Question GRO term

Thu Jun 15 14:19:05 EDT 2006

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.
--------------------------------------------------------------------------