[Ontology-editors] muscle relaxation

[Jennifer Deegan (nee Clark)]

Hi,

I have just received the response below from Paolo Lavader who is a 
muscle expert at CRIBI in Padua. He is cc'd here.

Thanks,

Jennifer

====================

Hi Jennifer,

Thank you for writing me. I do not have very much to say about muscle
relaxation:

At the MOLECULAR LEVEL Ruth Lovering is right: Relaxation of muscles is an
active process.  Before a muscle can contract again calcium needs to be
pumped back into the sarcoplasmic reticulum.  Consequently people with
mutations in ATP2A1 take longer to relax their muscles, not because nothing
is pulling the other way but because the calcium pump is not removing the
calcium from the cytosol quick enough.

However, at the ANATOMICAL LEVEL David Hill is not wrong: contraction of
agonistic muscles is coupled by relaxation of antagonistic ones (e.g. biceps
vs triceps).

This is matter for muscle physiologists...


I have something to ask you in the discussion about muscle development.

If "Individual somatic (skeletal) muscles in Drosophila consist of a single
cell" why drosophilists cannot use the terms muscle cell development or
muscle fiber development to annotate their genes? I would simply change the
current definition of muscle fiber development by adding "They can be
classed as slow, intermediate/fast or fast IN VERTEBRATES", as I am not sure
the same is true in insects.

I sit a simplistic view?

Paolo





David Hill wrote:
> Hopefully some of the muscle folks will respond.
> 
> Ruth Lovering wrote:
>> I object to this decision.
>>
>> Relaxation of muscles is an active process.  Before a muscle can 
>> contract again calcium needs to be pumped back into the sarcoplasmic 
>> reticulum.  Consequently people with mutations in ATP2A1 take longer 
>> to relax their muscles, not because nothing is pulling the other way 
>> but because the calcium pump is not removing the calcium from the 
>> cytosol quick enough.
>>
>> See SF item for reference to Brody's disease.
>>
>> Ruth
>>
>> On 4 Jun 2009, at 13:54, Midori Harris wrote:
>>
>>> Hi David,
>>>
>>> That makes sense, and would mean that we should rename GO:0060085 and 
>>> GO:0060087, and merge GO:0055119 into GO:0055118.
>>>
>>> Any objections?
>>>
>>> Midori
>>>
>>> On Thu, 4 Jun 2009, David Hill wrote:
>>>
>>>> Hi Midori,
>>>>
>>>> This is because muscles don't actively relax per se. The stop 
>>>> contracting and then some other force causes the muscle tissue to 
>>>> expand. In skeletal muscle this is done by having opposing pairs of 
>>>> muscles like the biceps and the triceps. I think describing muscle 
>>>> relaxation as a negative regulation of contraction is actually the 
>>>> way it really works.
>>>>
>>>> David
>>>>
>>>> Midori Harris wrote:
>>>>> Hello,
>>>>> Prompted by a SourceForge request from Ruth, I've noticed that we 
>>>>> haven't been consistent about representing muscle relaxation. We 
>>>>> have three terms that use 'relaxation' in the names, but all have 
>>>>> definitions that are worded much like regulation term defs 
>>>>> (especially the latter two):
>>>>> [Term]
>>>>> id: GO:0055119
>>>>> name: relaxation of cardiac muscle
>>>>> namespace: biological_process
>>>>> def: "The process whereby the extent of cardiac muscle contraction 
>>>>> is reduced." [GOC:ed]
>>>>> is_a: GO:0055118 ! negative regulation of cardiac muscle contraction
>>>>> [Term]
>>>>> id: GO:0060085
>>>>> name: smooth muscle relaxation of the bladder outlet
>>>>> namespace: biological_process
>>>>> def: "Any process that stops, prevents or reduces the frequency, 
>>>>> rate or extent of smooth muscle contraction in the bladder outlet 
>>>>> that contributes to the expulsion of urine from the body." 
>>>>> [GOC:dph, PMID:15827347]
>>>>> synonym: "synaptic transmission involved in urination" EXACT []
>>>>> is_a: GO:0045986 ! negative regulation of smooth muscle contraction
>>>>> relationship: part_of GO:0060073 ! micturition
>>>>> [Term]
>>>>> id: GO:0060087
>>>>> name: relaxation of vascular smooth muscle
>>>>> namespace: biological_process
>>>>> def: "Any process that stops, prevents or reduces the frequency, 
>>>>> rate or extent of vascular smooth muscle contraction." [GOC:dph, 
>>>>> PMID:15867178]
>>>>> synonym: "vascular smooth muscle relaxation" EXACT []
>>>>> is_a: GO:0045986 ! negative regulation of smooth muscle contraction
>>>>> relationship: part_of GO:0042311 ! vasodilation
>>>>> On the other hand, for uterine smooth muscle and the generic smooth 
>>>>> muscle parent, 'relaxation' is a related synonym for the negative 
>>>>> regulation of contraction term:
>>>>> [Term]
>>>>> id: GO:0045986
>>>>> name: negative regulation of smooth muscle contraction
>>>>> namespace: biological_process
>>>>> def: "Any process that stops, prevents or reduces the frequency, 
>>>>> rate or extent of smooth muscle contraction." [GOC:go_curators]
>>>>> synonym: "smooth muscle relaxation" RELATED []
>>>>> is_a: GO:0006940 ! regulation of smooth muscle contraction
>>>>> is_a: GO:0045932 ! negative regulation of muscle contraction
>>>>> relationship: negatively_regulates GO:0006939 ! smooth muscle 
>>>>> contraction
>>>>> [Term]
>>>>> id: GO:0070473
>>>>> name: negative regulation of uterine smooth muscle contraction
>>>>> namespace: biological_process
>>>>> def: "Any process that modulates the frequency, rate or extent of 
>>>>> uterine smooth muscle contraction." [GOC:go_curators]
>>>>> synonym: "uterine smooth muscle relaxation" RELATED [GOC:mah]
>>>>> is_a: GO:0045986 ! negative regulation of smooth muscle contraction
>>>>> is_a: GO:0070472 ! regulation of uterine smooth muscle contraction
>>>>> relationship: negatively_regulates GO:0070471 ! uterine smooth 
>>>>> muscle contraction
>>>>> Not only is the term naming inconsistent, the related scope of the 
>>>>> relaxation synonyms is at odds with the fact that GO:0045986 is an 
>>>>> is_a parent of GO:0060085 and GO:0060087 (I would expect exact or 
>>>>> narrow scope).
>>>>> There is also no generic parent named 'muscle relaxation', although 
>>>>> Ruth has requested one as part of the SF item, nor is 'muscle 
>>>>> relaxation' a synonym for 'negative regulation of muscle 
>>>>> contraction' (GO:0045932). I think we should make this area of the 
>>>>> graph consistent before we add any new terms.
>>>>> So, my question is: which way should we standardize, separate terms 
>>>>> or synonyms for muscle relaxation? Any comments are welcome.
>>>>> SF link:
>>>>> https://sourceforge.net/tracker/?func=detail&aid=2800451&group_id=36855&atid=440764 
>>>>> ccing ontdev list for archiving
>>>>> cheers,
>>>>> midori
>>>>
>>>>
>>
>