ETHZ

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[[Image:Eth_zh_logo_2.png|800px]]
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<center>[[Image:Eth_zh_logo_4.png|900px]]</center>
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__TOC__
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== Team Members ==
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<center>[[ETHZ/Main_page | Main Page]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Biology | Biology Pespective]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Engineering | Engineering Perspective]] &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>
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<div style="float:right">
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{|  
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|-
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| class="taxo-image" | [[Image:|thumb|398px|'''Picture:''' The ETH Zuerich iGEM Team 2007 ''(left to right: )'']]
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|}</div>
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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.
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__NOTOC__
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<P><b>Instructors:</b></P>
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<center><font size = '+2'><b> .:: ETH Zurich - EducatETH ''E.coli'' ::. </b></font></center><br>
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[https://2007.igem.org/User:sven Sven Panke], Joerg Stelling
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<P><b>Students:</b></P>
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=='''.:: Introduction ::.'''==
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[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], [http://leemnan.spaces.live.com Nan Li], [https://2007.igem.org/User:Stefan Stefan Luzi]
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<p>It is the third time the [http://www.ethz.ch ETH Zurich] takes part in [https://2007.igem.org/wiki/index.cgi International Genetically Engineered Machine Competition] (iGEM). This year, our combined team of biologists and engineers has undertaken the task of educating <i>E.coli</i> ! More specifically, in our project (Fig. 1)  [[Image:Educateth_Ecoli.png|thumb|The ETH Zurich team undertook the task of engineering a learning mechanism for <i>E.coli</i>. '''(Fig. 1)'''|500px]] we are trying to create <i>E.coli</i> which have the ability to distinguish between two chemicals they may be exposed to after they have undergone a training phase.</p>
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<P><b>Graduate Students:</b></P>
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<p>Stay in this page for an overview of how EducatETH <i>E.coli</i> works, the motivation behind it and its possible future applications. If you want to see the biological design of our system and the parts that it consists of, or if you are interested in building it yourself and want to read the lab protocols, the [[ETHZ/Biology | Biology Perspective]] will be of interest to you. If you want to know more on how EducatETH <i>E.coli</i> has been modeled and simulated, or on its equivalences to systems such as flip-flops and finite state machines, please visit the [[ETHZ/Engineering | Engineering Perspective]]. You may also want to visit [[ETHZ/Meet_the_team | Meet the Team]] for information regarding the team and [[ETHZ/Pictures | Pictures!]] for our photo gallery. Finally, in [[ETHZ/Internal | Team Notes]] you can read the notes exchanged by the team during preparation for the competition.</p>
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[http://christos.bergeles.net Christos Bergeles], [http://www.tik.ee.ethz.ch/~sop/people/thohm/ Tim Hohm], [http://fm-eth.ethz.ch/eth/peoplefinder/FMPro?-db=phonebook.fp5&-format=pf%5fdetail%5fde.html&-lay=html&-op=cn&Typ=Staff&Suche%5fText=kemmer&Suche%5fText%5fpre=kemmer&-recid=3772770936&-find=/ Christian Kemmer], [https://2007.igem.org/User:JoeKnight Joseph Knight], [https://2007.igem.org/User:uhrm Markus Uhr], [http://www.ricomoeckel.de Rico Möckel]
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== Introduction to Synthetic Biology ==
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====='''.:: Team Members ::.'''=====
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In order to get an initial understanding of the concepts of synthetic biology, we read and presented
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publications on various topics. A representative list of the topics that we covered on this “boot-camp” is listed in the following:
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* Introduction to synthetic biology
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<p>As [https://2007.igem.org/wiki/index.cgi iGEM] is a synthetic biology competition, the ETH Zurich team consists of balanced numbers of biology and engineering students. Our team members are: </p><ul>
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* DNA de novo design
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<li><i>Project advisors</i>: [https://2007.igem.org/User:sven Sven Panke], Joerg Stelling
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* DNA circuits
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<li><i>Undergraduate students</i>: [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:LiNan Nan Li], [https://2007.igem.org/User:Stefan Stefan Luzi]
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* Hysteresis
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<li><i>Graduate students</i>: [http://christos.bergeles.net Christos Bergeles], [http://www.tik.ee.ethz.ch/~sop/people/thohm/ Tim Hohm], [http://fm-eth.ethz.ch/eth/peoplefinder/FMPro?-db=phonebook.fp5&-format=pf%5fdetail%5fde.html&-lay=html&-op=cn&Typ=Staff&Suche%5fText=kemmer&Suche%5fText%5fpre=kemmer&-recid=3772770936&-find=/ Christian Kemmer], [https://2007.igem.org/User:JoeKnight Joseph Knight], [https://2007.igem.org/User:uhrm Markus Uhr], [http://www.ricomoeckel.de Rico Möckel]
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* Oscillators
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</ul>
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* Zinc fingers
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<p>For more information on the team members, follow the links or visit [[ETHZ/Meet_the_team | Meet the Team]].</p>
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* Noise in single cell measurements
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* Distance communication
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* Parameter manipulations
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* Protein logic
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* Orthogonal systems
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* mRNA engineering
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* RNA regulators
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== Choosing the Project ==
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====='''.:: Motivation ::.'''=====
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=== Step 1: Brainstorming ===
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<p> Learning plays a major role for living organisms, as it enables them to survive by adapting to an ever-changing environment. Engineering a simple biological system which exhibits learning behavior is of great interest, as it can support our understanding of this procedure by comparison with natural systems. On the other hand, learning and memorizing plays an equally big role in engineering; from handwriting recognition on PDAs to plain logical circuits storing their binary state on computers, it can be found on numerous everyday life applications. Constructing a biological analogue of a simple memory as known from logic design can hopefully function as a biological building block from which more complex systems may be constructed. We therefore think that EducatETH <i>E.coli</i> operates on an exciting interface between engineering and biology.</p>
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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:
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# Defer judgment - the rules of nature don't apply
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# Encourage wild ideas
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# Build on the ideas of others
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# Be visual
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# Go for quantity
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# Stay focused on topic
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The ideas that we came up with, as were presented in the following meetings, were:
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====='''.:: <i>E.coli</i> Intelligence (E.I) - Specifications and analogies ::.'''=====
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* '''PID Controller''': Design a PID controller out of biological elements. The P component can be a simple 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?
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* '''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 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.
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* '''Analog-to-Digital Converter''': Compare the level of protein concentration with thresholds, and digitize the output.
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* '''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 evolution can be a sort of feedback, but we want to avoid this. (This idea was the basis for the “learning project”)
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* '''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.
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* '''Cell Batteries''': Cells are able to create and store large quantities of ATP, during a “storing process”. 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 ATP that they have accumulated.
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* '''Flashing Bacteria''': Cells are grown on a light pattern. The cells that are on the bright parts of the image are oscillating in phase, while the others are remaining dark. This results in the observation of a flashing pattern.
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* '''Biocam''': Visible to Fluorescent light converter.
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* '''BioCD''': “Print” cells on a film, then read them out and “reconstruct” the original data. Basically, it is an analog to digital converter, followed by a system that can interpret the digitized data. (This idea was the basis for the “Music of life project”, where cells would produce fluorescent proteins based on an analog input. Then, the amount and type of fluorescence would code some music).
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* '''Clock''': A follow-the-leader system. We have to groups of cells. The first group creates something that repels the second group. The second group creates a protein that attracts the first group. This way, they first group wants to “catch” the second group, whereas the second group wants to “avoid” the first group. This results in them moving around. We can say that the second group is the leader, and the first group exhibits a "follow-the-leader” behavior.
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* '''Sensors''': Various systems that can sense PH, pressure, temperature, meat quality, moisture e.t.c. have been proposed.
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=== Step 2: Preferred Projects ===
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<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>
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We decided that three of the above ideas were worth a deeper examination. Namely, we split again in three
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<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>
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teams, so that we can come up with an initial system, with remarks on its feasibility and coolness. Our results
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(Want to read more about this? Visit the [[ETHZ/Engineering| Engineering Perspective]]!)</p>
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were presented on all the team members, so that we could then limit the potential projects down to two and
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one, and proceed with constructing the DNA sequence. The three projects and the presentations that we did
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were:
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# '''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 music is created on the fly.  
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# '''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.
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Idea two, even though it was fancy, was fairly simple, as, creating two switches is a straightforward and well understood process. As a result, it was discarded. We could try to make the system more complex, but making something more complex just for the sake of it, is not a good engineering approach ;)
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<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>
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(Want to see the biological design of our modified toggle? Visit the [[ETHZ/Biology | Biology Perspective]]!)</p>
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== The Project ==
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====='''.:: A short system description ::.'''=====
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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 (teaching substance). 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.
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<p>EducatETH <i>E.coli</i> is able to recognize between two chemical substances (aTC and IPTG) it has previously been exposed with help of an external chemical signal (AHL).
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We aim to implement our system using a toggle switch consisting of different repressor and activator proteins coupled with double regulatory regions.
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In the first part of the training phase (“meeting”), the system is exposed to one of the two chemicals (aTC and IPTG) and AHL is added, causing a steady system behavior. In the second part of the training phase (“memorizing”), all chemicals but AHL are removed, allowing the system to maintain its state. Finally, in the testing phase (“recognizing”), 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. As seen on Table , 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 , YFP for ) and two others to control whether the system sees the same chemical as it did in the training phase (GFP) or not (RFP). Thus, the system response is determined uniquely. </p>
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Our biological system was inspired from the toggle of [?], and its binary logic equivalent. In order to understand that, one should think of learning as a "switching of behavior". As a response to an external stimulus, the behavior changes. If we approach the problem with the tools of binary logic, we can see that we want to implement a JK flip-flop with a latch. At the learning process, the JK flip-flop will stabilize at its final state Q. At the recognition phase, the flip-flop is latched, and recognition is performed (see figure below):
 
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[[Image:logic_circuit.png|center]]
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{| 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;"                   
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! Training <br>chemical             
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! Testing <br>chemical             
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! Fluorescence <br>during training
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! Fluorescence <br> during testing
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|-   
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| aTc
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| aTc
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| CFP or YFP?
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| GFP
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|-     
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| aTc                   
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| IPTG
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| CFP or YFP?
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| RFP
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|-   
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| IPTG                   
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| aTc                     
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| CFP or YFP?
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| RFP
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|-       
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| IPTG
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| IPTG
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| CFP or YFP?
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| GFP
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|}
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Based on the toggle from [?], we discussed our prototype system (see figure below), which the resulted in the refined system that we describe in the next section.
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====='''.:: References ::.'''=====
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[1]: Toggle Switch
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(picture of initial draft of the bio system, as taken from Joe, --here--)
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====='''.:: Acknowledgements ::.'''=====
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<ul>
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<li><p>[http://europa.eu The European Union]</p>
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<li><p>[http://www.ethz.ch The ETH Zurich]</p>
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<li><p>[http://www.geneart.com GENEART]</p>
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</ul><br>
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====='''.:: Links ::.'''=====
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<ul>
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<li><p>[https://2006.igem.org/wiki/index.php/ETH_Zurich_2005 The ETH Zurich 2005 project]</p>
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<li><p>[https://2006.igem.org/wiki/index.php/ETH_Zurich_2006 The ETH Zurich 2006 project]</p></ul><br>
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=='''.:: To Do ::.'''==
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====='''.:: New ones ::.'''=====
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=== System Models ===
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<p><ul>
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[[Image:new_learning_system3.png|center]]
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<li> Change banner on top of page.
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<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.
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<li> Possibly put table of contents.
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<li> Possibly take EducatETH <i>E.coli</i> from Figure.
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<li> Change Figure 2.
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<li> Possibly change figure caption format from xxx (Fig. x) to Fig.x: xxx. Put second format on Figure 2 for all to check.
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<li> Fix table showing possible system states and reporters. Maybe with some color?
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<li> Put cross-reference on table.
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<li> Align table left
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<li> Add which reporters do what in paragraph.
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<li> Put (compressed!) team photo instead of Fig.1
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<li> Fix paragraph with system description, looks somehow bulky. Maybe italics or bold on important things?
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<li> Fix reference on toggle switch.
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<li> Possibly remove Introduction heading altogether, and just start with the text.
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</ul></p>
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=== Simulations ===
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====='''.:: Old ones ::.'''=====
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* [[ETHZ/Modeling Basics| basic modeling principles]]<BR>
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<p><ul>
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* [[ETHZ/Simulations| detailed information on the simulations]]<BR>
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<li>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'')
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<li>Need picture: Einstein ecoli (''Sylke: does Stefan have the layer file?'')
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=== Sensitivity Analysis ===
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<li>Stupidity: All E. Colis are equal, but our E. Colis are more equal than the others :D
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<li>''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.
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== Lab Work ==
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<li>''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)
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</ul></p>
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Here we can write when each one will be available. For example:
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*<b>Christos:</b><br> Can be available everyday after 18:00, till 00:00. Weekends as well.
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*<b>Tim:</b><br> 13.08.-15.08. after 17:30<br> away from 17.08. until 02.09.
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*<b>Martin:</b><br> Every day, also weekends, for half a day or even more if it's requiered. The last week of August and the first one in September I have only time for aproximately 5-6 h a day due to learning for the exams.
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*<b>Katerina:</b><br> Not available 5.09-7.09 (final exams). Otherwise available after 17:30. Possible also in the morning, if I know in advance that I will be needed.
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*<b>Christian:</b><br> Not available 5.10-24.10.2007 --> holidays, I can do most of the labwork during the day in my lab
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*<b>Sylke:</b><br> Not available 21.09-14.10.2007 --> holidays
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=== Cloning Plan ===
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The system consists of 11 parts. These are:
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{| class="wikitable" border = "1" style="text-align:left"
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|+ '''System parts'''
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|-
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! 1
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| TetR production(constitutive part of system)
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|-
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! 2
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| LacI production (constitutive part of system)
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|-
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! 3
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| LuxR production(constitutive part of system)
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! 4
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| 1st half of p22/YFP production (outer part of system, reporting)
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! 5
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| 2nd half of p22/YFP production (outer part of system, reporting)
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!6
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| CI production (inner part of system)
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! 7
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| p22 production (inner part of system)
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|-
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! 8
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| 1st half of CI/CFP production (outer part of system, reporting)
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! 9
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| 2nd half of CI/CFP production (outer part of system, reporting)
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|-
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! 10
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| RFP production (reporting)
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! 11
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| GFP production (reporting)
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|}
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3 plasmids will be used for the 11 system parts as follows:
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{| class="wikitable" border = "1" style="text-align:left"
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|+'''Plasmids and contents'''
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|-
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! plasmid !! resistance !! copy type!! contents !! comments
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|-
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| [[ETHZ/pbr322| pbr322]] || ampicillin || high || 1,2,3 || constitutive part
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|-
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| [[ETHZ/pck01| pck01]] || chloramphenicol|| low || 4,5,8,9 || outer part
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|-
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| [[ETHZ/pacyc177| pacyc177]] || kanamycin|| low || 6,7,10,11 || inner part, reporting
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|-
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|}
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The standard BioBrick assembly will be used to put the parts in the plasmids. Detailed information on how the BioBrick part fabrication works can be found  [http://openwetware.org/wiki/Synthetic_Biology:BioBricks/Part_fabrication here]. For a shorter explanation of how to assemble 2 parts together check [http://partsregistry.org/Assembly:Standard_assembly here]. Note that the composite part is constructed from the end to the beginning, i.e. each new part is inserted ''before'' the existing one. In the following, the plasmid containing the new part to be inserted will be referred to as the ''donor'' and the plasmid accepting the new part will be referred to as the ''acceptor''. Composite pars made of parts '''a''' and '''b''' are denoted '''a.b'''.
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==== '''Plasmid 1 ''(pbr322ap)'' ''' ====
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# Put parts 1,2,3 in  pbr322ap plasmids.
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# Merge plasmid containing part '''2''' ''(donor)'' with plasmid containing part '''3''' ''(acceptor)''. You should get a plasmid containing a '''2.3''' composite part.
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# Merge plasmid containing part '''1''' ''(donor)'' with plasmid containing composite part '''2.3'''  ''(acceptor)''. You should get a plasmid containing a '''1.2.3''' composite part.
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==== '''Plasmid 2 ''(pck01cm)'' ''' ====
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# Put parts 4,5,8,9 in  pck01cm plasmids.
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# Merge plasmid containing part '''4''' ''(donor)'' with plasmid containing part '''5''' ''(acceptor)''. You should get a plasmid containing a '''4.5''' composite part.
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# Merge plasmid containing part '''8''' ''(donor)'' with plasmid containing part '''9''' ''(acceptor)''. You should get a plasmid containing a '''8.9''' composite part. ''Note'': this step can be done simultaneously with the above.
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# Merge plasmid containing composite part '''4.5''' ''(donor)'' with plasmid containing composite part '''8.9''' ''(acceptor)''. You should get a plasmid containing a '''4.5.8.9''' composite part.
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==== '''Plasmid 3 ''(pacyc177km)'' ''' ====
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# Put parts 6,7,10,11 in  pacyc177km plasmids.
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# Merge plasmid containing part '''6''' ''(donor)'' with plasmid containing part '''7''' ''(acceptor)''. You should get a plasmid containing a '''6.7''' composite part.
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# Merge plasmid containing part '''10''' ''(donor)'' with plasmid containing part '''11''' ''(acceptor)''. You should get a plasmid containing a '''10.11''' composite part. ''Note'': this step can be done simultaneously with the above.
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# Merge plasmid containing composite part '''6.7''' ''(donor)'' with plasmid containing composite part '''10.11''' ''(acceptor)''. You should get a plasmid containing a '''6.7.10.11''' composite part.
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==== '''Linkers''' ====
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# [[ETHZ/pCK01-1| pck01-1]]
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# [[ETHZ/pCK01-2| pck01-2]]
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# [[ETHZ/pacyc177-1| pacyc177-1]]
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# [[ETHZ/pacyc177-2| pacyc177-2]]
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# [[ETHZ/pbr322-1| pbr322-1]]
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# [[ETHZ/pbr322-2| pbr322-2]]
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# [[ETHZ/pbr322-3| pbr322-3]]
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# [[ETHZ/pbr322-4| pbr322-4]]
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We have got 4 linkers for pbr322, because there are two for the tetracycline version of pbr333 and two for the ampicillin version.
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=== Lab Instructions and Methods ===
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=== Lab Schedule ===
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<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>
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[[ETHZ/labnotes| lab schedule week 1]]<BR>
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<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>
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[[ETHZ/labnotes| lab schedule week 2]]<BR>
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<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>
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[[ETHZ/labnotes| lab schedule week 3]]<BR>
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<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>
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[[ETHZ/labnotes| lab schedule week 4]]<BR>
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<font face="DejaVu Sans" size="3"><b>Week 5</b></font> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <b>03.08.07 - 09.09.07</b><br>
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[[ETHZ/labnotes| lab schedule week 5]]<BR>
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<font face="DejaVu Sans" size="3"><b>Week 6</b></font> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <b>10.09.07 - 16.09.07</b><br>
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[[ETHZ/labnotes| lab schedule week 6]]<BR>
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<font face="DejaVu Sans" size="3"><b>Week 7</b></font> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <b>17.09.07 - 23.09.07</b><br>
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[[ETHZ/labnotes| lab schedule week 7]]<BR>
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<font face="DejaVu Sans" size="3"><b>Week 8</b></font> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <b>24.09.07 - 30.09.07</b><br>
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[[ETHZ/labnotes| lab schedule week 8]]<BR>
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<font face="DejaVu Sans" size="3"><b>Week 9</b></font> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <b>01.10.07 - 07.10.07</b><br>
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[[ETHZ/labnotes| lab schedule week 9]]<BR>
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=== Lab Notes / Log Book ===
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Here we can write down every day a detailed version of the work we have done (it should be the same stuff we write in the "real lab book" which stays in the lab). In this way everyone can see in detail what was done in the lab.
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[[ETHZ/Lab book| detailed lab notes]]<BR>
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== Task List ==
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The things to do, from the most pressing (timewise), to the least pressing (timewise) is below. Please put your name next to the task that you believe that you can undertake.
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# '''Team descriptions (overdue) and team photograph''' <br> ''Christian'': I guess I am the only semiprofessional photographer of the group. I can do some group pictures etc. but for this we need some ideas... - I would like to do something special. I also made the group-pics of the Synth. Biology 3.0 conference. Some references  ;-)  : [http://www.fotocommunity.de/pc/pc/mypics/461397] <br> ''Raphael'': What about a short movie of us?
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# '''Team rosters due (1.9.)'''<br> ''Martin'': Does somebody know, what exactly should be done here? <br> ''Nan'': A list of team members, including some basic personal info.? (e.g. nationality, background, pet peeves...? )<br>''Katerina'': Guys, to make this easier, either write things about you on your personal page on the wiki or link to a page about you. This way it'll be easy to put it all together afterwards.
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# '''Labwork (parts have to be at the registry in Boston on 26.10.)''' <br> ''Joe'': I can be in the lab at least 2 evenings a week and some times through the weekdays. <br> ''Martin'': From Monday I can work every day for the whole day. At the moment I only work for several hours... <br> ''Rico'': I have my exam on Tuesday. Afterwards I can assist.<br> ''Christian'': I can do the introduction of the polylinker into the vectors beside my normal labwork on the Hoenggerberg. I could also do the whole biobrick assembly if you want this (I will go on holiday from the 5.10-24.10.07) <br> ''Raphael'': That's the part where I will mainly contribute, from 14.09. on I can work several days/week<br> ''Christos'': I can assist at the afternoons, if needed. <br> ''Katerina'': 7.09 - 30.09 generally plenty of time, apart from when I do my semester project presentation, will keep you posted when that is. <br> ''Sylke'': I'll not be available until 14th of October but from then on I can work several days per week fulltime.
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# '''Testing/ Analysis/ Detection (due to 02.11.)''' <br> ''Sylke'': Meeting with Alfredo Franco-Obregon (FACS guy from center) on 18.09. concerning devices available for detection of GFP/ derivatives.
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# '''Simulation and sensitivity analysis'''<br> ''Martin'': From 10. Sept. I've got plenty time to work on it. I think Markus would join here too ;-)  <br> ''Tim'': I can contribute in running stuff and help identify parameters from literature <br> ''Rico'': I can do simulations, sensitivity analysis. <br> ''Nan'': I would like to do simulations and sensitivity analysis. <br> ''Christos'': Yeap, I guess I can be here too. I will check some toolboxes to automate things, this weekend. <br> ''Katerina'': Want to help (parameter identification, programming, sensitivity analysis). Discuss in upcoming meeting tasks, versioning and ask Christian about parameters.
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# '''Presentation''' <br> ''Joe'': I'm American... I can sale anything.<br> ''Martin'': I'm bad in Layout stuff, but maybe I can help as an idea supplier or so. <br> ''Rico'': I like giving presentations. For preparation we will need a mixture of different background and excellent pictures!!! <br> ''Christian'': I can provide the molecular biology knowledge and part. <br> ''Nan'': I can work on the slides. <br> ''Christos'': I like this part, I guess everyone will contribute anyway...<br> ''Katerina'': I believe I can be of help in structure, layout and fancy stuff. Could help train a bit the people we decide to do the presentation (question answering, style). I also think that Joe and Christos could be good for doing the presentation (structured, pleasant voices and lively), can discuss this in a meeting. <br> ''Sylke'': I can help with the bio-part and I'm good at doing graphics and stuff. Can be a help when it needs to look good :-)
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#''' Poster''' <br> ''Joe'': See 5. above <br> ''Rico'': I can help. <br> ''Christian'': I can provide the molecular biology knowledge and part. <br> ''Nan'': Partly art. I will help. <br> ''Christos'': You can sell, but can you trick? lol :)<br> ''Katerina'': Not my strong point, but have an eye for typos, fonts, layout etc, so can help in final checking. <br> ''Sylke'': See above. Good at layout.
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# '''Wiki (Project and part documentation due on 26.10)''' <br> ''Martin'': See the points above, from next Monday I will give everything, now I'm doing my best... <br> ''Rico'': I can help. I guess this will have to contain the materials that we will also use for poster and presenttion anyway. <br> ''Nan'': Shouldn't it be updated with every going on process? <br> ''Christos'': I am trying to put stuff in, as it comes along. I will update the bio pages with the presentation material, this weekend (I hope). <br> ''Katerina'': You guys have done a great job so far, will help with whatever needed.
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# '''T-Shirts''' <br> ''Sylke'': in print (2007-09-24)
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== Testing new wiki look ==
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I just need a fresh page folks. (Christos)
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[[ETHZ/Wiki_rel]] Click me
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Revision as of 14:54, 15 October 2007

Eth zh logo 4.png
Main Page      Biology Pespective      Engineering Perspective      Meet the Team      Team Notes      Pictures!


.:: ETH Zurich - EducatETH E.coli ::.

.:: Introduction ::.

It is the third time the [http://www.ethz.ch ETH Zurich] takes part in International Genetically Engineered Machine Competition (iGEM). This year, our combined team of biologists and engineers has undertaken the task of educating E.coli ! More specifically, in our project (Fig. 1)

The ETH Zurich team undertook the task of engineering a learning mechanism for E.coli. (Fig. 1)
we are trying to create E.coli which have the ability to distinguish between two chemicals they may be exposed to after they have undergone a training phase.

Stay in this page for an overview of how EducatETH E.coli works, the motivation behind it and its possible future applications. If you want to see the biological design of our system and the parts that it consists of, or if you are interested in building it yourself and want to read the lab protocols, the Biology Perspective will be of interest to you. If you want to know more on how EducatETH E.coli has been modeled and simulated, or on its equivalences to systems such as flip-flops and finite state machines, please visit the Engineering Perspective. You may also want to visit Meet the Team for information regarding the team and Pictures! for our photo gallery. Finally, in Team Notes you can read the notes exchanged by the team during preparation for the competition.

.:: Team Members ::.

As iGEM is a synthetic biology competition, the ETH Zurich team consists of balanced numbers of biology and engineering students. Our team members are:

  • Project advisors: Sven Panke, Joerg Stelling
  • 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://fm-eth.ethz.ch/eth/peoplefinder/FMPro?-db=phonebook.fp5&-format=pf%5fdetail%5fde.html&-lay=html&-op=cn&Typ=Staff&Suche%5fText=kemmer&Suche%5fText%5fpre=kemmer&-recid=3772770936&-find=/ Christian Kemmer], Joseph Knight, Markus Uhr, [http://www.ricomoeckel.de Rico Möckel]

For more information on the team members, follow the links or visit Meet the Team.

.:: Motivation ::.

Learning plays a major role for living organisms, as it enables them to survive by adapting to an ever-changing environment. Engineering a simple biological system which exhibits learning behavior is of great interest, as it can support our understanding of this procedure by comparison with natural systems. On the other hand, learning and memorizing plays an equally big role in engineering; from handwriting recognition on PDAs to plain logical circuits storing their binary state on computers, it can be found on numerous everyday life applications. Constructing a biological analogue of a simple memory as known from logic design can hopefully function as a biological building block from which more complex systems may be constructed. We therefore think that EducatETH E.coli operates on an exciting interface between engineering and biology.

.:: E.coli Intelligence (E.I) - Specifications and analogies ::.

How can we make E.coli bacteria able to report us about their environment? Can we teach bacteria to tell if they have seen before a specific chemical?

Fig. 2: EducatETH E. Coli System

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.
(Want to read more about this? Visit the Engineering Perspective!)

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.
(Want to see the biological design of our modified toggle? Visit the Biology Perspective!)

.:: A short system description ::.

EducatETH E.coli is able to recognize between two chemical substances (aTC and IPTG) it has previously been exposed with help of an external chemical signal (AHL). In the first part of the training phase (“meeting”), the system is exposed to one of the two chemicals (aTC and IPTG) and AHL is added, causing a steady system behavior. In the second part of the training phase (“memorizing”), all chemicals but AHL are removed, allowing the system to maintain its state. Finally, in the testing phase (“recognizing”), 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. As seen on Table , 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 , YFP for ) and two others to control whether the system sees the same chemical as it did in the training phase (GFP) or not (RFP). Thus, the system response is determined uniquely.


Training
chemical 		Testing
chemical 		Fluorescence
during training 		Fluorescence
during testing
aTc aTc CFP or YFP? GFP
aTc IPTG CFP or YFP? RFP
IPTG aTc CFP or YFP? RFP
IPTG IPTG CFP or YFP? GFP
.:: References ::.

[1]: Toggle Switch

.:: Acknowledgements ::.

  • [http://europa.eu The European Union]

  • [http://www.ethz.ch The ETH Zurich]

  • [http://www.geneart.com GENEART]


.:: Links ::.

.:: To Do ::.

.:: New ones ::.

  • Change banner on top of page.
  • 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.
  • Possibly put table of contents.
  • Possibly take EducatETH E.coli from Figure.
  • Change Figure 2.
  • Possibly change figure caption format from xxx (Fig. x) to Fig.x: xxx. Put second format on Figure 2 for all to check.
  • Fix table showing possible system states and reporters. Maybe with some color?
  • Put cross-reference on table.
  • Align table left
  • Add which reporters do what in paragraph.
  • Put (compressed!) team photo instead of Fig.1
  • Fix paragraph with system description, looks somehow bulky. Maybe italics or bold on important things?
  • Fix reference on toggle switch.
  • Possibly remove Introduction heading altogether, and just start with the text.

.:: Old ones ::.

  • 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)
  • Need picture: Einstein ecoli (Sylke: does Stefan have the layer file?)
  • 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)

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