From owner-rapd@net.bio.net Sun May 02 23:00:00 1993 Path: biosci!esvax.dnet.dupont.com!rafalski From: rafalski@esvax.dnet.dupont.com Newsgroups: bionet.molbio.rapd Subject: Coupling/repulsion Message-ID: <9305032000.AA15417@esds01.es.dupont.com> Date: 3 May 93 20:00:13 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 20 In response to a question about RAPD band being in coupling or repulsion to the trait: IN coupling: Trait: + + + - - - + RAPD: + + + _ _ _ + In repulsion: Trait as above RAPD: - - - + + + - or: Coupling: RAPD band comes from the trait donor parent Repulsion: RAPD band comes from the other parent Hope this helps. Antoni rafalski@esvax.dnet.dupont.com From owner-rapd@net.bio.net Thu May 06 23:00:00 1993 Path: biosci!UNIXG.UBC.CA!hobbs From: hobbs@UNIXG.UBC.CA Newsgroups: bionet.molbio.rapd Subject: RAPD primers from UBC Message-ID: <9305071946.AA05509@unixg.ubc.ca> Date: 7 May 93 20:46:15 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 66 Alas, I said I was new to e-mail, and did not realise that the Greek symbol for micro would not be transmitted. This recorrects the earlier posting, with micrograms replacing grams! May, 1993 Dear Colleague, RE: SOURCE OF 10mers FOR RAPD MARKER RESEARCH In response to the need for a variety of 10mer primers for RAPD analyses at low cost, over the past eighteen months Dr. John Carlson designed, and we prepared, 700 primers according to the sequence specifications of Williams et al. (1990, Nucl Acids Res 18:6531). Dr. Carlson processed and distributed these at cost as kits of 100 unique primers. Participants expressed satisfaction with the primers and even after they were completely sold out, new and repeat orders kept arriving. Due to this popular demand, we are continuing the UBC RAPD primer project. We are firstly resynthesizing the same 700 primers as before. We will then move on to additional primer sets. As before we ship them as sterile, dry 10 microgram aliquots. Each set contains the sequence information for the primers. We plan to offer these primer sets on a continuing basis. Sets of 100 primers cost $300 Canadian (or $250US). This cost covers materials for the syntheses, purification, aliquotting, and packaging. Airmail costs are added: US$4 to most parts of the world. For courier delivery in the US, we add an additional $18US ($10CN for shipments within Canada). Courier delivery to other parts of the world is added at the rate charged to us: $23 to the UK, $24 to Western Europe, $28 to Australasia, $24 to the Far East, $42 to China and South America, and $47 to Africa (all prices in US$). Sets of 50 primers can be ordered from any set of 100 at a cost of $165 Canadian (US$140 ). The first, second, third, fourth, fifth and sixth sets of 100 primers (set #1, lot #2, set #2, lot #2, set #3, lot #2, set #4, lot #2, set #5 lot #2 and set#6 lot#2) are now being distributed. Set #7 lot #2 should become available in June. Individual primers from any of the kits available can be supplied at US$10 for each 10 microgram sample. The responsibility for the UBC RAPD primer project has been transferred, with Dr. Carlson's agreement, to the University of British Columbia's Nucleic Acid - Protein Service (NAPS) Unit, although Dr. Carlson remains in close touch with the project. As Director of the Unit, 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. For UBC RAPD Primer Orders: Mailing Address: Or Contact: University of British Columbia Dr. John Hobbs Attn: Dr. John Hobbs Director, NAPS Unit The Biotechnology Laboratory University of British Columbia #237 - 6174 University Boulevard voice phone: (604)822-6373 Vancouver, B.C. V6T 1Z3 Fax number: (604)822-5437 CANADA e-mail: hobbs@unixg.ubc.ca From owner-rapd@net.bio.net Thu May 06 23:00:00 1993 Path: biosci!UNIXG.UBC.CA!hobbs From: hobbs@UNIXG.UBC.CA Newsgroups: bionet.molbio.rapd Subject: RAPD primers from UBC Message-ID: <9305070029.AA07364@unixg.ubc.ca> Date: 6 May 93 09:29:06 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 50 May, 1993 Dear Colleague, RE: SOURCE OF 10mers FOR RAPD MARKER RESEARCH In response to the need for a variety of 10mer primers for RAPD analyses at low cost, over the past eighteen months Dr. John Carlson designed, and we prepared, 700 primers according to the sequence specifications of Williams et al. (1990, Nucl Acids Res 18:6531). Dr. Carlson processed and distributed these at cost as kits of 100 unique primers. Participants expressed satisfaction with the primers and even after they were completely sold out, new and repeat orders kept arriving. Due to this popular demand, we are continuing the UBC RAPD primer project. We are firstly resynthesizing the same 700 primers as before. We will then move on to additional primer sets. As before we ship them as sterile, dry 10 g aliquots. Each set contains the sequence information for the primers. We plan to offer these primer sets on a continuing basis. Sets of 100 primers cost $300 Canadian (or $250US). This cost covers materials for the syntheses, purification, aliquotting, and packaging. Airmail costs are added: US$4 to most parts of the world. For courier delivery in the US, we add an additional $18US ($10CN for shipments within Canada). Courier delivery to other parts of the world is added at the rate charged to us: $23 to the UK, $24 to Western Europe, $28 to Australasia, $24 to the Far East, $42 to China and South America, and $47 to Africa (all prices in US$). Sets of 50 primers can be ordered from any set of 100 at a cost of $165 Canadian (US$140 ). The first, second, third, fourth, fifth and sixth sets of 100 primers (set #1, lot #2, set #2, lot #2, set #3, lot #2, set #4, lot #2, set #5 lot #2 and set#6 lot#2) are now being distributed. Set #7 lot #2 should become available in June. Individual primers from any of the kits available can be supplied at US$10 for each 10 g sample. The responsibility for the UBC RAPD primer project has been transferred, with Dr. Carlson's agreement, to the University of British Columbia's Nucleic Acid - Protein Service (NAPS) Unit, although Dr. Carlson remains in close touch with the project. As Director of the Unit, 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. John Hobbs, Nucleic Acid - Protein Service (NAPS) Unit, Biotechnology Laboratory, University of British Columbia, Canada. FAX (604)822-5437; Tel. (604)822-6373 From owner-rapd@net.bio.net Thu May 06 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: hobbs@unixg.ubc.ca Newsgroups: bionet.molbio.rapd Subject: RAPD primers from UBC Message-ID: <1993May7.161922.19916@gserv1.dl.ac.uk> Date: 7 May 93 01:15:36 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 64 Original-To: rapd@uk.ac.daresbury Sorry, I'm still relatively new to e-mail and got the ending wrong on my earlier posting: the contact information was incomplete. This corrects the earlier posting! May, 1993 Dear Colleague, RE: SOURCE OF 10mers FOR RAPD MARKER RESEARCH In response to the need for a variety of 10mer primers for RAPD analyses at low cost, over the past eighteen months Dr. John Carlson designed, and we prepared, 700 primers according to the sequence specifications of Williams et al. (1990, Nucl Acids Res 18:6531). Dr. Carlson processed and distributed these at cost as kits of 100 unique primers. Participants expressed satisfaction with the primers and even after they were completely sold out, new and repeat orders kept arriving. Due to this popular demand, we are continuing the UBC RAPD primer project. We are firstly resynthesizing the same 700 primers as before. We will then move on to additional primer sets. As before we ship them as sterile, dry 10 g aliquots. Each set contains the sequence information for the primers. We plan to offer these primer sets on a continuing basis. Sets of 100 primers cost $300 Canadian (or $250US). This cost covers materials for the syntheses, purification, aliquotting, and packaging. Airmail costs are added: US$4 to most parts of the world. For courier delivery in the US, we add an additional $18US ($10CN for shipments within Canada). Courier delivery to other parts of the world is added at the rate charged to us: $23 to the UK, $24 to Western Europe, $28 to Australasia, $24 to the Far East, $42 to China and South America, and $47 to Africa (all prices in US$). Sets of 50 primers can be ordered from any set of 100 at a cost of $165 Canadian (US$140 ). The first, second, third, fourth, fifth and sixth sets of 100 primers (set #1, lot #2, set #2, lot #2, set #3, lot #2, set #4, lot #2, set #5 lot #2 and set#6 lot#2) are now being distributed. Set #7 lot #2 should become available in June. Individual primers from any of the kits available can be supplied at US$10 for each 10 g sample. The responsibility for the UBC RAPD primer project has been transferred, with Dr. Carlson's agreement, to the University of British Columbia's Nucleic Acid - Protein Service (NAPS) Unit, although Dr. Carlson remains in close touch with the project. As Director of the Unit, 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. For UBC RAPD Primer Orders: Mailing Address: Or Contact: University of British Columbia Dr. John Hobbs Attn: Dr. John Hobbs Director, NAPS Unit The Biotechnology Laboratory University of British Columbia #237 - 6174 University Boulevard voice phone: (604)822-6373 Vancouver, B.C. V6T 1Z3 Fax number: (604)822-5437 CANADA e-mail: hobbs@unixg.ubc.ca From owner-rapd@net.bio.net Thu May 06 23:00:00 1993 Path: biosci!UNIXG.UBC.CA!hobbs From: hobbs@UNIXG.UBC.CA Newsgroups: bionet.molbio.rapd Subject: RAPD primers from UBC Message-ID: <9305071607.AA13019@unixg.ubc.ca> Date: 7 May 93 01:07:09 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 65 Sorry, I'm still relatively new to e-mail and got the ending wrong on my earlier posting: the contact information was incomplete. This corrects the earlier posting! May, 1993 Dear Colleague, RE: SOURCE OF 10mers FOR RAPD MARKER RESEARCH In response to the need for a variety of 10mer primers for RAPD analyses at low cost, over the past eighteen months Dr. John Carlson designed, and we prepared, 700 primers according to the sequence specifications of Williams et al. (1990, Nucl Acids Res 18:6531). Dr. Carlson processed and distributed these at cost as kits of 100 unique primers. Participants expressed satisfaction with the primers and even after they were completely sold out, new and repeat orders kept arriving. Due to this popular demand, we are continuing the UBC RAPD primer project. We are firstly resynthesizing the same 700 primers as before. We will then move on to additional primer sets. As before we ship them as sterile, dry 10 g aliquots. Each set contains the sequence information for the primers. We plan to offer these primer sets on a continuing basis. Sets of 100 primers cost $300 Canadian (or $250US). This cost covers materials for the syntheses, purification, aliquotting, and packaging. Airmail costs are added: US$4 to most parts of the world. For courier delivery in the US, we add an additional $18US ($10CN for shipments within Canada). Courier delivery to other parts of the world is added at the rate charged to us: $23 to the UK, $24 to Western Europe, $28 to Australasia, $24 to the Far East, $42 to China and South America, and $47 to Africa (all prices in US$). Sets of 50 primers can be ordered from any set of 100 at a cost of $165 Canadian (US$140 ). The first, second, third, fourth, fifth and sixth sets of 100 primers (set #1, lot #2, set #2, lot #2, set #3, lot #2, set #4, lot #2, set #5 lot #2 and set#6 lot#2) are now being distributed. Set #7 lot #2 should become available in June. Individual primers from any of the kits available can be supplied at US$10 for each 10 g sample. The responsibility for the UBC RAPD primer project has been transferred, with Dr. Carlson's agreement, to the University of British Columbia's Nucleic Acid - Protein Service (NAPS) Unit, although Dr. Carlson remains in close touch with the project. As Director of the Unit, 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. For UBC RAPD Primer Orders: Mailing Address: Or Contact: University of British Columbia Dr. John Hobbs Attn: Dr. John Hobbs Director, NAPS Unit The Biotechnology Laboratory University of British Columbia #237 - 6174 University Boulevard voice phone: (604)822-6373 Vancouver, B.C. V6T 1Z3 Fax number: (604)822-5437 CANADA e-mail: hobbs@unixg.ubc.ca From owner-rapd@net.bio.net Thu May 06 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: hobbs@unixg.ubc.ca Newsgroups: bionet.molbio.rapd Subject: RAPD primers from UBC Message-ID: <1993May7.003147.29913@gserv1.dl.ac.uk> Date: 6 May 93 09:31:30 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 49 Original-To: rapd@uk.ac.daresbury May, 1993 Dear Colleague, RE: SOURCE OF 10mers FOR RAPD MARKER RESEARCH In response to the need for a variety of 10mer primers for RAPD analyses at low cost, over the past eighteen months Dr. John Carlson designed, and we prepared, 700 primers according to the sequence specifications of Williams et al. (1990, Nucl Acids Res 18:6531). Dr. Carlson processed and distributed these at cost as kits of 100 unique primers. Participants expressed satisfaction with the primers and even after they were completely sold out, new and repeat orders kept arriving. Due to this popular demand, we are continuing the UBC RAPD primer project. We are firstly resynthesizing the same 700 primers as before. We will then move on to additional primer sets. As before we ship them as sterile, dry 10 g aliquots. Each set contains the sequence information for the primers. We plan to offer these primer sets on a continuing basis. Sets of 100 primers cost $300 Canadian (or $250US). This cost covers materials for the syntheses, purification, aliquotting, and packaging. Airmail costs are added: US$4 to most parts of the world. For courier delivery in the US, we add an additional $18US ($10CN for shipments within Canada). Courier delivery to other parts of the world is added at the rate charged to us: $23 to the UK, $24 to Western Europe, $28 to Australasia, $24 to the Far East, $42 to China and South America, and $47 to Africa (all prices in US$). Sets of 50 primers can be ordered from any set of 100 at a cost of $165 Canadian (US$140 ). The first, second, third, fourth, fifth and sixth sets of 100 primers (set #1, lot #2, set #2, lot #2, set #3, lot #2, set #4, lot #2, set #5 lot #2 and set#6 lot#2) are now being distributed. Set #7 lot #2 should become available in June. Individual primers from any of the kits available can be supplied at US$10 for each 10 g sample. The responsibility for the UBC RAPD primer project has been transferred, with Dr. Carlson's agreement, to the University of British Columbia's Nucleic Acid - Protein Service (NAPS) Unit, although Dr. Carlson remains in close touch with the project. As Director of the Unit, 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. John Hobbs, Nucleic Acid - Protein Service (NAPS) Unit, Biotechnology Laboratory, University of British Columbia, Canada. FAX (604)822-5437; Tel. (604)822-6373 From owner-rapd@net.bio.net Thu May 06 23:00:00 1993 Path: biosci!kristoff From: kristoff@net.bio.net (David Kristofferson) Newsgroups: bionet.molbio.rapd Subject: Duplicates on RAPD? Message-ID: Date: 7 May 93 23:46:01 GMT References: <9305070029.AA07364@unixg.ubc.ca> Distribution: bionet Organization: BIOSCI International Newsgroups for Biology Lines: 10 I received a report of duplicates from RAPD, but after looking into this, it appears simply that one user had some local problems sending mail today. The messages were not exact duplicates. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net From owner-rapd@net.bio.net Thu May 06 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: hobbs@unixg.ubc.ca Newsgroups: bionet.molbio.rapd Subject: RAPD primers from UBC Message-ID: <1993May7.194751.2026@gserv1.dl.ac.uk> Date: 7 May 93 20:47:37 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 65 Original-To: rapd@uk.ac.daresbury Alas, I said I was new to e-mail, and did not realise that the Greek symbol for micro would not be transmitted. This recorrects the earlier posting, with micrograms replacing grams! May, 1993 Dear Colleague, RE: SOURCE OF 10mers FOR RAPD MARKER RESEARCH In response to the need for a variety of 10mer primers for RAPD analyses at low cost, over the past eighteen months Dr. John Carlson designed, and we prepared, 700 primers according to the sequence specifications of Williams et al. (1990, Nucl Acids Res 18:6531). Dr. Carlson processed and distributed these at cost as kits of 100 unique primers. Participants expressed satisfaction with the primers and even after they were completely sold out, new and repeat orders kept arriving. Due to this popular demand, we are continuing the UBC RAPD primer project. We are firstly resynthesizing the same 700 primers as before. We will then move on to additional primer sets. As before we ship them as sterile, dry 10 microgram aliquots. Each set contains the sequence information for the primers. We plan to offer these primer sets on a continuing basis. Sets of 100 primers cost $300 Canadian (or $250US). This cost covers materials for the syntheses, purification, aliquotting, and packaging. Airmail costs are added: US$4 to most parts of the world. For courier delivery in the US, we add an additional $18US ($10CN for shipments within Canada). Courier delivery to other parts of the world is added at the rate charged to us: $23 to the UK, $24 to Western Europe, $28 to Australasia, $24 to the Far East, $42 to China and South America, and $47 to Africa (all prices in US$). Sets of 50 primers can be ordered from any set of 100 at a cost of $165 Canadian (US$140 ). The first, second, third, fourth, fifth and sixth sets of 100 primers (set #1, lot #2, set #2, lot #2, set #3, lot #2, set #4, lot #2, set #5 lot #2 and set#6 lot#2) are now being distributed. Set #7 lot #2 should become available in June. Individual primers from any of the kits available can be supplied at US$10 for each 10 microgram sample. The responsibility for the UBC RAPD primer project has been transferred, with Dr. Carlson's agreement, to the University of British Columbia's Nucleic Acid - Protein Service (NAPS) Unit, although Dr. Carlson remains in close touch with the project. As Director of the Unit, 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. For UBC RAPD Primer Orders: Mailing Address: Or Contact: University of British Columbia Dr. John Hobbs Attn: Dr. John Hobbs Director, NAPS Unit The Biotechnology Laboratory University of British Columbia #237 - 6174 University Boulevard voice phone: (604)822-6373 Vancouver, B.C. V6T 1Z3 Fax number: (604)822-5437 CANADA e-mail: hobbs@unixg.ubc.ca From owner-rapd@net.bio.net Fri May 07 23:00:00 1993 Path: biosci!MERCURY.UARK.EDU!DRHOADS From: DRHOADS@MERCURY.UARK.EDU ("Doug Rhoads") Newsgroups: bionet.molbio.rapd Subject: Re: RAPD primers from UBC Message-ID: Date: 8 May 93 14:36:09 GMT Sender: daemon@net.bio.net Distribution: bionet Organization: University of Arkansas Lines: 141 > Alas, I said I was new to e-mail, and did not realise that the Greek symbol > for micro would not be transmitted. This recorrects the earlier posting, > with micrograms replacing grams! > > May, 1993 > > Dear Colleague, > > RE: SOURCE OF 10mers FOR RAPD MARKER RESEARCH > > In response to the need for a variety of 10mer primers for RAPD analyses > at low cost, over the past eighteen months Dr. John Carlson designed, and > we prepared, 700 primers according to the sequence specifications of > Williams et al. (1990, Nucl Acids Res 18:6531). Dr. Carlson processed and > distributed these at cost as kits of 100 unique primers. Participants > expressed satisfaction with the primers and even after they were completely > sold out, new and repeat orders kept arriving. > > Due to this popular demand, we are continuing the UBC RAPD primer projec .... > The responsibility for the UBC RAPD primer project has been transferred, > with Dr. Carlson's agreement, to the University of British Columbia's > Nucleic Acid - Protein Service (NAPS) Unit, although Dr. Carlson remains in > close touch with the project. As Director of the Unit, 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. > Dr. Hobbs- We have been purchasing the UBC RAPD primer sets and are very satisfied with the results. A number of RAPDers (including us) have also utilized primers based on only 2 or 3 bases rather than all 4. I was wondering whether there are any plans at UBC to include the 2 or 3 base primers in sets in the future? We had a custom synthesis of 28 2-base primers and have found them to be very informative on lower eukaryotes. Others have expressed an interest in these primers but I don't know how wide spread the interest is. The following text is a post I made to the RAPD group last year for your information. I am posting this to the RAPD discussion group. How many of you netters would be interested?? ************original message to RAPD Listserv************* Hello RAPDers- When last we talked I was embarking on an investigation of 2- base primers and their utility in RAPD analyses. As a reintroduction I submit the following passage restated from my last posting on this subject: Theory on 2 base primers Analyze all possible 10mers comprising two non-complementary bases (one purine and one pyrimidine). Oligos discarded which: i) had less than 7 of 10 C or G, ii) the 3' most base was not C or G, iii) contained internal repeats comprising 4 or more bases, and iv) had no homopolymeric runs of greater than 3 bases. These criteria were based somewhat on intuitive thoughts about the primers most likely to give problems in PCR (slippage of priming site and melting temp). Some observations: i) 8 different base patterns satisfied these criteria giving a total of 32 possible primers (8 patterns x 4 pairs of bases), and ii) if the CG/AT ratio is allowed to drop to 60% the number of patterns jumps to 53 x 4 pairs of bases = 212 oligos. Added the criteria that neither the last 2 or 3 bases must be direct repeats (no NNNNRYRRYR) to further minimize priming site slippage (this last criteria was only based on intuition). This reduces the number of 70% GC/AT oligos to 28. Sixteen of the 28 have been synthesized bit # pattern oligo 4 919CA CCCACAACCC GA GGGAGAAGGG CT CCCTCTTCCC GT GGGTGTTGGG 5 923CA CCACCAACCC GA GGAGGAAGGG CT CCTCCTTCCC GT GGTGGTTGGG 6 935CA CCCAACACCC GA GGGAAGAGGG CT CCCTTCTCCC GT GGGTTGTGGG 7 947CA CCAACCACCC GA GGAAGGAGGG CT CCTTCCTCCC GT GGTTGGTGGG We have now tested these 16 primers in RAPDs on three different species of fungi and one canid DNA. With 20 primers from Operon (set X) success rates (i.e., amplification of >4 well separated and clear bands) typically were of 4-5 primers/set on fungi and 7-8 primers/set with canid or chicken DNA. The new set of 16 has given success rates of 12 to 14 of the 16 primers. Early data suggest that the CA primers all give nice well separated bands, GA primers give slightly fewer bands, and the CT primers hardly work at all. The GT primers give a multitude of bands which look like smearing on mini-gels but on longer gels actually give great patterns. I do not know the reason but the total yield of DNA using the GT primers seems much higher. At first I thought that the GT primers would be the worst as GU base pairs could lead to unanticipated base pairing and thus smearing, perhaps I was wrong. The upshot is that these primers appear to have a far higher success rate than four-base primers (I know my data set is so small that no statistics could ever back that last statement, it is just an impression). What about detectable polymorphisms? For the Operon primers only one of the 5 successful primers detected a single polymorphism between three different races of Colletotrichum orbiculare (my test fungus). Be advised these three races are virtually indistinguishable by mtDNA RFLP or nuclear fingerprint probes and so are very closely related. With the 2 base primers preliminary data are: i) the CA primers detect only a few polymorphisms, ii) the GA and GT primers ALL detect polymorphisms. These polymorphisms are not in minor bands but in major bands and several bands per reaction. BE ADVISED: this is preliminary data from only a few isolates but where tested on multiple samples has repeated. Therefore, at this time I believe that the 2 base primers are directing the RAPD to polymorphic DNAs as one would expect for repeat sequences of limited base composition. I have a fair stock of these primers but I didn't spend $720 to mail it all out. I would be interested in exchanges for other primer(s) on a limited basis and especially in finding out whether the CA vs GA vs GT results in other organisms. **********************end of edited message*************** 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 Sat May 08 23:00:00 1993 Path: biosci!MACC.WISC.EDU!ROC From: ROC@MACC.WISC.EDU (Raul O Castillo) Newsgroups: bionet.molbio.rapd Subject: RAPD uses in detecting genetic integrity in genebanks Message-ID: <23050909364500@vms2.macc.wisc.edu> Date: 9 May 93 15:36:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 11 Dear all: We are interesting in a project to detect genetic integrity in regenerated seed collections in genebanks. Do you think RAPD will be the best way to go? We will use original stored seeds, 3-4 cycles of regeneration and new collections done in the exact place where the first collections were done. This work will be done in potato (wild relatives). Then we hope to move to other crops. Thank you Raul Castillo From owner-rapd@net.bio.net Sat May 08 23:00:00 1993 Path: biosci!MACC.WISC.EDU!ROC From: ROC@MACC.WISC.EDU (Raul O Castillo) Newsgroups: bionet.molbio.rapd Subject: Raul Castillo's Email Message-ID: <23050909433917@vms2.macc.wisc.edu> Date: 9 May 93 15:43:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 5 I forgot to put my Email address in the last message concerning RAPD uses in genebanks. This is: ROC@macc.wisc.edu = From owner-rapd@net.bio.net Sun May 09 23:00:00 1993 Path: biosci!ACD.TUSK.EDU!PRAKASH From: PRAKASH@ACD.TUSK.EDU Newsgroups: bionet.molbio.rapd Subject: RE:RAPD uses in detecting genetic integrity in genebanks Message-ID: <01GY0K9QM2AA0000ST@Acd.Tusk.Edu> Date: 10 May 93 20:44:19 GMT Sender: daemon@net.bio.net Distribution: bionet Organization: Tuskegee University Lines: 15 Dr. Raul Castillo has recently posted a message enquiring about the utility RAPDs in verifying the genetic integrity of the seedlots in genebanks. I think RAPDs certainly provide the quick, cost effective and least cumbersome way to analyze large amount of samples. We are working on sweetpotato germplasm and trying to come up with means to identify accessions in an unambigous manner and to facilitate eliminations of duplicates and also to compute genetic distances. We find DAF approach very helpful in this (Caeteno-Anolles et al. Bio/TEchnology 9:553). Essentially this approach uses 8-mer primers and DNA electrophoresis is conducted on polyacrylamide rather than agarose gels. DNA visualization is done by silver stainin g rather than ethidium bromide. We find that 2 to 3 primers can identify nearly seventy genotypes we have tested. Hope you find this info useful. C. S. PRAKASH TUSKEGEE UNIVERSITY PRAKASH@TUSK.EDU PH: 205 727 8023 From owner-rapd@net.bio.net Mon May 10 23:00:00 1993 Path: biosci!MUSKWA.UCS.UALBERTA.CA!dchong From: dchong@MUSKWA.UCS.UALBERTA.CA (Chong Daniel) Newsgroups: bionet.molbio.rapd Subject: Re: RAPD uses in detecting genetic integrity in genebanks Message-ID: <9305112323.AA26587@muskwa.ucs.ualberta.ca> Date: 11 May 93 23:23:23 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 13 There is one positive response to this question I would like to add a negative one. I agree that RAPDs are the best way to analyze a large number of samples. However, utilization of RAPDs in detecting genetic integrity in genebank has a problem. Two individual plants having an identical RAPD profile (or banding pattern) do not always possess identical genotypes because of the co-dominant feature of RAPDs (i.e. genotypes AA and Aa will have the same RAPD profile.). But RAPDs could be used to detect genetic integrity if that species has very high homozygosity (barley) or heterozygosity (conifers). Daniel Chong Department of Forest Science University of Alberta From owner-rapd@net.bio.net Mon May 10 23:00:00 1993 Path: biosci!YVAX.BYU.EDU!FARMERJ From: FARMERJ@YVAX.BYU.EDU Newsgroups: bionet.molbio.rapd Subject: Re: RAPD primers from UBC Message-ID: <01GY1Z6PD68Y8Y7DK4@yvax.byu.edu> Date: 11 May 93 21:53:15 GMT Sender: daemon@net.bio.net Distribution: bionet Organization: Brigham Young University Lines: 15 In response to Doug Rhoads' question, I would very much like to purchase some two-base primers. In my experience, they are much better for Drosophila work than the four-base primers. I make my own, but I can only afford a small number at $40+ per primer. 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 From owner-rapd@net.bio.net Tue May 11 23:00:00 1993 Path: biosci!MUSKWA.UCS.UALBERTA.CA!dchong From: dchong@MUSKWA.UCS.UALBERTA.CA (Chong Daniel) Newsgroups: bionet.molbio.rapd Subject: AmpliTaq DNA Polymerase, Stoffel Fragment Message-ID: <9305122214.AA06548@muskwa.ucs.ualberta.ca> Date: 12 May 93 22:14:50 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 8 PERKIN ELMER has a new product, AmpliTaq DNA Polymerase, Stoffel Fragment, which is almost half price of its original AmpliTaq DNA Polymerase ($341.00 for 1000 units). Has anybody tried this enzyme in RAPDs ? DAniel Chong Department of Forest Science University of Alberta From owner-rapd@net.bio.net Tue May 11 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: datherto@crc.ac.uk (Mr. D.J. Atherton) Newsgroups: bionet.molbio.rapd Subject: FAQ available? Message-ID: <1993May12.145239.18426@gserv1.dl.ac.uk> Date: 12 May 93 14:43:00 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 10 Original-To: rapd@uk.ac.daresbury Is there a FAQ available somwhere out there on RAPD and associated methods? Hopefully David Atherton datherton@uk.ac.ox.path.vax Univ. Dept. Pharmacology Univ. Oxford Oxford U.K. From owner-rapd@net.bio.net Wed May 12 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!darwin.sura.net!haven.umd.edu!uunet!pipex!sunic!news.lth.se!news.lu.se!buster.hik.se!hik.se!fm91hn From: fm91hn@hik.se (HENRIK NORSELL) Newsgroups: bionet.molbio.rapd Subject: OPINION POLL! Message-ID: Date: 13 May 93 11:43:07 GMT Sender: news@tintin.hik.se Organization: University of Kalmar Lines: 29 Net citizens! This is a desperate try to save our last course in university. We are writing a study about the Net, how it all started, about the people living in it, however trying to explain the basics of how it all works. That includes you, reader of this message. We would be more than grateful if we could get your answers to the following questions; 1. For how many years have you known that Internet existed? 2. How often do you use the Net? (occasions per month) 3. Whatfor? (hobby, in your profession, socialy...) 4. How do you access the Net? (university, profession, friends, private...) 5. Has the Net taken over roles that other media played before? (telephone, newspapers, TV, girlfriend...) 6. What newsgroups/type of information do you take part of? 7. Male or Female? 8. Age? If you have the time; 9. What's your future visions about the Net? Limits and/or possibilities. 10.How do you think/hope law and censorship will change over time ahead? We also want to apologize for taking up so much bandwidth with this. This request has been spread to 60 newsgroups, chosen at random, but, you know how it is, term end is closing up, panic spreads. Email address: fm91hn@hik.se (or if thats busy) fm91pb@hik.se Sincere Respect And May The Force Be With You All! Peter & Henrik From owner-rapd@net.bio.net Wed May 12 23:00:00 1993 Path: biosci!esvax.dnet.dupont.com!rafalski From: rafalski@esvax.dnet.dupont.com Newsgroups: bionet.molbio.rapd Subject: Stoffel fragment Message-ID: <9305131203.AA04468@esds01.es.dupont.com> Date: 13 May 93 12:03:47 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 11 In response to a question about Stoffel fragment by Daniel Chong: Mike McClelland's / Bruno Sobral's group published on the use of Stoffel fragment for AP-PCR. We now use Stoffel for RAPDs, in preference to AmpliTaq. Stoffel gives a different distribution of fragments (shifted towards smaller size) and requires higher Mg then Taq (we currently use 2.5 mM Mg with Stoffel). There is some evidence that reproducibility is better with Stoffel. Antoni Rafalski rafalski@esvax.dnet.dupont.com From owner-rapd@net.bio.net Mon May 17 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!noc.near.net!uunet!newsflash.concordia.ca!nstn.ns.ca!dragon.acadiau.ca!ace.acadiau.ca!msnyder From: msnyder@ace.acadiau.ca (MARLENE SNYDER) Newsgroups: bionet.molbio.rapd Subject: Info on RAPD primers available from UBC ? Message-ID: Date: 18 May 93 18:19:17 GMT Sender: news@dragon.acadiau.ca Organization: Acadia University Lines: 4 Nntp-Posting-Host: 131.162.69.36 Could someone either post or mail info on RAPD primers as available from UBC? Thanks! From owner-rapd@net.bio.net Mon May 17 23:00:00 1993 Path: biosci!YVAX.BYU.EDU!Anderswr From: Anderswr@YVAX.BYU.EDU (W. Ralph Andersen) Newsgroups: bionet.molbio.rapd Subject: Re: AmpliTaq DNA Polymerase, Stoffel Fragment Message-ID: <01GYBBHUZ82Q8WXI71@yvax.byu.edu> Date: 18 May 93 18:25:37 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 9 At 4:14 PM 5/12/93 -0600, Chong Daniel wrote: > PERKIN ELMER has a new product, AmpliTaq DNA Polymerase, Stoffel Fragment, >which is almost half price of its original AmpliTaq DNA Polymerase ($341.00 for >1000 units). Has anybody tried this enzyme in RAPDs ? > >DAniel Chong >Department of Forest Science >University of Alberta From owner-rapd@net.bio.net Tue May 18 23:00:00 1993 Path: biosci!ABRSLE.AGR.CA!HACHEY From: HACHEY@ABRSLE.AGR.CA (john hachey) Newsgroups: bionet.molbio.rapd Subject: re:stoffel frag Message-ID: <01GYCX2N8NV600251G@GW.AGR.CA> Date: 19 May 93 16:56:53 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 16 > PERKIN ELMER has a new product, AmpliTaq DNA Polymerase, Stoffel Fragment, >which is almost half price of its original AmpliTaq DNA Polymerase ($341.00 for >1000 units). Has anybody tried this enzyme in RAPDs ? > >DAniel Chong >Department of Forest Science >University of Alberta I haven't tried it but one group has : Sobral, B.W. et al. 1993. High Output Genetic mapping of polyploids using PCR-generated markers. TAG 86:105-112. john From owner-rapd@net.bio.net Tue May 18 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!news.cac.psu.edu!psuvm!frmop11.cnusc.fr!barilvm!aristo.tau.ac.il!ccsg.tau.ac.il!idotan From: idotan@ccsg.tau.ac.il (dotan iris) Newsgroups: bionet.molbio.rapd Subject: replica plating of cultured mammalian cells Message-ID: <1993May19.104232.4121@aristo.tau.ac.il> Date: 19 May 93 10:42:32 GMT Sender: usenet@aristo.tau.ac.il (USENET) Organization: Tel-Aviv University Computation Center Lines: 2 Has anyone performed replica plating of HeLa cells? Tips would be appreciated. From owner-rapd@net.bio.net Tue May 18 23:00:00 1993 Path: biosci!MERCURY.UARK.EDU!DRHOADS From: DRHOADS@MERCURY.UARK.EDU ("Doug Rhoads") Newsgroups: bionet.molbio.rapd Subject: RAPD primers from UBC and 2 base primers Message-ID: <2EE12DA5CD3@uamercury.uark.edu> Date: 19 May 93 23:10:58 GMT Sender: daemon@net.bio.net Distribution: bionet Organization: University of Arkansas Lines: 83 On Tue, 11 May 1993 10:10:36 -0800 John Hobbs asked: > Hi, Doug! Thank you for your e-mail. I'm sending this as a preliminary to > a longer and more detailed message, for which I need to do a bit of > research in our collection of data (I won't dignify it with the term > "database" yet). Briefly, we have never deliberately generated sets based > on only 2 or 3 bases rather than all 4, but all our sets contain a number > of sequences using only 3 of the bases, and a quick inspection of the sets > shows that the 700 sequences we've made contain 6 which have only 2 of the > 4 bases. We have not done any systematized generation of 2-base-only sets > like yourself, but since we plan to start creating some new sets shortly, I > was very interested in your findings. Did your results with the full 28 > sequences maintain your preliminary success rate with the first 16? In answer to a question of John Hobbs I am providing the following information on our experience with 4-base and 2-base primers. The data are for RAPDs on tomato DNA. We are looking for markers linked to a disease resistance in an introgressed line. For these comparisons we evaluated the RAPD products yielded by a set of 100 4-base primers (set 401-500) obtained from UBC and 28 2-base primers synthesized for us. I have included the sequences of these primers in previous posts and will not repeat them here but they all conform with my theories on what might make for good RAPD 2- base primers. RAPD product yield was rated on the following scale: rating description 0 no bands or weak bands only 1 1-3 good scorable bands 2 4-6 good scorable bands 3 7-10 good scorable bands 4 >10 good scorable bands rating 4 could be construed as a smear if not separated on a long gel (>15cm) UBC primers 401-500 rating number of primers ------ ----------------- 0 29 1 30 2 18 3 12 4 11 2-base primers: broken down by base composition pattern CA GA CT GT ------- -- -- -- -- 823 4 4 4 4 827 4 3 2 4 883 4 4 4 3 919 4 3 3 2 923 2 2 1 2 935 3 2 4 4 947 4 4 2 2 totals for 2-base primers: score CA GA CT GT totals ----- -- -- -- -- ------ 0 0 0 0 0 0 (0%) 1 0 0 1 0 1 (3.6%) 2 1 2 2 3 8 (28.6%) 3 1 2 1 1 5 (17.9%) 4 5 3 3 3 14 (50%) All reactions were performed in an Idaho cycler in a 10ul in Idaho 1x buffer with 50-100ng DNA and 0.5uM primer. Annealing parameters were either 5x35c then 35x45c, or 40x35c. Our results vary with these two alternatives but the rating is not affected greatly. The results on tomato contrast with our data on fungi in that no particular base composition preference is observed. This may derive from the smaller fungal genome possibly containing fewer short VNTR sequences in comparison with the larger (more complex?) genome of tomato. I must admit I do not know the significance of these initial observations but the numbers speak for themselves. Whether the 2- base primers give higher numbers of polymorphisms is not known as the tomato line is highly introgressed and few polymorphisms have been identified with either the 28 2-base primers or the >600 4- base primers we have tested. Doug Rhoads || Dept. of Biological Sciences drhoads@mercury.uark.edu || 601 Science Engineering drhoads@uafsysb.uark.edu || University of Arkansas 501-575-3251 || Fayetteville, AR 72701 From owner-rapd@net.bio.net Mon May 24 23:00:00 1993 Path: biosci!enterpoop.mit.edu!gatech!howland.reston.ans.net!wupost!uhog.mit.edu!grapevine.lcs.mit.edu!ai-lab!hal.gnu.ai.mit.edu!not-for-mail From: bw@hal.gnu.ai.mit.edu (Bruce Waldman) Newsgroups: bionet.jobs,bionet.molbio.rapd,bionet.population-bio,bionet.molbio.evolution Subject: Research assistant position/New Zealand frogs Message-ID: <1ts89h$pu9@hal.gnu.ai.mit.edu> Date: 25 May 93 04:45:37 GMT Organization: dis Lines: 24 Xref: biosci bionet.jobs:1869 bionet.molbio.rapd:72 bionet.population-bio:433 bionet.molbio.evolution:945 NNTP-Posting-Host: hal.ai.mit.edu A research assistant position, to study behavioural ecology and population genetics of native New Zealand frogs (genus Leiopelma), is available starting 1 July 1993 (or later date to be negotiated). The successful candidate will be involved in various research projects concerned with the behaviour (e.g. parental care of brood) and ecology (e.g. dispersal) of these unique frogs. A major portion of the work will involve analyses of genetic variation within and among populations using PCR and various fingerprinting techniques. The application of these methodologies to conservation biology, both with respect to these endangered frogs and other threatened New Zealand fauna, will be stressed. Work on other endemic fauna (e.g. wetas) will be encouraged. Initial funding is available for a full-time research assistant for one year, and funding for future years is possible. Applicants with experience in methods of DNA purification and analyses, and/or with experience working on problems of behaviour or ecology in the field, will be given preference. Please contact me if you are interested, or would like further details. Bruce Waldman Department of Zoology University of Canterbury Christchurch, New Zealand Telephone: +64 3 364 2066 FAX: +64 3 364 2024 Email: bw@gnu.ai.mit.edu From owner-rapd@net.bio.net Mon May 24 23:00:00 1993 Path: biosci!YVAX.BYU.EDU!FARMERJ From: FARMERJ@YVAX.BYU.EDU Newsgroups: bionet.molbio.rapd Subject: Re: SSCP analysis Message-ID: <01GYLL17E8IA9368IA@yvax.byu.edu> Date: 25 May 93 22:43:37 GMT Sender: daemon@net.bio.net Distribution: bionet Organization: Brigham Young University Lines: 14 The original SSCP reference is Orita et al, Genomics 5:874-879 (1989). There have been a lot of papers since then which should be easily obtained from Science Citation Index, ENTREZ, etc. 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 From owner-rapd@net.bio.net Mon May 24 23:00:00 1993 Path: biosci!YVAX.BYU.EDU!FARMERJ From: FARMERJ@YVAX.BYU.EDU Newsgroups: bionet.molbio.rapd Subject: Re: A few basic questions... Message-ID: <01GYLKMIT67M9361LJ@yvax.byu.edu> Date: 25 May 93 22:31:50 GMT Sender: daemon@net.bio.net Distribution: bionet Organization: Brigham Young University Lines: 23 In response to Tim Chipman: I am surveying individual flies from Drosophila pseudoobscura populations. I have seen polymorphism with every 2-base primer I have used. In a sample of 24 flies from the same population, I can usually see several different, reproducible RAPD patterns. Three or four individuals is usually enough to see polymorphism. If you are using laboratory or domestic populations, the levels of polymorphism may be lower. For instance, I looked at six flies from a "wild-type" population which I obtained from a stock center. I could detect no polymorphism in these six flies with the two or three primers I tried on them. 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 From owner-rapd@net.bio.net Mon May 24 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!ux1.cso.uiuc.edu!sdd.hp.com!news.cs.indiana.edu!nstn.ns.ca!dragon.acadiau.ca!axe.acadiau.ca!901106c From: 901106c@axe.acadiau.ca (TIM CHIPMAN) Newsgroups: bionet.molbio.rapd Subject: A few basic questions re: RAPD primer use Message-ID: <901106c.455.738360146@axe.acadiau.ca> Date: 25 May 93 21:02:22 GMT Sender: news@dragon.acadiau.ca Organization: Acadia University Lines: 16 Nntp-Posting-Host: 131.162.69.36 I have a few questions about the usage of RAPD primers, hopefully which will be obvious to someone who is willing to help. (1) How many organisms need to be surveyed to determine if there is a usefull RFLP ? (2) Are primers used individually initially, or can you do batch jobs to speed the process? Thanks! I appreciate your help. ........ Tim Chipman .................................. .......... 901106c@axe.acadiau.ca .................................. From owner-rapd@net.bio.net Mon May 24 23:00:00 1993 Path: biosci!VTVM1.CC.VT.EDU!JOFTOPSM From: JOFTOPSM@VTVM1.CC.VT.EDU (Donna Jensen) Newsgroups: bionet.molbio.rapd Subject: SSCP analysis Message-ID: <9305251743.AA19024@net.bio.net> Date: 25 May 93 17:30:23 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 10 Hi! Can anyone out there give me any information on Single-Stranded Conformation Polymorphism (SSCP) analysis to detect point mutations? I am interested in possibly using this technique to detect mutations in bacteria. I would appreciate any information, including references explaining the technique and the principles behind it, as well as information from those of you that have used this technique as far as how well it works and what its limitations are. Thanks in advance!! :-> Donna JOFTOPSM@VTVM1.CC.VT.EDU From owner-rapd@net.bio.net Tue May 25 23:00:00 1993 Path: biosci!EQUINOX.UNR.EDU!hoelzer From: hoelzer@EQUINOX.UNR.EDU (Guy A Hoelzer) Newsgroups: bionet.molbio.rapd Subject: Re: Hoefer TKO 100 fluorometer Message-ID: Date: 26 May 93 15:56:15 GMT References: <0096D0BF.50479D80.10279@lewis.umt.edu> Sender: daemon@net.bio.net Distribution: bionet Lines: 10 Donna Leeper asked about using the Hoefer TKO flourometer for quantitating DNA samples. I like this instrument. I find it to be faster, easier, and more accurate than a spectrophotometer. I have not tried their special capillary tube arrangement for quantitating very low concentrations (<10ug/ml) and I am curious how well this works. There are also a couple of kits that only require spotting 1 ul of sample onto a surface (e.g. the DNA dipstick by Invitrogen). These kits also claim great sensitivity. Has anyone tried one of these kits and how well do they work? From owner-rapd@net.bio.net Tue May 25 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!ux1.cso.uiuc.edu!news.cs.indiana.edu!nstn.ns.ca!dragon.acadiau.ca!axe.acadiau.ca!901106c From: 901106c@axe.acadiau.ca (TIM CHIPMAN) Newsgroups: bionet.molbio.rapd Subject: Re: re:basic questions Message-ID: <901106c.456.738421148@axe.acadiau.ca> Date: 26 May 93 13:59:07 GMT References: <1993May26.093234.289@gserv1.dl.ac.uk> Sender: news@dragon.acadiau.ca Distribution: bionet Organization: Acadia University Lines: 25 Nntp-Posting-Host: 131.162.69.36 >The questions you raise can only be answered if more info is given. >Is the organism diploid or haploid? Is there info on genetic variation >of the organism (in general that is, allozymes, RFLP, sequences)? >What is a useful polymorphism? A rare one? A 50%-one? >In diploids, it maybe hard to detect a polymorphism if the amplifiable >allele is much more frequent than the not amplifiable allele. The organism is a little invertibrate critter called Corophium, which lives out in the Mud Flats. As far as I know, no other DNA work has been done with these little guys (ie: very little know about them...) However, I believe they are diploid. Ideally, it would be nice to be able to distinguish between individuals using RAPD methods. However, if that is not feasable, it would be also usefull to be able to distinguish between different populations. Thanks! Tim ........ Tim Chipman .................................. .......... 901106c@axe.acadiau.ca .................................. From owner-rapd@net.bio.net Tue May 25 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: ZANDE@RUGR86.RUG.nl Newsgroups: bionet.molbio.rapd Subject: re:basic questions Message-ID: <1993May26.093234.289@gserv1.dl.ac.uk> Date: 26 May 93 10:21:00 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 16 X-Envelope-To: rapd@daresbury.AC.UK Content-Identifier: re:basic ques... X-Vms-Cc: ZANDE Original-To: rapd@uk.ac.daresbury Content-Transfer-Encoding: 7BIT X-Vms-To: IN%"rapd@daresbury.ac.uk" Dear Tim The questions you raise can only be answered if more info is given. Is the organism diploid or haploid? Is there info on genetic variation of the organism (in general that is, allozymes, RFLP, sequences)? What is a useful polymorphism? A rare one? A 50%-one? In diploids, it maybe hard to detect a polymorphism if the amplifiable allele is much more frequent than the not amplifiable allele. Do not mix primers for tha t will generate a different but not a composite pattern. Hope this will help a little. Louis v.d.ZAnde From owner-rapd@net.bio.net Tue May 25 23:00:00 1993 Path: biosci!MUSKWA.UCS.UALBERTA.CA!dchong From: dchong@MUSKWA.UCS.UALBERTA.CA (Chong Daniel) Newsgroups: bionet.molbio.rapd Subject: Hoefer TKO 100 minifluorometer Message-ID: <9305262201.AA28898@muskwa.ucs.ualberta.ca> Date: 26 May 93 22:01:49 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 6 Can someone tell me where to buy and how much Hoefer TKO 100 minifluorometer is? Does CTAB affect its reading? Daniel Chong University of Alberta From owner-rapd@net.bio.net Tue May 25 23:00:00 1993 Path: biosci!EQUINOX.UNR.EDU!hoelzer From: hoelzer@EQUINOX.UNR.EDU (Guy A Hoelzer) Newsgroups: bionet.molbio.rapd Subject: Hoefer TKO miniflourometer Message-ID: Date: 26 May 93 19:56:36 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 9 Thanks to everybody for the info about the DNA dipstick. I would like to add one more bit of information about the Hoefer miniflourometer. Instability in the readout seems to be exaggerated by using the more concentrated dye solution recommended by Hoefer. I find that using the less concentrated dye solution, suggested for less concentrated samples, works fine for all DNA concentrations the machine can deal with (up to 2mg/ml) and the readings are much more stable. From owner-rapd@net.bio.net Tue May 25 23:00:00 1993 Path: biosci!uwm.edu!ux1.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: Re: Hoefer TKO 100 fluorometer Message-ID: Date: 26 May 93 17:42:27 GMT References: <0096D0BF.50479D80.10279@lewis.umt.edu> Sender: root@nrcnet0.nrc.ca (Operator) Distribution: bionet Organization: National Research Council of Canada Lines: 27 Nntp-Posting-Host: 132.246.164.10 In article hoelzer@EQUINOX.UNR.EDU (Guy A Hoelzer) writes: >From: hoelzer@EQUINOX.UNR.EDU (Guy A Hoelzer) >Subject: Re: Hoefer TKO 100 fluorometer >Date: 26 May 93 15:56:15 GMT >Donna Leeper asked about using the Hoefer TKO flourometer for quantitating >DNA samples. I like this instrument. I find it to be faster, easier, and >more accurate than a spectrophotometer. I have not tried their special >capillary tube arrangement for quantitating very low concentrations >(<10ug/ml) and I am curious how well this works. There are also a couple >of kits that only require spotting 1 ul of sample onto a surface (e.g. the >DNA dipstick by Invitrogen). These kits also claim great sensitivity. >Has anyone tried one of these kits and how well do they work? Yeah... a colleague bought a DNA dipstick kit. IMHO, it is as sensitive as the old-fashioned ethidium bromide plate method, and takes 10 times longer (I keep a "coupladozen" EB plates in my fridge). cheers, John John Nash | Email: Nash@biologysx.lan.nrc.ca. Institute for Biological Sciences, | National Research Council of Canada, Cell Physiology Group. | Ottawa, Ontario, Canada. *** Disclaimer: All opinions are mine, not NRC's! *** From owner-rapd@net.bio.net Tue May 25 23:00:00 1993 Path: biosci!ACD.TUSK.EDU!PRAKASH From: PRAKASH@ACD.TUSK.EDU Newsgroups: bionet.molbio.rapd Subject: Re: TKO 100 fluorometer Message-ID: <01GYMR9CDW20000A0K@Acd.Tusk.Edu> Date: 26 May 93 17:56:20 GMT Sender: daemon@net.bio.net Distribution: bionet Organization: Tuskegee University Lines: 14 Donna Leeper and also Guy Holezer asked by about using TKO 100 fluorometer for quantitating DNA samples and also about DNA dipstick. There was a series of discussion on the reliability of Hoeffer flurometer on the net a month ago and looks like it basically comes down to how well you clean the cuvettes. There were several suggested recipes, and I have a print out of the summary, if any one is interested. Regarding DNA dipstick from Invitrogen, we tried it about two years ago and were very disasspointed about it. I don't think it is reliable or sensitive. C. S. Prakash Tuskegee University Prakash@acd.tusk.edu From owner-rapd@net.bio.net Tue May 25 23:00:00 1993 Path: biosci!LEWIS.UMT.EDU!bi__dkl From: bi__dkl@LEWIS.UMT.EDU (Donna) Newsgroups: bionet.molbio.rapd Subject: Hoefer TKO 100 fluorometer Message-ID: <0096D0BF.50479D80.10279@lewis.umt.edu> Date: 26 May 93 01:57:41 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 3 Hello, I was wondering if anyone has had experience with the Hoefer tko100 fluorometer. I have tried quantifying DNA in the past and gave it up as a bad effort, and now I need to try to optimize so that SOME of my reactions will work. I'd appreciate any input. Thanks much Donna Leeper U MT :-) From owner-rapd@net.bio.net Tue May 25 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: Re: Hoefer TKO fluorometer Message-ID: <01GYMRPII1IQ002O3V@GW.AGR.CA> Date: 26 May 93 18:05:45 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 16 26-May-1993 In response to Donna Leepers request for info on the Hoefer TKO 100, our initial attempts to use the fluorometer were frustrating as the values danced around and were very sensitive to hand movement near the machine. These problems were corrected by turning the machine so it's back was toward the window (North facing, so no direct sun). The values stabilized and we have been fairly pleased with the resulting quantitations. 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 Wed May 26 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!mrccrc!datherto From: datherto@crc.ac.uk (Mr. D.J. Atherton) Newsgroups: bionet.molbio.rapd Subject: Re: Hoefer TKO 100 fluorometer Summary: DNA quantification Message-ID: <1993May27.152257.25111@crc.ac.uk> Date: 27 May 93 15:22:57 GMT References: <0096D0BF.50479D80.10279@lewis.umt.edu> Sender: Datherton Distribution: bionet Organization: MRC Human Genome Resource Centre Lines: 45 Nntp-Posting-Host: tin Hi All With regards to Invitrogen dipsticks and do they work. Answer:- well yes pretty much, although the exact accuracy is dependant on human judgement. An advantage is that they can be kept as proof of the 'experiment'. However, a word of warning - they are expensive, and IMHO a bit of a rip-off. My point is this: The kit arrives and you use it, so far so good. BTW if you are careful you can get many more sample spots on the dipstick than I.gen say. Despite this you quickly run out of dipsticks, and these are not sold seperately, hence you are left with three bottles of nigh on useless development solutions, (In order to get more dipsticks you buy another kit, so get more solutions as well), and a look at the product information tells you nothing since it is all 'an industrial secret'. I decided to do something about this some time ago when I had some spare time (The moon was a distinct shade of blue I recall :-). The dipsticks detect concentrations of ds/ss DNA, RNA, DNA/RNA hybrids and any nucleotide or mix thereof. The only thing these have in common is a sugar phosphate 'backbone' ergo it is probably some part of this which is being detected and quantified The question was what part, and did the dipsticks play any part in it's detection? My working hypothesis was that the dipsticks do nothing except hold the DNA, and the solutions detect and quantify. An attempt at substituting a strip of DNA blotting nylon membrane for the dipstick showed this to be true since, although background was high distinct spots could still be seen. I assume that the solutions actually detect the sugar moiety of the DNA/RNA bases, (Nitrocellulose membrane gives even higher background), hence a suitable substitute for the dipsticks would be something which does not contain any form of 'sugar' and can bind DNA - ie something like a ground glass coating. I moved out of the job I was in before I had a chance to test this, and my new position does not have anybody around who uses I.gen dipsticks. If any body out there has tried this or similar I'd like to know. Hope this helps. Regards David Atherton datherton@uk.ac.ox.path.vax Univ. Oxford Oxford Geneticists do it with large populations! Oxon UK ! . From owner-rapd@net.bio.net Wed May 26 23:00:00 1993 Path: biosci!UNR.EDU!hoelzer From: hoelzer@UNR.EDU (Guy A Hoelzer) Newsgroups: bionet.molbio.rapd Subject: Re: Hoefer TKO 100 minifluorometer Message-ID: Date: 27 May 93 16:23:36 GMT References: <9305262201.AA28898@muskwa.ucs.ualberta.ca> Sender: daemon@net.bio.net Distribution: bionet Lines: 14 On Wed, 26 May 1993, Chong Daniel wrote: > Can someone tell me where to buy and how much Hoefer TKO 100 minifluorometer > is? Does CTAB affect its reading? > > Daniel Chong > University of Alberta You can buy directly from Hoefer (800-227-4750) and I believe that Hoefer products are also carried by VWR. The unit costs about $2000. From owner-rapd@net.bio.net Wed May 26 23:00:00 1993 Path: biosci!GMUVAX.GMU.EDU!LADAMKEW From: LADAMKEW@GMUVAX.GMU.EDU ("LAURA ADAMKEWICZ") Newsgroups: bionet.molbio.rapd Subject: basic questions from T. Chipman Message-ID: <9305271838.AA29170@net.bio.net> Date: 27 May 93 19:33:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 9 KKK From owner-rapd@net.bio.net Thu May 27 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: ZANDE@RUGR86.RUG.nl Newsgroups: bionet.molbio.rapd Subject: more basics Message-ID: <1993May28.094750.7982@gserv1.dl.ac.uk> Date: 28 May 93 10:18:00 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 7 X-Envelope-To: rapd@daresbury.AC.UK Content-Identifier: more basics X-Vms-Cc: ZANDE Original-To: rapd@uk.ac.daresbury Content-Transfer-Encoding: 7BIT X-Vms-To: IN%"rapd@daresbury.ac.uk" Well Tim The proof of the pudding is in the eating. Just start RAPDing your creatures and the answers will come out RAPDly. Louis From owner-rapd@net.bio.net Fri May 28 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!darwin.sura.net!news.udel.edu!chopin.udel.edu!daschaff From: daschaff@chopin.udel.edu (Dennis A Schaff) Newsgroups: bionet.molbio.rapd,bionet.molbio.yeast,bionet.photosynthesis Subject: Call for Abstracts MAPMBS meeting Message-ID: Date: 29 May 93 14:20:06 GMT Sender: usenet@news.udel.edu Organization: University of Delaware Lines: 241 Xref: biosci bionet.molbio.rapd:90 bionet.molbio.yeast:112 bionet.photosynthesis:43 Nntp-Posting-Host: chopin.udel.edu Call for Abstracts 10th Annual Meeting Mid-Atlantic Plant Molecular Biology Society July 15-16, 1993 University of Delaware, Clayton Hall Newark, Delaware Please return Registration and Abstracts by June 25, 1993. Keynote Address Sheila McCormick, USDA/ARS--Plant Gene Expression Center Molecular analysis of gametogenesis in plants. Gene Regulation Becky Boston--North Carolina State University--Regulation and function of maize ribosome inactivating proteins. Michael Dobres--Drexel University--A transcriptional marker for epidermal differentiation in Pisum sativum. Carroll Vance--USDA/ARS, University 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. Plant/Microbe Interactions Jim Carrington--Texas A&M--Replication and movement of a potyvirus that expresses GUS. 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. Transformation/Techniques Ted Klein--Du Pont Co.--Maize transformation: An industrial perspective. Antoni Rafalski--Du Pont Co.--Technology for molecular breeding: RAPD markers, microsatellites, and machines. Developing Technologies Paul Gilna--Los Alamos--The latest advances in community-based access to sequence data submission and maintenance technologies for GenBank. Post-meeting Tour Friday evening, July 16, 1993. We are planning a tour of Longwood Gardens, Kennett Square, PA (18 miles from the University of Delaware). Tenth Annual Meeting of the Mid-Atlantic Plant Molecular Biology Society Univerity of Delaware, Newark, DE July 15-16, 1993 Registration due by June 25, 1993 The Mid-Atlantic Plant Molecular Biology Society (MAPMBS) was formed to provide a high quality, accessible, and affordable plant molecular biology meeting each year for scientists in the Mid-Atlantic region. The society wishes especially to encourage presentations by postdoctoral fellows and graduate students. Toward this goal, and as a special incentive, the registration fee for students who are presenting short talks or posters (one presenter per abstract please) includes only the cost of food and beverages. This year's keynote address on Thursday July 15 will be given by Dr. Sheila McCormick, USDA, ARS, Plant Gene Expression Center, Albany, CA. Dr. McCormick's lecture will be followed by an informal social hour and dinner. Registration for the conference will open at 8:00 a.m. on Thursday inside Clayton Hall. Talks will begin promptly at 9:00 a.m. Thursday and 8:00 a.m. Friday. Two platform sessions will be held each day. Each platform session consists of two or three 30-minute talks by invited speakers followed by short contributed talks of approximately 15-20 minutes. Poster presentations are also encouraged. Time will be reserved for poster presentation and discussion. To present either a talk or a poster please submit an abstract (see directions for format). If you prefer to give a talk, please indicate the session you feel would be most appropriate. Accommodations for participants requiring overnight lodging can be made at the University of Delaware on-campus housing. A block of rooms has been reserved for participants. Arrangements must be made by participants through the Conference Center at Clayton Hall (housing form enclosed). Lodging will be available for Wednesday and Thursday nights at the conference rate (additional nights may be arranged on an individual basis). Breakfast can be bought at the Cafeteria (breakfast $4.50). If you prefer other accommodations, please make your own arrangements. Pre-registration is strongly encouraged. Please note that this is the only announcement and call for abstracts that will be mailed. For those who register in advance, lunches and dinner will be provided and are included in the pre-registration fees. Ample parking is available in the Conference Center parking lot. Walk-in registration will also be available at the door on Thursday morning July 15. ABSTRACT FORMAT (Abstracts are photocopied without modification) TITLE IN CAPITAL LETTERS: Author(s) Name; Author(s) Affiliation, and Address. Please type your abstract on 8.5" x 11" white paper leaving a 1.5" margin on all sides. Mail the original abstract and one copy to the address listed on the registration form. Be sure to check the appropriate spaces on the registration form to indicate your preference for presentation format (short talk or poster) and session. You will be notified of the session, time, and format for your presentation. Posters should fit within a 4' x 4' area. Please return your abstract by June 25, 1993. Your attendance and participation are essential to the continued growth and productivity of the MAPMBS. We look forward to meeting you in July! For further information, contact: Send Abstracts to: Dennis A. Schaff Ben Matthews Department of Plant and Soil Sciences MAPMBS University of Delaware c/o USDA-ARS, PMBL Newark, Delaware 19717-1303 B-006, BARC-West Phone: (302) 831-2534 10300 Baltimore Avenue FAX: (302) 831-3651 Beltsville, MD 20705-2350 E-mail: daschaff@brahms.udel.edu Registration Form Please return by June 25, 1993 Please photocopy this page and mail the registration and housing forms SEPARATELY; MAPMBS will not guarantee forwarding of housing forms sent to Beltsville. Name _________________________________ I am interested in presenting: Institution __________________________ _____ A short talk Department __________________________ _____ A poster Address ______________________________ (Be sure abstract is enclosed) City ________________________________ State ________________________________ Platform session preference: Zip Code _____________________________ _____ Gene Regulation Telephone ____________________________ _____ Plant/Microbe Interactions FAX __________________________________ _____ Transformation/Techniques E-mail _______________________________ Pre-registration: Late registration (after June 25): Presenting Student.......... $50 N/A Student..................... $65 $75 Regular registration........ $80 $90 Total amount enclosed....... $_______ Make Checks Payable to MAPMBS Pre-registration includes meeting attendance, 2 lunches, social hour, and Thursday banquet. ______ Please check if interested in the post-meeting tour to Longwood Gardens (Friday July 16). ______ Special dietary requirements. Please specify:_____________________ Choice of meals for banquet (check one) ______ Chinese Flank Steak ______ Vegetarian Platter ______ Delaware Combo (Crabcake and Chicken Breast ) Mail Registration Materials to: Ben Matthews MAPMBS Meeting c/o USDA-ARS, PMBL B-006, BARC-West 10300 Baltimore Avenue Beltsville, MD 20705-2350 Housing Reservation Form 10th Annual Meeting: Mid-Atlantic Plant Molecular Biology Society July 15-16, 1993 Name_________________________________ Title/position____________________ Affiliation_____________________________________________________________ Address_________________________________________________________________ City____________________________________State__________Zip______________ Telephone Numbers (work)_________________ (home)_______________________ Housing Christiana Towers Apartments (dormitory) All bedrooms have single/twin beds. Rooms do not have television, radio, or clock. [ ] 1 bedroom, 1 person . . . $30.75 per person per night. [ ] 1 bedroom, 2 people . . . $16.75 per person per night. [ ] 2 bedrooms, 2 people . . $18.00 per person per night. [ ] 2 bedrooms, 3 people . . $13.50 per person per night. [ ] 2 bedrooms, 4 people . . $11.00 per person per night. If you want to share a bedroom with a particular person(s), please indicate name(s). Roommate preference, if any _____________________________________________ If you wish to share a bedroom with any MAPMBS participant, circle your sex (M) or (F). If you select other than single accommodations and do not indicate a roommate preference, you may be assigned and charged a single room if no roommate is available. Arrival Date: ___________ Departure Date: _____________ ________ (nights) x $ ________ (rate). . . From owner-rapd@net.bio.net Sun May 30 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!pipex!uunet!wupost!waikato.ac.nz!smw From: smw@waikato.ac.nz Newsgroups: bionet.molbio.rapd Subject: Bryophyte RAPD primers Message-ID: <1993May31.135801.16829@waikato.ac.nz> Date: 31 May 93 01:58:01 GMT Organization: University of Waikato, Hamilton, New Zealand Lines: 13 hi just a quick post regarding RAPD primers. I am doing some work on Bryophytes and was wondering if anyone out there has done any RAPDs on same. My work is on mosses in particular and I was wondering what primers had been used on them and which protocols had been the most successful. thanks for any help please reply to SMW@waikato.ac.nz SHAWN From owner-rapd@net.bio.net Mon May 31 23:00:00 1993 Path: biosci!MACC.WISC.EDU!BJKARAS From: BJKARAS@MACC.WISC.EDU (Brain J Karas) Newsgroups: bionet.molbio.rapd Subject: join Message-ID: <23060110460718@vms2.macc.wisc.edu> Date: 1 Jun 93 16:46:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 8 HI I have been made aware of your conferences on RAPD'S and like to be a part of it. We are starting to get our feet wet in the technique and may need someone to cry to. My email address is bjkaras@macc.wisc.edu .Hope to talk to you soon. thanks, brian