NTR PMID:34666001 localization to sites of mechanical stress

[ValWood]

normal protein localization to site of mechanical stress descendent of FYPO:0003627 | normal protein localization |

A cell phenotype in which the localization of a protein at a site of mechanical stress on the cell surface (i.e. indistinguishable from wild type).

and abolished protein localization to site of mechanical stress A cell phenotype in which a protein does not localize to a site of mechanical stress on the cell surface.

[ValWood]

Also,

inviable vegetative cell during mechanical stress

[manulera]

For abolished protein localization to site of mechanical stress, should it be a child of 'abnormal protein localization to cell surface'?

normal protein localization to cell surface does not exist, so I will put it as child of FYPO:0003627 as you said.

[manulera]

I haved added the two first terms, and replaced them in the curation session.

I did not add the inviable vegetative cell during mechanical stress, I had not seen it. I will add it on next one.

There is also a term request in the curation session for decreased lateral diffusion in membrane, but I think it should be increased lateral diffusion in membrane. What they measure is the recovery timescale (a proxy of how long it takes for receptors to diffuse to the part of the membrane that was bleached).

Wsc1DWSC-GFP and Wsc1DSTR-GFP, which are incapable of clustering, exhibited much smaller half-times—closer to that of mCherry-Psy1 (Figures 6A, 6B, and S6A).

The lower recovery time reported for the Dwsc and Dstr mutants implies that they diffuse faster.

I will add this term as well, as a child of abnormal dynamic protein localization pattern as you requested.

[manulera]

For 'inviable vegetative cell during mechanical stress', the definition could be: "A cell phenotype in which a vegetative cell dies at a level of mechanical stress that wild-type cells can normally withstand"

However, I wonder whether we have cell phenotypes similar to the population phenotypes children of FYPO:0000304 - 'sensitive to stress during vegetative growth'. Since the mechanical stress can be of different amounts, and wild type cells would also die at high mechanical stress, maybe sensitive is more accurate than inviable cell, even for a cell phenotype.

[ValWood]

I agree. I wasn't really sure what to do with this one!

[ValWood]

So in this case do you think I should use just FYPO:0000304 - 'sensitive to stress during vegetative growth' or would you add also

• 'sensitive to mechanical stress during vegetative growth'

[manulera]

The problem is that the phenotypes that mention stress are population phenotypes, and this feels like a cell phenotype. Also because the stress is applied at the cellular level, it's not a matter of observation method only. But maybe I am wrong and this can be considered a population phenotype, since overall you would measure the percentage of cells that die under a given mechanical stress?

Perhaps for now we can add it as a child of FYPO:0000304, and figure out the right placement and logical definition in the future with uPheno. Since this is a new term anyway, I don't think it will be problematic to postpone its right placement as long as we keep it in mind.

[ValWood]

I think you are right. I should do these as inviable vegetative cell in response to mechanical stress with the appropriate penetrance. Does that sound OK?

[manulera]

I am not sure, I think we could ask this to uPheno, for what I said before:

Since the mechanical stress can be of different amounts, and wild type cells would also die at high mechanical stress, maybe sensitive is more accurate than inviable cell, even for a cell phenotype.

I think this could be something like increased sensitivity to cellular-level perturbation or something in these lines. Some perturbation that is applied at the cellular level and kills the mutants, but at higher intensity would also kill wild-type cells.

[ValWood]

I see what you mean.

maybe "increased cell death in response to mechanical stress" ?

uPheno might not be able to help so much with questions like these. They are more concerned with making sure that our logical definitions match the design patterns of similar phenotypes used by other groups, and are consistent within our ontology. MAinly they are ontologists rather than biologists so figuring out what we want to describe will be largely on us. Also, most of the other phenotype ontologies are based on developmental processes or disease phenotypes rather than cell level phenotypes, we have probably the largest collection of cell level phenotypes. so there will usually be no precedent.

They will help us with how to construct a logical definition. When that part of the OBO academy comes up let me know. I'm should learn about this.

[manulera]

Hi @ValWood, I will create an abnormal cell phenotype called cell sensitive to mechanical stress, and we can figure out placement and logical definition in the future.

[manulera]

Addressed in Protege

[manulera]

Forgot to add increased lateral diffusion in membrane, still pending

[ValWood]

I just spotted this in Nico's e-mail

In the cases where you mention inviable vegetative cell and vegetative cell lysis, the % indicated correspond to situations when cells are grown under mechanical stress. Can we modify this?

This would also require a term

"vegetative cell lysis during mechanical stress"

[manulera]

I had annotated

To sensitive to mechanical stress and added a comment (25% cell death).

And there is still

I could annotate both penetrance phenotypes to "vegetative cell lysis during mechanical stress", I imagine the inviable cell was also lysed?

Should these phenotypes be output_of "cell sensitive to mechanical stress"?

But then I am wondering, is being sensitive to mechanical stress the same thing as cell lysis during mechanical stress? As in, do they determine the sensitivity to mechanical stress by seeing how many cells die/lyse under those conditions? Or is there another readout?