New terms in PO

[Leonore Reiser]

On Fri, 3 Sep 2004, Pankaj Jaiswal wrote:

> My comments are follow Leonore's.
> -Pankaj
>
> Leonore Reiser wrote:
>
> > On Thu, 2 Sep 2004, Felipe Zapata wrote:
> >
> >
> >>Cauline leaf:
> >> From the definition it looks like it refers to a regular leaf. Only it
> >>has a particular name because "is before flowering" and "lacks a
> >>petiole".  Lacking a petiole shouldn't pose a problem as not all the
> >>parts of leaf have to be present (we still follow the sometimes part of
> >>rule, right?). So a leaf may or may not have petiole.  In regards to
> >>"before flowering" I wonder if this event makes a "regular leaf" (in
> >>terms of anatomy and structure) a different type of leaf. I don't think
> >>so.  This is more like a...developmental stage term?
> >
> >
> > This term typically refers to the leaves which are borne on the elongated
> > inflorescence branches in Arabidopsis. It is a VERY commonly used term in
> > desrcribing Arabidopsis both wild type and mutant form.They almost always
> > have 'adult' characteristics.
>
> I consider this as a generic leaf but present on the cauline internodes.
> Going by the TAIR definition as follows it is an equivalent of "flag
> leaf" in cereal plants.
> Def: Stem leaf, produced before the transition to flowering, lacking a
> petiole.

Gah- no one in the Arabidopsis community would use the term flag leaf to
define this body part. Nor are the leaves produced before the transition
to flowering - most are borne on a flowering plant. The reason I added the
statement about origins/initiation is because its likely that these leaves
are produced AFTER the transition to flowering has occured (though some
are initiated before BOLTING).

>
> However, if there are more than one instances of this leaf in a plant
> (answer is possibly YES) , then we can create this as an instance of the
> leaf at the same level as
> PO:0006340 : adult leaf
> PO:0020103 : flag leaf
> PO:0020043 : compound leaf
> PO:0006338 : embryonic leaf
> PO:0006339 : juvenile leaf
> PO:0020042 : simple leaf
>
>
>
> >>Rosette leaf:
> >>Once again, from the definition, it looks like it refers to a regular
> >>(normal) leaf growing in certain arrangement, not to a different type
> >>of leaf.  If the internodes between leaves elongate or not, that's a
> >>different issue.  Some plants grow characteristically as rosette plants
> >>(e.g. plants in the high peaks), nonetheless the leaves are "normal
> >>leaves".  If rosette leaf is introduced to POC, why not alternate leaf?
> >>opposite leaf?
> >
> > Again- this is a very commonly used term to describe leaves that are
> > formed prior to elongation of the primary stem. Well, actually, I think
> > Fred Hempell may have shown that some of these leaves are initiated before
> > stem elongation. So maybe defining as leaves which are below the elongated
> > internode.
> >
>
> I think this refers to the generic leaf present in the Arabidopsis or in
> any other organism, often found in the region of stem, where internode
> elongation is either absent or minimal. In cases of Maize as Marty is
> suggesting, it is due to the defective in Gibberellic Acid synthesis,
> where possibly due to this effect the plant may never enters the "stem
> elongation growth stage". However, in case of Arabidopsis this is a
> normal phenomenon and so as in cabbage or many of the other Brassicales.
> These are definitely different than cauline leaves in terms of position
> which are present towards the top of the stalk/stem with elongated
> internodes also called as cauline region.
>

Aren't we describing normal development in these ontologies.


> A generic definition of a rosette leaves is "A group of leaves arising
> closely together from a short stem, forming a radiating cluster on or
> near the ground".
>
> Therefore, I would consider rosette leaves as synonym of the term
> PO:0009025 : leaf.
>
>
>
> >
> >>Hypocothyl hook:
> >>I am not what it refers to, but if it is indispensable...
> >>
> >
> >
> > Oh yes- it is indespensable- particularly when describing ethylene
> > responses. Part of the so called triple response is hypocotyl hook
> > curvature. This would be an example of a term that refers to a region
> > (defined by a physiological response).
> > Leonore
> >
>
> In most of the descriptions I have found, if refers to the upper region
> of hypocotyl next to the cotyledons, found mainly in the germinating
> seeds of dicots only, that undergo epigeal type of germination. e.g. in
> many beans. However, in those seeds undergoing hypogeal type of
> germination, e.g. in peas, the hook forms in epicotyl and cotyledons
> stay in ground. In these cases it is called "epicotyl hook".
>
> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=search&term=epicotyl+hook
>
> Plant Cell Physiol. 2001 Sep;42(9):952-8 says:
> ...The intensity of the yieldin signal in the hypocotyls was highest in
> the apical pre-elongation region (the hook region) and decreased toward
> the elongated mature base indicating that the yieldin disappeared with
> the ceasing of cell elongation....
>
> Physiol Plant. 2000 Feb;108(2):208-15.  suggests evidence of term usage
> hypocotyl/epicotyl hook.
>
> more on epicotyl hook.
> Photochem Photobiol. 1992;55(2):313-8.
> Plant Physiol. 1996 Jan;110(1):163-70.
>
> Going by the majority cases, it is part of a hypocotyl or rather it is
> the hypocotyl and the curved portion of the hypocotyl, which straigtens
> out once the cotyledons emerge from the ground/soil. Once it
> straightens, no one calls it s hook, it is hypocotyl. It is just a short
> phase of germination when the hypocotyl is maintained as a hook.
>
> My suggestion is to create a synonym "hypocotyl hook" for hypocotyl.
>
>
I dont think that is going to work. Yes it is  a region of the hypocotyl
that is curved for a period of time during development. Oh and how about
apical
hook (more commonly used in describing this body part)  with hypocotyl
hook as a synonym. There needs to be some way of describing this very
special part/stage in seedling development. Yes it is a developmental
stage (apical hook formation or whatever) but there are genes that are
expressed specifically in this domain...
leonore

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Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
The Arabidopsis Information Resource	FAX: (650) 325-6857
Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
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