Question GRO term

Shuly Avraham shuly at cshl.edu
Thu Jul 6 15:00:55 EDT 2006 

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Shuly.

On Jul 6, 2006, at 11:53 AM, Pankaj Jaiswal wrote:

> In the version 1.25 of the po_anatomy.obo file the following new  
> terms were added. The same will be available for browsing in the  
> next release of the ontology soon.
>
> -Pankaj
>
> [Term]
> id: PO:0006090
> name: organogenic callus
> namespace: plant_structure
> def: "A type of cultured callus that has competence to form any  
> organ such as root\, leaf\, shoot\, leafless\nshoot/bare stem\,  
> etc." [POC:curators]
> synonym: "meristematic callus" []
> is_a: PO:0000009 ! cultured callus
>
> [Term]
> id: PO:0006091
> name: embryogenic callus
> namespace: plant_structure
> def: "A type of cultured callus that form embryo-like structures  
> such as somatic embryos." [POC:curators]
> is_a: PO:0000009 ! cultured callus
>
> Added additonal parent for somatic embryo PO:0000011
>
> embryogenic callus PO:0006091
> --developsfrom--somatic embryo PO:0000011
>
> ---------------------------------------------------------------------- 
> -----
>
>
> Shoshi Kikuchi wrote:
>> 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.
>>> -------------------------------------------------------------------- 
>>> ------
>>>
>
>
> -- 
> Pankaj Jaiswal
> G-15, Bradfield Hall
> Dept. of Plant Breeding and Genetics
> Cornell University
> Ithaca, NY-14853, USA
>
> Ph. +1-607-255-3103 / 4199
> fax: +1-607-255-6683
>

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