From owner-rapd@net.bio.net Wed Jul 05 23:00:00 1995 Newsgroups: bionet.molbio.rapd Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!spool.mu.edu!uwm.edu!msunews!harbinger.cc.monash.edu.au!newsroom.utas.edu.au!ml.csiro.au!mac-1305.ml.csiro.au!chris.bolch From: Christopher J. S. Bolch Subject: Britestar posting X-Nntp-Posting-Host: mac-1305.ml.csiro.au Message-ID: X-Xxmessage-Id: X-Xxdate: Mon, 3 Jul 95 13:15:29 GMT Sender: news@ml.csiro.au Organization: CSIRO Division of Fisheries, Hobart, Tasmania X-Useragent: Version 1.1.3 Date: Mon, 3 Jul 1995 03:11:40 GMT Lines: 25 Thr recent posting from britestar which advertises a range of products, mostly office products, is very irritating. I tried to reply to the address, telling them that they are decreasing their chances of sales by doing this, and couldn't get through. Can someone else try to mail my message for me. This sort of junk should be killed at the source if possible. Thanks Dear Britestar Inc. If you are trying to capture some of the science market for your material then this is a bad way to do it!! Please refrain from commercial advertising of products on the net. I, and most of my colleagues, find that this sort of material only makes me determined to never buy anything from the company concerned, particularly when the information is completely irrelevent to the particular list I received this through. Congratulations, Britestar Inc is now etched on my, and many other memories, as a company to avoid in perpetuity!! From owner-rapd@net.bio.net Thu Jul 06 23:00:00 1995 Newsgroups: bionet.molbio.rapd Path: biosci!rutgers!uwm.edu!reuter.cse.ogi.edu!netnews.nwnet.net!ns1.nodak.edu!plains!comstock From: comstock@plains.NoDak.edu (Clay Comstock) Subject: Storage of DNA Sender: usenet@ns1.nodak.edu (Usenet login) Message-ID: Date: Fri, 7 Jul 1995 22:02:37 GMT Nntp-Posting-Host: plains.nodak.edu Organization: North Dakota Higher Education Computing Network (NDHECN) X-Newsreader: TIN [version 1.2 PL2] Lines: 31 Hello, I am extracting DNA from spiders using a Chelex-100 Resin and Proteinase K Protocol. To prepare for the digestion all sample are ground in 500ul. of TE. Could anyone tell me how long the DNA lasts when frozen at -20C. Thanks, Clay Comstock ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ____________ /| /| "The Necker Cube / |_________/_| Reminds Us, That /__/________/ | All Situations | / | / Can Be Viewed |/ | / From Two Different Perspectives" |__________|/ Clay Comstock Dickinson State University Dickinson, ND 58601 e-mail comstock@plains.nodak.edu homepage http://murphy217.math.dsu.nodak.edu/dsu/comstock.htm ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-rapd@net.bio.net Thu Jul 06 23:00:00 1995 Newsgroups: bionet.molbio.rapd Path: biosci!agate!spool.mu.edu!uwm.edu!uwvax!newssinet!news.u-tokyo.ac.jp!tkyex1.phys.s.u-tokyo.ac.jp!news.tisn.ad.jp!riksun!postman.riken.go.jp!biog024.riken.go.jp!user From: cgrunau@rkna50.riken.go.jp (Christoph Grunau) Subject: Is there experimental proof for Nei&Li (1979)? 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: biog024 Content-Transfer-Encoding: 8bit Organization: RIKEN Tokyo Mime-Version: 1.0 Date: Fri, 7 Jul 1995 08:35:43 GMT Lines: 26 Hi RFLPers! Does anyone knows a paper about the experimental proof for Nei & Li's paper from 1979 "Mathematical model for studying genetic variations in terms of restriction endonucleases"? What I am doing is: #1) PCR amplification of hsp70 from a mixed population #2) RFLP of the obtained clones to reduce data redundancy by estimating the substitutions per nucleotide site (Nei & Li) and hierarchical clustering #3) choosing a type clone for each cluster and sequencing the type clones #4) sequence comparison Problem: RFLP and sequence comparison gives SAME tree topology but more than one order of magnitude DIFFERENT distance values (substitutions per nucleotide site). The RFLP tree is "smaller" than the sequence tree. I would appreciate to hear your opinion. Thanks in advance. Christoph Grunau From owner-rapd@net.bio.net Mon Jul 10 23:00:00 1995 Path: biosci!ACD1.BYU.EDU!HECKMANR From: HECKMANR@ACD1.BYU.EDU ("RICHARD A. HECKMANN") Newsgroups: bionet.molbio.rapd Subject: Want to be included in the net Date: 11 Jul 1995 15:15:17 -0700 Organization: Brigham Young University Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <1CC501D0FED@acd1.byu.edu> NNTP-Posting-Host: net.bio.net Hello: Can anyone tell me how to be included in this net? I am a graduate student from Bolivia and I will need some information about RAPD's. I am using my proffesor e-mail. Victor H. Inchausty Zoology Dept. Brigham Young University Provo, UT 84602 e-mail: Heckmanr@acd1.byu.edu (801)378-2495 From owner-rapd@net.bio.net Mon Jul 10 23:00:00 1995 Path: biosci!YVAX.BYU.EDU!anderswr From: anderswr@YVAX.BYU.EDU (W. Ralph Andersen) Newsgroups: bionet.molbio.rapd Subject: Extracting DNA from small organisms Date: 11 Jul 1995 09:29:01 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HSQOAXP35KAAU8UD@yvax.byu.edu> NNTP-Posting-Host: net.bio.net Hello: Anyone know of- or have a method for extracting DNA from individual small animals such as fish eye flukes for RAPD or PCR? Victor Inchausty, from Bolivia (Altiplano region and Bolivian lowlands, rain forest etc.,), is needing a method to analyze the genetic structure of such parasites. Please let me know. Thank you. Ralph Andersen, 297 WIDB, BYU Provo, Ut. 84602. Ph: 801 378 2468, Fax: 801 378 7499. From owner-rapd@net.bio.net Thu Jul 13 23:00:00 1995 Path: biosci!agate!overload.lbl.gov!emf.emf.net!gatech!news.sprintlink.net!uunet!in1.uu.net!newsflash.concordia.ca!news.mcgill.ca!news From: mfortin@nrs.mcgill.ca (M. Fortin) Newsgroups: bionet.molbio.rapd Subject: Source of oligos for microsatellites in plants Date: Fri, 14 Jul 95 15:23:08 GMT Organization: McGill University Computing Centre Lines: 8 Distribution: world Message-ID: <3u61re$ci4@sifon.cc.mcgill.ca> NNTP-Posting-Host: 132.216.21.68 X-Newsreader: News Xpress Version 1.0 Beta #2.1 We are looking for a supplier of oligos for repeats in plants; GATA and the like. Can you provide us with the name etc... of some suppiers. We figure it would be cheaper to buy them than to have them synthesized. Marc Fortin Mary dePauw genelab@nrs.mcgill.ca From owner-rapd@net.bio.net Thu Jul 13 23:00:00 1995 Newsgroups: bionet.molbio.rapd Path: biosci!agate!newsxfer.itd.umich.edu!zip.eecs.umich.edu!umn.edu!mac20.agoff.umn.edu!user From: vergelv@puccini.CRL.umn.edu (Vergel Concibido) Subject: Cost estimates of PCR-based markers vs. RFLP Message-ID: Sender: news@news.cis.umn.edu (Usenet News Administration) Nntp-Posting-Host: mac20.agoff.umn.edu Organization: Univ. of Minnesota Date: Fri, 14 Jul 1995 08:39:11 GMT Lines: 8 I am comparing the cost per data point/ per polymorphism using RFLPs vs using PCR-based markers in a marker-assisted selection strategy in plant breeding. I have done an estimate for RFLPs based on my experience in our lab. It amounted to about $2.00 per data point and the cost goes down depending on the number of probings my Southern blots can last. Does anybody have done estimates for these type of markers? The only reference I am aware of is: Beckmann and Soller, 1983 TAG. I appreciate your input on this. From owner-rapd@net.bio.net Fri Jul 14 23:00:00 1995 Path: biosci!SASK.USASK.CA!ganeshan From: ganeshan@SASK.USASK.CA Newsgroups: bionet.molbio.rapd Subject: Intriguing intense band Date: 15 Jul 1995 14:35:04 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hi all: I am performing RAPDs on isolates of two fungal species. I have got a polymorphic band for species A, but there are few isolates of species B that show the same band, albeit very, very faint. So to eliminate all unwanted bands and retain only my polymorphic band, I cranked up the annealing temperature from 36 degrees to 51 degrees, leaving all the other conditions same as in my previous RAPD conditions. Well, sure enough all unwanted bands disappeared, but the few isolates of species B that showed the very faint band previously, have now become very intense. Does anyone have an explanation for this or any speculations? One speculation may be that at the higher annealing temperature more resources are available for the primer to bind to strictly complementary sites on the template. However, this does not explain why at 36 degrees annealing temp. the bands were so faint. Your input will be very much appreciated. Pooba U of S Saskatoon From owner-rapd@net.bio.net Mon Jul 17 23:00:00 1995 Path: biosci!UOW.EDU.AU!Al_Griskaitis From: Al_Griskaitis@UOW.EDU.AU ("Al Griskaitis") Newsgroups: bionet.molbio.rapd Subject: Any ideas? Date: 17 Jul 1995 22:06:54 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear RAPDers Can one use RAPDs to determine whether species hitherto classified as different are in fact the same? On three southern continents exist three ascidian species which are casually indistinguishable in terms of morphology. I'm certain RAPDs (or RFLPs for that matter) will be able to distinguish between these populations. But my question is: how similar must the RAPD (or RFLP) profiles be in order to group these [pseudospecies] as one? More to the point, is RAPDs an appropriate approach? and if it is not, what are the alternatives? Any ideas would be greatly appreciated. Cheers, Al Griskaitis University of Wollongong, NSW, Australia. From owner-rapd@net.bio.net Mon Jul 17 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!news.cac.psu.edu!news.tc.cornell.edu!travelers.mail.cornell.edu!newsstand.cit.cornell.edu!NewsWatcher!user From: Warren_Lamboy@cornell.edu (Warren Frank Lamboy) Newsgroups: bionet.molbio.rapd Subject: Re: Any ideas? Date: Mon, 17 Jul 1995 08:41:04 -1200 Organization: Cornell University Lines: 44 Sender: wfl1@cornell.edu (Verified) Distribution: world Message-ID: References: NNTP-Posting-Host: 132 In article , Al_Griskaitis@UOW.EDU.AU ("Al Griskaitis") wrote: > Dear RAPDers > Can one use RAPDs to determine whether species hitherto classified as > different are in fact the same? > On three southern continents exist three ascidian species which are casually > indistinguishable in terms of morphology. I'm certain RAPDs (or RFLPs for that > matter) will be able to distinguish between these populations. But my question > is: how similar must the RAPD (or RFLP) profiles be in order to group these > [pseudospecies] as one? More to the point, is RAPDs an appropriate approach? > and if it is not, what are the alternatives? > Any ideas would be greatly appreciated. > Cheers, > Al Griskaitis > University of Wollongong, NSW, Australia. Dear Al: The question you are asking is possibly the most important question in biological systematics, namely, how different do organisms need to be in order for us to classify them as different. This question arises whether one is using RAPD data, isozyme data, morphological data, etc. All characteristics of the organisms (interbreeding, habitat, DNA, life cycle, etc.) must be considered when one makes a decision as to whether they should be treated as separate species or not. If, however, one were going to make the determination solely on the basis of similarities based on RAPD fragment profiles [something I do not necessary think is a good idea, but something that we systematists are sometimes called upon to do anyway] , one would need first to determine the range of RAPD similarity values between known unequivocally-accepted species in the group or in closely related groups. Then, after computing RAPD similarities between the "species" that are the taxa of interest, one can compare those similarity values to values found for known accepted species. If the similarities are significantly greater than those between known different species, then one has some justification for arguing that the "species" in question probably do not deserve that rank. If the similarities are within the range of similarity values for accepted known different species, then the populations in question could justifiably be deemed to be different species. I hope you find my comments helpful. -Warren From owner-rapd@net.bio.net Mon Jul 17 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!news.sprintlink.net!demon!tank.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: BANANA & PLANTAIN Newsgroups: bionet.molbio.rapd Subject: What is retrotransposon? Date: 18 Jul 1995 09:32:17 +0100 Lines: 20 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3ufrih$oj3@mserv1.dl.ac.uk> MIME-Version: 1.0 Original-To: RAPD , Methods-and-Reagents Hello Netters, Can anybody described in brief retrotransposon? Also, is it possible to use retrotrasnposon mediated fingerprinting to assess the magnitude of somaclonal variation? Thanks. -Naresh ------------------------------------------------------------------------- NARESH PANCHOLI AGRICULTURAL BOTANY PHONE: +44 1734 875123 EXT. 4087 SCHOOL OF PLANT SCIENCES FAX: +44 1734 316577 UNIVERSITY OF READING READING RG6 6AS ENGLAND N.C.PANCHOLI@READING.AC.UK ------------------------------------------------------------------------- From owner-rapd@net.bio.net Wed Jul 19 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!geraldo.cc.utexas.edu!usenet From: Kreblon@ccwf.cc.utexas.edu (Robert Nagy) Newsgroups: bionet.molbio.rapd Subject: Seed formation in an intergeneric rice hybrid Date: 20 Jul 1995 20:43:41 GMT Organization: The University of Texas at Austin Lines: 19 Message-ID: <3umf5t$2su@geraldo.cc.utexas.edu> NNTP-Posting-Host: kreblon.botany.utexas.edu X-Newsreader: WinVN 0.90.4 Dear colleagues: In the last Annual Conference of the Bangladesh Association for Plant Tissue Culture (BAPTC) held in Dhaka in April last, a paper was presented reporting for the first time a hybrid at the tetraploid level in the combination, colchicine-induced tetraploid rice, c-4x Oryza sativa (2n=4x=48) x a natural tetraploid, Porteresia coarctata (2n+48), which grows wild in the coastal areas of the Indian subcontinent. The author said that in spite of a large number of backcrosses to either of the parents and self-pollination, not a single seed was formed. Surprisingly, Pollen stainability was better and there was less variation in the size of pollen compared to those of the c-4x O. sativa. Could anyone please suggest of any modern technique which will promote the setting of seeds because if the researcher obtains one viable seed, it will open an unlimited possibility of creating rice varieties suitable for growing in the saline coastal soil where no food crops grows at present. I shall very much appreciate receiving a reply which I would like to communicate to the researcher who does not have facility to an internet connection. Thanks again. Sincerely, Ahmad Islam From owner-rapd@net.bio.net Mon Jul 31 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!panix!zip.eecs.umich.edu!caen!uwm.edu!msunews!harbinger.cc.monash.edu.au!news.uwa.edu.au!perth.highway1.com.au!usenet From: biotech@highway1.com.au Newsgroups: bionet.molbio.rapd Subject: Alcohol Interference in PCR Date: 1 Aug 1995 10:06:03 GMT Organization: Highway1 Pty Ltd Lines: 26 Message-ID: <3vkuab$io0@perth.highway1.com.au> NNTP-Posting-Host: biotech.highway1.com.au X-Newsreader: AIR News 3.X (SPRY, Inc.) Dear ALL, I am trying to find some information on the levels of ethanol and butanol which cause interference in PCR reactions. If you have any information or you know of a reference which covers this problem please contact me. Thank you for your help. Keith Norman Research Scientist E-mail to either : Biotechperth@attmail.com Biotech@highway1.com.au Postal Address : Biotech International Ltd. Unit 9, 4 Brodie Hall Drive Technology Park Bentley Western Australia 6102 Phone : (619) 470-4322 Fax : (619) 470-4283