Question GRO term

Thu Jun 15 21:19:02 EDT 2006

Dear Katica and all

> Dr. Kikuchi (and others), please let me know if this would work for
> annotation purposes.

Thank you very much for your discusiion and very quick arrangement.

We agree the annotation and it will work.

Sincerely yours,

Shoshi Kikuchi

***********************************
Shoshi Kikuchi Ph.D
Plant Genome Research Unit
Division of Genome and Biodiversity Research
National Institute of Agrobilogical Sciences (NIAS)
Kan'non dai 2-1-2
Tsukuba Ibaraki 305-8602 Japan
TEL/FAX +81-29-838-7007
Email: skikuchi at nias.affrc.go.jp
WEB: ?(RMOS) http://microarray.rice.dna.affrc.go.jp
          (KOME) http://cdna01.dna.affrc.go.jp/cDNA/
************************************

----- Original Message ----- 
From: <katica at acoma.Stanford.EDU>
To: "AUGUSTINE, ALICE CLARA [AG/8042]" <alice.clara.augustine at monsanto.com>
Cc: <po-dev at plantontology.org>; "SATOH, Kouji" <ksatoh at nias.affrc.go.jp>;
"Pankaj Jaiswal" <pj37 at cornell.edu>; "Shoshi Kikuchi"
<skikuchi at nias.affrc.go.jp>
Sent: Friday, June 16, 2006 3:19 AM
Subject: RE: Question GRO term

>
> Hi Clare,
>
> Thanks for explanation.
>
> Based on the responses we got so far, my suggestion would be to add two
> terms, 'embryogenic callus' and 'organogenic callus':
>
> PO:0000004 : in vitro cultured cell, tissue and organ
>    (i) PO:0000009 : cultured callus
>   (i) embryogenic callus
>   (i) organogenic callus (syn. meristematic callus)
>
> I need to double check about the synonym for the latter term.
>
> Since both callus types can originate (be induced) from a variety of
> tissues, I would ignore this aspect, it can get really complicated,
> (triggering large proliferation of terms).
> Also, at this point, I would suggest not to propagate term 'meristemoid'
> under 'in vitro cultured cell, tissue and organ' node. This term is
already
> in the PSO,
>
> PO:meristemoid, PO:0000070,
>
> Def: A cell or a group of cells constituting an active locus of
> meristematic activity in a tissue composed of somewhat older,
differentiating
> cells.
>
> The definition describes all meristemoid cell, regardless of location.
> However, if 'in vitro meristemoid cell' is required for accurate
> annotations (in cases where term' meristemoid' is not sufficiently
> granular), we will add it to PSO.
>
> Dr. Kikuchi (and others), please let me know if this would work for
> annotation purposes.
>
> Best regards,
>
> Katica
>
> On Wed, 14 Jun 2006, AUGUSTINE, ALICE CLARA [AG/8042] wrote:
>
> > Katica and all,
> >
> > There is a clear distinction between embryogenic callus and organogenic
> > callus and the usage is pretty consistent amidst the tissue culture
> > community.
> >
> > Organogenic - has competence to form any organ (root, leaf, shoot,
leafless
> > shoot/bare stem etc). In the embryogenic callus type, embryo-like
structures
> > develop, called somatic embryos, that then simultaneously develop shoots
and
> > roots.
> >
> > Then there is also the question of "meristematic callus". This type of
> > callus that produces meristemoids (meristematic cell masses)
> > Meristemoid: A localized group of callus cells, characterized by their
> > accumulation of starch, RNA and protein, and giving rise to adventitious
> > shoots or roots.
> > Would it make sense to put organogenic callus and meristematic callus as
> > synonyms?
> >
> > Another point to note is Meristemoids occur in 2 contexts:
> > One as progenitors of stomata and the other as defined above.
> >
> > Cheers
> > Regards,
> > Alice Clara Augustine
> >
> > -----Original Message-----
> > From: owner-po-dev at plantontology.org
[mailto:owner-po-dev at plantontology.org]
> > On Behalf Of katica at acoma.Stanford.EDU
> > Sent: Wednesday, June 14, 2006 11:26 PM
> > To: POC-dev; katica at acoma.Stanford.EDU
> > Cc: SATOH, Kouji; Pankaj Jaiswal; Shoshi Kikuchi
> > Subject: RE: Question GRO term
> >
> > Satoh,
> >
> > Sorry I wasn't specific enough regardng embryogenic callus,
> > 'embryogenic callus' should describe callus with demonstrable competence
> > to form somatic embryos. 'organogenic callus' has competence to form
roots
> > and/or shoots.
> >
> > I vaguely remember that some people referred to embryogenic callus even
> > though regeneration of shoots/roots took place from such callus. My
> > recollection goes back to literature that was published some 12 or more
> > years ago.
> >
> > Is there a clear distinction in plant tissue culture community regarding
> > proper use of this terminology, 'embryogenic callus' and 'organogenic
> > callus'?
> >
> > Katica
> >
> >
> > On Wed, 14 Jun 2006 katica at acoma.stanford.edu wrote:
> >
> >> Dear Satoh,
> >>
> >> On Wed, 14 Jun 2006, SATOH, Kouji wrote:
> >> ....
> >>> I have question for you: you described the callus as embryogenic, does
> >>>> this refer to callus that will give rise to somatic embryos, or
> >>>> to the callus
> >>>> induced from embryo tissue within seed, or both? I don't know
> >>>> enough about
> >>>> callus induction from rice seeds, some clarification would help with
> >>>> defining parent terms for the new term 'embryogenic callus'.
> >>>
> >>> "Embryogenic callus" is the callus is able to generate somatic embryo,
> > does
> >>> not indicate the callus derived from embryo tissue.
> >>
> >> OK, 'embryogenic calus' refers to callus with demonstrable
morphogenetic
> >> competence (either organogenesis or embryogenesis). Coincidentally, in
the
> >
> >> particular case of the callus induced from rice seeds, it originated
from
> >> embryonic tissue too (which is relevant for placing the new term under
> > proper
> >> parent term).
> >>
> >>> And I think  "Embryogenic callus" is one of organogenic callus.
> >>> Three type of tissues are generated from callus.They are adventitious
> >>> shoot,
> >>> root, and embryo(same as soamtic embryo).
> >>> Because plant call has "totipotency".
> >>> Therefore the methods of re-diffrerentiation of plant from callus are
> > two.
> >>> One is direct induced somatic embryo from callus.
> >>> This callus is embryogenic callus
> >>>
> >>> Other is two step method, at first, the induction of adventitious
shoot
> > (or
> >>> root), and after that, induced root (or shoot).
> >>> This callus is "organogenic callus"
> >>>
> >>> Can I answer the your question?
> >>
> >> Yes, you did. Thank you very much for clarification.
> >> Best regards,
> >>
> >> Katica
> >>>
> >>> best regards
> >>> Satoh
> >>>
> >>> ++++++++++++++++++++++++++++++++++++
> >>> SATOH, Kouji (º´Æ£¹ÀÆó) Ph. D
> >>> Unit of Plant Genome Research
> >>> National Institute of Agrobiological Sciences
> >>> Mail: ksatoh at nias.affrc.go.jp
> >>> Tel: 029-838-7007
> >>> ++++++++++++++++++++++++++++++++++++
> >>>
> >>>> -----Original Message-----
> >>>> From: katica at acoma.stanford.edu [mailto:katica at acoma.stanford.edu]
> >>>> Sent: Wednesday, June 14, 2006 2:27 AM
> >>>> To: POC-dev; Pankaj Jaiswal
> >>>> Cc: Shoshi Kikuchi; º´Æ£ ¹ÀÆó
> >>>> Subject: Re: Question GRO term
> >>>>
> >>>>
> >>>> Dear Kikuchi,
> >>>>
> >>>> Pankaj Jaiswal forwarded your request to POC. Currently, we only
> >>>> have term
> >>>> 'cultured callus' and 'cultured embryo' in Plant structure ontology
> > (PSO).
> >>>> New term, embryogenic callus, would need to be introduced to PSO.
> >>>>
> >>>> I have question for you: you described the callus as embryogenic,
does
> >>>> this refer to callus that will give rise to somatic embryos, or
> >>>> to the callus
> >>>> induced from embryo tissue within seed, or both? I don't know
> >>>> enough about
> >>>> callus induction from rice seeds, some clarification would help with
> >>>> defining parent terms for the new term 'embryogenic callus'.
> >>>>
> >>>> Also, there are no Growth stage terms for in vitro cultures. Since
Plant
> >>>> Growth Stages are pertinent to a whole plant, we intentionally
> >>>> ommitted dealing with staging for tissue culture entities.
> >>>>
> >>>> Best Regards,
> >>>>
> >>>> Katica
> >>>>
> >>>>> Shoshi Kikuchi wrote:
> >>>>>> Dear Pankaj
> >>>>>>
> >>>>>> We are now preparing for the ontology-based description of our
> >>>> full-length
> >>>>>> cDNA clones.
> >>>>>>
> >>>>>> I have a question. What is the appropriate description of
embryogenic
> >>>>>> callus. Many of our full-length cDNA libraries are originated from
> > rice
> >>>>>> callus induced from mature seed.
> >>>>>>
> >>>>>> 21 day-old callus after induction on the medium containing
> >>>> 2,4-D as auxin
> >>>>>> from a mature seed.
> >>>>>>
> >>>>>> What kind of GRO term is the most appropriate one?
> >>>>>>
> >>>>>> Sincerely yours,
> >>>>>>
> >>>>>> Shoshi
> >>>>>> ***********************************
> >>>>>> Shoshi Kikuchi Ph.D
> >>>>>> Plant Genome Research Unit
> >>>>>> Division of Genome and Biodiversity Research
> >>>>>> National Institute of Agrobilogical Sciences (NIAS)
> >>>>>> Kan'non dai 2-1-2
> >>>>>> Tsukuba Ibaraki 305-8602 Japan
> >>>>>> TEL/FAX +81-29-838-7007
> >>>>>> Email: skikuchi at nias.affrc.go.jp
> >>>>>> WEB: ¡£¡£(RMOS) http://microarray.rice.dna.affrc.go.jp
> >>>>>>           (KOME) http://cdna01.dna.affrc.go.jp/cDNA/
> >>>>>> ************************************
> >>>>>>
> >>>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>
> >>>> --
> >>>>
>
> --------------------------------------------------------------------------
> >>>> 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/
> >>>> 260 Panama St.
> >>>> Stanford, CA 94305
> >>>> U.S.A.
> >>>>
>
> --------------------------------------------------------------------------
> >>>>
> >>>
> >>
> >>
> >
> >
>
> -- 
> --------------------------------------------------------------------------
> 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/
> 260 Panama St.
> Stanford, CA 94305
> U.S.A.
> --------------------------------------------------------------------------
>