From owner-rapd@net.bio.net Tue Sep 05 23:00:00 1995 Path: biosci!PUCCINI.CRL.UMN.EDU!paulz From: paulz@PUCCINI.CRL.UMN.EDU (Paul Zambino) Newsgroups: bionet.molbio.rapd Subject: Re: PCR Analysis of Fungi in Wood Date: 6 Sep 1995 10:55:06 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 85 Sender: daemon@net.bio.net Distribution: world Message-ID: <199509061753.MAA03945@puccini.crl.umn.edu> NNTP-Posting-Host: net.bio.net >From: mltajs@VAXD.DCT.AC.UK ("Alan J. Score") Newsgroups: >bionet.molbio.rapd Subject: PCR Analysis of Fungi in Wood Date: 1 Sep 1995 >03:59:39 -0700 Organization: BIOSCI International Newsgroups for Molecular >Biology Message-ID: <00995BEA.803FCFDC.33@vaxd.dct.ac.uk >Dear All, > >I am a third year postgraduate research student working on the biocontrol of >the dry rot fungus Serpula lacrymans by Trichoderma species. I would like >to use the PCR reaction to map the spread of both fungal species through wood >(pine sapwood, taken from a large scale interaction experiment and a field >trial) whoch contains othr fungi. I was wondering whether anyone had experience >in extracting fungal DNA from infected wood and amplifying the DNA using RAPD >PCR. >There doesn't seem to be any problem in extracting the DNA but I am having >severe problems in using the PCR as nothing appears on the gel afterwards (!). >I would be grateful for any assistance that can be provided. Thanks. >Phone : (01382) 308000 Ext 8675/2918/2917 Alan, I haven't extracted from wood, but would be interested in your technique, as I will soon be extracting DNA from pine to detect blister rust DNA before symptoms are apparent. About your problem and approach: RAPDs can be very sensitive to inhibitors and differences in DNA concentration in the DNA extracts. You may or may not be able to remove whatever is causing the problem by further cleaning up the DNA and adjusting the DNA in the reactions. I would take one of a number of different approaches. I would abandon RAPDs and instead amplify regions of the ribosomal gene repeat, preferably using primers specific to the two genera, or at least to basidiomycetes vs. ascomycetes. Then if you get bands, restrict the products from your wood samples and from positive controls that include DNA from your cultures, to check to see if they match. Fungus-specific and basidiomycete-specific primers are available (see Gardes and Bruns, 1993, Molecular Ecology 2:113-118). If there is nothing that has been developed specifically for Trichoderma, there may be sequences available on GENBANK that you could align to design your own primers. I have used a rust-specific primer in the large-subunit rDNA region paired with a "universal" primer in the small subunit to detect rust DNA in some plants, and am pleased with the results (Kropp et al, 1995,Weed Science 43(3):467-472, detects an asymptomatic rust in a crucifer). If you amplify using the primers specific to fungi, and the Serpula and Trichoderma are the most predominant DNA, you may get bands that identify the two species. From past experience using universal primers that span the internal transcribed spacer (one primer in the small subunit, one in the large subunit rDNA), the fragment that amplifies for Trichoderma may likely be a different length than that for Serpula. You would still want to run restrictions on your products to confirm their identity, however. On the other hand, if you don't get the expected bands, you could be amplifying rDNAs from other fungi present in small amounts. At any rate, I think you would have even more difficulties interpreting RAPDs in which there may be competition for primer sites. Since rDNA primers are longer than RAPD primers, have higher annealing temperatures, and rDNA is present in greater copy numbers, you may find that you can fiddle with PCR conditions to amplify from somewhat "dirty" samples. And you can also sequence the rDNA fragments using the same two primers that you used to amplify. One other article that might serve as an example: Robb et al., 1993-4? (Verticillium). Aside from PCR amplification, ITS regions of the ribosomal gene from different species can be used as probes in dot blots of sample DNA. Here you still have the advantages of trying to detect the relatively abundant rDNA, using a portion of the ribosomal region that varies a lot among fungi. Well, hope this will give you some alternatives. Good luck. Paul Paul Zambino USDA Forest Service Forestry Sciences Lab 5985 Highway K Rhinelander, WI 54501 PH:(715)362-1178 FAX: (715)362-1166 EMAIL: paulz@puccini.crl.umn.edu DG:p.zambino:R09F06A From owner-rapd@net.bio.net Tue Sep 05 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!elna.ethz.ch!usenet From: ROKOE@EZINFO.VMSMAIL.ETHZ.CH (KOELLIKER,ROLAND) Newsgroups: bionet.molbio.rapd Subject: Help!!! Inconsistent RAPD results! Date: 6 Sep 1995 14:27:17 GMT Organization: ETH ZUERICH Lines: 9 Distribution: world Message-ID: <42kb45$qhq@elna.ethz.ch> NNTP-Posting-Host: ezinfo.ethz.ch X-News-Reader: VMS NEWS 1.24 I'm working on the genetic variability of meadow fescue and try to find suitable RAPD markers. Since I didn't have any experience in molecular biology I did get assistance from other laboratorys. People also provided me with suitable RAPD protocols. The problem I have is, that sometimes the reaction works and sometimes - with exactly the same experimental conditions - it doesn't. I tried almost everything (different thermocyclers, different protocols, etc.) and finally I think it has something to do with the preparation of the master mix. Did anybody have the same problems? Who could help me? From owner-rapd@net.bio.net Tue Sep 05 23:00:00 1995 Path: biosci!WAIKATO.AC.NZ!marys From: marys@WAIKATO.AC.NZ (Mary Skotnicki) Newsgroups: bionet.molbio.rapd Subject: Teaching RAPDs Date: 6 Sep 1995 14:53:59 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net I've found an enormous variety of wonderful papers on RAPDs in the database, but what I'm really after (and haven't located) is a nice simple methods or review paper on RAPDs which would be suitable for 2nd year undergraduate teaching. Can anyone point me in the right direction please? Mary L. Skotnicki Dept. of Biological Sciences School of Science and Technology University of Waikato Hamilton New Zealand mary.skotnicki@waikato.ac.nz From owner-rapd@net.bio.net Wed Sep 06 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!serra.unipi.it!giuditta!vassallo From: vassallo@cli.di.unipi.it (Fabrizio Vassallo) Newsgroups: bionet.molbio.rapd Subject: music & DNA Date: 7 Sep 1995 16:41:04 GMT Organization: Dipartimento di Informatica, Universita' di Pisa Lines: 6 Distribution: world Message-ID: <42n7b0$1d6g@serra.unipi.it> NNTP-Posting-Host: giuditta.cli.di.unipi.it X-Newsreader: TIN [version 1.2 PL2] Hallo! Have anyone heard of relations betw. music & DNA? please post me Fabrizio From owner-rapd@net.bio.net Wed Sep 06 23:00:00 1995 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!EU.net!howland.reston.ans.net!agate!usenet.kornet.nm.kr!news.kreonet.re.kr!news.dacom.co.kr!usenet From: Hong Kyung-nak Newsgroups: bionet.molbio.rapd Subject: Re: Help!!! Inconsistent RAPD results! Date: 7 Sep 1995 08:18:37 GMT Organization: DACOM Internet Lines: 19 Message-ID: <42m9st$fda@nis.dacom.co.kr> References: <42kb45$qhq@elna.ethz.ch> NNTP-Posting-Host: magicall.dacom.co.kr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Windows; I; 16bit) To: bionet.molbio.rapd ROKOE@EZINFO.VMSMAIL.ETHZ.CH (KOELLIKER,ROLAND) wrote: >I'm working on the genetic variability of meadow fescue and try to find >suitable RAPD markers. Since I didn't have any experience in molecular biology >I did get assistance from other laboratorys. People also provided me with >suitable RAPD protocols. The problem I have is, that sometimes the reaction >works and sometimes - with exactly the same experimental conditions - it >doesn't. I tried almost everything (different thermocyclers, different >protocols, etc.) and finally I think it has something to do with the >preparation of the master mix. Did anybody have the same problems? Who could >help me? Did you check your template DNA, especillay its purity? The purity of DNA is the most important conditon for the reproducibility of RAPD results. Have a good luck... From owner-rapd@net.bio.net Wed Sep 06 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!swrinde!tank.news.pipex.net!pipex!warwick!bham!bcs88.bham.ac.uk!user From: A.C.Hilton@bham.ac.uk (Wiggy) Newsgroups: bionet.molbio.rapd Subject: Re: Teaching RAPDs Date: 7 Sep 1995 10:10:56 GMT Organization: The University of Birmingham Lines: 30 Distribution: world Message-ID: References: NNTP-Posting-Host: bcs88.bham.ac.uk In article , marys@WAIKATO.AC.NZ (Mary Skotnicki) wrote: > I've found an enormous variety of wonderful papers on RAPDs in the > database, but what I'm really after (and haven't located) is a nice simple > methods or review paper on RAPDs which would be suitable for 2nd year > undergraduate teaching. Can anyone point me in the right direction please? > > Mary L. Skotnicki > Dept. of Biological Sciences > School of Science and Technology > University of Waikato > Hamilton > New Zealand > > mary.skotnicki@waikato.ac.nz You may like to have a browse through : 1. Caetano-Anolles, G., Bassam, B. J. and Gresshoff, P. M. (1991) Bio/Technology, 9, 553-557. 2. Caetano-Anolles, G., Bassam, B. J. and Gresshoff, P. M. (1991) Plant Molecular Biology Reporter, 9(4), 294-307. 3. Caetano-Anollés, G. (1993) , PCR Methods and Applications, Vol. 3, pp. 85-94. Hope this helps, Wig. From owner-rapd@net.bio.net Wed Sep 06 23:00:00 1995 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!EU.net!news.sprintlink.net!cs.utexas.edu!news.tamu.edu!news From: jbielawski@tamu.edu () Newsgroups: bionet.molbio.rapd Subject: Re: Teaching RAPDs Date: Thu, 07 Sep 1995 20:17:13 GMT Organization: Texas A&M University, College Station, TX Lines: 32 Message-ID: <42nngr$iis@news.tamu.edu> References: NNTP-Posting-Host: minnow.tamu.edu X-Newsreader: Forte Free Agent v0.55 marys@WAIKATO.AC.NZ (Mary Skotnicki) wrote: >I've found an enormous variety of wonderful papers on RAPDs in the >database, but what I'm really after (and haven't located) is a nice simple >methods or review paper on RAPDs which would be suitable for 2nd year >undergraduate teaching. Can anyone point me in the right direction please? >Mary L. Skotnicki >Dept. of Biological Sciences >School of Science and Technology >University of Waikato >Hamilton >New Zealand >mary.skotnicki@waikato.ac.nz Here are two possibilities: 1. Hadrys et al. 1992. Applications of random amolified polymorphic DNA (RAPD) in molecular ecology. Mol. Ecol. 1:55-63. (This is a good general review paper) 2. Bielawski et al. 1995. Reproducible amplification of RAPD merkers from vertabrate DNA. Biotechniques., 18:856-860. (methods papaer) Good luck, J. Bielawski From owner-rapd@net.bio.net Wed Sep 06 23:00:00 1995 Path: biosci!BRAHMS.UDEL.EDU!pgaffney From: pgaffney@BRAHMS.UDEL.EDU (Patrick Gaffney) Newsgroups: bionet.molbio.rapd Subject: Re: music & DNA Date: 7 Sep 1995 12:11:47 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <42n7b0$1d6g@serra.unipi.it> NNTP-Posting-Host: net.bio.net Some years ago, I believe Susumu Ohno put DNA sequences to music. I've never heard them, but I was told that particular motifs are pretty catchy. Patrick Gaffney | pgaffney@udel.edu College of Marine Studies | (302) 645-4364 University of Delaware | FAX: (302) 645-4028 Lewes, DE 19958 | - This space for rent - On 7 Sep 1995, Fabrizio Vassallo wrote: > Hallo! > Have anyone heard of relations betw. music & DNA? > please post me > > Fabrizio > > From owner-rapd@net.bio.net Sat Sep 09 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!newsfeed.internetmci.com!tank.news.pipex.net!pipex!in1.uu.net!news.compuserve.com!news.production.compuserve.com!news From: Patrick R. Jones <102570.2734@CompuServe.COM> Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.molluscs,bionet.molbio.proteins,bionet.molbio.rapd,bionet.molbio.yeast Subject: Need Help!! Date: 10 Sep 1995 20:13:45 GMT Organization: Personal Lines: 19 Message-ID: <42vgtp$9h8$1@mhafm.production.compuserve.com> Xref: biosci bionet.molbio.methds-reagnts:33310 bionet.molbio.molluscs:143 bionet.molbio.proteins:5587 bionet.molbio.rapd:1280 bionet.molbio.yeast:3709 I am a undergraduate student in biology. Some day I hope to go to graduate school in biochemistry. My grades are good enough but I am afraid that this may not be enough to get in. I am looking for something to set myself apart from the other students. At this point I am at a loss on what to do. I have no real resources to work on projects in the areas that interest me. Does anybody have any ideas? I do have one useful skill. I am a professional computer programmer. I don’t mean someone who has taken a FORTRAN class and is working as a work-study student, but a 10 year application programming veteran in the computing industry. If I could use this skill great if not, I don’t care. I need something to further my career; something good. Please help!!! I know that somebody out there knows of something I could do. Thank you for your time!!! Patrick R. Jones -- <> From owner-rapd@net.bio.net Sun Sep 10 23:00:00 1995 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!EU.net!newsfeed.internetmci.com!news.sprintlink.net!cs.utexas.edu!usc!news.cerf.net!coh.Coh.ORG!usenet From: gerald forrest Newsgroups: bionet.molbio.rapd Subject: Re: music & DNA Date: 11 Sep 1995 17:02:43 GMT Organization: Beclman Research Institute at the City of Hope Lines: 31 Message-ID: <431q3j$e8b@coh.coh.org> References: <42n7b0$1d6g@serra.unipi.it> <42v9kv$r4@taco.cc.ncsu.edu> NNTP-Posting-Host: 151.152.5.81 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) To: vassallo@cli.di.unipi.it X-URL: news:42v9kv$r4@taco.cc.ncsu.edu Dr. Susumu Ohno, Department of Biology, Beckman Res.Inst./City of Hope Medical Center, Duarte, CA 91010 has published many articles on music and DNA. For example: Ohno, S. and Jabara, M Chemica Scripta, 1986, 26B:43-49 Ohno,S Leukemia J. 1993, 7:S157-S159 Ohno, S. Haematology and Blood Transfusion Vol.31 in Modern Trends in Human Leukemia VII Edited by Neth, Gallo, Greaves and Kabisch, Springer-Vertag, Berlin Heidelberg 1987. Ohno, S. and Ohno, M. Immunogenetics, 1986, 24:71-78 Ohno, S. Animal Genetics, 1988, 19:305-316 Ohno, S. Nato ASI Series, Vol. H23, The Semiotics of Cellular Communication in the Immune System, Edited by E.E. Sercarz et al. Springer-Verlag Berlin Heidleberg 1988 131-147 Gerald ForrestSusan Jane Hogarth wrote: >-- vassallo@cli.di.unipi.it (Fabrizio Vassallo) wrote: > >>Have anyone heard of relations betw. music & DNA? > >I'm afraid this won't be of much help, but a year or two ago, I heard a story >(on US National Public Radio?) about a music student who "translated" some >sequences from HIV and human genes and played them together. They played some >of the "music" on the program. It was haunting, strange, and beautiful. But >then, I'm not a very good music critic, I'm afraid. > >Susan Jane Hogarth > From owner-rapd@net.bio.net Sun Sep 10 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!in1.uu.net!cis.ohio-state.edu!magnus.acs.ohio-state.edu!lerc.nasa.gov!purdue!news.bu.edu!taco.cc.ncsu.edu!news From: Susan Jane Hogarth Newsgroups: bionet.molbio.rapd Subject: Re: music & DNA Date: 10 Sep 1995 18:09:35 GMT Organization: North Carolina State University Lines: 12 Message-ID: <42v9kv$r4@taco.cc.ncsu.edu> References: <42n7b0$1d6g@serra.unipi.it> NNTP-Posting-Host: sparc5b-2203gardnr.ppath.ncsu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; SunOS 5.4 sun4m) To: vassallo@cli.di.unipi.it X-URL: news:42n7b0$1d6g@serra.unipi.it -- vassallo@cli.di.unipi.it (Fabrizio Vassallo) wrote: >Have anyone heard of relations betw. music & DNA? I'm afraid this won't be of much help, but a year or two ago, I heard a story (on US National Public Radio?) about a music student who "translated" some sequences from HIV and human genes and played them together. They played some of the "music" on the program. It was haunting, strange, and beautiful. But then, I'm not a very good music critic, I'm afraid. Susan Jane Hogarth From owner-rapd@net.bio.net Sun Sep 10 23:00:00 1995 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!EU.net!howland.reston.ans.net!cs.utexas.edu!usc!news.cerf.net!coh.Coh.ORG!usenet From: gerald forrest Newsgroups: bionet.molbio.rapd Subject: Re: music & DNA Date: 11 Sep 1995 17:02:20 GMT Organization: Beclman Research Institute at the City of Hope Lines: 31 Message-ID: <431q2s$e8b@coh.coh.org> References: <42n7b0$1d6g@serra.unipi.it> <42v9kv$r4@taco.cc.ncsu.edu> NNTP-Posting-Host: 151.152.5.81 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) To: vassallo@cli.di.unipi.it X-URL: news:42v9kv$r4@taco.cc.ncsu.edu Dr. Susumu Ohno, Department of Biology, Beckman Res.Inst./City of Hope Medical Center, Duarte, CA 91010 has published many articles on music and DNA. For example: Ohno, S. and Jabara, M Chemica Scripta, 1986, 26B:43-49 Ohno,S Leukemia J. 1993, 7:S157-S159 Ohno, S. Haematology and Blood Transfusion Vol.31 in Modern Trends in Human Leukemia VII Edited by Neth, Gallo, Greaves and Kabisch, Springer-Vertag, Berlin Heidelberg 1987. Ohno, S. and Ohno, M. Immunogenetics, 1986, 24:71-78 Ohno, S. Animal Genetics, 1988, 19:305-316 Ohno, S. Nato ASI Series, Vol. H23, The Semiotics of Cellular Communication in the Immune System, Edited by E.E. Sercarz et al. Springer-Verlag Berlin Heidleberg 1988 131-147 Gerald ForrestSusan Jane Hogarth wrote: >-- vassallo@cli.di.unipi.it (Fabrizio Vassallo) wrote: > >>Have anyone heard of relations betw. music & DNA? > >I'm afraid this won't be of much help, but a year or two ago, I heard a story >(on US National Public Radio?) about a music student who "translated" some >sequences from HIV and human genes and played them together. They played some >of the "music" on the program. It was haunting, strange, and beautiful. But >then, I'm not a very good music critic, I'm afraid. > >Susan Jane Hogarth > From owner-rapd@net.bio.net Sun Sep 10 23:00:00 1995 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!EU.net!howland.reston.ans.net!usc!news.cerf.net!coh.Coh.ORG!usenet From: gerald forrest Newsgroups: bionet.molbio.rapd Subject: Re: music & DNA Date: 11 Sep 1995 16:58:41 GMT Organization: Beclman Research Institute at the City of Hope Lines: 18 Message-ID: <431ps1$e8b@coh.coh.org> References: <42n7b0$1d6g@serra.unipi.it> <42v9kv$r4@taco.cc.ncsu.edu> NNTP-Posting-Host: 151.152.5.81 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) To: vassallo@cli.di.unipi.it X-URL: news:42v9kv$r4@taco.cc.ncsu.edu Dr. Susumu Ohno, Department of Biology, Beckman Res.Inst./City of Hope Medical Center, Duarte, CA 91010 has published many articles on music and DNA. For example: Ohno, S. and Jabara, M Chemica Scripta, 1986, 26B:43-49 Ohno,S Leukemia J. 1993, 7:S157-S159 Ohno, S. Haematology and Blood Transfusion Vol.31 in Modern Trends in Human Leukemia VII Edited by Neth, Gallo, Greaves and Kabisch, Springer-Vertag, Berlin Heidelberg 1987. Ohno, S. and Ohno, M. Immunogenetics, 1986, 24:71-78 Ohno, S. Animal Genetics, 1988, 19:305-316 Ohno, S. Nato ASI Series, Vol. H23, The Semiotics of Cellular Communication in the Immune System, Edited by E.E. Sercarz et al. Springer-Verlag Berlin Heidleberg 1988 131-147 Gerald Forrest From owner-rapd@net.bio.net Sun Sep 10 23:00:00 1995 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!EU.net!howland.reston.ans.net!usc!news.cerf.net!coh.Coh.ORG!usenet From: gerald forrest Newsgroups: bionet.molbio.rapd Subject: Re: music & DNA Date: 11 Sep 1995 16:54:22 GMT Organization: Beclman Research Institute at the City of Hope Lines: 18 Message-ID: <431pju$e8b@coh.coh.org> References: <42n7b0$1d6g@serra.unipi.it> <42v9kv$r4@taco.cc.ncsu.edu> NNTP-Posting-Host: 151.152.5.81 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) To: vassallo@cli.di.unipi.it X-URL: news:42v9kv$r4@taco.cc.ncsu.edu Dr. Susumu Ohno, Department of Biology, Beckman Res.Inst./City of Hope Medical Center, Duarte, CA 91010 has published many articles on music and DNA. For example: Ohno, S. and Jabara, M Chemica Scripta, 1986, 26B:43-49 Ohno,S Leukemia J. 1993, 7:S157-S159 Ohno, S. Haematology and Blood Transfusion Vol.31 in Modern Trends in Human Leukemia VII Edited by Neth, Gallo, Greaves and Kabisch, Springer-Vertag, Berlin Heidelberg 1987. Ohno, S. and Ohno, M. Immunogenetics, 1986, 24:71-78 Ohno, S. Animal Genetics, 1988, 19:305-316 Ohno, S. Nato ASI Series, Vol. H23, The Semiotics of Cellular Communication in the Immune System, Edited by E.E. Sercarz et al. Springer-Verlag Berlin Heidleberg 1988 131-147 Gerald Forrest From owner-rapd@net.bio.net Sun Sep 10 23:00:00 1995 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!EU.net!newsfeed.internetmci.com!news.sprintlink.net!cs.utexas.edu!usc!news.cerf.net!coh.Coh.ORG!usenet From: gerald forrest Newsgroups: bionet.molbio.rapd Subject: Re: music & DNA Date: 11 Sep 1995 17:03:05 GMT Organization: Beclman Research Institute at the City of Hope Lines: 31 Message-ID: <431q49$e8b@coh.coh.org> References: <42n7b0$1d6g@serra.unipi.it> <42v9kv$r4@taco.cc.ncsu.edu> NNTP-Posting-Host: 151.152.5.81 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) To: vassallo@cli.di.unipi.it X-URL: news:42v9kv$r4@taco.cc.ncsu.edu Dr. Susumu Ohno, Department of Biology, Beckman Res.Inst./City of Hope Medical Center, Duarte, CA 91010 has published many articles on music and DNA. For example: Ohno, S. and Jabara, M Chemica Scripta, 1986, 26B:43-49 Ohno,S Leukemia J. 1993, 7:S157-S159 Ohno, S. Haematology and Blood Transfusion Vol.31 in Modern Trends in Human Leukemia VII Edited by Neth, Gallo, Greaves and Kabisch, Springer-Vertag, Berlin Heidelberg 1987. Ohno, S. and Ohno, M. Immunogenetics, 1986, 24:71-78 Ohno, S. Animal Genetics, 1988, 19:305-316 Ohno, S. Nato ASI Series, Vol. H23, The Semiotics of Cellular Communication in the Immune System, Edited by E.E. Sercarz et al. Springer-Verlag Berlin Heidleberg 1988 131-147 Gerald ForrestSusan Jane Hogarth wrote: >-- vassallo@cli.di.unipi.it (Fabrizio Vassallo) wrote: > >>Have anyone heard of relations betw. music & DNA? > >I'm afraid this won't be of much help, but a year or two ago, I heard a story >(on US National Public Radio?) about a music student who "translated" some >sequences from HIV and human genes and played them together. They played some >of the "music" on the program. It was haunting, strange, and beautiful. But >then, I'm not a very good music critic, I'm afraid. > >Susan Jane Hogarth > From owner-rapd@net.bio.net Sun Sep 10 23:00:00 1995 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!EU.net!news.sprintlink.net!cs.utexas.edu!usc!news.cerf.net!coh.Coh.ORG!usenet From: gerald forrest Newsgroups: bionet.molbio.rapd Subject: Re: music & DNA Date: 11 Sep 1995 17:06:10 GMT Organization: Beclman Research Institute at the City of Hope Lines: 31 Message-ID: <431qa2$e8b@coh.coh.org> References: <42n7b0$1d6g@serra.unipi.it> <42v9kv$r4@taco.cc.ncsu.edu> NNTP-Posting-Host: 151.152.5.81 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) To: vassallo@cli.di.unipi.it X-URL: news:42v9kv$r4@taco.cc.ncsu.edu Dr. Susumu Ohno, Department of Biology, Beckman Res.Inst./City of Hope Medical Center, Duarte, CA 91010 has published many articles on music and DNA. For example: Ohno, S. and Jabara, M Chemica Scripta, 1986, 26B:43-49 Ohno,S Leukemia J. 1993, 7:S157-S159 Ohno, S. Haematology and Blood Transfusion Vol.31 in Modern Trends in Human Leukemia VII Edited by Neth, Gallo, Greaves and Kabisch, Springer-Vertag, Berlin Heidelberg 1987. Ohno, S. and Ohno, M. Immunogenetics, 1986, 24:71-78 Ohno, S. Animal Genetics, 1988, 19:305-316 Ohno, S. Nato ASI Series, Vol. H23, The Semiotics of Cellular Communication in the Immune System, Edited by E.E. Sercarz et al. Springer-Verlag Berlin Heidleberg 1988 131-147 Gerald ForrestSusan Jane Hogarth wrote: >-- vassallo@cli.di.unipi.it (Fabrizio Vassallo) wrote: > >>Have anyone heard of relations betw. music & DNA? > >I'm afraid this won't be of much help, but a year or two ago, I heard a story >(on US National Public Radio?) about a music student who "translated" some >sequences from HIV and human genes and played them together. They played some >of the "music" on the program. It was haunting, strange, and beautiful. But >then, I'm not a very good music critic, I'm afraid. > >Susan Jane Hogarth > From owner-rapd@net.bio.net Sun Sep 10 23:00:00 1995 Path: biosci!greb.ulaval.ca!Christian.Mouton From: Christian.Mouton@greb.ulaval.ca (Christian Mouton) Newsgroups: bionet.molbio.rapd Subject: Help Date: 11 Sep 1995 12:54:13 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 28 Sender: daemon@net.bio.net Distribution: world Message-ID: <9509111953.AA10105@hermes.ulaval.ca> NNTP-Posting-Host: net.bio.net I would like to know if someone could give me any explanation about my unexpected result: I have exploited the ability of RAPD to generate species-specific fragments which could be used to develop specific DNA probes. Once a species-specific RAPD marker was found, it was cloned and sequenced, and we used that sequence to select a primer pair allowing PCR amplification. For one target species I have studied, when I analyze the product of PCR by using a selected primer pair, I obtain a double band (2 bands of very closely size) of expected size instead of a single band. That "doublet" of expected size is vizualized with different primer pairs.(I tried 4 primer pairs). Thanks for your help! Emmanuelle Guillot -----------------------------Christian Mouton----------------------------- Groupe de Recherche en Écologie Buccale tél. (418)656-5872 Faculté de médecine dentaire fax. (418)656-2861 Université Laval Email: Christian.Mouton@greb.ulaval.ca Québec (Québec) G1K 7P4 CANADA From owner-rapd@net.bio.net Sun Sep 10 23:00:00 1995 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!EU.net!newsfeed.internetmci.com!news.sprintlink.net!cs.utexas.edu!usc!news.cerf.net!coh.Coh.ORG!usenet From: gerald forrest Newsgroups: bionet.molbio.rapd Subject: Re: music & DNA Date: 11 Sep 1995 17:03:32 GMT Organization: Beclman Research Institute at the City of Hope Lines: 31 Message-ID: <431q54$e8b@coh.coh.org> References: <42n7b0$1d6g@serra.unipi.it> <42v9kv$r4@taco.cc.ncsu.edu> NNTP-Posting-Host: 151.152.5.81 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) To: vassallo@cli.di.unipi.it X-URL: news:42v9kv$r4@taco.cc.ncsu.edu Dr. Susumu Ohno, Department of Biology, Beckman Res.Inst./City of Hope Medical Center, Duarte, CA 91010 has published many articles on music and DNA. For example: Ohno, S. and Jabara, M Chemica Scripta, 1986, 26B:43-49 Ohno,S Leukemia J. 1993, 7:S157-S159 Ohno, S. Haematology and Blood Transfusion Vol.31 in Modern Trends in Human Leukemia VII Edited by Neth, Gallo, Greaves and Kabisch, Springer-Vertag, Berlin Heidelberg 1987. Ohno, S. and Ohno, M. Immunogenetics, 1986, 24:71-78 Ohno, S. Animal Genetics, 1988, 19:305-316 Ohno, S. Nato ASI Series, Vol. H23, The Semiotics of Cellular Communication in the Immune System, Edited by E.E. Sercarz et al. Springer-Verlag Berlin Heidleberg 1988 131-147 Gerald ForrestSusan Jane Hogarth wrote: >-- vassallo@cli.di.unipi.it (Fabrizio Vassallo) wrote: > >>Have anyone heard of relations betw. music & DNA? > >I'm afraid this won't be of much help, but a year or two ago, I heard a story >(on US National Public Radio?) about a music student who "translated" some >sequences from HIV and human genes and played them together. They played some >of the "music" on the program. It was haunting, strange, and beautiful. But >then, I'm not a very good music critic, I'm afraid. > >Susan Jane Hogarth > From owner-rapd@net.bio.net Mon Sep 11 23:00:00 1995 Path: biosci!ns1.faseb.org!lamarck.sura.net!ra.nrl.navy.mil!news.math.psu.edu!psuvax1!gvls1!udel!news.udel.edu!strauss.udel.edu!not-for-mail From: mcdonald@strauss.udel.edu (John H McDonald) Newsgroups: bionet.molbio.rapd Subject: Re: Help Date: 11 Sep 1995 22:46:40 -0400 Organization: University of Delaware Lines: 31 Message-ID: <432sag$slm@strauss.udel.edu> References: <9509111953.AA10105@hermes.ulaval.ca> NNTP-Posting-Host: strauss.udel.edu In article <9509111953.AA10105@hermes.ulaval.ca>, Christian Mouton wrote: >I would like to know if someone could give me any explanation about my >unexpected result: >I have exploited the ability of RAPD to generate species-specific fragments >which could be used to develop specific DNA probes. Once a species-specific >RAPD marker was found, it was cloned and sequenced, and we used that >sequence to select a primer pair allowing PCR amplification. >For one target species I have studied, when I analyze the product of PCR by >using a selected primer pair, I obtain a double band (2 bands of very >closely size) of expected size instead of a single band. That "doublet" of >expected size is vizualized with different primer pairs.(I tried 4 primer >pairs). >Thanks for your help! >Emmanuelle Guillot One possibility is that the DNA that you've made primers for is in multiple copies in the genome, and the copies differ slightly in length. Another possibility is that there are two alleles that differ slightly in length. It probably depends on the organism, but in my experience junk DNA has a lot of length variation that is big enough to see on an agarose gel. If it's two alleles, run a few individuals and you should see some single-banded homozygotes. If you try to gel-purify the two bands and sequence them separately, be aware of one thing: the two alleles may be close enough in size that they run together, while the heteroduplex runs as the slower band. If that's the case, direct sequencing of either band will yield a mishmash of both alleles. John H. McDonald Department of Biology University of Delaware From owner-rapd@net.bio.net Mon Sep 11 23:00:00 1995 Newsgroups: bionet.molbio.rapd Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!paladin.american.edu!news.ecn.uoknor.edu!news.uoknor.edu!ns1.nodak.edu!beangenes.cws.ndsu.nodak.edu!mcclean From: mcclean@PROBLEM_WITH_INEWS_DOMAIN_FILE (Phil McClean) Subject: Re: Help!!! Inconsistent RAPD results! Sender: usenet@ns1.nodak.edu (Usenet login) Message-ID: Date: Tue, 12 Sep 1995 13:22:21 GMT References: <42kb45$qhq@elna.ethz.ch> <42m9st$fda@nis.dacom.co.kr> Nntp-Posting-Host: beangenes.cws.ndsu.nodak.edu Organization: I need to put my ORGANIZATION here. X-Newsreader: TIN [version 1.2 PL2] Lines: 30 Hong Kyung-nak (honeutal@chollian.dacom.co.kr) wrote: : ROKOE@EZINFO.VMSMAIL.ETHZ.CH (KOELLIKER,ROLAND) wrote: : >I'm working on the genetic variability of meadow fescue and try to find : >suitable RAPD markers. Since I didn't have any experience in molecular biology : >I did get assistance from other laboratorys. People also provided me with : >suitable RAPD protocols. The problem I have is, that sometimes the reaction : >works and sometimes - with exactly the same experimental conditions - it : >doesn't. I tried almost everything (different thermocyclers, different : >protocols, etc.) and finally I think it has something to do with the : >preparation of the master mix. Did anybody have the same problems? Who could : >help me? : Did you check your template DNA, especillay its purity? : The purity of DNA is the most important conditon for the reproducibility : of RAPD results. I would have to disagree with this statement, although only slightly. From our experience, the purity of DNA is not as important as the consistency of purity. It is not good to try to compare a CsCl purified sample with a crude extract when using RAPDs. Be consistent in the level of quality of DNA would be my advise. Phil McClean Dept. of Plant Sciences North Dakota State University Fargo, ND 58105 mcclean@beangenes.cws.ndsu.nodak.edu From owner-rapd@net.bio.net Tue Sep 12 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!tank.news.pipex.net!pipex!dispatch.news.demon.net!demon!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: a_arzani@cc.iut.ac.ir (AHMAD ARZANI) Newsgroups: bionet.molbio.rapd Subject: Molecu Molecular marker study of disease resistance genes Date: 13 Sep 1995 12:03:05 +0100 Lines: 9 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <436dp9$aro@mserv1.dl.ac.uk> Original-To: rapd@dl.ac.uk Dear sir/Madanm, Could you provide me some information or scientist address, who can help me with above subject. Yours sincerely, Ahmad arzani, Assist. Prof., Genetics and Plkant Breeding, College of Agric. Isfahan university of  Technologfy, Isfahan, Iran From owner-rapd@net.bio.net Tue Sep 12 23:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!in1.uu.net!zib-berlin.de!news.rrz.uni-hamburg.de!rzaix05!pz4a004 From: pz4a004@rzaix05.uni-hamburg.de (Aquiles Luna-Rodriguez) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.molluscs,bionet.molbio.proteins,bionet.molbio.rapd,bionet.molbio.yeast Subject: Re: Need Help!! Followup-To: bionet.molbio.methds-reagnts,bionet.molbio.molluscs,bionet.molbio.proteins,bionet.molbio.rapd,bionet.molbio.yeast Date: 13 Sep 1995 13:43:30 GMT Organization: University of Hamburg -- Germany Lines: 29 Message-ID: <436n62$8dk@rzsun02.rrz.uni-hamburg.de> References: <42vgtp$9h8$1@mhafm.production.compuserve.com> NNTP-Posting-Host: rzaix05.rrz.uni-hamburg.de X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.molbio.methds-reagnts:33462 bionet.molbio.molluscs:145 bionet.molbio.proteins:5616 bionet.molbio.rapd:1293 bionet.molbio.yeast:3732 In article <42vgtp$9h8$1@mhafm.production.compuserve.com> you wrote: : I am a undergraduate student in biology. Some day I hope to go to : graduate school in biochemistry. : I am a professional computer programmer. Hi Patrick! I may have just what your4re looking for. I4m a psycho- logy student, and I write neural simulation programs since many years. Now, I4m developing a tool-box to simulate neural behavior, a kind of formal lenguage to describe brain theories. It can be used to simulate small subsystems, maybe even the "learning" part of animal models like Aplysia, Hermissenda or C. elegans. The idea is using a "chemical" learning algorithm, and test the model against empirical data, either neural or behavioral. I need contact with people interested in molecular biology, neurophisio- logy/anatomy, computer programming, behavior science, etc. Don4t worry if you4re less than a specialist in all these fields, modesty is a disadvantage if you4re shooting at a Nobel Prize. If you4re interested, I can send you C source for Turbo C 3.0, just email me. *********************************** * Aquiles Luna-Rodriguez * * Universitaet Hamburg, Germany * * pz4a004@rrz.uni-hamburg.de * *********************************** From owner-rapd@net.bio.net Wed Sep 13 23:00:00 1995 Path: biosci!SERVIDOR.DGSCA.UNAM.MX!carvalho From: carvalho@SERVIDOR.DGSCA.UNAM.MX (Carvalho Torres Alexandro cassio-UACPYP) Newsgroups: bionet.molbio.rapd Subject: RAPD nad homozygotes Date: 13 Sep 1995 20:23:11 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear netters. Please a need a reference that discuss step by step homozygotes or heterozygotes and RFLP or RAPD. Thanks a lot. Alexandro carvalho depertment of Infectious Diseases. Mexico City From owner-rapd@net.bio.net Wed Sep 13 23:00:00 1995 Path: biosci!agate!boulder!tali.UCHSC.edu!Guy.Oshiro From: oshiro_G@defiance.hsc.colorado.edu (Guy Oshiro) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.molluscs,bionet.molbio.proteins,bionet.molbio.rapd,bionet.molbio.yeast Subject: Re: Need Help!! Date: 13 Sep 1995 19:25:57 GMT Organization: University of Colorado Health Sciences Center Lines: 31 Sender: -Not-Authenticated-[6503] Message-ID: <437b85$s49@tali.UCHSC.edu> References: <42vgtp$9h8$1@mhafm.production.compuserve.com> NNTP-Posting-Host: brbmt8.uchsc.edu X-Posted-From: InterNews 7.2@tali.uchsc.edu. Xdisclaimer: No attempt was made to authenticate the sender's name. Xref: biosci bionet.molbio.methds-reagnts:33508 bionet.molbio.molluscs:146 bionet.molbio.proteins:5623 bionet.molbio.rapd:1295 bionet.molbio.yeast:3738 Patrick, My a 10 year computer programmer ventran and you want to pursue a career in biological sciences. Hmmm...are you sure this is what you want to do with your life? I hope that you realize that science is not a money-making carreer. I hope that you are prepared to make less than a fast-food worker - for the next 7-10 years that it takes you to finish your PhD and then a post-doc. Then of course the next step would be to find a position. But enough lamenting about the current state of affairs and things may change in the next few years. You can definitely set yourself apart with your programming skill if you want to continue with it in your biology-computer science career. The first thought that comes to mind is computer modeling of protein structures. The dream of a lot of biologists would be able to enter the primary DNA sequence and have a computer algorithm convert it into its functional tertiary structure. There are many other possibilities but you should look into groups near your area that are doing computer modeling to get some hands on experience. Good Luck. Guy Oshiro EMAIL: Oshiro_G@defiance.hsc.colorado.edu /\ /\ /\ / \/ \/\/ \ Science in the Rockies. / \ \/ \ From owner-rapd@net.bio.net Thu Sep 14 23:00:00 1995 Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.molluscs,bionet.molbio.proteins,bionet.molbio.rapd,bionet.molbio.yeast Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!usenet.eel.ufl.edu!warwick!yama.mcc.ac.uk!thor.cf.ac.uk!news From: Jami Grossfield Subject: Re: Need Help!! Sender: news@cf.ac.uk (USENET News System) Message-ID: Date: Fri, 15 Sep 1995 12:57:55 GMT To: 102570.2734@CompuServe.COM X-Nntp-Posting-Host: d014.anat.cf.ac.uk Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii References: <42vgtp$9h8$1@mhafm.production.compuserve.com> Mime-Version: 1.0 X-Mailer: Mozilla 1.1N (Windows; I; 16bit) Organization: Cardiff University of Wales Lines: 11 Xref: biosci bionet.molbio.methds-reagnts:33576 bionet.molbio.molluscs:149 bionet.molbio.proteins:5640 bionet.molbio.rapd:1296 bionet.molbio.yeast:3747 Patrick- I would strongly reccommend working in a lab as a technician for at least a year. this will give you a better idea of what you are getting yourself into, and give you lab skills that your furture thesis advisor will want you to know. I did not do this before entering grad school (in the u.s.) and really regretted it. also read,read, read! journal articles, that is. the more you know, the better. good luck! jami From owner-rapd@net.bio.net Thu Sep 14 23:00:00 1995 Path: biosci!greb.ulaval.ca!Christian.Mouton From: Christian.Mouton@greb.ulaval.ca (Christian Mouton) Newsgroups: bionet.molbio.rapd Subject: Immunomagnetic PCR\ DNA Probe\ Porphyromonas gingivalis Date: 15 Sep 1995 14:01:27 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 44 Sender: daemon@net.bio.net Distribution: world Message-ID: <9509152100.AA21968@hermes.ulaval.ca> NNTP-Posting-Host: net.bio.net The following is the summary of a paper which has been accepted for publication by J. Clin. Microbiol. Of particular interest is the fact that the DNA probe and the PCR protocol specific for Porphyromonas gingivalis were derived from the sequence of a random amplified polymorphic DNA (RAPD) species-specific fragment. We are currently developing similar procedures for the diagnosis of other fastidious gram negative anaerobes in mixed infections. Immunomagnetic PCR and a DNA Probe for the Detection and Identification of Porphyromonas gingivalis. Riad M. Benkirane, Emmanuelle Guillot, and Christian Mouton The aim of this study that we describe was to combine an immunomagnetic separation and a polymerase chain reaction followed by dot blot hybridization with a DNA probe for the detection and identification of Porphyromonas gingivalis. Immunomagnetic particles were coated with monoclonal antibody specific for P. gingivalis and incubated with a suspension of seven oral bacterial species spiked with various dilutions of P. gingivalis. Beads with their load of bound bacteria were boiled in water, and the target DNA in the supernatant was amplified with a primer pair to generate a 593-bp PCR fragment specific for P. gingivalis. Finally, the product of amplification was detected by dot-blot hybridization with a digoxigenin-labeled 593-bp probe. The detection limit was determined at 100 bacterial cells/ml. The immunomagnetic-PCR/DNA probe procedure described here should be useful for the rapid, specific and sensitive detection and identification of P. gingivalis in clinical samples. -----------------------------Christian Mouton----------------------------- Groupe de Recherche en Écologie Buccale tél. (418)656-5872 Faculté de médecine dentaire fax. (418)656-2861 Université Laval Email: Christian.Mouton@greb.ulaval.ca Québec (Québec) G1K 7P4 CANADA From owner-rapd@net.bio.net Fri Sep 15 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!btnet!dispatch.news.demon.net!demon!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: "Dijk, Peter van" Newsgroups: bionet.molbio.rapd Subject: PhD position available Date: 16 Sep 1995 02:04:14 +0100 Lines: 67 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <43d7qe$ai1@mserv1.dl.ac.uk> Encoding: 67 TEXT Original-To: RAPD PhD POSITION AVAILABLE FOR A POPULATION BIOLOGIST A 4-years PhD position is available at the Netherlands Institute of Ecology (NIE-CTE) for the project 'Genetic founder effects in tree species of the Krakatau islands (Indonesia)'. Because of ongoing fragmentation of the tropical rain forest it is impor- tant to get more insight in the effects of reduced gene flow and inbreeding in tropical forest trees. The recolonization of the Krakatau islands (Indonesia) after the 1883 volcanic eruption, provides an ideal opportunity to study these processes. A population genetic study is proposed on five tree species. Plant material will be collected during a number of expeditions to the Krakatau islands. Collected material will be grown and analyzed in the Netherlands. Genetic variation on the islands will be quantified with allozymes and DNA markers, and com- pared to the levels in populations on Java and Sumatra. This will provide information on founder effects and inter-island gene flow. Greenhouse experiments will be conducted to determine the relationship between inbreeding and growth. The project will participate in the Krakatau Research Programme, and more particularly there will be cooperation with the universities of Oxford and Leeds (UK). The salary will be around Dfl 2000 per month in the first year, increasing to around Dfl 3700 in the last year. The work will begin at December 1st 1995. We are looking for a population biologist. It is desirable that candidates have a population genetic background and have experience with DNA techniques. With respect of the field-work in Indonesia we are looking for somebody who is able to work independently in an international expedition-team under primitive conditions. Furthermore candidates should be able to combine fieldwork in Indonesia with labwork in the Netherlands. Interested applicants should send their CV and the names of two referees by regular post. Inquieries will be answered by email. Ap- plications are due in Heteren by October 9th 1995. For information and application letters contact Dr. Peter van Dijk, NIE-CTE, Dept of Plant Population Biology, PO Box 40, NL-6666 ZG, Heteren, The Nether- lands (email: pjvandijk@nioo.nl, tel: +31.8306.91208, fax:+31.8306.23227). From owner-rapd@net.bio.net Mon Sep 18 23:00:00 1995 Path: biosci!LIFSCI.SDSU.EDU!MCCLELLAND From: MCCLELLAND@LIFSCI.SDSU.EDU Newsgroups: bionet.molbio.rapd Subject: postdoc position Leptospira Date: 19 Sep 1995 13:54:16 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <950919060421.20201dac@LIFSCI.SDSU.EDU> NNTP-Posting-Host: net.bio.net Dr. David Ralph at Urocor in Oklahoma City has a postdoctoral position available to study an ORF in the 23S rRNA gene of Leptospira and also to develop diagnostics for bacterial infections of the urinary tract. Contact me or him at dralph@ionet.net Michael McClelland From owner-rapd@net.bio.net Mon Sep 18 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!in1.uu.net!olivea!charnel.ecst.csuchico.edu!csusac!csus.edu!hh-bio-22.sfsu.edu!user From: rzebell@sfsu.edu (Randy K. Zebell) Newsgroups: bionet.molbio.rapd Subject: DNA Quantitation Date: 19 Sep 1995 17:40:13 GMT Organization: San Francisco State University Lines: 5 Message-ID: NNTP-Posting-Host: @hh-bio-22.sfsu.edu Does anyone have an opinion about Hoefer Scientific Instrument's DyNA Quant 200 flourometer? Given our small lab, it seems appropriate for rapidly quantifying DNA without the added size and expense of a spectrophotometer. I'm wondering how accurate and reliable the instrument is in practice. From owner-rapd@net.bio.net Tue Sep 19 23:00:00 1995 Path: biosci!ACD.TUSK.EDU!Prakash From: Prakash@ACD.TUSK.EDU (C. S. Prakash) Newsgroups: bionet.molbio.rapd Subject: New FAO Email Groups in Plant Genetic Resources Date: 19 Sep 1995 07:26:04 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 352 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HVGEHSND6A0007XQ@Acd.Tusk.Edu> I am forwarding the following information I received from Dr. Charles Spillane about the FAO Email series on Plant Genetic Diversity, Plant Germplasm, Plant Breeding and other topics. -C. S. Prakash Tuskegee University. >-----------INVITATION TO JOIN FAO E-MAIL CONFERENCES--------------- > >FAO is convening the Fourth International Technical Conference >on Plant Genetic Resources in Leipzig, Germany on 17-23 June 1996. The Con >ference Secretariat is currently preparing two major documents for this >intergovernmental event: (1) the first Report on the State of the >Worlds Plant Genetic Resources and (2) a costed Global Plan of Action for the >Conservation and Sustainable Utilization of Plant Genetic Resources. > >The Report on the State of the Worlds Plant Genetic Resources will cover >both the conservation and utilisation of plant genetic resources. Such >utilisation will be considered in a broad sense which includes use by >breeders and farmers. > >I attach below details of a number of e-mail conferences we have established >on plant breeding/improvement, plant genetic diversity, genebanks, etc, so >as to get broader input to the two documents we are preparing and, perhaps >as importantly, to provide a forum for discussion between individuals >interested in any aspect of plant genetic resources conservation and >utilisation. > >We would welcome your participation in these conferences on any topic you >feel should be included in a Report on the State of the Worlds PGR or in a >Global Plan of Action or indeed any topic related to PGR. Please feel free to >circulate this invitation to join our e-mail conferences to other >of your colleagues in this area or whomever you feel may be interested in >the conference topics. We would wish for as broad a participation as >possible, particularly from developing countries, so if you >know of any developing country individuals, with access to e-mail facilities, >who may be interested let us know or else directly cc our invitation >to them yourselves. > >If you have Internet facilities you may be interested in visiting our >home page http://web.icppgr.fao.org/ where we are displaying a number >of the 125 national reports on the state of plant genetic resources >conservation and utilisation which we have received, to date, as input for >the Technical Conference in 1996. > >Best regards, > >Dr. Charlie Spillane, >Commission on Plant >Genetic Resources / ICPPGR, FAO, >Room: C-710 or B-752,Viale delle terme di Caracalla, >00100 Rome,ITALY. >Tel: 39-6-52255392, Fax: 39-6-52255533 >E-mail: Charles.Spillane@FAO.ORG > > >-----------WHAT FOLLOWS IS INFORMATION ON FAO ELECTRONIC CONFERENCES--------- > > > >(ICPPGR). Presentation of the Bulletin Board Network (BBN) > > >Content of this message: >------------------------ > > A- Introduction of the ICPPGR BBN > B- Content of the Conferences available on the > ICPPGR BBN > C- How can you join us: > C-1 EMail and Telnet users > C-2 TCP-IP and modem users > > Annex 1: Background Information on the ICPPGR > Annex 2: Presentation of FirstClass Software > > > >A- Introduction: >----------------- > >The Food and Agriculture Organization of the United Nations (FAO), >through its "International Conference and Programme for Plant >Genetic Resources" (ICPPGR) is organizing the Fourth International >Technical Conference on Plant Genetic Resources to be held in Leipzig, >Germany, 17-23 June 1996. The ICPPGR is formulating the First >Report on the State of the World's Plant Genetic Resources and a >Global Plan of Action for the Conservation and Sustainable Utilization >of Plant Genetic Resources for Food and Agriculture. Further >information about the ICPPGR is provided in Annex 1. > >To promote the broadest participation in the preparatory process, the >ICPPGR secretariat has establish an electronic bulletin board to allow >interested organizations and individuals to contribute to this process. > This "Bulletin Board Network" (BBN), will support all major types of >communication tools and will provide discussion groups on a set of >topics, as well as providing access to documents, reports, and databases. > >This forum will serve as an input into the formulation of FAO's Report >on the State of the World's Plant Genetic Resources and the >development of a Global Plan of Action. Moreover, the bulletin board >will encourage the plant genetic resources community to communicate >and work together to analyze and solve problems. > >The FAO invites you to join this Forum. You will find in this document >the information you need to subscribe to our Bulletin Board Network. > >The BBN is working now with a Listserv linked to a powerful BBS >named FirstClass. This system supports EMail, Modem and TCP-IP >access for DOS and Macintosh users. All informations, conferences, >databases,reports, notes, etc... are available for each type of user. > >We will also provide to EMail users access to all the information >accessible on our Server: documents, reports, databases and maps as >they become available. By the end of May, this information will also be >available through our Web site (Web.ICPPGR.FAO.ORG). > >----------------------------------------------------------------------------- >Please feel free to contact our Administrator at this addresses for any >help about ICPPGR's Bulletin Board Network: Samy.Gaiji@fao.org >----------------------------------------------------------------------------- > >----------------------------------------------------------------------------- >If you are looking for general information about the preparatory process >for the Fourth International Technical Conference on Plant Genetic >Resources or ICPPGR's activities, please send EMail to: >ICPPGR@fao.org >----------------------------------------------------------------------------- > > >B - Content of the Conferences: >------------------------------------------- > >Six discussion groups are operating now. More will be added later. > >Here is the list of conferences you can subscribe to immediately: > >---------------------------------------------------------------------------- >ICPPGR Conference on "Genetic Diversity" > > >We do not know how much diversity once existed, so we do not know >how much has been lost. Similarly, we do not know how much >genetic diversity of uutility to humankind exists today, so we cannot say for >sure how much remains to be collected. When and how will we know that we >have enough genetic diversity in relation to the types of characters plant >breeders or farmers are interested in? How would such criteria >aid us in conserving for future, unperceived needs? When thinking >about conserving diversity, should we focus on genes, genotypes or >phenotypes? Is genetic erosion a major problem today either in ex situ, in >situ or in farmers fields? If so what are the forces causing it? What can we >do to minimize them? Is there a need for early-warning >systems? What would such a systems look like? > >--------------------------------------------------------------------------- > >ICPPGR Conference on "Plant Breeding" > > >The value of plant genetic resources for food and agriculture ultimately >lies in their utilization. Promoting plant breeding and improvement is >one way of sharing the benefits of these resources. What needs and >problems should the Global Plan of Action address regarding this area? >What kind of linkages need to be made between conservation programmes >and breeding, biotechnology or seed production efforts? What role should the >CGIAR play? The "Green Revolution" succeeded in raising yields, particularly >in high-potential areas. Are different breeding approaches needed for more >marginal areas? Will resources poor farmers in developing countries >benefit from the new biotechnologies? Can more genetic diversity be utilized >in plant breeding? What are the bottlenecks to increasing the use of ex situ >collection by breeders or biotechnologists? Can plant breeding strategies be >changed to maintain more diversity in new varieties? Do farmers still have a >role to play in crop improvement in partnership with scientific plant >breeders? > >---------------------------------------------------------------------------- >ICPPGR Conference on "Ex-Situ Collections": > > >The maintenance of genebank collections is expensive; yet, the number >of genebanks has increased rapidly in the last two decades; and, now, >there are hundreds of thousands of accessions stored in genebanks >around the world. Do we have enough genebanks? Should and can >every country have a long-term storage facility which meets >international standards? Should there be a more limited number of long- >term facilities storing material on behalf of others? Should collections >be "rationalized" and "excess" material be discarded? How could this best be >done? What would a multilateral system of genebanks look like? How should ex- >situ conservation be linked to in-situ strategies? What are the major >obstacles to greater use of ex-situ collections? > >---------------------------------------------------------------------------- >ICPPGR Conference on "Regeneration" > > >Periodically, according to factors peculiar to a species, an accession, or >the conditions under which seed is stored, all genebank accessions must >be regenerated. Regeneration, however, carries with it a number of >risks, including selection, genetic drift or bottlenecking. FAO's Global Plan >of Actionshould include the first safe regeneration of existing ex-situ >collections. What would such a programme look like? What is the scope of the >need? Should all accessions needing regeneration be regenerated >(original and all duplicates)? What are the financial and operational >implications of such initiative? What criteria should define which crops >are regenerated first? > >---------------------------------------------------------------------------- >ICPPGR Conference on "Training/Education" > > >Developing countries need qualified personnel to operate genetic >conservation programmes, engage in plant breeding and >improvement, and handle the many complex policy and legal questions involved >in >this field. What type of training/educational programmes are needed in >the Global Plan of Action? Should short, intensive courses be organized >around specific topics or are longer term courses needed? Should we >concentrate resources onhigher academic levels (University) or practical >technical levels? Which topics are most critical? Which or what kind of >instructor should be involved [professionals and/or practitioners >and/or farmers]? Who should the target audience for such training be? >What would the goals of such efforts be? Is there a need for advanced >courses to be established in developing countries? At what level >[regional/sub-regional]? > >---------------------------------------------------------------------------- >ICPPGR Conference on "In-Situ Conservation" > > >Interest in in-situ (including on-farm) conservation/plant improvement >has exploded in recent years; yet, experience is limited. The Global Plan >of Action must address this area and propose what to do, what direction >to take, what activities to engage in, who to involve, what goals to >pursue. Given the current state of knowledge, what are the next steps to >take in this area? Should in-situ efforts focus only on conservation or >on a mix of conservation and development potential? Can effective >incentives for conservation be introduced? How should in-situ >conservation be linked to ex-situ programmes? > >--------------------------------------------------------------------------- > >Each conferences will be managed by two or more topic managers from >different organizations (FAO, IPGRI and others). They will provide >regularly summaries to participants in each conference. > > >C- How can you join us: >----------------------- > >The Bulletin Board Network is works in three ways: > > - access by EMail > - access through a BBS (Modem or TCP-IP users) > - access through a WEB server (not yet available) > >You must check with your Computer specialist, to know if you have a >TCP-IP or SLIP connection (full internet access). This option can give >you access to our BBS named FirstClass, or to our WEB server soon. >These methods have more facilities to manage the information available >on our BBN. However, you can have access to all the information >through all three methods. > > > > A- You are an E-Mail participant: > --------------------------------- > >This is probably the easiest way to join our BBN. > >If you are in this category, you will use your current EMail software >and conventional Listserv commands to subscribe to Conferences. > >The address of our Listserv is: MAILSERV@MAILSERV.FAO.ORG. > >Here are the available Conferences now: > > - ICPPGR-EX-SITU-L > - ICPPGR-IN-SITU-L > - ICPPGR-DIVERSITY-L > - ICPPGR-REGEN-L > - ICPPGR-TRAINING-L > - ICPPGR-BREEDING-L > >and: > > - ICPPGR-NEWS-L for the ICPPGR newsletter. If you subscribe to >one of the above Conferences, you will be added automatically to this >newsletter. > > ................................. > >To subscribe to one of these conferences: > >1) address your e-mail to MAILSERV@MAILSERV.FAO.ORG > >2) leave the subject line in your header blank > >3) at the beginning of the first line in the body of your > mail, type the following command: > > subscribe > >Example: > > subscribe ICPPGR-BREEDING-L > >4) Once you have successfully subscribed to the Conference, you will >receive a welcome message from the Listserv, with all the details you >need to understand the specific aims of the conference, how you can get >the last report on the conference, how you can find information about, >how you can unsubscribe, etc.... > >Don't delete this message, it will be very useful in the future. > >5) you may post messages to the selected conference by sending them >as an >EMail to: > >@MAILSERV.FAO.ORG > >Example: > > ICPPGR-BREEDING-L@MAILSERV.FAO.ORG > >(Please don't send individual contributions to : >MAILSERV@MAILSERV.FAO.ORG) > > ................................. > >New conferences will be added in a few weeks. To get the up-to-date >list please send an email as follows to: > >MAILSERV@MAILSERV.FAO.ORG > >leave the subject blank, and write in the body: > >LIST > >The Listserv will send you all the available Conference and the >instruction for >subscription. > > > C. S. Prakash Voice (334) 727 - 8023 Tuskegee University Fax (334) 727 - 8067 School of Agriculture,Tuskegee Email: Prakash@Acd.Tusk.Edu Alabama 36088 USA From owner-rapd@net.bio.net Thu Sep 21 23:00:00 1995 Path: biosci!ZOOL.CANTERBURY.AC.NZ!SMITH From: SMITH@ZOOL.CANTERBURY.AC.NZ ("Dr.D.Smith") Newsgroups: bionet.molbio.rapd Subject: Micro DNA extract Date: 21 Sep 1995 20:53:01 -0700 Organization: Zoology, University of Canterbury Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <186252462E0E@zool.canterbury.ac.nz> Reply-To: d.smith@zool.canterbury.ac.nz NNTP-Posting-Host: net.bio.net We're starting some DNA extractions for PCR using the protocol of Rose et al., (Molecular Ecology 3:275). Has anyone had success with this protocol using plant or other animal tissue; also; what is a "sterile pellet mixer", and are there suppliers with a broader ambit than ScotLab which carry them? Thanks, David Smith Zoology Department University of Canterbury, N.Z. From owner-rapd@net.bio.net Sun Sep 24 23:00:00 1995 Path: biosci!nbri.sirnetd.ernet.in!sar From: sar@nbri.sirnetd.ernet.in ("Shirish A. Ranade") Newsgroups: bionet.molbio.rapd Subject: microsatellite primer pcr Date: 24 Sep 1995 20:28:32 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 32 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hi Netters! I have been carrying out amplifications of several plant DNAs using the microsatellite sequences such as (GAA)6, (CAC)5 and (TG)10 as single primers. Of the three primers (GAA)6 and (CAC)5 have revealed specific amplification products while the (TG)10 gave only smears on the gel. Surprisingly when I use these same primer oligonucleotides as end-labelled probes on a S-blot of the same plant DNAs digested with restriction endonucleases, (TG)10 in many cases has revealed a "fingerprint" like profile. Any similar experiences? Any views? In my earlier post to this net I had enquired about similar experiences. Unfortunately for me our e-mail system stopped functioning because of modem faults and I seemingly have missed any replies that may have been sent. Would the colleagues on the net respond once again? Sorry for this extra demand on your time. Thanks in advance. Shirish RANADE >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DR. SHIRISH A. RANADE SNAIL MAIL : CENTRE FOR PLANT MOLECULAR BIOLOGY NATIONAL BOTANICAL RESEARCH INSTITUTE RANA PRATAP MARG, LUCKNOW 226001. (U.P.) INDIA. FAX NOS. : (91) 522 282881 OR 282849 E-MAIL (PERSONAL) : SAR@NBRI.SIRNETD.ERNET.IN E-MAIL (PUBLIC) : MANAGER@NBRI.SIRNETD.ERNET.IN <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< From owner-rapd@net.bio.net Thu Sep 28 23:00:00 1995 Path: biosci!nbri.sirnetd.ernet.in!SAR From: SAR@nbri.sirnetd.ernet.in ("Shirish A. Ranade") Newsgroups: bionet.molbio.rapd Subject: RE : INCONSISTENT RAPD RESULTS Date: 28 Sep 1995 21:13:21 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 34 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hi Netters! Some days back there was a post about inconsistent RAPD results. Sorry I have lost that thread on my mailserver. I too have observed some inconsistencies when working with different plant DNAs. I agree with Phil McClean, North Dakota State University, ND 58105, that the DNA purity is not the criterion as was suggested earlier. In fact if one has to CsCl-purify each DNA and one is analysing a large population, the work involved is tremendous. However, I am not clear by what he means when he says "..be consistent in the level of quality of DNA...". Any elaboration please? Could this simply be an experimental error? If so what should be the best way to inrease reproducibility of the profiles? I am a late entrant to this network. If these questions have already been asked and well answered too, my apologies. In this last instance however, could some one be kind enough to post me some of the dialogue that has already taken place? Thanking you in advance. S.A.Ranade >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DR. SHIRISH A. RANADE SNAIL MAIL : CENTRE FOR PLANT MOLECULAR BIOLOGY NATIONAL BOTANICAL RESEARCH INSTITUTE RANA PRATAP MARG, LUCKNOW 226001. (U.P.) INDIA. FAX NOS. : (91) 522 282881 OR 282849 E-MAIL (PERSONAL) : SAR@NBRI.SIRNETD.ERNET.IN E-MAIL (PUBLIC) : MANAGER@NBRI.SIRNETD.ERNET.IN <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< From owner-rapd@net.bio.net Fri Sep 29 23:00:00 1995 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!EU.net!news.sprintlink.net!gatech!taco.cc.ncsu.edu!news From: David Ley Newsgroups: bionet.molbio.rapd Subject: RAPD Analysis Date: 29 Sep 1995 13:34:16 GMT Organization: North Carolina State University Lines: 11 Message-ID: <44gsko$ade@taco.cc.ncsu.edu> NNTP-Posting-Host: faeppc2.cvm.ncsu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) X-URL: news:bionet.molbio.rapd I am interested in digital imaging methodology for analysis and comparison of RAPD profiles. Does anyone know if/how NIH-Image (freeware for the Mac) can be used to analyze photos of DNA banding patterns resulting from Random Amplified Polymorphic DNA (RAPD) analysis? In particular, I wonder if the Plotting Analysis tool can be used to compare banding patterns from gels run at different times not just within the same gel. I seems to me that some sort of calibration or standardization based on DNA size markers would be needed. Thanks for any help, dl.