From 2007.igem.org

Revision as of 15:56, 21 October 2007

Introduction

"ALL ANIMALS ARE EQUAL BUT SOME ANIMALS ARE MORE EQUAL THAN OTHERS" (Animal Farm by George Orwell)

In this year's iGEM, the ETH team is interested in quite small but well known animals, E.coli 's. And even for these, Orwell's remark holds (although in a somewhat more positive way): We have been working on teaching E.coli 's in order to make them capable of deliberately recognizing their environment.

In detail, our combined team of biologists and engineers was working on the E.coli 's ability, first, to recognize two different inputs (here we used two different chemicals), second, to remember which input was presented to them, and third, when confronted with a new input to recognize if it is the same as before. Thereby, the educatETH E.coli 's provide a first step towards the development of biological equivalents to complex engineering building blocks like, e.g. , flip-flops and other logical circuits. The concept of learning and recognition plays a major role in different high-level applications like, e.g., recognition of handwriting on a [http://en.wikipedia.org/wiki/Personal_digital_assistant PDA]. On the other hand, learning plays a major role for living organisms, as well: it enables them to survive by adapting to an ever-changing environment. Therefore, engineering a simple biological system which exhibits learning behavior (e.g. epigenetics) is of great interest as it can support our understanding of this procedure by comparison with natural systems.

In the following, we would like to present 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 find some further information on the team, some more details about ideas we developed before we came up with the system we finally implemented, and some pictures documenting our work.

Team Members

ETHZ iGEM2007 Team

The ETH Zurich team consists of 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://csb.inf.ethz.ch/people/uhr.html Markus Uhr], [http://www.ricomoeckel.de Rico Möckel]
• 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 by the ETH iGEM 2007 team. For making it possible, we would like to thank the people in [http://www.ipe.ethz.ch/laboratories/bpl/index Sven Panke's Lab], especially Andreas Meyer PhD, who was always there for us, when we had a problem in the lab, [http://www.fussenegger.ethz.ch/ Martin Fussenegger's lab] for their patience concerning our questions, and [http://www.facs.ethz.ch Alfredo Franco-Obregóns lab] and Oralea Büchi for the help with the flow cytometry.

We would also like to acknowledge the following three companies and organizations for their financial support:

Site Map

• Modeling of the learning system
• Implementation using flip-flops
• Representation with finite state machines
• tutorial?
• Model simulations and theoretical considerations
• Biological implementation
• epigenetic?
• Lab notes

• Team page
• Pictures
• Other ideas we developed
• others I forgot?

• The ETH Zurich 2005 project
• The ETH Zurich 2006 project

.:: TODOs ::.

• put a fancy picture in the intro
• link Stefan's Epigenetic Page
• put all Links to subpages including a short description in the "site map" section
• check if you like the contents of your personal pages

.:: to be removed ::.

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!)

EducatETH E.coli is able to recognize between two chemical substances (aTC and IPTG) it has previously been exposed to with the help of an external chemical signal (AHL).
In the first part of the training phase (“learning”), the system is exposed to one of the two chemicals (aTc and IPTG), causing a steady system behavior. In the second part of the training phase (“memory”), AHL, is added while all other chemicals are removed, allowing the system to maintain its state. Finally, in the testing phase (“recognition”), the system is exposed to any of the two chemicals again. Via comparison of the toggle's steady state with the system response the new chemical causes, the system recognizes if it has been exposed to this chemical before or not.
As seen in Table 1, four system states are possible in the testing phase. We chose to use two reporters to control which chemical educatETH E.coli is exposed to during the training phase (CFP for IPTG, YFP for aTc). When the system recognizes the same chemical substance in the "recognition phase" as in the "learning phase ", it will respond with the same reporter output as in the learning phase (YFP for aTc learned and recognized, CFP for IPTG learned and recognized). However, when the system recognizes a different chemical substance, than previously learned, it will respond with either a GFP (when aTc is learned and IPTG is recognized) or a RFP output (when IPTG is learned and aTc is recognized). Thus, the system response is determined uniquely.

[http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html [1] Elowitz MB and Leibler S] "A synthetic oscillatory network of transcriptional regulators", Nature 403:335-338, 2000

• How about changing "educatETH E.coli to all italics "educatETH E.coli"
  • ( might be kinda late now, we have already had "educatETH E.coli" on the T-shirts... ?)
  • (Not really because the font on the T-shirts is all italics, for all who want to know: Bitstream Charter Bold Italic Not-Rotated)
• Change the name of p22cII to only cII (its a cI analog) p22 just means that it derives from the phage p22.
• IMPORTANT: THE COLOURS ARE TOTALLY WRONG IN THE SIMULATION PART. Please refer to the table on the main page. Changed it just now, it was wrong before!!!
• Change banner on top of page. Stefan: Can we please change the banner back to the old version?!? It was MUCH nicer.
• 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.
  • ( by "Figure", you mean the Einstein figure on the banner? )
• 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? --> No colour please.
• Put cross-reference on table. Is there something like a description function for tables? An automatic "Tab. 1" as in "Fig. 1"?
• Align table left
• Add which reporters do what in paragraph.
• Put (compressed!) team photo instead of Fig.1
  • ( can we leave it and add team pic? Fig.1 is somehow our brand.)
• 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.
• These two lines are kinda confusing...
  • " Main Page / Biology Pespective / Engineering Perspective / Meet the Team / Team Notes / Pictures!"
  • "Main Page / System Modeling / Simulations / System Implementation / Lab Notes / Meet the Team / Team Notes / Pictures!
• (19th Oct.) Just notice that we have different header styles under different sub-wikipage...
• BTW, can we label the solved problems to blue ?

• 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)