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nitrogen shift terms / endosulphine. (Noctua modelling subticket) #2787

Open ValWood opened 4 years ago

ValWood commented 4 years ago

review

These terms indicate a change from a (good) glutamate to a bad (proline) nitrogen source but that is difficult to parse from the terms. Also it is difficult to understand that the cells are dividing early or late.

1 | abolished cell division timing change upon nitrogen source shift (FYPO:0004701) [single allele genotypes] | ...   | 3 | normal mitotic cell cycle regulation upon nitrogen source shift (FYPO:0005207) [single allele genotypes] | ...   | 9 | abnormal mitotic cell cycle regulation upon nitrogen source shift (FYPO:0005206) [single allele genotypes]

These should be either 1?

  1. normal entry into mitosis during nitrogen starvation
  2. abnormal normal entry into mitosis during nitrogen starvation (either advanced or delayed)
mah11 commented 4 years ago

When the phenotype terms were requested, Antonia thought the N source change was different from full-blown nitrogen starvation - https://github.com/pombase/fypo/issues/2508#issuecomment-172860032 (plus the rest of that ticket); also see https://github.com/pombase/fypo/issues/3009 and https://github.com/pombase/fypo/issues/2236.

ValWood commented 4 years ago

It is different from full blown starvation but this doesn't really indicate that the change in source is a mechanism to introduce 'nitrogen stress' by changing from a good nitrogen source to a bad nitrogen source. It not about the source change per. se.

ValWood commented 4 years ago

I think one of the main things is that the shift it isn't clear the direction of the shift either. So it's difficult to interpret the phenotypes, and it's quite head-melty anyway trying to figure what the changes in division time of cell length mean.

ValWood commented 2 years ago

I can speak to Janni about this in the New Year because we will need the correct conditions for her datasets.