Quorum Sensing based

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Back to [[ETH Zurich]] main page.
Back to [[ETH Zurich]] main page.
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=Design Group=
=Design Group=
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Design group defined during teammeeting on Thu. 2005.08.04
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This is the subpage of the temporary design group defined during the team meeting on Thu. 2005.08.04
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==Purpose==
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* Discuss those projects assigned to us and develop them further, both conceptually (modularity, coolness, usefulness) and implementation-wise (feasability, availability of components).
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* Agree on some favored existing solution or merge current concepts into a new one.
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==Current Project Variants==
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==Purpose==
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*[[Sorting Bacteria]]
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* To discuss those projects assigned to us (detailed below under "Initial Project Variants") and develop them further, both conceptually (modularity, coolness, usefulness) and implementation-wise (feasability, availability of components).
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*[[Pulser]]
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* Agree on some favored existing solution or merge current concepts into a new one, [[Project X]].
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*[[Constructor Bacteria]]
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*[[Controlled Cell Division]]
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*[[Predator-Prey Behavior]]
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==Current Members==
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==Permanent Members==
* [[Dominic Frutiger]]
* [[Dominic Frutiger]]
* [[Giorgia Valsesia]]
* [[Giorgia Valsesia]]
* [[Herve Vanderschuren]]
* [[Herve Vanderschuren]]
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==New Members==
 
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New members: please add your name here so that we know that you want to join.
 
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* [[User:realUACM|Urs A. Müller]]
 
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* [[Simon_Barkow|Simon Barkow]]
 
==Discussion Meetings==
==Discussion Meetings==
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  '''2005.08.09, Tuesday, 16:00, Discussion of feasability/implementation regarding modules'''
  '''2005.08.09, Tuesday, 16:00, Discussion of feasability/implementation regarding modules'''
  '''2005.08.10, Wednesday, 09:00, Discussion of concept (Dominic, Simon)'''
  '''2005.08.10, Wednesday, 09:00, Discussion of concept (Dominic, Simon)'''
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'''2005.08.10, Wednesday, 17:00, Introduction of current status to Alex (by Dominic)'''
  '''2005.08.10, Wednesday, 17:30, Discussion of modules (Giorgia, Dominic) @polyterrasse'''
  '''2005.08.10, Wednesday, 17:30, Discussion of modules (Giorgia, Dominic) @polyterrasse'''
  '''2005.08.11, Thursday, 09:00, Discussion of presentation preps (all)'''
  '''2005.08.11, Thursday, 09:00, Discussion of presentation preps (all)'''
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'''2005.08.11, Thursday, 11:15, Discussion of presentation preps and story line (all)'''
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'''2005.08.11, Thursday, 14:30, Assigning tasks for presentation, @polyterrasse'''
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==Progress==
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==Progress History==
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During the first two meetings we mainly developed the existing concepts further or added variants. On monday we tried to find useful categories to identify what makes the projects similar and what makes them different - in order to reduce the number of true variants and merge interesting functions into a new project idea. We started to divide the existing project ideas further into certain behavior states and their possible expression:
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During the first two meetings we mainly developed the existing concepts (see "Initial Project Variants" below) further or added variants.  
 +
 
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===Initial Project Variants===
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Here you find a list of the initial projects that were assigned to this group. These projects have their own page. We developed them a little further at first, but now we are merging some of them into [[Project X]]. Thus those projects are no longer maintained by our development group members.
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*[[Sorting Bacteria]] (outdated -> [[Project_X]])
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*[[Pulser]] (outdated -> [[Project_X]])
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*[[Constructor Bacteria]] (outdated -> [[Project_X]])
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*[[Controlled Cell Division]] (outdated -> [[Project_X]])
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*[[Predator-Prey Behavior]] (outdated -> see section below "Problems with Pred-Prey")
===Behavior States===
===Behavior States===
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On monday we tried to find useful categories to identify what makes the projects similar and what makes them different - in order to reduce the number of true variants and merge interesting functions into a new project idea. We started to divide the existing project ideas further into certain behavior states and their possible expression:
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* pattern formation
* pattern formation
** oscillation behavior and/or dynamic equilibria
** oscillation behavior and/or dynamic equilibria
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* the resulting population dynamics would be interesting, but neither very useful nor extendable.
* the resulting population dynamics would be interesting, but neither very useful nor extendable.
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===Convergence===
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===Convergence / Current Development Stage===
The remaining project ideas, however, seem to share many modules and can be merged into the following new project variant [[Project_X]].
The remaining project ideas, however, seem to share many modules and can be merged into the following new project variant [[Project_X]].
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==Project X==
 
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===Basic Concept I===
 
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Two engineered strains of E.coli, A and B, in a tank. B's cell division is inhibited. Population  A is either much larger than population B in the beginning, or growing much faster.
 
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* Stage 1:
 
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** 1.1  A constitutively expresses aggregation factor for A
 
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** 1.2  A and B constitutively express fluorescence genes (different colors)
 
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** 1.3  A constitutively releases some signaling substance a1, B constitutively expresses b1
 
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* Stage 2:
 
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** 2.1  A starts to aggregate and form clusters
 
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** 2.2  B senses concentration of substance a1
 
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* Stage 3:
 
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** 3.1  The clusters of A reach a critical size. This leads to a certain concentration of a1 in the vicinity of the cluster
 
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** 3.2  The threshold of a1 is reached and sensed by B. This triggers intensive cell division of B.
 
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** 3.3  In parallel, B expresses an aggregation factor that makes B attach to A
 
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* Stage 4:
 
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** 4.1  A shell of B forms around the clusters of A.
 
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** 4.2  a1 and b1 reach certain concentrations at the B-shell-A-core boundary, which triggers the production of cellulose in both types. Either as AND-implementation or more simply just by b1 triggering A and a1 triggering B.
 
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* Stage 5:
 
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** 5.1  Due to the growing thickness of the cellulose shell, the A-core gets isolated and starts to express some different fluorescence gene.
 
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That is only a rough status for now, but there are various variations possible, e.g. to reduce complexity if desired or use alternative solutions. Also, not all stages are dependent on each other, i.e. one could simulate the result of a previous stage and still get a result. We are confident that some variant of this concept would be fairly feasable and still lead to interesting results.
 
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===Next Steps===
 
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Checking out the individual modules and their feasability.
 
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* Herve: aggregation behavior, cell division control
 
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* Giorgia: quorum sensing, AND dependence
 
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* Dominic: cellulose, physical structures
 
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===Basic Concept II===
 
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This is an attempt to break down the concept into clearer and more elaborate steps, open questions, and pros and cons.
 
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Note: some things have slightly changed. The stages have new, somewhat arbitrary names and assignement of subaspects.
 
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----
Back to [[ETH Zurich]] main page.
Back to [[ETH Zurich]] main page.

Revision as of 11:46, 11 August 2005

Back to ETH Zurich main page.

Contents

Design Group

This is the subpage of the temporary design group defined during the team meeting on Thu. 2005.08.04

Purpose

  • To discuss those projects assigned to us (detailed below under "Initial Project Variants") and develop them further, both conceptually (modularity, coolness, usefulness) and implementation-wise (feasability, availability of components).
  • Agree on some favored existing solution or merge current concepts into a new one, Project X.

Permanent Members

Discussion Meetings

Everybody is more than welcome to join in! 

2005.08.05, Friday, 15:30, Discussion/development of group topics, Giorgia & Dominic
2005.08.07, Sunday, 16:00, Discussion/development of group topics, Herve & Dominic
2005.08.08, Monday, 10:00, Discussion/development of group topics, all (visitors welcome)
2005.08.09, Tuesday, 16:00, Discussion of feasability/implementation regarding modules
2005.08.10, Wednesday, 09:00, Discussion of concept (Dominic, Simon)
2005.08.10, Wednesday, 17:00, Introduction of current status to Alex (by Dominic)
2005.08.10, Wednesday, 17:30, Discussion of modules (Giorgia, Dominic) @polyterrasse
2005.08.11, Thursday, 09:00, Discussion of presentation preps (all)
2005.08.11, Thursday, 11:15, Discussion of presentation preps and story line (all)
2005.08.11, Thursday, 14:30, Assigning tasks for presentation, @polyterrasse

Progress History

During the first two meetings we mainly developed the existing concepts (see "Initial Project Variants" below) further or added variants.

Initial Project Variants

Here you find a list of the initial projects that were assigned to this group. These projects have their own page. We developed them a little further at first, but now we are merging some of them into Project X. Thus those projects are no longer maintained by our development group members.

Behavior States

On monday we tried to find useful categories to identify what makes the projects similar and what makes them different - in order to reduce the number of true variants and merge interesting functions into a new project idea. We started to divide the existing project ideas further into certain behavior states and their possible expression:

  • pattern formation
    • oscillation behavior and/or dynamic equilibria
    • convergence to specific end states with distinct intermediate states
  • pattern display
    • fluorescence
    • physical structures

The first step would always be pattern formation. The difficulty with approaches aiming at oscillation behavior and/or dynamic equilibria (such as the Pulser or the Predator-Prey_Behavior) is that we can not break them down to intermediate stages and thus there is no step-wise increase of risk: either all aspects work at once and the interplay is balanced leading to some dynamic stability or the whole concept miserably fails. Also, it is more difficult to prove success.

As a result our discussions more and more converged towards approaches with specific static end states and intermediate layers.

Modules

Also, we tried to break down the existing variants into modules fulfilling a specific function:

quorum sensing aggregation / sticking killer behavior
cell division sensing cell division control induced apoptosis
chemotaxis (+/-) nutrition production nutrition dependence

Then we discussed the estimated (!) feasability and general usefulness of these modules to get a better feeling of what should be used and what will prove difficult to implement.

Problems with Pred-Prey

We quickly found that the implementation of true Predator-Prey behavior would be very interesting, but that there are serious drawbacks:

  • there are no layers: all functions would have to be successfully implemented at the same time (e.g. production of nutrients in pop A, dependence on nutrients of pop B, balancing the killing behavior of B vs. A) otherwise the whole project would fail.
  • the resulting population dynamics would be interesting, but neither very useful nor extendable.

Convergence / Current Development Stage

The remaining project ideas, however, seem to share many modules and can be merged into the following new project variant Project_X.


Back to ETH Zurich main page.

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