ETHZ

From 2007.igem.org

(Difference between revisions)
(Lab Notes)
(Multipurpose Cell Lines)
 
(320 intermediate revisions not shown)
Line 1: Line 1:
-
[[Image:Eth_zh_logo_2.png|800px]] __TOC__
+
[[Image:ETHZ_banner.png|830px]]
-
== Team Members ==
+
<!--
-
<div style="float:right">
+
<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__
-
| class="taxo-image" | [[Image:|thumb|398px|'''Picture:''' The ETH Zuerich iGEM Team 2007 ''(left to right: )'']]
+
<html>
-
|}</div>
+
<script type="text/javascript" src="http://christos.bergeles.net/eth_dropdowntabs.js">
-
For the International Competition on Genetically Engineered Machines, the teams should be composed of both biologist and engineers. That way, the engineers will try to develop new systems in a bottom-up fashion and run numerical simulations, while the biologists will be able to assess the feasibility of such systems, and construct them from biological parts.
+
/***********************************************
 +
* 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
 +
***********************************************/
-
<P><b>Instructors:</b></P>
+
</script>
-
[https://2007.igem.org/User:sven Sven Panke]
+
-
Joerg Stelling
+
<!-- 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>
-
<P><b>Students:</b></P>
+
<!--1st drop down menu -->
-
Martin Brutsche
+
<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>
-
Katerina Dikaiou
 
-
[https://2007.igem.org/User:Raphael Raphael Guebeli]
+
<!--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>
-
[https://2007.igem.org/User:hoehnels Sylke Hoehnel]
+
<!--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>
-
[https://2007.igem.org/User:LiNan Nan Li]
+
<!--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>
-
[https://2007.igem.org/User:Stefan Stefan Luzi]
+
<!--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>
-
<P><b>Graduate Students:</b></P>
+
<script type="text/javascript">
-
[https://2007.igem.org/User:cbergeles Christos Bergeles]
+
//SYNTAX: tabdropdown.init("menu_id", [integer OR "auto"])
 +
tabdropdown.init("colortab", 3)
 +
</script>
-
[http://www.tik.ee.ethz.ch/~sop/people/thohm/ Tim Hohm]
+
</html>
-
Christian Kemmer
+
__NOTOC__
-
[https://2007.igem.org/User:JoeKnight Joseph Knight]
+
<html>
 +
<p align="center"><font size="6"><b>ETH Zurich - educatETH <i>E.coli</i> System</b></font></p>
 +
</body>
 +
</html>
-
[https://2007.igem.org/User:uhrm Markus Uhr]
+
=Introduction=
 +
<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> 
-
== Introduction to Synthetic Biology ==
+
... 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 order to get an initial understanding of the concepts of synthetic biology, we read and presented
+
-
publications on various topics. A representative list of the topics that we covered on this “boot-camp” is listed in the following:
+
-
* Introduction to synthetic biology
+
==Motivation==
-
* DNA de novo design
+
-
* DNA circuits
+
-
* Hysteresis
+
-
* Oscillators
+
-
* Zinc fingers
+
-
* Noise in single cell measurements
+
-
* Distance communication
+
-
* Paramter manipulations
+
-
* Protein logic
+
-
* Orthogonal systems
+
-
* Minimal genomes
+
-
* mRNA engineering
+
-
* RNA regulators
+
-
== Choosing the Project ==
+
[[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]]
-
=== Step 1: Brainstorming ===
+
-
Initially, we wanted to come up with as many ideas as possible, in order to be able to choose among them the best, and find a cool project to carry out. For this reason, we had brainstorming sessions. We split up in three teams, and each team tried to come up with many fancy and showy ideas, which was facilitated by keeping in mind the following brainstorming guidelines:
+
-
# Defer judgment - the rules of nature don't apply
+
-
# Encourage wild ideas
+
-
# Build on the ideas of others
+
-
# Be visual
+
-
# Go for quantity
+
-
# Stay focused on topic
+
-
The ideas that we came up with, as were presented in the following meetings, were:
+
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.  
-
* '''PID Controller''': Design a PID controller out of biological elements. The P component can be a simple
+
In other words, in this project '''we are educating the <i>E.coli</i>'''!
-
output to a regulatory protein, and the I component can be the overall protein production at a time
+
 
-
period. What can the D component be?
+
===Multipurpose Cell Lines===
-
* '''Motion Detector''': Cells are grown on a petri dish. Below the dish, moving images are displayed. A 3-
+
 
-
state automaton is proposed. Output A is created when light is present. Output B is created when light
+
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.  
-
is absent. Moving patterns will cause some cells to create both outputs over time. This will result in
+
 
-
some “inspector” cells producing output C, by collecting outputs A and B.
+
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.  
-
* '''Analog-to-Digital Converter''': Compare the level of protein concentration with thresholds, and digitize
+
 
-
the output.
+
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.
-
* '''Neural Network''': Create a sort of biological neural network with bacteria. We should address the issue
+
 
-
of learning, and find a way to incorporate the feedback in the cell decision making process. Directed
+
===Link to Epigenetics===
-
evolution can be a sort of feedback, but we want to avoid this. (This idea was the basis for the
+
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.
-
“learning project”)
+
 
-
* '''Central Pattern Generation''': Coordinate two oscillators, so that they are in phase. This can be achieved
+
===Intelligent Biosensors and Self-Adaptation===
-
through diffusion between the different cell types. (This idea was the basis for the “spatial oscillations
+
 
-
project”).
+
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.
-
* '''Paramedic Cells''': Some cells are able to detect signals coming from other cells, and create food for
+
 
-
them, or create proteins in order to save them and make them function better.
+
==Team Members==
-
* '''Cell Batteries''': Cells are able to create and store large quantities of ATP, during a “storing process”.
+
[[Image:ETHZ_Group_photo_6.png|right|thumb|The ETH Zurich iGEM2007 Team|270px]]
-
Afterwards, they can detect a signal and give back all the energy they stored, in a short burst, like a
+
 
-
capacitor. Other ideas are that the cells can “blow up” and emit large amounts of GFP, based on the
+
The ETH Zurich team consists of a good mixture between biologists and engineering students.  
-
ATP that they have accumulated.
+
We are:
-
* '''Flashing Bacteria''': Cells are grown on a light pattern. The cells that are on the bright parts of the
+
<ul>
-
image are oscillating in phase, while the others are remaining dark. This results in the observation of a
+
<li><i>Undergraduate students</i>: <br>
-
flashing pattern.
+
[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>
-
* '''Biocam''': Visible to Fluorescent light converter.
+
[https://2007.igem.org/Nan_Li Nan Li],  
-
* '''BioCD''': “Print” cells on a film, then read them out and “reconstruct” the original data. Basically, it is
+
[https://2007.igem.org/User:Stefan Stefan Luzi]
-
an analog to digital converter, followed by a system that can interpret the digitized data. (This idea
+
<li><i>Graduate students</i>: <br>
-
was the basis for the “Music of life project”, where cells would produce fluorescent proteins based on
+
[http://christos.bergeles.net Christos Bergeles],
-
an analog input. Then, the amount and type of fluorescence would code some music).
+
[http://www.tik.ee.ethz.ch/~sop/people/thohm/ Tim Hohm], <br>
-
* '''Clock''': A follow-the-leader system. We have to groups of cells. The first group creates something that
+
[http://www.fussenegger.ethz.ch/people/kemmerc Christian Kemmer],  
-
repels the second group. The second group creates a protein that attracts the first group. This way,
+
[https://2007.igem.org/User:JoeKnight Joseph Knight], <br>
-
they first group wants to “catch” the second group, whereas the second group wants to “avoid” the
+
[http://www.ricomoeckel.de Rico Möckel],
-
first group. This results in them moving around. We can say that the second group is the leader, and
+
[http://csb.inf.ethz.ch/people/uhr.html Markus Uhr]
-
the first group exhibits a “follow-the-leader” behavior.
+
<li><i>Project advisors</i>: <br>
-
* '''Sensors''': Various systems that can sense PH, pressure, temperature, meat quality, moisture e.t.c. have
+
[http://www.ipe.ethz.ch/laboratories/bpl/people/panke Sven Panke], <br>
-
been proposed.
+
[http://csb.inf.ethz.ch/people/stelling.html Joerg Stelling]
 +
</ul>
-
=== Step 2: Preferred Projects ===
+
For more information about us, visit our [[ETHZ/Meet_the_team | Meet the Team]] page.
-
We decided that three of the above ideas were worth a deeper examination. Namely, we split again in three
+
==Acknowledgments==
-
teams, so that we can come up with an initial system, with remarks on its feasibility and coolness. Our results
+
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.
-
were presented on all the team members, so that we could then limit the potential projects down to two and
+
-
one, and proceed with constructing the DNA sequence. The three projects and the presentations that we did
+
-
were:
+
-
# '''Spatial Oscillations''': Should I put something here?
+
-
# '''Music of Life''': The basic idea is that instead of having an analog-to-digital converter with four outputs (three fluorescent proteins, and no output), we can have two switches. When switch A is on, RFP is produced. When switch B is on, GFP is produced. When both switches A and B are on, a yellowish output is observed. By recording these outputs, we can later create music, by assigning each fluorescent protein to a chord. For example, RFP would correspond to a G chord. The strength of the fluorescence can signify the strength of the chord. If the cells are placed on a spinning disk, we can have something like a vinyl player. A camera is observing the cells, and created music on the fly.
+
-
# '''Learning''': Based on the idea of the neural network, we want to create a biological system, where the cells can learn a specific behavior. In order to simplify the system, we decided that the cells can learn to recognize a specific type of other cells. We divide the process in a learning phase, and a recognition phase. First, cells A are put together with cells B. Then, cells A are “learning” to recognize cells B. If afterwards they are put in a petri dish with cells B, they will emit GPF. Otherwise, they will stay dark.
+
-
We decided that ideas one and three were worth further exploration. Idea two, even though it was fancy, it
+
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]:
-
was fairly simple, as, creating two switches is a straightforward and well understood process. As a result, it
+
<center>
-
was discarded. We could try to make the system more complex, but making something more complex just for
+
{| border="0"
-
the shake of it, is not a good engineering approach ;)
+
|-
 +
| [http://europa.eu http://www.tik.ee.ethz.ch/~thohm/EU.gif]
 +
| width="40" |
 +
| [http://www.ethz.ch http://www.tik.ee.ethz.ch/~thohm/ethlogo.jpg]
 +
| width="40" |
 +
| [http://www.geneart.com http://www.tik.ee.ethz.ch/~thohm/geneart.gif]
 +
|}
 +
</center>
-
== The Project ==
+
==Site Map==
-
We decided to proceed with the '''Learning Project'''. Our goal is to design an E.coli strain, able to distinguish between two chemical substances after an assigned learning process, induced by an external chemical signal. After the bacterial strain was taken to a testing phase, the output will result in either yellow or cyan fluorescence, depending on whether the bacteria recognized the same chemical substance in the testing phase as it was trained in the learning phase or a different one.
+
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.
-
We aim to implement our system using a toggle switch consisting of different repressor and activator proteins coupled with double regulatory regions.
+
-
=== System Models ===
+
The site map of our wiki is the following:
-
[[Image:ethz_system_1.png]]
+
-
<br>
+
-
<br>
+
-
[[Image:ethz_system_2.png]]
+
-
=== Simulations ===
+
{| 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;"
 +
!width="34%"| Modeling Pages                       
 +
!width="22%"| Biology Pages
 +
!width="22%"| ETHZ Team Pages
 +
!width="22%"| Links
 +
|-
 +
| [[ETHZ/Model | Modeling of the learning system]]
 +
| [[ETHZ/Biology | Biological implementation]]
 +
| [[ETHZ/Meet_the_team | Team page]]
 +
| [https://2006.igem.org/wiki/index.php/ETH_Zurich_2005 The ETH Zurich 2005 project]
 +
|-
 +
| [[ETHZ/FlipFlop | Representation using flip-flops]]
 +
| [[ETHZ/Biology/parts | Biobricks/parts]]
 +
| [[ETHZ/Pictures | Pictures]]
 +
| [https://2006.igem.org/wiki/index.php/ETH_Zurich_2006 The ETH Zurich 2006 project]
 +
|-
 +
| [[ETHZ/FSM | Representation using finite state machines]]
 +
| [[ETHZ/Biology/Lab | Lab notes]]
 +
| [[ETHZ/Internal | Brainstorming sessions]]
 +
|
 +
|-
 +
| [[ETHZ/Simulation | Model simulations and theoretical considerations]]
 +
|
 +
|
 +
|
 +
|-
 +
| [[ETHZ/Parameters | Parameters used in our simulations]]
 +
|
 +
|
 +
|
 +
|-
 +
|}
-
=== Sensitivity Analysis ===
+
== References ==
-
== Lab Work ==
+
[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 />
 +
[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 />
-
Here we can write when each one will be available. For example:
 
-
*Christos: Can be available everyday after 17:30, till 00:00. Weekends as well. If that is not possible, I will take days off, one per week, to work in the lab (if supervisor agrees, that is...)
 
-
=== Cloning Plan ===
 
-
=== Lab Notes ===
+
<html><body>
-
<font face="DejaVu Sans" size="3"><b>Week 1</b></font> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <b>06.08.07 - 12.08.07</b><br>
+
<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'" />
-
[[ETHZ/labnotes| detailed lab notes]]<BR>
+
</a>
-
<font face="DejaVu Sans" size="3"><b>Week 2</b></font> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <b>13.08.07 - 19.08.07</b><br>
+
-
[[ETHZ/labnotes| detailed lab notes]]<BR>
+
<html><body>
-
<font face="DejaVu Sans" size="3"><b>Week 3</b></font> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <b>20.08.07 - 26.08.07</b><br>
+
<a>
-
[[ETHZ/labnotes| detailed lab notes]]<BR>
+
<img src="http://www.easycounter.com/counter.php?stefanluzi"
-
<font face="DejaVu Sans" size="3"><b>Week 4</b></font> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <b>27.08.07 - 02.09.07</b><br>
+
border="0" alt="Welcome to ETHz - iGEM07"></a>
-
[[ETHZ/labnotes| detailed lab notes]]<BR>
+
</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 [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

The ETH Zurich iGEM2007 Team

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

  • Undergraduate students:
    Martin Brutsche, Katerina Dikaiou,
    Raphael Guebeli, Sylke Hoehnel,
    Nan Li, Stefan Luzi
  • Graduate students:
    [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], Joseph Knight,
    [http://www.ricomoeckel.de Rico Möckel], [http://csb.inf.ethz.ch/people/uhr.html Markus Uhr]
  • Project advisors:
    [http://www.ipe.ethz.ch/laboratories/bpl/people/panke Sven Panke],
    [http://csb.inf.ethz.ch/people/stelling.html Joerg Stelling]

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 [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]:

[http://europa.eu http://www.tik.ee.ethz.ch/~thohm/EU.gif] [http://www.ethz.ch http://www.tik.ee.ethz.ch/~thohm/ethlogo.jpg] [http://www.geneart.com 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

[http://www.nature.com/nature/journal/v447/n7143/abs/nature05913.html;jsessionid=62903C604764B175945C03DB8639ECBD [1] Bird A] "Perceptions of epigenetics", Nature 447:396-398, 2007
[http://linkinghub.elsevier.com/retrieve/pii/S096098220701007X [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