search

pombase / fypo

Fission Yeast Phenotype Ontology
Creative Commons Attribution 4.0 International
14 stars 6 forks source link

viable vegetative cells with circular(ized) chromosomes #795

Closed fypoadmin closed 9 years ago

fypoadmin commented 11 years ago

viable vegetative cells with circular(ized) chromosomes

Original comment by: Antonialock

fypoadmin commented 11 years ago

We don't have very many other terms that mix cell viability in with subcellular structure abnormalities. The descendants of abnormal subcellular structure describe what's wrong with the structure, and most don't say anything about whether the cell is viable (and the exceptions so far only mention the nucleus or the septum, not any other subcellular structures).

So I will have to add a term for circularized chromosome, and it would be more consistent with existing terms to leave it at that.

Original comment by: mah11

fypoadmin commented 11 years ago

ok....I just thought it was a cool phenotype. Cells that do not circularize their chromosomes die, and the ones that do stay viable..

Original comment by: Antonialock

fypoadmin commented 11 years ago

I was thinking about this. This is pot1 isn't it, but the same thing happens when you look the sub telomeric helicases that look like transposons.....

so can this pot1 delete survive indefinitely with circularized chromosomes? how does that work? i think for the other telomeric ones eventually some recombination event replaces the telomeres, although I would have to check on that....

Original comment by: ValWood

fypoadmin commented 11 years ago

yeah it is pot1...I suppose it is safer to omit the viable bit, they don't really comment on if they go on indefinitely or not as far as i can remember

Original comment by: Antonialock

fypoadmin commented 11 years ago

I wonder if there is some way to capture "survivors", more generally.

I think this is the things jacky has listed as "possibly acquired suppressor" etc (which I am ignoring for now), where things look almost dead, and then are rescued by some other mutation, or event....any ideas anyone?

Or would we just capture this temporally? although presumably in these cases, because they are dependent on a random event occurring, sometimes you will get survivors, and sometimes you won't, but it won't always be reproducible.....

Original comment by: ValWood

fypoadmin commented 11 years ago

We had a brief discussion about this, just to summarize. We think that this is no longer pot1(delta) only because there is the +chromosome circularization, which has changed the genotype (slightly)...no idea HOW we would represent this.

Don't know what to suggest for now, whether we should annotate rare survivors as "viable", but definitely it is information we should capture...but how?

Original comment by: ValWood

fypoadmin commented 11 years ago

ok yes, I do not know if they have acquired an additional mutation, or if it is just the topology that has changed.

I don't think we should annotate to 'can be rescued by a suppressor but we don't know which one' because that is what we cover with a genetic interaction once it IS known...

Original comment by: Antonialock

fypoadmin commented 10 years ago

I'm submitting this paper for approval. Let me know if you want me to get this phenotype in somehow, Val?

http://curation.pombase.org/pombe/curs/0afc32dc747285ae

otherwise I guess this can be closed?

Original comment by: Antonialock

fypoadmin commented 10 years ago

I think, as this is quite a significant observation we should add a phenotype for now of "circularized chromosomes"

(but not combine it with viability)

Original comment by: ValWood

fypoadmin commented 10 years ago

Original comment by: mah11

fypoadmin commented 10 years ago

OK, that makes sense. Added:

circularized chromosome FYPO:0002702

Original comment by: mah11