From owner-rapd@net.bio.net Tue Aug 01 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!newsfeed.internetmci.com!news.uoregon.edu!vixen.cso.uiuc.edu!uwm.edu!msunews!harbinger.cc.monash.edu.au!news.uwa.edu.au!perth.highway1.com.au!usenet From: biotech@highway1.com.au Newsgroups: bionet.molbio.rapd Subject: Alcohol Interference in PCR Date: 2 Aug 1995 04:31:16 GMT Organization: Highway1 Pty Ltd Lines: 27 Message-ID: <3vmv2k$q7m@perth.highway1.com.au> NNTP-Posting-Host: biotech.highway1.com.au X-Newsreader: AIR News 3.X (SPRY, Inc.) Dear All, I am trying to find some information on the levels of ethanol and butanol which cause interference in PCR. If you have any information or you know of a reference which covers this problem please contact me. Thank you for your help. Keith Norman Research Scientist E-mail to either : Biotechperth@attmail.com Biotech@highway1.com.au Postal Address : Biotech International Ltd. Unit 9, 4 Brodie Hall Drive Technology Park Bentley Western Australia 6102 Phone : (619) 470-4322 Fax : (619) 470-4283 From owner-rapd@net.bio.net Wed Aug 02 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!usenet.eel.ufl.edu!news.gmi.edu!msunews!harbinger.cc.monash.edu.au!bunyip.cc.uq.oz.au!dingo.cc.uq.oz.au!zzrhowde From: zzrhowde@dingo.cc.uq.oz.au (Ross Howden) Newsgroups: bionet.molbio.rapd Subject: Biotechnology company positions Date: 3 Aug 1995 04:41:53 GMT Organization: University of Queensland Lines: 81 Message-ID: <3vpk2h$dee@dingo.cc.uq.oz.au> NNTP-Posting-Host: localhost X-Newsreader: TIN [version 1.2 PL1] ForBio Research is a key part of the ForBio group of companies based in Brisbane which now has branches in Europe, Malaysia and China, with operations planned to commence in the USA within 12 months. The Australian operations currently employ over 50 staff, and it is planned that the international group will expand to 250 personnel within three years. ForBio Research Pty Ltd is the largest private Australian plant biotechnology group, and the largest forest biotechnology research company worldwide. It has a staff of over 30 which will expand to about 40. The company has an overriding commitment to excellence, and operates in well-equipped laboratories in Brisbane, with linkages to the University of Queensland. Applications are sought from outstanding PhD level scientists to strengthen our gene transformation and marker-aided selection programs. Talented Research Assistants are also being appointed in each of these areas as well as to our molecular biology programs. RESEARCH SCIENTISTS (MOLECULAR BREEDING) Quantitative Geneticist or Breeder with a PhD qualification and experience in use of molecular markers is sought for a senior role in our mapping team, developing correlations between quantitative trait loci and map markers using advanced software packages. This group is one of the most productive in the world and expects to generate over a million RAPD reactions per year using automated methods. Ability to manage a dynamic team and to interact with other professionals both within and external to the ForBio group is desirable. The group is also developing capabilities in positional cloning and there is potential for appointees to have direct or indirect participation in this program. RESEARCH SCIENTIST (PLANT TRANSFORMATION) Our transformation team is involved in development of robust transformation systems for an increasing variety of woody plants. Both Agrobacterium and particle bombardment systems are currently used by the group. It is expected that the team will be involved in the development of methods for robot-assisted subculture in association with ForBio Robotics. Interest in the longer-term goal of developing targeted gene insertion methods would be well regarded. A PhD qualified scientist is sought who has relevant technical skills and who will also be able to provide team coordination and communication in areas of responsibility. TECHNICAL SERVICES OFFICER (SCIENTIFIC EQUIPMENT SPECIALIST) An experienced and talented equipment specialist is sought who can provide hands-on maintenance, service and modification of advanced biotechnological equipment worth over a million dollars. A variety of background experience could suit this role, including electronics or operational experience with laboratory equipment, but a strong interest in the operation of computer-controlled biotechnology equipment is essential. The appointee will be broadly responsible for the physical maintenance of equipment (with appropriate outside services), and for assisting in development of new applications. PROGRAM COORDINATOR /COMMUNICATOR A biotechnologist with good writing and communication skills is sought to assist scientists in an active research group, particularly the CEO, with project scoping, reporting and general communication. It is likely that the successful applicant will have a PhD and experience in plant biotechnology or a related field of research, but now wishes to pursue a career in a non-laboratory role. Other skills, such as in documentation of intellectual property, will be well regarded. RESEARCH ASSISTANTS (MOLECULAR BIOLOGY) Graduates, preferably with BSc(Hons) or MSc qualifications, are required to assist molecular biology research studies involving isolation and characterisation of genes, preparation of gene constructs, sequencing, mapping with molecular markers, and related studies. Laboratory research experience will be well regarded, but is not essential for individuals who are eager to learn. ForBio Research has a philosophy of supporting individual creativity to address agreed team goals in a cooperative and harmonious environment. Attractive remuneration packages commensurate with the responsibilities of the respective positions will be negotiated with successful candidates. Applications including a detailed curriculum vitae and the names of three referees should be forwarded by 13 August 1995 to ForBio Research Pty Ltd, 50 Meiers Road, Indooroopilly, Qld, 4068, Email:S.Hedley@forbio.com.au. Further information can be obtained from Ms Edith Mendelle or Professor Bob Teasdale on +61-7-870 5888, fax: +61-7-870 5777 or email: S.Hedley@forbio.com.au. From owner-rapd@net.bio.net Thu Aug 03 23:00:00 1995 Path: biosci!DOLPHIN.UPENN.EDU!stein From: stein@DOLPHIN.UPENN.EDU Newsgroups: bionet.molbio.rapd Subject: postdoc position-wanted Date: 3 Aug 1995 17:39:32 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 37 Sender: daemon@net.bio.net Distribution: world Message-ID: <199508040037.UAA26891@dolphin.upenn.edu> NNTP-Posting-Host: net.bio.net From stein Thu Aug 3 19:54:23 1995 >From stein@dolphin.upenn.edu Thu Aug 3 19:54:23 1995 Received: by dolphin.upenn.edu id TAA25423; Thu, 3 Aug 1995 19:54:23 -0400 Posted-Date: Thu, 3 Aug 1995 19:54:23 -0400 Received-Date: Thu, 3 Aug 1995 19:54:23 -0400 Subject: tr To: stein@dolphin.upenn.edu Date: Thu, 3 Aug 1995 19:54:23 -0400 (EDT) From: stein@alumni.upenn.edu X-Sender: "stein" X-Mailer: ELM [version 2.4 PL23-upenn2.9] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 430 Status: RO *** Please, don't response by command 'reply' *** SUBJECT: Seeking for postdoctoral position in US FIELD: Molecular Biology & Genetics of Oncogenes or Antioncogenes SKILLS: Cloning, sequencing, mutagenesis, PCR (RT-PCR), Southern & Northern blotting, immunoprecipitation, CAT, tissue culture, tumor induction, PC, publications registered in CC, etc. WHEN: available immediately, further information upon request ADDRESS: stein@dolphin.upenn.edu From owner-rapd@net.bio.net Sun Aug 06 23:00:00 1995 Path: biosci!cabi.org!D.BRAYFORD From: D.BRAYFORD@cabi.org ("David Brayford ", IMI) Newsgroups: bionet.molbio.rapd Subject: list of restrictions Date: 7 Aug 1995 04:11:29 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <3025F561@msm.cgnet.com> NNTP-Posting-Host: net.bio.net Dear All I'd like to put together a file listing restriction enzymes and their recognition sequences. Can anyone direct me to an ftp or web site where such a list might be found? I did a search but nothing popped up. Many thanks. Dave Brayford, IMI d.brayford@cabi.org From owner-rapd@net.bio.net Sun Aug 06 23:00:00 1995 Path: biosci!PIRA.CENA.USP.BR!DAVHMOON From: DAVHMOON@PIRA.CENA.USP.BR Newsgroups: bionet.molbio.rapd Subject: Extraction of mite DNA Date: 7 Aug 1995 07:14:13 -0700 Organization: CENA/USP Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <17806A747D4@pira.cena.usp.br> NNTP-Posting-Host: net.bio.net Dear Netters, I have some colleagues trying to extract DNA from whole mites. I would be grateful if anyone out there has any experience or knows of any protocols that have been published. Here are the specific details that were passed to me:- Specie: Brevipalpus phoenicis Family: Tenuipalpidae Super-family: Tetranychoidea Order : Acari Thankyou in advance David H. Moon From owner-rapd@net.bio.net Sun Aug 06 23:00:00 1995 Path: biosci!UKCC.UKY.EDU!EQUIGENE From: EQUIGENE@UKCC.UKY.EDU (Teri Lear) Newsgroups: bionet.molbio.rapd Subject: gene maps Date: 7 Aug 1995 15:17:01 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <199508072216.PAA18950@net.bio.net> NNTP-Posting-Host: net.bio.net Does anyone know if the Yale Human Gene Map Library is still in service? I am having difficulties subscribing. Thanks. Teri L. Lear Dept. of Veterinary Science Gluck Eequine Research Center University of Kentucky Lexington, KY 40546-0099 USA equigene@ukcc.uky.edu From owner-rapd@net.bio.net Sun Aug 06 23:00:00 1995 Path: biosci!CURAGEN.COM!mmckenna From: mmckenna@CURAGEN.COM (Michael McKenna) Newsgroups: bionet.molbio.rapd Subject: Re: list of restrictions Date: 7 Aug 1995 05:57:48 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 31 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Try http://www.gdb.org/Dan/rebase/rebase.html. There is an excellent searchable HTTP version of the REBASE database cross-referenced with vendor availability. It's maintained by Dan Jacobson. -MPM At 4:11 AM 8/7/95, "David Brayford ", IMI wrote: * Dear All * * I'd like to put together a file listing restriction enzymes and their * recognition sequences. * Can anyone direct me to an ftp or web site where such a list might be found? * I did a search but nothing popped up. * Many thanks. * * Dave Brayford, IMI * d.brayford@cabi.org ====================================================================== Michael P. McKenna Senior Research Scientist mmckenna@curagen.com CuraGen Corporation p: (203) 481-1104 x34 322 E. Main Street f: (203) 481-1106 Branford, CT 06405 From owner-rapd@net.bio.net Mon Aug 07 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!newsie.wis.com!NewsWatcher!user From: echtc@wis.com (Craig S. Echt) Newsgroups: bionet.molbio.rapd Subject: Re: list of restrictions Followup-To: bionet.molbio.rapd Date: Mon, 07 Aug 1995 19:18:29 -0500 Organization: Forest Service Research Lines: 62 Distribution: world Message-ID: References: <3025F561@msm.cgnet.com> NNTP-Posting-Host: 199.3.241.121 In article <3025F561@msm.cgnet.com>, D.BRAYFORD@cabi.org ("David Brayford ", IMI) wrote: > > Dear All > > I'd like to put together a file listing restriction enzymes and their > recognition sequences. > Can anyone direct me to an ftp or web site where such a list might be found? > I did a search but nothing popped up. > Many thanks. > > Dave Brayford, IMI > d.brayford@cabi.org New England Biolabs has such a database. Here's information from thier information file: R E B A S E The Restriction Enzyme Database, is a collection of information about restriction enzymes, methylases, the microorganisms from which they have been isolated, recognition sequences, cleavage sites, methylation specificity, the commercial availability of the enzymes, and references - both published and unpublished observations (dating back to 1952). REBASE is updated daily. Each month, a set of REBASE data files are released publically and distributed to the scientific community at no charge via a regular monthly emailing list, and made available at our own anonymous ftp site (vent.neb.com). These data files are flat ASCII text files, many of which we designed specifically for use with a variety of software packages, such as GCG and IntelliGenetics. As REBASE expands, an ever-growing number of new data files are being provided. Requests for additional formats are welcome, as we are prepared to support each major sequence analysis package. REBASE is now accessible via WAIS directly from us as well. Dr. Richard J. Roberts New England BioLabs 32 Tozer Road Beverly, Massachusetts 01915 U.S.A. phone: (508) 927-5054 fax: (508) 921-1527 email: roberts@neb.com REVIEWS: See Nucleic Acids Research 21: 3125-3137, 1993. ****************************************************************************** -- Craig S. Echt Research Geneticist USDA Forest Service Research Rhinelander, WI From owner-rapd@net.bio.net Tue Aug 08 23:00:00 1995 Path: biosci!ns1.faseb.org!darwin.sura.net!mother.usf.edu!news From: tabibzadeh@rics.moffitt.usf.edu (SIAMAK TABIBZADEH) Newsgroups: bionet.molbio.rapd Subject: Frontiers in Bioscience, an electronic journal and virtual library Date: 9 Aug 1995 16:37:09 GMT Organization: Moffitt Cancer Center at USF Lines: 40 Message-ID: <40ao7l$rp6@mother.usf.edu> NNTP-Posting-Host: pc3160.moffitt.usf.edu Mime-Version: 1.0 X-Newsreader: WinVN 0.93.11 Frontiers in Bioscience, an electronic journal and virtual library An electronic journal and virtual library has been created in order to facilitate rapid dissemination of scientific data as well as to provide investigators with numerous online tools for use in their day-to-day research activities. The publication cost is minimized or completely eliminated. A section of the journal is dedicated to publishing manuscripts that contain real time events. Access to a large number of databases is quite easy from the journal. These include databases for analysis of scientific data, search strategies, dictionaries, atlases, tutorials, conferences, information on products of various manufacturers, links to online journals and many other valuable information. Access to the journal and these services is free. The staff members of the journal are in the process of creation of various databases. One such database on gene knockout is already online. The journal can be accessed at the following address on WWW: http://bayanet.com/bioscinece Although submission of data for publication in electronic platforms has just begun, this method of distribution of scientific information would certainly be the logical route of the future. The first volume of the journal to be published around Jan 1996 will contain excellent manuscripts. Please take a moment to examine the journal and consider to send manuscripts for publication in this new and novel forum. The address of the editorial office is as follows: Frontiers in Bioscience S Tabibzadeh, MD, Dept of Pathology University of South Florida 12901 Bruce B Downs Blvd Tampa, FL 33612 Tel: 813-979-7237 Fax: 813-979-3085 E-mail: tabibzadeh@rics.moffitt.usf.edu From owner-rapd@net.bio.net Wed Aug 09 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!convex!darwin.sura.net!mother.usf.edu!news From: tabibzadeh@rics.moffitt.usf.edu (SIAMAK TABIBZADEH) Newsgroups: bionet.molbio.rapd Subject: Frontiers in Bioscience, a journal and virtual library Date: 10 Aug 1995 14:29:23 GMT Organization: Moffitt Cancer Center at USF Lines: 40 Message-ID: <40d543$73c@mother.usf.edu> NNTP-Posting-Host: pc3160.moffitt.usf.edu Mime-Version: 1.0 X-Newsreader: WinVN 0.93.11 Frontiers in Bioscience, a journal and virtual library An electronic journal and virtual library has been created in order to facilitate rapid dissemination of scientific data as well as to provide investigators with numerous online tools for use in their day-to-day research activities. The publication cost is minimized or completely eliminated. A section of the journal is dedicated to publishing manuscripts that contain real time events. Access to a large number of databases is quite easy from the journal. These include databases for analysis of scientific data, search strategies, dictionaries, atlases, tutorials, conferences, information on products of various manufacturers, links to online journals and many other valuable information. Access to the journal and these services is free. The staff members of the journal are in the process of creation of various databases. One such database on gene knockout is already online. The journal can be accessed at the following address on WWW: http://bayanet.com/bioscience Although submission of data for publication in electronic platforms has just begun, this method of distribution of scientific information would certainly be the logical route of the future. The first volume of the journal to be published around Jan 1996 will contain excellent manuscripts. Please take a moment to examine the journal and consider to send manuscripts for publication in this new and novel forum. The address of the editorial office is as follows: Frontiers in Bioscience S Tabibzadeh, MD, Dept of Pathology University of South Florida 12901 Bruce B Downs Blvd Tampa, FL 33612 Tel: 813-979-7237 Fax: 813-979-3085 E-mail: tabibzadeh@rics.moffitt.usf.edu From owner-rapd@net.bio.net Tue Aug 15 23:00:00 1995 Path: biosci!AXE.ACADIAU.CA!002846M From: 002846M@AXE.ACADIAU.CA ("FLYIN' BRIAN") Newsgroups: bionet.molbio.rapd Subject: What bands should be used in Pop. analysis? Date: 16 Aug 1995 13:05:34 -0700 Organization: Acadia University Lines: 26 Sender: daemon@net.bio.net Distribution: world Message-ID: <70A8873323@axe.acadiau.ca> NNTP-Posting-Host: net.bio.net I'm stumped on how to analyze populations using RAPD fragments. I'm not finished collecting the data but it looks like I'm going to have about 1 polymorphic band per primer used in the analysis. My question is how do I use the data to identify populations and generate a dendrogram, or simular tree analysis? Is it OK to simply use only the polymorphic bands for the analysis, use only the polymorphic bands that seem to be population specific (ie: the bands I like) or should I use all the bands generated by the polymorphic primers in a cluster analysis of some kind (suggestions here please if you think this is the way to go)? I have seen people publish using only the polymorphic bands that seemed population specific (Ballinger-Crabtree, M.E., C. Black IV and B.R. Miller 1992) and using all the polymorphic bands generated (Haig, S.M., J.M. Rhymer and D.G. Heckel 1994). Any insights into this question will likely be useful to others so please respond via RAPDnet. Thanks in advance, Brian Merry Acadia University Student From owner-rapd@net.bio.net Wed Aug 16 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!howland.reston.ans.net!gatech!newsxfer.itd.umich.edu!news.emich.edu!emuvax!bio_hannan From: bio_hannan@emuvax.emich.edu Newsgroups: bionet.molbio.rapd Subject: Re: What bands should be used in Pop. analysis? Date: 17 Aug 95 10:12:19 EST Organization: EASTERN MICHIGAN University Lines: 36 Distribution: world Message-ID: <1995Aug17.101219.1@emuvax.emich.edu> References: <70A8873323@axe.acadiau.ca> NNTP-Posting-Host: laurel.emich.edu In article <70A8873323@axe.acadiau.ca>, 002846M@AXE.ACADIAU.CA ("FLYIN' BRIAN") writes: > I'm stumped on how to analyze populations using RAPD fragments. I'm > not finished collecting the data but it looks like I'm going to have > about 1 polymorphic band per primer used in the analysis. > > My question is how do I use the data to identify populations and > generate a dendrogram, or simular tree analysis? Is it OK to simply > use only the polymorphic bands for the analysis, use only the > polymorphic bands that seem to be population specific (ie: the bands > I like) or should I use all the bands generated by the polymorphic > primers in a cluster analysis of some kind (suggestions here please > if you think this is the way to go)? > > I have seen people publish using only the polymorphic bands that > seemed population specific (Ballinger-Crabtree, M.E., C. Black IV and > B.R. Miller 1992) and using all the polymorphic bands generated > (Haig, S.M., J.M. Rhymer and D.G. Heckel 1994). > > Any insights into this question will likely be useful to others so > please respond via RAPDnet. > > Thanks in advance, > Brian Merry > > > Acadia University > Student I would say that it depends on what your sampling scheme was, and what you are asking the data to tell you. Do you have multiple samples per population? Are you somehow summarizing samples to give one set of bands for each population? Do you want some "phenetic" measure of similarity among samples? (then use all markers). Have you thought about using Shannon diversity measure approach for quantifying variation within vs among populations? Gary Hannan From owner-rapd@net.bio.net Wed Aug 16 23:00:00 1995 Newsgroups: bionet.molbio.rapd Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!EU.net!news.sprintlink.net!newsfeed.internetmci.com!qns3.qns.com!news.ecn.uoknor.edu!news.uoknor.edu!ns1.nodak.edu!badlands!wsargent From: wsargent@badlands.NoDak.edu (Wsargent) Subject: ?? ROBOCYCLER ?? Sender: usenet@ns1.nodak.edu (Usenet login) Message-ID: Date: Thu, 17 Aug 1995 19:54:46 GMT Nntp-Posting-Host: badlands.nodak.edu Organization: North Dakota Higher Education Computing Network X-Newsreader: TIN [version 1.2 PL2] Lines: 19 We are in the market for a new thermal cycler and I would appreciate any thoughts, comments or experiences concerning Statagene's Robocycler. It uses a robotic arm to move plate/tubes from block to block, thus eliminating ramping time. Thanx in advance.... WAS ======================================================================== Wayne Sargent Department of Plant Sciences Loftsgard Hall, Room 166 phone : 701-231-8057 North Dakota Sate University fax : 701-231-8474 Fargo, ND 58105 e-mail: wsargent@badlands.NoDak.edu ======================================================================== From owner-rapd@net.bio.net Thu Aug 17 23:00:00 1995 Path: biosci!rutgers!gatech!news.sprintlink.net!EU.net!news2.EUnet.fr!ceph.cephb.fr!linehan From: linehan@ceph.cephb.fr (Paul Linehan) Newsgroups: bionet.molbio.rapd Subject: Robocycler Date: 18 Aug 1995 13:56:22 +0200 Organization: Fondation J. Dausset - CEPH Lines: 30 Distribution: world Message-ID: <411v56$f5a@ceph.cephb.fr> NNTP-Posting-Host: ceph.cephb.fr We are in the market for a new thermal cycler and I would appreciate any thoughts, comments or experiences concerning Statagene's Robocycler. It uses a robotic arm to move plate/tubes from block to block, thus eliminating ramping time. Thanx in advance.... WAS ======================================================================== Wayne Sargent Department of Plant Sciences Loftsgard Hall, Room 166 phone : 701-231-8057 North Dakota Sate University fax : 701-231-8474 Fargo, ND 58105 e-mail: wsargent@badlands.NoDak.edu ======================================================================== Yes, it seems like a good idea But! What about the messy oil step (both before and after)? Paul... From owner-rapd@net.bio.net Thu Aug 17 23:00:00 1995 Path: biosci!agate!news.ucdavis.edu!library.ucla.edu!europa.chnt.gtegsc.com!howland.reston.ans.net!news.sprintlink.net!sunic!sunic.sunet.se!columba.udac.uu.se!populus.slu.se!newsmgr From: Alfred.Szmidt@genfys.slu.se (Alfred E. Szmidt) Newsgroups: bionet.molbio.rapd Subject: Re: What bands should be used in Pop. analysis? Date: 18 Aug 1995 14:18:36 GMT Organization: http://linne.genfys.slu.se Lines: 58 Distribution: world Message-ID: <4127fs$l2g@populus.slu.se> References: <70A8873323@axe.acadiau.ca> NNTP-Posting-Host: b209.genfys.slu.se Mime-Version: 1.0 Content-Type: Text/Plain; charset=ISO-8859-1 X-Newsreader: WinVN 0.99.5 Please read recent papers by Lynch M. and Milligan B. 1994. Analysis of population genetic structure with RAPD markers. Molecular Ecology 3: 91-99. and Clark A. G. and Lanigan C. M. S. 1993. Prospects for Estimating Nucleotide Divergence with RAPDs. Mol. Biol. Evol. 10: 1096-1111. to find answers to your questions. In general, I would suggest to use both poly- and monomorphic bands (and only those that do not show intensity variation, please see our recent paper Lu M.-Z., Szmidt A. E. and Wang X.-R. 1995. Inheritance of RAPD fragments in haploid and diploid tissues of Pinus sylvestris (L.). Heredity 74: 582-589 for details). Our recent study has also demonstrated that in conifers RAPD loci often show departures from H-W which seriously limits usefulnes of such markers for analysis of genetic structure of diploid populations. Best wishes, Alfred E. Szmidt WWW Home Page: http://linne.genfys.slu.se In article <70A8873323@axe.acadiau.ca>, 002846M@AXE.ACADIAU.CA says... > >I'm stumped on how to analyze populations using RAPD fragments. I'm >not finished collecting the data but it looks like I'm going to have >about 1 polymorphic band per primer used in the analysis. > >My question is how do I use the data to identify populations and >generate a dendrogram, or simular tree analysis? Is it OK to simply >use only the polymorphic bands for the analysis, use only the > polymorphic bands that seem to be population specific (ie: the bands > I like) or should I use all the bands generated by the polymorphic > primers in a cluster analysis of some kind (suggestions here please >if you think this is the way to go)? > >I have seen people publish using only the polymorphic bands that >seemed population specific (Ballinger-Crabtree, M.E., C. Black IV and >B.R. Miller 1992) and using all the polymorphic bands generated >(Haig, S.M., J.M. Rhymer and D.G. Heckel 1994). > >Any insights into this question will likely be useful to others so >please respond via RAPDnet. > >Thanks in advance, >Brian Merry > > >Acadia University >Student From owner-rapd@net.bio.net Thu Aug 17 23:00:00 1995 Path: biosci!YVAX.BYU.EDU!anderswr From: anderswr@YVAX.BYU.EDU (W. Ralph Andersen) Newsgroups: bionet.molbio.rapd Subject: Verifying RAPD bands in various genotypes. Date: 18 Aug 1995 08:12:37 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HU7OPW9SYIAFUDI3@yvax.byu.edu> NNTP-Posting-Host: net.bio.net Several workers (including us) are using 4-cutters to verify band similarities in RAPD band positions when comparing species relationships. Most of the time (I'd say maybe 90%+) bands in like positions show similarity by this method. I can see the usual difficulties of certainty even with this added assurance. I am wondering if it is really worth the effort when we are using a pretty big data base anyway----say 5500 scored bands on 5 species. I'd like some feed back. Thanks. Ralph Andersen From owner-rapd@net.bio.net Thu Aug 17 23:00:00 1995 Path: biosci!bcm!news.msfc.nasa.gov!europa.chnt.gtegsc.com!howland.reston.ans.net!news.sprintlink.net!sunic!sunic.sunet.se!columba.udac.uu.se!populus.slu.se!newsmgr From: Alfred.Szmidt@genfys.slu.se (Alfred E. Szmidt) Newsgroups: bionet.molbio.rapd Subject: Re: What bands should be used in Pop. analysis? Date: 18 Aug 1995 14:31:52 GMT Organization: http://linne.genfys.slu.se Lines: 51 Distribution: world Message-ID: <41288o$ljt@populus.slu.se> References: <70A8873323@axe.acadiau.ca> NNTP-Posting-Host: b209.genfys.slu.se Mime-Version: 1.0 Content-Type: Text/Plain; charset=ISO-8859-1 X-Newsreader: WinVN 0.99.5 Please read recent papers by Lynch M. and Milligan B. 1994. Analysis of population genetic structure with RAPD markers. Molecular Ecology 3: 91-99. and Clark A. G. and Lanigan C. M. S. 1993. Prospects for Estimating Nucleotide Divergence with RAPDs. Mol. Biol. Evol. 10: 1096-1111. to find answers to your questions. In general, I would suggest to use both poly- and monomorphic bands (and only those that do not show intensity variation, please see our recent paper Lu M.-Z., Szmidt A. E. and Wang X.-R. 1995. Inheritance of RAPD fragments in haploid and diploid tissues of Pinus sylvestris (L.). Heredity 74: 582-589 for details). Our recent study has also demonstrated that in conifers RAPD loci often show departures from H-W which seriously limits usefulnes of such markers for analysis of genetic structure of diploid populations. Best wishes, Alfred E. Szmidt WWW Home Page: http://linne.genfys.slu.se In article <70A8873323@axe.acadiau.ca>, 002846M@AXE.ACADIAU.CA says... > >I'm stumped on how to analyze populations using RAPD fragments. I'm >not finished collecting the data but it looks like I'm going to have >about 1 polymorphic band per primer used in the analysis. > >My question is how do I use the data to identify populations and >generate a dendrogram, or simular tree analysis? Is it OK to simply >use only the polymorphic bands for the analysis, use only the > polymorphic bands that seem to be population specific (ie: the bands > I like) or should I use all the bands generated by the polymorphic > primers in a cluster analysis of some kind (suggestions here please >if you think this is the way to go)? > > >Thanks in advance, >Brian Merry > > >Acadia University >Student From owner-rapd@net.bio.net Thu Aug 17 23:00:00 1995 Path: biosci!agate!news.ucdavis.edu!library.ucla.edu!info.ucla.edu!news.bc.net!news.uoregon.edu!europa.chnt.gtegsc.com!howland.reston.ans.net!news.sprintlink.net!sunic!sunic.sunet.se!columba.udac.uu.se!populus.slu.se!newsmgr From: Alfred.Szmidt@genfys.slu.se (Alfred E. Szmidt) Newsgroups: bionet.molbio.rapd Subject: Re: What bands should be used in Pop. analysis? Date: 18 Aug 1995 14:34:27 GMT Organization: SLU, Umeå Lines: 42 Message-ID: <4128dj$lk2@populus.slu.se> References: <70A8873323@axe.acadiau.ca> NNTP-Posting-Host: b209.genfys.slu.se X-Newsreader: WinVN 0.92.1 Sorry for repeated postings, I just got mixed up. Please read recent papers by Lynch M. and Milligan B. 1994. Analysis of population genetic structure with RAPD markers. Molecular Ecology 3: 91-99. and Clark A. G. and Lanigan C. M. S. 1993. Prospects for Estimating Nucleotide Divergence with RAPDs. Mol. Biol. Evol. 10: 1096-1111. to find answers to your questions. In general, I would suggest to use both poly- and monomorphic bands (and only those that do not show intensity variation, please see our recent paper Lu M.-Z., Szmidt A. E. and Wang X.-R. 1995. Inheritance of RAPD fragments in haploid and diploid tissues of Pinus sylvestris (L.). Heredity 74: 582-589 for details). Our recent study has also demonstrated that in conifers RAPD loci often show departures from H-W which seriously limits usefulnes of such markers for analysis of genetic structure of diploid populations. Best wishes, Alfred E. Szmidt WWW Home Page: http://linne.genfys.slu.se In article <70A8873323@axe.acadiau.ca>, 002846M@AXE.ACADIAU.CA ("FLYIN' BRIAN") says: > >I'm stumped on how to analyze populations using RAPD fragments. I'm >not finished collecting the data but it looks like I'm going to have >about 1 polymorphic band per primer used in the analysis. >Thanks in advance, >Brian Merry > > >Acadia University >Student From owner-rapd@net.bio.net Thu Aug 17 23:00:00 1995 Path: biosci!bcm!news.msfc.nasa.gov!newsfeed.internetmci.com!news.uoregon.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!tank.news.pipex.net!pipex!oleane!jussieu.fr!news-rocq.inria.fr!news2.EUnet.fr!ceph.cephb.fr!linehan From: linehan@ceph.cephb.fr (Paul Linehan) Newsgroups: bionet.molbio.rapd Subject: Verifying RAPD bands Date: 18 Aug 1995 18:04:00 +0200 Organization: Fondation J. Dausset - CEPH Lines: 24 Distribution: world Message-ID: <412dlg$ilk@ceph.cephb.fr> NNTP-Posting-Host: ceph.cephb.fr Several workers (including us) are using 4-cutters to verify band similarities in RAPD band positions when comparing species relationships. Most of the time (I'd say maybe 90%+) bands in like positions show similarity by this method. I can see the usual difficulties of certainty even with this added assurance. I am wondering if it is really worth the effort when we are using a pretty big data base anyway----say 5500 scored bands on 5 species. I'd like some feed back. Thanks. Ralph Andersen Could someone (maybe Ralph Andersen himself) explain the use of "4 cutters to verify band similarities". I don't fully understand the idea behind this technique. Thanks. Paul... From owner-rapd@net.bio.net Thu Aug 17 23:00:00 1995 Path: biosci!bcm!news.msfc.nasa.gov!europa.chnt.gtegsc.com!gatech!news.sprintlink.net!sunic!sunic.sunet.se!columba.udac.uu.se!populus.slu.se!newsmgr From: Alfred.Szmidt@genfys.slu.se (Alfred E. Szmidt) Newsgroups: bionet.molbio.rapd Subject: Re: What bands should be used in Pop. analysis? Date: 18 Aug 1995 14:28:09 GMT Organization: http://linne.genfys.slu.se Lines: 42 Distribution: world Message-ID: <41281p$l5o@populus.slu.se> References: <70A8873323@axe.acadiau.ca> NNTP-Posting-Host: b209.genfys.slu.se Mime-Version: 1.0 Content-Type: Text/Plain; charset=ISO-8859-1 X-Newsreader: WinVN 0.99.5 Please read recent papers by Lynch M. and Milligan B. 1994. Analysis of population genetic structure with RAPD markers. Molecular Ecology 3: 91-99. and Clark A. G. and Lanigan C. M. S. 1993. Prospects for Estimating Nucleotide Divergence with RAPDs. Mol. Biol. Evol. 10: 1096-1111. to find answers to your questions. In general, I would suggest to use both poly- and monomorphic bands (and only those that do not show intensity variation, please see our recent paper Lu M.-Z., Szmidt A. E. and Wang X.-R. 1995. Inheritance of RAPD fragments in haploid and diploid tissues of Pinus sylvestris (L.). Heredity 74: 582-589 for details). Our recent study has also demonstrated that in conifers RAPD loci often show departures from H-W which seriously limits usefulnes of such markers for analysis of genetic structure of diploid populations. Best wishes, Alfred E. Szmidt WWW Home Page: http://linne.genfys.slu.se In article <70A8873323@axe.acadiau.ca>, 002846M@AXE.ACADIAU.CA says... > >I'm stumped on how to analyze populations using RAPD fragments. I'm >not finished collecting the data but it looks like I'm going to have >about 1 polymorphic band per primer used in the analysis. >Thanks in advance, >Brian Merry > > >Acadia University >Student From owner-rapd@net.bio.net Mon Aug 21 23:00:00 1995 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!EU.net!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!news.bc.net!info.ucla.edu!news.ucdavis.edu!dale!ez049617 From: ez049617@dale.ucdavis.edu (Anne Gillen) Newsgroups: bionet.molbio.rapd Subject: Re: Verifying RAPD bands in various genotypes. Date: 22 Aug 1995 02:38:21 GMT Organization: University of California, Davis Lines: 20 Distribution: world Message-ID: <41bfut$heo@mark.ucdavis.edu> References: <01HU7OPW9SYIAFUDI3@yvax.byu.edu> NNTP-Posting-Host: dale.ucdavis.edu X-Newsreader: TIN [version 1.2 PL2] W. Ralph Andersen (anderswr@YVAX.BYU.EDU) wrote: : Several workers (including us) are using 4-cutters to verify band : similarities in RAPD band positions when comparing species relationships. : Most of the time (I'd say maybe 90%+) bands in like positions show : similarity by this method. I can see the usual difficulties of certainty : even with this added assurance. I am wondering if it is really worth the : effort when we are using a pretty big data base anyway----say 5500 scored : bands on 5 species. I'd like some feed back. Thanks. Ralph Andersen I'd say that given the notorious non repeatability of RAPDs anything that shows that bands are truely similar is useful. What is the use of 5500 scored bands if no one else can repeat them. I attempted to replicate the results of another lab and it was marginally successful. The most prominent polymorphism that I found was the reverse of what was expected. This is just an opinion. For your purposes repeatablity may not be as key as it is for us. Anne From owner-rapd@net.bio.net Tue Aug 22 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: Papers. Date: 22 Aug 1995 22:22:58 -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 please I am looking for some complete reference of the follows articles. 1) Kubelik mentioned in teh paper of Williams et al., 1990. 2)Williams & Kresovich cited in Akopyanz et al., NAR:20:19, 1992. 3)a work of welsh et al., discuting strains having some ancestral antigens. I would like to receive any information. thanks in advance. Alexandro carvalho. INNSZ. Mx From owner-rapd@net.bio.net Wed Aug 23 23:00:00 1995 Path: biosci!LIFSCI.SDSU.EDU!MCCLELLAND From: MCCLELLAND@LIFSCI.SDSU.EDU Newsgroups: bionet.molbio.rapd Subject: inappropriate e-mail Date: 23 Aug 1995 18:24:20 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <950823103458.202012a3@LIFSCI.SDSU.EDU> NNTP-Posting-Host: net.bio.net Does anyone know how to get an e-mail address from the following data? I would like to deluge the person advertising a 900 number with e-mail complaining that a sincere person would use the free e-mail to protest Internet restrictions rather than set up a 900 number. From: SMTP%"johnbach@net" To: MCCLELLAND CC: Subj: Government Restricts Internet!! To: rapd@net.bio.net From: johnbach@net (Restrict) Subject: Government Restricts Internet!! Date: Wed, 23 Aug 1995 15:41:38 GMT Message-ID: <41fi2n$afv@ixnews4.ix.netcom.com> NNTP-Posting-Host: ix-val-ca1-11.ix.netcom.com X-Newsreader: Forte Free Agent 1.0.82 Thanks, Michael From owner-rapd@net.bio.net Wed Aug 23 23:00:00 1995 Path: biosci!ASRR.ARSUSDA.GOV!abartlet From: abartlet@ASRR.ARSUSDA.GOV ("Alan C. Bartlett") Newsgroups: bionet.molbio.rapd Subject: Re: inappropriate e-mail Date: 24 Aug 1995 09:15:25 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <950823103458.202012a3@LIFSCI.SDSU.EDU> NNTP-Posting-Host: net.bio.net We might try to send a message to the address: 41fi2n$afv@ixnews4.ix.netcom.com If that fails, we could try to get information from Netcom. They are a commercial supplier of Internet software and services. In fact, they might be the ones generating the message. I agree that we should do something about such commercial messages on this forum. Alan C. Bartlett "GENES-R-US" "ALTERATIONS AVAILABLE!^" "^some restrictions may apply:)" From owner-rapd@net.bio.net Wed Aug 23 23:00:00 1995 Path: biosci!PIRA.CENA.USP.BR!DAVHMOON From: DAVHMOON@PIRA.CENA.USP.BR Newsgroups: bionet.molbio.rapd Subject: Contact Date: 24 Aug 1995 06:44:04 -0700 Organization: CENA/USP Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <30F8DBE1A22@pira.cena.usp.br> NNTP-Posting-Host: net.bio.net Dear netters, I am not sure if this is the right place to ask this but here goes anyway. I am trying to make contact with Dr. Timothy C. Hall who was at the dept. of genetics, University of Wisconsin about a gene that he cloned, french bean phaseolin. I have tried writting to his address but have received no answer. If anyone has any idea of his whereabouts please let me know. Thanks in advance David From owner-rapd@net.bio.net Thu Aug 24 23:00:00 1995 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.rapd Subject: UNSUBSCRIBING, BIOSCI ARCHIVES, ADDRESS DATABASE & BIOSCI FAQ Date: 25 Aug 1995 02:00:51 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 347 Sender: daemon@net.bio.net Distribution: world Message-ID: <199508250900.CAA18519@net.bio.net> NNTP-Posting-Host: net.bio.net Four important items follow: How to cancel e-mail subscriptions to BIOSCI newsgroups, BIOSCI archive searching, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our BIOSCI user directory, please take a few minutes to complete and return the form below. If your personal information has changed since you listed yourself, please send us a complete new updated form. We can not make manual revisions to existing entries. 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Thanks again for your cooperation! --------------- please cut here and return portion below --------------- New information or Update to old record (enter N or U): date (DD-MM-YY): first name: middle initial: family name: job title: e-mail address: e-mail network: phone number: FAX number: institution: address1: address2: address3: city: state/province: country: postal code: research interest: research interest: comment: comment: comment: comment: comment: From owner-rapd@net.bio.net Sun Aug 27 23:00:00 1995 Path: biosci!DEAKIN.EDU.AU!huangbx From: huangbx@DEAKIN.EDU.AU (Bixing Huang) Newsgroups: bionet.molbio.rapd Subject: How to sequence a RAPD fragment? Date: 28 Aug 1995 00:29:56 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <199508280727.RAA05173@hestia.ccs.deakin.edu.au> NNTP-Posting-Host: net.bio.net Hello Netters, Due to the two ends of RAPD fragment are the same, how do you think to get it sequenced? Wethether it should be cloned or some of other ways to do it. Your suggestions will be very appreciated! Thank you. Bixing Huang This is a sig From owner-rapd@net.bio.net Sun Aug 27 23:00:00 1995 Path: biosci!SASK.USASK.CA!ganeshan From: ganeshan@SASK.USASK.CA Newsgroups: bionet.molbio.rapd Subject: Re: How to sequence a RAPD fragment? Date: 28 Aug 1995 08:04:03 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <199508280727.RAA05173@hestia.ccs.deakin.edu.au> NNTP-Posting-Host: net.bio.net On Mon, 28 Aug 1995, Bixing Huang wrote: > Hello Netters, > > Due to the two ends of RAPD fragment are the same, how do you think to get > it sequenced? Wethether it should be cloned or some of other ways to do it. > Your suggestions will be very appreciated! > > Thank you. > > Bixing Huang > This is a sig > > > I have successfully cloned a RAPD fragment by TA cloning and sequenced it on an ABI 377. Although the ends are same, you will still have the A overhangs, assuming you used a polymerase lacking 3' to 5' exonuclease activity. In fact, to make cloning easy I cranked up the annealing temperature from 36 to 51 degrees C ( the temp. at which only my polymorphic band remained ) and after PCRing, used the reaction straight for cloning without any further purification or manipulation. You can try increasing the annealing temp. few degrees every time and see if you can retain only the fragment of interest. If not, then you have to excise from the gel.... Hope this helps. Pooba U of S From owner-rapd@net.bio.net Sun Aug 27 23:00:00 1995 Path: biosci!MERCURY.UARK.EDU!DRHOADS From: DRHOADS@MERCURY.UARK.EDU ("Douglas Rhoads") Newsgroups: bionet.molbio.rapd Subject: Re: Reptile species via DNA. Date: 28 Aug 1995 09:16:37 -0700 Organization: University of Arkansas Lines: 42 Sender: daemon@net.bio.net Distribution: world Message-ID: <1A93AD03B7@mercury.uark.edu> NNTP-Posting-Host: net.bio.net > To: molecular-evolution@net.bio.net > From: Gregory_Russell.PEDIATRICS@MAILGW.SURG.MED.UMICH.EDU ("Gregory Russell") > Subject: Reptile species via DNA. > Date: 28 Aug 1995 08:10:49 -0700 > REGARDING Reptile species via DNA. > > I am interested in conducting a study on various reptile species and > "sub-species" within one genus in an attempt to sort out the phylogeny and > evolution of species within the genus. > I intend to use RAPDs on nuclear DNA to do this as an initial study. > I would also like to examine a nuclear gene that has a high mutation rate in > an attempt to detect any differences. Sequencing huge chunks of DNA is beyond > the scope of this initial study however, I was wondering if there is a small > region in reptiles (or vertebrates) that would be worth looking at (maybe a > small protein or a highly variable region). > Does anyone have any suggestions???? > > Thanks. > Greg Russell PhD. > (Research Fellow) My favorite would be a ribosomal protein gene using conserved primers. Many ribosomal protein genes are highly conserved and generally single copy functional genes with several pseudogenes. Limited evidence suggests that intron position is conserved for most vertebrates. This allows one to PCR amplify a region containing an intron. The intron containing fragment is distinguished from the PCR products from the pseudogenes. As long as you are dealing with millions of years of evolution a few hundred bases of intron sequence should be informative. No nuclear gene should have a mutation rate as high as a non-coding intron. //========================================================\\ ||Doug Rhoads || Dept. of Biological Sciences|| ||drhoads@mercury.uark.edu || 601 Science Engineering || ||drhoads@uafsysb.uark.edu || University of Arkansas || ||501-575-3251 || Fayetteville, AR 72701 || ==========================================================|| || My Dogma Just Got Run Over by Someone's Karma || \\========================================================// From owner-rapd@net.bio.net Sun Aug 27 23:00:00 1995 Path: biosci!GNU.AI.MIT.EDU!bw From: bw@GNU.AI.MIT.EDU (Bruce Waldman) Newsgroups: bionet.molbio.rapd Subject: Research Position/ New Zealand herps Date: 28 Aug 1995 01:25:50 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 36 Sender: daemon@net.bio.net Distribution: world Message-ID: <199508280823.EAA00146@pogo.gnu.ai.mit.edu> NNTP-Posting-Host: net.bio.net MOLECULAR ECOLOGY OF NEW ZEALAND FROGS AND SKINKS A research position to study behavioural ecology and population genetics of native New Zealand frogs and skinks is available immediately. The successful candidate will be involved in various research projects concerned with the behaviour (e.g. parental care of frog brood) and ecology (e.g. dispersal) of these animals. A major portion of the work will involve analyses of genetic variation within and among populations using PCR-based methodologies (e.g. microsatellites, RAPDs) and other fingerprinting techniques (minisatellites, mtDNA). The application of these methodologies to conservation biology, both with respect to these endangered frogs and skinks, and other threatened New Zealand fauna, will be stressed. Applicants should have experience in methods of DNA purification and analyses. Knowledge of techniques for constructing and screening genomic libraries would be an advantage. Research will also involve fieldwork, surveying behaviour of animals in natural conditions. Funding is initially for one year, with possibilities of extension for a further two years. Applicants should have an M.Sc. or B.Sc. (Honours) in which they have had experience using molecular techniques. Please contact me if you are interested, or would like further details. Letters of application should include details of previous experience with molecular methods, c.v., and names and contact information (phone/fax/email) of referees who know your work. Bruce Waldman Department of Zoology University of Canterbury Christchurch, New Zealand Telephone: +64 3 364 2066 FAX: +64 3 364 2024 Email: bw@gnu.ai.mit.edu From owner-rapd@net.bio.net Mon Aug 28 23:00:00 1995 Path: biosci!VIR.BEKKOAME.OR.JP!shigeos From: shigeos@VIR.BEKKOAME.OR.JP (Shigeo SUGITA) Newsgroups: bionet.molbio.rapd Subject: (none) Date: 29 Aug 1995 04:10:36 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <199508291107.UAA00936@bekkoame.bekkoame.or.jp> NNTP-Posting-Host: net.bio.net shigeos@vir.bekkoame.or.jp From owner-rapd@net.bio.net Wed Aug 30 23:00:00 1995 Path: biosci!rutgers!gatech!udel!news.udel.edu!chopin.udel.edu!not-for-mail From: mcdonald@chopin.udel.edu (John H McDonald) Newsgroups: bionet.molbio.rapd Subject: Re: How to sequence a RAPD fragment? Date: 30 Aug 1995 20:05:39 -0400 Organization: University of Delaware Lines: 21 Message-ID: <422ucj$g9r@chopin.udel.edu> References: <199508280727.RAA05173@hestia.ccs.deakin.edu.au> NNTP-Posting-Host: chopin.udel.edu In article <199508280727.RAA05173@hestia.ccs.deakin.edu.au>, Bixing Huang wrote: > >Due to the two ends of RAPD fragment are the same, how do you think to get >it sequenced? Wethether it should be cloned or some of other ways to do it. >Your suggestions will be very appreciated! > This technique works well for us: 1) Gel purify the fragment to be sequenced. 2) Try a number of 4-cutter restriction enzymes on the fragment. Find an enzyme that cuts the fragment into two pieces that are unequal in size. 3) Gel purify the two fragments, and sequence each one separately by cycle sequencing. John H. McDonald Department of Biology University of Delaware From owner-rapd@net.bio.net Thu Aug 31 23:00:00 1995 Path: biosci!VAXD.DCT.AC.UK!mltajs 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 Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <00995BEA.803FCFDC.33@vaxd.dct.ac.uk> NNTP-Posting-Host: net.bio.net 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. Alan J. Score E-mail : A.J.Score@Abertay-Dundee.Ac.Uk Postal Address : Scottish Institute for Wood Technology, University of Abertay Dundee, Bell Street, Dundee. DD1 1HG. Phone : (01382) 308000 Ext 8675/2918/2917