From owner-rapd@net.bio.net Sun Aug 15 23:00:00 1993 Path: biosci!ACD.TUSK.EDU!PRAKASH From: PRAKASH@ACD.TUSK.EDU Newsgroups: bionet.molbio.rapd Subject: Software for analysis of digitized RAPD fingerprints? Message-ID: <01H1T9VQVQDK0001EA@Acd.Tusk.Edu> Date: 16 Aug 93 17:22:57 GMT Sender: daemon@net.bio.net Distribution: bionet Organization: Tuskegee University Lines: 16 Dear Fellow RAPD scientists: We are working on DNA amplification fingeprinting, a subset of RAPD procedure. We normally see 15-20 bands per lane and a very high degree of polymorphism in sweetpotato. We are using computer scanning to to store the images. Now, does any one know a computer software that can read through these images, compare bands, and determine the extent of similarity between lanes? I came across in ad in the Science magazine for a program called "Gel Marker" for RFLP analysis. Has any one used this software and any comments? Any info and assistance would be appreciated. C. S. Prakash Tuskegee University Prakash@acd.tusk.edu (205) 727-8023 From owner-rapd@net.bio.net Sun Aug 15 23:00:00 1993 Path: biosci!UNR.EDU!hoelzer From: hoelzer@UNR.EDU (Guy A Hoelzer) Newsgroups: bionet.molbio.rapd Subject: Postdoctoral Position Message-ID: Date: 16 Aug 93 18:02:53 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 16 POSTDOCTORAL POSITION. A postdoctoral position is available at the University of Nevada, Reno to participate in a field and laboratory study of dispersal and genetic population structure of Mexican Spotted Owls. Applicants should be familiar with modern molecular genetic techniques, including mtDNA sequencing and microsatellite characterization. The project is funded by NSF and is part of a rapidly developing program at the University of Nevada, Reno in population and conservation biology. The successful candidate will be expected to participate in on-going studies and to pursue his/her own research. Send CV, description of previous laboratory and field experience, and names of three references to: Dr. Peter B. Stacey, Program in EEC Biology, University of Nevada, 1000 Valley Road, Reno NV 89512. Phone (702) 784-1436. Applications accepted until position filled. An Equal Opportunity/Affirmative Action Employer. From owner-rapd@net.bio.net Mon Aug 16 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: daj@uk.ac.ic.nhm ((David Johnston) daj) Newsgroups: bionet.molbio.rapd Subject: >Subject: Re: Software for analysis of digitized RAPD fingerprints? Message-ID: <1993Aug17.093121.9823@gserv1.dl.ac.uk> Date: 17 Aug 93 10:33:35 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 28 Precedence: first-class Original-To: rapd@uk.ac.daresbury X-Popmail-Charset: British Original-Cc: daj@nhm.ic.ac.uk UltraViolet Products Ltd sell a couple of packages: GELMATCH works under MS Windows. You use a scanner to create the gel image and it calculates fragment sizes etc and allows comparison between gels. However, as I remember it, it can only work with a few (6?) gels at a time and as it always works with the scanned image, each gel occupies a lot of memory/disk space. Alternately MOLMATCH runs under MS DOS and uses a graphics tablet/digitiser (so you have to enter the origin and fragment positions by hand but this is very quick and the graphics tablet (Summasketch) is included and comes with MS Windows drivers so it can also be used with MS Windows drawing packages etc). This also calculates fragment sizes etc and permits you to build up databases of fragment patterns for comparisons. These store patterns as lists of band sizes and whether they are singles, doublets or triplets so each record takes up minimal memory/disk space. IMHO it is dead easy to use and allows you to adjust the sensitivity of the comparison (% variation in calculated band size acceptable for match and % of bands which must match). We have just bought one for our RAPD work. Hope this helps, if you need the address of UVP drop me an email, Cheers DAJ David A. Johnston Dept of Zoology, The Natural History Museum, Cromwell Road, South Kensington, London SW7 5DB. (tel 071 9389297, fax 071 9388754, email daj@nhm.ic.ac.uk) From owner-rapd@net.bio.net Mon Aug 16 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: S.P.Harrison@uk.ac.bath.gdr (S P Harrison) Newsgroups: bionet.molbio.rapd Subject: Research Position Message-ID: <1993Aug17.163743.9062@gserv1.dl.ac.uk> Date: 17 Aug 93 16:36:52 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 28 Precedence: first-class Original-To: rapd@uk.ac.daresbury RESEARCH FELLOW DNA FINGERPRINTING OF HORSES. One of three positions remain in this area for 1993. This three year appointment is funded by The Leverhulme Trust. The project is concerned with the use and further development of DNA fingerprinting by RAPDs and microsatellites for the study of various horse populations. The candidate will join an expanding research group and should have a good first degree in Genetics or Biological Sciences. An MSc or PhD is desirable, but not essential. Applicants not possessing a higher degree would register for a PhD. 11,571. Full superannuation will be added to this. Please submit applications in the form of a detailed CV to: Dr.S.P.Harrison, The Royal Agricultural College, Cirencester, GL7 6JS. (Tel. 0285 652531, Fax. 0285 650219). Closing Date: 27th August, 1993. From owner-rapd@net.bio.net Mon Aug 16 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!europa.eng.gtefsd.com!uunet!psgrain!ee.und.ac.za!hippo.ru.ac.za!mimq From: mimq@hippo.ru.ac.za (Molapo Qhobela) Newsgroups: bionet.molbio.rapd Subject: Re: Software for analysis of digitized RAPD fingerprints? Message-ID: Date: 17 Aug 93 16:08:15 GMT References: <01H1T9VQVQDK0001EA@Acd.Tusk.Edu> Distribution: bionet Organization: Rhodes University, Grahamstown, South Africa Lines: 35 In <01H1T9VQVQDK0001EA@Acd.Tusk.Edu> PRAKASH@ACD.TUSK.EDU writes: >Dear Fellow RAPD scientists: >We are working on DNA amplification fingeprinting, a subset of RAPD >procedure. We normally see 15-20 bands per lane and a very high degree >of polymorphism in sweetpotato. We are using computer scanning to >to store the images. Now, does any one know a computer software >that can read through these images, compare bands, and determine >the extent of similarity between lanes? I came across in ad in the >Science magazine for a program called "Gel Marker" for RFLP analysis. >Has any one used this software and any comments? >Any info and assistance would be appreciated. >C. S. Prakash >Tuskegee University > Hi, You could try GEL MATCH which is sold by UVP or GelManager, which was developed bby Peter Jackman and its sold by Biosystematica. Both will allow you to compare lanes of gels and determine the degree to similarity. They both read TIFF files and most scanning facilities allow you to store the image in that format. Best of luck Molapo -- Molapo Qhobela PhD. | Dept. of Microbiology Internet: mimq@hippo.ru.ac.za | Rhodes University Telephone: +27 (461) 318447 | PO Box 94, Grahamstown 6140 Telefax: +27 (0461) 24377 | South Africa From owner-rapd@net.bio.net Wed Aug 18 23:00:00 1993 Path: biosci!CABELL.VCU.EDU!bio2dle From: bio2dle@CABELL.VCU.EDU (David L. Erickson) Newsgroups: bionet.molbio.rapd Subject: subscribtion to RAPD billboard Message-ID: <9308191826.AA16359@cabell.vcu.edu> Date: 19 Aug 93 18:26:55 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 13 I am interested in subscribing to a billboard concerning the use of Randomly Amplified Polymorphic DNA. If I am correct in assuming this is the address to which subscription requests should be sent, please sign me on. If this is in fact not the correct address, if you could send me a message with the correct address, I would greatly appreciate it. Thank you, David Erickson bio2dle@cabell.vcu.edu From owner-rapd@net.bio.net Wed Aug 18 23:00:00 1993 Path: biosci!LIFSCI.SDSU.EDU!SOBRAL From: SOBRAL@LIFSCI.SDSU.EDU Newsgroups: bionet.molbio.rapd Subject: POST-DOCTORAL POSITION IN PLANT GENETICS Message-ID: <930819104301.24608347@LIFSCI.SDSU.EDU> Date: 19 Aug 93 17:43:01 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 18 A two or three year post-doctoral position is available immediately to study genetics and evolution of sugarcane and its relatives (the Saccharum complex). The position is at the California Institute of Biological Research, 11099 North Torrey Pines Rd., Suite 300, La Jolla, CA, 92037. CIBR is a private, non-profit research institution funded mainly by governmental grants. The applicant should have a Ph.D. in genetics, population biology, or related area; expertise with statistical analysis would be a plus and experience with RFLP and PCR techniques is a must. Salary competitive\ and commesurate with experience. Applications will be accepted until the position is filled. Contact: Dr. Bruno WS Sobral, CIBR, at the above address, or via phone at (619)535-5483 (office) or 535-5491 (lab). Fax: (619)535-5472. E-mail: sobral@lifsci.sdsu.edu. Please send 3 letters of reference and relevant reprints of work. Interviews will be during September 8-15 and October 15-November 15. Latest start date is January 1994, or until the position is filled. Bruno Sobral From owner-rapd@net.bio.net Wed Aug 18 23:00:00 1993 Path: biosci!ACD.TUSK.EDU!PRAKASH From: PRAKASH@ACD.TUSK.EDU Newsgroups: bionet.molbio.rapd Subject: Re: Software for Digitized Gel Images Message-ID: <01H1XJ90KCQK0003E6@Acd.Tusk.Edu> Date: 19 Aug 93 18:28:11 GMT Sender: daemon@net.bio.net Distribution: bionet Organization: Tuskegee University Lines: 7 Around August 19, some one sent me an e-mail asking me for my reprint on DNA Amplified Fingerprinting. Unfortunately, due to the printer goof I lost his address. Could that individual please send me another request? From hazy memory, the individual's name may have been Dr. Mitchell. Thanks Prakash@acd.tusk.edu From owner-rapd@net.bio.net Wed Aug 18 23:00:00 1993 Path: biosci!YVAX.BYU.EDU!anderswr From: anderswr@YVAX.BYU.EDU (W. Ralph Andersen) Newsgroups: bionet.molbio.rapd Subject: MJ Research thermocyclers Message-ID: <01H1XBH7JF0Y90VAJU@yvax.byu.edu> Date: 19 Aug 93 15:45:11 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 23 Maybe some of you would be interested in our thermocycling profile. We are useing the Stoffel fragment on two MJ Research machines. We are also using MJ's 96-well polycarbonate plates. Costar's work equally well. In both cases you have to watch out for "funny" batches of plates. Here's our profile. The temp settings are as programed in the machine and are not thermocouple measures in the reaction chambers. Begin: 96 C 3 min (I doubt if this is necessary but we do it anyway---doesn't hurt) 1. 94 C < 2 sec 2. Ramp at maximum delta temperature to 34 C < 2 sec (no dwell time in the program) 3. Ramp at 0.3 degrees per sec to 72 C (you could use .25 degrees per sec ramp speed)(no dwell time at 72) 4. From 72 C we ramp to 94 C at the rate of .2 degrees per sec. Cycle 1 through 4 40 times. Finish with a 4 min 72 C extension. The profile as measured with a small thermocouple and recorder is a lazy, fat Zee. The cycle time from peak to peak is ca. 4.6 min or about 3.2 hours. We like it. From owner-rapd@net.bio.net Wed Aug 18 23:00:00 1993 Path: biosci!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!torn!nott!nrcnet0!10.164.nrc.ca!nash From: nash@biologysx.lan.nrc.ca (John Nash) Newsgroups: bionet.molbio.rapd Subject: RAPD fingerprinting - algorithms for similarity? Message-ID: Date: 19 Aug 93 12:14:08 GMT Sender: root@nrcnet0.nrc.ca (Operator) Organization: National Research Council of Canada Lines: 16 Nntp-Posting-Host: 132.246.164.10 Hi, Does anybody use RAPDs for bacterial fingerprinting? What sort of algorithms or formulae are used to determine whether 2 species are the same? I'd expect they'd count # similar bands vs # diff. bands with respect to total # bands and create some sort of index. Thanks, cheers, John John Nash | Email: Nash@biologysx.lan.nrc.ca. Institute for Biological Sciences | National Research Council of Canada | Email to my other NRC accounts Ottawa, Ontario, Canada. | is usually forwarded here. *** Disclaimer: All opinions are mine, not NRC's! *** From owner-rapd@net.bio.net Wed Aug 18 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!munnari.oz.au!uniwa!uniwa!not-for-mail From: mitch@uniwa.uwa.edu.au (Michelle Waycott) Newsgroups: bionet.molbio.rapd Subject: Software... Message-ID: <24v9rl$l3i@uniwa.uwa.edu.au> Date: 19 Aug 93 07:24:37 GMT Organization: The University of Western Australia Lines: 25 NNTP-Posting-Host: uniwa.uwa.edu.au X-Newsreader: TIN [version 1.2 PL1] Hi there everyone, I thought I should get a bid in for a WONDERFUL program from NIH for the Mac called IMAGE. This program is public domain and accepts images from many input sources. I use a flatbed scanner to generate images of my gels to work with then import them into IMAGE. There are many different ways of analysing these images depending on what you want to do with them. There is also good support through an Internet user group and a direct line to the programmer (via the same) for bugs/new ideas/info (can't get better than that!). Image is easy to use and had a good manual you can print out yourself. Try it before you spend lots of money on something that does less! Good luck Mitch PS I don't work for NIH! I'm just a humble student :-) ** Michelle Waycott ** ** Uni of Western Australia ** ** mitch@uniwa.uwa.edu.au ** From owner-rapd@net.bio.net Wed Aug 18 23:00:00 1993 Path: biosci!YVAX.BYU.EDU!anderswr From: anderswr@YVAX.BYU.EDU (W. Ralph Andersen) Newsgroups: bionet.molbio.rapd Subject: Oops! Error in our profile report Message-ID: <01H1XE84GNFM90UPV3@yvax.byu.edu> Date: 19 Aug 93 17:03:23 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 13 I may have said something misleading in myfirst letter. Try to follow this addendum. Begin @ 94 C 3 min. 1. 94 C < 2 sec. Then ramp at maximum machine rate to 34 C. No dwell time. 2. Ramp to 72 C @ the rate of 0.3 degrees per second (could try 0.25 deg. per sec) 3. No dwell time at 72C but at this point ramp from 72 C to 94 C at 0.2 degrees per second. Repeat 1-3 40 cycles. If you try it let know what you think. Thanks. As I said, it works OK or us. From owner-rapd@net.bio.net Wed Aug 18 23:00:00 1993 Path: biosci!JOPLIN.BIOSCI.ARIZONA.EDU!rsheehy From: rsheehy@JOPLIN.BIOSCI.ARIZONA.EDU ("Bob Sheehy") Newsgroups: bionet.molbio.rapd Subject: (none) Message-ID: <9308192043.AA06615@joplin.biosci.arizona.edu> Date: 19 Aug 93 20:43:43 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 31 Hey there! For those interested in computer analysis of gels, and in possession of Macs, try looking into NCSA gelreader2. This program takes a digitized photo of your autorad or EtBr stained gel and, using standards on the gel will determine the molecular weight of bands. Like most Macintosh based programs it is user condescending and fairly interactive. There is a manual which, for the most part, is unnecessary. The program is public domain and is available via anonymous FTP from a number of places including: 1) fly.bio.indiana.edu (129.79.224.25) Location: /molbio/mac/gelreader FILE rw-r--r-- 322859 May 15 1992 gelreader2.hqx 2) Host evolution.bchs.uh.edu (129.7.2.43) Location: /pub/gene-server/mac FILE rw-r--r-- 322859 Jun 23 18:00 gelreader2.hqx This program, in conjunction with Image (mentioned in an earlier post) works great for the determination of molecular weights. There should be a program available in about a month for using the output from gelreader2 to perform the band sharing analysis between individuals Ala. Michael Lynch. For IBM fans check out past issues of Bio Techniques. I'm not sure how far back to look (less than a year) but someone has a public domain program for reading digitized fingerprint gels and determining the similarity index. Cheers bob . From owner-rapd@net.bio.net Sun Aug 22 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!spool.mu.edu!news.cs.indiana.edu!nstn.ns.ca!dragon.acadiau.ca!901106c From: 901106c@dragon.acadiau.ca (Timothy Chipman) Newsgroups: bionet.molbio.rapd Subject: Inquiry: temp. cycle. protocols, ramp times, etc...? Message-ID: <1993Aug23.205036.11413@dragon.acadiau.ca> Date: 23 Aug 93 20:50:36 GMT Organization: Acadia University Lines: 24 I am currently using RAPD primers on honeybees to generate banding patterns. However, the protocol I am using with an MJ-Research thermal cycler takes about 4.5 hrs to complete a reaction of 40 cycles. I am curious what sort of procedures other people are using, to what degree of success, and if they have any recommendations to make if I wish to trim the reaction time without significantly decreasing yield. My current procedure is: 2 min@93 deg.C (start loop) 1 min@93 1 min@35 2 min@72 (end loop-40 repeats) 5 min@72 hold@4 I appreciate any help I get! Tim Chipman 901106c@dragon.acadiau.ca From owner-rapd@net.bio.net Sun Aug 22 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!darwin.sura.net!gatekeeper.es.dupont.com!esds01.es.dupont.com!TINGEYSV@esvx12.es.dupont.com From: tingeysv@esvx12.es.dupont.com Newsgroups: bionet.molbio.rapd Subject: Drawing Genetic Maps Message-ID: <1993Aug23.124558.18301@es.dupont.com> Date: 23 Aug 93 12:45:58 GMT Sender: news@es.dupont.com (USENET News System) Reply-To: tingeysv@esvx12.es.dupont.com Organization: DuPont (Opinions are those of the writer only) Lines: 31 Nntp-Posting-Host: esvx12.es.dupont.com Dear Mappers, We have had several inquires into whether we have a 'generic' program for drawing genetic maps. We don't but John Proctor, the programmer that created MapMaker Macintosh V1.0 and V2.0, would be willing to develop one if there is sufficient interest. If you would like to see a generic program for drawing genetic maps on the Macintosh, the IBM, or UNIX workstations please fill out the questionnaire indicating your preferences and return it to me. Scott Tingey P.O. Box 80402 Wilmington, DE 19880-0402 Email: tingeysv@esvax.dnet.dupont.com QUESTIONNAIRE: Preferred hardware platform: Current System Version: Printer: Preferred Input file format: Graphic file formats for export (e.g.. PICT, tiff, etc.): What graphic drawing software are you currently using: Graphic file formats for export (e.g.. PICT, tiff, etc.): From owner-rapd@net.bio.net Sun Aug 22 23:00:00 1993 Path: biosci!rutgers!utcsri!utnut!torn!nott!nrcnet0!10.164.nrc.ca!nash From: nash@biologysx.lan.nrc.ca (John Nash) Newsgroups: bionet.molbio.rapd Subject: Re: RAPD fingerprinting - algorithms for similarity? Message-ID: Date: 23 Aug 93 20:32:33 GMT References: Sender: root@nrcnet0.nrc.ca (Operator) Organization: National Research Council of Canada Lines: 107 Nntp-Posting-Host: 132.246.164.10 In article nash@biologysx.lan.nrc.ca (John Nash) writes: >Does anybody use RAPDs for bacterial fingerprinting? What sort of >algorithms or formulae are used to determine whether 2 species are the >same? I'd expect they'd count # similar bands vs # diff. bands with respect >to total # bands and create some sort of index. I asked this question a few days ago. Thank you to the folk who answered. It makes the whole struggle seem worthwhile when complete strangers mail you helpful answers! As is USENET custom, I'll summarise the responses. =========== SNIP ============================================ From: Scott Lyell Gardner Don't know if you got much response from your note, but here in my lab I use the NTSYS-PC package. You can do clustering on the similarity or dissimilarity matrices that are generated from your raw data. We basically code the gels by presence-absence of bands for each taxon. You have to make your own guess as to the level of genetic similarity for taxonomic identifcation or diagnosis. Good luck. I wouild be interested in your success at diagnosis of species or strains. Some stuff that the software does: It does lots more too. CVA Canonical variates analysis. POOLVCV Compute pooled within-groups variance-covariance matrix (used by the CVA program). New options have been added to existing programs: TRANSF - DIV, SHAPET, SHAPETU, 1TO2, 2TO1, 1TO3, 3TO1 transformations added. MXPLOT - Option for biplots added when in graphics mode. Option added to allow both axes in same scale. MOD3D - Option added to allow three axes not be in the same scale. Option added to control display of fill pattern on the base. Graphics programs - direct "native" support for a large number of printers and graphic ouptut file formats have been added. ------------- Problems? For scientific questions: F. James Rohlf Department of Ecology and Evolution State University of New York Stony Brook, NY 11794 USA 516-632-8580 BITNET: ROHLF@SBBIOVM FAX: 516-632-7626 For problems with your order, bills, condition of the disks, etc.: Exeter Publishing, Ltd. 100 North Country Road Setauket, NY 11733 USA Phone: 516-689-7838 Toll-free: 800-842-5892 FAX: 516-751-3435 ============================================================================== From: Neal Stewart John, One way we did it was to use a variety of genetic distances in the program ntsys-pc. With this you can also make trees to graphically represent your data. ============================================================================== From: (J Russell Stothard) jrs I have read your e-mail comment on RAPD's, I have been doing RAPD's for phylogenetics studies on african snails and have come to the conclusion that it will be nescessary to explore other algorithms for calculating similarity (of which there are many -- all of which will have different geometric properties). In my own example I have used percentage similarity as a measure, unfortunately the data I derive isn't fully 'additive', and in my case is very important as the clustering methods that I use to generate dendrograms have requirements that the data fits the 'additive model'. As a word of warning I would stay off UPGMA as a clustering method for your similarity matrix as it would assume a molecular clock (i.e.. ultrametric data). It is at present difficult to say if this non-additivity is inherent in the data (homoplasy) or merely an artifact of the similarity algorithm, hence there may be an algorithm that has better geometric properties than % age similarity. Hope this hasn't been too confusing, and if I come up with anything I'll get back in touch. ============================================================================== From: PAB5SUS@UK.AC.LEEDS.BIO.VAX (Sue Crossland) The exact algorithm you have described is Nei and Li's percentage similarity index, which you should be able to find in a standard numerical taxonomy book. Its sometimes called thr F-statistic. I have used this on Molluscs, and it works fine. ============================================================================== cheers, John John Nash | Email: Nash@biologysx.lan.nrc.ca. Institute for Biological Sciences | National Research Council of Canada | Email to my other NRC accounts Ottawa, Ontario, Canada. | is usually forwarded here. *** Disclaimer: All opinions are mine, not NRC's! *** From owner-rapd@net.bio.net Tue Aug 24 23:00:00 1993 Path: biosci!uwm.edu!math.ohio-state.edu!sol.ctr.columbia.edu!destroyer!nntp.cs.ubc.ca!newsserver.sfu.ca!sfu.ca!mckaya From: mckaya@fraser.sfu.ca (Sheldon McKay) Newsgroups: bionet.molbio.rapd Subject: Negative controls(?) Message-ID: Date: 25 Aug 93 19:57:22 GMT Sender: news@sfu.ca Organization: Simon Fraser University, Burnaby, B.C., Canada Lines: 31 I have recently started doing RAPDs using an Idaho Technologies Air thermocycler. Despite using double distilled, UV-irradiated and autoclaved water and being extremely careful with reagents, etc., 7 my negative control reaction (no template) often has amplification products. They rarely correspond to the products in the other lanes. Is this normal, or is there a way to get around this problem? I would also like to know if anyone has attempted to reproduce results from this or a similar Air cycler on a more conventional PCR machine 7 7 7 I am curious as to whether my results would be the same if I could reproduce the thermal profile on another machine. Please respond by email if you have any advice, Thanks, Sheldon McKay mckaya@fraser.sfu.ca :Will :wq PS- I'm sorry about the extra '7's etc, I an confounded by this editor :wq 7 PS I'm sorry about all the extra 7n From owner-rapd@net.bio.net Tue Aug 24 23:00:00 1993 Path: biosci!agate!doc.ic.ac.uk!uknet!pipex!sunic!corax.udac.uu.se!zeta.bmc.uu.se!daresbury!daresbury!news From: datherto@uk.ac.crc (Mr. D.J. Atherton) Newsgroups: bionet.molbio.rapd Subject: microtitre plate PTCs Message-ID: <1993Aug25.145525.18218@gserv1.dl.ac.uk> Date: 25 Aug 93 14:54:54 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 18 Precedence: first-class Original-To: rapd@uk.ac.daresbury Hi Netters, Call for information on thermal cyclers with microtitre plate accesories. Any comments on best/worst, cheapest/costly, simplest/complex, adaptability/value for money blah blah blah gratefully recieved. If I may suggest respondants reply rather than follow up to the BB, and I will post a precis at a later date, to save on band space, repeatition etc. Thanks in advance. Regards datherton@uk.ac.ox.path.vax David Atherton Univ Oxford Old professors never die..... Oxford Oxon ....They just lose their faculties! UK ! From owner-rapd@net.bio.net Tue Aug 24 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: CHRIS@za.ac.uovs.wwg3 Newsgroups: bionet.molbio.rapd Subject: Re: Inquiry: temp. cycle. protocols, ramp times, etc...? Message-ID: <1993Aug25.082907.3856@gserv1.dl.ac.uk> Date: 24 Aug 93 18:49:14 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Organization: Computer Sience, UOFS, Bfn, RSA Lines: 45 Precedence: first-class Original-To: rapd@uk.ac.daresbury Priority: normal X-Mailer: Pegasus Mail v2.3 (R5). I am currently using RAPD primers on honeybees to generate banding patterns. However, the protocol I am using with an MJ-Research thermal cycler takes about 4.5 hrs to complete a reaction of 40 cycles. I am curious what sort of procedures other people are using, to what degree of success, and if they have any recommendations to make if I wish to trim the reaction time without significantly decreasing yield. My current procedure is: 2 min@93 deg.C (start loop) 1 min@93 1 min@35 2 min@72 (end loop-40 repeats) 5 min@72 hold@4 I appreciate any help I get! Tim Chipman 901106c@dragon.acadiau.ca Dear Tim, You can replace the 1 min@93 with 15 secs@ 95,96. You may also find that reducing to 35 cycles does not significantly reduce yield. Chris@wwg3.uovs.ac.za ___________________________________________________________________ |Chris Viljoen | Dept. of Microbiology & | |Internet: chris@wwg3.uovs.ac.za | Biochemistry | |Telephone: (051) 401-2875 | Univ. of the Orange Freestate | |Telefax: 27/51/482004 | P.O. Box 339, Bloemfontein, 9300| | | South Africa | ------------------------------------------------------------------- From owner-rapd@net.bio.net Tue Aug 24 23:00:00 1993 Path: biosci!NET.BIO.NET!kristoff From: kristoff@NET.BIO.NET (David Kristofferson) Newsgroups: bionet.molbio.rapd Subject: IMPORTANT BIOSCI INFORMATION Message-ID: <9308250900.AA26808@net.bio.net> Date: 25 Aug 93 09:00:03 GMT Sender: kristoff@net.bio.net Distribution: bionet Lines: 243 Three important items follow: BIOSCI archive searching by e-mail, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our e-mail address directory, please take a few minutes to complete and return the form below. If your address information has changed since you listed yourself, please send us an updated form. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net **** SEARCHING BIOSCI ARCHIVES WITH WAISMAIL **** E-mail users can search the BIOSCI archives by using our waismail e-mail server. For instructions send the message help to waismail@net.bio.net. Leave the Subject: line blank. Other methods of searching the archives via WAIS and gopher are described in the BIOSCI FAQ. **** BIOSCI FREQUENTLY ASKED QUESTIONS (FAQ) SHEET **** New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and is available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/biosci.FAQ. It may also be requested by sending e-mail to biosci@net.bio.net (use plain English for your request). 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Using Gopher to complete the form --------------------------------- If you don't want to use a text editor, you can also use Dan Jacobson's gopher site to fill out the address database form as follows. Otherwise skip this section on gopher and proceed to the instructions for filling out the form below. > To add yourself to the database just point your > gopher client at merlot.welch.jhu.edu and select the following: > > --> 15. Searching For Biologists/ > > --> 9. E-mail Addresses of Biosci-Bionet Users/ > > --> 1. Add (or Correct) Your Address to the BIOSCI User Address > Data.. > > > And fill out the form. or Rob Harper's gopher site in Europe as follows: > Europeans can point their gopher client at gopher.csc.fi and add their > information to the database. All entries will be mailed directly to > Dave for incorporation in a wais source. > > The path to the questionare is as follows. > > ---> 10. Finnish EMBnet BioBox/ > > ---> 8. FAQ Files/ > > FAQ Files > > 1. EMBnet: Information. > 2. EMBnet: Internet resources guide. > 3. A Biologist's Guide to Internet Resources/ > 4. All FAQs (Frequently Asked Questions) Searches and Archives/ > --->5. Bionauts Address Database (questionaire) IMPORTANT INSTRUCTIONS - PLEASE READ CAREFULLY Please enter all responses after the : on each line, leaving one (1) blank space after the : (i.e., before the start of your text). Please do NOT extend your responses past the end of each line (80 characters) or alter any of the field identifiers such as "first name: ". Several lines are provided at the end of the form for comments, but, please adhere to the line length restriction. On the date: line, please enter the date in the DD-MM-YY format, e.g., 05-05-93 for 5 May 1993. This line will tell others when the information was last updated. Please be sure to include the 0's for single digit days or months, e.g., 05-05-93, not 5-5-93. 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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 Tue Aug 24 23:00:00 1993 Path: biosci!uwm.edu!rpi!batcomputer!cornell!newsstand.cit.cornell.edu!newsstand.cit.cornell.edu!usenet From: kh11@cornell.edu (Kathie Hodge) Newsgroups: bionet.molbio.rapd Subject: Re: Inquiry: temp. cycle. protocols, ramp times, etc...? Message-ID: <25gmb7INNgig@newsstand.cit.cornell.edu> Date: 25 Aug 93 21:41:59 GMT References: <1993Aug23.205036.11413@dragon.acadiau.ca> Sender: kh11@cornell.edu (Verified) Organization: Cornell University Lines: 24 NNTP-Posting-Host: 128.253.27.147 X-UserAgent: Nuntius v1.1.1d7 X-XXDate: Wed, 25 Aug 93 20:44:42 GMT Timothy Chipman writes: >the protocol I am using with an MJ-Research thermal cycler takes >about 4.5 hrs to complete a reaction of 40 cycles. Check out: Yu, K. and K.P. Pauls. 1992. Optimization of the PCR program for RAPD analysis. Nucleic Acids Res. 20 (10): 2606. The authors describe a program for the MJ Research PTC-100 thermocycler that takes only 2.5 hours. They claim to get sharper bands than with the traditional program. Their profile is 35 cycles of: 94 C for 5 sec 36 C for 30 sec 72 C for 60 sec I've tried it and it works fine (but note that I have an in-sample temperature probe which controls the cycling - so it's the sample itself that is held at 94 C for 5 sec, not just the block as in most other machines). Good luck. Kathie Hodge kh11@cornell.edu From owner-rapd@net.bio.net Wed Aug 25 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!darwin.sura.net!haven.umd.edu!purdue!mentor.cc.purdue.edu!inet.d48.lilly.com!mcvax4.d48.lilly.com!swift From: swift@mcvax4.d48.lilly.com Newsgroups: bionet.molbio.rapd Subject: subscription to RAPD board Message-ID: <1993Aug26.150953.1@mcvax4.d48.lilly.com> Date: 26 Aug 93 20:09:53 GMT Lines: 4 Nntp-Posting-Host: mcvax4.d48.lilly.com Please sign me on to the RAPD board. Thank you. Has anyone applied RAPD to bivales? From owner-rapd@net.bio.net Wed Aug 25 23:00:00 1993 Path: biosci!UICVM.UIC.EDU!LIMARMG%BRUFMG From: LIMARMG%BRUFMG@UICVM.UIC.EDU ("Roberto G.Lima") Newsgroups: bionet.molbio.rapd Subject: subscription Message-ID: <9308261545.AA27303@net.bio.net> Date: 26 Aug 93 15:45:58 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 19 Dear Sir, I am workimg with rapd techniques typing domestic animals from diferent breeds. I would really appreciate participating in this discussion group. As soon as possible , please send me a message of my request. Yours sincerely, Roberto Gil de Lima ****************************************************************** * Roberto Gil de Lima * * Departamento de Zootecnia, Veterinary School * * Universidade Federal de Minas Gerais-Belo Horizonte, MG * * BITNET LIMARMG@BRUFMG * * BRAZIL * ****************************************************************** From owner-rapd@net.bio.net Wed Aug 25 23:00:00 1993 Path: biosci!UNR.EDU!hoelzer From: hoelzer@UNR.EDU (Guy A Hoelzer) Newsgroups: bionet.molbio.rapd Subject: Re: Negative controls(?) Message-ID: Date: 26 Aug 93 16:34:55 GMT References: <9308252035.AA05432@net.bio.net> Sender: daemon@net.bio.net Distribution: bionet Lines: 24 On 25 Aug 1993, Sheldon McKay wrote: > I have recently started doing RAPDs using an Idaho Technologies Air > thermocycler. Despite using double distilled, UV-irradiated and > autoclaved water and being extremely careful with reagents, etc., > my negative control reaction (no template) often has amplification > products. They rarely correspond to the products in the other > lanes. Is this normal, or is there a way to get around this problem? Ironically, the worst PCR contamination problem I ever dealt with, which appeared as anomolous bands in my negative control, was the result of autoclaving. It turned out that other labs were autoclaving bacterial waste in the same autoclave and that produced alot of fragmented prokaryotic DNA in the air and interior surfaces of the autoclave. This DNA then contaminated other items placed in the same unit. This DNA was totally unrelated to the template I was using, and must have been highly degraded, but the use of short RAPD primers and the power of PCR amplification still produced bands in the negative control. Solution - stop autoclaving tubes, tips, water, etc., used in the RAPD reaction. It worked for me. From owner-rapd@net.bio.net Thu Aug 26 23:00:00 1993 Path: biosci!YVAX.BYU.EDU!FARMERJ From: FARMERJ@YVAX.BYU.EDU Newsgroups: bionet.molbio.rapd Subject: E-mail subscriptions to this newsgroup Message-ID: <01H28VS76HTU95OJA4@yvax.byu.edu> Date: 27 Aug 93 22:25:38 GMT Sender: daemon@net.bio.net Distribution: bionet Organization: Brigham Young University Lines: 16 I have recently received a fairly large number of requests for e- mail subscriptions to rapd@net.bio.net (Americas and Pacific rim) or rapd@daresbury.ac.uk (Europe and elsewhere). PLEASE send these requests, in plain English, to biosci@net.bio.net or biosci@daresbury.ac.uk and the people there will add your name to the list. Since your message will be read by a human being, there is no need for a special format. Be sure to tell them that you wish to subscribe to the rapd newsgroup. If you wish to end your subscription, please send them a message in plain English telling them to remove your name. Please pass this information on to your colleagues who may be interested. Jim Farmer farmerj@yvax.byu.edu From owner-rapd@net.bio.net Thu Aug 26 23:00:00 1993 Path: biosci!UICVM.UIC.EDU!LIMARMG%BRUFMG From: LIMARMG%BRUFMG@UICVM.UIC.EDU (Roberto Gil de Lima) Newsgroups: bionet.molbio.rapd Subject: subscription Message-ID: <9308272321.AA07058@net.bio.net> Date: 27 Aug 93 23:21:40 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 19 DEAR SIR, I am working with RAPD techniques typing domestic animals (especialy catlle) from different breeds. I would really appreciate participating in this discussion group. As soon as possible, please send me e message of my request. Yours sincerely, Roberto Gil de Lima *************************************************************** Roberto Gil de Lima Departamento de Zootecnia, Veterinary School Universidade Federal de Minas Gerais - Belo Horizonte - MG BITNET LIMARMG@BRUFMG Brazil From owner-rapd@net.bio.net Thu Aug 26 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!uunet!haven.umd.edu!purdue!mentor.cc.purdue.edu!inet.d48.lilly.com!mcvax4.d48.lilly.com!swift From: swift@mcvax4.d48.lilly.com Newsgroups: bionet.molbio.rapd Subject: RAPD and Bivalves Message-ID: <1993Aug27.102020.1@mcvax4.d48.lilly.com> Date: 27 Aug 93 15:20:20 GMT Lines: 2 Nntp-Posting-Host: mcvax4.d48.lilly.com Is anyone applying RAPD to bivalves? Inquiring minds want to know. From owner-rapd@net.bio.net Thu Aug 26 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!europa.eng.gtefsd.com!uunet!munnari.oz.au!news.Hawaii.Edu!uhunix.uhcc.Hawaii.Edu!stiles From: stiles@uhunix.uhcc.Hawaii.Edu (John Stiles) Newsgroups: bionet.molbio.rapd Subject: Re: Negative controls(?) Message-ID: Date: 25 Aug 93 23:27:24 GMT References: Sender: news@news.Hawaii.Edu Organization: University of Hawaii Lines: 25 In article mckaya@fraser.sfu.ca (Sheldon McKay) writes: >I have recently started doing RAPDs using an Idaho Technologies Air >thermocycler. Despite using double distilled, UV-irradiated and >autoclaved water and being extremely careful with reagents, etc., >7 > my negative control reaction (no template) often has amplification >products. They rarely correspond to the products in the other >lanes. Is this normal, or is there a way to get around this problem? > >I would also like to know if anyone has attempted to reproduce results >from this or a similar Air cycler on a more conventional PCR machine >7 >I am curious as to whether my results would be the same if I could >reproduce the thermal profile on another machine. Please respond >by email if you have any advice, Thanks, > >Sheldon McKay >mckaya@fraser.sfu.ca Sheldon, We (ant others I have talked with) have also seen this. It appears to be due to small amounts of DNA in the reagents (eg. Taq pol). These bands are not seen when sample DNA is included as it out competes the samll amount in the reagent. We don't worry about it. John stiles@uhunix.uhcc.hawaii.edu From owner-rapd@net.bio.net Thu Aug 26 23:00:00 1993 Path: biosci!YVAX.BYU.EDU!FARMERJ From: FARMERJ@YVAX.BYU.EDU Newsgroups: bionet.molbio.rapd Subject: Re: Negative controls Message-ID: <01H28UPLFKSE95OL99@yvax.byu.edu> Date: 27 Aug 93 21:56:42 GMT Sender: daemon@net.bio.net Distribution: bionet Organization: Brigham Young University Lines: 5 The labs here have also seen bands in negative controls. This was discussed at some length on RAPD-L (see the old archives, available from BIOSCI). Our experience is that everything "cures" the problem-- temporarily. We also no longer worry about them. They don't correspond to bands in the experimental tubes. Jim Farmer, farmerj@yvax.byu.edu From owner-rapd@net.bio.net Fri Aug 27 23:00:00 1993 Path: biosci!UMACMAIL.APLDBIO.COM!Janet_Ziegle From: Janet_Ziegle@UMACMAIL.APLDBIO.COM ("Janet Ziegle") Newsgroups: bionet.molbio.rapd Subject: Negative Controls Message-ID: <9308272241.AA19906@apldbio.com> Date: 27 Aug 93 07:40:31 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 14 Subject: Time:3:25 PM OFFICE MEMO Negative Controls Date:27 08 93 This is in response to Sheldon McKay's questions about negative controls. The amplification you are seeing in your negative control is probably coming from DNA contamination in the taq prep, that is DNA from the bacteria it was grown in, either T.aq. or E. cloi.. When amplifying for many cycles, at a low annealing temp, with a short primer, as in RAPDs, you may see amplification. Perkin Elmer now makes a Amplitaq LD (for Low DNA) which they say will contain less than 10 copies of the bacterial genome per tube. This amplitaq prep includes some column purification to remove most/all bacterial DNA. From owner-rapd@net.bio.net Sun Aug 29 23:00:00 1993 Path: biosci!qut.edu.au!P.HOEBEN From: P.HOEBEN@qut.edu.au (HOEBEN) Newsgroups: bionet.molbio.rapd Subject: (none) Message-ID: Date: 30 Aug 93 23:44:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 7 Dear rapd network, Could you please add me to your mailing list. Thank you Peter Hoeben Hoeben@qut.edu.au From owner-rapd@net.bio.net Mon Aug 30 23:00:00 1993 Path: biosci!waite.adelaide.edu.au!tmaguire From: tmaguire@waite.adelaide.edu.au (Tina Maguire) Newsgroups: bionet.molbio.rapd Subject: scanner for a mac Message-ID: <9308310122.AA04950@schooner.waite.adelaide.edu.au> Date: 31 Aug 93 01:22:39 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 6 Could anyone help me I am looking for a hand scanner that can image gels (agarose and polyacrylamide) and is compatible with a macintosh computer Thank you in advance Email tmaguire@waite.adelaide.edu.au From owner-rapd@net.bio.net Mon Aug 30 23:00:00 1993 Path: biosci!uoguelph.ca!boulding From: boulding@uoguelph.ca (Elizabeth BOULDING) Newsgroups: bionet.molbio.rapd Subject: RAPD (fwd) Message-ID: Date: 31 Aug 93 02:20:50 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 21 This is in response to the enquiry about who is doing RAPD on bivalves. Elizabeth Boulding boulding@uoguelph.ca ---------- Forwarded message ---------- Date: Mon, 30 Aug 1993 13:55:30 -0400 (AST) From: "Dr. Ellen Kenchington" To: boulding@uoguelph.ca Subject: RAPD We are doing RAPD on Placopecten magellanicus (sea scallop) as part of a population genetic study. Ellen Rice Kenchington (Dept. Fisheries & Oceans Canada) Carolyn Bird/Moshin Patwary (National Research Council Canada) Eleftherios Zouros/Marty Ball (Dalhousie University) We have over 113 positive primers and have tested them on families. From owner-rapd@net.bio.net Mon Aug 30 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!uunet!destroyer!newsrelay.iastate.edu!cobra.uni.edu!jurgenson From: jurgenson@cobra.uni.edu Newsgroups: bionet.molbio.rapd Subject: primers Message-ID: <1993Aug31.173731.16169@cobra.uni.edu> Date: 31 Aug 93 22:37:31 GMT Organization: University of Northern Iowa Lines: 5 During the past summer one or two postings advertized sources of primer sets or kits for doing rapds. I am interested in starting a project to race ty0pe cultivars of several fungal species and would appreciate any information which could direct me to ready made primer kits that we could use to begin our research. From owner-rapd@net.bio.net Mon Aug 30 23:00:00 1993 Path: biosci!uoguelph.ca!boulding From: boulding@uoguelph.ca (Elizabeth BOULDING) Newsgroups: bionet.molbio.rapd Subject: RE: RAPD and Bivalves (fwd) Message-ID: Date: 31 Aug 93 02:17:17 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 24 I enclose a couple of messages that came from posting the enquiry aboout RAPD on bivalves on the mollusc-molecular-news@sfu.ca Elizabeth Boulding boulding@uoguelph.ca ---------- Forwarded message ---------- Date: Mon, 30 Aug 1993 12:54:13 -0400 From: etter@umbsky.cc.umb.edu To: boulding@uoguelph.ca Subject: RE: RAPD and Bivalves (fwd) We are using RAPDs on deep-sea protobranch bivalves, but have also tried them on the oyster C. virginica and the mussel Mytilus edulis. We are mostly interested in looking at genetic structure of deep-sea populations. If you want any more info, let me know. Ron Etter etter@umbsky.cc.umb.edu From owner-rapd@net.bio.net Tue Aug 31 23:00:00 1993 Path: biosci!MERCURY.UARK.EDU!DRHOADS From: DRHOADS@MERCURY.UARK.EDU ("Doug Rhoads") Newsgroups: bionet.molbio.rapd Subject: Re: primers Message-ID: <38E21B42E82@uamercury.uark.edu> Date: 1 Sep 93 13:44:18 GMT Sender: daemon@net.bio.net Distribution: bionet Organization: University of Arkansas Lines: 60 >To: rapd@net.bio.net >From: jurgenson@cobra.uni.edu >Subject: primers >Date: 31 Aug 93 22:37:31 GMT >During the past summer one or two postings advertized sources of primer sets or >kits for doing rapds. I am interested in starting a project to race ty0pe >cultivars of several fungal species and would appreciate any information which >could direct me to ready made primer kits that we could use to begin our >research. > The best source of primers is to contact Dr. John Hobbs Nucleic Acid - Protein Service Unit Biotech Lab room 237, Wesbrook Building 6174 University Boulevard Univ. of British Columbia Vancouver, V6T 1Z3, Canada FAX 604-822-5437 Tel 604-822-6373 email hobbs@unixg.ubc.ca It usually takes longer but You get sets of 100 primers not 20. And the cost per primer is much better. However, if you want to synthesize your own you should contact Integrated DNA Technologies or Biosynthesis rates are at $2.50/base with no setup. For primers that are `guaranteed' to work you may want to consider 2 base primers. In our hands primers with all 4 bases generally give an average of 3-4 bands and range from 0 to 12 scorable bands. 2-base primers of the form: ********************************************************* 70% GC no 3' 2 or 3 base repeats bit primers # pattern CA GA CT GT 1 823 CCCACCAACC GGGAGGAAGG CCCTCCTTCC GGGTGGTTGG 2 827 CCACCCAACC* GGAGGGAAGG CCTCCCTTCC GGTGGGTTGG 3 883 CCAACCCACC GGAAGGGAGG CCTTCCCTCC GGTTGGGTGG 4 919 CCCACAACCC GGGAGAAGGG CCCTCTTCCC GGGTGTTGGG 5 923 CCACCAACCC GGAGGAAGGG CCTCCTTCCC GGTGGTTGGG 6 935 CCCAACACCC GGGAAGAGGG CCCTTCTCCC GGGTTGTGGG 7 947 CCAACCACCC GGAAGGAGGG CCTTCCTCCC GGTTGGTGGG In our hands these primers give on average 10 bands with a range from 2 to 20. This data is largely from larger genomes, avian and plant. In less comprehensive tests on 4 species of fungi the two base primers still average 5-7 bands where 4 base primers average 2-3. 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 Aug 31 23:00:00 1993 Path: biosci!PARGVA.AGR.CA!MACKENZIED From: MACKENZIED@PARGVA.AGR.CA ("DONALD MACKENZIE, SPQS") Newsgroups: bionet.molbio.rapd Subject: test Message-ID: <01H2FKS4S3J6000W85@GW.AGR.CA> Date: 1 Sep 93 16:25:43 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 1 test From owner-rapd@net.bio.net Tue Aug 31 23:00:00 1993 Path: biosci!YVAX.BYU.EDU!anderswr From: anderswr@YVAX.BYU.EDU (W. Ralph Andersen) Newsgroups: bionet.molbio.rapd Subject: Measuring heterozygosity in nat. pops. Message-ID: <01H2FVCSMSSY9105FT@yvax.byu.edu> Date: 1 Sep 93 22:28:34 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 19 Can any of you guide me on this question? Suppose I intend to use RAPDs to identify genetic variation among individuals in a population and further suppose I intend to convert selected RAPD loci to PCR-identified sequences by making PCR primers from the sequence information derived from the RAPD locus. My particular reason for doing this is to add heterozygosity estimates to my population DNA polymorphism data. My question is: how do you determine the best numbers to sample heterozygosity....in a wind- or an insect- pollinated population (number of loci and number of individuals sampled----if you sample 10 individuals, how many loci would give a reasonable estimate, 10? 40?, 80 loci?---- or would 10 loci measured on 40 individuals be a better estimate....that sort of question). You can see this deals with good science vs. the cruel realities of research economics. Appreciate any help or guidance. Thank you. Ralph A.