HP Modularity

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Revision as of 21:10, 12 June 2008 by RobMills (talk | contribs) (sketched an outline of what to touch on in the abstract/proposal)

Host-Pathogen Modularity

This is the working space for our project. Everything written is a work in progress.

Title Ideas

  • Evolution of modularity in a host-pathogen system
  • Modularity: a pathogen's answer to host interactions
  • more here

Major Questions

  1. Does modularity in pathogen genes responsible for an interaction with a host increase its ability to adapt to a host?
  2. Is modularity in the host required for pathogen modularity to arise/emerge?
  3. additional ones here

Questions to answer in proposal

  1. why are we studying host-pathogen interactions?
  2. what evidence suggests that modular allelic dependencies might be advantageous in such a host-pathogen system?
  3. give a one-line description of this type of modularity
  4. what conditions do we aim to test to show a benefit to modular dependencies/interaction structures?
  5. what are our null models, i.e. why is (this) result a surprise?
  6. what impact does this have for the understanding of host-pathogen interactions, and evolvability in general?

Model Details

Discrete or continuous?

  1. Pros for discrete: easier to run iterated simulations; possible to run experiments on explicit graph structures
  2. Pros for continuous: mathematical derivations cleaner


Modularity Concepts

I'm quite sure that there is some overloading here; but these are the types of modularity that have come up in our discussions:

  1. Modularity for reassortment (Molly)
  2. Modularity for independence (Molly) (I call this 'functional decomposition' - Rob)
  3. Repeated modularity: eg where a body segment occurs many times in an organism (Rob)
  4. Modularity for robustness to antagonistic pleiotrophy (Molly)

Pathogen-related terms

  1. Epitope : the phenotype of a pathogen that interacts with a host
    1. only need to consider a portion of the host's genome since the pathogen only targets a specialised portion of that genome.