important -- question for PAMGO

[Brett Tyler]

Hi Alex,

>I agree that we should carefully review the types of organisms that 
>warrant response to terms.  My omission of oomycetes and others was 
>not meant to exclude them, but rather to avoid complexity while we 
>were deciding on the basic DAG structure.

I understand

>I think in particular we need input on which organisms need 
>"response to symbiotic [organism]" terms, as well as "defense 
>response to [organism]" terms.

I think this will have to be an evolution.

>
>The existence of the yeast terms is due to me, unfortunately 
>("response to yeast" and "detection of yeast").  I'll accept any 
>proper advice about whether the terms valid or not.  I guess the 
>question is really whether there are additional or different 
>pathways for responses to yeast versus multicellular fungi.

Many fungal pathogens of plants and animals undergo a dimorphic shift 
between a unicellular (yeast) form and a hyphal (syncytial) or 
pseudohyphal (multicellular) form.  In some cases the shift is 
essential for pathogenicity - Candida is a good example. So even the 
yeast versus multicellular distinction is murky.

Cheers

Brett


>
>Thanks,
>
>Alex
>
>At 1:58 PM -0500 3/30/05, Brett Tyler wrote:
>>Alex,
>>
>>Looks good. I agree that this is ready to put out for further 
>>discussion by the wider community.
>>
>>Here is some further discussion right away :-)
>>
>>There should be terms for oomycete (organisms that we work on that 
>>look like fungi but are in a different kingdom), apicomplexans 
>>(malaria, Toxoplasma etc), which belong to different kingdoms than 
>>those listed in your diagram, plus something like protist or 
>>protozoa (Leishmania, trypanosomes, Giardia etc etc)
>>
>>At some point GO will have to decide how deeply into the tree of 
>>life to specify terms like "response to <some organism>" - it's 
>>similar to the sensu issue.  Perhaps it should be left at the 
>>kingdom level (easy for crown eukaryotes, but tough for 
>>"protists"), which would eliminate yeast, until evidence is 
>>obtained that a host organism really has a response that is more 
>>specific than that.
>>
>>A related issue is whether common names like "yeast" are 
>>appropriate in this context - and maybe that issue has already been 
>>decided in the context of "sensu" terms.
>>
>>Cheers
>>
>>Brett
>>
>>
>>--
>>*****************
>>Brett Tyler
>>Professor
>>Virginia Bioinformatics Institute
>>Virginia Polytechnic Institute and State University
>>Washington Street
>>Blacksburg, VA 24061-0447
>>
>
>
>--
>Alexander Diehl, Ph.D.
>Scientific Curator
>Mouse Genome Informatics
>The Jackson Laboratory
>600 Main Street
>Bar Harbor, ME  04609
>
>email:  adiehl at informatics.jax.org
>work:  +1 (207) 288-6427
>fax:  +1 (207) 288-6131


-- 
*****************
Brett Tyler
Professor
Virginia Bioinformatics Institute
Virginia Polytechnic Institute and State University
Washington Street
Blacksburg, VA 24061-0447

Telephone: (540) 231-7318
Fax: (540) 231-2606
Email: bmtyler at vt.edu
Web: https://www.vbi.vt.edu/article/articleview/141
*****************
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