cell projection - inappropriate relationship to plasma membrane

[krchristie]

While looking into this ticket:
#13181

I noticed that 'cell projection' currently has this relationship:

has_part some 'plasma membrane region'

but it shouldn't since it includes bacterial and archaeal type flagella, neither of which is bound by plasma membrane.

[dosumis]

Maybe worth adding ‘plasma membrane bounded cell projection’ has a new subclass?

…

On Mar 20, 2017, at 3:43 PM, Karen R Christie ***@***.***> wrote: While looking into this ticket: #13181 <#13181> I noticed that 'cell projection' currently has this relationship: has_part some 'plasma membrane region' but it shouldn't since it includes bacterial and archaeal type flagella, neither of which is bound by plasma membrane. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#13193>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAG4xxxRpxEo2byM0F3TYUdoBIwnjk47ks5rnp63gaJpZM4MinLu>.

[krchristie]

Regarding:

Maybe worth adding ‘plasma membrane bounded cell projection’ has a new subclass?

seems sensible to me. Objections @ukemi ?

[ukemi]

Sounds ok to me.

[krchristie]

I have created the new class @dosumis suggested:

 [Term]
+id: GO:0120025
+name: plasma membrane bounded cell projection
+namespace: cellular_component
+def: "A prolongation or process extending from a cell and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon." [GOC:krc]
+intersection_of: GO:0042995 ! cell projection
+intersection_of: has_part GO:0098590 ! plasma membrane region
+relationship: has_part GO:0098590 ! plasma membrane region
+created_by: kchris
+creation_date: 2017-03-21T17:26:07Z

I have moved most of the child terms of 'cell projection' to be under this new subclass, either by changing the explicit SubClass relationship or the Equivalence axiom as appropriate, or sometimes both.

There are a few terms, I am not confident I can move without further checking, so I won't move those till I have time to check.

@tberardini

• From what I could glean quickly from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3355688/ the 'plant cell papilla' look like a cell wall structure, so I think it may be correct to leave this as a 'cell project' that is not PM bounded.
• 'pollen tube' did look like a plasma membrane bounded cell projection, so I have changed its parentage, but let me know if this is incorrect

@paolaroncaglia

• Do you know if 'dinoflagellate peduncle' is PM bound?
• Also, I was wondering if there should be a relationship between 'dinoflagellate peduncle' and 'oral apparatus'. From the definitions, it looks like they may be the same thing, or perhaps the first is a type of 'oral apparatus'

Also have to check on:

• 'haustorium'

[tberardini]

@krchristie

so I think it may be correct to leave this [plant cell papilla] as a 'cell project[ion]' that is not PM bounded.

Agreed.

'pollen tube' did look like a plasma membrane bounded cell projection, so I have changed its parentage, but let me know if this is incorrect

Yes, pollen tubes are PM (and cell wall) bounded. (One ref: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3510122/)

Thanks.

[krchristie]

thanks @tberardini !!

[krchristie]

reminder for KRC:

• 'neuron projection' still has an asserted 'cell projection' relationship that should be removed

[paolaroncaglia]

Hi @krchristie ,
Wrt
"Do you know if 'dinoflagellate peduncle' is PM bound?"
I think so, but am not 100% sure. The original ticket doesn't really specify (#11553), and Google images don't help much. You could ask the submitter, Anne Thessen. Her username on GitHub seems to be diatomsRcool.
Then,
"Also, I was wondering if there should be a relationship between 'dinoflagellate peduncle' and 'oral apparatus'. From the definitions, it looks like they may be the same thing, or perhaps the first is a type of 'oral apparatus'"
Sort of, but 'oral apparatus' has a definition comment that refers to ciliated protozoans, so the dinoflagellate term wouldn't fit. (Note that it's hard to create a taxon constraint for protozoans as they encompass so many groups.)
Thanks.

[krchristie]

Hi Anne (@diatomsRcool),

Do you know if the dinoflagellate peduncle is bound by the plasma membrane? We recently created a sub-category of 'cell projection' for ' plasma membrane bounded cell projection', so I'm trying to figure out if 'dinoflagellate peduncle' belongs in this more specific class. I'm having a hard time with researching this though as I don't have subscription access to journal articles that come up in PubMed when I search.

thanks,

Karen

[diatomsRcool]

I don't know off hand. If you point me to the articles you found, I can likely get them.

[krchristie]

@diatomsRcool: Thanks for the offer! Funnily enough, I happened to do a really general Google search looking for info about the difference between dinoflagellates and ciliated protozoans and came up with this paper:

Lee RE, Kugrens P. Relationship between the flagellates and the ciliates. Microbiol Rev. 1992 Dec;56(4):529-42. Review. PubMed PMID:1480107 and it says this:

A second type of feeding apparatus in the dinoflagellates involves the extension of a peduncle 
(70, 118) or pseudopod (38, 67) that attaches to, or engulfs, the prey organism (Fig. 7). A 
peduncle is a projection of cytoplasm that contains an array of microtubules (70).

so based on that, I feel pretty comfortable saying a dinoflagellate peduncle is bound by plasma membrane. Let me know if you're not convinced by this and we can do more research. The two papers cited for the peduncle in the quote above would be a good start, plus one more I've come across.

Also, what do you think about the idea of adding this info into the definition?

Current def:
A small, flexible, finger-like appendage located near the flagellar pores in some photosynthetic as well as nonphotosynthetic dinoflagellate species. Its functions are not fully understood, but it has been associated with feeding behavior (phagotrophy).

Possible new def
A small, flexible, finger-like projection of cytoplasm containing an array of microtubles and located near the flagellar pores in some photosynthetic as well as nonphotosynthetic dinoflagellate species. Its functions are not fully understood, but it has been associated with feeding behavior (phagotrophy).

[diatomsRcool]

Yes, I do feel comfortable saying that the peduncle is bound by the plasma membrane. The new definition is also acceptable to me. a

…

On 3/23/2017 9:08 PM, Karen R Christie wrote: @diatomsRcool <https://github.com/diatomsRcool>: Thanks for the offer! Funnily enough, I happened to do a really general Google search looking for info about the difference between dinoflagellates and ciliated protozoans and came up with this paper: *Lee RE, Kugrens P.* Relationship between the flagellates and the ciliates. Microbiol Rev. 1992 Dec;56(4):529-42. Review. PubMed PMID:1480107 and it says this: A second type of feeding apparatus in the dinoflagellates involves the extension of a peduncle (70, 118) or pseudopod (38, 67) that attaches to, or engulfs, the prey organism (Fig. 7). A peduncle is a projection of cytoplasm that contains an array of microtubules (70). so based on that, I feel pretty comfortable saying a dinoflagellate peduncle is bound by plasma membrane. Let me know if you're not convinced by this and we can do more research. The two papers cited for the peduncle in the quote above would be a good start, plus one more I've come across. Also, what do you think about the idea of adding this info into the definition? *Current def:* A small, flexible, finger-like appendage located near the flagellar pores in some photosynthetic as well as nonphotosynthetic dinoflagellate species. Its functions are not fully understood, but it has been associated with feeding behavior (phagotrophy). *Possible new def* A small, flexible, finger-like projection of cytoplasm containing an array of microtubles and located near the flagellar pores in some photosynthetic as well as nonphotosynthetic dinoflagellate species. Its functions are not fully understood, but it has been associated with feeding behavior (phagotrophy). — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#13193 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AE5wSO1rZ4EWWSZMy72hmy22Rb5blF0Sks5roxeFgaJpZM4MinLu>.

-- Anne E. Thessen, Ph.D. The Data Detektiv, Owner and Founder Ronin Institute, Research Scholar 443.225.9185

[krchristie]

Great. Thanks for your input @diatomsRcool

I'm at a meeting this week, so I won't get to this till later in the week, or maybe next week.

[krchristie]

@diatomsRcool - I've made the agreed upon changes to 'dinoflagellate peduncle'. Thanks again for taking a look.

also fixed asserted parentage of 'neuron projection', so this term is good now.

[krchristie]

@ukemi - I wanted to get you input on ticket management. I have done everything that is related to the initial issue I brought up, i.e that the term 'cell projection' had an inappropriate relationship to the term 'plasma membrane'. This includes making the more granular term @dosumis suggested to group all the cell projections that are PM bound.

There are two remaining issues, but I was wondering if it might make more sense to make individual tickets for each of these issues, at least partly for keeping track of different issues that ontology editors deal with, so I wanted to check with you on what the preferred procedure is.

Two remaining issues:
'oral apparatus' - I don't think this structure should be under 'cell projection at all since it seems that the 'oral apparatus' is a complex structure which contains cell projections, but is not only a projecition. A review by Lee & Kugrens P. (Relationship between the flagellates and the ciliates. Microbiol Rev. 1992 PMID:1480107) says this:

Most ciliates are phagotrophic, taking food particles or organisms in through a mouth (cytosome, 
cytopharynx) that is commonly surrounded by rows of cilia (oral kinetids) (Fig. 2). The mouth and 
the oral cilia make up the oral apparatus, which can be on the cell surface or in a depression of 
the cell surface.

'haustorium' - There are at least two kinds:

• one in plant parasites of other plants roots. From what I have gleaned so far, these may be more appropriate as a cellular bridge.
  From PMID:26322059

Parasitic plants form a haustorium, a unique multicellular invasion organ common to all 
parasitic plants. In the Orobanchaceae root parasites, globular-shaped haustoria invade host 
roots and form direct vascular connections with host plants, which likely enables nutrient transfer 
(Hibberd and Jeschke, 2001; Yoshida and Shirasu, 2012). 

• one in fungal parasites of plants:
  From PMID:25699068

On the leaf surface rust spores produce germ tubes which grow on the plant surface. Over 
a stoma an appressorium is formed, a special structure from which the infection hypha is invading 
the leaf tissue (Hoch and Staples, 1987). Within the substomatal vesicle intercellular hyphae 
spread the plant tissue and haustorial mother cells are formed adjacent to mesophyll cells. 
Haustoria are formed after penetrating the plant cell wall without vulnerating the plant plasma 
membrane. The haustoria grow within the living plant cells and constitute an intimate contact to 
the plant cells cytoplasm. As a result the cytoplasm of host and fungus remain separated by the 
host plasma membrane, the fungal plasma membrane and between the so-called extrahaustorial 
matrix (Voegele et al., 2009).

[ukemi]

I think with the new procedure of closing tickets with a merge, it makes sense to go ahead and open separate tickets for these. That way if we ever want to simply search on the tickets and connect them to the diffs for the commits, it is easy. I'd like to start keeping track of everything we do through the ticket system.

[krchristie]

I've done more than one commit for this ticket, but these remaining issues seem like separate problems, so I like putting them into new tickets too. I will do that and close this one.

[ukemi]

Yes. If all of the commits concern the same issue, then the diffs will be grouped in the ticket. But in the case where there is additional work that is not really related to the original ticket, then a separate ticket is better.