Cellular Slime Mold Simulation

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News

• 062507: Next meeting tomorrow (Tuesday) at 6.30 pm. in the cafeteria.

• 062007: Next meeting: today (Wednesday) at 5.30 pm. in the cafeteria.

• 061407: Meeting today after the lecture at 8 pm. Place: Cafeteria first floor Peterson Student Center /Johan

• 061107: I've developed a simple graphical viewer that does the job of displaying the individual CA cells, color coded the same way as in the article. It's not great, but if anyone is interested, let me know and I'll make the code avaliable. /Johan

• Meeting on Thursday the 14th before dinner

Old news

First meeting will be on Monday the 11th at 6 pm. Lets meet outside the dining room. "Homework" till then will be to read the original article(see list below) and think a little of what we want to get out of the project. /Johan

Background

One of the most widely studied and relatively simple organisms in which to study morphogenesis (the shapes of organisms and the positions in the organisms of various specialized cell types) is the so-called cellular slime mold. It provides a simple model organism for studying many general developmental processes, including chemotaxis (behavioral response by an organism to a directional chemical stimulus), cell sorting, pattern formation and complex behavior through self-organization.

Normally, slime mold is a unicellular amoeba, but when food resources become scarce, they aggregate and form multicellular organisms that can move towards food sources.

Proposition

There is an article by N. J. Savill and P. Hogeweg where a model of the morphogenesis of these slime mold organisms is presented. What amazes me with this article is that the model seems to be relatively simple, but that it can still account for the whole morphogenetic process from single cells to a larger aggregate of cells, and finally to a multicellular organism capable of coordinated motion.

I propose a project group for implementing this model and possibly extend it in directions that we find suitable. I’m sure some very interesting questions will pop up along the way.

More about the model

The simulations are based on a cellular automata (CA) model, where each amoeba is represented as a collection of CA cells. A Monte Carlo simulation is performed, where amoebae of different types have a tendency to group together. This results in a cell sorting behavior. Another mechanism in the model is communication between amoebae via cAMP (cyclic adenosine monophosphate) chemicals, modelled by a partial differential equation. This results in aggregation of the amoebae into a ”multicellular organism” (interesting philosophical/biological question if this really counts as a multicellular organism). Without any change of parameters, the slime mold eventually starts to move guided by cAMP waves. The whole process seems to very much resemble what happens for living slime mold.

Participants

• Johan Nyström (nystjoha@chalmers.se)
• Will Ludington
• Tim Johann
• Ryan Chisholm
• Dan Lester - maybe before we get together on monday, have a think about scope for this project, especially something of biological importance
• Natasha - I would like to know the date and time of meeting.
• (add your name here)

Reading material

On the Cellular Automaton model:

• Original article: [1]
• A continuation of the original article: [2]. Have a look at picture 2 on page 7. They make their slime mold follow a thermal gradient.
• Computing an organism: on the interface between informatic and dynamic processes, P. Hogeweg, Biosystems 64 (2002) 97-109: This article contains an overview of the work done using the model.
• How amoeboids self-organize into a fruiting body: multicellular coordination in Dictyostelium discoideum Proc. Natl. Acad. Sci. USA 98 (7), 3879-3883: [[3]]

Biologically relevant articles:

If someone know any article, please add it here.

I suggest the following reading material(Natasha)

• Try the following links for some biologically relevant articles:

 http://www.mycologia.org/cgi/content/full/97/1/178 (Behavior of cellular slime molds in the
 soil)
 http://www.ucmp.berkeley.edu/protista/slimemolds.html (Introduction to the slime molds)
 http://www.ias.ac.in/jbiosci/march1999/99bc
 http://www.biolbull.org/cgi/reprint/122/1/13 (Aggregation of territories in the cellular
 slime molds)
 jcs.biologists.org/cgi/reprint/22/1/41.pdf (CYCLIC ADENOSINE MONOPHOSPHATE AND THE
 DEVELOPMENT OF POLYSPHONDYLIUM)

• For comprehensive information on Dictyostelium discoideum, visit http://dictybase.org/

 For an overview of world-wide research on D.discoideum,visit http://dictyworkbench.sdsc.edu/
 For some kool videos of Dicty, try http://dictybase.org/Multimedia/index.html

• And the comprehensive one: A Cellular Automata model for D.Discoideum (http://www.cs.york.ac.uk/ftpdir/reports/YCS-2005-393.pdf)

 Phototaxis during the slug stage of Dictyostelium discoideum: a 
 model study (http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1690080&blobtype=pdf)

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