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allergene annotation

Suparna Mundodi smundodi at acoma.Stanford.EDU
Wed Mar 15 12:43:55 PST 2006


Thanx Michelle. Well, I had a quick discussion with Shauna Somerville 
here, who is an expert on necrotroph-plant interactions. Looks like 
pathogens do seem to have mechanisms(such as secreting toxic compounnds 
etc) to induce HR in plants and then live off of the dead cells. 
However, Shauna didn't know of any gene product directly associated with 
it. So, if the existence of a process such as this warrants a term, then 
I am for it.

Here is another review on this issue.
PMID: 11524110

Cheers,
Suparna

Michelle Gwinn Giglio wrote:
> 
> Hi Suparna,
> 
> Sure - it's PMID:12410814.
> However, these may not be the best examples, in fact I'm sure they are 
> not, I know very little about this, only what I've learned from PAMGO 
> folks over relatively brief discussions of papers they were annotating.
> 
> Michelle
> 
> 
> 
> Suparna Mundodi wrote:
> 
>> Michelle,
>>
>> Do you have the P.sojae reference by any chance?
>>
>> Suparna
>>
>> Michelle Gwinn Giglio wrote:
>>
>>>
>>>
>>>
>>> Hi Alex,
>>>
>>> Yeah - I'm not sure there was a specific gene for the Botrytis 
>>> cinerea case yet identified - but it shows a system exists even if 
>>> they haven't found the exact genes.  However, they have found such 
>>> candidate genes in the P. sojae system.
>>>
>>> Michelle
>>>
>>>
>>> Alexander D. Diehl wrote:
>>>
>>>> Michelle,
>>>>
>>>> Great paper, although I don't think they actually identified a 
>>>> specific Botrytis cinerea gene that promotes the HR response in the 
>>>> host to which one could tie the "induction of hypersensitive 
>>>> response in other organism" annotation.  But maybe I skimmed too 
>>>> quickly or that's coming in the next paper.
>>>>
>>>> -- Alex
>>>>
>>>>
>>>> Michelle Gwinn Giglio wrote:
>>>>
>>>>>
>>>>>
>>>>> Hi Suparna,
>>>>>
>>>>> I'm not an expert on this either - I'm hoping Candace will chime in.
>>>>>
>>>>> In the meantime, according to my understanding of what was 
>>>>> discussed at the recent PAMGO workshop, some pathogens 
>>>>> intentionally induce the HR in plants.   Some of these are 
>>>>> necrotrophic and require (or at least can use) dead tissues for 
>>>>> growth.   Check out the abstract for this paper PMID:10898976 - it 
>>>>> describes how the HR response allows Botrytis cinerea to grow on 
>>>>> plants.  In addition, some pathogens shift from biotrophy (living 
>>>>> on live tissue) to necrotrophy during an infection (hemibiotrophs) 
>>>>> and at least one gene has been found in P. sojae which is expressed 
>>>>> at this transition and is believed to induce HR.  That's examples 
>>>>> from two systems - I imagine there are more.
>>>>>
>>>>> But Candace should be the one to comment on this as she knows much 
>>>>> more about it.
>>>>>
>>>>> Michelle
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Alexander D. Diehl wrote:
>>>>>
>>>>>> Suparna,
>>>>>>
>>>>>> I don't know if this is true as I am not an expert here, but 
>>>>>> Michelle wrote "it appears that pathogens (or at least plant ones) 
>>>>>> have the ability to manipulate and effect MANY plant systems," and 
>>>>>> mentioned the hypersensitive response in her discussion, I thought 
>>>>>> she was implying that manipulating the hypersensitive response is 
>>>>>> in fact done by certain microbes for their benefit.
>>>>>>
>>>>>> -- Alex
>>>>>>
>>>>>>
>>>>>> Suparna Mundodi wrote:
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> 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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