Meeting Notes 3

From GO Wiki
Revision as of 12:54, 31 August 2007 by Dhowe (talk | contribs) (→‎otolith)
Jump to navigation Jump to search

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?
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?

Plan


spores

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

People:

Val
Maria Costanzo
Jim Hu
Michelle
Midori

Questions:

Same question as cell walls.
What are the distinguishing features of the walls?
or What are the distinguishing features of the assembly of the walls?


Plan:


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:


cell polarity

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.

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?


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.

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:


spores

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

People:

Pascale
Jen
Michelle
Jim Hu
Tanya
Midori
Val


Questions:
Ask Chris Brett if he knows difference between plant, bacterial, and fungal cell walls. Also relevant to cell walls. [Jen]

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:

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: