Meeting Notes 3

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Nematode development

negative regulation of vulval development (sensu Nematoda)
positive regulation of vulval development (sensu Nematoda)
regulation of vulval development (sensu Nematoda)
vulval development (sensu Nematoda)
tail tip morphogenesis (sensu Nematoda)

People:
Kimberly
Doug-perhaps only with respect to 'tail tip morphogenesis'
David

Questions:

What is the distinguishing feature of the anatomical structure vulva between species?
Do we want a term just called vulval development?
Can we handle this by making cross references to anatomical dictionaries?
For tail tip morph, do we even need the sensu Nematode?

Comments:

The tail tip morphogenesis term appears to refer to morphogenesis of the nematode tail tip resulting in development of reproductive structures. Such a process does not occur in fish or vertebrates that I can think of. Fish won't need this term, so I think the resolution of this term can be left to Kimberly's discretion.
-Doug

Plan

spores

spore wall assembly (sensu Bacteria)
spore wall assembly (sensu Fungi)
spore wall (sensu Fungi)

sporulation (sensu Bacteria)
sporulation (sensu Fungi)
spore development (sensu Magnoliophyta)

People:

Val
Maria Costanzo
Michelle
Midori
Pascale
Jen
Jim Hu
Tanya

Questions:

What are the distinguishing features of the walls?
or What are the distinguishing features of the assembly of the walls?
Ask Chris Brett if he knows difference between plant, bacterial, and fungal cell walls.
Also relevant to cell walls. [Jen]


Plan:

Michelle speaking - I see from below the "sporulation" terms still have sensu designations - didn't we talk once about making terms that were "reproductive sporulation" and "stress-induced sporulation" or something along those lines? If so, could we carry that into these terms? I fear that there might be so much heterogeneity in spore wall structures (even within bacteria) that getting good defs based on that may be hard. But I need to do more checking.... that was just a first thought.

Eurie: The introduction in this publication - PMID:15590821 - has a nice description of what is unique about S. cerevisiae spores.

Chromosome

chromosome organization and biogenesis (sensu Bacteria)
chromosome organization and biogenesis (sensu Eukaryota)

People:

Michelle
Jim Hu
Eurie

Questions:

What are the distinguishing features?
Do we lump mitochondrial and plastid with bacterial?

Plan:


Michelle speaking - It seems to me that these processes are really the same - yes different genes and proteins are involved in the different types of organism, but I don't see why there needs to be separate terms. Can these just be merged into their parent? I think you would want to keep mitochondrial and plastid terms separate as they are "auxillary" chromosomes, not the primary genome of the organism (not that they aren't important).

cell polarity - DONE

establishment and/or maintenance of cell polarity (sensu Fungi)
establishment of cell polarity (sensu Fungi)
maintenance of cell polarity (sensu Fungi)

People:

David
Midori
Rex

Questions:

Plan:

Merge these terms with their non-sensu parents. Fungal cell polarity is the model system for everything on polarity.

Val confirms that merges also work for pombe; see SF 1796071.

Merge done 2007-09-18. [mah]

neural rod

neural rod cavitation (sensu Teleost)
neural rod formation (sensu Teleost)


People:

Doug
David

Questions:

How do we distinguish neural rods in Teleosts and other things. Does anything else have neural rods?

Comments:

Neurulation in teleosts is a bit different than it is in other verts. For example, many verts have a clear distinction b/t primary neurulation (epithelial folding etc..) vs. secondary neurulation (mesenchymal cavitation process). In the case of teleosts, they form a 'neural rod' which has an epithelial origin, so is primary neurulation like, but the cell movements are slightly different. Epithelial cells form a solid dorsal structure (the neural keel) which then morphs into a tube (the neural rod) which then cavitates to form the neural tube. It's like primary neurulation in that it has epithelial origins, but is sort of like secondary neurulation in that it is a cavitation process rather than a folding process to form the tube. From what I can find in the literature, the 'neural rod' refers to the developing teleost neural tube structure of epidermal origin. Other verts that use the more conventional primary and secondary neurulation mechanism won't have this structure. Long story short: I think we might be able to simply drop (sensu Telost) from both of these terms.

-Doug

We might be more correct to move 'neural keel formation' to the same level as 'neural rod formation' rather than them having a 'part of' relation to each other. The neural keel develops into the neural rod through a morphogenetic change, but perhaps they are to be considered distinct anatomical structures.

-Doug

Plan:

gastrulation

gastrulation (sensu Vertebrata)
gastrulation (sensu Mammalia)


People:

David
Doug
Victoria

Questions:

What distinguishes mammalian gastrulation from other organisms?

Plan:

Find distinguishing feature or merge terms.


pigment

pigment cell differentiation (sensu Nematoda and Protostomia)
pigment cell differentiation (sensu Vertebrata)

People:

Kimberly
David
Doug
Victora
Susan Tweedie
Becky Foulger

Questions:

Should we have a sensu designation or should we just enumerate the types of pigment cells underneath the parent pigment term.
Look to the cell ontology for guidance.

Comments:

I vote for a single pigment cell differentiation parent term with individual cell type-specific differentiation terms as children. Merge the sensu Vertebrata (GO:0043358) and sensu Nematoda and Protostomia (GO:0043357) terms with 'pigment cell differentiation' (GO:0043358).

-Doug

Plan:

larval development

larval development (sensu Amphibia)
larval development (sensu Nematoda)


People:

Becky Foulger
Kimberly

Questions:

What are the distinguishing features?
Is it worth having separate terms for each?

Plan:


genderization

hermaphrodite germ-line sex determination (sensu Nematoda)
feminization of hermaphroditic germ-line (sensu Nematoda)
masculinization of hermaphroditic germ-line (sensu Nematoda)
hermaphrodite somatic sex determination (sensu Nematoda)
feminization of hermaphrodite soma (sensu Nematoda)
masculinization of hermaphrodite soma (sensu Nematoda)


People:

Kimberly


Questions:

Is there any other type or can we just merge into the generic parent?

Plan:


proteasome

proteasome core complex (sensu Eukaryota)
cytosolic proteasome core complex (sensu Eukaryota)
proteasome regulatory particle (sensu Eukaryota)
cytosolic proteasome regulatory particle (sensu Eukaryota)
proteasome regulatory particle, base subcomplex (sensu Eukaryota)
cytosolic proteasome regulatory particle, base subcomplex (sensu Eukaryota)
proteasome regulatory particle, lid subcomplex (sensu Eukaryota)
cytosolic proteasome regulatory particle, lid subcomplex (sensu Eukaryota)
proteasome complex (sensu Eukaryota)
cytosolic proteasome complex (sensu Eukaryota)
proteasome core complex (sensu Bacteria)
proteasome core complex, alpha-subunit complex (sensu Eukaryota)
cytosolic proteasome core complex, alpha-subunit complex (sensu Eukaryota)
proteasome core complex, beta-subunit complex (sensu Eukaryota)
cytosolic proteasome core complex, beta-subunit complex (sensu Eukaryota)
proteasome regulatory particle (sensu Bacteria)


People:

Rama
Jim Hu
Michelle

Questions:

Plan:



cytosolic ribosome

cytosolic large ribosomal subunit (sensu Eukaryota)
cytosolic large ribosomal subunit (sensu Archaea)
cytosolic large ribosomal subunit (sensu Bacteria)
cytosolic ribosome (sensu Archaea)
cytosolic ribosome (sensu Bacteria)
cytosolic ribosome (sensu Eukaryota)

cytosolic small ribosomal subunit (sensu Archaea)
cytosolic small ribosomal subunit (sensu Bacteria)
cytosolic small ribosomal subunit (sensu Eukaryota)


People:

Harold
Michelle
Jim Hu

Questions:

Plan:


From Harold's e-mail:


The cytosolic ribosomes of prokaryotic and eukaryotic cells differ basically by size, number of proteins, and number or RNA strands.
Prokaryotic ribosomes have three strands, typically called 5s, 16s, and 23s. These are generated from post-transcriptional processing of a single rRNA precursor. Prokaroytic ribosomes contain about 50 proteins. The 5s is 120 nt, 16s about 1500nt, and 23s about 2900nt)
Eukaryotic ribosomes have four strands, typically called 5s, 5.8s, 18s, and 28s. The 5.8, 18, and 28s chains are post-transcriptionally processed from a single rRNA precursor. The 5s RNA is generated separately from a differerent promoter. The 5s RNA is synthesized by RNA polymerase III, whereas the large transcript containing the other three is synthesized by RNA polymerase I. The large rRNA, typically called “28s”, is in fact much larger than it's bacterial counterpart (~4700 nt vs ~2900nt,). The 18 sRNA is about 1900nt, 5s 120nt, and 5.8s about 160nt. Eukaryotic ribosomes contain 70-80 proteins.
I would think that the most single feature is the 3 vs 4 chain.
Although basically, mitochondrial ribosomes are thought to be “prokaryote-like”, some fungal and animal mitochondrial ribosomes lack 5 sRNA, and are thus only 2 chain). However, if you base the definition on the fact that these are found within the organelle, then you would b safe).
The archebacteria vs prokaroytic is harder; it's mostly a size and number difference, in that the archebacteria have an intermediate number of proteins, etc. The expert I spoke to would not be adverse to a system that lumped the archebacteria and prokaroytic together.
I propose
1. Three-RNA chain containg ribosome (prokaryotic-type to include prokaroytic and archebacteria ribosomes)
2. Four-RNA chain containing ribosomes. ( 5.8s-, eukarytotic-type)
Note, I have tried to get away from using exact S-values in the term name. Using them in the def would be fine, I hope. Although I wouldn't be adverse to using “5.8s-containing ribosome vs ??).
Now, the large subunit of each class is where you will have the 3 vs 4 chain difference. The small subunit is the hard one: more prokaryotic like than eukaryotic, but a work around would be
small subunit of a three-chain containing ribosome
smll subunit of a four-chain containg ribosome.

References:
Personal communication Dr. Caroline Kohler, Dept. of Biology, MIT, and
Lewin, Genes VII ISBN:019879276-X

The Ribosome, ISBN:0879696206




Find previous notes from e-mail.


NADH and reaction centre

NADH dehydrogenase complex (plastoquinone) (sensu Cyanobacteria)
NADH dehydrogenase complex (quinone) (sensu Bacteria)
NADH dehydrogenase complex (ubiquinone) (sensu Bacteria)


People:

Michelle
Jim Hu


Questions:

Plan:




plasmid partitioning (sensu Bacteria)

People:

Eurie
Michelle
Midori


Questions:

Plan:


somitomeric trunk muscle development (sensu Mammalia)

People:

David
Victoria
Emily


Questions:

Plan:

Probably merge with parent.

otolith

otolith mineralization (sensu Actinopterygii)
otolith mineralization (sensu Tetrapoda)


People:

David Fashena
https://sourceforge.net/tracker/index.php?func=detail&aid=1109256&group_id=36855&atid=440764
Midori
David
Emily
Victoria
Doug (I can consult with Dave F. as he is in the next office over)

Questions:

Comments:

I believe the initial introduction of the 'sensu Actinopterygii' term was because fish otoliths continue to grow throughout the life of the fish. It was my understanding that this was not true for tetrapods. If this distinction doesn't hold water, then perhaps a merge could happen.

-Doug

Plan:

outer membrane biogenesis (sensu ProteoBacteria)

People:

Jim Hu
Michelle


Questions:

Check how we distinguish the outer membrane in the component ontology.

Plan:


invasive growth (sensu Saccharomyces)

People:

Maria Costanzo
Val


Questions:

https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1583546&group_id=36855
Also consider pseudohyphal growth and filamentous growth.

Plan:

reaction center (sensu ProteoBacteria)

People:


Jim Hu
Michelle
Jen

Questions:

Plan: