From owner-rapd@net.bio.net Sun Dec 01 22:00:00 1996 Path: biosci!MAILSERV.CUHK.EDU.HK!b086712 From: b086712@MAILSERV.CUHK.EDU.HK (PC Shaw) Newsgroups: bionet.molbio.rapd Subject: Rapd data analysis Date: 2 Dec 1996 02:54:19 -0800 Organization: CUHK Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <199612021054.SAA20496@hpg50a.csc.cuhk.edu.hk> NNTP-Posting-Host: net.bio.net I am a RAPD user. I encounter a problem in analysis the RAPD data for phylogenetic studies. The similarity indexes ( the ratio between the common bands shared in two samples and the total number of bands of the two samples) from different primers show different results. Some primers show that they are very similar while other show they are not. So What should I do ? How many primers should be tried in order to give a confident result ? Could anyone solve my problem, please send to s941800@mailserv.cuhk.hk Thank you very much! K.Ngan From owner-rapd@net.bio.net Sun Dec 01 22:00:00 1996 Path: biosci!EMUVAX.EMICH.EDU!bio_hannan From: bio_hannan@EMUVAX.EMICH.EDU (Gary Hannan) Newsgroups: bionet.molbio.rapd Subject: Re: Rapd data analysis Date: 2 Dec 1996 06:42:38 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 26 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <199612021054.SAA20496@hpg50a.csc.cuhk.edu.hk> NNTP-Posting-Host: net.bio.net >I am a RAPD user. I encounter a problem in analysis the RAPD data for >phylogenetic studies. The similarity indexes ( the ratio between the >common bands shared in two samples and the total number of bands of >the two samples) from different primers show different results. Some >primers show that they are very similar while other show they are not. So >What should I do ? How many primers should be tried in order to give a >confident result ? > >Could anyone solve my problem, please send to s941800@mailserv.cuhk.hk > >Thank you very much! > >K.Ngan I believe that RAPD band data are inappropriate for phylogenetic analysis, regardless of the method used to analyze the data. The fatal problem with RAPD data is the serious issue concerning homology. There is no way to establish the homology of bands without (at least) performing southerns of all bands used, and in all taxa studied. An even this is only a rough guide to homology- small insertions/deletions/point mutations could go undetected. We have already seen in the literature examples of apparently identical bands being non-homologous using southerns. Gary Hannan From owner-rapd@net.bio.net Sun Dec 01 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: Louis van de Zande Newsgroups: bionet.molbio.rapd Subject: Re: Rapd data analysis Date: 2 Dec 1996 15:06:39 -0000 Organization: Department of Biology RuG Lines: 23 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <57ur9v$3rc@mserv1.dl.ac.uk> Reply-To: L.P.W.G.M.van.de.Zande@biol.RUG.NL Original-To: rapd@dl.ac.UK > I am a RAPD user. I encounter a problem in analysis the RAPD data for > phylogenetic studies. The similarity indexes ( the ratio between the > common bands shared in two samples and the total number of bands of > the two samples) from different primers show different results. Some > primers show that they are very similar while other show they are not. So > What should I do ? How many primers should be tried in order to give a > confident result ? > > Could anyone solve my problem, please send to s941800@mailserv.cuhk.hk > > Thank you very much! > > K.Ngan > Stop using RAPD for phylogenetic analysis (unless you have very closely related species). They will not give you sound quantitative data. See: Journal of Evolutionary Biology 8, 645-656, 1995. Louis van de Zande From owner-rapd@net.bio.net Sun Dec 01 22:00:00 1996 Path: biosci!esvax.dnet.dupont.com!rafalski From: rafalski@esvax.dnet.dupont.com (Antoni Rafalski) Newsgroups: bionet.molbio.rapd Subject: RAPDs fo phylogenetic analysis Date: 2 Dec 1996 08:39:24 -0800 Organization: DuPont Co. Agricultural Biotechnology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <32A2C02A.53F4@esvax.dnet.dupont.com> Reply-To: rafalski@esvax.dnet.dupont.com NNTP-Posting-Host: net.bio.net Regarding message by Gary Hannan: There are several examples in the literature of successful use of RAPDs for phylogenetic analysis (for example Tibayrenc, M., Neubauer, K., Barnabe, C., Guerrini, F., Skarecky, D., Ayala, F.J. Genetic characterization of six parazitic protozoa: Parity between random-primer DNA typing and multilocus enzyme electrophoresis PNAS 1993 90: 1335-1339). Of course, the method is more appropriate for relatively closely realted individuals. Non-homologous similar-sized bands could pose a problem, however, they are usually in minority and contribute to some noise in the data, the more polymorphic bands you analyse the better off you are. Methods exist to confirm homology of the bands, if deemed necessary (for example Williams et al. Methods in Enzymology 218(1993) 704-740). Classical methods of phylogenetic analysis, of course, suffer from similar problems: something that looks similar is not always homologous (for example a phenotypic characteristic that may have evolved independently) To answer the originally asked question, the more polymoprhic bands you analyze the better it is. Try to analyze the data after collecting 50, 100, 150 polymorphic bands and see if your results are consistent. Antoni Rafalski From owner-rapd@net.bio.net Sun Dec 01 22:00:00 1996 Path: biosci!EM.AGR.CA!vincentd From: vincentd@EM.AGR.CA (Daniel Vincent) Newsgroups: bionet.molbio.rapd Subject: Inhibitor of Taq polymerase Date: 2 Dec 1996 11:16:40 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Last year, someone wrote that vitamin E used as a stabilizing agent in some mineral and paraffin oil inhibits Taq polymerase. If that person recognizes him/herself, please write me back. I would like to have more information. Thanks. From owner-rapd@net.bio.net Mon Dec 02 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: Roland Koelliker Newsgroups: bionet.molbio.rapd Subject: Genetic variability in 4n grasses Date: 3 Dec 1996 12:08:46 -0000 Lines: 19 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <58158e$mrt@mserv1.dl.ac.uk> X-Sender: rkoellik@patho1 content-length: 664 Original-To: rapd@dl.ac.uk Dear netters I'm working on genetic variability of meadow fescue (2n) using RAPD markers. For comparison I'd like to investigate some Lolium perenne cultivars. Since most of these cultivars are 4n I wonder if I ran in difficulties comparing data from meadow fescue with the one of 4n Lolium perenne. What do you think about that? Is there any literature to this subject? Thank you for your help. Roland Koelliker Swiss Fed Inst Technol Plant Sciences ETH-Zentrum, LFW-C47 CH-8092 Zurich Tel ++41-1-632 3888 Fax ++41-1-632 1153 e-mail: koelliker@ipw.agrl.ethz.ch From owner-rapd@net.bio.net Mon Dec 02 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.erols.net!feed1.news.erols.com!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!cpk-news-feed1.bbnplanet.com!ox.mc.edu!usenet From: Robert Hamilton Newsgroups: bionet.molbio.rapd Subject: Re: Rapd data analysis Date: 3 Dec 1996 23:09:07 GMT Organization: Mississippi College Lines: 15 Message-ID: <582buj$t3f@ox.mc.edu> References: NNTP-Posting-Host: mobo.mc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) Homology is a >sticky issue, and even the same-sized fragment does not necessarily mean >the fragments are homologous. > >Gary Hannan > > > This is true. SIMILARITY is NEVER a good measure of homolgy. Just because two fragments DON'T hybridize in a Southern does not mean that they are NOT homologous, particularly in closely realted species. An assessment of homology requires more knowledge than sequence similarity provides, be it via RAPDs or actual sequence data. From owner-rapd@net.bio.net Mon Dec 02 22:00:00 1996 Path: biosci!EMUVAX.EMICH.EDU!bio_hannan From: bio_hannan@EMUVAX.EMICH.EDU (Gary Hannan) Newsgroups: bionet.molbio.rapd Subject: Re: Rapd data analysis Date: 2 Dec 1996 16:35:32 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 51 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net >Dear Gary, >I'm interested by your reply, I wonder if I could trouble you to dig out >some of the references you refer to. I've only seen one so far and >wasn't quite happy with the methodoloy used. However I did have a long >chat with someone at a conference recently who left me pretty convinced that >her rapd bands were not homologous. Still, I'm baffled - why should, >non-homologous bands in a fingerprint be, quite coincidentally, >the same size?. It keeps me awake at night, not least because I've just >spent several months generating rapd fingerprints with a view to making >phylogenetic inferences. > >Yours sleeplessly, >Alastair > >: *************************************************************************** >: Alastair Hamilton | **. .***. .***. .***. . >: Institute of Aquaculture | | | * * | | | * | | | * * | | | * | >: University of Stirling | | | | * * | | | * * | | | * * | | | * * >: Stirling | * | | | * | | | * * | | | * | | | * >: FK9 4LA | '***' '***' '***' '***' >: >: Tel: 01786 467878 X7919 Fax: 01786 472133 > > *************************************************************************** > > Quiros, et al. 1995. Analysis of a set of RAPD markers by hybridization sequencing in Brassica: a note of caution. Plant Cell Rep. 14:630-634. Ayliffe, et al. 1994. Heteroduplex molecules formed between allelic sequences cause nonparental RAPD bands. Nucleic Acids Res. 22:1632-1636. Clark & Lanigan. 1993. Prospects for estimating nucleotide divergence with RAPDs. Mol. Biol. Evol. 10:1096-1111. My question in response to your homology question would be: why should same (or undetectably different size) bands in a fingerprint be, quite conicidentally, homologous? or, why should two bands that are similar enough in size to run at nearly the same rate (at least close enough to not be judged as different sizes) be assuemd to _be_ homologous? Homology is a sticky issue, and even the same-sized fragment does not necessarily mean the fragments are homologous. I just think RAPDs have a place as a tool, but phylogeny reconstruction is a very risky application for it. Gary Hannan From owner-rapd@net.bio.net Tue Dec 03 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.erols.net!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!uunet!in3.uu.net!192.89.123.24!nntp.inet.fi!news.funet.fi!news.helsinki.fi!news From: Kari.Kammiovirta@Helsinki.Fi (Kari Kammiovirta) Newsgroups: bionet.molbio.rapd Subject: Re: Rapd data analysis Date: 4 Dec 1996 14:29:44 GMT Organization: Helsingin Yliopisto Lines: 29 Distribution: world Message-ID: <5841so$ckc@oravannahka.Helsinki.FI> References: <199612021054.SAA20496@hpg50a.csc.cuhk.edu.hk> NNTP-Posting-Host: mmkab-06512.pc.helsinki.fi Mime-Version: 1.0 X-Newsreader: WinVN 0.93.14 In article <199612021054.SAA20496@hpg50a.csc.cuhk.edu.hk>, b086712@MAILSERV.CUHK.EDU.HK says... > >I am a RAPD user. I encounter a problem in analysis the RAPD data for >phylogenetic studies. The similarity indexes ( the ratio between the >common bands shared in two samples and the total number of bands of >the two samples) from different primers show different results. Some >primers show that they are very similar while other show they are not. So >What should I do ? How many primers should be tried in order to give a >confident result ? > >Could anyone solve my problem, please send to s941800@mailserv.cuhk.hk > >Thank you very much! > >K.Ngan > Hi, You don't tell are you trying to investigate among one species or between. Among species I have heard someone said something about 10-20 primers is enough. After that dendrograms don't change anymore. Between species you should try something else, like microsatellites, because the checking of the bands is too enormous task. Good luck, Kari From owner-rapd@net.bio.net Tue Dec 03 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!news-peer.gsl.net!news.gsl.net!news-penn.gsl.net!news.gsl.net!news.NetVision.net.il!news From: Martin Sanders Newsgroups: bionet.molbio.rapd Subject: FREE pH Measurement booklet Date: 4 Dec 1996 17:58:45 GMT Organization: NetVision LTD. Lines: 8 Message-ID: <584e4l$n4d@news.NetVision.net.il> NNTP-Posting-Host: ts002p12.pop2a.netvision.net.il Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.2N (Windows; I; 16bit) A free pH booklet is available which contains valuable information on basic pH measurement theory, pH measurement techniques, selecting the proper pH electrode for a particular application, and a pH troubleshooting guide. The booklet is available from Lazar Research Labs. Inc. by emailing service@lazarlab.com or faxing 1-213-931-1434. The booklet can also be obtained from the Lazar web site at http://www.lazarlab.com From owner-rapd@net.bio.net Wed Dec 04 22:00:00 1996 Path: biosci!MVET.UNIZAR.ES!pcatalan From: pcatalan@MVET.UNIZAR.ES (PILAR CATALAN RODRIGUEZ) Newsgroups: bionet.molbio.rapd Subject: micro-sat Dioscoriaceae Date: 5 Dec 1996 02:09:28 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <961205.110843.45665@mvet.unizar.es> NNTP-Posting-Host: net.bio.net Dear Sir/Madam, I am interested in getting information on microsatellite of species of the plant family Dioscoriaceae. Any help on primers' design, efficiency, and obtained results would be very appreciate. Yours faithfully, Pilar Catalan Dr. Pilar Catalan Department of Agriculture University of Zaragoza (Spain) From owner-rapd@net.bio.net Thu Dec 05 22:00:00 1996 Path: biosci!rutgers!uwm.edu!www.nntp.primenet.com!nntp.primenet.com!feed1.news.erols.com!worldnet.att.net!uunet!in3.uu.net!132.205.106.4!newsflash.concordia.ca!feed.umontreal.ca!alize.ERE.UMontreal.CA!landryp From: landryp@ERE.UMontreal.CA (Landry Pierre-Alexandre) Newsgroups: bionet.molbio.rapd Subject: Re: Rapd data analysis Date: 6 Dec 96 15:07:57 GMT Organization: Universite de Montreal Lines: 37 Distribution: world Message-ID: References: <199612021054.SAA20496@hpg50a.csc.cuhk.edu.hk> NNTP-Posting-Host: alize.ere.umontreal.ca b086712@MAILSERV.CUHK.EDU.HK (PC Shaw) writes: >I am a RAPD user. I encounter a problem in analysis the RAPD data for >phylogenetic studies. The similarity indexes ( the ratio between the >common bands shared in two samples and the total number of bands of >the two samples) from different primers show different results. Some >primers show that they are very similar while other show they are not. So >What should I do ? How many primers should be tried in order to give a >confident result ? >Could anyone solve my problem, please send to s941800@mailserv.cuhk.hk >Thank you very much! >K.Ngan The use of RAPD bands in phylogenetic studies raises many questions. The choice of the similarity index is critical. I have worked with RAPD distance to reconstruct phylogenies for the last 8 months. Basically, I found that relationships among closely-related taxa are usually correctly recovered (i.e. below the level of the family), but that over this taxonomical limit the results become unreliable. For the number of primers to use, I think that it depends of the specimens you are comparing. I would suggest to make a little bootstrap among the primers you have used, and to verify the stability of the calculated distances for an increasing number of primers. When your estimates become stable (you can assess that rapidly by looking at it graphically), you can consider that the addition of new information will not change the results. For my part, I saw that 12 primers were sufficient. Anyways, I have submitted a paper comparing 4 different similarity indexes (JAccard, Dice, Russel & Rao and simple matching) with increasing number of primers, in an experimental design including specimens of increasing phylogenetic distances. It was sent to Zoologica scripta about 7 weeks ago. Ax From owner-rapd@net.bio.net Thu Dec 12 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!news.sprintlink.net!news-peer.sprintlink.net!worldnet.att.net!uunet!in3.uu.net!136.142.185.26!newsfeed.pitt.edu!newsflash.concordia.ca!feed.umontreal.ca!lagrande.IRO.UMontreal.CA!lemieuxs From: lemieuxs@IRO.UMontreal.CA (Sebastien Lemieux) Newsgroups: bionet.molbio.rapd Subject: RAPDs for phylogenetic analysis... Date: 12 Dec 1996 21:35:54 GMT Organization: Universite de Montreal Lines: 11 Distribution: world Message-ID: <58ptrq$54a@epervier.CC.UMontreal.CA> NNTP-Posting-Host: lagrande.iro.umontreal.ca X-Newsreader: TIN [version 1.2 PL2] Hi all, I've been listening to the recent discussion about the analysis of RADP band pattern for phylogeny reconstruction and I've been wondering if any one has ever summarized the major arguments against the use of RAPD for phylogeny reconstruction? ------------------ Sebastien Lemieux, Microbio/CS ------------------- Breaking the Second Half of the Genetic Code ctggaagggt taatttactc ccataaaaga gcagaaatcc tggatctttg ggtgtataac From owner-rapd@net.bio.net Thu Dec 12 22:00:00 1996 Path: biosci!BRADLEY.BRADLEY.EDU!rrs From: rrs@BRADLEY.BRADLEY.EDU (Robert Stephens) Newsgroups: bionet.molbio.rapd Subject: Re: RAPDs for phylogenetic analysis... Date: 13 Dec 1996 07:33:06 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 24 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <58ptrq$54a@epervier.CC.UMontreal.CA> NNTP-Posting-Host: net.bio.net I believe there was a paper in Cladistics within the last several issues. rrs@bradley.bradley.edu Robert Rhea Stephens Biology Department Bradley University Peoria, IL 61625 On 12 Dec 1996, Sebastien Lemieux wrote: > Hi all, > > I've been listening to the recent discussion about the analysis of > RADP band pattern for phylogeny reconstruction and I've been wondering > if any one has ever summarized the major arguments against the use of > RAPD for phylogeny reconstruction? > > ------------------ Sebastien Lemieux, Microbio/CS ------------------- > Breaking the Second Half of the Genetic Code > > ctggaagggt taatttactc ccataaaaga gcagaaatcc tggatctttg ggtgtataac > > From owner-rapd@net.bio.net Thu Dec 12 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!www.nntp.primenet.com!nntp.primenet.com!news.bbnplanet.com!su-news-hub1.bbnplanet.com!arclight.uoregon.edu!news.uoregon.edu!newsfeed.orst.edu!news.orst.edu!sslab.FSL.ORST.EDU!krutovsk From: krutovsk@fsl.orst.edu (Konstantin Krutovskii) Newsgroups: bionet.molbio.rapd Subject: Faculty Research Assistant/Plant Molecular Geneticist Date: Wed, 11 Dec 1996 23:05:50 Organization: Forestry Sciences Lab Lines: 102 Message-ID: NNTP-Posting-Host: sslab.fsl.orst.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Position Number: 002-825 Faculty Research Assistant/Research Associate, Plant Molecular Genetics Location: Department of Forest Science, Oregon State University, Corvallis, OR Date Available: March 1, 1997 Closing Date: January 13, 1997 Position Responsibilities: We seek a molecular geneticist to work as part of the Tree Genetic Engineering Research Cooperative (TGERC) at Oregon State University. The TGERC is a consortium supported by 13 Members, mostly forest industries, that are seeking improved means for genetic manipulation of poplar trees. The applicant's primary responsibility in the Coop will be production of novel plasmid constructs to be used in Agrobacterium transformation, and analysis of the transgenic trees produced. They will work closely with other TGERC staff doing tissue culture, transformation, and gene isolation. The constructs will be composed primarily of floral homeotic genes intended for induction of sexual sterility; however, they will also work with other genes relevant to ongoing Cooperative projects on insect, disease, and herbicide resistance. Specifically, responsibilities will include: 1. Development of strategies for producing binary constructs with various genes for Agrobacterium transformation of poplar. 2. Configuration of genes and plasmid vectors, verifying structure/sequence, and transformation into Agrobacterium strains. 3. Analysis of transgenic plants for gene incorporation, expression, and delivery of desired traits. 5. Supervision of students, technicians, and other workers to help carry out laboratory studies. 6. Participation in writing Coop reports and publications for scientific journals. 7. Effective oral communication of results at annual Coop meeting and other scientific forums. 8. Collaboration with Coop staff to write grants to obtain supplemental funding for research. Education and experience: A B.S. degree in molecular genetics or a related field, and at least two years of experience with recombinant DNA manipulation, are essential. Knowledge of plant molecular biology and experience in plant transformation techniques are desirable. Experience and demonstrated competence in the following areas are particularly important: 1. Advanced recombinant DNA manipulation of plasmid vectors. 2. Molecular analyses, including DNA sequencing, PCR, and Southern, northern, and western blots. 3. Written and oral communication. 4. Collaboration with colleagues, subordinates, and superiors. 5. Long- and short-term organization and planning of work. Employment conditions: The job will be filled at the rank of either Research Assistant (B.S., M.S., or Ph.D.) or Research Associate (Ph.D.), depending upon career track of candidate, in the Department of Forest Science at Oregon State University. We are also open to the applicant taking a more scientific role in the work, as would Ph.D.s in a Research Associate position (e.g., writing papers for publication), or a more technical role, as would most with only a B.S. (limited writing, mostly directed lab work). The appointment is a full-time, 12-month, fixed-term position; reappointment is at the discretion of the Dean. The employee will report directly to Cooperative Director. The salary will be in the range of $24,000 to $32,004/year, depending on qualifications. Medical, dental, and life insurance plans are available. To apply: Send a letter of application describing your qualifications and interests in the position, a resume, transcripts, and the names, email addresses, and fax numbers of four references by January 13, 1997 to Sandra Lewis, Office Manager, Dept. of Forest Science, 020 Forestry Sciences Laboratory, Oregon State University, Corvallis, OR 97331-7501. For more information contact Prof. Steve Strauss, phone 541/737-6578, email strauss@FSL.orst.edu, fax 541/737-1393. OREGON STATE UNIVERSITY IS AN AFFIRMATIVE ACTION/EQUAL OPPORTUNITY EMPLOYER AND HAS A POLICY OF BEING RESPONSIVE TO THE NEEDS OF DUAL-CAREER COUPLES. From owner-rapd@net.bio.net Mon Dec 16 22:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.rapd Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 17 Dec 1996 02:00:48 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199612171000.CAA23520@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. 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However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-rapd@net.bio.net Tue Dec 17 22:00:00 1996 Path: biosci!rutgers!gatech!csulb.edu!hammer.uoregon.edu!arclight.uoregon.edu!news.uoregon.edu!newsfeed.orst.edu!news.orst.edu!gus.FSL.ORST.EDU!krutovsk From: krutovsk@fsl.orst.edu (Konstantin Krutovskii) Newsgroups: bionet.molbio.rapd Subject: GRADUATE ASSISTANTSHIPS - PLANT/TREE MOLECULAR GENETICS Date: Tue, 17 Dec 1996 21:16:12 Organization: Forestry Sciences Lab Lines: 44 Message-ID: NNTP-Posting-Host: gus.fsl.orst.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] GRADUATE ASSISTANTSHIPS - PLANT/TREE MOLECULAR GENETICS Two Graduate Research Assistantships are available in the Department of Forest Science at Oregon State University beginning July 1997. Students must apply and be accepted into either the Department of Forest Science, the Molecular and Cellular Biology Program, or the Genetics Program at OSU. Doctoral students are preferred, but outstanding students who lack a Masters are also encouraged to apply. Students should have excellent grades and GRE scores; strong course and/or research experience in molecular genetics; and demonstrated ability to write and speak English well. Three to five years of half-time support, and tuition remission, are available subject to adequate performance in research and coursework. Students may work on a variety of topics related to gene identification, genetic engineering, and genome mapping. Most work in the laboratory deals with poplars and Douglas-fir. Students may develop other areas for research, however, current topics of interest include: - Isolation and manipulation of floral homeotic genes for engineering of reproductive development -Effects of matrix attachment regions on gene silencing in transgenic poplars -Population genetic studies of gene diversity and gene flow using microsatellite markers -Genetic engineering of systems for inducible sterility/fertility -Molecular engineering of genotype independent transformation systems -Ecophysiological consequences of genetic engineering for lignin modification -Development of microsatellite marker-maps and use for QTL analysis For information or an application form (specify department), contact Steve Strauss, Dept. of Forest Science, Oregon State University, Corvallis, OR 97331-7501, fax 541 737 1393, phone -6578, strauss@FSL.orst.edu From owner-rapd@net.bio.net Sun Dec 22 22:00:00 1996 Path: biosci!rutgers!news.sgi.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!newsfeed.internetmci.com!masternews.telia.net!newssrv.ita.tip.net!news.keyworld.net!news From: Kenneth Briffa Newsgroups: bionet.molbio.yeast,bionet.molbio.rapd Subject: Method of DNA extraction from yeast Date: Mon, 23 Dec 1996 23:17:28 -0800 Organization: ESI, Malta. Lines: 9 Message-ID: <32BF8388.19C3@keyworld.net> Reply-To: kennbrif@keyworld.net NNTP-Posting-Host: ppp40.keyworld.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win16; I) Xref: biosci bionet.molbio.yeast:6285 bionet.molbio.rapd:1760 Hello, I'm an undergraduate preparing my dissertation project. The project involves RAPD from brewer's yeast. I've been trying to extract the DNA from the yeasts using benzyl chloride but the yield is not good enough. Does anyone know any method to extract the DNA from yeasts without using any enzymes? Cheers, Kenneth Briffa University of Malta From owner-rapd@net.bio.net Thu Dec 26 22:00:00 1996 Path: biosci!rutgers!cnn.Princeton.EDU!udel-eecis!gatech!csulb.edu!hammer.uoregon.edu!arclight.uoregon.edu!news.uoregon.edu!newsfeed.orst.edu!news.orst.edu!gus.FSL.ORST.EDU!krutovsk From: krutovsk@fsl.orst.edu (Konstantin Krutovskii) Newsgroups: bionet.molbio.rapd Subject: GRADUATE ASSISTANTSHIPS - PLANT/TREE MOLECULAR GENETICS Date: Tue, 17 Dec 1996 21:16:12 Organization: Forestry Sciences Lab Lines: 44 Message-ID: NNTP-Posting-Host: gus.fsl.orst.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] GRADUATE ASSISTANTSHIPS - PLANT/TREE MOLECULAR GENETICS Two Graduate Research Assistantships are available in the Department of Forest Science at Oregon State University beginning July 1997. Students must apply and be accepted into either the Department of Forest Science, the Molecular and Cellular Biology Program, or the Genetics Program at OSU. Doctoral students are preferred, but outstanding students who lack a Masters are also encouraged to apply. Students should have excellent grades and GRE scores; strong course and/or research experience in molecular genetics; and demonstrated ability to write and speak English well. Three to five years of half-time support, and tuition remission, are available subject to adequate performance in research and coursework. Students may work on a variety of topics related to gene identification, genetic engineering, and genome mapping. Most work in the laboratory deals with poplars and Douglas-fir. Students may develop other areas for research, however, current topics of interest include: - Isolation and manipulation of floral homeotic genes for engineering of reproductive development -Effects of matrix attachment regions on gene silencing in transgenic poplars -Population genetic studies of gene diversity and gene flow using microsatellite markers -Genetic engineering of systems for inducible sterility/fertility -Molecular engineering of genotype independent transformation systems -Ecophysiological consequences of genetic engineering for lignin modification -Development of microsatellite marker-maps and use for QTL analysis For information or an application form (specify department), contact Steve Strauss, Dept. of Forest Science, Oregon State University, Corvallis, OR 97331-7501, fax 541 737 1393, phone -6578, strauss@FSL.orst.edu From owner-rapd@net.bio.net Thu Dec 26 22:00:00 1996 Path: biosci!rutgers!news.cis.ohio-state.edu!nntp.sei.cmu.edu!bb3.andrew.cmu.edu!newsfeed.pitt.edu!portc02.blue.aol.com!howland.erols.net!newsfeed.internetmci.com!masternews.telia.net!newssrv.ita.tip.net!news.keyworld.net!news From: Kenneth Briffa Newsgroups: bionet.molbio.yeast,bionet.molbio.rapd Subject: Method of DNA extraction from yeast Date: Mon, 23 Dec 1996 23:17:28 -0800 Organization: ESI, Malta. Lines: 9 Message-ID: <32BF8388.19C3@keyworld.net> Reply-To: kennbrif@keyworld.net NNTP-Posting-Host: ppp40.keyworld.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win16; I) Xref: biosci bionet.molbio.yeast:6334 bionet.molbio.rapd:1762 Hello, I'm an undergraduate preparing my dissertation project. The project involves RAPD from brewer's yeast. I've been trying to extract the DNA from the yeasts using benzyl chloride but the yield is not good enough. Does anyone know any method to extract the DNA from yeasts without using any enzymes? Cheers, Kenneth Briffa University of Malta From owner-rapd@net.bio.net Mon Dec 30 22:00:00 1996 Path: biosci!MBCRR.HARVARD.EDU!bsturner From: bsturner@MBCRR.HARVARD.EDU (Bradley Turner) Newsgroups: bionet.molbio.rapd Subject: Re: Rapd data analysis->Similarity vs homology Date: 31 Dec 1996 08:52:51 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 48 Sender: daemon@net.bio.net Distribution: world Message-ID: <199612311652.LAA22215@mbcrr.harvard.edu> NNTP-Posting-Host: net.bio.net Hi Robert Hamilton, I'm very interested in your comment differentiating Homology and Similarity, I was wondering if you (or other RAPD netters) would be able to share some references that would discuss these differences at greater length or depth? Thank You, Brad Turner ************************************************************** Bradley Turner Beth Israel Deaconess Medical Center Harvard Medical School 617-667-1215 phone Division of Gastroenterology 617-667-2767 fax Room Dana 536 bsturner@mbcrr.harvard.edu 330 Brookline Avenue bturner@bidmc.harvard.edu Boston, MA 02215, USA turner@sprcore.bidmc.harvard.edu ************************************************************** BEGIN INCLUDED MESSAGE------------------------------------------------------- From rhamilton@mc.edu Wed Dec 4 02:59:24 1996 To: rapd@net.bio.net From: Robert Hamilton Subject: Re: Rapd data analysis Date: 3 Dec 1996 23:09:07 GMT Homology is a >sticky issue, and even the same-sized fragment does not necessarily mean >the fragments are homologous. > >Gary Hannan > > > This is true. SIMILARITY is NEVER a good measure of homolgy. Just because two fragments DON'T hybridize in a Southern does not mean that they are NOT homologous, particularly in closely realted species. An assessment of homology requires more knowledge than sequence similarity provides, be it via RAPDs or actual sequence data. END OF INCLUDED MESSAGE------------------------------------------------------ From owner-rapd@net.bio.net Mon Dec 30 22:00:00 1996 Path: biosci!agate!howland.erols.net!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!cpk-news-feed1.bbnplanet.com!ox.mc.edu!usenet From: Robert Hamilton Newsgroups: bionet.molbio.rapd Subject: Re: Rapd data analysis->Similarity vs homology Date: 31 Dec 1996 19:50:52 GMT Organization: Mississippi College Lines: 3 Message-ID: <5abqqs$si9@ox.mc.edu> References: <199612311652.LAA22215@mbcrr.harvard.edu> NNTP-Posting-Host: mobo.mc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) This issue has not been fully discussed with reference to the type of data associated with RAPDs.