From owner-rapd@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!CHARLY.UCDAVIS.EDU!cushwa From: cushwa@CHARLY.UCDAVIS.EDU Newsgroups: bionet.molbio.rapd Subject: RAPDs and insitu hybridization Date: 2 Jun 1995 07:22:21 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <00991441.EC92BE00.22675@charly.ucdavis.edu> NNTP-Posting-Host: net.bio.net Does anyone know of references that involve physical mapping of RAPD markers using insitu hybridization techniques? If so, I would appreciate receiving the information. Thanks for your help. Willy Cushwa wtcushwa@ucdavis.edu From owner-rapd@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!usc!cs.utexas.edu!howland.reston.ans.net!Germany.EU.net!EU.net!Austria.EU.net!newsfeed.ACO.net!swidir.switch.ch!univ-lyon1.fr!jussieu.fr!oleane!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: Newsgroups: bionet.molbio.rapd Subject: RAPDs and insitu hybridization Date: 2 Jun 1995 15:24:55 +0100 Lines: 7 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3qn6vn$gaq@mserv1.dl.ac.uk> Original-To: rapd@dl.ac.uk Does anyone know of references that involve physical mapping of RAPD markers using insitu hybridization techniques? If so, I would appreciate receiving the information. Thanks for your help. Willy Cushwa wtcushwa@ucdavis.edu From owner-rapd@net.bio.net Thu Jun 01 23:00:00 1995 Newsgroups: bionet.molbio.rapd Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!reuter.cse.ogi.edu!cs.uoregon.edu!usenet.ee.pdx.edu!news.reed.edu!sun.lclark.edu!netnews.nwnet.net!ns1.nodak.edu!plains!comstock From: comstock@plains.NoDak.edu (Clay Comstock) Subject: PCR Protocols Sender: usenet@ns1.nodak.edu (Usenet login) Message-ID: Date: Fri, 2 Jun 1995 16:29:41 GMT Nntp-Posting-Host: plains.nodak.edu Organization: North Dakota Higher Education Computing Network (NDHECN) X-Newsreader: TIN [version 1.2 PL2] Lines: 37 Dear Netters, My name is Clay Comstock and I am an undergrad at Dickinson State University in Dickinson, North Dakota. I am currently using RAPD Primers from the University of British Columbia on my spiders which are from the genus Zelotes. It seems that I have run into some problems with my primers binding to the DNA. I am using a MJ Research PTC-150 Minicycler with cycling temperatures of 94;38;70. If anyone has any suggestions on my thermal cycling temperatures or any other information please contact me as soon as possible. Thanks Clay Comstock -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ____________ /| /| "The Necker Cube / |_________/_| Reminds Us, That /__/________/ | All Situations | / | / Can Be Viewed |/ | / From Two Different Perspectives" |__________|/ Clay Comstock Dickinson State University Dickinson, ND 58601 e-mail comstock@plains.nodak.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-rapd@net.bio.net Sun Jun 04 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: (Russell Stothard) Newsgroups: bionet.molbio.rapd Subject: RESTSITE Date: 5 Jun 1995 12:58:44 +0100 Lines: 12 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3qurhk$7h3@mserv1.dl.ac.uk> X-POPmail-Charset: English Original-To: rapd@dl.ac.uk Hi Does anyone have a copy of J.C.Miller's RESTSITE program. The program is freeware and I have been unable to find a copy located on the net. Thanks Russ Stothard Russ Stothard@nhm.ac.uk Dept Zoology Natural History Museum London From owner-rapd@net.bio.net Mon Jun 05 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!fnnews.fnal.gov!overload.lbl.gov!s27w007.pswfs.gov!dmh From: dmh@pswfs.gov (Derek M. Harkins) Newsgroups: bionet.molbio.rapd Subject: Re: primers Date: 6 Jun 1995 21:38:34 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 43 Message-ID: <3r2hsr$fio@overload.lbl.gov> References: <3r1pd1$3po@whitbeck.ncl.ac.uk> NNTP-Posting-Host: s27w007.pswfs.gov X-Newsreader: TIN [version 1.2 PL2] H.Tyler-Walters (H.Tyler-Walters@ncl.ac.uk) wrote: : I'm trying to start some work that will use RAPD markers. Could some-one : be so kind as to post the address for Operon Technologies. Are there any : other companies that supply RAPD primers. Would I be better synthesizing : my own. : Thanks in Advance. : H. Tyler-Walters. There are several sources for RAPD primers. The address for OPERON is: OPERON Technologies, Inc. 1000 Atlantic Ave Alameda, CA 94501 phone: (800) 688-2248 FAX: (510) 865-5525 e-mail: dna@operon.com There is also a source for RAPD primers at the University of British Columbia. The person to contact is John Hobbs. University of British Columbia Biotechnology Laboratory Room 237 Wesbrook Building 6174 University Boulevard Vancouver, B.C. Canada V6T1Z3 Phone: (604) 822-6373 e-mail: hobbs@unixg.ubc.ca There is also Genosys, which has recently started making RAPD primers, but I can't seem to find the address. Anyone out there care to help? Good luck, I hope this helped. Derek -- * Derek M. Harkins __ * * United States Department of Agriculture | | /\ / \ * * Forest Service | | //\\ | * * Pacific Southwest Research Station | | ///\\\ \__ * * Institute of Forest Genetics | | ////\\\\ \ * * 2480 Carson Road | | /////\\\\\ | * * Placerville, CA 95667 USA (916) 622-1225 \__/ || \__/ * From owner-rapd@net.bio.net Mon Jun 05 23:00:00 1995 Path: biosci!CCMAIL.LLU.EDU!blangridge From: blangridge@CCMAIL.LLU.EDU ("blangridge") Newsgroups: bionet.molbio.rapd Subject: testing Date: 5 Jun 1995 19:09:44 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: <9505058024.AA802404449@ccmail.llu.edu> NNTP-Posting-Host: net.bio.net this is just a test , ignore From owner-rapd@net.bio.net Mon Jun 05 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!news.sprintlink.net!pipex!warwick!news.ncl.ac.uk!eata!nhtw From: "H.Tyler-Walters" Newsgroups: bionet.molbio.rapd Subject: primers Date: 6 Jun 1995 14:40:33 GMT Organization: University of Newcastle upon Tyne Lines: 6 Message-ID: <3r1pd1$3po@whitbeck.ncl.ac.uk> NNTP-Posting-Host: eata.ncl.ac.uk X-Newsreader: TIN [version 1.2 PL2] I'm trying to start some work that will use RAPD markers. Could some-one be so kind as to post the address for Operon Technologies. Are there any other companies that supply RAPD primers. Would I be better synthesizing my own. Thanks in Advance. H. Tyler-Walters. From owner-rapd@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!daresbury!is.bbsrc.ac.uk!news From: Your Name Newsgroups: bionet.molbio.rapd Subject: Re: primers Date: 7 Jun 1995 13:42:04 GMT Organization: BBSRC Biotechnology and Biological Sciences Research Council Lines: 23 Message-ID: <3r4abc$9jl@is.bbsrc.ac.uk> References: <3r1pd1$3po@whitbeck.ncl.ac.uk> <3r2hsr$fio@overload.lbl.gov> NNTP-Posting-Host: pc717.res.bbsrc.ac.uk dmh@pswfs.gov (Derek M. Harkins) wrote: > There is also Genosys, which has recently started making RAPD primers, but I > can't seem to find the address. Anyone out there care to help? The address for Genosys is as follows: Genosys Biotechnologies Inc., 162A Cambridge Science Park Milton Road Cambridge CB4 4GH, U.K. I haven't got round to actually trying out any of their RAPD primers as yet. If anyone has done so I wouldn't mind hearing from them as I seem to remember a posting to this group stating that in order to get results of a similar standard to those obtained with Operon primers, larger quantities of the Genosys primers had to be used. Cheers, Simon fosters@bbsrc.ac.uk From owner-rapd@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: "C.S.Wilding" Newsgroups: bionet.molbio.rapd Subject: Re: primers Date: 7 Jun 1995 11:26:23 +0100 Lines: 59 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3r3usf$sj9@mserv1.dl.ac.uk> X-Sender: osp086@picard Original-To: rapd@dl.ac.uk Genosys can be contacted via e-mail at: genosys@genosys.co.uk ******************************************************************** * CRAIG WILDING, E-mail: OSP086@SOS.BANGOR.AC.UK * * SCHOOL OF OCEAN SCIENCES, Phone: (0)1248 351151 ext.2899 * * UNIVERSITY OF WALES (BANGOR), Fax: (0)1248 716367 * * MENAI BRIDGE, * * GWYNEDD, LL59 5EY, * * WALES, U.K. * ******************************************************************** On Tue, 6 Jun 1995 CBS%UK.AC.DARESBURY.PSERV1::GOV.PSWFS::DMH@clvax.bangor.ac.uk wrote: > > H.Tyler-Walters (H.Tyler-Walters@ncl.ac.uk) wrote: > : I'm trying to start some work that will use RAPD markers. Could some-one > : be so kind as to post the address for Operon Technologies. Are there any > : other companies that supply RAPD primers. Would I be better synthesizing > : my own. > : Thanks in Advance. > : H. Tyler-Walters. > > There are several sources for RAPD primers. The address for OPERON is: > > OPERON Technologies, Inc. > 1000 Atlantic Ave > Alameda, CA 94501 > phone: (800) 688-2248 > FAX: (510) 865-5525 > e-mail: dna@operon.com > > There is also a source for RAPD primers at the University of British > Columbia. The person to contact is John Hobbs. > > University of British Columbia > Biotechnology Laboratory > Room 237 Wesbrook Building > 6174 University Boulevard > Vancouver, B.C. Canada V6T1Z3 > Phone: (604) 822-6373 > e-mail: hobbs@unixg.ubc.ca > > There is also Genosys, which has recently started making RAPD primers, but I > can't seem to find the address. Anyone out there care to help? > > Good luck, I hope this helped. > > Derek > > -- > * Derek M. Harkins __ * > * United States Department of Agriculture | | /\ / \ * > * Forest Service | | //\\ | * > * Pacific Southwest Research Station | | ///\\\ \__ * > * Institute of Forest Genetics | | ////\\\\ \ * > * 2480 Carson Road | | /////\\\\\ | * > * Placerville, CA 95667 USA (916) 622-1225 \__/ || \__/ * > > > From owner-rapd@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!usc!news.cerf.net!newsserver.sdsc.edu!news.tc.cornell.edu!travelers.mail.cornell.edu!newsstand.cit.cornell.edu!NewsWatcher!user From: pts3@cornell.edu (phil) Newsgroups: bionet.molbio.rapd Subject: Help!! Paper Wasps Needed Followup-To: bionet.molbio.rapd Date: 7 Jun 1995 02:53:39 GMT Organization: cornell Lines: 24 Sender: pts3@cornell.edu (Verified) Message-ID: NNTP-Posting-Host: cu-dialup-0615.cit.cornell.edu Hello. My name is Phil Starks. I am a graduate student at Cornell University in the field of NeuroBiology and Behavior. I am currently examining paper wasps, specifically Polistes dominulus. I am evaluating their nesting behavior and population genetics. I want to compare animals from different regions -- mostly from the Northeast in areas between Boston, MA and Ithaca, NY. My problem is finding these critters. They tend to congregate in the eves of man-made structures. I have searched state parks and some universities but have only found 4 usable sites. A usable site is one that has been relatively undisturbed (not sprayed with insecticides) for a few years and contains 18 or more colonies. These wasps make un-enveloped nests -- you can plainly see the cells of the comb (it looks much like a gray honeycomb). P. dominulus is the more yellow and smaller of the 2 Polistes species in this region (P. fuscatus is dark brown and the larger of the two animals). At this time of year you may see colonies with anywhere from 1 to 10 individuals, and nests that may contain 8 to 100 cells. If you know of any potential sites please email me. I am offering a $20.00 finder fee for useful sites. Thanks for reading this message Phil Starks (pts3@cornell.edu) From owner-rapd@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!uwm.edu!msunews!harbinger.cc.monash.edu.au!newshost.anu.edu.au!newsmaster From: johna@rsbs-central.anu.edu.au Newsgroups: bionet.molbio.rapd Subject: RAPD Software Date: 7 Jun 1995 01:34:21 GMT Organization: rsbs - anu Lines: 20 Message-ID: <3r2vmt$hvs@manuel.anu.edu.au> NNTP-Posting-Host: 150.203.38.97 Keywords: RAPD X-Newsreader: RAPDistance Package A group at the Research School of Biological Sciences, Australian National University, Canberra under the direction of Prof. Adrian Gibbs has developed a software package called RAPDistance for the analysis of RAPD data. It has a comprehensive range of options for creating data files, editing them and using application programs to analyse them. The third version has just been released on the Internet. The first version was made available in October 1994. It is intended to maintain and extend the package as resources allow. The following files are available :- 1) README.DOC Getting started. 2) INTRO.DOC Brief details of scope of package and modifications. 3) RAPD103.EXE Self extracting archive file containing the package. Accessed from the Internet via :- 1) Anonymous ftp ftp://life.anu.edu.au/pub/RAPDistance or 2) WWW http://life.anu.edu.au/molecular/software/rapd.html Please register with me if you use the package so that I can keep you informed of new versions, bugs etc. Regards. John Armstrong From owner-rapd@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!sunic!sunic.sunet.se!news.funet.fi!news.csc.fi!news.helsinki.fi!kruuna!petterss From: petterss@cc.Helsinki.FI (Jouko Kalevi Pettersson) Newsgroups: bionet.molbio.rapd Subject: Re: primers Date: 7 Jun 1995 15:09:40 GMT Organization: University of Helsinki Lines: 17 Message-ID: <3r4ffk$gse@oravannahka.Helsinki.FI> References: <3r1pd1$3po@whitbeck.ncl.ac.uk> NNTP-Posting-Host: kruuna.helsinki.fi Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: TIN [version 1.2 PL0] H.Tyler-Walters (H.Tyler-Walters@ncl.ac.uk) wrote: > I'm trying to start some work that will use RAPD markers. Could some-one > be so kind as to post the address for Operon Technologies. Are there any > other companies that supply RAPD primers. And you can check, what is available. URL: gopher://s27w007.pswfs.gov/1/.Data/.Primers/.RAPD URL: gopher://poplar1.cfr.washington.edu/11/pub/primers Good luck! -- Jouko Pettersson Internet: Jouko.Pettersson@Helsinki.FI Division of Biochemistry FAX: +358 0 708 59068 Department of Biosciences Phone: +358 0 708 59012 University of Helsinki From owner-rapd@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!LIFSCI.SDSU.EDU!MCCLELLAND From: MCCLELLAND@LIFSCI.SDSU.EDU Newsgroups: bionet.molbio.rapd Subject: posting Date: 7 Jun 1995 13:10:04 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <950607052325.2020074c@LIFSCI.SDSU.EDU> NNTP-Posting-Host: net.bio.net When I reply to an inquiry on this board does it always get posted for everone on the board or does it only go to the person with the inquiry? The reason I ask is that the last twenty or so replies I have made were not posted as far as I could tell, though most were acknowledged by the inquirer. If this is not the right address to ask this question could you give me the correct address. Thanks, Michael From owner-rapd@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: Newsgroups: bionet.molbio.rapd Subject: sequence of OPERON RAPD OPEQ2 (Kit Q) Date: 7 Jun 1995 15:56:19 +0100 Lines: 4 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3r4emj$crp@mserv1.dl.ac.uk> Original-To: rapd@dl.ac.uk Hello I am a PhD student in ORSAY (FRANCE) and I am looking for the sequence of OPERON RAPD primer OPEQ2.If someone could send me that sequence, i would appreciate. Thanks in advance From owner-rapd@net.bio.net Wed Jun 07 23:00:00 1995 Path: biosci!cbr.for.csiro.au!charlie.bell From: charlie.bell@cbr.for.csiro.au (Charlie Bell) Newsgroups: bionet.molbio.rapd Subject: Re: sequence of OPERON RAPD OPEQ2 (Kit Q) Date: 7 Jun 1995 19:58:34 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 30 Sender: daemon@net.bio.net Distribution: world Message-ID: <199506080254.AA23278@acacia.cbr.for.csiro.au> NNTP-Posting-Host: net.bio.net asked, >Hello >I am a PhD student in ORSAY (FRANCE) and I am looking for the sequence of >OPERON RAPD primer OPEQ2.If someone could send me that sequence, i would appreciate. >Thanks in advance > The sequence is, " Q-02","TCTGTCGGTC" and was retrieved from, URL: gopher://s27w007.pswfs.gov/1/.Data/.Primers/.RAPD where all the Operon and UBC primer sequences are available. You could also try, URL: gopher://poplar1.cfr.washington.edu/11/pub/primers Charlie Bell ****************************************************** Charlie Bell Phone 06-2818324 (International) +616-2818324 CSIRO Fax 06-2818312 (International) +616-2818312 Division of Forestry E-mail charlie.bell@cbr.for.csiro.au PO Box 4008 QVT Canberra ACT 2600 Australia ****************************************************** From owner-rapd@net.bio.net Wed Jun 07 23:00:00 1995 Path: biosci!cabi.org!D.BRAYFORD From: D.BRAYFORD@cabi.org ("David Brayford ", IMI) Newsgroups: bionet.molbio.rapd Subject: RE: primers Date: 8 Jun 1995 07:05:23 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: <2FD70383@msm.cgnet.com> NNTP-Posting-Host: net.bio.net H.Tyler-Walters (H.Tyler-Walters@ncl.ac.uk) wrote: > I'm trying to start some work that will use RAPD markers. Could some-one > be so kind as to post the address for Operon Technologies. Are there any > other companies that supply RAPD primers. Hi Changing the subject slightly, we've been buying custom primers (not kits) from Pharmacia Biotech in UK and have been very pleased with the service, price and yeilds. They are at: Pharmacia Biotech Ltd. 23 Grosvenor Road St. Albans Hertsfordshire AL1 3AW, UK Phone: (01727) 814000 FAX: (01727) 814001 I hasten to add that I don't work for them! Dave Brayford International Mycological Institute d.brayford@cabi.org From owner-rapd@net.bio.net Sat Jun 10 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!news2.near.net!news.delphi.com!usenet From: lonnie Newsgroups: bionet.molbio.rapd Subject: Re: posting Date: Sun, 11 Jun 95 01:22:34 -0500 Organization: Delphi (info@delphi.com email, 800-695-4005 voice) Lines: 16 Message-ID: References: <950607052325.2020074c@LIFSCI.SDSU.EDU> NNTP-Posting-Host: bos1c.delphi.com X-To: writes: >When I reply to an inquiry on this board does it always get posted for >everone on the board or does it only go to the person with the inquiry? > I subscibe to the Internet through Delphi and that is the only service I have ever had, so it's possible that another service may be different. However, when I am looking at newsgroups and I type "reply", the system prompts me to type in my message followed by a "Control-Z". After I type the Control-Z, the system gives me a choice of "post, list, or cancel". When I pick "post", the reply gets posted FOR EVERYBODY to see, including me. On my system there is an option other than REPLY to send a private message to the writer of the message that I am responding to. The latter method will not post for all to see. Lonnie From owner-rapd@net.bio.net Sun Jun 11 23:00:00 1995 Path: biosci!CCR.DSI.UANL.MX!jpmtz From: jpmtz@CCR.DSI.UANL.MX Newsgroups: bionet.molbio.rapd Subject: About primers and peptides Date: 12 Jun 1995 15:35:50 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 25 Sender: daemon@net.bio.net Distribution: world Message-ID: <00991C6B.84E1CF80.51@ccr.dsi.uanl.mx> NNTP-Posting-Host: net.bio.net Dear netters, Days ago somebody wanted information about companies (reliable) making oligos. Well... I have some experience with some of them. I have found BIO-SYNTHESIS, INC as the best... by far. I have tested custom oligos and their 10-mer primer kits. No problem what so ever. 100% efficiency, reproducibility and extremely fast. Take this example... I order 5 oligos by e-mail on friday and I got them today (Monday) in MEXICO !! And the price...$ 1.19 per base no setup charge. Their e-mail is Biosyn@aol.com Fax (214) 420-0442 or toll free (800) 227-0627 or check their ad in SCIENCE for snail mail address. Juan Pablo Martinez-Soriano Monterrey, MEXICO .....>>>> I am only a satisfied customer, no ties of any kind with Bio-Synthesis, Inc. From owner-rapd@net.bio.net Tue Jun 13 23:00:00 1995 Path: biosci!EM.AGR.CA!SPRASHAR From: SPRASHAR@EM.AGR.CA (Suvira Prashar) Newsgroups: bionet.molbio.rapd Subject: re:DGGE: Ethidium bromide stain. Date: 14 Jun 1995 05:28:36 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Does anybody know why acrylamide gels won't stain with eithidium bromide but the same gel will stain nicely with silver stain. Conditions of gel running are overnight at 60 C. Buffer being used is TAE pH 7.4. (Buffer recirculates during the run by means of perastalic pump. Imp: Using the same conditions these DGGE gels used to stain perfectly. We have tried changing :Fresh stain 0.5ug/ml. :Prepared all reagents from brand new chem. bottles. :Double checked the pH of Buffer. NOW I AM LOOKING FOR ANY SUGGESTIONS YOU HAVE. From owner-rapd@net.bio.net Tue Jun 13 23:00:00 1995 Path: biosci!UNIXG.UBC.CA!hobbs From: hobbs@UNIXG.UBC.CA (John Hobbs) Newsgroups: bionet.molbio.rapd Subject: RAPD 10-mer Primers Date: 14 Jun 1995 16:57:21 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 183 Sender: daemon@net.bio.net Distribution: world Message-ID: <199506142356.QAA25008@unixg.ubc.ca> NNTP-Posting-Host: net.bio.net This is a long posting, and I'm told that people tend not to read long postings, so maybe it's wasted effort. Anyway, briefly: the first part is this blurb; the second part tries to answer a recent query to the newsgroup; the third part describes how UBC primers are made and processed vis-a-vis those from Operon and GenoSys, and the fourth part considers recommendations on storing primers. If none of these are of interest, please file this posting in the trash. ************************************************************************* In a recent posting, it was asked why Operon's primers appear to be used more widely than UBC primers. Possibly the answer is that Operon is a commercial concern and advertises widely in major scientific journals. UBC Primers emanate from the core facility at UBC, the Nucleic Acid - Protein Service Unit, which is not a commercial firm. We do not advertise (in fact I am expressly forbidden to do so) other than through postings to relevant newsgroups on the InterNet, and these have been restricted to relatively few postings to this newsgroup and (for our insect mitochondrial DNA primer set) bug-net. ********************************************************************** I have been concerned to read the recent postings regarding the need to use a higher concentration of UBC primer concentrations than recommended in order to attain reasonable banding patterns. If users of UBC primers feel that they have received lower quantities of primer than expected, I would like to hear from them. However, I would like to make the following points: First, regarding the way we process our primers: after synthesis and cleavage/deprotection, the crude oligo 10-mer is dissolved in 0.5 ml. TE buffer and applied to a NAP-5 column (Pharmacia; pre-equilibrated with phosphate buffer). NAP-5 columns are essentially Sephadex G-25: the oligo passes through and the low mol. wt. impurities from the synthesis are retained. We elute the oligo with 0.5 ml. aliquots of TE buffer, collecting five fractions. The first never contains any oligo, and we normally just measure the A260 values in fractions 2,3,and 4, by diluting a 10-microlitre aliquot 1:100 with water. The densest fraction is nearly always fraction #3. We then combine the two fractions with highest OD content (nearly always #2 and #3: the fourth fraction is usually discarded), and re-measure the OD content of the combined fractions as above. It should be the mean of the values for the two constituent fractions, of course. If it is not, within reasonable error, we check again. This allows us an internal check on the previous figures. If all is OK, we plug the figure for the OD of the combined fractions into a Microsoft Excel file in which the formulae are set up, with extinction coefficients allowing for base composition, to permit the calculation of the yield of oligo in micrograms, and the volume of TE buffer which still needs to be added to the combined fractions to give a solution containing 1 microgram of DNA per microlitre. (By the way, the calculation assumes that the volume of the combined fractions is two 0.5 ml. volumes minus the number of microlitres used in the A260 determinations. Obviously this is predicated on the operator having pipetted 0.5 ml. of TE buffer accurately on to the column to obtain each 0.5 ml. fraction at the bottom, but our checks indicate that the assumption is not seriously in error). The calculated volume of TE buffer is then added and the solution mixed. We then pipette 10 microlitre aliquots of this diluted solution into Eppendorf tubes using a repeating autopipette and allow the solution to air-dry in a running sterile flow hood (all solutions, pipette tips, etc. have been sterilized, of course). The number of tubes which you can pipette from a single fill of the pipette tip gives a check on the repetitive accuracy of the delivery of the solution, and we have found it to be constant. The mean molecular weight of a primer is close to 3000. Obviously this varies with the base composition, the extremes (for 50-80% G+C 10-mers) being 2861 (C8 T2) and 3199 (G8 A2), i.e. the weights can be plus or minus 5.6% on either side of a mean of 3030. Since we have calculated to deliver 10 microgram aliquots, an aliquot should contain around 3.3 nmoles, though this figure could be as high as 3.495 (for C8 T2) or as low as 3.125 (for G8 A2). Let us suppose it is 3.3 nmoles. On the basis of an "average" value for the extinction coefficient, this figure equates to about 0.3 A260 units. Our primers nearly all have G+C content in the range 50-80%, rather than the 60-70% used by Operon (judged by the requests for further aliquots of individual primers, this wider range of G+C content is justified: the number of requests for 50% and 80% G+C primers is slightly less than, but comparable to that for 60-70% G+C primers). The variability associated with the optical density of the primers is much greater than that for the molecular weight, with the extremes represented by C8 T2 (with a rather low extinction coefficient at 260nm) and G5 A5 (with a rather high one) The variations from the "mean" value are such that for C8 T2 an A260 value of around 0.26 would be expected, and for G5 A5 a value of around 0.39, without the aliquotted quantity being in error. I should add that the A280 and A260/A280 values will of course also vary with base composition of the primer. At times we perform random checks on the quantities of primers in individual tubes, and have rarely found them to be other than the advertised amounts. Operon's kits contain larger quantities of individual primers than ours. I understand that Operon's aliquots contain 0.5 A260 units of each primer, and the primers contain 60 or 70% G+C. The quantity in nanomoles provided in the aliquots will therefore vary appreciably with base composition: the largest quantity would be for an oligo of composition C7 T3 (6.45 nmoles) and the smallest for an oligo of composition G6 A4 (3.79 nmoles). I do not know what recommendations are provided with Operon's kits as to dissolving the primers and the quantities to use. To obtain equimolar concentrations in each incubation using different primers, the volume of suspension buffer will need to be adjusted for each primer. Our approach has been to provide closely similar molar quantities of each primer to obviate the need to adjust concentrations with individual primers. I am told that Operon's primers were prescreened using a lettuce and lettuce fungus test system: only primers which gave patterns with the test system were included in primer sets. Ours are not prescreened in this way: it might give a bias towards use with a certain genomic type which would be fine if your genome of interest was a related one, but maybe less applicable if it were not. We would normally expect about 60% of our primers to give useful scorable bands with any given genome, and sometimes the incidence is reportedly much higher. That the policy of distributing non-prescreened primers is reasonable may be justified by the finding that 85 of the hundred primers in set #2 and 87 of the hundred primers in set #3 have been the subjects of individual reorders at different times, so a high proportion of the primers in the sets are presumably proving useful for somebody. ********************************************************************** Back before Xmas, there was some discussion among the newsgroup regarding the stability of RAPD primers. I would like to offer some second-hand recommendations, and some first-hand results and suggestions. The second-hand information: the earlier discussion called to mind some data which Genosys distributes regarding storage conditions of primers and their stability, and after some rummaging I found them. They are as follows: Lyophilized (-20C) 6mos.- several years Lyophilized (25C) 2mos.- 1 year Dissolved (-20C) 1mo.- 6 mos. Dissolved (25C) 1wk. - 1 mo. (Resuspension buffers are taken to be sterile water or TE buffer). Before you throw your RAPD primers away, I should say that the length of the primers for which the recommendations are given is not defined: I suspect that Genosys based the recommendations on assumed primer lengths of 20 bases upwards (the lifetimes are likely to be substantially longer for short primers such as RAPD primers), and that the figures given are fairly conservative anyway. In partial substantiation, some first-hand information: I recently came across a box of RAPD 10-mers, lyophilized, which had been sitting around at room temperature for around 2.5 years (our clients will be glad to know that we do not send out primers remotely approaching this age!), and thought they would be a good test of stability: they were dissolved in water and examined by hplc, comparing the elution profiles against those of identical sequences of much more recent synthesis. The old primers showed surprisingly good long-term stability in a dried state, with degradation being usually substantially less than 20% even after 2.5 years, and they generally exhibited good banding patterns in my colleague John Carlson's test system. In a dried state, at least, there did not seem to be any predominant breakdown mode as judged from the elution profiles - by which I mean that no particular peak assignable to a breakdown product seemed to predominate. Such degradation as occurs appears to be random. So much for the dried state - what about primers stored frozen or in solution? Here I do not have hplc data, but it seems to be common experience that RAPD primers stored frozen in solution at -20C or lower retain good long-term function, at least for much longer than the above figures suggest. The hplc profiles of some of our standard sequencing 18-mers stored frozen for two years show no appreciable degradation. However, the Genosys figures at least highlight the fact that primers do not last forever, and will slowly become degraded however they are stored, and while most primer users are aware of this, some are not. Primers to be used should be dissolved in resuspension buffer or water and divided among a number of sterile stock tubes. Only one tube should be used as the working sample, the others being frozen. Flash freezing by dipping in a dry ice/acetone or ethanol (or similar low temperature) bath is to be preferred over slow freezing by simply putting the samples in a freezer, but take care not to wash any ink markings off the tubes! The working tube is stored frozen and then thawed for use, and re-frozen after use, until evident deterioration as judged by poor results is seen (freeze-thaw cycles accelerate deterioration, according to lore), when it is discarded and a fresh stock tube taken. Alternatively the aliquots subdivided into the sterile stock tubes could simply be stored dry by letting them evaporate in a running sterile flow hood - typically a volume of 10-20 microlitres will evaporate overnight at ambient temperature. This is probably the best option for longer storage. John Hobbs. Dr. John Hobbs Nucleic Acid - Protein Service (NAPS) Unit Biotechnology Laboratory Room 237, Wesbrook Building 6174 University Boulevard University of British Columbia Vancouver, V6T 1Z3 Canada. FAX (604)822-5437 or (604)822-0676; Tel. (604)822-6373 From owner-rapd@net.bio.net Tue Jun 13 23:00:00 1995 Path: biosci!SERVIDOR.DGSCA.UNAM.MX!carvalho From: carvalho@SERVIDOR.DGSCA.UNAM.MX (Carvalho Torres Alexandro cassio-UACPYP) Newsgroups: bionet.molbio.rapd Subject: re:DGGE: Ethidium bromide stain. Date: 14 Jun 1995 07:52:06 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net On 14 Jun 1995, Suvira Prashar wrote: > Does anybody know why acrylamide gels won't stain with eithidium > bromide but the same gel will stain nicely with silver stain. > Conditions of gel running are overnight at 60 C. Buffer being used > is TAE pH 7.4. (Buffer recirculates during the run by means of > perastalic pump. > Imp: Using the same conditions these DGGE gels used to stain > perfectly. > We have tried changing :Fresh stain 0.5ug/ml. > :Prepared all reagents from brand > new chem. bottles. > :Double checked the pH of Buffer. > > NOW I AM LOOKING FOR ANY SUGGESTIONS YOU HAVE. > > > Dear Prashar. Try use TBE 1X! What is your concentration of Acrylamide. Silver staining is more sensitivy than ethidium bromide. I have good results with the latter staining. Good luck Alexandro Carvalho Mexico City. INNSZ. From owner-rapd@net.bio.net Wed Jun 14 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!gaia.ucs.orst.edu!sslab.FSL.ORST.EDU!sceppa From: sceppa@fsl.orst.edu (Jennifer Sceppa) Newsgroups: bionet.molbio.rapd Subject: long PCR Date: Thu, 15 Jun 1995 11:41:56 Organization: Forestry Sciences Lab Lines: 4 Message-ID: NNTP-Posting-Host: sslab.fsl.orst.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] I was wondering if anyone knows of any references dealing with applications of long PCR. Any help would be greatly appreciated. Jen Sceppa From owner-rapd@net.bio.net Wed Jun 14 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!pipex!oleane!jussieu.fr!jouy.inra.fr!usenet From: Yves Bertheau Newsgroups: bionet.molbio.rapd Subject: (no subject) Date: 15 Jun 1995 17:05:36 GMT Organization: INRA Lines: 24 Message-ID: <3rpp90$bad@saphir.jouy.inra.fr> NNTP-Posting-Host: solair.inapg.inra.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1b3 (X11; I; SunOS 5.3 sun4c) X-URL: news:bionet.molbio.rapd?ALL Hello, I tried several times to retrieve the rapd program (rapd103.exe) from the gopher server: life.anu.edu.au by the netscape client or by a direct ftp from /pub/RAPDistance but ever succeed.. Each time, after several hours at a very low flow, I obtained 350 to 700 ko of this program of more than 1 Mo... then the ftp/gopher server resetted the communication. Although I ftped since several years a lot of files/software I am really unsuccesfull with this program and I am looking for an alternative to retrieve this program. Is there any other source of this software to analyse RAPD data ? Thanking you in advance for your help. -- Yves Bertheau, INRA INA P-G, Pathologie Vegetale, 16 rue Claude Bernard, 75231 PARIS cedex 05, FRANCE, Tel +33 (1) 44.08.16.98 or 44.08.17.04 Fax: +33 (1) 44.08.17.00 or 16.31, Internet: bertheau@inapv.inapg.inra.fr http://inapv.inapg.inra.fr/gcg/WWW/server_root/Welcome.html From owner-rapd@net.bio.net Sun Jun 18 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!usc!cs.utexas.edu!news.sprintlink.net!EU.net!uknet!warwick!news.coventry.ac.uk!rowan!apx085 From: Ralph Rapley Newsgroups: bionet.molbio.rapd Subject: RNA analysis & PCR methods courses Date: Mon, 19 Jun 1995 18:49:39 +0100 Organization: Coventry University Lines: 46 Message-ID: NNTP-Posting-Host: apx085@rowan-fddi.coventry.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: apx085@rowan RNA Extraction & Analysis ========================= 20 September 1995 & 19th December 1995 PCR Methods & Applications ========================== 21 September 1995 & 20th December 1995 Coventry University, UK These are two one day laboratory based practical courses that may be attended alone or as a two day course. They provide a basic introduction into the extraction and characterisation of RNA and the techniques and applications of the PCR. The practical component is supplemented by seminars and demonstrations in related topics such as ; Northern blotting, mRNA isolation, RPA & S1 mapping, rRNA isolation, cDNA synthesis & RT-PCR etc. for the RNA course. For the PCR course, Microbe identification, probe preparation, PCR cloning & sequencing and primer design will be among the topics. These introductory courses will be of interest to those initiating work in these areas or wishing to update their knowledge. Fees are GBP100 for each course inclusive of lunch, tea/coffee. For attendance at both courses the fee is GBP160. Further Information and Registration forms: Debbie Elliott, Commercial Development Unit, Coventry University, Priory Street, Coventry, CV1 5FB United Kingdom. Tel. 01203 838145 Fax. 01203 221396 email Dr Ralph Rapley (rapley@coventry.ac.uk) ************************************************************************* From owner-rapd@net.bio.net Mon Jun 19 23:00:00 1995 Path: biosci!LIFSCI.SDSU.EDU!MCCLELLAND From: MCCLELLAND@LIFSCI.SDSU.EDU Newsgroups: bionet.molbio.rapd Subject: patents/ corrected e-mail address Date: 20 Jun 1995 15:24:54 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 5 Sender: daemon@net.bio.net Distribution: world Message-ID: <950620073900.2020121c@LIFSCI.SDSU.EDU> NNTP-Posting-Host: net.bio.net The e-mail address for Stratagene is ronni_sherman@stratagene.com Sorry for any inconvenience. Michael From owner-rapd@net.bio.net Mon Jun 19 23:00:00 1995 Newsgroups: bionet.molbio.rapd Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!qns3.qns.com!news.ecn.uoknor.edu!news.uoknor.edu!ns1.nodak.edu!plains!comstock From: comstock@plains.NoDak.edu (Clay Comstock) Subject: Chelex 100 Resin Sender: usenet@ns1.nodak.edu (Usenet login) Message-ID: Date: Tue, 20 Jun 1995 16:42:07 GMT Nntp-Posting-Host: plains.nodak.edu Organization: North Dakota Higher Education Computing Network (NDHECN) X-Newsreader: TIN [version 1.2 PL2] Lines: 32 Hello, I was wondering if anyone had any extraction protocols using Chelex 100 Resin (by BioRad). Preferrably, a protocol for spider DNA but anything close will help. I have one publication from Biotechniques 10:1991. It deals with DNA extraction from blood and semen. Thanks, Clay Comstock ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ____________ /| /| "The Necker Cube / |_________/_| Reminds Us, That /__/________/ | All Situations | / | / Can Be Viewed |/ | / From Two Different Perspectives" |__________|/ Clay Comstock Dickinson State University Dickinson, ND 58601 e-mail comstock@plains.nodak.edu homepage http://murphy217.math.dsu.nodak.edu/dsu/comstock.htm ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-rapd@net.bio.net Mon Jun 19 23:00:00 1995 Path: biosci!LIFSCI.SDSU.EDU!MCCLELLAND From: MCCLELLAND@LIFSCI.SDSU.EDU Newsgroups: bionet.molbio.rapd Subject: patenting arbitrarily primed PCR Date: 20 Jun 1995 14:27:22 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: <950620064124.202011cf@LIFSCI.SDSU.EDU> NNTP-Posting-Host: net.bio.net I have heard rumours that DuPont has sold the rights to RAPDs to an Australian company and that they are asking 50 cents a reaction from companies and even asking Universities for money. Does anyone know if this is true? I do not want to lower the tone of RAPD net but I wanted to relate the following information. DuPont filed in March 1990 and published later that year (along with a paper by John Welsh and I that was accepted first). Our competing patent (which included RNA fingerprinting) was not filed until October 1990. However, in the USA it is first to conceive and reduce to practice that has priority, not the first to file. I am confident that our patent has USA priority for conception and for reduction to practice for both RNA and DNA. No doubt priority will be disputed, perhaps in court. Unfortunately, I do not have control over this possibility because our patent is not owned by me but by CIBR and Stratagene. More information might be available from Stratagene at 619 535 5400 or e-mail: ronnie_sherman@stratagene.com. Michael McClelland From owner-rapd@net.bio.net Tue Jun 20 23:00:00 1995 Path: biosci!UNIXG.UBC.CA!lijuan From: lijuan@UNIXG.UBC.CA (Lijuan Sun) Newsgroups: bionet.molbio.rapd Subject: Help Date: 20 Jun 1995 21:49:37 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 39 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hi, Dear rapders, I've beening working with Endocronartium harknessii (syn:Peridermium harknessii), a fungus causes gall rust on hard pine. Its common name is western gall rust. My project focused on the population structure of this fungus in British Columbia. Since there is a dispute about the reproductive system of this pathogen, it makes hard to interpret the results right now. This rust species only has one prominent spore type, termed aecioid teliospore or aeciospores by different group of people who held different opinion on reproductive system. The former claimed that meiosis occured in aeciospore-like teliospore, and the geminated tubes resemble to basidiospores; The other considered aeciospores are true aeciospores, like other rust, Cronartium sp. but has short life cycle. Enough for the introduction. Sorry for keep it so long. I did some work to check the reproductive system by using RAPD. The work started with the idea of mother gall-progeny test. 'Mother' gall spore collected and inoculated to 20 more seedlings. After 2 years, these progeny galls produced spores. Spores were collected from each seedling as separeted 'single gall'. Then RAPD applied to both mother gall and progeny galls. Primers are those showing polymorphisms with population study. The results showed variations among progeny galls as well as among mother galls with 6 primers. There is very low chance of identity of mothers and their progenies.Total 15 mothers and 79 progenies (from 300 inoculated seedlings) were screened. Can someone rule out sexual reproduction from this results? Or this assumption is not valid? In addition, mycelium in the infected tissue is uninucleate and spores are binucleate. Axenic culture on the stage of very little mycelium produced. Pycnia stage has been found but very rare event in nature. Thanks in advance for any open suggestions. Lijuan Sun (Grad.) Faculty of forestry/Biotechnology University of British Columbia 270-2357 Main Mall Vancouver, BC V6T 1Z4 From owner-rapd@net.bio.net Tue Jun 20 23:00:00 1995 Path: biosci!LIFSCI.SDSU.EDU!MCCLELLAND From: MCCLELLAND@LIFSCI.SDSU.EDU Newsgroups: bionet.molbio.rapd Subject: correction Date: 21 Jun 1995 12:38:36 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: <950621024450.2020133f@LIFSCI.SDSU.EDU> NNTP-Posting-Host: net.bio.net The e-mail address for Stratagene is ronni_sherman@stratagene.com Sorry for any inconvenience. I understand that the company in Australia is ForBio Systems and they are claiming exclusive rights for forestry. I am told that DuPont is contacting companies in other areas of research, directly. From owner-rapd@net.bio.net Tue Jun 20 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!news.u.washington.edu!toby From: toby@u.washington.edu ('Toby' H D Bradshaw) Newsgroups: bionet.molbio.rapd Subject: Re: patenting arbitrarily primed PCR Date: 20 Jun 1995 23:33:25 GMT Organization: University of Washington, Seattle Lines: 40 Message-ID: <3s7ls5$4o6@nntp1.u.washington.edu> References: <950620064124.202011cf@LIFSCI.SDSU.EDU> NNTP-Posting-Host: saul3.u.washington.edu NNTP-Posting-User: toby In article <950620064124.202011cf@LIFSCI.SDSU.EDU>, wrote: > >I have heard rumours that DuPont has sold the rights to RAPDs to an >Australian company and that they are asking 50 cents a reaction >from companies and even asking Universities for money. Does >anyone know if this is true? Nobody I know has seen the license agreement between ForBio (Bob Teasdale's company) and DuPont, but ForBio claims to have an exclusive license for the RAPD process *in forest trees*. AFIK that's all ForBio got from DuPont. And, yes, ForBio wants a "small fee" (their language) of $0.50/rxn. I don't feel like typing in the whole letter, but I'll make a scan available by ftp if there's sufficient interest. ForBio now claims that academic research will not be charged the "small fee". How basic and applied research will be distinguished is an open question. >I do not want to lower the tone of RAPD net but I wanted to >relate the following information. DuPont filed in March 1990 and >published later that year (along with a paper by John Welsh and I >that was accepted first). Our competing patent (which included RNA >fingerprinting) was not filed until October 1990. However, in the USA it is >first to conceive and reduce to practice that has priority, not the first to >file. I am confident that our patent has USA priority for >conception and for reduction to practice for both RNA and DNA. > >No doubt priority will be disputed, perhaps in court. This matters to me only if one patent holder plans to charge a smaller royalty than the other. I'll not hold my breath :) Toby Bradshaw | (206)616-1796 (voice) Center for Urban Horticulture | (206)616-1826 (FAX) Box 354115 | toby@u.washington.edu University of Washington | 47.39.496N 122.17.404W Seattle WA 98195 | Will make linkage maps for food. From owner-rapd@net.bio.net Wed Jun 21 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!cam.news.pipex.net!pipex!edi.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!news.rediris.es!acebo.sdi.uam.es!chotis!dopazo From: dopazo@samba.cnb.uam.es (Joaquin Dopazo) Newsgroups: bionet.molbio.rapd Subject: NEW SOFTWARE: Gel Manager Date: Thu, 22 Jun 1995 14:51:06 Organization: CNB-UAM Lines: 66 Message-ID: NNTP-Posting-Host: chotis.cnb.uam.es X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Finally a program for analysis of gels which includes a mathematical treatment for RAPD data!! ----------------------------------------------------------------------------- GEL MANAGER 1.1 A Program For the Analysis of Electrophoretic 1D Gels Developed at : Centro Nacional de Biotecnología, CSIC. Universidad Autónoma, Madrid, SPAIN Under a contract of TDI SA Authors: Carlos Vaquerizo and Joaquín Dopazo The program We present a new concept in the field of comparison and analysis of electrophoretic profiles. Gel Manager is a user friendly program which runs in Microsoft Windows environment. It includes advanced techniques of image processing along with sophisticated options for data analysis. It can deal with different kinds of data such as: RFLP, RAMM, RAPD, microsatellites and other fingerprinting techniques. Their capacities of data processing make of Gel Manager a multipurpose program extremely useful for many types of studies including the definition of genetic relationships, taxonomy and classification , epidemiology, etc. Image processing Using the digitalized image of a gel or a film, Gel Manager performs a cleaning of the image removing noise by means of different advanced methods of image processing. Images can be retrieved in many standard graphic formats (BMP, PCX, TIFF, etc.). Next, the program automatically finds the positions of the bands of every lane, by means of a high precision algorithm, and estimates their molecular weights using as reference any marker of electrophoretic migration. Every selected lane is presented as a profile of intensity with the detected bands marked. The program provides a series of tools to manually define, remove or move peaks. The threshold of detection is very easy to use and can be changed to detect very weak bands over a noisy background. Distortion in gels can be easily corrected by defining base lines which allows the recalculation of the positions of every band by interpolation. Each image with all the operations performed over it can be stored as a session which can be reloaded later. On the other hand, all the molecular weights obtained can be stored in databases which allow to perform different comparisons between the lanes. Data analysis Considering the most recent scientific literature, Gel manager provides different indexes appropriate for the comparison of samples studied by means of different techniques. Results of the comparisons can be displayed as a divergence matrix or as a dendrogram, obtained by the UPGMA method. All these characteristics set to Gel Manager among the most advanced software in the field of digital analysis of electrophoretic gels for PC computers. AVAILABILITY Have a look to gel manager in our Web page at the URL: HTTP://WWW.CNB.UAM.ES/WWW/PROGRAMAS/GEL_MAN/GM.HTML You can retrieve a DEMO copy in out FTP at the internet address: FTP.CNB.UAM.ES in the directory SOFTWARE/MOLBIOL Alternatively you can send your requests to 100626.13@compuserve.com You are kindly invited to visit our Software Web page at the URL: HTTP://WWW.CNB.UAM.ES/www/programas/pag-soft.html From owner-rapd@net.bio.net Wed Jun 21 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!mcrcim.mcgill.edu!news.mcgill.ca!VM1.MCGILL.CA From: "LECLERC-POTVIN,CAROLE,MS" Newsgroups: bionet.molbio.rapd Subject: UBC and OPERONS primers Date: 22 JUN 95 10:41:47 EST Organization: McGill University Lines: 12 Sender: usenet@MUSICB.MCGILL.CA Message-ID: <22JUN95.11552373.0106@VM1.MCGILL.CA> NNTP-Posting-Host: vm1.mcgill.ca I'm sorry...I read the message on UBC and OPERONS primers yesturday. Of course I did not have a diskette to save the message and this morning it was gone! Mr. Hobbs or anybody that copied it, would you please send me a copy via e-mail. Thank you very much, Merci Carole Leclerc-Potvin xp7x@musicb.mcgill.ca From owner-rapd@net.bio.net Thu Jun 22 23:00:00 1995 Newsgroups: bionet.molbio.rapd Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!agate!news.Stanford.EDU!nntp-hub2.barrnet.net!newshost.ea.com!psinntp!psinntp!psinntp!psinntp!nntp.hk.super.net!news.ust.hk!usthk.ust.hk!boningli From: boningli@usthk.ust.hk Subject: postdoctoral position available Message-ID: <1995Jun22.220046.1@usthk.ust.hk> Lines: 24 Sender: usenet@uxmail.ust.hk Nntp-Posting-Host: ustcc3.ust.hk Organization: The Hong Kong University of Science & Technology (HKUST) Date: Thu, 22 Jun 1995 14:00:46 GMT Postdoctoral Position A postdoctoral position is available immediately to study: 1) the temporal and spatial regulation of ACC synthase and ACC oxidase gene expression during plant development and differentiation; 2) the genetic engineering of banana plant with reduced ethylene production. Successful candidates should have experience in plant molecular biology and/or protein biochemistry. Appointment will be for two years with possible renewal for up to one additional year. The monthly salary is at least HK$21000 plus a standard health-care benefit. The Hong Kong University of Science and Technology campus locates right on the beach of clear water bay of Hong Kong and offers an exciting environment, the state of art equipment and modern libraries for doing cutting-edge researches. Interested individuals should send CV to : Drs Ning Li / Shang Fa Yang Department of Biology The Hong Kong University of Science and Technology Clear Water Bay Hong Kong E-mail: BONINGLI@usthk.ust.hk FAX: 852-358-1559 TEL: 852-358-7335; 852-358-7311 From owner-rapd@net.bio.net Thu Jun 22 23:00:00 1995 Path: biosci!YVAX.BYU.EDU!anderswr From: anderswr@YVAX.BYU.EDU (W. Ralph Andersen) Newsgroups: bionet.molbio.rapd Subject: horses and RAPDs Date: 22 Jun 1995 10:45:50 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HS04VBYHHMA8C2TE@yvax.byu.edu> Yes, I know I can do a library search, and I will (when I catch up), but do any of you know of recent papers on DNA polymorphism in horses (RFLP, RAPD, AFLP and other genetic acronyms, etc.)? I would appreciate any help you could give me along these lines. Thanks. Ralph Andersen 297 WIDB, BYU, Provo, Ut. 84602. Phone: 801 378 2468 or Fax: 801 378 7499. From owner-rapd@net.bio.net Thu Jun 22 23:00:00 1995 Path: biosci!rutgers!uwm.edu!msunews!harbinger.cc.monash.edu.au!newshost.anu.edu.au!newsmaster From: johna@rsbs-central.anu.edu.au Newsgroups: bionet.molbio.rapd Subject: RAPDistance software/Netscape Date: 23 Jun 1995 05:06:08 GMT Organization: ANU, Canberra, Oz Lines: 9 Message-ID: <3sdi40$g7b@manuel.anu.edu.au> NNTP-Posting-Host: 150.203.38.97 X-Newsreader: Hi, Yves Bertheau on 15 June noted some problems with downloading the RAPDistance software using Netscape. I have had a similar message from a colleague in New Zealand. I don't know the reason for this. The traffic has been heavy with over 200 accessions in one week. Suggest if you continue to have problems you contact me again. At a last resort I will send out discs. The software consists of two text files and one binary file. In all approx 1.2Mb. Cheers John A From owner-rapd@net.bio.net Thu Jun 22 23:00:00 1995 Path: biosci!POPGEN.DBS.UMT.EDU!donna From: donna@POPGEN.DBS.UMT.EDU (Donna Leeper) Newsgroups: bionet.molbio.rapd Subject: Re: RAPDistance software/Netscape Date: 23 Jun 1995 10:59:40 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <3sdi40$g7b@manuel.anu.edu.au> Greetings The software downloaded fine from the ftp site. Donna Leeper University of Montana On 23 Jun 1995 johna@rsbs-central.anu.edu.au wrote: > Hi, Yves Bertheau on 15 June noted some problems > with downloading the RAPDistance software using Netscape. > I have had a similar message from a colleague in New > Zealand. I don't know the reason for this. The traffic > has been heavy with over 200 accessions in one week. > Suggest if you continue to have problems you contact > me again. At a last resort I will send out discs. > The software consists of two text files and one binary > file. In all approx 1.2Mb. Cheers John A > From owner-rapd@net.bio.net Sat Jun 24 23:00:00 1995 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.rapd Subject: UNSUBSCRIBING, BIOSCI ARCHIVES, ADDRESS DATABASE & BIOSCI FAQ Date: 25 Jun 1995 02:00:10 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 347 Sender: daemon@net.bio.net Distribution: world Message-ID: <199506250900.CAA17564@net.bio.net> NNTP-Posting-Host: net.bio.net Four important items follow: How to cancel e-mail subscriptions to BIOSCI newsgroups, BIOSCI archive searching, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our BIOSCI user directory, please take a few minutes to complete and return the form below. 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Thanks again for your cooperation! --------------- please cut here and return portion below --------------- New information or Update to old record (enter N or U): date (DD-MM-YY): first name: middle initial: family name: job title: e-mail address: e-mail network: phone number: FAX number: institution: address1: address2: address3: city: state/province: country: postal code: research interest: research interest: comment: comment: comment: comment: comment: From owner-rapd@net.bio.net Sun Jun 25 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!Norway.EU.net!EU.net!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!news.u.washington.edu!toby From: toby@u.washington.edu ('Toby' H D Bradshaw) Newsgroups: bionet.molbio.rapd Subject: ForBio letter/RAPD patent Date: 26 Jun 1995 14:55:20 GMT Organization: University of Washington, Seattle Lines: 81 Message-ID: <3smhoo$1vb@nntp3.u.washington.edu> NNTP-Posting-Host: saul3.u.washington.edu NNTP-Posting-User: toby I have scanned in the letter received by my University from ForBio regarding the use of RAPDs in forest trees. The image can be found in encapsulated PostScript (.eps) and TIFF (.tif) formats, and is available by anonymous ftp from poplar1.cfr.washington.edu in the /pub/tmp directory. Included below is the email I received later from ForBio after a considerable volume of complaint from those of us engaged in basic research about the potential doubling of the cost of a RAPD reaction. -Toby Bradshaw toby@u.washington.edu Begin included text: _______________________________________________________________________ From rdt@research.forbio.com.au Wed May 17 19:50:11 1995 Return-Path: Received: from mx5.u.washington.edu by stein2.u.washington.edu (5.65+UW95.05/UW-NDC Revision: 2.33 ) id AA25407; Wed, 17 May 95 19:50:10 -0700 Received: from eucalypt.client.uq.edu.au by mx5.u.washington.edu (5.65+UW95.05/UW-NDC Revision: 2.31 ) id AA21897; Wed, 17 May 95 19:50:06 -0700 Received: (from rdt@localhost) by research.forbio.com.au (8.6.11/8.6.11) id MAA00888 for Toby@u.washington.edu; Thu, 18 May 1995 12:51:48 +1000 Date: Thu, 18 May 1995 12:51:48 +1000 Message-Id: <199505180251.MAA00888@research.forbio.com.au> From: rdt@research.forbio.com.au (Robert Teasdale) To: Toby@u.washington.edu Subject: Cc: Status: RO X-Status: 17 May 1995 Dear Sir, Random Amplification Polymorphic DNA I refer to the above and my previous correspondence of May 1995. It has been brought to my attention that you may be concerned or confused about the role of ForBio in the use and monitoring of the RAPD process. ForBio is a major user of the RAPD system, and as such has been able to negotiate a competitive royalty with Du Pont, the owner of the RAPD patent. In order to be able to do this we have taken on the responsibility of monitoring and licensing other users of this patented system (attached is a copy of a letter of authority from Du Pont). We are asking that all uses of the RAPD process be declared, although naturally where the use is not commercially funded or for a commercial purpose it is unlikely that we will seek to recover royalties. Would you please provide me with details of your use of the RAPD process so that we may update our Users Register and that where necessary we can arrange for a formal licence to be put in place. Your co-operation in this matter is appreciated. Yours faithfully, Christine Olds Legal Executive To whom it may concern ForBio limited has been licensed by E.I. DuPont de Nemours and Company of Wilmington, Delaware, USA with respect to DuPont's "RAPD" methodology claimed in U.S. Patent 5,126,239 and its foreign counterparts. This licence to ForBio Limited grants exclusive worldwide rights to perform research and product development in certain fields, particularly in forestry. ForBio Limited has the right to sublicense under the DuPont RAPD license, subject to the terms of it s license agreement with DuPont. Sincerely Dr Robert T. Giaquinta Manager, Biotechnology Business Development original by post. From owner-rapd@net.bio.net Mon Jun 26 23:00:00 1995 Path: biosci!oitunix.oit.umass.edu!ebeer From: ebeer@oitunix.oit.umass.edu (Eric N Beer) Newsgroups: bionet.molbio.rapd Subject: subscribe Date: 27 Jun 1995 09:54:29 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <199506262053.QAA10368@titan.oit.umass.edu> NNTP-Posting-Host: net.bio.net subscribe rapd From owner-rapd@net.bio.net Mon Jun 26 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!torn!ccshst05.cs.uoguelph.ca!ccshst01.cs.uoguelph.ca!mapsimon From: mapsimon@uoguelph.ca (Michele ApSimon) Newsgroups: bionet.molbio.rapd Subject: rat DNA?? Date: 26 Jun 1995 19:45:51 GMT Organization: University of Guelph Lines: 5 Message-ID: <3sn2pf$dj@ccshst05.cs.uoguelph.ca> NNTP-Posting-Host: ccshst01.cs.uoguelph.ca X-Newsreader: TIN [version 1.2 PL2] We are assaying for DNA content in various rat tissues and we would like to know if anyone knows the DNA content of rat somatic cells ie ug DNA/million cells??? Thank you. From owner-rapd@net.bio.net Wed Jun 28 23:00:00 1995 Path: biosci!agate!library.ucla.edu!psgrain!quagga.ru.ac.za!wabe.csir.co.za!pukrs7.puk.ac.za!blpc34.uovs.ac.za!paam From: paam@rs.uovs.ac.za (Mnr AA Myburg (Plant & Dierkunde x2818)) Newsgroups: bionet.molbio.rapd Subject: Separation of RAPD fragments on agarose Date: Thu, 29 Jun 1995 11:08:54 GMT Organization: Computer Services University of the Orange Free-State Lines: 26 Message-ID: NNTP-Posting-Host: blpc34.uovs.ac.za Anybody doing RAPDs out there, I am experiencing problems separating my RAPDs on agarose. I am screening wheat DNA for resistance markers using AB taq and I am running the samples in 2% agarose on the Hoefer HE100 Supersub. I am separating my samples at 5 V/cm (150V/30cm for 3h - 15 cm gels) When I use 1XTAE buffer, the bands (especially those larger than 1 kb) are fuzzy and distorted, } - shaped. The HE 100 manual suggests the use of TBE instead of TAE because of the lower buffer capacity of TAE. I have tried TBE buffer, but all the bands larger than 1 kb are smiling, ) - shaped. The lower bands are perfect. I have changed the loading buffer from a glycerol base to 15 % Ficoll BFB. This has improved the seperation, but only for the lower bands. I have also tried lowering the agarose concentration to 1.6% and running the gel at lower V (3 V/cm), but the >1 kb bands are still smiling and smeared. I have also lowered my sample concentration to avoid overloading. I would appreciate any suggestions which you might have. I still have to screen 3 segregating populations (100 plants each) and I am desperate! Zander Myburg paam@rs.uovs.ac.za From owner-rapd@net.bio.net Thu Jun 29 23:00:00 1995 Path: biosci!daresbury!is.bbsrc.ac.uk!news From: fosters@bbsrc.ac.uk (Sim) Newsgroups: bionet.molbio.rapd Subject: Re: Separation of RAPD fragments on agarose Date: 30 Jun 1995 11:59:13 GMT Organization: Institute of Arable Crops Research, Rothamsted Lines: 19 Message-ID: <3t0ouh$jef@is.bbsrc.ac.uk> References: NNTP-Posting-Host: pc748.res.bbsrc.ac.uk X-Newsreader: WinVN 0.92.6+ In article , paam@rs.uovs.ac.za (Mnr AA Myburg (Plant & Dierkunde x2818)) says: >I am experiencing problems separating my RAPDs on agarose. > >When I use 1XTAE buffer, the bands (especially those larger than 1 kb) are >fuzzy and distorted, } - shaped. Hi, Don't know if this is any help or not, just letting you know what I've experienced so far with RAPDs. I've found that I often get the fuzzy distorted } - shaped large bands when either the Taq concn or the amount of template DNA is too high. For example in 25ul reaction mixes, 0.5 Units Taq gives fine results, but an increase to 0.6 Units gives the fuzzy bands. Hope this is of some help. Cheers, Simon. From owner-rapd@net.bio.net Thu Jun 29 23:00:00 1995 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!news.sprintlink.net!gatech!emf.emf.net!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.molbio.rapd Subject: Dendrome list of 3040 10-mers Date: 30 Jun 1995 21:55:29 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 27 Distribution: world Message-ID: <3t1rsh$jsm@overload.lbl.gov> NNTP-Posting-Host: s27w007.pswfs.gov The Dendrome project at the Institute of Forest Genetics provides a list of commercially available 10-mer kits. You can access these via our gopher at s27w007.pswfs.gov or on the WWW at http://s27w007.pswfs.gov/Data/. Thanks to Dr. Simon Sims at Genosys Biotechnologies for providing us with sequence data for their new release of 1040 decamers. Apart from separate lists by vendor, you will find a list of all 10-mers sorted alphabetically by sequence and a (short) list of the duplicates found in the list. Please inform us of any new collections of primers that should be included. We will be happy to correct any mistakes or to provide any omitted credits or citations. --bks -- Bradley K. Sherman | Institute of Forest Genetics bks@s27w007.pswfs.gov | P.O. Box 245 510-559-6437 FAX:510-559-6440 | Berkeley, CA 94701 USA Dendrome Project