#9899 protection from anoxia

closed-accepted
5
2013-01-07
2012-12-13
alan_bridge
No

Hi GO

I'd like to annotate the role of some genes in survival to anoxia - oxygen deprivation (not hypoxia, oxygen reduction).

C.elegans can survive for around 48 hrs with almost no oxygen (see PubMed ), and this requires a specific ceramide synthase hyl-2. Mutants in hyl-2 survive anoxia for much shorter periods, and this correlates with loss of specific ceramides.

I just wondered if GO would consider protection from anoxia to be a "biological process". We already have GO:0034059, "response to anoxia", but this is not quite what I wanted to express (although you would assume that the organism would need to mount a response to anoxia in order to survive anoxia). Here, it's the "base state" of the organism that determines whether it survives and for how long: a lack of hyl-2 makes it more susceptible to anoxia.

Thanks for your insight, Cheers, Alan

Discussion

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  • alan_bridge
    alan_bridge
    2012-12-13

    Sorry I forgot the PubMed: it's 19372430, "Protection of C. elegans from anoxia by HYL-2 ceramide synthase."

     
    • labels: --> New term request
    • assigned_to: nobody --> tairtb
     
  • I'm consulting with WormBase curators to see how to best address this issue and whether a new term is warranted. Thanks for your patience.

     
  • alan_bridge
    alan_bridge
    2012-12-14

    thanks Tanya!

     
  • Hi Alan,

    With her consent, I'm adding the comments of Kimberly Van Auken, a WormBase curator, to this SF item. I consulted her about the addition of a new term and annotation using this paper.

    "I've had a look at the C. elegans anoxia paper.

    To be honest, I'm not sure I would annotate to either a 'protection from'
    or a 'response to' anoxia term for hyl-2.

    I couldn't get a good sense from the paper of whether this was an active
    role for hyl-2 or whether this was a downstream effect on signaling
    pathways as a result of not having ceramides (see the last paragraph of
    the paper.)

    Maybe we could ask Alan if he has more information about the mechanism
    that would address whether or not this is an active role, or a downstream
    effect, of hyl-2 activity.

    I was also looking at the other 'protection' terms we have in GO, like UV
    protection and DNA protection, and wondering if those terms have been used
    for cases where the mechanism might not be known yet, but there is some
    connection between the gene and protection of the organism. If this is a
    similar situation, maybe a 'protection from' term would be okay for now
    and when details of the pathway become clearer a more precise annotation
    for hyl-2 could be made.

    Let me know if you need any more info."

    Do you have any additional data about hyl-2 and its relationship with anoxia?

    Thanks,

    Tanya

     
  • alan_bridge
    alan_bridge
    2012-12-20

    Hi Tanya and Kimberley,

    thanks for your thoughts, unfortunately there is no more precise data available yet on the mechanism, so I was wondering if a high level GO term might be appropriate in the meantime, in spite of the fact that the mechanism is not well understood. Alterations in the lipidome could in principle affect a multitude of pathways, through signaling pathways and trafficking, hopefully the elegans genetics might help elucidate this...

    Thanks again, Alan

     
  • Added:

    [Term]
    +id: GO:0090519
    +name: anoxia protection
    +namespace: biological_process
    +def: "Any process in which an organism or cell protects itself from anoxia, which may also result in resistance to repeated exposure to anoxia." [GOC:tb, PMID:19372430]
    +is_a: GO:0034059 ! response to anoxia
    +created_by: tanyaberardini
    +creation_date: 2012-12-21T15:37:37Z

     
    • status: open --> closed-accepted
     
  • alan_bridge
    alan_bridge
    2012-12-23

    thanks Tanya, have a good xmas!

     
  • alan_bridge
    alan_bridge
    2012-12-23

    • status: closed-accepted --> open-accepted
     
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