ntr: small vegetative cell with advanced mitosis and M phase arrest #2818
Comments
No, smallness, like everything else, is defined relative to wild type under the same conditions. As noted in #2544, we haven't linked FYPO:0000648 to FYPO:0001046 because we're waiting for you and Jacky to figure out whether there's any way to define premature mitosis using criteria other than cell size, or any way to get a small cell other than by premature mitosis. We'll need to know that for this ticket, too, to tell whether the new term will simply be "small vegetative cell with cell cycle arrest in M phase" or if the "premature mitosis" part actually adds any further distinction. There's more background in an older ticket in SourceForge (one of the few that missed out on the move to GitHub) - https://sourceforge.net/p/pombase/fission-yeast-phenotype/1770/ |
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you can get small cells in G0 too I think sometimes it is difficult to differentiate in a mixed population..... But I see what you mean leave this with me. I'll get it eventually.... not to self: I'm not even sure about the viability here..... |
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I think a premature mitosis could also be defined as a shorter than normal G2 phase Sent from my iPhone On 20 Sep 2016, at 17:51, Midori Harris <notifications@github.commailto:notifications@github.com> wrote: IIRC we could not put FYPO:0000648 viable small vegetative cell as an output [of] FYPO:0001046 premature mitosis because cells can be small also if entering G0 or grown on non-rich media? No, smallness, like everything else, is defined relative to wild type under the same conditions. As noted in #2544#2544, we haven't linked FYPO:0000648 to FYPO:0001046 because we're waiting for you and Jacky to figure out whether there's any way to define premature mitosis using criteria other than cell size, or any way to get a small cell other than by premature mitosis. We'll need to know that for this ticket, too, to tell whether the new term will simply be "small vegetative cell with cell cycle arrest in M phase" or if the "premature mitosis" part actually adds any further distinction. There's more background in an older ticket in SourceForge (one of the few that missed out on the move to GitHub) - https://sourceforge.net/p/pombase/fission-yeast-phenotype/1770/ You are receiving this because you are subscribed to this thread. The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 215 Euston Road, London NW1 2BE. |
But (if I understand correctly) that's a normal feature of G0, and therefore not what we're trying to represent with the implicitly-abnormal "small cell".
Always, always compare to wild type cells treated the same way. If you have an experiment that doesn't show wt you may be stuffed, unfortunately ... |
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Yes but I think sometimes you might have small cells because some have entered G0, but you didn't know this was the reason they were small. This was my worry. I think I have seen such situations .... |
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If all you have is pictures of cells where the mutant ones look smaller than the wild type ones, you have to just annotate to a "small cell" term because that's what the pictures show. The annotation could be removed later if additional evidence reveals that they've entered G0, and we could add a "premature G1 to G0 transition" term if it's warranted for those cases. |
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curs/9442751303a5f327 |
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anything to do for this, or should we close it? |
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Lets close |
This term is analogous to
the inviable elongated cell with mitotic transition delay and cell cycle arrest in M-phase
it will be a child of both
FYPO:0001046 premature mitosis
and
FYPO:0000648 viable small vegetative cell
which are often concurrently annotated (see comment)
This more precise phenotype will be useful. IIRC we could not put FYPO:0000648 viable small vegetative cell as an output or FYPO:0001046 premature mitosis because cells can be small also if entering G0 or grown on non-rich media?
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