HDTenEightyP/NetNews huggingface dataset:
From: ftmx@acad3.alaska.edu
Newsgroups: bionet.population-bio
Subject: data needed
Date: 18 Aug 92 18:12:09 GMT
Organization: University of Alaska Fairbanks


   Anyone who has data or other materials about the relations of introcellular
organs? I am interested in the research of interorgan-relationship. Anyone who
has information about this please tell me. Thank you very much. Anyone who is
interested in this please don't hesitate to contact me.
   Thank you very much.	 
Organization: Doctoral student, Biology, Carnegie Mellon, Pittsburgh, PA
Newsgroups: bionet.immunology
Date: Tue, 18 Aug 1992 18:54:52 -0400 
From: Paul Grigore Hodor <ph20+@andrew.cmu.edu>
Subject: IgG assembly?


Can anybody indicate me some references about IgG assembly? I am
particularly interested in what happens if different fragments of heavy
and light chains are expressed together in myeloma cells, and if heavy
chains of different IgG subclasses can combine to form hybrid molecules.


Paul Hodor
Carnegie Mellon U, Dept Bio Sci
Pittsburgh, PA, USA
From: shiv@scrapie.med.umn.edu (Shiv Prasad)
Newsgroups: bionet.immunology
Subject: Re: Journal Watch: MHC and intracellular self
Date: 21 Aug 92 15:44:38 GMT
Organization: University of Minnesota

In article <92234.085803FORSDYKE@QUCDN.QueensU.CA> <FORSDYKE@QUCDN.QueensU.CA> writes:
>Continuing the discussion on intracellular self/not-self discrimination....
>
>                 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?

For some proteins for which a long half-life is necessary, evolution may have
selected for mutations that increased stability without severely affecting 
function.  Other ways that protein stability is increased are:
	1.  Compartmentalization - sequestering that protein away from
		proteases.
	2.  Forming complexes - such as ribosomal proteins with rRNA, and
		protein-protein complexes.
	3.  Modification - (hand-waving on my part) phosphorylation, 
		glycosylation, or other additions may increase stability.
		On the other hand, some modifications may "mark" proteins
		for degradation (and the resulting peptides would be presented
		by MHC...).

Shiv


>
>>>>>>>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
		     Forsdyke, D. (1992) Bionet.immunology, 858 edt
 
>[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.]
Newsgroups: bionet.immunology
From: shiv@tsp.med.umn.edu (Shiv Prasad)
Subject: Re: Ig and Protein A question
Organization: University of Minnesota
Date: Mon, 17 Aug 1992 17:23:07 GMT

Speaking of Ig's and Ig-binding proteins, does anyone know of a reference
that compiles data on which Ig subclasses of several species bind the various
Proteins-A/G/X/Y/Z?  Also is there a table somewhere of which isotypes fix
C'?  It seems that one of these immunochemistry companies (like Pierce) should
have a promotional wall-chart with this information.  The only table I can find
is in a textbook that shows which human isotypes fix C'.  This isn't very
useful, since we never use Hu-Ab for FACS or cell depletions.  Any help
would be appreciated.

Shiv Prasad
shiv@lenti.med.umn.edu

Newsgroups: bionet.immunology
From: bshum@miasun.med.miami.edu (Benny Shum)
Subject: NK cells
Organization: University Of Miami, School Of Medicine
Date: Fri, 14 Aug 1992 14:55:36 GMT


I am happy for the establishment of bionet.immunology.

I was reading an NK cell article in the July issue of 
Immunology Today. The author (Roger Versteeg) suggests
that NK-MHC/peptide interaction may predate Tcell-MHC/peptide
interaction.  Is there anyone on netland working with NK
and can provide the latest concerning NK-receptor? 
Is there another molecule recognizing MHC/peptide other
than TCR?
-- 
  Benny P.Shum
  Graduate Student
  Department of Microbiology and Immunology
  University of Miami, School of Medicine
Newsgroups: bionet.immunology
From: shiv@tsp.med.umn.edu (Shiv Prasad)
Subject: Re: Journal Watch: MHC and intracellular self
Organization: University of Minnesota
Date: Fri, 14 Aug 1992 15:16:45 GMT

In article <92225.094723FORSDYKE@QUCDN.QueensU.CA> <FORSDYKE@QUCDN.QueensU.CA> writes:
>Journal Watch. "Dawn of the Hunt for Nonclassical MHC Function" by
>Stephen M. Hedrick. Cell vol 70, p. 177-180. 24th July 1992.
>
>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
>
>    Sincerely,  Don Forsdyke


It seems that self-nonself discrimination at the level of peptide-MHC
binding would add another (unnecessary?) level of complexity to the immune
system.  We  all know how specificity is governed by T cell selection, and
the question of tolerance to extra-thymic self Ag can be explained by
clonal anergy, or perhaps even suppression.  I find it difficult however
to envision the MHC molecules, or some other component of presentation,
as discriminating between self and nonself.

It is becoming more apparent that there are common motifs in peptides that
bind certain MHC molecules, and these motifs appear to be present in both
the self and nonself peptides that have been eluted and sequenced from MHC.
Therefore binding still appears to be somewhat promiscuous, and this makes
sense (that MHC-peptide binding doesn't discriminate) or else thymic selection
wouldn't be what it is.  However it seems that you suggest discrimination at
the peptide-transporter level.  Let's use thymic selection as a model for
analyzing this.

Self-peptides are presented by thymic APC, allowing the deletion of autorx
thymocytes.  Hence in these APC self-peptides would be bound and transported
by the intracellular complex.  At this point we are unable to determine what
would happen to a non-self peptide, until we look at neonatal tolerance
experiments.  Presumeably in these models the foreign Ag is transported to
the thymus by the blood and then is processed, presented, and the resulting
Ag-MHC complexes can delete thymocytes with cognate receptors.  The same
processing events occur with the injected peptide as with the self-peptides
(again a presumption, but with little evidence to think otherwise).  So it
appears that the thymic APC cannot discriminate between self and non-self
peptides.

If ONLY foreign peptides were expressed in conjunction with MHC on the cell
surface, that would be more efficient.  But we know from the peptide elution
experiments that this doesn't occur.  Therfore it is logical for the APC
to express "every" peptide capable of binding MHC, and letting the T cell
determine what is self and what is foreign.

Shiv
shiv@lenti.med.umn.edu

P.S.
Don, I could have read your J. Theor. Biol. paper, but that wouldn't make
for an interactive net-discussion.
Organization: Queen's University at Kingston
Date: Wednesday, 12 Aug 1992 09:41:43 EDT
From: <FORSDYKE@QUCDN.QueensU.CA>
Newsgroups: bionet.immunology
Subject: Journal Watch: a new type of contribution

Journal Watch =JW.

  Here is an idea for a new type of contribution to Bionet.immunology.
Reading the new journal literature is often a very individual thing. If
something strikes one as being of particular interest one may communicate
it to a colleague, but often it stops there.     Perhaps your thoughts
might be of interest to others. Why not give it a try? I suggest that
items in this category carry the header JW or journal watch before the
subject title.
                Sincerely,
                Don Forsdyke. Discussion Leader.
From: shiv@tsp.med.umn.edu (Shiv Prasad)
Newsgroups: bionet.immunology
Subject: Re: Journal Watch: MHC and intracellular self
Date: 21 Aug 92 00:56:13 GMT
Organization: University of Minnesota

In article <92233.085821FORSDYKE@QUCDN.QueensU.CA> <FORSDYKE@QUCDN.QueensU.CA> writes:
>
>              You anticipate me! What determines a promoter, enhancer, mRNA
>              stability, and rate of translation?
>
This tangent is going too far into the nucleus for my knowledge.  I don't 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.


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


Shiv

>>>>>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
>
Organization: Queen's University at Kingston
Date: Wednesday, 19 Aug 1992 10:19:20 EDT
From: <FORSDYKE@QUCDN.QueensU.CA>
Newsgroups: bionet.immunology
Subject: Re: Journal Watch: MHC and intracellular self
 <1992Aug18.013306.4745@news2.cis.umn.edu>
 <92231.161618FORSDYKE@QUCDN.QueensU.CA>
 <1992Aug19.040540.21000@news2.cis.umn.edu>

In article <1992Aug19.040540.21000@news2.cis.umn.edu>, shiv@tsp.med.umn.edu
(Shiv Prasad) says:
>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?
>
>Prasad: Synthesis - Turnover would give us the number of copies of protein X

  Forsdyke: Yes, synthesis and degradation (turnover).  OK. Now be patient and
            tell me what determines rates of synthesis and degradation.

>> Under what conditions would the virus be in "excess"?

  Prasad:
>Depends on the virus.

  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.

>  Prasad:           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.
>
 Forsdyke: At this stage it should be noted that one of the "other factors",
           as implied in my original test-tube scenario , is the concentration
           of other proteins in the crowded cytosol. More of this later.
>
>>          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
>               Forsdyke, D. (1992) Bionet.immunology 818, 1616edt
                Prasad, S. (1992) Bionet.immunology 819, 405gmt
From: ruslan@DS5000.DGSCA.UNAM.MX
Newsgroups: bionet.immunology
Subject: subscribe
Date: 12 Aug 92 21:40:47 GMT
Distribution: bionet


Please Subscribe me.

	Ruslan Gomez Nesterkin. 
	Supercomputer Department
	DGSCA-UNAM - Mexico City .
Organization: Queen's University at Kingston
Date: Thursday, 20 Aug 1992 09:47:03 EDT
From: <FORSDYKE@QUCDN.QueensU.CA>
Newsgroups: bionet.immunology
Subject: Journal watch: MHC and intracellular self

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: wetsel_r@wums.wustl.edu
Newsgroups: bionet.immunology
Subject: RE: meetings
Date: 14 AUG 92 09:54:27 GMT
Organization: MIT PLASMA FUSION CENTER
NNTP-Posting-Host: msnews.wustl.edu

Greetings Ralph:

My personal favorites would be either the FASEBs, now Experimental Biology,
meeting where AAI meets (Except for this year, of course where AAI is meeting
independently of ExBo in Denver).  The downside to FASEB style meetings is
that soooo much is going on, chances are that you will miss something of
interest to you.  However, the meetings will cover a broad range of topics.
Another one to consider is the mid-winter conference of immunologist held each
January at the Asilomar conference grounds in Pacific Grove California.  The
nice thing about the MWCI is that only one thing is going on at a time.
However, the MWCI has "themes" for the meeting and one year's meeting may
interest you greatly while another may bore you.  I can dig up the address
for the MWCI to which you can request information about the upcoming meeting,
if you like.

Best wishes,

David
Newsgroups: bionet.immunology
From: shiv@tsp.med.umn.edu (Shiv Prasad)
Subject: Re: Journal Watch: MHC and intracellular self
Organization: University of Minnesota
Date: Tue, 18 Aug 1992 01:33:06 GMT

In article <92230.175700FORSDYKE@QUCDN.QueensU.CA> <FORSDYKE@QUCDN.QueensU.CA> writes:

>  Start, by forgetting about cells and imagine placing a set of "self"
>cytosolic proteins in a test tube (A,B,C,D,E,F,G,H). Now add a not-self
>protein (X). The problem is to find a way of specifically selecting X for
>degradation. Double the concentration of all the proteins. Nothing
>happens. Double again, and again. Something is now happening. One of the
>proteins is aggregating. It is doing this specifically, self with self.
>The mechanism for this is set out in Lauffer's book "Entropy-driven
>Processes in Biology (Springer. 1975). Now, as we have it set up,
>there is no particular reason for any one protein to be the first to
>aggregate. It could be one of A to H. It could be X. But once it has
>aggregated, it has marked itself as different. As such, it might be
>recognized by a specific proteolytic complex (proteosome?) and some of
>its peptides made available for coupling to MHC protein.
>
>                          Sincerely,
>                               Don Forsdyke, Department of Biochemistry,
>                                             Queen's University, Kingston
>                                             Canada.

In your experiment it would seem that whichever protein aggregates first
would depend on the initial concentration of each protein, and the homotypic
affinities.  A situatioon in which the non-self would be in excess (to move
this back into the cell) is a viral infection, where certain viral proteins
are made far in excess of the cellular proteins.  If the viral proteins are
more quickly degraded by proteolytic complexes, this may be a simple question
of availability and competition.  For this cell to be recognized as a target
the infecting virus must not lyse the cell.  So we are left to ponder viruses
that make a large quantity of their own proteins while not being lytic.  My
knowledge of viruses doesn't include this information however.

Going back to the cell-free scenario (i.e. this just popped into my mind)
the viral proteins may be in excess of the cellular proteins, and they may
also aggregate more easily, since an aggregate of one protein often forms
a viral capsid.  So I can see there where X would aggregate before A-H.
But again, recognition of this non-self aggregate would be the proteolytic
complex binding to the aggregate that is more in abundance.  This form of
discrimination would be (through my T cell eyes) a rather loose useage
of the term self-nonself discrimination.  For example if two or more
foreign protein were present, let's say the capsid protein and the viral
polymerase (packaged at low numbers per virion), the capsid protein would
outcompete the self proteins and the polymerase.  The polymerase would not
necessarily outcompete the self-proteins, as it may not be present in large
enough quantities to aggregate before the self molecules do.

Is this close to the point that you're trying to make?

Shiv
From: wetsel_r@wums.wustl.edu
Newsgroups: bionet.immunology
Subject: RE: Analysis of FACS data
Date: 14 AUG 92 10:00:33 GMT
Organization: MIT PLASMA FUSION CENTER
NNTP-Posting-Host: msnews.wustl.edu

King:

This may be of no help but I'll toss it your way...  I had a similar situation
as I wanted to get data from a Coulter EPICS to my PC.  I had to use a "null"
modem cable as the i/o was a serial connection.  The EPICs already had "data
export" software.  I had to use communication software on the PC in order to receive the data, specifically I used Procom.  It took a couple of tries
to get the two to talk as I had to work out all the communication parameters,
like baud, data bits, parity - once I did, it worked like a charm.  I hope
that's of some use as most of the detail have left me since that was four
years ago!!!

I hope it can help...

David
Organization: Queen's University at Kingston
Date: Tuesday, 18 Aug 1992 16:16:18 EDT
From: <FORSDYKE@QUCDN.QueensU.CA>
Newsgroups: bionet.immunology
Subject: Re: Journal Watch: MHC and intracellular self
 <1992Aug14.151645.4343@news2.cis.umn.edu>
 <92230.175700FORSDYKE@QUCDN.QueensU.CA>
 <1992Aug18.013306.4745@news2.cis.umn.edu>


In article <1992Aug18.013306.4745@news2.cis.umn.edu>, shiv@tsp.med.umn.edu (Shiv
Prasad) says:
>
>In article <92230.175700FORSDYKE@QUCDN.QueensU.CA> <FORSDYKE@QUCDN.QueensU.CA>
>writes:
>
>>  Start, by forgetting about cells and imagine placing a set of "self"
>>cytosolic proteins in a test tube (A,B,C,D,E,F,G,H). Now add a not-self
>>protein (X). The problem is to find a way of specifically selecting X for
>>degradation. Double the concentration of all the proteins. Nothing
>>happens. Double again, and again. Something is now happening. One of the
>>proteins is aggregating. It is doing this specifically, self with self.
>>The mechanism for this is set out in Lauffer's book "Entropy-driven
>>Processes in Biology (Springer. 1975). Now, as we have it set up,
>>there is no particular reason for any one protein to be the first to
>>aggregate. It could be one of A to H. It could be X. But once it has
>>aggregated, it has marked itself as different. As such, it might be
>>recognized by a specific proteolytic complex (proteosome?) and some of
>>its peptides made available for coupling to MHC protein.

  Prasad replies:

>In your experiment it would seem that whichever protein aggregates first
>would depend on the initial concentration of each protein, and the homotypic
>affinities.  A situatioon in which the non-self would be in excess (to move

   Yes. So, what determines the concentration of self proteins in a cell?

>this back into the cell) is a viral infection, where certain viral proteins
>are made far in excess of the cellular proteins.  If the viral proteins are

  Yes. So what determines the concentration of viral proteins in a cell?

>Going back to the cell-free scenario (i.e. this just popped into my mind)
>the viral proteins may be in excess of the cellular proteins, and they may
>also aggregate more easily, since an aggregate of one protein often forms
>a viral capsid.  So I can see there where X would aggregate before A-H.

 Under what conditions would the virus be in "excess"?

          Sincerely,
          Don Forsdyke

              Prasad, S. (1992) Bionet.immunology 814 1516gmt
              Forsdyke, D. (1992) Bionet.immunology 817 1757edt
              Prasad, S. (1992) Bionet.immunology 818 133gmt
Newsgroups: bionet.immunology
From: bz965@cleveland.Freenet.Edu (Richard Hatch)
Subject: Re: Ig and Protein A question
Organization: Case Western Reserve University, Cleveland, Ohio, (USA)
Date: Mon, 17 Aug 92 16:05:47 GMT


I don't have a reference handy, but the pH dependence of binding
of IgG to protein A is apparently well known. An ex-coworker in 
my lab was aware of it and succeeded in separating four type of
monoclonal IgGs in a pH gradient run on silica immobilized Prot-A
The antibodies were the well known MOPC21, UPC10, FLOPC21, and 
MOPC141. The increased binding at higher pH for many murine IgGs
is also well known, as is increased binding with higher salt
concentrations. I will look for a reference if you are still
interested.
Newsgroups: bionet.immunology