HDTenEightyP/NetNews huggingface dataset:
From: shiv@scrapie.med.umn.edu (Shiv Prasad)
Subject: Re: Journal Watch: MHC and intracellular self
Organization: University of Minnesota
Date: Wed, 19 Aug 1992 20:19:32 GMT

In article <92232.101920FORSDYKE@QUCDN.QueensU.CA> <FORSDYKE@QUCDN.QueensU.CA> writes:
>
>  Forsdyke: Yes, synthesis and degradation (turnover).  OK. Now be patient and
>            tell me what determines rates of synthesis and degradation.
>
Ok, rates of transcription and translation determine synthesis (I hope we're
not going to get into promoters and enhancers).  As far as degredation, protein
stability, i.e. maintaining it's conformation, is certainly a factor, as de-
natured proteins may be degraded, but I'm not really sure what controls the 
half-lives of proteins.  I'm not exactly sure where you're going with this.
Are you going to suggest that viral proteins have longer half-lives, which may
lead to higher relative concentrations in the cell?
>
>  Forsdyke: OK. Let's just take a "generic" virus which goes about its
>            business within the cell and eventually lyses the cell.
>            It will make some viral proteins more than others, but a minimum
>            of one protein would be     necessary in order to get a foreign
>            peptide displayed at the cell surface with MHC class I.
>

So back to the original question, what is the system that prevents all of
the cellular self-proteins from competing with the viral non-self protein.

>>>References:   Forsdyke, D. (1992) Bionet.immunology 812 947edt
>>>              Prasad, S. (1992) Bionet.immunology 814 1516gmt
>>>              Forsdyke, D. (1992) Bionet.immunology 817 1757edt
>>>              Prasad, S. (1992) Bionet.immunology 818 133gmt
>>               Forsdyke, D. (1992) Bionet.immunology 818, 1616edt
>                Prasad, S. (1992) Bionet.immunology 819, 405gmt


P.S.  How are we doing on the citation indices :-).
Organization: Queen's University at Kingston
Date: Friday, 21 Aug 1992 08:58:03 EDT
From: <FORSDYKE@QUCDN.QueensU.CA>
Newsgroups: bionet.immunology
Subject: Re: Journal Watch: MHC and intracellular self
 <1992Aug19.201932.27235@news2.cis.umn.edu>
 <92233.085821FORSDYKE@QUCDN.QueensU.CA>
 <1992Aug21.005613.10403@news2.cis.umn.edu>

Continuing the discussion on intracellular self/not-self discrimination....

>>  Forsdyke:   You anticipate me! What determines a promoter, enhancer, mRNA
>>              stability, and rate of translation?
    Prasad:
>This tangent is going too far into the nucleus for my knowledge.  I don't     w
>follow
>how things such as zinc-fingers and CAAT boxes determine self from nonself in
>the intracellular compartment.  Perhaps you could elaborate more on this.
>
>>  Forsdyke:   What determines that protein A will live longer than protein B?
    Prasad:
>I really don't know, does anyone?
>Conformation may have something to do with it, as some proteins may expose
>protease sites.  But until the intracellular half-lives of proteins can be
>compared to their 3-D structures this may just be conjecture.

    Forsdyke: Sorry, I wasn't looking for the details. I was just trying to
              get you to make the general point that the final concentration
              of self-protein A relative to self-protein B is determined by
              the respective genes. The genes encode not only information on
              function, but information determining the final concentration of
              the gene product. For example, the sequence of the 3' non-coding
              region of the mRNA determines, in part, the mRNA life span,
              which, in turn, determines how long the mRNA is around to code
              for the synthesis of the corresponding protein.
                 So, the next question I offer is: What evolutionary forces,
              acting by modifying the gene sequence, mould the encoded life-
              span of a particular gene product?

>>>>>>References:   Forsdyke, D. (1992) Bionet.immunology 812 947edt
>>>>>>              Prasad, S. (1992) Bionet.immunology 814 1516gmt
>>>>>>              Forsdyke, D. (1992) Bionet.immunology 817 1757edt
>>>>>>              Prasad, S. (1992) Bionet.immunology 818 133gmt
>>>>>               Forsdyke, D. (1992) Bionet.immunology 818, 1616edt
>>>>                Prasad, S. (1992) Bionet.immunology 819, 405gmt
>>>                 Forsdyke, D. (1992) Bionet.immunology 819 1019edt
>>>                 Prasad, S. (1992) Bionet.immunology 819, 2019gmt
>                   Forsdyke, D. (1992) Bionet.immunology 820, 858edt
>>                  Prasad, S. (1992) Bionet.immunology 821, 56gmt
[Footnote for sharp-eyed David K. whose note informs us of the previous
 advise he gave regarding citations in BioNet. To this I replied that
 eventually the paper and electronic media are going to merge and it is
 likely that the existing format in the paper literature will be generally
 adopted. In my opinion, the format David sets out is far too cumbersome.
 But this is another area of discussion and should not really continue under
 this heading.]
From: anazerad@cnedcu51.bitnet (Pascal A. AZERAD)
Newsgroups: bionet.immunology
Subject: hemostasis
Date: 13 Aug 92 10:50:31 GMT
Organization: University of Neuchatel, Switzerland

A close friend of mine asked me whether factor XII is either a fibrinolytic 
or coagulant agent in hemostasis. Thanks for answers!

-- 
	Pascal Azerad                 "Les mathematiques sont simples,
	Institut de mathematiques      c'est nous qui sommes compliques."
	Universite de Neuchatel
	Switzerland.

	Pascal.Azerad@maths.unine.ch
From: shiv@tsp.med.umn.edu (Shiv Prasad)
Newsgroups: bionet.immunology
Subject: Re: Journal Watch: MHC and intracellular self
Date: 19 Aug 92 04:05:40 GMT
Organization: University of Minnesota

In article <92231.161618FORSDYKE@QUCDN.QueensU.CA> <FORSDYKE@QUCDN.QueensU.CA> writes:
>
>
>   Yes. So, what determines the concentration of self proteins in a cell?
>
>  Yes. So what determines the concentration of viral proteins in a cell?

	Synthesis - Turnover would give us the number of copies of protein X
>
>
> Under what conditions would the virus be in "excess"?
>
Depends on the virus.  Picorna viruses "take over" the cell's protein
synthesis machinery and  make gobs of viral proteins.  However these infections
are lytic, and the infected cell may not have loaded class I sufficiently
to be a target before it is lysed.  Other viruses don't make as much viral 
proteins, especially those that, at a point in their life cycle, are in the
proviral form.  A single viral protein would be in molar xs of any other
single cellular protein when that v-protein is required in large copy
numbers for packaging the viral nucleic acid.  As I mentioned before, an 
example may be the viral capsid protein.  If a capsid is made of aggregted
protein X, and the infected cell will produce a large number of virions, then
I assume that protein X would be in molar xs of any other single protein,
cellular of viral.  Goerge Chacko indicated earlier that homotypic adhesion
was dependent on protein concentration, pH, and the notorious "other factors."
Since we realy can't say for certain which proteins agggregate better at
cellular pH, and how the "other factors" play a role, we seem to be left with
[protein] as the only thing that we can grasp.

Are there any virologists out there who can give examples of which viral 
proteins may in in large xs.  Seems that someone should have tried a 
Comassie stain on PAGE'd lysates of infected cells, only to find a big, blue
blob that was absent from the uninfected cells, yet dominated the infected-cell
lane on the gel.

>          Sincerely,
>          Don Forsdyke
>
>References:   Forsdyke, D. (1992) Bionet.immunology 812 947edt
>              Prasad, S. (1992) Bionet.immunology 814 1516gmt
>              Forsdyke, D. (1992) Bionet.immunology 817 1757edt
>              Prasad, S. (1992) Bionet.immunology 818 133gmt

Shiv
Organization: Queen's University at Kingston
Date: Thursday, 20 Aug 1992 08:58:21 EDT
From: <FORSDYKE@QUCDN.QueensU.CA>
Newsgroups: bionet.immunology
Subject: Re: Journal Watch: MHC and intracellular self
 <1992Aug19.040540.21000@news2.cis.umn.edu>
 <92232.101920FORSDYKE@QUCDN.QueensU.CA>
 <1992Aug19.201932.27235@news2.cis.umn.edu>


>>  Forsdyke: Yes, synthesis and degradation (turnover).  OK. Now be patient
>>            tell me what determines rates of synthesis and degradation.
>>
>Ok, rates of transcription and translation determine synthesis (I hope we're
>not going to get into promoters and enhancers).

              You anticipate me! What determines a promoter, enhancer, mRNA
              stability, and rate of translation?

>As far as degradation
>stability, i.e. maintaining it's conformation, is certainly a factor, as de-
>natured proteins may be degraded, but I'm not really sure what controls the
>half-lives of proteins.

              What determines that protein A will live longer than protein B?

>Are you going to suggest that viral proteins have longer half-lives, which may
>lead to higher relative concentrations in the cell?

              Longer half-lives? No. Higher relative concentrations? Depends
              what you mean by "relative" (more later).

>So back to the original question, what is the system that prevents all of
>the cellular self-proteins from competing with the viral non-self protein?

              I have not forgotten it.

>>>>References:   Forsdyke, D. (1992) Bionet.immunology 812 947edt
>>>>              Prasad, S. (1992) Bionet.immunology 814 1516gmt
>>>>              Forsdyke, D. (1992) Bionet.immunology 817 1757edt
>>>>              Prasad, S. (1992) Bionet.immunology 818 133gmt
>>>               Forsdyke, D. (1992) Bionet.immunology 818, 1616edt
>>                Prasad, S. (1992) Bionet.immunology 819, 405gmt
>                 Forsdyke, D. (1992) Bionet.immunology 819 1019edt
>                 Prasad, S. (1992) Bionet.immunology 819, 2019gmt

>P.S.  How are we doing on the citation indices :-).

       [Seriously, Bionet files are stored at at least two sites and are
        in principle citable in the paper literature. One day the powers that
        be will decide on a suitable citation format. In the meantime, it makes
        some sense to use a format somewhat like that seen in the paper litera-
        ture. The notion that one's words are stored for "all time" may
        dissuade some from contribution. On the other hand, it may make for
        more "responsible" postings, when communicating in the public domain.]
From: gchacko@magnus.acs.ohio-state.edu (George W Chacko)
Subject: Re: Journal Watch: MHC and intracellular self
Organization: The Ohio State University
Date: Tue, 18 Aug 1992 01:58:45 GMT


In article <1992Aug18.013306.4745@news2.cis.umn.edu> shiv@tsp.med.umn.edu (Shiv Prasad) writes:

>In your experiment it would seem that whichever protein aggregates first
>would depend on the initial concentration of each protein, and the homotypic
>affinities.  

I'm not sure what 'homotypic affinities' means but if it indicates the
affinity of a protein molecule for another molecule of the same
protein which can also be expressed in terms of concentration, e.g.

A + A  <-> 2A  => Keq = [2A]/{[A]*[A]}

then the first protein to aggregate would be the one with the highest
homotypic affinity as defined above. That of course, is dictated
principally by its primary amino acid sequence as well as standard 'other
factors' like pH and ionic strength. Right?

George
Organization: Queen's University at Kingston
Date: Wednesday, 12 Aug 1992 09:47:23 EDT
From: <FORSDYKE@QUCDN.QueensU.CA>
Newsgroups: bionet.immunology
Subject: Journal Watch: MHC and intracellular self

Journal Watch. "Dawn of the Hunt for Nonclassical MHC Function" by
Stephen M. Hedrick. Cell vol 70, p. 177-180. 24th July 1992.

   The following statement left me purring with pleasure: "A troublesome
concept concerns the competition among peptides for binding to the
available MHC molecules. It is hard to understand how peptides derived
from foreign antigens can compete with the tide of self peptides, and
there is currently a considerable amount of speculation concerning the
possibility that such a system could, in theory, function efficiently.
Perhaps there is a mechanism that could help to sort peptides into those
originating from self and those originating from foreign proteins."

   Having been pushing such a mechanism for some time (J.Theoret.Biol.
vol 115, 471-473. 1985), I was pleased that at least the possibility of
the existence of such a mechanism was being acknowledged. However, my
spirits were dampened by Stephen Hedrick's volte face at the end of the
article: "..there is no known way of distinguishing viral and host
peptides a priori, and therefore the immune system is largely saddled
with the necessity of presenting all peptides and allowing the population
of T cells to choose those to ignore".

    Sincerely,  Don Forsdyke
Newsgroups: bionet.immunology
From: dordaz@magnus.acs.ohio-state.edu (Donald E Ordaz Jr)
Subject: Immunology text
Organization: The Ohio State University
Distribution: na
Date: Mon, 17 Aug 1992 20:03:06 GMT


Hello All,

I'm conducting a quick survey regarding textbooks used in teaching an
introductory Immunology course.

The question :

What, if any, text do you use or have you used for an introductory immunology
course, at the undergraduate level?

Would you recommend the text?

Any strong or weak points about the text?

Please e-mail me directly, I'l post the results for anyone interested.

Thanks

Don Ordaz
Department of Microbiology
The Ohio State University

dordaz@magnus.acs.ohio-state.edu
From: birchall@pilot.njin.net (Shag)
Newsgroups: bionet.immunology
Subject: Request for Information: CMV
Summary: I'm not a doctor.  Layman's terms are best.
Keywords: Cytomegalovirus
Date: 18 Aug 92 01:51:19 GMT
Organization: Screaming in Digital, the Queensryche Net Digest

Greetings.

	In late November of 1990, I took ill, and was tested for Mono.  The
doctor informed me that I didn't have Mono, but _did_ have CMV.  I asked him
what it was, he told me to go look it up.  He then went on vacation [to
Bermuda, I believe].  I looked it up, grasped the basic concept of it, and
spent 3 weeks sleeping, trying to eat jello, and taking Nuprin.  After that
I felt pretty much better, and went on with life.  The doctor returned from
his vacation, and asked me to come in for further blood tests.  I [politely]
told him to pack sand.  [I don't appreciate doctors who won't give me
information about illnesses, particularly the going-on-vacation ones].

	Recently, I had a cold, and a friend of mine also had a cold.  We
spend large amounts of time in each other's company, colds or not.  She now
has some of the preliminary symptoms of a CMV infection - swollen lymph
nodes in her neck, extreme fatigue, high fever.  She's getting tested
tomorrow.  We are, as the song says, hoping for the best but expecting the
worst.

	I have been told in recent days that CMV has a tendency to remain
in someone, latent or inactive, and reactivate if their immune system drops
or if the CMV is transferred into someone else's body.  I've also been told
that I may not be immune to CMV, and may only have an inactive case of it.

	Right now, as a 'CMV survivor' I have a good bit more general 
knowledge of the critter than the average man on the street.  However, I
don't know as much about it as the average expert.  I'd like to learn more.

	I'm very concerned as to what the current risk is, both to myself
and to those around me.  I'd like to find out how it can be transmitted,
exactly how much damage it does to what, what triggers it, and what 
secondary infections should be guarded against.  I'd _especially_ like to
find out whether there's any way to zap it when it's inactive.

	-Shag
-- 

     Freedom belongs to only those without video screens for eyes and mouth.
		- Queensryche
From: lzett@CARROLL1.CC.EDU (Leslie D Zettergren)
Newsgroups: bionet.immunology
Subject: Subscribe
Date: 15 Aug 92 13:00:37 GMT
Distribution: bionet

SUBSCRIBE Leslie D. Zettergren
From: kristoff@genbank.bio.net (David Kristofferson)
Newsgroups: bionet.immunology
Subject: Re: Journal Watch: MHC and intracellular self
Date: 20 Aug 92 22:12:37 GMT
Organization: GenBank Online Service

FORSDYKE@QUCDN.QueensU.CA writes:

>     [Seriously, Bionet files are stored at at least two sites and are
>      in principle citable in the paper literature. One day the powers that
>      be will decide on a suitable citation format. In the meantime, it makes
>      some sense to use a format somewhat like that seen in the paper litera-
>      ture. The notion that one's words are stored for "all time" may
>      dissuade some from contribution. On the other hand, it may make for
>      more "responsible" postings, when communicating in the public domain.]


I bring the following old poosting on this topic to your attention:

From bionet.general Thu May  7 18:11:45 1992
From: kristoff@GENBANK.BIO.NET (Dave Kristofferson)
Newsgroups: bionet.general
Subject: Citing BIOSCI/bionet postings
Date: 18 Dec 91 00:41:52 GMT
Distribution: bionet


Donald,

	If one wanted to cite a posting I would suggest a format which
includes the name and e-mail address of the person posting the
message, the Subject: line of the message, the newsgroup name, and the
date/time stamp.  If one really wants to become fanatical, note that
each message has a unique message id line.

(yours was:   Message-Id: <9112171614.AA22659@genbank.bio.net>  )

This latter info is not much use to humans though.  I would not
advocate using article numbers from your newsreader because this
varies from site to site.  An example reference for your posting would
thus be:

Forsdyke, Donald R. (FORSDYKE@QUCDN.QueensU.CA), "Reorganization:
implication for electronic journal." USENET/bionet.general, 17 Dec 91
15:48:09 GMT.


Hope this helps.  Just writing it down in that format gives it a bit
more authority, doesn't it 8-)?!  One could also potentially have
priority fights get down to the second, too (what fun).

Dave
From: henikoff@milton.u.washington.edu (Steven Henikoff)
Newsgroups: bionet.announce
Subject: New e-mail server for homology searching
Date: 18 Aug 92 18:12:28 GMT
Distribution: bionet
Organization: University of Washington, Seattle


        ___________               ___________               ___________ 
       |\ __________\            |___________|            /__________ /|
       | |           |           |           |           |           | |
       | | **********|           |***********|           |********** | |
       | | * BLOCKS  |           |   E-MAIL  |           |SEARCHER * | |
       | | **********|           |***********|           |********** | |
        \|___________|___________|___________|___________|___________|/
                     |\ __________\         /__________ /|
                     | | JC Wallace|       | Copyright | |
                     | |   S Agus  |       |    Fred   | |
                     | |JG Henikoff|       | Hutchinson| |
                     | | S Henikoff|       |   Center  | |
                      \|___________|       |____1992___|/

As an aid to detection and verification of protein sequence homology, we
introduce the BLOCKS e-mail searcher, which compares a protein or DNA sequence
to the current database of protein blocks. Blocks are short multiply aligned
ungapped segments corresponding to the most highly conserved regions of
proteins. A database of blocks has been constructed by successive application
of the automated PROTOMAT system to individual entries in the PROSITE catalog
of protein groups keyed to the SWISS-PROT protein sequence databank. The
rationale behind searching a database of blocks is that information from
multiply aligned sequences is present in a concentrated form, reducing
background and increasing sensitivity to distant relationships. If a particular
block scores highly, it is possible that the sequence is related to the group
of sequences the block represents. Typically, a group of proteins has more than
one region in common and their relationship is represented as a series of
blocks separated by unaligned regions. If a second block for a group also
scores highly in the search, the evidence that the sequence is related to the
group is strengthened, and is further strengthened if a third block also scores
it highly, and so on.

For a detailed help file, send a blank e-mail message as follows:

To: blocks@howard.fhcrc.org
Subject: help

Or just send a protein or DNA sequence in FASTA, Genepro, GenBank, EMBL, SWISS-
PROT, or PIR formats (DNA is automatically translated in all 6 reading frames 
for searching).  Here is an example of a protein query in FASTA format:

To: blocks@howard.fhcrc.org
Subject:
>YCZ2_YEAST   Hypothetical 40.1 KD protein in HMR 3' region
MKAVVIEDGKAVVKEGVPIPELEEGFVLIKTLAVAGNPTDWAHIDYKVGPQGSILGCDAA
GQIVKLGPAVDPKDFSIGDYIYGFIHGSSVRFPSNGAFAEYSAISTVVAYKSPNELKFLG
EDVLPAGPVRSLEGAATIPVSLTTAGLVLTYNLGLNLKWEPSTPQRNGPILLWGGATAVG
QSLIQLANKLNGFTKIIVVASRKHEKLLKEYGADQLFDYHDIDVVEQIKHKYNNISYLVD
CVANQNTLQQVYKCAADKQDATVVELTNLTEENVKKENRRQNVTIDRTRLYSIGGHEVPF
GGITFPADPEARRAATEFVKFINPKISDGQIHHIPARVYKNGLYDVPRILEDIKIGKNSG
EKLVAVLN
From: kristoff@genbank.bio.net (David Kristofferson)
Newsgroups: bionet.announce
Subject: CALL FOR DISCUSSION: bionet.maize
Date: 21 Aug 92 22:46:54 GMT
Distribution: bionet
Organization: GenBank Online Service

We have received a proposal for a new newsgroup, bionet.maize
(e-mail address: MAIZE).

Discussion will now be open through 31 August on BIOFORUM/bionet.general
(*not* on BIONEWS/bionet.announce).

Please do not post one-line messages saying only "I am in favor of
such a newsgroup".  We will collect votes later.  The discussion
period is an opportunity for anyone to bring up reservations about the
proposed charter and to propose modifications prior to the vote.  The
discussion leader may submit a revised proposal in light of the
discussion, and the new charter would be included in the call for votes
which will go out on September 1st.

Please be aware that only one vote is counted per e-mail address, so
it is necessary to have your own account in order to vote.  Multiple
votes from the same address are not accepted.  If you are interested
in the following newsgroup, but do not have an e-mail address of your
own, please obtain one from your computer center before the call for
votes is issued in ten days.

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

Proposal to establish bionet.maize

Purpose: Discussions/inquiries regarding the breeding, genetics,
biochemistry, evolution, and ethnobotany of maize, including
information exchange regarding mutants, mapping, and methodology.

Discussion Leader: Allen Wright  <adwright@iastate.edu>
                   Iowa State Unversity

----------------------------------------------------------------------
From: POSTMAST@GUNBRF.BITNET
Newsgroups: bionet.announce
Subject: Restoration of Network Access to PIR
Date: 13 Aug 92 21:52:05 GMT


                 Announcement of Restoration of Access to
                   The Protein Identification Resource

The National Biomedical Research Foundation has restored access to the
Protein Identification Resource Network Server and the On-line System.

Requests may again be sent to FILESERV@GUNBRF on BITNET.

We regret any inconvenience this temporary loss of service may have caused.
------------------------------------------------------------------------
                                 Dr. John S. Garavelli
                                 Database Coordinator
                                 Protein Identification Resource
                                 National Biomedical Research Foundation
                                 Washington, DC  20007
                                 POSTMASTER@GUNBRF.BITNET