HDTenEightyP/NetNews huggingface dataset:
From: robert@arbo.microbiol.uwa.oz.au (Robert Coelen)
Newsgroups: bionet.molbio.methds-reagnts
Subject: Virology textbook
Date: 9 Sep 1992 02:50:18 GMT
Organization: University of Western Australia
NNTP-Posting-Host: mve.microbiol.uwa.edu.au

I consider Fields VIROLOGY (second edition) one of the best text
books on virology. It is comprehensive and reasonably in depth.

Details: Fields VIROLOGY
         Fields, Knipe (Editors-in-Chief)
         Raven Press, New York
	 ISBN 0-88167-552-0

Any university with ANY biological sciences departments SHOULD have this
2 volume piece in their library.


I hope you netters out there will sharpen your email pencils to vote for
bionet.virology when it comes up again in October !


Robert Coelen
Dept of Microbiology
Newsgroups: bionet.molbio.methds-reagnts
From: bchs1b@Elroy.UH.EDU (Michael Benedik)
Subject: Re: TYE Medium?
Reply-To: bchs1b@Elroy.UH.EDU
Organization: University of Houston
Date: Mon, 14 Sep 1992 02:33:19 GMT

In article <13SEP199207092503@aardvark.ucs.uoknor.edu>, broe@aardvark.ucs.uoknor.edu (Bruce Roe) writes:
>In article <1992Sep11.171500.1@hmivax.humgen.upenn.edu>, dreyfuss@hmivax.humgen.upenn.edu writes...
>>Hello--
>> 
>>Does anyone out there know about the composition of TYE medium for growing
>>E.coli TG1 cells?
>> 
>>Thanks,
>>Jeong-Kook Kim
>>Howard Hughes Medical Institute/University of Pennsylvania
>>Internet:  dreyfuss@hmivax.humgen.upenn.edu
>>(215)898-0172
>
>Hi,
>	The following is what we use for TYE plates and TYE medium:
>
>TYE plates:  
>       10 g. of Bacto-tryptone, 5 g. of yeast extract, 8 g. of NaCl,
>       15 g. of nutrient agar, distilled water to 1 liter; autoclave
>       to sterilize.
>       Cool to 55 deg C, add antibiotic if desired, pour into sterile
>       petri dishes.  (approx. 20 ml/plate)
>
>TYE medium:
>       Same as TYE plates but without any agar.
>
>  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> \  Bruce A. Roe                     Dept. Chemistry and Biochemistry /
> /  BROE@aardvark.ucs.uoknor.edu     University of Oklahoma           \
>  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Bruce,
	I think there is a typo in your response. Are you sure you
mean to say 15g nutrient agar. Don't you just mean plain agar??
Nutrient agar is already a rich media all by itself. 

	---------------------------------------------------
	 Michael Benedik
	 Department of Biochemical and Biophysical Sciences
	 University of Houston
	 INTERNET: Benedik@UH.EDU	BITNET: Benedik@UHOU
Newsgroups: bionet.molbio.methds-reagnts
From: schumann@rhrk.uni-kl.de (Klaus Schumann [Biologie])
Subject: Re: AT Biochem - address etc??
Organization: University of Kaiserslautern, Germany
Distribution: eunet
Date: Fri, 11 Sep 1992 10:54:42 GMT



>Hello M&M's..

>Recently, lurking in the back of Nature, I found a mention of
>a product called Hydrolink MDE (mutation detection enhancement)
>gel. It is purportedly capable of resolving heteroduplex fragments
>with 1 bp change in 900.

>However, Nature failed to give the address, phone, fax, email (hah hah)
>of this company - I suspect they're on t'other side of the pond.

>Can any of you help. If anyone has any experience of this product, I'd
>like to hear from you too.

>Rob Beynon, Biochemistry, Liverpool


There was an article in Biotech Forum Europe (BFE) 8 (11), p. 694-695
: New formulations for improved DNA electrophoresis, by Schiffer R.,  
1991, in which they write that Hydrolink was developed by the J.T Baker
company.
Their adress is:
J.T. Baker B.V.
Rijsterborgherweg 20
POB I
7400 AA Deventer
The Netherlands
Phone +31 5700 87500
Fax   +31 5700 11342


Hope this helps

(Disclaimer: I am in no way connected to the above mentioned company)


Klaus Schumann                    
Fachbereich Biologie
Universitaet Kaiserslautern
D-6750 Kaiserslautern

Internet: schumann@rhrk.uni-kl.de
Newsgroups: bionet.molbio.methds-reagnts
Subject: Re: ssDNA sequencing preps: NaOAc or NOT ?READ/NEXT
From: cytogen@chmeds.ac.nz (Martin Kennedy)
Date: 10 Sep 92 11:01:44 +1300
Followup-To: bionet.molbio.methds-reagnts

In article <jgraham-080992184800@end.chem.indiana.edu>, jgraham@sunflower.bio.indiana.edu (Jim Graham) writes:
> Maybe it's a worn thread but :
> 
> I recently have been using what was describe in a bulletin from Stratagene
> as an improvement in the organic extraction procedure for cleaning up
> phagemid templates. I am using it with Sequenase single stranded
> sequencing. They claim that a SINGLE phenol-CIA extraction is sufficient if
> the PEG phage pellet from a 1.5 ml culture supernatant is resuspended in a
> 400ul of  0.3 M NaOAc. Others in my lab agree, but I find that more than
> half of my samples show a large grey smear instead of a ladder. Must I
> return to the laborious 2 phenol/CIA, 3 CIA extraction procedure ? I have
> always found that to work, but it is a real pain in the @#$#.
> 
> Thanks for your help,
> 
> Jim
> J. E. Graham
> Biology/Chemistry Departments
> Indiana University -Bloomington

Jim-

I never use more than a single phenol extraction for M13 ss preps; I add 100ul
of TE to the PEG pellet (without resuspending) then add 50ul of phenol (not
phenol-CIA), vortex the hell out of them for about 10-20", sit on bench for
5-15', then vortex again for 10-20". Spin and aspirate S/N into a new tube into
which I've already added 10ul of 3M NaOAc, and ppt with 250ul EtOH.  This works
well and consistently.

Cheers, 

Martin
From: beynonrj@uxb.liv.ac.uk (Dr. R.J. Beynon)
Newsgroups: bionet.molbio.methds-reagnts
Subject: AT Biochem - address etc??
Date: 8 Sep 92 16:45:15 GMT
Organization: The University of Liverpool
X-Newsreader: Tin 1.1 PL5

Hello M&M's..

Recently, lurking in the back of Nature, I found a mention of
a product called Hydrolink MDE (mutation detection enhancement)
gel. It is purportedly capable of resolving heteroduplex fragments
with 1 bp change in 900.

However, Nature failed to give the address, phone, fax, email (hah hah)
of this company - I suspect they're on t'other side of the pond.

Can any of you help. If anyone has any experience of this product, I'd
like to hear from you too.

Rob Beynon, Biochemistry, Liverpool
From: byrne@soma.umdnj.edu (Bruce Byrne)
Newsgroups: bionet.molbio.methds-reagnts
Subject: Re: HIV
Date: 14 Sep 92 14:36:08 GMT
Distribution: bionet

BMA14432@VAX1.UTULSA.EDU writes:


>Dear Netters,
>Our NEWS group does not allow posting to the HIV thread so I am forced to post here.
>Does anyone have recent references for HIV replication, transcriptional
>regulation, and splicing? Any and ALL responses are greatly 
>appreciated. Thanks in advance.

Mark, 
  I assume you're referring to bionet.molbio.hiv   That group has been very
quiet, and certainly without references to the things you're asking about.
I've wondered if specific groups in a field as competitive as HIV research
might suffer from people being afriad that good thoughts will be taken up by
competitors.  Sorry state.

Bruce Byrne
From: skspoidn@susssys1.reading.ac.uk
Newsgroups: bionet.molbio.methds-reagnts
Subject: HgiE II
Date: 7 Sep 92 14:33:48 GMT
Distribution: bionet
Original-To: methods@uk.ac.daresbury

The subject line says it all :)

After several subclonings into an already complicated vector,
 HgiE II is the only enzyme on the plasmid map which will 
linearize it appropriately. Unfortunately, the map
 is the only place I can find any reference to it!

If anyone has heard or knows of a commercial source
 of this enzyme, I would appreciate it.

HgiE II:  recognition is ACCNNNNNNGGT

ps plasmid is pXT1 from Stratagene
From: BMA14432@VAX1.UTULSA.EDU
Newsgroups: bionet.molbio.methds-reagnts
Subject: HIV
Date: 14 Sep 92 13:34:58 GMT
Distribution: bionet


Dear Netters,
Our NEWS group does not allow posting to the HIV thread so I am forced to post here.
Does anyone have recent references for HIV replication, transcriptional
regulation, and splicing? Any and ALL responses are greatly 
appreciated. Thanks in advance.
Mark Brudnak
INTERNET: BMA14432@VAX1.UTULSA.EDU
From: jmv@canctr.mc.duke.edu
Newsgroups: bionet.molbio.methds-reagnts
Subject: 33-P: how well does it work?
Date: 10 Sep 92 21:42:07 GMT
Reply-To: jmv@canctr.mc.duke.edu
Organization: Duke U. Med. Ctr., Durham, NC

As recently noted by several netters, NEN has offered 33-P as an
alternative to 32-P. Our lab has tried it for PCR & it worked.
Is available in gamma (end-labeling) form?
Has anyone used it for sequencing? Or Probe labeling? I'd
appreciate news on this!

czesc!
DB, Duke U. Med/Neurology
From: MURPHY@JII.AFRC.AC.UK
Newsgroups: bionet.molbio.methds-reagnts
Subject: pam tables
Date: 8 Sep 92 10:41:00 GMT
Distribution: bionet
Original-To: METHODS@UK.AC.DARESBURY

Does anybody out there have a set of GCG-format peptide comparison tables at
different PAM levels, or even better a VMS equivalent of "pam" in the blast
suite which has a GCG-format output?
Thanks,
George Murphy
********************************************************************************
George Murphy                     |Snailmail: 
                                  |     Molecular Genetics,
JANET:murphy@uk.ac.afrc.jii       |     Cambridge Laboratory,
INTERNET:murphy@jii.afrc.ac.uk    |     JI Centre for Plant Science Research,
                                  |     Colney Lane,
Telephone: +44 603 52571          |     Norwich NR4 7UJ,
Fax:       +44 603 505725         |     U.K.
********************************************************************************
From: thsiao@ANOLIS.BNR.USU.EDU (Ting H. Hsiao)
Newsgroups: bionet.molbio.methds-reagnts
Subject: PCR enhancers
Date: 10 Sep 92 16:32:55 GMT
Distribution: bionet

Dear Netters,

I am interested in the use of PCR enhancers.  I would like to know if any one
has experience with the use of Stratagene's Perfect Match Polymerase Enhancer.
Is this a single-stranded DNA binding protein?  What is the difference with
USB's single-stranded DNA binding protein or GP 32?  How effective are these
products in getting better PCR yields?  Any suggestion and tips will be
appreciated.



   +---------------Ting H. Hsiao ---------------+
   | Dept. of Biology, Utah State University    |
   | Logan, UT 84322-5303, U.S.A.               |
   | PHONE: (801) 750-2549; FAX: (801) 750-1575 |
   | E-MAIL: thsiao@anolis.bnr.usu.edu          |
   +--------------------------------------------+
Wed, 9 Sep 1992 12: 36:26 +0200
               Wed, 9 Sep 1992 15: 42:18 +0200
From: suter@VAX.MPIZ-KOELN.MPG.dbp.de
Newsgroups: bionet.molbio.methds-reagnts
Subject: contaminant
Date: 9 Sep 92 13:42:18 GMT
Distribution: bionet
Content-Identifier: 12
Original-To: methods@uk.ac.daresbury
Conversion: Prohibited

dear netters,
i have a completely rediculous observation, which could be meaningful in some 
way.
the problem is the following: i prepare a stock solution of 1 M MgSO4,
autoclave, poor out (under sterile conditions) half of the contents, and
store the remainder on my bench. 
guess what happens: after half a year at RT, a fungus (diameter 2 cm, biomass
unknown) is floating around.
this happens only with this chemical. i accept that the initial infection is due
to my sloppy handling (i am not that bad tho...).

my question however is: where does the biomass come from ? from:
1. CO2 in the air above the solution (this would mean c-fixation!)
2. a contaminant in the MgSO4 (this would be bad news, since the experiment
is reproducible with several different MgSO4 lots from diff. companies) could
a contaminant explain the apperant high biomass?
3. somehow a carbon source is introduced into the bottle during autoclaving
or extremely sloppy handling (i only notice this with this solution !)

you are probably all grinning at this stage....any microbiologists out there
with an explanation ?

cheers, clemens
----------------------------------> cut here <----------------------------------
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. xx49-221-5062.21
suter@vax.mpiz-koeln.mpg.dbp.de
------------------------------------------------------------------------------- 
     ! all job offers should include a self-addressed, stamped envelope !
-------------------------------------------------------------------------------
From: rmkdhhp@ucl.ac.uk (Dr Huaizheng Peng)
Newsgroups: bionet.molbio.methds-reagnts
Subject: gene amplification
Date: 15 Sep 92 10:20:22 GMT
Distribution: bionet
Original-To: methods@uk.ac.daresbury

Hi, group:

Do you have the experience to use double-labelling probes to detect gene amplification? Would you please pass me some reference?

Thank you in advance.

Dr. Peng HZ
 RMKDHHP@uk.ac.ucl
From: bsh@MED.PITT.EDU (Basavaraju Shankarappa)
Newsgroups: bionet.molbio.methds-reagnts
Subject: Re: Frozen competent RecA- strains
Date: 10 Sep 92 20:12:40 GMT
Distribution: bionet

LOTS OF STUFF DELETED
> > I'm not sure how important the method of freezing is. If you make your own > cells, it is probably safest to freeze in liquid N2 or in a dry ice/ethanol
 
One comment:
I follow the simple CaCl2 protocol in Methods Enzymology.  One observation 
that may be significant to people who freeze cells slwoly.  In the procedure
I follow, after treating the cells with CaCl2, I incubate cells on ice for
about 24 hours in the refrigerator.  One common mistake I have seen people do
at this stage when snap freezing on LN2 or dry ice is that people forget to
look at the bottom of the tubes.  If you just take a glance you can see all
the cells pelleted at the bottom.  So do a quick vortexing of cells before
snap freezing.  

Is this something that may be going unnoticed.  I am not sure how much time
it does take for the cells to settle down.  But if the cells do settle down
will it adversely affect the viability of cells because of clumping?

I would be grateful if someone can expand on this.  

Raj Shankarappa
Univ of Pittsburgh
Newsgroups: bionet.molbio.methds-reagnts
From: John.Hardham@bbs.oit.unc.edu (John Hardham)
Subject: Re: Ligation trouble...
Organization: Extended Bulletin Board Service
Date: Wed, 9 Sep 1992 12:43:53 GMT

Dispite all of the advances in science, ligations are still like vodoo
magic.  Once you get them working, you don't ask too many questions...

Anyway, here are a few questions/tips that have helped us in the past.

     1)  You don't mention anything about controls in your post.  It
         is helpful to use a cut(not alk. phos.) vector control in your
         ligations.  This will tell you if your vector can undergo at
         least a first order ligation.  If this fails to work, there
         could be a number of things wrong.  Some of these include
         the following:  single stranded nuclease in the restriction
         enzyme, metal contaminants, phenol carry-over.

     2)  Try cutting something like lambda DNA with your restriction
         enzyme, clean it up, and try to ligate it back together again.
         This may help to get your ligations working without burning
         up your vector and insert stocks.

     3)  Try switching brands of restriction enzyme.  This may sound
         funny, but we had a batch of enzyme with a single stranded
         nuclease contaminant that chewed up our overhangs.

     4)  What type of alkaline phosphatase are you using?  Is it
         possible that you are not totally inactivating the enzyme?
         We have had good luck with Artic Shrimp AP (from USB).
         This enzyme can be added to the restriction digestion, or
	 after the vector is digested.  It is totally inactivated
	 at 65oC, which can make experiments much shorter.

     5)  How clean are your insert and vector DNAs?


     6)  Pray to the gods of science for it to work!


--
   The opinions expressed are not necessarily those of the University of
     North Carolina at Chapel Hill, the Campus Office for Information
        Technology, or the Experimental Bulletin Board Service.
           internet:  bbs.oit.unc.edu or 152.2.22.80
Newsgroups: bionet.molbio.methds-reagnts
From: apk@phoenix.oulu.fi (Ari-Pekka Kvist)
Subject: Chromosomes on disk(ette)?
Organization: University of Oulu, Finland
X-Newsreader: Tin 1.1 PL4
Date: Tue, 15 Sep 1992 06:27:19 GMT

Hello folks

Does anyone have human chromosomes already drawn to diskette? I mean
G-banded chromosomes at metaphase state (the very usual ones which you 
can find in every textbook). It would be better if they are in vector-
graphichs format (CorelDraw, Arts&Letters, Designer...) but bitmaps
will do also (bmp, gif, pcx..) or HPGL, Tiff or postscript-format. 

Thanks in advance



      Researcher           (Bitnet   : lbio-apk at finou.bitnet)
      Ari-Pekka Kvist      (IBM      : lbio-apk at finou.oulu.fi)
                           (UNIX     : apk@phoenix.oulu.fi or
      Oulu university                  kvist@convex.csc.fi)
      Department of Medical Biochemistry
      Kajaanintie 52 A
      SF-90220 Oulu
      Finland

      Tel. 358-(9)81-5375840
From: robison1@husc10.harvard.edu (Keith Robison)
Newsgroups: bionet.molbio.methds-reagnts
Subject: Re: N-ter labelling of proteins
Date: 14 Sep 92 22:33:25 GMT
Distribution: bionet.molbio.methds-reagnts

justman@husc10.harvard.edu (Craig Justman) writes:


>i have seen allusions in the current literature to label the n-terminus
>specifically by controlling the pH of the reaction, but have found no 
>references.  before i go re-inventing the wheel and trying to determine the
>optimal pH (by wasting protein and reagent), i would like to know if anyone
>has seen such a reference (or am i missing something obvious?)

Not the method you suggest, but heres one:

  Jay, DG.  1984.  JBC 259:15572-15578.
	A general procedure for the end labeling of proteins and positioning
	of amino acids in the sequence.


Keith Robison
Harvard University
Department of Cellular & Developmental Biology
Department of Genetics / HHMI

robison@ribo.harvard.edu
From: adavies@vax.oxford.ac.uk (Anthony Davies)
Newsgroups: bionet.molbio.methds-reagnts
Subject: re: Epstein Barr
Date: 9 Sep 92 07:46:08 GMT
Organization: Institute of Virology, Oxford, UK

> Epstein-Barr virus (EBV) is a herpes virus and is an aetiological agent of
> glandular fever (infectious mononucleosis). The virus is also strongly 
> implicated as having a causal relationship to African Burkitt's lymphoma
> and to nasopharyngeal cancer (note other cofactors are generally present !)
> The major route of transmission of EBV in young adults appears to be kissing
> with exchange of saliva (not the kiss on the cheek variety !). Evidence from
> cases on a submarine indicates that close contact (but not kissing) is not
> sufficient to transmit the virus. Whilst the virus appears not to be very contagious,
> one of the early cases of infectious mononucleosis attributed to EBV was in
> a technician in a lab where they worked with it. Present day biohazard hoods
> and good microbiological practices (gloves, alcohol wiping surfaces, etc) should
> be sufficient to keep you free of EBV. 

                                       |||One of the Klein's worked with EBV for a
> lifetime and never seroconverted !|||

Actually Eva Klein did convert a few years ago - - from her granddaughter!!
________________________________________________________________________________

Anthony Davies                Voice: 865-512361
Institute of Virology         Fax:   865-59962
Mansfield Road                Vax:   adavies%uk.ac.oxford.vax
Oxford OX1 3SR
UK
________________________________________________________________________________
From: BECKERM@SIMSC.BITNET
Newsgroups: bionet.molbio.methds-reagnts
Subject: ammonia cleavage from proteins
Date: 5 Sep 92 18:52:00 GMT
Distribution: bionet

I'm not sure if my first message got throught, I think I had the wrong address
nor do I know what format to use, but  I'm looking for references to ammonia
cleavage from proteins, specifically light induced reactions (UV & visible)
and whether one mechanism is preferential to another for a particular
amino acid in the sequence.  I'd appreciate any help, mary
beckerm@simsc.bitnet
From: mcgraw%gandal.dnet@SERVER.UGA.EDU
Newsgroups: bionet.molbio.methds-reagnts
Subject: lambda won't cut
Date: 9 Sep 92 14:48:16 GMT
Distribution: bionet



Hello netters,

A colleague provided us with some lambda clone DNAs "purified" from plate
lysates.  They won't cut with EcoR1.  We tried further purification with
additional phenol/chloroform extractions.  The uncut DNA looks good on a
gel, and the OD's are good.  The inserts should cut out with EcoR1 based on
the way the library was made (R1 linkers).  We haven't worked with lambda
in quite a while, but I imagine that some of you out there are cutting
yours successfully as you read this.

What do you suggest?

                                Mike Grosse
                                McGraw lab
                                University of Georgia

Newsgroups: bionet.molbio.methds-reagnts
From: num208ww@MBDS.NRC.CA (Warren Wakarchuk)
Subject: Re: non-specific cleavage of X-gal
Reply-To: num208ww@MBDS.NRC.CA
Organization: NRC, OTTAWA, ONTARIO, CANADA.
Date: Fri, 11 Sep 92 02:04:01 GMT

In article <1992Sep9.110653.202722@uctvax.uct.ac.za>, coyne@uctvax.uct.ac.za writes:
stuff deleted..
>If X-gal is such a sensitive substrate for detecting beta-galactosidase
>activity, and if most gram negative bacteria possess other glycosidases which
>are capable of cleaving X-gal, is it ever possible to get truly "white" 
>colonies where lacZ is NOT expressed from an upstream promoter (as in operon
>fusions) in a lac- gram negative strain grown on media containing X-gal?
stuff deleted..

Vernon I would agree with Michael that this response is strain
dependant, and that you should "screen" other strains for the ability
the turn blue on X-gal.  You might also want to try other substrates. 
X-gal is not very sensitive compared to ONPG for example, except you
can't use ONPG in plates.  You might try
4-Methyl-umbelliferyl-galactoside "MUG" (SIGMA sells this) as an
alternative.  It is florecescent when cleaved under 304 nm UV. You may
see that the enzyme in your Vibrio which cleaves X-gal doesn't work as
well with MUG (it might also work just as well).  Some of these
enzymes are quite picky about the aglycon (non-sugar) part of these
substrates.
Good Luck...

*************************************************************************
Dr. Warren Wakarchuk   Prefered email: wakarchu@biologysx.lan.nrc.ca
                       Alternate     : NUM208WW@MBDS.NRC.CA
National Research Council Canada, Protein Structure and Design
Ottawa, Ont., Canada K1A 0R6 ***THESE ARE MY OPINIONS NOT THOSE OF NRC***
From: wmelchior@NTBTOX.NCTR.FDA.GOV ("Bill Melchior, NCTR/FDA")
Newsgroups: bionet.molbio.methds-reagnts
Subject: Re: Epstein Barr
Date: 15 Sep 92 17:37:53 GMT
Reply-To: wmelchior@NTDOC.NCTR.FDA.GOV
Distribution: bionet

>We also use EBV for the same purpose; our employee-health department required 
>a blood test to demonstrate a positive anti-EBV antibody titer before working
>with it. Evidently most folks (at least in the U.S.) have titers from exposures
>during childhood/adolescence. 

I once heard that the Salk polio vaccine was contaminated with EBV, so that 
many people who took it became anti-EBV positive.  Does anyone know if this
is indeed true?
________________________________________________________________________________
The opinions stated are mine, not those of NCTR or its sponsoring organizations.

Bill Melchior                                ||   "You have lawyers the way
National Center for Toxicological Research   ||    other people have mice."
Jefferson, AR  72079                         ||
(501) 543-7206                               ||   -Kenneth Duncan, English
                                             ||    Health & Safety Executive,
WMELCHIOR@NTDOC.NCTR.FDA.GOV                 ||    to US regulators
Newsgroups: bionet.molbio.methds-reagnts