From owner-rapd@net.bio.net Thu Apr 01 23:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!zaphod.mps.ohio-state.edu!malgudi.oar.net!news.ysu.edu!psuvm!cunyvm!yvax.byu.edu!farmerj From: farmerj@yvax.byu.edu Newsgroups: bionet.molbio.rapd Subject: RE: Old RAPD-L archives Message-ID: <1993Apr2.104338.1709@yvax.byu.edu> Date: 2 Apr 93 17:43:38 GMT Organization: Brigham Young University Lines: 5 The old RAPD-L archives will be available on bionet as soon as the biosci people retrieve them. I have made them available by anonymous FTP from yvax.byu.edu (user:anonymous, password:rapd). They will be there for a few weeks, at least. RAPD-L itself will shut down on or about Monday 5 April 1993. Jim Farmer From owner-rapd@net.bio.net Sun Apr 04 23:00:00 1993 Path: biosci!LIFSCI.SDSU.EDU!SOBRAL From: SOBRAL@LIFSCI.SDSU.EDU Newsgroups: bionet.molbio.rapd Subject: Re: Multiple RAPD primers Message-ID: <930401125912.24600355@LIFSCI.SDSU.EDU> Date: 1 Apr 93 20:59:12 GMT Sender: kristoff@net.bio.net Distribution: bionet Lines: 8 Jim, we essentially see what Michael McClelland and John Welsh reported in the cited NAR paper; i.e., that about 2/3 or 3/4 of the bands generated with pairs of primers are novel with respect to the bands generated using the primers singly. So, it is worth it if you want to save $$$ on primers. However, we usually find that polymerase is the big $$$, so we don't usually skimp on primers. You need to pick primers that son't self anneal in the least, however. Bruno Sobral From owner-rapd@net.bio.net Wed Apr 07 23:00:00 1993 Path: biosci!lhc!darwin.sura.net!haven.umd.edu!uunet!munnari.oz.au!hp9000.csc.cuhk.hk!hkuxb.hku.hk!hkuxa.hku.hk!h9107446 From: h9107446@hkuxa.hku.hk (Ko Wing Kin) Newsgroups: bionet.molbio.rapd Subject: Help on assay Message-ID: Date: 8 Apr 93 14:18:25 GMT Sender: usenet@hkuxb.hku.hk (USENET News System) Distribution: bionet Organization: The University of Hong Kong Lines: 10 Nntp-Posting-Host: hkuxa.hku.hk Hello, My lecturer ask me to write a short review on "RNA-binding proteins", can anyone suggest what topics should I include in the assay ? Any suggestions are welcome. (including the references) Thanks in advance, Best regards, Wing-kin From owner-rapd@net.bio.net Wed Apr 07 23:00:00 1993 Path: biosci!lhc!darwin.sura.net!newsserver.jvnc.net!howland.reston.ans.net!news.cac.psu.edu!psuvm!cunyvm!yvax.byu.edu!farmerj From: farmerj@yvax.byu.edu Newsgroups: bionet.molbio.rapd Subject: Are there 0.5 ml screw-cap tubes? Message-ID: <1993Apr7.121058.1732@yvax.byu.edu> Date: 7 Apr 93 19:10:58 GMT Organization: Brigham Young University Lines: 7 As I reported some time ago, I have gotten an incredible improvement in RAPD reactions using a thermal cycler with an "evaporation control device" (top heater) which allows me to omit the oil overlay. The cost is that about 15-25% of the tubes evaporate. I am willing to pay that price, but I would rather not. Does anyone know of a source for 0.5-0.6 ml tubes with a screw cap? I have tried several snap-cap tubes and all of them fail at about the same rate. Jim Farmer From owner-rapd@net.bio.net Wed Apr 07 23:00:00 1993 Path: biosci!esvax.dnet.dupont.com!rafalski From: rafalski@esvax.dnet.dupont.com Newsgroups: bionet.molbio.rapd Subject: screw caps? Message-ID: <9304081201.AA01651@esds01.es.dupont.com> Date: 8 Apr 93 12:01:43 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 7 In response to a question by Jim Farmer about screw cap tubes: 0.5 ml screw cap tubes are available (for example Stratagene 410010, $60 per 1000), but these are tubes "with skirt" and would not fit in your thermocycler. Antoni Rafalski From owner-rapd@net.bio.net Thu Apr 08 23:00:00 1993 Path: biosci!s.u-tokyo!news.u-tokyo.ac.jp!wnoc-tyo-news!nec-tyo!nec-gw!sgiblab!darwin.sura.net!zaphod.mps.ohio-state.edu!malgudi.oar.net!news.ysu.edu!psuvm!cunyvm!yvax.byu.edu!farmerj From: farmerj@yvax.byu.edu Newsgroups: bionet.molbio.rapd Subject: RE: Are there 0.5 ml screw-cap tubes? Message-ID: <1993Apr8.105030.1736@yvax.byu.edu> Date: 8 Apr 93 17:50:30 GMT Organization: Brigham Young University Lines: 17 Thanks to the people who responded to the original question. There appears to be at least one source (thanks to Michael Wooten): MIDWEST SCIENTIFIC P.O. Box 458 Valley Park, MO 63088 800 227-9997 Thermal Reactor Tubes TC-10 500/cs $50/case They are sending me samples. Others of you may want to check them out also. Jim farmer From owner-rapd@net.bio.net Sun Apr 11 23:00:00 1993 Path: biosci!kristoff From: kristoff@net.bio.net (David Kristofferson) Newsgroups: bionet.molbio.rapd Subject: Re: Subscription Message-ID: Date: 12 Apr 93 22:26:13 GMT References: <9304121836.AA15604@esds01.es.dupont.com> Distribution: bionet Organization: BIOSCI International Newsgroups for Biology Lines: 18 russelsh@esvax.dnet.dupont.com writes: >I would like to subscribe to the RAPD newsgroup. >Sandra H. Russell >DuPont Life Sciences >RUSSELSH@ESVAX.DNET.DUPONT.COM >Thank you. Subscription mail should be sent to one of the following two addresses depending upon your location, *not* to the newsgroup posting address. Address Location ------- -------- biosci@daresbury.ac.uk Europe, Africa, and Central Asia biosci@net.bio.net Americas and the Pacific Rim From owner-rapd@net.bio.net Sun Apr 11 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!zaphod.mps.ohio-state.edu!darwin.sura.net!news.udel.edu!chopin.udel.edu!daschaff From: daschaff@chopin.udel.edu (Dennis A Schaff) Newsgroups: bionet.molbio.rapd Subject: Mid-Atlantic Plant Molecular Biology Society Meeting Message-ID: Date: 12 Apr 93 15:10:51 GMT Sender: usenet@news.udel.edu Organization: University of Delaware Lines: 95 Nntp-Posting-Host: chopin.udel.edu First Announcement 10th Annual Meeting Mid-Atlantic Plant Molecular Biology Society July 15-16, 1993 University of Delaware Clayton Hall Newark, Delaware Keynote Address Sheila McCormick USDA/ARS-Plant Gene Expression Center Molecular analysis of gametogenesis in plants. Invited Speakers Becky Boston (North Carolina State University) Regulation and function of maize ribosome inactivating proteins. Jim Carrington (Texas A&M) Replication and movement of a potyvirus that expresses GUS. Michael Dobres (Drexel University) A transcriptional marker for epidermal differentiation in Pisum sativum. Ted Klein (Du Pont Co.) Maize transformation: An industrial perspective. Antoni Rafalski (Du Pont Co.) Technology for molecular breeding: RAPD markers, microsatellites, and machines. Dan Roberts (USDA/ARS~Beltsville) Molecular basis of rhizosphere colonization by the plant beneficial bacterium, Enterobacter cloacae. Barbara Valent (Du Pont Co.) Two cloned genes for host specificity in the rice blast fungus, Magnaporthe grisea. Carroll Vance (USDA/ARS-Univ. of Minnesota) Primary assimilation of nitrogen in alfalfa nodules: Molecular features of the enzymes involved. John Watson (University of Maryland) Photo-regulated expression of protein kinase genes. Sessions Plenary sessions will include 30-minute presentations by the invited speakers and shorter talks by interested participants. Student and post-doctoral presentations are particularly encouraged. Poster sessions will be held in conjunction with plenary sessions. Commercial exhibitors will be present to highlight key products and developing technologies. Developing Technologies Paul Gilna (Los Alamos) The latest advances in community-based access to sequence data submission and maintenance technologies for GenBank. Housing Housing will be available on-campus or at local motels. Dinner A social hour and dinner will follow Sheila McCormick's address (July 15). Registration A call for abstracts, registration forms, and housing requests will be sent in May. Tour We are planning a tour of Longwood Gardens, Kennett Square PA (18 miles from the University of Delaware) after the meeting. Further Information If you have any questions or need further information, please contact the organizer: Dennis A. Schaff Department of Plant and Soil Sciences University of Delaware Newark, DE 19717-1303 (302) 831-2534 (302) 831-3651 (FAX) daschaff@brahms.udel.edu (e-mail) Please copy this announcement and pass it on to interested colleagues. From owner-rapd@net.bio.net Sun Apr 11 23:00:00 1993 Path: biosci!esvax.dnet.dupont.com!russelsh From: russelsh@esvax.dnet.dupont.com Newsgroups: bionet.molbio.rapd Subject: Subscription Message-ID: <9304121836.AA15604@esds01.es.dupont.com> Date: 12 Apr 93 18:36:02 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 7 I would like to subscribe to the RAPD newsgroup. Sandra H. Russell DuPont Life Sciences RUSSELSH@ESVAX.DNET.DUPONT.COM Thank you. From owner-rapd@net.bio.net Mon Apr 12 23:00:00 1993 Path: biosci!NET.BIO.NET!kristoff From: kristoff@NET.BIO.NET (Dave Kristofferson) Newsgroups: bionet.molbio.rapd Subject: RAPD-L archives now available for FTP from net.bio.net Message-ID: Date: 13 Apr 93 00:05:46 GMT Sender: kristoff@net.bio.net Distribution: bionet Lines: 24 The archives of the former RAPD-L list are now available for anoynmous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/RAPD (Note the case! This is a UNIX machine and is case sensitive.). The files available are listed by date, YYMM, where YY is the year and MM is the month: 9201 9203 9205 9208 9210 9212 9302 9304 9202 9204 9207 9209 9211 9301 9303 current There was no 9206 file. Recent messages posted to RAPD/bionet.molbio.rapd are in the "current" file and can also be searched by WAIS/gopher as described in the BIOSCI FAQ. If you want a copy of the FAQ, please send a request to biosci@net.bio.net regardless of your geographical location. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net From owner-rapd@net.bio.net Tue Apr 13 23:00:00 1993 Path: biosci!BCRSSU.AGR.CA!WIERSMA From: WIERSMA@BCRSSU.AGR.CA ("Paul A. Wiersma; Summerland, B.C.") Newsgroups: bionet.molbio.rapd Subject: use of microtitre plates in PCR Message-ID: <01GX0GEO763M00C77X@GW.AGR.CA> Date: 15 Apr 93 00:15:45 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 13 14-Apr-1993 I'd appreciate hearing your comments about use of 96-well microtitre plates for RAPD-PCR. The ease of setting up reactions appears useful but are there any problems with plates warping or wells evaporating? Thanks. Paul A. Wiersma, Ph.D. Agriculture Canada Research Station phone: (604) 494-7711 Summerland, BC fax : (604) 494-0755 Canada V0H 1Z0 Internet: wiersma@bcrssu.agr.ca From owner-rapd@net.bio.net Tue Apr 13 23:00:00 1993 Path: biosci!NET.BIO.NET!kristoff From: kristoff@NET.BIO.NET (Dave Kristofferson) Newsgroups: bionet.molbio.rapd Subject: Change from LISTSERV Message-ID: Date: 14 Apr 93 22:25:03 GMT Sender: kristoff@net.bio.net Distribution: bionet Lines: 24 I received the following question which I should call to the attention of those of you who are primarily familiar with LISTSERV: ---------------------------------------------------------------------- > Also, when I reply to a message from rapd@net.bio.net, the reply > function of my system will put the author's address of that message in > the To: field. Will my message (reply) be seen in the > rapd@net.bio.net group? The behavior above is standard for Internet mailing lists while BITNET LISTSERV lists would default to a reply to the group. You must explicitly add the newsgroup address (or else use a "reply all" function in your mail program if one exists to automatically include the newsgroup address). The Internet adopted this standard to prevent the waste of bandwidth, i.e., people have to make a conscious decision to reply to the list and not just broadcast messages by default. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net From owner-rapd@net.bio.net Wed Apr 14 23:00:00 1993 Path: biosci!esvax.dnet.dupont.com!rafalski From: rafalski@esvax.dnet.dupont.com Newsgroups: bionet.molbio.rapd Subject: microplates for RAPDs Message-ID: <9304151130.AA13189@esds01.es.dupont.com> Date: 15 Apr 93 11:30:40 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 16 In reply to a question about using 96-well plates for RAPDs: There is no problem using 96-well plates, as long as the plate is compatible with the thermocycler - stable at dentauration temperatures, etc. MJ research advertises a plate designed for thermocycling, several other companies have such plates, too. Polycarbonate is a suitable material, polystyrene is not. In general, you will have to use oil to prevent evaporation. Several labs are experimenting with small volume multi-well plates that do not require oil. Ther is a 4x96 well plate from Hans Lehrach's lab (see recent article in Nature), available from Genetix 44-202-4902-03, 44-202-4902-06 fax, and a 9x96 well plate, available from Helix (c/o Skip Garner General Atomics/Helix "garner@vaxd.gat.com") - see recent a rticle in Bio/Techniques. We use a polypropylene plate of our own design that is 2x96 and does not require oil (but it does not fit in standard 96-well format). Antoni Rafalski From owner-rapd@net.bio.net Fri Apr 16 23:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!gatech!pitt.edu!zxxst From: zxxst+@pitt.edu (Zhihua Xie) Newsgroups: bionet.molbio.rapd Subject: Re: Are there 0.5 ml screw-cap tubes? Message-ID: <9228@blue.cis.pitt.edu> Date: 17 Apr 93 02:21:13 GMT References: <1993Apr7.121058.1732@yvax.byu.edu> Sender: news+@pitt.edu Organization: University of Pittsburgh Lines: 1 test, please ignore From owner-rapd@net.bio.net Fri Apr 16 23:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!gatech!pitt.edu!zxxst From: zxxst+@pitt.edu (Zhihua Xie) Newsgroups: bionet.molbio.rapd Subject: Re: test Message-ID: <9230@blue.cis.pitt.edu> Date: 17 Apr 93 02:34:03 GMT References: <1993Apr7.121058.1732@yvax.byu.edu> <9228@blue.cis.pitt.edu> <9229@blue.cis.pitt.edu> Sender: news+@pitt.edu Organization: University of Pittsburgh Lines: 1 Test again! From owner-rapd@net.bio.net Fri Apr 16 23:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!gatech!pitt.edu!zxxst From: zxxst+@pitt.edu (Zhihua Xie) Newsgroups: bionet.molbio.rapd Subject: test Message-ID: <9229@blue.cis.pitt.edu> Date: 17 Apr 93 02:29:12 GMT References: <1993Apr7.121058.1732@yvax.byu.edu> <9228@blue.cis.pitt.edu> Sender: news+@pitt.edu Organization: University of Pittsburgh Lines: 1 This is a test From owner-rapd@net.bio.net Sun Apr 25 23:00:00 1993 Path: biosci!esvax.dnet.dupont.com!scolnipa From: scolnipa@esvax.dnet.dupont.com Newsgroups: bionet.molbio.rapd Subject: (none) Message-ID: <9304262139.AA01725@esds01.es.dupont.com> Date: 26 Apr 93 21:39:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 22 >I was wondering if someone out there could explain to me in layman's terms >the difference between a RAPD marker being linked to a trait in repulsion >vs in coupling and how this would affect the segregation ratios in an F2 >population. >Thanks for any and all info, >John John: in coupling or cis phase the positive RAPD allele (the allele that gives rise to the RAPD band) is in the same homologous chromosome as the mutant allele, whereas it's in the other in repulsion or trans. RAPDs in general are dominant, thus you can't tell the difference between hets and homozygous dominants. Dominant markers in trans are not very useful for linkage analysis (see Reiter et al., PNAS 89,1477-1481, 1992). Cheers Pablo Scolnik From owner-rapd@net.bio.net Sun Apr 25 23:00:00 1993 Path: biosci!ABRSLE.AGR.CA!HACHEY From: HACHEY@ABRSLE.AGR.CA (john hachey) Newsgroups: bionet.molbio.rapd Subject: marker segregation Message-ID: <01GXH2WQIQ8I0009DJ@GW.AGR.CA> Date: 26 Apr 93 21:58:12 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 13 Hello, I was wondering if someone out there could explain to me in layman's terms the difference between a RAPD marker being linked to a trait in repulsion vs in coupling and how this would affect the segregation ratios in an F2 population. Thanks for any and all info, John From owner-rapd@net.bio.net Sun Apr 25 23:00:00 1993 Path: biosci!AGCS.PSU.EDU!Mark_Guiltinan From: Mark_Guiltinan@AGCS.PSU.EDU (Mark Guiltinan) Newsgroups: bionet.molbio.rapd Subject: RE: RAPD Variation Message-ID: <01GXH6QW7S3M935GU0@psupen.psu.edu> Date: 26 Apr 93 22:45:17 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 9 I would like to start a discussion thread on the amount of, sources and solutions to variation in RAPD analysis. Please make all postings to the RAPD group. Thanks, Mark Guiltinan Penn State Biotechnology Institute mjg@psupen.psu.edu From owner-rapd@net.bio.net Wed Apr 28 23:00:00 1993 Path: biosci!YVAX.BYU.EDU!ZOOLOGYFTP From: ZOOLOGYFTP@YVAX.BYU.EDU Newsgroups: bionet.molbio.rapd Subject: RAPD references Message-ID: <01GXKY61MGSY8Y5V19@yvax.byu.edu> Date: 29 Apr 93 17:20:03 GMT Sender: daemon@net.bio.net Distribution: bionet Organization: Brigham Young University Lines: 37 I have extracted references with abstracts to RAPD and RAPDS from ENTREZ 4.0, the current release. If anyone is interested, they are in two files that are available by anonymous FTP. RAPD_ENTREZ.REFS RAPD_NEIGHBORS_ENTREZ.REFS The first file is references that were found by searching the terms RAPD or RAPDS. The second file is "neighbors" to the RAPDS articles, some of which are on RAPD and some of which are on related topics. These files are available from yvax.byu.edu USER: anonymous PASSWORD: rapd I recommend ENTREZ. It has all the nucleic acid and protein sequences, a National Library of Medicine reference database on sequences, and software to use them. It comes on a CD-ROM, updated four times a year, for about US$ 55/year. You can get information from info@ncbi.nlm.nih.gov James L. Farmer Department of Zoology 571 WIDB Brigham Young University Provo, Utah 84602, USA (801) 378-2153 (OFFICE) (801) 378-7499 (FAX) FARMERJ@YVAX.BYU.EDU FARMERJ@BYUVAX.BITNET