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allergene annotation

Suparna Mundodi smundodi at acoma.Stanford.EDU
Wed Mar 15 09:59:25 PST 2006



Alexander D. Diehl wrote:
> Michelle,
> 
> I think it's very important to distinguish between microbial products 
> that enable a microbe to manipulate its environment within a host 
> organism in a way that benefits the microbe, and products that are 
> simply responded to because of the inherent ability of the host to 
> recognize specific molecular patterns evolutionarily associated with the 
> presence and potential danger of a microbe and mount a response intended 
> to protect the host.  The first type is a valid microbial process of 
> inducing a response in another organism, whereas as the second process 
> is strictly a host process acting upon a substrate in the environment.  
> The second situation corresponds to the recognition of 
> antigens/allergens by a vertebrate immune system.  The only process 
> involved is a host process.
> 
> Clearly in the case of induction of the plant hypersensitive response by 
> microbes, if that induction benefits the microbe in some way, it is a 
> valid process for the microbe, 

Alex,

I am not sure if I have heard of a situation where plant hypersensitive 
response benefitting a microbe. Is there such a thing?

Suparna



otherwise it is simply a host defense
> response.  We need to maintain the distinction here in how we annotate 
> to the GO, and in some situations the existing experimental evidence may 
> not support an annotation to a microbial process.
> 
> -- Alex
> 
> 
> Michelle Gwinn Giglio wrote:
> 
>>
>>
>>
>> Hi Jane, Alex, and all,
>>
>> It's funny this is coming up now since at the recent PAMGO workshop 
>> held here at TIGR, we needed to annotate a gene from a pathogen to the 
>> process of inducing hypersensitive response in a plant.
>>
>> In fact we were planning on requesting just such a term as "induction 
>> of hypersensitive response in other organisms".
>> However, we also then started into a discussion of whether this was 
>> the best annotation approach to deal with this kind of situation - as 
>> it appears that pathogens (or at least plant ones) have the ability to 
>> manipulate and effect MANY plant systems and we fear a duplication of 
>> much of the process tree under "interaction between organism" - so we 
>> were wondering if the dual-taxon thing could work for this too.
>>
>> Anyway - my point here was really to say that, yes indeed, there are 
>> cases where organims have proteins which induce the hypersensitive 
>> response in orther organisms.
>>
>> I forget why they do this (at least the ones we were looking at) - its 
>> not my field - but I think it has to do with feeding - but I'm not sure.
>>
>> Michelle
>>
>>
>>
>>
>>
>> Jane Lomax wrote:
>>
>>> LOL!
>>>
>>> Okay, okay - I take your point - the hay-fever example wasn't 
>>> entirely serious. Although I do remain to be convinced that there are 
>>> _no_ cases where inducing a hypersensitive response in another 
>>> organism doesn't confer some selective advantage, but I don't know 
>>> enough about this field and will bow to your superior knowledge ;)
>>>
>>> Out of interest (and I remember having this discussion with you 
>>> before Alex, I just can't remember the conclusion) what's the 
>>> rationale behind having GO:0016068 (type I hypersensitivity) in the 
>>> ontology if all hypersensitivities are disregulations?
>>>
>>> thanks,
>>>
>>> jane
>>>
>>>
>>>
>>> On Tue, 14 Mar 2006, Alexander Diehl wrote:
>>>
>>>  
>>>
>>>> No,
>>>>
>>>> Allergen and antigens are simply the substrates of the immune 
>>>> system.  What makes something an allergen or an antigen is  
>>>> dependent on the responding immune system, and varies by both 
>>>> individual and species.  A response to a particular allergen or 
>>>> antigen is a phenotypic quality of the responding organism.  
>>>> Furthermore, allergies are far more prevalent in "western" human 
>>>> populations than in societies with less well-developed systems of 
>>>> sanitation and medicine, and thus reflect largely an inappropriate 
>>>> refocusing of the immune system in the absence of the threats humans 
>>>> faced in evolution, primarily parasites.  The suggestion that an 
>>>> allergen confers an advantage to plant reproduction also seems 
>>>> amazingly far fetched, given that the vast majority of plant pollen 
>>>> ends up somewhere else than up a person's nose.  Even in sneezing 
>>>> (if I am to pursue what may be intended facetiously here), the 
>>>> pollen would be primarily expelled covered in mucus and probably 
>>>> inactivated.
>>>>
>>>> Allergies are pathogenic disregulations of the normal 
>>>> "hypersensitivity" responses.  We should not be stretching the GO to 
>>>> become a disease ontology unless that is what we want to do with 
>>>> it.  If we want to make the GO into a disease ontology then let's do 
>>>> it officially and not on the sly.
>>>>
>>>> -- Alex
>>>>
>>>>
>>>> Jane Lomax wrote:
>>>>  
>>>>
>>>>> I concede that the argument doesn't hold up as well for allergens 
>>>>> as it does for pathogenic organisms.
>>>>>
>>>>> But aren't you making a value judgement about what constitutes a 
>>>>> 'normal' interaction? How do we know that the fact that the plant 
>>>>> protein induces a hypersensitive response in another organism 
>>>>> doesn't confer some advantage to the plant? Perhaps hay-fever 
>>>>> promotes the spreading of pollen?!
>>>>>
>>>>> jane
>>>>>
>>>>>
>>>>> On Tue, 14 Mar 2006, Alexander Diehl wrote:
>>>>>
>>>>>  
>>>>>    
>>>>>
>>>>>> Sorry to be a few minutes late on this.
>>>>>>
>>>>>> The function of a protein, any protein, is not to be an allergen, 
>>>>>> or antigen, for another organism's immune system.  This is not 
>>>>>> appropriate annotation at all.  Indeed, nearly any protein can be 
>>>>>> made antigenic when given in the right context.  The plant 
>>>>>> proteins in question may be known allergens, but that is not their 
>>>>>> natural role in the plant or for the plant.  Annotation of 
>>>>>> allergenic potential would be appropriate with an ontology focused 
>>>>>> on disease and pathology, but not for the GO.
>>>>>>
>>>>>> We can discuss at the meeting, but I am quite firm in my 
>>>>>> conviction here,
>>>>>>
>>>>>> Alex
>>>>>>
>>>>>>
>>>>>> Jane Lomax wrote:
>>>>>>         
>>>>>>
>>>>>>> But I think when you're talking about interactions between 
>>>>>>> organisms, there really isn't a 'normal' or 'abnormal' - the 
>>>>>>> interaction just occurs. And remember that you'll record two 
>>>>>>> taxon ids; one for the species producing the allergen, and one 
>>>>>>> for the 'allergic' species. So it isn't the usual case of 'is it 
>>>>>>> normal for the species I'm annotating' because you're annotating 
>>>>>>> both.
>>>>>>>
>>>>>>> jane
>>>>>>>
>>>>>>> On Tue, 14 Mar 2006, Harold Drabkin wrote:
>>>>>>>
>>>>>>>  
>>>>>>>             
>>>>>>>
>>>>>>>> Yes, a new term would work much better.  However, it may or may 
>>>>>>>> not be the "normal " function or process.
>>>>>>>> A virus or symbiont host interaction is a bit different, because 
>>>>>>>> those interactions are most likely critical for the life cycle 
>>>>>>>> (eg, if you don't have a host, the virus can't replicate, 
>>>>>>>> etc.).  Many people are allergic to gluten, but is that a normal 
>>>>>>>> function/process of  gluten?
>>>>>>>>
>>>>>>>> Jane Lomax wrote:
>>>>>>>>                    
>>>>>>>>
>>>>>>>>> Unfortunately that term only works where one organism is living 
>>>>>>>>> in symbiosis with another organism (e.g. host/pathogen) which 
>>>>>>>>> is why I suggested that new term...
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Tue, 14 Mar 2006, Harold Drabkin wrote:
>>>>>>>>>
>>>>>>>>>  
>>>>>>>>>                          
>>>>>>>>>
>>>>>>>>>> But, I did find this term, and related?
>>>>>>>>>>
>>>>>>>>>> GO term:     *induction of host defense response*
>>>>>>>>>> GO id:     *GO:0044416*
>>>>>>>>>> Definition:     *The elicitation by an organism of the defense 
>>>>>>>>>> response of the host. The host is defined as the larger of the 
>>>>>>>>>> organisms involved in a symbiotic interaction. *
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> which I think might be more in line with a direct annotation 
>>>>>>>>>> to something like this???
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Harold Drabkin wrote:
>>>>>>>>>>                                   
>>>>>>>>>>
>>>>>>>>>>> I would not; they are the a cause, but they are not involved 
>>>>>>>>>>> in the process (which is not occurring in the plant).
>>>>>>>>>>> The GO is used to indicate the normal function and process of 
>>>>>>>>>>> a gene product. You need to look at it from the point of view 
>>>>>>>>>>> of the organism that produces the gene product. If these 
>>>>>>>>>>> perform some function for the plant, that is what you would 
>>>>>>>>>>> annotate them to. Perhaps there are terms associated with 
>>>>>>>>>>> defense in a plant (ie, along the lines of something that is 
>>>>>>>>>>> released to deter the plant from being eaten???__?
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> adepto at cribi.unipd.it wrote:
>>>>>>>>>>>                                           
>>>>>>>>>>>
>>>>>>>>>>>> Hi All
>>>>>>>>>>>> I have to annotate plant genes described as "allergenic 
>>>>>>>>>>>> peptides" in pFam these
>>>>>>>>>>>> genes are described as:
>>>>>>>>>>>> "Allergies are hypersensitivity reactions of the immune 
>>>>>>>>>>>> system to specific
>>>>>>>>>>>> substances called allergens (such as pollen, stings, drugs, 
>>>>>>>>>>>> or food) that, in
>>>>>>>>>>>> most people, result in no symptoms. A nomenclature system 
>>>>>>>>>>>> has been established
>>>>>>>>>>>> for antigens (allergens) that cause IgE-mediated atopic 
>>>>>>>>>>>> allergies in humans..."
>>>>>>>>>>>>
>>>>>>>>>>>> So, where may I annotate these allergenes? It is GO:0016068 
>>>>>>>>>>>> (type I
>>>>>>>>>>>> hypersensitivity) the right term? Thanks in advance.
>>>>>>>>>>>> Alessandro
>>>>>>>>>>>>  
>>>>>>>>>>>>                                                    
>>>>>>>>>>
>>>>>>>>>>                                    
>>>>>>>>>
>>>>>>>>> Dr Jane Lomax
>>>>>>>>> GO Editorial Office
>>>>>>>>> EMBL-EBI
>>>>>>>>> Wellcome Trust Genome Campus
>>>>>>>>> Hinxton
>>>>>>>>> Cambridgeshire, UK
>>>>>>>>> CB10 1SD
>>>>>>>>>
>>>>>>>>> p: +44 1223 492516
>>>>>>>>> f: +44 1223 494468
>>>>>>>>>
>>>>>>>>>  
>>>>>>>>>                           
>>>>>>>>
>>>>>>>>                     
>>>>>>>
>>>>>>> Dr Jane Lomax
>>>>>>> GO Editorial Office
>>>>>>> EMBL-EBI
>>>>>>> Wellcome Trust Genome Campus
>>>>>>> Hinxton
>>>>>>> Cambridgeshire, UK
>>>>>>> CB10 1SD
>>>>>>>
>>>>>>> p: +44 1223 492516
>>>>>>> f: +44 1223 494468
>>>>>>>
>>>>>>>  
>>>>>>>              
>>>>>>
>>>>>> -- 
>>>>>> 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
>>>>>>
>>>>>>          
>>>>>
>>>>> Dr Jane Lomax
>>>>> GO Editorial Office
>>>>> EMBL-EBI
>>>>> Wellcome Trust Genome Campus
>>>>> Hinxton
>>>>> Cambridgeshire, UK
>>>>> CB10 1SD
>>>>>
>>>>> p: +44 1223 492516
>>>>> f: +44 1223 494468
>>>>>
>>>>>  
>>>>>     
>>>>
>>>> -- 
>>>> 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
>>>>
>>>>   
>>>
>>>
>>> Dr Jane Lomax
>>> GO Editorial Office
>>> EMBL-EBI
>>> Wellcome Trust Genome Campus
>>> Hinxton
>>> Cambridgeshire, UK
>>> CB10 1SD
>>>
>>> p: +44 1223 492516
>>> f: +44 1223 494468
>>>
>>>  
>>>
> 
> 



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