From owner-rapd@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.sprintlink.net!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!lll-winken.llnl.gov!enews.sgi.com!decwrl!tribune.usask.ca!quartz.ucs.ualberta.ca!unixg.ubc.ca!leblanc From: leblanc@unixg.ubc.ca (Heidi N LeBlanc) Newsgroups: bionet.molbio.ageing,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.rapd,bionet.molbio.yeast,bionet.molbio.gene-linkage Subject: Re: controversies & ethics Followup-To: bionet.molbio.ageing,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.rapd,bionet.molbio.yeast,bionet.molbio.gene-linkage Date: 2 Feb 1995 17:45:59 GMT Organization: University of British Columbia, Vancouver, B.C., Canada Lines: 9 Message-ID: <3gr5on$amt@nnrp.ucs.ubc.ca> References: <3gk3au$pdp@rebecca.albany.edu> <3gm7u9$t5e@nntp1.u.washington.edu> NNTP-Posting-Host: interchg.ubc.ca X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.molbio.ageing:1224 bionet.molbio.bio-matrix:537 bionet.molbio.embldatabank:439 bionet.molbio.evolution:2394 bionet.molbio.gdb:285 bionet.molbio.genome-program:1148 bionet.molbio.hiv:865 bionet.molbio.rapd:954 bionet.molbio.yeast:2287 bionet.molbio.gene-linkage:519 One of the problems isn't so much what we *do* with biotechnology, as how what we do is generally perceived. We as scientists think "Oh, what a clever idea, putting an arctic fish gene into strawberries". Non-scientists, with whatever level of education, often seem to think this is just monstrous. The issue might not really be whether what we are doing is ethical, or whether the ethics are unique to biotech, but rather that the level of tinkering we can achieve is vaguely felt to be just plain unnatural. The ethical problems might really be PR problems, and no less real for that. From owner-rapd@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!agate!newsxfer.itd.umich.edu!gatech!swiss.ans.net!emi.com!pauling.wadsworth.org!rebecca!labonnes From: labonnes@csc.albany.edu (S. LaBonne) Newsgroups: bionet.molbio.ageing,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.rapd,bionet.molbio.yeast,bionet.molbio.gene-linkage Subject: Re: controversies & ethics Date: 2 Feb 1995 21:41:47 GMT Organization: University at Albany, SUNY Lines: 21 Message-ID: <3grjir$n5d@rebecca.albany.edu> References: <3gm7u9$t5e@nntp1.u.washington.edu> <3gr5on$amt@nnrp.ucs.ubc.ca> NNTP-Posting-Host: bathsheba.albany.edu Xref: biosci bionet.molbio.ageing:1227 bionet.molbio.bio-matrix:539 bionet.molbio.embldatabank:442 bionet.molbio.evolution:2397 bionet.molbio.gdb:287 bionet.molbio.genome-program:1154 bionet.molbio.hiv:867 bionet.molbio.rapd:956 bionet.molbio.yeast:2301 bionet.molbio.gene-linkage:523 In article <3gr5on$amt@nnrp.ucs.ubc.ca>, Heidi N LeBlanc wrote: >One of the problems isn't so much what we *do* with biotechnology, as how >what we do is generally perceived. We as scientists think "Oh, what a >clever idea, putting an arctic fish gene into strawberries". >Non-scientists, with whatever level of education, often seem to think >this is just monstrous. The issue might not really be whether what we >are doing is ethical, or whether the ethics are unique to biotech, but >rather that the level of tinkering we can achieve is vaguely felt to be >just plain unnatural. The ethical problems might really be PR problems, >and no less real for that. I quite agree, and my fear is that we needlessly _exacerbate_ these PR problems if we single out biotechnology for the kind of special treatment exemplified by the proposed course that started this discussion. Then naturally laypeople conclude, "Gee, even the scientists think this stuff is especially problematical, so we _certainly_ should be worried". -- Steve LaBonne *********************** (labonnes@csc.albany.edu) "It can never be satisfied, the mind, never." - Wallace Stevens From owner-rapd@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!swiss.ans.net!emi.com!pauling.wadsworth.org!rebecca!labonnes From: labonnes@csc.albany.edu (S. LaBonne) Newsgroups: bionet.molbio.ageing,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.rapd,bionet.molbio.yeast,bionet.molbio.gene-linkage Subject: Re: controversies & ethics Date: 2 Feb 1995 16:43:49 GMT Organization: University at Albany, SUNY Lines: 34 Message-ID: <3gr245$i9p@rebecca.albany.edu> References: <3gm7u9$t5e@nntp1.u.washington.edu> <3gml85$fb5@rebecca.albany.edu> NNTP-Posting-Host: freia.albany.edu Xref: biosci bionet.molbio.ageing:1226 bionet.molbio.bio-matrix:538 bionet.molbio.embldatabank:440 bionet.molbio.evolution:2395 bionet.molbio.gdb:286 bionet.molbio.genome-program:1152 bionet.molbio.hiv:866 bionet.molbio.rapd:955 bionet.molbio.yeast:2298 bionet.molbio.gene-linkage:522 In article , Howard M. Bomze wrote: > Steve Bonne has been saying that there are no new ethical >considerations for agricultural biotechnologies. However, he has been >missing one very important one, that is the possibility of an engineered >gene to be transfered to a different species. The transgenic plant not >only has the sequences of the desired gene, it also contains the >sequences which are necesary to insert the gene into the genome. So a >question which must be looked at is this: If a gene for herbicide >resistance has been put into a corn plant so that that herbicide can be >used to kill all of the crab grass in the corn field, what happens if >the gene is transfered to the crab grass? Is there an _ethical_ problem here? I guess I can parse this as meaning, "if we failed to be concerned about this possibility and released the engineered corn without satisfying ourselves that it won't happen, we would be behaving unethically". Certainly I agree. Since comparable transfers of desired traits have been performed by selective breeding since the Neolithic (not to mention that horizontal gene transfers occur all the time in nature), I still don't see the _qualitatively_ new ethical considerations that you seem to think exist here. (Introducing rabbits into Australia is a good pre-biotechnology example of failing to anticipate massive undesired consequences of an environmental manipulation.) Don't get me wrong- we clearly need to start thinking a lot more seriously about the potential undesired impacts of _all_ new technologies. I just think that to single out biotechnology as some kind of special case borders on superstition. -- Steve LaBonne *********************** (labonnes@csc.albany.edu) "It can never be satisfied, the mind, never." - Wallace Stevens From owner-rapd@net.bio.net Fri Feb 03 22:00:00 1995 Path: biosci!LABATT.COM!48169 From: 48169@LABATT.COM (Rob.Stewart@Labatt.Com) Newsgroups: bionet.molbio.rapd Subject: Blank Lanes Date: 3 Feb 1995 07:37:30 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <9502031437.AA18238@ldn71.lboc.com> With repsect to failed rapd reactions we have experienced similar problems in the past. Our goal is to fingerprint bacteria for identification. We did two things which solved the problem. First we went to a larger PCR reaction volume-from 25 microlitres to 50 microlitres. This reduced the impact of pipetting errors. I believe that pipetting error is a major concern, since we find that changes in reaction conditions such as enzyme and magnesium concentration and particularly template DNA concentration greatly influnces the complexity of the RAPD pattern. Secondly, we prepare master mixes in batches containing primer and store at -20 C. The batches are made up for 10 samples. We aliquot 40 microlitres and add 10 microlitres of template DNA. We find our patterns much more reproducilble and do not have any failed reactions. As a bonus the cross contamination of the water blanks is also much less. In addition, we find that the master mix can be freze-thawed 1-2 times without affecting the efficiency of reaction i.e. no change in the fingerprint is observed. I hope this helps you with your problem. Yours sincerly, Robert J. Stewart From owner-rapd@net.bio.net Fri Feb 03 22:00:00 1995 Path: biosci!hubcap.clemson.edu!biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!swiss.ans.net!emi.com!pauling.wadsworth.org!rebecca!labonnes From: labonnes@csc.albany.edu (S. LaBonne) Newsgroups: bionet.molbio.ageing,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.gene-linkage,bionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.rapd,bionet.molbio.yeast Subject: Re: controversies & ethics Date: 31 Jan 1995 01:21:34 GMT Organization: University at Albany, SUNY Lines: 39 Message-ID: <3gk3au$pdp@rebecca.albany.edu> References: NNTP-Posting-Host: freia.albany.edu Xref: biosci bionet.molbio.ageing:1230 bionet.molbio.bio-matrix:541 bionet.molbio.embldatabank:444 bionet.molbio.evolution:2403 bionet.molbio.gdb:288 bionet.molbio.gene-linkage:529 bionet.molbio.genome-program:1158 bionet.molbio.hiv:869 bionet.molbio.rapd:957 bionet.molbio.yeast:2304 In article , Phandaal wrote: >I've been asked to give a lecture to upper-division college students on >the controversies and ethical considerations in producing transgenic >organisms, especially transgenic plants. It's been a while since I gave >this lecture, and so I was wondering if anybody had any good examples of >controversies or ethical considerations that I could incorporate into the >talk. > >Two I can think of off-hand are: > >1) introducing insecticidal proteins (such as the Bacillus thuringiensis >protein) into plants may create resistant insect populations (under the >force of heavy selection pressure), which could then overrun the resistant >plants and make worthless the efforts by conventional growers who *use* Bt >protein as a topical pesticidal spray. > >2) altering fatty acid metabolism in oil-crops (like canola) so that they >produce oils found chiefly in palm and coconut could severely damage the >palm oil and coconut oil industries in Third World countries... thus >severely depressing the economies of these already struggling countries. My problem with these examples is that I see nothing about them that is unique to transgenic technology. Similar sorts of problems are raised all the time by "conventional" technologies, including very ancient ones like selective breeding. An analogue to 1 is simply overuse of pesticides (or antibiotics for that matter), which can render them worthless in the way you describe. And 2 in no way raises ethical issues different from, say, starting a palm oil industry in Key West, possibly after selective breeding of oil palms to produce strains that give high yields there. Indeed, I doubt that there _are_ any ethical issues which depend _specifically_ on agricultural use of biotechnology as opposed to agricultural technologies in general. -- Steve LaBonne *********************** (labonnes@csc.albany.edu) "It can never be satisfied, the mind, never." - Wallace Stevens From owner-rapd@net.bio.net Sat Feb 04 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!news.uh.edu!uuneo.neosoft.com!Starbase.NeoSoft.COM!mckee From: mckee@starbase.neosoft.com (George McKee) Newsgroups: bionet.molbio.ageing,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.rapd,bionet.molbio.yeast,bionet.molbio.gene-linkage Subject: Re: controversies & ethics Followup-To: bionet.molbio.ageing,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.rapd,bionet.molbio.yeast,bionet.molbio.gene-linkage Date: 5 Feb 1995 15:25:32 GMT Organization: NeoSoft Internet Services +1 713 968 5800 Lines: 24 Message-ID: <3h2qlc$d6o@uuneo.neosoft.com> References: <3gk3au$pdp@rebecca.albany.edu> <3gm7u9$t5e@nntp1.u.washington.edu> NNTP-Posting-Host: starbase.neosoft.com X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.molbio.ageing:1236 bionet.molbio.bio-matrix:543 bionet.molbio.embldatabank:445 bionet.molbio.evolution:2412 bionet.molbio.gdb:290 bionet.molbio.genome-program:1164 bionet.molbio.hiv:871 bionet.molbio.rapd:960 bionet.molbio.yeast:2314 bionet.molbio.gene-linkage:530 Howard M. Bomze (hb10+@andrew.cmu.edu) wrote: : Steve Bonne has been saying that there are no new ethical : considerations for agricultural biotechnologies. However, he has been : missing one very important one, that is the possibility of an engineered : gene to be transfered to a different species. The transgenic plant not : only has the sequences of the desired gene, it also contains the : sequences which are necesary to insert the gene into the genome. This is one of those "ethical" problems that are really biological problems in disguise. Injecting new genes into the genomes of other organisms is precisely what retroviruses such as HIV have been doing for eons longer than biologists. To consider genetic engineering per se to be unethical is the same as considering crossbreeding unethical. The ethical considerations come into play when the new variety, however it was created, is being considered for introduction into the ecosystem. Introducing the gypsy moth into North America as a silk producer was far more disastrous than any frost-free tomato is likely to be. - George McKee -- Internet: mckee@neosoft.com Voice: +1 713 890 8122 From owner-rapd@net.bio.net Sun Feb 05 22:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.sprintlink.net!howland.reston.ans.net!gatech!newsxfer.itd.umich.edu!jobone!lynx.unm.edu!dns1.NMSU.Edu!usenet From: "Roy G. Cantrell" Newsgroups: bionet.molbio.rapd Subject: Re: Blank Lanes Date: 6 Feb 1995 15:37:10 GMT Organization: New Mexico State University Lines: 24 Message-ID: <3h5fn6$g7c@dns1.NMSU.Edu> References: <9502031437.AA18238@ldn71.lboc.com> NNTP-Posting-Host: mac-cantrell.nmsu.edu 48169@LABATT.COM (Rob.Stewart@Labatt.Com) wrote: > > With repsect to failed rapd reactions we have experienced similar problems > in the past. Our goal is to fingerprint bacteria for identification. We > did two things which solved the problem. First we went to a larger PCR > reaction volume-from 25 microlitres to 50 microlitres. This reduced the > impact of pipetting errors. I believe that pipetting error is a major > concern, since we find that changes in reaction conditions such as enzyme > and magnesium concentration and particularly template DNA concentration > greatly influnces the complexity of the RAPD pattern. Secondly, we prepare > master mixes in batches containing primer and store at -20 C. The batches > are made up for 10 samples. We aliquot 40 microlitres and add 10 > microlitres of template DNA. We find our patterns much more reproducilble > and do not have any failed reactions. As a bonus the cross contamination of > the water blanks is also much less. In addition, we find that the master > mix can be freze-thawed 1-2 times without affecting the efficiency of > reaction i.e. no change in the fingerprint is observed. I hope this helps > you with your problem. > Yours sincerly, > Robert J. Stewart > We have considered doing this. A question that I have? Is your Taq polymerase stable if stored in this manner in a "master mix"? Your master mix contains everything but DNA template , right? From owner-rapd@net.bio.net Sun Feb 05 22:00:00 1995 Path: biosci!SERVIDOR.DGSCA.UNAM.MX!carvalho From: carvalho@SERVIDOR.DGSCA.UNAM.MX (Carvalho Torres Alexandro cassio-UACPYP) Newsgroups: bionet.molbio.rapd Subject: GelCompar Date: 6 Feb 1995 10:58:54 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 4 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <3h5fn6$g7c@dns1.NMSU.Edu> NNTP-Posting-Host: net.bio.net Dear Netters Who have some experience between RAPD bands and the program GelCompar? Alexandro Cassio T. Carvalho Departamento de Infectologia-INNSZ.Mexico, DF From owner-rapd@net.bio.net Mon Feb 06 22:00:00 1995 Path: biosci!biotech.lan.nrc.ca!peloquin From: peloquin@biotech.lan.nrc.ca ("Peloquin, Marc") Newsgroups: bionet.molbio.rapd Subject: (none) Date: 7 Feb 1995 12:05:28 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <2F37D278@coursmtp.nrc.ca> NNTP-Posting-Host: net.bio.net A practical question? I would like to line up 40 profiles on an electrophoresis gel, does anybody out there have good results using a box with forthy wells ? What kind? Is it practical to load 2 x 20 well containing gels? Marc Peloquin peloquin@biotech.lan.nrc.ca From owner-rapd@net.bio.net Mon Feb 06 22:00:00 1995 Newsgroups: bionet.molbio.rapd Path: biosci!rutgers!gatech!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!netnews.nwnet.net!ns1.nodak.edu!plains!zcheng From: zcheng@plains.NoDak.edu (Zongming Cheng) Subject: PhD position available! Sender: usenet@ns1.nodak.edu (Usenet login) Message-ID: Date: Tue, 7 Feb 1995 17:56:06 GMT Nntp-Posting-Host: plains.nodak.edu Organization: North Dakota Higher Education Computing Network X-Newsreader: TIN [version 1.2 PL2] Lines: 21 GRADUATE FELLOWSHIP AVAILABLE. Department of Plant Sciences, North Dakota State University, has one fellowship available for a Ph.D candidate beginning fall semester 1995. This fellowship is part of the Department of Energy (DOE)/ND EPSCoR traineeship designed to award top students and to encourage work with DOE related research. This particular candidate will work specifically on either the molecular mechanism of adventitious root formation in hardwood cuttings of aspen, a woody energy plant, or the phytoremediation of heavy metals. Students who are US CITIZENS OR PERMANENT RESIDENTS with a strong background in plant molecular biology and (bio)chemistry are encouraged to apply. GRE General Test is required and Subject Test in Biology is encouraged. Annual stipend is $16,000 per year plus tuition waiver and health insurance coverage. The Department of Plant Sciences, located in a newly constructed building, has state-of-the-art facilities to carry out the research. For further information on research or program contact: Dr. Zong-Ming Cheng (phone: (701©231-7405, fax: (701©231-8474, e-mail: zcheng@plains.nodak.edu), Department of Plant Sciences, North Dakota State University, Fargo, ND 58105. For application materials contact: The Graduate School, North Dakota State University, Fargo, ND 58105. From owner-rapd@net.bio.net Mon Feb 06 22:00:00 1995 Path: biosci!biotech.lan.nrc.ca!peloquin From: peloquin@biotech.lan.nrc.ca ("Peloquin, Marc") Newsgroups: bionet.molbio.rapd Subject: (none) Date: 7 Feb 1995 11:15:10 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <2F37C6AF@coursmtp.nrc.ca> NNTP-Posting-Host: net.bio.net Hi I am a new member of RAPD so I thought I would introduce myself (like I do with my other discussion groups). My name is Marc Peloquin, I am a graduate student (PhD) at McGill university in Montreal. RAPD are a sideline for me but currently, I can tell you that I have done a lot of work on RAPD of vibrio isolates from the coast of Newfoundland. I have just purchased the program Dendron from Solltech and hope to analyze a lot of stuff. Is anybody out there familiar with the program? Also I was wondering if someone could send me some good references on a possible review and a typical use of RAPD PCR. Marc Peloquin peloquin@biotech.lan.nrc.ca From owner-rapd@net.bio.net Mon Feb 06 22:00:00 1995 Path: biosci!jab000.uesp.ansp.br!gkuhar From: gkuhar@jab000.uesp.ansp.br (GORAN KUHAR JEZOVSEK) Newsgroups: bionet.molbio.rapd Subject: dna purity Date: 7 Feb 1995 00:32:32 -0800 Organization: UNESP Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <2f3671da@jab000.uesp.ansp.br> Reply-To: GORAN KUHAR JEZOVSEK Dear netters, Is there any relationship between DNA purity and RAPD results ? In the literature there seems to conflictant opinions. Thanks Goran -- 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 Tue Feb 07 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!torn!ccshst05.cs.uoguelph.ca!ccshst01.cs.uoguelph.ca!jdulson From: jdulson@uoguelph.ca (Jacqueline Dulson) Newsgroups: bionet.molbio.rapd Subject: Re: (none) Date: 8 Feb 1995 18:14:42 GMT Organization: University of Guelph Lines: 24 Distribution: world Message-ID: <3hb1mi$4i0@ccshst05.cs.uoguelph.ca> References: <2F37D278@coursmtp.nrc.ca> NNTP-Posting-Host: ccshst01.cs.uoguelph.ca X-Newsreader: TIN [version 1.2 PL2] Peloquin, Marc (peloquin@biotech.lan.nrc.ca) wrote: : A practical question? : I would like to line up 40 profiles on an electrophoresis gel, does anybody : out there have good results using a box with forthy wells ? What kind? Is it : practical to load 2 x 20 well containing gels? : Marc Peloquin : peloquin@biotech.lan.nrc.ca We routinely run out this many lanes on a gel and more. We had a gel tray made (in house, sorry) to fit our BRL gel box that is 1 1/2 times the size of the tray that came with the box that will take 3 combs and about 60 samples per gel. We run it slowly (it takes about 6 hours to complete a run), but the resolution of the bands remains comparable to more standard set-ups. We use 1.4 % agarose (of course?) so there is little problem with diffusion over the course of loading; you can always run each line of wells into the agarose before loading the next line if you are really concerned about this (load your markers with the lanes of course). Hope this helps. -Jackie Dulson Univ. of Guelph From owner-rapd@net.bio.net Tue Feb 07 22:00:00 1995 Path: biosci!daresbury!trane.uninett.no!sunic!news.funet.fi!news.csc.fi!news.helsinki.fi!MMKAB-01208.pc.Helsinki.FI!kkammiov From: kkammiov@viikki21.helsinki.fi (KARI KAMMIOVIRTA (MMKAB)) Newsgroups: bionet.molbio.rapd Subject: HELP: Old insects Date: Wed, 8 Feb 1995 12:37:10 GMT Organization: University of Helsinki Lines: 12 Message-ID: NNTP-Posting-Host: mmkab-01208.pc.helsinki.fi Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Hi everybody, I have run out of imagination with my newest samples. They are OLD insects from one University collection. Problem is that I can't get any DNA out of those beasties. They are from 10 to 90 years old, and they have been stored in quite dry, room temperature, but not exactly for this purpose. So can somebody give me a hint how to extract, or am I banging my head to the wall just for nothing. Thanks to anybody who wants to comment. Kari From owner-rapd@net.bio.net Thu Feb 09 22:00:00 1995 Path: biosci!agate!dog.ee.lbl.gov!news.cs.utah.edu!news.cc.utah.edu!corona!patrick From: Patrick O'Neil Newsgroups: bionet.molbio.ageing,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.gene-linkage,bionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.rapd,bionet.molbio.yeast Subject: Re: controversies & ethics Date: Thu, 9 Feb 1995 23:44:24 -0700 Organization: University Of Utah Computer Center Lines: 25 Message-ID: References: <3gk3au$pdp@rebecca.albany.edu> <3gm7u9$t5e@nntp1.u.washington.edu> NNTP-Posting-Host: corona.med.utah.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: <3gm7u9$t5e@nntp1.u.washington.edu> Xref: biosci bionet.molbio.ageing:1269 bionet.molbio.bio-matrix:554 bionet.molbio.embldatabank:451 bionet.molbio.evolution:2430 bionet.molbio.gdb:296 bionet.molbio.gene-linkage:544 bionet.molbio.genome-program:1179 bionet.molbio.hiv:888 bionet.molbio.rapd:973 bionet.molbio.yeast:2370 On 31 Jan 1995, Jared Roach wrote: > 2) The human race as a whole (or national governments, or > individuals) is slow to reach consensus on ethical issues (i.e. > religion, abortion, the creation of new species, etc.) Science > should slow its pace of discovery to allow Ethics to catch up. I could never go along with this point. What, tell us all that we should quit looking at this? Stop research concerning that? Take up a new trade, like house painting? I do and will continue to study and learn just as quickly as I am physically capable. I could never say, "well, that result sure does point to a VERY exciting, very interesting, line of research that would increase my understanding of x. Well, maybe I'll just cool my jets and let it go for a decade or so. Sure don't want to upset those who can't handle the fast pace of scientific understanding." In any case, it is a pointless thought since if this or that or those countries stopped research on x, then some other country or group would take it up because there would be a possible economic boon tied to it. If not us, then someone else. Humans have never and will never all agree to the same extent on ANYTHING. I would go to any location that would support what I am interested in researching, be it transgenics or gene therapy, etc. From owner-rapd@net.bio.net Thu Feb 09 22:00:00 1995 Path: biosci!agate!dog.ee.lbl.gov!news.cs.utah.edu!news.cc.utah.edu!corona!patrick From: Patrick O'Neil Newsgroups: bionet.molbio.ageing,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.gene-linkage,bionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.rapd,bionet.molbio.yeast Subject: Re: controversies & ethics Date: Thu, 9 Feb 1995 23:28:35 -0700 Organization: University Of Utah Computer Center Lines: 52 Message-ID: References: NNTP-Posting-Host: corona.med.utah.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: Xref: biosci bionet.molbio.ageing:1267 bionet.molbio.bio-matrix:553 bionet.molbio.embldatabank:450 bionet.molbio.evolution:2429 bionet.molbio.gdb:295 bionet.molbio.gene-linkage:543 bionet.molbio.genome-program:1178 bionet.molbio.hiv:887 bionet.molbio.rapd:972 bionet.molbio.yeast:2369 On Mon, 30 Jan 1995, Phandaal wrote: > I've been asked to give a lecture to upper-division college students on > the controversies and ethical considerations in producing transgenic > organisms, especially transgenic plants. It's been a while since I gave > this lecture, and so I was wondering if anybody had any good examples of > controversies or ethical considerations that I could incorporate into the > talk. I spent a year working in a plant molec bio lab that was being partially funded by a private company to produce a more fungal resistent sugarbeet. Technically, it would be a transgenic in that a gene, VERY closely related to an already present gene, from Arabidopsis was/is to be introduced into the sugarbeet and overexpressed, thus bolstering the sugarbeet's fungal resistence. I enjoyed the work very much and saw absolutely nothing wrong with it. It was making use of an already existent defensive gene that resides in many plants and simply increasing its output by using an easy to maniplate gene from a common lab plant. This sugarbeet will allow, hopefully, less use of chemical fungicides. You could argue that it will simply apply selective pressure for fungi to evolve resistence...but then, so does the use of fungicides or natural defenses. A more resistent fungi will, conversely, select for more fungal-resistent plants. This can be applied to your first point below too. > > Two I can think of off-hand are: > > 1) introducing insecticidal proteins (such as the Bacillus thuringiensis > protein) into plants may create resistant insect populations (under the > force of heavy selection pressure), which could then overrun the resistant > plants and make worthless the efforts by conventional growers who *use* Bt > protein as a topical pesticidal spray. The use of the spray itself puts selective pressure on insects to develop resistence. The point is moot. > > 2) altering fatty acid metabolism in oil-crops (like canola) so that they > produce oils found chiefly in palm and coconut could severely damage the > palm oil and coconut oil industries in Third World countries... thus > severely depressing the economies of these already struggling countries. If business was nice, then companies would never be put out of business. It may be tough but I could not support artificially supporting a weakly-based economy by ignoring a possible economic boon here. Any economy that ties itself to one commodity is *automatically* doomed to bite it pretty hard. Look at Louisiana and the effects of it having placed all its economic eggs in the oil business basket -- the state is only now beginning to recover from over a decade of depressed economy and hard times. Patrick From owner-rapd@net.bio.net Thu Feb 09 22:00:00 1995 Path: biosci!agate!dog.ee.lbl.gov!news.cs.utah.edu!news.cc.utah.edu!corona!patrick From: Patrick O'Neil Newsgroups: bionet.molbio.ageing,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.rapd,bionet.molbio.yeast,bionet.molbio.gene-linkage Subject: Re: controversies & ethics Date: Thu, 9 Feb 1995 23:52:53 -0700 Organization: University Of Utah Computer Center Lines: 20 Message-ID: References: <3gk3au$pdp@rebecca.albany.edu> <3gm7u9$t5e@nntp1.u.washington.edu> <3gml85$fb5@rebecca.albany.edu> NNTP-Posting-Host: corona.med.utah.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: Xref: biosci bionet.molbio.ageing:1270 bionet.molbio.bio-matrix:555 bionet.molbio.embldatabank:452 bionet.molbio.evolution:2431 bionet.molbio.gdb:297 bionet.molbio.genome-program:1180 bionet.molbio.hiv:889 bionet.molbio.rapd:974 bionet.molbio.yeast:2371 bionet.molbio.gene-linkage:545 On Wed, 1 Feb 1995, Howard M. Bomze wrote: > Steve Bonne has been saying that there are no new ethical > considerations for agricultural biotechnologies. However, he has been > missing one very important one, that is the possibility of an engineered > gene to be transfered to a different species. This already happens in nature by various means, one of which is viral. There is no absolute genetic sanctity in nature. As for transgenics, especially in plants, one tool for introducing foreign genes is agrobacteria. This microbe is fully capable of vectoring interspecific DNA without lab manipulation. The DNA so introduced in the lab does not carry any special DNA destabilizer, rather, it depends on the rather scattershot and low-yield natural method of homologous recombination or illegitimate recombination. Another method has absolutely no danger of transfering a new DNA transfer method to nature: the gene gun. DNA of interest bound to microscopic gold beads and shot into cells offers absolutely no threat of tranfering into an uncontrollable means of interspecific gene transfer in the wild. From owner-rapd@net.bio.net Sat Feb 11 22:00:00 1995 Path: biosci!newshost.lanl.gov!news.ttu.edu!aurora.LaTech.edu!darwin.sura.net!nntp.st.usm.edu!whale.st.usm.edu!sywang From: sywang@whale.st.usm.edu (Shiao Y. Wang) Newsgroups: bionet.molbio.rapd Subject: 35S in RAPD? Date: 12 Feb 1995 06:49:45 GMT Organization: University of Southern Mississippi Lines: 12 Message-ID: <3hkb29$m1e@server.st.usm.edu> NNTP-Posting-Host: whale.st.usm.edu X-Newsreader: TIN [version 1.2 PL1] My limited experience with RAPD has been with the use of EtBr-stained agarose gels to visualize the PCR products. I've been wondering whether the use of 35S-dNTP and autoradiography would improve the resolution? I would appreciate comments by those with more experience and perhaps protocols (such as to how much labeled dNTP to use or ratio of hot/cold dNTP). Thank you. Shiao Wang sywang@whale.st.usm.edu From owner-rapd@net.bio.net Sat Feb 11 22:00:00 1995 Path: biosci!MERCURY.UARK.EDU!DRHOADS From: DRHOADS@MERCURY.UARK.EDU ("Douglas Rhoads") Newsgroups: bionet.molbio.rapd Subject: Re: dna purity Date: 11 Feb 1995 13:13:21 -0800 Organization: University of Arkansas Lines: 44 Sender: daemon@net.bio.net Distribution: world Message-ID: <75DDED70CB@uamercury.uark.edu> In our experience the major problem can be in quantitation of DNA vs RNA. Loads of RNA, especially as small oligo RNAs, can be a problem since under the low annealing stringencies employed you can get false priming by oligo RNAs in place of the RAPD primers you add. This leads to lots of targets that can then increase alternative targets. As we view it, RAPD is based on the product of target complementarity and target concentration. Increase the concentration and you get increased chance of priming. Lots of RNAs increase the concentration of degenerate primers during initial cycles. > To: rapd@net.bio.net > From: gkuhar@jab000.uesp.ansp.br (GORAN KUHAR JEZOVSEK) > Subject: dna purity > Date: 7 Feb 1995 00:32:32 -0800 > Reply-to: GORAN KUHAR JEZOVSEK > Dear netters, > > Is there any relationship between DNA purity and RAPD results ? > In the literature there seems to conflictant opinions. > > Thanks > > Goran > -- > > 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 > > > //========================================================\\ ||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 || ==========================================================|| || My Dogma Just Got Run Over by Someone's Karma || \\========================================================// From owner-rapd@net.bio.net Sun Feb 12 22:00:00 1995 Path: biosci!EMUVAX.EMICH.EDU!BIO_HANNAN From: BIO_HANNAN@EMUVAX.EMICH.EDU Newsgroups: bionet.molbio.rapd Subject: re:dna purity Date: 13 Feb 1995 07:09:47 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <950213100933.202033df@emuvax.emich.edu> NNTP-Posting-Host: net.bio.net Goran, We have found that we must use Bioclean (US Biochemical) before amplification, or we just get streaking, no bands (regardless of template amount used). We think there is some contaminating polysaccharides, or something that we have been unable to remove any other way. We are working on a species of Iris (I. lacustris and I. cristata). Gary Hannan From owner-rapd@net.bio.net Sun Feb 12 22:00:00 1995 Path: biosci!ALPHAC.CIMMYT.MX!RBIRD From: RBIRD@ALPHAC.CIMMYT.MX ("rbird@cimmyt.mx") Newsgroups: bionet.molbio.rapd Subject: connection with rapd Date: 13 Feb 1995 09:55:37 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HN008MVYGOA3C8FS@ALPHAC.CIMMYT.MX> NNTP-Posting-Host: net.bio.net 13 Feb 95 rapd folk, I am starting RAPD analysis of ancient maize from Peru and of traditional maize from the same area and elsewhere, preparatory to doing analysis of SSRs and targeted sequences. I just was forwarded a message passed thru rapd@net.bio.net and would like to know more about this connection. Thanks, Robert Bird, rbird@cimmyt.mx (the "alphac" that may head this message before "cimmyt.mx" is not needed). ----------------------------------------------------------------- CENTRO INTERNACIONAL DE MEJORAMIENTO DE MAIZ Y TRIGO (CIMMYT,INT) International Maize and Wheat Improvement Center Note new INTERNET address: username@CIMMYT.MX Lisboa 27 Apdo. Postal 6-641 CP 06600 Mexico, D.F. MEXICO Telephone: +52(5)726-9091 FAX: +52(5)726-7559 ----------------------------------------------------------------- From owner-rapd@net.bio.net Mon Feb 13 22:00:00 1995 Path: biosci!qmrelay.mail.cornell.edu!warren_lamboy From: warren_lamboy@qmrelay.mail.cornell.edu ("Warren Lamboy") Newsgroups: bionet.molbio.rapd Subject: 260/280 ratios Date: 14 Feb 1995 14:22:48 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 30 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Subject: Time:17:56 OFFICE MEMO 260/280 ratios Date:13/02/1995 Dear netters: I have a question about 260/280 ratios for checking for contamination of DNA with proteins (and I presume other contaminants as well). I have read conflicting statements about what values of the ratio correspond to "pure" DNA. I was taught that a ratio of 1.8 corresponds to pure double-stranded DNA, and that a ratio of 2.0 represented single-stranded (I presumed) RNA. But I have seen a number of papers lately that stated they had great double-stranded DNA with ratios close to 2.0. Does that suggest that the DNA was contaminated with RNA? Or was what I was taught incorrect? We used to consider ratios between 1.6 and 1.8 pretty good DNA, with 1.8 the maximum values possible (barring contamination). There was also a paper recently in Biotechniques that dealt with this issue, but it actually raised more questions in my mind than it answered. I know that if I could find published values for extinction coefficients, I could work this all out for myself, a la the paper in Biotechniques (sorry, I don't have the reference at hand), so can anyone please tell me where I can find published values for extinction coefficients for DNA and RNA (and oligos as well)? I would like to hear anyone's thoughts and experiences with this issue. I will collate all responses (assuming there are any) and send them out to all RAPDer's. Thanks for your help on this. - Warren P.S. Of course, I could take some commercially available DNAs and see what results I get at 260 and 280, but I wanted to hear of researchers' experiences before I went ahead with empirical studies myself. Thanks. From owner-rapd@net.bio.net Mon Feb 13 22:00:00 1995 Path: biosci!IPST.EDU!Mike.Wood From: Mike.Wood@IPST.EDU Newsgroups: bionet.molbio.rapd Subject: RE: dna purity Date: 14 Feb 1995 08:52:37 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 31 Sender: daemon@net.bio.net Distribution: world Message-ID: <42743.mwood@pop.ipst.edu> NNTP-Posting-Host: net.bio.net In message 7 Feb 1995 00:32:32 -0800, gkuhar@jab000.uesp.ansp.br (GORAN KUHAR JEZOVSEK) writes: > Dear netters, > > Is there any relationship between DNA purity and RAPD results ? > In the literature there seems to conflictant opinions. > > Thanks > > Goran > -- Dear Goran, This is just based on personal experience, but there does seem to be a relationship between DNA purity and reaction results. When I was using a poor DNA isolation procedure to isolate DNA from Pinus tadea needles and buds, there were differences in reaction products for the two tissues. This was the case even though the tissue samples were from the same branch of the same tree. Once the samples were cleaned up, purified with a better procedure, the reaction products were the same for both tissues. In addition with some samples, impurities can prevent reactions from running. These same samples will produce reaction products when diluted (presumably the contaminant is diluted to the point where it no longer interfers). I don't know if this is all true, it's just what I've seen. Mike From owner-rapd@net.bio.net Mon Feb 13 22:00:00 1995 Path: biosci!MESSEL.EMSE.FR!dkarlin From: dkarlin@MESSEL.EMSE.FR (david) Newsgroups: bionet.molbio.rapd Subject: is RAPD directed molecular evolution ? Date: 14 Feb 1995 09:05:32 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <9502141700.AA03645@messel.emse.fr.emse.fr> NNTP-Posting-Host: net.bio.net Hello ! I'm a french student in engeering and I have a real passion for biology. I have read in several scientific magazines articles called "Directed molecular evolution" or "Darwin's medicine" who talked about the creation of new molecules with a cycle of mutations/selection ... and I think (if I dare say so) that it is mere GENIOUS ! Therefore, I'd like to know whether Directed Molecular Evolution and RAPD are the same thing ; I'd also appreciate some information about the RAPD net ! Hopefully you won't waste your time, because I have some ideas about the relationship between Directed Molecular Evolution and the theory of complexity ... Thanking you in advance, David Karlin (dkarlin@messel.emse.fr) From owner-rapd@net.bio.net Tue Feb 14 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!pipex!uunet!in1.uu.net!newsflash.concordia.ca!nstn.ns.ca!ac!cox.nsac.ns.ca!b92270 Newsgroups: bionet.molbio.rapd Subject: DNA fingerprinting of scallops Message-ID: From: b92270@cox.nsac.ns.ca Date: Wed, 15 Feb 1995 08:12:21 Organization: NS Agr College Keywords: scallops, DNA Nntp-Posting-Host: 198.166.16.122 Lines: 2 Could anyone givee an address for someone doing DNA work with scallops? also an address for a marine biology listserver would be nice... From owner-rapd@net.bio.net Tue Feb 14 22:00:00 1995 Path: biosci!UKCC.UKY.EDU!EQUIGENE From: EQUIGENE@UKCC.UKY.EDU ("Teri L. Lear") Newsgroups: bionet.molbio.rapd Subject: rapd sequences Date: 15 Feb 1995 15:06:09 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: <199502152305.PAA27237@net.bio.net> NNTP-Posting-Host: net.bio.net Having searched the literature I can find no reference where someone has compared the sequences of co-migrating RAPD markers between species mammalian systems. We are trying to find out more about the nature of these "shared" RAPD bands and if they are indeed the same sequences. I am aware of the use of Southern blots, etc. for the characterization of RAPD markers. In previous RAPD network discussions several researchers noted that they planned to further characterize markers shared between species by sequencing and I was curious if anyone had done this? Any references or comments are greatly appreciated. Thanks. Teri L. Lear Department of Veterinary Science Gluck Equine Research Center University of Kentucky Lexington, KY 40546-0099 e-mail: equigene@ukcc.uky.edu From owner-rapd@net.bio.net Tue Feb 14 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: Louis van de Zande Newsgroups: bionet.molbio.rapd Subject: RE: dna purity Date: 15 Feb 1995 09:18:02 -0000 Organization: Department of Biology, RUGroningen Lines: 13 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3hsgsa$85u@mserv1.dl.ac.uk> Reply-To: ZANDELPW@BIOL.rug.nl Original-To: rapd@dl.ac.uk > Dear netters, > > Is there any relationship between DNA purity and RAPD results ? > In the literature there seems to conflictant opinions. > > Thanks > > Goran > -- There certainly is!!! Louis van de Zande From owner-rapd@net.bio.net Wed Feb 15 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!uunet!newstf01.news.aol.com!newsbf02.news.aol.com!not-for-mail From: loggins@aol.com (Loggins) Newsgroups: bionet.molbio.rapd Subject: Re: HELP: Old insects Date: 15 Feb 1995 23:39:39 -0500 Organization: America Online, Inc. (1-800-827-6364) Lines: 2 Sender: root@newsbf02.news.aol.com Message-ID: <3hukub$dbp@newsbf02.news.aol.com> References: Reply-To: loggins@aol.com (Loggins) NNTP-Posting-Host: newsbf02.mail.aol.com Did you try Chelex? I heard that it works quite well with mounted/stuffed fish...Haven't tried that one myself tough. From owner-rapd@net.bio.net Wed Feb 15 22:00:00 1995 Newsgroups: bionet.molbio.ageing,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.gene-linkage,bionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.rapd,bionet.molbio.yeast Path: biosci!daresbury!trane.uninett.no!ugle.unit.no!news.uit.no!pclab12.hibo.no!FG1 From: FG1@stud.hibo.no Subject: Re: controversies & ethics Sender: news@news.uit.no (News admin.) Message-ID: Date: Thu, 16 Feb 1995 10:34:11 GMT Lines: 58 References: Organization: Bodoe College X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Xref: biosci bionet.molbio.ageing:1331 bionet.molbio.bio-matrix:557 bionet.molbio.embldatabank:457 bionet.molbio.evolution:2449 bionet.molbio.gdb:301 bionet.molbio.gene-linkage:562 bionet.molbio.genome-program:1199 bionet.molbio.hiv:914 bionet.molbio.rapd:987 bionet.molbio.yeast:2405 In article Patrick O'Neil writes: >From: Patrick O'Neil >Subject: Re: controversies & ethics >Date: Thu, 9 Feb 1995 23:28:35 -0700 >On Mon, 30 Jan 1995, Phandaal wrote: >> I've been asked to give a lecture to upper-division college students on >> the controversies and ethical considerations in producing transgenic >> organisms, especially transgenic plants. It's been a while since I gave >> this lecture, and so I was wondering if anybody had any good examples of >> controversies or ethical considerations that I could incorporate into the >> talk. > I spent a year working in a plant molec bio lab that was being partially >funded by a private company to produce a more fungal resistent >sugarbeet. Technically, it would be a transgenic in that a gene, VERY >closely related to an already present gene, from Arabidopsis was/is to be >introduced into the sugarbeet and overexpressed, thus bolstering the >sugarbeet's fungal resistence. I enjoyed the work very much and saw >absolutely nothing wrong with it. It was making use of an already >existent defensive gene that resides in many plants and simply increasing >its output by using an easy to maniplate gene from a common lab plant. >This sugarbeet will allow, hopefully, less use of chemical fungicides. > You could argue that it will simply apply selective pressure for fungi >to evolve resistence...but then, so does the use of fungicides or natural >defenses. A more resistent fungi will, conversely, select for more >fungal-resistent plants. This can be applied to your first point below too. >> >> Two I can think of off-hand are: >> >> 1) introducing insecticidal proteins (such as the Bacillus thuringiensis >> protein) into plants may create resistant insect populations (under the >> force of heavy selection pressure), which could then overrun the resistant >> plants and make worthless the efforts by conventional growers who *use* Bt >> protein as a topical pesticidal spray. >The use of the spray itself puts selective pressure on insects to develop >resistence. The point is moot. >> >> 2) altering fatty acid metabolism in oil-crops (like canola) so that they >> produce oils found chiefly in palm and coconut could severely damage the >> palm oil and coconut oil industries in Third World countries... thus >> severely depressing the economies of these already struggling countries. >If business was nice, then companies would never be put out of business. >It may be tough but I could not support artificially supporting a >weakly-based economy by ignoring a possible economic boon here. Any >economy that ties itself to one commodity is *automatically* doomed to bite >it pretty hard. Look at Louisiana and the effects of it having placed >all its economic eggs in the oil business basket -- the state is only now >beginning to recover from over a decade of depressed economy and hard times. >Patrick From owner-rapd@net.bio.net Wed Feb 15 22:00:00 1995 Path: biosci!UKCC.UKY.EDU!EQUIGENE From: EQUIGENE@UKCC.UKY.EDU ("Teri L. Lear") Newsgroups: bionet.molbio.rapd Subject: rapd sequences Date: 16 Feb 1995 07:12:21 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <199502161512.HAA15127@net.bio.net> NNTP-Posting-Host: net.bio.net I recently sent a note about rapd markers shared between species/individuals. I realize that shared bands (same size) are not always the same sequence. Perhaps a better question would have been "how often does this occur?". Has anyone examined this in mammalian systems at the DNA sequence level (ie cloned and sequenced a shared band across several closely related species)? Thanks. Teri L. Lear Dept. of Veterinary Science Gluck Equine Research Center University of Kentucky Lexington, KY 40546-0099 e-mail: equigene@ukcc.uky.edu From owner-rapd@net.bio.net Wed Feb 15 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: Louis van de Zande Newsgroups: bionet.molbio.rapd Subject: Re: rapd sequences Date: 16 Feb 1995 08:11:42 -0000 Organization: Department of Biology, RUGroningen Lines: 30 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3hv1bu$gjg@mserv1.dl.ac.uk> Reply-To: ZANDELPW@BIOL.rug.nl Original-To: rapd@dl.ac.uk > Having searched the literature I can find no reference where someone has > compared the sequences of co-migrating RAPD markers between species > mammalian systems. We are trying to find out more about the nature of these > "shared" RAPD bands and if they are indeed the same sequences. I am aware of > the use of Southern blots, etc. for the characterization of RAPD markers. > In previous RAPD network discussions several researchers noted that they > planned to further characterize markers shared between species by sequencing > and I was curious if anyone had done this? Any references or comments are > greatly appreciated. > > Thanks. > > Teri L. Lear > Department of Veterinary Science > Gluck Equine Research Center > University of Kentucky > Lexington, KY 40546-0099 > e-mail: equigene@ukcc.uky.edu > In Drosophila (keep on reading) fragments of similar size are homologous between closely related species but not for less related species. And even in closely related species same size does not invariably mean same locus. Shortly the Journal of evolultionary biology will contain an article in which southerns are shown to demonstrate the above. In the meantime: do not count on similar size equals similar sequence in RAPDs. cheers Louis van de Zande From owner-rapd@net.bio.net Thu Feb 16 22:00:00 1995 Path: biosci!SERVIDOR.DGSCA.UNAM.MX!carvalho From: carvalho@SERVIDOR.DGSCA.UNAM.MX (Carvalho Torres Alexandro cassio-UACPYP) Newsgroups: bionet.molbio.rapd Subject: Re: rapd sequences Date: 17 Feb 1995 07:48:57 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 38 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <3hv1bu$gjg@mserv1.dl.ac.uk> NNTP-Posting-Host: net.bio.net On 16 Feb 1995, Louis van de Zande wrote: > > Having searched the literature I can find no reference where someone has > > compared the sequences of co-migrating RAPD markers between species > > mammalian systems. We are trying to find out more about the nature of these > > "shared" RAPD bands and if they are indeed the same sequences. I am aware of > > the use of Southern blots, etc. for the characterization of RAPD markers. > > In previous RAPD network discussions several researchers noted that they > > planned to further characterize markers shared between species by sequencing > > and I was curious if anyone had done this? Any references or comments are > > greatly appreciated. > > > > Thanks. > > > > Teri L. Lear > > Department of Veterinary Science > > Gluck Equine Research Center > > University of Kentucky > > Lexington, KY 40546-0099 > > e-mail: equigene@ukcc.uky.edu > > > > In Drosophila (keep on reading) fragments of similar size are > homologous between closely related species but not for less related > species. And even in closely related species same size does not > invariably mean same locus. Shortly the Journal of evolultionary > biology will contain an article in which southerns are shown to > demonstrate the above. In the meantime: do not count on similar size > equals similar sequence in RAPDs. > > cheers > Louis van de Zande > > Please send us the complete reference of hte article. Thanks a lot. Alexandro C. T. Carvalho From owner-rapd@net.bio.net Sun Feb 19 22:00:00 1995 Path: biosci!SASK.USASK.CA!LEES From: LEES@SASK.USASK.CA Newsgroups: bionet.molbio.rapd Subject: RAPD analysis program Date: 20 Feb 1995 14:46:14 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hello, It'll be appreciated if anyone show me how to get or where I can find some programs for RAPD analysis, from which site of FTP ? Thanks very much, Sun Lee National Research Council Saskatoon, SK Canada S7N 0W9 e-mail: lees@skyfox.usask.ca From owner-rapd@net.bio.net Sun Feb 19 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!dundee.ac.uk!sfh.biolsci.dundee.ac.uk!rdjbutcher From: rdjbutcher@biolsci.dundee.ac.uk (ROBERT BUTCHER) Newsgroups: bionet.molbio.rapd Subject: Microsatellite polymorphisms Date: Mon, 20 Feb 1995 17:12:15 GMT Organization: University of Dundee Lines: 32 Message-ID: NNTP-Posting-Host: sfh.biolsci.dundee.ac.uk Keywords: microsatellites, Hello, A few very basic and obviouse questions for which i apologise, but i simply just dont happen to know the answers! Thus all help (replies, on news or personal) will be greatly appreciated. (1) At what length (either number of nucleotides in total or the number of nucleotide repeat units) does a repetatative sequence become definable as a microsatellite? Thus, for example {with respect to one strand only} (dGT)60 or (dCAC)40 are clearly so, (dGT)10 and (dCAC)8 probably so, but what about (dGT)6 or (dCAC)4? Likewise for mononucleotide (eg (dC)n), tetranucleotide etc repeat units! (2) With reference to the generation of microsatellite locus(i) length polymorphism:- are there any studies or other evidence upon the rate (probability) of generation of length polymorphism of any locus with respect to (a) the original microsatellite length? (i.e does a larger microsatellite stand a greater chance of slippage and thus show more rapid polymorphism development within the constraints allowed) (b) sequences flanking the microsatellite (c) the microsatellite core repeat unit (i.e. will a say (gt)n alter more frequently than a say (gc) repeat, all other conditions being essentially identical? Well there we go. Nothing of great interst to anyone but myself.. your replies still apreciated all the more for it Thanks Rob Robert Butcher Department of Biological Sciences Dundee University Dundee Scotland e-mail:- R.D.J.BUTCHER@DUNDEE.AC.UK From owner-rapd@net.bio.net Mon Feb 20 22:00:00 1995 Path: biosci!cabi.org!D.BRAYFORD From: D.BRAYFORD@cabi.org ("David Brayford ", IMI) Newsgroups: bionet.molbio.rapd Subject: newt preserve Date: 21 Feb 1995 06:25:34 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: <2F49F76B@msm.cgnet.com> NNTP-Posting-Host: net.bio.net Can I ask a stupid question? Just don't laugh, OK. As I understand it, the rRNA gene ITS regions are regarded as a selectively neutral segments of DNA which can accumulate mutations over time and hence be used for phylogenetic analysis. What I don't understand is:- if an organism has e.g. 100 copies of its rRNA gene, each with its own ITS regions, how come we don't find 100 different ITS sequences in each organism we study? Or at least how can we expect them to all be the same? How can we say "This isolate has this sequence"? If the mutations are selectively neutral, how could one mutant sequence come to predominate? I must be missing something fairly fundamental here. You can probably guess I'm not a molecular person. I mean, while we're at it, what preserves microsatellite sequences? Look, I'm losing sleep over this, so please put me out of my misery somebody. Give me a reference to Noddy's Beginners Guide to Molecular Biology or something. Thanks, Dave Brayford d.brayford@cabi.org From owner-rapd@net.bio.net Mon Feb 20 22:00:00 1995 Path: biosci!OSF1.GMU.EDU!ladamkew From: ladamkew@OSF1.GMU.EDU ("S. LAURA ADAMKEWICZ") Newsgroups: bionet.molbio.rapd Subject: Re: DNA fingerprinting of scallops Date: 21 Feb 1995 11:50:27 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net On Wed, 15 Feb 1995 b92270@cox.nsac.ns.ca wrote: > Could anyone givee an address for someone doing DNA work with scallops? > also an address for a marine biology listserver would be nice... > > People at SUNY Stoney Brook were a couple of years ago. So is Elizabeth Boulding of mollusc-molecular news. From owner-rapd@net.bio.net Mon Feb 20 22:00:00 1995 Path: biosci!OSF1.GMU.EDU!ladamkew From: ladamkew@OSF1.GMU.EDU ("S. LAURA ADAMKEWICZ") Newsgroups: bionet.molbio.rapd Subject: Re: newt preserve Date: 21 Feb 1995 11:49:27 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <2F49F76B@msm.cgnet.com> NNTP-Posting-Host: net.bio.net On 21 Feb 1995 D.BRAYFORD@cabi.org wrote: > > Can I ask a stupid question? Just don't laugh, OK. Definitely NOT stupid. You want a clear account of concerted evolution, but I am not the one to give it. The idea is that periodically one sequence is amplified and used to replace all others, thus rapid change but apparent uniformity. Presumably the same sort of thing happens in mtDNA with high rates of change but low amounts of heteroplasmy. Someone knowledgeable please explain the mechanism to both of us. > As I understand it, the rRNA gene ITS regions are regarded as a selectively > neutral segments of DNA which can accumulate mutations over time and hence > be used for phylogenetic analysis. What I don't understand is:- if an > organism has e.g. 100 copies of its rRNA gene, each with its own ITS > regions, how come we don't find 100 different ITS sequences in each organism > we study? Or at least how can we expect them to all be the same? How can > we say "This isolate has this sequence"? If the mutations are selectively > neutral, how could one mutant sequence come to predominate? I must be > missing something fairly fundamental here. You can probably guess I'm not a > molecular person. I mean, while we're at it, what preserves microsatellite > sequences? > Look, I'm losing sleep over this, so please put me out of my misery > somebody. Give me a reference to Noddy's Beginners Guide to Molecular > Biology or something. > > Thanks, > Dave Brayford > d.brayford@cabi.org > > From owner-rapd@net.bio.net Mon Feb 20 22:00:00 1995 Path: biosci!agate!news.duke.edu!godot.cc.duq.edu!hudson.lm.com!news.pop.psu.edu!news.cac.psu.edu!news.tc.cornell.edu!travelers.mail.cornell.edu!newsstand.cit.cornell.edu!NewsWatcher!user From: bir1@cornell.edu (Bruce Reisch) Newsgroups: bionet.molbio.rapd Subject: Re: 260/280 ratios Date: Tue, 21 Feb 1995 08:47:20 -0500 Organization: Cornell University Lines: 19 Sender: bir1@cornell.edu (Verified) Distribution: world Message-ID: References: NNTP-Posting-Host: 132.236.10.52 In article , warren_lamboy@qmrelay.mail.cornell.edu ("Warren Lamboy") wrote: > Subject: Time:17:56 > OFFICE MEMO 260/280 ratios Date:13/02/1995 > > Dear netters: I have a question about 260/280 ratios for checking for > contamination of DNA with proteins (and I presume other contaminants as well). > I have read conflicting statements about what values of the ratio correspond > to "pure" DNA. I was taught that a ratio of 1.8 corresponds to pure > double-stranded DNA, and that a ratio of 2.0 represented single-stranded (I > presumed) RNA. But I have seen a number of papers lately that stated they had > great double-stranded DNA with ratios close to 2.0. Does that suggest that > the DNA was contaminated with RNA? Or was what I was taught incorrect? We > used to consider ratios between 1.6 and 1.8 pretty good DNA, with 1.8 the > maximum values possible (barring contamination). snip snip Doesn't anybody have a thoughtful response for this important question? From owner-rapd@net.bio.net Mon Feb 20 22:00:00 1995 Path: biosci!LIFSCI.SDSU.EDU!MCCLELLAND From: MCCLELLAND@LIFSCI.SDSU.EDU Newsgroups: bionet.molbio.rapd Subject: postdoc Date: 21 Feb 1995 11:34:30 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 35 Sender: daemon@net.bio.net Distribution: world Message-ID: <950221113222.20203f3d@LIFSCI.SDSU.EDU> NNTP-Posting-Host: net.bio.net Please post Postdoctoral Position DNA and RNA fingerprinting in mammalian cells. Available any time in the next year. Please submit curriculum vitae to: Michael McClelland, California Institute of Biological Research, 11099 North Torrey Pines Road, La Jolla, CA 92037. FAX 619 535 5472. References: (1) Mclelland et al., 1994. Interactions among regulators of RNA abundance characterized using RNA fingerprinting by arbitrarily primed PCR. Nucleic Acids Res. 22:4419. Ionov et al., 1993. Ubiquitous somatic mutations in simple repeated sequences reveal a new mechanism for colonic carcinogenesis. Nature, 363:558-561; Peinado et al., 1992. Isolation and characterization of allelic losses and gains in colorectal tumors by arbitrarily primed polymerase chain reaction. Proc. Natl. Acad. Sci. USA, 89:10065; Welsh et al., 1992. Arbitrarily primed PCR fingerprinting of RNA. Nucleic Acids Res. 20:4965-4970; Ralph et al., 1993. RNA fingerprinting using arbitrarily primed PCR identifies differentially expressed genes in Mink lung (Mu1Lv) cells growth arrested by transforming growth factor-beta1. Proc. Natl. Acad. Sci. USA, 90 :10710-10714; Wong, et al., 1993. Identification of differentially expressed RNA in human ovarian carcinoma cells by arbitrarily primed PCR fingerprinting of total RNAs. Int. J. Oncology 3:13-17; Wong et al., 1994. Stress-inducible gene of Salmonella typhimurium identified by arbitrarily primed PCR of RNA. Proc. Natl. Acad. Sci. U.S.A. 91: 639-643. CIBR is a not-for-profit basic molecular biology research institute From owner-rapd@net.bio.net Tue Feb 21 22:00:00 1995 Path: biosci!SASK.USASK.CA!LEES From: LEES@SASK.USASK.CA Newsgroups: bionet.molbio.rapd Subject: RAPD analysis program Date: 21 Feb 1995 22:20:01 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Anyone know how to find Image 1.55 program from FTP site? Thanks, Sun Lee Plant Biotechnology Institute National Research Council Saskatoon, Saskatchewan Canada S7N 0W9 Phone: 1 306/975-6594 Fax: 1 306/975-4839 E-mail: lees@skyfox.usask.ca From owner-rapd@net.bio.net Tue Feb 21 22:00:00 1995 Path: biosci!ISA0.ISA.UTL.PT!crismoniz From: crismoniz@ISA0.ISA.UTL.PT Newsgroups: bionet.molbio.rapd Subject: (none) Date: 22 Feb 1995 02:49:27 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: <0098C5D3.05775E20.16959@isa0.isa.utl.pt> NNTP-Posting-Host: net.bio.net I am working with plants. I would like to know if there any studies on RAPDs and tissue culture and if you think that this methodology can be used to detect somaclonal variation ... thanks From owner-rapd@net.bio.net Tue Feb 21 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: (Dave Johnston) Newsgroups: bionet.molbio.rapd Subject: Re: tempos fudge it (return of the newt) Date: 22 Feb 1995 16:30:34 -0000 Lines: 21 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3ifora$9er@mserv1.dl.ac.uk> X-POPmail-Charset: British Original-To: D.BRAYFORD%cabi.org@earn-relay.ac.uk, rapd@dl.ac.uk On 22 Feb 1995 06:37:25 -0800, "David Brayford ", IMI writes: Does this mean >all those bods merrily constructing phylogenies from rDNA sequences are as >much looking at the vagaries of DNA repair as at a ticking molecular clock? David, be very cautious about assuming molecular clock mechanisms to be valid for ANY gene system. Unless the data can be shown to fit certain criteria (namely that methods which assume a molecular clock give identical phylogenies to those that don't - if I remember correctly, this means that the data must be both additive and ultrametric!) then molecular clocks are a load of b*ll*cks as far as that gene is concerned. Certainly in schistosomes neither 18S or 28S rDNA sequences fit a clock model. DAJ David A. Johnston Research Fellow, Dept of Zoology, The Natural History Museum, Cromwell Road, South Kensington, London SW7 5DB. England (tel 071 9389297, fax 071 9388754, email daj@nhm.ac.uk) From owner-rapd@net.bio.net Tue Feb 21 22:00:00 1995 Path: biosci!cabi.org!D.BRAYFORD From: D.BRAYFORD@cabi.org ("David Brayford ", IMI) Newsgroups: bionet.molbio.rapd Subject: tempos fudge it (return of the newt) Date: 22 Feb 1995 06:37:25 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: <2F4B4BB7@msm.cgnet.com> NNTP-Posting-Host: net.bio.net Dear All I'd just like to say a big thanks to all those who responded so kindly to my outburst regarding synchronicity of ITS sequences. This means I now have a different idea to lose sleep over -- Concerted Evolution. Does this mean all those bods merrily constructing phylogenies from rDNA sequences are as much looking at the vagaries of DNA repair as at a ticking molecular clock? I can't help wondering how much DNA repair processes are open to selection and whether taxa lacking meiosis (such as many fungi) might adapt to allow more sequence variation, hence changing the apparent "clock speed". Anyway, thanks again. Dave Brayford d.brayford@cabi.org From owner-rapd@net.bio.net Tue Feb 21 22:00:00 1995 Path: biosci!esvax.dnet.dupont.com!rafalski From: rafalski@esvax.dnet.dupont.com Newsgroups: bionet.molbio.rapd Subject: RAPDs and somaclonal variation Date: 22 Feb 1995 04:57:12 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <9502221248.AA16833@esds01.es.dupont.com> NNTP-Posting-Host: net.bio.net In response to a recent question concerning RAPDs and somaclonal variation: I have seen some work (posters at the Amsterdam ISPMB congress last June) using RAPDs in an attempt to detect somaclonal variation. I am very sceptical. While not too much is known about the molecular nature of somaclonal variation, it is likely to involve a very small fraction of the genome. If so, RAPDs, which essentailly "throw darts at the genome" would be very unlikely to detect it. Recently I heard a presentation from H. Hirochika (NIAR, Tsukuba, Japan, who claimed that retrotransposons seem to increase in copy number in tissue culture, and that some somaclonal variation can be explained by retrotransposon activity. He had some retrotransposaon- directed primers that detect such variation. Maybe you should use this kind of primers instead of RAPDs for this particular application? H. Hirochiks's paper on retrotransposon-directed primers appeared in EMBO Journal , June or July 1993. Antoni Rafalski From owner-rapd@net.bio.net Tue Feb 21 22:00:00 1995 Newsgroups: bionet.molbio.rapd Path: biosci!daresbury!hgmp.mrc.ac.uk!sunsite.doc.ic.ac.uk!doc.news.pipex.net!pipex!uknet!liv!htownson From: htownson@liverpool.ac.uk (Prof H. Townson) Subject: Re: newt preserve Message-ID: Sender: news@liverpool.ac.uk (News System) Nntp-Posting-Host: uxd.liv.ac.uk Organization: The University of Liverpool X-Newsreader: TIN [version 1.2 PL2] References: <2F49F76B@msm.cgnet.com> Date: Wed, 22 Feb 1995 11:02:46 GMT Lines: 35 David Brayford ", IMI (D.BRAYFORD@cabi.org) wrote: : Can I ask a stupid question? Just don't laugh, OK. : As I understand it, the rRNA gene ITS regions are regarded as a selectively : neutral segments of DNA which can accumulate mutations over time and hence : be used for phylogenetic analysis. What I don't understand is:- if an : organism has e.g. 100 copies of its rRNA gene, each with its own ITS : regions, how come we don't find 100 different ITS sequences in each organism : we study? ... ... etc This is an important and certainly not a stupid question and has been extensively examined, particularly by Gabriel Dover. The homogenization of members of multi-gene arrays is due to DNA turnover processes and it and the related process of molecular drive is described in Dover,G.A. and Flavell, R.B.(ed.) (1982) Genome Evolution. Academic Press. The processes are examined more briefly and simply in Hoelzel, A.R. and Dover, G.A. (1991) Molecular Genetic Ecology IRL Press. Basically unequal crossing over occurs at rates greater than the base substitution rates leading to homogenization. I suggest you read the detailed accounts that deal with rates of generation of new spacer lengths etc The latter book is a good introduction to molecular approaches to the study of naturally occurring genetic variation. Hope this helps. -- -------------------------------------------------------------------------- Harold Townson | Liverpool School of Tropical Medicine htownson@liverpool.ac.uk | Pembroke Place 0151-708-9393 voice | Liverpool L3 5QA 0151-708-8733 fax | UK __________________________________________________________________________ From owner-rapd@net.bio.net Wed Feb 22 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!uunet!newstf01.news.aol.com!newsbf02.news.aol.com!not-for-mail From: dlegard@aol.com (DLegard) Newsgroups: bionet.molbio.rapd Subject: What PCR machine do you recommend Date: 23 Feb 1995 14:48:16 -0500 Organization: America Online, Inc. (1-800-827-6364) Lines: 8 Sender: root@newsbf02.news.aol.com Message-ID: <3iioq0$a47@newsbf02.news.aol.com> Reply-To: dlegard@aol.com (DLegard) NNTP-Posting-Host: newsbf02.mail.aol.com I am starting up a program to look at RAPD variation in my favorite fungus Colletotricum. I recall seeing a discussion on the merits of different PCR machines in this newsgroup but don't recall the make of the concensus choice (it wasn't P & K). If anyone has a recommendation or a copy of the previous discussion results I would appreciate it. Thanks Dan Legard University of Florida From owner-rapd@net.bio.net Wed Feb 22 22:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.nysernet.net!news.sprintlink.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!news.rediris.es!obelix.cica.es!lucano!bv1pevir From: Rafael Perez Vicente Newsgroups: bionet.molbio.rapd Subject: expensive kit from Invitrogen Date: Tue, 21 Feb 1995 13:40:25 +0100 Organization: Centro Informatico Cientifico de Andalucia Lines: 24 Message-ID: NNTP-Posting-Host: lucano.uco.es Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: bv1pevir@lucano Hi netters, Our dealer in Spain is selling the invitrogen pCR-Script SK(+) cloning kit at about 580$ per unit. That is expensive for most of us here in Spain. Could someone tell me the price of this kit in the States. It is not the first time that the Spaniard dealers increase the price without any reason but to make more money. Thanks for your support Rafael Perez Vicente Div. Fisiologia Vegetal Fac. Ciencias. Univ. Cordoba 14071-Cordoba SPAIN Phone: (57) 218610 218611 Fax: (57) 218606 From owner-rapd@net.bio.net Wed Feb 22 22:00:00 1995 Path: biosci!TEOSINTE.AGRON.MISSOURI.EDU!byrne From: byrne@TEOSINTE.AGRON.MISSOURI.EDU (Patrick Byrne) Newsgroups: bionet.molbio.rapd Subject: Journal of Quantitative Trait Loci Date: 23 Feb 1995 08:15:50 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 154 Sender: daemon@net.bio.net Distribution: world Message-ID: <199502231614.KAA07508@teosinte.agron.missouri.edu> NNTP-Posting-Host: net.bio.net ANNOUNCING THE JOURNAL OF QUANTITATIVE TRAIT LOCI The Journal of Quantitative Trait Loci (JQTL), sponsored by the Crop Science Society of America (CSSA), will provide a peer-reviewed, fully electronic forum in which articles dealing with the theory and practice of QTL analysis will be published. The publication format will facilitate links to related publications and databases, and will permit the inclusion of more complete analyses than is generally feasible in bound media. Improved publication speed, easy and inexpensive access, and flexibility should make JQTL a preferred journal for the publication of papers dealing with the analysis of the inheritance of quantitative traits. PURPOSE OF THE JOURNAL 1. JQTL will publish articles relevant to the analysis, manipulation, and use of genes modifying quantitative characters in any species. We are defining quantitative characters as those for which the phenotypic variation among genotypes is continuous and cannot be separated into discrete classes. This definition of QTL makes no assumptions regarding the number of genes controlling such characters, nor the magnitude of genetic effects. When appropriate, authors will be encouraged to include datasets upon which their analyses depend. 2. JQTL will serve as a medium for announcing, describing, and storing new software developed for QTL analysis. 3. JQTL will publish secondary analyses of primary datasets when such analyses prove novel and illuminating. 4. JQTL will publish worthy editorial commentaries and review articles as space and interest warrant. GENERAL STANDARDS Papers will be submitted either electronically or on diskette. They will consist of ASCII text, with .gif files holding images. Papers will be written in general accordance with style standards of CROP SCIENCE (Publications Handbook and Style Manual, 1988, American Society of Agronomy, Madison, WI). Papers will be submitted to the Editor, who will then request review by two Technical Editors. 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They will be asked to review the manuscript for compliance with the above criteria, to judge suitability of the article for inclusion in JQTL, and to write brief critiques of the manuscript to be returned to the author. The editors will attempt to evaluate the performance of submitted software. SUBMISSION PROTOCOL Articles may consist of text, tables, and data sets (all in ASCII format) and figures (in .gif format). Other acceptable formats may be announced in the future. There are no size limitations. Prior to submission, authors should e-mail the Editor (current address: blake@hordeum.oscs.montana.edu) to request a submission number. Files should then be renamed to include the submission number (e.g., text##.asc, fig1##.gif, fig2##.gif, tabl##.asc, data##.asc, etc.). This will avoid the problem of one submission over-writing another. Submit files via ftp to hordeum.oscs.montana.edu Login as jqtlsubm Password: your e-mail address. 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Each accepted manuscript will then be sent to CSSA headquarters for HTML formatting, and thence to the U.S. National Agricultural Library for immediate publication. JQTL will be continuously updated with new articles. JOURNAL ACCESS Beginning April 1, 1995, JQTL will be available for public on-line access from the National Agricultural Library via World Wide Web at http://probe.nalusda.gov:8000/ under the heading Newsletters, Journals, and Other Publications. No charge will be levied for publication or for journal access during 1995, although nominal fees may be assessed at a later date. JQTL will be indexed in the AGRICOLA bibliographic database and by other biological indexing services. JOURNAL ANNUAL By the end of the first year of publication we hope to have the capacity to make annual CDs of the journal available for a nominal fee. JQTL Editor: Thomas Blake, Montana State University JQTL Technical Editors: Jim Anderson, North Dakota State University Doug Bigwood, USDA, National Agricultural Library Cynthia Bottema, Waite Institute (Australia) Pat Byrne, USDA, Agricultural Research Service Rebecca Doerge, Cornell University Jon Geadelmann, Holden's Foundation Seeds, Inc. Dave Matthews, Cornell University Phil McClean, North Dakota State University Laura Oberthur, Montana State University Andrew Paterson, Texas A&M University Mark Sorrells, Cornell University CSSA Editor-in-chief: P. Stephen Baenziger, University of Nebraska CSSA Board of Directors: R.C. Shearman, President A.B. Maunder, President-Elect V.B. Cardwell, Past President R.F. Barnes, Executive Vice President From owner-rapd@net.bio.net Wed Feb 22 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!uunet!in1.uu.net!comp.vuw.ac.nz!zephyr.grace.cri.nz!Crop.cri.nz!BulmanS From: BulmanS@Crop.cri.nz (Simon Bulman) Newsgroups: bionet.molbio.rapd Subject: SSR-anchored PCR Date: Thu, 23 Feb 1995 03:59:07 GMT Organization: Crown Research Institute Lines: 9 Message-ID: NNTP-Posting-Host: 161.65.3.175 Hello, if anyone out there is using SSR-anchored PCR (note the anchored bit :-), Genomics 20, 176-), particularly for population differentiation, I'd very much like to exchange some ideas on technique and analysis. Further, can somebody out there supply me with an e-mail address for Dr. Antoni Rafalski ? Thanks, Simon Bulman bulmans@crop.cri.nz From owner-rapd@net.bio.net Thu Feb 23 22:00:00 1995 Path: biosci!ik.hist.no!BJORN From: BJORN@ik.hist.no ("Bjorn Arne Nass") Newsgroups: bionet.molbio.rapd Subject: subscription wanted Date: 24 Feb 1995 02:24:24 -0800 Organization: Institutt for Kjemi, HIST Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: Reply-To: bjorn@ik.hist.no NNTP-Posting-Host: net.bio.net Can Yuo please give me more information about this group ? Thank You ! Bjoern. Bjorn Arne Naess Sor-Trondelag College, Dep. Engeneering and Foodtechnology inst. of Chemistry Chemical-engeneering/Biotechnolgy 7005 Trondheim NORWAY tel.: + 45 73 89 64 29 // 73 89 62 00 fax.: + 45 73 89 64 73 // 73 89 62 25 Email.: Bjorn@IK.HIST.NO From owner-rapd@net.bio.net Thu Feb 23 22:00:00 1995 Newsgroups: bionet.molbio.rapd Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!caen!msunews!harbinger.cc.monash.edu.au!bunyip.cc.uq.oz.au!munnari.oz.au!newsroom.utas.edu.au!ml.csiro.au!mac-1305.ml.csiro.au!chris.bolch From: Christopher J. S. Bolch Subject: Aust Supplier for USB Message-ID: <1995Feb24.054933.8673@ml.csiro.au> X-Xxmessage-Id: X-Xxdate: Fri, 24 Feb 95 16: 52:40 GMT Sender: news@ml.csiro.au Organization: CSIRO Division of Fisheries, Hobart, Tasmania X-Useragent: Version 1.1.3 Date: Fri, 24 Feb 1995 05:49:33 GMT Lines: 9 Hi RAPD bods Everyone except the Australians can probably ignore this. Anyone got any idea who the Australian suppliers are for US Biochemicals. I want to purchase a restriction enzyme called Nsp I which is only available from USB. Thanks in advance. From owner-rapd@net.bio.net Fri Feb 24 22:00:00 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 Feb 1995 02:00:18 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 338 Sender: daemon@net.bio.net Distribution: world Message-ID: <199502251000.CAA07060@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. If your personal information has changed since you listed yourself, please send us a complete new updated form. 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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 Feb 26 22:00:00 1995 Path: biosci!agate!library.ucla.edu!csulb.edu!nic-nac.CSU.net!charnel.ecst.csuchico.edu!news.xmission.com!news.cc.utah.edu!corona!patrick From: Patrick O'Neil Newsgroups: bionet.molbio.ageing,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.gene-linkage,bionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.rapd,bionet.molbio.yeast Subject: Re: controversies & ethics Date: Sun, 26 Feb 1995 20:33:58 -0700 Organization: University Of Utah Computer Center Lines: 55 Message-ID: References: <3gk3au$pdp@rebecca.albany.edu> <3gm7u9$t5e@nntp1.u.washington.edu> NNTP-Posting-Host: corona.med.utah.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: <3gm7u9$t5e@nntp1.u.washington.edu> Xref: biosci bionet.molbio.ageing:1462 bionet.molbio.bio-matrix:561 bionet.molbio.embldatabank:459 bionet.molbio.evolution:2494 bionet.molbio.gdb:304 bionet.molbio.gene-linkage:583 bionet.molbio.genome-program:1231 bionet.molbio.hiv:937 bionet.molbio.rapd:1011 bionet.molbio.yeast:2477 On 31 Jan 1995, Jared Roach wrote: > Now one might argue that the speed of recombinant research > has two dangers: > 1) The rest of the ecosystem is not changing as fast to > modify itself so as to maintain some kind of ecological "balance." > Furthermore, scientists may be slower to understand ecological impact > than they are in developing new organisms. This is not just restricted to transgenics. Chemical companies and farmers don't want nature to catch up to pesticides too quickly (if at all) so would it be bad if DOW, for instance, came up with a pesticide that insects or fungi were extremely slow to catch up to? (Leaving the debate over the use of such chemicals aside for the moment) The whole basis of farming is one of a state of unbalance. A field made up of only one species of plant is not, itself, natural and is unbalanced. Plants being protected by human interventions from predators is unbalanced. If it was all let alone then balance would come but at the expense of food for the populous. Where and what is a good state of unbalance, then? Even organic farming requires human-induced unbalancing through the artificial increased mass of fertilizing manure, introduction of unnatural numbers of beneficial insects, etc. > 2) The human race as a whole (or national governments, or > individuals) is slow to reach consensus on ethical issues (i.e. > religion, abortion, the creation of new species, etc.) Science > should slow its pace of discovery to allow Ethics to catch up. > Some of these areas will NEVER be an area of consensus. The new species that I have seen/read about are incredibly specialized and always based on natural examples (hydrocarbon consuming bacteria). A beefalo isn't itself so odd, for instance, except in name. They are a melding of two very closely related species and like cattle, are not set up to take over the world...just dinner tables. I am no fan of the cattle industry but is such specialized living food really any worse than any domesticated food animal, bred for sloth, even temper, tender haunches, etc? In any case, the idea, "Science should slow down discovery" is disturbing. I again ask, what do you do, tell a scientist that he or she is doing too well and finding out too much? Knowledge is deadly and bad? More disturbing to me than any talk of _unthinking_ tampering with lifespan to any significant degree is the idea that one can know too much. One can learn too much. Religions tend to take that position when their particular belief system is threatened by some bit of knowledge. So, just cover your eyes and ears and pretend that what is so is NOT so? Knowledge is NEVER the problem, it is how you use it. That said, transgenics is not, in and of itself, bad unless it is done foolishly and for the wrong reasons. I presently work with transgenic mice in a cancer research lab. They are indespensible to the research. Patrick From owner-rapd@net.bio.net Sun Feb 26 22:00:00 1995 Path: biosci!GPU.SRV.UALBERTA.CA!vbailey From: vbailey@GPU.SRV.UALBERTA.CA (Vanessa Bailey) Newsgroups: bionet.molbio.rapd Subject: re: RAPD-PCR in Soil Date: 27 Feb 1995 13:16:43 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net I am doing my Ph.D in Soil Biology and Biochemistry, specifically bioremediation. A professor in microbiology suggested that I could use RAPD-PCR to "fingerprint" the microbial consortium which is degrading the contaminant. Unfortunately, I have found no account of RAPD being done in soil in the literature, and am hoping that somebody on this network will be able to help me. Thanks, Vanessa vbailey@gpu.srv.ualberta.ca From owner-rapd@net.bio.net Sun Feb 26 22:00:00 1995 Path: biosci!cabi.org!G.SADDLER From: G.SADDLER@cabi.org ("Gerry Saddler ", IMI) Newsgroups: bionet.molbio.rapd Subject: (none) Date: 27 Feb 1995 08:22:47 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 32 Sender: daemon@net.bio.net Distribution: world Message-ID: <2F51FB96@msm.cgnet.com> NNTP-Posting-Host: net.bio.net Dear All, This is a plea for help, if ever there was one! We are currently working on a project to characterise/identify/detect phytopathogenic coryneform bacteria (no mean feat!) using amongst other things molecular fingerprinting techniques. The methods we have tried and are currently banging our heads against a brick wall with are; PFGE, and PCR-fingerprinting techniques such as RAPD's and using repeat sequence primers such as ERICs, BOX & REP. Most of our limited experience with all of these methods has been on Gram negative bacteria and not without problems! However, this work has been easy compared with the coryneform work. We know we can get all of the above to work on these bacteria, it all boils down to reproducibility; when its good its very, very good but when its bad its....... We've tried laborious/exhaustive DNA extractions, carefully monitoring DNA concentration, ensuring the integrity etc. of our reagent stocks, but nothing seems to get over the reproducibility problem. Our latest ploy is to hang rosary beeds on the PCR machine and play Elvis Costello very loud, but this has met with only limited success. If there is anyone out there who has experienced similar problems we would like to hear from you, believe me! From owner-rapd@net.bio.net Mon Feb 27 22:00:00 1995 Path: biosci!BIOLOGY.UTAH.EDU!jevans From: jevans@BIOLOGY.UTAH.EDU Newsgroups: bionet.molbio.rapd Subject: Re: Microsatellite polymorphisms Date: 27 Feb 1995 21:42:00 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 81 Sender: daemon@net.bio.net Distribution: world Message-ID: <199502280541.WAA00390@fcom.cc.utah.edu> NNTP-Posting-Host: net.bio.net ok, i'll take a stab at the questions posed by Robert Butcher, please pardon this note if you feel this should be strictly a RAPD forum: > (1) At what length (either number of nucleotides in total or >the number of nucleotide repeat units) does a repetitive sequence become >definable as a microsatellite? Thus, for example {with respect to one strand >only} (dGT)60 or (dCAC)40 are clearly so, (dGT)10 and (dCAC)8 probably so, >but what about (dGT)6 or (dCAC)4? Likewise for mononucleotide (eg (dC)n), >tetranucleotide etc repeat units! The consensus seems to be eight to ten repeats for dinucleotides, 6+ for tri's and tetra's. While repeats of (CA)4 or (CA)6 might deserve to be called "satellites" since they are anomalous stretches, a more functional definition "microsatellites are inherently unstable stretches consisting tandem repeats of one to six nucleotides" seems more useful. > > (2) With reference to the generation of microsatellite locus(i) >length polymorphism:- are there any studies or other evidence upon the >rate (probability) of generation of length polymorphism of any locus with >respect to >(a) the original microsatellite length? (i.e does a larger >microsatellite stand a greater chance of slippage and thus show more rapid >polymorphism development within the constraints allowed) The number of tandem repeats composing a microsatellite is often linked to variability (Weber, Genomics 7, 524+). In the ants for which I have cloned microsatellites, loci whose clone sequences showed 30 or more CA repeats turned out to be most variable (30+ alleles). 15 repeats for a CA-repeat locus seems to be a good lower bound for highly polymorhic (Htz. > 0.8) loci, but this may be somewhat taxon-dependent. In the human genetic realm, longer repeats are consistently the ones that give rise to highly variable disease alleles (Sutherland and Richards, J. Med. Genet. 30,978+, Nelson and Warren, Nature Genetics 4, 107+). Specifically, mutations increase drastically when the repeat number reaches a threshold (models to explain this threshold are discussed and proposed in Eichler et al, Nature Gen. 8, 88+) > (b) sequences flanking the microsatellite Strand et al (Nature 365,274+) showed an interesting difference in mutation rates between repeats inserted into a plasmid vector vs. yeast chromosomes. In strains of each which also contained a broken mismatch repair gene (mutation pms1), the plasmid repeats mutated at a much higher rate, perhaps implying that sequences flanking the chromosome-inserted locus inhibit mutation. Other studies (e.g., Ionov et al., Natuure 363,558+) indicate that global (trans-acting) factors (as oposed to flanking sequence) are most important for predicting mutation rates. There is good evidence that interspersed non-repetitive DNA can lower mutation rates; "imperfect" repeats (e.g., (CA)5(AT)(CA)5 vs. (CA)10 ) are more stable (Weber, Genomics 7, 524+, Eichler et al, Nature Gen. 8, 88+). > (c) the microsatellite core repeat unit (i.e. will a say (gt)n >alter more frequently than a say (gc) repeat, all other conditions >being essentially identical? Empirically, GT repeats seem to mutate at a faster rate, since that is presumably what drives the high frequency of GT vs. GC microsatellites. It's not as simple as just having a purine/pyrimidine pair, though, since AG repeats are common in plants (Condit and Hubbell, Genome 34,66+). hope this helps a bit Jay E Department of Biology University of Utah Salt Lake City, UT 84112 ph: (801) 581-8478 FAX (801) 581-4668 From owner-rapd@net.bio.net Mon Feb 27 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!gatech!news-feed-1.peachnet.edu!usenet.eel.ufl.edu!gmi!msunews!harbinger.cc.monash.edu.au!sol.ccs.deakin.edu.au!deakin.edu.au!drierac From: drierac@deakin.edu.au (Chris Driver) Newsgroups: bionet.molbio.rapd Subject: Human DNA Date: Tue, 28 Feb 1995 16:02:18 Organization: Deakin University Lines: 9 Message-ID: NNTP-Posting-Host: pc-rbp161.sci.deakin.edu.au X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Has anyone done RAPDS on human DNA. What primer(s) did you use? Chris Driver Chris Driver, Ph D School of Biology and Chemistry, Rusden Campus Deakin University 662 Blackburn Rd Clayton, VIC, 3168 AUSTRALIA From owner-rapd@net.bio.net Mon Feb 27 22:00:00 1995 Path: biosci!esvax.dnet.dupont.com!rafalski From: rafalski@esvax.dnet.dupont.com Newsgroups: bionet.molbio.rapd Subject: Human RAPD Date: 28 Feb 1995 04:54:29 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <9502281249.AA19825@esds01.es.dupont.com> NNTP-Posting-Host: net.bio.net In response to a question by Chris Driver about RAPDs on human DNA. Yes, we did that long time ago - I believe there are two lanes of human RAPD in our first RAPD paper (Nucleic Acids Research, 18 (1990) 6531-6535, Williams et al. The primer used was acggtacact, but it does not matter - the essence of the RAPD method is to use many primers of arbitrary sequence - you can buy them as kits of ten from Operon (Operon Technologies, Inc. Alameda, CA, USA (510) 865-8644 fax (510) 865-5255 ). Mike McClelland and his colleagues did a lot of AP-PCR on human DNA -also see work by Manuel Perucho on detection of large deletions in colon carcinomas. Antoni Rafalski From owner-rapd@net.bio.net Tue Feb 28 22:00:00 1995 Path: biosci!CHARLY.UCDAVIS.EDU!cushwa From: cushwa@CHARLY.UCDAVIS.EDU Newsgroups: bionet.molbio.rapd Subject: quantifying similarity in RAPD fingerprints Date: 1 Mar 1995 08:15:43 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 30 Sender: daemon@net.bio.net Distribution: world Message-ID: <0098CB34.E591DF60.9924@charly.ucdavis.edu> NNTP-Posting-Host: net.bio.net We have screened a group of parents and identified a number of RAPD polymorphisms that segregate in their respective offspring. Several of the parents share a common father while others are unrelated. In a number of cases, the unrelated parents have what appears to be a common polymorphism. Since we do not have a common relative to show the origin of the polymorphism, we want to provide some quantitative data to support our assumption that the same RAPD locus is being scored in all families. The most obvious source of evidence for each polymorphism is the high degree of similarity in the parental RAPD fingerprints. I am aware of one statistic used to quantifying the similarity (or alternatively the difference) called the Average Percent Difference (APD). This value is obtained by first calculating the Percentage Difference (PD) by making a series of pairwise comparisons (PD =Nab/Na + Nb x 100, where Nab is the number of fragments that differ between two individuals for a single primer, Na is the number of fragments scored in individual "a", and Nb is the number of fragments scored in individual "b". The APD value is C obtained by the following: 1/C< PD where C is the number of comparisons < i i=1 (Sorry about the poor summation sign!) I would appreciate any suggestions, comments, and/or references. We have too many polymorphisms to check by doing Southerns for each one. Thanks, Willy Cushwa wtcushwa@ucdavis.edu From owner-rapd@net.bio.net Tue Feb 28 22:00:00 1995 Path: biosci!ASRR.ARSUSDA.GOV!abartlet From: abartlet@ASRR.ARSUSDA.GOV ("Alan C. Bartlett") Newsgroups: bionet.molbio.rapd Subject: Re: Human DNA Date: 1 Mar 1995 03:27:31 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net In a very small study, we got good banding patterns with Operon A02, A11, and A15 tenmers. Alan C. Bartlett "GENES-R-US" "ALTERATIONS AVAILABLE!^" "^some restrictions may apply:)" From owner-rapd@net.bio.net Tue Feb 28 22:00:00 1995 Newsgroups: bionet.molbio.rapd Path: biosci!rutgers!uwm.edu!uwvax!sinetnews!news.u-tokyo.ac.jp!news.tisn.ad.jp!riksun!postman!mbs405.riken.go.jp!user From: cgrunau@rkna50.riken.go.jp (Christoph Grunau) Subject: RFLP analysis program? Content-Type: text/plain; charset=ISO-8859-1 Message-ID: Followup-To: bionet.molbio.rapd Sender: news@postman.riken.go.jp (News Administrator) Nntp-Posting-Host: mbs405 Content-Transfer-Encoding: 8bit Organization: RIKEN Tokyo Mime-Version: 1.0 Date: Wed, 1 Mar 1995 14:12:24 GMT Lines: 7 Hi Netters, does anyone know a program for the analysis of RFLPs? Thanks for answering! Christoph Grunau