From owner-rapd@net.bio.net Sun Oct 02 23:00:00 1994 Path: biosci!UNAMVM1.DGSCA.UNAM.MX!carvalho From: carvalho@UNAMVM1.DGSCA.UNAM.MX (Carvalho Torres Alexandro cassio-UACPYP) Newsgroups: bionet.molbio.rapd Subject: Re: Sequencing PCR product Date: 3 Oct 1994 16:30:28 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 67 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net On 23 Sep 1994, Stephen A. Karl wrote: > On Thu, 22 Sep 1994, Christopher J. S. Bolch wrote: > > > I have heard recently that it is possible to sequence PCR products > > directly either by usual means or by cycle sequencing. Is it as simple > > as that or does one need to clone the fragments first? Does sequencing > > of the product directly have any pitfalls or problems? I imagine that > > excess primer could be a problem. > > > > Chris > > > > > We are currently using US Biochemicals PCR Sequenase Sequencing Kit > (Actually, we have ordered the missing enzymes separately and have > "converted" our existing Sequenase V2.0 kits). It uses Exonuclease I to > digest single stranded DNA (i.e. primers) in ~5 microL of PCR amplified > DNA (directly). The free nucleotides (from the exo reaction and the dNTP > added for the PCR) are dephosphorylated with Shrimp alk-Phosphatase and > the resulting DNA is used directly in a standard Sequenase reaction. In > addition, we have been using AT Biochem (1-800-282-4626) Long Ranger Gel > solution under standard conditions (i.e. NOT glycerol tolerant - the new > Sequenase protocol has the Sequenase and Pyrophos. enzymes mixed in a > glycerol buffer and suggests that a glycerol tolerant gel be used). We > have tried both the standard Sequenase labeling and a modified 3 nt > labeling approach when the sequence just after the primer is known > (details are available in the kit directions or from USB). The 3 nt > techniques seems to give better results but both work well. With the 3 > nt technique we easily get to within 2 nt of the labeled primer. > Although we have only made 3 sequencing attempts (30 independent > reactions) the gels are working very, very well (i.e. easily 300 bp of good > sequence, few if any "hard stops" that are normally observed in PCR > template sequencing, short exposure times with 35S - 2 days on average > and nice even band intensities). > Like everyone, I have tried everything (cycle sequencing, Lambda exo, > standard Sequenase, single stranded amps, spin col. etc) and this is by > far the easiest and BEST (that is results wise) technique that I have > used. Just in case you are now wondering - I do not work for USB (and in > fact have a general dislike and contempt for these companies that are > making so much money from so little work!). > > FYI, > Steve > > > Stephen Karl > Department of Biology > University of South Florida > 4202 East Fowler Ave, LIF 169 > Tampa, Florida 33620-5150 > Voice (813) 974-1592 > Fax (813) 974-3263 > EMail Karl@.chuma.cas.usf.edu > > > > Dear Stephen Karl and rapd investigators, Who have some success in direct sequence rapd bands. What is the most easy protocol or Kit to do a sequence of a rapd band, using a randomic primer? Alexandro Cassio Torres de Carvalho Departamento de Infectologia Instituto Nacional de la Nutricion Salvador Zubiran. Mexico, DF From owner-rapd@net.bio.net Mon Oct 03 23:00:00 1994 Path: biosci!URIACC.URI.EDU!MKI101 From: MKI101@URIACC.URI.EDU ("Marian R. Goldsmith") Newsgroups: bionet.molbio.rapd Subject: merger Date: 4 Oct 1994 03:10:31 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <199410041010.DAA16970@net.bio.net> If the question of merging with the Chromosome Bionet user group is still open, I suggest that people listen in to it for awhile to see if it really covers the same territory as the RAPD group. From the description it sounded to me to be strongly aimed at mammalian systems, which might mean there is a lot of technical or specific info that's not of general interest to this group. Marian R. Goldsmith Dept. of Zoology University of Rhode Island Kingston, RI 02881-0816, USA (401) 792-2637; FAX 792-4256 From owner-rapd@net.bio.net Mon Oct 03 23:00:00 1994 Path: biosci!s.u-tokyo!news.tisn.ad.jp!news.u-tokyo.ac.jp!sinetnews!daffy!uwvax!uwm.edu!news.moneng.mei.com!howland.reston.ans.net!europa.eng.gtefsd.com!uhog.mit.edu!sgiblab!sgigate.sgi.com!enews.sgi.com!decwrl!netcomsv!ix.netcom.com!netnews From: Bhupi@ix.netcom.com (Bhupinder Singh) Newsgroups: bionet.molbio.rapd Subject: Need help: information of plague vaccine Date: 4 Oct 1994 05:51:26 GMT Organization: Netcom Lines: 6 Distribution: world Message-ID: <36qqgu$lm8@ixnews1.ix.netcom.com> NNTP-Posting-Host: ix-sj14-07.ix.netcom.com Due to sudden break in of the plague epidamic in India, there are lot of anxities for demand of vaccine for human plague. Any information regading such vaccine from any agency would help save hundreds of thousands lives. Please get in touch with me as soon as possible. Bhupi Ph.(408) 383-0800 From owner-rapd@net.bio.net Tue Oct 04 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!swrinde!howland.reston.ans.net!swiss.ans.net!nntp.sunbelt.net!udel!news-4.nss.udel.edu!strauss.udel.edu!not-for-mail From: mcdonald@strauss.udel.edu (John H McDonald) Newsgroups: bionet.molbio.rapd Subject: Re: Sequencing PCR product Date: 5 Oct 1994 12:52:16 -0400 Organization: University of Delaware Lines: 23 Message-ID: <36ulk0$27a@strauss.udel.edu> References: NNTP-Posting-Host: strauss.udel.edu In article , Wiggy wrote: > >I have a bit of a problem understanding how you could directly sequence a >RAPD product using the same primers for the PCR and the sequencing because >both of the strands contain the same priming sites. You can not >distinguish in my mind between the two strands when doing the sequencing >reaction. Without cloning how would people do this? You can't use >asymmetric PCR as there is only one primer, nor labelled primers such as >biotin as again the biotinilated primers would be incorporated in both >strands. Am I missing something obvious? When we want to sequence a PCR product with the same primer at both ends, we find a restriction enzyme that cuts it once, gel purify the two fragments, then sequence each one separately. Another possibility is to sequence with primers that are your PCR primer plus one or two more bases at the 3' end, but that could get expensive if you want to sequence a lot of different bands. Or you could clone the fragments, but hey, it's the '90s, who clones anymore? John H. McDonald Department of Biology University of Delaware From owner-rapd@net.bio.net Tue Oct 04 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!library.ucla.edu!europa.eng.gtefsd.com!howland.reston.ans.net!doc.news.pipex.net!pipex!lyra.csx.cam.ac.uk!warwick!bham!bcs88.bham.ac.uk!user From: A.C.Hilton@bham.ac.uk (Wiggy) Newsgroups: bionet.molbio.rapd Subject: Re: Sequencing PCR product Date: 5 Oct 1994 16:23:50 GMT Organization: The University of Birmingham Lines: 79 Distribution: world Message-ID: References: NNTP-Posting-Host: bcs88.bham.ac.uk In article , carvalho@UNAMVM1.DGSCA.UNAM.MX (Carvalho Torres Alexandro cassio-UACPYP) wrote: > On 23 Sep 1994, Stephen A. Karl wrote: > > > On Thu, 22 Sep 1994, Christopher J. S. Bolch wrote: > > > > > I have heard recently that it is possible to sequence PCR products > > > directly either by usual means or by cycle sequencing. Is it as simple > > > as that or does one need to clone the fragments first? Does sequencing > > > of the product directly have any pitfalls or problems? I imagine that > > > excess primer could be a problem. > > > > > > Chris > > > > > > > > We are currently using US Biochemicals PCR Sequenase Sequencing Kit > > (Actually, we have ordered the missing enzymes separately and have > > "converted" our existing Sequenase V2.0 kits). It uses Exonuclease I to > > digest single stranded DNA (i.e. primers) in ~5 microL of PCR amplified > > DNA (directly). The free nucleotides (from the exo reaction and the dNTP > > added for the PCR) are dephosphorylated with Shrimp alk-Phosphatase and > > the resulting DNA is used directly in a standard Sequenase reaction. In > > addition, we have been using AT Biochem (1-800-282-4626) Long Ranger Gel > > solution under standard conditions (i.e. NOT glycerol tolerant - the new > > Sequenase protocol has the Sequenase and Pyrophos. enzymes mixed in a > > glycerol buffer and suggests that a glycerol tolerant gel be used). We > > have tried both the standard Sequenase labeling and a modified 3 nt > > labeling approach when the sequence just after the primer is known > > (details are available in the kit directions or from USB). The 3 nt > > techniques seems to give better results but both work well. With the 3 > > nt technique we easily get to within 2 nt of the labeled primer. > > Although we have only made 3 sequencing attempts (30 independent > > reactions) the gels are working very, very well (i.e. easily 300 bp of good > > sequence, few if any "hard stops" that are normally observed in PCR > > template sequencing, short exposure times with 35S - 2 days on average > > and nice even band intensities). > > Like everyone, I have tried everything (cycle sequencing, Lambda exo, > > standard Sequenase, single stranded amps, spin col. etc) and this is by > > far the easiest and BEST (that is results wise) technique that I have > > used. Just in case you are now wondering - I do not work for USB (and in > > fact have a general dislike and contempt for these companies that are > > making so much money from so little work!). > > > > FYI, > > Steve > > > > > > Stephen Karl > > Department of Biology > > University of South Florida > > 4202 East Fowler Ave, LIF 169 > > Tampa, Florida 33620-5150 > > Voice (813) 974-1592 > > Fax (813) 974-3263 > > EMail Karl@.chuma.cas.usf.edu > > > > > > > > > Dear Stephen Karl and rapd investigators, > Who have some success in direct sequence rapd bands. What is the most > easy protocol or Kit to do a sequence of a rapd band, using a randomic > primer? > Alexandro Cassio Torres de Carvalho > Departamento de Infectologia > Instituto Nacional de la Nutricion Salvador Zubiran. Mexico, DF I have a bit of a problem understanding how you could directly sequence a RAPD product using the same primers for the PCR and the sequencing because both of the strands contain the same priming sites. You can not distinguish in my mind between the two strands when doing the sequencing reaction. Without cloning how would people do this? You can't use asymmetric PCR as there is only one primer, nor labelled primers such as biotin as again the biotinilated primers would be incorporated in both strands. Am I missing something obvious? Wig. From owner-rapd@net.bio.net Tue Oct 04 23:00:00 1994 Path: biosci!CHUMA.CAS.USF.EDU!karl From: karl@CHUMA.CAS.USF.EDU ("Stephen A. Karl") Newsgroups: bionet.molbio.rapd Subject: Re: Sequencing PCR product Date: 5 Oct 1994 10:15:47 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 24 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net To all: Unfortunately there was some confusion (on my part) about the original question about sequencing PCR products. Essentially, it amounts to me not being sensitive to the type of group that this is. I do not, nor have I ever, sequenced RAPD PCR amplifications. I primarily do single copy nuclear DNA analysis and have PAIRS of primers that amplify my loci. The sequencing method that I relayed to this group works fine under those conditions (i.e. where you have defined, unique ends), but I do not know how it will work with single primer amplification. I stand by the method and am very sorry if I mislead. Sincerely, Steve Stephen Karl Department of Biology University of South Florida 4202 East Fowler Ave, LIF 169 Tampa, Florida 33620-5150 Voice (813) 974-1592 Fax (813) 974-3263 EMail Karl@.chuma.cas.usf.edu From owner-rapd@net.bio.net Wed Oct 05 23:00:00 1994 Path: biosci!agate!spool.mu.edu!olivea!news.bu.edu!wyc From: wyc@bu.edu (Yecheng Wu) Newsgroups: bionet.molbio.rapd Subject: Re: Automatic Data Collection Date: 6 Oct 1994 15:58:32 GMT Organization: Boston University Lines: 29 Message-ID: <3716r8$jf8@news.bu.edu> References: NNTP-Posting-Host: crsa.bu.edu X-Newsreader: TIN [version 1.2 PL0] Kevin O'Donnell (odonnell@sasa.gov.uk) wrote: : We are interested in constructing a RAPD band library for potato : varieties and would like to use a system for automatically : registering and characterising the bands generated on RAPD gels, : and entering this information into a database which can then be : interogatted to identify unknown varieties in blind tests. in other words, : once the data is entered, it will be able to identify any of the : varieties from their banding patterns. : Has anyone tried using a gel scanner to construct a library : of RAPD band patterns for use in variety testing? If so, would you like : to share your experiences? I am particularly interested in how many : varieties your software was able to descriminate between and how reliably. : Is there a particular type of hardware or software that you would : recommend,and so on. : : Kevin O'Donnell : Scottish Agricultural Science Agency : Edinburgh : Scotland We have a package commercially available for doing exactly what you are looking for. The software is called RFLPscan which does automatic band scoring from scanned gels and save the processed results into a Microsoft Access compatible database. The database can be queried to identify unknown varieties and much more. For more information call 508-663-7598 (USA) or E-mail scan_info@cspi.com From owner-rapd@net.bio.net Wed Oct 05 23:00:00 1994 Path: biosci!vt.edu!fishgen From: fishgen@vt.edu (Bruce J. Turner) Newsgroups: bionet.molbio.rapd Subject: (none) Date: 6 Oct 1994 13:22:59 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <199410062022.NAA16316@net.bio.net> NNTP-Posting-Host: net.bio.net We are interested in corresponding with anyone who has successfully obtained amplifiable DNA from the leaves of trees in the family Fagaceae, especially oaks and chestnuts. We are having difficulty obtaining good DNA from these organisms, and we wonder if anyone has worked out a protocol. Thanks to all. From owner-rapd@net.bio.net Wed Oct 05 23:00:00 1994 Path: biosci!PNFI.FORESTRY.CA!ldeverno From: ldeverno@PNFI.FORESTRY.CA (LDEVERNO 613-589-2880) Newsgroups: bionet.molbio.rapd Subject: Metaphor agarose Date: 6 Oct 1994 06:01:07 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <7834000906101994.A19191.PNFI.118A32401F00*@MHS> NNTP-Posting-Host: net.bio.net This product can be obtained from FMC BioProducts, 191 Thomaston Street, Rockland, Maine USA 04841. I have used this agarose for all of my RAPD analysis and find that it gives excellent resolution and is easy to use. A 2% gel in TBE buffer has similar resolution to 4% polyacrylamide. This agarose comes with a handy booklet describing the resolving power, how to prepare gels, standard electrophoresis conditions and staining procedures, as well as tips for optimizing resolution in Metaphor agarose gels. Linda DeVerno Petawawa National Forestry Institute Chalk River, Ontario Canada K0J 1J0 ldeverno@pnfi.forestry.ca From owner-rapd@net.bio.net Wed Oct 05 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: Louis van de Zande Newsgroups: bionet.molbio.rapd Subject: metaphor Date: 6 Oct 1994 09:19:40 +0100 Organization: Department of Biology, RUGroningen Lines: 11 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <370bus$c12@mserv1.dl.ac.uk> Reply-To: ZANDELPW@BIOL.RUG.nl Original-To: rapd@dl.ac.uk Hello, Has anybody heard of or even better has experience with Metaphor agarose for separation of fragments that differ only by 4-10 bp? If it is good, where can it be obtained. I like to know this for the possible use of this type of agarose in detecting more RAPD polymorphisms and for microsatellite separation. Louis van de Zande Dept. Genetics University of Groningen. From owner-rapd@net.bio.net Wed Oct 05 23:00:00 1994 Path: biosci!CHUMA.CAS.USF.EDU!karl From: karl@CHUMA.CAS.USF.EDU ("Stephen A. Karl") Newsgroups: bionet.molbio.rapd Subject: Forgotten Soldier Date: 6 Oct 1994 12:59:06 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 28 Sender: daemon@net.bio.net Distribution: world Message-ID: Reply-To: "Stephen A. Karl" NNTP-Posting-Host: net.bio.net To All: One more important piece of information about sequencing PCR products with the USB PCR Sequenase kit. Susan Brandon (BIO) (brandon@chuma.cas.usf.edu) is THE goddess and queen of all molecular biology and everything she touches. It is she who originally brought this sequencing protocol to my attention and it is I who never even thought to mention her name when passing it along to you. For this, I owe her an apology and hope that this message will correct my egregious oversight. Yours humbly, Steve Karl Stephen Karl Department of Biology University of South Florida 4202 East Fowler Ave, LIF 169 Tampa, Florida 33620-5150 Voice (813) 974-1592 Fax (813) 974-3263 EMail Karl@.chuma.cas.usf.edu From owner-rapd@net.bio.net Thu Oct 06 23:00:00 1994 Path: biosci!agate!msuinfo!netnews.upenn.edu!gopher.cs.uofs.edu!jaguar.uofs.edu!chengss1 From: chengss1@jaguar.uofs.edu Newsgroups: bionet.molbio.rapd Subject: RADP-Cloning Date: 6 Oct 94 22:05:29 EST Organization: University of Scranton Lines: 8 Message-ID: <1994Oct6.220529.1@jaguar.uofs.edu> NNTP-Posting-Host: jaguar.cs.uofs.edu Hi! Does any one think it is worth to clone RADP-DNA fragment? Does any one know the terminal sequences of RADP-DNA fragment?-- changed or not? I have got some cloned DNA from bacterial RADP & try to find what it like in the amplified sequences. Shuqiu Cheng -- CHENGS1@lion.uofs.edu From owner-rapd@net.bio.net Thu Oct 06 23:00:00 1994 Path: biosci!UNAMVM1.DGSCA.UNAM.MX!carvalho From: carvalho@UNAMVM1.DGSCA.UNAM.MX (Carvalho Torres Alexandro cassio-UACPYP) Newsgroups: bionet.molbio.rapd Subject: Re: Forgotten Soldier Date: 6 Oct 1994 18:44:06 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 40 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net On 6 Oct 1994, Stephen A. Karl wrote: > To All: > > One more important piece of information about sequencing PCR products > with the USB PCR Sequenase kit. > > Susan Brandon (BIO) (brandon@chuma.cas.usf.edu) is THE goddess and queen > of all molecular biology and everything she touches. It is she who > originally brought this sequencing protocol to my attention and it is I > who never even thought to mention her name when passing it along to you. > For this, I owe her an apology and hope that this message will correct my > egregious oversight. > > Yours humbly, > Steve Karl > Stephen Karl > Department of Biology > University of South Florida > 4202 East Fowler Ave, LIF 169 > Tampa, Florida 33620-5150 > Voice (813) 974-1592 > Fax (813) 974-3263 > EMail Karl@.chuma.cas.usf.edu > > > Dear friends, I loved in receive some protocols or idea to sequence directally a rapd fragments, if it is not possible do do something like that I loved to do small primers or sequences of the extreme. Aftyer that I will intend and make all the sequence of the fragment, please send me suggestion and idea. Thanks a lot. Best regards, Alexandro Carvalho Dept of Infectious Diseases. INNSZ. Mexico DF. From owner-rapd@net.bio.net Sat Oct 08 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!newsfeed.ksu.ksu.edu!moe.ksu.ksu.edu!hobbes.physics.uiowa.edu!cobra.uni.edu!palasj9579 From: palasj9579@cobra.uni.edu Newsgroups: bionet.molbio.rapd Subject: Idaho Tech. RAPD analysis Message-ID: <1994Oct9.142405.33133@cobra.uni.edu> Date: 9 Oct 94 14:24:05 -0500 Organization: University of Northern Iowa Lines: 9 We are in the process of looking at an Idaho Technology thermocycler which runs 10 ul samples. We're wanting to use the thermalcycler to run RAPD analysis. Has anyone had any experience in using this thermalcycler for RAPDs, and what kind of protocol was used for successful amplification? Thanks, Jeff Palas University of Northern Iowa Cedar Falls, IA 50614 From owner-rapd@net.bio.net Mon Oct 10 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!news.funet.fi!news.csc.fi!news.helsinki.fi!HAMBI-9101.pc.Helsinki.FI!kaijalai From: kaijalai@viikki.helsinki.fi (SEPPO KAIJALAINEN (MMETT)) Newsgroups: bionet.molbio.rapd Subject: Primer-program Date: Tue, 11 Oct 1994 17:06:56 GMT Organization: University of Helsinki Lines: 9 Message-ID: NNTP-Posting-Host: hambi-9101.pc.helsinki.fi Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Anybody out there, who could explain what following terms of Primers (Whitehead inst.) output means: any self 3' s.k. From owner-rapd@net.bio.net Mon Oct 10 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!uknet!daresbury!not-for-mail From: Louis van de Zande Newsgroups: bionet.molbio.rapd Subject: re:metaphor Date: 11 Oct 1994 10:18:47 +0100 Organization: Department of Biology, RUGroningen Lines: 91 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <37dl9n$br2@mserv1.dl.ac.uk> Original-To: rapd@dl.ac.uk My question about MetaPhor agarose resulted in the following useful answers. Thanks to all the generous senders. Louis van de Zande This product can be obtained from FMC BioProducts, 191 Thomaston Street, Rockland, Maine USA 04841. I have used this agarose for all of my RAPD analysis and find that it gives excellent resolution and is easy to use. A 2% gel in TBE buffer has similar resolution to 4% polyacrylamide. This agarose comes with a handy booklet describing the resolving power, how to prepare gels, standard electrophoresis conditions and staining procedures, as well as tips for optimizing resolution in Metaphor agarose gels. Linda DeVerno Petawawa National Forestry Institute Chalk River, Ontario Canada K0J 1J0 ldeverno@pnfi.forestry.ca ---------------------------------------------------------------------- We have used Metaphor agarose. It comes from a company called FMC but I only have the address of their U.K distributer. U would certainly recommend giving it a go. We used it to look at the products of microsatelite amplification although we moved on to acrylamide to do the actual sizing of our products. good luck Frankie Bligh Nottingham ---------------------------------------------------------------------- I have been using Metaphor Agarose for the separation of PCR product restriction digests, in the range 10-500 bp. I have recently compared Perkin Elmer PE-Express gel (prepared for PE by FMC bioproducts), Nusieve GTG and Metaphor (FMC Bioproducts.). All three are considerably better resolution than other standard or high qualilty agaroses. Nusieve GTG (3% gel) is very good but Metaphor (3%) is better at resolving very small bp differences. I have confirmed the separation of a 4bp difference between the 242 and 238 bp bands of a pBR322/Msp1 digest. This can be achieved with a 1 hour run on a 14x10cm minigel (3%) at 5V/cm; as they claim in the small booklet that comes with the agarose. In the booklet they claim separation of 3 bp microsatellite pair of 97bp and 94bp. I have no doubt that this is possible with the rapid gel conditions I use. I was able to obtain an 8 gm sample from my local Australian agent for FMC. This was adequate for me to determine how useful the gel was going to be. I do not know who your supplier is likely to be however. It appears that from comparisons with acrylamide minigels that the resolution is equivalent to a 6% acrylamide gel but if using slab horizontal gels you need about 5 times as much DNA (for visualising RFLP fragments). Hope this is helpful Christopher Bolch ___________________________ Christopher J. S. Bolch, Experimental Scientist CSIRO Division of Fisheries, GPO Box 1538, Hobart, Tasmania, Australia, 7001. ---------------------------------------------------------------------- Metaphor is marketed by FMC Bioproducts whose European base is in Denmark. Tel: 45 43 73 11 22 fax: 45 43 73 56 92. They should be able to provide info re: local suppliers. We have used Metaphor up to 3% to separate RAPD and mtDNA PCR/RFLP fragments. We have not tried separating fragments below 100bp but appear to get resolution of fragments differing by 5bp in the 100-200bp range. Metaphor is claimed by FMC to separate to within 2% in the 200-800bp range. Hope this is of some help. Harry Townson htownson@liverpool.ac.uk Liverpool School of Tropical Medicine ---------------------------------------------------------------------- We have excellent luck with metaphor agarose for microsatellites - we have on aoccasion separated fragments differing by 2 bp (in 100-150), 4 bp is not difficult. It is sold by FMC. Antoni Rafalski From owner-rapd@net.bio.net Mon Oct 10 23:00:00 1994 Path: biosci!CABI.org!D.BRAYFORD From: D.BRAYFORD@CABI.org ("David Brayford ", IMI) Newsgroups: bionet.molbio.rapd Subject: RFLPscan software and IGS primers Date: 11 Oct 1994 04:42:01 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <2E9A7AB3@smtp-gateway.cgnet.com> NNTP-Posting-Host: net.bio.net I'm quite interested getting info on the RFLPscan software, but the email address scan_info@cspi.com came back as undeliverable. Does anyone know an updated/correct email address? While I'm here, can anyone let me know some primer sequences for the rRNA IGS region that work with fungi? Thanks. Dave Brayford International Mycological Institute Bakeham Lane Egham Surrey TW20 9TY UK d.brayford@cabi.org From owner-rapd@net.bio.net Wed Oct 12 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!EU.net!uunet!newsflash.concordia.ca!tsunami.cc.mcgill.ca!VM1.MCGILL.CA From: "MONTESCLAROS,LUZ,MISS" Newsgroups: bionet.molbio.rapd Subject: direct sequencing of PCR products Date: 13 OCT 94 16:56:06 EST Organization: McGill University Lines: 11 Sender: usenet@MUSICB.MCGILL.CA Message-ID: <13OCT94.18289838.0157@VM1.MCGILL.CA> NNTP-Posting-Host: vm1.mcgill.ca Hello Everyone! We would appreciate any information on direct sequencing of PCR products without cloning. Is there a protocol? or a kit available? Thank you! Carole and Luz xp17@musicb.mcgill.ca From owner-rapd@net.bio.net Thu Oct 13 23:00:00 1994 Path: biosci!COMP.UARK.EDU!wetges From: wetges@COMP.UARK.EDU (William J. Etges) Newsgroups: bionet.molbio.rapd Subject: Re: Linkage Disequilibrium-Software? Date: 14 Oct 1994 12:52:08 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 58 Sender: daemon@net.bio.net Distribution: world Message-ID: <199410141951.OAA05803@comp.uark.edu> NNTP-Posting-Host: net.bio.net At 6:46 PM 10/14/94 +0000, David MacHugh wrote: >Hi, > > >Is anybody of aware of a program that provides statistical analysis of >allelic association (linkage or gametic disequilibrium) between multialleic >genetic markers for population data? A program capable of generating random >reshuffled bilocus genotypic distributions would be particularly desirable. >This would create an synthetic distribution to compare the observed data >with and would allow meaningful statistical assessment of populations with >small sample sizes (approx. 50 individuals). >We have data from a large number of microsatellites typed in 20 >populations, hence source code would be useful as we could then port it to >a DEC alpha to cut down the runtime. > >I would try a develop a program myself except that I am trying to finish my >PhD thesis and anyway I can't write a single line of code ;-) > >Thanks in advance for your help. > >-- > ********************************************************************* > * (__) David MacHugh, E-mail: dmachugh@mail.tcd.ie * > * (@*) Bovine Genetics, Phone: (353)-1-7021088 * > * /-------\u' Genetics Department, Fax: (353)-1-6798558 * > * / | || Trinity College, * > * ||----|| Dublin 2. * > * ^^ ^^ Ireland. * > ********************************************************************* David, I have a copy of a FORTRAN program written by Dave Foltz in the "old days" based on Bruce Weir's 1979 paper in Biometrics (Biometrics 35:235-254). There MUST be something more recent out there in someone's statistical package. Tom Whittam at Penn State, Biology Dept. used to work on linkage disequilibrium in bacteria and wrote his own programs. You might check with him. If you want to get prehistoric and dust off your FORTRAN compiler, let me know. Bill ------------------------------------------------------------------------- William J. Etges "When scientists are Department of Biol. Sciences under attack, they circle University of Arkansas 'round, wagon train Fayetteville, AR 72701 USA style. The physicists wetges@comp.uark.edu aim outward at their voice: (501) 575-6358 opponents. Biologists FAX (501) 575-4010 on the other hand, aim inward, at each other." Dr. Janet V. Dorigan Dept. of Energy ------------------------------------------------------------------------- From owner-rapd@net.bio.net Thu Oct 13 23:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!pipex!sunic!columba.udac.uu.se!pc01.fysbot.uu.se!HAKTAELIM From: HAKTAELIM@fysbot.uu.se (HAKTAE LIM) Newsgroups: bionet.molbio.rapd Subject: Somatic hybrids and RAPD Date: Fri, 14 Oct 1994 15:42:53 GMT Organization: Uppsala University Lines: 3 Message-ID: NNTP-Posting-Host: pc01.fysbot.uu.se I would like to contact with those who are involved in somatic hybrids in plants and RAPD analyses. Thanks for your attention. With best wishes, Haktae Lim, Ph.D. From owner-rapd@net.bio.net Thu Oct 13 23:00:00 1994 Newsgroups: bionet.molbio.rapd Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!EU.net!ieunet!tcdcs!news.tcd.ie!gen024.gen.tcd.ie!user From: dmachugh@mail.tcd.ie (David MacHugh) Subject: Linkage Disequilibrium-Software? Message-ID: Followup-To: bionet.molbio.rapd Sender: usenet@news.tcd.ie (TCD News System ) Organization: Genetics Department, Trinity College, Dublin 2. IRELAND Date: Fri, 14 Oct 1994 18:46:10 GMT Lines: 29 Hi, Is anybody of aware of a program that provides statistical analysis of allelic association (linkage or gametic disequilibrium) between multialleic genetic markers for population data? A program capable of generating random reshuffled bilocus genotypic distributions would be particularly desirable. This would create an synthetic distribution to compare the observed data with and would allow meaningful statistical assessment of populations with small sample sizes (approx. 50 individuals). We have data from a large number of microsatellites typed in 20 populations, hence source code would be useful as we could then port it to a DEC alpha to cut down the runtime. I would try a develop a program myself except that I am trying to finish my PhD thesis and anyway I can't write a single line of code ;-) Thanks in advance for your help. -- ********************************************************************* * (__) David MacHugh, E-mail: dmachugh@mail.tcd.ie * * (@*) Bovine Genetics, Phone: (353)-1-7021088 * * /-------\u' Genetics Department, Fax: (353)-1-6798558 * * / | || Trinity College, * * ||----|| Dublin 2. * * ^^ ^^ Ireland. * ********************************************************************* From owner-rapd@net.bio.net Thu Oct 13 23:00:00 1994 Path: biosci!UNIXG.UBC.CA!hobbs From: hobbs@UNIXG.UBC.CA Newsgroups: bionet.molbio.rapd Subject: UBC SSR Primer Set (Set #9) Date: 14 Oct 1994 16:25:58 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 174 Sender: daemon@net.bio.net Distribution: world Message-ID: <9410142325.AA11879@unixg.ubc.ca> NNTP-Posting-Host: net.bio.net A number of users of the UBC RAPD primer sets have expressed an interest in using a set of SSR-targeted primers for genomic analysis, if one were made available. We have therefore assembled set #9 for this purpose. The sequences are shown below, together with a reminder of the abbreviations for mixed-base positions. As with previous sets, the oligos were purified by elution with Tris/EDTA buffer through NAP-5 drip columns. Aliquots (10-20 microlitres each) calculated to be 3 nanomoles (see below) were made near the bottom of the tubes and air-dried in a running sterile flow-hood. The primers were quantitated by u.v. spectrophotometry and two assumptions were made in converting the A260 figures to concentrations: first, that at mixed base positions, equal quantities of the mixed bases are incorporated, and second, that no secondary structure is present, i.e. that no hypochromicity is occurring. Nucleic acid chemists will appreciate that these are necessarily approximations, and the second, particularly, is likely to be inaccurate for some sequences. However, in these cases the error is likely to be in favour of the recipient, with the actual quantity of primer probably being between 3 and 4 nmoles. Many of the sequences are 2-base repeats reported in the literature as having been used for genomic mapping, with the repeat sequence interrupted at the 3'- or 5'- end by bases which in type or identity are "out-of-phase" with the repeat and can thus act as anchors (for use of primers of this type, see Zietkiewicz, Rafalski and Labuda, Genomics, 20,176-183 (1994)). A number of 3-, 4-, and 5- base repeats, without putative anchors, have also been included: all have been reported as SSRs for various species. A number of oligonucleotides described as general genomic amplification primers have also been included in the set. References to these are as follows: #892 Hadano et al., Genomics, 11, 364-373 (1991) #893 Zhang et al., Proc. Natl. Acad. Sci. USA, 89, 5847-5851 (1992) #894, 895 Bohlander et al., Genomics, 13, 1322-1324 (1992) #896,897 Telenius et al., Genomics, 13, 718-725 (1992) #898 Breneman et al., Chromosoma, 102, 591-598 (1993) I thank those who have taken the time and trouble to provide suggestions for sequences to be included in this set. Despite the higher production costs (the average length of a primer here is 17.62), to save confusion I am holding the price at the level asked for our 10-mer primer sets for RAPD analysis, viz. US$ 235 (or Can. $300) plus carriage: airmail costs are US$4 to most parts of the world, while for courier delivery in the US we add an additional $11US ($7Can. for shipments within Canada). Courier delivery to other parts of the world is also added at the rate charged to us: $16 to the UK, $16 to Western Europe, $17 to Australasia, $17 to the Far East, $25 to China, South America, and Africa (all prices in US$, based on orders of one or two sets [i.e. up to 500g.]). If you are interested in obtaining a set, I am accepting purchase orders by fax, mail or e-mail. Orders must specify your mailing address, the name of the person to be billed (i.e. grant holder), your preference as to shipment via courier or air mail, and either an official Purchase Order Number or your cheque in advance (made out to "University of British Columbia"). If an order is phoned in, a copy of the P.O. for our records is still required. Our UBC 10-mer sets #1 to #8 for use in RAPD, and also our DDRT-PCR kit, remain available despite apparent rumours to the contrary! Please contact me if you require further details of these. John Hobbs. ****************************************************************************** UBC Primer Set #9 801 ATA TAT ATA TAT ATA TT 851 GTG TGT GTG TGT GTG TYG 802 ATA TAT ATA TAT ATA TG 852 TCT CTC TCT CTC TCT CRA 803 ATA TAT ATA TAT ATA TC 853 TCT CTC TCT CTC TCT CRT 804 TAT ATA TAT ATA TAT AA 854 TCT CTC TCT CTC TCT CRG 805 TAT ATA TAT ATA TAT AC 855 ACA CAC ACA CAC ACA CYT 806 TAT ATA TAT ATA TAT AG 856 ACA CAC ACA CAC ACA CYA 807 AGA GAG AGA GAG AGA GT 857 ACA CAC ACA CAC ACA CYG 808 AGA GAG AGA GAG AGA GC 858 TGT GTG TGT GTG TGT GRT 809 AGA GAG AGA GAG AGA GG 859 TGT GTG TGT GTG TGT GRC 810 GAG AGA GAG AGA GAG AT 860 TGT GTG TGT GTG TGT GRA 811 GAG AGA GAG AGA GAG AC 861 ACC ACC ACC ACC ACC ACC 812 GAG AGA GAG AGA GAG AA 862 AGC AGC AGC AGC AGC AGC 813 CTC TCT CTC TCT CTC TT 863 AGT AGT AGT AGT AGT AGT 814 CTC TCT CTC TCT CTC TA 864 ATG ATG ATG ATG ATG ATG 815 CTC TCT CTC TCT CTC TG 865 CCG CCG CCG CCG CCG CCG 816 CAC ACA CAC ACA CAC AT 866 CTC CTC CTC CTC CTC CTC 817 CAC ACA CAC ACA CAC AA 867 GGC GGC GGC GGC GGC GGC 818 CAC ACA CAC ACA CAC AG 868 GAA GAA GAA GAA GAA GAA 819 GTG TGT GTG TGT GTG TA 869 GTT GTT GTT GTT GTT GTT 820 GTG TGT GTG TGT GTG TC 870 TGC TGC TGC TGC TGC TGC 821 GTG TGT GTG TGT GTG TT 871 TAT TAT TAT TAT TAT TAT 822 TCT CTC TCT CTC TCT CA 872 GAT AGA TAG ATA GAT A 823 TCT CTC TCT CTC TCT CC 873 GAC AGA CAG ACA GAC A 824 TCT CTC TCT CTC TCT CG 874 CCC TCC CTC CCT CCC T 825 ACA CAC ACA CAC ACA CT 875 CTA GCT AGC TAG CTA G 826 ACA CAC ACA CAC ACA CC 876 GAT AGA TAG ACA GAC A 827 ACA CAC ACA CAC ACA CG 877 TGC ATG CAT GCA TGC A 828 TGT GTG TGT GTG TGT GA 878 GGA TGG ATG GAT GGA T 829 TGT GTG TGT GTG TGT GC 879 CTT CAC TTC ACT TCA 830 TGT GTG TGT GTG TGT GG 880 GGA GAG GAG AGG AGA 831 ATA TAT ATA TAT ATA TYA 881 GGG TGG GGT GGG GTG 832 ATA TAT ATA TAT ATA TYC 882 VBV ATA TAT ATA TAT AT 833 ATA TAT ATA TAT ATA TYG 883 BVB TAT ATA TAT ATA TA 834 AGA GAG AGA GAG AGA GYT 884 HBH AGA GAG AGA GAG AG 835 AGA GAG AGA GAG AGA GYC 885 BHB GAG AGA GAG AGA GA 836 AGA GAG AGA GAG AGA GYA 886 VDV CTC TCT CTC TCT CT 837 TAT ATA TAT ATA TAT ART 887 DVD TCT CTC TCT CTC TC 838 TAT ATA TAT ATA TAT ARC 888 BDB CAC ACA CAC ACA CA 839 TAT ATA TAT ATA TAT ARG 889 DBD ACA CAC ACA CAC AC 840 GAG AGA GAG AGA GAG AYT 890 VHV GTG TGT GTG TGT GT 841 GAG AGA GAG AGA GAG AYC 891 HVH TGT GTG TGT GTG TG 842 GAG AGA GAG AGA GAG AYG 892 TAG ATC TGA TAT CTG AAT TCC C 843 CTC TCT CTC TCT CTC TRA 893 NNN NNN NNN NNN NNN 844 CTC TCT CTC TCT CTC TRC 894 TGG TAG CTC TTG ATC ANN NNN 845 CTC TCT CTC TCT CTC TRG 895 AGA GTT GGT AGC TCT TGA TC 846 CAC ACA CAC ACA CAC ART 896 AGG TCG CGG CCG CNN NNN NAT G 847 CAC ACA CAC ACA CAC ARC 897 CCG ACT CGA GNN NNN NAT GTG G 848 CAC ACA CAC ACA CAC ARG 898 GAT CAA GCT TNN NNN NAT GTG G 849 GTG TGT GTG TGT GTG TYA 899 CAT GGT GTT GGT CAT TGT TCC A 850 GTG TGT GTG TGT GTG TYC 900 ACT TCC CCA CAG GTT AAC ACA SINGLE LETTER ABBREVIATIONS FOR MIXED BASE POSITIONS N = (A,G,C,T) R = (A,G) Y = (C,T) B = (C,G,T) (i.e. not A) D = (A,G,T) (i.e. not C) H = (A,C,T) (i.e. not G) V = (A,C,G) (i.e. not T) K = (G,T) (Keto in large groove) M = (A,C) (aMino in large groove) S = (G,C) (Strong [3 H-bonds]) W = (A,T) (Weak [2 H-bonds[) Dr. John Hobbs Nucleic Acid - Protein Service (NAPS) Unit Biotechnology Laboratory Room 237, Wesbrook Building 6174 University Boulevard University of British Columbia Vancouver, V6T 1Z3 Canada. FAX (604)822-5437 or (604)822-0676; Tel. (604)822-6373 From owner-rapd@net.bio.net Sat Oct 15 23:00:00 1994 Path: biosci!IRRI.CGNET.COM!SKATIYAR From: SKATIYAR@IRRI.CGNET.COM Newsgroups: bionet.molbio.rapd Subject: Mailing list Date: 15 Oct 1994 20:33:08 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HICAFLIR000026XO@irri.cgnet.com> NNTP-Posting-Host: net.bio.net Please include me in your mailing list. From owner-rapd@net.bio.net Sat Oct 15 23:00:00 1994 Path: biosci!sfu.ca!corley From: corley@sfu.ca ("Graham Corley-Smith") Newsgroups: bionet.molbio.rapd Subject: Hoechst 33258 Date: 16 Oct 1994 14:19:48 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 26 Sender: daemon@net.bio.net Distribution: world Message-ID: <51754.corley@sfu.ca> Reply-To: corley@sfu.ca NNTP-Posting-Host: net.bio.net Hi, A few months ago I wrote some comments on DNA quantification. In that post, I stated that Hoeschst 33258 bound in the minor groove to a particular tetranucleotide sequence. In response, someone asked me what the sequence that Hoescht 33258 recognizes, is. At the time, I could not locate the reference where I had read the information and could not remember the sequence. Today, I came across the reference. However, I do not recall who asked the question, therefore I am making this a general post. Reference: Blackburn, G. Michael and Michael J. Gait. 1990. Nucleic Acids in Chemistry and Biology. IRL Press at Oxford University Press. Oxford, New York, Tokyo. The sequence it recognizes is ATTC. p307-308 of above. Sorry for the long delay in supplying the info. ------------------------- Graham E. Corley-Smith Institute of Molecular Biology and Biochemistry Biological Sciences Department Simon Fraser University Burnaby, B.C., V5A 1S6 Canada Phone: (604) 291-3021 Fax: (604) 291-5583 e-mail: corley@sfu.ca From owner-rapd@net.bio.net Sun Oct 16 23:00:00 1994 Path: biosci!UBVMS.CC.BUFFALO.EDU!V226UHBQ From: V226UHBQ@UBVMS.CC.BUFFALO.EDU Newsgroups: bionet.molbio.rapd Subject: Keystone Symposium on Molecular Approaches in Marine Ecology Date: 17 Oct 1994 13:03:56 -0700 Organization: University at Buffalo Lines: 112 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HIDZYRR9G28WWO1O@ubvms.cc.buffalo.edu> NNTP-Posting-Host: net.bio.net Dear Colleague, We are organizing a Keystone Symposium entitled, "Molecular Approaches to Marine Ecology and Evolution." The symposium will be held in Santa Fe, March 5-11,1995. The meeting will consist of morning and evening invited plenary talks and early evening contributed poster sessions. The deadline for submission of abstracts for posters is NOVEMBER 1. We will accept posters after that but it will not be posssible to include those abstracts in the abstracts volume. If you are interested in contributiong a poster or attending the meeting please contact either of us or the Keystone Symposium office directly. Keystone - (303)262-1230 - [FAX (303) 262- 1525]. For more information about the meeting contact either: Howard Lasker email - biolask@ubvms.cc.buffalo.edu or Mary Alice Coffroth email - v226uhbq@ubvms.cc.buffalo.edu Dept. of Biological Sciences SUNY at Buffalo Buffalo, NY 14260 (716) 645-2881 (716) 645-2975 FAX *********************************************************************** MOLECULAR APPROACHES TO MARINE ECOLOGY AND EVOLUTION INTRODUCTION Howard R. Lasker - SUNY at Buffalo Introductory remarks -structure of the problem and the symposium. Dennis Powers - Stanford University New frontiers in molecular marine biology. SPEAKER TO BE ANNOUNCED John Avise - University of Georgia Conservation genetics for the 21st century. THE ECOLOGY AND EVOLUTION OF FERTILIZATION - John Pearse - University of California-Santa Cruz Patterns of spawning and fertilization among marine invertebrates. Victor Vacquier - University of California-San Diego Speciation in abalone is linked to the molecular evolution of sperm lysin. Steven Palumbi - University of Hawaii Evolution of gamete recognition in the speciation process. Don Levitan - Florida State University Ecological correlates of fertilization success in free spawning marine invertebrates. Howard Lasker - SUNY at Buffalo Fertilization success among broadcast spawning benthic invertebrates: the interaction between clonal propagation, flow regime and success. Michael McCartney - University of California at Davis Determinants of competitive male fertilization success in benthic marine invertebrates. Dan Howard - New Mexico State University Rapid evolution of barriers to fertilization in insects: parallels to marine species. Development - Eric Davidson - California Institute of Technology Understanding development of marine embryos: gene transfer and experimental control of gene expression. R. Andrew Cameron - California Institute of Technology Molecular aspects of sea urchin development. Matthew Dick - Yale University Homeoboxes among invertebrates. Larval Dispersal - Steven Gaines - University of California-Santa Barbara Patterns of dispersal among sessile marine invertebrates. Thomas Kocher - University of New Hampshire Identifying the planktonic players. Robert Cowen - SUNY at Stony Brook Dispersal of marine fishes. Dan Morse - University of California -Santa Barbara Molecular cues from the environment controlling site specific recruitment: morphogen based flypaper for larvae as a tool for manipulative experiments. POPULATION STRUCTURE - Dennis Hedgecock - University of California -Davis Population genetic consequences of variance in reproductive success for marine animals. Richard Grosberg -University of California -Davis Population structure, competition and cooperation in benthic invertebrates. Mary Alice Coffroth - SUNY at Buffalo Clonal population structure of a coral reef gorgonian. Sean Nee - Oxford University Inferring population history from molecular phylogenies. Harilaos Lessios - Smithsonian Tropical Research Inst. Direct evidence about bottlenecks in marine organisms: the 1983 Diadema pandemic. Eldredge Bermingham- Smithsonian Tropical Research Inst. The isthmus of Panama, molecular clocks, and fish biogeography. Curtis Suttle - University of Texas at Austin To be announced ADAPTATION TO THE ENVIRONMENT - Dennis Powers - Stanford Molecular mechanisms that populations use to adapt to changing environments. Nancy Knowlton - Smithsonian Tropical Research Institute Ecologic significance of cryptic diversity in coral-algal symbioses. TO BE ANNOUNCED TO BE ANNOUNCED CONCLUSIONS Jeremy B.C. Jackson - Smithsonian Tropical Research Institute The fossil record of speciation in the sea. Round Table Discussion From owner-rapd@net.bio.net Sun Oct 16 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!swrinde!pipex!uunet!psinntp!hk.super.net!news.ust.hk!hpg30a.csc.cuhk.hk!slip072.csc.cuhk.hk!b137795 From: b137795@mailserv.cuhk.hk Newsgroups: bionet.molbio.rapd Subject: bionet.molbio.methods-reagent? Date: Mon, 17 Oct 1994 16:06:12 GMT Organization: dept biol cuhk Lines: 15 Message-ID: NNTP-Posting-Host: slip072.csc.cuhk.hk Summary: looking for the bionet.methods-reagent Keywords: methods-reagent Dear bionetters, Do anyone know where to find the bionet.methods-reagent? I use to read this group. However, I can't find this group anymore. I can just find the bionet.molbio.hiv than follow with the bionet.molbio.protein. Usually the methods-reagent is in between hiv and protein. Is there any thing wrong with the network, or any thing wrong with my program? Anyone know the answer, please let me know. I highly appreciate your help. Thank you very much. Ming-Chiu FUNG mingchiufung@cuhk.hk From owner-rapd@net.bio.net Tue Oct 18 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!swrinde!sgiblab!uhog.mit.edu!news.mtholyoke.edu!news.amherst.edu!not-for-mail From: walin@unix.amherst.edu (Athena Wen-chuan Lin) Newsgroups: bionet.molbio.rapd Subject: test Date: 18 Oct 1994 19:55:41 -0400 Organization: Amherst College, Amherst MA, USA Lines: 1 Message-ID: <381n9t$888@amhux3.amherst.edu> NNTP-Posting-Host: amhux3.amherst.edu X-Newsreader: TIN [version 1.2 PL0] From owner-rapd@net.bio.net Tue Oct 18 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!uhog.mit.edu!news.mtholyoke.edu!news.amherst.edu!not-for-mail From: walin@unix.amherst.edu (Athena Wen-chuan Lin) Newsgroups: bionet.molbio.rapd Subject: test Date: 18 Oct 1994 19:57:57 -0400 Organization: Amherst College, Amherst MA, USA Lines: 1 Message-ID: <381ne5$8a3@amhux3.amherst.edu> NNTP-Posting-Host: amhux3.amherst.edu X-Newsreader: TIN [version 1.2 PL0] From owner-rapd@net.bio.net Wed Oct 19 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!ucsnews!sol.ctr.columbia.edu!howland.reston.ans.net!gatech!newsxfer.itd.umich.edu!jobone!lynx.unm.edu!triton.unm.edu!not-for-mail From: dkim@unm.edu Newsgroups: bionet.molbio.rapd Subject: Re: bionet.molbio.methods-reagent? Date: 19 Oct 1994 16:49:53 -0600 Organization: University of New Mexico, Albuquerque Lines: 11 Sender: dkim@triton.unm.edu Message-ID: <3847qh$irl@triton.unm.edu> References: NNTP-Posting-Host: triton.unm.edu Keywords: methods-reagent Hello: the problem you may be having with the methods and reagents newsgroup is that it uses an odd spelling for the name. it is: bionet.molbio.methds-reagnts There is also information on current discussions in this group to be found in the "Computer Corner" column of TIBS, written by Paul Hengen. Daniel Kim dkim@triton.unm.edu From owner-rapd@net.bio.net Wed Oct 19 23:00:00 1994 Path: biosci!YVAX.BYU.EDU!FARMERJ From: FARMERJ@YVAX.BYU.EDU Newsgroups: bionet.molbio.rapd Subject: Name change (was "RAPD amplification) Date: 20 Oct 1994 10:10:09 -0700 Organization: Brigham Young University Lines: 67 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HIHWVEVWS294DZZ0@yvax.byu.edu> NNTP-Posting-Host: net.bio.net I have been extremely busy this fall and have not had time until now to address the question of renaming this news group. I am concerned that broadening this group too much will make it unwieldy and redundant to other news groups. For instance, PCR is one of the major topics in the methods and reagents newsgroup. As another example, PCR and RAPD are both discussed at length on bug-net, which has a lot of information on PCR and RAPD as applied to insects. I assume that other specialized news groups exist as well. There is no point trying to duplicate their services. At some point, this newsgroup will become unnecessary as the RAPD technique becomes standardized and more specialized news groups proliferate. However, it seems to me that we have not yet reached that point. It seems to me that this group still provides a service to new users and to researchers who are seeking others who are working with the same organisms. I do not necessarily object to a new name, but if we do choose one, it should be unambiguous in order to reduce extraneous postings and serious overlap with other, established news groups. For instance, I would object strongly to "PCR". Some interesting suggestions have been made, but I am not convinced that any of them is clearly preferable to the present name. If there is serious interest in a name change, I suggest that we propose a new news group to the bionet administration, define its purpose, and suggest a name. If approved, the new news group would replace this one if it were approved. That way there will be general announcements, comments, and a vote of all bionet users. This is the process we went through to create the RAPD newsgroup. Our charter has not been changed, but it should be if we are going to change the purpose of this group. I do not have the time to pursue this process again. If someone else would like to be the "owner" of the new news group, and take care of all administrative chores involved in the process I have just described, please contact me or, if you prefer, contact the bionet administration. I don't intend to cut off discussion of a name change or of a change in emphasis. I see much merit in recognizing the de facto expansion of topics to include markers in addition to RAPD markers. I would just like to see things done in a way that maintains the integrity and usefulness of this news group. In the meantime, I would like to compile a list of all specialized news groups (other than those on bionet) which discuss RAPD and PCR markers in particular organisms or groups of organisms. If you will send me information on any that you know, I will compile the information and post it. If we know how many such groups exist, it might help us to make an intelligent decision. Please send this information directly to me rather than posting it. 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 Wed Oct 19 23:00:00 1994 Path: biosci!vt.edu!fishgen From: fishgen@vt.edu (Bruce J. Turner) Newsgroups: bionet.molbio.rapd Subject: SYBR Green I Date: 20 Oct 1994 09:57:57 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <199410201657.JAA04882@net.bio.net> NNTP-Posting-Host: net.bio.net Has anyone tried the new "Sybr Green I" nucleic acid stain, a product of Molecular Probes, Inc.? I'd appreciate it if you could share your experiences. This looks like a "dream stain" but appears a bit pricey. I'm particularly concerned because it apparently works best when excited at about 254 nm; my light box is at 300 nm. At that wavelength, I'd apparently only get about 8 fold the sensitivity of EtBr (vs about 25 fold at 256). Also, even if I had one, I'm not sure that 254 nm UV is a particularly good thing for lab people to be exposed to. Any comments on this? From owner-rapd@net.bio.net Thu Oct 20 23:00:00 1994 Path: biosci!UBVMS.CC.BUFFALO.EDU!V226UHBQ From: V226UHBQ@UBVMS.CC.BUFFALO.EDU Newsgroups: bionet.molbio.rapd Subject: PCR Machines Date: 21 Oct 1994 06:01:58 -0700 Organization: University at Buffalo Lines: 30 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HIJ6OYQXRM9AMH0Y@ubvms.cc.buffalo.edu> NNTP-Posting-Host: net.bio.net Hi All, I am getting ready to purchase a thermocyler. I know that the pros and cons of various machines has been discussed occassionally here, but I would appreciate any input into the merits of the various machines out there. I now have a Coy and am getting reproducible data ( I am doing RAPDs), but with 6 bodies demanding machine time, it's time to get a second machine. I am looking for something with a few more wells than the Coy (i.e., >35) and a bit faster ramp times (our runs take 8+ hours --yikes!). The considerations are the usual -- reliability, ability to cycle to 0 C and of course cost. I remember awhile back a bit of discussion about the MJ research 96 well machine-- are these giving reproducible results (with the microtiter plates). Are there any disadvantages to the MJ Research machine? At the moment the feedback I get is that the choice is between the MJ and PE. At any rate, I'd apprecaite any comments. If you send your replies to me, I'll summarize them and post them to the group. Thanks in advance for your help! Mary Alice Coffroth Department of Biological Sciences SUNY at Buffalo Buffalo, NY 14260 716-645-2881 716 645-2975 [fax] V226uhbq@ubvms.cc.buffalo.edu From owner-rapd@net.bio.net Thu Oct 20 23:00:00 1994 Path: biosci!DEAKIN.EDU.AU!huangbx From: huangbx@DEAKIN.EDU.AU Newsgroups: bionet.molbio.rapd Subject: Please help me to get right DMSO concentration in PCR Date: 20 Oct 1994 17:55:46 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <199410210055.KAA06966@hestia.ccs.deakin.edu.au> NNTP-Posting-Host: net.bio.net Dear netters, It is said that DMSO can help the GC rich region amplified. I have a GC rich (65%) minisatellite to look into, which stops me for a while. I shoud try DMSO soon, but I do not have any clue for this. It will be very appreciated for me to have a protocol or direct me a reference from anyone on the net. Many thanks. Bixing Huang huangbx@deakin.edu.au Department of Biology, Deakin University of Australia From owner-rapd@net.bio.net Thu Oct 20 23:00:00 1994 Path: biosci!UKCC.UKY.EDU!VSC003 From: VSC003@UKCC.UKY.EDU (Ernie Bailey) Newsgroups: bionet.molbio.rapd Subject: Coy Thermocyclers Date: 21 Oct 1994 15:07:43 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <199410212207.PAA11308@net.bio.net> NNTP-Posting-Host: net.bio.net 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 owner-rapd@net.bio.net Thu Oct 20 23:00:00 1994 Path: biosci!BADLANDS.NODAK.EDU!jweiland From: jweiland@BADLANDS.NODAK.EDU (John J Weiland) Newsgroups: bionet.molbio.rapd Subject: Microtitre PCR blocks and MJR Date: 21 Oct 1994 15:23:32 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net 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 $93.00 for 25 plates (polycarbonate) for use in the 96-well unit. Any cheaper prices out there for a plate that is manufactured for use in a thermocycler? Thanks John Weiland jweiland@badlands.nodak.edu From owner-rapd@net.bio.net Thu Oct 20 23:00:00 1994 Path: biosci!EMUNIX.EMICH.EDU!bio_hannan%emuvax.dnet.emich.edu From: bio_hannan%emuvax.dnet.emich.edu@EMUNIX.EMICH.EDU Newsgroups: bionet.molbio.rapd Subject: re: thermocycler Date: 21 Oct 1994 09:24:09 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <9410211624.AA15100@emunix.emich.edu> NNTP-Posting-Host: net.bio.net Mary, We have a Coy50 that has gone back for repair twice- first for cooling block problem, now for heating problem. It won't get up to set points above about 35 degrees. Have you had similar problems and is that why you are not considering another Coy (e.g. 60)? We have also had the usual experiences of having amplifications stop completely for no apparent reason (although this seems to happen to everyone at times). Gary Hannan bio_hannan@emunix.emich.edu From owner-rapd@net.bio.net Mon Oct 24 22:00:00 1994 Path: biosci!rutgers!uwm.edu!news.moneng.mei.com!howland.reston.ans.net!europa.eng.gtefsd.com!uhog.mit.edu!news.mtholyoke.edu!news.amherst.edu!not-for-mail From: walin@unix.amherst.edu (Athena Wen-chuan Lin) Newsgroups: bionet.molbio.rapd Subject: RAPD on bacteria Date: 24 Oct 1994 22:45:13 -0400 Organization: Amherst College, Amherst MA, USA Lines: 1 Message-ID: <38hrfp$ieb@amhux3.amherst.edu> NNTP-Posting-Host: amhux3.amherst.edu X-Newsreader: TIN [version 1.2 PL0] From owner-rapd@net.bio.net Mon Oct 24 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!EU.net!uunet!newsflash.concordia.ca!nstn.ns.ca!nstn.ns.ca!nntp-user From: Newsgroups: bionet.molbio.rapd Subject: ATCC Date: 24 Oct 1994 23:17:21 -0300 Organization: Nova Scotia Technology Network Lines: 11 Sender: news@nstn.ns.ca Message-ID: <92984.pmcauley@fox.nstn.ns.ca> Reply-To: X-Minuet-Version: Minuet1.0_Beta_14.1 X-POPMail-Charset: English Can anyone out there on the Net help us find the ATCC catalogue number for the VHL probe that is a 1.5 kb EcoRI cDNA insert, denoted g7, encoding part of the human von Hippel-Lindau disease tumor suppressor gene on chromosome 3p25-26 [see: Latif, F. et al (1993) Science 260, 1317-1320.] If this is the wrong NEWS group, where should I send my request. Thank you. -- Peter McAuley pmcauley@fox.nstn.ns.ca From owner-rapd@net.bio.net Mon Oct 24 22:00:00 1994 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.rapd Subject: UNSUBSCRIBING, BIOSCI ARCHIVES, ADDRESS DATABASE & BIOSCI FAQ Date: 25 Oct 1994 02:00:19 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 322 Sender: daemon@net.bio.net Distribution: world Message-ID: <199410250900.CAA04488@net.bio.net> NNTP-Posting-Host: net.bio.net Four important items follow: How to cancel e-mail subscriptions to BIOSCI newsgroups, BIOSCI archive searching, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our BIOSCI user directory, please take a few minutes to complete and return the form below. If your personal information has changed since you listed yourself, please send us a complete new updated form. We can not make manual revisions to existing entries. 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Thanks again for your cooperation! --------------- please cut here and return portion below --------------- New information or Update to old record (enter N or U): date (DD-MM-YY): first name: middle initial: family name: job title: e-mail address: e-mail network: phone number: FAX number: institution: address1: address2: address3: city: state/province: country: postal code: research interest: research interest: comment: comment: comment: comment: comment: From owner-rapd@net.bio.net Mon Oct 24 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!swrinde!sgiblab!uhog.mit.edu!news.mtholyoke.edu!news.amherst.edu!not-for-mail From: walin@unix.amherst.edu (Athena Wen-chuan Lin) Newsgroups: bionet.molbio.rapd Subject: RAPD on bacteria Date: 24 Oct 1994 22:52:46 -0400 Organization: Amherst College, Amherst MA, USA Lines: 9 Message-ID: <38hrtu$iun@amhux3.amherst.edu> NNTP-Posting-Host: amhux3.amherst.edu X-Newsreader: TIN [version 1.2 PL0] Sorry about the empty post :) I have read an article using RAPD to differentiate Helicobacter pyrori (64 isolates from the same hospital). All six(?) primers were able to differentiate all the isolates tested. A Japanese group also used the same set of primers to differentiate Yersinia isolates. has anybody else tried these primers? I don't seem to have much good luck with them. From owner-rapd@net.bio.net Tue Oct 25 22:00:00 1994 Path: biosci!SDSUMUS.SDSTATE.EDU!PX52 From: PX52@SDSUMUS.SDSTATE.EDU (THOMAS E CHASE) Newsgroups: bionet.molbio.rapd Subject: PCR Machines Date: 25 Oct 1994 20:38:38 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <25OCT94.24424064.0042.MUSIC@SDSUMUS.SDSTATE.EDU> NNTP-Posting-Host: net.bio.net 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 owner-rapd@net.bio.net Tue Oct 25 22:00:00 1994 Path: biosci!COSMAIL2.CTD.ORNL.GOV!ygl From: ygl@COSMAIL2.CTD.ORNL.GOV ("Lee E. Gunter") Newsgroups: bionet.molbio.rapd Subject: Position Available Date: 26 Oct 1994 09:46:31 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 43 Sender: daemon@net.bio.net Distribution: world Message-ID: <125.ygl@cosmail2.ctd.ornl.gov_POPMail.PC_3.2.2> Reply-To: NNTP-Posting-Host: net.bio.net DNA CHARACTERIZATION OF UV-B DAMAGED FOREST TREE POLLEN Post-Masters' Position Environmental Sciences Division Oak Ridge National Laboratory Starting Date: January 1, 1995 Duration: 2 years Salary: Starting at $25,000 per year, increasing with qualifications Project Description: DNA structural damage associated with elevated UV-B radiation will be characterized using three different quantitative assays. The three assays are: an alkaline unwinding assay, a restriction digest/median fragment length assay, and a PCR-based thymine-dimer assay. Pollen from a wind and an insect pollinated species, each from various elevational and latitudinal origins, will be exposed to UV-B radiation. We have determined that normal pollen function and development are interrupted under such conditions. After exposure, DNA will be isolated, the assays conducted, and the results correlated to pollen function and genetic origin. Qualifications: Research experience and/or training involving DNA isolation, PCR techniques, and gel electrophoresis are required. A knowledge of forest tree reproduction is desirable. An availability and willingness to travel during the course of this study is also required. The successful candidate needs to have demonstrated an ability to work independently. If you are interested in the job, please forward your resume and three letters of recommendation to me at the following address. E-mail responses are acceptable. Dr. Gerald A. Tuskan gtk@ornl.gov : e-mail Biofuels Feedstock Development Program (615) 576-8141 : phone Oak Ridge National Laboratory (615) 576-8143 : fax P.O. Box 2008, MS-6352 Bldg 1503, Rm 1F Oak Ridge, TN 37831 From owner-rapd@net.bio.net Tue Oct 25 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!EU.net!uunet!newstf01.cr1.aol.com!newsbf01.news.aol.com!not-for-mail From: mmassoudi@aol.com (MMASSOUDI) Newsgroups: bionet.molbio.rapd Subject: Re: PCR Machines Date: 26 Oct 1994 13:21:04 -0400 Organization: America Online, Inc. (1-800-827-6364) Lines: 8 Sender: news@newsbf01.news.aol.com Message-ID: <38m360$c7d@newsbf01.news.aol.com> References: <01HIJ6OYQXRM9AMH0Y@ubvms.cc.buffalo.edu> NNTP-Posting-Host: newsbf01.news.aol.com In article <01HIJ6OYQXRM9AMH0Y@ubvms.cc.buffalo.edu>, V226UHBQ@UBVMS.CC.BUFFALO.EDU writes: HI DEAR: 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 owner-rapd@net.bio.net Tue Oct 25 22:00:00 1994 Path: biosci!CFL.FORESTRY.CA!HAMELIN From: HAMELIN@CFL.FORESTRY.CA Newsgroups: bionet.molbio.rapd Subject: MJ-Research cyclers Date: 26 Oct 1994 06:03:49 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: <941026090240.19b07@CFL.FORESTRY.CA> NNTP-Posting-Host: net.bio.net 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? From owner-rapd@net.bio.net Wed Oct 26 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!uknet!daresbury!not-for-mail From: dudy bar-zvi Newsgroups: bionet.molbio.rapd Subject: RoboCycler? Date: 27 Oct 1994 15:02:36 -0000 Lines: 14 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <38ofec$mri@mserv1.dl.ac.uk> Original-To: methods@dl.ac.uk, rapd@dl.ac.uk Dear Netters, I am thinking to purchase a new cycler to my lab. The features of Stratagene RoboCycler appear to be promising. i would be thankful to learn from RoboCycler users about their experience and recommendation. Also, does this machine have a test tube probe to monitor the temperature in the test tube in addition to the blocks' temperature? Thanks, Dudy Bar-Zvi Dept. of Life Sciences Ben-Gurion University Beer-Sheva, Israel. From owner-rapd@net.bio.net Wed Oct 26 22:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!torn!news.ccs.queensu.ca!qucdn!forsdyke Organization: Queen's University at Kingston Date: Thu, 27 Oct 1994 10:09:24 EDT From: Message-ID: <94300.100924FORSDYKE@QUCDN.QueensU.CA> Newsgroups: bionet.molbio.rapd Subject: Re: MJ-Research cyclers Distribution: world References: <941026090240.19b07@CFL.FORESTRY.CA> Lines: 2 After 11 months of use our MJ heat-pump just collapsed. But it worked very nicely before then. From owner-rapd@net.bio.net Wed Oct 26 22:00:00 1994 Path: biosci!UNIX.AMHERST.EDU!walin From: walin@UNIX.AMHERST.EDU (Athena Wen-chuan Lin) Newsgroups: bionet.molbio.rapd Subject: Re: RAPD on bacteria Date: 27 Oct 1994 16:32:27 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <199410272332.AA21949@amhux3.amherst.edu> NNTP-Posting-Host: net.bio.net Dear Alexandro, Could you tell me how many polymorphic patterns did you get using these primers? I will write mote later on to discuss with you about the problems I have. Thank you very much for the reply :) Athena From owner-rapd@net.bio.net Wed Oct 26 22:00:00 1994 Path: biosci!UNAMVM1.DGSCA.UNAM.MX!carvalho From: carvalho@UNAMVM1.DGSCA.UNAM.MX (Carvalho Torres Alexandro cassio-UACPYP) Newsgroups: bionet.molbio.rapd Subject: Re: RAPD on bacteria Date: 27 Oct 1994 11:12:29 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 25 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <38hrtu$iun@amhux3.amherst.edu> NNTP-Posting-Host: net.bio.net On 24 Oct 1994, Athena Wen-chuan Lin wrote: > Sorry about the empty post :) > I have read an article using RAPD to differentiate Helicobacter pyrori > (64 isolates from the same hospital). All six(?) primers were able > to differentiate all the isolates tested. A Japanese group also used > the same set of primers to differentiate Yersinia isolates. > has anybody else tried these primers? I don't seem to have much > good luck with them. > > > > Dear Lin, I used this primers and I get a lot of results, you should to try the good conditions to do your amplifications. The same lot of primers a used to amplify Pseudomonoas, the best one was 1283 primer. If you have some additional question write to me. \\\\\\\\\\\\\\\\\ Alexandro Carvalho INNSZ, Mexico City From owner-rapd@net.bio.net Thu Oct 27 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: Vancoppenolle@bota.ucl.ac.be (Benoit Van Coppenolle) Newsgroups: bionet.molbio.rapd Subject: How to use NIH Image (version 1.55) for RAPDs images analysis Date: 28 Oct 1994 15:35:26 -0000 Lines: 33 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <38r5nu$agr@mserv1.dl.ac.uk> X-Sender: vancoppe@fisher.sc.ucl.ac.be Original-To: rapd@dl.ac.uk Hi netters, I am brand new in here. Maybe the question I have has already been answered many times but I have vital needs for answers. I posted this message to bio-software as well. I have been collecting RAPD data from the analysis of a germplasm collection (more than 300 individuals) of an aquatic fern, with 10 Random primers. The diversity I obtained is quite large and the number of bands is tremendous. Now, I am trying to use a computer software for the analysis of all these data, for classification purposes. I would like to transform the banding data into scores of presence or absence of bands (0 and 1 codes) for each gel lane. Someone told me about NIH Image (version 1.55) but also said that it would require substantial manipulations (like pointing the bands to score), therefore being quite slow. Is there anybody who used or is using NIH Image for the same purpose, and add problems or not at all? Any tip for an adequate and fast way to use it for my purpose? Are there alternative software available (Mac) for a reasonable amount of money? Rapidly, Benoit ====================================================================== Benoit Van Coppenolle Tel: 32-10-473468 Plant Biology Laboratory Fax: 32-10-473471 Universite Catholique de Louvain E-Mail: Vancoppenolle@bota.ucl.ac.be 5, Place Croix du Sud B- 1348 Louvain-la-Neuve, Belgium / "What's life without plants?" ======================================================================