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Contents 1 Design Group 1.1 Purpose 1.2 Current Project Variants 1.3 Current Members 1.4 New Members 1.5 Discussion Meetings 1.6 Progress 1.6.1 Behavior States 1.6.2 Modules 1.6.3 Problems with Pred-Prey 1.6.4 Convergence 1.7 Project X 1.7.1 Basic Concept 1.7.2 Next Steps

Design Group

Design group defined during teammeeting on Thu. 2005.08.04

Purpose

• Discuss those projects assigned to us 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.

Current Project Variants

• Sorting Bacteria
• Pulser
• Constructor Bacteria
• Controlled Cell Division
• Predator-Prey Behavior

Current Members

• Dominic Frutiger
• Giorgia Valsesia
• Herve Vanderschuren

New Members

New members: please add your name here so that we know that you want to join.

• Urs A. Müller
• Simon Barkow

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, 17:30, Discussion of modules (Giorgia, Dominic)
2005.08.11, Thursday, 09:00, Discussion of presentation preps (all)

Progress

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:

Behavior States

• 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

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

Project X

Basic Concept

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.

• Stage 1:
  • 1.1 A constitutively expresses aggregation factor for A
  • 1.2 A and B constitutively express fluorescence genes (different colors)
  • 1.3 A constitutively releases some signaling substance a1, B constitutively expresses b1
• Stage 2:
  • 2.1 A starts to aggregate and form clusters
  • 2.2 B senses concentration of substance a1
• Stage 3:
  • 3.1 The clusters of A reach a critical size. This leads to a certain concentration of a1 in the vicinity of the cluster
  • 3.2 The threshold of a1 is reached and sensed by B. This triggers intensive cell division of B.
  • 3.3 In parallel, B expresses an aggregation factor that makes B attach to A
• Stage 4:
  • 4.1 A shell of B forms around the clusters of A.
  • 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.
• Stage 5:
  • 5.1 Due to the growing thickness of the cellulose shell, the A-core gets isolated and starts to express some different fluorescence gene.

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.

Next Steps

Checking out the individual modules and their feasability.

• Herve: aggregation behavior, cell division control
• Giorgia: quorum sensing, AND dependence
• Dominic: cellulose, physical structures

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