From owner-rapd@net.bio.net Mon Apr 01 23:00:00 1996 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!news-feed.iguide.com!news.delphi.com!usenet From: lonnie Newsgroups: bionet.molbio.rapd Subject: email address in University of Bielefeld Date: Tue, 2 Apr 96 00:48:53 -0500 Organization: Delphi (info@delphi.com email, 800-695-4005 voice) Lines: 4 Message-ID: NNTP-Posting-Host: bos1f.delphi.com I am lookin gfor the email address for Achim Muller at the University of Bielefeld in Germany. I fyou can help, please email me. Thanks, Lonnie From owner-rapd@net.bio.net Tue Apr 02 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!newsfeed.sunet.se!news00.sunet.se!sunic!mn6.swip.net!plug.news.pipex.net!pipex!tank.news.pipex.net!pipex!newsfeed.internetmci.com!gatech!concert!news-server.ncren.net!taco.cc.ncsu.edu!news From: Susan Jane Hogarth Newsgroups: bionet.molbio.rapd Subject: need software to track primers Date: Tue, 02 Apr 1996 11:17:02 -0500 Organization: North Carolina State University Lines: 27 Message-ID: <316152FE.7DE@unity.ncsu.edu> NNTP-Posting-Host: sparc5c-2203gardnr.ppath.ncsu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; SunOS 5.4 sun4m) Hey, What software do you all use to keep track of your RAPD primers? Something free would be nice. Please email me. thanks lots -- Susan Jane Hogarth "Luck is the residue of design." -- Freddy the Fish "Personally, I'm always ready to learn, although I do not always like being taught." -- Winston Churchill http://www4.ncsu.edu/~sjhogart/public/home.html . .-~\ / `-'\.' `- : | / `._ | | .-. { \ | `-' `. . \ | / ~-.`. \| .-~_ `.\-.\ .-~ \ `-'/~~ -.~ / .-~/|`-._ /~~-.~ -- ~ / | \ ~- . _\ From owner-rapd@net.bio.net Wed Apr 03 23:00:00 1996 Path: biosci!ALPHAC.CIMMYT.MX!ASERRATOS From: ASERRATOS@ALPHAC.CIMMYT.MX ("J. Antonio Serratos", by way of Prakash@Acd.Tusk.edu (C. S. Prakash)) Newsgroups: bionet.molbio.rapd Subject: Proceedings distribution: maize/teosinte gene flow Date: 4 Apr 1996 12:36:22 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 131 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net I am forwarding this announcement posted to a FAO newsgroup as I am confident that this will be of interest to many of you. C. S. Prakash ---------------------------------------------------------------------------- ------------ ANNOUNCING A NEW PUBLICATION By the Mexican National Institute of Forestry, Agriculture and Livestock Research (INIFAP), the Mexican National Agricultural Biosafety Committee (CNBA), and the International Maize and Wheat Improvement Center (CIMMYT): MAIZE-TEOCINTLE AND MAIZE-MAIZE GENE FLOW: IMPLICATIONS FOR TRANSGENIC MAIZE Proceedings of a forum held at CIMMYT headquarters, El Batan, Mexico, in September 1995, involving some 20 biotech and genetic resource specialists -- including Mexican and invited foreign experts. Specific topics include the distribution of teosinte in Mexico, the frequency and intensity of gene flow between maize and teosinte, the flow of genes from improved maize to landraces, and the regulation and risk assessment of the release of transgenic maize in the center of origin of this crop and teosinte The publication will be of interest to a varied readership, including researchers in genetic engineering, private seed company representatives, policymakers in Mexico and other countries wherein are found centers of genetic origin for crop species, and farmers who may eventually wish to sow transgenic seed. Approximately 130 pages, letter size. Spanish and English versions. To request a free copy, send a message to mlistman@cimmyt.mx with your name(and institution or company, where appropriate), address, and other contact information (phone, fax, e-mail address), and the title "Gene Flow Proceedings Request" in the "Re" or "Subject" slot of your message. UNA NUEVA PUBLICACION Del Instituto Nacional de Investigaciones Forestales y Agropecuarias (INIFAP), y el Comite Nacional de Bioseguridad Agricola (CNBA) de Mexico, con la colaboracion del Centro Internacional de Mejoramiento de Maiz y Trigo (CIMMYT): FLUJO GENETICO ENTRE MAIZ MEJORADO, MAIZ CRIOLLO Y TEOCINTLE: IMPLICACIONES PARA EL MAIZ TRANSGENICO Es la memoria de un foro que se llevo a cabo en la sede del CIMMYT, en El Batan, Mexico, en Septiembre de 1995. En este foro participaron aproximadamente 20 especialistas en biotecnologia y recursos geneticos, de Mexico y otros paises. Los temas tratados incluyeron la distribucion del teocintle en Mexico, la frecuencia y la intensidad del flujo genetico entre maiz y teocintle, el flujo de genes de variedades mejoradas e hibridos a razas indigenas, y la reglamentacion y estimacion de riesgos relacionados con la liberacion de maiz transgenico en el centro de origen de este cultivo y del teocintle. La publicacion sera de interes para un publico diverso, que incluye a investigadores de la ingenieria genetica, representantes de empresas semilleras, funcionarios en Mexico y otros paises donde se encuentren los centros de origen de los cultivos domesticados, y los productores que algun dia siembren la semilla transgenica. Aproximadamente 130 paginas, tamano carta. Disponible en Ingles y Espanol Para solicitar un ejemplar gratis, envie un mensaje a mlistman@cimmyt.mx con su nombre (y la institucion o compania , en su caso), direccion, y otra informacion de contacto (numero telefonico o de fax, direccion de correo electronico), y el titulo "Gene Flow Proceedings Request" en la seccion "Re" o "Subject" de su correo electronico. ---------------------------------------------------------------------------- ----------- Take note there is a limited number of copies. J. Antonio Serratos Instituto Nacional de Investigaciones Forestales y Agropecuarias Campo Experimental Valle de Mexico. Km. 38.5 Carretera Mexico-Veracruz via Texcoco. A.P. 10, Chapingo C.P. 56230, edo. de Mexico. MEXICO. Tel. 52-5-9542499 Fax. 52-5-9546728 ----------------------------------------------------------------- CENTRO INTERNACIONAL DE MEJORAMIENTO DE MAIZ Y TRIGO (CIMMYT,INT) International Maize and Wheat Improvement Center - Sustainable Maize and Wheat Systems for the Poor - Lisboa 27 Apdo. Postal 6-641 CP 06600 Mexico, D.F. MEXICO Telephone: +52(5)726-9091 FAX: +52(5)726-7559 ----------------------------------------------------------------- From owner-rapd@net.bio.net Thu Apr 04 23:00:00 1996 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!in1.uu.net!svc.portal.com!news1.best.com!nntp1.best.com!usenet From: Kay Brown Newsgroups: bionet.molbio.rapd Subject: Etiquette for posting a message Date: Thu, 04 Apr 1996 18:01:53 -0800 Organization: Best Internet Communications Lines: 60 Message-ID: <31647F11.6043@best.com> NNTP-Posting-Host: biosoft.vip.best.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win16; I) Dear moderator: I just mailed this reply: ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ We have developed a primer design software package, Primer Premier, which helps you design PCR, sequencing primers and hybridization probes. The program runs on both Windows and Power Macintosh. It has a database facility which can be used to store primers. You can use the program to analyze any stored primers for secondary structures and primer properties such as melting temperature. You can store unlimited number of primers and you can keep them categorized by using separate file for each type. It will automatically generate synthesis forms for easy reordering of primers in the database. Please visit our web site http://www.PremierBiosoft.com for a free demonstration copy. Please contact me if you have any questions or need further assistance. Kay Brown +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ to this inquiry: > Hey, > What software do you all use to keep track of your RAPD primers? > Something free would be nice. Please email me. thanks lots > -- > > Susan Jane Hogarth I would like to know if it would have been acceptable to this news group to POST this reply? I would also like to know if there are any news groups that would welcome the announcement of our new release of version 4 of Primer Premier. Thank you. Kay Brown =============================================================== Premier Biosoft International Developing intuitive software for the molecular biologist 3786 Corina Way, Palo Alto, CA 94303 Phone: 415.856.2703 Fax: 415.843.1250 http://www.PremierBiosoft.com/ =============================================================== From owner-rapd@net.bio.net Sat Apr 06 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!news.cis.okstate.edu!newsfeed.ksu.ksu.edu!news.physics.uiowa.edu!news.uiowa.edu!black.weeg.uiowa.edu!akumar From: "A. Kumar" Newsgroups: bionet.molbio.rapd Subject: sequencing from membranes Date: Sun, 7 Apr 1996 15:39:18 -0500 Organization: University of Iowa, Iowa City, IA, USA Lines: 24 Distribution: world Message-ID: NNTP-Posting-Host: black.weeg.uiowa.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: akumar@black.weeg.uiowa.edu Hi ! I need to sequence same proteins from PVDF blots of 2D gels. Is there a company or University facility that can do this for me ? Kindly post response or send me an email. Thanx Ashish WORKPLACE DEN Dept. of Anatomy, 735 Michael St. Apt 34 College of Medicine, Iowa City University of Iowa, IA 52246-5523 Iowa City, IA 52242 Dial (319)335-7739 (319)338-0529 e : akumar@blue.weeg.uiowa.edu From owner-rapd@net.bio.net Sun Apr 07 23:00:00 1996 Path: biosci!ent.umass.edu!swerle From: swerle@ent.umass.edu (Sean Werle) Newsgroups: bionet.molbio.rapd Subject: Gut fauna of Scarab beetle larvae Date: 7 Apr 1996 19:56:15 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <31689AC5.7455@ent.umass.edu> NNTP-Posting-Host: net.bio.net Hi there, Could anyone refer me to work that has been done looking at the microbes that reside in the guts of Scarabaeid larvae? I know it's a long shot but I figured someone on this list might be able to narrow my search. Any help is greatly appreciated. Sincerely, -- Sean F. Werle Graduate student Department of Entomology UMass, Amherst Work: (413)-545-0268 Web: http://www-unix.oit.umass.edu/~swerle/ **** Finger for PGP public key block **** From owner-rapd@net.bio.net Sun Apr 07 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: Roland Koelliker Newsgroups: bionet.molbio.rapd Subject: Strange smile Date: 8 Apr 1996 09:13:22 +0100 Lines: 15 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4kahr2$bu8@mserv1.dl.ac.uk> X-Sender: rkoellik@patho1 content-length: 539 Original-To: rapd@dl.ac.uk Hi there I always did get nice flat RAPD gels but all of a sudden the second half of the gel seems to run slower than the first and the patterns are bent to the lower right corner of the gel. Does anyone have an idea what could be going on? Thank you for your help. Roland Roland Koelliker Swiss Fed Inst Technol Plant Sciences ETH-Zentrum, LFW-C47 CH-8092 Zurich Tel ++41-1-632 4890 Fax ++41-1-632 1153 e-mail: koelliker@ipw.agrl.ethz.ch From owner-rapd@net.bio.net Mon Apr 08 23:00:00 1996 Path: biosci!ACD1.BYU.EDU!FARMERJ From: FARMERJ@ACD1.BYU.EDU ("James L. Farmer") Newsgroups: bionet.molbio.rapd Subject: summer scientific meeting? Date: 9 Apr 1996 13:16:15 -0700 Organization: Brigham Young University Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <362F08C74B9@acd1.byu.edu> NNTP-Posting-Host: net.bio.net I have funds to attend a scientific meeting but I am not free to go anywhere until July and the funds must be spent by the end of August. Unfortunately, all of the meetings I am aware of on genetics and/or evolution are in April, June, and October. Does anyone know of meetings in July or August? My interests are Drosophila genetics, human genetics, ancient DNA, genetic diversity of natural populations, and evolutionary genetics, not necessarily in that order. Thanks for what I hope will be some good suggestions. James Farmer Dept. of Zoology, 571 WIDB Brigham Young University Provo, Utah 84604-5255, USA FARMERJ@BYU.EDU 801-378-2153 (voice) 801-378-7423 (FAX) From owner-rapd@net.bio.net Mon Apr 08 23:00:00 1996 Path: biosci!daresbury!imbb1.imbb.forth.gr!nefeli.imbb.forth.gr!ANASTASO From: anastaso@nefeli.imbb.forth.gr Newsgroups: bionet.genome.chromosomes,bionet.molbio.rapd Subject: tobacco mutant seeds Date: Tue, 09 Apr 1996 18:37:04 GMT Organization: Imbb-forth,CREtE, creece Lines: 25 Message-ID: <009A0999.B853B614@nefeli.imbb.forth.gr> Reply-To: anastaso@nefeli.imbb.forth.gr NNTP-Posting-Host: nefeli.imbb.forth.gr Xref: biosci bionet.genome.chromosomes:1114 bionet.molbio.rapd:1559 Dear Netters, we are to mutagenise TOBACCO seeds and then select for the mutants In order to map the position of the mutation we would need to tobacco plants that carry known markers; ones that are known to reside at particular chromosomes would be very usefull to our mapping effort. Therefore may we ask anyone who has seeds from such plants to send us some to the address mentioned below. Thank you for your help. Elias Anastassopoulos, Foundation of Research and Technology-Hellas Institute of Molecular Biology and Biotechnology P.O.Box 1527, Heraklion, 711 10, Crete, HELLAS. Fax # (081) 230469 email:anastaso@nefeli.imbb.froth.gr From owner-rapd@net.bio.net Mon Apr 08 23:00:00 1996 Path: biosci!daresbury!imbb1.imbb.forth.gr!nefeli.imbb.forth.gr!ANASTASO From: anastaso@nefeli.imbb.forth.gr Newsgroups: bionet.molbio.rapd Subject: tobacco mutant seeds (email correction) Date: Tue, 09 Apr 1996 22:23:21 GMT Organization: Imbb-forth,CREtE, creece Lines: 25 Message-ID: <009A09B9.55466547@nefeli.imbb.forth.gr> Reply-To: anastaso@nefeli.imbb.forth.gr NNTP-Posting-Host: nefeli.imbb.forth.gr Dear Netters, we are to mutagenise TOBACCO seeds and then select for the mutants In order to map the position of the mutation we would need tobacco plants that carry known markers; ones that are known to reside at particular chromosomes would be very usefull to our mapping effort. Therefore may we ask anyone who has seeds from such plants to send us some to the address mentioned below. Thank you for your help. Elias Anastassopoulos, Foundation of Research and Technology-Hellas Institute of Molecular Biology and Biotechnology P.O.Box 1527, Heraklion, 711 10, Crete, HELLAS. Fax # (081) 230469 email:anastaso@nefeli.imbb.forth.gr From owner-rapd@net.bio.net Wed Apr 10 23:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!pasteur.fr!univ-lyon1.fr!in2p3.fr!swidir.switch.ch!swsbe6.switch.ch!surfnet.nl!howland.reston.ans.net!gatech!taco.cc.ncsu.edu!news From: Susan Jane Hogarth Newsgroups: bionet.molbio.rapd Subject: Re: Strange smile Date: Thu, 11 Apr 1996 06:35:38 -0400 Organization: North Carolina State University Lines: 33 Message-ID: <316CE07A.41C67EA6@unity.ncsu.edu> References: <4kahr2$bu8@mserv1.dl.ac.uk> NNTP-Posting-Host: fliegen.ent.ncsu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; SunOS 4.1.3_U1 sun4m) Caprice Rosato wrote: > We have been using > silver-stained acrylamide to visualize our RAPD results, and we have seen > some bending around the edges. Our analysis would > be enhanced by being able to get the lanes to run closer to parallel > (that is, we could then take advantage of digital analysis rather than > scoring by hand). Isn't there image analysis software that can compensate for "smiling" gels? -- Susan Jane Hogarth "Luck is the residue of design." -- Freddy the Fish "Personally, I'm always ready to learn, although I do not always like being taught." -- Winston Churchill http://www4.ncsu.edu/~sjhogart/public/home.html . .-~\ / `-'\.' `- : | / `._ | | .-. { \ | `-' `. . \ | / ~-.`. \| .-~_ `.\-.\ .-~ \ `-'/~~ -.~ / .-~/|`-._ /~~-.~ -- ~ / | \ ~- . _\ From owner-rapd@net.bio.net Wed Apr 10 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!newsfeed.sunet.se!news00.sunet.se!sunic!mn6.swip.net!plug.news.pipex.net!pipex!tank.news.pipex.net!pipex!newsfeed.internetmci.com!news.uoregon.edu!newsfeed.orst.edu!news.orst.edu!ucs.orst.edu!rosatoc From: Caprice Rosato Newsgroups: bionet.molbio.rapd Subject: Re: Strange smile Date: Wed, 10 Apr 1996 11:50:43 -0700 Organization: Oregon State University Lines: 35 Message-ID: References: <4kahr2$bu8@mserv1.dl.ac.uk> NNTP-Posting-Host: ucs.orst.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: <4kahr2$bu8@mserv1.dl.ac.uk> Hi. Are you running in agarose or acrylamide? We have been using silver-stained acrylamide to visualize our RAPD results, and we have seen some bending around the edges. Currently we are exploring alternative gel matricies (lifted from the literature), with the understanding that our problem may be due to 'drying' at the edges. At the moment we haven't explored this theory other than to take note. Our analysis would be enhanced by being able to get the lanes to run closer to parallel (that is, we could then take advantage of digital analysis rather than scoring by hand). What is the voltage/amperage for your electrophoresis? Caprice Rosato, Fac. Res. Asst., Oregon State University On 8 Apr 1996, Roland Koelliker wrote: > Hi there > I always did get nice flat RAPD gels but all of a sudden the second half of > the gel seems to run slower than the first and the patterns are bent to the > lower right corner of the gel. Does anyone have an idea what could be going on? > Thank you for your help. > Roland > Roland Koelliker > Swiss Fed Inst Technol > Plant Sciences > ETH-Zentrum, LFW-C47 > CH-8092 Zurich > Tel ++41-1-632 4890 > Fax ++41-1-632 1153 > e-mail: koelliker@ipw.agrl.ethz.ch > > > From owner-rapd@net.bio.net Thu Apr 11 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: Louis van de Zande Newsgroups: bionet.molbio.rapd Subject: Re: Strange smile Date: 12 Apr 1996 13:23:53 +0100 Organization: Department of Biology, RUGroningen Lines: 9 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4kli0p$qct@mserv1.dl.ac.uk> Reply-To: L.P.W.G.M.van.de.Zande@biol.RUG.NL Original-To: rapd@dl.ac.UK On Smiling (or frowning) Suppose everything is OK. Gel thickness, tank position, evenly distributed agarose concentration and uniform ion strength. In that case you could check the electrodes for corrosion, salt sedementation or even breaks. Electrophoretic mobility is depending on the electric field so it is crucial that the field is uniform. good luck Louis van de Zande From owner-rapd@net.bio.net Thu Apr 11 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!swrinde!newsfeed.internetmci.com!in2.uu.net!nntp.inet.fi!news.funet.fi!news.helsinki.fi!news From: Kari.Kammiovirta@Helsinki.Fi (Kari Kammiovirta) Newsgroups: bionet.molbio.rapd Subject: Re: Strange smile Date: 12 Apr 1996 08:32:10 GMT Organization: Helsingin Yliopisto Lines: 17 Distribution: bionet Message-ID: <4kl4ea$6it@oravannahka.Helsinki.FI> References: <4kahr2$bu8@mserv1.dl.ac.uk> NNTP-Posting-Host: mmkab-06512.pc.helsinki.fi Mime-Version: 1.0 X-Newsreader: WinVN 0.93.14 In article <4kahr2$bu8@mserv1.dl.ac.uk>, koelliker@ipw.agrl.ethz.ch says... >I always did get nice flat RAPD gels but all of a sudden the second half of >the gel seems to run slower than the first and the patterns are bent to the >lower right corner of the gel. Does anyone have an idea what could be going on? If you are running in agarose horizontal gels it might be that either the gel is little bit thicker on the other side, or that the running 'tank' is little bit tilted on the other side. I always check the position of the casting table and the place where I put the tank and have never suffered so bad tilting that it matters. Cheers, Kari From owner-rapd@net.bio.net Thu Apr 11 23:00:00 1996 Path: biosci!WSUNIX.WSU.EDU!stiff From: stiff@WSUNIX.WSU.EDU (Carol Stiff, by way of Prakash@acd.tusk.edu (C. S. Prakash)) Newsgroups: bionet.molbio.rapd Subject: Post-doc position in Marker Assisted Breeding of Legumes Date: 12 Apr 1996 11:10:07 -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 Please route the following post-doc announcement to anyone interested: Postdoc - Marker Assisted Breeding of Legumes: Candidates must have a Ph.D. in plant breeding or genetics and molecular biology or related fields. Demonstrated experience in use of molecular markers to evaluate progency and germplasm. Responsibilities include introduction of specific traits into Glycine and Vigna lines, assist graduate student research projects, prepare grant proposals and research papers, and evaluate germplasm field plots. Experience in transgenics and interest in East Asian agriculture desirable. Send letter of application, resume, transcripts, addresses and telephone numbers for three references, personal addresses and telephone numbers by 1 June 1996 to: Dr. Thomas Lumpkin, Chair Department of Crop and Soil Sciences Washington State University Pullman, WA 99164-6420 509-335-3471 FAX 509-335-8674 lumpkin@wsu.edu * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Carol M. Stiff Horticulture/Crop Science Plant Tissue Culture Lab 26 Johnson Hall Washington State University, Pullman, WA 99164-6420 509-335-3404 (lab) 208-882-8131 (home) FAX 509-335-8674 stiff@wsunix.wsu.edu * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * From owner-rapd@net.bio.net Sat Apr 13 23:00:00 1996 Newsgroups: bionet.molbio.rapd Path: biosci!rutgers!uwm.edu!cs.utexas.edu!swrinde!howland.reston.ans.net!ix.netcom.com!netcom.com!bks From: bks@netcom.com (Bradley K. Sherman) Subject: Re: Strange smile Message-ID: Organization: {D|R}NA + Sunlight References: <4kli0p$qct@mserv1.dl.ac.uk> Distribution: bionet Date: Sat, 13 Apr 1996 16:28:51 GMT Lines: 10 Sender: bks@netcom18.netcom.com No expert on this but I do recall a seminar where the top three problems in image processing of gels were enumerated as: o gels tilted during run o uneven heat dissipation o uneven initial drag caused by suboptimal comb shape Hope this helps, --bks From owner-rapd@net.bio.net Sun Apr 14 23:00:00 1996 Path: biosci!nbri.sirnetd.ernet.in!sar From: sar@nbri.sirnetd.ernet.in ("Shirish A. Ranade") Newsgroups: bionet.molbio.rapd Subject: Gel Doc. System. Date: 15 Apr 1996 09:10:29 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 42 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hello Netters! Some months back I had posted a query re: a Gel Doc. System. Based on the replies I got then as well as a survey of the various models available for ssale to India, I have narrowed down the possible models of choice for me to just 2. 1. The system from Pharmacia 2. The Nighthawk system from PDI. While the Camera and other system details are comparable, what I wish to know is the utility of the respective softwares of these 2 firms for carrying out RAPD analysis. Pharmacia gives IMAGEMASTER software while PDI is offering me DISCOVERY ssoftware. Are there any among you who have used either or noth of these systemms and softwares? If so, I would be happy to receive any feedback from you about these ssystems. I will be finalising my Indent in the next 10 to 15 days. I DO NOT WAAANNT ANY INFORMATION FROM THE MANUFACTURERS OR THEIR REPRESENTATIVES SINCE I ALREADY HAVE A LOT OF LITERATURE AND FLIERS FROM THEM. Reply at my personal e-mail address as given below. Thanks in advance for any help and information received. 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 Mon Apr 15 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!news.cais.net!newsfeed.internetmci.com!news.cyberhighway.net!usenet From: raclark@cyberhighway.net (Robert Clark) Newsgroups: bionet.molbio.rapd Subject: Re: Strange smile Date: 16 Apr 1996 15:03:21 GMT Organization: CyberHighway Internet Services Lines: 13 Distribution: bionet Message-ID: <4l0crp$s41@host-3.cyberhighway.net> References: <4kahr2$bu8@mserv1.dl.ac.uk> NNTP-Posting-Host: filerpm1-5.cyberhighway.net Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.6 We found a simple way to eliminate migration distortion from submarine agarose gels. If your gel tank has a space between the lid and the wall of the tank (e.g. Owl Scientific apparatus), you can force room temp air into the space to help remove the heat that collects in the air space between the buffer and the lid. We use a very small cheapo-cheapo desktop fan, and direct the airstream at the aforementioned space. We can now increase the voltage, which greatly shortens the run time, and still obtain very straight patterns. Best regards and good luck! --Bob in the Idaho high desert From owner-rapd@net.bio.net Tue Apr 16 23:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.rapd Subject: IMPORTANT - BIOSCI Fundraising Update! Date: 17 Apr 1996 02:00:23 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 154 Sender: daemon@net.bio.net Distribution: world Message-ID: <199604170900.CAA29634@net.bio.net> NNTP-Posting-Host: net.bio.net BIOSCI is about halfway to its funding goal!! I'm interrupting the usual monthly posting of the BIOSCI miniFAQ to bring you up to date on BIOSCI fundraising progress, a topic of concern to your future use of this resource. Thank you in advance for taking the time to read this message carefully. Last year we announced that BIOSCI was going to adopt the U.S. Public Broadcasting System model to fund its operations after our DOE/NSF grant runs out later this year. Unlike PBS, we are not soliciting contributions from users; we are only selling ads on our Web pages solely to cover our operating costs. Our goal is to seek sponsorships until we build up an operating reserve of about $100,000 and then cease further promotions until we need to build the reserve back up. (The accountants among our readership will be familiar with the problem of deferred revenue which we can not safely utilize until ads have been displayed for a period of time.) We are only about halfway to our funding goal and need to raise further funds to avoid having to curtail services at net.bio.net. Fundraising is time-consuming, however, and we need your help as explained further below. Our operating costs consist of our network connection, phone lines, hardware maintenance (we will be getting newer and faster hardware soon!), plus 0.7 FTE of salaries covering UNIX systems admin, technical support, quality assurance, i.e., testing, of our system, and administrative costs (such as the time it takes to actually find/write/call potential sponsors and raise money!). Although the BIOSCI staff does get compensated for a portion of the work that they do, this project has always received a lot of free after-hours and "vacation" time labor, so we hope that no one will begrudge the time that we do charge to the project to serve you. All of the three part-time staff members, Dave Mack, Julie Lawrence, and myself, have full time day jobs and families in addition to working hard to keep this service running for all of you. Julie and Dave Mack are subcontractors for BIOSCI; my time that is charged to the project defrays a portion of my regular salary instead of adding to my income. Besides having to relocate the project, we were very busy this last year building new infrastructure such as our WWW hypermail interface to the system. This was released last December along with scores of WAIS indices for the newsgroups. Virtually everything is complete, although we do continue to find and fix bugs (many through your helpful feedback!). We are still having some problems with our WAIS indexing. The archives continue to grow rapidly. We are running over 100 indexes now versus three previously and any systems crashes cause greater havoc with the indexing than before! We are still working to fix this as fast as our resources permit and appreciate your patience, but we have been able to automate a lot of the infrastructure to reduce labor as compared to past requirements. We have also implemented new software to make moderation of BIOSCI/bionet newsgroups much easier and combat the growing problem of Internet junk mail and USENET "spamming." About 20% of our groups are now moderated, many of them by the BIOSCI staff! This, for example, made a major difference last year in the quality of content in our EMPLOYMENT/bionet.jobs.offered newsgroup which many commercial concerns and recruiting firms are using **without charge** to recruit candidates for positions in the biological sciences. We are also now in a position to have sponsors for individual newsgroups as you will have noticed if you have visited http://www.bio.net/ and clicked on "Access the BIOSCI/bionet newsgroups" recently. So, how can you help?? ---------------------- As noted above it can take a lot of time to contact potential sponsors if I have to do it all myself. Our request is quite simple. You can do two important things which will take very little time for you individually. First, please use our WWW system at http://www.bio.net/ to access the archives. You can now post or reply to messages via your Web browser. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. Our hope is to quickly raise several large corporate/institutional sponsors on our heavily-used WWW locations (some stats appended below), and then end this sponsorship campaign so that our resources can continue to be used for service provision, not fundraising. Many of our specialty newsgroup WWW archives are still used by small communities of scientists (and they haven't been heavily promoted yet). While these may be valuable niche markets to some advertisers, it will generate more labor and overhead having to find these sponsors, fairly price the locations, and deal with lots of smaller sponsorships than fewer mid-to large sponsors. We are striving to keep our operation as lean and efficient as possible since we are not trying to make careers out of running BIOSCI. We are trying if at all possible to avoid the administrative overhead entailed with processing lots of small payments to reach our fundraising goals. I'd like to thank all of you for your help in advance. In helping us, you are also helping yourselves, not only in keeping this resource available for all of the both large and small research communities that we serve, but also by alleviating the need for us to go back and compete with researchers for tight grant dollars! We promised NSF when we were awarded the BIOSCI grant that we would carry out this mission to make the service self-supporting. With your help, we will succeed in continuing BIOSCI's work into its second decade. Thank you very much! Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net A list of our prime WWW sponsorship locations follow. Please contact us for further details. ---------------------------------------------------------------------- The overall BIOSCI WWW pages are currently visited by users from close to 5500 unique computer hosts per week. Web servers only log the Internet computer/host name and frequently more than one individual can connect to us from a particular host. Main home page, http://www.bio.net, visited recently by about 2100 unique hosts per week Main Newsgroups archives page, http://www.bio.net/archives.html, visited recently by about 1200 Unique hosts per week BIO-JOURNALS archive page, http://www.bio.net/BIO-JOURNALS.html, visited recently by about 1000 unique hosts per week. EMPLOYMENT archive pages: http://www.bio.net:80/hypermail/EMPLOYMENT/ and monthly header pages, visited recently by about 800 unique hosts per week. Address database search page, http://www.bio.net/addrsearch.html, visited recently by about 450 unique hosts per week. Methods newsgroup archive pages, http://www.bio.net:80/hypermail/METHDS- REAGNTS/ and monthly header pages, visited recently by about 350 unique hosts per week. Ads can also be displayed on various combinations of other BIOSCI/bionet newsgroups. Please contact us at biosci-help@net.bio.net for details. ---------------------------------------------------------------------- From owner-rapd@net.bio.net Sun Apr 21 23:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!news.belnet.be!swsbe6.switch.ch!swidir.switch.ch!in2p3.fr!oleane!plug.news.pipex.net!pipex!tank.news.pipex.net!pipex!swrinde!cs.utexas.edu!newshost.convex.com!news.onramp.net!usenet From: "Cynthia S. Smagula" <" biota"@onramp.net> Newsgroups: bionet.molbio.rapd Subject: Rapid access to web bioresources Date: Sat, 20 Apr 1996 20:18:53 -0600 Organization: BIOTA Publications Lines: 15 Message-ID: <31799B0D.1608@onramp.net> Reply-To: biota@onramp.net NNTP-Posting-Host: dal25.onramp.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Macintosh; I; PPC) BIOINFORMATION ON THE WORLD WIDE WEB: An Annotated Directory of Molecular Biology Tools comes with URLinks software for instant access to over 600 selected web sites. Just plug it into Netscape and take off! The book contains three core chapters on nucleic acid analysis, genome resources, and protein structural and imaging resources followed by sections on neurobiology & cell biology, medical resources, biotechnology resources, career opportunities and research and funding resources. More information is available at http://www.biota.com/biota Cynthia Smagula biota@onramp.net From owner-rapd@net.bio.net Sun Apr 21 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!info.ucla.edu!news.bc.net!news.sfu.ca!creslab2.biol.sfu.ca!user From: crespi@sfu.ca (Bernard Crespi) Newsgroups: bionet.molbio.rapd Subject: f-statistics Date: Mon, 22 Apr 1996 09:44:07 +0000 Organization: Biological Sciences, Simon Fraser University Lines: 7 Message-ID: References: <009A0999.B853B614@nefeli.imbb.forth.gr> NNTP-Posting-Host: creslab2.biol.sfu.ca Our lab is interested in recommendations for software (any platform, Mac preferred) to do f-statistics on rapd data. Is there a last word on using AMOVA? Thank you in advance, Dave Carmean carmean@sfu.ca From owner-rapd@net.bio.net Mon Apr 22 23:00:00 1996 Path: biosci!GOODALL.UNCG.EDU!nstewart From: nstewart@GOODALL.UNCG.EDU ("Neal Stewart") Newsgroups: bionet.molbio.rapd Subject: amova for rapds Date: 23 Apr 1996 07:38:32 -0700 Organization: University of NC at Greensboro Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <7090C7A098C@goodall.uncg.edu> NNTP-Posting-Host: net.bio.net Hi: One of the latter words about amova, is that Laurant Excoffier and I have a manuscript in press that deals with the use of amova for rapds. It will be published very soon in the Journal of Evolutionary Biology. At last word, the changes we suggest in the analysis will be incorporated into the amova program. More later. Cheers, Neal dnatransgenicsplantsphysiologycanolasoy * * * C. Neal Stewart, Jr. * * Assistant Professor of Biology * * * * Department of Biology * * 312 Eberhart Building * * The University of North Carolina * * Greensboro, NC 27412-5001 USA * * * * voice: 910 334 5391 ext. 22 * * fax: 910 334 5839 * * email: nstewart@goodall.uncg.edu * * http://www.uncg.edu/~cnstewar/ * * * ecologytobaccocranbioreactorinsectbtcry From owner-rapd@net.bio.net Wed Apr 24 23:00:00 1996 Path: biosci!rutgers!concert!news-server.ncren.net!taco.cc.ncsu.edu!news From: Susan Jane Hogarth Newsgroups: bionet.molbio.rapd Subject: Re: RAPD Quality Date: Thu, 25 Apr 1996 12:47:44 -0400 Organization: North Carolina State University Lines: 29 Message-ID: <317FACB0.4AF2@unity.ncsu.edu> References: <317F15D5.6B00@ozemail.com.au> 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 2.0 (X11; I; SunOS 5.4 sun4m) Gary Lum wrote: > > A paper I submitted a while ago criticised my use of RAPD and said I should have performed PFGE. PFGE how? Did they want you to anchor some RAPDs by hybridising to chromosome blots, or what? What organism are you working with? -- Susan Jane Hogarth "Luck is the residue of design." -- Freddy the Fish "Personally, I'm always ready to learn, although I do not always like being taught." -- Winston Churchill http://www4.ncsu.edu/~sjhogart/public/home.html . .-~\ / `-'\.' `- : | / `._ | | .-. { \ | `-' `. . \ | / ~-.`. \| .-~_ `.\-.\ .-~ \ `-'/~~ -.~ / .-~/|`-._ /~~-.~ -- ~ / | \ ~- . _\ From owner-rapd@net.bio.net Wed Apr 24 23:00:00 1996 Path: biosci!rutgers!concert!news-server.ncren.net!taco.cc.ncsu.edu!news From: Susan Jane Hogarth Newsgroups: bionet.molbio.rapd Subject: Re: RAPD Quality Date: Thu, 25 Apr 1996 12:46:10 -0400 Organization: North Carolina State University Lines: 32 Message-ID: <317FAC52.9EB@unity.ncsu.edu> References: <317F15D5.6B00@ozemail.com.au> 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 2.0 (X11; I; SunOS 5.4 sun4m) Gary Lum wrote: > > A paper I submitted a while ago criticised my use of RAPD and said I should have performed PFGE. What can I > do to increase the robustness of my RAPD besides using separate primers, a constant technique and a constant > thermal cycler? > *Vary* all of the parameters you metioned above, and get the same results. That would be impressive... -- Susan Jane Hogarth "Luck is the residue of design." -- Freddy the Fish "Personally, I'm always ready to learn, although I do not always like being taught." -- Winston Churchill http://www4.ncsu.edu/~sjhogart/public/home.html . .-~\ / `-'\.' `- : | / `._ | | .-. { \ | `-' `. . \ | / ~-.`. \| .-~_ `.\-.\ .-~ \ `-'/~~ -.~ / .-~/|`-._ /~~-.~ -- ~ / | \ ~- . _\ From owner-rapd@net.bio.net Wed Apr 24 23:00:00 1996 Path: biosci!.rfhsm.ac.uk!k9mhc From: k9mhc@.rfhsm.ac.uk (Mr Vid Mohan-Ram) Newsgroups: bionet.molbio.rapd Subject: pfge Date: 25 Apr 1996 00:36:16 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: <199604250722.IAA00618@rfhsun2.rfhsm.ac.uk> NNTP-Posting-Host: net.bio.net what IS pfge?? cheers vid From owner-rapd@net.bio.net Wed Apr 24 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!OzEmail!OzEmail!usenet From: Gary Lum Newsgroups: bionet.molbio.rapd Subject: RAPD Quality Date: Thu, 25 Apr 1996 15:34:05 +0930 Organization: OzEmail Pty Ltd - Australia Lines: 8 Message-ID: <317F15D5.6B00@ozemail.com.au> NNTP-Posting-Host: sldar1p28.ozemail.com.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01Gold (Win95; I) A paper I submitted a while ago criticised my use of RAPD and said I should have performed PFGE. What can I do to increase the robustness of my RAPD besides using separate primers, a constant technique and a constant thermal cycler? Any help appreciated. -- Hope you're having a good day Why don't you visit my Home Page http://www.ozemail.com.au/~glum/ From owner-rapd@net.bio.net Fri Apr 26 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!info.ucla.edu!csulb.edu!not-for-mail From: lgeller@csulb.edu (Louis Geller) Newsgroups: bionet.molbio.rapd Subject: Re: pfge Date: 27 Apr 1996 06:49:49 GMT Organization: Cal State Long Beach Lines: 24 Distribution: world Message-ID: <4lsg2d$6av@hatathli.csulb.edu> References: <199604250722.IAA00618@rfhsun2.rfhsm.ac.uk> NNTP-Posting-Host: jaeger.csulb.edu X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Mr Vid Mohan-Ram (k9mhc@.rfhsm.ac.uk) wrote: : what IS pfge?? : : cheers : : vid : -- pfge is Pulsed Field Gel Electrophoresis. It is a technique for the separation of large DNA pieces, even whole Chromosomes. It uses electrical fields that go in many directions, not just up and down. The gel is placed in a circle, and the fields run through the gel, in many directions. By doing so, the DNA molecules are permitted to re-orient themselves periodically, since the direction of the field is changed every few seconds or so. Perhaps for a better explanation, try Biorad or Hoeffer scientific - they probably have a technical bulletin that can be of more help. Hope this helps some Louis Geller Graduate Student, Department of Biology lgeller@csulb.edu From owner-rapd@net.bio.net Sat Apr 27 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!newsflash.concordia.ca!news.nstn.ca!coranto.ucs.mun.ca!news.unb.ca!usenet From: sgriffit@rpc.unb.ca (Steve Griffiths) Newsgroups: bionet.molbio.rapd Subject: RAPD / AP PCR and Context effect Date: 28 Apr 1996 16:35:11 GMT Organization: RPC Lines: 31 Message-ID: <4m06nv$gk6@sol.sun.csd.unb.ca> NNTP-Posting-Host: 198.164.84.57 Summary: Reproducibility of simple profiles Keywords: RAPD ,AP PCR ,Stoffel X-Newsreader: News Xpress Version 1.0 Beta #3 I have been using various manifestations of RAPD for about 3 years to characterize bacterial pathogens affecting aquaculture. Recently I have attempted to use it to characterize an avirulent mutant of Renibacterium salmoninarum causative agent of bacterial kidney disease(BKD) in salmonid fish.The idea was that I would go trough about 120 10mers and see if i could spin out some bands that would distinguish between the wild type and the mutant-- I would subsequently sequence these bands and then extend back over the site on the genome which had been found by a distinguishig primer. The hope was that iwould find either a bp del./sub. or a bonafide deletion.This information would then be used to design a specific PCR test to monitor the persistance of the avirulent mutant in field tials if it was used as a vaccine. Having found that Stoffel fragment generated simpler patterns than regular Taq I stuck with it for this project .Furthermore it always produced LMW profiles with bands suitable for direct cloning( ie 300-700) in pCR II. Of 120 10mers, 4 produced strikingly different profiles for the mutant and wild type; the other profiles were in general identical. The distinguising profiles however were all characterized by their simplicity ie 1 intense band and a afew other minor bands. Although i was aware of the context effect i still had hopes that it would provide me with some pointers to a distinguishing region.Unfortunately,the profiles were not very reproducible,seemingly affected by the batch of mastermix used (!!). Regardless wew cloned 1 of the distinguishing bands and typical luck, it was AT rich and would only amplify when I added TMAC in with the selected primers. This has become a rather longwinded posting (it's my first attempt to get on a naws page) but i would appreciate any observations or suggestions regarding the validity of simple profiles . As usual I suppose there is no generalization! Thank you for your time folks. STEVE G