http://www.ricomoeckel.de Rico Möckel],  
-
<li><i>Project advisors</i>:  
+
[http://csb.inf.ethz.ch/people/uhr.html Markus Uhr]
-
[http://www.ipe.ethz.ch/laboratories/bpl/people/panke Sven Panke],  
+
<li><i>Project advisors</i>: <br>
 +
[http://www.ipe.ethz.ch/laboratories/bpl/people/panke Sven Panke], <br>
[http://csb.inf.ethz.ch/people/stelling.html Joerg Stelling]
[http://csb.inf.ethz.ch/people/stelling.html Joerg Stelling]
</ul>
</ul>
-
For more information about us, visit our [[ETHZ/Meet_the_team | Meet the Team]] page.
 
-
==='''.:: Acknowledgements ::.'''===
+
For more information about us, visit our [[ETHZ/Meet_the_team | Meet the Team]] page.
-
The idea for the project as well as its implementation was done by the ETH iGEM 2007 team. Nevertheless, we would like to thank the people in [http://www.ipe.ethz.ch/laboratories/bpl/index Sven Panke's Lab], especially Andreas Meyer PhD, who was always there for us, when we had a problem in the lab, [http://www.fussenegger.ethz.ch/ Martin Fussenegger's lab] for their patience concerning our questions, and [http://www.facs.ethz.ch Alfredo Franco-Obregóns lab] and Oralea Büchi for the help with the flow cytometry.
+
-
We would also like to acknowledge the following three companies and organizations for their financial support:
+
==Acknowledgments==
 +
The idea for the project as well as its implementation was done solely by the ETH iGEM 2007 team. We would like to thank the people in [http://www.ipe.ethz.ch/laboratories/bpl/index Sven Panke's Lab], especially Andreas Meyer who was always there for us when we had a problem. Additionally, we would like to thank [http://www.facs.ethz.ch Alfredo Franco-Obregón's lab] and Oralea Büchi for the help with the flow cytometry.
 +
We would also like to acknowledge the financial support by [http://europa.eu EU], the [http://www.ethz.ch ETH Zurich], and [http://www.geneart.com GeneArt]:
 +
<center>
{| border="0"
{| border="0"
|-
|-
| [http://europa.eu http://www.tik.ee.ethz.ch/~thohm/EU.gif]
| [http://europa.eu http://www.tik.ee.ethz.ch/~thohm/EU.gif]
-
| width="50" |
+
| width="40" |
| [http://www.ethz.ch http://www.tik.ee.ethz.ch/~thohm/ethlogo.jpg]
| [http://www.ethz.ch http://www.tik.ee.ethz.ch/~thohm/ethlogo.jpg]
-
| width="50" |
+
| width="40" |
| [http://www.geneart.com http://www.tik.ee.ethz.ch/~thohm/geneart.gif]
| [http://www.geneart.com http://www.tik.ee.ethz.ch/~thohm/geneart.gif]
|}
|}
 +
</center>
-
==='''.:: Site Map ::.'''===
+
==Site Map==
-
* [[ETHZ/Model | Modeling of the learning system]]
+
-
* [[ETHZ/FlipFlop | Implementation using flip-flops]]
+
-
* [[ETHZ/FSM | Representation with finite state machines]]
+
-
* tutorial?
+
-
* [[ETHZ/Simulation | Model simulations and theoretical considerations]]
+
-
* [[ETHZ/Biology | Biological implementation]]
+
-
* epigenetic?
+
-
* [[ETHZ/Biology/Lab | Lab notes]]
+
-
* [[ETHZ/Meet_the_team | Team page]]
+
In this wiki, we will present to you a detailed description of the proposed system: starting with the [[ETHZ/Model | modeling of the system]], we describe both, [[ETHZ/Simulation | simulations and theoretical considerations]] of the system, as well as the actual [[ETHZ/Biology | implementation using bio-bricks]] accompanied by our [[ETHZ/Biology/Lab | lab notes]]. Additionally, you will find further [[ETHZ/Meet_the_team | information on the team]], more details about [[ETHZ/Internal | ideas we developed]] before we came up with the system we finally implemented, and some [[ETHZ/Pictures | pictures]] documenting our work.
-
* [[ETHZ/Pictures | Pictures]]
+
-
* [[ETHZ/Internal | Other ideas we developed]]
+
-
* others I forgot?
+
-
* [https://2006.igem.org/wiki/index.php/ETH_Zurich_2005 The ETH Zurich 2005 project]
+
The site map of our wiki is the following:
-
* [https://2006.igem.org/wiki/index.php/ETH_Zurich_2006 The ETH Zurich 2006 project]
+
-
==='''.:: TODOs ::.'''===
+
{| class="wikitable" width="100%" border="1" cellspacing="0" cellpadding="2" style="text-align:left; margin: 1em 1em 1em 0; background: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;"
-
* put a fancy picture in the intro
+
!width="34%"| Modeling Pages                       
-
* link Stefan's Epigenetic Page
+
!width="22%"| Biology Pages
-
* put all Links to subpages including a short description in the "site map" section
+
!width="22%"| ETHZ Team Pages
-
* check if you like the contents of your personal pages
+
!width="22%"| Links
-
 
+
|-
-
 
+
| [[ETHZ/Model | Modeling of the learning system]]
-
======'''.:: to be removed ::.'''======
+
| [[ETHZ/Biology | Biological implementation]]
-
 
+
| [[ETHZ/Meet_the_team | Team page]]
-
<p>How can we make <i>E.coli</i> bacteria able to report us about their environment? Can we teach bacteria to tell if they have seen before a specific chemical? [[Image:System_blended4.png|thumb|350px| '''Fig. 2: '''educatETH ''E.coli'' System ]]</p>
+
| [https://2006.igem.org/wiki/index.php/ETH_Zurich_2005 The ETH Zurich 2005 project]
-
 
+
|-
-
<p>This problem is essentially broken down to constructing a toggle switch which can maintain the state it acquired during a training phase. In Logic Design, this is done using a JK flip-flop with a latch. With this approach, reporting in the testing phase may be implemented with AND gates using the state of the toggle and the current chemical as inputs.<br>
+
| [[ETHZ/FlipFlop | Representation using flip-flops]]
-
(Want to read more about this? Visit the [[ETHZ/Engineering| Engineering Perspective]]!)</p>
+
| [[ETHZ/Biology/parts | Biobricks/parts]]
-
 
+
| [[ETHZ/Pictures | Pictures]]
-
<p>Back to biology, a toggle switch has been successfully implemented in [1]. This toggle switch, however, changes states according to one input only as it has one operator site and therefore loses its previous state whenever the system is exposed to a different chemical. This means that it cannot memorize information. To overcome this, we modified the toggle switch in [1] using two operator sites. In this way, a second chemical acting as a “helper” substance present only in the training phase may be used so that the toggle maintains its state during testing.<br>
+
| [https://2006.igem.org/wiki/index.php/ETH_Zurich_2006 The ETH Zurich 2006 project]
-
(Want to see the biological design of our modified toggle? Visit the [[ETHZ/Biology | Biology Perspective]]!)<br><br><br></p>
+
|-
-
 
+
| [[ETHZ/FSM | Representation using finite state machines]]
-
<p>EducatETH <i>E.coli</i> is able to recognize between two chemical substances (aTC and IPTG) it has previously been exposed to with the help of an external chemical signal (AHL).
+
| [[ETHZ/Biology/Lab | Lab notes]]
-
<br>In the first part of the training phase (''“learning”''), the system is exposed to one of the two chemicals (aTc and IPTG), causing a steady system behavior. In the second part of the training phase (''“memory”''), AHL, is added while all other chemicals are removed, allowing the system to maintain its state. Finally, in the testing phase (''“recognition”''), the system is exposed to any of the two chemicals again. Via comparison of the toggle's steady state with the system response the new chemical causes, the system recognizes if it has been exposed to this chemical before or not.
+
| [[ETHZ/Internal | Brainstorming sessions]]
-
<br>As seen in Table 1, four system states are possible in the testing phase. We chose to use two reporters to control which chemical educatETH ''E.coli'' is exposed to during the training phase (CFP for IPTG, YFP for aTc). When the system recognizes the same chemical substance in the "recognition phase" as in the "learning phase ", it will respond with the same reporter output as in the learning phase (YFP for aTc learned and recognized, CFP for IPTG learned and recognized). However, when the system recognizes a different chemical substance, than previously learned, it will respond with either a GFP (when aTc is learned and IPTG is recognized) or a RFP output (when IPTG is learned and aTc is recognized). Thus, the system response is determined uniquely. </p>
+
|
-
 
+
|-
-
{| class="wikitable" border="1" cellspacing="0" cellpadding="2" style="text-align:left; margin: 1em 1em 1em 0; background: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;"                  
+
| [[ETHZ/Simulation | Model simulations and theoretical considerations]]
-
! Training <br>chemical             
+
|
-
! Testing <br>chemical             
+
|
-
! Fluorescence <br>during training
+
|
-
! Fluorescence <br> during testing
+
|-
-
|-    
+
| [[ETHZ/Parameters | Parameters used in our simulations]]
-
| aTc
+
|
-
| aTc
+
|
-
| YFP
+
|
-
| YFP
+
|-
-
|-     
+
|}
-
| aTc                   
+
-
| IPTG
+
-
| YFP
+
-
| GFP
+
-
|-    
+
-
| IPTG                   
+
-
| aTc                     
+
-
| CFP
+
-
| RFP
+
-
|-      
+
-
| IPTG
+
-
| IPTG
+
-
| CFP
+
-
| CFP
+
-
|}
+
-
 
+
-
[1]: Toggle Switch
+
-
 
+
-
<p><ul>
+
-
<li> How about changing "educatETH <i>E.coli</i> to all italics "<i>educatETH E.coli</i>"
+
-
*<span style=color:#cc1177;>( might be kinda late now, we have already had "educatETH <i>E.coli</i>" on the T-shirts... ?)</span>
+
-
*<span style=color:#cc1177;>(Not really because the font on the T-shirts is all italics, for all who want to know: Bitstream Charter Bold Italic Not-Rotated)</span>
+
-
<li> Change the name of p22cII to only cII (its a cI analog) p22 just means that it derives from the phage p22.
+
-
<li> IMPORTANT: THE COLOURS ARE TOTALLY WRONG IN THE SIMULATION PART. Please refer to the table on the main page. Changed it just now, it was wrong before!!!
+
-
<li> Change banner on top of page. Stefan: Can we please change the banner back to the old version?!? It was MUCH nicer.
+
-
<li> Decide on headings type. I like larger headings more, I also like the horizontal line because it separates, put it only on Introduction for you to see how it is.
+
-
<li> Possibly put table of contents.
+
-
<li> Possibly take educatETH <i>E.coli</i> from Figure.
+
-
*<span style=color:#cc1177;>( by "Figure", you mean the Einstein figure on the banner? )</span>
+
-
 
+
-
<li> Change Figure 2.
+
-
<li> <span style=color:blue;>Possibly change figure caption format from xxx (Fig. x) to Fig.x: xxx. Put second format on Figure 2 for all to check.</span>
+
-
<li> <span style=color:blue;>Fix table showing possible system states and reporters. Maybe with some color? --> No colour please. </span>
+
-
<li> Put cross-reference on table. Is there something like a description function for tables? An automatic "Tab. 1" as in "Fig. 1"?
+
-
<li> <span style=color:blue;>Align table left</span>
+
-
<li> <span style=color:blue;>Add which reporters do what in paragraph.</span>
+
-
<li> Put (compressed!) team photo instead of Fig.1
+
-
*<span style=color:#cc1177;>( can we leave it and add team pic? Fig.1 is somehow our brand.)</span>
+
-
<li> <span style=color:blue;>Fix paragraph with system description, looks somehow bulky. Maybe italics or bold on important things?</span>
+
-
<li> Fix reference on toggle switch.
+
-
<li> Possibly remove Introduction heading altogether, and just start with the text.
+
-
<li> These two lines are kinda confusing...
+
== References ==
-
*" Main Page / Biology Pespective / Engineering Perspective / Meet the Team / Team Notes / Pictures!"
+
-
*"Main Page / System Modeling / Simulations / System Implementation / Lab Notes / Meet the Team / Team Notes / Pictures!
+
-
<li> '''(19th Oct.)''' Just notice that we have different header styles under different sub-wikipage...
+
-
<li><span style=color:red;>'''BTW, can we label the solved problems to </span><span style=color:blue;>blue </span><span style=color:red;>?'''</span>
+
-
</ul></p>
+
-
*Need picture: Bacteria red, Bacteria Green, two pictures showing different exposure to chemicals (''Sylke: see my presentation Sven will hold for me tonight (20.09) -> the FACS guy wants probes of our XFP expressing E.coli - the one who brings it to him can just put it under the microscope and take a few pictures for the wiki'')
+
[http://www.nature.com/nature/journal/v447/n7143/abs/nature05913.html;jsessionid=62903C604764B175945C03DB8639ECBD &#91;1&#93; Bird A] <i>"Perceptions of epigenetics"</i>, Nature 447:396-398, 2007 <br />
-
*Need picture: Einstein ecoli (''Sylke: does Stefan have the layer file?'')
+
[http://linkinghub.elsevier.com/retrieve/pii/S096098220701007X &#91;2&#93; Ptashne M] <i>"On the use of the word ‘epigenetic’"</i>, Current Biology 17(7):R233-R236, 2007 <br />
-
*Stupidity: All E. Colis are equal, but our E. Colis are more equal than the others :D
+
-
*''Katerina'': 2. If we have a separate "Meet the team" page (which is good that we have), we have to make sure that all data about each one of us (short bio+photo) appear also on each one's user page-the same version would be the best, in my opinion.
+
-
*''Katerina'': 3. Figure 2, bottom right part needs to be a bit larger/more clear, in my opinion, as it's important. (Christos: If you click, then it becomes larger. Will have the same at the bio part as well... Should I make it bigger anyway? I will change it, it is wrong anyway :D)
+
-
<html><body>
 
-
<a href="http://www3.clustrmaps.com/counter/maps.php?url=https://2007.igem.org/ETHZ" id="clustrMapsLink"><img src="http://www3.clustrmaps.com/counter/index2.php?url=https://2007.igem.org/ETHZ" style="border:0px;" alt="Locations of visitors to this page" title="Locations of visitors to this page" id="clustrMapsImg" onError="this.onError=null; this.src='http://www2.clustrmaps.com/images/clustrmaps-back-soon.jpg'; document.getElementById('clustrMapsLink').href='http://www2.clustrmaps.com'" />
 
-
</a>
 
-
<html><body>
+
<html><body>
-
<a>
+
<a href="http://www3.clustrmaps.com/counter/maps.php?url=https://2007.igem.org/ETHZ" id="clustrMapsLink"><img src="http://www3.clustrmaps.com/counter/index2.php?url=https://2007.igem.org/ETHZ" style="border:0px;" alt="Locations of visitors to this page" title="Locations of visitors to this page" id="clustrMapsImg" onError="this.onError=null; this.src='http://www2.clustrmaps.com/images/clustrmaps-back-soon.jpg'; document.getElementById('clustrMapsLink').href='http://www2.clustrmaps.com'" />
-
<img src="http://www.easycounter.com/counter.php?stefanluzi"
+
</a>
-
border="0" alt="Welcome to ETHz - iGEM07"></a>
+
 +
<html><body>
 +
<a>
 +
<img src="http://www.easycounter.com/counter.php?stefanluzi"
 +
border="0" alt="Welcome to ETHz - iGEM07"></a>
</body></html>
</body></html>

Latest revision as of 20:20, 26 October 2007

ETHZ banner.png

 


ETH Zurich - educatETH E.coli System

Introduction

"All E.coli 's are equal, but some E.coli 's are more equal than others..." (freely adapted from "Animal Farm" by George Orwell)

... this is what George Orwell would have written, were he a synthetic biologist. In the E.coli colonies on petri dishes, all bacteria are equal; except for some special ones. Our project is about designing such special E.coli that are "more equal" than the rest: they have the ability to be trained in order to memorize and recognize their environment in the future. Their story will be presented through this wiki ...

Motivation

Fig. 1: Artist's approach to the different stages of the development. We started by modeling and simulating the system. We continued by specifying the DNA strands for its implementation. Finally in the end, our system should report with different fluorescent proteins (image edited)

Our combined team of biologists and engineers is coping with the problem of implementing memory capabilities in bacterial colonies. First, E.coli are able to respond differently (with distinct fluorescent proteins) to two different inputs (we used chemicals). Second, they remember which input was presented to them. Finally, when confronted with a new input, they are able to recognize whether it is the one that they were trained with or not. In other words, in this project we are educating the E.coli!

Multipurpose Cell Lines

Our system has the ability to behave in different ways according to an internal toggle inside it switching states based on the chemical substances that the system is exposed to. The toggle states could generally be used to trigger events such as enzyme synthesis, transcriptional regulation, virion production, or even cell death. Therefore, one may view the bacterial cell line containing this system as a multipurpose cell line. By adding a certain chemical to a cell line, the latter may be trained to exhibit a desired behavior, and then it is not necessary any more to construct two independent cell lines.

This means that one applies an “input engineering” instead of a “DNA engineering” approach. If one extends this idea to several multi-inducible toggle switches being harbored in the same cell line, the number of possible phenotypes increases to 2n, where n equals the number of toggle switches. For example, if one would have 5 such toggle switches inside a cell line, 32 different behavior patterns would be possible.

For the purpose of creating a toggle switch that is activated in a specific phase only and not always (a multi-inducible toggle switch), as is required for stable biological automatons, we introduced the concept of double promoters to the Registry of Standard Biological Parts, which can be helpful for engineering systems which exhibit a desired behavior only at specific times.

Link to Epigenetics

Epigenetics refers to features like chromatin or DNA modifications that do not involve changes in the underlying DNA sequence and are stable over many cell divisions [1],[2]. If one has a closer look at our proposed system, one can also view it as a model-system for epigenetics: Although the DNA sequence itself stays the same, two different subpopulations of cells with different phenotypes can develop from it. Put simply, depending in which state (subpopulation) the toggle switch is, the cells will produce different fluorescent proteins upon addition of two different inducer molecules. Therefore, the epigenetic feature here is the binding of specific repressor proteins whose production is dependent on the toggle switch state.

Intelligent Biosensors and Self-Adaptation

The system is capable of sensing different chemicals and producing different fluorescent proteins. Since the cells can be trained to produce one of several specific fluorescent protein types when a certain chemical is present, one can also view those cells as intelligent biosensors which recognize chemical substances according to a training phase. The intelligent biosensors are not limited to detect chemicals; temperature, pH, light, pressure could be detected with an appropriate system as well. Such an application could be especially of interest when the environment to be probed is harmful for humans, for example due to high toxicity.

Team Members

The ETH Zurich iGEM2007 Team

The ETH Zurich team consists of a good mixture between biologists and engineering students. We are:

For more information about us, visit our Meet the Team page.

Acknowledgments

The idea for the project as well as its implementation was done solely by the ETH iGEM 2007 team. We would like to thank the people in Sven Panke's Lab, especially Andreas Meyer who was always there for us when we had a problem. Additionally, we would like to thank Alfredo Franco-Obregón's lab and Oralea Büchi for the help with the flow cytometry.

We would also like to acknowledge the financial support by EU, the ETH Zurich, and GeneArt:

http://www.tik.ee.ethz.ch/~thohm/EU.gif http://www.tik.ee.ethz.ch/~thohm/ethlogo.jpg http://www.tik.ee.ethz.ch/~thohm/geneart.gif

Site Map

In this wiki, we will present to you a detailed description of the proposed system: starting with the modeling of the system, we describe both, simulations and theoretical considerations of the system, as well as the actual implementation using bio-bricks accompanied by our lab notes. Additionally, you will find further information on the team, more details about ideas we developed before we came up with the system we finally implemented, and some pictures documenting our work.

The site map of our wiki is the following:

Modeling Pages Biology Pages ETHZ Team Pages Links
Modeling of the learning system Biological implementation Team page The ETH Zurich 2005 project
Representation using flip-flops Biobricks/parts Pictures The ETH Zurich 2006 project
Representation using finite state machines Lab notes Brainstorming sessions
Model simulations and theoretical considerations
Parameters used in our simulations

References

[1] Bird A "Perceptions of epigenetics", Nature 447:396-398, 2007
[2] Ptashne M "On the use of the word ‘epigenetic’", Current Biology 17(7):R233-R236, 2007


Locations of visitors to this page Welcome to ETHz - iGEM07