HDTenEightyP/NetNews huggingface dataset:
From: mwitten@HERMES.CHPC.UTEXAS.EDU
Newsgroups: bionet.molbio.bio-matrix
Subject: Re: Please Renew!!! (fwd)
Date: 18 Aug 92 21:42:18 GMT
Distribution: bionet

Well, to be brutally honest, I've paid for the past three years
and gotten nothing but one newsletter. I don't know what this is
about and I am feeling rather foul (fowl) about it!

Matthew

> Forwarded message:
> > From BIOSCI-REQUEST@genbank.bio.net Mon Jul 27 10:32:26 1992
> > Date: Mon, 27 Jul 92 10:18:45 CDT
> > From: dbd@theory.BCHS.UH.EDU (Dan Davison)
> > Message-Id: <9207271518.AA02085@theory.BCHS.UH.EDU>
> > To: bio-matrix@genbank.bio.net
> > Subject: Please Renew!!!
> > 
> > Dear Biomatrix members,
> > 
> > at the moment we only have 10 renewals on the biomatrix memberships
> > that went out in the last newsletter.  It's hard to keep an organization
> > going with that few people...if you want to discuss the relative merits
> > of being a member vs. a lurker, this is the forum to do it.  Post notes
> > to	
> > 	bio-matrix@genbank.bio.net
> > 
> > 
> > dan "I'm a member" davison
> > 
> > 
> --------
> 
> Matthew, did you renew our gentools biomatrix subscription?  Does CHPC pay
> for it?
> 
> (In the dark.........).....Sarah
> 


-- 

_____________________________________________________________________

Matthew Witten, Ph.D. MED
Director, Applications Research & Development
Associate Director, 
UT System Center For High Performance Computing
Balcones Research Center, 1.154 CMS
10100 Burnet Road, Austin, TX 78758-4497 USA

Phone: (512) 471-2472  FAX: (512) 471-2445  

E-MAIL  MWITTEN@CHPC.UTEXAS.EDU
      or
        MWITTEN@UTHERMES.BITNET

"some intellectuals make their living by creating 
obscurities for the rest of us to puzzle over"
_____________________________________________________________________
Newsgroups: bionet.molbio.methds-reagnts
Subject: Re: NaOAc in seq gels
From: cytogen@chmeds.ac.nz (Martin Kennedy)
Date: 20 Aug 92 17:25:03 +1300
Distribution: bionet

In article <9208190147.AA28423@cscgpo.anu.edu.au>,
 Klaus.Matthaei@anu.edu.au writes:> 

> I have had quite a bit of E-mail about my comment on the Na acetate method.
>  I make the solution up in water and don't bother to Ph it.  Most comments
> to me say that they also use the acetate but use a final concentration of
> 1M in the bottom tank.  I found my addition so good that I didn't bother to
> try anything else.  It is possible of course that other concentrations are
> better.  Maybe someone else out there has direct comparisons?

I've done the same thing for years, using NaOAC in H2O, at final conc
1M in bottom tank, only I add it one hour from the end of the run, 
and turn the power down a little as the gel temperature seems to 
creep up a bit high otherwise (I normally run at 40W in a BioRad
Sequigen, but turn it down to 35W after adding NaOAc).  I've
compared it with other gels run in buffer gradients, and the compression
is about the same, and a lot easier to achieve!

I've given up fixing my gels beore drying - I simply transfer the gel
direct onto 3MM paper after separating the plates, and dry for a bit
longer than usual.  This seems to work fine, although they can
be a little sticky in places.

Cheers,

Martin
From: derekr@yang.earlham.edu
Newsgroups: bionet.molbio.methds-reagnts
Subject: MacVector
Date: 13 Aug 92 14:46:22 EST
Organization: Earlham College, Richmond, Indiana

We've been experiencing difficulties with the program MacVector.  Does
anyone know of a similar program for the Macintosh that aligns sequences?
Thank you.

Derek Reubish
Dept. of Biology
Earlham College
Newsgroups: bionet.molbio.methds-reagnts
From: Elliot Lefkowitz <Lefkowitz@orion.cmc.uab.edu>
Subject: Re: Peltier PCR Instruments - Possible explaination of mixed reviews
X-Xxmessage-Id: <A6B6D342F5012D46@satf.cmc.uab.edu>
X-Xxdate: Tue, 18 Aug 92 16: 18:10 GMT
Organization: University of Alabama
X-Useragent: Nuntius v1.1.1d8
Date: Tue, 18 Aug 1992 21:14:19 GMT

In article <1992Aug18.185916.15290@fccc.edu> Randy Hardy,
hardy@mighty.facs.fccc.edu writes:

>Well, we got an early MJ cycler several years ago which eventually
developed
>problems and was "upgraded" with a new element (under warranty),  Since
then we
>have had ZERO problems; this on a cycler that we use every day (often
several
>times/day).  A very satisfied user.

Ditto. Same Experience.


**************************************************************
*  Elliot Lefkowitz, Ph.D.     |  University of Alabama      *
*  Lefkowitz@Orion.cmc.uab.edu |  Department of Microbiology *
*  Lefkowitz@Uabcmc.Bitnet     |  Birmingham, AL  35294      *
*                              |  205-934-1946               *
**************************************************************
From: PHILLIPSA@UK.AC.AFRC.LARS (Andy Phillips)
Newsgroups: bionet.molbio.methds-reagnts
Subject: Ligation in melted Nusieve
Date: 12 Aug 92 14:54:00 GMT
Distribution: bionet
Original-To: METHODS@UK.AC.DARESBURY.DLGM

The booklet that comes with Nusieve GTG agarose claims that ligation
of isolated fragment to vector can be carried out in melted Nusieve.
Some guys here have tried this with plasmid vectors and it works fine.
My question is: will this technique work with lambda insertion vectors
(eg ZapII), or will the agarose interfere with ligation and/or
packaging (I could test this myself, but Gigapack Gold isn't
the cheapest ingredient ever).
Thanks
Andy Phillips
Cell Biology Dept, LARS, Bristol, UK
From: botbvk@lure.latrobe.edu.au
Newsgroups: bionet.molbio.methds-reagnts
Subject: Dictyostelium viruses?
Date: 19 Aug 92 07:42:18 GMT
Organization: VAX Cluster, Computer Centre, La Trobe University

Hi there,
does anybody know anything about viruses or other extrachromosomal
nucleic acids in Dictyostelium discoideum or any other molds?
I was not able to find any references and it may be that nobody
published anything. However, I know people have cloned strange genes
out of molds.
If there is anybody willing to communicate about this matter, please
contact me.

thank you in advance:  Beat von Kanel

Email:botbvk@lure.latrobe.edu.au

Beat von Kanel
Department of Botany
la Trobe University
Bundoora, Victoria
Australia, 3084
From: penas@ucbeh.san.uc.edu
Newsgroups: bionet.molbio.methds-reagnts
Subject: screening cDNA libraries
Date: 13 Aug 92 16:58:57 EST
Distribution: world
Organization: Univ. of Cincinnati

I just finished reading an article on Molecular  Pharmacology where the authors
describe a solution-phase library screening method to scree a lamda gt10 cDNA
library.  I personally thought the method to be neet for the isolation of
clones with low representation in the library.  Does anyone else have any
experience doing this type of screening?  If so, could you send me your
thoughts and comments?  They will be greatly appreciated.

Sincerely,
-- 
Sandra Pena de Ortiz     : penas@ucbeh.bitnet
University of Cincinnati
College of Medicine
Toxicology Program
Newsgroups: bionet.molbio.methds-reagnts
From: leanne@arbo.microbiol.uwa.oz.au (Lee Sammels)
Subject: re: MacVector
Organization: University of Western Australia
Date: Fri, 14 Aug 1992 08:33:39 GMT

In article <1992Aug13.144622.19374@yang.earlham.edu> derekr@yang.earlham.edu writes:
>We've been experiencing difficulties with the program MacVector.  Does
>anyone know of a similar program for the Macintosh that aligns sequences?
>Thank you.
>
>Derek Reubish
>Dept. of Biology
>Earlham College
We use MACAW version 1.05 for Win 3.1 and we believe somebody has ported it to the Macintosh platform, maybe the authors of this program can help you. Email address: schuler@ncbi.nlm.nih.gov


Good Luck

Lee
Dept of Microbiology
UWA
From: coutavas@mcclb0.med.nyu.edu
Newsgroups: bionet.molbio.methds-reagnts
Subject: pET9 vector sequence
Summary: Need pET9 vector sequence
Keywords: pET9c
Date: 17 Aug 92 00:53:44 GMT
Reply-To: Coutavas@mcclb0.nyu.med
Organization: NYU Medical Center, New York, NY 10016, USA



	Does anyone out there have the sequence for pET9 vector, or
know how I might be able to get it?  Many thanks in advance.


XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
Elias Coutavas				Phone: (212) 263-5127
					Fax: (212) 263-8166
NYU Medical Center 
Biochemistry Dept. 			E-mail: coutavas@mcclb0.med.nyu.edu
550 First Av. NY NY  10016  			coutavas@nyumed.bitnet 
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
Newsgroups: bionet.molbio.methds-reagnts
From: kramer@umigw.miami.edu (Jack Kramer)
Subject: polyclar AT
Organization: University of Miami, RSMAS
Date: Wed, 19 Aug 92 00:39:37 GMT

I have seen references to "Polyclar AT" for use in cleaning up 
plant DNA extractions.  I can't find it anywhere.  Does anyone know of
a vendor or another name for the reagent?
From: bsh@MED.PITT.EDU (Basavaraju Shankarappa)
Newsgroups: bionet.molbio.methds-reagnts
Subject: Re: Automated sequencing
Date: 19 Aug 92 21:33:06 GMT
Distribution: bionet

> Hello out there,
> Automated DNA sequencers are used for sequencing DNA, and can also be
> used for say determining the size of labeled DNA fragments.
> I was wondering if anyone is aware of other possible or potential
> applications of these machines. Any ideas?
> 
> Johan de Boer 
> jdboer@sol.uvic.ca
> 
Use of automated sequencer and/or the principle IMHO is presently
the big thing in forensics to correct for the so called
BAND SHIFTING.  This is done by incorporating size markers which
have been labeled differently along with the sample.  This sample
is usually PCR products obtained from using primers  that are again 
labeled differently with different fluorescent labels.  Thus each primer
that is specific for each gene will generate specific bands the size of
which is internally controlled for.  
This is also being attempted to be used in VNTR mapping.
and possibly for identifying the gene responsible for a genetic disease 
using mapping techniques similar to those above.  

ABI has software currently available for doing such kind of work.  But
I do not know whether anyone has standardized the different techniques.

Also the other use is in diagnostics for use with multiplex PCR; where
you amplify with different primers and even if the products overlap,
because of the different fluorescent tags on them, you should be very
easily possible to identify the presence of a specific pathogen.

I think this technology is going to revolutionize almost all the 
applications that would require or benefit from electrophoretic analysis.
Raj Shankarappa.
From: READY@UTBC01.CM.UTEXAS.EDU
Newsgroups: bionet.molbio.methds-reagnts
Subject: Super Broth
Date: 19 Aug 92 17:55:47 GMT
Distribution: bionet

Andrew Cockburn writes...

>I saw an article a few weeks ago in a biotech company's newletter
>touting the advantages of growing plasmids in rich media.  The 
>newletter went the way of all such things, but now I wonder if I
>should have kept it.

>Does anyone have experience using rich media (eg 2x or 3x L broth)
>for growing plasmids in E. coli?  Do the specific vector and host
>matter?  Are the yields high enough to justify switching from L
>broth?  What is your media recipe?  Do you use the same plasmid
>prep as before?

Andrew - 
	For plasmid preps (both large scale and mini) I habitually use
2xYT + 0.2% glucose. 2x YT is (per liter):  16 g Difco Tryptone
                                            10 g Difco Yeast Extract
                                             5 g NaCl

I confess I have never quantitated the difference in yield between this and
standard broth, but eyeball measurement has indicated it to be significant.
Typical yields for 10 ml minipreps are 50-100 ug for pUC-like plasmids. My best
1 liter prep was > 9 mg plasmid. We get different yields from different strains,
but in general we get better yields from "upscale" media. Whether it's worth
it is up to you and probably depends on what your plasmid copy number is. 
Most of us would not use up 9 mg of plasmid in a century, so it may be overkill.
(However, we use pUC for restriction and transformation controls all the time - 
my 9 mg only lasted about 2 years.)

Good luck,
Mike R.

    _______________________________________________________________________
   | Dr. Michael P. Ready                     | READY@UTBC01.CM.UTEXAS.EDU |
   | Clayton Foundation Biochemical Institute | Phone: (512)471-3625       |
   | University of Texas                      | FAX:   (512)471-8696       |
   | Austin, Texas 78737                      |                            |
   |__________________________________________|____________________________|
  
Newsgroups: bionet.molbio.methds-reagnts
From: ca566@cleveland.Freenet.Edu (Michael Holloway)
Subject: Re: promoter sequence listings
Reply-To: ca566@cleveland.Freenet.Edu (Michael Holloway)
Organization: Case Western Reserve University, Cleveland, OH (USA)
Date: Sun, 16 Aug 92 02:09:43 GMT


In a previous article, DMEIER@mis.mcw.edu () says:

>Enter your message below. Press CTRL/Z when complete, or CTRL/C to quit:
>Hello all,  Can you help me?  I am looking for a listing of eukarotic promoter
>sequences.  For example, although estrogen response elements are similar, a
>number of bona fide EREs have been identified which differ at specific bases.
>Is there a list that has all the permutations of EREs, and other elements?      Thanks mucho in advance.       ...Dan Meier, DMEIER@mis.mcw.edu
>
By now you must be deluged in responses but I'll repeat the obvious one
anyway and throw in a couple of journal references that others may not have
given.  By far the easiest, and most extensive, way of getting what you
want is to ftp to ncbi.nlm.nih.gov, the NIH archives, and download the TFD
and EPD databases.  If you're lucky enough to have access to a Unix box,
there's even software for using the darn things to their full extent (I am
not so fortunate).
References:
David Ghosh, New developments of a Transcription Factors Database, 1990, TIBS
16:445-447.
	-Previous Ghosh references are sited. You may have even been 
	contacted by him by now.
Edgar Wingender, Compilation of transcription regulating proteins, 1988 NAR
16:1879-1903.
	-I seem to recall that this fella was also making a database but I
	can't recall the particulars at the moment.
J.Locker and G.Buzard, A dictionary of transcription control sequences,
1990, DNA Sequence-J. DNA Sequencing and Mapping 1:3-11
	-Interesting in that the authors set out to limit their list to
	just vertebrates and pol II promoters.

If you're scanning a sequence I can recommend the GCG similarity search
programs.  They're arkward to use, frustrating sometimes, but they get the
job done.

Warning: Do not, under any circumstances, start typing in your own
database.  It will take you much longer than you can imagine.  Use what's
out there already.

Mike
-- 
E-mail: mhollowa@ccmail.sunysb.edu (mail to freenet is forwarded)
phone:  (516)444-3612
I would claim to speak for my university but no one is likely to
believe it.
From: bioysl@lure.latrobe.edu.au
Newsgroups: bionet.molbio.methds-reagnts
Subject: YEp13 primers????????  URGENT!!!!!
Date: 19 Aug 92 01:26:56 GMT
Organization: VAX Cluster, Computer Centre, La Trobe University

Hi! Friends!
	I need to know if anyone has got PRIMERS at BamHI site of YEp13 vector.
	I am going to screen a YEp13 yeast genomic library by using PCR.

Thanks in advance.

Yong Shu LIU
Biochem Dept
La Trobe Uni.
Bundoora, Vic. 
Australia 3083
Newsgroups: bionet.molbio.methds-reagnts
From: ca566@cleveland.Freenet.Edu (Michael Holloway)
Subject: Re: Scientific Spelling
Reply-To: ca566@cleveland.Freenet.Edu (Michael Holloway)
Organization: Case Western Reserve University, Cleveland, OH (USA)
Date: Mon, 17 Aug 92 23:52:10 GMT


In a previous article, tcritchl@sdcc3.ucsd.edu (Tod Critchlow) says:

>I was wondering if anyone new of a list of Scientific
>terms that could be loaded into or were already in
>a format usable by Microsoft Word's spelling checker.
>

I recall seeing a medical dictionary file for Wordperfect though I guess
that this probably wouldn't fit the bill.  Do you know of any way it could
be converted?  I would assume that you could use a dic file from someone
else in the same field.  Even a dic file for science, in general, would
probably be inadequate for words within a specific field.  

If you get any useful responses please post them.

Mike

-- 
E-mail: mhollowa@ccmail.sunysb.edu (mail to freenet is forwarded)
phone:  (516)444-3612
I would claim to speak for my university but no one is likely to
believe it.
From: wmelchior@NTBTOX.NCTR.FDA.GOV ("Bill Melchior, NCTR/FDA")
Newsgroups: bionet.molbio.methds-reagnts
Subject: EB assay for DNA (was InVitrogen Dipsticks)
Date: 20 Aug 92 14:14:26 GMT
Reply-To: wmelchior@NTDOC.NCTR.FDA.GOV
Distribution: bionet

>If working with Ethidium Bromide holds no fear for
>you, you might try a fluorescence spot test we often use. Briefly, 2 ul
>droplet of the DNA whose concentration is spotted on saran wrap layed on a 
>UV transilluminator. An 8 ul droplet of a .5 ug/ml solution of EtBr is mixed
>by pipetting up-and-down. A series of droplets containing known quantities
>of DNA are also spotted. The fluorescence of the test sample is then compared
>to the knowns. Like the Dipstick, the best response is obtained with amounts
>as low as 1 ng an as high as 10 ng. A picture can taken with the appropriate
>filter for a permanent record (and also to avoid having to stare at a UV box).
>When quantitating, be sure to include a zero ng control, since the EtBr itself
>can fluoresce. Also, ignore the fluorescence seen at the edges of the sample.
>Once the solutions of EtBr and the known samples are prepared, this method
>takes only a few minutes to do.

I use essentially the same method.  I have a microscope slide, the surface
of which I treated with silicone grease (which practically never comes off)
to keep the drops from spreading.  After running the test, I just wipe off
the droplets and stick the slide back in the drawer.

I've not made a careful study, but feel that I get the best results, over
a wider range of DNA amounts, when the WEIGHT of the added ethidium bromide
is roughly equal to to the WEIGHT of the DNA.  As stated above, it's crucial
to have a blank spot in the series.
________________________________________________________________________________
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
From: daryl@RT2.MENZIES.SU.EDU.AU (Daryl Webb)
Newsgroups: bionet.molbio.methds-reagnts
Subject: HOS cells
Date: 21 Aug 92 15:34:44 GMT
Distribution: bionet


Sorry if this is a little off beat for this newsgroup but I'm hoping that its
wide readership might come up with something.  grovel, suck :-)*

We wish to obtain the following cell line for virological studies:

HOS (human osteogenic sarcoma) cell line described in RM McAllister et al
Cancer (1971) 27:397-402 and listed as ATCC CRL 1543

Though this cell line is available from ATCC, it would be more convenient (no
AQIS etc) to obtain it from another Australian institution.

So all you Aussie Labbies do me a favour and have a look in the bottom of
that LN2 tank in the corner eh.   Please :-)*

To stop me wasting any more bandwidth please E_mail replies.

Ta muchly

-- 
                                                     |      |
  Daryl Webb  (daryl@menzies.su.edu.au)               \    / 
  Menzies School of Health Research                    \__/   
  P.O. Box 41096                                        ||   <<
  Casuarina N.T. 0811            ----------------------- *  <<
  Australia                                             ||   <<
  Voice : 61_89_228196                                 /||\ 
  Fax   : 61_89_275187                                * || o
                                                     /  ||  \    
Newsgroups: bionet.molbio.methds-reagnts
From: robert@arbo.microbiol.uwa.oz.au (Robert Coelen)
Subject: Re: Two Sequencing questions:
Organization: University of Western Australia
Date: Thu, 13 Aug 1992 03:44:18 GMT

In article <zsha.713469334@sanger.bb.iastate.edu> zsha@iastate.edu (Zhengyu Sha) writes:
>In <1992Aug10.154723.23852@magnus.acs.ohio-state.edu> rrumpf@magnus.acs.ohio-state.edu (Robert Rumpf) writes:
>
>>I have two questions regarding sequencing protocols:
>
>>1.  Our 35-S gels are still sticky after drying; the saran wrap sticks to them 
>>and is difficult to remove.  Why?  We also noticed that removing the saran wrap
>>and placing film directly on the gels apparently causes some damage to the 
>>film from the moisture or urea in the gel...
This is the nth time I've heard of people wanting to remove the saran wrap
of gels containing 35S. Why ? We don't fix our gels, nor take of the wrap. We
peel the gels of the glass with Whatman 3MM and dry them under wrap in a vacuum gel dryer. Than expose them to Fuji RX (not a very sensitive film !) and get good results from an overnight exposure. Just make sure your reactions are good (CLEAN template and good template to primer ratio)
>
>>2.  Anyone have any experience with 33-P yet?  We would like to know if the 
>>energy from this isotope is sufficient to pass through saran wrap so we can 
>>expose films without taking the wrap off.
>	You mean 32-P? The answer is yes. Even with 35-S sequencing gel we exposure the dried gel without removing the saran wrap. The results are satisfied if you labeling reaction is good. 
>

We are about to develop some film from a 33P run. We'll let you know tomorrow
what our findings are.............................

Robert (semi-mature Gouda CHEESE) Coelen
Dept of Microbiology
From: BACKD@QUCDN.QueensU.CA
Newsgroups: bionet.molbio.methds-reagnts
Subject: Re: scanners
Date: 12 Aug 92 12:07:05 GMT
Distribution: bionet
Organization: Queen's University at Kingston

Jim,

Check the following article for scanner software. You may wish to call Cary
Mariash and ask his advise.

Correa-Rotter,R., Mariash, C.N. & Rosenberg, M.E. (1992) "Loading and transfer
control for northern hybridization." BioTechniques 12:154-158.

Don Back
Department of Biochemistry
Queen's University
Kingston, Ontario
From: MPB@CBR.DWE.CSIRO.AU (Mark Bradley)
Newsgroups: bionet.molbio.methds-reagnts
Subject: RE: Immunoprecipitation
Date: 13 Aug 92 14:37:33 GMT
Distribution: bionet

We have found that anti-rabbit IgG sepharose gives very good
results with immunoprecipitation.  Some years ago we changed
to this after finding that Staph Protein A alone wopuld precipitate
quite a number of non-specific proteins from tissue culture media.
Good luck, MARK BRADLEY
From: miguel@aclcb.purdue.edu (PHILLIP_SANMIGUEL)
Newsgroups: bionet.molbio.methds-reagnts
Subject: Re: Baby powder those sticky gels
Date: 21 Aug 92 18:37:38 GMT
Reply-To: miguel@aclcb.purdue.edu
Organization: Purdue University AIDS Center

In article <1992Aug21.002612.16567@usenet.ins.cwru.edu>, ca566@cleveland.Freenet.Edu (Michael Holloway) writes:
>
>I've received an E-mail message about the "sticky sequencing gel" problem
>that I was asked to pass on.  Seems like a perfectly reasonable solution.
>
  I just throw the gel in the -80 oC for the exposure.  Frozen, the gel 
does not stick to the film.  But I also fix (60 min.) and dry my wedge 
gels much longer than most (several hours).  So this method may not cut 
it for some of you.  
  Actually, I've quit doing wedge gels since I started using HydroLink's 
Long Ranger acrylamide.  Seems to do the same thing the Na Acetate in the 
bottom buffer would do.  (But I've not tried Na Acetate so I can't say from 
personal experience.)
Newsgroups: bionet.molbio.methds-reagnts