From owner-rapd@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: Newsgroups: bionet.molbio.rapd Subject: new Date: 2 Mar 1995 16:46:29 -0000 Lines: 9 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3j4sp5$mr2@mserv1.dl.ac.uk> Original-To: rapd@dl.ac.uk Hi I tried once before to get into the RAPDs group, but address given to me was wrong...Now I run in new problems and I would like to ask people working longer with RAPDs then me, for some , possible ,tips... This time I will be very short as I am still not sure how good is address that I have... I hope I will gwt through this time Maja From owner-rapd@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!gatech!news-feed-1.peachnet.edu!hobbes.cc.uga.edu!news From: bernhardt@bscr.uga.edu Newsgroups: bionet.molbio.rapd Subject: SSLP Primers for genome mapping? Date: 2 Mar 1995 15:45:57 GMT Organization: University of Georgia, Athens, Ga Lines: 10 Message-ID: <3j4p7l$sqa@hobbes.cc.uga.edu> Reply-To: bernhardt@bscr.uga.edu NNTP-Posting-Host: bscr.cc.uga.edu I'm trying to find the name and address of a company that makes SSLP (microsatellite) primers for genome mapping in Drosophila. One of my advisors recently saw an ad of theirs, but can't find it. This company makes these primers for a variety of systems, e.g. mammalian and Drosophila. It *may* have been located in Alabama. (Take this with a grain of salt.) Anyone else have any idea what I'm talking about? :-) Thanks much. -- Matt Bernhardt University of Georgia Fools multiply folly. bernhardt@bscr.uga.edu From owner-rapd@net.bio.net Thu Mar 02 22:00:00 1995 Path: biosci!biotech.lan.nrc.ca!peloquin From: peloquin@biotech.lan.nrc.ca ("Peloquin, Marc") Newsgroups: bionet.molbio.rapd Subject: temp blitz Date: 2 Mar 1995 08:32:32 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: <2F55F31D@coursmtp.nrc.ca> Okay everybody, it's RAPD PCR profile blitz time, heeeee haaaa! Tell me 1- What are your temperature profil? 2- What type of machine do you use? 3- What is the size of your primer and the kind of template? 4- Are you happy with your results? 1- hot start, 1 second at 96, 3 min ramp to 35, 30 second hold at 35, straight to 72, 30 second hold at 72, straight to 96. 30 cycles 2- Perkin elmer thermal cycler 480 3- 9mers (we sell'em by the way), total genomic DNA from bacteria 4- Sure! C'mon don't be shy! Marc Peloquin PhD candidate National Research Council peloquin@biotech.lan.nrc.ca From owner-rapd@net.bio.net Thu Mar 02 22:00:00 1995 Path: biosci!biotech.lan.nrc.ca!peloquin From: peloquin@biotech.lan.nrc.ca ("Peloquin, Marc") Newsgroups: bionet.molbio.rapd Subject: RFLP analysis program? Date: 2 Mar 1995 08:31:40 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 32 Sender: daemon@net.bio.net Distribution: world Message-ID: <2F55F2DD@coursmtp.nrc.ca> ------------------------------------------------------------------------------ REPLY FROM: Peloquin, Marc Return-Path: To: rapd@net.bio.net From: cgrunau@postman.riken.go.jp (Christoph Grunau) Subject: RFLP analysis program? Content-Type: text/plain; charset=ISO-8859-1 Message-Id: Followup-To: bionet.molbio.rapd Sender: news@postman.riken.go.jp (News Administrator) Nntp-Posting-Host: mbs405 Content-Transfer-Encoding: 8bit Mime-Version: 1.0 Date: Wed, 1 Mar 1995 14:12:24 GMT ------------------------------------------------------------------------------ Hi Netters, does anyone know a program for the analysis of RFLPs? Thanks for answering! Christoph Grunau We have just received and are using a program called dendron, (Solltech, around 7000$ US) this is just for the software. e-mail for more detail Marc Peloquin NRC peloquin@biotech.lan.nrc.ca From owner-rapd@net.bio.net Thu Mar 02 22:00:00 1995 Newsgroups: bionet.molbio.rapd Path: biosci!adam.cc.sunysb.edu!news.nysernet.net!news.sprintlink.net!alfa02.medio.net!netnews.nwnet.net!ns1.nodak.edu!beangenes.cws.ndsu.nodak.edu!mcclean From: mcclean@PROBLEM_WITH_INEWS_DOMAIN_FILE (Phil McClean) Subject: Linux version of Mapmaker Sender: usenet@ns1.nodak.edu (Usenet login) Message-ID: Date: Fri, 3 Mar 1995 15:20:24 GMT Nntp-Posting-Host: beangenes.cws.ndsu.nodak.edu Organization: I need to put my ORGANIZATION here. X-Newsreader: TIN [version 1.2 PL2] Lines: 10 Does anyone know if a version of Mapmaker compiled for Linux exists anywhere? If so, please let me know, I would like to get a copy of it. Phil McClean Dept. of Plant Sciences North Dakota State University Fargo, ND 58105 mcclean@beangenes.cws.ndsu.nodak.edu From owner-rapd@net.bio.net Thu Mar 02 22:00:00 1995 Path: biosci!cabi.org!G.SADDLER From: G.SADDLER@cabi.org ("Gerry Saddler ", IMI) Newsgroups: bionet.molbio.rapd Subject: FW: Date: 3 Mar 1995 08:14:49 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 38 Sender: daemon@net.bio.net Distribution: world Message-ID: <2F572B31@msm.cgnet.com> NNTP-Posting-Host: net.bio.net ---------- From: Gerry Saddler (IMI) To: DIAGNOST; RAPDS Date: 27 February 1995 16:07 Dear All, This is a plea for help, if ever there was one! We are currently working on a project to characterise/identify/detect phytopathogenic coryneform bacteria (no mean feat!) using amongst other things molecular fingerprinting techniques. The methods we have tried and are currently banging our heads against a brick wall with are; PFGE, and PCR-fingerprinting techniques such as RAPD's and using repeat sequence primers such as ERICs, BOX & REP. Most of our limited experience with all of these methods has been on Gram negative bacteria and not without problems! However, this work has been easy compared with the coryneform work. We know we can get all of the above to work on these bacteria, it all boils down to reproducibility; when its good its very, very good but when its bad its....... We've tried laborious/exhaustive DNA extractions, carefully monitoring DNA concentration, ensuring the integrity etc. of our reagent stocks, but nothing seems to get over the reproducibility problem. Our latest ploy is to hang rosary beeds on the PCR machine and play Elvis Costello very loud, but this has met with only limited success. If there is anyone out there who has experienced similar problems we would like to hear from you, believe me! From owner-rapd@net.bio.net Thu Mar 02 22:00:00 1995 Path: biosci!cabi.org!D.BRAYFORD From: D.BRAYFORD@cabi.org ("David Brayford ", IMI) Newsgroups: bionet.molbio.rapd Subject: test - please ignore Date: 3 Mar 1995 01:18:43 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <2F56DDF1@msm.cgnet.com> NNTP-Posting-Host: net.bio.net test- sorry for the inconvenience From owner-rapd@net.bio.net Thu Mar 02 22:00:00 1995 Newsgroups: bionet.molbio.rapd Path: biosci!daresbury!trane.uninett.no!eunet.no!nuug!Norway.EU.net!EU.net!howland.reston.ans.net!news.sprintlink.net!alfa02.medio.net!netnews.nwnet.net!ns1.nodak.edu!beangenes.cws.ndsu.nodak.edu!mcclean From: mcclean@PROBLEM_WITH_INEWS_DOMAIN_FILE (Phil McClean) Subject: ANNOUNCEMENT: BeanGenes Sender: usenet@ns1.nodak.edu (Usenet login) Message-ID: Date: Fri, 3 Mar 1995 22:35:26 GMT Nntp-Posting-Host: beangenes.cws.ndsu.nodak.edu Organization: I need to put my ORGANIZATION here. X-Newsreader: TIN [version 1.2 PL2] Lines: 106 BeanGenes --- A Phaseolus/Vigna sp. Database Phillip E. McClean Department of Plant Sciences North Dakota State University Fargo, ND 58105 mcclean@beangenes.cws.ndsu.nodak.edu Plant Genome Databases Plant genome databases have been designed for a number of important crop species. The goal of these databases is to provide "one-stop shopping" for information that is relevant to a species or group of species. Examples of these databases include GrainGenes (for cereal groups), SolGenes (for Solanaceous species), and SoyBase (for Glycine species). Information that is contained in these databases include molecular mapping data, germplasm information, trait studies, identified quantitative trait loci, pathogen descriptions, relevant publication citations, images pertaining to all aspects of the crop, and colleague addresses. These efforts are each funded by the USDA Plant Genome project. BeanGenes BeanGenes is a plant genome data base which currently contains information relevant to Phaseolus and Vigna species. The BeanGenes project was funded by the USDA/ARS Plant Genome project through the SoyBase project administered by Dr. Randy Shoemaker (USDA/ARS, Ames, Iowa). The hardware component of BeanGenes is a computer containing a Pentium P90 processor, 64 mByte RAM, 2 GByte hard drive, and 8 GByte tape backup drive. The machine is running under the Linux operating system. Linux is a Unix-based operating system designed to run on machines using the Intel X86 series of processors. Internet domain name of the machine is beangenes.cws.ndsu.nodak.edu. The IP address of the machine is 134.129.117.50. Currently, all of the BeanGenes information is stored in the ACeDB software application. This is the most frequently used plant genome database application. Richard Durbin (MRC, England) and Jean Thierry-Mieg (CNRS, France) initially developed ACeDB (an acronym for A C. elegans database) to archive information about Caenorhabditis elegans (Durbin and Thierry-Mieg, 1995). The database runs under the X-Windows environment on machines utilizing some flavor of a UNIX operating system. To access the database as an X-window application, the user must login on the server. Alternatively, a user can obtain a copy of the database and install it on a local X-Windows server. Remote users will need to access the database from a computer running a form of X-Windows. The database can be accessed from any personal computer or MacIntosh computer which has X-Windows emulation software. BeanGenes contains several classes of information. All of the published molecular maps of P. vulgaris are represented in the database. These include the restriction fragment length polymorphism (RFLP) map developed by Dr. Eduardo Vallejos at the University of Florida (Vallejos et al., 1992) and the RFLP map developed by Dr. Paul Gepts at the University of California, Davis (Gepts et al., 1993). The combined RFLP and randomly amplified polymorphic DNA (RAPD) developed by Dr. Michel Dron at University of Paris, Sud can also be accessed. Dr. Nevin Young of the University of Minnesota has provided RFLP maps of mung bean (Vigna radiata) and cowpea (V. unguiculata). Associated with each molecular map are loci and probe information. The loci information describes the probes or RAPDs used to define the locus, and the probe data provides specific information about a given probe. BeanGenes also contains all of the gene information that was complied by Dr. Mark Bassett, University of Florida. This is identical to the recent published list (Bassett, 1993) All published references to the genes are also included. Accessing BeanGenes The BeanGenes database can be accessed in three manners. For those users with X-Windows capability, a login on the BeanGenes server can be established. If you would like to have an account on the BeanGenes machine contact Phil McClean at mcclean@beangenes.cws.ndsu.nodak.edu and an account will be established. Two methods of accessing the database are available that do not require X-Windows capability. The ACeDB form of BeanGenes can be searched on the Agricultural Genome World Wide Web Server at URL http://probe.nalusda.gov:8300/. This WWW site can be accessed by such client software as Mosaic and Netscape. Once the site is reached, find the BeanGenes entry and the database can be navigated using standard point-and-click techniques. The database is also accessible using the Gopher application. The gopher address is probe.nalusda.gov. When the database is accessed via Gopher, the user will able to search for information using the WAIS (Wide Area Information Search) application. Use the following menu steps to find the searchable version of BeanGenes. 2. Plant Genome Informaton 2. Access to Genome Databases 19. Search BeanGenes (Phaseolus sp.) References Bassett, M.J. 1993. List of genes - Phaseolus vulgaris L. Ann. Report of Bean Imp. Coop. 36:vi-xxiii. Durbin, R. and J. Thierry Mieg. 1995. A. C. elegans database. Documentation, code and data available from anonymous FTP servers at lirmm.lirmm.fr, cele.mrc-lmb.cam.ac.uk and ncbi.nlm.nih.gov. Gepts, P., R. Nodari, S.M. Tsai, E.M.K. Kinage, V. Llaca, R. Gilbertson, and P. Guzmán. 1993. Linkage mapping in common bean. Ann. Report of Bean Imp. Coop. 36:xxiv-xxxviii. Vallejos, C.E., N.S. Sakiyama, C.D. Chase. 1992. A molecular-marker-based linkage Map of Phaseolus vulgaris L. Genetics 131:733-740. From owner-rapd@net.bio.net Thu Mar 02 22:00:00 1995 Path: biosci!rutgers!uwm.edu!msunews!harbinger.cc.monash.edu.au!news.cs.su.oz.au!metro!unsw.edu.au!NewsWatcher!user From: R.Oweyoung@cfi.unsw.edu.au (Robert Owe-Young) Newsgroups: bionet.molbio.rapd Subject: Re: Aust Supplier for USB Date: 3 Mar 1995 01:42:55 GMT Organization: CFI/UNSW Lines: 15 Message-ID: References: <1995Feb24.054933.8673@ml.csiro.au> NNTP-Posting-Host: 129.94.200.8 Amersham are the new distributors for USB, but the old distributors Trace Scientific (03-543-1255) are the agents for a crowd called Toyobo, which they say USB buys their enzymes from. In article <1995Feb24.054933.8673@ml.csiro.au>, Christopher J. S. Bolch wrote: > Hi RAPD bods > > Everyone except the Australians can probably ignore this. > > Anyone got any idea who the Australian suppliers are for US Biochemicals. > I want to purchase a restriction enzyme called Nsp I which is only > available from USB. > > Thanks in advance. From owner-rapd@net.bio.net Fri Mar 03 22:00:00 1995 Path: biosci!ABACUS.BATES.EDU!dagrawal From: dagrawal@ABACUS.BATES.EDU (Dileep Agrawal) Newsgroups: bionet.molbio.rapd Subject: Need LAB to work on DAF of Orobanche Date: 3 Mar 1995 20:38:25 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: <9503040438.AA18555@abacus.bates.edu> NNTP-Posting-Host: net.bio.net HI! I am a research scientist at Research Laboratory for Agricultural Biotechnology and Biochemistry located in Kathmandu, Nepal. I have received a UNESCO short-term fellowship for 3 months to work on DNA amplification fingerprinting (DAF) of Orobanche ecotypes. I have already extracted DNA samples. Unfortunately, the grant only covers travel and living expenses. So, if someone is willing to donate me lab supplies and lab space, I would be very grateful. Please reply to: dagrawal@bates.edu Sincerely, Arvind Kesari Research Scientist Res. Lab. for Agric. Biotech. and Biochem. From owner-rapd@net.bio.net Sat Mar 04 22:00:00 1995 Path: biosci!Citadel.edu!WHITEHURSTM From: WHITEHURSTM@Citadel.edu Newsgroups: bionet.molbio.rapd Subject: Re:SSLP Primers for genome mapping Date: 5 Mar 1995 10:13:54 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 5 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HNS0UJ2KNQ8Y7YJ9@Citadel.edu> NNTP-Posting-Host: net.bio.net Matt Bernhard asked for the address of the Alabama company which makes microsatellite primers. We recently bought canine primers from: Research Genetics, Inc., Fax 205-536-9016, Phone 800-533-4363 22130 Memorial Parkway SW, Huntsville, AL 35801. Hope this helps. Maureen Whitehurst From owner-rapd@net.bio.net Sat Mar 04 22:00:00 1995 Path: biosci!MERCURY.UARK.EDU!DRHOADS From: DRHOADS@MERCURY.UARK.EDU ("Douglas Rhoads") Newsgroups: bionet.molbio.rapd Subject: Re: SSLP Primers for genome mapping? Date: 5 Mar 1995 06:41:05 -0800 Organization: University of Arkansas Lines: 40 Sender: daemon@net.bio.net Distribution: world Message-ID: <827811FFB@uamercury.uark.edu> NNTP-Posting-Host: net.bio.net > To: rapd@net.bio.net > From: bernhardt@bscr.uga.edu > Subject: SSLP Primers for genome mapping? > Date: 2 Mar 1995 15:45:57 GMT > Reply-to: bernhardt@bscr.uga.edu > I'm trying to find the name and address of a company that makes SSLP > (microsatellite) primers for genome mapping in Drosophila. One of my advisors > recently saw an ad of theirs, but can't find it. This company makes these > primers for a variety of systems, e.g. mammalian and Drosophila. It *may* have > been located in Alabama. (Take this with a grain of salt.) > Anyone else have any idea what I'm talking about? :-) Thanks much. > -- > Matt Bernhardt > University of Georgia Fools multiply folly. > bernhardt@bscr.uga.edu I would suggest contacting John Hobbs at UBC. He has a set of SSLP based primers called set #9. Try: Dr. John Hobbs Nucleic Acid - Protein Service (NAPS) Unit Biotechnology Laboratory Room 237, Wesbrook Building 6174 University Boulevard University of British Columbia Vancouver, V6T 1Z3 Canada. FAX (604)822-5437 or (604)822-0676; Tel. (604)822-6373 hobbs@unixg.ubc.ca //========================================================\\ ||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 Mar 05 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.cac.psu.edu!news.tc.cornell.edu!news.graphics.cornell.edu!newsstand.cit.cornell.edu!usenet From: sg19@cornell.edu (Silvana Grandillo) Newsgroups: bionet.molbio.rapd Subject: Re: Linux version of Mapmaker Date: 6 Mar 1995 14:55:37 GMT Organization: Cornell University Lines: 11 Sender: sg19@cornell.edu (Verified) Message-ID: <3jf7p9$pcg@newsstand.cit.cornell.edu> References: NNTP-Posting-Host: cu-dialup-0230.cit.cornell.edu X-Newsreader: WinVN 0.90.5 Same problem but in the Microsoft Windows environment (IBM/PC). Does anybody know of a MAPMAKER and MAPMAKER QTL for it ? Silvana Grandillo sg19@cornell.edu From owner-rapd@net.bio.net Mon Mar 06 22:00:00 1995 Path: biosci!CCR.DSI.UANL.MX!jpmtz From: jpmtz@CCR.DSI.UANL.MX (The PCR Cruncher) Newsgroups: bionet.molbio.rapd Subject: Single step PCR to detect Brucella spp. Date: 6 Mar 1995 16:48:41 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 49 Sender: daemon@net.bio.net Distribution: world Message-ID: <0098CF7B.285B0340.18@ccr.dsi.uanl.mx> NNTP-Posting-Host: net.bio.net Brucellosis is still a health problem in Mexico. Because it is a zoonosis, it is known that the effort to prevent or eradicate the disease relies on an early and efficient diagnosis (of infected cattle). The disease is caused by more than one species of the genus Brucella. Differentiation of species and biovars is important not only for taxonomy or phylogenetic analysis but to trace the source of infection as well Here in Mexico, at the Centro de Investigacion Biomedica del IMSS and the Instituto Nacional de Investigaciones Forestales y Agropecuarias (see addresses below) we designed primer pairs that are efficient in detecting all biovars of every Brucella species. The primers are specific and apparently do not amplify from other closely related bacteria. Our PCR is also very sensitive and we have used it to detect Brucella from blood and milk from infected animals. Very rarely we need to use nested PCR or to reamplify in a second round. We also found that using multiplex PCR it easy to find clear genetic differences that later could help in a taxonomic identification of the pathogen. We already published one article on this matter (and couple more have been submitted). At this moment we would like to see our primers and PCR conditions tried in different labs. The idea is to evaluate them in ring test trials, use them with other biovars or field isolates. In human brucellosis is worth a try. If somebody is interested in collaborative research or would like to use our test and primers please state your request and intention in a FAX to Diana Sara Leal-Klevezas CIBIN-IMSS Mexico fax no. (528) 344-4116 Please forward this message to any interested people. Best regards from sunny Mexico ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Juan Pablo Martinez-Soriano, Ph.D. Laboratorio de Patologia Molecular Convenio INIFAP-UANL Apartado postal 128-F Ciudad Universitaria San Nicolas de los Garza, N.L. MEXICO Voice and fax (528) 376-6320 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-rapd@net.bio.net Mon Mar 06 22:00:00 1995 Path: biosci!esvax.dnet.dupont.com!rafalski From: rafalski@esvax.dnet.dupont.com Newsgroups: bionet.molbio.rapd Subject: Primers from Alabama Date: 6 Mar 1995 05:03:45 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <9503061300.AA10762@esds01.es.dupont.com> Research Genetics 2130 Memorial Pkw SW Huntsville, AL 35801 1-800-533-4363 fax 205-536-9016 makes a variet of primers for microsatellite (SSLP or whatever) polymorphisms. Antoni Rafalski From owner-rapd@net.bio.net Wed Mar 08 22:00:00 1995 Path: biosci!ASRR.ARSUSDA.GOV!dkaplan From: dkaplan@ASRR.ARSUSDA.GOV Newsgroups: bionet.molbio.rapd Subject: Re: SCARs Date: 9 Mar 1995 11:55:47 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 30 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <1995Mar9.112438.1@leif> NNTP-Posting-Host: net.bio.net You are correct, a SCAR is a "Sequence Characterized Amplified Region" and it refers to primers that are made to specific RAPD fragments. They differe form STS (Sequence Tagged Sites) in that they contain the original primer used to amplify the original RAPD D. Kaplan On 9 Mar 1995 kegger@leif.ucs.mun.ca wrote: > I'm trying to find out what the acronym SCARs stands for. > My impression is that it stands for "Sequence Characterized > Amplified Regions" and refers to RAPD fragments that have > been sequenced and the sequence used to design more specific > PCR primers to amplify the region spanned by the RAPD primer. > > Does anyone have more insight into this term? Is the term > in widespread use? Has it ever been published? > > Thanks > > -------------------------------------- > Keith N. Egger > Department of Biology > Memorial University > St. John's, Newfoundland > A1B 3X9 CANADA > -------------------------------------- > Tel: 709-737-4478 FAX: 709-737-3018 > Email: KEgger@kean.ucs.mun.ca > -------------------------------------- > > From owner-rapd@net.bio.net Wed Mar 08 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!torn!news.unb.ca!coranto.ucs.mun.ca!leif!kegger From: kegger@kean.ucs.mun.ca Newsgroups: bionet.molbio.rapd Subject: SCARs Date: 9 Mar 95 11:24:38 -0330 Organization: Memorial University. St.John's Nfld, Canada Lines: 21 Message-ID: <1995Mar9.112438.1@leif> NNTP-Posting-Host: leif.ucs.mun.ca I'm trying to find out what the acronym SCARs stands for. My impression is that it stands for "Sequence Characterized Amplified Regions" and refers to RAPD fragments that have been sequenced and the sequence used to design more specific PCR primers to amplify the region spanned by the RAPD primer. Does anyone have more insight into this term? Is the term in widespread use? Has it ever been published? Thanks -------------------------------------- Keith N. Egger Department of Biology Memorial University St. John's, Newfoundland A1B 3X9 CANADA -------------------------------------- Tel: 709-737-4478 FAX: 709-737-3018 Email: KEgger@kean.ucs.mun.ca -------------------------------------- From owner-rapd@net.bio.net Wed Mar 08 22:00:00 1995 Path: biosci!esvax.dnet.dupont.com!rafalski From: rafalski@esvax.dnet.dupont.com Newsgroups: bionet.molbio.rapd Subject: SCARs Date: 9 Mar 1995 11:28:22 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <9503091926.AA00197@esds01.es.dupont.com> NNTP-Posting-Host: net.bio.net You are correct as to the acronym. It means "Sequence characterized amplified regions" It has been published by Paran and Michelmore, TAG 85(1993) 985-993. I suggested to Rich (half-jokingly) that the acronym has somewhat unpleasant connotations and should be changed to STARS (Sequence-Tagged Amplified Regions, see Trends in Genetics 9 (1993) 275-280). Antoni Rafalski From owner-rapd@net.bio.net Thu Mar 09 22:00:00 1995 Path: biosci!UNIXG.UBC.CA!hobbs From: hobbs@UNIXG.UBC.CA (John Hobbs) Newsgroups: bionet.molbio.rapd Subject: Insect mtDNA primer set. Date: 10 Mar 1995 14:38:58 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 120 Sender: daemon@net.bio.net Distribution: world Message-ID: <199503102238.OAA11469@unixg.ubc.ca> NNTP-Posting-Host: net.bio.net Insect molecular phylogenists who use RAPD but do not subscribe to bug-net may be interested to know that we have an insect mitochondrial primer set available: details are given in the posting below which was made to bug-net on 21st. February. **************************************************************************** ****We are happy to announce the availability of the insect mtDNA primer set that has been a topic of conversation on the net for some time. The set has been designed following the advice and input of Dr. Bernard J. Crespi (Simon Fraser University, Burnaby, B.C., Canada) and Dr. Chris Simon (University of Connecticut, Storrs, Connecticut, U.S.A.). Most of the sequences are taken from among those identified in C. Simon, F. Frati, P. Flook, A. Beckenbach, B. J. Crespi and H. Liu, "Evolution, weighting and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers", Annals of the Entomological Society of America, 1994, 87, 651-701. Each set contains 10 nmoles each (which is enough for 1 ml of 10uM solution of each primer) of 37 oligos marked mtD-1 to mtD-37. Also enclosed are a copy of the invoice, and the complete sequence list for the set, showing concordance between tube marking, conventional designation, alias (where applicable) and sequence. The oligonucleotides were purified by elution with Tris/EDTA buffer through NAP-5 drip columns. Aliquots of 10 nmoles (10-20 microlitres) each were made near the bottom of the tubes and air dried. All manipulations were conducted in a sterile laminar flow hood. We suggest dissolving your oligos in water or buffer as required, dividing them into portions of adequate size for each intended set of experiments, and storing these as stock solutions at -20 C, thawing portions only when needed. Oligonucleotides subjected to repeated freeze-thaw cycles will become degraded. Concordance: Tube Label / Standard Designation / Alias / Sequence Tube / Designation / Alias (if any) / Sequence (5 prime to 3 prime) mtD-1 TI-N-24 t-Iso ATT TAC CCT ATC AAG GTA A mtD-2 TM-J-206 Frank GCT AAA TAA GCT AAC AGG TTC AT mtD-3 TM-N-193 met-20 TGG GGT ATG AAC CCA GTA GC mtD-4 TY-J-1460 TAC AAT TTA TCG CCT AAA CTT CAG CC mtD-5 C1-N-1560 TGT TCC TAC TAT TCC GGC TCA mtD-6 C1-J-1718 GGA GGA TTT GGA AAT TGA TTA GTT CC mtD-7 C1-J-1751 Ron GGA TCA CT GAT ATA GCA TTC CC mtD-8 C1-J-2183 Jerry CAA CAT TTA TTT TGA TTT TTT GG mtD-9 C1-N-2191 Nancy CCC GGT AAA ATT AAA ATA TAA ACT TC mtD-10 C1-J-2195 CO1-RLR TTG ATT TTT TGG TCA TCC AGA AGT mtD-11 C1-N-2329 K525 ACT GTA AAT ATA TGA TGA GCT CA mtD-12 L2-N-3014 Pat TCC AAT GCA CTA ATC TGC CAT ATT A mtD-13 TL2-J-3034 AAT ATG GCA GAT TAG TGC A mtD-14 C2-J-3279 A-171 GGT CAA ACA ATT GAG TCT ATT TGA AC mtD-15 C2-N-3389 Marilyn TCA TAA GTT CAR TAT CAT TG mtD-16 C2-J-3400 A-298 ATT GGA CAT CAA TGA TAT TGA mtD-17 C2-N-3494 B-434 GGT AAA ACT ACT CGA TTA TCA AC mtD-18 C2-N-3661 Barbara CCA CAA ATT TCT GAA CAT TGA CCA mtD-19 C2-J-3696 A-611 GAA ATT TGT GGA GCA AAT CAT AG mtD-20 TK-N-3785 B-tLYS GTT TAA GAG ACC AGT ACT TG mtD-21 C3-J-5014 CO3a TTA TTT ATT GCA TCA GAA GT mtD-22 C3-N-5460 CO3b TCA ACA AAG TGT CAG TAT CA mtD-23 N4-N-8924 ND4rev AAA GCT CAT GTT GAA GCT CC mtD-24 N4-J-8944 ND4 GGA GCT TCA ACA TGA GCT TT mtD-25 CB-J-10612 CB1L CCA TCC AAC ATC TCA GCA TGA TGA AA mtD-26 CB-J-10933 CB1 TAT GTA CTA CCA TGA GGA CAA ATA TC mtD-27 CB-N-10920 CB2-H CCC TCA GAA TGA TAT TTG TCC TCA mtD-28 CB-N-11367 CB2 ATT ACA CCT CCT AAT TTA TTA GGA AT mtD-29 N1-J-12585 ND1A-Colorado GGT CCC TTA CGA ATT TGA ATA TAT CCT mtD-30 N1-N-12595 ND1 GTA GCA TTT TTA ACT TTA TTA GAA CG mtD-31 LR-N-12866 16Sb ACA TGA TCT GAG TTC AAA CCG G mtD-32 LR-J-12887 16Sbr CCG GTC TGA ACT CAG ATC ACG T mtD-33 LR-J-13417 16Sa ATG TTT TTG TTA AAC AGG CG mtD-34 LR-N-13398 16Sar CGC CTG TTT AAC AAA AAC AT mtD-35 SR-J-14233 12Sbi AAG AGC GAC GGG CGA TGT GT mtD-36 SR-N-14588 12Sai AAA CTA GGA TTA GAT ACC CTA TTA T mtD-37 SR-N-14925 TTA AAG TTT TAT TTT GGC The cost of the set is: for Canadian clients Can.$280 plus applicable taxes (GST for Canadian clients, plus PST for B.C. clients, unless you are fortunate enough to be exempt from these nuisances (in which case, please tell me!)); or US$220 for others. Individual primers can be ordered for Can.$20 (plus taxes, for Canadians) or $US 15. Carriage costs are added: airmail costs (small packet category) are US$3 for for the US, or US$4 to most parts of the world, while for courier delivery in the US we add an additional $11US ($8Can. for shipments within Canada). Courier delivery to other parts of the world is also added at the rate charged to us: $16 to the UK, $16 to Western Europe, $17 to Australasia, $17 to the Far East, $25 to China, South America, and Africa (all prices in US$, based on orders of one or two sets [i.e. up to 500g.]). ****************************************************************************** My thanks to Bernie for suggesting and stimulating the assembly of this set. At present we have enough material to make up around 30 sets, though less if there are major inroads on stocks of individual primers. First come, first served. Of course if demand is sustained we shall be remaking the primers. I can accept orders by fax, mail or e-mail to the address below. Orders should specify your mailing address, the name of the person to be billed (i.e. grant holder), your preference as to shipment via courier or air mail, and either an official Purchase Order Number or your cheque in advance (made out to "University of British Columbia"). If you request carriage by courier, please note that our couriers do not deliver to box numbers - a full mailing address is required - and also usually request a contact telephone number. If an order is phoned in, a copy of the P.O. for our records is still required. Our 10-mer primer sets for RAPD, our DDRT-PCR kit and our SSR-directed primer set continue to be available. Please contact me if you require details. John Hobbs. Dr. John Hobbs Nucleic Acid - Protein Service (NAPS) Unit Biotechnology Laboratory Room 237, Wesbrook Building 6174 University Boulevard University of British Columbia Vancouver, V6T 1Z3 Canada. FAX (604)822-5437 or (604)822-0676; Tel. (604)822-6373 From owner-rapd@net.bio.net Thu Mar 09 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: Marta Ceroni Newsgroups: bionet.molbio.rapd Subject: RAPDs and conservation Date: 10 Mar 1995 14:59:01 -0000 Lines: 17 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3jppfl$bie@mserv1.dl.ac.uk> Original-To: rapd@dl.ac.uk Hello, I'm a PHD student in Ecology; I'm studying genetic structure of an italian beech (Fagus sylvatica L.) population with RAPD and SSLP markers. I'm also interested in conservation problems and I'd like to know if there is someone out there studying genetic diversity of threatened plant species with these techniques. Thanks in advance, marta ceroni -- Marta Ceroni Istituto di Ecologia Direct phone: +39-521-905615 Universita' di Parma FAX: +39-521-905402 Viale delle Scienze e.mail: marta@eagle.bio.unipr.it 43100 Parma, Italy From owner-rapd@net.bio.net Thu Mar 09 22:00:00 1995 Path: biosci!SERVIDOR.DGSCA.UNAM.MX!carvalho From: carvalho@SERVIDOR.DGSCA.UNAM.MX (Carvalho Torres Alexandro cassio-UACPYP) Newsgroups: bionet.molbio.rapd Subject: Re: RFLP analysis program? Date: 9 Mar 1995 21:07:10 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net On Thu, 9 Mar 1995, Gary C. Donaldson wrote: > In article <2F55F2DD@coursmtp.nrc.ca> peloquin@biotech.lan.nrc.ca ("Peloquin, Marc") writes: > >From: peloquin@biotech.lan.nrc.ca ("Peloquin, Marc") > >Subject: RFLP analysis program? > >Date: 2 Mar 1995 08:31:40 -0800 > --- > >Hi Netters, > > >does anyone know a program for the analysis of RFLPs? > > >Thanks for answering! > > >Christoph Grunau > > > Millipore sells a software package called BioImage. The Windows version is > due to be out this summer. The version I've used runs on a Sun SparcStation - > basically, you scan in your gel photographs, and tell the machine to find the > bands. With the standards on the gel, you can get pretty good size > estimations. This package does a pile of neat things, and costs a small > fortune I'm sure. > > > Dear Netters, You could try the GelCompar programs. It have a lot of alternative analysis and it cost more a small price when comapared with the Millipore. Alexandro Carvalho Dept. Infectious Diseases - INNSZ. Mexico City. From owner-rapd@net.bio.net Thu Mar 09 22:00:00 1995 Path: biosci!agate!news.mindlink.net!news.bc.net!unixg.ubc.ca!port34.annex3.net.ubc.ca!garyd From: garyd@unixg.ubc.ca (Gary C. Donaldson) Newsgroups: bionet.molbio.rapd Subject: Re: RFLP analysis program? Date: Thu, 9 Mar 1995 17:23:10 UNDEFINED Organization: University of British Columbia Lines: 21 Distribution: world Message-ID: References: <2F55F2DD@coursmtp.nrc.ca> NNTP-Posting-Host: port34.annex3.net.ubc.ca X-Newsreader: Trumpet for Windows [Version 1.0 Rev B] In article <2F55F2DD@coursmtp.nrc.ca> peloquin@biotech.lan.nrc.ca ("Peloquin, Marc") writes: >From: peloquin@biotech.lan.nrc.ca ("Peloquin, Marc") >Subject: RFLP analysis program? >Date: 2 Mar 1995 08:31:40 -0800 --- >Hi Netters, >does anyone know a program for the analysis of RFLPs? >Thanks for answering! >Christoph Grunau Millipore sells a software package called BioImage. The Windows version is due to be out this summer. The version I've used runs on a Sun SparcStation - basically, you scan in your gel photographs, and tell the machine to find the bands. With the standards on the gel, you can get pretty good size estimations. This package does a pile of neat things, and costs a small fortune I'm sure. From owner-rapd@net.bio.net Fri Mar 10 22:00:00 1995 Path: biosci!BIOMED.NUS.SG!bchtantw From: bchtantw@BIOMED.NUS.SG (Dr Tan Tin Wee) Newsgroups: bionet.molbio.rapd Subject: Primer sets for food pathogens Date: 10 Mar 1995 17:23:30 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <199503102238.OAA11469@unixg.ubc.ca> NNTP-Posting-Host: net.bio.net I have been asked by a colleague at our Primary Production Dept's food analysis laboratory about PCR primer sets for detection of food pathogens in food products. Any pointers will be gratefully received. Thank you in advance. Rgds Tin Wee --- Dr Tan Tin Wee Head, Technet Unit, Computer Centre, NUS 65-772-4690 Senior Lecturer, Dept of Biochemistry, Fac of Medicine, NUS 65-772-3678 Resident Fellow, Sheares Hall, NUS 65-778-2119 National University of Singapore, Kent Ridge, SINGAPORE 0511 Fax: 65-773-6812 Internet: tinwee@technet.sg URL: http://biomed.nus.sg and http://www.technet.sg CUSeeMe: 137.132.9.61 biomed.nus.sg From owner-rapd@net.bio.net Sat Mar 11 22:00:00 1995 Path: biosci!VM1.MCGILL.CA!SMTPB From: SMTPB@VM1.MCGILL.CA Newsgroups: bionet.molbio.rapd Subject: RFLP performed using PCR: FABLE method Date: 12 Mar 1995 10:00:42 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 51 Sender: daemon@net.bio.net Distribution: world Message-ID: <199503121800.KAA04527@net.bio.net> NNTP-Posting-Host: net.bio.net >Hello Netters, >I have thought of and tried a new technique. It involves the >use of PCR to perform RFLP. It eliminates the need for >Southerns, DNA digestion ect. > >The technique, in theory is simple. DNA extension, during PCR, >is halted by blockers. These blockers can have the same sequence >as restriction enzymes or not. The primer is the probe used for >regular RFLP. > >Problems to be addressed were high affinity binding of >the blockers (4 to 8 baase pairs), PCR extension of greater than >100bp, dimerization and non-extension of the blockers, and use of large sized primers. >The high affinity binding can be obtained with the use of peptide >nucleic acids. PCR extension is much larger than previously >due to proof reading, use of new buffers with appropriate pH >at PCR cycling temperatures and so on. Shorter probe fragments can be >used for PCR (that is one way to get around the large size of probes >used in RFLP, if PCR technology is to be applied). >I do not know if the blockers dimerize but they may not extend >during PCR cycling. I tried the technique with short >DNA fragmentsts, blocked by a sort peptide chain, but >it did not work. The resolved fragments were of inappropriate >size (the same size as the parent DNA strand and were R.E cleaved where the blocker was supposed to bind to (and block R.E cleavage). > >This idea came about due to the laborius work of RFLP. It was due >to the advances made in PCR extension by Brown and others >(I had gained this information off of this news group earlier) >and Ergholm et al (correct spelling?) who made the peptide >nucleic acids. He is now at BioSearch, a subsidiary of Millipore. >Anyways, you can see the adverts for Peptide nucleic acids in several >journals. > >I am not affiliated with any of the companies that produce the >PCR products and extra long PCR, or with companies that make >peptide nucleic acids. The use and development of this procedure, >which I call FABLE fragment extension and blocked long >extension, is permitted provided that I am credited. >I believe thatt science will benefit more from >shared ideas, freely distributed rather than jealously guarded >secrets (extreme personal opinion). >If anyone tries this method I would be interested in hearing of it. > >Ian Murray >McGill University >e-mail: BKPK@musicb.mcgill.ca From owner-rapd@net.bio.net Sat Mar 11 22:00:00 1995 Path: biosci!Citadel.edu!WHITEHURSTM From: WHITEHURSTM@Citadel.edu Newsgroups: bionet.molbio.rapd Subject: re insect mtDNA primer set Date: 12 Mar 1995 15:50:40 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HO24J8Q0AE8ZGJ9Y@Citadel.edu> NNTP-Posting-Host: net.bio.net "bug-net" was mentioned in the original post. Please send information on accessing "bug-net". Thanks Maureen Whitehurst From owner-rapd@net.bio.net Sun Mar 12 22:00:00 1995 Path: biosci!AVA.BCC.ORST.EDU!bakalina From: bakalina@AVA.BCC.ORST.EDU (Alan Bakalinsky) Newsgroups: bionet.molbio.rapd Subject: RADP reproducibility Date: 13 Mar 1995 10:18:47 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 61 Sender: daemon@net.bio.net Distribution: world Message-ID: <9503131820.AA22060@BCC.ORST.EDU> NNTP-Posting-Host: net.bio.net Colleagues, From time to time, discussion has focused on the reproducibility of the RAPD assay and on all the parameters that have an affect on the reaction. From our limited experience, we have found that reproducibility is a major problem of RAPDs and will be a source of difficulty if one expects to share data between labs and over long periods of time. The major conclusions of our work with grape RAPDs and SCARSs are: 1. RAPDs are too unreliable for use as endpoints. 2. RAPDs are very good for quickly screening polymorphisms (and artifacts). 3. As soon as a RAPD is detected, clone and sequence it (or its ends), and convert it into a sequence specific marker that will be stable and useful. 4. All the reaction parameters such as choice of polymerase, magnesium concentration, etc. that are known to affect RAPDs should be viewed as ways of increasing the range of polymorphisms that can be detected. 5. SCARs are useful about 50% of the time, but until a better way is found of exploiting the poplymorphisms that RAPDs detect, they ought to be used. I have appended the abstract of our in press paper (J. Amer. Soc. Hort. Sci., 1995) and will be happy to provide preprints. Sequence-specific PCR markers derived from RAPDs for fingerprinting grape (Vitis) rootstocks. Hong Xu, Diane J. Wilson, S. Arulsekar, and Alan T. Bakalinsky Abstract: Random amplified polymorphic DNA (RAPD) markers were generated for identifying grape (Vitis) rootstocks. A total of 77 primers (of ten base length) were screened using CsCl-purified leaf DNA derived from multiple field samples of nine rootstocks sampled in successive years. A total of nine RAPD markers were detected from six primers, and in combination, distinguished all nine rootstocks tested. Because inconsistencies were encountered in performing the RAPD assay, sequence-specific primers were derived from cloned RAPD bands for use under more stringent amplification conditions. Southern hybridization analysis of the RAPD gels with cloned RAPD bands as probes revealed deficiencies of scoring RAPD bands based solely on ethidium bromide staining. In some cases, bands of the same size generated by the same primer in different rootstocks--normally scored as the same marker--failed to cross-hybridize, implying lack of homology between the bands. More commonly, bands scored as absent based on ethidium bromide staining were detected by hybridization. Six of the nine cloned RAPD bands were partially sequenced, and sequence-specific primer pairs were synthesized. Three of the most useful primer pairs amplified apparent length variants in some accessions. Two amplified a product the same size as the original RAPD band in all rootstocks, resulting in loss of polymorphism. Two other pairs of sequence-specific primers derived from the same marker failed to amplify the expected band consistently. Alan T. Bakalinsky Department of Food Science and Technology Wiegand Hall Oregon State University Corvallis, OR 97331-6602 Phone: (503) 737-6510 FAX: (503) 737-1877 Internet: bakalina@bcc.orst.edu From owner-rapd@net.bio.net Sun Mar 12 22:00:00 1995 Path: biosci!U.WASHINGTON.EDU!walterh From: walterh@U.WASHINGTON.EDU (Walter Hill) Newsgroups: bionet.molbio.rapd Subject: Re: Primer sets for food pathogens Date: 13 Mar 1995 12:29:34 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 26 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net On 10 Mar 1995, Dr Tan Tin Wee wrote: > > I have been asked by a colleague at our Primary Production Dept's > food analysis laboratory about PCR primer sets for detection > of food pathogens in food products. Because most foodborne pathogens are also of concenr in the clinical laboratory, I would suggest the following chapter: Mahbubani and Bej: Applications of PCR Methodlogy in Clinical Diagnostics. in PCR Technology: Current Innovations (ed by Griffin and Griffin), CRC press, Chap. 31, pp 307-365. The is a rather extensive table listing organisms, primer sequences, targets and references which should prove useful for anyone wanting to get started in the PCR-based detection of microbial pathogens. [insert the usual disclaimers here] walterh@u.washington.edu (primary) (secondary) hillw@par66.par.ora.fda.gov Food & Drug Admin., Seafood Products Research Center, Bothell, WA 98041-3012 Affiliate Associate Professor of Microbiology University of Washington VOICE:(206) 483-4892 "Cook it first" (206) 483-4996:FAX > From owner-rapd@net.bio.net Sun Mar 12 22:00:00 1995 Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.rapd Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!uunet!world!chi From: chi@world.std.com (Cambridge Healthtech Institute) Subject: Genetic Diagnostics/Infectious Diseases Conference Message-ID: Organization: Cambridge Healthtech Institute X-Newsreader: TIN [version 1.2 PL2] Date: Mon, 13 Mar 1995 19:48:40 GMT Lines: 57 Xref: biosci bionet.molbio.methds-reagnts:25875 bionet.molbio.rapd:1047 Cambridge Healthtech Institute is sponsoring a meeting, "Advances in Genetic Diagnostics for Infectious Diseases," to be held April 19-20, 1995 in Washington, DC. Genetic diagnostics provide significant advantages with infectious agents that are difficult to culture or in cases including the emergence of multi-drug resistant strains, where it is critical to distinguish between closely related strains of the agent. Increasingly, quantification of viral or infectious load is being used as surrogate markers in clinical trials, to monitor disease progression or response to therapy, in order to tailor therapy to the individual patient. These and other key diagnostic issues, including results with newly developed tests, will be discussed in detail. --Session Chairs-- Dr. Thomas M. Shinnick, Centers for Disease Control and Prevention --Speakers-- Dr. Kathleen D. Eisenach, University of Arkansas for Medical Sciences Dr. Thomas R. Gingeras, Affymetrix Dr. Steven A. Herman, Roche Molecular Systems, Inc. Dr. Indira K. Hewlett, CBER, FDA Dr. Craig S. Hill, Gen-Probe Incorporated Dr. Helen H. Lee, Abbott Laboratories Dr. Richard D. Press, Oregon Health Sciences University Dr. Ira Schwartz, New York Medical College Dr. Mathias Uhlén, Royal Institute of Technology Dr. Mickey S. Urdea, CHIRON CORPORATION Dr. Gerard F. Vovis, Genome Therapeutics Corporation Dr. G. Terrance Walker, Becton Dickinson Research Center Abbott Laboratories Organon Teknika Exhibitors: Digene, Gen-Probe Coming soon: "New Applications of Emerging Molecular Diagnostics for Infectious Diseases:" June 26-27, The Regent London, London England. For more information on either meeting, contact: chi@world.std.com. Please provide fax number for quick response. *********************************************************************** *>>>>>>>>>>>> Cambridge Healthtech Institute <<<<<<<<<<<<<* *>>>>> 1000 Winter Street, Suite 3700 <<<<<* *~~~~~~~~~~~~~~~~~ Waltham, MA 02154 ~~~~~~~~~~~~~~~~~* *tel: 617.487.7989 fax: 617.487.7937* *e-mail: chi@world.std.com ++++++++ ftp: ftp.std.com: /pub/chi* *>>>>>World Wide Web: http://www.xensei.com/users/chi/homepg.html<<<<<* *********************************************************************** From owner-rapd@net.bio.net Mon Mar 13 22:00:00 1995 Path: biosci!U.WASHINGTON.EDU!walterh From: walterh@U.WASHINGTON.EDU (Walter Hill) Newsgroups: bionet.molbio.rapd Subject: Re: Primer sets for food pathogens Date: 13 Mar 1995 16:35:02 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net In my previous reply to Dr. Wee, I described the wrong chapter in the book edited by Griffin and Griffin. The correct chapter is by Jones and Bej (Chapter 33, not 31). The pages are 341-365. My apologies for the error and the waste of bandwidth. walterh@u.washington.edu (primary) (secondary) hillw@par66.par.ora.fda.gov Food & Drug Admin., Seafood Products Research Center, Bothell, WA 98041-3012 Affiliate Associate Professor of Microbiology University of Washington VOICE:(206) 483-4892 "Cook it first" (206) 483-4996:FAX From owner-rapd@net.bio.net Tue Mar 14 22:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.nysernet.net!news.sprintlink.net!pipex!sunsite.doc.ic.ac.uk!dundee.ac.uk!sfh.biolsci.dundee.ac.uk!rdjbutcher From: rdjbutcher@biolsci.dundee.ac.uk (ROBERT BUTCHER) Newsgroups: bionet.molbio.rapd Subject: Re: re insect mtDNA primer set Date: Wed, 15 Mar 1995 23:37:39 GMT Organization: University of Dundee Lines: 11 Distribution: world Message-ID: References: <01HO24J8Q0AE8ZGJ9Y@Citadel.edu> NNTP-Posting-Host: sfh.biolsci.dundee.ac.uk In article <01HO24J8Q0AE8ZGJ9Y@Citadel.edu> WHITEHURSTM@Citadel.edu writes: >From: WHITEHURSTM@Citadel.edu >Subject: re insect mtDNA primer set >Date: 12 Mar 1995 15:50:40 -0800 >"bug-net" was mentioned in the original post. Please send information on >accessing "bug-net". Thanks Maureen Whitehurst Likewise..Please inform me also Rob e-mail:- R.D.J.BUTCHER@DUNDEE.AC.UK Thanks From owner-rapd@net.bio.net Wed Mar 15 22:00:00 1995 Path: biosci!SERVIDOR.DGSCA.UNAM.MX!carvalho From: carvalho@SERVIDOR.DGSCA.UNAM.MX (Carvalho Torres Alexandro cassio-UACPYP) Newsgroups: bionet.molbio.rapd Subject: prokaryotic mapping Date: 16 Mar 1995 15:58:13 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear netters I would like to know who have some experience and how can I make to mapping a bcaterial genome with rapd primers? Exist some special program or tips to do that. I read some papers for eukariotic cells but I don't see anything for bacterial genome. Sincerely, Alexandro Carvalho Deprtment of Infectious Diseases.-INNSZ. mexico, DF From owner-rapd@net.bio.net Wed Mar 15 22:00:00 1995 Path: biosci!rutgers!gatech!news-feed-1.peachnet.edu!news.duke.edu!solaris.cc.vt.edu!uunet!in1.uu.net!newstf01.news.aol.com!newsbf02.news.aol.com!not-for-mail From: mmassoudi@aol.com (MMASSOUDI) Newsgroups: bionet.molbio.rapd Subject: Lack of Hybridization Date: 16 Mar 1995 14:51:41 -0500 Organization: America Online, Inc. (1-800-827-6364) Lines: 18 Sender: root@newsbf02.news.aol.com Message-ID: <3ka4sd$9d2@newsbf02.news.aol.com> Reply-To: mmassoudi@aol.com (MMASSOUDI) NNTP-Posting-Host: newsbf02.mail.aol.com Dear Colleagues: I have been able to link four RAPD markers to an important fungal resistance trait in pepper. I have carried out the Southern hybridization analysis using the gel isolated the RAPD bands as probes to test that the amplified RAPD fragments are genomically driven. However, I have failed to cross hybridize one of the four probes (the probe is about 900 bp in size). I have repeated the hybridization steps a few times without any success. I have found many inconsistancies with this particular probe. The questions are: a. Does this imply that there is a lack of homology between the RAPD generated band with the genomic DNA? b. What are the possible reasons for lack of hybridization and how would I be able to solve the problem? Thanks for your comments. MM From owner-rapd@net.bio.net Thu Mar 16 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: Louis van de Zande Newsgroups: bionet.molbio.rapd Subject: Re: Lack of Hybridization Date: 17 Mar 1995 09:15:10 -0000 Organization: Department of Biology, RUGroningen Lines: 33 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3kbjuu$7mg@mserv1.dl.ac.uk> Reply-To: L.P.W.G.M.van.de.Zande@biol.rug.nl Original-To: rapd@dl.ac.uk > Dear Colleagues: > I have been able to link four RAPD markers to an important fungal > resistance trait in pepper. I have carried out the Southern hybridization > analysis using the gel isolated the RAPD bands as probes to test that the > amplified RAPD fragments are genomically driven. However, I have failed to > cross hybridize one of the four probes (the probe is about 900 bp in > size). I have repeated the hybridization steps a few times without any > success. I have found many inconsistancies with this particular probe. The > questions are: > > a. Does this imply that there is a lack of homology between the RAPD > generated band with the genomic DNA? Yes it does. However, maybe other factors are involved. The fragment could be generated from non-nuclear DNA and, due to extraction procedures, this DNA could be underrepresented in your blotted DNA. Alternatively, but you give no clue as to this, the DNA homologous to your probe could be digested into very short fragments by the restriction enzyme you use for the southern transfer. These fragments do not transfer efficiently to the filter and additionally give a less specific hybridization. > > b. What are the possible reasons for lack of hybridization and how would I > be able to solve the problem? > Try blotting the original RAPD pattern and see what happens when the probe is confronted with itself and other RAPD bands generated by the same primer. Try different restriction enzymes or even undigested DNA. Or just lower the stringgency of the hybridization and washing procedures. Louis van de Zande From owner-rapd@net.bio.net Thu Mar 16 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!news.cac.psu.edu!news.tc.cornell.edu!travelers.mail.cornell.edu!newsstand.cit.cornell.edu!NewsWatcher!user From: bir1@cornell.edu (Bruce Reisch) Newsgroups: bionet.molbio.rapd Subject: Re: RADP reproducibility Date: Fri, 17 Mar 1995 13:30:57 -0500 Organization: Cornell University Lines: 93 Sender: bir1@cornell.edu (Verified) Distribution: world Message-ID: References: <9503131820.AA22060@BCC.ORST.EDU> NNTP-Posting-Host: 132 In article <9503131820.AA22060@BCC.ORST.EDU>, bakalina@AVA.BCC.ORST.EDU (Alan Bakalinsky) wrote: > Colleagues, > {snip} > 1. RAPDs are too unreliable for use as endpoints. > 2. RAPDs are very good for quickly screening polymorphisms (and artifacts). > 3. As soon as a RAPD is detected, clone and sequence it (or its ends), > and convert it into a sequence specific marker that will be stable and > useful. > 4. All the reaction parameters such as choice of polymerase, magnesium > concentration, etc. that are known to affect RAPDs should be viewed as ways > of increasing the range of polymorphisms that can be detected. > 5. SCARs are useful about 50% of the time, but until a better way is > found of exploiting the poplymorphisms that RAPDs detect, they ought to be > used. {snip} Alan We have been in touch with you about your work in the past, and as you know, our findings are quite different. 1. We had a scientist from Spain reproduce his RAPD-Vitis fingerprinting work in our lab. 2. A scientist from Turkey now in our lab is finding identical results in fingerprinting as an earlier postdoc in our lab. He has been able to confirm some banding pattern differences seen last year between supposedly identical varieties. 3. This same scientist has picked up on earlier genetic mapping work and again has been able to produce banding patterns identical to those produced in 1992 and 1993. 4. In a detailed fingerprinting study, a portion of a large set of data was replicated over DNA extractions, separate reaction mixtures, and two different thermocyclers. No differences were seen between reactions from the same initial grape genotype. See abstract of pending manuscript below. The point I wish to make is that several labs, including mine, and one each in Israel, Spain, and France, have had good results with consistency of RAPDs. Alan's points are well taken that reproducibility may be a problem, but it is not insurmountable. Others have made the point that the following factors must be tightly controlled: 1) source and quantity of Taq polymerase, 2) template DNA quantity (DNA must be quantified carefully, fluorometer preferred), and 3) strict control on thermocycler temperature profile and ramping times based on direct measure of the amplification reaction mixture. Other factors are also involved, but the above factors seem to contribute to a number of cases of inconsistent results. Alan - hope you don't mind my adding another point of view to a good debate! But I don't want to give new researchers the impression that every lab has run into the problems you have had with unreliability of RAPD markers. Bruce Reisch manuscript in preparation: Analysis of the relationship between grapevine cultivars and clones via DNA fingerprinting Guang-Ning Ye, Norman F. Weeden, Robert M. Pool and Bruce I. Reisch Department of Horticultural Sciences, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456. Abstract DNA fingerprinting utilizing RAPD polymorphisms was employed to develop a reliable method for grapevine identification. The relationship among 16 clonally propagated cultivars and others believed to be sports from these cultivars was examined. From 53 primers, a total of 464 bands were generated, of which 29% were common to all cultivars and clones tested. Cluster analysis classified all tested cultivars into two main groups (V. vinifera L. and V. X Labruscana Bailey) as expected. No polymorphism was detected among known clones of 'Chardonnay' ('Chardonnay' clone 7, 'Chardonnay' clone 78 and 'Chardonnay' Geneva clone) or 'Pinot noir' ('Pinot noir' clone 29, 'Pinot noir' Geneva clone and 'Pinot noir' Pernand). 'Pinot Meunier' and 'Gamay Beaujolais' displayed patterns identical to 'Pinot noir'. Surprisingly, however, 'Pinot gris', and 'Auxerrois' showed unique patterns, contradicting the common belief that 'Pinot gris' is a berry color sport from 'Pinot noir', and that 'Auxerrois' is a clone of 'Chardonnay'. 'Chardonnay' clone 7 shared 81% of its bands with 'Pinot noir' Geneva. While RAPD banding patterns could not distinguish between known clones, they were useful to distinguish between phenotypically similar cultivars, and to help understand the origins of cultivars thought to have originated as sports. . . . Reproducibility of RAPD fingerprinting A portion of the data collected, generating 147 of the 386 markers within the 'Pinot'/'Chardonnay' group, was replicated by analyzing two DNA extractions per cultivar, each of which was amplified separately on two PTC-100 thermocyclers. The banding patterns obtained from these replicated samples were always identical for each primer/genotype combination (Figure 2). From owner-rapd@net.bio.net Thu Mar 16 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!pipex!warwick!bham!bcs88.bham.ac.uk!user From: A.C.Hilton@bham.ac.uk (Wiggy) Newsgroups: bionet.molbio.rapd Subject: Re: rapd sequences Date: 17 Mar 1995 15:16:39 GMT Organization: The University of Birmingham Lines: 32 Distribution: world Message-ID: References: <199502152305.PAA27237@net.bio.net> NNTP-Posting-Host: bcs88.bham.ac.uk In article <199502152305.PAA27237@net.bio.net>, EQUIGENE@UKCC.UKY.EDU ("Teri L. Lear") wrote: > Having searched the literature I can find no reference where someone has > compared the sequences of co-migrating RAPD markers between species > mammalian systems. We are trying to find out more about the nature of these > "shared" RAPD bands and if they are indeed the same sequences. I am aware of > the use of Southern blots, etc. for the characterization of RAPD markers. > In previous RAPD network discussions several researchers noted that they > planned to further characterize markers shared between species by sequencing > and I was curious if anyone had done this? Any references or comments are > greatly appreciated. > > Thanks. > > Teri L. Lear > Department of Veterinary Science > Gluck Equine Research Center > University of Kentucky > Lexington, KY 40546-0099 > e-mail: equigene@ukcc.uky.edu Hi, I have cloned and sequenced several bands (produced from RAPD of different serotypes of Salmonella) that co-migrate and have found that they are actually different sequence. I need to, however, sequence more fragments to be absolutely confident of this finding. Regards, Wiggy From owner-rapd@net.bio.net Thu Mar 16 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.cac.psu.edu!news.tc.cornell.edu!travelers.mail.cornell.edu!newsstand.cit.cornell.edu!CU-DIALUP-0623.CIT.CORNELL.EDU!bl14 From: bl14@cornell.edu (Barbara E. Liedl) Newsgroups: bionet.molbio.rapd Subject: Help free a Rwandan scientist imprionsed while on a humanitarian mission Date: Fri, 17 Mar 1995 03:20:36 UNDEFINED Organization: Cornell University Lines: 39 Sender: bl14@cornell.edu (Verified) Message-ID: NNTP-Posting-Host: cu-dialup-0623.cit.cornell.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev B] Dr. Martin Bicamumpaka is a Rwandan agricultural scientist, who has spent his life working to improve agriculture in Sub-Sahara Africa. During the recent unrest in Rwanda, he along with his family left Rwanda for a neighboring country. His current post is as the coordinator of PRAPACE, a regional network composed of the potato and sweetpotato research programs of six African countries: Burundi, Ethiopia, Kenya, Rwanda, Uganda and Zaire. PRAPACE provides established mechanisms for the lateral transfer of improved materials and technologies for potatoes and sweetpotatoes among the member countries. Because of his expertise, he was asked attend an international workshop on the "Seeds of Hope" program in Rwanda and after his arrival on February 2nd he was arrested. He is currently in Kigali Central Prison accused of serious crimes related to genocide. There are currently 6,500 prisoners begin held in this prison, a facility built for 2,500.People are sick and are dying in this prison every day. The justice system in Rwanda is understaffed and procedures for cases like Dr. Bicamumpaka's have not yet been worked out. The U.N. High Commission on Human Rights will follow his case- but a very important part of this process is to keep Dr. Bicamumpaka's name and case visible, by writing letters and makinginguiries. THIS IS WHERE YOU CAN MAKE A DIFFERENCE. PLEASE write a letter to: Dr. Augustine Iyamuremye Minister of Agriculture Rwanda This letter should mention that Dr. Bicamumpaka's whole career has been devoted to improving the agricultural situation in Rwanda and that the charges against him must be in error. It does not matter if you know Martin Bicamumpaka personally or not; what matters is the volume of letters that the Minister receives. Please take the time to write a letter and help Dr. Bicamumpaka survive this dangerous situation. Any questions about this situation should be directed to: Laurie_Hanley@qmrelay.mail.cornell.edu THANK YOU for your assistance. From owner-rapd@net.bio.net Thu Mar 16 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: Wolfgang Wuster Newsgroups: bionet.molbio.rapd Subject: Re: Help free a Rwandan scientist imprionsed while on a humanitarian mission Date: 17 Mar 1995 09:57:38 -0000 Lines: 40 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3kbmei$a13@mserv1.dl.ac.uk> X-Sender: bss166@clss1 Original-To: "Barbara E. Liedl" On Fri, 17 Mar 1995, Barbara E. Liedl wrote: > Dr. Martin Bicamumpaka is a Rwandan agricultural scientist, who has spent > his life working to improve agriculture in Sub-Sahara Africa. During the [snip] > countries. Because of his expertise, he was asked attend an international > workshop on the "Seeds of Hope" program in Rwanda and after his arrival on > February 2nd he was arrested. > > He is currently in Kigali Central Prison accused of serious crimes related to > genocide. There are currently 6,500 prisoners begin held in this prison, a ^^^^^^^^ [snip] > This letter should mention that Dr. Bicamumpaka's whole career has been devoted to > improving the agricultural situation in Rwanda and that the charges against > him must be in error. It does not matter if you know Martin Bicamumpaka ^^^^^^^^^^^^^^^^^ So this guy is in jail on suspicion of having participated in an act of genocidal madness that left close to a million people dead, as we are supposed to write to the ministry of his country to let him go because he is an expert in sweet potatoes? I'm sure he ordinarily is a nice fellow, and his family loves him. However, I do not see how his agricultural work necessarily means that he is innocent. Unfortunately, the Rwandan genocide is not the first time in history that acts of genocide were perpetrated by previously ordinary people. If there are grounds for suspicion against Dr. Bicamumpaka, he should go through the judicial process of his country like anyone else, and should not receive special treatment because he has some contacts abroad. Just my $ .02 Wolfgang Wuster Thought for the day: If you see a light at the end of the tunnel, it is probably a train. From owner-rapd@net.bio.net Sun Mar 19 22:00:00 1995 Path: biosci!nbri.sirnetd.ernet.in!manager From: manager@nbri.sirnetd.ernet.in (UDAY PATHRE) Newsgroups: bionet.molbio.rapd Subject: STR as primers Date: 19 Mar 1995 21:33:03 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 45 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Message dated March 15, 1995 Dear Netters, Hi! I have been using STRs such as (TG)10 , (GAA)6, (CAC)5, (GATA)4 and (GACA)4 for determining fingerprint patterns in some of the plant species. In the case of Amaranths, I get good fingerprint patterns when I use end-labelled (32P) (TG)10 as the probe. Using similar protocols but for (GAA)6 as a probe I get no or low signals. However, when I use (TG)10 as a single primer for an amplification reaction, I get just a smear while with (GAA)6 as the single primer, I get several products (4-9 distinct bands). Any ideas/views as to how this can be explained/interpreted? I think that in case of (TG)10 as a primer, the G-rich nature may have something to do with the failure to obtain discrete products and if so, I may have to try additives like DMSO or TEACL. Anyone out there having similar experiences? Your comments please. I will also greatly appreciate receiving protocol(s) using the additives like DMSO or TEACL. My thanks in advance. Shirish A. Ranade ******************************************************************* * "RAPD or DFP, SCAR or SPAR, DFP or RFLP * * ANOTHER KIND OF TO BE OR NOT TO BE" * * * * * * MESSAGE FROM DR. SHIRISH A. RANADE * * CENTRE FOR PLANT MOLECULAR BIOLOGY * * NATIONAL BOTANICAL RESEARCH INSTITUTE * * RANA PRATAP MARG, LUCKNOW 226 001. INDIA. * * * * FAX NO. : (91) 522 282881 OR 282849 * * * * E-MAIL : manager@nbri.sirnetd.ernet.in * * * ******************************************************************* From owner-rapd@net.bio.net Mon Mar 20 22:00:00 1995 Path: biosci!greb.ulaval.ca!Christian.Mouton From: Christian.Mouton@greb.ulaval.ca (Christian Mouton) Newsgroups: bionet.molbio.rapd Subject: What is SCAR ? Date: 21 Mar 1995 12:05:40 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: <9503212005.AA09529@hermes.ulaval.ca> NNTP-Posting-Host: net.bio.net On 21 Mar 1995 Alan T. Bakalinsky wrote: ..."our 3 year experience with grape RAPDs was a prolonged agony, until we began cloning those we could reproduce and converting them into SCARs." What do SCAR stand for? is any reference in the literature available? Christian Mouton Groupe de Recherche en Écologie Buccale Faculté de médecine dentaire Université Laval Québec (Québec) G1K 7P4 CANADA tél. (418)656-5872 fax. (418)656-2861 Email: Christian.Mouton@greb.ulaval.ca From owner-rapd@net.bio.net Mon Mar 20 22:00:00 1995 Path: biosci!AVA.BCC.ORST.EDU!bakalina From: bakalina@AVA.BCC.ORST.EDU (Alan Bakalinsky) Newsgroups: bionet.molbio.rapd Subject: RAPD reproducibility Date: 21 Mar 1995 10:17:44 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 37 Sender: daemon@net.bio.net Distribution: world Message-ID: <9503211819.AA11596@BCC.ORST.EDU> NNTP-Posting-Host: net.bio.net Colleagues, I am responding to the comments of Bruce Reisch, Michael McClelland, and W. Ralph Andersen concerning my earlier post about RAPD irreproducibility. I stated, in so many words, that our 3 year experience with grape RAPDs was a prolonged agony, until we began cloning those we could reproduce and converting them into SCARs. Bruce pointed out that he has had success with grape RAPDs and that problems of reproducibility have been minor or tamed. A couple thoughts come to mind: One explanation for our different results is that we isolated DNA late in the season and generally from mature leaves laced with polysaccharide. Although we used a CsCl-based method to purify the DNA and found it to be cuttable by the few restriction enzymes we tested, perhaps over time (1-3 years in TE at -20 C) the DNA became degraded in subtle ways such that it was still a substrate for the polymerase, but a changed one. Another possibility is that we used Tfl polymerase, not Taq. Quite recently, we switched to Taq for doing SCARs and found that it seems to give a cleaner background than Tfl. The switch was prompted by difficulties related to a bad batch of Tfl. A final note. Until we can determine the cause(s) of our reproducibility problems, we find it safer to use RAPDs only as a first screen for polymophisms. Once a RAPD is detected, we clone it and convert it into a SCAR or a similar stable marker. Alan T. Bakalinsky Department of Food Science and Technology Wiegand Hall Oregon State University Corvallis, OR 97331-6602 Phone: (503) 737-6510 FAX: (503) 737-1877 Internet: bakalina@bcc.orst.edu From owner-rapd@net.bio.net Mon Mar 20 22:00:00 1995 Newsgroups: bionet.molbio.rapd Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!sunserver.insinc.net!news.Direct.CA!scipio.cyberstore.ca!vanbc.wimsey.com!news.mindlink.net!news.bc.net!rover.ucs.ualberta.ca!tribune.usask.ca!canopus.cc.umanitoba.ca!newsflash.concordia.ca!nstn.ns.ca!dragon.acadiau.ca!pat426.acadiau.ca!msnyder From: msnyder@ace.acadiau.ca (MARLENE SNYDER) Subject: Temp. gradient gel elcetrophorsis/ G/C clamps Message-ID: Lines: 16 Sender: news@relay.acadiau.ca Nntp-Posting-Host: pat426.acadiau.ca Organization: Acadia University X-Newsreader: Trumpet for Windows [Version 1.0 Rev B final beta #1] Date: Tue, 21 Mar 1995 15:40:45 GMT Lines: 16 Hi, I am trying to figure out how TGGE works, and why the GC clamp facilitates TGGE detection of single base mis matches within a DNA fragment. It seems to me that the clamp would impede melting, but melting is the object of the excise, is it not? Any enlightenment would be appreciated. Marty Snyder Genetics Acadia From owner-rapd@net.bio.net Mon Mar 20 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!eru.mt.luth.se!news.luth.se!sunic!sunic.sunet.se!columba.udac.uu.se!strix.udac.uu.se!genpt From: genpt@strix.udac.uu.se (Peter Thoren) Newsgroups: bionet.molbio.rapd Subject: spermidine Date: 21 Mar 1995 14:32:29 GMT Organization: Uppsala University Lines: 12 Message-ID: <3kmo1t$16uk@columba.udac.uu.se> NNTP-Posting-Host: strix.udac.uu.se X-Newsreader: TIN [version 1.2 PL2] hi netters! I am going to test spermidine in order to improve my microsatellite PCR. I just want to know what final concentration is used by others. Thanks in advance, Peter Thoren Dept.of genetics, Uppsala University Sweden peter.thoren@genetik.uu.se From owner-rapd@net.bio.net Tue Mar 21 22:00:00 1995 Newsgroups: bionet.molbio.rapd Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!alfa02.medio.net!netnews.nwnet.net!ns1.nodak.edu!badlands!schnurr From: schnurr@badlands.NoDak.edu (Jeffrey P Schnurr) Subject: Female sterility gene? Sender: usenet@ns1.nodak.edu (Usenet login) Message-ID: Date: Wed, 22 Mar 1995 18:26:53 GMT Nntp-Posting-Host: badlands.nodak.edu Organization: North Dakota Higher Education Computing Network X-Newsreader: TIN [version 1.2 PL2] Lines: 1 From owner-rapd@net.bio.net Tue Mar 21 22:00:00 1995 Path: biosci!YVAX.BYU.EDU!FARMERJ From: FARMERJ@YVAX.BYU.EDU Newsgroups: bionet.molbio.rapd Subject: bug-net information Date: 22 Mar 1995 15:28:06 -0800 Organization: Brigham Young University Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HOFYHT9VPE90OR4O@yvax.byu.edu> NNTP-Posting-Host: net.bio.net For information, contact Bernie Crespi at crespi@sfu.ca. The actual bug-net address is bug-net@sfu.ca. This group is devoted to molecular markers for insect research, if I understand it correctly. Best wishes. James L. Farmer From owner-rapd@net.bio.net Tue Mar 21 22:00:00 1995 Path: biosci!CSHL.ORG!lodhi From: lodhi@CSHL.ORG (Muhammad Lodhi) Newsgroups: bionet.molbio.rapd Subject: Re: RAPD reproducibility Date: 22 Mar 1995 03:56:43 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 62 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net In response to Alan Bakalinsky; I think that standardization of RAPD conditions is the main point for reproducibility. I worked with grape RAPD markers for three years and most of the time I used the same DNA that I purified in the beginning of the project. The key to success was our modified DNA extraction protocol that got published in the Ist issue of Plant Molecular Biology Reporter in 1994 (it does not involve any CsCl purification) as well as the intensive standardization of all the RAPD components in the start of the project. I stored not only the stock but also the aliquats at -70C and never had any problem with it. The same DNA is being used by people coming after me to work on the same project. I did try to switch to Tfl one time due to some very tempting commercial offer but when I compared the results I gave up on the idea. I not only used RAPD markers to develop grape genetic map but also used it for southern hybridization and did not see any disparity in hybridization pattern of a particular marker purified from gel in different runs. Muhammad A. Lodhi McClintock Lab Cold Spring Harbor Laboratory Cold Spring Harbor, NY 11724 >Colleagues, > > I am responding to the comments of Bruce Reisch, Michael >McClelland, and W. Ralph Andersen concerning my earlier post about RAPD >irreproducibility. I stated, in so many words, that our 3 year experience >with grape RAPDs was a prolonged agony, until we began cloning those we >could reproduce and converting them into SCARs. Bruce pointed out that he >has had success with grape RAPDs and that problems of reproducibility have >been minor or tamed. > > A couple thoughts come to mind: > > One explanation for our different results is that we isolated DNA >late in the season and generally from mature leaves laced with >polysaccharide. Although we used a CsCl-based method to purify the DNA and >found it to be cuttable by the few restriction enzymes we tested, perhaps >over time (1-3 years in TE at -20 C) the DNA became degraded in subtle ways >such that it was still a substrate for the polymerase, but a changed one. > > Another possibility is that we used Tfl polymerase, not Taq. Quite >recently, we switched to Taq for doing SCARs and found that it seems to >give a cleaner background than Tfl. The switch was prompted by >difficulties related to a bad batch of Tfl. > > A final note. Until we can determine the cause(s) of our >reproducibility problems, we find it safer to use RAPDs only as a first >screen for polymophisms. Once a RAPD is detected, we clone it and convert >it into a SCAR or a similar stable marker. >Alan T. Bakalinsky >Department of Food Science and Technology >Wiegand Hall >Oregon State University >Corvallis, OR 97331-6602 >Phone: (503) 737-6510 >FAX: (503) 737-1877 >Internet: bakalina@bcc.orst.edu From owner-rapd@net.bio.net Thu Mar 23 22:00:00 1995 Path: biosci!rutgers!gatech!newsfeed.pitt.edu!uunet!in1.uu.net!news.claremont.edu!paris.ics.uci.edu!csulb.edu!library.ucla.edu!news.ucdavis.edu!hydrilla.ucdavis.edu!user From: fjryan@ucdavis.edu (Fred Ryan) Newsgroups: bionet.molbio.rapd Subject: fluorometers for DNA Followup-To: bionet.molbio.rapd Date: Thu, 23 Mar 1995 13:10:37 -0800 Organization: University of California, Davis Lines: 2 Message-ID: NNTP-Posting-Host: hydrilla.ucdavis.edu We are interested in acquiring a small fluorometer for the measurement of DNA, something like the Hoefer TKO. Does anyone have any recommendations? From owner-rapd@net.bio.net Thu Mar 23 22:00:00 1995 Path: biosci!daresbury!trane.uninett.no!Norway.EU.net!EU.net!news.sprintlink.net!howland.reston.ans.net!news.cac.psu.edu!usenet From: mmg6@psu.edu (mmg6) Newsgroups: bionet.molbio.rapd Subject: Re: What is SCAR ? Date: 24 Mar 1995 06:06:41 GMT Organization: Penn State University Lines: 21 Sender: mmg6@hearst.cac.psu.edu Distribution: world Message-ID: <3ktnhh$a7p@hearst.cac.psu.edu> References: <9503212005.AA09529@hermes.ulaval.ca> NNTP-Posting-Host: ppp98.cac.psu.edu X-Authinfo-User: mmg6@psu.edu X-Posted-From: InterNews 1.0.4@ppp98.cac.psu.edu X-Authenticated: mmg6 on INN host hearst.cac.psu.edu In article <9503212005.AA09529@hermes.ulaval.ca> Christian.Mouton@greb.ulaval.ca (Christian Mouton) writes: > ..."our 3 year experience with grape RAPDs was a prolonged agony, until we > began cloning those we > could reproduce and converting them into SCARs." > > What do SCAR stand for? is any reference in the literature available? SCAR is an acronym for Sequence Characterized Amplified Region. There was a recent publication in Phytopathology in which SCAR analysis was used. Sorry I can't recall the issue. As the name suggests, SCAR analysis involves sequencing a PCR amplified product. In the case of RAPDs, amplified segments of the same size may not be identical sequences thus SCAR analysis offers a higher level of resolution. Cheers, Michael From owner-rapd@net.bio.net Thu Mar 23 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!gatech!taco.cc.ncsu.edu!malcolm From: malcolm@unity.ncsu.edu (Malcolm Campbell) Newsgroups: bionet.molbio.rapd Subject: Re: What is SCAR ? Date: 24 Mar 1995 16:14:34 GMT Organization: North Carolina State University, Project Eos Lines: 38 Distribution: world Message-ID: <3kur5a$lor@taco.cc.ncsu.edu> References: <9503212005.AA09529@hermes.ulaval.ca> <3ktnhh$a7p@hearst.cac.psu.edu> Reply-To: malcolm@unity.ncsu.edu (Malcolm Campbell) NNTP-Posting-Host: forbt2.nrrc.ncsu.edu Originator: malcolm@forbt2.nrrc.ncsu.edu In article <3ktnhh$a7p@hearst.cac.psu.edu>, mmg6@psu.edu (mmg6) writes: Subject: Re: What is SCAR ? >> What do SCAR stand for? is any reference in the literature available? >SCAR is an acronym for Sequence Characterized Amplified Region. There >was a recent publication in Phytopathology in which SCAR analysis was >used. On a lighter note: Rumour has it that the term SCAR was developed at the facility for Fabulous Acronym Development (FAD) 8^). (Rumour attributable to Rick Kessli). Cheers, Malcolm +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + + + + Malcolm M.Campbell + malcolm@unity.ncsu.edu + + Forest Biotechnology Group + phone:(919)515-7799 + + Department of Forestry + (919)515-7800 + + North Carolina State University + (919)515-7801 + + Box 8008, 6113 Jordan Hall + FAX: (919)515-7801 + + Raleigh, North Carolina + + + USA + + + 27695-8008 + + + + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ -- +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + + + From owner-rapd@net.bio.net Thu Mar 23 22:00:00 1995 Path: biosci!esvax.dnet.dupont.com!rafalski From: rafalski@esvax.dnet.dupont.com Newsgroups: bionet.molbio.rapd Subject: SCARs Date: 24 Mar 1995 06:09:49 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 5 Sender: daemon@net.bio.net Distribution: world Message-ID: <9503241406.AA17556@esds01.es.dupont.com> NNTP-Posting-Host: net.bio.net The prper reference fo SCARs is: Paran and Michelmore Theor.Appl.Genet. (1993) vol 85, issue 8, 985-993. A. Rafalski From owner-rapd@net.bio.net Thu Mar 23 22:00:00 1995 Path: biosci!esvax.dnet.dupont.com!rafalski From: rafalski@esvax.dnet.dupont.com Newsgroups: bionet.molbio.rapd Subject: Fluorometers Date: 24 Mar 1995 06:06:24 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: <9503241403.AA17318@esds01.es.dupont.com> NNTP-Posting-Host: net.bio.net Regarding fluorometers for DNA quantitation: We use Millipore Cytofluor 2350 - it is a relatively large and expensive instrument, but it measures fluorescence in 96-well plates and provides the output in computer-readable format. Antoni Rafalski From owner-rapd@net.bio.net Thu Mar 23 22:00:00 1995 Path: biosci!CSHL.ORG!lodhi From: lodhi@CSHL.ORG (Muhammad Lodhi) Newsgroups: bionet.molbio.rapd Subject: Re: fluorometers for DNA Date: 24 Mar 1995 04:41:46 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Fred Ryan wrote, >We are interested in acquiring a small fluorometer for the measurement of >DNA, something like the Hoefer TKO. Does anyone have any recommendations? TKO is reliable and easy to use instrument. With the diposable cuvettes lot of time is saved especially in the cases where you have to measure concentration for hundreds of samples at a time as in our genome sequencing project. However, we do see minor variation in DNA concentration from time to time that may be due to diposable cuvettes. There is another similar instrument sold by Pharmacia called GeneQuant RNA/DNA Calculator. Even though I don't have any direct experience with it but the advertisement says that it reads absorbance at 230,260, 280 and 320 unlike TKO that reads only at 260. GeneQuant RNA/DNA Calculator also reads RNA, ssDNA, dsDNA and oligonucleotides in several different units and calulates 260/280 ratio whereas its TKO counterpart reads only dsDNA. I would like to have something like this in my lab too that will save me lots of time in calculations. Good luck Muhammad A. Lodhi Cold Spring Harbor Lab. From owner-rapd@net.bio.net Mon Mar 27 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!pipex!warwick!bham!bcs88.bham.ac.uk!user From: A.C.Hilton@bham.ac.uk (Wiggy) Newsgroups: bionet.molbio.rapd Subject: Re: What is SCAR ? Date: 28 Mar 1995 09:27:20 GMT Organization: The University of Birmingham Lines: 26 Distribution: world Message-ID: References: <9503212005.AA09529@hermes.ulaval.ca> NNTP-Posting-Host: bcs88.bham.ac.uk In article <9503212005.AA09529@hermes.ulaval.ca>, Christian.Mouton@greb.ulaval.ca (Christian Mouton) wrote: > On 21 Mar 1995 Alan T. Bakalinsky wrote: > > ..."our 3 year experience with grape RAPDs was a prolonged agony, until we > began cloning those we > could reproduce and converting them into SCARs." > > What do SCAR stand for? is any reference in the literature available? > > Christian Mouton > Groupe de Recherche en Écologie Buccale > Faculté de médecine dentaire > Université Laval > Québec (Québec) > G1K 7P4 CANADA > > tél. (418)656-5872 > fax. (418)656-2861 > Email: Christian.Mouton@greb.ulaval.ca SCAR stands for "Sequence Characterised Amplified Region" Wiggy. From owner-rapd@net.bio.net Wed Mar 29 23:00:00 1995 Path: biosci!biosci!not-for-mail From: Werner.Vogetseder@uibk.ac.at (Werner Vogetseder) Newsgroups: bionet.cellbiol,bionet.general,bionet.molbio.methds-reagnts,bionet.molbio.proteins,bionet.molbio.rapd,bionet.molbio.yeast,bionet.virology Subject: Help: I need a plasmid: pGFP-N3 (green fluorescent protein) Date: 30 Mar 1995 11:28:41 -0800 Organization: Universitdt Innsbruck Lines: 18 Sender: biohelp@net.bio.net Distribution: world Message-ID: <3lbhae$38m@news.uibk.ac.at> Reply-To: Werner.Vogetseder@uibk.ac.at (Werner Vogetseder) NNTP-Posting-Host: net.bio.net Xref: biosci bionet.cellbiol:1946 bionet.general:14408 bionet.molbio.methds-reagnts:26595 bionet.molbio.proteins:4128 bionet.molbio.rapd:1077 bionet.molbio.yeast:2696 bionet.virology:2061 Six weeks ago I have ordered the plasmid pGFP-N3 by our local distributor (Biotrade, Vienna) which is a product offered by Clontech, Inc. Until now the local distributor and Clontech, Inc. were not able to tell me, when I will get this plasmid. Since I need this very urgently, I would ask someone, if she/he could send me an aliquot or tell me from where I could obtain it very rapidely. Many thanks in advance Werner Vogetseder, MD Institute for Hygiene Fritz-Preglstr. 3 A 6020 Innsbruck AUSTRIA Tel.: +43/512/507-3438 Fax.: +43/512/507-2870 E-mail: Werner.Vogetseder@uibk.ac.at From owner-rapd@net.bio.net Wed Mar 29 23:00:00 1995 Path: biosci!YL05HP.TB.NODA.SUT.AC.JP!ohba From: ohba@YL05HP.TB.NODA.SUT.AC.JP (Hiroyoshi Ohba) Newsgroups: bionet.molbio.rapd Subject: Typing MHC by RAPD Date: 29 Mar 1995 20:39:52 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: <9503300426.AA16505@yl05hp.tb.noda.sut.ac.jp> NNTP-Posting-Host: net.bio.net Hello bionetters; Does anybody has experience or information about typing MHC (major histocompatibility complex) gene by RAPD or PCR? Hiroyoshi, ### # # # # # # # # # # # # # # # # # # # # # # Hiroyoshi Ohba, Ph.D. Laboratory of Immunology, Department of Biological Science & Technology, Science University of Tokyo 2641 Yamazaki, Noda, Chiba 278 Japan Tel: 81-471-24-1501 ext. 4429 FAX: 81-471-25-1841 e-mail: ohba@yl05hp.tb.noda.sut.ac.jp (domain name is y-el-zero-5hp not y-one-owe-5hp, sorry) ### # # # # # # # # # # # # # # # # # # # # # # From owner-rapd@net.bio.net Wed Mar 29 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!Norway.EU.net!EU.net!howland.reston.ans.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!news.dfn.de!gina.zfn.uni-bremen.de!alf.zfn.uni-bremen.de!g15q From: g15q@alf.zfn.uni-bremen.de (Ioannis Paspaltsis) Newsgroups: bionet.molbio.rapd Subject: Test Date: 30 Mar 1995 12:51:16 GMT Organization: Zentrum fuer Netze, Universitaet Bremen Lines: 2 Message-ID: <3le9g4$b3n@gina.zfn.uni-bremen.de> NNTP-Posting-Host: alf.zfn.uni-bremen.de X-Newsreader: TIN [version 1.2 PL2] Test. From owner-rapd@net.bio.net Thu Mar 30 23:00:00 1995 Path: biosci!agate!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!flh From: flh@mole.bio.cam.ac.uk (Frances Hannan (Zoology)) Newsgroups: bionet.cellbiol,bionet.general,bionet.molbio.methds-reagnts,bionet.molbio.proteins,bionet.molbio.rapd,bionet.molbio.yeast,bionet.virology Subject: Re: Help: I need a plasmid: pGFP-N3 (green fluorescent protein) Date: 31 Mar 1995 12:05:04 GMT Organization: University of Cambridge, England Lines: 22 Message-ID: <3lgr5g$mtm@lyra.csx.cam.ac.uk> References: <3lbhae$38m@news.uibk.ac.at> NNTP-Posting-Host: mole.bio.cam.ac.uk Xref: biosci bionet.cellbiol:1953 bionet.general:14422 bionet.molbio.methds-reagnts:26635 bionet.molbio.proteins:4141 bionet.molbio.rapd:1079 bionet.molbio.yeast:2697 bionet.virology:2070 Werner.Vogetseder@uibk.ac.at (Werner Vogetseder) writes: >Six weeks ago I have ordered the plasmid pGFP-N3 by our local distributor >(Biotrade, Vienna) which is a product offered by Clontech, Inc. Until now >the local distributor and Clontech, Inc. were not able to tell me, when I >will get this plasmid. Since I need this very urgently, I would ask >someone, if she/he could send me an aliquot or tell me from where I could >obtain it very rapidely. According to the Clontech people at last weeks seminar on GFP in London the GFP-N3 construct has not even been completed let alone put into production. So you will unfortunately have to wait for it. It may be quicker for you to use PCR to change the reading frame of your insert and stick it in one of the other N vectors.... -- Frances Hannan BILMS, Zoology, Downing St, Cambridge, CB2 3EJ, UK Phone (0223)336663, FAX (0223)461954 flh@mole.bio.cam.ac.uk From owner-rapd@net.bio.net Thu Mar 30 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!news From: dubear@whitewater (Dubear Kroening) Newsgroups: bionet.cellbiol,bionet.general,bionet.molbio.methds-reagnts,bionet.molbio.proteins,bionet.molbio.rapd,bionet.molbio.yeast,bionet.virology Subject: M13 ssDNA stability Date: 31 Mar 1995 13:22:50 GMT Organization: University of Wisconsin, Madison Lines: 14 Message-ID: <3lgvna$1l38@news.doit.wisc.edu> References: <3lbhae$38m@news.uibk.ac.at> <3lgr5g$mtm@lyra.csx.cam.ac.uk> NNTP-Posting-Host: whitewater.chem.wisc.edu Xref: biosci bionet.cellbiol:1954 bionet.general:14425 bionet.molbio.methds-reagnts:26638 bionet.molbio.proteins:4142 bionet.molbio.rapd:1080 bionet.molbio.yeast:2698 bionet.virology:2071 Hello, We are noticing degradation of M13 ssDNA when resuspended in water and heated at 90 degrees celcius for 10 minutes. We see no degradation when just resuspended in water (without heating) or when resuspended in TE (with or without heating). We were concerned that this may have something to do with magnesium in the prep. Does anyone have any ideas at all? Any comments or suggestions would be greatly appreciated. Dubear Kroening dubear@whitewater.chem.wisc.edu From owner-rapd@net.bio.net Thu Mar 30 23:00:00 1995 Path: biosci!DEAKIN.EDU.AU!huangbx From: huangbx@DEAKIN.EDU.AU (Bixing Huang) Newsgroups: bionet.molbio.rapd Subject: How do you calculate annealling temperature if DMSO added??? Date: 30 Mar 1995 21:14:30 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: <199503310513.PAA11624@hestia.ccs.deakin.edu.au> NNTP-Posting-Host: net.bio.net Hello netter's and friends, I am trying so hard to amplify 700-800bp fragement from a minisatellite region, which is 65% G-C rich part. The primer pair is 24 nt length. Everytime I just got very faint or none bands from it. Now I am going to use the method discussed on the net---addition DMSO in the reaction. But how do you calculate the annealling temperture if DMSO added to the mixture? Or do you people over there have any bright ideas to solve this problem?? Thank you very much for your kindness. With regards. Bixing Huang huangbx@deakin.edu.au Department of Biology Deakin University of Australia From owner-rapd@net.bio.net Fri Mar 31 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!f181-217.net.wisc.edu!user From: ppongam@students.wisc.edu (Patchara Pongam) Newsgroups: bionet.molbio.rapd Subject: test Date: 1 Apr 1995 19:31:15 GMT Organization: Plant Pathology Lines: 1 Message-ID: NNTP-Posting-Host: f181-217.net.wisc.edu test