HDTenEightyP/NetNews huggingface dataset:
From: KU@helix.nih.gov (Karen Usdin)
Subject: Re: Buffer Making Program
Followup-To: bionet.molbio.methds-reagnts
Organization: National Institutes of Health
Distribution: bionet
Date: Mon, 11 Jan 1993 21:05:49 GMT

In article <01GT7AY4TYIQ8WWEDO@mis.mcw.edu>, DMEIER@mis.mcw.edu wrote:
>   Is there a Mac program that will calculate weights to use for buffer 
> preps? 

I have created a set of Hypercard stacks primarily for data management for
molecular biologists. In addition to its data storage and retrieval
functions, it also automates a lot of tedious tasks such as calculations of
quantities of chemicals for solutions, calculations of Tms of oligos etc.
It also has a simple sequence entry feature with voice verification and
does some simple sequence manipulations. The stack set was described in
Computer Applications in the Biological Sciences (8/2,pp 107-111). If you
are interested you can contact me by e-mail at the above address.

Karen Usdin
Newsgroups: bionet.molbio.methds-reagnts
From: ALSOBROOK@biomed.med.yale.edu (John Alsobrook)
Subject: Lambda-gtWES restriction sites
Organization: Yale University
Date: Tue, 12 Jan 1993 15:53:23 GMT
X-News-Reader: VMS NEWS 1.20

Hello, net-folk. Can anyone steer me to a restriction map of Lambda-gtWES?
Also, it's size, etc? I've used the retriever at GENBANK (including their
vector database) and have not found any information. Any help would
be greatly appreciated. We just want to excise the insert, and would like
to know what to expect on the gel before we do it!

Thanks alot.


******************************************************************************
* John Alsobrook    Child Study Center    Yale University School of Medicine *
* internet: alsobrook@biomed.med.yale.edu / bitnet: alsobrook@yalemed.bitnet *
*----------------------------------------------------------------------------*
* "Giving money and power to the government is like giving whiskey and car   *
*  keys to teenage boys." -- P.J. O'Rourke                                   *
*----------------------------------------------------------------------------*
* If I was a spokesperson for Yale my secretaries would have typed this...   *
*----------------------------------------------------------------------------*
From: drm21@mbuk.bio.cam.ac.uk
Newsgroups: bionet.molbio.methds-reagnts
Subject: Musca/D.virilis cDNA
Date: 6 Jan 93 20:23:26 GMT
Distribution: bionet
Original-To: methods@uk.ac.daresbury
Return-Path: <drm21@mbuk.bio.cam.ac.uk>

Hi there all.  Happy New Year.

Does anyone have a housefly (Musca) and/or Drosophila virilis cDNA library
that I could scrounge a tiny tiny bit of???  I'm trying to clone the
homologues of a largish D. melanogaster gene to get some idea of which bits
are important .

Any help would be very much appreciated,
Cheers, David
___________________________________________________________
D.R.Micklem,
Wellcome/CRC Institute,       Time flies like an arrow...
Tennis Court Road,              
Cambridge CB2 1QR             Fruit flies like a banana.
UK                             
                drm21@mbuk.bio.cam.ac.uk
___________________________________________________________
Newsgroups: bionet.molbio.methds-reagnts
From: ALSOBROOK@biomed.med.yale.edu (John Alsobrook)
Subject: Re: Correction: Lambda-gtWES restriction sites 
Organization: Yale University
Date: Tue, 12 Jan 1993 16:02:33 GMT
X-News-Reader: VMS NEWS 1.20

In <1993Jan12.155323.26331@news.yale.edu> ALSOBROOK@biomed.med.yale.edu writes:

> Hello, net-folk. Can anyone steer me to a restriction map of Lambda-gtWES?
> Also, it's size, etc? I've used the retriever at GENBANK (including their
       ^^^^^^


Aaargh! Obviously I mean "its" size; I hate committing apostrophe abuse!



 ******************************************************************************
 * John Alsobrook    Child Study Center    Yale University School of Medicine *
 * internet: alsobrook@biomed.med.yale.edu / bitnet: alsobrook@yalemed.bitnet *
 *----------------------------------------------------------------------------*
 * "Giving money and power to the government is like giving whiskey and car   *
 *  keys to teenage boys." -- P.J. O'Rourke                                   *
 *----------------------------------------------------------------------------*
 * If I was a spokesperson for Yale my secretaries would have typed this...   *
 *----------------------------------------------------------------------------*
Newsgroups: bionet.molbio.methds-reagnts
From: BIOSEE@UKCC.UKY.EDU (Stephanie Edelmann)
Subject: Re: Glycogen for DNA Precipitation
Organization: University of Kentucky
Date: Fri, 8 Jan 1993 19:26:06 GMT

In article <9301072225.AA18226@net.bio.net>
KNECHT@UCONNVM.UCONN.EDU (Dave Knecht) writes:
 
>
>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
 
We also must be using the Glycogen from Boehringer Mannheim.  Add 1ml to
the DNA in ethanol and spin.  Glycogen is supposed to be a volume excluder
(as far as I know), but we in our lab are convinced, that its main
effect is a psychological one.  After adding glycogen, you all a sudden
see a pellet.  That might be mostly glycogen, but it's a PELLET as oppose
to nothing visible.  We haven't noticed any negative effects, yet. I've
used it on DNA that was supposed to be cut, ligated, electrophoresed and
probably others.
 
Stephanie
Newsgroups: bionet.molbio.methds-reagnts
From: BIOSEE@UKCC.UKY.EDU (Stephanie Edelmann)
Subject: Re: Glycogen for DNA Precipitation
Organization: University of Kentucky
Date: Fri, 8 Jan 1993 21:33:11 GMT

In article <16B50CB07.BIOSEE@UKCC.UKY.EDU>
BIOSEE@UKCC.UKY.EDU (Stephanie Edelmann) writes:
 
>
>In article <9301072225.AA18226@net.bio.net>
>KNECHT@UCONNVM.UCONN.EDU (Dave Knecht) writes:
>
>>
>>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
>
>We also must be using the Glycogen from Boehringer Mannheim.  Add 1ml to
                                                                   ===
Oops, I goofed, that's supposed to be 1ul (microliter!!!!)
 
>the DNA in ethanol and spin.  Glycogen is supposed to be a volume excluder
>(as far as I know), but we in our lab are convinced, that its main
>effect is a psychological one.  After adding glycogen, you all a sudden
>see a pellet.  That might be mostly glycogen, but it's a PELLET as oppose
>to nothing visible.  We haven't noticed any negative effects, yet. I've
>used it on DNA that was supposed to be cut, ligated, electrophoresed and
>probably others.
>
>Stephanie
From: bchs1b@Elroy.UH.EDU (Michael Benedik)
Newsgroups: bionet.molbio.methds-reagnts
Subject: Leucine zipper
Date: 7 Jan 1993 22:40:36 GMT
Organization: University of Houston
Reply-To: bchs1b@Elroy.UH.EDU
NNTP-Posting-Host: elroy.uh.edu

 I have 2 questions for you cognoscenti out there about leucine zippers... 

(1) are leucine zipper regions very hydrophobic in general or not? 
(2) are all leucine zipper proteins DNA binding proteins or not? 

Many thanks in advance
----------------------------------------------------------------------
 Michael Benedik				INTERNET: Benedik@uh.edu
 Dept. of Biochemical & Biophysical Sciences	
 University of Houston				BITNET: Benedik@uhou
-----------------------------------------------------------------------
Newsgroups: bionet.molbio.methds-reagnts
From: jgraham@bronze.ucs.indiana.edu (the End)
Subject: Re: DNA purification
Organization: Indiana University
Distribution: bionet
Date: Wed, 13 Jan 1993 03:55:22 GMT

I have used a similar technique with great success. It is even simpler.

Slice your gel (reg. or preferably lo-melt) and put it in an Eppendorf.
Freeze it min at -70C. Thaw it out and spin it hard in a microfuge.
Pour off the liquid. Again you have 10-50 ug/ul (in the super).

This DNA ligates well for me. Don't try to percipitate it or it will 
"disapear". Check a few ul on a gel to reassure yourself.

Hey I wonder if I could sell this to "Clonegouge" as a kit ?

Just kidding,

Jim
J. Graham
Biology/Chemistry Departments
Indiana University -Bloomington
Newsgroups: bionet.molbio.methds-reagnts
From: rrumpf@magnus.acs.ohio-state.edu (Robert Rumpf)
Subject: Use of *protein as probe for colony hyb
Organization: The Ohio State University
Date: Tue, 5 Jan 1993 18:10:32 GMT

Yet another question for a friend (really!  It's not me!):  Is it possible (has
it been done by someone else) to use a labelled DNA-binding protein as a probe 
for colony hybridization?  It seems logical that it would work, but opinions 
and comments would be appreciated.  Email to this account..

Bob
Newsgroups: bionet.molbio.methds-reagnts
From: BIOSEE@UKCC.UKY.EDU (Stephanie Edelmann)
Subject: Re: DNA purification
    <1993Jan11.112657.23798@crc.ac.uk>
Organization: University of Kentucky
Date: Mon, 11 Jan 1993 15:59:55 GMT

In article <1993Jan11.112657.23798@crc.ac.uk>
sbhattac@crc.ac.uk (Dr. S. Bhattacharya) writes:
 
>
>Hi all
>I got a few requests to explain this method in more detail so am posting it
>to the net.
>
>To siliconize glass wool:
>Place glass wool in beaker, and about 50 ml of dimethylsilane in another beaker.
>Put them both in a vacuum dessicator (in fume hood) and apply vacuum till dessicator
>is evacuated. Leave the glass wool to absorb the silicone vapor overnight.
>
>To extract DNA:
>1.Cut out band from agarose (1.5% or less in TBE, normal agarose).
>2.Briefly blot the agarose block dry.
>3.Pierce a hole using a green 21G needle at the bottom of a mini-eppendorf.
>  Pack the eppendorf with a small pinch of siliconized glass wool (so that there is about
>  4 mm of packed glass wool at the bottom of the tube).
>4.remove the cap from a larger Eppendorf and put the mini eppend. into it.
>5.Place agarose block containing your DNA into the small Eppendorf
>6.Spin 6500 rpm on bench top for 10 min
>7. Depending on size of agarose block you should get 50-100ul of aqueous phase
>buffer containing your DNA, usually at 10ng/ul, you can check recovery using
>UV fluorescence.
>8. You can clone or sequence directly; you can also concentrate and remove buffer salts
>using an Amicon Microcon of appropriate pore size membrane.
>
>A far cheaper and faster method than various kits on offer.
>
>Best of luck
>
>Shoumo
I used this method for a while after hearing about it from a friend.  It
seemed to give me decent recovery of DNA.  However, I could never use
DNA purified in this way for ligations.  I just would not ligate at all.
Any ideas?
 
Stephanie
Newsgroups: bionet.molbio.methds-reagnts
From: sbhattac@crc.ac.uk (Dr. S. Bhattacharya)
Subject: Re: DNA purification
Reply-To: sbhattac@crc.ac.uk (Dr. S. Bhattacharya)
Organization: MRC Human Genome Mapping Project Resource Centre, Harrow, UK
Date: Mon, 11 Jan 1993 11:26:57 GMT

Hi all
I got a few requests to explain this method in more detail so am posting it
to the net.

To siliconize glass wool:
Place glass wool in beaker, and about 50 ml of dimethylsilane in another beaker.
Put them both in a vacuum dessicator (in fume hood) and apply vacuum till dessicator
is evacuated. Leave the glass wool to absorb the silicone vapor overnight.

To extract DNA:
1.Cut out band from agarose (1.5% or less in TBE, normal agarose).
2.Briefly blot the agarose block dry.
3.Pierce a hole using a green 21G needle at the bottom of a mini-eppendorf.
  Pack the eppendorf with a small pinch of siliconized glass wool (so that there is about
  4 mm of packed glass wool at the bottom of the tube).
4.remove the cap from a larger Eppendorf and put the mini eppend. into it.
5.Place agarose block containing your DNA into the small Eppendorf
6.Spin 6500 rpm on bench top for 10 min
7. Depending on size of agarose block you should get 50-100ul of aqueous phase
buffer containing your DNA, usually at 10ng/ul, you can check recovery using
UV fluorescence.
8. You can clone or sequence directly; you can also concentrate and remove buffer salts
using an Amicon Microcon of appropriate pore size membrane.

A far cheaper and faster method than various kits on offer.

Best of luck

Shoumo
From: camdna@ubvmsb.cc.buffalo.edu (Darren Natale)
Newsgroups: bionet.molbio.methds-reagnts
Subject: Re: Purity of DNA (Ratio of OD = 1.8-2.0) ?
Date: 12 Jan 93 15:04:00 GMT
Organization: University at Buffalo
News-Software: VAX/VMS VNEWS 1.41

In article <1993Jan12.061103.2973@kudpc.kyoto-u.ac.jp>, a52041@sakura.kudpc.kyoto-u.ac.jp (Michael CHENG) writes...

>  Why is a preparation of DNA considered to be pure if OD260/OD280 => 1.8?
>  Actually, I've never thought of it myself so I went around asking my labmates.
>Well, nobody really knows the answer. Then I heard that there's possibly a
>theoretical formula that sets the above value range.
>  If this is true, I would appreciate it if someone out there can point me to
>the reference.
> 
Both proteins and nucleic acids absorb at 280 and 260. However, proteins
absorb more strongly at 280 than at 260, whereas the opposite is true for
nucleic acids. The formula you refer to is probably derived from the data
of Warburg and Christian in a paper (in German) from 1945 (?) or so. In that
paper, the authors were more interested in protein purity, and presented a
table of 280/260 ratios versus percent nucleic acid contamination. The 
contamination ranged from 0% to 20%, and a single value of 100%. I have
derived a graph of their data, and found a linear correspondence between 
the ratio and the %nucleic acid. 100% nucleic acid has a ratio (280/260)
of 0.49, which is a 2.04 260/280 ratio. Here is my formula for percent
nucleic acid using _280/260_:

	%NA = 2.06-1.18r
	      ----------
	    0.4962r-0.2274    where r = A280/A260

DN
From: salbert@gwdgv1.dnet.gwdg.de ("GWDGV1::SALBERT")
Newsgroups: bionet.molbio.methds-reagnts
Subject: Inosine in PCR primers
Date: 8 Jan 93 13:58:50 GMT
Distribution: bionet
Original-To: methods@uk.ac.daresbury

Hi netters,
I have just designed set of primers including inosine instead of third
wobbling base in some codons. Unfortunately, they don't work. Sure, problem
can be elsewhere, but I would appreciate any comment and\or experiences
about use of inosine in designing oligonucleotide primer.

Thanks in advance,
			Stefan
Newsgroups: bionet.molbio.evolution
From: danj@welchgate.welch.jhu.edu (Dan Jacobson)
Subject: Re: PAUP for ibm/dos
Organization: Johns Hopkins Univ. Welch Medical Library
Date: Tue, 5 Jan 1993 22:10:33 GMT

In article <1993Jan5.193553.16035@galileo.cc.rochester.edu> WERR@db1.cc.rochester.edu (JOHN WERREN) writes:
>we are looking for a PAUP software program that runs on Dos/ibm
>compatible machines.  We have a 386/33 system.  Swoffords old
>1bm version does not accept sequence strings longer than a few
>hundred bases, and we would very much like an updated version.
>thanks for any help.  
> j. werren   
>address  werr@db1.cc.rochester.edu

I don't know what version of Paup you have - I think the latest version
is 3.0 but I would suggest that you contact Swofford for the latest information
about Paup, he still reads his e-mail at swofford@uxh.cso.uiuc.edu.

Here's a little tidbit of information about Paup:

     1.  David Swofford (Illinois Natural  History  Survey,  Natural  Resources
Building,   607   East  Peabody  Drive,  Champaign,  Illinois   61820,  U.S.A.)
distributes PAUP (Phylogenetic Analysis Using Parsimony).
 
     Since  December,  1985,  Swofford  has  been  distributing  a  precompiled
executable object-code versions of PAUP for the IBM PC and other MSDOS systems.
As of this writing (May, 1991) he has released version  3  (PAUP/Mac)  for  the
Macintosh,  and  later  hopes  to  release  version  3  for  PCDOS  systems and
ultimately for mainframes.  Its cost is  $50.   Orders  received  for  the  Mac
version  will  be filled but the final printed documentation will arrive later,
as it is not completed yet.

     PAUP 3.0 is probably the most sophisticated parsimony program.  It  allows
multistate  characters,  user-defined  weights on individual state transitions,
Wagner,  Camin-Sokal  and  Dollo  parsimony   methods,   bootstrap   confidence
intervals,  and  finding  all  most parsimonious trees by branch-and-bound.  It
also has provision for computing Lake's linear phylogenetic invariants.


This was clipped out of Joe Felsenstein's documentation for PHYLIP - 
another package for doing all sorts of phylogeny.  You may want to
consider getting PHYLIP, it is well supported, extremely well documented,
and FREE.  You can get it by anonymous ftp at evolution.genetics.washington.edu
in the /pub directory. (Kudos to Joe)

Best of Luck,

Dan Jacobson

danj@welchgate.welch.jhu.edu
Newsgroups: bionet.molbio.evolution
Subject: Re: Dosage compensation in Z/W chromosome systems
From: robison1@husc10.harvard.edu (Keith Robison)
Date: 8 Jan 93 00:02:09 GMT

FORSDYKE@QUCDN.QueensU.CA writes:


>    I am looking for recent work on dosage compensation in birds, butterflies,
>snakes and other species with Z/W chromosome systems. The best references I
>have are Johnson and Turner (1979) Heredity 43, 71-77 and
>         Baverstock et al., (1982) Nature 296, 763-766.
>    I will be checking the Science Citation Index to see who is citing these
>papers now but there may be some papers I miss. Can anyone help?
>                                             Sincerely,
>                                                       Don Forsdyke



Uh, could you enlighten me as to why Z/W systems need dosage compensation
-- I thought the Z/W meant that the two chromosomes contained the
same genes except for the sex-determination factor.

You might also look into work on C.elegans and speculations as
to the evolution of dosage compensation and hermaphrodism there.
I believe Jonathon Hodgkin is a major author in the field.

(a really fuzzy thought -- I think I saw some speculation on
chromosomal sex determination recently in a "review" journal
-- Current Biology, Current Opinion in Genes and Development,
Trends in Genetics, or Bioessays [most likely Bioessays]).


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

robison@biosun.harvard.edu
Organization: Queen's University at Kingston
Date: Thu, 7 Jan 1993 16:23:20 EST
From: <FORSDYKE@QUCDN.QueensU.CA>
Newsgroups: bionet.molbio.evolution
Subject: Dosage compensation in Z/W chromosome systems

    I am looking for recent work on dosage compensation in birds, butterflies,
snakes and other species with Z/W chromosome systems. The best references I
have are Johnson and Turner (1979) Heredity 43, 71-77 and
         Baverstock et al., (1982) Nature 296, 763-766.
    I will be checking the Science Citation Index to see who is citing these
papers now but there may be some papers I miss. Can anyone help?
                                             Sincerely,
                                                       Don Forsdyke
From: boulding@sfu.ca
Newsgroups: bionet.molbio.evolution
Subject: Mollusc Molecular News
Date: 8 Jan 93 17:22:08 GMT
Distribution: bionet
Original-To: mol-evol@uk.ac.daresbury
X-Mailer: ELM [version 2.3 PL11]

I am putting together the second issue of the Mollusc
Molecular News (MMN).  The MMN is a free, informal
newsletter for researchers doing systematics or
population genetics using mollusc DNA.

In this issue there will be a list of polymerase chain
reaction (PCR) primers that have been used to amplify
mollusc DNA.  Please do not include unpublished PCR
primers if their use could compromise your research.
If you wish to contribute to the list of primers please
provide the following information: 1) your name and
affiliation 2) gene(s) amplified by primer pair, 3)
sequences of PCR primers listed 5' to 3' and labelled
as sense or antisense, 4) classes, families, and
species that primers have been successfully used on, 5)
useful level of variation {e.g., within species,
between orders} 6) end use of PCR product {e.g.,
restriction analysis, direct sequencing, cloning then
sequencing clones}.

If you want to be included in the directory of
researchers please send me the following information.
I keep this information in a database file that has the
following structure (numbers in parentheses refer to
maximum number of characters): surname (15), other
names and title (15), address line 1 (30), address line
2 (30), address line 3 (30), address line 4 (30), work
phone number (20), FAX number (20), electronic mail
address (54), keywords (54).

I will list separately all publications concerned with
mollusc DNA that are in press or have been published
since 1990.  Please write out journal names in full.

Please include a paragraph or two describing the
ongoing research in your laboratory for the Research
News section.  You also can solicit help from other
readers in the Technical Bulletin Board section.
Please send your contributions to the Research News or
Technical Bulletin Board sections via electronic mail
or print them using a letter quality printer on heavy
letter-size white paper leaving 2.5 cm margins and a
typeface of at least 9 pt.

Many people working on mollusc DNA do not have access
to electronic mail and I would be grateful if you would
bring this notice to their attention.  Please try to
get all contributions to me by the end of January 1993.
Please note my new electronic mail address.
     
     Elizabeth Boulding.
     elizabeth_boulding@sfu.ca
     
     Dr. Elizabeth Boulding
     Editor, Mollusc Molecular News
     Department of Biological Sciences
     Simon Fraser University
     Burnaby, B.C.
     V5A 1S6
     Canada
From: tomh@BAMBI.CCS.FAU.EDU (Tom Holroyd)
Newsgroups: bionet.molbio.evolution
Subject: Re: artificial networks
Date: 8 Jan 93 00:34:53 GMT
Distribution: bionet

andrick@rhrk.uni-kl.de (Ulf Andrick [Biologie]) writes:

>There seems to be enough work to be done to simulate `static' Neural
>Networks in simple organisms. An interesting question is, e. g.,
>what role the complex electrophysiological properties of the single
>neuron play for the behaviour of the whole network? What are
>the effects of neuromodulators? And these questions may
>also be of relevance in neural development.

Just a quick note, but to understand the functioning of a network
of neurons, you must sometimes study the whole network and not
the properties of single neurons.  Many of the complex electrophysiological
properties of the single neuron may be irrelevant at the network level,
since some functions may be emergent properties not present at the
single unit level.

This is also true for networks of interacting genes.  Studying how a
single gene codes for an enzyme may not help you understand how the
complex regulatory network functions, since some of the processes
are almost surely emergent, like a collective effect on a regulatory
process.

Growing simple network models won't tell you anything about individual
cells, but it will help you understand the types of interactions that
are possible, and you may find that the interactions produce forces that
outweigh any cellular level process.  There's a paper by Kauffman on
properties of genetic regulatory networks that is illustrative.  [ I don't
have it handy though; sorry. :-( ]

Tom Holroyd
Center for Complex Systems and Brain Sciences
Florida Atlantic University, Boca Raton, FL 33431 USA
tomh@bambi.ccs.fau.edu