Cryptococcus NTR: titan cell formation phenotype

[Achchuthan]

NTR

1) titan cell formation phenotype FAO cross-reference: id: FAO:0000063 name: titan cell def: "Large cells produced by fungi, such as Cryptococcus neoformans, that typically exhibit altered capsule structure, a thickened cell wall, increased ploidy, and resistance to nitrosative and oxidative stresses." [CGD:doi, PMID:21821718] is_a: FAO:0000032 ! vegetative cell created_by: mariacostanzo creation_date: 2013-04-03T11:15:35Z 2) altered titan cell formation (is_a titan cell formation phenotype) 3) increased titan cell formation (is_a altered titan cell formation) 4) decreased titan cell formation (is_a altered titan cell formation)

[dianeoinglis]

Titan cell is a child of "vegetative cell" and the FAO should be cross-referenced.

http://www.ncbi.nlm.nih.gov/pubmed/21821718 PMID: 21821718

[dianeoinglis]

And http://conservancy.umn.edu/handle/11299/131861

[Achchuthan]

FAO ID added above.

Thanks, Achchuthan

[dianeoinglis]

Excellent. Thank you. Diane

[dianeoinglis]

This term is fine to proceed with. Diane

[dsiegele]

Would these terms be children of 'cell development phenotype?'

http://microbialphenotypes.org/wiki/index.php/Category:OMP:0000070_!_cell_development_phenotype

[dianeoinglis]

Hello Debby,

I don't think so. Titan cells are not derived from another cell-type.

Terms for "development" and "cell development" are often used incorrectly all over the place. I am planning to discuss this issue with the GO editors as the same problem exists in the GO.

The definition in OMP: " the progression of a cell from an initial condition to a later condition"

The child terms under "cell development phenotype" do not formally match the definition. Technically, sporulation does not involve a change in a cell. Spores are generated by sporogenous cells. There is no cell that progresses (or changes) from an initial state or condition to a later state or condition that can be called a spore. However, if a new spore begins to form from a spore-bearing organ, then does not completely form a normal spore cell wall, that would be a "cell development/spore development" phenotype. But the process of sporulation does not involve cell development. Even endospore formation, though it occurs within a vegetative cell, is "generated" and does arise by a cell changing to another condition.

Spore germination is formally a type of "cell development" because the changes occur to the spore itself to form a germling or germ tube. When a germling undergoes nuclear division, the new cell is not a spore and technically did not change from a spore to another cell-type, it was generated by a spore process.

It is more accurate to call spore formation and heterocyst formation development.of the organism and not a cell. All the definitions refer to cyanobacteria forming heterocysts, spores being produced by bacteria (or fungi) and that is technically accurate. The use of the term "differentiated" when referring to these types of cells is not quite the same process as when "cell differentiation" is used for mammals.

Ugh!

This issue is pretty wormy and I have been dragging my feet as I prepare to discuss this with the GO editors because it may involve quite a few changes in parentage to be scientifically accurate for fungi and probably most microbes.

Diane

[dsiegele]

I made the following terms for titan cell phenotype: OMP:0007506 titan cell phenotype def:A cell morphology phenotype where a microbe, typically a fungus, produces large vegetative cells that typically exhibit altered capsule structure, a thickened cell wall, increased ploidy, and resistance to nitrosative and oxidative stresses. .....OMP:0007508 absence of titan cells def: A titan cell phenotype where a microbe cannot form titan cells. .....OMP:0007507 presence of titan cells def:A titan cell phenotype where a microbe is able to form titan cells. .....OMP:0007509 altered titan cell morphology def: A titan cell phenotype where the size, shape, or appearance of titan cells is altered relative to a designated control. .....OMP:0007510 altered titan cell formation def. A titan cell phenotype where the frequency, rate, timing, or extent of titan cell formation is altered relative to a designated control.

For increased and decreased total cell formation, are these for phenotypes affecting the fraction of a vegetative cell population that are titan cells?

[dianeoinglis]

Hi Debby,

Do you think specific "increased titan cell formation" and "decreased titan cell formation" phenotypes can be created as opposed to grouping them under with "altered?" I think "altered should be a "do not use for annotation" term. The only phenotype Iactually captured was "decreased..."

Diane