From owner-rapd@net.bio.net Mon Nov 01 22:00:00 1993 Path: biosci!UNIXG.UBC.CA!hobbs From: hobbs@UNIXG.UBC.CA Newsgroups: bionet.molbio.rapd Subject: UBC Primer Set #8 Message-ID: <9311020114.AA21766@unixg.ubc.ca> Date: 2 Nov 93 01:16:25 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 153 UBC Primer set #8 is a 2-base primer set of 100 decamers. Doug Rhoads, James Farmer and others have reported good results with 2-base 10-mers using a variety of species, and others have enquired as to their availability and presence among the UBC primers made previously. In fact, only six out of the previous 700 UBC primers are 2-base primers, and we felt it would be interesting to make a larger number of primers of this type to see whether the findings of high incidence of good banding patterns and ability to detect polymorphisms reported previously were further substantiated. Set #8 contains primers varying between 60% and 80% G or C content: most are 70%, a few are 80%, the remainder 60%. The mean G or C content is 67.6%. The sequences are pasted in below. Sixteen of the sequences are the same as those reported on favourably by Doug Rhoads, and posted to this newsgroup: as far as we are aware, the remainder are new. They have not appeared previously in UBC primer sets, or in the Operon primer sets that we know of - i.e. the Operon sequences posted to the bulletin board on 9th. September by Toby Bradshaw. UBC Primer set #8, prepared, purified, quantified and aliquotted as usual to give 10 micrograms of each primer, is now available at a cost of Can. $300 (or US $250), plus shipment costs (airmail or courier). We can also offer sets of 50 (which will be all the even numbers or all the odd numbers) at a cost of Can. $165 (US $140). Any individual primer may be ordered at $10 for 10 micrograms. UBC Primer sets #2 to #7 are all presently available; set #1 is presently sold out, but more is in preparation. The prices are the same as for set #8, above. The mean G+C contents of the sets are: set #2, 59.4%; set #3, 62.2%; set #4, 63.2%; set #5, 62.4%; set #6, 60.3%; set #7, 59.7% (and set #1, 69%). The sequences of all these sets were posted to the newsgroup on 9th. September. To obtain further information, or to order (I need a P.O. number, your full mailing address, billing address and an indication as to whether you prefer carriage by airmail (US$3 to USA, US$4 internationally, Can.$6.25 - 9.00 in Canada which doesn't have a "small packet" postal category, ridiculous isn't it?) or courier (US$11 to addresses in the US, Can. $7 to addresses in Canada, enquire for other destinations) please e-mail, or phone, fax or snail-mail to me at the address below. John Hobbs 10-Mers Set 100/8 (UBC RAPD Oligo Project) 701.CCCACAACCC 702.GGGAGAAGGG 703.CCAACCACCC 704.GGAAGGAGGG 705.GGAGGAAGGG 706.GGTGGTTGGG 707.CCCAACACCC 708.GGGTTGTGGG 709.CCTCCTCCCT 710.GGTGGTGGGT 711.CCCTCTCCCT 712.GGGTGTGGGT 713.CCCTCCCTCT 714.GGGTGGGTGT 715.CCACCACCCA 716.GGAGGAGGGA 717.CCCACACCCA 718.GGGAGAGGGA 719.CCCACCCACA 720.GGGAGGGAGA 721.CCCTTCCCTC 722.CCTCTCCCTC 723.CCCTCTCCTC 724.CTCCCTCCTC 725.GGGTTGGGTG 726.GGTGTGGGTG 727.GGGTGTGGTG 728.GTGGGTGGTG 729.CCCAACCCAC 730.CCACACCCAC 731.CCCACACCAC 732.CACCCACCAC 733.GGGAAGGGAG 734.GGAGAGGGAG 735.GGGAGAGGAG 736.GAGGGAGGAG 737.GGTGGGTGTG 738.GGTGGGTGGT 739.GGAGGGAGAG 740.GGAGGGAGGA 741.CCTCCCTCTC 742.CCTCCCTCCT 743.CCACCCACAC 744.CCACCCACCA 745.GGGAAGAGGG 746.GGGTGTTGGG 747.CCACCAACCC 748.CCCTTCTCCC 749.GGGAGGAGAG 750.GGGTGGTGTG 751.CCCACCACAC 752.CCCTCCTCTC 753.GGGAGGAGGA 754.GGGTGGTGGT 755.CCCACCACCA 756.CCCTCCTCCT 757.GGAAGGGAGG 758.GGTTGGGTGG 759.CCAACCCACC 760.CCTTCCCTCC 761.GAGAGGAGGG 762.GTGTGGTGGG 763.CACACCACCC 764.CTCTCCTCCC 765.AGGGAGGAGG 766.TGGGTGGTGG 767.ACCCACCACC 768.TCCCTCCTCC 769.GGGTGGTGGG 770.GGGAGGAGGG 771.CCCTCCTCCC 772.CCCACCACCC 773.GGGTTGTTGG 774.GGTGTGTGGT 775.GGTTTGGTGG 776.CTTCCCTCCT 777.GGAGAGGAGA 778.CCACACCACA 779.CCTTTCTCCC 780.CCTCTTCCTC 781.GGGAAGAAGG 782.GGGAAGAGAG 783.GGTGGGTTGT 784.GTGGGTGTTG 785.CACCCAACCA 786.TCCCTTCCTC 787.CCCTTCTTCC 788.CCTTCCCTCT 789.GGAAGGGAGA 790.GGGTGTGGTT 791.GTGGGTTGTG 792.CAACCCACAC 793.CTCCTCTCTC 794.GAGGGGAAAG 795.TGGTGTGGGT 796.AGAGGGAGGA 797.CCACCAACAC 798.GAGAGGAAGG 799.TGTGGTGGTG 800.TCTCCCTCCT 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; Tel. (604)822-6373 From owner-rapd@net.bio.net Tue Nov 02 22:00:00 1993 Path: biosci!YVAX.BYU.EDU!anderswr From: anderswr@YVAX.BYU.EDU (W. Ralph Andersen) Newsgroups: bionet.molbio.rapd Subject: (none) Message-ID: <01H4VEUH8CSI8X04Z9@yvax.byu.edu> Date: 3 Nov 93 15:25:21 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 9 We are attempting to extract DNA from Tilletia caries spores (a smut fungus). We have attempted a lit. search at our library and have not picked up a reference for successful DNA extraction from these very tough spores or anything like it. Any body out there see a recent paper or know of someone who has done this successfully? Got any ideas as to approaches, or an experienced lab we could contact? Sincerely yours, David Gang From owner-rapd@net.bio.net Tue Nov 02 22:00:00 1993 Path: biosci!CUCCFA.CCC.COLUMBIA.EDU!JIA From: JIA@CUCCFA.CCC.COLUMBIA.EDU Newsgroups: bionet.molbio.rapd Subject: Differential Display info needed! Message-ID: <931102152524.ce86@CUCCFA.CCC.COLUMBIA.EDU> Date: 2 Nov 93 20:25:24 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 9 Has any body used the Differential Display method to identify different gene expression? It is somehow similar to RAPD. However, does this method really work? Any comments, suggestions will be helpful. R. Jia Columbia Univ. jia@cuccfa.ccc.columbia.edu tel. 212-305-2704 fax. 212-568-8473 Thank you very much. From owner-rapd@net.bio.net Tue Nov 02 22:00:00 1993 Path: biosci!ABRSLE.AGR.CA!HACHEY From: HACHEY@ABRSLE.AGR.CA (john hachey) Newsgroups: bionet.molbio.rapd Subject: re:fungal dna Message-ID: <01H4VSO15H8Y000FNT@GW.AGR.CA> Date: 3 Nov 93 20:08:08 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 28 >We are attempting to extract DNA from Tilletia caries spores (a smut >fungus). We have attempted a lit. search at our library and have not >picked up a reference for successful DNA extraction from these very tough >spores or anything like it. Any body out there see a recent paper or know >of someone who has done this successfully? Got any ideas as to approaches, >or an experienced lab we could contact? > >Sincerely yours, David Gang The only refs I have on fungal DNA extraction are: Kim et al.,1990. Isolation of high molecular weight dna and double-stranded rnas from fungi. Can. J. Bot. 68:1898-1902. Moller et al.,1992. A simple and efficient protocol for isolation of high molecular weight dna from filamentous fungi,fruit bodies, and infected plant tissues. NAR 20:6115-6116 Both give rapdable dna , at least from hyphae of the Phoma spp. I have tried John -------- ,VV, : (OO) : /..\ : hachey@abrsle.agr.ca (~--~) : ---^^--- From owner-rapd@net.bio.net Tue Nov 02 22:00:00 1993 Path: biosci!GPU.SRV.UALBERTA.CA!ghawkins From: ghawkins@GPU.SRV.UALBERTA.CA (Glen Hawkins) Newsgroups: bionet.molbio.rapd Subject: rapd network Message-ID: Date: 3 Nov 93 23:17:06 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 3 subscribe rapd help From owner-rapd@net.bio.net Wed Nov 03 22:00:00 1993 Path: biosci!esvax.dnet.dupont.com!rafalski From: rafalski@esvax.dnet.dupont.com Newsgroups: bionet.molbio.rapd Subject: Microsatellites Message-ID: <9311042023.AA01841@esds01.es.dupont.com> Date: 4 Nov 93 20:23:48 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 8 In response to a question about microsatellite references: There are many papers on microsatellites. Please read the paper by Morgante and Olivieri in The Plant Journal vol 3 (1993) issue 1, 175-182, and you will find many references there. The title of the paper is "PCR_amplified microsatellites as markers in plant genetics". Antoni From owner-rapd@net.bio.net Wed Nov 03 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!sangam!vikram!usmani From: usmani@ern.doe.ernet.in (Prof Usmani) Newsgroups: bionet.population-bio,bionet.molbio.rapd,bionet.molbio.evolution,bionet.jobs Subject: Re: PostDoc Available Message-ID: <1993Nov4.070545.16053@ern.doe.ernet.in> Date: 4 Nov 93 07:05:45 GMT References: <2ammadINNuu@network.ucsd.edu> Followup-To: bionet.population-bio,bionet.molbio.rapd,bionet.molbio.evolution,bionet.jobs Organization: Department of Electronics Lines: 56 Xref: biosci bionet.population-bio:508 bionet.molbio.rapd:320 bionet.molbio.evolution:1239 bionet.jobs:2597 X-Newsreader: TIN [version 1.2 PL1] andy@pooh.ucsd.edu wrote: : POSTDOCTORAL RESEARCH FELLOW POSITION AVAILABLE : Southwest Fisheries Science Center : Marine Mammal Division : A one-year National Research Council Associateship : (renewable to three years) is available in the Marine Mammal : Molecular Genetics Laboratory of the Southwest Fishery Science : Center located in La Jolla, California. Ph.D. with experience : and/or interest in population genetics or modelling is sought to : formulate quantitative means for using genetic data to define : biologically meaningful stock units on which to base conservation : and management efforts for marine mammals. Stocks, not species, : are the units on which conservation and management efforts, by : law, must be focussed, yet how to do this remains one of the most : important questions in conservation biology today. : In spite of rapid progress in the molecular arena, : development of quantitative means for using the information : gained in the laboratory to define biologically meaningful stock : units has not been fully realized. Methodologies using molecular : data to estimate population-genetic parameters, molecular : phylogenies, gene flow and dispersal distance, etc., are : available, but there has been growing realization that this area : is much more complex and pitfall-ridden than had been thought, : especially when the methods are applied to incompletely isolated : populations. Nevertheless, the continuing rapid advances in : molecular methods, the reality of laboratory automation, and the : ability to measure genetic diversity directly from pooled samples : will provide data of heretofore unavailable breadth and scope. A : concentrated research effort focusing directly on how to use : these data to define stock units in potentially politically : controversial situations is needed. : Envisioned, for example, is the development of an : individual-based model of evolving and interchanging local : populations, which could be stochastically sampled in order to : test the utility of various analyses of population genetic : structure for defining management stocks. Such a model would : also serve as a means of designing practical sampling programs : for such purposes and, in the course of which, measures of the : statistical power of the quantitative indices should be : developed. : NRC Associates receive a stipend from the National Research : Council while carrying out his or her proposed research. The : current annual stipend for a Regular Associate (< 5yr from PhD) : is $30,000 per year. Suitable relocation reimbursement will be : determined for an awardee, and funds are available for : professional travel during tenure. Applicants should direct : initial inquires to Dr. Andrew Dizon (andy@pooh.ucsd.edu) or Dr. : William Perrin, PO Box 271, SWFSC, La Jolla, CA, 92038. : From owner-rapd@net.bio.net Wed Nov 03 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!swrinde!sdd.hp.com!decwrl!decwrl!usenet.coe.montana.edu!news.uoregon.edu!netnews.nwnet.net!news.u.washington.edu!stein2.u.washington.edu!toby From: toby@stein2.u.washington.edu (Toby Bradshaw) Newsgroups: bionet.molbio.rapd Subject: Re: Codominant markers Message-ID: <2bbhcj$k36@news.u.washington.edu> Date: 4 Nov 93 18:24:19 GMT References: <9311041640.AA25071@esds01.es.dupont.com> Distribution: bionet Organization: University of Washington, Seattle Lines: 25 NNTP-Posting-Host: stein.u.washington.edu In article <9311041640.AA25071@esds01.es.dupont.com>, wrote: >Toby Bradshaw desires co-dominant, PCR-based markers that could be used >together with RAPDs. Microsatellite (simple sequence repeat) markers >meet these criteria. Microsatellite maps are. of course, well developed in >vertebrates (human, mice, rat). We, and a few other groups are currently >working on microsatellites in plants (soybean, corn, arabidopsis, etc). Our >group is concentrationg on soybean, and indications are microsatellites >will be great in plants. Their abundance is lower then in mammals, but they >are much more informative then RFLPs, and are co-domonant and PCR-based. SO >far we are having best luck with (AG)n SSRs. The disadvantage is that a lot >of effort is required to develop each marker (cloning, sequencing, etc). I have little doubt that if sufficient funds were made available, microsatellite markers would be the markers of choice for most mapping projects. Except for the high initial cost, they leave little to be desired. RFLPs detected by Southerns are perhaps a little more easily translated across wide phylogenies than any PCR-based markers, and have that advantage. RAPDs are damn near unbeatable for pure trait mapping in a single family, if cost and speed are important, but things can fall apart quickly when trying to extend results from RAPDs to other pedigrees. -Toby Bradshaw toby@u.washington.edu From owner-rapd@net.bio.net Wed Nov 03 22:00:00 1993 Path: biosci!esvax.dnet.dupont.com!rafalski From: rafalski@esvax.dnet.dupont.com Newsgroups: bionet.molbio.rapd Subject: Codominant markers Message-ID: <9311041640.AA25071@esds01.es.dupont.com> Date: 4 Nov 93 16:40:01 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 12 Toby Bradshaw desires co-dominant, PCR-based markers that could be used together with RAPDs. Microsatellite (simple sequence repeat) markers meet these criteria. Microsatellite maps are. of course, well developed in vertebrates (human, mice, rat). We, and a few other groups are currently working on microsatellites in plants (soybean, corn, arabidopsis, etc). Our group is concentrationg on soybean, and indications are microsatellites will be great in plants. Their abundance is lower then in mammals, but they are much more informative then RFLPs, and are co-domonant and PCR-based. SO far we are having best luck with (AG)n SSRs. The disadvantage is that a lot of effort is required to develop each marker (cloning, sequencing, etc). Antoni Rafalski From owner-rapd@net.bio.net Wed Nov 03 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!decwrl!decwrl!usenet.coe.montana.edu!news.uoregon.edu!netnews.nwnet.net!news.u.washington.edu!stein2.u.washington.edu!toby From: toby@stein2.u.washington.edu (Toby Bradshaw) Newsgroups: bionet.molbio.rapd Subject: Re: Double Het RAPD markers Message-ID: <2bb7b1$g8a@news.u.washington.edu> Date: 4 Nov 93 15:32:49 GMT References: <199311041432.AA18824@postoffice.mail.cornell.edu> Distribution: bionet Organization: University of Washington, Seattle Lines: 29 NNTP-Posting-Host: stein.u.washington.edu In article <199311041432.AA18824@postoffice.mail.cornell.edu>, Muhammad A. Lodhi wrote: > What is the way of differentiating between heterozygous and >homozygous dominant RAPD markers, if any. By definition, a dominant genetic marker cannot distinguish between heterozygotes and dominant homozygotes. RAPD bands may be converted to codominance in the same way other DNA-based polymorphisms are detected -- e.g. restriction enzyme digestion, SSCP, DNA sequencing, allele-specific primers derived from STS data, etc. Sometimes RAPD bands can be used as probes on conventional Southern blots, but in genomes with a lot of repetitive DNA many RAPD bands will be found to contain repeats and not be informative as probes. >I think that may be very helpful >in linkage analysis with pseudotest crosses in woody plants. RAPDs have many advantages, but dominance is a major drawback. We have found that it takes relatively few codominant markers to join RAPDs linked in repulsion, so it is perhaps cost-effective to make maps largely with RAPDs and add one or two codominant markers per chromosome. Ideally, these codominant markers will be PCR-based, as well. Toby Bradshaw | Department of Biochemistry | Will make genetic linkage maps and College of Forest Resources | for food. University of Washington, Seattle | toby@u.washington.edu | From owner-rapd@net.bio.net Wed Nov 03 22:00:00 1993 Path: biosci!cornell.edu!mal5 From: mal5@cornell.edu (Muhammad A. Lodhi) Newsgroups: bionet.molbio.rapd Subject: Double Het RAPD markers Message-ID: <199311041432.AA18824@postoffice.mail.cornell.edu> Date: 4 Nov 93 10:36:05 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 17 Dear Friends What is the way of differentiating between heterozygous and homozygous dominant RAPD markers, if any. I think that may be very helpful in linkage analysis with pseudotest crosses in woody plants. This is a part of the problem that I am facing for linkage analysis that I posted earlier on this group. Thanks in advance ============================ Muhammad A. Lodhi Cornell University, NYSAES Geneva, NY 14456 Ph: 315 787 2239 Fax: 315 787 2216 e-mail:mal5@cornell.edu From owner-rapd@net.bio.net Wed Nov 03 22:00:00 1993 Path: biosci!MUSKWA.UCS.UALBERTA.CA!rcyang From: rcyang@MUSKWA.UCS.UALBERTA.CA (Yang Rong Cai) Newsgroups: bionet.molbio.rapd Subject: Re: Double Het RAPD markers Message-ID: <9311041700.AA01482@muskwa.ucs.ualberta.ca> Date: 4 Nov 93 17:00:44 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 18 >Dear Friends > What is the way of differentiating between heterozygous and >homozygous dominant RAPD markers, if any. You have to do progeny-testing or segregation analysis. I can't recall what species you are working on, but if you happen to work with conifers then segragation analysis can be very easily done by assaying megagametophytes and has become a routine in several genome mapping projects for conifer species. Other than that, you probably have to live with the assumption that outcrossing tree species show very high level of heterozygosity so that you are likely to have testcrosses in most cases. Rong-Cai Yang University of Alberta From owner-rapd@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!usc!howland.reston.ans.net!sol.ctr.columbia.edu!destroyer!nntp.cs.ubc.ca!utcsri!newsflash.concordia.ca!owl.nstn.ns.ca!dragon.acadiau.ca!pat426.acadiau.ca!901106c From: 901106c@axe.acadiau.ca (TIM CHIPMAN) Newsgroups: bionet.molbio.rapd Subject: Inquiry re: preparation of Powdered Glass (aka glassmilk) Message-ID: <901106c.627.2CDAA95F@axe.acadiau.ca> Date: 5 Nov 93 19:28:31 GMT Sender: news@dragon.acadiau.ca Organization: Acadia University Lines: 9 Nntp-Posting-Host: pat426.acadiau.ca I am curious: My advisor has `fond' recollections of when she had to make "do-it-yourself" glassmilk. However, she does not remember the recipie. Does anyone have a protocol for making powdered glass for use as glassmilk..? Thanks! Tim Chipman 901106c@axe.acadiau.ca From owner-rapd@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!esvax.dnet.dupont.com!rafalski From: rafalski@esvax.dnet.dupont.com Newsgroups: bionet.molbio.rapd Subject: Microsatellites Message-ID: <9311051248.AA28822@esds01.es.dupont.com> Date: 5 Nov 93 12:48:07 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 6 In response to Jim Farmer's question: I do not know about mirosatellite primers for Drosophila, but you may consider searching for simple sequence repeats in GenBank (Drosophila sequences). I bet there will be a few SSRs already "in the bank". Antoni From owner-rapd@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!usc!howland.reston.ans.net!agate!dog.ee.lbl.gov!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.molbio.rapd Subject: Alphabetical list of 10-mers Message-ID: <2bc84u$ih7@overload.lbl.gov> Date: 5 Nov 93 00:52:46 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 24 NNTP-Posting-Host: s27w007.pswfs.gov I have prepared a list of 1000 10-mers from Operon and 800 10-mers from University of British Columbia with the sequence as the first field and the primer name as the second. The list is in alphabetical order by sequence. The list can be retrieved from the Dendrome project Gopher server, s27w007.pswfs.gov, port 70 as ... 3. Data other than Images/ ... 2. Primers/ ... 4. alpha_list. --bks -- Bradley K. Sherman P.O. Box 245 Computer Scientist Berkeley, CA, 94701 Dendrome Project 510-559-6437 FAX: 510-559-6440 Institute of Forest Genetics Internet: bks@s27w007.pswfs.gov From owner-rapd@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!YVAX.BYU.EDU!FARMERJ From: FARMERJ@YVAX.BYU.EDU Newsgroups: bionet.molbio.rapd Subject: Re: Codominant markers Message-ID: <01H4XD6N90WU8Y6I3G@yvax.byu.edu> Date: 5 Nov 93 01:01:34 GMT Sender: daemon@net.bio.net Distribution: bionet Organization: Brigham Young University Lines: 1 Like Antoni Rafalski, I also plan to use microsatellite markers. Does anyone know of microsatellite primers for Drosophila pseudoobscura? It doesn't seem likely, but it doesn't hurt to ask. Jim Farmer, farmerj@yvax.byu.edu From owner-rapd@net.bio.net Fri Nov 05 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!newsflash.concordia.ca!mizar.cc.umanitoba.ca!hamel From: hamel@ccu.umanitoba.ca (Andre Hamel) Newsgroups: bionet.molbio.rapd Subject: Re: glassmilk Message-ID: Date: 5 Nov 93 23:02:16 GMT Sender: news@ccu.umanitoba.ca Organization: University of Manitoba, Winnipeg, Canada Lines: 27 Nntp-Posting-Host: castor.cc.umanitoba.ca If you have access to gopher (and know how to use it :-), try; gopher merlot.welch.jhu.edu then choose (each in successive order); -> 16 search usenet news and FAQs -> 7 search messages to usenet newsgroups -> 1 or 2 search bionet archives then enter search term (glassmilk) You should get 5 about 5 pages of postings involving this search term. I've taken liberty to email some of these to you (I checked these for my own curiousity ... to see if there were any new articles that I may have missed). best regards ******************** Andre Hamel email: hamel@ccu.umanitoba.ca Manitoba Veterinary Services lab tel.: (204) 945-7630 545 University Crescent, FAX:(204) 945-8062 Winnipeg, Manitoba, CANADA R3T 5S6 ******************** From owner-rapd@net.bio.net Sun Nov 07 22:00:00 1993 Path: biosci!cornell.edu!mal5 From: mal5@cornell.edu (Muhammad A. Lodhi) Newsgroups: bionet.molbio.rapd Subject: QTL analysis with pseudotest cross population Message-ID: <199311081919.AA01216@postoffice.mail.cornell.edu> Date: 8 Nov 93 15:23:19 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 15 Dear Friends How does QTL analysis work in linkage maps developed with pseudotest cross population. As in such populations we get separate linkage maps of each parent and as far as I know we can't combine them together to get one map. Whether QTL analysis is done separately on each map or there is some better strategy that I could use. Thanks in advance ====================== Muhammad A. Lodhi Cornell University NYSAES, Geneva, NY 14456 Ph : 315-787-2239 Fax : 315-787-2216 e-mail: mal5@cornell.edu From owner-rapd@net.bio.net Mon Nov 08 22:00:00 1993 Path: biosci!bcm!TAMUTS.TAMU.EDU!cs.utexas.edu!swrinde!emory!news-feed-2.peachnet.edu!gatech!news-feed-1.peachnet.edu!umn.edu!gaia.ucs.orst.edu!news.uoregon.edu!netnews.nwnet.net!news.u.washington.edu!stein2.u.washington.edu!toby From: toby@stein2.u.washington.edu (Toby Bradshaw) Newsgroups: bionet.molbio.rapd Subject: Re: QTL analysis with pseudotest cross population Message-ID: <2bmpgn$e35@news.u.washington.edu> Date: 9 Nov 93 00:50:31 GMT References: <199311081919.AA01216@postoffice.mail.cornell.edu> Distribution: bionet Organization: University of Washington, Seattle Lines: 24 NNTP-Posting-Host: stein.u.washington.edu In article <199311081919.AA01216@postoffice.mail.cornell.edu>, Muhammad A. Lodhi wrote: > How does QTL analysis work in linkage maps developed with >pseudotest cross population. As in such populations we get separate >linkage maps of each parent and as far as I know we can't combine them >together to get one map. The maps can be merged with as few as one codominant marker on each linkage group -- two would be better for orientation purposes. >Whether QTL analysis is done separately on each >map or there is some better strategy that I could use. Depends on the genetics of the trait in question. Those genes or QTLs with dominant modes of action are completely covered by normal RAPDs, with or without a map. Additive gene action makes RAPDs less informative when linkages in repulsion cannot be determined. Overdominant modes of gene action are very tough to find with dominant markers alone. Maps per se are not necessarily that helpful for trait mapping -- depends entirely on the genetics of the trait as to whether RAPDs alone will do you any good. -Toby Bradshaw toby@u.washington.edu From owner-rapd@net.bio.net Tue Nov 09 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!mrccrc!jclewley From: jclewley@crc.ac.uk (Dr. J.P. Clewley) Newsgroups: bionet.molbio.rapd Subject: Re: RAPD primers Summary: Program for RAPD/APPCR primer prediction Message-ID: <1993Nov9.234516.28425@crc.ac.uk> Date: 9 Nov 93 23:45:16 GMT References: <8725289607B@uamercury.uark.edu> Sender: news@crc.ac.uk Distribution: bionet Organization: MRC Human Genome Resource Centre Lines: 11 Nntp-Posting-Host: tin A colleague told me he'd heard of a program that predicts primers for RAPD/APPCR (based on genome GC/AT content & size, or sequence -if known, for a smallish genome- but he had no details, it was a *bar* conversation?). Can anyone shed any light on this? Thanks Jon Clewley From owner-rapd@net.bio.net Wed Nov 10 22:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!mcsun!uknet!pipex!howland.reston.ans.net!torn!nott!nrcnet0!nash From: nash@nrcbsa.bio.nrc.ca (John Nash) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.rapd Subject: Re: Are PCR contions different from RAPD? Message-ID: <1993Nov11.164106.17346@nrcnet0.nrc.ca> Date: 11 Nov 93 16:41:06 GMT References: <60904.huangbx@mail-g.deakin.edu.au> Sender: root@nrcnet0.nrc.ca (Operator) Followup-To: bionet.molbio.rapd Distribution: bionet Organization: National Research Council of Canada Lines: 63 Xref: biosci bionet.molbio.methds-reagnts:9015 bionet.molbio.rapd:332 Nntp-Posting-Host: nrcbsa.bio.nrc.ca In article <60904.huangbx@mail-g.deakin.edu.au>, Huang Bixing wrote: >Hello netters, > >I optimized my PCR reaction conditions with a specific primer set. Once >everything has been finalized, I changed to RAPD with random primers from >UBC (yes, the annealling temperature lowered to 35oC). Upto now I have >scaned 30 random primers. There are NO PRIMERS shown any good RAPD >results yet. > >Therefore I have questions: >Are PCR reaction conditions different from those of RAPD? If so, how can I >optimize my RAPD reaction conditions? Well, I will be very appreciated if >someone kindly email his RAPD protocol to me. Before I begin, another good place to read is the bionet.molbio.rapd newsgroup. I've set my Followup: to that newsgroup. Also... all my work is with bacterial DNA! What is your temp-cycler, and what is the time of each step? Also, what is your MgCl2 conc, and Taq pol. conc? What are your primer, dNTP, DNA concs? With respect to MgCl2, published reports (I'll dig them up if you want, but I'm at home because it's the Remembrance day holiday) say that 6 mM MgCl2 is good (although I still use 1.5 mM), and that 2.5 units of enzyme / 50 ul reaction is high --> a couple of pubs recommend 0.625 units/50 ul reaction. WIth my old (and crappy) COY TempCycler Model 60, I used: 94 deg/1 min; 30 deg/2 min; 72 deg/2 min. 30 deg was marginally better than 36 deg - which I started with. 25 deg made no difference. With my new, sleek, and totally unfashionable Perkin-Elmer 9600 ;-) I am currently trying: Step: Ramp: Temp: Hold: 1 0 94 1:00 2 0:30 30 0:30 3 0:30 40 0:30 4 0 72 1:00 (or 2:00) At first, I didn't have the 40 deg step, and I couldn't reproduce the COY parameters on the PE9600 (half the time I had NO bands), but after consultation with the PE rep, I put in the 40 deg step, and tweaked the step 2 ramp and hold, and step 4 hold, and things went from zero bands to very much like the COY's bands. The BIG difference is the primers. After RAPDs using 2 dozen different DNAs and at least 40 primers, I'd say at least 1/3 to 1/2 of the primers gave no bands. So, perservere with primers which may have been reported to work with systems similar to yours, and play with your conditions. Good luck -- John Nash (nash@nrcbsa.bio.nrc.ca) Institute for Biological Sciences, National Research Council of Canada, Yet another Aussie-in-exile ;-) *** Disclaimer: All opinions are mine, not NRC's! *** From owner-rapd@net.bio.net Wed Nov 10 22:00:00 1993 Path: biosci!daresbury!not-for-mail From: abetts@crc.ac.uk (Mr. A.M. Betts) Newsgroups: bionet.molbio.rapd Subject: differential display. Message-ID: <2bt33i$8au@mserv1.dl.ac.uk> Date: 11 Nov 93 10:10:58 GMT Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Lines: 3 Original-To: rapd@dl.ac.uk ..Hi all ..does anyone have any modifications to the differential display method designed by liang and pardee..... I am having a few problems getting it to work at the moment and would be interested to hear from anyone who is currently using the method ... From owner-rapd@net.bio.net Thu Nov 11 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!spool.mu.edu!agate!overload.lbl.gov!kam From: kam@s27w007.pswfs.gov (Kim Marshall) Newsgroups: bionet.molbio.rapd Subject: Forest Tree Molecular Protocols Wanted Message-ID: <2bulej$5sh@overload.lbl.gov> Date: 12 Nov 93 00:30:11 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 20 NNTP-Posting-Host: s27w007.pswfs.gov I am developing a database of molecular techniques and protocols which have been applied to forest trees. If you have any protocols that are specific to forest trees and would like to share with others, please forward them to me. Please include citations that the protocols may have been derived from. Source citations for the protocols will be shown in the database, which will be in the public domain. Kim Marshall Dendrome Project Institute of Forest Genetics USDA Forest Service P.O. Box 245 Berkeley CA, 94701 FAX: (510) 559-6440 Phone: (510) 559-6434 Internet: kam@s27w007.pswfs.gov FS-WAN: k.marshall:s27a From owner-rapd@net.bio.net Thu Nov 11 22:00:00 1993 Path: biosci!DEAKIN.EDU.AU!huangbx From: huangbx@DEAKIN.EDU.AU ("Huang Bixing") Newsgroups: bionet.molbio.rapd Subject: Is conditions of PCR different from RAPD? Message-ID: <60019.huangbx@mail-g.deakin.EDU.AU> Date: 11 Nov 93 21:39:58 GMT Sender: kristoff@net.bio.net Reply-To: Distribution: bionet Lines: 23 Hello netters, I optimized my PCR reaction conditions with a pair of specific primer set. Then I swithed to random primers from UBC to do RAPD (surely the annealing temperature lowered to 35oC). What happened is that I have not got any good RAPD results from 30 random primers. My questions are: Are the PCR reaction contions different from those of RAPD? If so, how do I optimize my RAPD reaction contions? Could anyone kindly email your RAPD protocol to me please? Thank you for your time. With regards. Bixing Huang huangbx@deakin.edu.au ----- School of Biological and Chemical Sciences, Deakin University, Geelong ----- From owner-rapd@net.bio.net Thu Nov 11 22:00:00 1993 Path: biosci!cornell.edu!mal5 From: mal5@cornell.edu (Muhammad A. Lodhi) Newsgroups: bionet.molbio.rapd Subject: QTL analysis with test cross population Message-ID: <199311122252.AA02381@postoffice.mail.cornell.edu> Date: 12 Nov 93 18:56:58 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 21 Dear Friends How does QTL analysis work in linkage maps developed with pseudotest cross population. As in such populations we get separate linkage maps of each parent and as far as I know we can't combine them together to get one map. Whether QTL analysis is done separately on each map or there is some better strategy that I could use. I heard there are some new software that people have been working with for sometimes. If someone has good experience with any of those please let me know. Also if someone wants to use my data for testing I will be very happy to talk about it. Thanks in advance ====================== Muhammad A. Lodhi Cornell University NYSAES, Geneva, NY 14456 Ph : 315-787-2239 Fax : 315-787-2216 e-mail: mal5@cornell.edu From owner-rapd@net.bio.net Wed Nov 17 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!agate!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.molbio.rapd,bionet.plants Subject: Forest Tree RAPD Data Wanted Message-ID: <2cghoq$194@overload.lbl.gov> Date: 18 Nov 93 19:17:46 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 276 Xref: biosci bionet.molbio.rapd:338 bionet.plants:2082 NNTP-Posting-Host: s27w007.pswfs.gov Introduction Dendrome is a forest tree genome informatics and database project. The Institute of Forest Genetics, USDA Forest Service, Albany CA is overseeing the project in collaboration with the National Agricultural Library. TreeGenes is the central database and it is intended that this database include genetic maps and associated information for all forest trees. At this time, we are focusing our efforts on collecting RAPD map data. This announcement is a request to tree genome researchers to submit RAPD map data for inclusion into the database. These data will be made publically available through distribution of the TreeGenes database. Contributors are encouraged to submit unpublished data but have the option of completely selected fields of the input file. Please contact David Neale or Bradley Sherman (contact information below) if you have any questions regarding submission of your data to the TreeGenes database. We look forward to your submissions and the development of a rich forest tree genome database for the forest genetics research community. Accepted Formats We are prepared to accept your data in almost any format. Below is a sample data file, but we would rather have your submission sooner, in your own format, than later in ours. If you do submit data in a local format please include a description of the meaning of the data, computer platform used and a contact person for clarification. Data may be submitted by FTP, email, or on diskette. For More Information David B. Neale (dbn@s27w007.pswfs.gov) Bradley K. Sherman (bks@s27w007.pswfs.gov) Institute of Forest Genetics USDA Forest Service P.O. Box 245, Berkeley, CA, 94701 Phone (510)559-6437 FAX (510)559-6440 Sample Submission A Sample file showing preferred format follows. Any line beginning with a sharp '#' is a comment. Please feel free to include as many comments as you like in a submission. We have indented all of the comments below, although this is not required. Each field is preceded by a comment which shows some sample data. Question marks '?' show where your data should go. Data tags are separated from the data by colons ':'. ----------------------Begin Sample File---------------------------- # # A Sample file demonstrating how to # submit data concerning a RAPD map # to the TreeGenes database. # # This is an attempt at an inclusive file, # you may wish to omit certain sections. # # The general rule is that a line has a tag name and a # value separated by a colon ':' # # # Give Latin name. For Hybrid show both species. # Species : Pinus taeda Species : ? # Tell us who you are and where you live # In the Laboratory Section. Use as many lines # As you like. # Laboratory : Institute of Forest Genetics # Laboratory : USDA Forest Service # Laboratory : P.O. Box 245, Berkeley, CA, 94701 # Laboratory : Phone 510-559-6347 # Laboratory : FAX 510-559-6440 Laboratory : ? Laboratory : ? Laboratory : ? # You may choose a Laboratory ID (3 letters) and an # Experiment ID (3 letters) or we will do it for you. # We use these do disambiguate data from different # laboratories and different experiments within # laboratories: # Laboratory ID : IFG # Experiment ID : QTL Laboratory ID : ? Experiment ID : ? # Name the investigators for the experiment # Use as many lines as you like: # Investigator : David B. Neale # Investigator : Andrew T. Groover # Investigator : Kathy D. Jermstad Investigator : ? Investigator : ? # Give the name of a contact for data clarification: # Contact : Bradley K. Sherman # Contact : (510) 559-6437 # Contact : bks@s27w007.pswfs.gov Contact : ? Contact : ? Contact : ? # If the map is published please give a citation # Paper : Groover, A.T., Jermstad, K.D. and Neale, D.B. (1999), # Paper : Genetics 411, 441-449. Paper : ? # Assign a descriptive name to the Genetic map: # Map : Loblolly Pine RAPD Base Map Map : ? # Describe the mapping population used in the # experiment; if a single tree give name of tree. # Specify number of individuals used. # # Mapping population : Single tree map from loblolly pine # Mapping population : tree 7-56. 60 megagametophytes # Mapping population : in segregating population. Mapping population : ? Mapping population : ? # How many Linkage groups and loci are there in your map? # This serves to double check the data entry process: # Total linkage groups : 3 # Total loci : 18 Total linkage groups : ? Total loci : ? # Candidates for units of distance on the map are, e.g. # recombination, centimorgan/Kosambi, centimorgan/Haldane: # Units : recombination Units : ? # The Genetic Map itself. # The Genetic Map is composed of Linkage groups # In the file the Linkage groups are separated from # one another by at least one blank line. # Give the name of the group the number of loci, then # List the Loci with primer name, molecular weight and position # and an error estimate. Please use a '-' for missing values. # If you do not have an error estimate you may omit the fourth # field. # # If you are using a primer that is not from UBC or Operon # please give its sequence as the locus name # # Note that positions are cumulative, not pairwise, distances! # # # Linkage group : QTL-1 # Number of loci : 10 # Locus : OPA-1 800 0.0 # Locus : OPD-3 750 15.1 # Locus : OPX-3 1250 15.9 # Locus : OPC-3 900 23.8 # Locus : OPN-3 775 50.0 # Locus : OPAA-3 625 55.2 # Locus : OPAD-3 700 55.2 # Locus : UBC-351 1180 70.1 # Locus : OPB-4 1500 80.8 # Locus : OPB-9 300 85.8 # # Leave a blank line between but not within linkage groups. # Linkage group : QTL-2 # Number of loci : 3 # Locus : OPA-1 550 0.0 # Locus : OPA-5 375 20.3 # Locus : OPAX-1 975 22.8 # # # Here is the 3rd linkage group. # Linkage group : QTL-5 # Number of loci : 5 # Locus : UBC-325 550 0.0 # Locus : UBC-550 375 20.3 # Locus : UBC-220 975 22.8 # Locus : UBC-340 850 22.8 # Locus : OPA-1 700 30.8 Linkage group : ? Number of loci : ? Locus : ? Locus : ? Locus : ? Locus : ? Locus : ? Linkage group : ? Number of loci : ? Locus : ? Locus : ? Locus : ? Locus : ? Locus : ? # Take as many or as few lines to describe your protocols # as you like. Please bracket this section by the tags # "Begin protocol :" and "End protocol : " # You may have multiple protocol sections if you like.: # Begin protocol: # # RAPD Reaction and Cycling Conditions # # This protocol was originally derived from the Perkin-Elmer # protocol for PCR amplification of DNA and then modified at # the Institute of Forest Genetics by various scientists. # # [...] # # Perkin-Elmer reaction: # 100 ul reaction scaled down to 25 ul; # # 10x PCR buffer 25 ul 1x # dNTP mix (1.25 mM each dNTP) 4 ul 200 uM # primer [10 mM] 1 ul 0.4 uM # Taq polymerase (reduced amt) 0.2 ul 1.0 units # Tween 20 0.13 ul 0.5 % # # [...] # # End protocol : Begin protocol : ? ? End protocol : # What software and hardware did you use? # Linkage analysis software : Mapmaker 2.0 # Hardware platform : Sun Microsystems SPARCstation Linkage analysis software : ? Hardware platform : ? # Following this please provide input file for the # linkage analysis program. It can be submitted in # a separate file if you like. Please bracket the # beginning and end of the file with the labels # "Begin input file" and "End input file": # # Begin input file : # * FAMILY LIST # *884 abc def jek [...] # # [...] # # *LOCUS NAME OP-A1-800 # *ABBREVIATION OPA1_800 # # [...] # # *END # End input file : Begin input file : ? ? End input file : ----------------End of sample submission file------------------ -- Bradley K. Sherman P.O. Box 245 Computer Scientist Berkeley, CA, 94701 Dendrome Project 510-559-6437 FAX: 510-559-6440 Institute of Forest Genetics Internet: bks@s27w007.pswfs.gov From owner-rapd@net.bio.net Wed Nov 17 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!spool.mu.edu!olivea!charnel!OAVAX.CSUCHICO.EDU!BMCNULTY From: bmcnulty@OAVAX.CSUCHICO.EDU (bob) Newsgroups: bionet.molbio.rapd,bionet.molbio.evolution,bionet.cellbiol Subject: I NEED HELP Message-ID: <2cf4nlINNkn4@charnel.ecst.csuchico.edu> Date: 18 Nov 93 06:29:09 GMT Reply-To: bmcnulty@OAVAX.CSUCHICO.EDU Organization: California State University, Chico Lines: 65 Xref: biosci bionet.molbio.rapd:336 bionet.molbio.evolution:1249 bionet.cellbiol:161 NNTP-Posting-Host: oavax.csuchico.edu I am the manager of a stockroom/lab facility which is responsible for servicing the needs (chemical, reagents, and equipment) of a Biology department in a small university (14 - 16000 students). The facility I manage supplies these items for over 80 laboratory class sections per week with only 3 personnel while at the same time managing a service/checkout window which is open for 6 hours each day (9:00am 'til 3:00pm). The department has 20 PHD faculty and several part time MS instructors or TAs. I seem to have found myself in the middle of a rather large debate with one faculty member who insists that he/she have unlimited access (a key and pass code) to the area I manage (which is currently under alarm and houses well over $1,000,000 worth of inventory) because she/he needs supplies to do unfunded research at hours other than those when the facility I manage is open. The other faculty are either supported by grants or are not actively involved in research. IN AN EFFORT TO SOLVE THIS DILEMMA I NEED YOUR HELP!!! I SEEK ONLY DATA. If you would be so kind.... please answer the following questions and e- mail them to me directly so I may scientifically support my position. I WILL USE NO NAMES OR ADDRESS IN MY REPORT, JUST THE DATA I COLLECT FROM THE QUESTIONS BELOW!!! ********************* CUT HERE ***************************************** With what academic institution are you affiliated? _______________________________ Do faculty at your institution have a key or unlimited access to the main stockroom/supply/support facility? __________________________________ *************************************************************************** Thank you for your time and the effort! BMCNULTY@OAVAX.CSUCHICO.EDU //////// "Adapt, Migrate, or Die" ( ) \ @ @ / BMCNULTY@OAVAX.CSUCHICO.EDU -------w---U---w---- Bob McNulty, CA. STATE UNIV., CHICO From owner-rapd@net.bio.net Wed Nov 17 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!math.ohio-state.edu!magnus.acs.ohio-state.edu!dstothar From: dstothar@magnus.acs.ohio-state.edu (Diane Stothard) Newsgroups: bionet.molbio.rapd,bionet.molbio.evolution,bionet.cellbiol Subject: Re: I NEED HELP Message-ID: <2cg8jm$9df@charm.magnus.acs.ohio-state.edu> Date: 18 Nov 93 16:41:26 GMT References: <2cf4nlINNkn4@charnel.ecst.csuchico.edu> Organization: The Ohio State University Lines: 69 Xref: biosci bionet.molbio.rapd:337 bionet.molbio.evolution:1250 bionet.cellbiol:162 NNTP-Posting-Host: top.magnus.acs.ohio-state.edu In article <2cf4nlINNkn4@charnel.ecst.csuchico.edu> bmcnulty@OAVAX.CSUCHICO.EDU writes: > > > I am the manager of a stockroom/lab facility which is responsible for >servicing the needs (chemical, reagents, and equipment) of a Biology >department in a small university (14 - 16000 students). The facility I >manage supplies these items for over 80 laboratory class sections per week >with only 3 personnel while at the same time managing a service/checkout >window which is open for 6 hours each day (9:00am 'til 3:00pm). The >department has 20 PHD faculty and several part time MS instructors or TAs. > >I seem to have found myself in the middle of a rather large debate with one >faculty member who insists that he/she have unlimited access (a key and >pass code) to the area I manage (which is currently under alarm and houses >well over $1,000,000 worth of inventory) because she/he needs supplies to >do unfunded research at hours other than those when the facility I manage >is open. The other faculty are either supported by grants or are not >actively involved in research. > > > > IN AN EFFORT TO SOLVE THIS DILEMMA I NEED YOUR HELP!!! > > I SEEK ONLY DATA. > >If you would be so kind.... please answer the following questions and e- >mail them to me directly so I may scientifically support my position. > >I WILL USE NO NAMES OR ADDRESS IN MY REPORT, JUST THE DATA I COLLECT FROM > > THE QUESTIONS BELOW!!! > >********************* CUT HERE ***************************************** > > >With what academic institution are you affiliated? > > _Ohio State University__ > > > >Do faculty at your institution have a key or unlimited access to the main > > > stockroom/supply/support facility? _____________NO_____________________ > We have about 15 stock rooms all over our campus and to the best of my knowledge, no one has a key to any of them. > > > > >*************************************************************************** > > >Thank you for your time and the effort! > >BMCNULTY@OAVAX.CSUCHICO.EDU > > > > > > //////// "Adapt, Migrate, or Die" > ( ) > \ @ @ / BMCNULTY@OAVAX.CSUCHICO.EDU >-------w---U---w---- >Bob McNulty, CA. STATE UNIV., CHICO From owner-rapd@net.bio.net Mon Nov 22 22:00:00 1993 Path: biosci!agate!howland.reston.ans.net!europa.eng.gtefsd.com!uunet!decwrl!decwrl!usenet.coe.montana.edu!news.uoregon.edu!netnews.nwnet.net!news.u.washington.edu!stein2.u.washington.edu!toby From: toby@stein2.u.washington.edu (Toby Bradshaw) Newsgroups: bionet.molbio.rapd Subject: Re: Double Het RAPD markers Message-ID: <2bb7b1$g8a@news.u.washington.edu> Date: 4 Nov 93 15:32:49 GMT References: <199311041432.AA18824@postoffice.mail.cornell.edu> Distribution: bionet Organization: University of Washington, Seattle Lines: 29 NNTP-Posting-Host: stein.u.washington.edu In article <199311041432.AA18824@postoffice.mail.cornell.edu>, Muhammad A. Lodhi wrote: > What is the way of differentiating between heterozygous and >homozygous dominant RAPD markers, if any. By definition, a dominant genetic marker cannot distinguish between heterozygotes and dominant homozygotes. RAPD bands may be converted to codominance in the same way other DNA-based polymorphisms are detected -- e.g. restriction enzyme digestion, SSCP, DNA sequencing, allele-specific primers derived from STS data, etc. Sometimes RAPD bands can be used as probes on conventional Southern blots, but in genomes with a lot of repetitive DNA many RAPD bands will be found to contain repeats and not be informative as probes. >I think that may be very helpful >in linkage analysis with pseudotest crosses in woody plants. RAPDs have many advantages, but dominance is a major drawback. We have found that it takes relatively few codominant markers to join RAPDs linked in repulsion, so it is perhaps cost-effective to make maps largely with RAPDs and add one or two codominant markers per chromosome. Ideally, these codominant markers will be PCR-based, as well. Toby Bradshaw | Department of Biochemistry | Will make genetic linkage maps and College of Forest Resources | for food. University of Washington, Seattle | toby@u.washington.edu | From owner-rapd@net.bio.net Wed Nov 24 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!spool.mu.edu!wupost!waikato!waikato.ac.nz!smw From: smw@waikato.ac.nz Newsgroups: bionet.molbio.rapd Subject: HELP Ive Lost It!!! Message-ID: <1993Nov25.182825.22598@waikato.ac.nz> Date: 25 Nov 93 05:28:25 GMT Organization: University of Waikato, Hamilton, New Zealand Lines: 13 hello a while ago someone posted a reference for a paper on RAPD analysis unfortunately I have lost the ref so if anyone out there has it or could point me in the right direction I would be most grateful Shawn Walsh Biology Dept University of Waikato New Zealand SMW@Waikato.ac.nz From owner-rapd@net.bio.net Thu Nov 25 22:00:00 1993 Path: biosci!MERCURY.UARK.EDU!DRHOADS From: DRHOADS@MERCURY.UARK.EDU ("Doug Rhoads") Newsgroups: bionet.molbio.rapd Subject: Re: HELP Ive Lost It!!! Message-ID: Date: 26 Nov 93 17:28:07 GMT Sender: daemon@net.bio.net Distribution: bionet Organization: University of Arkansas Lines: 32 >To: rapd@net.bio.net >From: smw@waikato.ac.nz >Subject: HELP Ive Lost It!!! >Date: 25 Nov 93 05:28:25 GMT >hello > >a while ago someone posted a reference for a paper on RAPD analysis >unfortunately I have lost the ref so if anyone out there has it or could >point me in the right direction I would be most grateful > > >Shawn Walsh >Biology Dept >University of Waikato >New Zealand > >SMW@Waikato.ac.nz > Shwan, you will have to be more specific. There are hundreds of papers on RAPD analysis. If you just want a paper describing the technique check out: Williams,JGK; Hanafey,MK; Rafalski,JA; Tingey,SV (1993): Genetic analysis using random amplified polymorphic DNA markers. Meth. Enzym. 218, 704-740. Good luck. 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 From owner-rapd@net.bio.net Fri Nov 26 22:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!howland.reston.ans.net!europa.eng.gtefsd.com!emory!news-feed-2.peachnet.edu!gatech!news-feed-1.peachnet.edu!umn.edu!gaia.ucs.orst.edu!news.uoregon.edu!netnews.nwnet.net!news.u.washington.edu!stein2.u.washington.edu!toby From: toby@stein2.u.washington.edu (Toby Bradshaw) Newsgroups: bionet.molbio.rapd Subject: Re: QTL analysis with pseudotest cross population Message-ID: <2bmpgn$e35@news.u.washington.edu> Date: 9 Nov 93 00:50:31 GMT References: <199311081919.AA01216@postoffice.mail.cornell.edu> Distribution: bionet Organization: University of Washington, Seattle Lines: 24 NNTP-Posting-Host: stein.u.washington.edu In article <199311081919.AA01216@postoffice.mail.cornell.edu>, Muhammad A. Lodhi wrote: > How does QTL analysis work in linkage maps developed with >pseudotest cross population. As in such populations we get separate >linkage maps of each parent and as far as I know we can't combine them >together to get one map. The maps can be merged with as few as one codominant marker on each linkage group -- two would be better for orientation purposes. >Whether QTL analysis is done separately on each >map or there is some better strategy that I could use. Depends on the genetics of the trait in question. Those genes or QTLs with dominant modes of action are completely covered by normal RAPDs, with or without a map. Additive gene action makes RAPDs less informative when linkages in repulsion cannot be determined. Overdominant modes of gene action are very tough to find with dominant markers alone. Maps per se are not necessarily that helpful for trait mapping -- depends entirely on the genetics of the trait as to whether RAPDs alone will do you any good. -Toby Bradshaw toby@u.washington.edu From owner-rapd@net.bio.net Sat Nov 27 22:00:00 1993 Path: biosci!DEAKIN.EDU.AU!huangbx From: huangbx@DEAKIN.EDU.AU ("Huang Bixing") Newsgroups: bionet.molbio.rapd Subject: Is any programme availble for RAPD? Message-ID: <53844.huangbx@mail-g.deakin.EDU.AU> Date: 28 Nov 93 19:57:05 GMT Sender: daemon@net.bio.net Reply-To: Distribution: bionet Lines: 22 Hello to all netters, Could anyone tell me there is any PC and Mac programme availble for RAPD result analysis, eg. sorting the band patterns, calculating genetic distance between species RAPD results? If you have any idea about how to sort the bands in the gel, that will also be very appreciated. Thank you in advance. With regards. Bixing Huang huangbx@deakin.edu.au Department of Biology Deakin University VIC 3217, Australia ----- School of Biological and Chemical Sciences, Deakin University, Geelong ----- From owner-rapd@net.bio.net Sat Nov 27 22:00:00 1993 Path: biosci!MERCURY.UARK.EDU!DRHOADS From: DRHOADS@MERCURY.UARK.EDU ("Doug Rhoads") Newsgroups: bionet.molbio.rapd Subject: Re: Is any programme availble for RAPD? Message-ID: Date: 28 Nov 93 16:48:41 GMT Sender: daemon@net.bio.net Distribution: bionet Organization: University of Arkansas Lines: 51 >From: "Huang Bixing" >Date: Sun, 28 Nov 93 14:57:05 EST >Reply-to: >To: rapd@net.bio.net >Subject: Is any programme availble for RAPD? >Hello to all netters, > >Could anyone tell me there is any PC and Mac programme availble for RAPD >result analysis, eg. sorting the band patterns, calculating genetic >distance between species RAPD results? > >If you have any idea about how to sort the bands in the gel, that will >also be very appreciated. > >Thank you in advance. > >With regards. > >Bixing Huang I am aware of three companies that sell software for varying levels of analysis you allude to. Millipore Corp. (high priced Sun-based system), UVP Life Sciences (800-452-6788) has a Windows based system that you can buy `piece- meal' including CCD camera, printer, and software for 2D analysis, Molecular sizing, storage, and RFLP band pattern. (This one runs about $600 per module I think) Applied Maths (Belgium +32 56 424144) also sells software packages ranging from $1200 to $2280) that they claim do alot of different things related to gel documentation, cluster analysis, comparisons, etc. Unfortunately, I have little experience with any of these as they all get pricey in putting together a system. I hope to get a look at the UVP system since I may be able to afford it in the near-future. The rest are `out-of-my-league' in price. Until then I will continue to use Graduate students `eyeball-scanning' and free-ware suites like Phyllip to do my cluster and phylogenetic analyses. Maybe some one else has experience with these commercial products. (the usual disclaimer of any monetary or fiduciary relationship to the afore-mentioned companies). 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 From owner-rapd@net.bio.net Sat Nov 27 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!spool.mu.edu!wupost!waikato!waikato.ac.nz!smw From: smw@waikato.ac.nz Newsgroups: bionet.molbio.rapd Subject: Re: HELP Ive Lost It!!! Message-ID: <1993Nov28.130134.22659@waikato.ac.nz> Date: 28 Nov 93 00:01:34 GMT References: Distribution: bionet Organization: University of Waikato, Hamilton, New Zealand Lines: 4 sorry for all the confusion, the paper I was after was about analysing the RAPD results for genetic distance information. Shawn From owner-rapd@net.bio.net Mon Nov 29 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!cs.utexas.edu!wupost!waikato!waikato.ac.nz!smw From: smw@waikato.ac.nz Newsgroups: bionet.molbio.rapd Subject: NaOH DNA RAPD extraction Message-ID: <1993Nov30.142132.22754@waikato.ac.nz> Date: 30 Nov 93 01:21:31 GMT Organization: University of Waikato, Hamilton, New Zealand Lines: 15 Hi Shawn again, Thanks for the help with the reference and I have got the one I was refering to I was reading a PCR DNA extraction method in NAR (1993 21(17):4153-4154) that simply involved grinding the plant tissue in 0.5M NaOH and then diluting the supernatant in TE buffer. I have tried this on moss and found the results to be quite good, and they compare with the CTAB type prep I have been using to date. Has anyone else out there tried this and if so what do you think of the technique? Shawn Walsh From owner-rapd@net.bio.net Mon Nov 29 22:00:00 1993 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!cs.utexas.edu!wupost!waikato!waikato.ac.nz!smw From: smw@waikato.ac.nz Newsgroups: bionet.molbio.rapd Subject: NaOH DNA RAPD extraction Message-ID: <1993Nov30.142132.22754@waikato.ac.nz> Date: 30 Nov 93 01:21:31 GMT Organization: University of Waikato, Hamilton, New Zealand Lines: 15 Hi Shawn again, Thanks for the help with the reference and I have got the one I was refering to I was reading a PCR DNA extraction method in NAR (1993 21(17):4153-4154) that simply involved grinding the plant tissue in 0.5M NaOH and then diluting the supernatant in TE buffer. I have tried this on moss and found the results to be quite good, and they compare with the CTAB type prep I have been using to date. Has anyone else out there tried this and if so what do you think of the technique? Shawn Walsh From owner-rapd@net.bio.net Tue Nov 30 22:00:00 1993 Path: biosci!cornell.edu!mal5 From: mal5@cornell.edu (muhammad a. lodhi) Newsgroups: bionet.molbio.rapd Subject: Re: AmpliTaq polymerase LD Message-ID: <199311302308.AA12764@postoffice.mail.cornell.edu> Date: 30 Nov 93 19:13:15 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 25 Huang Bixing wrote that; >I am trying every percaution to avoid non-specific bands in my RAPD >negative control. I have been running RAPD reactions for last two years and I saw the same problem with Taq polymerase (Promega), though not very consistently. I used to see non specific amplifications in negative control from time to time but those bands never matched with the amplification products from experimental reactions, i.e., non-specific amplification never interfered with scoring of specific bands for genetic analysis. I used some other polymerases (like Tfl) too and saw similar pattern. By varying temperature profiles there was no significant improvement and this 'hide and seek' continued. After a while I stopped worrying about them as they seemed 'friendly' to me. I could not find a single factor responsible for this amplification but some time it helped to work under laminar flow hood as mostly I worked on the bench-top without any further protection. I ran reactions in 2-3 replications and found very consistent results. Its probably one of those mysteries that come with RAPD. ================================================================================ Muhammad A. Lodhi Cornell University Geneva Campus,NYSAES Geneva, NY 14456 From owner-rapd@net.bio.net Tue Nov 30 22:00:00 1993 Path: biosci!PHIBRED.COM!murrayian From: murrayian@PHIBRED.COM (IAN MURRAY) Newsgroups: bionet.molbio.rapd Subject: Grinding of tissue for DNA or protein extraction Message-ID: <9312012056.AA03108@phibred.phibred.com> Date: 1 Dec 93 20:56:45 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 17 Hello and good day, I am looking for disposable/ resuable pestles to fit into the wells of a 96 well microtitre plate or a 1 ml tube, the ones that I have are supplied by Bio Rad. I have tried Kontes, Bel Art and a few others. I was wondering if anyone could shed some shed some light on the matter, OR give me some references as to which pestles they use. Your help is much appreciated. Murrayian@phibred.com *smile* From owner-rapd@net.bio.net Tue Nov 30 22:00:00 1993 Path: biosci!cornell.edu!mal5 From: mal5@cornell.edu (Muhammad A. Lodhi) Newsgroups: bionet.molbio.rapd Subject: Re: AmpliTaq polymerase LD Message-ID: <199312012104.AA11202@postoffice.mail.cornell.edu> Date: 1 Dec 93 17:09:04 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 26 Huang Bixing wrote that; >I am trying every percaution to avoid non-specific bands in my RAPD >negative control. I have been running RAPD reactions for last two years and I saw the same problem with Taq polymerase (Promega), though not very consistently. I used to see non specific amplifications in negative control from time to time but those bands never matched with the amplification products from experimental reactions, i.e., non-specific amplification never interfered with scoring of specific bands for genetic analysis. I used some other polymerases (like Tfl) too and saw similar pattern. By varying temperature profiles there was no significant improvement and this 'hide and seek' continued. After a while I stopped worrying about them as they seemed 'friendly' to me. I could not find a single factor responsible for this amplification but some time it helped to work under laminar flow hood as mostly I worked on the bench-top without any further protection. I ran reactions in 2-3 replications and found very consistent results. Its probably one of those mysteries that come with RAPD. ================================================================================ Muhammad A. Lodhi Cornell University Geneva Campus,NYSAES Geneva, NY 14456 From owner-rapd@net.bio.net Tue Nov 30 22:00:00 1993 Path: biosci!daresbury!not-for-mail From: abrpanch@reading.ac.uk (Naresh C. Pancholi) Newsgroups: bionet.molbio.rapd Subject: Re: NaOH DNA RAPD extraction Message-ID: <2dil03$f79@mserv1.dl.ac.uk> Date: 1 Dec 93 17:41:23 GMT Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Lines: 35 Original-To: rapd@dl.ac.uk On 30 Nov 1993 smw@nz.ac.waikato wrote: > Hi Shawn again, > I was reading a PCR DNA extraction method in NAR (1993 21(17):4153-4154) > that simply involved grinding the plant tissue in 0.5M NaOH and then diluting > the supernatant in TE buffer. > > I have tried this on moss and found the results to be quite good, and they > compare with the CTAB type prep I have been using to date. > > Has anyone else out there tried this and if so what do you think of the > technique? > > Shawn Walsh Hello, I am following the same methods which is mentioned above for potatoes and bananas. 0.1M NaOH works well for potatoes but it seems that NaOH extraction is difficult for banana. I have tried various concentrations of NaOH for banana but still no success. Anyway, the important point is that this procedure is much simpler and quicker than CTAB or similar methods. One should try this over the range of plants. If anyone over the net has something on banana DNA extraction, I will appreciate very much. Naresh Pancholi abrpanch@reading.ac.uk Agricultural Botany University of Reading UK From owner-rapd@net.bio.net Tue Nov 30 22:00:00 1993 Path: biosci!UNR.EDU!hoelzer From: hoelzer@UNR.EDU (Guy A Hoelzer) Newsgroups: bionet.molbio.rapd Subject: Re: Mystery bands in the Negative Control Message-ID: Date: 1 Dec 93 16:46:45 GMT References: <199311302308.AA12764@postoffice.mail.cornell.edu> Sender: daemon@net.bio.net Distribution: bionet Lines: 21 A couple of years ago I was having the same problem of mystery bands appearing in my negative control when running RAPD's. These bands never lined-up with those in my sample lanes, so I was also not very concerned about the data. However, I still did what I could to track down the source of the contamination. It turned out that the contaminating template was bacterial DNA that was deposited on tips, tubes and glassware during autoclaving. If I used pipet tips and microcentrifuge tubes that had not gone through the autoclave, the mystery bands disappeared. Has anybody else had this experience? How common is it to have "free" DNA in an autoclave used to sterilize bacterial cultures that can contaminate glassware, etc., subsequently placed in the autoclave? Guy Hoelzer Dept. of Biology University of Nevada Reno Reno, NV 89557 hoelzer@unr.edu