Microtubule pushing forces

[manulera]

Hi Manu,

As you will see I have assigned you lots of sessions. I think most of these will be relatively quick for curation; some, especially the Tolic ones will probably only have one or two GO terms, but these are useful because describing normal functions and processes of genes is one of our main aims.

For example this one

https://core.ac.uk/reader/33995484?utm_source=linkout

we can add GO process "nuclear positioning" fir kinesin-8 motors

currently GO:0007097 nuclear migration (exact synonym).

Nuclear positioning seems slightly broader to than migration to me and should be the exact synonym (or even primary term name) of the parent "nucleus localization", do you agree?

[manulera]

looking at something else entirely I just spotted :

GO:0098863 nuclear migration by microtubule mediated pushing forces

if the above is true, distinct a terms should exist for positioning and alsoo for migration (e.g. for the oscillatory movement in meiosis)?

Q Is all nuclear migration/positioning microtubule mediated? (in this case there would be no need for a specific term "by microtubule mediated pushing forces"

We also need to be mindful that term changes requested work across species.

[manulera]

Hi Val,

Replying here to your questions:

if the above is true, distinct a terms should exist for positioning and alsoo for migration (e.g. for the oscillatory movement in meiosis)?

I guess this depends on how broad the term is, really. In a way migration seems like you want to take the nucleus somewhere, while positioning is more to keep it in a certain place. This would not only apply to pombe, who wants to keep the nucleus in the center, but also to muscle cells or fungi that are multi-nucleated, where the cells aim to keep their nuclei evenly spaced, and to many cells that use microtubules to keep their nucleus centered in the cell. At the same time, I can see how positioning and migration can be merged in the big scheme of things.

Q Is all nuclear migration/positioning microtubule mediated? (in this case there would be no need for a specific term "by microtubule mediated pushing forces"

a) Regarding all transport being mediated by MTs:

No, for example in mouse oocytes the nuclei of the gametes are brought together by the drag of vesicles. These vesicles move along microtubules, so I guess one could say so, but the driving force is the drag:

https://www.researchgate.net/figure/Schematic-of-the-geometry-of-the-embryo-used-in-the-model-and-the-forces-involved-The_fig4_248385647

Actin can also move the nucleus in a way. Think of a migrating cell which has a lamelipodium, the cellular movements induced mostly by actin will https://www.cell.com/action/showPdf?pii=S0962-8924%2820%2930244-0

b) Regarding pushing forces, not all nuclear positioning is mediated by pushing forces:

Pushing forces are typically used to position the spindle in the center of cells, in pombe and mammalian cells:

On the other hand, to center nuclei in multinucleated cells, you will typically rely on motors transporting the nucleus. I find that the ontology as is makes a lot of sense, with the pushing forces GO term spawning from both nuclear positioning and polymerisation, and the “nuclear migration along microtubule” depending on transport along microtubule.

https://www.ebi.ac.uk/QuickGO/term/GO:0030473

[ValWood]

This shows the terms discussed in the graph view (there is also a term for oscillatory movement, we might be able to improve some of these terms slightly. I don't think it looks too bad. Probably the main issue is that positioning is an exact synonym of migration, and the oscillatory movement term is not a descendant of "nuclear migration by microtubule...

(tip, to see a bunch of terms of interest in the quickGO view, click the 'basket' icon to collect the items of interest)

[manulera]

I think it would be correct as is, for both forms of nuclear migration in pombe:

• Horsetail is mediated by dynein movement so it is nuclear migration along microtubule and not nuclear migration by microtubule pushing forces.
• The opposite is true for the nuclear positioning during interphase.

[manulera]

Also, thanks for the tip, I had not seen that and it is indeed very useful