From 2007.igem.org

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Latest revision as of 20:20, 26 October 2007

Introduction Team Members Acknowledgments Site map

Introduction Model Overview Detailed Model Final Model Modeling Basics Page Mathematical Model FSM View Page Flip-Flop View Page Parameters Page

Introduction Test Cases Sensitivity Analysis

Introduction The Complete System System Phases Current Cloning Status System Parts Page Lab Notes Page

The ETH Zurich 07 Team Team Description Brainstorming Page

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

@@ Line 93: / Line 93: @@
 <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>
-... 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 modeling and designing these special <i>E.coli</i> that are "more equal" than the rest: they have the ability to be trained, memorize, and recognize their environment, and their story will be presented through this wiki ...
+... 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 ...
 ==Motivation==
-[[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, and in the end, our system should report with different fluorescent proteins (image edited)|600px]]
+[[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]]
-Our combined team of biologists and engineers is working on the ''E.coli'' 's ability, first, to recognize two different inputs (here we use two different chemicals), second, to remember which input was presented to them, and third, when confronted with a new input, to recognize whether it is the one that it was trained with or not - in other words, '''we educated the <i>E. coli</i>'''.
+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 <i>E.coli</i>'''!
-It is obvious thus, that we are coping with the problem of implementing memory capabilities in bacterial colonies. Our system is a memorizing system, and it also has the ability to understand its environment through a recognition phase. If we assume that the training chemicals are harmful for humans, we can use the developed system to understand whether a particular environment is dangerous for humans or not. In this sense, our system can have applications in the health/safety sector, as is described below:
+===Multipurpose Cell Lines===
-===Intelligent Biosensors and Self-Adaptation===
+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.
-We constructed a system 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, able to change their properties in a training phase.
+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.
-It is also possible that the environment (and its chemicals) itself is the training phase, and hence, that the biosensors are adapting themselves to the existing environment. Eventually, the intelligent biosensors are not limited to detect chemicals. Temperature, pH, light, pressure etc. could be detected with an appropriate system as well.
-The main applications of our system however, lie in fully exploiting its memorizing potential, as can be understood from the following:
+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.
-===Multipurpose Cell Lines===
+===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.
-Our system can be trained to behave in a specific way, by setting its inducible toggle switch to one of its two states. This specific states can trigger specific and different events such as enzyme synthesis, transcriptional regulation, virion production, or even cell death. In this case, one can view the bacterial cell line containing this system, as a multipurpose cell line. One can add a certain chemical to a cell line, and train it to the desired behavior, instead of constructing two independent cell lines.
+===Intelligent Biosensors and Self-Adaptation===
-This means, one applies an “input engineering” instead of a “DNA engineering” approach. If one extends this idea to several inducible toggle switches being harbored in the same cell line, the number of possible phenotypes increases to 2<sup>n</sup>, where n equals the number of toggle switches. For example, if one would have 5 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 (we call this 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 future projects. As a concept, double promoters are expandable to handle multiple promoter sites, for the case of a greater number of toggle switches (stefan: this sentence is not so clear to me, can we formulate it differently?).
-==Link to Epigenetics==
+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.
-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 inducer molecules (aTc or IPTG). For example, if aTc is added one subpopulation will be red while the other will be yellow although both carry exactly the same DNA information. Therefore, the epigenetic feature here is the binding of specific repressor proteins whose production is dependent on the toggle switch state.
 ==Team Members==
-[[Image:ETHZ_Group_photo_6.png|right|thumb|ETHZ iGEM2007 Team|250px]]
+[[Image:ETHZ_Group_photo_6.png|right|thumb|The ETH Zurich iGEM2007 Team|270px]]
-The ETH Zurich team consists of good mixture between biologists and engineering students.
+The ETH Zurich team consists of a good mixture between biologists and engineering students.
 We are:
 <ul>
@@ Line 146: / Line 142: @@
 ==Acknowledgments==
-The idea for the project as well as its implementation was done 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.
+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]:
@@ Line 162: / Line 158: @@
 ==Site Map==
-In this wiki, we will 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.
+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.
 The site map of our wiki is the following:
 {| 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="25%"| Modeling Pages
+!width="34%"| Modeling Pages
-!width="25%"| Biology Pages
+!width="22%"| Biology Pages
-!width="25%"| ETHZ Team Pages
+!width="22%"| ETHZ Team Pages
-!width="25%"| Links
+!width="22%"| Links
 |-
 | [[ETHZ/Model | Modeling of the learning system]]

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