From owner-rapd@net.bio.net Wed Nov 02 22:00:00 1994 Path: biosci!daresbury!bioftp.unibas.ch!citi2.fr!jussieu.fr!cea.fr!usenet From: cisitm@albert.cad.cea.fr (Pierre Didierjean) Newsgroups: bionet.molbio.rapd Subject: *** Q: WHAT KIND OF PEOPLE ON THE NET ? Date: 3 Nov 1994 16:17:17 GMT Organization: SSII Lines: 28 Sender: cisitm@albert.cad.cea.fr Message-ID: <39b2ed$9po@anemone.saclay.cea.fr> NNTP-Posting-Host: nyassa.cad.cea.fr I'd like to know what kind of people i find on the net. Students, Commercials, Adminitrations, Scientifics or what ?? Is anybody knows that or have statistical results ? What are YOU doing in life ? I am a system administrator. Thanks for the answers and sorry for my english ..... Bye +-----------------------------------------------------------------------------+ | Pierre DIDIERJEAN | | | | Administrateur Systeme UNIX | | Cisi, Aix-en-Provence | | France | +-----------------------------------------------------------------------------+ | email : cisitm@albert.cad.cea.fr | +-----------------------------------------------------------------------------+ From owner-rapd@net.bio.net Wed Nov 02 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!pipex!uknet!daresbury!not-for-mail From: dudy bar-zvi Newsgroups: bionet.molbio.rapd Subject: TECHNE thermal cyclers Date: 3 Nov 1994 13:47:07 -0000 Lines: 13 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <39apkr$8tg@mserv1.dl.ac.uk> Original-To: methods@dl.ac.uk, rapd@dl.ac.uk Dear netters, We have got a nice offer from thermocyclers form Techne. I would like to get some information and experience with thermocyclers made by Techne. Are Techne cyclers users happy with it? Do they recommend to get it? Thanks, Dudy Bar-Zvi Ben-Gurion University Beer-Sheva, Israel From owner-rapd@net.bio.net Thu Nov 03 22:00:00 1994 Path: biosci!UBVMS.CC.BUFFALO.EDU!V226UHBQ From: V226UHBQ@UBVMS.CC.BUFFALO.EDU Newsgroups: bionet.molbio.rapd Subject: Summary of comments on PCR machines Date: 4 Nov 1994 11:02:10 -0800 Organization: University at Buffalo Lines: 285 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HJ316AOEUQ8X0RHM@ubvms.cc.buffalo.edu> NNTP-Posting-Host: net.bio.net Netters -- A few weeks ago I put out a request for advice on PCR machines. The following is a summary of those results. From the input, I am leaning towards the MJR machine, but will bench test several models. Thanks to everyone for your input! Mary Alice Coffroth Department of Biological Sciences SUNY at Buffalo Buffalo, NY 14260 716-645-2881 716 645-2975 [fax] V226uhbq@ubvms.cc.buffalo.edu -------------------------------------------------------------------------- SUMMARY OF COMMENTS ON "THE BEST PCR MACHINE" From: IN%"jfell@rsmas.miami.edu" 20-OCT-1994 15:32:45.76 To: IN%"V226UHBQ@ubvms.cc.buffalo.edu" CC: Subj: RE: Pcr machines we have been using the MJ - both models for several years and they have been great- no problems and the price is right - PS - MJ will send out one on trial - but I am sure that you will be happy with one. J. From: IN%"bio_hannan%emuvax.dnet.emich.edu@emunix.emich.edu" 21-OCT-1994 12:36:19.53 To: IN%"rapd@net.bio.net" CC: Subj: RE: thermocycler We have a Coy50 that has gone back for repair twice- first for cooling block problem, now for heating problem. It won't get up to set points above about 35 degrees. Have you had similar problems and is that why you are not considering another Coy (e.g. 60)? We have also had the usual experiences of having amplifications stop completely for no apparent reason (although this seems to happen to everyone at times). Gary Hannan bio_hannan@emunix.emich.edu From: IN%"UDBR150@BAY.CC.KCL.AC.UK" "DEVILISH DERVISH" 21-OCT-1994 12:46:21.43 To: IN%"V226UHBQ@ubvms.cc.buffalo.edu" CC: Subj: RE: PCR Machines In the lab we have had a Hybaid Tr1 'thermo cycler' for years and found it to be verry good for all amplification..including RAPD's found the same problem as your getting..pcr became more popular in the lab and adjoining labs and had to get another...tried the Hybaid tr2 found it to be too slow...due to an open top design making heating to 90+ a real problem..also found it to be unreliable...results not always reproducible but were reproducible in the tr1..no good for us called Hybaid and arranged a 'part exchange'...for a realativley small ammount we got rid of the tr2 and got a tr3...this was a verry different beast has 96well microtitre or eppendorph (small) capabilities..as well as able to do the insitue amplification work on microscope slides..ramp time is much faster...about 2/3 time of the tr2 and can be adjusted for individual programs...both ramp and increment (usefull for the longer porograms where Taq can loose activity) are programable, can hold up to 30 programs on 'smart-disc' and can also be coupled to the lab pc. if this wasnt enough it can have up to 2 satelite units slaved to it.. 'dumb' blocks under the copntroll of the primary unit..can perform 3 different amplifications simultaniously..satelites are about1/2 price of te controll module. Basically i like it..even has a groovey display showing possition in the program and predicted finish time. Only thing i dont know is the price..but i do know that Hybaid are quite cheep compared to many of the companies. Hope this is of help. Dave Roberts Kings College London p.s. I dont work for Hybaid..I work for peanuts !! From: IN%"boulding@uoguelph.ca" "Elizabeth Boulding" 21-OCT-1994 12:51:34.95 To: IN%"V226UHBQ@ubvms.cc.buffalo.edu" CC: Subj: RE: PCR Machines Hi, I like my MJ research machine very much and it is much easier to program and faster than a PE machine. Elizabeth Boulidng. From: IN%"JNAKAMOT@pediatrics.medsch.ucla.edu" "Nakamoto, M.D.,Jon" 21-OCT-1994 13:06:38.75 To: IN%"V226uhbq@ubvms.cc.buffalo.edu" CC: Subj: RE: thermal cycler info I happen to be in exactly the same boat (currently using a Coy and looking for a 96-well plate cycler, with the leading candidate being an MJ Research machine). I'll share my one small bit of info with you if you'll E-mail your summary of comments you get. Debra Farber's lab over at the Jules Stein Eye Institute here at UCLA are currently demo-ing both an MJ Research 100-96V with a "Hot Bonnet" lid, as well as a Stratagene Robocycler. They like them both very much (the MJ for the plates, and the RoboCycler for pure speed). Their previous MJ machine was very dependable and still used. One thing that surprised me was their comment that the heated lid option wasn't dependable enough to leave mineral oil out of the reaction --although they're still testing it, at this point they probably won't get this option. What's nice is that they were allowed to demo the unit with the heated lid for a few weeks -- something both you and I should probably do, too. Actually, I'm also going to demo the Ericomp Single-Block (a few hundred dollars cheaper), which the sales rep said I should run side-by-side with the MJ machine. He claims the well-to-well uniformity is better (who knows?). (Rich) People using the top of the line Perkin-Elmer 9600 (2 divisions in our dept) like it (great well-to-well uniformity/reproducibility), but you know the price. And the heated lid is again not as great as advertised (one lab still uses mineral oil). If you need more speed (and with 8 hour runs, it sound like you might), a lot of people have been enthusiastic about the units which physically move tubes from pre-equilibrated block to block. You've likely seen the ads for the Stratagene Robocycler (including the one that has a gradient block to test 8 diff annealing temps -- gee that sounds nice); I also asked for Inotech Biosystems to send me info on their Quarterbath Immersion Cycler ($4900 list) which does the same thing, only with water baths. The Stratagene unit doesn't support 96-well plates that I know of; the Quarterbath unit does. I'd love to hear what comments you get (I didn't get much response when I posted a similar question earlier). Thanks, Jon Jon Nakamoto, MD Clinical Instructor of Pediatrics/Endocrinology UCLA jnakamot@pediatrics.medsch.ucla.edu fax (310) 206-5843 From: IN%"VSC003@ukcc.uky.edu" 21-OCT-1994 18:11:46.02 To: IN%"rapd@net.bio.net" CC: Subj: Coy Thermocyclers We have one of the early Coy Thermocyclers. I'm at home and don't recall the model number. It has worked very well for RAPDs for us and is the machine of choice for one of my co-workers. We had a problem with the machine quitting on us in the middle of runs. We finally learned from the manufacturer that we needed to remove the front piece and use a soft pencil eraser to clean the "electrical points" (my word). Then it works great. Even the digital display is brighter. We've made a habit of cleaning the "points" once a month or so. I had a pick-up truck like that once. The Coy has performed well against other machines for PCR. It just has this one maintainance aspect that isn't described in the manual.--- From: IN%"jweiland@BADLANDS.NODAK.EDU" 21-OCT-1994 18:28:49.48 To: IN%"rapd@net.bio.net" CC: Subj: Microtitre PCR blocks and MJR First, we are really in love with the MJR machines. My S.O. first used one 4 years ago, and I went over to her lab to get away from the dinosaur Perkin-Elmer near our lab. I've used a 60 well MJR for the past two years and had no problems, and on a new project now, have ordered a 96-well unit. MJR's are very fast and quiet. No problems yet. They are very easy to program and start. So far, so good. Question for users of MJR or other 96-well blocks----WE've been quoted a price of $93.00 for 25 plates (polycarbonate) for use in the 96-well unit. Any cheaper prices out there for a plate that is manufactured for use in a thermocycler? Thanks John Weiland jweiland@badlands.nodak.edu From: IN%"GOVE002@TWNMOE10.Edu.TW" "WANG, WEI-YOUNG" 23-OCT-1994 20:04:53.66 To: IN%"V226UHBQ@ubvms.cc.buffalo.edu" CC: Subj: RE: PCR Machines I had an old Coy60 for several years. I used for RAPDs and regular PCR. It performed well for me although it has broken twice on me. The problem of using Coy60 for RAPDs is slow. I use 94Cx1m, 30Cx4m45s, 72Cx2m and 45 cycles which takes about 9 hrs to complete. Then, I got a Idaho Air Thermal Cycler which seals reaction mixtures in a glass capillary. The reaction is much faster and more reliable. I uses 94Cx1s, 37Cx7s, 72Cx70s and 45 cycles which takes about 2 hr to complete for RAPDs. As for PCR reaction, it usually takes less than half an hour to complete. The glass capillary is sealed with a mini-torch which is a little bit troblesome but since no oil is needed, latter application of RAPD samples into gel is easier. Also, capillary tubes costs much less than 0.5ml tubes or 96-well plates. (I'm in no way associated with the company that produce the Idaho Air Thermal Cycler). Wei-Young Wang Taiwan Forestry Research Institute gove002@twnmoe10.edu.tw From: IN%"PX52@SDSUMUS.SDSTATE.EDU" 25-OCT-1994 23:48:10.03 To: IN%"rapd@net.bio.net" CC: Subj: PCR Machines My lab's experience with the machines from M.J. Research has been outstanding. We have two 60-well models. Both have given very reproducible results and have been very reliable.The only problems we had were when we employed the external temperature probe; then there was a tendency for the programs to scram. So, we just don't use the external probes any more. The M.J. machines are also reasonably priced IMHO. -------------------------------------------------------- Thomas E. Chase px52@sdsumus.sdstate.edu South Dakota State University Voice 605-688-5550 Plant Science Department FAX: 605-688-4024 -------------------------------------------------------- From: IN%"HAMELIN@cfl.forestry.ca" 26-OCT-1994 09:50:08.83 To: IN%"rapd@net.bio.net" CC: Subj: MJ-Research cyclers We also use MJ-Research PTC100 60 wells machines and are very satisfied. However, last summer, 10 days before the end of the warranty, the element fried when the power came back after a power break-down. I hope this is not going to happen every time there is power failure...Anybody else had their elements burn in their MJ-Research cyclers? To: IN%"rapd@net.bio.net" CC: Subj: RE: PCR Machines I HAVE A PERKIN/ELMER 480. IT HAS BEEN WORKING ALMOST 24 HRS. A DAY FOR THE PAST 1.5 YEARS. IT HAS NEVER LET MY DOWN. ALWAYS GENERATE REPRODUCIBLE RESULTS. I CAN HIGHLY DEPEND ON IT, EVEN BETTER THAN MY USED CAR! MM From: IN%"FORSDYKE@QUCDN.QueensU.CA" 27-OCT-1994 17:24:13.03 To: IN%"rapd@net.bio.net" CC: Subj: RE: MJ-Research cyclers After 11 months of use our MJ heat-pump just collapsed. But it worked very nicely before then. From: IN%"harry@liverpool.ac.uk" "Mr H.A. Noyes" 1-NOV-1994 17:30:43.31 To: IN%"V226UHBQ@ubvms.cc.buffalo.edu" CC: Subj: RE: PCR Machines Here in Britain PE have a special offer on of two for the price of one. That would be enough for me as they are very sound machines. I also use the Hybaid Omnigene, that is fan cooled and therefore does not go to below ten degrees above ambient but is a more flexible machine taking 96 well plates and 500ul tubes on the same block as well as other alternatives. It is also cheaper than the PE. All the best Harry Noyes at Liverpool School of Tropical Medicine From owner-rapd@net.bio.net Sun Nov 06 22:00:00 1994 Path: biosci!YVAX.BYU.EDU!FARMERJ From: FARMERJ@YVAX.BYU.EDU Newsgroups: bionet.molbio.rapd Subject: Other sources of molecular marker information Date: 7 Nov 1994 09:31:10 -0800 Organization: Brigham Young University Lines: 34 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HJ70QWWP7S95OK0L@yvax.byu.edu> NNTP-Posting-Host: net.bio.net I received only one response to my query about newsgroups/mailing lists which concentrate on molecular markers and primers for particular species or higher level taxonomic categories. ----------------------------------------------- This group covers any DNA related protocols/discoveries/PCR primers of relevance to any and all molluscs. (Thanks to Craig Wilding) molluscs@net.bio.net ---------------------------------------------- The other group of which I am aware is devoted to molecular markers and primers in insects. bug-net@sfu.ca I believe that you can get subscription information from Bernie Crespi at crespi@crespi@sfu.ca ----------------------------------------------- James L. Farmer Department of Zoology 571 WIDB Brigham Young University Provo, Utah 84602, USA (801) 378-2153 (voice, phone mail) (801) 378-7499 (FAX) FARMERJ@YVAX.BYU.EDU From owner-rapd@net.bio.net Sun Nov 06 22:00:00 1994 Path: biosci!IPST.EDU!Mike.Wood From: Mike.Wood@IPST.EDU Newsgroups: bionet.molbio.rapd Subject: (none) Date: 7 Nov 1994 11:25:05 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: <51910.mwood@pop.ipst.edu> NNTP-Posting-Host: net.bio.net I would like to be included in the RAPD newsgroup. Thanks From owner-rapd@net.bio.net Mon Nov 07 22:00:00 1994 Path: biosci!YVAX.BYU.EDU!FARMERJ From: FARMERJ@YVAX.BYU.EDU Newsgroups: bionet.molbio.rapd Subject: RE:Other sources of molecular marker information Date: 8 Nov 1994 10:13:08 -0800 Organization: Brigham Young University Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HJ8GH33ETE95OM06@yvax.byu.edu> NNTP-Posting-Host: net.bio.net I apologize for my university's text editor. The information address for bug-net should be (obviously) crespi@sfu.ca. Sorry. Jim Farmerz From owner-rapd@net.bio.net Wed Nov 09 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!howland.reston.ans.net!torn!nermal.cs.uoguelph.ca!gadwall.cs.uoguelph.ca!mlagace From: mlagace@uoguelph.ca (Mark C Lagace) Newsgroups: bionet.molbio.rapd Subject: Has anyone cloned a RAPD band? Date: 10 Nov 1994 14:51:54 GMT Organization: University of Guelph Lines: 14 Message-ID: <39tc2a$s40@nermal.cs.uoguelph.ca> NNTP-Posting-Host: gadwall.cs.uoguelph.ca X-Newsreader: TIN [version 1.2 PL2] I am trying to clone a RAPD band and was wondering if anyone had experience with this. More specifically I was wondering what cloning vector would be suited to this purpose. An article reference would be ideal. Thanks for any help you can offer. Mark. -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- I think the surest sign that | Mark Lagace intelligent life exists else- | Molecular Biology + Genetics where in the universe is that | University of Guelph none of it has tried to contact | Guelph, Ontario, Canada us. -- Calvin (and Hobbes) | mlagace@uoguelph.ca -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From owner-rapd@net.bio.net Wed Nov 09 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!grapevine.lcs.mit.edu!uhog.mit.edu!europa.eng.gtefsd.com!news.umbc.edu!haven.umd.edu!purdue!gatech!howland.reston.ans.net!nctuccca.edu.tw!netnews.ntu.edu.tw!news From: khwu@ccms.ntu.edu.tw (Kae-kang Hwu) Newsgroups: bionet.molbio.rapd Subject: Better separation medium Date: Thu, 10 Nov 94 08:53:47 MST Organization: National Taiwan Univ. Lines: 36 Message-ID: <39rri7$i8r@netnews.ntu.edu.tw> NNTP-Posting-Host: @140.112.74.1 Mime-Version: 1.0 X-Newsreader: WinVN 0.93.02 Hi All, Has anybody been using SynerGel to separate RAPD products? We are looking for a better separation medium than NewSieve 3:1, and no polyacrylamide please. We have been working on one major band in our RAPD analysis of watermelon for more than two weeks. Today we fond out in horror today that it is actually composed of two very close bands. We regularly use NewSieve 3:1 for gel electrophoresis. The separation was usually satisfying but today's run was exceptionally well (judging from the sharpness of markers). However, the two bands in question can only be distinguished in 5 of the total 6 samples still. First we thought that after 2 times of re-amplification, the slightly shorter band was a product of mismatch near the priming site. But restriction digests reveled that they are indeed two different sequences. So these two bands were there from the beginning. Checking with earlier photo records than we noticed that 'this band' did look to be a little wider then others in the similar molecular weight range. This finding brings out a horrifying question: Are those major bands in our analysis all composed of more than one bands? We have to re-exam some of those to clarify this potential disaster, but we are certainly happy that we caught this one before starting sequence them. So, any body care to comment? =========================================== Kae-kang Hwu Dept. of Agronomy National Taiwan Univ. ============================================ From owner-rapd@net.bio.net Wed Nov 09 22:00:00 1994 Newsgroups: bionet.molbio.rapd Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!vixen.cso.uiuc.edu!newsfeed.ksu.ksu.edu!moe.ksu.ksu.edu!osuunx.ucc.okstate.edu!David.Demezas From: demed@vms.ucc.okstate.edu. (David Demezas) Subject: Re: Better separation medium Message-ID: X-Posted-From: InterNews 1.0@osuunx.ucc.okstate.edu. Lines: 9 Sender: -Not-Authenticated-[4455] Nntp-Posting-Host: lse421-1.microb.okstate.edu Organization: Oklahoma State University, Stillwater OK References: <39rri7$i8r@netnews.ntu.edu.tw> Date: Thu, 10 Nov 1994 19:00:27 GMT Xdisclaimer: No attempt was made to authenticate the sender's name. Kae-Kang, we have been using FMC's Metaphor agarose. FMC claims very good resolution for small products. We have found this so in our hands as well. I would suggest that you call your FMC supplier and see if you can get a sample to try it out. ============================== David Demezas Demed@vms.ucc.okstate.edu. ============================== From owner-rapd@net.bio.net Thu Nov 10 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: "Renato Fani" Newsgroups: bionet.molbio.rapd Subject: RE: Has anyone cloned a RAPD band? Date: 11 Nov 1994 12:36:05 -0000 Lines: 38 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <39vofl$i8s@mserv1.dl.ac.uk> Reply-To: dibagef1@idg.fi.cnr.it X-Nupop-Charset: English Original-To: rapd@dl.ac.uk In message 10 Nov 1994 14:51:54 GMT, mlagace@uoguelph.ca (Mark C Lagace) writes: > I am trying to clone a RAPD band and was wondering if anyone had > experience with this. More specifically I was wondering what cloning > vector would be suited to this purpose. An article reference would be > ideal. Thanks for any help you can offer. > > Mark. > > -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- > I think the surest sign that | Mark Lagace > intelligent life exists else- | Molecular Biology + Genetics > where in the universe is that | University of Guelph > none of it has tried to contact | Guelph, Ontario, Canada > us. -- Calvin (and Hobbes) | mlagace@uoguelph.ca > -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- > Mark, We have cloned and sequenced some RAPD markers from the nitrogen fixing bacterium Azospirillum brasilense. You can find all the informations dealing with the cloning strategy and the plasmid(s) used in the following paper by Fani et al published last year in Mol. Ecology 2, 243-250: "Use of the Random amplified polymorphic DNA (RAPD) for generating specific DNA probes for microorganisms". Best regards and good luck. Renato ------------------------------------------------------- Renato Fani Dipartimento di Biologia Animale e Genetica "Leo Pardi" Universita' degli Studi di Firenze via Romana 17 I-50125 Firenze, Italy Phone: +39 55 220498 Fax: +39 55 222565 ------------------------------------------------------- From owner-rapd@net.bio.net Thu Nov 10 22:00:00 1994 Path: biosci!ns1.faseb.org!darwin.sura.net!mother.usf.edu!com1!jpaciga From: jpaciga@com1.med.usf.edu (June Paciga) Newsgroups: bionet.molbio.rapd Subject: Re: Better separation medium Date: 10 Nov 1994 17:58:09 GMT Organization: University of South Florida Lines: 44 Message-ID: <39tmvi$a62@mother.usf.edu> References: <39rri7$i8r@netnews.ntu.edu.tw> NNTP-Posting-Host: com1.med.usf.edu X-Newsreader: TIN [version 1.2 PL2] Kae-kang Hwu (khwu@ccms.ntu.edu.tw) wrote: : Hi All, : Has anybody been using SynerGel to separate RAPD : products? We are looking for a better separation medium : than NewSieve 3:1, and no polyacrylamide please. : We have been working on one major band in our RAPD : analysis of watermelon for more than two weeks. Today we : fond out in horror today that it is actually composed of two : very close bands. We regularly use NewSieve 3:1 for gel : electrophoresis. The separation was usually satisfying but : today's run was exceptionally well (judging from the : sharpness of markers). However, the two bands in question : can only be distinguished in 5 of the total 6 samples still. : First we thought that after 2 times of re-amplification, the : slightly shorter band was a product of mismatch near the : priming site. But restriction digests reveled that they are : indeed two different sequences. So these two bands were : there from the beginning. Checking with earlier photo : records than we noticed that 'this band' did look to be a little : wider then others in the similar molecular weight range. This : finding brings out a horrifying question: Are those major : bands in our analysis all composed of more than one bands? : We have to re-exam some of those to clarify this potential : disaster, but we are certainly happy that we caught this one : before starting sequence them. : So, any body care to comment? : =========================================== : Kae-kang Hwu : Dept. of Agronomy : National Taiwan Univ. : ============================================ Try using FMC's MetaPhor agarose. I have been using it for ddrt/pcr products. It is supposedly capable of separating products differing in size by 2%. June Eva Paciga Dept. Pathology Univ. So. Florida Tampa From owner-rapd@net.bio.net Thu Nov 10 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: "Renato Fani" Newsgroups: bionet.molbio.rapd Subject: RE: Has anyone cloned a RAPD band? Date: 11 Nov 1994 12:22:34 -0000 Lines: 38 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <39vnma$hjk@mserv1.dl.ac.uk> Reply-To: dibagef1@idg.fi.cnr.it X-Nupop-Charset: English Original-To: rapd@dl.ac.uk In message 10 Nov 1994 14:51:54 GMT, mlagace@uoguelph.ca (Mark C Lagace) writes: > I am trying to clone a RAPD band and was wondering if anyone had > experience with this. More specifically I was wondering what cloning > vector would be suited to this purpose. An article reference would be > ideal. Thanks for any help you can offer. > > Mark. > > -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- > I think the surest sign that | Mark Lagace > intelligent life exists else- | Molecular Biology + Genetics > where in the universe is that | University of Guelph > none of it has tried to contact | Guelph, Ontario, Canada > us. -- Calvin (and Hobbes) | mlagace@uoguelph.ca > -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- > Mark, We have cloned and sequenced some RAPD markers from the nitrogen fixing bacterium Azospirillum brasilense. You can find all the informations dealing with the cloning strategy and the plasmid(s) used in the following paper by Fani et al published last year in Mol. Ecology 2, 243-250: "Use of the Random amplified polymorphic DNA (RAPD) for generating specific DNA probes for microorganisms". Best regards and good luck. Renato ------------------------------------------------------- Renato Fani Dipartimento di Biologia Animale e Genetica "Leo Pardi" Universita' degli Studi di Firenze via Romana 17 I-50125 Firenze, Italy Phone: +39 55 220498 Fax: +39 55 222565 ------------------------------------------------------- From owner-rapd@net.bio.net Tue Nov 15 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!grapevine.lcs.mit.edu!uhog.mit.edu!sgiblab!swrinde!gatech!newsxfer.itd.umich.edu!emuvax!bio_hannan From: bio_hannan@emuvax.emich.edu Newsgroups: bionet.molbio.rapd Subject: Message-ID: <1994Nov16.000234.3061@emuvax.emich.edu> Date: 16 Nov 94 00:02:34 EST Organization: EASTERN MICHIGAN University Lines: 28 Ok, here goes. Has _anyone_ really ever figured out why their RAPD amplifications mysteriously stop working for periods of time (days to weeks) while trying new batches of everythinkg imaginable?? We have had about four bouts of amplification failures in the last year or so and we have never come up with a very satisfying explanation for it. We end up saying "well, it's working again. Let's not worry about why it stopped and concentrate on generating data until it stops again." I know from talking to many other people doing RAPDs that it happens to everyone at some time. Yes, we have tried new Taq, different dNTPs, new 10x buffer, new MgCl, water from other sources, checking pipetter calibration, different 500uL tubes, another Coy50 (I know, I know), glycerol instead of mineral oil in wells, different positive control templates (that have worked well in the past), PCR of other tmeplates with known primers, different mineral oil ovelay (that has worked in past- although we are now forced to use a new batch that we found to work once while trying to sort out our amp. problems). Taq, dNTPs, 10x buffer, MgCl all Perkin-Elmer. Any words of wisdom would help alleviate much frustration lately. Thanks Gary Hannan Bio_hannan@emuvax.emich.edu From owner-rapd@net.bio.net Tue Nov 15 22:00:00 1994 Newsgroups: bionet.molbio.rapd Path: biosci!agate!hilbert.dnai.com!nic.scruz.net!cruzio!agaricus From: agaricus@cruzio.com Subject: DEAD? Reply-To: agaricus@cruzio.com Organization: Cruzio Community Networking System, Santa Cruz, CA Date: Wed, 16 Nov 1994 21:04:48 GMT Message-ID: Keywords: Anyone out there Sender: agaricus@cruzio.com (Erik Legg) Lines: 7 Is this group dead, or is it the technique which has died? -- ------------------------------------------------------------------------------- "Mushrooms have genes?!" Erik Legg phone 408 728 8321 Amycel/SpawnMate Biotechnical Group fax 408 728 8385 From owner-rapd@net.bio.net Tue Nov 15 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!grapevine.lcs.mit.edu!uhog.mit.edu!sgiblab!swrinde!gatech!newsxfer.itd.umich.edu!emuvax!bio_hannan From: bio_hannan@emuvax.emich.edu Newsgroups: bionet.molbio.rapd Subject: No amp. Why??? Message-ID: <1994Nov16.000400.3062@emuvax.emich.edu> Date: 16 Nov 94 00:03:59 EST Organization: EASTERN MICHIGAN University Lines: 5 Sorry for the lack of subject in my first post- still learning the ropes of our news reader. Gary Hannan From owner-rapd@net.bio.net Wed Nov 16 22:00:00 1994 Newsgroups: bionet.molbio.rapd Path: biosci!bloom-beacon.mit.edu!gatech!newsxfer.itd.umich.edu!zip.eecs.umich.edu!umn.edu!news From: "austi012@gold.tc.umn.edu" Subject: Viruses/DNA/Cancer To: austi012@gold.tc.umn.edu Message-ID: <50111.austi012@gold.tc.umn.edu> X-Minuet-Version: Minuet1.0_Beta_16 Sender: news@news.cis.umn.edu (Usenet News Administration) Nntp-Posting-Host: dialup-5-93.gw.umn.edu X-Popmail-Charset: English Organization: University of Minnesota, Twin Cities Date: Wed, 16 Nov 1994 16:11:36 GMT Lines: 43 What follows are questions and a line of reasoning. (1) Can or will a given virus enter/invade a cell that has already been invaded by one of the virus' sisters? If not, has the first virus somehow coded the surface of the infected cell so as to discourage further infiltrations? (2) Every cell's DNA coding has many miles of code that does nothing. Included in the DNA chain are 'switches' that tell the cell not to read or act on the code, although it is replicated when the cell reproduces. Where does this extra coding come from? (a) We know that, in general, viruses reproduce by attaching thier own genetic material to the cells and thereby forcing the cell to use its machinery to replicate many more viruses. Is it possible that some of the 'extra' coding in cells is DNA that was injected into the cell or its predecessor by a virus, incorporated into the cell's DNA coding, and then switched off by the cell (as a defense mechanism) with one of the "Do not read" switches mentioned above? (b) Additionally, if (1) and (2a) are correct, could not the cell be using the virus as a means of shutting down infiltration by sister viruses? That is, having incorporated the virus into its own DNA and having rendered the virus coding impotent with the "off" switch, could not the cell and its successors use the virus' own "do not invade' coding to ward off sister virus infiltrations? Alternatively, another approach: the cell, having incorporated the virus' coding, and rendered it impotent with the "off" switch, reads the virus and uses it as a comparison piece-- as part of a defense strategem against viruses that attempt to infiltrate-- in much the same way as the virus program my computer uses. That is, when a virus similar to one already incorporated attemptsto infiltrate the cell, the cell is able somehow to recognize the virus and deny it venue. (3) A possible cause of cancers: faulty "off" switches. The incorporated viral coding is left in a partly "on" state, and that coding forces the cell to replicate out of control. Thanks for reading this post. If anybody would like to respond to me, I'll look forward to reading same. Thaddeus Austin Imagine a witty quote here: virtual humor! austi012@gold.tc.umn.edu From owner-rapd@net.bio.net Thu Nov 17 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!newsxfer.itd.umich.edu!jobone!lynx.unm.edu!pegasus.unm.edu!not-for-mail From: dkim@unm.edu Newsgroups: bionet.molbio.rapd Subject: Re: Viruses/DNA/Cancer Date: 18 Nov 1994 09:14:24 -0700 Organization: University of New Mexico, Albuquerque Lines: 65 Sender: dkim@triton.unm.edu Message-ID: <3aijt0$42so@pegasus.unm.edu> References: <50111.austi012@gold.tc.umn.edu> NNTP-Posting-Host: pegasus.unm.edu Hello: WRT two viruses in one cell: There is the case of suppressor genes in bacteriophages which prevent a phage from successfully infecting a bacterium already harboring another phage. This is the basis for some recombinant selection strategies in lambda phage cloning (for instance, the EMBL3 phage has a sequence in its "insert" region that prevents nonrecombinant phage from infecting a particular host which is already harboring a prophage in its genome. If the "insert" region is replaced by a recombinant sequence, then that phage can infect.). This suppression may not exist, or may have exceptions in other viruses. WRT viral sequences incorporated into genomes: This does happen. One well-known case is the virus-like sequence found in rodents called "VL-30". It has many of the structural elements of a retrovirus provirus, including long terminal repeat (LTR) elements that contain growth hormone-responsive enhancer elements. The VL-30 is so old that its genes are no longer functional. It no longer has the ability to replicate itself as an RNA virus, nor can it encode viral proteins such as reverse transcriptase or coat proteins. Other viral sequences of this type have been found and characterized, but I am not familiar with them. WRT provirus-induced immunity: I don't know of anything like this in mammalian systems. Plants have something like this (recently reviewed in _The Plant Cell_) that uses the unusual plant property of "sense suppression". In sense suppression, if a plant has some active gene in its own genome, and a similar gene is introduced (by transfection/transformation in the lab, for instance), the plant will inactivate the expression of both genes. The mechanism is unknown. Using this phenomenon, it is possible, in some cases, to make a plant "immune" to viral infection by previously transfecting it with an essential viral gene. When the virus infects, its own gene will be suppressed. WRT virus-induced cancer: This does happen in a way. RNA viruses (retroviruses) in mammalian cells contain enhancer elements ("on"-switches) in their LTRs that respond to growth factors and growth-related transcriptional activating proteins. One good example is the "AP-1" site, which is bound by the fos/jun complex (AP-1) and stimulates gene expression in a nearby gene. By having these elements, retroviral genes are activated by cell growth. If a provirus inserts itself close to some growth-stimulating gene, the proximity of LTR-enhancers or of the viral promoters themselves may cause the cellular gene to be activated inappropriately, stimulating the cell into a growth cycle. I think the mouse mammary tumor virus (MMTV) may work in this way, preferentially incorporating close to a mouse mammary growth gene. In addition, parts of growth-related genes can be accidentally incorporated into the viral genome, thus falling under the control of viral transcription. The expression of these genes during the viral life cycle can cause a cell to enter a growth phase. This is the basis of the "oncogene" concept, which was first(?) characterized in the avian "src" gene. I hope this was helpful. I believe I am at least 89% correct in what I wrote. Daniel Kim dkim@triton.unm.edu From owner-rapd@net.bio.net Sun Nov 20 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!howland.reston.ans.net!swrinde!pipex!sunic!trane.uninett.no!daresbury!not-for-mail From: fernley.symons@st-hughs.oxford.ac.uk Newsgroups: bionet.molbio.rapd Subject: Lepidoptera RAPDs Date: 21 Nov 1994 17:38:46 -0000 Lines: 19 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3aqlv6$4i7@mserv1.dl.ac.uk> Original-Sender: fernley.symons@uk.ac.oxford.st-hughs Original-To: rapd@dl.ac.uk Hi, folks I'm interested in doing RAPD on Leps (genus *Papilio*). I'm hoping to get enough markers for both intra- and inter- population work. Jim Mallet and his Lep. group at University college, London have advised me against RAPDs as they've had difficulties with them. Wonder if anyone else would like to comment? Is anyone else out there looking at Leps? How about this Dutch company's a-RAPD system - guess it's much more expensive but might it solve my marker problem for me? If I could get the things to work it'd be great as I'm likely to have v. limited funds/time. RAPD seems to offer the best system for what I want to do. TIA for any suggestions and/or contacts in the field FERNLEY SYMONS (fernley.symons@st-hughs.ox.ac.uk) From owner-rapd@net.bio.net Mon Nov 21 22:00:00 1994 Path: biosci!esvax.dnet.dupont.com!vogeljm From: vogeljm@esvax.dnet.dupont.com (Julie Vogel) Newsgroups: bionet.molbio.rapd Subject: (none) Date: 22 Nov 1994 12:43:25 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: <9411222043.AA05050@esds01.es.dupont.com> NNTP-Posting-Host: net.bio.net subscribe RAPD From owner-rapd@net.bio.net Tue Nov 22 22:00:00 1994 Path: biosci!MERCURY.UARK.EDU!DRHOADS From: DRHOADS@MERCURY.UARK.EDU ("Douglas Rhoads") Newsgroups: bionet.molbio.rapd Subject: Re: Stratagen Taq Extender Date: 23 Nov 1994 05:57:44 -0800 Organization: University of Arkansas Lines: 24 Sender: daemon@net.bio.net Distribution: world Message-ID: <19EBB2C5905@uamercury.uark.edu> NNTP-Posting-Host: net.bio.net > To: rapd@net.bio.net > From: krutovskiik@fsl.orst.edu (Konstantin Krutovskii) > Subject: Stratagen Taq Extender > Date: Tue, 22 Nov 1994 19:32:28 > Stratagen recently introduced very effective PCR-enhancement reagent, Taq > Extender PCR additive (see Nielson et al., 1994: Strategies 7: 26 or 7:64). > We use it in the same amount per reaction as Taq. It really improves the > amplification of different templates and increases the yield of many PCRs > (especially for long products). I hope it would be interesting for RAPD folks > who got headache with difficult templates. > > Kostya But will Taq extender work under RAPD conditions?? Has anyone tried? Some enzyme preps of Taq contain lots of contaminating fragmented DNAs that generate smears under RAPD conditions with most primers and no additional input template DNA. We have measured as high as 300ng/ul DNA in some commercial preps of Taq Pol. 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 Tue Nov 22 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!uhog.mit.edu!europa.eng.gtefsd.com!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!gaia.ucs.orst.edu!sslab.FSL.ORST.EDU!krutovskiik From: krutovskiik@fsl.orst.edu (Konstantin Krutovskii) Newsgroups: bionet.molbio.rapd Subject: Stratagen Taq Extender Date: Tue, 22 Nov 1994 19:32:28 Organization: fsl.orst.edu Lines: 8 Message-ID: NNTP-Posting-Host: sslab.fsl.orst.edu Keywords: Stratagen Taq Extender X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Stratagen recently introduced very effective PCR-enhancement reagent, Taq Extender PCR additive (see Nielson et al., 1994: Strategies 7: 26 or 7:64). We use it in the same amount per reaction as Taq. It really improves the amplification of different templates and increases the yield of many PCRs (especially for long products). I hope it would be interesting for RAPD folks who got headache with difficult templates. Kostya From owner-rapd@net.bio.net Wed Nov 23 22:00:00 1994 Path: biosci!PIRA.CENA.USP.BR!DAVHMOON From: DAVHMOON@PIRA.CENA.USP.BR Newsgroups: bionet.molbio.rapd Subject: microsatellites Date: 24 Nov 1994 10:47:17 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Netters, I am looking for the sequences of micro satellite repeats. Has any one seen any reviews or publications with lists of the repeat sequences. I would be pleased to receive any information on this subject. Thanks in advance David H. Moon From owner-rapd@net.bio.net Thu Nov 24 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: Newsgroups: bionet.molbio.rapd Subject: re: microsatellites Date: 25 Nov 1994 11:26:27 -0000 Lines: 5 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3b4hl3$25s@mserv1.dl.ac.uk> Original-To: rapd@dl.ac.uk e.g.: GCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGC Why is anyone interested in a microsatellite sequence? K. Louis From owner-rapd@net.bio.net Thu Nov 24 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!uhog.mit.edu!europa.eng.gtefsd.com!newsxfer.itd.umich.edu!nntp.cs.ubc.ca!alberta!quartz.ucs.ualberta.ca!news From: mhicks@gpu.srv.ualberta.ca (Mark Hicks - Genetics Group/University of Alberta) Newsgroups: bionet.molbio.rapd Subject: re: microsatellites Date: 25 Nov 1994 17:32:02 GMT Organization: Dept. of Biology/University of Alberta Lines: 28 Message-ID: <3b572i$666@quartz.ucs.ualberta.ca> References: <3b4hl3$25s@mserv1.dl.ac.uk> Reply-To: mhicks@gpu.srv.ualberta NNTP-Posting-Host: dna.biology.ualberta.ca X-Newsreader: WinVN 0.92.6 In article <3b4hl3$25s@mserv1.dl.ac.uk>, says: > > >e.g.: GCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGC > >Why is anyone interested in a microsatellite sequence? >K. Louis K. Louis I'm interested in microsatellites because I will be using them to quantify genetic variation in lodgepole pine. They are easy to use because they are small enough to allow them to be PCRed. As a result once a microsatellite sequence has been located it makes it very easy to look at biodiversity and phylogenetic relationships. Your microsatellite lover, *********************************************************************************** Mark Hicks * * Dept. of Genetics * /*\ <- lodgepole pine University of Alberta * /***\ Edmonton, Alberta * /*****\ my favorite tree. CANADA * * e-mail: mhicks@gpu.srv.ualberta.ca * * ************************************************************************************* From owner-rapd@net.bio.net Sun Nov 27 22:00:00 1994 Path: biosci!ccmail.orst.edu!krutovsk From: krutovsk@ccmail.orst.edu Newsgroups: bionet.molbio.rapd Subject: Re[2]: Stratagen Taq Extender Date: 27 Nov 1994 23:32:57 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 56 Sender: daemon@net.bio.net Distribution: world Message-ID: <9410277860.AA786007881@ccmail.orst.edu> NNTP-Posting-Host: net.bio.net Received: by ccmail from ccmbox1.ucs.orst.edu From DRHOADS@mercury.uark.edu X-Envelope-From: DRHOADS@mercury.uark.edu Received: from cornus.FSL.ORST.EDU (root@FSL.ORST.EDU [128.193.112.105]) by ccmbo x1.ucs.orst.edu (8.6.9/8.6.9) with ESMTP id FAA02105 for ; Wed, 23 Nov 1994 05:57:45 -0800 Received: from wizard.uark.edu (wizard.uark.edu [130.184.7.93]) by cornus.FSL.ORS T.EDU (8.6.9/8.6.9) with SMTP id FAA07589 for ; Wed, 23 Nov 1994 05:57:43 -0800 Received: from uamercury.uark.edu by wizard.uark.edu with SMTP (1.37.109.4/15.6) id AA06478; Wed, 23 Nov 94 07:57:34 -0600 Received: from MERCURY/MERCURY by uamercury.uark.edu (Mercury 1.13); Wed, 23 Nov 94 7:57:25 GMT-6 Received: from MERCURY by MERCURY (Mercury 1.13); Wed, 23 Nov 94 7:56:55 GMT-6 From: "Douglas Rhoads" Organization: University of Arkansas To: rapd@net.bio.net, krutovskiik@fsl.orst.edu (Konstantin Krutovskii) Date: Wed, 23 Nov 1994 07:56:53 CST Subject: Re: Stratagen Taq Extender Priority: normal X-Mailer: Pegasus Mail/Windows (v1.11a) Message-Id: <19EBB2C5905@uamercury.uark.edu> > To: rapd@net.bio.net > From: krutovskiik@fsl.orst.edu (Konstantin Krutovskii) > Subject: Stratagen Taq Extender > Date: Tue, 22 Nov 1994 19:32:28 > Stratagen recently introduced very effective PCR-enhancement reagent, Taq > Extender PCR additive (see Nielson et al., 1994: Strategies 7: 26 or 7:64). > We use it in the same amount per reaction as Taq. It really improves the > amplification of different templates and increases the yield of many PCRs > (especially for long products). I hope it would be interesting for RAPD folks > who got headache with difficult templates. > > Kostya But will Taq extender work under RAPD conditions?? Has anyone tried? Actually, we use it for RAPD and it works. Some enzyme preps of Taq contain lots of contaminating fragmented DNAs that generate smears under RAPD conditions with most primers and no additional input template DNA. We have measured as high as 300ng/ul DNA in some commercial preps of Taq Pol. I would not disagree, but this is another point and has nothing to do with Taq extender. Kostya 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 Mon Nov 28 22:00:00 1994 Path: biosci!vt.edu!fishgen From: fishgen@vt.edu (Bruce J. Turner) Newsgroups: bionet.molbio.rapd Subject: "FSCP" Help! Date: 29 Nov 1994 08:51:28 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <199411291651.IAA00612@net.bio.net> NNTP-Posting-Host: net.bio.net I thought I was fairly up-t0--date on acronyms, but I need help figuring out what "FSCP" is and finding a good reference to the technique. An anonymous reviewer of a grant proposal suggested that I use this technique to find noncanonical monomer satellite DNA variants rather than brute force cloning and sequencing, but he/shge failed to define or reference the technique. I would suppose that the "F" and the "S" stand for "flanking sequences" or some such, but amy mystified by the rest. Any hints would be much appreciated. From owner-rapd@net.bio.net Mon Nov 28 22:00:00 1994 Path: biosci!DARWIN.EEB.UCONN.EDU!kent From: kent@DARWIN.EEB.UCONN.EDU (Kent Holsinger) Newsgroups: bionet.molbio.rapd Subject: Re: "FSCP" Help! Date: 29 Nov 1994 10:47:14 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: <9411291847.AA15999@darwin.eeb.uconn.edu> References: <199411291651.IAA00612@net.bio.net> NNTP-Posting-Host: net.bio.net >>>>> "Bruce" == Bruce J Turner writes: Bruce> I thought I was fairly up-t0--date on acronyms, but I need Bruce> help figuring out what "FSCP" is and finding a good Bruce> reference to the technique. An anonymous reviewer of a Bruce> grant proposal suggested that I use this technique to find Bruce> noncanonical monomer satellite DNA variants rather than Bruce> brute force cloning and sequencing, but he/shge failed to Bruce> define or reference the technique. I would suppose that Bruce> the "F" and the "S" stand for "flanking sequences" or some Bruce> such, but amy mystified by the rest. Any hints would be Bruce> much appreciated. Is it possible that the reviewer meant SSCP (single-strand sequence conformation polymorphism, or something like that)? If so, I can dig up some references. If not, I have no idea. -- Kent +------------------------------------------------------------------------+ | Kent E. Holsinger Internet: Kent@Darwin.EEB.UConn.Edu | | Department of Ecology & Holsinge@UConnVM.UConn.Edu | | Evolutionary Biology BITNET: Holsinge@UConnVM | | University of Connecticut, U-43 | | Storrs, CT 06269-3043 | +------------------------------------------------------------------------+ From owner-rapd@net.bio.net Mon Nov 28 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!sunic!umdac!news From: Xiao-Ru.Wang@genfys.slu.se (Xiao-Ru.Wang) Newsgroups: bionet.molbio.rapd Subject: re: microsatellites Date: 29 Nov 1994 15:55:51 GMT Organization: SLU, Umeå Lines: 8 Message-ID: <3bfiu7$cj3@kitten.umdc.umu.se> References: <3b4hl3$25s@mserv1.dl.ac.uk> <3b572i$666@quartz.ucs.ualberta.ca> NNTP-Posting-Host: sko212.genfys.slu.se X-Newsreader: WinVN 0.92.1 >Your microsatellite lover, Hi Mark, Have you found any microsatellite sequences in logipole pine? Xiao-Ru Wang From owner-rapd@net.bio.net Tue Nov 29 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!uunet!jabba.fdn.org!jussieu.fr!univ-lyon1.fr!serra.unipi.it!sirio.cineca.it!eagle!villa From: villa@eagle.bio.unipr.it (Ferdinando Villa) Newsgroups: bionet.molbio.rapd Subject: HELP - Ethidium Bromide contamination Date: 30 Nov 1994 15:45:46 GMT Organization: Cineca Lines: 27 Message-ID: <3bi6na$ofj@sirio.cineca.it> NNTP-Posting-Host: eagle.bio.unipr.it X-Newsreader: TIN [version 1.2 PL0] Hello, I need urgent advice. A friend working in our lab got contaminated with diluted (1ml in 1l water) ethidium bromide (a single finger got wet with the solution, because of a hole in the glove). She washed her hands after a minute or so, when she realized the problem, with water and soap. No trace of remaining ethidium was shown under UV light on her finger. We need to know urgently which controls she should carry out after that. The security instruction refer to the following book: Sambrook et al, "Molecular Cloning, A Lab Manual", Cold Spring Harbor labs 1989. As we don't own the book and would take some time ordering it, we would be most grateful to anyone who cares to give any advice on what to do. With best wishes and thanks in advance, Ferdinando Villa -- Ferdinando Villa, Ph.D. Institute of Ecology Direct phone: +39-521-905615 University of Parma FAX: +39-521-905402 Viale delle Scienze Home phone (voice mail): +39-521-604013 43100 Parma, Italy e.mail: villa@eagle.bio.unipr.it From owner-rapd@net.bio.net Wed Nov 30 22:00:00 1994 Path: biosci!PBS.DFO.CA!"PBS::NELSONJ" From: "PBS::NELSONJ"@PBS.DFO.CA Newsgroups: bionet.molbio.rapd Subject: fuzzy pcr Date: 1 Dec 1994 15:38:58 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <941201153921.20e00c04@PBS.DFO.CA> NNTP-Posting-Host: net.bio.net Hi, I am doing microsatellite amplification from genomic dna and I find for one of the microsatellites I'm amplifying the bands (around 100-200 bp) always seem to be fuzzy on a 3% nusieve/1% BRL gel. I don't think it is the gel as the marker looks ok and other microsatelites amplified of approx this size amplify up as more distinct bands. Any ideas out there on this? John nelsonj@pbs.dfo.ca From owner-rapd@net.bio.net Wed Nov 30 22:00:00 1994 Path: biosci!PBS.DFO.CA!"PBS::NELSONJ" From: "PBS::NELSONJ"@PBS.DFO.CA Newsgroups: bionet.molbio.rapd Subject: Rene Guyomard's address Date: 1 Dec 1994 15:25:53 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <941201152609.20e00bba@PBS.DFO.CA> NNTP-Posting-Host: net.bio.net Hello, Does anyone out the have Rene Guyomard's (Laboratoire de Biologie et Genetique Evolutives, CNRS) email address or phone number? Thanks, John Nelson nelsonj@pbs.dfo.ca