vascular bundle

Mon Aug 30 17:19:08 EDT 2004

Anu,

I am curently looking at the annotations for Arabidopsis associated
with term 'vascular bundle, and will come up with details soon.

Can you tell me exactly how many annotations (how many genes are annotated
to it and how many annotations) do you have in the Gramene that are
associated to the term 'vascular bundle'?

Let's start from the bottom up, find out if we need to add this term,
and if so, how many different terms for vascular bundle we need to have in
PO, in order not to lose any annotations. Please look thoroughly in the
literature for details.

The term 'vascular bundle' will not be needed for microarray expressions
studies (for obvious reasons). It's mainly is situ hybridization studies
and gene expressions involving GUS, and often, authors (although using
term vascular bundles) are more specific in their descriptions and they
refer to the particular tissue withing vascular bundle (xylem, phloem
or transfussion tissue) whenever possible. Otherwords, this is not the
most granular term that will be often used for the annotations.
In a couple of references I looked, whenever they just say vascular bundle,
they mean in the leaf, which in my opinion, is a leaf vein.

Also, I will talk to some experts in the field and see what they
think.

Katica

On Mon,
30 Aug 2004, Anuradha Pujar wrote:

>
> A few genes whose expression is related to vascular
> tissue/pattern/development/differentiation are listed below.
>
> Due to the use of the term ‘vascular bundle’ by these authors it would be
> difficult to clearly annotate them to a particular vascular cell type.
>
> CVP1 genes: involved in vascular tissue pattern, the author has shown
> whole leaf pictures and refers to vasculature/vein as the vascular bundle
> Fig 1, and also  with reference to the cross section  it is referred to as
> the anatomy of “cotyledon vascular bundle” Fig 6.
>
> http://www.plantcell.org/cgi/content/full/11/11/2123
>
> AtPIN1 gene: involved in the regulation of polar auxin transport,  in Fig
> 4 the authors mention that the anti AtPIN1 formed continuous vertical cell
> strands in vascular bundle.
> http://www.sciencemag.org/cgi/content/full/282/5397/2226
>
> ATHB 8 gene: the gene involved in regulation of vascular development, the
> authors   refer to vascular bundle in the cross-section Fig 5
> http://www.plantphysiol.org/cgi/content/full/126/2/643
>
> COV1 gene: this gene is involved with the regulation of vascular pattern
> refer to Fig 1.
> http://dev.biologists.org/cgi/content/full/130/10/2139
>
> These genes are from Arabidopsis, my concern is with genes/gene products
> related to cereal plants wherein the localization within vascular tissue
> is not clear such as the Glutamine synthase in rice and barley. And auxin
> related genes.
>
> GS1: Glutamate synthase is specific to vascular bundle according this paper.
> http://jxb.oupjournals.org/cgi/reprint/52/356/591
>
> anu
>
> > Isn't "vascular bundle" simply the term applied to a vein when viewed in
> > cross section?  I agree with Katica's earlier message that the term
> > vascular bundle should remain obsolete.  The gene in question can be
> > annotated to vein or vascular tissue if it can't be annotated to one of
> > the parts of the vein.  I haven't checked the publication myself, but I'd
> > be pretty surpirsed if it were actually expressed in every cell of the
> > vein.
> >
> > If the group decides to un-obsolete (great verb!) the term, then the
> > ontology would have to be considerably more complex than Pankaj outlined
> > earlier.  I think it would be more like:
> >
> > Sporophyte
> > --p--vascular bundle
> > -----i--leaf VB
> > -----i--stem VB
> > -----i--root VB
> > -----i--stamen VB
> > -----i--petal VB
> > -----i--sepal VB
> > -----i---etc., one each for every organ
> > -----p--xylem
> > -----p--phloem
> > -----p--cambium
> > -----p--bundle sheath
> > ---------i--mestome sheath
> > ---------i--parenchyma sheath
> > -----p--parenchyma
> > -----p--schlerenchyma
> > --p--shoot
> > -----p--stem
> > --------p--stem VB
> > -----p--leaf
> > --------p--root VB
> > --p--root
> > -----p--root VB
> >
> > Finally, to respond to an earlier message in this thread - veins (vascular
> > bundles) are present in all plants, not just C4s.
> > Toby
> >
> >
> > -----Original Message-----
> > From:	owner-po-dev at brie4.cshl.org on behalf of Pankaj Jaiswal
> > Sent:	Fri 8/27/2004 9:55 AM
> > To:	po-dev at plantontology.org
> > Cc:
> > Subject:	Re: vascular bundle
> >
> > The purpose for asking this term was, that they are present in all kinds
> > of organs and not just limited to the leaves.
> >
> > In leaves mid veins are representing the vasculature and the leaf VB is
> > a part of that network of vasculature and as Dave pointed out there are
> > many other parts as well.
> >
> > My suggestion is to include this term. If agreed, the other question
> > would be, where should we place it, it's not just a tissue, but contains
> > a lot of tissue types. Thus it is an organized structure or a region in
> > an organ.
> >
> > The proposed structure is
> > i = instance of
> > p = part of
> >
> >
> > Sporophyte
> > --p--vascular bundle
> > -----i--leaf VB
> > -----i--stem VB
> > -----i--root VB
> > -----i--stamen VB
> > -----p--xylem
> > -----p--phloem
> > -----p--cambium
> > --p--shoot
> > -----p--stem
> > --------p--stem VB
> > -----p--leaf
> > --------p--root VB
> > --p--root
> > -----p--root VB
> >
> > I am not sure....
> >
> > #1
> > Its true that that the three terms xylem, phloem and cambium are not
> > always part of VB.
> >
> > But as we know the PART of relationship we have suggests that, a child
> > is a partof but not always a partof parent term. Thus this lineage seems
> > correct.
> >
> > #2
> > Do gametophytes also have VB?
> >
> >
> >
> > Suggested definitions for VB are
> >
> > by Fahn: A strand of conducting tissue
> >
> > By Essau: A strand like part of the vascular system composed of xylem
> > and phloem. occurs in stem, leaf and flower.
> >
> > By Dickison: A strand like association of primary xylem and phloem that
> > extends throughout the plant body.
> >
> > http://www.cogsci.princeton.edu/cgi-bin/webwn?stage=1&word=vascular+bundle
> > a unit strand of the vascular system in stems and leaves of higher
> > plants consisting essentially of xylem and phloem
> >
> >
> >
> > If that is an accepted structure then we may need a further
> > instantiation of the terms xylem, phloem and cambium, because as of now
> > these are the generic terms. But that is a topic for another request to
> > be sent on the mailing list.
> >
> >
> > Thanks
> > Pankaj
> >
> >
> >
> >
> > Anuradha Pujar wrote:
> >
> >>
> >> Hello,
> >>
> >> These are just a couple of references, please have a look.
> >>
> >>
> >> http://www.plantphysiol.org/cgi/content/full/129/3/1019
> >>
> >> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14630956
> >>
> >> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15258165
> >> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14614507
> >> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12615934
> >> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2102372
> >>
> >> anu
> >>
> >>
> >
> > --
> > ************************
> > Pankaj Jaiswal, PhD
> > G15-Bradfield Hall
> > Dept. of Plant Breeding
> > Cornell University
> > Ithaca, NY-14853, USA
> >
> > Tel: +1-607-255-3103
> >       +1-607-255-4109
> > Fax: +1-607-255-6683
> > http://www.gramene.org
> > ************************
> >
> >
> >
> >
>
>

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Katica Ilic             		katica at acoma.stanford.edu
The Arabidopsis Information Resource 	Tel: (650) 325-1521 ext. 253
Carnegie Institution of Washington 	FAX: (650) 325-6857
Department of Plant Biology 		URL: http://arabidopsis.org/
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