HDTenEightyP/NetNews huggingface dataset:
From: hunter@work.nlm.nih.gov (Larry Hunter)
Newsgroups: bionet.biology.computational
Subject: Re: hybrid representations of protein structures
Date: 29 Jul 92 02:23:07 GMT
Distribution: bionet
Organization: National Library of Medicine
Originator: biocomp@lerkim.umiacs.umd.edu


Sajeev Batra asks:

  I noticed that in the 2nd Albany Conf on Computational Biology David Waltz is
  giving a talk on protein secondary structure prediction using hybrid
  representations.  Does anyone know more about this?  I am relatively new in
  this area.  What exactly is a hybrid representation?

I think they call it a "Hybrid System," rather than representation.  Zhang,
Mesirov & Waltz use a collection of different representations and inference
methods, and then combine all of their outputs with a neural network, something
like GRAIL does for gene finding.  There is an article in a recent Journal of
Molecular Biology: JMB (1992) 225: 1049-1063.

						Larry
--
Lawrence Hunter, PhD.
National Library of Medicine
Bldg. 38A, MS-54
Bethesda. MD 20894
(301) 496-9300
(301) 496-0673 (fax)
hunter@nlm.nih.gov (internet)
From: shenkin@avogadro.barnard.columbia.edu (Peter S. Shenkin)
Newsgroups: bionet.biology.computational
Subject: Re: Are viruses alive?
Date: 24 Jul 92 03:23:27 GMT
Distribution: bionet
Organization: Dept. of Chem, Barnard College, Columbia U, New York
Originator: biocomp@lerkim.umiacs.umd.edu


In article <3605@fcs280s.ncifcrf.gov> toms@ncifcrf.gov (Tom Schneider) writes:
>
>In article <CMM.0.90.2.711650592.pkarp@Rockaway.AI.SRI.COM> pkarp@ai.sri.com
>(Peter Karp) writes:
>
>|Harold Morowitz' forthcoming book, "Metabolism Recapitulates
>|Biogenesis: The Beginnings of Cellular Life" has a succinct definition
>|of living systems.  To paraphrase from a draft of the book, an
>|autonomous biological self-replicating system is a molecular
>|self-replicating entity that is capable of evolving, and that operates
>|in the absence of other self-replicating entities.  Therefore, a virus
>|is not an autonomous biological self-replicating system because it
>|requires the presence of other self-replicating entities to replicate.
>|Whether it is alive or not depends on whether you equate life with an
>|autonomous biological self-replicating system, or simply a biological
>|self-replicating system.
>
>Hmm.  So humans must not be "autonomous biological self-replicating systems"
>because we depend on oxygen, vitamin C and various amino acids.  

Morawitz specifies that live things cannot depend on other *self-replicating*
entitities.  "Oxygen, vitamin C and various amino acids" are not 
self-replicating, so they don't count.  The real reason we're not alive
is that we eat plants and animals.

>   .... But I think
>that most people would claim to be alive (or object violently if someone else
>claimed that they were not!)....

Now, now.... just because we claim to be alive, or object violently if
someone else claims we're not, doesn't mean we really ARE alive....  :-)

  -P.
-- 
************************f*u*cn*rd*ths*u*cn*gt*a*gd*jb*************************
Peter S. Shenkin, Department of Chemistry, Barnard College, New York, NY 10027
(212)854-1418    shenkin@avogadro.barnard.columbia.edu   shenkin@cunixf.BITNET
******************** The singular of "media" is "medium". ********************
From: paulk@garfield.cs.mun.ca (Paul E. King)
Newsgroups: bionet.biology.computational
Subject: Re: Are viruses alive?
Date: 23 Jul 92 21:10:08 GMT
Distribution: bionet
Organization: CS Dept., Memorial University of Newfoundland
Originator: biocomp@lerkim.umiacs.umd.edu


Yes, but viruses can be isolated from the cell, crystallized into viral
"cakes," separated from all other living things, and be stored indefinitely
at room temperature, where it doesn't do anything: esentially dead.

BUT, these same viruses can be taken out of isolation, palced inside the host,
and is "alive" again (i.e., replicating). 

Viruses are just a hunk of protein with DNA inside it. They are not really
"living things," unless you mean that the ONLY proof of something being alive
is that it is replicating, regardless of the mechanism, or the prescence of
any biological reactions which are unique to it. 
And, as far as I know, viruses are not classified under any of the 5
kingdoms of living things. 

paulk :-)
From: henebry@matt.ksu.ksu.edu (Geoffrey M Henebry)
Newsgroups: bionet.biology.computational
Subject: Re: Are viruses alive?
Date: 23 Jul 92 20:58:10 GMT
Distribution: bionet
Organization: Kansas State University
Originator: biocomp@lerkim.umiacs.umd.edu

jk13+@andrew.cmu.edu (Joanne M. Karohl) writes:

>Peter writes:

>>Harold Morowitz' forthcoming book, "Metabolism Recapitulates
>>Biogenesis: The Beginnings of Cellular Life" has a succinct definition
>>of living systems.  To paraphrase from a draft of the book, an
>>autonomous biological self-replicating system is a molecular
>>self-replicating entity that is capable of evolving, and that operates
>>in the absence of other self-replicating entities.       ^^^^^^^^^^^^^
  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>This definition of life does exclude many symbiotic organisms, such as
>the malaria parasite and others, which require host organisms to
>complete their life
>cycles . . .

>Joanne

the definition is in need of spatio-temporal bounds to make sense. every
living thing depends upon other living things for necessary supplies of 
nutrients and energy from which to self-replicate. i can think of no instances
in which organisms persist in environments untouched by the influence of other
organisms. 

Robert Rosen offers a provocative view of what sort of thing is an organism
in his recent book "Life Itself".  

from a passage toward the end of the book: 

"A material system is an organism if, and only if, it is closed to efficient
causation.  That is, if F is any component of such a system, the question
'Why F?' has an answer within the system, which corresponds to the category of
efficient cause of F. ... We claim that everything else about organisms,
everything studied in biology by biologists, and much else besides, arises
from and devolves upon this property. ... This is indeed biology from a new
and different perspective.  For one thing, it places the heart of biology 
entirely outside the scope of mechanism.  This is in itself illuminating; it
allows us finally to understand why the initial presumption of mechanism has
made the basic question 'What is life' inaccessible and unanswerable."

any comments? :)
                  geoff
+=+=+=+=+
 Geoffrey M. Henebry                voice: (913) 532-7997   fax: (913) 532-6653 
 Konza Prairie LTER                 BITNET:     HENEBRY@KSUVM                   
 Division of Biology/Ackert Hall    internet:   gmh@andro.konza.ksu.edu         
 Kansas State University                        henebry@matt.ksu.ksu.edu        
 Manhattan, KS 66506 USA            Heraclitus: PANTA HREI
From: batra@boulder.colorado.edu (sajeev batra)
Newsgroups: bionet.biology.computational
Subject: hybrid representations of protein structures
Date: 28 Jul 92 00:48:48 GMT
Distribution: bionet
Organization: University of Colorado, Boulder
Originator: biocomp@lerkim.umiacs.umd.edu

I noticed that in the 2nd Albany Conf on Computational Biology David Waltz
is giving a talk on protein secondary structure prediction using hybrid
representations.  Does anyone know more about this?  I am relatively new
in this area.  What exactly is a hybrid representation? 

Any references on this approach to protein secondary structure prediction
that anybody knows of???



______________________________________________________________________________
sajeev batra
comp sci & mcd biology
univ of colorado @ boulder
From: axh@cs.bham.ac.uk (Alex Hooper)
Newsgroups: bionet.biology.computational
Subject: Help needed for Mackey-Glass
Date: 29 Jul 92 02:24:36 GMT
Distribution: bionet
Organization: University of Birmingham
Originator: biocomp@lerkim.umiacs.umd.edu


Does anyone out there have experience of calculating the values for the
Mackey-Glass equation (any values for parameters). If anybody has executable
files that could calculate a series of x(t) values for it, they could uuencode
and compress it and mail it to me (wishful thinking). Otherwise any helpful hints
to a non-mathematician would be appreciated. (Having x(t) and x(t-delay) terms in
the differential equation confuses me utterly)

		Thanks


____________________________________________
Its long been a hobby of mine
A new value for PI to assign
I'd set it at three
For its easier you see
Than 3.14159...
                   (Alexander Hooper)
                   (axh@cs.bham.uk.ac)
____________________________________________
From: jk13+@andrew.cmu.edu (Joanne M. Karohl)
Newsgroups: bionet.biology.computational
Subject: Re: Are viruses alive?
Date: 21 Jul 92 00:00:09 GMT
Distribution: bionet
Originator: biocomp@lerkim.umiacs.umd.edu

Peter writes:

>Harold Morowitz' forthcoming book, "Metabolism Recapitulates
>Biogenesis: The Beginnings of Cellular Life" has a succinct definition
>of living systems.  To paraphrase from a draft of the book, an
>autonomous biological self-replicating system is a molecular
>self-replicating entity that is capable of evolving, and that operates
>in the absence of other self-replicating entities.  Therefore, a virus
>is not an autonomous biological self-replicating system because it
>requires the presence of other self-replicating entities to replicate.
>Whether it is alive or not depends on whether you equate life with an
>autonomous biological self-replicating system, or simply a biological
>self-replicating system.

This definition of life does exclude many symbiotic organisms, such as
the malaria parasite and others, which require host organisms to
complete their life
cycles . . .

Joanne
From: kristoff@genbank.bio.net (David Kristofferson)
Newsgroups: bionet.journals.contents
Subject: Re: Survey on the Future of Electronic Information Distribution
Date: 27 Jul 92 21:06:26 GMT
Distribution: usa
Organization: GenBank Online Service

Two additional points - 

(1) NSF, not Don, is the only group empowered to define when and how
Boston Consulting Group or anyone else may use the networks.  Don has
no authority to negotiate conditions for Boston Consulting Group.

(2) bionet.journals.contents is for posting TOCs, not for discussions.


				Sincerely,

				Dave Kristofferson
				GenBank Manager

				kristoff@genbank.bio.net
From: VJIMENEZ@UCRVM2.BITNET ("Victor M. Jimenez")
Newsgroups: bionet.journals.contents
Subject: Agrobacterium tumefaciens information
Date: 24 Jul 92 22:41:37 GMT
Distribution: bionet
Organization: Universidad de Costa Rica


Dear friends:
     I'm looking for a recent article about the subject ~Biology of Agrobacteri
um tumefaciens~ or related.
     1992's references would be so helpful.
                                   Thanking in advance,
                              ^^^^^^^^^^^^^^^^^^^^^^
                               VICTOR M. JIMENEZ G.
                              VJIMENEZ@UCRVM2.BITNET
                              ^^^^^^^^^^^^^^^^^^^^^^
From: D31@EARN.TRANAVM1 (suleyman aydin)
Newsgroups: bionet.journals.contents
Subject: j. mice ?
Date: 30 Jul 92 15:58:01 GMT
Distribution: bionet
Original-To: BIO-JRNL@UK.AC.DARESBURY


 
Dear friends,
 
Is there any journal related to mice(rat) and lab. animals?
 
which can you recommend to publish the observation(s) about morphological
and physiological changes?
 
or
 
if the observation(s) related to morphology then shall I go to morphology if
immunology to the immunological area (e.g.  J. anatomy and J. immunology ?)
 
suleyman AYDIN (student of pharmacology)
d31@tranavm1.bitnet
-=-=- ah, yes, a pharmacology journal is full of papers  of rat&mice -=-=-
-=-=- but what if a "j. mice" exists?  :-))                          -=-=-
From: chai_z@wehi.edu.au
Newsgroups: bionet.molbio.gene-org
Subject: <None>
Date: 23 Jul 92 05:04:31 GMT
Organization: Walter & Eliza Hall Institute

SORRY, THIS IS A TEST
From: zauhar@SHIVA.PSU.EDU (Dr. Randy Zauhar)
Newsgroups: bionet.molbio.bio-matrix
Subject: Renewal
Date: 27 Jul 92 15:28:02 GMT
Distribution: bionet



I believe I am presently on the biomatrix newsgroup, but I never recall
receiving any sort of membership notice (I am relatively new to BIONET).
Could someone explain the "Please Renew!!!" message?

   Randy Zauhar
   Center for Computational Biology 
   Penn State
From: dbd@THEORY.BCHS.UH.EDU (Dan Davison)
Newsgroups: bionet.molbio.bio-matrix
Subject: Please Renew!!!
Date: 27 Jul 92 15:18:45 GMT
Distribution: bionet

Dear Biomatrix members,

at the moment we only have 10 renewals on the biomatrix memberships
that went out in the last newsletter.  It's hard to keep an organization
going with that few people...if you want to discuss the relative merits
of being a member vs. a lurker, this is the forum to do it.  Post notes
to	
	bio-matrix@genbank.bio.net


dan "I'm a member" davison
From: Davison@UH.EDU (Dan Davison)
Newsgroups: bionet.molbio.bio-matrix
Subject: Re: Renewal
Date: 27 Jul 92 15:58:03 GMT
Distribution: bionet

Dr. Randy Zauhar said:
> I believe I am presently on the biomatrix newsgroup, but I never recall
> receiving any sort of membership notice (I am relatively new to BIONET).
> Could someone explain the "Please Renew!!!" message?

The Bio-matrix news group is one of the services of the Biomatrix
Society. The newsgroup is a FREE service.  My note was directed to the
member of the Biomatrix Society, not the Bio-matrix newsgroup.

Membership information for the Biomatrix Society (not the newsgroup)
can be obtained from Ms. Ginger Richardson, grr@sfi.santafe.edu.

dan
-- 
dr. dan davison/dept. of biochemical and biophysical sciences/univ. of
Houston/4800 Calhoun/Houston,TX 77204-5934/davison@uh.edu/DAVISON@UHOU

-----RIP Isaac Asimov 1920-1992     I'll miss him --------------------

Disclaimer: As always, I speak only for myself, and, usually, only to
myself.
From: pkarp@AI.SRI.COM (Peter Karp)
Newsgroups: bionet.molbio.bio-matrix
Subject: electronic publication
Date: 30 Jul 92 17:09:57 GMT
Distribution: bionet

Those of you interested in electronic journals may find the
following paper of interest:

Gaines, B.R., "Social Dynamics of Scholarly Publication," AAAI-92
workshop on communicating scientific and technical knowledge.

To obtain a copy you might contact Gaines at

Knowledge Science Institute
University of Calgary
Calgary, Alberta, Canada T2N 1N4

gaines@cpsc.ucalgary.ca
From: PARSONS_A@uk.co.pcr.snd01
Newsgroups: bionet.molbio.bio-matrix
Subject: Bulletin Boards for Vector Sequences
Date: 27 Jul 92 13:56:05 GMT
Distribution: bionet
Original-To: BIOMATRX <BIOMATRX@UK.AC.DARESBURY>

Hi Mol-Bio-Netters,

I seem to recall some companies that provided BBS access to their vector 
sequencesn (Invitrogen,Promega?).  Could some kind soul refresh my memory as to
which companies provide these services and the modem nmbers to attach to?

Many thanks,

Tony P.

 +----------------------------------------------------------------------------+
 | Dr.Tony Parsons,			VOX   : + 44 304 616871	              |
 | IT Department,			FAX   : + 44 304 616670               |
 | Pfizer Central Research,				 		      |
 | Ramsgate Road,  +----------------------   e-mail   ------------------------+
 | Sandwich,       |JANET      : parsons_a@uk.co.pcr.snd01                    |
 | KENT	           |Internet   : parsons_a@snd01.pcr.co.uk	       	      |
 | CT13 9NJ UK	   |Compuserve : 100064,765    PSImail:234216700127.parsons_a |
 +-----------------+----------------------------------------------------------+
From: kim@m44.unm.edu
Newsgroups: bionet.molbio.methds-reagnts
Subject: Re: SS Phagemid gradients, KI or CsCl?
Date: 23 Jul 92 16:41:32 GMT
Reply-To: kim@m44.unm.edu
Organization: UNM Cancer Center, Albuquerque, NM

In article <1992Jul23.025622.9263@menudo.uh.edu>, bchs1b@Elroy.UH.EDU (Michael Benedik) writes:
>In article <1992Jul21.154049.25431@usenet.ins.cwru.edu>, djt2@po.CWRU.Edu (Dennis J. Templeton) writes:


<Stuff about ss phagemid DNA preps omitted>

Instead of using gradient centrifugation or PEG, there is a method that uses
Glacial Acetic Acid and Sodium Perchlorate.  It is a glass-binding type DNA
purification, like Geneclean.  I have never tried it, but the reference is:

Nucleic Acids Research 15:5507-5516

A modification of this method was posted a while ago as:

1. In a 1.5 ml tube, mix 1 ml cleared phagemid supernatant with 10 microliters
of glacial acetic acid.  Sit r.t. for 5 minutes to precipitate phage.

2.  Spin out the phage pellet.  Drain.

3.  Resuspend in 4.5 M Sodium Perchlorate (I didn't get the volume to use),
made up in TE buffer.  Sit 50 C for 10 minutes.

4.  Add 5 microliters glassmilk from Geneclean or home-made.  Rock on ice 10
minutes.  (So the volume to resuspend should be maybe 100 - 300 microliters, I
would guess).

5.  Spin out the glass.  Drain.  Do NEW wash 3 times.

6.  Thoroughly drain the glass pellet, and elute the ss DNA in 50 microliters
water.


If you try this, post a report on how it works/doesn't work.  I'd like to know.

Daniel Kim
KIM@FLOVAX.LANL.GOV
From: NWHETT@NCSUMVS.BITNET
Newsgroups: bionet.molbio.methds-reagnts
Subject: re: RAPD PCR method
Date: 30 Jul 92 15:44:00 GMT
Distribution: bionet

Phillip Lowrey asked about RAPD as a means of obtaining markers
for genetic mapping studies. Our group (Forest Biotechnology Group
at North Carolina State University) has used RAPD markers extensively
in genetic mapping in pines, which are particularly well suited to
the use of dominant markers because haploid tissue can be obtained
from the megagametophyte in the seeds. We generated a map with 191
markers covering a total of 1687 cM in twelve linkage groups using
60 open-pollinated seed in about two months (which strikes me as
fairly high efficiency). Other experiments in the lab have shown
RAPDs are most useful on species with high levels of genetic variability,
such as populations of forest trees. A student using RAPDs to map in
a horticultural species has had to look through more primers to find
markers segregating in his crosses. RAPDs are definitely easier and
faster to screen for than virtually any other molecular marker, though,
so this is not a devastating criticism. We have found reproducibility
to be good (98%), as long as you're careful in choosing which bands
to score as markers. The thing to remember about RAPD is that what you
see on the gel is a _phenotype_, not a genotype. There is a lot
of variation on the gels, and not all of it is due to genetic
variation between the individuals sampled. Choose markers that
segregate in Mendelian ratios and reproducibility is very good.
Ross Whetten
From: jdboer@SOL.UVIC.CA (Johan deBoer)
Newsgroups: bionet.molbio.methds-reagnts
Subject: Site directed mutagenesis
Date: 23 Jul 92 05:12:33 GMT
Distribution: bionet

Hello,
There is a kit on the market called Transformer for the site directed
mutagenesis of any double stranded plasmid. It uses two mutagenic primers
one to introduce the desired mutation and one to destroy a unique 
restriction site. This way all original plasmid can be destroyed by
restriction digestion.
This looks a very nice method. My question is, has anyone used this
method and does it live up to its promise or is it just another method
like so many others?
I would appreciate any comments from people who have used the kit.
Johan de Boer.
From: horton@molbio.cbs.umn.edu (Robert Horton)
Subject: Re: RAPD PCR sequencing
Organization: University of Minnesota
Distribution: bionet
Date: Fri, 24 Jul 1992 18:21:13 GMT

The following scheme might be worth a try:
	Make a set of new primers identical to your RAPD primers EXCEPT
extend the 3' end by one base: add A to one, C to another, and G to the
third.
	In 75% of randomly chosen cases, the next base past the primer
should be different at the two ends of the PCR product (if its A at one
end, there's only a 25% chance that it will be A at the other end, too,
etc.). Unless the next base past the primer is the same at both ends, one
of the extended RAPD primers should prime uniquely at only one end, so 
you should be able to sequence with it.
	Note that you only have to make three such primers (i.e., any 
product that has a T at only one end by default has one of the other
bases uniquely at the other end.).
	The 25% of products that you couldn't sequence this way you might
have to go ahead and clone, but its better than cloning all of them. 
Alternatively, you could make a set of 15 primers with permutations of two
base additions which would allow you to directly seqeunce all but 1/16th
of randomly chosen products...

Good luck.
-Bob Horton
-- 
Bob Horton            /\ "Crash programs fail because of the theory that
U. of Minnesota, CBS  || with nine women pregnant you get a baby a month" 
1479 Gortner Ave.    /||\   -Werner von Braun.  Disclaimer:"Bob who?"
St. Paul, MN 55108    ^^   horton@molbio.cbs.umn.edu/(612) 624-3790
From: afc@gnv.ifas.ufl.edu (Andrew F. Cockburn)
Newsgroups: bionet.molbio.methds-reagnts
Subject: Re: ethanol precipitation
Date: 17 Jul 92 11:16:09 -0500
Distribution: bionet
Organization: USDA/ARS/MAVERL

In article <9207152209.AA22355@phobos.med.pitt.edu>, bsh@MED.PITT.EDU (Basavareju Shankarappa) writes:
>>>I have observed that using NaCl for pptn of DNA often results in 
>>>precipitation of salt specially after prolonged incubation at 
>>>-20 C.  I learnt this from my experience rather than anything.
   ^^^^^
Flame on.

My answer is simple: you shouldn't be precipitating DNA at -20 C (or
worse yet, at -80 C).  DNA is insoluble in 60% ethanol at 4 C (with 
the proper salt concentration).  It doesn't become "more insoluble"
at lower temperatures, this is impossible.  The idea that nucleic 
acids precipitate faster at low temperatures is a myth.

The process of insoluble DNA aggregating to form precipitates is a 
chemical reaction, and like other chemical reactions occurs more
rapidly at higher temperatures.  Putting it in the freezer SLOWS the
precipitation, it does not speed it up.

BTW, BRL tested this seven or eight years ago and published the results
is Focus.  Overnight precipitation at 4 C was the best.  The most 
critical factor in recovery was how long and hard the centrifuge
spin was.

Flame off.

Andrew Cockburn
USDA/ARS/MAVERL
Disclaimer: Of course, my grad students put their DNA into the freezer
to precipitate...
Newsgroups: bionet.molbio.methds-reagnts
From: djt2@po.CWRU.Edu (Dennis J. Templeton)
Subject: Charms (Was: Tracer dyes in agarose gels)
Reply-To: djt2@po.CWRU.Edu (Dennis J. Templeton)
Organization: Case Western Reserve University, Cleveland, OH (USA)
Date: Thu, 30 Jul 92 15:53:36 GMT


In a previous article, themmen@nl.eur.fgg.endov ("Axel P.N. Themmen") says:
>
> Yes There is such a dye. It is Orange G (Sigma O 1625). We use it instead
> of the bromophenolblue and xylene cyanol in Ficoll based loading dye.
> Works as a charm.
        ^^

Axel probably doesn't have the (?dis)advantage of hearing people say often:
"works *like* a charm", but his version is refreshing and maybe more accurate.

So my question:  Does Orange G function as well as a charm functions, or 
is the role of this dye in electrophoresis to provide charm (and other
quarks too?)

I'm hoping the latter, since we could use a little charm.

dennis
Newsgroups: bionet.molbio.methds-reagnts