From owner-rapd@net.bio.net Sun Jan 01 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!news2.near.net!howland.reston.ans.net!swiss.ans.net!newsgate.advantis.net!news-m01.ny.us.ibm.net!news From: albersh@ibm.net Newsgroups: bionet.molbio.rapd Subject: Manipulation of gene and protein sequences Date: 2 Jan 1995 20:59:39 GMT Lines: 10 Message-ID: <3e9pfr$2i4e@news-s01.ny.us.ibm.net> Reply-To: albersh@ibm.net NNTP-Posting-Host: slip18-156.ga.us.ibm.net X-Newsreader: IBM NewsReader/2 v1.03 I am seeking advice on the best available and easiest to use (graphics interface) software for comparing nucleotide and amino acid sequences, searching for repeated motifs, preparing graphic outputs (for example, for publication), and so forth. Ease of transferring sequences from searches of the international data bases is important. My direct e-mail address is palbersh@mond1.ccrc.uga.edu. Thank you for your assistance. Peter Albersheim Complex Carbohydrate Research Center University of Georgia 706-542-4404 From owner-rapd@net.bio.net Mon Jan 02 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!howland.reston.ans.net!torn!nermal.cs.uoguelph.ca!gadwall.cs.uoguelph.ca!jpopi From: jpopi@uoguelph.ca (Jon Popi) Newsgroups: bionet.molbio.rapd Subject: RAPDs and maize populations Date: 3 Jan 1995 14:38:54 GMT Organization: University of Guelph Lines: 7 Message-ID: <3ebnhu$p06@nermal.cs.uoguelph.ca> NNTP-Posting-Host: gadwall.cs.uoguelph.ca X-Newsreader: TIN [version 1.2 PL2] I would like to evaluate the diversity existing within and among 16 maize populations by RAPD analyses. Since the number of populations is pretty high, I would like to analize the smallest number of plants per population that would give reliable results. Does anybody have any information about the number of plants that should be analized? Thank you! Jon From owner-rapd@net.bio.net Tue Jan 03 22:00:00 1995 Path: biosci!newshost.lanl.gov!news.ttu.edu!seas.smu.edu!convex!insosf1.infonet.net!solaris.cc.vt.edu!swiss.ans.net!gatech!news-feed-1.peachnet.edu!hobbes.cc.uga.edu!news From: joesilva@uga.cc.uga.edu Newsgroups: bionet.molbio.rapd Subject: TesT...pls ignore Date: 4 Jan 1995 17:43:38 GMT Organization: University of Georgia, Athens Lines: 6 Message-ID: <3eemoa$jrr@hobbes.cc.uga.edu> Reply-To: joesilva@uga.cc.uga.edu NNTP-Posting-Host: pc57.ccrc.uga.edu X-Newsreader: IBM NewsReader/2 v1.02 This is only a test... --------------------- JoE Silva silva@mond1.ccrc.uga.edu "BanG BanG" - MaxWeLL From owner-rapd@net.bio.net Tue Jan 03 22:00:00 1995 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!pipex!news.oleane.net!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!news.rediris.es!news.cica.es!lucano!bv1pevir From: Rafael Perez Vicente Newsgroups: bionet.molbio.rapd Subject: mtDNA RAPD Date: Tue, 3 Jan 1995 17:40:49 +0100 Organization: Centro Informatico Cientifico de Andalucia Lines: 22 Message-ID: NNTP-Posting-Host: lucano.uco.es Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: bv1pevir@lucano Dear netters, I am looking for information about RAPD as markers to distinguish between mitochondrial genomes. Could any of you refer me to any paper, journal, book etc. to start with? Thanks in advance Rafa Perez Div. Fisiologia Vegetal Fac. Ciencias Univ. Cordoba 14071-Cordoba Spain From owner-rapd@net.bio.net Wed Jan 04 22:00:00 1995 Path: biosci!LIFSCI.SDSU.EDU!MCCLELLAND From: MCCLELLAND@LIFSCI.SDSU.EDU Newsgroups: bionet.molbio.rapd Subject: mapmaker Date: 5 Jan 1995 12:06:38 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 5 Sender: daemon@net.bio.net Distribution: world Message-ID: <950105120442.2020761e@LIFSCI.SDSU.EDU> NNTP-Posting-Host: net.bio.net Dr. Bruno Sobral used Mapmaker extensively on arbitrarily primed PCR products (RAPDs). His number is 619 535 5486. He had a paper on this in Genetics recently. I think his e-mail address is sobral@lifsci.sdsu.edu From owner-rapd@net.bio.net Wed Jan 04 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!netnews.nwnet.net!news.u.washington.edu!toby From: toby@u.washington.edu (Toby Bradshaw) Newsgroups: bionet.molbio.rapd Subject: Re: FAQ??? on band segregation Date: 5 Jan 1995 18:43:41 GMT Organization: University of Washington, Seattle Lines: 26 Message-ID: <3ehekt$9g6@nntp1.u.washington.edu> References: <2F0F7FB29E7@uamercury.uark.edu> NNTP-Posting-Host: stein3.u.washington.edu In article <2F0F7FB29E7@uamercury.uark.edu>, Douglas Rhoads wrote: >This has been discussed in the past but I would be interested in what >computer programs people prefer for determining linkage between RAPD >bands in segregating populations. I have looked at MapMaker and >think it may be able to do what we want but haven't spent that much >time. I am sure there must be a setting to indicate that the entries >are all co-dominant. Hey, who can understand all these manuals and >stuff?? MAPMAKER can deal with all-dominant, all-codominant, and mixed marker sets in an F2. If there is an "H" genotype, the program assumes codominance. Dominant markers are coded A/C (C = "not A", i.e., the "with-band" RAPD phenotype where A is the null homozygote) and B/D, depending on linkage phase. MAPMAKER can group dominant markers with codominant, and can even group repulsion phase dominant markers given sufficient numbers. It has a hard time ordering repulsion phase dominant markers, of course, so you generally end up with coupling-only maps if you use a mixed marker set. Toby Bradshaw | (206)616-1796 (voice) Center for Urban Horticulture GF-15 | (206)616-1826 (FAX) University of Washington | toby@u.washington.edu Seattle WA 98195 | Will make linkage maps for food. From owner-rapd@net.bio.net Wed Jan 04 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!uhog.mit.edu!nntp.club.cc.cmu.edu!newsfeed.pitt.edu!uunet!fonorola!inforamp.net!woody16.inforamp.net!intermed From: intermed@inforamp.net (Ian Clarke) Newsgroups: bionet.molbio.rapd Subject: Attention Canadian Researchers Date: Thu, 5 Jan 1995 12:58:33 Organization: InfoRamp Inc. Lines: 19 Message-ID: NNTP-Posting-Host: woody16.inforamp.net X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Inter Medico is the Canadian distributor for many of the world's leading molecular biology companies. Inter Medico represents Genzyme(cytokines, chemokines, cell adhesion molecules), Novagen (pET bacterial expression systems, mRNA purification systems), Amresco (fine chemicals, thermostable DNA polymerases, nucleic acid isolation kits), SLT (ELISA readers, fluorometers, microplate washers), BioDesign (a huge selection of biologically important antibodies), and The Binding Site ( clinically-relevant antibody-based diagnostic systems). As part of Inter Medico's continuing dedication to the Canadian research community, we have established a user-group to share the latest information about molecular biology products designed to save you time and money. There are valuable discounts available only to subscribers. There is no charge to join. If you are interested in joining, please send an e-mail message to Majordomo@inforamp.net. In the body of the letter, type Subscribe Research . Join today, and start enjoying the benefits immediately. From owner-rapd@net.bio.net Wed Jan 04 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!torn!nermal.cs.uoguelph.ca!gadwall.cs.uoguelph.ca!jpopi From: jpopi@uoguelph.ca (Jon Popi) Newsgroups: bionet.molbio.rapd Subject: Re: RAPDs and maize populations Date: 5 Jan 1995 16:40:36 GMT Organization: University of Guelph Lines: 33 Message-ID: <3eh7e4$m1d@nermal.cs.uoguelph.ca> References: <3ebnhu$p06@nermal.cs.uoguelph.ca> NNTP-Posting-Host: gadwall.cs.uoguelph.ca X-Newsreader: TIN [version 1.2 PL2] Phil McClean (mcclean@PROBLEM_WITH_INEWS_DOMAIN_FILE) wrote: : Jon Popi (jpopi@uoguelph.ca) wrote: : : I would like to evaluate the diversity existing within and among 16 maize : : populations by RAPD analyses. Since the number of populations is pretty : : high, I would like to analize the smallest number of plants per population : : that would give reliable results. Does anybody have any information : : about the number of plants that should be analized? : Before this question can be answered, we would need to know what is the level of : inbreeding, or what is the genetic structure of the lines? Only then can a estimate : be made of the amount of residual variation exists in your lines and how many : plants be line need to be sampled. : Phil McClean : Dept. of Plant Sciences : North Dakota State University : Fargo, ND 58105 USA : mcclean@plains.nodak.edu First of all, thank you for trying to help me. Here is a little clarification of my problem: I am not dealing with inbred lines, but with populations, which possess quite a bit of variability. So, I would like to know what is the smallest number of plants that I need for RAPD analyses in order to have that variability represented accurately enough. Thank you again! Jon Popi Crop Science Department University of Guelph Guelph, Ontario N1G 2W1, Canada jpopi@crop.uoguelph.ca From owner-rapd@net.bio.net Wed Jan 04 22:00:00 1995 Path: biosci!MERCURY.UARK.EDU!DRHOADS From: DRHOADS@MERCURY.UARK.EDU ("Douglas Rhoads") Newsgroups: bionet.molbio.rapd Subject: FAQ??? on band segregation Date: 5 Jan 1995 08:05:00 -0800 Organization: University of Arkansas Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <2F0F7FB29E7@uamercury.uark.edu> NNTP-Posting-Host: net.bio.net This has been discussed in the past but I would be interested in what computer programs people prefer for determining linkage between RAPD bands in segregating populations. I have looked at MapMaker and think it may be able to do what we want but haven't spent that much time. I am sure there must be a setting to indicate that the entries are all co-dominant. Hey, who can understand all these manuals and stuff?? //========================================================\\ ||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 Wed Jan 04 22:00:00 1995 Newsgroups: bionet.molbio.rapd Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!netnews.nwnet.net!ns1.nodak.edu!beangenes.cws.ndsu.nodak.edu!mcclean From: mcclean@PROBLEM_WITH_INEWS_DOMAIN_FILE (Phil McClean) Subject: Re: RAPDs and maize populations Sender: usenet@ns1.nodak.edu (Usenet login) Message-ID: Date: Thu, 5 Jan 1995 14:58:53 GMT References: <3ebnhu$p06@nermal.cs.uoguelph.ca> Nntp-Posting-Host: beangenes.cws.ndsu.nodak.edu Organization: I need to put my ORGANIZATION here. X-Newsreader: TIN [version 1.2 PL2] Lines: 18 Jon Popi (jpopi@uoguelph.ca) wrote: : I would like to evaluate the diversity existing within and among 16 maize : populations by RAPD analyses. Since the number of populations is pretty : high, I would like to analize the smallest number of plants per population : that would give reliable results. Does anybody have any information : about the number of plants that should be analized? Before this question can be answered, we would need to know what is the level of inbreeding, or what is the genetic structure of the lines? Only then can a estimate be made of the amount of residual variation exists in your lines and how many plants be line need to be sampled. Phil McClean Dept. of Plant Sciences North Dakota State University Fargo, ND 58105 USA mcclean@plains.nodak.edu From owner-rapd@net.bio.net Wed Jan 04 22:00:00 1995 Newsgroups: bionet.molbio.rapd Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!netnews.nwnet.net!ns1.nodak.edu!beangenes.cws.ndsu.nodak.edu!mcclean From: mcclean@PROBLEM_WITH_INEWS_DOMAIN_FILE (Phil McClean) Subject: Re: mtDNA RAPD Sender: usenet@ns1.nodak.edu (Usenet login) Message-ID: Date: Thu, 5 Jan 1995 14:56:22 GMT References: Nntp-Posting-Host: beangenes.cws.ndsu.nodak.edu Organization: I need to put my ORGANIZATION here. X-Newsreader: TIN [version 1.2 PL2] Lines: 20 Rafael Perez Vicente (bv1pevir@lucano.uco.es) wrote: : Dear netters, : I am looking for information about RAPD as markers to distinguish between : mitochondrial genomes. You will not be able to distinguish between nuclear and organelle polymorphisms with a total DNA prep. Therefore to score mtDNA variation you will have to isloate mtDNA separately from the remaining DNA. If you to do that, I would think it would be cheaper to just use restricition enzymes to cut the DNA. BTW---what species are you working with, that would help also for us to provide suggestions. Phil McClean Dept. of Plant Sciences North Dakota State University Fargo, ND 58105 USA mcclean@plains.nodak.edu From owner-rapd@net.bio.net Wed Jan 04 22:00:00 1995 Path: biosci!MERCURY.UARK.EDU!DRHOADS From: DRHOADS@MERCURY.UARK.EDU ("Douglas Rhoads") Newsgroups: bionet.molbio.rapd Subject: Re: mtDNA RAPD Date: 4 Jan 1995 07:38:18 -0800 Organization: University of Arkansas Lines: 31 Sender: daemon@net.bio.net Distribution: world Message-ID: <2D884CE50A7@uamercury.uark.edu> > To: rapd@net.bio.net > From: Rafael Perez Vicente > Subject: mtDNA RAPD > Date: Tue, 3 Jan 1995 17:40:49 +0100 > > Dear netters, > > I am looking for information about RAPD as markers to distinguish between > mitochondrial genomes. > > Could any of you refer me to any paper, journal, book etc. to start with? > > Thanks in advance > > Rafa Perez > Div. Fisiologia Vegetal I wouldn't recommend RAPD as a method for looking at mtDNA. Since the mt genome is less than 0.01% of the total genome complexity in most eukaryotes (<0.001% in a lot) then less than 1 in 10000 RAPD bands will be from mtDNA. Why not design specific PCR primers based on known mtDNA sequences? //========================================================\\ ||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 Wed Jan 04 22:00:00 1995 Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins,bionet.molbio.rapd,bionet.molbio.yeast,bionet.mycology,bionet.n2-fixation,bionet.neuroscience,bionet.photosynthesis,bionet.plants,bionet.population-bio,bionet.software,bionet.software.acedb,bionet.software.gcg,bionet.users.addresses,bionet.virology,bionet.women-in-bio,bionet.xtallography,biz.americast,biz.books.technical,biz.comp.hardware Path: biosci!bloom-beacon.mit.edu!gatech!newsfeed.pitt.edu!uunet!xnet!quake.xnet.com!research From: crta@xnet.com (Norman Fraley) Subject: New Research & Testing Association Formed Message-ID: Sender: news@amiserv.chi.il.us Nntp-Posting-Host: research.crta.org Organization: Contract Research & Testing Association X-Newsreader: News Xpress Version 1.0 Beta #2 Date: Thu, 5 Jan 1995 20:53:53 GMT Lines: 66 Xref: biosci bionet.molbio.methds-reagnts:22623 bionet.molbio.proteins:3374 bionet.molbio.rapd:925 bionet.molbio.yeast:2110 bionet.mycology:1351 bionet.neuroscience:5641 bionet.photosynthesis:527 bionet.plants:4862 bionet.population-bio:1001 bionet.software:10553 bionet.software.acedb:518 bionet.software.gcg:897 bionet.users.addresses:2135 bionet.virology:1302 bionet.women-in-bio:1694 bionet.xtallography:1410 biz.americast:1037 biz.books.technical:741 biz.comp.hardware:7143 As the primary resource of research information, the Internet was the primary choice for making all concerned individuals aware of the formation of the Contract Research & Testing Association. CRTA is an International Association designed to serve the needs of contract research, product and process development organizations and consultants throughout the world. Contract research organizations have specific public, governmental, and industry perception and promotion needs which are not addressed by existing scientific industry associations. CRTA operates as a non-profit, tax-exempt, corporation eligible for scientific research and public awareness charitable organization contributions as provided for in the IRC 501(c)(3) provisions. Being a scientific research and public awareness related organization, CRTA exists to benefit its members by providing: 1) An organization devoted to the promotion of Contract Research. 2) A unified voice on matters of common interest or concern. 3) Point of contact for media relations relative to contract research. 4) Business opportunity referrals as a research clearinghouse. 5) Professional networking opportunities for its members. 6) Periodic publishing of information beneficial to the membership. 7) Periodic dissemination of applicable research results to the public. 8) Governmental representation on issues affecting CRO's. 9) Public promotion of the strengths of its membership. 10) A directory of Contract Research Organizations and Consultants. CRTA will provide: 1) A forum for the exchange of information. 2) Formal recognition to the CRO's role in business. 3) Standards for the professionals so engaged. 4) Representation the profession in matters of common interest. 5) The development of techniques and methods to improve the practice and management of CROs. CRTA will also offer: 1) A monthly news publication. 2) Annual meetings 3) Active promotional media publicity programs. 4) A professional placement service 5) A Contract Research Service Directory. 6) Media topics and contacts directory If you have an interest in joining the Contract Research & Testing Association, please E-mail your reply to crta@xnet.com. Please include: 1) The word "membership" in your RE: or header information, 2) Your interest in the association / your area of work, 3) Your dues payment preference (check, money order, credit card, company check, wire xfer, etc.) DO NOT INCLUDE ANY CREDIT CARD INFORMATION! Only your preference for the manner of payment. 4) Most importantly, your email address, and additional contact information if you desire. We will then e-mail membership information and ALL FURTHER INFORMATION directly to you at your email location. Thank you for taking the time to read this announcement. If membership in this program this does not appeal to you, thank you for your patience and understanding. Sincerely, Membership Department Contract Research & Testing Association Best Regards, Norman Fraley CRTA@xnet.com Executive Director BBS:708-515-0494 Contract Research & Testing Association From owner-rapd@net.bio.net Thu Jan 05 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!hookup!uwm.edu!psuvax1!news.pop.psu.edu!hudson.lm.com!netline-fddi.jpl.nasa.gov!nntp-server.caltech.edu!ingber From: ingber@alumni.caltech.edu (Lester Ingber) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins,bionet.molbio.rapd,bionet.molbio.yeast,bionet.mycology,bionet.n2-fixation,bionet.neuroscience,bionet.photosynthesis,bionet.plants,bionet.population-bio,bionet.software,bionet.software.acedb,bionet.software.gcg,bionet.users.addresses,bionet.virology,bionet.women-in-bio,bionet.xtallography,biz.americast,biz.books.technical,biz.comp.hardware Subject: Re: New Research & Testing Association Formed Date: 6 Jan 1995 14:04:51 GMT Organization: California Institute of Technology, Alumni Association Lines: 165 Message-ID: <3ejim3$eiq@gap.cco.caltech.edu> References: Reply-To: ingber@alumni.caltech.edu NNTP-Posting-Host: alumni.caltech.edu Xref: biosci bionet.molbio.methds-reagnts:22646 bionet.molbio.proteins:3383 bionet.molbio.rapd:927 bionet.molbio.yeast:2117 bionet.mycology:1356 bionet.neuroscience:5655 bionet.photosynthesis:528 bionet.plants:4871 bionet.population-bio:1002 bionet.software:10566 bionet.software.acedb:519 bionet.software.gcg:898 bionet.users.addresses:2136 bionet.virology:1305 bionet.women-in-bio:1699 bionet.xtallography:1412 biz.americast:1044 biz.books.technical:744 biz.comp.hardware:7159 Norman: I like the concept of what you are trying to form, and so I would like to explain why I will not join now, but might be interested at some future time. My criticism is meant to be constructive, and I hope it will be accepted in this context. Since I think your organization is a great idea, I'm making my response public so that other researchers who might be turned off by some of these problems in your presentation also will keep an open mind to joining your organization in the future. (You really did span quite few bulletin boards!) : From crta@xnet.com Thu Jan 5 21:47:00 1995 : Return-Path: : Date: Thu, 5 Jan 1995 23:46:55 -0600 : From: Norman Fraley : To: ingber@alumni.caltech.edu : Subject: Membership information for CRTA : : Dear Mr. Ingber : : WHAT IS CRTA? : : CRTA, formally known as the Contract Research and Testing Association, is : an : international scientific organization whose primary objective is to build : awareness of the role of contract research in industry and in society, : represent the industry in matters of common interest and to provide a forum : for the exchange of ideas and techniques in the fields of Testing and : Applied : Research. If you are appealing to a large audience over the InterNet, you should follow some commonly accepted guidelines, e.g., delivering text in a most readable format, e.g., limiting lines to 79 characters, so that lines do not spill over on most 80-character screens. This is the most vital context of my critique, that you will not come across as a knowledgeable and professional organization unless you present yourself as such. For example, I put your 424-line e-mail reply to my follow-up to this posting through ispell, and here is a partial list which also does not register in `webster`: copywrite lnternational nonanalytical nonmicrobiology proovided spectroscopists toxicologists : CRTA is known for the efforts it has made in helping to promote the new and : rapidly growing industry of contract research. This is accomplished by a : network of nearly 700 commercial, industry, government, and academic : laboratories and individual product and process development consultants. : These promotional activities and other CRTA programs offer you, the : technical : professional, avenues for professional growth and recognition that only an : organization of CRTA's caliber can provide ... plus access to a wellspring : of : analytical, research and technical information. I question whether you already have such a membership, or this is what you aspire to? This is a reasonable question. Many people, like myself, are more sympathetic to an honest statement from a new operation, than to misleading advertisements. I note a number of journals and publications you (intend to?) make available, and I expect they have a price. Your fees for members of $125/yr is fair, if all these services are available now. All this is fine, but those prices should be stated up front. : Email: crta@xnet.com : WWW: www.xnet.com/~crta I tried this site, http://www.xnet.com/~crta, and found a short notice that it is under construction. I think it better to first do your homework, before advertising such a site, especially since you really are charging commercial rates for a commercial venture, your non-profit status notwithstanding. : copywrite 1994 Contract Research & Testing Association. This one is a real killer, demonstrating that you are not sensitive to one of the main concerns of contract research, the copyright (not the "copywrite"). Lester In article , Norman Fraley wrote: :As the primary resource of research information, the Internet was the :primary choice for making all concerned individuals aware of the formation :of the Contract Research & Testing Association. : :CRTA is an International Association designed to serve the needs of contract :research, product and process development organizations and consultants :throughout the world. Contract research organizations have specific public, :governmental, and industry perception and promotion needs which are not addressed :by existing scientific industry associations. CRTA operates as a non-profit, :tax-exempt, corporation eligible for scientific research and public awareness :charitable organization contributions as provided for in the IRC 501(c)(3) provisions. : :Being a scientific research and public awareness related organization, CRTA :exists to benefit its members by providing: : : 1) An organization devoted to the promotion of Contract Research. : 2) A unified voice on matters of common interest or concern. : 3) Point of contact for media relations relative to contract research. : 4) Business opportunity referrals as a research clearinghouse. : 5) Professional networking opportunities for its members. : 6) Periodic publishing of information beneficial to the membership. : 7) Periodic dissemination of applicable research results to the public. : 8) Governmental representation on issues affecting CRO's. : 9) Public promotion of the strengths of its membership. : 10) A directory of Contract Research Organizations and Consultants. : :CRTA will provide: : 1) A forum for the exchange of information. : 2) Formal recognition to the CRO's role in business. : 3) Standards for the professionals so engaged. : 4) Representation the profession in matters of common interest. : 5) The development of techniques and methods to improve the practice and : management of CROs. : :CRTA will also offer: : 1) A monthly news publication. : 2) Annual meetings : 3) Active promotional media publicity programs. : 4) A professional placement service : 5) A Contract Research Service Directory. : 6) Media topics and contacts directory : :If you have an interest in joining the Contract Research & Testing Association, :please E-mail your reply to crta@xnet.com. Please include: : :1) The word "membership" in your RE: or header information, :2) Your interest in the association / your area of work, :3) Your dues payment preference (check, money order, credit card, company check, wire xfer, etc.) : DO NOT INCLUDE ANY CREDIT CARD INFORMATION! Only your preference for the manner of payment. :4) Most importantly, your email address, and additional contact information if you desire. : :We will then e-mail membership information and ALL FURTHER INFORMATION :directly to you at your email location. Thank you for taking the time :to read this announcement. If membership in this program this does not :appeal to you, thank you for your patience and understanding. : :Sincerely, :Membership Department :Contract Research & Testing Association : : :Best Regards, : :Norman Fraley CRTA@xnet.com :Executive Director BBS:708-515-0494 :Contract Research & Testing Association -- /* Prof. Lester Ingber * * Lester Ingber Research E-Mail: ingber@alumni.caltech.edu * * P.O. Box 857 WWW: http://alumni.caltech.edu/~ingber/ * * McLean, VA 22101 Archive: ftp.alumni.caltech.edu:/pub/ingber/ */ From owner-rapd@net.bio.net Thu Jan 05 22:00:00 1995 Path: biosci!esvax.dnet.dupont.com!rafalski From: rafalski@esvax.dnet.dupont.com Newsgroups: bionet.molbio.rapd Subject: Commercial message - inappropriate Date: 6 Jan 1995 05:15:17 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: <9501061311.AA02171@esds01.es.dupont.com> NNTP-Posting-Host: net.bio.net I believe the commercial message from "intermed@inforamp.net" "Ian Clarke" recently sent to the RAPD forum on Bionet is entirely inappropriate. These guys want to benefit from Bionet by advertising their distributorship and other services. Antoni Rafalski From owner-rapd@net.bio.net Fri Jan 06 22:00:00 1995 Newsgroups: bionet.molbio.rapd Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!usc!howland.reston.ans.net!pipex!news.oleane.net!oleane!jussieu.fr!univ-lyon1.fr!ghost.dsi.unimi.it!news.graphics.cornell.edu!newsstand.cit.cornell.edu!travelers.mail.cornell.edu!cornell!uw-beaver!netnews.nwnet.net!ns1.nodak.edu!plains!comstock From: comstock@plains.NoDak.edu (Clay Comstock) Subject: Research Methods Sender: usenet@ns1.nodak.edu (Usenet login) Message-ID: Date: Sat, 7 Jan 1995 19:32:36 GMT Nntp-Posting-Host: plains.nodak.edu Organization: North Dakota Higher Education Computing Network X-Newsreader: TIN [version 1.2 PL2] Lines: 1 From owner-rapd@net.bio.net Fri Jan 06 22:00:00 1995 Path: biosci!GPU.SRV.UALBERTA.CA!ryang From: ryang@GPU.SRV.UALBERTA.CA (Rong Yang) Newsgroups: bionet.molbio.rapd Subject: Re: RAPDs and maize populations Date: 7 Jan 1995 09:15:45 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 59 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <3eh7e4$m1d@nermal.cs.uoguelph.ca> NNTP-Posting-Host: net.bio.net On 5 Jan 1995, Jon Popi wrote: > Date: 5 Jan 1995 16:40:36 GMT > From: Jon Popi > To: rapd@net.bio.net > Subject: Re: RAPDs and maize populations > > Phil McClean (mcclean@PROBLEM_WITH_INEWS_DOMAIN_FILE) wrote: > : Jon Popi (jpopi@uoguelph.ca) wrote: > : : I would like to evaluate the diversity existing within and among 16 maize > : : populations by RAPD analyses. Since the number of populations is pretty > : : high, I would like to analize the smallest number of plants per population > : : that would give reliable results. Does anybody have any information > : : about the number of plants that should be analized? > > : Before this question can be answered, we would need to know what is the level of > : inbreeding, or what is the genetic structure of the lines? Only then can a estimate > : be made of the amount of residual variation exists in your lines and how many > : plants be line need to be sampled. > > : Phil McClean > : Dept. of Plant Sciences > : North Dakota State University > : Fargo, ND 58105 USA > : mcclean@plains.nodak.edu > > First of all, thank you for trying to help me. Here is a little > clarification of my problem: I am not dealing with inbred lines, but > with populations, which possess quite a bit of variability. So, I would > like to know what is the smallest number of plants that I need for RAPD > analyses in order to have that variability represented accurately enough. > > Thank you again! > > Jon Popi > Crop Science Department > University of Guelph > Guelph, Ontario > N1G 2W1, Canada > jpopi@crop.uoguelph.ca > > Let's assume your populations are in Hardy-Weinberg equilibrium. This is probably a reasonable assumption for outcrossing maize. In this case, you can estimate frequency of null allele from your RAPD data. The question is: How large a sample should be to detect a rare allele (i.e. alleles with low frequencies)? Let's say you want to detect allele with frequencies >= 0.05 with 95% certainty, then 60 (~ log(1-0.95) / log(1-0.05)) accessions are required. If you wish to do multilocus analysis, you definitely need a much larger sample size. See Tony Brown's paper on this aspect (Theor. Pop. Biol. 8:184-201. 1975). Hope this will help. Rong-Cai Yang Renewable Resources University of Alberta From owner-rapd@net.bio.net Sun Jan 08 22:00:00 1995 Path: biosci!YVAX.BYU.EDU!FARMERJ From: FARMERJ@YVAX.BYU.EDU Newsgroups: bionet.molbio.rapd Subject: Re: commercial postings Date: 9 Jan 1995 15:58:45 -0800 Organization: Brigham Young University Lines: 4 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HLNEM6UF4O8X8Z9Z@yvax.byu.edu> NNTP-Posting-Host: net.bio.net I agree completely with Rafalski that commercials are objectionable. Please send your objections directly to the perpetrator so he/she will understand our displeasure. The guilty ones probably don't read bionet, so posting here won't reach them. Best wishes. James Farmer From owner-rapd@net.bio.net Wed Jan 11 22:00:00 1995 Path: biosci!LIFSCI.SDSU.EDU!MCCLELLAND From: MCCLELLAND@LIFSCI.SDSU.EDU Newsgroups: bionet.molbio.rapd Subject: advertising Date: 12 Jan 1995 13:23:59 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <950112132151.20207dcd@LIFSCI.SDSU.EDU> NNTP-Posting-Host: net.bio.net I think everyone should send an e-mail to bbs.america@loa.com and to david.paulo@loa.com to protest the use of the internet for adverts. I cannot distinguish mail related to my work from unsolicited ads until waste time reading them. A single person can waste a few seconds of time for millions of people and at no cost. We should make sure that it is not worth their time. Michael McClelland From owner-rapd@net.bio.net Sun Jan 15 22:00:00 1995 Newsgroups: bionet.molbio.rapd Path: biosci!bcm!cs.utexas.edu!swrinde!pipex!sunic!news.chalmers.se!news.gu.se!news From: Subject: RAPD with internal labelling Message-ID: Sender: news@news.gu.se (USENET News System) Nntp-Posting-Host: mac6.marbot.gu.se Organization: Gothenburg University Date: Mon, 16 Jan 1995 17:50:16 GMT Lines: 2 Has anyone succesfully performed RAPD on a ABI 373 (or any other system of that kind) using internal labelling From owner-rapd@net.bio.net Sun Jan 15 22:00:00 1995 Newsgroups: bionet.molbio.rapd Path: biosci!agate!howland.reston.ans.net!pipex!news.oleane.net!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!rzusuntk.unizh.ch!NewsWatcher!user From: joni@systbot.unizh.ch (Josef Niederberger) Subject: Amplification of RNA instead of DNA? Message-ID: Sender: newsadm@rzu-news.unizh.ch (CNEWS ADMINISTRATION) Organization: Systematsiche Botanik, Uni Zuerich Date: Mon, 16 Jan 1995 15:54:42 GMT Lines: 23 Hello in the past weeks I tried several DNA extractions to examine their applicability for RAPD procedure. With a CTAB protocol from a friend of mine I got few DNA but great amounts of RNA. I recognized that many researchers published RAPD results with similar extraction procedures not using RNAse. Now I found an article in Gassen et al.1994, Gustav Fischer Verlag Stuttgart Germany, that refers to the reverse transcriptase activity of the Taq polymerase. This has been prooved by W.T.Tse & B.G.Forget 1990. I asked myself if it would be possible that one works with RNA as the main substrate instead of DNA or together with DNA. I think this would falsify the results. Does somebody know anything about this item? Many thanks. Kurt Eichenberger Institut fuer systematische Botanik Zollikerstrasse 107 CH 8008 Zuerich E-mail: aerob@systbot.unizh.ch From owner-rapd@net.bio.net Sun Jan 15 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!gatech!udel!news-4.nss.udel.edu!strauss.udel.edu!not-for-mail From: mcdonald@strauss.udel.edu (John H McDonald) Newsgroups: bionet.molbio.rapd Subject: Re: RAPD with internal labelling Date: 16 Jan 1995 16:29:48 -0500 Organization: University of Delaware Lines: 15 Message-ID: <3feogc$joa@strauss.udel.edu> References: NNTP-Posting-Host: strauss.udel.edu In article , wrote: >Has anyone succesfully performed RAPD on a ABI 373 >(or any other system of that kind) using internal labelling You can use the dye TOTO, available from Molecular Probes (503-465-8353). The excitation wavelength is pretty close to the laser used in the ABI 373, and the emission wavelength is close to the "blue" filter. The dye binds dsDNA, so you have to run a non-denaturing gel. It's been working fairly well for us on restriction fragments; I don't know why it wouldn't work on RAPDs. I'd be interested to hear from anyone else who's doing this. John H. McDonald Department of Biology University of Delaware From owner-rapd@net.bio.net Sun Jan 15 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!EU.net!uknet!daresbury!s-crim1!mbgxr From: mbgxr@s-crim1.dl.ac.uk (G. Ramsay) Newsgroups: bionet.molbio.rapd Subject: Re: Amplification of RNA instead of DNA? Date: 16 Jan 1995 18:50:48 GMT Organization: SERC Daresbury Lab, Warrington, U.K. Lines: 16 Distribution: bionet Message-ID: <3fef68$c14@mserv1.dl.ac.uk> References: NNTP-Posting-Host: s-crim1.dl.ac.uk X-Newsreader: TIN [version 1.2 PL2] Kurt RNA (or its RT copy) will be single-stranded, hence only linear copies could be made, all facing the same way. No 'Chain Reaction'. Gavin. Gavin Ramsay cggr@scri.sari.ac.uk Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK Phone: +44 1382 562731 Fax: +44 1382 562426 From owner-rapd@net.bio.net Mon Jan 16 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!EU.net!uknet!daresbury!s-crim1!mbgxr From: mbgxr@s-crim1.dl.ac.uk (G. Ramsay) Newsgroups: bionet.molbio.rapd Subject: Re: Amplification of RNA instead of DNA? Date: 17 Jan 1995 17:51:17 GMT Organization: SERC Daresbury Lab, Warrington, U.K. Lines: 14 Distribution: world Message-ID: <3fh02l$m5o@mserv1.dl.ac.uk> References: NNTP-Posting-Host: s-crim1.dl.ac.uk X-Newsreader: TIN [version 1.2 PL2] Quite right. (sound of humble pie being eaten!) Thanks to others too for pointing this out. Even one primer can serve as forward and reverse off a single-stranded cDNA template - especially under low stringency conditions, as you can read in Welsh et al Nucleic Acids Res. 20:4965-70 if you wish. Anyone have any views about the RT activity of TaqP? Gavin Ramsay cggr@scri.sari.ac.uk Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK Phone: +44 1382 562731 Fax: +44 1382 562426 From owner-rapd@net.bio.net Mon Jan 16 22:00:00 1995 Path: biosci!Oberon.HSC.Colorado.edu!COHRS-R From: COHRS-R@Oberon.HSC.Colorado.edu ("Randall J. Cohrs") Newsgroups: bionet.molbio.rapd Subject: Re: Amplification of RNA instead of DNA? Date: 16 Jan 1995 13:53:43 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 4 Sender: daemon@net.bio.net Distribution: world Message-ID: > RNA (or its RT copy) will be single-stranded, hence only linear copies > could be made, all facing the same way. No 'Chain Reaction'. > Unless two gene specific primers are used for PCR. From owner-rapd@net.bio.net Mon Jan 16 22:00:00 1995 Path: biosci!ATGENOME.BIO.UPENN.EDU!jecker From: jecker@ATGENOME.BIO.UPENN.EDU (Joe Ecker) Newsgroups: bionet.molbio.rapd Subject: Instruments for large scale PCR Date: 17 Jan 1995 15:00:28 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: <9501172254.AA03909@atgenome.bio.upenn.edu> NNTP-Posting-Host: net.bio.net Dear Colleagues, We are in need of a reliable system for large-scale PCR (>1000 samples run). We are currently testing the Intelligent Automation Thermocycler- TC1600 (16 x 192 format). I would appreciate any advice from users of this instrument as to how they like it. Our primary use of the machine is for STS content mapping of YAC/P1 libraries and SSLP typing on recombinant inbred populations. However, I would be very interested if anyone has experience using the TC1600 for cycle sequencing. I would also be interested in hearing from anyone using a robotic cycler for the above tasks. I've seen a recent review of the Sanger Center conference on automation that describes several machines. However, I'm looking for an instrument that is currently available commercially. Thanks in advance, Joe Ecker From owner-rapd@net.bio.net Mon Jan 16 22:00:00 1995 Path: biosci!IPST.EDU!Mike.Wood From: Mike.Wood@IPST.EDU Newsgroups: bionet.molbio.rapd Subject: Re: Amplification of RNA instead of DNA? Date: 17 Jan 1995 10:21:49 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 47 Sender: daemon@net.bio.net Distribution: world Message-ID: <48108.mwood@pop.ipst.edu> NNTP-Posting-Host: net.bio.net In message 16 Jan 1995 18:50:48 GMT, mbgxr@s-crim1.dl.ac.uk (G. Ramsay) writes: > Kurt > > RNA (or its RT copy) will be single-stranded, hence only linear copies > could be made, all facing the same way. No 'Chain Reaction'. > > Gavin. > > Gavin Ramsay > cggr@scri.sari.ac.uk > > Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK > Phone: +44 1382 562731 > Fax: +44 1382 562426 > Hello, I don't think this will be the case. For example, suppose we have a mRNA with the following sequence, (- = any base) ------AUGCAGUCGU---------------------------------ACGACUGCAU------------ Site 1 Site 2 Now suppose the primer sequence is TACGTCAGCA. In the first cycle, the primer would bind to site one, and produce the following product. ------AUGCAGUCGU---------------------------------ACGACUGCAU---- RNA TACGTCAGCA---------------------------------TGCTGACGTA---> Strand 1 (Primer) In the second cycle, the primer could bind at site two on DNA Strand 1 to produce Strand 2 which could then be amplified exponentially. (Primer) ATGCAGTCGT---------------------------------ACGACTGCAT Strand 2 TACGTCAGCA---------------------------------TGCTGACGTA---> Strand 1 I'm not sure if this is occuring, but if Taq does indeed have reverse transcriptase activity, I can see little reason for this not to occur in RAPDS. This could go toward explaining some of the variation seen in RAPDS. M Wood From owner-rapd@net.bio.net Wed Jan 18 22:00:00 1995 Newsgroups: bionet.molbio.rapd Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!pipex!uunet!zib-berlin.de!gs.dfn.de!fauern!news.th-darmstadt.de!muster!hamster.hrz.uni-giessen.de!gh54 From: Andreas Langsdorf Subject: reusing microtiter plates for rapds ? Sender: news@muster.hrz.uni-giessen.de Message-ID: X-Sender: gh54@hamster.hrz.uni-giessen.de Date: Thu, 19 Jan 1995 12:42:29 GMT Content-Type: TEXT/PLAIN; charset=US-ASCII Mime-Version: 1.0 Organization: Uni-Giessen Lines: 9 Hello, Are there any problems in reusing microtiter plates for rapd analysis? I autoclaved them twice but wasn`t able to obtain the same results. Any comments appreciated. thanks Andreas From owner-rapd@net.bio.net Thu Jan 19 22:00:00 1995 Path: biosci!daresbury!bioftp.unibas.ch!rc1.vub.ac.be!ben!wmoens From: wmoens@ben.vub.ac.be (Moens William) Newsgroups: bionet.molbio.rapd Subject: Testing thermocycles for RAPD Date: 20 Jan 1995 17:04:39 GMT Organization: Brussels Free Universities (VUB/ULB), Belgium Lines: 14 Message-ID: <3foqf7$5bd@rc1.vub.ac.be> NNTP-Posting-Host: ben.vub.ac.be. X-Newsreader: TIN [version 1.2 PL2] Hi, Do you have any experience of ussing the Stratagene's robocycler for RAPD's? Or Did hear something about its usability? Thank you for reply, W. Moens Ph. D. Biosafety& Biotechnology IHE Brussels Belgium aly From owner-rapd@net.bio.net Fri Jan 20 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.cac.psu.edu!news.pop.psu.edu!hudson.lm.com!godot.cc.duq.edu!ddsw1!ns2.mainstreet.net!ablecom!decwrl!tribune.usask.ca!quartz.ucs.ualberta.ca!news From: mhicks@gpu.srv.ualberta.ca (Mark Hicks - Genetics Group/University of Alberta) Newsgroups: bionet.molbio.rapd Subject: Re: Testing thermocycles for RAPD Date: 21 Jan 1995 20:01:36 GMT Organization: Dept. of Biology/University of Alberta Lines: 41 Message-ID: <3frp70$16b3@quartz.ucs.ualberta.ca> References: <3foqf7$5bd@rc1.vub.ac.be> Reply-To: mhicks@gpu.srv.ualberta NNTP-Posting-Host: dna.biology.ualberta.ca Mime-Version: 1.0 X-Newsreader: WinVN 0.93.11 In article <3foqf7$5bd@rc1.vub.ac.be>, wmoens@ben.vub.ac.be says... > >Hi, > >Do you have any experience of ussing the Stratagene's robocycler for >RAPD's? >Or Did hear something about its usability? > >Thank you for reply, > >W. Moens Ph. D. >Biosafety& Biotechnology >IHE Brussels Belgium > > >aly Hi, I have used the robocycler from stratagene for RAPD analysis of lodgepole pine and I have not had any problems with it. The advantage using a temp. block type termocycler vs. a water based version is that it is easier to do a hot-start type PCR. I have also used the Grant termocycler, a water based version, for RAPDS and it too works equally well as the stratagene model. The advantage the Grant has over the stratgene model is the fact that it is approx. $2000 dollar Cdn. cheaper! -- ************************************************************************* ************ Mark Hicks * * Dept. of Genetics * /*\ <- lodgepole pine University of Alberta * /***\ Edmonton, Alberta * /*****\ my favorite tree. CANADA * * e-mail: mhicks@gpu.srv.ualberta.ca * * ************************************************************************* ************ From owner-rapd@net.bio.net Fri Jan 20 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.tamu.edu!rigel.tamu.edu!grl6732 From: grl6732@rigel.tamu.edu (Gerard R. Lazo) Newsgroups: bionet.molbio.rapd Subject: Re: reusing microtiter plates for rapds ? Date: 20 Jan 1995 22:32 CST Organization: Texas A&M University OpenVMScluster Lines: 22 Distribution: world Message-ID: <20JAN199522323561@rigel.tamu.edu> References: NNTP-Posting-Host: rigel.tamu.edu News-Software: OpenVMS/VAX VNEWS 1.41 >Are there any problems in reusing microtiter plates for rapd analysis? >I autoclaved them twice but wasn`t able to obtain the same results. > Why create more problems? With the sensitivity of the PCR to amplify almost any remnant DNA in your wells I would think you were asking for trouble. If PCR is working in your microtiter dishes; what kind are you using? I've tried mixing PCR reactions in the standard microtiter plates, trying to avoid those treated for tissue culture, and have found some batches of plates work and others do not. In the marketplace, there are now microtiter dishes deemed PCR-reliable, but they cost twice as much. I just want a reliable dish for mixing reactions, not running the PCR in them. If you can recommend a reliable brand and catalog number, I'd like to hear about it. I can post the brands and catalog numbers of the inconsistent ones that I've run into later. / Gerard R. Lazo . %. (=) GLAZO@tam2000.tamu.edu USDA-ARS (.( .) / Off: 409-260-9533 Southern Crops Research Lab. ( ( .) .) -> (=) Lab: 409-260-9522 2765 F&B Road %_( ._) / Fax: 409-260-9333 College Station, TX 77845 //\| (=) (( / From owner-rapd@net.bio.net Thu Jan 26 22:00:00 1995 Path: biosci!UBVMS.CC.BUFFALO.EDU!V226UHBQ From: V226UHBQ@UBVMS.CC.BUFFALO.EDU Newsgroups: bionet.molbio.rapd Subject: Blank Lanes Date: 26 Jan 1995 17:53:05 -0800 Organization: University at Buffalo Lines: 29 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HMBDRS6C8Y8X9NPV@ubvms.cc.buffalo.edu> NNTP-Posting-Host: net.bio.net The RAPD demon strikes again!!! I'm not sure if this question has been posted before, but we are having trouble with RAPDs samples that do not amplify at all--the lanes are completely blank. This appears to happen arbitrarily. By running replicates, we know it is not the DNA source, the primers, the Taq or any of the other materials used in the soup, the particular wells in the thermal cycler, the gels, or the gel boxes. Our procedure is very clean (e.g., we're working in a plexiglass box, all materials are autoclaved immediately before beginning the reaction) and contamination in the controls is very low. Although this has happened once in a while in the past, for the past week we have been consistently losing 1 to 8 lanes in each run of 35 samples. Does anyone have any advice? Thanks! Sincerely, Mary Alice Coffroth Department of Biological Sciences SUNY at Buffalo Buffalo, NY 14260 716-645-2881 716 645-2975 [fax] V226uhbq@ubvms.cc.buffalo.edu From owner-rapd@net.bio.net Thu Jan 26 22:00:00 1995 Newsgroups: bionet.molbio.rapd Path: biosci!rutgers!gatech!swrinde!pipex!uunet!zib-berlin.de!gs.dfn.de!zeus.rbi.informatik.uni-frankfurt.de!terra.wiwi.uni-frankfurt.de!news.th-darmstadt.de!muster!hamster.hrz.uni-giessen.de!gh54 From: Andreas Langsdorf Subject: Re: reusing microtiter plates for rapds ? Sender: news@muster.hrz.uni-giessen.de Message-ID: X-Sender: gh54@hamster.hrz.uni-giessen.de In-Reply-To: Date: Thu, 26 Jan 1995 13:25:23 GMT Content-Type: TEXT/PLAIN; charset=US-ASCII References: Mime-Version: 1.0 Organization: Uni-Giessen Lines: 28 On Tue, 24 Jan 1995, In C. Kim wrote: > In article you wrote: > > : Hello, > > : Are there any problems in reusing microtiter plates for rapd analysis? > : I autoclaved them twice but wasn`t able to obtain the same results. > > Hi, > > Please excuse my ignorance. Please tell me what is rapd about? I am > very curious. I would appreciate your feedback. Thanks. > > > -- > In C. Kim > University of New Mexico School of Medicine > Albuquerque, New Mexico Hi In C. Kim, RAPD = Random Amplified Polymorphic DNA any questions ? bye Andreas From owner-rapd@net.bio.net Fri Jan 27 22:00:00 1995 Path: biosci!ASRR.ARSUSDA.GOV!abartlet From: abartlet@ASRR.ARSUSDA.GOV ("Alan C. Bartlett") Newsgroups: bionet.molbio.rapd Subject: Re: Blank Lanes Date: 27 Jan 1995 14:58:44 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <01HMBDRS6C8Y8X9NPV@ubvms.cc.buffalo.edu> Take a look at your dNTP mixture. We recently had trouble with a batch of dNTP's from Perkin-Elmer where we would get 50% or more blank lanes. After trying all other possiblities we switched to another brand of dNTP's and found every reaction would be there. PE denied that their products would have this effect, but it did. Good luck - that is a frustrating thing to have to endure!:( Alan C. Bartlett "GENES-R-US" "ALTERATIONS AVAILABLE!^" "^some restrictions may apply:)" From owner-rapd@net.bio.net Fri Jan 27 22:00:00 1995 Path: biosci!MERCURY.UARK.EDU!DRHOADS From: DRHOADS@MERCURY.UARK.EDU ("Douglas Rhoads") Newsgroups: bionet.molbio.rapd Subject: Re: Blank Lanes Date: 27 Jan 1995 08:54:51 -0800 Organization: University of Arkansas Lines: 53 Sender: daemon@net.bio.net Distribution: world Message-ID: <2A6D5212C@uamercury.uark.edu> > To: rapd@net.bio.net > From: V226UHBQ@UBVMS.CC.BUFFALO.EDU > Subject: Blank Lanes > Date: 26 Jan 1995 17:53:05 -0800 > > > The RAPD demon strikes again!!! I'm not sure if this question has been > posted before, but we are having trouble with RAPDs samples that do not amplify > at all--the lanes are completely blank. This appears to happen > arbitrarily. By running replicates, we know it is not the DNA > source, the primers, the Taq or any of the other materials used in > the soup, the particular wells in the thermal cycler, the gels, > or the gel boxes. Our procedure is very clean (e.g., we're working > in a plexiglass box, all materials are autoclaved immediately > before beginning the reaction) and contamination in the controls is > very low. Although this has happened once in a while in the past, > for the past week we have been consistently losing 1 to 8 lanes in > each run of 35 samples. Does anyone have any advice? Thanks! > > > Sincerely, > > > Mary Alice Coffroth > Department of Biological Sciences > SUNY at Buffalo > Buffalo, NY 14260 > > 716-645-2881 > 716 645-2975 [fax] > V226uhbq@ubvms.cc.buffalo.edu Tubes, tips or pipeting errors are most likely the cause. If you set up a single cocktail with all reagents and then pipet that into several tubes and then run you can eliminate the tubes and tips pretty easily. If it is none of those then it is tube to tube variation in pipeting or mixing of the cocktail prior to PCR. I have known autoclaving of tubes to tarnish tubes if the tubes get coated unevenly from a campus steam supply. They put all sorts of polyanions and stuff in campus steam to keep pipes clean. I have also known of batches of tubes that were tainted when shipped from the supplier. The tubes smelled of processing oils when you autoclaved them. //========================================================\\ ||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 Jan 29 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!ix.netcom.com!netcom.com!csus.edu!news.ucdavis.edu!rocky!ez006804 From: Phandaal Newsgroups: bionet.molbio.ageing,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.gene-linkage,bionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.rapd,bionet.molbio.yeast Subject: controversies & ethics Date: Mon, 30 Jan 1995 11:59:15 -0800 Organization: University of California, Davis Lines: 37 Message-ID: NNTP-Posting-Host: rocky.ucdavis.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: ez006804@rocky Xref: biosci bionet.molbio.ageing:1203 bionet.molbio.bio-matrix:531 bionet.molbio.embldatabank:430 bionet.molbio.evolution:2374 bionet.molbio.gdb:279 bionet.molbio.gene-linkage:513 bionet.molbio.genome-program:1135 bionet.molbio.hiv:850 bionet.molbio.rapd:949 bionet.molbio.yeast:2260 I've been asked to give a lecture to upper-division college students on the controversies and ethical considerations in producing transgenic organisms, especially transgenic plants. It's been a while since I gave this lecture, and so I was wondering if anybody had any good examples of controversies or ethical considerations that I could incorporate into the talk. Two I can think of off-hand are: 1) introducing insecticidal proteins (such as the Bacillus thuringiensis protein) into plants may create resistant insect populations (under the force of heavy selection pressure), which could then overrun the resistant plants and make worthless the efforts by conventional growers who *use* Bt protein as a topical pesticidal spray. 2) altering fatty acid metabolism in oil-crops (like canola) so that they produce oils found chiefly in palm and coconut could severely damage the palm oil and coconut oil industries in Third World countries... thus severely depressing the economies of these already struggling countries. If you are aware of any other similar cases, or simply have a point which you think would be useful for the lecture, I'd appreciate hearing from you! Thanks, Peter Schuerman plschuerman@ucdavis.edu />>/>>/>> In nature there are neither rewards nor <<\<<\<<\ \>>\>>\>> punishments--there are consequences. <>/>>/>> <>\>>\>> From owner-rapd@net.bio.net Mon Jan 30 22:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!swiss.ans.net!emi.com!pauling.wadsworth.org!rebecca!labonnes From: labonnes@csc.albany.edu (S. LaBonne) Newsgroups: bionet.molbio.ageing,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.gene-linkage,bionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.rapd,bionet.molbio.yeast Subject: Re: controversies & ethics Date: 31 Jan 1995 01:21:34 GMT Organization: University at Albany, SUNY Lines: 39 Message-ID: <3gk3au$pdp@rebecca.albany.edu> References: NNTP-Posting-Host: freia.albany.edu Xref: biosci bionet.molbio.ageing:1206 bionet.molbio.bio-matrix:532 bionet.molbio.embldatabank:431 bionet.molbio.evolution:2376 bionet.molbio.gdb:280 bionet.molbio.gene-linkage:514 bionet.molbio.genome-program:1138 bionet.molbio.hiv:851 bionet.molbio.rapd:950 bionet.molbio.yeast:2266 In article , Phandaal wrote: >I've been asked to give a lecture to upper-division college students on >the controversies and ethical considerations in producing transgenic >organisms, especially transgenic plants. It's been a while since I gave >this lecture, and so I was wondering if anybody had any good examples of >controversies or ethical considerations that I could incorporate into the >talk. > >Two I can think of off-hand are: > >1) introducing insecticidal proteins (such as the Bacillus thuringiensis >protein) into plants may create resistant insect populations (under the >force of heavy selection pressure), which could then overrun the resistant >plants and make worthless the efforts by conventional growers who *use* Bt >protein as a topical pesticidal spray. > >2) altering fatty acid metabolism in oil-crops (like canola) so that they >produce oils found chiefly in palm and coconut could severely damage the >palm oil and coconut oil industries in Third World countries... thus >severely depressing the economies of these already struggling countries. My problem with these examples is that I see nothing about them that is unique to transgenic technology. Similar sorts of problems are raised all the time by "conventional" technologies, including very ancient ones like selective breeding. An analogue to 1 is simply overuse of pesticides (or antibiotics for that matter), which can render them worthless in the way you describe. And 2 in no way raises ethical issues different from, say, starting a palm oil industry in Key West, possibly after selective breeding of oil palms to produce strains that give high yields there. Indeed, I doubt that there _are_ any ethical issues which depend _specifically_ on agricultural use of biotechnology as opposed to agricultural technologies in general. -- Steve LaBonne *********************** (labonnes@csc.albany.edu) "It can never be satisfied, the mind, never." - Wallace Stevens From owner-rapd@net.bio.net Mon Jan 30 22:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!pipex!uunet!news.u.washington.edu!roach From: roach@u.washington.edu (Jared Roach) Newsgroups: bionet.molbio.ageing,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.gene-linkage,bionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.rapd,bionet.molbio.yeast Subject: Re: controversies & ethics Date: 31 Jan 1995 20:52:25 GMT Organization: University of Washington Lines: 28 Message-ID: <3gm7u9$t5e@nntp1.u.washington.edu> References: <3gk3au$pdp@rebecca.albany.edu> NNTP-Posting-Host: saul3.u.washington.edu Xref: biosci bionet.molbio.ageing:1212 bionet.molbio.bio-matrix:533 bionet.molbio.embldatabank:432 bionet.molbio.evolution:2379 bionet.molbio.gdb:282 bionet.molbio.gene-linkage:515 bionet.molbio.genome-program:1140 bionet.molbio.hiv:853 bionet.molbio.rapd:951 bionet.molbio.yeast:2273 While it is true that there is to a first approximation nothing that one can do with transgenic agriculture that could not be done with traditional plant breeding, there is no denying that recombinant DNA is MUCH faster. This to me is the crux of the ethical issue. Not what, or even why, but how fast. It would presumably take a very long time to breed arctic fish with strawberries to get frost resistant strawberries (or more likely, to select over umpteen generations of strawberries for the same trait). Now one might argue that the speed of recombinant research has two dangers: 1) The rest of the ecosystem is not changing as fast to modify itself so as to maintain some kind of ecological "balance." Furthermore, scientists may be slower to understand ecological impact than they are in developing new organisms. 2) The human race as a whole (or national governments, or individuals) is slow to reach consensus on ethical issues (i.e. religion, abortion, the creation of new species, etc.) Science should slow its pace of discovery to allow Ethics to catch up. There are excellnt counterpoints, but I will allow others to continue the dialectic. Jared Roach Dept. of Molecular Biotechnology University of Washington roach@u.washington.edu From owner-rapd@net.bio.net Tue Jan 31 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!swiss.ans.net!emi.com!pauling.wadsworth.org!rebecca!labonnes From: labonnes@csc.albany.edu (S. LaBonne) Newsgroups: bionet.molbio.ageing,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.gene-linkage,bionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.rapd,bionet.molbio.yeast Subject: Re: controversies & ethics Date: 1 Feb 1995 00:39:33 GMT Organization: University at Albany, SUNY Lines: 37 Message-ID: <3gml85$fb5@rebecca.albany.edu> References: <3gk3au$pdp@rebecca.albany.edu> <3gm7u9$t5e@nntp1.u.washington.edu> NNTP-Posting-Host: bathsheba.albany.edu Xref: biosci bionet.molbio.ageing:1216 bionet.molbio.bio-matrix:534 bionet.molbio.embldatabank:433 bionet.molbio.evolution:2381 bionet.molbio.gdb:283 bionet.molbio.gene-linkage:516 bionet.molbio.genome-program:1141 bionet.molbio.hiv:856 bionet.molbio.rapd:952 bionet.molbio.yeast:2275 In article <3gm7u9$t5e@nntp1.u.washington.edu>, Jared Roach wrote: > Now one might argue that the speed of recombinant research >has two dangers: > 1) The rest of the ecosystem is not changing as fast to >modify itself so as to maintain some kind of ecological "balance." >Furthermore, scientists may be slower to understand ecological impact >than they are in developing new organisms. This is not an ethical issue until the ecological problems are shown to be more concrete than vague forebodings. Even then, it is not an ethical problem of a new _kind_, being nothing more than the familiar tradeoffs between benefits and environmental impact that must be considered in the case of virtually _any_ technological change. > 2) The human race as a whole (or national governments, or >individuals) is slow to reach consensus on ethical issues (i.e. >religion, abortion, the creation of new species, etc.) Science >should slow its pace of discovery to allow Ethics to catch up. There is much to be said for this contention, but again biotechnology is not unique in giving rise to such considerations. I still say there are _no_ ethical considerations that are _unique to biotechnology as such_, and I fail to see the case for singling out biotechnology in an ethics course; what's more, this tends to give scientifically naive students, and members of the public, an irrational fear of biotechnology over and above other technologies. Naturally, biotechnology can serve as a valuable source of _examples_ in discussions of the ethics of applying new technologies in general. -- Steve LaBonne *********************** (labonnes@csc.albany.edu) "It can never be satisfied, the mind, never." - Wallace Stevens From owner-rapd@net.bio.net Tue Jan 31 22:00:00 1995 Path: biosci!daresbury!trane.uninett.no!sunic!pipex!pipex!howland.reston.ans.net!news2.near.net!das-news2.harvard.edu!casaba.srv.cs.cmu.edu!bb3.andrew.cmu.edu!andrew.cmu.edu!hb10+ From: "Howard M. Bomze" Newsgroups: bionet.molbio.ageing,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.rapd,bionet.molbio.yeast,bionet.molbio.gene-linkage Subject: Re: controversies & ethics Date: Wed, 1 Feb 1995 17:31:58 -0500 Organization: Doctoral student, Biology, Carnegie Mellon, Pittsburgh, PA Lines: 15 Message-ID: References: <3gk3au$pdp@rebecca.albany.edu> <3gm7u9$t5e@nntp1.u.washington.edu> <3gml85$fb5@rebecca.albany.edu> NNTP-Posting-Host: po2.andrew.cmu.edu In-Reply-To: <3gml85$fb5@rebecca.albany.edu> Xref: biosci bionet.molbio.ageing:1221 bionet.molbio.bio-matrix:535 bionet.molbio.embldatabank:434 bionet.molbio.evolution:2387 bionet.molbio.gdb:284 bionet.molbio.genome-program:1144 bionet.molbio.hiv:858 bionet.molbio.rapd:953 bionet.molbio.yeast:2278 bionet.molbio.gene-linkage:518 Steve Bonne has been saying that there are no new ethical considerations for agricultural biotechnologies. However, he has been missing one very important one, that is the possibility of an engineered gene to be transfered to a different species. The transgenic plant not only has the sequences of the desired gene, it also contains the sequences which are necesary to insert the gene into the genome. So a question which must be looked at is this: If a gene for herbicide resistance has been put into a corn plant so that that herbicide can be used to kill all of the crab grass in the corn field, what happens if the gene is transfered to the crab grass? There are also ethical problems with other non-agricultural biotechnology. Howard Bomze