HDTenEightyP/NetNews huggingface dataset:
From: PARSONS_A@snd01.pcr.co.uk
Newsgroups: bionet.molbio.bio-matrix
Subject: Psoriatic Arthropathy
Date: 8 Jan 93 14:26:42 GMT
Distribution: bionet
Original-To: BIOMATRX <BIOMATRX@UK.AC.DARESBURY>

Hi Networkers,

Sorry if this is an inappropriate posting but I am trawling the net!

A friend of mine has been suffering (since age 11) with what appeared to be
rheumatoid arthritis.  Recently this has been diagnosed as a psoriatic
arthropathy which has all the characteristics of chronic-relapsing rheumatoid
arthritis. 

Recently the periods of remission have become shorter and some researchers in
Middlesex (Northwick Park?) have suggested that this condition as well as being
an autoimmune condition may be triggered by changes in the gut flora/fauna, in
particular levels of Candida in the alimentary canal and also its
morphologoical state (budding vs. pseudomycelial form). 

The diet (I understand Candida diets are all the rage) is quite restrictive:

No sugary foods
High Complex carbohydrate diet
High Protein
No alcohol

In addition to the diet a prophylactic dose of nystatin is taken to counter 
the Candida in the gut.

Does anyone know where I can find out who might be working on this particular
autoimmune condition, the efficacy of the diet and what the actual metabolic
rationale behind it is.

Many thanks,

Tony Parsons

 +----------------------------------------------------------------------------+
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 | Pfizer Central Research,				 		      |
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From: kab@WELCHGATE.WELCH.JHU.EDU (Kerryn Brandt)
Newsgroups: bionet.molbio.gdb
Subject: GnomeView: Visual Representation of Data
Date: 6 Jan 93 14:05:05 GMT
Distribution: bionet

AU$  GDB staff
LT$  NEWSLETTER
SO$  Human Genome News, November 1992;4(4):8
TI$  GnomeView: Visual Representation of Data
YR$  1992
AB$  
         GnomeView, developed by Richard Douthart's team at Pacific
   Northwest Laboratory (PNL) is undergoing beta testing as a user
   interface to access information generated by the Human Genome
   Project. GnomeView provides graphical and textual styles of data
   presentation and displays color representations of genomic maps for
   review, analysis, and manipulation. It supports both chromosome and
   DNA sequence maps with data from Genome Data Base and
   GenBank, respectively. The standard representation of a
   chromosome map in GnomeView is a stylized depiction of the
   chromosome's banding pattern. DNA sequence is represented as a
   number line with features from GenBank as regions and the base
   pairs as tick marks or letters. GnomeView also provides density
   maps, a type of color-coded histogram indicating the distribution of
   objects over an associated genomic map.
         GnomeView addresses the problem of moving among databases
   by using cross references to achieve smooth transition across
   databases and among different levels of data. Given a GDB locus,
   for example, GnomeView can retrieve all the associated GenBank 
   sequences, and vice versa. Another unique feature is the ability to
   magnify any region and scroll maps interactively in either
   direction. Overlapping labels become separable as the
   magnification increases. Regions, tick marks, and letters are color
   coded so that patterns can be discerned more easily. The
   GnomeView window-based query interface allows the user to specify
   complex queries through the use of buttons and menus, with
   minimal text entry.
          ASCII flat files are downloaded from the public databases to
   a local disk via anonymous FTP over the Internet. The local 
   GnomeView database is then loaded from these flat files. The user
   interacts with the local GnomeView database via a graphical user
   interface.
          GnomeView will be demonstrated at the February DOE
   Contractor-Grantee meeting in Santa Fe, New Mexico, and will be
   available to the general community in 1993. For more
   information, contact Richard Douthart; Life Sciences Center; PNL;
   Richland, WA 99352 (509/375-2653, Fax: 509/375-3649, Internet:
   dick@gnome.pnl.gov).
From: kab@WELCHGATE.WELCH.JHU.EDU (Kerryn Brandt)
Newsgroups: bionet.molbio.gdb
Subject: GDB Standard Reports Available via FTP
Date: 6 Jan 93 14:03:33 GMT
Distribution: bionet

AU$  GDB staff
LT$  NEWSLETTER
SO$  Human Genome News, November 1992;4(4):11
TI$  GDB Standard Reports Available via FTP
YR$  1992
AB$  
        A series of standard reports will be generated regularly for
   the GDB FTP server (mendel.welch.jhu.edu or 128.220.59.42). The 
   first set is based on the content and style of tables accompanying
   the HGM 11 chromosome summary reports. Each report will contain a
   specific extract of GDB data and will be available in these formats:
   (1) PostScript files (very large) can be sent to the user's local
   PostScript printer to produce a formatted document of near-typeset
   quality. (2) Formatted ASCII files (smaller than PostScript files)
   produce human-readable copy. (3) Tab-delimited ASCII tables are
   in computer-readable format for input to the user's computer
   program. The README file in the <gdb/report> directory will
   describe the location and filenaming conventions for the report
   series. For information about FTP access or to suggest report
   enhancements or subjects for new reports, contact GDB User
   Support in Baltimore at 410/955-7058 or Fax 410/614-0434.
From: kab@WELCHGATE.WELCH.JHU.EDU (Kerryn Brandt)
Newsgroups: bionet.molbio.gdb
Subject: GDB 5.0 Data Conversion Aids for Software Developers
Date: 6 Jan 93 14:00:22 GMT
Distribution: bionet

AU$  GDB staff
LT$  NEWSLETTER
SO$  Human Genome News, November 1992;4(4):10
TI$  GDB 5.0 Data Conversion Aids for Software Developers
YR$  1992
AB$  
      When GDB version 5.0 is released, the FTP server flat files and
    the SQL server database (both generated weekly from the online
    GDB) will reflect the 5.0 format. To help developers test programs
    for converting from 4.2 to 5.0 format, GDB plans to set up two
    new FTP directories containing flat files with equivalent data in
    two formats:
        GDB 4.2 data at time of conversion and
        GDB 5.0 data just after conversion.
    The README file in the top-level directory will describe the
    location of these new test files.
       A second SQL server containing 4.2 data at the time of
    conversion will also be available. Information about this test server
    will be sent via e-mail to everyone with an SQL account.
       The test files and server will be accessible for 3 months.
    Developers interested in obtaining the 5.0 schema and accompanying
    data dictionary should contact GDB User Support in Baltimore.
From: dwen@sci.wfeb.edu
Newsgroups: bionet.molbio.methds-reagnts
Subject: Human beta-actin clone
Date: 11 Jan 93 20:08:33 GMT
Organization: Worcester Fndn. for Exptl. Biol.


I am looking for a genomic clone of human beta-actin in
an SP6/T7 transcription vector.  If anyone has one or knows
where I can find one, I would greatly appreciate it if you 
would e-mail me.

Thanks.

Paulette Dwen
Worcester Foundation for Experimental Biology
Dwen@wfeb2.bitnet
Dwen@sci.wfeb.edu
From: SHANELT@BIOLAN.UNI-KOELN.DE (Sabine Hanelt)
Newsgroups: bionet.molbio.methds-reagnts
Subject: Lambda nm 1149
Date: 12 Jan 93 14:27:09 GMT
Distribution: bionet
X-Vmsmail-To: smtp%"methods@daresbury.ac.uk"
Original-To: methods@uk.ac.daresbury

Hey netters,
does anybody know anything about the phage Lambda nm 1149 and the
host Pop 13?
Thanks for your help.
Sabine
Newsgroups: bionet.molbio.methds-reagnts
From: BIOSEE@UKCC.UKY.EDU (Stephanie Edelmann)
Subject: Re: Glycogen for DNA Precipitation
    <9301072225.AA18226@net.bio.net> <1ikuofINNq43@usenet.INS.CWRU.Edu>
Organization: University of Kentucky
Date: Fri, 8 Jan 1993 22:57:22 GMT

In article <1ikuofINNq43@usenet.INS.CWRU.Edu>
ccy@po.CWRU.Edu (Cheung C. Yue) writes:
 
>
>
>In a previous article, BIOSEE@UKCC.UKY.EDU (Stephanie Edelmann) says:
>
>
>>We also must be using the Glycogen from Boehringer Mannheim.  Add 1ml to
>                                                                    ^^
>Surely you must mean 1 microliter!!  Otherwise it would have cost you
>$50 or more per precipitation!  :-)
>
Well, that would explain why my advisor complains that we spend too much
money all the time.  :-)   Just kidding, I did post a correction as soon
as I found the minor mishaps.
 
Stephanie
 
>ccy@po.cwru.edu
>--
Newsgroups: bionet.molbio.methds-reagnts
From: A8101DAL@vm.univie.ac.at (Martin Hetzer)
Subject: DNA purification
Organization: University of Vienna
Date: Mon, 4 Jan 1993 15:00:18 GMT

Geneclean II glassmilk efficiently removes DNA 200 bases or longer from
agarose gels. Who has tried to isolate shorter (50-200) fragments.

Thank you in advance
       Martin
From: pnj@stein.u.washington.edu (JnP)
Newsgroups: bionet.molbio.methds-reagnts
Subject: PvuII plasmid
Date: 7 Jan 1993 23:10:50 GMT
Organization: University of Washington, Seattle
Distribution: world
NNTP-Posting-Host: stein.u.washington.edu

Thanks for any suggestions or help!  

-Fred
From: DAC050@MUVMS3.MU.WVNET.EDU
Newsgroups: bionet.molbio.methds-reagnts
Subject: subscribe to the group
Date: 11 Jan 93 20:59:00 GMT
Distribution: bionet

Please include my email address in the mailing list.

Thanks
Dinakar
From: vrati@dbe.csiro.au (Sudhanshu Vrati)
Newsgroups: bionet.molbio.methds-reagnts
Subject: email/fax no. of HenrikGaroff/PeterLiljestorm of Karolinska
Date: 6 Jan 93 22:20:46 GMT
Distribution: bionet


I need the email address and fax no. of Prof. Henrik Garoff and Dr. Peter
Liljestrom who are at the Department of Molecular Biology, Huddinge Hospital,
Karolinska Institute, Stockholm, Sweden.  Any body out there who may help ?

Thanks in anticipation,

Sudhanshu


********************************************************************************
    Sudhanshu Vrati, PhD                                  Tel: 61-2-8864964
    CSIRO Division of Biomolecular Engg.,                 Fax: 61-2-8864805
    PO Box 184, North Ryde, NSW 2113              Email: vrati@dbe.csiro.au
    Sydney (Australia) 
********************************************************************************
From: pamaga@biobase.aau.dk (Paulo Magalhaes)
Newsgroups: bionet.molbio.methds-reagnts
Subject: DNA from muscle (1993 version...)
Date: 5 Jan 93 10:25:21 GMT
Organization: The Danish BioBase

Hi,

Last year (!) I asked for some help on DNA extraction from muscle
biopsies. I got some answers, but I'm afraid no real help. So, for
the time being anyway, I'll stick to my present method.

I did, however, get a number of requests for my method. To save me
the trouble of replying individually, I thought it would be a good idea
to post it here. I have to apologise, but my knowledge of
mainframes and the likes is not what I would like it to be... Perhaps
what follows is readable (modems, tab spaces and various other
gremlins always play tricks on me...); any questions, doubts, etc,
just drop me a line.

Again I would like to reiterate my request. If there's anyone out there
who knows of a faster/simpler/more efficient method, I'd very much
like to hear about it. My interest is only in mtDNA, by the way.

Regards from Denmark.

Paulo
Rigshospitalet 4062
Copenhagen - Denmark


====

ISOLATION OF DNA FROM MUSCLE BIOPSIES.


Day 1

	1)	Rinse homogenisers in H2O and soak in 0.1 M HCl for 30'.
	2)	Rinse in H2O, ethanol and let dry.

	3)	Thaw biopsy and transfer to homogeniser
	4)	Add 1 ml of DB and homogenise well.

	5)	Transfer homogenate to an epp.
	6)	Add 25 ul of 20% SDS
	7)	Add 20 ul of 20 mg/ml ProK
	8)	Mix well and incubate O/N at 370C.

	9)	Rinse homogenisers in H2O and soak O/N in 20% Extran.

Day 2

	0)	This is just a reminder to wash the homogenisers and store them away...

	1)	Divide the contents of the O/N digestion into 2 equal portions.

	2)	Add 500 ul of PhOH and vortex briefly.
	3)	Add 500 ul of Chlorof. and vortex briefly.

	4)	Spin for 3'.

	5)	Remove 530 ul of the aqueous phase and transfer it to a new eppendorf.
	6)	Add 530 ul of Chlorof. and vortex briefly.

	7)	Spin for 3'.

	8)	Transfer 430 ul of the aqueous phase to a new eppendorf tube.
	9)	Add 215 ul of 7.5 M NH4Ac.
	10)	Add 860 ul of 100% EtOH.
	11)	Mix gently but thoroughly (keep at 40C if necessary)

	12)	Spin for 15'.
	13)	Remove supernatant carefully.

	14)	Add 1 ml of 70% EtOH.

	15)	Spin for 15'.
	16)	Remove supernatant carefully and dry under a lamp (30 - 40')

	17)	Dissolve the DNA in 50 5l of T-4E.

======
From: axa12@po.CWRU.Edu (Ashok Aiyar)
Newsgroups: bionet.molbio.methds-reagnts
Subject: Re: DNA purification
Date: 4 Jan 1993 18:33:27 GMT
Organization: Case Western Reserve University, Cleveland, OH (USA)
Reply-To: axa12@po.CWRU.Edu (Ashok Aiyar)
NNTP-Posting-Host: thor.ins.cwru.edu


In a previous article, A8101DAL@vm.univie.ac.at (Martin Hetzer) says:

>Geneclean II glassmilk efficiently removes DNA 200 bases or longer from
>agarose gels. Who has tried to isolate shorter (50-200) fragments.

I routinely isolate 100 - 200 bp dsDNA from 2 % agarose gels.
I find that electroelution onto DEAE-cellulose paper (Whatman DE-81)
works well for me.

Ashok
-- 
  Ashok Aiyar   Department of Biochemistry, CWRU   axa12@po.cwru.edu
For Internet Access (Telnet/FTP) in Cleveland, contact info@wariat.org
           Telnet to wariat.wariat.org and login as bbs
   Dial (216) 481-9425/9445 (V.32bis) or (216) 481-9436 (2400 bps)
Newsgroups: bionet.molbio.methds-reagnts
From: wjb1@ellis.uchicago.edu (William J. Buikema)
Subject: Freezer storage of microtiter plates
Reply-To: wjb1@midway.uchicago.edu
Organization: University of Chicago
Date: Mon, 11 Jan 1993 22:05:40 GMT

We are experiencing severe freezer space shortage, in part due to several
cosmid banks in microtiter plates stored there.  We would like to be able 
to efficiently store these plates in the freezer (chest type) in a similar
manner to our freezer boxes of microtubes--in vertical racks that are easily
accessed and organized.  However, I have been unable to find any source for
racks that are designed for microtiter plates.  Considering the large number 
of banks people are storing now, someone out there must have a solution to
our problem.  I would appreciate any help in tracking down a vendor.  Thanks.


William J. Buikema              internet: wjb1@midway.uchicago.edu
University of Chicago               or    w-buikema@uchicago.edu
Dept. of Molecular Genetics &       or    hetman@uchicago.edu 
    Cell Biology, CLSC 313
920 E. 58th St.
Chicago, IL  60637

Newsgroups: bionet.molbio.methds-reagnts
From: rrumpf@magnus.acs.ohio-state.edu (Robert Rumpf)
Subject: Colony Hyb:  DNA conformation?
Organization: The Ohio State University
Date: Tue, 5 Jan 1993 18:06:18 GMT

A friend of mine would like to know in what conformation DNA binds to 
nitrocellulose (ie, one end down, punctured through vertically, horizontally 
splayed out, etc etc...?).  Does anyone know the answer or where we might 
obtain the answer?  Email replies to this account, please...

Bob
From: suter@VAX.MPIZ-KOELN.MPG.dbp.de
Newsgroups: bionet.molbio.methds-reagnts
Subject: re: glycogen
Date: 8 Jan 93 09:51:40 GMT
Distribution: bionet
Content-Identifier: 12
Original-To: methods@uk.ac.daresbury
Conversion: Prohibited

Subj:	glycogen	
--------------------------------------------------------------------------------

+>I remember reading somewhere of people using glycogen as a carrier for precipit
+>ation of DNA.  Can someone enlighten me as to a concentration to use, purity re
+>quired and any pluses or minuses of this procedure that you have encountered? J
+>Dave

+I feel awful about saying this, but I just buy this stuff called Molecular
+Biology Grade glycogen from Boehringer Mannheim.  I don't know the
+concentration, but add 1 ul of it to precipitations of any volume.  It works,
+and hasn't negatively interfered in any noticible may with any subsequent
+steps such as restriction digestion, ligation, or in vitro transcription with
+T7 RNA pol.
+
+Ashok

the boehringer glycogen has a conc. of 20 mg/ml, so you should add something
like 20 ug. this is also the range that i used, but i ordered from Renner (a
german based firm, doesn't matter). glycogen does not interfere with any 
reaction as far as i know, as we used it for preparation of small amounts
of rna, which were then used for various enzymatic reactions, like cDNA
synthesis etc. it does have a disavantage tho: the pellet does not cling
very well to the eppendorf anymore, and may be washed away. this was the
reason that i stopped using glycogen, and started working with 'invisible',
EtOH + LiCl or AmAc produced pellets.... 

cheers

clemens
===============================================================================
Clemens Suter-Crazzolara, PhD
Max-Planck-Institut fuer Zuechtungsforschung
Abteilung Genetische Grundlagen der Zuechtungsforschung
Carl-von-Linne Weg 10
5000 Koeln 30
Tel. xx49-221-5062.221       Fax. xx49-221-5062.213      Priv. xx49-221-581.794
e-mail: suter@vax.mpiz-koeln.mpg.dbp.de
===============================================================================
From: DMEIER@mis.mcw.edu
Newsgroups: bionet.molbio.methds-reagnts
Subject: Buffer Making Program
Date: 6 Jan 93 21:06:40 GMT
Distribution: bionet
Organization: Medical College of Wisconsin (Milwaukee, WI)

Hello All,
  Welcome back to work after these holidays!
  Is there a Mac program that will calculate weights to use for buffer 
preps?  For example, I have a buffer which is 18 mM NaPO4, 10 mM HEPES, 
2 mM KCl, 5 mM MgCl2....etc.  It sure would be nice if I could give a 
program the final molarity and volume desired, and it would crank out 
the weights.  I know this is easy to due but it is so tedious it drives 
me crazy...
  Thanks, and wishing you all a 1993 full of successful experiments, 
lots of papers, and a sprinking of grants!

Dan
dmeier@mis.mcw.edu
From: djt2@po.CWRU.Edu (Dennis J. Templeton)
Newsgroups: bionet.molbio.methds-reagnts
Subject: Re: Subtraction and PCR? [differential display cloning]
Date: 5 Jan 1993 16:37:31 GMT
Organization: Case Western Reserve University, Cleveland, OH (USA)
Reply-To: djt2@po.CWRU.Edu (Dennis J. Templeton)
NNTP-Posting-Host: slc12.ins.cwru.edu


In a previous article, hardy@mighty.facs.fccc.edu (Randy Hardy) says:

>A question for PCR experts: can one generate subtracted libraries using RT-PCR?
> Our problem is that the starting amounts of message are very tiny (ie, from
>rare normal cells) so that traditional RNA subtraction is not feasible.  Seems
>like I've heard some discussion before on using anchored PCR to generate large
>amounts of material for subtraction, just wondered whether anyone has any
>experience and/or recommendations.  Thanks in advance...
>

Hmmm.  one related method is the differential display procedure that was
reported this past summer by Liang and Pardee (Science 257, 967-71/Aug 14
92)

this approach uses RT pcr with one anchored primer (T10-(GAC)-(GATC)) and a
short "random primer" to generate lots (ca 150 -200) of "nonspecifically
amplified" products that are then displayed on a sequencing gel (they label
with 35S-dATP).

by starting with different sources of mRNA, they can view and compare about
150 messages at a time, and with about 100 or so reactions could get close
to looking at nearly all expressed genes.  

We are toying with setting this up, but I would be greatly reassured if
someone out there had a positive experience with theis procedure.
Have any of you tried this reaction??

thanks for your input,

dennis
From: camdna@ubvmsb.cc.buffalo.edu (Darren Natale)
Newsgroups: bionet.molbio.methds-reagnts
Subject: Re: supercoiled DNA migration in agrose [TBE vs. TAE or TPE gels]
Date: 4 Jan 93 17:04:00 GMT
Organization: University at Buffalo
News-Software: VAX/VMS VNEWS 1.41

In article <1992Dec30.100500.2007@gnv.ifas.ufl.edu>, afc@gnv.ifas.ufl.edu writes...
>In article <1hn8b6INN5ee@usenet.INS.CWRU.Edu>, djt2@po.CWRU.Edu (Dennis J. Templeton) writes:
>> 
>> In a previous article, vjongene@isrec-sun1.unil.ch (Victor Jongeneel) says:
>>>migrates fastest, followed by linear and nicked circles.  Linear does
>>>not always separate from supercoiled, nicked circles usually do.  This
>>>does of course not exclude the presence of miniphage (see other
>>>response in thread).  The best way to find out is to start
>>>with freshly purified (CsCl/EtBr) supercoiled DNA and treat it so as
>>>to make linears and nicked circles.
>>>
>> 
>The relative mobilities of the three different forms is affected by just
>about everything: buffer, agarose concentration, voltage, and probably
>moon phase.  In my hands, running TBE gels a la Maniatis, the following
>generalities hold.
> 
>Open circles run slowest.  A 15 kb mitochondrial molecule runs behind even
>uncut genomic DNA.
> 
>Supercoiled plasmids run at about the same mobility as linear DNA of 1/2
>the length.  I assume that this is because they are, in fact, linear 
>molecules of 1/2 the length of a linearized plasmid.  This is highly 
>dependent on the concentration of ethidium bromide in the gel.
> 
>There are lots of papers that discuss this issue rigorously.  I have one
>by Beverly (Nucleic Acids Res 16:925-939, 1988) that talks about pulse
>field gels, but also references the earlier literature.
> 

Another reference: Johnson and Grossman (1977) Biochemistry 16:4217-4224.
 This paper discusses affect of size, conformation, field strength, ionic
strength, and EthBr on migration.