From owner-rapd@net.bio.net Sat Sep 03 23:00:00 1994 Newsgroups: bionet.molbio.rapd Path: biosci!daresbury!trane.uninett.no!eunet.no!nuug!EU.net!uunet!munnari.oz.au!news.Hawaii.Edu!uhunix.uhcc.Hawaii.Edu!stiles From: stiles@uhunix.uhcc.Hawaii.Edu (John Stiles) Subject: Re: Next PLANT GENOME meetings Message-ID: Sender: news@news.Hawaii.Edu Organization: University of Hawaii References: Date: Thu, 25 Aug 1994 23:05:14 GMT Lines: 27 In article wfl1@cornell.edu (Warren Frank Lamboy) writes: >Does anyone know when the next Plant Genome meetings will be held, >and whom I might contact for more information? Thank you. > >-- >Warren F. Lamboy >Dept. of Horticultural Sciences and > USDA-ARS Plant Genetic Resources Unit >Cornell University >Geneva, NY 14456-0462 >warren_lamboy@cornell.edu Plant Gemone III January 15-19 Town & Country Hotel San Diego, CA For information contact: Scherago International, Inc. Tel. (212) 643-1750 Fax. (212) 643-1758 Email Scherago@Biotechnet.com John stiles@uhunix.uhcc.hawaii.edu From owner-rapd@net.bio.net Mon Sep 05 23:00:00 1994 Newsgroups: bionet.molbio.rapd Path: biosci!agate!library.ucla.edu!europa.eng.gtefsd.com!newsxfer.itd.umich.edu!gatech!swrinde!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!netnews.nwnet.net!ns1.nodak.edu!badlands!dahleen From: dahleen@badlands.NoDak.edu (Lynn S Dahleen) Subject: Re: codominance take 2 (or more!) Sender: usenet@ns1.nodak.edu (Usenet login) Message-ID: Date: Tue, 6 Sep 1994 16:31:13 GMT References: Nntp-Posting-Host: badlands.nodak.edu Organization: North Dakota Higher Education Computing Network X-Newsreader: TIN [version 1.2 PL2] Lines: 38 : In my lab we are having trouble with the cutting oout and re-amplification : bit, do you have any suggestions? Kath, Try cutting the band out and placing the agarose/acrylamide fragment in 50 to 100 microliters of water. Let that sit overnight. The next day, set up a 100 ul PCR reaction using the original primers and 2 ul of the eluate from the gel frag. This should give you a pretty substantial amount of the band you are interested in. People are also trying to clone the band : for sequencing. As for cloning, add 1 ul (about 5 units) of Klenow to the above reaction, and incubate 30 minutes at 37 degrees C. This should effectivly blunt end the amplification product. (Yes, klenow seems to work fine in both Taq, Tfl, and Vent buffer). Run the resulting DNA out on a gel, cut out the band (there should be lots of it if all worked well). Take a 0.5 ml eppi and punch a small hole in the bottom of it. Plug the hole with glass wool, and place your gel fragment in the modified tube. Then place the whole set-up in a 1.5 ml eppi and spin for 15 min at max speed. Extract the resulting liquid 2X with phenol and 2X with CHCl3 and then EtOH precipitate. Mix with the blunt ended vector of choice and ligate (use an excess of ligase) overnight at room temp. Transform using any standard method. Hope this helps. Dave Horvath USDA/ARS/NCSL Fargo, ND PS. I am also curious as to how one gets a heteroduplex with PCR. : Kath Nesbitt : P.s. It seems that I have to make more text than I'm replying to for this : news-server to post my questions. Sometimes I just don't understand : computers!!! I wonder if that's enough text for it. From owner-rapd@net.bio.net Tue Sep 06 23:00:00 1994 Path: biosci!JOPLIN.BIOSCI.ARIZONA.EDU!mount From: mount@JOPLIN.BIOSCI.ARIZONA.EDU ("Dr. David Mount") Newsgroups: bionet.molbio.rapd Subject: (none) Date: 7 Sep 1994 12:22:09 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <9409071818.AA11649@joplin.biosci.arizona.edu> NNTP-Posting-Host: net.bio.net unsubscribe From owner-rapd@net.bio.net Wed Sep 07 23:00:00 1994 Path: biosci!ACAD.URSINUS.EDU!kgoddard From: kgoddard@ACAD.URSINUS.EDU Newsgroups: bionet.molbio.rapd Subject: seeking human primers Date: 8 Sep 1994 12:45:03 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <009842B8.DF60D2E0.1108@acad.ursinus.edu> NNTP-Posting-Host: net.bio.net We would be most grateful if anyone could recommend some primers which reveal differences within human populations. From owner-rapd@net.bio.net Thu Sep 08 23:00:00 1994 Path: biosci!zoology.uni-frankfurt.d400.de!Streit From: Streit@zoology.uni-frankfurt.d400.de (PCN-Benutzer) Newsgroups: bionet.molbio.rapd Subject: request Date: 9 Sep 1994 08:05:07 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <61513.streit@watson.rz.uni-frankfurt.de> NNTP-Posting-Host: net.bio.net Sorry, if we do not keep up to your normal standarts of communication. We are a group of molecular ecologists and we are interested in information about joining your network. We do not even know, if this is the right adress, but if there's anybody out there please respond. (Our e-mail system is now installed for about 1 hour and therefore we are very proud that we can handle it.) thank you in advance AK ™K™LOGIE Uni-Frankfurt/Deutschland From owner-rapd@net.bio.net Sun Sep 11 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!sunic!trane.uninett.no!daresbury!not-for-mail From: J R Beeching Newsgroups: bionet.molbio.rapd Subject: RFLP / RAPD band profile database Date: 12 Sep 1994 13:44:41 +0100 Lines: 22 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <351ifp$7be@mserv1.dl.ac.uk> MIME-Version: 1.0 Original-To: BIO-SOFTWARE Dear All, I am looking for some software, preferably public domain, which can be used to store and compare RFLP and/or RAPD band profile data. Ideally it should be able to accept cumulative date from different probes or primers. It should also have the capability to be interrogated in order to determine whether or not a pattern from a new organism is already in the database. If there is much interest and many replies I will post a compilation. Thank you for your help. John ------------------------------------------------------------------- | John Beeching E-mail: J.R.Beeching@bath.ac.uk | | Biology & Biochemistry | | University of Bath | | Bath BA2 7AY Phone: +44 (0)225 826826 ext 5193| | U.K. Fax: +44 (0)225 826779 | ------------------------------------------------------------------- From owner-rapd@net.bio.net Tue Sep 13 23:00:00 1994 Path: biosci!YVAX.BYU.EDU!FARMERJ From: FARMERJ@YVAX.BYU.EDU Newsgroups: bionet.molbio.rapd Subject: Re: There is no rapd FAQ, but... (addresses) Date: 14 Sep 1994 08:32:10 -0700 Organization: Brigham Young University Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HH3IY8S2769382H3@yvax.byu.edu> NNTP-Posting-Host: net.bio.net In my last posting, I did not have the address for users in the European-Africa area. You can request assistance from either of the addresses below. biosci-help@net.bio.net biosci@daresbury.ac.uk Best wishes. James Farmer FARMERJ@YVAX.BYU.EDU From owner-rapd@net.bio.net Tue Sep 13 23:00:00 1994 Path: biosci!YVAX.BYU.EDU!FARMERJ From: FARMERJ@YVAX.BYU.EDU Newsgroups: bionet.molbio.rapd Subject: There is no FAQ, but... Date: 14 Sep 1994 08:12:29 -0700 Organization: Brigham Young University Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HH3IACTP8I91XBTP@yvax.byu.edu> NNTP-Posting-Host: net.bio.net In a recent message, Hilton referred to rapd FAQ. I would like to remind everyone, especially newcomers, that there is no FAQ. However, it is possible to search the archives. If you do not know how, request information from BIOSCI-HELP@NET.BIO.NET or the equivalent address at DANSBURY for the European and African users. Jim Farmer FARMERJ@YVAX.BYU.EDU From owner-rapd@net.bio.net Tue Sep 13 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!uknet!fulcrum!bham!bcs88.bham.ac.uk!user From: A.C.Hilton@bham.ac.uk (Wiggy) Newsgroups: bionet.molbio.rapd Subject: Re: RFLP / RAPD band profile database Date: 14 Sep 1994 08:43:59 GMT Organization: University of Birmingham Lines: 39 Distribution: bionet Message-ID: References: <351ifp$7be@mserv1.dl.ac.uk> NNTP-Posting-Host: bcs88.bham.ac.uk In article <351ifp$7be@mserv1.dl.ac.uk>, J R Beeching wrote: > Dear All, > > I am looking for some software, preferably public domain, which can be > used to store and compare RFLP and/or RAPD band profile data. Ideally it > should be able to accept cumulative date from different probes or primers. > It should also have the capability to be interrogated in order to determine > whether or not a pattern from a new organism is already in the database. > > If there is much interest and many replies I will post a compilation. > > Thank you for your help. > > John > > ------------------------------------------------------------------- > | John Beeching E-mail: J.R.Beeching@bath.ac.uk | > | Biology & Biochemistry | > | University of Bath | > | Bath BA2 7AY Phone: +44 (0)225 826826 ext 5193| > | U.K. Fax: +44 (0)225 826779 | > ------------------------------------------------------------------- There was some discussion on this topic a few months ago and a compilation of possible analysis software posted to this group. You may want to check the FAQ. Wig. -- ********************************************************** ** It's because I come from Wigan that my name is Wiggy,** ** and nothing to do with my head................Honest!** ** ** ** A.C.Hilton@bham.ac.uk ** ********************************************************** From owner-rapd@net.bio.net Tue Sep 13 23:00:00 1994 Path: biosci!jab000.uesp.ansp.br!gkuhar From: gkuhar@jab000.uesp.ansp.br (GORAN KUHAR JEZOVSEK) Newsgroups: bionet.molbio.rapd Subject: info primers Date: 13 Sep 1994 23:46:56 -0700 Organization: UNESP Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <2e746181@jab000.uesp.ansp.br> Reply-To: GORAN KUHAR JEZOVSEK NNTP-Posting-Host: net.bio.net I would like to know if anybody has the information about random or specific primers for maize fingerprinting, or any microsattelite sequences? Thanks a lot. Goran Kuhar. -- GORAN KUHAR JEZOVSEK E-mail: gkuhar@jab000.uesp.ansp.br FACULDADE CIENCIAS AGRARIAS E VETERINARIAS Fone : (0163) 23-2500 JABOTICABAL/ UNESP Endereco: Rod. Carlos Tonanni,Km 5 14870-000 Jaboticabal SP From owner-rapd@net.bio.net Wed Sep 14 23:00:00 1994 Path: biosci!EMUNIX.EMICH.EDU!bio_hannan%emuvax.dnet.emich.edu From: bio_hannan%emuvax.dnet.emich.edu@EMUNIX.EMICH.EDU Newsgroups: bionet.molbio.rapd Subject: RE: RAPD for plant ID Date: 15 Sep 1994 10:27:14 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <9409151726.AA01823@emunix.emich.edu> NNTP-Posting-Host: net.bio.net Stewart, I have been working on developing clone-specific profiles in Iris lacustris and have been able to find consistent banding patterns for all shoots within single clones that also differ between clones. We had to sample multiple shoots from single clones to find those fragments that consistently appeared in all shoots. We always find a number of bands that sho w up only inconsistently within clones. Gary Hannan bio_hannan@emunix.emich.edu From owner-rapd@net.bio.net Wed Sep 14 23:00:00 1994 Path: biosci!FAPQ.FAPESP.BR!Carteiro From: Carteiro@FAPQ.FAPESP.BR Newsgroups: bionet.molbio.rapd Subject: Mail not delivered yet. Please do not reply. Date: 15 Sep 1994 11:00:07 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: <1F08307840019900@fapq.fapesp.br> Reply-To: Carteiro@fapq.fapesp.br NNTP-Posting-Host: net.bio.net -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- begin- ------------------------------------------------------------------------------- This mail was not delivered yet. Some "daemon" in the system may be hung. The system will retry later. Virtually, Fapesp's PostPerson. ------------------------------------------------------------------------------- `From gkuhar Mon, 12 Sep 94 10:11:13 C remote from jab000 `Received: by jab000.uesp.ansp.br (UUPC/extended 0.0); ` Mon, 12 Sep 94 10:11:13 C `Message-id: <2e746181@jab000.uesp.ansp.br> `Date: Mon, 12 Sep 94 10:11:13 C `From: GORAN KUHAR JEZOVSEK `Organization: UNESP `Reply-To: GORAN KUHAR JEZOVSEK `To: rapd@net.bio.net `Subject: info primers ` `I would like to know if anybody has the information about random or specific p `rimers for maize fingerprinting, or any microsattelite sequences? `Thanks a lot. ` `Goran Kuhar. `-- ` ` GORAN KUHAR JEZOVSEK E-mail: gkuhar@jab000.uesp.ansp. `br `FACULDADE CIENCIAS AGRARIAS E VETERINARIAS Fone : (0163) 23-2500 ` JABOTICABAL/ UNESP Endereco: Rod. Carlos Tonanni,Km ` 5 ` 14870-000 Jaboticabal SP ` -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- end- From owner-rapd@net.bio.net Wed Sep 14 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!cs.utexas.edu!uunet!panix!ddsw1!godot.cc.duq.edu!newsfeed.pitt.edu!dsinc!netnews.upenn.edu!msuinfo!harbinger.cc.monash.edu.au!news.uwa.edu.au!newsman.csu.murdoch.edu.au!Stewart.Washer From: Washer@csuvax1.murdoch.edu.au (Stewart Washer) Newsgroups: bionet.molbio.rapd Subject: RAPD for plant ID Date: 15 Sep 1994 06:53:30 GMT Lines: 11 Sender: -Not-Authenticated-[4689] Message-ID: <358r1aINNup@newsman.csu.murdoch.edu.au> NNTP-Posting-Host: subcmac4.csu.murdoch.edu.au X-Posted-From: InterNews 1.0@newsman.csu.murdoch.edu.au. Xdisclaimer: No attempt was made to authenticate the sender's name. I wish to use RAPD to compare a group of plants to see if any are from the same original clone. Are RAPDs stable enough to do this beyond "reasonable" doubt ? Also, what sort of sensitivity do they have in regards to picking up differences between closely related individuals ? Any help or advice would be greatly appreciated ! Stewart Washer Murdoch University Western Australia email (Washer@csuvax1.murdoch.edu.au) From owner-rapd@net.bio.net Sun Sep 18 23:00:00 1994 Newsgroups: bionet.celegans,bionet.molbio.rapd Path: biosci!bcm!cs.utexas.edu!news.uta.edu!wbar.uta.edu!patrick From: patrick@wbar.uta.edu (Patrick Phillips) Subject: RAPD on C. elegans Message-ID: <1994Sep19.180655.9508@news.uta.edu> Sender: news@news.uta.edu (USENET News System) Nntp-Posting-Host: wbar.uta.edu Organization: /usr/local/lib/news/organization Date: Mon, 19 Sep 1994 18:06:55 GMT Lines: 19 Xref: biosci bionet.celegans:111 bionet.molbio.rapd:775 We are just starting a project using RAPDs with everyone's favorite nematode, C. elegans. Is anyone out there working with this method in C. elegans? I would like to know which primers should for sure work with N2 before I do a lot of playing around. For those experienced RAPDers in b.m.rapd, what seems to be the probability that a particular primer will amplify at all? I've only tried four primers so far, and none have amplified (I know the DNA and PCR reagents are good). I have no way of knowing whether something is going wrong with the PCR (like the annealing temp), or if the primers just aren't hitting anything. Before I try 100 more primers, I'd like to know what others have experienced. Patrick Phillips Biology Department University of Texas at Arlington patrick@wbar.uta.edu (817) 273-2409 From owner-rapd@net.bio.net Mon Sep 19 23:00:00 1994 Path: biosci!cbr.for.csiro.au!charlie.bell From: charlie.bell@cbr.for.csiro.au (Charlie Bell) Newsgroups: bionet.molbio.rapd Subject: Re: RAPD on C. elegans Date: 20 Sep 1994 16:06:40 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <199409202305.AA12799@acacia.cbr.for.csiro.au> NNTP-Posting-Host: net.bio.net >For those experienced RAPDers in b.m.rapd, what seems to be the probability >that a particular primer will amplify at all? I've only tried four >primers so far, and none have amplified (I know the DNA and PCR reagents >are good). I have no way of knowing whether something is going wrong with >the PCR (like the annealing temp), or if the primers just aren't hitting >anything. Before I try 100 more primers, I'd like to know what others have >experienced. > >Patrick Phillips >Biology Department >University of Texas at Arlington >patrick@wbar.uta.edu >(817) 273-2409 > > We have screened the first 520 Operon primers on DNA from Pinus Radiata and Eucalyptus nitens and found that only about 10% do not amplify under the conditions that we have standardised on. We can usually get these 10% to work by just changing the MgCl2 concentration. From owner-rapd@net.bio.net Mon Sep 19 23:00:00 1994 Path: biosci!EMUNIX.EMICH.EDU!bio_hannan%emuvax.dnet.emich.edu From: bio_hannan%emuvax.dnet.emich.edu@EMUNIX.EMICH.EDU Newsgroups: bionet.molbio.rapd Subject: E. elegans RAPDs Date: 20 Sep 1994 07:31:52 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: <9409201433.AA20749@emunix.emich.edu> NNTP-Posting-Host: net.bio.net Over what time period have you tried the four primers? It is possible that amplifications just stop for a while for no apparent reason. But if other systems in the same lab were working, the lack of amplification is not as likely to be a random shutdown of amplification reactions. gary Hannan From owner-rapd@net.bio.net Tue Sep 20 23:00:00 1994 Path: biosci!GNU.AI.MIT.EDU!bw From: bw@GNU.AI.MIT.EDU (Bruce Waldman) Newsgroups: bionet.molbio.rapd Subject: Research Position/ Molecular Ecology of New Zealand Frogs Date: 21 Sep 1994 05:18:16 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 38 Sender: daemon@net.bio.net Distribution: world Message-ID: <9409211213.AA03638@apple-gunkies.gnu.ai.mit.edu> NNTP-Posting-Host: net.bio.net Research Scientist/Postdoctoral Fellow BEHAVIOUR, ECOLOGY AND POPULATION GENETICS OF NEW ZEALAND FROGS A research position to study behavioural ecology and population genetics of native New Zealand frogs (genus Leiopelma) is available starting 1 November 1994 (or other date to be negotiated). The successful candidate will be involved in various research projects concerned with the behaviour (e.g. parental care of brood) and ecology (e.g. dispersal) of these unique frogs. A major portion of the work will involve analyses of genetic variation within and among populations using PCR-based methodologies (e.g. microsatellites, RAPDs) and other fingerprinting techniques (minisatellites, mtDNA). The application of these methodologies to conservation biology, both with respect to these endangered frogs and other threatened New Zealand fauna, will be stressed. Applicants should have experience in methods of DNA purification and analyses. Knowledge of techniques for constructing and screening genomic libraries would be an advantage. Research will also involve fieldwork, surveying behaviour of frogs in natural conditions. Funding is initially for one year, with possibilities of extension for a further two years. Appointment may be made as a Research Scientist, Postdoctoral Fellow, or Research Assistant, depending on applicant's qualifications and final budget allocation. Please contact me if you are interested, or would like further details. Letters of application should include details of previous experience with molecular methods, c.v., and names and contact information (phone/fax/email) of referees who know your work. Bruce Waldman Department of Zoology University of Canterbury Christchurch, New Zealand Telephone: +64 3 364 2066 FAX: +64 3 364 2024 Email: waldman_b@ix.wcc.govt.nz From owner-rapd@net.bio.net Wed Sep 21 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!uunet!news.delphi.com!usenet From: Tony Newsgroups: bionet.molbio.rapd Subject: Anyone here can help me with RFLP Linkage Analysis Date: Wed, 21 Sep 94 22:21:35 -0500 Organization: Delphi (info@delphi.com email, 800-695-4005 voice) Lines: 3 Message-ID: NNTP-Posting-Host: bos1b.delphi.com Could anyone assist me in info about this procedure, that is-- RFLP Linkage Analysis. Thanks From owner-rapd@net.bio.net Wed Sep 21 23:00:00 1994 Path: biosci!jab000.uesp.ansp.br!gkuhar From: gkuhar@jab000.uesp.ansp.br (GORAN KUHAR JEZOVSEK) Newsgroups: bionet.molbio.rapd Subject: (none) Date: 22 Sep 1994 04:19:18 -0700 Organization: UNESP Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: <2e807123@jab000.uesp.ansp.br> Reply-To: GORAN KUHAR JEZOVSEK NNTP-Posting-Host: net.bio.net Do someone have information about the use of PCR-RFLPs in plants ? If so, in which references? Thanks Goran Kuhar -- GORAN KUHAR JEZOVSEK E-mail: gkuhar@jab000.uesp.ansp.br FACULDADE CIENCIAS AGRARIAS E VETERINARIAS Fone : (0163) 23-2500 JABOTICABAL/ UNESP Endereco: Rod. Carlos Tonanni,Km 5 14870-000 Jaboticabal SP From owner-rapd@net.bio.net Wed Sep 21 23:00:00 1994 Newsgroups: bionet.molbio.rapd Path: biosci!agate!howland.reston.ans.net!swrinde!sgiblab!munnari.oz.au!newsroom.utas.edu.au!ml.csiro.au!mac-1303.ml.csiro.au!chris.bolch From: Christopher J. S. Bolch Subject: Sequencing PCR product Message-ID: <1994Sep22.063608.16290@ml.csiro.au> X-Xxmessage-Id: X-Xxdate: Thu, 22 Sep 94 16: 38:28 GMT Sender: news@ml.csiro.au Organization: CSIRO Division of Fisheries, Hobart, Tasmania X-Useragent: Version 1.1.3 Date: Thu, 22 Sep 1994 06:36:08 GMT Lines: 7 I have heard recently that it is possible to sequence PCR products directly either by usual means or by cycle sequencing. Is it as simple as that or does one need to clone the fragments first? Does sequencing of the product directly have any pitfalls or problems? I imagine that excess primer could be a problem. Chris From owner-rapd@net.bio.net Thu Sep 22 23:00:00 1994 Path: biosci!vt.edu!fishgen From: fishgen@vt.edu (Bruce J. Turner) Newsgroups: bionet.molbio.rapd Subject: expanding the subject base of the rapd network Date: 23 Sep 1994 11:38:53 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <199409231834.LAA23867@net.bio.net> NNTP-Posting-Host: net.bio.net In postings today, Kevin O'Donnell and David MacHugh both suggested that the subject base of the rapd network be expanded to other sorts of molecular markers. I agree, especially since microsatellites are very likely going to have an enormous impact on the field. I think we should become something like a "molecular techniques in population genetics" net, with members employing, and discussing the relative merits of, different techniques as they become available. Rapds are still of interest to many people, but I think it fair to say that they are now one of several different techniquess one might use, rather than a focal technique that nearly all people will use. It is likely that very nearly all the future molecular markers will be based on pcr amplification (some are already referring to them as "amplicons") and this technique, and the ever-present problems inherent in isolating good DNA from many different organisms, can serve as a common thread for discussions even if different people are using different markers. From owner-rapd@net.bio.net Thu Sep 22 23:00:00 1994 Path: biosci!MERCURY.UARK.EDU!drhoads From: drhoads@MERCURY.UARK.EDU (doug rhoads) Newsgroups: bionet.molbio.rapd Subject: Re: RAPD Newsgroup Date: 23 Sep 1994 11:16:16 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 49 Sender: daemon@net.bio.net Distribution: world Message-ID: <1CE1B2807C6@uamercury.uark.edu> NNTP-Posting-Host: net.bio.net At 05:12 PM 9/23/94 GMT, David MacHugh wrote: >In article , odonnell@sasa.gov.uk (Kevin >O'Donnell) wrote: > >> >> I find this newsgroup the most useful of all of the BIONET newsgroups, >> (along with the Diagnostics list), and have a suggestion as to how it >> could be made even more useful, to me at least. >> >> As all of the participants seem to be using RAPDs for much the same >> sort of purpose, would it make sense to expand the subject matter of >> the group to take in AFLPs, SSRs, RFLPs etc.? This would mean a >> molecular markers group rather than a RAPDs group but this would make >> sense to me. >> >> This may be one of those questions which gets flogged to death >> every so often, so apologies if I am going over old ground. However, >> I would be interested in what others think of this idea. >> >> Kevin O'Donnell >> Scottish Agricultural Science Agency >> Edinburgh >> Scotland > >I reckon this is a worthwile idea. Without meaning to demean RAPDs, VNTRs >(in the broad sense) are much more widely used. SSRs are the workhorses of >gene mapping and are undoubtedly about to revolutionise population and >evolutionary genetics too. Basically it would be great to have a forum for >all types of molecular markers, not just RAPDs. > ********************************************************************* > * (__) David MacHugh, E-mail: dmachugh@mail.tcd.ie * Well, I guess I need to throw away all my RAPD primers. We're working in the dark ages. I believe all of the techniques are similar enough in the general approach perhaps a molecular mapping forum is what is desired. After all we can only deal with the `I don't have bands in my RAPDs any more' or `there are bands in my negative control' questions. Do we really need a name change?? I would speculate that would only be with recruitment of new newsies. Perhaps our network leaders could comment on what happens with a name change. I have seen similar discussions in other groups and I would hate for us to fragment to far and wide. Doug Rhoads || Dept. of Biological Sciences drhoads@mercury.uark.edu || 601 Science Engineering drhoads@uafsysb.uark.edu || University of Arkansas 501-575-3251 || Fayetteville, AR 72701 From owner-rapd@net.bio.net Thu Sep 22 23:00:00 1994 Newsgroups: bionet.molbio.rapd Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!pipex!jura.sasa.gov.uk!news From: odonnell@sasa.gov.uk (Kevin O'Donnell) Subject: RAPD Newsgroup Organization: Scottish Agricultural Science Agency Date: Fri, 23 Sep 1994 15:09:55 GMT Message-ID: X-Newsreader: WinVN 0.91.3 Sender: news@jura.sasa.gov.uk (Usenet) Lines: 19 I find this newsgroup the most useful of all of the BIONET newsgroups, (along with the Diagnostics list), and have a suggestion as to how it could be made even more useful, to me at least. As all of the participants seem to be using RAPDs for much the same sort of purpose, would it make sense to expand the subject matter of the group to take in AFLPs, SSRs, RFLPs etc.? This would mean a molecular markers group rather than a RAPDs group but this would make sense to me. This may be one of those questions which gets flogged to death every so often, so apologies if I am going over old ground. However, I would be interested in what others think of this idea. Kevin O'Donnell Scottish Agricultural Science Agency Edinburgh Scotland From owner-rapd@net.bio.net Thu Sep 22 23:00:00 1994 Newsgroups: bionet.molbio.rapd Path: biosci!agate!howland.reston.ans.net!pipex!jura.sasa.gov.uk!news From: odonnell@sasa.gov.uk (Kevin O'Donnell) Subject: Automatic Data Collection Organization: Scottish Agricultural Science Agency Date: Fri, 23 Sep 1994 15:01:34 GMT Message-ID: X-Newsreader: WinVN 0.91.3 Sender: news@jura.sasa.gov.uk (Usenet) Lines: 19 We are interested in constructing a RAPD band library for potato varieties and would like to use a system for automatically registering and characterising the bands generated on RAPD gels, and entering this information into a database which can then be interogatted to identify unknown varieties in blind tests. in other words, once the data is entered, it will be able to identify any of the varieties from their banding patterns. Has anyone tried using a gel scanner to construct a library of RAPD band patterns for use in variety testing? If so, would you like to share your experiences? I am particularly interested in how many varieties your software was able to descriminate between and how reliably. Is there a particular type of hardware or software that you would recommend,and so on. Kevin O'Donnell Scottish Agricultural Science Agency Edinburgh Scotland From owner-rapd@net.bio.net Thu Sep 22 23:00:00 1994 Newsgroups: bionet.molbio.rapd Path: biosci!rutgers!gatech!howland.reston.ans.net!EU.net!ieunet!tcdcs!news.tcd.ie!gen033.gen.tcd.ie!user From: dmachugh@mail.tcd.ie (David MacHugh) Subject: Re: RAPD Newsgroup Message-ID: Followup-To: bionet.molbio.rapd Sender: usenet@news.tcd.ie (TCD News System ) Organization: Genetics Department, Trinity College, Dublin 2. IRELAND References: Date: Fri, 23 Sep 1994 17:12:17 GMT Lines: 41 In article , odonnell@sasa.gov.uk (Kevin O'Donnell) wrote: > > I find this newsgroup the most useful of all of the BIONET newsgroups, > (along with the Diagnostics list), and have a suggestion as to how it > could be made even more useful, to me at least. > > As all of the participants seem to be using RAPDs for much the same > sort of purpose, would it make sense to expand the subject matter of > the group to take in AFLPs, SSRs, RFLPs etc.? This would mean a > molecular markers group rather than a RAPDs group but this would make > sense to me. > > This may be one of those questions which gets flogged to death > every so often, so apologies if I am going over old ground. However, > I would be interested in what others think of this idea. > > Kevin O'Donnell > Scottish Agricultural Science Agency > Edinburgh > Scotland I reckon this is a worthwile idea. Without meaning to demean RAPDs, VNTRs (in the broad sense) are much more widely used. SSRs are the workhorses of gene mapping and are undoubtedly about to revolutionise population and evolutionary genetics too. Basically it would be great to have a forum for all types of molecular markers, not just RAPDs. -- ********************************************************************* * (__) David MacHugh, E-mail: dmachugh@mail.tcd.ie * * (@*) Bovine Genetics, Phone: (353)-1-7021088 * * /-------\u' Genetics Department, Fax: (353)-1-6798558 * * / | || Trinity College, * * ||----|| Dublin 2. * * ^^ ^^ Ireland. * ********************************************************************* From owner-rapd@net.bio.net Thu Sep 22 23:00:00 1994 Path: biosci!CHUMA.CAS.USF.EDU!karl From: karl@CHUMA.CAS.USF.EDU ("Stephen A. Karl") Newsgroups: bionet.molbio.rapd Subject: Re: Sequencing PCR product Date: 23 Sep 1994 09:27:33 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 53 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <1994Sep22.063608.16290@ml.csiro.au> NNTP-Posting-Host: net.bio.net On Thu, 22 Sep 1994, Christopher J. S. Bolch wrote: > I have heard recently that it is possible to sequence PCR products > directly either by usual means or by cycle sequencing. Is it as simple > as that or does one need to clone the fragments first? Does sequencing > of the product directly have any pitfalls or problems? I imagine that > excess primer could be a problem. > > Chris > > We are currently using US Biochemicals PCR Sequenase Sequencing Kit (Actually, we have ordered the missing enzymes separately and have "converted" our existing Sequenase V2.0 kits). It uses Exonuclease I to digest single stranded DNA (i.e. primers) in ~5 microL of PCR amplified DNA (directly). The free nucleotides (from the exo reaction and the dNTP added for the PCR) are dephosphorylated with Shrimp alk-Phosphatase and the resulting DNA is used directly in a standard Sequenase reaction. In addition, we have been using AT Biochem (1-800-282-4626) Long Ranger Gel solution under standard conditions (i.e. NOT glycerol tolerant - the new Sequenase protocol has the Sequenase and Pyrophos. enzymes mixed in a glycerol buffer and suggests that a glycerol tolerant gel be used). We have tried both the standard Sequenase labeling and a modified 3 nt labeling approach when the sequence just after the primer is known (details are available in the kit directions or from USB). The 3 nt techniques seems to give better results but both work well. With the 3 nt technique we easily get to within 2 nt of the labeled primer. Although we have only made 3 sequencing attempts (30 independent reactions) the gels are working very, very well (i.e. easily 300 bp of good sequence, few if any "hard stops" that are normally observed in PCR template sequencing, short exposure times with 35S - 2 days on average and nice even band intensities). Like everyone, I have tried everything (cycle sequencing, Lambda exo, standard Sequenase, single stranded amps, spin col. etc) and this is by far the easiest and BEST (that is results wise) technique that I have used. Just in case you are now wondering - I do not work for USB (and in fact have a general dislike and contempt for these companies that are making so much money from so little work!). FYI, Steve Stephen Karl Department of Biology University of South Florida 4202 East Fowler Ave, LIF 169 Tampa, Florida 33620-5150 Voice (813) 974-1592 Fax (813) 974-3263 EMail Karl@.chuma.cas.usf.edu From owner-rapd@net.bio.net Thu Sep 22 23:00:00 1994 Path: biosci!rutgers!gatech!swrinde!howland.reston.ans.net!news.cac.psu.edu!news.tc.cornell.edu!travelers.mail.cornell.edu!newsstand.cit.cornell.edu!NewsWatcher!user From: wfl1@cornell.edu (Warren Frank Lamboy) Newsgroups: bionet.molbio.rapd Subject: Re: RAPD Newsgroup Followup-To: bionet.molbio.rapd Date: Fri, 23 Sep 1994 02:18:31 -1200 Organization: Cornell University Lines: 17 Sender: wfl1@cornell.edu (Verified) Message-ID: References: NNTP-Posting-Host: 132.236.3.42 In article , odonnell@sasa.gov.uk (Kevin O'Donnell) wrote: > > I find this newsgroup . . . (text deleted) I don't see any need for a name change for the group, but I, too would welcome extending the subject matter discussed to other types of molecular markers. -- Warren F. Lamboy "It's easy if you know how to Dept. of Horticultural Sciences and do it, but it's impossible if USDA-ARS Plant Genetic Resources Unit you don't know how to do it." Cornell University Geneva, NY 14456-0462 warren_lamboy@cornell.edu From owner-rapd@net.bio.net Thu Sep 22 23:00:00 1994 Path: biosci!CSCGPO.ANU.EDU.AU!lce652 From: lce652@CSCGPO.ANU.EDU.AU (Livinus Emebiri) Newsgroups: bionet.molbio.rapd Subject: Re: RAPD Newsgroup Date: 23 Sep 1994 16:44:19 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <9409232346.AA16334@cscgpo.anu.edu.au> NNTP-Posting-Host: net.bio.net >I find this newsgroup the most useful of all of the BIONET newsgroups, >(along with the Diagnostics list), and have a suggestion as to how it >could be made even more useful, to me at least. I agree with you that this news group has been most useful and informative (to me at least), and welcome the suggestion to expand its subject matter coverage. No doubt it will be even more informative, but will this not amount to an encroachment into the Diagnostics List field of interest ? Livinus Emebiri From owner-rapd@net.bio.net Sun Sep 25 23:00:00 1994 Newsgroups: bionet.molbio.rapd Path: biosci!agate!howland.reston.ans.net!pipex!jura.sasa.gov.uk!news From: odonnell@sasa.gov.uk (Kevin O'Donnell) Subject: Re: RAPD Newsgroup Organization: Scottish Agricultural Science Agency Date: Mon, 26 Sep 1994 07:53:37 GMT Message-ID: X-Newsreader: WinVN 0.91.3 References: <9409232346.AA16334@cscgpo.anu.edu.au> Sender: news@jura.sasa.gov.uk (Usenet) Lines: 32 In article <9409232346.AA16334@cscgpo.anu.edu.au>, lce652@CSCGPO.ANU.EDU.AU (Livinus Emebiri) says: > >I agree with you that this news group has been most useful and informative >(to me at least), and welcome the suggestion to expand its subject matter >coverage. No doubt it will be even more informative, but will this not >amount to an encroachment into the Diagnostics List field of interest ? > No, I don't think so. However, as a few people have mailed me to ask about the Diagnostics list, perhaps I should say what it is. Diagnost is a prototype bionet group i.e. currently available as an email list only. It provides a forum for discussion about using and developing techniques for the detection and identification of pests and pathogens. The group covers all techniques from antibodies (ELISA) to DNA (PCR, LCR etc.). Subscribers come from a variety of backgrounds -plant, vet, medical, where people are using the same techniques for the same purpose. If you are interested, you can subscribe to diagnost by sending the message: subscribe diagnost to this address: biosci-server@net.bio.net leaving the subject line blank. I should declare an interest by saying that I am one of the discussion leaders for diagnost. As for overlap, well diagnostics uses some of the techniques used for molecular markers but in a different context, IMO. I am interested in both groups because I have an interest in variety testing of plants, as well as their diseases. Kevin O'Donnell Scottish Agricultural Science Agency Edinburgh Scotland From owner-rapd@net.bio.net Sun Sep 25 23:00:00 1994 Path: biosci!YVAX.BYU.EDU!FARMERJ From: FARMERJ@YVAX.BYU.EDU Newsgroups: bionet.molbio.rapd Subject: Comment on expanding this newsgroup Date: 26 Sep 1994 09:00:24 -0700 Organization: Brigham Young University Lines: 92 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HHKBFEKDJM91WEHY@yvax.byu.edu> NNTP-Posting-Host: net.bio.net In light of the current discussion about expanding this newsgroup, I posted the following message to BIOSCI-HELP@NET.BIO.NET and received the following response. What do you think? James Farmer farmerj@yvax.byu.edu >> There is some discussion in the rapd newsgroup about >> expanding the scope to include other techniques of >> molecular mapping. I do not know where it will lead. >> If the decision were made to expand, it would be a good >> idea to change the name of the group. Is that >> feasible? If so, what would be required to obtain >> permission? I would like to know the answers to these >> questions, and your general advice, before the >> discussion goes much further. >> >> Thanks >> >> James Farmer >> farmerj@yvax.byu.edu >> > >I include the charter for the CHROMOSOMES group. Please look it over >and see if you think whether or not you would be duplicating the >purpose of that group. If so, then those discussions should be held in >the CHROMOSOMES group. > > Sincerely, > > Dave Kristofferson > BIOSCI/bionet Manager > > biosci-help@net.bio.net > > >Information for CHROMOSOMES/bionet.genome.chromosomes > >USENET newsgroup name: bionet.genome.chromosomes > >Mailing list name: CHROMOSOMES > >E-mail addresses: bio-chrom@net.bio.net > bio-chrom@daresbury.ac.uk > >Discussion leaders: > >Greg Lennon >Human Genome Center, L-452 >Lawrence Livermore National Laboratory >Livermore, CA 94550 >greg@mendel.llnl.gov > >Bruce A. Roe >Department of Chemistry and Biochemistry >University of Oklahoma >620 Parrington Oval >Norman, Oklahoma 73019 >broe@aardvark.ucs.uoknor.edu > > >CHROMOSOMES/bionet.genome.chromosomes charter: > >Name: bio-chrom MAPPING AND SEQUENCING OF EUCARYOTE CHROMOSOMES > > Greg Lennon and Bruce Roe propose to be discussion leaders >for a new news group that would replace the .chromosome22 news group >and the autoseqs@net.bio.net e-mail list. > >The topics open for discussion in this new, combined, news group include: > > 1. Physical mapping of human, mouse, and other eucaryote chromosomes > > 2. Large-scale sequencing of cDNAs and chromosomes > > 3. Mapping of human, mouse, and other eucaryote cDNAs to chromosomes > > 4. Selection of chromosome-specific cDNAs > > 5. Generation of chromosome-specific clones and sequences > (STSs, microsatellites, etc.) > > 6. Announcements and requests for probes. > >with an emphasis on theory, techniques and discoveries. The overall >purpose of this new, combined news group is to bring research groups >with an interest in genomic-level research and automated methods for >studying eucaryote genomes together to exchange ideas and protocols, >probes and mapping information, and to discuss other issues relevant >to large scale mapping and sequencing. > From owner-rapd@net.bio.net Mon Sep 26 23:00:00 1994 Path: biosci!CABI.org!D.BRAYFORD From: D.BRAYFORD@CABI.org ("David Brayford ", IMI) Newsgroups: bionet.molbio.rapd Subject: RAPD amplification Date: 27 Sep 1994 00:27:18 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <2E87C9BB@smtp-gateway.cgnet.com> NNTP-Posting-Host: net.bio.net There does seem to be potential overlap between an expanded RAPD group and the Eukaryotic Chromosomes newsgroup. One possibility would be to merge the whole lot into one. However, I feel that this would then be too broad. Also, we use PCR methodologies to analyse variation in fungi and plant pathogenic bacteria. Where would the prokaryotic interests of users such as us then fit in?? I venture to suggest that the RAPD newsgroup should be expanded to cover all PCR-based methodologies as applied to eukaryotic and prokaryotic organisms, and that it should be kept separate from the Eukaryotic Chromosomes newsgroup. The name could then be changed from RAPD to PCR. I think this would keep the group focussed, whilst reflecting the expanding horizons of how these techniques are being used. Dave Brayford International Mycological Institute From owner-rapd@net.bio.net Mon Sep 26 23:00:00 1994 Path: biosci!PIRA.CENA.USP.BR!DAVHMOON From: DAVHMOON@PIRA.CENA.USP.BR Newsgroups: bionet.molbio.rapd Subject: Re. Robocycler Date: 27 Sep 1994 12:00:45 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hi netters, Is any one out there using a Stratagene Robocycler?? They are just launching this model in Brasil with claims of reduced cycling times of up to 30%, extended block life etc. etc. etc. I would be grateful to receive any feed back about this machine. Thanks in advance, David H. Moon From owner-rapd@net.bio.net Tue Sep 27 23:00:00 1994 Path: biosci!FAPQ.FAPESP.BR!Carteiro From: Carteiro@FAPQ.FAPESP.BR Newsgroups: bionet.molbio.rapd Subject: Mail not delivered yet. Please do not reply. Date: 28 Sep 1994 15:05:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 36 Sender: daemon@net.bio.net Distribution: world Message-ID: <86C19B5EA004763B@fapq.fapesp.br> Reply-To: Carteiro@fapq.fapesp.br NNTP-Posting-Host: net.bio.net -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- begin- ------------------------------------------------------------------------------- This mail was not delivered yet. Some "daemon" in the system may be hung. The system will retry later. Virtually, Fapesp's PostPerson. ------------------------------------------------------------------------------- `From gkuhar Mon, 26 Sep 94 11:44:15 C remote from jab000 `Received: by jab000.uesp.ansp.br (UUPC/extended 0.0); ` Mon, 26 Sep 94 11:44:15 C `Message-id: <2e86ec4f@jab000.uesp.ansp.br> `Date: Mon, 26 Sep 94 11:44:15 C `From: GORAN KUHAR JEZOVSEK `Organization: UNESP `Reply-To: GORAN KUHAR JEZOVSEK `To: rapd@net.bio.net `Subject: looking for position ` `I am looking for a laboratory to extend my knowledge on the use of RAPD and PC `R related molecular markers. I would be interested in a two or three year peri `od of working. No restrictions. A PhD course would also be desirable. `Thanks a lot. ` `Goran Kuhar ` `email: gkuhar@jab000.uesp.ansp.br `-- ` ` GORAN KUHAR JEZOVSEK E-mail: gkuhar@jab000.uesp.ansp. `br `FACULDADE CIENCIAS AGRARIAS E VETERINARIAS Fone : (0163) 23-2500 ` JABOTICABAL/ UNESP Endereco: Rod. Carlos Tonanni,Km ` 5 ` 14870-000 Jaboticabal SP ` -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- end- From owner-rapd@net.bio.net Tue Sep 27 23:00:00 1994 Newsgroups: bionet.molbio.rapd Path: biosci!agate!library.ucla.edu!europa.eng.gtefsd.com!howland.reston.ans.net!EU.net!ieunet!tcdcs!news.tcd.ie!gen033.gen.tcd.ie!user From: dmachugh@mail.tcd.ie (David MacHugh) Subject: Re: RAPD amplification Message-ID: Followup-To: bionet.molbio.rapd Sender: usenet@news.tcd.ie (TCD News System ) Organization: Genetics Department, Trinity College, Dublin 2. IRELAND References: <2E87C9BB@smtp-gateway.cgnet.com> Date: Wed, 28 Sep 1994 11:42:07 GMT Lines: 39 In article <2E87C9BB@smtp-gateway.cgnet.com>, D.BRAYFORD@CABI.org ("David Brayford ", IMI) wrote: > > There does seem to be potential overlap between an expanded RAPD group and > the Eukaryotic Chromosomes newsgroup. One possibility would be to merge the > whole lot into one. However, I feel that this would then be too broad. > Also, we use PCR methodologies to analyse variation in fungi and plant > pathogenic bacteria. Where would the prokaryotic interests of users such as > us then fit in?? > > I venture to suggest that the RAPD newsgroup should be expanded to cover all > PCR-based methodologies as applied to eukaryotic and prokaryotic organisms, > and that it should be kept separate from the Eukaryotic Chromosomes > newsgroup. The name could then be changed from RAPD to PCR. I think this > would keep the group focussed, whilst reflecting the expanding horizons of > how these techniques are being used. A broad-based newsgroup pertaining to PCR would perhaps overlap with the methds-reagnts group to a great extent. More appropriate titles might be "bionet.molbio.mol-polymorphs" or "bionet.molbio.mol-markers", even "bionet.molbio.PCR-polymorphs" etc. I think a name change along these lines would expand the scope of the newsgroup without attracting too many irrelevant postings. David. -- ********************************************************************* * (__) David MacHugh, E-mail: dmachugh@mail.tcd.ie * * (@*) Bovine Genetics, Phone: (353)-1-7021088 * * /-------\u' Genetics Department, Fax: (353)-1-6798558 * * / | || Trinity College, * * ||----|| Dublin 2. * * ^^ ^^ Ireland. * ********************************************************************* From owner-rapd@net.bio.net Tue Sep 27 23:00:00 1994 Newsgroups: bionet.molbio.rapd Path: biosci!daresbury!trane.uninett.no!sunic!pipex!jura.sasa.gov.uk!news From: odonnell@sasa.gov.uk (Kevin O'Donnell) Subject: Re: Comment on expanding this newsgroup Organization: Scottish Agricultural Science Agency Date: Wed, 28 Sep 1994 14:00:14 GMT Message-ID: X-Newsreader: WinVN 0.91.3 References: <01HHKBFEKDJM91WEHY@yvax.byu.edu> Sender: news@jura.sasa.gov.uk (Usenet) Lines: 37 In article <01HHKBFEKDJM91WEHY@yvax.byu.edu>, FARMERJ@YVAX.BYU.EDU says: > >In light of the current discussion about expanding this newsgroup, I posted the following >message to BIOSCI-HELP@NET.BIO.NET and received the following response. What >do you think? (From D. Kristofferson:) >>I include the charter for the CHROMOSOMES group. Please look it over >>and see if you think whether or not you would be duplicating the >>purpose of that group. If so, then those discussions should be held in >>the CHROMOSOMES group. >> (from chromosomes charter:) >>>with an emphasis on theory, techniques and discoveries. The overall >>purpose of this new, combined news group is to bring research groups >>with an interest in genomic-level research and automated methods for >>studying eucaryote genomes together to exchange ideas and protocols, >>probes and mapping information, and to discuss other issues relevant >>to large scale mapping and sequencing. >> Oh dear. I started the ball rolling on this and it has had the totally unintended effect of calling the existence of the group into question. In answer to the above query, the bits I've copied state clearly that bionet.chromosomes is about sequencing and mapping genomes. I see this as completely different to the subject matter of RAPD as that is concerned with variation within and between populations (broadly speaking). So, whereas I'm still keen to see other methods included I don't think that a merger with chromosomes is a good idea. Kevin O'Donnell Scottish Agricultural Science Agency Edinburgh Scotland From owner-rapd@net.bio.net Wed Sep 28 23:00:00 1994 Newsgroups: bionet.molbio.rapd Path: biosci!bcm!cs.utexas.edu!swrinde!elroy.jpl.nasa.gov!netline-fddi.jpl.nasa.gov!nntp-server.caltech.edu!news.claremont.edu!paris.ics.uci.edu!csulb.edu!library.ucla.edu!news.mic.ucla.edu!unixg.ubc.ca!quartz.ucs.ualberta.ca!tribune.usask.ca!sue!news From: DURKIN@Meena.CC.URegina.CA (192403285) Subject: Query: Looking for good orthopteran CytB & 16s rDNA primers Sender: news@sue.cc.uregina.ca Message-ID: Date: Thu, 29 Sep 1994 05:02:18 GMT X-News-Reader: VMS NEWS v1.25 Organization: University of Regina, Regina, Sask., Canada Lines: 15 Greetings: I am working on a project to determine the phylogeny of Acrididae grasshoppers via RFLPs. I have looked in the Simple Fool's Guide for appropriate primers to amplify the 16s rDNA and CytB regions of the mitochondrial DNA. The closest match they give is for Drosophila; I was wondering if anyone has had personal experience with the Drosophila primers for orthopterans and if so, how they have worked out. If anyone has information regarding appropriate orthopteran primers or knows of a suitable recent reference, please contact me via E-mail. Thanks in advance, Jonathan Durkin durkin@meena.cc.uregina.ca From owner-rapd@net.bio.net Wed Sep 28 23:00:00 1994 Path: biosci!UCONNVM.UCONN.EDU!CSIMON From: CSIMON@UCONNVM.UCONN.EDU (Chris) Newsgroups: bionet.molbio.rapd Subject: Good orthopteran Cytb & 16S primers Date: 29 Sep 1994 08:44:51 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <199409291544.IAA24910@net.bio.net> NNTP-Posting-Host: net.bio.net Hi Jonathan- My colleagues and I have just finished a paper that contains an appendix of over 70 "universal" PCR primers. These primers are presented in comparative format to show how conserved they are. We compare the primers to human (or cow), xenopus, urchin, nematode, fly, bee, locust, and sometimes additional taxa. The body of the paper reviews weighting DNA data for phylogenetic analysis, mitochondrial gene evolution, and the phylogenetic usefulness of various mitochondrial genes (with an emphasis on insects). The reference is: Simon, C., F. Frati, A. Beckenbach, B. Crespi, H. Liu, and P. Flook. 1994. Evolution, Weighting, and phylogene- tic usefulness of mitochondrial genes with a compilation of conserved PCR primers. Annals of the Entomological Society of America in press [November 1994, pp. 1-51]. You might also wish to join Bug-net, the insect molecular systematics network by sending a message to Crespi@SFU.CA Good Luck, Chris CHRIS SIMON PHONE: 203-486-4640 ECOL. EVOL. BIOLOGY U-43 FAX: 203-486-6364 UNIVERSITY OF CONNECTICUT BITNET: CSIMON@UCONNVM STORRS, CT 06269 INTERNET: CSIMON@UCONNVM.UCONN.EDU From owner-rapd@net.bio.net Wed Sep 28 23:00:00 1994 Path: biosci!jab000.uesp.ansp.br!gkuhar From: gkuhar@jab000.uesp.ansp.br (GORAN KUHAR JEZOVSEK) Newsgroups: bionet.molbio.rapd Subject: looking for position Date: 28 Sep 1994 18:07:12 -0700 Organization: UNESP Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: <2e86ec4f@jab000.uesp.ansp.br> Reply-To: GORAN KUHAR JEZOVSEK NNTP-Posting-Host: net.bio.net I am looking for a laboratory to extend my knowledge on the use of RAPD and PCR related molecular markers. I would be interested in a two or three year period of working. No restrictions. A PhD course would also be desirable. Thanks a lot. Goran Kuhar email: gkuhar@jab000.uesp.ansp.br -- GORAN KUHAR JEZOVSEK E-mail: gkuhar@jab000.uesp.ansp.br FACULDADE CIENCIAS AGRARIAS E VETERINARIAS Fone : (0163) 23-2500 JABOTICABAL/ UNESP Endereco: Rod. Carlos Tonanni,Km 5 14870-000 Jaboticabal SP