HDTenEightyP/NetNews huggingface dataset:
From: danj@welchgate.welch.jhu.edu (Dan Jacobson)
Subject: Welchlab Gopher going offline for a day
Organization: Johns Hopkins Univ. Welch Medical Library
Date: Mon, 21 Dec 1992 14:23:35 GMT

The gopher hole at the Welchlab (merlot.welch.jhu.edu) will be going
off-line today while we move to a new building.  Hopefully it will be
up again tomorrow as we get settled into our new space.  Sorry for any
inconvenience that this may cause, I'll post another note when the gopher
hole is back on-line.

Regards,

Dan Jacobson

danj@welchgate.welch.jhu.edu
From: francis@monod.Biol.McGill.CA (Francis Ouellette)
Newsgroups: bionet.general
Subject: Holiday greetings from CH I central!
Date: 21 Dec 92 16:47:55 GMT
Organization: McGill University


Here is a sequence for the holiday season:

       1  atggagcgac gttattgtca ccgaatttcc acaatggctt cagcaaacga 
      51  tgcgcacgca cccccttata acgagtggta cgaggcaaga 

it was sent to me From Irmi at MIPS in Munich
(becker@vax1.mips.mpg.dbp.de) but I am sure she would not mind me passing
it along to the net ...

happy holidays to all,

francis

--
| B.F. Francis Ouellette  
| manager, yeast chromosome I project
| dept of biology, McGill university, Montreal, Qc, Canada
| francis@monod.biol.mcgill.ca
--
| B.F. Francis Ouellette  
| manager, yeast chromosome I project
| dept of biology, McGill university, Montreal, Qc, Canada
| francis@monod.biol.mcgill.ca
From: choy@skorpio.usask.ca (I am a terminator.)
Newsgroups: bionet.general
Subject: Role of radiation?
Date: 28 Dec 1992 23:31:28 GMT
Organization: University of Saskatchewan, Saskatoon, Canada
Distribution: world
NNTP-Posting-Host: skorpio.usask.ca

What role does natural radioactive decay and other particle physics
play in the function of organisms?

-- 

Henry Choy
choy@cs.usask.ca

"The Log Song", from Ren & Stimpy
 
   "What rolls down stairs alone or in pairs
    Rolls over your neighbor's dog?
    What's great for a snack and fits on your back?
    It's Log, Log, Log!
 
    It's Log, Log, it's big, it's heavy, it's wood.
    It's Log, Log, it's better than bad, it's good!
    Everyone wants a log! You're gonna love it, Log!
    Come on and get your log! Everyone needs a Log!"


"Math is tough!"

      -- Barbie
Xref: sparky bionet.general:2004 bionet.software:2317
From: davison@menudo.uh.edu (Dan Davison)
Newsgroups: bionet.general,bionet.software
Subject: New Joural: Computational Biology
Date: 22 Dec 1992 21:57:05 GMT
Organization: University of Houston
Distribution: bionet
NNTP-Posting-Host: menudo.uh.edu


Feel free to contact me or D. Kingsbury about this announcement.

dan davison
----------------------------------------------------------------------------

Announcing an important new quarterly peer-review journal.

March 1993

COMPUTATIONAL BIOLOGY

The Journal of Computational Molecular Cell Biology

Editors

Daniel B. Davison, Ph.D.   David T. Kingsbury, Ph.D. Thomas Marr, Ph.D.
University of Houston	   Johns Hopkins University  Cold Springs Harbor Labs
                           School of Medicine

Goals: First, to provide a forum for communication of scientific and 
technical issues  associated with the analysis, management, and 
visualization of cellular information at the molecular level.  
COMPUTATIONAL BIOLOGY will accept papers on: algorithms, 
genomics; mathematical modeling and simulation of biological 
processes; new methods for sequence analysis, including, for example, 
parallel methods; design and implementation of biological databases; 
biological expert system design and use; reasoning by analogy; 
hypothesis formation and testing by machine; and, information 
theory.

Second, is the communication of significant biological problems 
to investigators traditionally outside of biology, but otherwise 
in appropriate areas of science and technology.  This will be accomplished 
by soliciting mini-reviews in diverse areas, and by providing a forum 
for the informal exchange of theories and experimental approaches.

The growth of molecular cell biology has created large amounts of 
complex data, and challenges to data handling, data analysis, and 
interpretation.  The mounting volume and richness of data require 
quantitative and multidisciplinary approaches for analysis and 
interpretation.

For submission of manuscripts send three copies to: David T. Kingsbury, 
The Welch Laboratory, The Johns Hopkins University School of 
Medicine, 1830 East Monument, 3rd Floor, Baltimore, MD 21205-2100.  
Phone: (410) 995-9705. E-mail: dkingsbu@library.welch.jhu.edu.

Subscription rate:  Volume 1 quarterly 1993.
Publisher: Mary Ann Leibert, Inc.

--
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: kristoff@NET.BIO.NET (Dave Kristofferson)
Newsgroups: bionet.general
Subject: Re: THANKS!!!
Date: 24 Dec 92 18:05:41 GMT
Distribution: bionet


Thanks, Sam.  I should also explicitly extend these thanks to Alan
Bleasby, Steve Marshall, Paul Griffiths, and David Hines at Daresbury
who, despite being less vocal than Kenton and myself on the net, are
vitally important in serving their half of the BIOSCI community.

Happy Holidays everyone!

				Sincerely,

				Dave Kristofferson
				BIOSCI/bionet Manager

				kristoff@net.bio.net
Newsgroups: bionet.general
From: nsmca@acad3.alaska.edu
Subject: Genetic Specific Organisms/Builders.
Organization: University of Alaska Fairbanks
Date: Tue, 29 Dec 1992 12:28:28 GMT

I wonder how hard it would be to design specific organisms to get, process,
design builingd and other products from the elements up..

Similiar to the way reefs are made, but faster and more specific. More specific 
products that is.. Such as the build a house, or a artificial heart (?)..

Any ideas or am I posting on the wrong discussion group?

I know this is near to the ideas of NANO tech, but what I suggest is using
biological organisms to build natural products..

(c) 1989 Michael Adams alias Ghost Wheel/Morgoth NSMCA@acad3.alaska.edu
From: kristoff@NET.BIO.NET (Dave Kristofferson)
Newsgroups: bionet.general
Subject: Re: Request: Recruiting/Luring biologists to the Nets
Date: 23 Dec 92 01:04:30 GMT
Distribution: bionet


> 1) I'm astonished and thrilled by the response - over 30 people
> responded, with nicely detailed examples.  This has really been
> an eye-opener; network useage is far more robust than I would have
> ever guessed.  

Everyone always seems to be astonished 8-).  The bottom line is that 

			 ***BIOSCI works!!***

Happy Holidays everyone!!

Dave Kristofferson

Xref: sparky bionet.general:2022 bionet.software:2337
From: davison@menudo.uh.edu (Dan Davison)
Newsgroups: bionet.general,bionet.software
Subject: Re: New Joural: Computational Biology
Date: 30 Dec 1992 20:32:43 GMT
Organization: University of Houston
NNTP-Posting-Host: menudo.uh.edu
In-reply-to: Robert.H.Gross@dartmouth.edu's message of 23 Dec 92 19:49:59 GMT

In article <1992Dec23.194959.17413@dartvax.dartmouth.edu> Robert.H.Gross@dartmouth.edu (Robert H. Gross) writes:

   Could you please provide more info on how to subscribe to this new
   journal. How much is a subscription and who do we contact to actually
   subscribe.

I did not think I could provide the subscription information due to
NSFNet commercial rules.  For information, contact:

Mary Ann Leibert, Inc.
1651 Third Avenue
New York, NY 10128
212-289-2300
212-289-4697

If Dave K. says it's OK I will post the subscription info.

dan davison



--
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: GC.GGG@forsythe.stanford.edu (Gwyn Gordon)
Newsgroups: bionet.general
Subject: FUNDING ANNOUNCEMENT
Date: 29 Dec 1992 14:47:34 -0800
Organization: Stanford University
NNTP-Posting-Host: morrow.stanford.edu


***FUNDING OPPORTUNITY***

Research Expeditions International is accepting applications for
funding for research projects scheduled for 1994.

Research Expeditions International specializes in Participatory
Research, in which well-educated lay people provide funding and
volunteer as the on-site work force. Studies best suited for
Participatory Research involve data collection or unskilled labor
which is easily taught to one or several groups of adults.
Preference will be given to studies in the following areas: animal
behavior; archaeological excavation; and tourist impact on culture,
economy and ecology. Studies in other fields will certainly be
considered if appropriate.

Applications for the 1994 season are due February 1, 1993.

For informational materials and application, contact:

Gwyn Gordon
gwyn.gordon@forsythe.stanford.edu
415-494-2515
806 Los Robles Avenue
Palo Alto, CA 94306
From: pathology@mscf.med.upenn.edu
Newsgroups: bionet.xtallography
Subject: "Grid Screen" Crystallization Kit
Date: 22 Dec 92 16:05:17 GMT
Organization: Univ of Penn - Med School Computer Facility

Can anyone comment on the usefulness of the crystallization reagent kit called 
"Grid Screen", which is sold by Hampton Research?  I am new to the field of
macromolecular crystallization and am trying to get started with a protein of
about 200 amino acids.  The Hampton Research kit seems like a smooth way to
begin testing a wide variety of crystallization conditions. Any comments
from present or previous users? 

Gregg Wells
Department of Pathology
University of Pennsylvania
Philadelphia, PA  19104
e-mail:  pathology@a1.mscf.upenn.edu
From: o6y@vax5.cit.cornell.edu
Newsgroups: bionet.xtallography
Subject: stereo in "O"
Date: 30 Dec 92 13:57:38 EST
Distribution: bionet
Organization: Cornell University




	I am using Jones' macromelecular modelling program O on an SGI Indigo 
RU4000 with the CrystalEyes stereo viewing system.  When I go into stereo 
mode (by pressing F1) the displayed molecules and density look flat, as if 
the stereo matrix is not quite right.
	Has anyone else had this experience, and if so were you able to 
fix it so that the molecules look three-dimensional?

			Kristin Fox
			o6y@vax5.cit.cornell.edu
From: ksugiyam@gan.ncc.go.jp (Kenji Sugiyama)
Newsgroups: bionet.xtallography
Subject: (none)
Date: 25 Dec 92 05:27:01 GMT
Distribution: bionet

help
D
Newsgroups: bionet.xtallography
From: joe@GENETICS.WASHINGTON.EDU (Joe Felsenstein)
Newsgroups: bionet.population-bio
Subject: Re: BIOSYS and DIPBIG(SMALL) help...
Date: 21 Dec 92 23:33:32 GMT
Distribution: bionet


Thor Brickman wrote --

> Help!
> 
>   I have a grad student who needs to use the BIOSYS and DIPBIG programs
> for her project analysis, but the executables she obtained did not have
> any documentation.  She assures me these are in the public domain and
> are widely used.  That being the case, can anyone send/tell me how to
> get said documentation?  She is, of course, under a time constraint or I
> wouldn't waste bandwidth with this. Her executables are for a PC.

Her assurance for BIOSYS may be wrong.  I am not aware that it is in the
public domain.  It is sold by David Swofford (send $25 to the Center
for Biodiversity, Illinois Natural History Survey, 607 East Peabody Drive,
Champaign, Illinois  61820, U.S.A.).  Swofford's other offering, PAUP, is
definitely NOT in the public domain and not freely copyable.  I do not know
for sure for BIOSYS but she might check with the people in Illinois (Swofford
has moved to the Smithsonian Institution but distribution of his programs
is from Illinois).

-----
Joe Felsenstein, Dept. of Genetics, Univ. of Washington, Seattle, WA 98195
 Internet:         joe@genetics.washington.edu     (IP No. 128.95.12.41)
 Bitnet/EARN:      felsenst@uwavm
Newsgroups: bionet.population-bio
From: ritland@gpu.utcs.utoronto.ca (K. Ritland)
Subject: Programs for estimating outcrossing
Organization: UTCS Public Access
Distribution: bionet.population-bio,bionet.plants,bionet.software
Date: Mon, 21 Dec 1992 16:52:17 GMT

Three programs for estimating outcrossing with genetic markers are
now available from Don Gilbert's ftp.bio.indiana.edu archive. They 
are compiled for PCs and are archived in biology/ibmpc/ml.ZIP (you
will need to unzip these files).  All programs assume data is collected
as progeny arrays, and all compute both single- and multilocus estimates
of outcrossing, do family estimates, use the bootstrap, etc. (further
details are in the documentation provided).  The three programs are:
  1.  mlt - program for diploids using co-dominant markers
  2.  mldt - program for diploids using dominant markers such as RAPDs
             (co-dominant markers also allowed)
  3.  mltet - program for autotetraploids (co-dominant markers only)

Kermit Ritland
Dept. of Botany
University of Toronto
ritland@utcs.utoronto.ca
Newsgroups: bionet.population-bio
From: thor@teetot.acusd.edu (Thor Brickman)
Subject: BIOSYS and DIPBIG(SMALL) help...
Organization: usd
Distribution: usa
Date: Mon, 21 Dec 92 22:57:07 GMT

Help!

  I have a grad student who needs to use the BIOSYS and DIPBIG programs
for her project analysis, but the executables she obtained did not have
any documentation.  She assures me these are in the public domain and
are widely used.  That being the case, can anyone send/tell me how to
get said documentation?  She is, of course, under a time constraint or I
wouldn't waste bandwidth with this. Her executables are for a PC.

Thanks in advance,
Thor@eetot.acusd.edu
--
From: GC.GGG@forsythe.stanford.edu (Gwyn Gordon)
Newsgroups: bionet.population-bio
Subject: FUNDING ANNOUNCEMENT
Date: 29 Dec 1992 14:48:08 -0800
Organization: Stanford University
NNTP-Posting-Host: morrow.stanford.edu


***FUNDING OPPORTUNITY***

Research Expeditions International is accepting applications for
funding for research projects scheduled for 1994.

Research Expeditions International specializes in Participatory
Research, in which well-educated lay people provide funding and
volunteer as the on-site work force. Studies best suited for
Participatory Research involve data collection or unskilled labor
which is easily taught to one or several groups of adults.
Preference will be given to studies in the following areas: animal
behavior; archaeological excavation; and tourist impact on culture,
economy and ecology. Studies in other fields will certainly be
considered if appropriate.

Applications for the 1994 season are due February 1, 1993.

For informational materials and application, contact:

Gwyn Gordon
gwyn.gordon@forsythe.stanford.edu
415-494-2515
806 Los Robles Avenue
Palo Alto, CA 94306
From: fgarbrec@POST.ITS.MCW.EDU (GARBRECHT)
Newsgroups: bionet.immunology
Subject: Re: ER - resident proteins
Date: 21 Dec 92 14:40:33 GMT
Distribution: bionet

On Mon, 21 Dec 1992 Mark.OLeary@newcastle.ac.uk wrote:

> Date: Mon, 21 Dec 92 10:39:51 GMT
> From:Mark.OLeary@newcastle.ac.uk
> To: GARBRECHT <fgarbrec@post.its.mcw.edu>
> Cc: immunology@net.bio.net
> Subject: Re: ER - resident proteins
> 
> Hi,
>    Thanks for replying to my post. My problem is (and I must phrase this delic
> ately, as I am under a non-disclosure agreement...) that I have an antibody th
> at recognises a common feature of several ER-resident proteins. I wish to conf
> irm its continued activity (I re-generated it from an old stock of the cell li
> ne in storage), and I attempted to do so by lysing some cells, hoping to see
> numerous bands on a western of the lysate when probed using this antibody and
> an alkaline phosphatase-linked secondary ab. This failed. So, I need to know a
>  way to enhance, ER-resident proteins in the mixture I apply to the gel...
> 
> My latest plan is to isolate ER-derived microsomes by sucrose gradient centrif
> ugation, and hope that they retain a good level of their resident proteins.
> 
> I also have another cell line in culture that may be 'leaking' ER-proteins, an
> d I'd like to use the same antibody to check the culture s/n for their presenc
> e, but a simple blot of the s/n doesnt show anything either: I shall have to i
> nvent some concentration protocol that also removes the fetal calf serum compo
> nents as well....
> 
> 
> It seems quite a hard pair of problems to me (I'm just starting my PhD) and th
> ats why I turned to the net for help...
> 
> I hope you can give me a lead or two... 8)

As far as concentrating your ER proteins goes, your plan sounds reasonable
to me.  In terms of seeing if your antibody has activity, well, thats another
problem.  Several things come to mind;  first, if the hybridoma is old but
viable, it probably would benefit from re-cloning as hybridomas tend to spit
out chromosomes along the way. (Obviously you need a screening method to
do the recloning.)  Also, check the hybridoma for mycoplasma contamination;
this is a problem in lots of labs, and can lead to poor antibody secretion
in otherwise viable cultures.  It might be helpful to talk to the person who
originally did the fusion for details on their original screening protocol.
The best way to check your detection system for problems would be to run
a control antibody that you know has activity (of the same subclass) against
some other protein known to be expressed by your cell line (or tissue); you
can troubleshoot the assay from there.  Make sure all of your antibody
reagents etc are reasonably fresh and have been stored appropriately.
Good luck,
Fred Garbrecht
Medical College of Wisconsin
fgarbrec@post.its.mcw.edu
Newsgroups: bionet.immunology
Subject: ####### TEST ########
From: louisd@dec5.ulb.ac.be (Louis Droogmans)
Date: 22 Dec 92 17:48:18 GMT
Distribution: world
Organization: Free University Brussels  - Belgium -  Department of Molecular Biology
Keywords: PS

Bonjour,

Je suis francophone.
Ceci est juste un test
From: Ed.Van.Hezik@f0.n0.z0.wlink.nl (Ed Van.Hezik)
Newsgroups: bionet.immunology
Subject: cytokines in mesothelioma
Date: 24 Dec 92 00:53:02 GMT

Maybe someone is involved in diagnosis or treatment of malignant mesothelioma
Recent papers show some interesting features in cytokine actvities in this
disease. Anyone who's interested please contact me.Thanx Ed van Hezik MD
From: Mark.OLeary@newcastle.ac.uk
Newsgroups: bionet.immunology
Subject: Re: ER - resident proteins
Date: 21 Dec 92 10:39:51 GMT
Distribution: bionet

Hi,
   Thanks for replying to my post. My problem is (and I must phrase this delic
ately, as I am under a non-disclosure agreement...) that I have an antibody th
at recognises a common feature of several ER-resident proteins. I wish to conf
irm its continued activity (I re-generated it from an old stock of the cell li
ne in storage), and I attempted to do so by lysing some cells, hoping to see
numerous bands on a western of the lysate when probed using this antibody and
an alkaline phosphatase-linked secondary ab. This failed. So, I need to know a
 way to enhance, ER-resident proteins in the mixture I apply to the gel...

My latest plan is to isolate ER-derived microsomes by sucrose gradient centrif
ugation, and hope that they retain a good level of their resident proteins.

I also have another cell line in culture that may be 'leaking' ER-proteins, an
d I'd like to use the same antibody to check the culture s/n for their presenc
e, but a simple blot of the s/n doesnt show anything either: I shall have to i
nvent some concentration protocol that also removes the fetal calf serum compo
nents as well....


It seems quite a hard pair of problems to me (I'm just starting my PhD) and th
ats why I turned to the net for help...

I hope you can give me a lead or two... 8)
From: kristoff@NET.BIO.NET (David Kristofferson)
Newsgroups: bionet.announce
Subject: BIOSCI Newsgroups - Changes
Date: 1 Jan 93 09:00:01 GMT
Distribution: bionet


			  HAPPY NEW YEAR!!!

From now on, two BIOSCI FAQs (Frequently Asked Questions compilations)
will follow the info sheet postings on the first of each month in this
newsgroup.  The BIOSCI info sheets have been revised to reflect this
and also to list the prototype newsgroups at net.bio.net.

A short reminder notice about the FAQ sheets will be sent to each
BIOSCI/bionet newsgroup once each month.  The message will be mailed
to one group each day from the 1st to the 28th (on a few days of each
month the reminder will be posted to two newsgroups).  Those of you
who read many of the newsgroups by e-mail will receive a copy of this
reminder message from each newsgroup that you subscribe to, but never
more than two copies on any particular day.  Our apologies in the
advance for the redundancy, but this is necessary to get the word out
to all of our readers.  Simply delete the message once you are
familiar with its contents; its subject line will be
	     "BIOSCI/bionet Frequently Asked Questions."


Two new newsgroups were brought on-line during the month of December.

----------------------------------------------------------------------
USENET Name:            bionet.virology

Pending E-mail addresses:	virology@daresbury.ac.uk
				virology@net.bio.net

One-line description:   Discussions about research in virology

----------------------------------------------------------------------
USENET Name: bionetjournals.note

Pending  E-mail addresses:	jrnlnote@daresbury.ac.uk
                   		jrnlnote@net.bio.net

One line description:

        Practical advice on dealing with professional journals in biology
----------------------------------------------------------------------

David Kristofferson
BIOSCI/bionet Manager
From: kristoff@net.bio.net (David Kristofferson)
Newsgroups: bionet.announce
Subject: 1991 BIOSCI readership distribution
Date: 31 Dec 92 23:00:03 GMT
Organization: BIOSCI International Newsgroups for Biology


Geographical Distribution of Fall 1991 BIOSCI Survey Respondents 
----------------------------------------------------------------

Total Responses Received (after removing duplicates from same address) = 597

Estimated response rate ~65%.  This was not determined directly but is
the average of the 66% response rate in 1990 and 64% response rate in
1992.

Estimated BIONEWS/bionet.general readership = approx. 920.  This is
about a 15% increase from June 1990 (~800) to October 1991 (~920).


Breakdown by Country
--------------------

No.	Country		  %
---	-------		 ---
332	USA		55.6%	(non-U.S. is 44.4%)
75	UK		12.5
36	Canada		 6.0
29	Germany		 4.9
15	France		 2.5
12	Australia	 2.0
9	Finland		 1.5
9	Japan		 1.5
8	Belgium		 1.3
8	Netherlands	 1.3
7	Switzerland	 1.2
6	Austria		 1.0
6	New Zealand	 1.0
5	Brazil		 0.8
5	Israel		 0.8
5	Norway		 0.8
5	Spain		 0.8
3	Sweden		 0.5
3	Taiwan		 0.5
3	Turkey		 0.5
2	Denmark		 0.3
2	Ireland		 0.3
2	South Africa	 0.3
2	Soviet Union	 0.3
1	Columbia	 0.2
1	Czechoslovakia	 0.2
1	Egypt		 0.2
1	Greece		 0.2
1	Hong Kong	 0.2
1	India		 0.2
1	Italy		 0.2
1	Uruguay		 0.2