New terms in PO

[Katica Ilic]

Hi,

I agree with Leonore and here is one more point to the discussion
about hypocotyl hook. If the term 'hypocotyl hook' end up being a synonym
of 'hypocotyl' in PO, (which I think is not right, even with different kinds of synonymy
currently in use by GO), all the annotations to this term would show up
under hypocotyl. So, if curators could use term hypocotyl, we wouldn't
have had their request for this term at the first place.

Cauline and rosette leaf:
Felipe, I understand you rationale, and those were the reasons that these
terms did not make it to the PO in the first round (back in May), but now,
we are talking about a need to facilitate annotations. Perhaps I was not
specific enough when I included info about gene annotations in TAIR. Genes
annotated to the term cauline leaf are not necessarily the same as those
annotated to rosette leaf (although, four out of five genes are expressed
in both, cauline and rosette leaves). They would all show up if you query
term 'leaf', but unless we have the cauline and rosette leaf as separate
terms, we can never see the annotation to each, nor would we be able to
ask which genes are expressed in cauline leaves, but not in rosette leaves
(for instance PPCK1 is expressed in mainly in rosette leaves, while PPCK2
is expressed in roots and cauline leaves, see Plant, Cell and Environment,
2002, 25:115-122). This is the reason it wouldn't work if we make rosette
leaf a synonym of term leaf, as Pankaj suggested.

Katica



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.
>
> 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.
>
> 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.
>
>
>
>
>
>

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Katica Ilic             		katica at acoma.stanford.edu
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