[Taxacom] DNA extraction from herbarium specimens

Monique Reed monique at mail.bio.tamu.edu
Thu Dec 27 13:06:42 CST 2007


We have supplied material that has yielded good results for workers in
our Biology Department.  For Brassicaceae, at least, the best results
come from material that was pressed very soon after collection, which
was dried very quickly, and which is less than five years old.  This
material has been frozen at least once at -80 C, so that does not seem
to affect DNA recovery.  When I return to the office from vacation, I
will contact the lab that has been having the good luck and see if they
can post something about their protocol.

Monique Reed
TAMU,  Texas A&M University  

>>> <taxacom-request at mailman.nhm.ku.edu> 12/27/07 12:00 PM >>>
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Today's Topics:

   1. DNA extraction from herbarium specimens
      (Vitor Fernandes de Miranda)
   2. Re: Help sought - re. spelling of Rhamnoides. (Torbj?rn Tyler)
   3. Re: Help sought - re. spelling of Rhamnoides. (Mario Blanco)
   4. Re: Help sought - re. spelling of Rhamnoides.
      (Paul van Rijckevorsel)
   5. Re: Help sought - re. spelling of Rhamnoides. (Jacques Melot)
   6. Re: Help sought - re. spelling of Rhamnoides.
      (Paul van Rijckevorsel)
   7. Re: Help sought - re. spelling of Rhamnoides.
      (Paul van Rijckevorsel)


----------------------------------------------------------------------

Message: 1
Date: Wed, 26 Dec 2007 19:58:48 -0300
From: "Vitor Fernandes de Miranda" <vmiranda at umc.br>
Subject: [Taxacom] DNA extraction from herbarium specimens
To: <taxacom at mailman.nhm.ku.edu>
Message-ID: <56A14BDF60B86444A53B1F8C23179958295879 at exchange.umc.br>
Content-Type: text/plain;	charset="iso-8859-1"

Dear friends,

 

I've experimented to extract DNA from herbarium specimens, but the
results are always disappointing. 

DNAzol and CTAB methods were tried but with no success.

 

Please, does anyone have any suggestion? Any protocol or even clues will
be very welcome.

 

Best wishes,

V?tor

 

 

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Prof.Dr. V?tor Fernandes Oliveira de Miranda
Curador HUMC
Universidade de Mogi da Cruzes - UMC
Laborat?rio de Sistem?tica Vegetal
Herbarium Mogiense - HUMC (Sala 21.16 - Pr?dio II)
Av. Dr. C?ndido Xavier de Almeida Souza, n.200
CEP 08780-911 - Moji das Cruzes - SP - Brasil
Tel.: +55 (11) 4798-7000 Ramal 7313
http://www.umc.br/~vmiranda

e-mail: vmiranda at umc.br

 



------------------------------

Message: 2
Date: Thu, 27 Dec 2007 09:23:16 +0100
From: Torbj?rn Tyler <Torbjorn.Tyler at sysbot.lu.se>
Subject: Re: [Taxacom] Help sought - re. spelling of Rhamnoides.
To: taxacom at mailman.nhm.ku.edu
Message-ID: <l0313030ec39910f455d9@[130.235.149.84]>
Content-Type: text/plain; charset="iso-8859-1"

Or, with a more Latin/European and less Anglo-/American pronounciation:
ram-no-EE-dees!

/ Torbj?rn Tyler


At 04.47 +0100 on 07-12-23, Thomas Lammers wrote:


> Over the e or over the i?  I think it's a dieresis:
> http://en.wikipedia.org/wiki/Diaeresis
> This tells us that the o and i are to be pronounced separately, not as
a diphthong:
> 
> "ram-no-EYE-dees" not "ram-NOI-dees"
> 
> ----- Original Message -----
> From: john.steel at botany.otago.ac.nz
> Date: Saturday, December 22, 2007 6:33 pm
> Subject: [Taxacom] Help sought - re. spelling of Rhamnoides.
> To: taxacom at mailman.nhm.ku.edu, taxacom-bounces at mailman.nhm.ku.edu
> 
> > I have occasionally come across Rhamnoides spelt with an umlaut 
> > over the -e- in 
> > english language texts.
> > 
> > Can anyone help me as to the justification, correctness (?), 
> > authority, or whatever, of 
> > this spelling?
> > 
> > Thanks in advance and compliments of the season to you all.
> > 
> > John Steel.
> > 
> > _______________________________________________
> > Taxacom mailing list
> > Taxacom at mailman.nhm.ku.edu
> > http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> >
> _______________________________________________
> Taxacom mailing list
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom


-------------------------------------------------------------------

Torbj?rn Tyler, Ph.D, 

- Curator at herbarium LD.
- Editor in Chief of Nordic Journal of Botany.
- Deputy secretary of Lund Botanical Society, with special
responsibility for Projekt Sk?nes Mossor.
- Responsible for the project The Hieracia of Sweden.


Botanical Museum
?. Vallgatan 18
SE-223 61 Lund

tel. +(0)46-222 89 65

					
e-mail: torbjorn.tyler at ekol.lu.se

Private address: Bredgatan 12B, SE-243 32 H??r (=Hoeoer), tel.
+(0)413-23123.
___________________________________________________________________





------------------------------

Message: 3
Date: Thu, 27 Dec 2007 03:08:38 -0600
From: Mario Blanco <mblanco at flmnh.ufl.edu>
Subject: Re: [Taxacom] Help sought - re. spelling of Rhamnoides.
To: TAXACOM <taxacom at mailman.nhm.ku.edu>
Message-ID: <47736B96.90102 at flmnh.ufl.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

According to Article 60.6 of the latest version of the International 
Code of Botanical Nomenclature, diacritical signs are to be suppressed 
from Latin plant names. However, the use of the diaeresis is permissible

(that is, optional; you can choose to use it or not).

"60.6. Diacritical signs are not used in Latin plant names. In names 
(either new or old) drawn from words in which such signs appear, the 
signs are to be suppressed with the necessary transcription of the 
letters so modified; for example ?, ?, ? become, respectively, ae, oe, 
ue; ?, ?, ? become e, or sometimes ae; ? becomes n; ? becomes oe; ? 
becomes ao. The diaeresis, indicating that a vowel is to be pronounced 
separately from the preceding vowel (as in Cepha?lis, Iso?tes), is 
permissible; the ligatures -?- and -?-, indicating that the letters are 
pronounced together, are to be replaced by the separate letters -ae- and

-oe-."

-- 
Mario A. Blanco
Department of Botany
University of Florida
220 Bartram Hall
Gainesville, FL 32611-8526
U.S.A.


Peter Bostock wrote:
>  W.T. Stearn in Botanical Latin edn 4 page 257 (with Greek
>  transliterated):
>
>  "Transliterated into Latin, the masculine and feminine ending
>  "oeides" (long e in final syllable) and the neuter "oeides" (short e
>  in final syllable) become -oides. This comprises two parts: the -o-
>  which belongs to the stem and -eides (having the nature of,
>  resembling) [written in Greek script in Stearn] from eidos (shape,
>  kind, nature). The -oi- of -oides should accordingly be pronounced as
>  two short vowels oi, and not as a dipthong (ie not as in English
>  'adenoid')..."
>
>  I think that use of the diaeresis would be helpful to indicate the
>  separate vowels, much as in Is?etes, but this rarely (never?) seems
>  to be applied to generic names possessing this ending (eg Nymphoides
>  and perhaps a hundred others).
>
>  Cheers,
>
>  Peter
>
>  At 01:47 PM 23/12/2007, Thomas Lammers wrote:
> > Over the e or over the i? I think it's a dieresis:
> > http://en.wikipedia.org/wiki/Diaeresis This tells us that the o and
> > i are to be pronounced separately, not as a diphthong:
> >
> > "ram-no-EYE-dees" not "ram-NOI-dees"
> >
> > ----- Original Message ----- From: john.steel at botany.otago.ac.nz
> > Date: Saturday, December 22, 2007 6:33 pm Subject: [Taxacom] Help
> > sought - re. spelling of Rhamnoides. To:
> > taxacom at mailman.nhm.ku.edu, taxacom-bounces at mailman.nhm.ku.edu
> >
> >> I have occasionally come across Rhamnoides spelt with an umlaut
> >> over the -e- in english language texts.
> >>
> >> Can anyone help me as to the justification, correctness (?),
> >> authority, or whatever, of this spelling?
> >>
> >> Thanks in advance and compliments of the season to you all.
> >>
> >> John Steel.
> >>
> >> _______________________________________________ Taxacom mailing
> >> list Taxacom at mailman.nhm.ku.edu
> >> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> >>
> > _______________________________________________ Taxacom mailing
> > list Taxacom at mailman.nhm.ku.edu
> > http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>
>  ------------------------------------------------------- Peter
>  Bostock, Principal Botanist, Queensland Herbarium, Brisbane,
>  Australia pbostock at ozemail.com.au (also peter.bostock at epa.qld.gov.au)
>  Web http://www.ozemail.com.au/~pbostock (TRANSLAT Bot. Latin
>  translation program (freeware) available at web site)
>
>  _______________________________________________ Taxacom mailing list
>  Taxacom at mailman.nhm.ku.edu
>  http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>
>





------------------------------

Message: 4
Date: Thu, 27 Dec 2007 13:28:51 +0100
From: "Paul van Rijckevorsel" <dipteryx at freeler.nl>
Subject: Re: [Taxacom] Help sought - re. spelling of Rhamnoides.
To: "taxacom" <taxacom at mailman.nhm.ku.edu>
Message-ID: <001a01c84884$3e8a19a0$2b4c4451 at magnifica2>
Content-Type: text/plain; format=flowed; charset="Windows-1252";
	reply-type=original

Well, "permissible" is not the same as "to be encouraged". In the
Species 
Plantarum of 1753 (page 1023/24) Linnaeus uses, side by side, Hippopha?
and 
Rhamnoides (the latter both as a generic name and to indicate the
species), 
with a diaeresis in Hippopha? but not in Rhamnoides.

If I may hazard a guess, I would say that a diaeresis is judged to be
bad 
form in -oides as everybody knows (or is supposed to know) how to
pronounce 
it, it being a regularly formed (and frequently occurring) ending. On
the 
other hand Hippopha? is irregular and the user can do with a reminder on
how 
to pronounce it.

Paul

----- Original Message ----- 
From: "Mario Blanco" <mblanco at flmnh.ufl.edu>
To: "TAXACOM" <taxacom at mailman.nhm.ku.edu>
Sent: Thursday, December 27, 2007 10:08 AM
Subject: Re: [Taxacom] Help sought - re. spelling of Rhamnoides.


According to Article 60.6 of the latest version of the International
Code of Botanical Nomenclature, diacritical signs are to be suppressed
from Latin plant names. However, the use of the diaeresis is permissible
(that is, optional; you can choose to use it or not).

"60.6. Diacritical signs are not used in Latin plant names. In names
(either new or old) drawn from words in which such signs appear, the
signs are to be suppressed with the necessary transcription of the
letters so modified; for example ?, ?, ? become, respectively, ae, oe,
ue; ?, ?, ? become e, or sometimes ae; ? becomes n; ? becomes oe; ?
becomes ao. The diaeresis, indicating that a vowel is to be pronounced
separately from the preceding vowel (as in Cepha?lis, Iso?tes), is
permissible; the ligatures -?- and -?-, indicating that the letters are
pronounced together, are to be replaced by the separate letters -ae- and
-oe-."

-- 
Mario A. Blanco
Department of Botany
University of Florida
220 Bartram Hall
Gainesville, FL 32611-8526
U.S.A.


Peter Bostock wrote:
>  W.T. Stearn in Botanical Latin edn 4 page 257 (with Greek
>  transliterated):
>
>  "Transliterated into Latin, the masculine and feminine ending
>  "oeides" (long e in final syllable) and the neuter "oeides" (short e
>  in final syllable) become -oides. This comprises two parts: the -o-
>  which belongs to the stem and -eides (having the nature of,
>  resembling) [written in Greek script in Stearn] from eidos (shape,
>  kind, nature). The -oi- of -oides should accordingly be pronounced as
>  two short vowels oi, and not as a dipthong (ie not as in English
>  'adenoid')..."
>
>  I think that use of the diaeresis would be helpful to indicate the
>  separate vowels, much as in Is?etes, but this rarely (never?) seems
>  to be applied to generic names possessing this ending (eg Nymphoides
>  and perhaps a hundred others).
>
>  Cheers,
>
>  Peter
>
>  At 01:47 PM 23/12/2007, Thomas Lammers wrote:
> > Over the e or over the i? I think it's a dieresis:
> > http://en.wikipedia.org/wiki/Diaeresis This tells us that the o and
> > i are to be pronounced separately, not as a diphthong:
> >
> > "ram-no-EYE-dees" not "ram-NOI-dees"
> >
> > ----- Original Message ----- From: john.steel at botany.otago.ac.nz
> > Date: Saturday, December 22, 2007 6:33 pm Subject: [Taxacom] Help
> > sought - re. spelling of Rhamnoides. To:
> > taxacom at mailman.nhm.ku.edu, taxacom-bounces at mailman.nhm.ku.edu
> >
> >> I have occasionally come across Rhamnoides spelt with an umlaut
> >> over the -e- in english language texts.
> >>
> >> Can anyone help me as to the justification, correctness (?),
> >> authority, or whatever, of this spelling?
> >>
> >> Thanks in advance and compliments of the season to you all.
> >>
> >> John Steel.
> >>
> >> _______________________________________________ Taxacom mailing
> >> list Taxacom at mailman.nhm.ku.edu
> >> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> >>
> > _______________________________________________ Taxacom mailing
> > list Taxacom at mailman.nhm.ku.edu
> > http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>
>  ------------------------------------------------------- Peter
>  Bostock, Principal Botanist, Queensland Herbarium, Brisbane,
>  Australia pbostock at ozemail.com.au (also peter.bostock at epa.qld.gov.au)
>  Web http://www.ozemail.com.au/~pbostock (TRANSLAT Bot. Latin
>  translation program (freeware) available at web site)
>
>  _______________________________________________ Taxacom mailing list
>  Taxacom at mailman.nhm.ku.edu
>  http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>
>



_______________________________________________
Taxacom mailing list
Taxacom at mailman.nhm.ku.edu
http://mailman.nhm.ku.edu/mailman/listinfo/taxacom 





------------------------------

Message: 5
Date: Thu, 27 Dec 2007 12:42:53 +0000
From: Jacques Melot <jacques.melot at isholf.is>
Subject: Re: [Taxacom] Help sought - re. spelling of Rhamnoides.
To: TAXACOM <taxacom at mailman.nhm.ku.edu>
Cc: john.steel at botany.otago.ac.nz, Torbj?rn Tyler
	<Torbjorn.Tyler at sysbot.lu.se>
Message-ID: <p06230901c3994b0fc254@[192.168.1.1]>
Content-Type: text/plain; charset="iso-8859-1" ; format="flowed"

  Le 27/12/07, ? 3:08 -0600, nous recevions de Mario Blanco :

>According to Article 60.6 of the latest version of the International
>Code of Botanical Nomenclature, diacritical signs are to be suppressed
>from Latin plant names. However, the use of the diaeresis is
permissible
>(that is, optional; you can choose to use it or not).
>
>"60.6. Diacritical signs are not used in Latin plant names. In names
>(either new or old) drawn from words in which such signs appear, the
>signs are to be suppressed with the necessary transcription of the
>letters so modified; for example ?, ?, ? become, respectively, ae, oe,
>ue; ?, ?, ? become e, or sometimes ae; ? becomes n; ? becomes oe; ?
>becomes ao. The diaeresis, indicating that a vowel is to be pronounced
>separately from the preceding vowel (as in Cepha?lis, Iso?tes), is
>permissible; the ligatures -?- and -?-, indicating that the letters are
>pronounced together, are to be replaced by the separate letters -ae-
and
>-oe-."


[J. M.]   Je ne suis pas s?r que cet article 
s'applique au cas de Rhamnoides. En effet, tout 
botaniste est cens? savoir que ? oi ? est 
prononc? ? la latine (o-i, en s?parant les 
voyelles) et non ? la fran?aise (oi = wa), par 
exemple.

    La di?r?se sert ? indiquer qu'une succession 
de voyelles a-e ou o-e, qui pourrait provenir des 
ligatures ae (?) ou oe (?), est a prononcer 
s?par?ment.

    En d'autres termes :

Cepha?lis signifie que ae n'est pas la ligature ae (?).
Iso?tes signifie que oe n'est pas la ligature oe (?).

    L'?criture Rhamno?des n'est pas conforme au 
Code (il n'existe aucune ligature oi). Il s'agit 
d'un r?sidu d'une ancienne ?criture utilis?e 
notamment en France, pour aider ? la 
prononciation. La seule ?criture acceptable est 
donc Rhamnoides.

    Meilleurs salutations,

    Jacques Melot


>--
>Mario A. Blanco
>Department of Botany
>University of Florida
>220 Bartram Hall
>Gainesville, FL 32611-8526
>U.S.A.
>
>
>Peter Bostock wrote:
>>   W.T. Stearn in Botanical Latin edn 4 page 257 (with Greek
>>   transliterated):
>>
>>   "Transliterated into Latin, the masculine and feminine ending
>>   "oeides" (long e in final syllable) and the neuter "oeides" (short
e
>>   in final syllable) become -oides. This comprises two parts: the -o-
>>   which belongs to the stem and -eides (having the nature of,
>>   resembling) [written in Greek script in Stearn] from eidos (shape,
>>   kind, nature). The -oi- of -oides should accordingly be pronounced
as
>>   two short vowels oi, and not as a dipthong (ie not as in English
>>   'adenoid')..."
>>
>>   I think that use of the diaeresis would be helpful to indicate the
>>   separate vowels, much as in Is?etes, but this rarely (never?) seems
>>   to be applied to generic names possessing this ending (eg
Nymphoides
>>   and perhaps a hundred others).
>>
>>   Cheers,
>>
>>   Peter
>>
>>   At 01:47 PM 23/12/2007, Thomas Lammers wrote:
>>  > Over the e or over the i? I think it's a dieresis:
>>  > http://en.wikipedia.org/wiki/Diaeresis This tells us that the o
and
>>  > i are to be pronounced separately, not as a diphthong:
>>  >
>>  > "ram-no-EYE-dees" not "ram-NOI-dees"
>>  >
>>  > ----- Original Message ----- From: john.steel at botany.otago.ac.nz
>>  > Date: Saturday, December 22, 2007 6:33 pm Subject: [Taxacom] Help
>>  > sought - re. spelling of Rhamnoides. To:
>>  > taxacom at mailman.nhm.ku.edu, taxacom-bounces at mailman.nhm.ku.edu
>>  >
>>  >> I have occasionally come across Rhamnoides spelt with an umlaut
>>  >> over the -e- in english language texts.
>>  >>
>>  >> Can anyone help me as to the justification, correctness (?),
>>  >> authority, or whatever, of this spelling?
>>  >>
>>  >> Thanks in advance and compliments of the season to you all.
>>  >>
>  > >> John Steel.

------------------------------

Message: 6
Date: Thu, 27 Dec 2007 16:13:44 +0100
From: "Paul van Rijckevorsel" <dipteryx at freeler.nl>
Subject: Re: [Taxacom] Help sought - re. spelling of Rhamnoides.
To: "taxacom" <taxacom at mailman.nhm.ku.edu>
Message-ID: <001801c8489b$3093c320$2b4c4451 at magnifica2>
Content-Type: text/plain; format=flowed; charset="iso-8859-1";
	reply-type=original

From: "Jacques Melot" <jacques.melot at isholf.is>
    La di?r?se sert ? indiquer qu'une succession
de voyelles a-e ou o-e, qui pourrait provenir des
ligatures ae (?) ou oe (?), est a prononcer
s?par?ment.

    En d'autres termes :

Cepha?lis signifie que ae n'est pas la ligature ae (?).
Iso?tes signifie que oe n'est pas la ligature oe (?).

    L'?criture Rhamno?des n'est pas conforme au
Code (il n'existe aucune ligature oi). Il s'agit
d'un r?sidu d'une ancienne ?criture utilis?e
notamment en France, pour aider ? la
prononciation. La seule ?criture acceptable est
donc Rhamnoides.

    Meilleurs salutations,

    Jacques Melot

***
That is not quite right, as the diaeresis on -a?- can be found in texts
that
also use the ligature -?- (for example Catesb?a and Cepha?lis in
http://www.botanicus.org/viewer/vieweronly.asp?cat=botanicus3&client=b1199485x/31753000645157/jp2&image=31753000645157_0161.jp2).
If that were all there were to it, the text could have used the separate
letters -ae- instead of -a?- to make the distinction.

The ligature -?- dropped out of use only decades ago, and the diaeresis
has
been around since long before that.

Paul





------------------------------

Message: 7
Date: Thu, 27 Dec 2007 17:52:21 +0100
From: "Paul van Rijckevorsel" <dipteryx at freeler.nl>
Subject: Re: [Taxacom] Help sought - re. spelling of Rhamnoides.
To: "taxacom" <taxacom at mailman.nhm.ku.edu>
Cc: Jacques Melot <jacques.melot at ISHOLF.IS>
Message-ID: <003401c848a8$e0fa1310$2b4c4451 at magnifica2>
Content-Type: text/plain; format=flowed; charset="iso-8859-1";
	reply-type=original

The more I think about it, the more I feel that Jacques Melot is
entirely
right, after all. The classic Latin texts that use both the ligature -?-
and
the diaeresis -a?- do not use separate letters -ae- (except in
capitals).

So, please disregard my previous post. Apologies!

Paul

* * *
From: "Jacques Melot" <jacques.melot at isholf.is>
    La di?r?se sert ? indiquer qu'une succession
de voyelles a-e ou o-e, qui pourrait provenir des
ligatures ae (?) ou oe (?), est a prononcer
s?par?ment.

    En d'autres termes :

Cepha?lis signifie que ae n'est pas la ligature ae (?).
Iso?tes signifie que oe n'est pas la ligature oe (?).

    L'?criture Rhamno?des n'est pas conforme au
Code (il n'existe aucune ligature oi). Il s'agit
d'un r?sidu d'une ancienne ?criture utilis?e
notamment en France, pour aider ? la
prononciation. La seule ?criture acceptable est
donc Rhamnoides.

    Meilleurs salutations,

    Jacques Melot


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------------------------------

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