neuronal ion channel clustering

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Hi,

Does this process happen anywhere other than in the neurons? Perhaps in muscle fibres?

Term: neuronal ion channel clustering ; GO:0045161 def: The process by which voltage-gated sodium and potassium ion channels become localized to distinct subcellular domains in the neuron. Specific targeting, clustering, and maintenance of these channels in their respective domains are essential to achieve high conduction velocities of action potential propagation.

Thanks,

Jen

Reported by: jenclark

Original Ticket: "geneontology/ontology-requests/2794":https://sourceforge.net/p/geneontology/ontology-requests/2794

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Original comment by: jenclark

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Definitively in muscle, but also in other excitable cells, such as cochlear hair cells (in the inner ear). Although in the epithelial cell of the kidney glomeruli, there is a differential targeting of channels.

That said, I disagree with the term. Channel clustering is different from differential localisation. We use clustering only when the channel are gathered together in cluster. That imply a rigid contact, direct, or through linker proteins. This is different from a segregation by a lipid raft, or a system of picket-fences (as in the neuromuscular junction).

Original comment by: lenov

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Hi Nicolas,

Thanks for your comment. Can you suggest an alternative structure that you'd be happy with?

Thanks,

Jen

Original comment by: jenclark

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This item was orignally opened to see if the name and definition of the term needed to stipulate that this process occurred in the neuron. Clearly it does, and the name and definition have been modified. If Nicolas does not have time to contribute a better model then I will close the item in one week.

Thanks,

Jen

Original comment by: jenclark

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Some comments:

1)

GO:0042551 ; nerve maturation

should be "neuron maturation"

A nerve is not a neuron. Therefore the lineage should be

neuron differentiation [p] neuron development [p] neuron maturation

to follow the superclass

cell differentiation [p] cell development [p] cell maturation

(none of my business, but how comes cell development is "part-of" diffentiation. It is the way around. Cell development comprises cell differentiation (the acquisition of the molecular identity of the cell), cell morphogenesis, cell migration etc.)

2) neuronal ion channel clustering must be made "part-of" neuron maturation, not "is-a"

Original comment by: lenov

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Hi Nicolas,

Thanks for getting back to me on this. The answer to your question about differentiation is documented at:

http://www.geneontology.org/GO.process.guidelines.shtml\#diffdev

Would you agree with that?

Jen

Original comment by: jenclark

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I have fixed all of this now.

Jen

Original comment by: jenclark

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Nicholas,

Could you have a look at the relationship between nerve (neuron) maturation and nerve ensheathment? I wonder if we should rename nerve ensheathment to be neuron ensheathment. It seems odd to me to have a process that is occurring at the level of the nerve be a part of neuron maturation.

David

Original comment by: ukemi

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Ouch! You are quite right. Easy to fix though (I think)

"nerve maturation" (GO:004551) should become a part-of "nervous system development" (GO:0007399) instead of "neuron development" (GO:48666)

And the relation between "nerve maturation" (GO:004551) with "cell maturation" (GO:0048469) should be suppressed.

On the other side "nerve ensheatment" should have two is-a kids:

"nerve ensheatment by oligodendrocyte" (GO:new)
"nerve ensheatment by Schwann cell" (GO:new)

Those should become also part-of kids of:

"oligodendrocyte development" (GO:new)
"Schwann cell development" (GO:new)

themselves kids of

"oligodendrocyte differentiation" (GO:0048709) "Schwann cell differentiation" (GO:new)

Finally "Schwann cell differentiation" (GO:new) should be kid of "glial cell differentation"

Here I follow the current term lineage, that is also the one of neuron.

differentiation ----[i] development

Jen, I think there is an alternative way of interpreting the doc.

"Cell development should NOT include the steps involved in committing a cell to a specific fate. Differentiation includes the processes involved in commitment. Development is what the cell does once it is committed to a given fate. " A logical structure would then be:

cellgenesis ----[p] cell differentiation --------[p] cell fate commitment ------------[p] cell fate specification ------------[p] cell fate determination[] ----[p] cell development --------[p] cell migration --------[p] cell morphogenesis

Original comment by: lenov

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awesome.

The problem I see with the differentiation structure at the bottom is that differentiation includes not only the committment steps, but also the development of the cell.

Interesting idea would be to include cell genesis, cytogenesis and cytogeny as some type of synonyms to cell differentiation??

David

David

Original comment by: ukemi

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Ouch! You are quite right. Easy to fix though (I think)

"nerve maturation" (GO:004551) should become a part-of "nervous system development" (GO:0007399) instead of "neuron development" (GO:48666)

And the relation between "nerve maturation" (GO:004551) with "cell maturation" (GO:0048469) should be suppressed.

On the other side "nerve ensheatment" should have two is-a kids:

"nerve ensheatment by oligodendrocyte" (GO:new)
"nerve ensheatment by Schwann cell" (GO:new)

Those should become also part-of kids of:

"oligodendrocyte development" (GO:new)
"Schwann cell development" (GO:new)

themselves kids of

"oligodendrocyte differentiation" (GO:0048709) "Schwann cell differentiation" (GO:new)

Finally "Schwann cell differentiation" (GO:new) should be kid of "glial cell differentation"

Here I follow the current term lineage, that is also the one of neuron.

differentiation ----[i] development

Jen, I think there is an alternative way of interpreting the doc.

"Cell development should NOT include the steps involved in committing a cell to a specific fate. Differentiation includes the processes involved in commitment. Development is what the cell does once it is committed to a given fate. " A logical structure would then be:

cellgenesis ----[p] cell differentiation --------[p] cell fate commitment ------------[p] cell fate specification ------------[p] cell fate determination[] ----[p] cell development --------[p] cell migration --------[p] cell morphogenesis

Original comment by: lenov

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"The problem I see with the differentiation structure at the bottom is that differentiation includes not only the committment steps, but also the development of the cell. "

Not according to the doc pointed to by Jen.

"Differentiation includes the processes involved in commitment."

"Development is what the cell does once it is committed to a given fate."

I don't say I agree with those definitions. In particular, for many cells, migration, morphogenesis and differentiation are concommitent, so the notion "once it is commited" is flawed.

But they are definition. And here we have a discrepancy between the definitions and the current state of GO.

Original comment by: lenov

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"Differentiation includes the processes involved in commitment."

"Development is what the cell does once it is committed to a given fate."

This is a slip of the tongue that I hadn't noticed. It's meant to imply "Differentiation includes the processes involved in commitment, in addition to the cell development steps."

Original comment by: jenclark

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"The problem I see with the differentiation structure at the bottom is that differentiation includes not only the committment steps, but also the development of the cell. "

Not according to the doc pointed to by Jen.

"Differentiation includes the processes involved in commitment."

"Development is what the cell does once it is committed to a given fate."

I don't say I agree with those definitions. In particular, for many cells, migration, morphogenesis and differentiation are concommitent, so the notion "once it is commited" is flawed.

But they are definition. And here we have a discrepancy between the definitions and the current state of GO.

Original comment by: lenov

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The conceptual difficulty here was deciding when the development of x begins and when it ends. One could argue that fertilization is part of heart development, but the utility is not very great. So, the decision with respect to cells was that we would consider the begining once the cell is committed. Otherwise, it could be the development of another cell. Differentiation contains both this committment phase and the subsequent development.

David

Original comment by: ukemi

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It's meant to imply "Differentiation includes the processes involved in commitment, in addition to the cell development steps."

Yep. Unfortunately. It seems that we have at the level of the cell, what we had at the level of the organ some weeks ago: "development" is synonymous of "morphogenesesis" rather than "genesis".

I don't want to start a similar debate again. But GO is really changing all the meanings. By definition "development" is the sum of all the processes that lead to the final state of an entity. While "differentiation" is the process that from identical entities leads to different entities. Therefore, by definition, X differentiation is a part of X development. Those concepts are used absolutely everywhere. There are not even specific to biology.

If we refocuss on the neuron "generation", you can consider for instance the changing fate of mature neurons (cathecholamine to acetylcholine in the autonomous system). You could argue that the differentiation covers everything from the neuroblast to the cholinergic phenotype. But since it implies migration and morphogenesis steps, it is more than that. In addition, the generation of the cholinergic neuron actually comprises several differentiations (differentiation of a neuroblast into a neuron, differentiation of a cathecolaminergic neuron into a cholinergic neuron ...)

Original comment by: lenov

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"development" is the sum of all the processes that lead to the final state of an entity.

The problem here is that of the chicken and the egg. From a practical standpoint for the development of any "entity" X, we have to define beginning and end points for the process. Otherwise, the embryogeneisis of my mother is part of my development, or gastrulation is a part of kidney development. Although my mother's embryogenesis led to the final state that was me, and gastrulation leads to the final state of a kidney, clearly there has to be a cut-off somewhere. That cut off is determined by how the class development differs from the class X development. Clearly for the case of me from a biological perspective, X can be set at the fertilized egg (although that is still argued in legal circles). But what about for a cell? Does it not make sense to make it after the cell undegoes commitment?

Is the development of a neuron part of the development of a neuroblast since that is what the neuroblast turns into? Or, is the development of a neuroblast part of the development of a neuron since that is where it came from? Where is the transition? It is at the commitment stage of differentiation when the decision is made. That is when the neuroblast ends and the neuron begins. Differentiation is still a developmental process, but we needed to decide when the development of an X cell starts. If it starts after the cell is committed to become X (quite reasonable I think), and differentiation is:The process whereby relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history.(consistent with both developmental biologists and cell biologists). Then X cell development is a part of its differentiation.

I think that lineage relationships are better represented in other ontologies such as in the cell ontology or in an anatomical ontology. The sum of all processes that lead up to something can then be computed based on those relationships. So, if you want neuron development to include everything, ask for neuron development to include the development and differentiation of all the precursors of a neuron as well as the neuron itself. If you want to learn about kidney development, choose the anatomical structures that you want to start with that develop into structures that eventually form the kidney and sum up all the processes.

David

Original comment by: ukemi

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I have made some new documentation for the website using material from that discussion.

Now I'm trying to figure where we've got to with

the question that started it off:

Nicholas,

Could you have a look at the relationship between nerve (neuron) maturation and nerve ensheathment? I wonder if we should rename nerve ensheathment to be neuron ensheathment. It seems odd to me to have a process that is occurring at the level of the nerve be a part of neuron maturation.

David

Thanks,

Jen

Original comment by: jenclark

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Hi Nicolas and David,

Is this information from Nicolas still good? I have summarised it below to make it easier to read. Please note that nerve maturation is actually called neuron maturation.

"nerve maturation" (GO:004551) should become a part-of "nervous system development" (GO:0007399) instead of "neuron development" (GO:48666)

And the relation between "nerve maturation" (GO:004551) with "cell maturation" (GO:0048469) should be suppressed.

On the other side "nerve ensheatment" should have two is-a kids:

"nerve ensheatment by oligodendrocyte" (GO:new)
"nerve ensheatment by Schwann cell" (GO:new)

Those should become also part-of kids of:

"oligodendrocyte development" (GO:new)
"Schwann cell development" (GO:new)

themselves kids of

"oligodendrocyte differentiation" (GO:0048709) "Schwann cell differentiation" (GO:new)

Finally "Schwann cell differentiation" (GO:new) should be kid of "glial cell differentation"

Here I follow the current term lineage, that is also the one of neuron.

differentiation ----[i] development

summary:

relationships added:

[i]nervous system development ; GO:0007399 ---[p]nerve maturation ; GO:004551

[i]nerve ensheatment ; ---[i]nerve ensheatment by oligodendrocyte ; GO:new
---[i]nerve ensheatment by Schwann cell ; GO:new

[i]oligodendrocyte differentiation ; GO:0048709 ---[p]oligodendrocyte development ; GO:new ------[p]nerve ensheatment by oligodendrocyte ; GO:new

[i]glial cell differentation ; ---[i]Schwann cell differentiation ; GO:new ------[p]Schwann cell development ; GO:new
---------[p]nerve ensheatment by Schwann cell ; GO:new

Relationships removed:

[i]nerve maturation ; GO:004551 ---[p]neuron development ; GO:48666

[i]cell maturation ; GO:0048469 ---[i]nerve maturation ; GO:004551

Original comment by: jenclark

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"oligodendrocyte differentiation" should also be kid of "glial cell differentation"

Original comment by: lenov

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Hi Jen,

Yes.

David

Original comment by: ukemi

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Great! I'll do that then.

Jen

Original comment by: jenclark

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I have made those changes and figured out defs with Nicolas. I'll check my changes again tomorrow and commit.

Jen

Original comment by: jenclark

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I've committed that now.

new terms:

[Term] id: GO:0048756 name: nerve ensheathment by oligodendrocyte namespace: biological_process def: "The process by which the axon of a neuron is insulated in the central nervous system and that insulation maintained\, thereby preventing dispersion of the electrical signal. This process is carried out by the oligodendrocyte\, a class of large neuroglial (macroglial) cell." [BIOMD:nln, GO:jic, MESH:A.08.637.600, MGI:dph] is_a: GO:0008366 ! nerve ensheathment relationship: part_of GO:0048758 ! oligodendrocyte development

[Term] id: GO:0048757 name: nerve ensheathment by Schwann cell namespace: biological_process def: "The process by which the axon of a neuron is insulated in the peripheral nervous system and that insulation maintained\, thereby preventing dispersion of the electrical signal. This process is carried out by the Schwann cells." [BIOMD:nln, GO:jic, MESH:A.08.637.800, MGI:dph] is_a: GO:0008366 ! nerve ensheathment relationship: part_of GO:0048760 ! Schwann cell development

[Term] id: GO:0048758 name: oligodendrocyte development namespace: biological_process def: "The process aimed at the progression of an oligodendrocyte over time\, from initial commitment of the cell to a specific fate\, to the fully functional differentiated cell. Oligodendrocyte is a class of large neuroglial (macroglial) cells in the central nervous system. They form the insulating myelin sheath of axons in the central nervous system." [BIOMD:nln, GO:jic, MGI:dph] relationship: part_of GO:0048709 ! oligodendrocyte differentiation

[Term] id: GO:0048759 name: Schwann cell differentiation namespace: biological_process def: "The process whereby a relatively unspecialized cell acquires specialized features of a Schwann cell. A Schwann cell is a neuroglial cell of the peripheral nervous system that forms the insulating myelin sheaths of peripheral axons." [BIOMD:nln, GO:jic, MESH:A.08.637.800, MGI:dph] is_a: GO:0010001 ! glial cell differentiation

[Term] id: GO:0048760 name: Schwann cell development namespace: biological_process def: "The process aimed at the progression of a Schwann cell over time\, from initial commitment of the cell to a specific fate\, to the fully functional differentiated cell. A Schwann cell is a neuroglial cell of the peripheral nervous system that forms the insulating myelin sheaths of peripheral axons." [BIOMD:nln, GO:jic, MESH:A.08.637.800, MGI:dph] relationship: part_of GO:0048759 ! Schwann cell differentiation

This item is now finished.

Thanks for all your work on this.

Jen

Original comment by: jenclark

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• status: open --> closed-accepted

Original comment by: jenclark

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Original comment by: cooperl09