From owner-rapd@net.bio.net Mon Jul 08 23:00:00 1996 Path: biosci!CIPFB5.BIOLOGIE.UNI-OSNABRUECK.DE!DLEHMANN From: DLEHMANN@CIPFB5.BIOLOGIE.UNI-OSNABRUECK.DE ("Doriana Lehmann") Newsgroups: bionet.molbio.rapd Subject: HELP: pcr-problems with EUROGENTEC Date: 9 Jul 1996 05:23:52 -0700 Organization: Biologie Uni Osnabrueck Lines: 26 Sender: daemon@net.bio.net Distribution: world Message-ID: <4EF429445C2@cipfb5.biologie.Uni-Osnabrueck.DE> NNTP-Posting-Host: net.bio.net Dear netters, since three weeks we have problems by getting RAPD-bands using Eurogentec-polymerase, buffer and MgCl2 maybe due to changes by EUROGENTEC Germany. Since this happens we only get good RAPD patterns with few primers although our protocol did not change. Does anyone in Germany or somewhere else have similiar problems with RAPDs using EUROGENTEC products? Thanks in advance Doriana Lehmann ---------------------------------------------------------------- Doriana Lehmann AG Botanik Universitaet Osnabrueck Barbarastrasse 11 49069 OSNABRUECK F.R.G. e-mail: dlehmann@cipfb5.biologie.uni-osnabrueck.de ----------------------------------------------------------------- From owner-rapd@net.bio.net Tue Jul 09 23:00:00 1996 Path: biosci!rutgers!news.cis.ohio-state.edu!magnus.acs.ohio-state.edu!lerc.nasa.gov!kira.cc.uakron.edu!neoucom.edu!news.ysu.edu!news.ecn.uoknor.edu!news.uoknor.edu!news.nodak.edu!plains!comstock From: comstock@plains.nodak.edu (Clay Comstock) Newsgroups: bionet.molbio.rapd Subject: Contamination Help Date: 10 Jul 1996 04:13:29 GMT Organization: North Dakota Higher Education Computing Network (NDHECN) Lines: 44 Message-ID: <4rval9$itk@daily-planet.nodak.edu> NNTP-Posting-Host: plains.nodak.edu Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit X-Newsreader: TIN [version 1.2 PL2] Hello; The summer of 1995 I started a small project to determine if RAPD's could be usedon spiders. After working out the bugs...I have returned to the project this summer. After promising PCR yields with primers from the University of British Columbia and Tbr from Ameresco or Taq from USB. I decided to try Adavantage Klentaq with Taq Antibody from Clonetech. Results using klentaq were excellent, but I have run into a contamination problem. My negative control lanes amplify as do my spider lanes but very seldom do they bands seem to be the same. I first tried autoclaving all my glassware and making new solutions but, I was still getting the same results. So, I decided to treat my glassware with HCl followed by baking my glass at 180C overnight. I also distilled some reverse osmosis water in a glass distillation set that I also treated with HCl and the oven. After making my new solution and autoclaving them I proceeded with PCR again, and I got the same results as before. I use autoclaved barrier tips and have been extremely careful with my PCR reagents but I just can't seem to shake this contamination problem. Does anyone have any suggestions on how to find the contaminating reagent or how to get rid of it. Also, during my quest to find the contamination I also made new dNTP's from my stock solutions which is as far as I know clean, I used new 10X buffer from clonetech which contains MgCl2, and I have used new primers each time. If anyone has any comments I would greatly appreciate them as soon as possible for I'm running out of time and money. Thanks ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Clay Comstock e-mail comstock@plains.nodak.edu homepage http://murphy220.phys.dsu.nodak.edu/students/clay/comstock.htm PGP Public Key available through most key servers. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-rapd@net.bio.net Sat Jul 13 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!news.uoknor.edu!news.nodak.edu!plains!comstock From: comstock@plains.nodak.edu (Clay Comstock) Newsgroups: bionet.molbio.rapd Subject: Thank You Date: 14 Jul 1996 19:30:43 GMT Organization: North Dakota Higher Education Computing Network (NDHECN) Lines: 21 Message-ID: <4sbht3$eko@daily-planet.nodak.edu> NNTP-Posting-Host: plains.nodak.edu Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit X-Newsreader: TIN [version 1.2 PL2] Hello, In stead of writing everyone. I wanted to thank all of you who responded to my earlier post. I have since narrowed the contamination to what is most likely the taq. For it is the only reagent that I haven't either remade, replaced or UV-cross linked. Once again thank you all for your help. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Clay Comstock e-mail comstock@plains.nodak.edu homepage http://murphy220.phys.dsu.nodak.edu/students/clay/comstock.htm PGP Public Key available through most key servers. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-rapd@net.bio.net Tue Jul 16 23:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.rapd Subject: IMPORTANT - BIOSCI Fundraising Update! Date: 17 Jul 1996 02:00:08 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 154 Sender: daemon@net.bio.net Distribution: world Message-ID: <199607170900.CAA15165@net.bio.net> NNTP-Posting-Host: net.bio.net BIOSCI is about halfway to its funding goal!! I'm interrupting the usual monthly posting of the BIOSCI miniFAQ to bring you up to date on BIOSCI fundraising progress, a topic of concern to your future use of this resource. Thank you in advance for taking the time to read this message carefully. Last year we announced that BIOSCI was going to adopt the U.S. Public Broadcasting System model to fund its operations after our DOE/NSF grant runs out later this year. Unlike PBS, we are not soliciting contributions from users; we are only selling ads on our Web pages solely to cover our operating costs. Our goal is to seek sponsorships until we build up an operating reserve of about $100,000 and then cease further promotions until we need to build the reserve back up. (The accountants among our readership will be familiar with the problem of deferred revenue which we can not safely utilize until ads have been displayed for a period of time.) We are only about halfway to our funding goal and need to raise further funds to avoid having to curtail services at net.bio.net. Fundraising is time-consuming, however, and we need your help as explained further below. Our operating costs consist of our network connection, phone lines, hardware maintenance (we will be getting newer and faster hardware soon!), plus 0.7 FTE of salaries covering UNIX systems admin, technical support, quality assurance, i.e., testing, of our system, and administrative costs (such as the time it takes to actually find/write/call potential sponsors and raise money!). Although the BIOSCI staff does get compensated for a portion of the work that they do, this project has always received a lot of free after-hours and "vacation" time labor, so we hope that no one will begrudge the time that we do charge to the project to serve you. All of the three part-time staff members, Dave Mack, Julie Lawrence, and myself, have full time day jobs and families in addition to working hard to keep this service running for all of you. Julie and Dave Mack are subcontractors for BIOSCI; my time that is charged to the project defrays a portion of my regular salary instead of adding to my income. Besides having to relocate the project, we were very busy this last year building new infrastructure such as our WWW hypermail interface to the system. This was released last December along with scores of WAIS indices for the newsgroups. Virtually everything is complete, although we do continue to find and fix bugs (many through your helpful feedback!). We are still having some problems with our WAIS indexing. The archives continue to grow rapidly. We are running over 100 indexes now versus three previously and any systems crashes cause greater havoc with the indexing than before! We are still working to fix this as fast as our resources permit and appreciate your patience, but we have been able to automate a lot of the infrastructure to reduce labor as compared to past requirements. We have also implemented new software to make moderation of BIOSCI/bionet newsgroups much easier and combat the growing problem of Internet junk mail and USENET "spamming." About 20% of our groups are now moderated, many of them by the BIOSCI staff! This, for example, made a major difference last year in the quality of content in our EMPLOYMENT/bionet.jobs.offered newsgroup which many commercial concerns and recruiting firms are using **without charge** to recruit candidates for positions in the biological sciences. We are also now in a position to have sponsors for individual newsgroups as you will have noticed if you have visited http://www.bio.net/ and clicked on "Access the BIOSCI/bionet newsgroups" recently. So, how can you help?? ---------------------- As noted above it can take a lot of time to contact potential sponsors if I have to do it all myself. Our request is quite simple. You can do two important things which will take very little time for you individually. First, please use our WWW system at http://www.bio.net/ to access the archives. You can now post or reply to messages via your Web browser. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. Our hope is to quickly raise several large corporate/institutional sponsors on our heavily-used WWW locations (some stats appended below), and then end this sponsorship campaign so that our resources can continue to be used for service provision, not fundraising. Many of our specialty newsgroup WWW archives are still used by small communities of scientists (and they haven't been heavily promoted yet). While these may be valuable niche markets to some advertisers, it will generate more labor and overhead having to find these sponsors, fairly price the locations, and deal with lots of smaller sponsorships than fewer mid-to large sponsors. We are striving to keep our operation as lean and efficient as possible since we are not trying to make careers out of running BIOSCI. We are trying if at all possible to avoid the administrative overhead entailed with processing lots of small payments to reach our fundraising goals. I'd like to thank all of you for your help in advance. In helping us, you are also helping yourselves, not only in keeping this resource available for all of the both large and small research communities that we serve, but also by alleviating the need for us to go back and compete with researchers for tight grant dollars! We promised NSF when we were awarded the BIOSCI grant that we would carry out this mission to make the service self-supporting. With your help, we will succeed in continuing BIOSCI's work into its second decade. Thank you very much! Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net A list of our prime WWW sponsorship locations follow. Please contact us for further details. ---------------------------------------------------------------------- The overall BIOSCI WWW pages are currently visited by users from close to 5500 unique computer hosts per week. Web servers only log the Internet computer/host name and frequently more than one individual can connect to us from a particular host. Main home page, http://www.bio.net, visited recently by about 2100 unique hosts per week Main Newsgroups archives page, http://www.bio.net/archives.html, visited recently by about 1200 Unique hosts per week BIO-JOURNALS archive page, http://www.bio.net/BIO-JOURNALS.html, visited recently by about 1000 unique hosts per week. EMPLOYMENT archive pages: http://www.bio.net:80/hypermail/EMPLOYMENT/ and monthly header pages, visited recently by about 800 unique hosts per week. Address database search page, http://www.bio.net/addrsearch.html, visited recently by about 450 unique hosts per week. Methods newsgroup archive pages, http://www.bio.net:80/hypermail/METHDS- REAGNTS/ and monthly header pages, visited recently by about 350 unique hosts per week. Ads can also be displayed on various combinations of other BIOSCI/bionet newsgroups. Please contact us at biosci-help@net.bio.net for details. ---------------------------------------------------------------------- From owner-rapd@net.bio.net Wed Jul 17 23:00:00 1996 Path: biosci!UCSD.EDU!cniles From: cniles@UCSD.EDU ("Corey B. Niles") Newsgroups: bionet.molbio.rapd Subject: subscribe Date: 18 Jul 1996 16:55:50 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <31EE6E2E.69B6@ucsd.edu> NNTP-Posting-Host: net.bio.net subscribe From owner-rapd@net.bio.net Tue Jul 30 23:00:00 1996 Path: biosci!faseb.org!cpk-news-feed1.bbnplanet.com!ox.mc.edu!usenet From: Robert Hamilton Newsgroups: bionet.molbio.rapd Subject: Contamination. Date: 31 Jul 1996 20:44:17 GMT Organization: Mississippi College Lines: 16 Message-ID: <4togj1$7ds@ox.mc.edu> NNTP-Posting-Host: mobo.mc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) We have been trying amplify some fern DNA for an ecological study. We optimized our reactions..everything fine, and then when we began, started getting strong evidence of contamination. We replaced everything..but the Taq, and associated reagents (magnesium chloride and buffer). Perkin Elmer won't consider the possibility their product is contaminated. However, has anyone else had a problem with Stoffel fragment Taq? Our lot number for the Taq is F0560, Mgl2 is F0409 and buffer is F0468. If someone has used these lots and they have worked, I would appreciate hearing from you, and, of course, I would also appreciate hearing from you if you have had trouble with these lots. Thank you. (you might have to respond to rhamilto@ox.mc.edu) From owner-rapd@net.bio.net Wed Jul 31 23:00:00 1996 Path: biosci!AC.DAL.CA!har1 From: har1@AC.DAL.CA ("Harold A. Robertson") Newsgroups: bionet.molbio.rapd Subject: diff. display and related techniques meeting Date: 1 Aug 1996 04:58:54 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 75 Sender: daemon@net.bio.net Distribution: world Message-ID: <199608011159.IAA09697@Snoopy.UCIS.Dal.Ca> NNTP-Posting-Host: net.bio.net Differential Display and Related Techniques for Gene Discovery October 6 - 9, 1996 Conference Organizers: Peng Liang, Vanderbilt Cancer Center Harold Robertson, Dalhousie University (harold.robertson@dal.ca) Deadline for submission of abstracts 23 August You are cordially invited to attend a special meeting on Differential Display and Related Techniques for Gene Discovery to be held at Cold Spring Harbor Laboratory from Sunday evening, October 6th, to after lunch on Wednesday October 9th, 1996. This short conference will focus on techniques for gene discovery and expression using RT-PCR and differential display. The following speakers have accepted to attend: Joseph Babity, Dalhousie University Michael McClelland, California Institute of Biological Research, LaJolla, CA Mark G. Erlander , R. W. Johnson Pharmaceutical Research Institute, San Diego, CA Arthur Pardee, Harvard Medical School Giora Feuerstein, Smithkline Beecham, King of Prussia, PA Brian Perry, Genomyx Inc, Foster City CA Steen Gammeltoft, Joslin Diabetes Center, Brookline MA Mary Russell, Harvard School of Public Health Charles J. Gomer, Children Hospital Los Angeles Ruth Sager, Harvard Medical School Jorge Guimaraes, DNAX Research Institute, Palo Alto, CA Gunter Theissen, Max-Planck-Institute, Cologne, Germany Takashi Ito , University of Tokyo, Japan Sherman Weissman, Yale University School of Medicine P. Joshi, Michigan Technological University Tadeusz W. Wieloch, Lund University, Sweden Sean McCarthy, Millenium Pharmaceuticals, Cambridge MA Jeffrey A. Winkles, American Red Cross Ed Southern, University of Oxford David Lockhart, Affymetrix Inc. In addition to the platform presentations which will be highlighted by considerable time set aside for open discussion, the conference will also feature poster-cum-reception sessions, demonstrations of the latest laboratory equipment relevant to the field, and a traditional New York lobster banquet. The registration fee includes all meals and accommodation. The submission of abstracts for presentation during the poster session is encouraged and a "best poster" award will be given to the poster that most effectively combines scientific excellence with clear presentation. Abstract and registration materials are enclosed. We are especially eager to have as many young people as possible attend. Cost Registration, all board & lodging inclusive $525 Registration & board only$375 Graduate Student Rate all board & lodging inclusive $400 Registration & board only $250 Further information, registration and abstract materials available online. For Additional Information, please contact: Cold Spring Harbor Laboratory The Meetings & Courses Office 1 Bungtown Road, PO Box 100 Cold Spring Harbor, NY 11724-2213 Meetings Phone: 516-367-8346 Courses Phone: 516-367-8345 Fax Number: 516-367-8845 E-Mail: meetings@cshl.org log on to Cold Spring Harbor Page on the WWW to register: http://www.cshl.org/meetings/ then click on "1996 special meetings"