ETH Zurich 2006

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Contents

Introduction

People

Students

Simon Barkow Christophe Dessimoz Zlatko Franjcic
Dominic Frutiger Robin Künzler Urs A. Müller
Jonas Nart Kristian Nolde Alexander Roth
Tamara Ulrich Giorgia Valsesia Herve Vanderschuren

Supervisors

Jörg Stelling Sven Panke Eckart Zitzler

Advisors

Uwe Sauer Martin Fussenegger Andreas Hierlemann
Kay-Uwe Kirstein Ruedi Aebersold

Events & Timeline


Project Ideas

This is the brainstorming section. In this section you will find random ideas and comments without too much consideration of feasability etc. Crazy ideas and wild dreams are welcome!

Individual Phenomena

Designing and tweaking so that the individual behaves in a desired way.

Oscillator-based Phenomena

Some clocking behaviors, such as counters and integrators etc.

Collaborative Phenomena

Some of us have a great interest in some form of emergent phenomena and group dynamics based on simple local rules and external stimulae. Examples would be behaviors like sorting, pattern detections, flocking etc.


Development Groups

We decided to cluster related projects and to form groups which will dedicate their time to this cluster. The goal is to converge to some single preferred solution based on these project ideas while keeping an eye on feasability, coolness, usefulness, and modular architecture on the way.

If you are in no group yet, please choose one.

Quorum Sensing based (Dominic, Giorgia, Herve)

Oscillator based (Urs, Christophe, Jonas)

Generation based (-)

Other projects (Jonas, Simon, Dominic)

Merged Projects

The two projects below are the outcome of the work of our two remaining development groups. They both have their pros and cons and the discussion continues until at least Monday evening.



Ballot

Please everybody make your vote (1 means "forget it" and 10 means "definitely a Nature paper") on the four criteria.

Constructor (aka Project X)

CONSTRUCTOR Urs Tamara Jonas Zlatko Giorgia Simon Kristian Herve Dominic Alexander Christophe Robin
Usefulness 6 4 - - - 6 - - - - - -
Feasability 4 8 - - - 5 - - - - - -
Modularity 10 8 - - - 9 - - - - - -
Coolness 9 7 - - - 9 - - - - - -

Additional Comments:
Tamara:
 As an engineer, I think the counter is completely useful and totally cool as well. I'm really      excited at the prospect that it might actually work 
 (which I frankly still doubt a little bit at     the moment). The SO-Constructor definitely is cool as well, but I don't see it's usefulness yet,        
 but as I'm no bilogist, it is not mine to judge.
 
 Talking about modularity, I see that the SO-Constructor has a lot of modules, but they are not         'parallel' modules, but 'serial' modules, i.e. 
 if one module fails, the overlaying modules won't    work as well. They strongly depend on each other. I also see the problem of tunig, because there 
 is   a real lot of tuning to do and nearly everything needs to be tuned. For me, some questions arise   like: Can you simply change the threshold for a 
 certain protein in quorum sensing? Anyway, the   probability that we have some results to present in the end is still relatively high.

 I don't think the counter is really modular, altough it is a combination of one basic part (the   'thing'). The point is, if that basic part works, the 
 whole counter probably works as well. If it   doesn't, then we don't have anything at all. But shouldn't we just take the risk and try it? No   risk,
 no fun :-)

 Conclusion: The SO-Constructor is in my opinion the 'safer' option, meaning that we are much more    probable to get something that actually works. 
 Whereas the Counter is much more useful and   revolutionary, at least when we get to work it somehow.



Dominic:
As I already have said during the meeting, I am a little bit concerned about the effects of the 
different presentation styles and levels of detail: it is hard to judge the feasability of one or
the other, since for the SO-Constructor I can see a clear stepwise approach with controllable
biological units to implement, but I am doubtful about the tuning and proper interplay of all these
components - although I am confident that to some degree this can be achieved. 
As for the Counter I am also not sure about the basic biological assumptions, e.g. whether the
toggle switch units are available and will work as well as the symmetric repression/activation
that is necessary, although the modeling part suggests everything is straightforward - but this
might be deceiving.
It is hard for me to judge the biological unpredictabilites and risks, but from an engineering
point of view the Counter building block is of the more useful thing to do, since it has a broad 
application range thanks to the clear interfaces. 
Last but not least such a technical unit seems more suitable in the context of Synthetic Biology.

Urs:
I think if the whole thing works this project is astonishing. But I'm in doubt about it. The fact
that you could model each step seperatly is of course a big advantage of this project. The 
probability that at least a few of the steps work is quite high and so you will see some results at 
the end. I'm not so sure about the usefulness. To encapsulate some bacterias which produce a 
certain substance could be usefull but I'm not an expert in this stuff.

Counter (aka The Thing)

COUNTER Urs Tamara Jonas Zlatko Giorgia Simon Kristian Herve Dominic Alexander Christophe Robin
Usefulness 10 10 - - - 8 - - - - - -
Feasability 6 7 - - - 7 - - - - - -
Modularity 7 5 - - - 8 - - - - - -
Coolness 8 10 - - - 9 - - - - - -
Additional Comments:
Urs:
From the engineer's point of few a counter like this is of course a crucial brick. As you can take 
the concentration of any substance you like (by transforming it to our input S) and also add for 
every single counter step a specific gene needed for an application this counter can be used 
whereever you want. The big disadvantage is of course that if the counter doesn't work there will be
no result you can see.

Christophe:
About feasibility: i don't agree with much of what has been said here. The counter is made of two 
toggle switches. These switches exist in the nature (lambda repressor) and have also been synthetized 
(Gardner et al., partly also on MIT registry). Now, the only think we need to come with are A) a way 
of having 4 different types of road blocks, which is, as Sven said, possible using zinc-fingers that 
target different dna seqs, and B) a way to have S working as an inducer and as a repressor, in a 
roughly symmetrical manner. And that's all. I am not saying that it is trivial, but seriously, it is 
really doable. And even if we don't manage it to do it for the jamboree, finishing it later could  
still be academically very rewarding.

Bottom line: The difference between the two projects, i guess, is that most of the work in the QS project
would be at the assembling/tuning of existing parts for a very cool final effect, while in the the counter,
we would focus the energy of the whole group into realizing a little module that is reliable and reusable. Both
projects are cool, both teams have done an increadible amount of preparatory work until now and so at this 
point, i would be very excited working on either projects.

External Information

Links

Papers

bulter04, atkinson03, bates05, keiler01, suetsugu03, sudesh00, römling02, ross91, sutherland01, Lai04, zogaj01, miller01, basu05, goryachev05,

you04,

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