HDTenEightyP/NetNews huggingface dataset:
From: harper@convex.csc.FI (Rob Harper)
Subject: Re: BIOSCI/bionet Frequently Asked Questions
Organization: Finnish Academic and Research Network Project - FUNET
Distribution: bionet
Date: Mon, 4 Jan 93 10:30:49 GMT

You can now read  BIOSCI FAQ I and BIOSCI FAQ II on the Finnish EMBnet gopher
Both files have been slightly modified so that you can read individual
questions and answers rather than having to scroll through the whole text
to get to what you want. You will find them in the FAQ FILES directory.

%%%%%%%%%%%%%%%%%%%%%%%%%%%% CLIP %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

                          The BIOSCI FAQ II

      1.  BIOSCI FAQ II (Contents).
      2.  What is BIOSCI and bionet?.
      3.  What newsgroups are available on BIOSCI/bionet?.
 -->  4.  What is USENET?.
      5.  How can I get news software at my site?.
      6.  Requesting or canceling e-mail subscriptions to BIOSCI newsgroups?.
      7.  Why are BIOSCI e-mail subscription requests not processed by machi...      8.  Why are there two BIOSCI sites?.
      9.  How does one know to which newsgroup a message was posted?.
      10. What is the "BIOSCI-REQUEST" address?.
      11. How does one post a message?.
      12. How can I get a list of newsgroups or my subscriptions?.
      13. Why have I stopped getting messages?.
      14. I posted a message and got back an error message from a daemon!!.
      15. Where (and how many times) should I post my messages?.
      16. How do I find back issues of BIOSCI postings?.
      17. Is there a summary of METHODS-AND-REAGENTS postings?.
      18. How does one start a new BIOSCI newsgroup/mailing list?.
--
 ~ Rob Harper                    ~ E-mail:          harper@convex.csc.fi    
 ~ Finnish State Computer Centre ~ Molbio/software: harper@nic.funet.fi
 ~ P.O. Box 40                   ~ Telephone:       +358 0 457 2076
 ~ SF-02101 Espoo Finland        ~ Fax:             +358 0 457 2302
Xref: sparky bionet.general:2053 bionet.molbio.embldatabank:67
From: blitz@embl-heidelberg.de
Newsgroups: bionet.general,bionet.molbio.embldatabank
Subject: MPsrch:  announcing a new service.
Date: 12 Jan 93 16:50:48 GMT
Organization: EMBL, European Molecular Biology Laboratory


                             MPsrch
                             ------

       (C) Biocomputing Research Unit, University of Edinburgh, 1992

     Smith and Waterman Protein Sequence Database searches on a MasPar  


  MPsrch (by Shane Sturrock and John Collins), the fastest implementation
  of the exhaustive Best Local Similarity algorithm for Sequence Database
  searching, is now available through BLITZ, a new e-mail service from the
  EMBL.  MPsrch runs on the 4096-processor MasPar MP-1 machine at the EMBL,
  using the Smith & Waterman algorithm, performing up to 140,000,000 cell
  updates per second.

    Typical search times on the MasPar against Swiss-Prot 23 are:

  5037 residues  RYNR_RABIT  340 seconds  (134,000,000 cell updates/second)
   377   "       ACTS_HUMAN   40 seconds  ( 85,000,000 cell updates/second)


  To get current help information, e-mail the word HELP in a mail message to
  the Internet address:

	Blitz@EMBL-Heidelberg.DE


  To run a search, using default weight matrix and INDEL cost settings, try
  sending an e-mail message with the word SEQ on the first line and the 
  sequence in free format on succeeding lines.   The end of the sequence is 
  determined either by the end of your mail message, if you do not use an 
  automatic mail signature, or by inserting a new line beginning with the 
  word END. 
  For example:

SEQ
	STKKKPLTQE QLEDARRLKA IYEKKKNELG LSQESVADKM GMGQSGVGAL
	FNGINALNAY NAALLAKILK VSVEEFSPSI AREIYEMYEA VSMQPSLRSE
	YEYPVFSHVQ AGMFSPELRT FTKGDAERWV STTKKASDSA FWLEVEGNSM
	TAPTGSKPSF PDGMLILVDP EQAVEPGDFC IARLGGDEFT FKKLIRDSGQ
	VFLQPLNPQY PMIPCNESCS VVGKVIASQW PEETFG
END


  The Help information explains how you can specify a PAM matrix between 1
  and 500 PAM's, an INDEL cost and the number of alignments to be returned
  in the output.

  The sensitivity of MPsrch depends on the choice of parameters, and
  searches with default parameter settings alone may not always find the
  most interesting results.  Even with the same query sequence, one set of
  parameters may find strong alignments best, while a different setting may
  show up weaker relationships better.  Because the search is so fast, we would
  encourage you to experiment with your own choice of parameter settings.

  In future developments, we hope to provide searches of other databases,
  including a nucleotide search facility.  


  John Collins & Shane Sturrock,                      Des Higgins (Data Library)
  Biocomputing Research Unit,                       & Roy Omond (Computer Group)
  University of Edinburgh,                            EMBL,
  Scotland,                                           Heidelberg,
  U.K.                                                Germany.
From: EZIZOO02@TREARN.BITNET (Petek Settar)
Newsgroups: bionet.general
Subject: (none)
Date: 13 Jan 93 00:35:32 GMT
Distribution: bionet


Dear researchers,

I study on Tibial Dyscondroplasia (TD) in broilers.
I want to contact someone who study TD.
Please let me know if you are interesting.
                                Thanks,
                              Petek SETTAR


E-mail address:
ezizoo02&TREARN

Address:
EGE UNIV. AGRICULTURAL FAC.
BIOMETRY_GENETIC
BORNOVA (35100)-IZMIR
TURKEY

Newsgroups: bionet.general
From: mazzucch@ghost.dsi.unimi.it (massimo mazzucchi)
Subject: info 2
Organization: Computer Science Dep. - Milan University
Date: Tue, 12 Jan 1993 12:29:57 GMT


HI

I am Max from Milan.

I have already write in thin newsgroup but now i explain exactly what i
want.

My friend Olga is looking for

STUDIES AND INFORMATION ON VEGETATION AND FAUNA INDICATORS AND INDEXES

IN ENVIRONMENTAL IMPACT ASSESSMENT.


Thaks for your help and if you want write 

to e-mail to


-------------------------------------------------------------------------------
!  Massimo Mazzucchi                        E-mail:                           !
!  University of State                       mazzucch@ghost.dsi.unimi.it      !
!  Computer Science Departement             internet:                         ! 
!  Via Comelico, 41 -  20133 MILAN ITALY     149.132.2.1                      !
-------------------------------------------------------------------------------

and to letter or telephone

OLGA CHITOTTI

VIA LOMELLINA, 56

20133 - MILANO - ITALY

Telephone 01139-2-7386495

FAx       01139-2-90634143
From: omond@embl-heidelberg.de
Newsgroups: bionet.general
Subject: "Thick fog on Channel; Continent cut off"
Date: 12 Jan 93 16:43:48 +0100
Organization: EMBL, European Molecular Biology Laboratory

*sigh* ... just to warn everyone that e-mail to UK sites serviced
by the infamous nsfnet-relay.ac.uk is bouncing (again) with the stupid
error message 

Addressee: xxxx@institute-of-cancer-research.ac.uk (for example)
Remote system's reason for rejecting:

(NAUTH) Bad authorization for address "xxxx@institute-of-cancer-research.ac.uk"
Sender 'netserv@embl-heidelberg.de' not authorized.


When are these guys finally going to fix this problem ?  It's happened
a few times before (admittedly not for a while);  my experience trying
to talk to the people in charge of nsfnet-relay.ac.uk have been VERY
negative.  They don't appear to take e-mail very seriously;

"what ?  we dropped e-mail into the bit bucket ?  Ah, well, let's have
another cup of tea and then go home ..."  (not quite a direct quotation,
but you get the gist)

*sigh* again ...

Roy Omond
System Manager/PostMaster etc. etc.
European Molecular Biology Laboratory
Heidelberg, Germany.
From: cliff@WATSON.IBM.COM ("Cliff Pickover ", 914 945-3630)
Newsgroups: bionet.general
Subject: Quick species question
Date: 6 Jan 93 18:54:46 GMT
Distribution: bionet

Can anyone give me a rough estimate as to the number of species that
are being lost every year as a result of human encroachment,
pollution, etc?

If you respond, please send a note to cliff@watson.ibm.com as
I sometimes have difficulty reading the forum.

Thanks, Cliff
From: NEWEB2@VAX2.CONCORDIA.CA
Newsgroups: bionet.general
Subject: publicathion ethics
Date: 4 Jan 93 20:08:00 GMT
Distribution: bionet

I agree that the head of the laboratory always has the final say. However
there are many times when students and advisors cannot reach an agree-
ment and in our department, they are helped a great deal by the official
committee which is set up for every graduate student. We have 2 faculty members
   i
in addition to the supervisor  in charge of every graduate student. This committ
   ee doesn't do much while times are good
but it meets and discusses when there are difficulties. It seems to me
that the problems described here would be relatively easy to settle if
outsiders were in on the discussion. The supervisor has a lot at stake,
if he/she ever wants another graduate student.
Elaine Newman
Biology Dept. Concordia University.
From: german@ucbeh.san.uc.edu
Newsgroups: bionet.general
Subject: International Congress of Vertebrate Morphology
Date: 4 Jan 93 20:39:00 GMT
Organization: Univ. of Cincinnati

International Congress of Vertebrate Morphology 
 
     The 4th International Congress of Vertebrate Morphology is
planned for July 31 - Aug 4, 1994 at the University of Chicago. 
This will be the first ICVM held in North America.  In addition
to contributed oral and poster papers, there will be plenary
speakers (Sharon Emerson, Brian Hall, J-P Gasc, Lou Guillette, R.
Holland), workshops (amphioxus, teaching comparative anatomy, and
3-D reconstruction) and symposia.  The symposia include
functional design of musculoskeletal systems (organized by W.A.
Weijs and A. Biewener), the evolution of neural systems
(organized by K. Nishikawa and G. Northcutt), segmentation in
vertebrates (Krumlauf and  Russell), genetics and morphology
(Cheverud and Atchley), adaptations of marine amniotes
(Pfeiffer), and amphibian-amniote transition (Sumida and Martin). 

     We are also establishing the ICVM as a formal organization
for membership and ongoing activities. 
 
     For information on the Chicago meeting and membership in the
ICVM (a bargin at $5), please contact: 
 
Sue Herring 
Chair, ICVM Organizing Committee 
Dept. of Orthodontics, SM-46 
University of Washington 
Seattle, WA  98195 
 
HERRING@U.WASHINGTON.EDU 
Phone: (206) 543-3203 
Fax:  (206) 685-8163
From: pathology@a1.mscf.upenn.edu (PATHOLOGY & LAB. MEDICINE)
Newsgroups: bionet.xtallography
Subject: Re: Grid Screen crystallization kit
Date: 11 Jan 1993 11:33:07 -0600
Organization: UTexas Mail-to-News Gateway
NNTP-Posting-Host: cs.utexas.edu



Here is another response to my inquiry about the Grid Screen kit.

Gregg Wells
Department of Pathology
University of Pennsylvania
Philadelphia, PA
email:  pathology@a1.mscf.upenn.edu

__________________________

Re: Grid Screen kits from Hampton Research

I have tried the equivalent of the "quick screen" kit sold by Hampton Research.
We had the reference to the method before the company started marketing the
kit so we just made up all of our solutions and set up 50 conditions
as outlined.  One protein yielded beautiful crystal that diffract to 2A, the
other has not yet crystallized.  My coworkers have also had success with
this method so I would highly recommend it as a quick way to see if the protein 
crystallizes.  A post doc in our lab also set up a simple neural net based
program that will take the results of the screen and predict what you should
try next (outlined in the paper by Jancarik and Kim).  No one has made
much use of this.  We just did the guessing by hand and it worked.  Give it
a try.

Evelyn Jabri
Cornell University
AIW@VAX5.CIT.CORNELL.EDU
From: katz@a.chem.upenn.edu (Darin Scott Katz)
Newsgroups: bionet.xtallography
Subject: P.E. Stein's current address
Date: 12 Jan 93 15:38:13 GMT
Distribution: bionet.xtallography
Organization: University of Pennsylvania

Thank you-

Darin Katz
Univ. of Pennsylvania
From: katz@a.chem.upenn.edu (Darin Scott Katz)
Newsgroups: bionet.xtallography
Subject: Re: P.E. Stein's current address
Date: 12 Jan 93 15:41:25 GMT
Distribution: bionet.xtallography
Organization: University of Pennsylvania




My mailer messed up.  Let's try this again.  I'm looking for Penelope
Stein's (solved ovalbumin structure) current address or Martha Teeter's
directory of crystallographers.  Could anyone with this information please
forward it to me.

Thanks-

Darin Katz
University of Pennsylvania
From: pathology@a1.mscf.upenn.edu (Gregg Wells)
Newsgroups: bionet.xtallography
Subject: Re: "Grid Screen" crystallization kit
Date: 8 Jan 93 19:14:18 GMT
Organization: University of Pennsylvania
X-UserAgent: Nuntius v1.1.1d16
X-XXMessage-ID: <A7733CCB3B011278@path1j.med.upenn.edu>
X-XXDate: Fri, 8 Jan 93 14:14:35 GMT

Below are the responses that I received to my inquiry about the
usefulness of "Grid Screen" crystallization kits from Hampton Research. 
Thanks to everyone who responded.   

Gregg Wells
Department of Pathology
University of Pennsylvania
Philadelphia, PA
USA
email:  pathology@a1.mscf.upenn.edu
____________________________________________________


Subject: Crystqallization screens
The Hampton Research crystallization screens are very good!  If you are
starting your search for initial crystallization conditions, I recommend
the Crystal Screen kit.  I've had terrific results with it!  It contains
50 different combinations of salts, alcohols, PEGs, etc---& is one of the
best screens around.  I have not used the AS or PEG Grid Screens as much
(they haven't been on the market very long), but did use them at the Cold
Spring Harbor Lab. Macromolecular Crystallography course this Oct. with
good  results.  So I would also recommend them too.  Bob Cudney at
Hampton Res. is extremely helpful----so if have any questions, call him. 
Or if I can help--

e mail me at      amh12478@usav01.glaxo.com

GOOD LUCK!!

Annie Hassell
Glaxo Research Institute
RTP, NC



 


Subject: Xtal Screen Kits
Regarding your questions about the Hampton xtal screening kits: I'm a
cloner in a structure function lab, but I can tell you (a) our
xtallographers us'em and (b) they love them - great time savers. The vast
majority of your boss's expenses are probably salary and benefits, and
these kits apparently save enormous amounts of time. Big productivity
improvement. That's about the limit of my knowledge. For more info,
contact one of our xtal people by email.
Try batalia@utbc01.cm.utexas.edu - he'll be here over the holidays.

Regards,
Mike
READY@UTBC01.CM.UTEXAS.EDU |
Clayton Foundation Biochemical Institute    

   
   
Subject: RE: "Grid Screen" Crystallization Kit
not cheap but it does work.  good luck.  

epr@leland.Stanford.EDU



Subject: Grid screen
This is about your query on bionet.xtallography about the grid screen
from  Hampton. It is my personal experience that it is extremely helpful.
Since it is very representative of the conditions under which the
proteins have bee crystallized so far, the probability of hitting
conditions close to optimum for a new protein arisgood. So when working
on a new protein I would definitely use the grid screen to begin with.
However, I would also set up plates with ammonium sulfate, PEG (400,
3350, 8000).  By the way, I am a graduate student in the Dept. of Biochem
and Biophy at the Texas A&M University.

Ketan
n053gf@tamuts.tamu.edu
From: johnreed@carson.u.washington.edu (John Reed)
Newsgroups: bionet.population-bio
Subject: Plant riparian population genetics
Date: 13 Jan 1993 02:09:33 GMT
Organization: University of Washington, Seattle
Distribution: world
NNTP-Posting-Host: carson.u.washington.edu


Hi,
	I am doing research on the population genetics of black cottonwood
(Populus trichocarpa) in some river valleys in the Cascade Mountains.  I
have searched for references on population genetics of plants (trees are
preferable) in a linear spatial system (a river or stream), but have had
virtually no luck in finding any.  It seems to me that the genetics of
such a system may be different than a typical 2-d system.  I would
appreciate any leads on references or studies you may know of concerning
population genetics of plants in a riparian setting.
Thanks
--------------------------------------------------------------------------
John Reed
College of Forest Resources, AR-10
University of Washington
Seattle, WA 98195
Internet: johnreed@u.washington.edu
--------------------------------------------------------------------------
From: johnreed@carson.u.washington.edu (John Reed)
Newsgroups: bionet.population-bio
Subject: Plant riparian population genetics
Date: 7 Jan 1993 18:28:40 GMT
Organization: University of Washington, Seattle
Distribution: world
NNTP-Posting-Host: carson.u.washington.edu

Newsgroups: sci.bio,bionet.plants,bionet.population-bio
Subject: Plant riparian population genetics
Summary: 
Followup-To: 
Distribution: 
Organization: University of Washington, Seattle
Keywords: 

Hi,
	I am doing research on the population genetics of black cottonwood
(Populus trichocarpa) in some river valleys in the Cascade Mountains.  I
have searched for references on population genetics of plants (trees are
preferable) in a linear spatial system (a river or stream), but have had
virtually no luck in finding any.  It seems to me that the genetics of
such a system may be different than a typical 2-d system.  I would
appreciate any leads on references or studies you may know of concerning
population genetics of plants in a riparian setting.
Thanks
John Reed
(E-mail: johnreed@u.washington.edu)
From: fgarbrec@POST.ITS.MCW.EDU (GARBRECHT)
Newsgroups: bionet.immunology
Subject: Re: Lymphocyte transformation by EBV - help wanted
Date: 6 Jan 93 00:36:41 GMT
Distribution: bionet

We use cyclosporin routinely without much problem (assuming you're
starting with cells from a normal individual).  Transformation
efficiency is usually high.  I never heard of using OKT3; I would guess
that the early morphologic changes that you see are the result of T cell
activation induced by the antibody; the method may actually work by
inducing anergy in any potentially EBV reactive T cells present.  The
other method that works very well is to deplete your culture of T cells
prior to transformation.

Fred Garbrecht
Medical College of Wisconsin
fgarbrec@post.its.mcw.edu
 On 5 Jan 1993, Cheung C. Yue wrote:

> Date: 5 Jan 93 23:51:15 GMT
> From: Cheung C. Yue <ccy@po.CWRU.Edu>
> To: immunology@net.bio.net
> Subject: Lymphocyte transformation by EBV - help wanted
> 
> 
> It has been a while since I did EBV transformation.  Previously I had
> used OKT3 (?to shut off autologous CTL response), but the last several
> times I did this (in '89!!), I used cyclosporin as per a number of 
> people's suggestions.  Well, the last 3 times I used cyclosporin I got
> no transformed cell lines, but using OKT3, I had at least 1 out of 4
> tries.  When I look at the cells, the OKT3 treated cultures developed
> clustering of cells by the second day, and the media gets quite acidic
> within a week.  In contrast there is not much cell clustering in the
> cyclsporin treated cells even after 1 week.  Interestingly the cyclosporin
> treated cells have on several occassions developed a bunch of large
> granular-appearing cells which tended to stream together forming a
> streak of cells (looks like a cotton fiber when out of focus, but is
> actually a bunch of cells that line up in a tubular kind of structure).
> Are these macrophages?  Have others observed this phenomenon?  Are the
> clusters of cells in the OKT3-treated samples early transformed cells?
> I kind of doubt the last point since the clusters do not have the same
> appearance of the clusters of LCL, and they appear way too soon.
> 
> Anyone care to comment?  I would welcome getting in touch with anybody
> on the net with experience transforming lymphocytes.  As it turns out,
> nobody in Cleveland is actually doing lymphocyte transformation at present,
> so I can't bug anybody local about this.  Thanks for all info.
> 
> C Cho Yue
> ccy@po.cwru.edu
> -- 
>
From: reason@garnet.berkeley.edu
Newsgroups: bionet.immunology
Subject: phage expression systems
Date: 10 Jan 93 19:32:10 GMT
Organization: University of California, Berkeley
NNTP-Posting-Host: garnet.berkeley.edu

Donald C. Reason, Ph.D.
reason@garnet.berkeley.edu


i
From: U56149@uicvm.uic.edu
Newsgroups: bionet.immunology
Subject: Goodpasture's
Date: 9 Jan 93 18:18:10 GMT
Organization: University of Illinois at Chicago

Can anyone explain to me why Goodpasture's Syndrome is
classified as a Type II hypersensitivity disease?  The
classical definition for Type II reactions is that they are
due to antibodies directed toward cell surface antigens.
The pathogenesis of Goodpastures is always described as
being due to antibodies directed toward basement membrane
antigens (renal and pulmonary), resulting in the lung in
hemorrhage and in the kidney in glomerulonephritis.  I am
always amazed that textbooks can then classify Goodpasture's
as a Type II disease without any attempt to present it as an
exception or to explain the apparent discrepancy.  In the
kidney, at least, and I suspect in the lung, the
pathogenesis sounds much more like a Type III reaction
(tissue injury and inflammation due to activation of
complement at the site of Ag-Ab complexes) than like a Type
II reaction.

Any ideas?  Thanks!!

Jerry Bartlett
Department of Pathology
U of IL @ Chicago, Coll Med @ Peoria

Reply        u56149@uicvm.cc.uic.edu
Or post to   bionet.immunology
From: ULIMJ@CSPUNI12.EARN (Milan Jira)
Newsgroups: bionet.immunology
Subject: Lymphocyte transformation (EBV, anti-CD3...)
Date: 7 Jan 93 11:51:53 GMT
Distribution: bionet
Original-To: immuno@UK.AC.DARESBURY

Subject:      Re: Lymphocyte transformation by EBV - help wanted
 
    I also believe that the lymphocyte transformation induced by anti-CD3
antibody has (if long acting..) temporarly effect on EBV-induced transformation
The procedure of T cell depletion certainly increase the level of EBV induced
transformation, as described.
 
The receptor on B cells for EBV is type II complement receptor (CD21). Does
anybody know if anti-CD21 has specific stimulatory effect of B cells?
 
Milan Jira, M.D., Ph.D.
Dept. of Immunology
3rd Medical Faculty, Charles University
Prague, Czech Republic
From: ccy@po.CWRU.Edu (Cheung C. Yue)
Newsgroups: bionet.immunology
Subject: Lymphocyte transformation by EBV - help wanted
Date: 5 Jan 1993 23:51:15 GMT
Organization: Case Western Reserve University, Cleveland, OH (USA)
Reply-To: ccy@po.CWRU.Edu (Cheung C. Yue)
NNTP-Posting-Host: slc12.ins.cwru.edu


It has been a while since I did EBV transformation.  Previously I had
used OKT3 (?to shut off autologous CTL response), but the last several
times I did this (in '89!!), I used cyclosporin as per a number of 
people's suggestions.  Well, the last 3 times I used cyclosporin I got
no transformed cell lines, but using OKT3, I had at least 1 out of 4
tries.  When I look at the cells, the OKT3 treated cultures developed
clustering of cells by the second day, and the media gets quite acidic
within a week.  In contrast there is not much cell clustering in the
cyclsporin treated cells even after 1 week.  Interestingly the cyclosporin
treated cells have on several occassions developed a bunch of large
granular-appearing cells which tended to stream together forming a
streak of cells (looks like a cotton fiber when out of focus, but is
actually a bunch of cells that line up in a tubular kind of structure).
Are these macrophages?  Have others observed this phenomenon?  Are the
clusters of cells in the OKT3-treated samples early transformed cells?
I kind of doubt the last point since the clusters do not have the same
appearance of the clusters of LCL, and they appear way too soon.

Anyone care to comment?  I would welcome getting in touch with anybody
on the net with experience transforming lymphocytes.  As it turns out,
nobody in Cleveland is actually doing lymphocyte transformation at present,
so I can't bug anybody local about this.  Thanks for all info.

C Cho Yue
ccy@po.cwru.edu
--
From: UBABCA01@EBCESCA1.BITNET (EMC)
Newsgroups: bionet.immunology
Subject: (none)
Date: 12 Jan 93 19:06:34 GMT
Distribution: bionet

SUBS IMMUNOLOGY Eva Marinez