HDTenEightyP/NetNews huggingface dataset:
From: bchs1b@Elroy.UH.EDU (Michael Benedik)
Subject: Re: Acid Precipitation
Reply-To: bchs1b@Elroy.UH.EDU
Organization: University of Houston
Date: Thu, 23 Jul 1992 03:04:34 GMT

In article <q2fm66=@lynx.unm.edu>, kim@m44.unm.edu writes:
>Hello group:
>
>Last year, I posted a question about TCA precipitation, and got several useful
>replies.  . . .  I lost them :(
>
>So here are a few questions.
>
>When one filters the acid-precipitated material through a glass filter, does
>the material actually _stick_ to the glass, or is this a simple particulate
>filtration?  If the latter, Why do we use glass?  Is it just for acid
>resistance?
>
>Can acid precipitated nucleic acids be pelleted and washed as a pellet?  How
>hard do they have to be centrifuged for this?  Has anyone tried this before?  I
>would like to try precipitating in 96-well dishes and spinning using a plate
>carrier in my refrigerated centrifuge, but the maximum RCF is about 2500 x g. 
>Does this sound sufficient?
>
>Thanks for your patience.  
>
>Daniel Kim
>KIM@FLOVAX.LANL.GOV
>

Yes, you certainly can precipitate nucleic acids with TCA in a centrifuge.
Standard DNAse assays are based on the efficient removal of large DNA
and the measuring of the acid soluble (small fragments) left in the sup.
I am not sure if you have enough G force for the microtiter dishes or not,
I guess it is worth a try. It may be quite dependent on the DNA concentration,
in fact I would strongly guess that it is.

	---------------------------------------------------
	 Michael Benedik
	 Department of Biochemical and Biophysical Sciences
	 University of Houston
	 INTERNET: Benedik@UH.EDU	BITNET: Benedik@UHOU
From: wmelchior@NTBTOX.NCTR.FDA.GOV ("Bill Melchior, NCTR/FDA")
Newsgroups: bionet.molbio.methds-reagnts
Subject: Re: E. coli strains
Date: 23 Jul 92 16:27:51 GMT
Reply-To: wmelchior@NTDOC.NCTR.FDA.GOV
Distribution: bionet

>Can anyone tell me of a source where I can find E.coli strains and 
>their genotypes?  Also are E. coli GM48 methylation defective (dam/dcm)? 

Two places to try:

1)  The ATCC Catalogue of Bacteria, Phages, and rDNA Vectors.
This gives some, though not very many, genotypes.  What it does have is
references for each strain, which should generally lead you to the
genotype.

2)  Frederick C. Neidhardt et al's two volume "Escherichia coli and
Salmonella typhimurium", published 1987 by the Amer. Soc. Microbiology.
One of the chapters is devoted to extensive pedigrees of different strains,
showing their derivations and genotypes.

When I ordered several strains from the E. coli genetic stock center at Yale,
each came with a complete genotype, but I knew what I wanted; I don't know 
whether they have a catalog.
________________________________________________________________________________
The opinions stated are mine, not those of NCTR or its sponsoring organizations.

Bill Melchior                                ||   "You have lawyers the way
National Center for Toxicological Research   ||    other people have mice."
Jefferson, AR  72079                         ||
(501) 543-7206                               ||   -Kenneth Duncan, English
                                             ||    Health & Safety Executive,
WMELCHIOR@NTDOC.NCTR.FDA.GOV                 ||    to US regulators
________________________________________________________________________________
The opinions stated are mine, not those of NCTR or its sponsoring organizations.

Bill Melchior                                ||   "You have lawyers the way
National Center for Toxicological Research   ||    other people have mice."
Jefferson, AR  72079                         ||
(501) 543-7206                               ||   -Kenneth Duncan, English
                                             ||    Health & Safety Executive,
WMELCHIOR@NTDOC.NCTR.FDA.GOV                 ||    to US regulators
From: ABOLA@PB1.PDB.BNL.GOV
Newsgroups: bionet.molbio.evolution
Subject: re: how many hemagglutinins 3D structures?
Date: 23 Jul 92 18:50:28 GMT
Distribution: bionet

>Does anybody know how many influenza strain A hemagglutinins have
>been crystallized and their structure determined? I don't have access
>to the Brookhaven structural database. Can I log-in somewhere to access
>this database on an anonymous basis?
> 
>Thanks,
> 
>Yannick Pouliot
>Montreal Neurological Institute
>

The following are in the current PDB release:


1HGD  HEMAGGLUTININ MUTANT(G135(A)R)          D.WILEY ET AL.   
1HGE  HEMAGGLUTININ MUTANT(G135(A)R)/NEU5AC2MED.WILEY ET AL.
1HGF  HEMAGGLUTININ                           D.WILEY ET AL.
1HGG  HEMAGGLUTININ/ALPHA(2,3)SIALYLLACTOSE   D.WILEY ET AL.
1HGH  HEMAGGLUTININ/NEU5AC(ALPHA)2BAC         D.WILEY ET AL.
1HGI  HEMAGGLUTININ/4-ACETYL-NEU5AC(ALPHA)2ME D.WILEY ET AL.
1HGJ  HEMAGGLUTININ/9-AMINO-NEU5AC(ALPHA)2ME  D.WILEY ET AL.


You can get further information by using WAIS - 

	PDB source can be accessed using the following:

	Internet name: irisc2.pdb.bnl.gov
        Internet address: 130.199.144.8
        TCP port: 210
        Database-name: protein-data-bank


enrique
________________________________________________________________                                 
				 | 
enrique e. abola                 |   BITNET:    abola@bnlchm 
Protein Data Bank                |   INTERNET:  abola1@bnl.gov 
Department of Chemistry          |   Tel:	(516)-282-4383 
Brookhaven National Laboratory   |   Fax:       (516)-282-5751
Upton NY 11973                   |
________________________________________________________________
From: CX13@MUSICA.MCGILL.CA ("Yannick@CX13")
Newsgroups: bionet.molbio.evolution
Subject: how many hemagglutinins 3D structures?
Date: 23 Jul 92 01:04:01 GMT
Distribution: bionet

Does anybody know how many influenza strain A hemagglutinins have
been crystallized and their structure determined? I don't have access
to the Brookhaven structural database. Can I log-in somewhere to access
this database on an anonymous basis?

Thanks,

Yannick Pouliot
Montreal Neurological Institute
Xref: sparky bionet.molbio.evolution:285 bionet.general:1470
From: asljl@acad2.alaska.edu
Newsgroups: bionet.molbio.evolution,bionet.general
Subject: NEED R&D INFO PLEASE HELP!!!
Date: 22 Jul 92 22:15:27 GMT
Organization: University of Alaska


#21 SMTP@INTERBIT       Mon 20 Jul 1992  21:55:51  (  37/ 1917)

Subject:  Request
From:     dhaley@MIHI.UNE.EDU.AU

MAIL FROM:<dhaley@mihi.une.edu.au> 
Received: from CORNELLC by CORNELLC (Mailer R2.08A) with BSMTP id 2380; Tue, 21 
 Jul 92 01:55:45 EDT 
Received: from grivel.une.edu.au by CORNELLC.cit.cornell.edu (IBM VM SMTP V2R2) 
   with TCP; Tue, 21 Jul 92 01:55:43 EDT 
Received: from mihi.une.edu.au by grivel.une.edu.au (4.0/25) 
	id AA06001; Tue, 21 Jul 92 15:57:10 EST 
Received: by mihi.une.edu.au (5.57/Ultrix3.0-C) 
	id AA20341; Tue, 21 Jul 92 15:57:09 +1000 
From: dhaley@mihi.une.edu.au (Dean) 
Message-Id: <9207210557.AA20341@mihi.une.edu.au> 
Subject: Request 
To: ASLJL%ALASKA.BITNET@cornellc.cit.cornell.edu (LINDA J LOCKWOOD) 
Date: Tue, 21 Jul 92 15:57:08 EST 
 16, 92 8:38 pm 
X-Mailer: ELM [version 2.3 PL11] 
  
Linda, 
    I need the following information but can not post to the newsgroups.. 
Could you post the following to bionet.general 
                                bionet.molbio.evolution 
  
 I have often wondered about intra-specific fosters. I once saw pn television 
where a horse successfully carried and birthed a zebra, whose embryo had 
been implanted in the horses womb. 
 My question is this. 
 How closely must the two species be related to aviod the foster parent 
aborting the fetus? Would it be possible, say, for a camel to carry the 
young of a llama. Both these species are of the Camel family. 
Direct email to dhaley@mihi.une.edu.au 
--------------------------------------------------------------------------- 
| Dean Haley              | University Of New England, Armidale  _--_|\   | 
| dhaley@mihi.une.edu.au  | N.S.W, Australia.                   /      \  | 
|                         |                                     \_.--.^/  | 
Please help my friend, and send the mail to him. If any of you have been
following the Federation postings and would like to get in touch please
direct your mail to me.

Signed 
Lady Rhavyn
From: DRBH@DB1.CC.ROCHESTER.EDU
Newsgroups: bionet.molbio.evolution
Subject: Request for suggestions to improve Molecular Biology and Evolution
Date: 21 Jul 92 16:05:00 GMT
Distribution: bionet

July 21, 1992

Dear Colleagues,
	I will assume responsibility for editing Molecular 
Biology and Evolution starting with Volume 11 (1994).  
Because of the usual gap between acceptance and publication 
my responsibilities will actually start about a year from 
now.
	You are the community that is served by MBE, and it would 
therefore be very helpful to me to learn how you feel about 
the journal.  Do you currently read MBE?  What are we doing 
well that you don't want to see changed?  What are we not 
doing well?  What should we change, and how?  Do you publish 
in MBE?  If not, what sorts of changes would encourage you to 
do so?  If so, what can we do to facilitate your authorship?  
Are there areas of Molecular Evolution that we over 
emphasize?  Are there areas that are under-represented?
	Please consider this an open invitation, both now and in 
the future, to suggest improvements.
	Those suggestions will be welcome by phone 
(716)J275P0721, by FAX (716) 275-2070, by E-mail (Bitnet: 
DRBH@UORDBV, or Internet:DRBH@DB1.CC.ROCHESTER.EDU), or by 
regular mail (Barry G. Hall, Biology Dept., River Campus, 
University of Rochester, Rochester, NY 14627, USA).

Sincerely,
Barry G. Hall
From: rybicki@uctvax.uct.ac.za
Newsgroups: bionet.molbio.evolution
Subject: re: are viruses alive?  You bet your genome....
Date: 21 Jul 92 11:25:43 GMT
Organization: University of Cape Town

So, Una:

Viruses are alive because they EVOLVED from living organisms?  I think we need
a definition of organism here:

"An organism is the unit element of a continuous lineage with an individual
evolutionary history."
- Salvador Luria, JE Darnell Jr, David Baltimore & A Campbell; General
Virology, 3rd Edn.

People all too often think of life in terms of a"top-down" approach: going from
things with legs or leaves to less complex forms, until they reach viruses and
say: "hey, these things are just molecules, anyway!" 

More definition:

"A material is living if, after isolation, it retains a specific configuration
that can be reintegrated into the cycle of genetic matter."
- Salvador Luria, 1953 (Virology, 1st Edn)

Prescient, wouldn't you say?  And describes viruses as organisms as life,
succinctly and aptly.

It is quite possible that many viruses evolved from cellular organisms (not
living orgs); it is equally possible that there are some viruses around now
which descend from bits of nucleic acid that may have been part of the very
first self-replicating (acellular) systems - some of the simpler (not
primitive) RNA viruses or parts thereof are very good candidates for direct
linear descendants of the ancestral RNA molorgs (molecular organisms).

And who's Una, anyway?  And why does she get so cranky when people try to show
a bit of respect by calling her Ms?  Methinks the lady doth protest too much.
 _________________________________________________________________________
|                                 |                                       |
|  Ed Rybicki                     |    Now you've got the hang of it      |
|  Dept Microbiology              | There's nothing you can't do with it  |
|  University of Cape Town        |         If you're very into it        |
|  PB Rondebosch 7700             |         You can't go wrong....        |
|  South Africa                   |                                       |
|  fax 27 21 650 4023             |              - Mad John               |
|  ed@micro.uct.ac.za             | (Ogden's Nut-Gone Flake, Small Faces) |
|_________________________________|_______________________________________|
From: JMILLER%BIOVX1.SPAN@STAR.STANFORD.EDU
Newsgroups: bionet.molbio.evolution
Subject: Age of Earth and Origin of Life
Date: 29 Jul 92 05:58:17 GMT
Distribution: bionet


 Actually, the time for life to evolve is much shorter than 1 billion years.
After the earth formed, it was subjected to intense bombardment by smaller
bodies, and possibly had a collision with a Mars-sized body, resulting in
the formation of the moon. The surface was completely melted during this time,
until about 4.1 billion years. There are some possible rocks from this period
(embedded in younger rocks). The first sedimentary rocks are from 3.7-3.8
billion years ago. If you believe water was necessary for the origin of life,
only a couple of hundred million years pass between the first life and the
fairly sophisticated (ie., it already has a completel intermediate metabolism
and is probably photo or chemosynthetic) last common ancestor of all life.

-Peter Markiewicz
Newsgroups: bionet.molbio.evolution
From: jlogsdon@sunflower.bio.indiana.edu (John Logsdon)
Subject: Age of Earth and Origins of Life
Organization: Indiana University
Date: Tue, 28 Jul 92 16:49:45 GMT

The following is a modified duplication  of a post that I intended to cross-post
to talk.origins AND bionet.molbio.evolution, but somehow it  never made it to
the latter.

_____
Alright, here's a question for you geologists out there.
Young earth creationists, please do not bother.
PLEASE educate this molecular evolutionary biologist.

I am wondering; what serious values have been proposed for the age of earth?
In casual converstion, I usually hear values ca. 4.5 Billion years.
In a quick check of a few paleobotany texts (all I have at my immediate
disposal) this is close to what they cite in their "geological columns." 
In a nutshell,on which isotopes are these based and what statistical errors 
correspond to these measures? 

In a recent paper in  _Science_ (v257: 232-235, 10 July 1992), the authors
claim to have found fossil eukaryotic algae that are ca. 2.1 BY old. This 
is striking to me because this lineage likely represents a fairly derived
eukaryotic lineage itself.  In other words, there are a number of eukaryote
lineages which branched off before this one did.  This makes these other euks
older than 2.1 BY.  In fact, Archaezoa (euks with out mitochondria, ie:
_Giardia_, that wonderful intestinal parasite) are probably MUCH older than 
the Algae they found (_Grypania_).  Given this and that the root of the 
tree of life is EVEN DEEPER (between eubacteria and 
archaebacteria+eukaryotes), this seems to put "life" (ie: the common ancestor 
of all life: the "progenote") fairly ancient, perhaps ca. 3.5 BYA.  

This, as I read it, apparent ca. ONE billion year gap between the Earth's
origin and the origin of life is the impetus of this post. From a VERY
naive point of view, this doesn't seem very long. If in fact there
is significant statistical error associated with the Age of the Earth, or the
Dating of the fossils in question for that matter, perhaps there is a longer
time period between the Earth origin and Life origin. If not, are there any
problems with such an apparently limited time frame for evolution of life
theories? 

Any primary literature (biology) and/or review/popular (geology) references 
are much appreciated.

Thanks!
John

_____________

___________________________________________________________
John Logsdon         Department of Biology
                     Indiana University
                     Bloomington, IN  47405
                     (812) 855-2549
                     (812) 855-6705 fax

jlogsdon@sunflower.bio.indiana.edu
____________________________________________________________
From: curtis@eos.ncsu.edu (SUSAN J CURTIS)
Newsgroups: bionet.molbio.hiv
Subject: Re: Mailing- outta here.
Date: 29 Jul 92 17:16:18 GMT
Reply-To: curtis@eos.ncsu.edu (SUSAN J CURTIS)
Distribution: bionet
Organization: North Carolina State University, Project Eos
Originator: curtis@c00127-100lez.eos.ncsu.edu


Super.  I've got plenty to chew on, can sleep a little better after
I would hope.   Thanks to JP Capitano, to Mika, and to Brian for their
input.  I'll shut up and tell my friends not to bug you guys.  

Until they next earth-shattering SPIN article,
yours undereducatedly,
Curtis.
--
Newsgroups: 
Distribution: world
Followup-To: 
From: curtis@eos.ncsu.edu (Abba Jones)
Reply-To: curtis@eos.ncsu.edu (Abba Jones)
Organization: Project EOS - North Carolina State University
Newsgroups: bionet.molbio.hiv
From: bhjelle@vaxine.unm.edu (Brian Hjelle)
Subject: Re: Mailing
Date: Wed, 29 Jul 92 14:43:39 GMT
Organization: University of New Mexico, Albuquerque
Distribution: bionet

In article <1992Jul28.203317.23129@ncsu.edu> curtis@eos.ncsu.edu writes:
>
>Well, I wrote a letter inquiring about duesberg some six weeks ago, asking
>that I have mail sent (not wishing to disturb the repartee herien -- I even
>disclaimed vis my unscientific nature).
>
>	I asked for: some paper outlining WHY Duesberg was wrong --
>		...some paper that worked as the "proof" for the HIV
>		   hypothesis.

There is a ton of data supporting the *association* between HIV
and AIDS, far too much to recount here. However, Koch's postulates
require that you reproduce the disease by introducing the agent
into uninfected patients. This can't be done ethically even
if Peter Duesberg volunteers to be the inoculee.

The closest thing we have now is the observation that *molecularly
cloned* (ie, utterly pure) SIV (a close monkey relative of HIV)
causes fatal immunodeficiency disease when introduced into
pigtail macaques (Nature 1990;345:636).

That is considered the best single bit of evidence supporting
the idea that lentiviruses, in utterly pure form, can unilaterally
cause AIDS.

Accidental innoculations of humans by needlestick have resulted
in AIDS. This also supports the causative role of HIV, but can
never be as pure and controlled as when molecular clones of
virus are directly introduced into animals. Recently it has
been discovered that HIV-1 can also infect pigtails. If the
preliminary suggestions that disease will ensue prove true,
the next step would be to show that molecular clones cause
disease as well.


>	I asked wether the reports that there were many (far more than the 
>12 you mentioned) AIDS patients w/o HIV I or II  (non-seropositive, I think 
>is the word).

These reports are highly preliminary to say the least. They
appear to be a mishmash of patients with different types of
risk behavior (many with none at all), and, most important,
it is less than clear that they have been examined for HIV
DNA or antibodies by good labs using state-of-the-art
technology.

>SO, as I can see, NOBODY seems to write to this board anymore, scientific or
>otherwise.  As far as I can see, there seems to be nothing to do but go back
>to listening to the AP bullshit that has assumed that HIV=AIDS with all of the
>witless, careless abandon that the average idiot such as myself deserves.  The
>illuminated will take care of everything.  Dont ask questions.
>
All the silence reveals is that the overwhelming majority of the
scientific community considers the evidence overwhelming that HIV-1
and HIV-2 cause AIDS. This is not equivalent to saying that there
can be no other agent that causes AIDS.

Brian
From: philstas@BE.AC.VUB
Newsgroups: bionet.molbio.hiv
Subject: Mailing
Date: 27 Jul 92 10:38:34 GMT
Distribution: bionet

Hi,
 
I dont know if anyone could answer this, but a good way to keep
this group alive seems to me to change the reply-field.
If I see a question, I reply to it as fast as I can, but
the answer goes only to the person who asked the question, not to
the whole group. Should'nt it be possible to have all replies and
discussion in the maiun bionet-group, and if one whishes
he can send a copy to person itself.
 
This might help in nhaving some more mail in the HIV-group.
 
btw, anyone has some interesting comments on the international
congress in Amsterdam, last week. From out lab two persons went there,
but their seminar will be only in september.
 
Most intreaging point seems to me the lack of consideration for the
theorie of Duesberg  (see also Nature from june 12). The existance of
a third HIV virus maid the press, alltough noting is proven .
How can one take 12 different cases to base a theorie about AIDS and
HIV.
IMHO, We live in a time where all AIDS patient are toroughly submitted to
several medical tests, the 12 out of 500.000 cases could form a unknown, very
rare immuno-disease.
 
Or are the 499.988 other cases exeptions that prove the rule?
 
Yours,
 
Johor
 
"If Man is five, Then the devil is six"
"And if the devil is six, Then GOD is seven"
"This monkey is going to heaven"
-------------------------------------------------------------
-  Philippe Stas                        philstas@vub.ac.be  -
-  Dept. of Cellular Immunology                             -
-  Free University of Brussels          tel: 32-2-359.03.58 -
-  Paardenstraat 65                     Fax: 32-2-359.03.90 -
-  B1640 St.Genesius Rode             Modem: 32-2-359.03.59 -
-  Belgium, Europe                           (2400,1,N,8,1) -
-------------------------------------------------------------
From: philstas@BE.AC.VUB
Newsgroups: bionet.molbio.hiv
Subject: Duesberg again
Date: 29 Jul 92 08:46:48 GMT
Distribution: bionet
Original-To: curtis@EDU.NCSU.EOS
Original-Cc: hiv-molbiol@UK.AC.DARESBURY
X-Mailer: ELM [version 2.3 PL11]

>Well, I wrote a letter inquiring about duesberg some six weeks ago, asking
>that I have mail sent (not wishing to disturb the repartee herien -- I even
>disclaimed vis my unscientific nature).
>
>       I asked for: some paper outlining WHY Duesberg was wrong --
>               ...some paper that worked as the "proof" for the HIV
>                  hypothesis.
 
I think I remember the paper, with some rather evident questions as I remember.
Weren't this questions in the trend of "why is a table called a table?"
 
>       I asked wether the reports that there were many (far more than the
>12 you mentioned) AIDS patients w/o HIV I or II  (non-seropositive, I think
>is the word).
>
I heard this number very recently, maybe there are 16 cases, please proof
other cases with some article (scientific, not of the sunday times please)
 
>       I feel like the elephant's child.
>SO, as I can see, NOBODY seems to write to this board anymore, scientific or
>otherwise.  As far as I can see, there seems to be nothing to do but go back
>to listening to the AP bullshit that has assumed that HIV=AIDS with all of the
>witless, careless abandon that the average idiot such as myself deserves.  The
>illuminated will take care of everything.  Dont ask questions.
>
How come you use a citatation from the pixies I used some weeks ago,
do you like the pixies ?
 
Sorry for this non scientifical part.
 
Philippe
 
"If Man is five, Then the devil is six"
"And if the devil is six, Then GOD is seven"
"This monkey is going to heaven"
-------------------------------------------------------------
-  Philippe Stas                        philstas@vub.ac.be  -
-  Dept. of Cellular Immunology                             -
-  Free University of Brussels          tel: 32-2-359.03.58 -
-  Paardenstraat 65                     Fax: 32-2-359.03.90 -
-  B1640 St.Genesius Rode             Modem: 32-2-359.03.59 -
-  Belgium, Europe                           (2400,1,N,8,1) -
-------------------------------------------------------------