inviable following spore germination, cell cycle arrest as elongated cells (or smth)

[fypoadmin]

inviable following spore germination, cell cycle arrest as elongated cells (or smth)

these cells arrest elongated following spore gerination, no cell divisions

Original comment by: Antonialock

[fypoadmin]

I think you want one of the children of FYPO:0000313 either inviable after spore germination with elongated germ tube inviable after spore germination with elongated, septated germ tube

(it is under inviable after spore germination, what did you search on? maybe there is a parent missing?)

These terms should be under "elongated inviable vegetative cell" too and i couldn't see them immediately under there.

(Q is it a DNA replication gene?)

Original comment by: ValWood

[fypoadmin]

yeah, elongated germ tube is fine I think

just asking before closing - would this not also be a cell cycle arrest phenotype (elongated germ tube)? Perhaps not always? When if so?

it is cdc2∆ btw

Original comment by: Antonialock

[fypoadmin]

Yes I have been thinking about this.

The elongation is what you see, and this allows us to infer a cell cycle arrest somewhere in interphase*

We would not necessarily in all cases want to annotate to a GO "regulation of cell cycle" without more information, but I think we want to represent the "cell cycle arrest" as a phenotype. I think Midori's solution in these cases is to have a parent child relationship cell cycle arrest has_output--elongated vegetative cell related

which makes sense

but then we also need to ensure that the annotations are inherited over "has output" (at present they are not)

(* we can't be more specific about the block at present, but I think once the genome project elongated are mapped more specifically we might be able to...this one seems to correlate with DNA replication, its regulation, and splicing ...presumably an essential gene is spliced).

P.s cdc2 from phenotype project is getting: inviable after spore germination with elongated germ tube (High penetrance)
AND FYPO:0002149 elongated inviable vegetative cell population

Original comment by: ValWood

[fypoadmin]

1. P.s cdc2 from phenotype project is getting: was just to show we are on the same page...

2. What is (or smth)?

v

Original comment by: ValWood

[fypoadmin]

Re> - would this not also be a cell cycle arrest phenotype

Yes, in fission yeast, every type of increased cellular elongation indicates a cell cycle transition defect (cells keep growing and don't divide, no other known explanation). ...although I wonder.. thinking ..... because for cells which are viable, but slightly elongated, maybe the defect just related to regulation of growth, and not division...but I guess it has to be regulation of division too, because reaching a certain size is the trigger for division.....I'm confusing myself...will ask Jacky...

certainly for small cells there are 2 explanations. Cells can be small because they don't grow (these are inviable), or they can be viable and divide at small size (wee) and these are a cell division defect.

Original comment by: ValWood

[fypoadmin]

What is (or smth)?

smth = something I meant 'or something along similar lines' :)

I didn't think I could annotate to elongated inviable vegetative cell population from the same experiment because 'inviable after spore germination with elongated germ tube' is a child of 'inviable after spore germination, no cell divisions' (=they never get to the point of a growing vegetative population?)

Original comment by: Antonialock

[fypoadmin]

Re: I didn't think I could annotate to elongated inviable vegetative cell population from the same experiment because 'inviable after spore germination with elongated germ tube' is a child of 'inviable after spore germination, no cell divisions' (=they never get to the point of a growing vegetative population?)

I discussed this in detail with Jacky. We think that as soon as a cell has germinated it can be considered as growing vegetatively, because it is not longer in sporulation. It is difficult to know when a cell has successfully germinated without staining the proteins where the germ tub emerge, they may heve germinated before anything is visible by simple microscopy, however as soon as the spore has "broken symmetry" and the germ tube is visible it is definitely in vegetative growth phase. Does this make sense ? This probably means that Midori will need to revisit a few existing terms to make them children of vegetative.

Original comment by: ValWood

[fypoadmin]

so division is not a prequisite. A cell can be growing vegetatively if it hasn't divided.

Original comment by: ValWood

[fypoadmin]

ok I see

Original comment by: Antonialock

[fypoadmin]

I've added:

inviable after spore germination, cell cycle arrest, elongated cells FYPO:0002263

do we need to do anything else? (inviable after spore germination is now is_a inviable vegetative cell anyway)

Original comment by: mah11

[fypoadmin]

• labels: --> new ontology term
• assigned_to: Midori Harris

Original comment by: mah11

[fypoadmin]

I think that's OK. Will open a new ticket if anything outstanding once but I can't find anything in my script notes outstanding for this one

VAL

Original comment by: ValWood

[fypoadmin]

• status: open --> closed-accepted

Original comment by: mah11