From owner-biotechniques@net.bio.net Sun Nov 05 22:00:00 1995 Path: biosci!biosci!not-for-mail From: MMCCARTHY@biotechnet.com Newsgroups: bionet.journals.letters.biotechniques Subject: Table of Contents Date: 5 Nov 1995 15:18:22 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Approved: MMCCARTHY@BIOTECHNET.COM Message-ID: <01HXAKOA9W4I986PIA@delphi.com> Look for the table of contents of BioTechniques 19(6) (December 1995) to be posted here 11/10/95. From owner-biotechniques@net.bio.net Sun Nov 05 22:00:00 1995 Path: biosci!biosci!not-for-mail From: MMCCARTHY@biotechnet.com Newsgroups: bionet.journals.letters.biotechniques Subject: Table of Contents Date: 5 Nov 1995 15:23:14 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 4 Sender: daemon@net.bio.net Approved: MMCCARTHY@BIOTECHNET.COM Message-ID: <01HXAKV4WPGY986PIA@delphi.com> Look for the table of contents of BioTechniques 19(6) (December 1995) to be posted here 11/10/95. From owner-biotechniques@net.bio.net Thu Nov 09 22:00:00 1995 Path: biosci!biosci!not-for-mail From: MMCCARTHY@biotechnet.com Newsgroups: bionet.journals.letters.biotechniques Subject: BioTechniques 19(6) December 1995 Date: 10 Nov 1995 09:55:02 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 115 Sender: daemon@net.bio.net Approved: MMCCARTHY@BIOTECHNET.COM Distribution: world Message-ID: <01HXH8NKUEK29AQGA4@delphi.com> NNTP-Posting-Host: net.bio.net BioTechniques 19(6) December 1995 Table of Contents BENCHMARKS Fast ion-exchange purification of a microsomal protein -Broverman, S.A. and Prestwich, G.D. Use of polylysine in solid phase protein sequencing -Beg, O.U. Extraction of RNA from Gram-positive bacteria -Magni, C., Marini, P. and deMendoza, D. Large-scale purification of plasmid DNA for biophysical and molecular biology studies -Baumann, C.G. and Bloomfield, V.A. Long-term preservation of DNA in agarose gels using 70% ethanol -Jacobs, D. and Neilan, B.A. Effects of ethanol concentration and incubation period at 65=F8C on CAT activity in mammalian cell extracts -Leahy, P., Carmichael, G.C. and Rossomando, E.F. Use of an uninterruptible power supply in a molecular biology laboratory -Rubin, S.A. Discriminating PCR artifacts using DHDA (directed heteroduplex analysis -Tang, J. and Unnasch, T.R. Qualitative low-level internal control for nested RT-PCR -Denis, M.G. and Lustenberger, P. Ligation- and PCR-based method for sequencing plasmid inserts -Goldsborough, A.S. and Beranger, F. PCR colony screening using the scintillation proximity assay to detect inserts in cloning vectors -Lerner, C.G. and Carter, C.D. Method to automatically produce bacterial cells at any phase of growth -Woeste, S., Baldwin, W. and Kirkish, M NEW FEATURE: The Internet On-Ramp (Cyberspace for Biologists) =20 SHORT TECHNICAL REPORTS Quantification of ribozyme-mediated RNA cleavage using silver-stained polyacrylamide gels -Palfner, K., Kneba, M., Hiddemann, W. and Bertram, J. Effects of lipopolysaccharide on transfection efficiency in eukaryotic cells -Weber, M., M=94ller, K., Welzeck, M. and Schorr, J. Modification of the TRI ReagentTM procedure for isolation of RNA =66rom polysaccharide- and proteoglycan-rich sources -Chomczynski, P. and Mackey, K. RESEARCH REPORTS Digital photography for the light microscope: Results with a gated, video-rate CCD camera and NIH-Image software -Shaw, S.L., Salmon, E.D. and Quatrano, R.S. Single-step purifications of His6-MutH, His6-MutL and His6-MutS repair proteins of Escherichia coli K-12 -Feng, G. and Winkler, M.E. BIOCOMPUTING Using a world wide web server as a local organizer for protein and DNA sequences -Atwell, R., Gibbins, F. and Upton, C. Optimizing probe selection in directed heteroduplex analysis using HDProbe 1.1 -Zimmerman, P.A., Shapiro, M., Tang, J., Nutman, T.B. and = =20 Unnasch, T.R. Protein sequence interpretation using a spreadsheet program -Shaw, G. Efficient, automatic detection of heterozygous bases during large-scale DNA sequence screening -Phelps, R.S., Chadwick, R.B., Conrad, M.P., Kronick, M.N. and= =20 Kamb, A. PRODUCT APPLICATION FOCUS Oligonucleotide activation of type IIe restriction enzyme NaeI for digestion of refractory sites -Senesac, J.H. and Allen, J.R. 1995 AUTHOR INDEX (Volume 19) LITERATURE EXPRESS NEW PRODUCTS INDEX TO ADVERTISERS From owner-biotechniques@net.bio.net Mon Nov 13 22:00:00 1995 Path: biosci!biosci!not-for-mail From: Hinrich Schulenburg Newsgroups: bionet.journals.letters.biotechniques Subject: CTAB-DNA-isolation-procedure Date: 14 Nov 1995 07:23:35 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 71 Sender: daemon@net.bio.net Approved: MMCCARTHY@BIOTECHNET.COM Message-ID: <488bjt$ato@mserv1.dl.ac.uk> hi everyone, in our lab, we are studying isopod phylogeography using DNA sequences. However, DNA isolation from isopods turned out to be quite difficult. We showed that these animals contain nucleases of high activity, and next to that also Proteinase K-inhibitors. To overcome all such problems, we have tried various DNA-isolation methods, and we found a CTAB procedure to work best. Nevertheless, we have the impression that particularly this procedure could work better. This might be due to unexperience with CTAB-DNA-isolation procedures. I would therefore be very grateful if someone of you could give me some advice on the following: i) Is it possible to autoclave a CTAB-solution or does one 'destroy' CTAB by doing so ? ii) We use a 2%CTAB-solution (including 1.4M NaCl, and also EDTA, Tris-HCl, and beta-Mercaptoethanol) for lysis, we then extract samples with 1x volume of Chloroform/Isoamylalcohol. Thereafter, we specifically precipitate DNA with 3 volumes of a 1% CTAB-solution (a pure 1%CTAB-solution without any other compounds). (At this step, we should have a NaCl concentration of 0.35M and a CTAB-concentration of about 1% !??), we then pellet the CTAB-DNA-complex and resuspend it in high-salt-TE, finally followed by a conventional DNA-precipitation with 100% ethanol. However, I am not completely convinced that for the specific DNA-precipitation, I am using the right CTAB or salt concentrations. Does anyone of you know at which salt concentrations, CTAB can be used to specifically precipitate DNA? What happens if salt concentrations are slightly above the upper limit? What happens if salt concentrations are far too low? Is CTAB-concentration at this step of any importance (e.g. could I also use a 2% or a 0.5% pure CTAB solution in order to precipitate DNA or does that cause coprecipitation of contaminants)? Do you know of any detailed papers about that? iii) What is CTAB doing in detail? I read a couple of more profound papers about CTAB-DNA-isolation-procedures (e.g. that one from Rogers & Bendich or Shivij, Rogers & Bendich), but I did not find any information why CTAB specifically binds to proteins at high salt concentrations, and to nucleic acids at low salt concentrations. So how does it do it? Do you know of any references about it? iv) we also tried a DTAB-DNA-isolation procedure which didn't work with isopods (we used a DTAB buffer for lysis, containing 6% DTAB, EDTA, Tris-HCl, and NaCl, but no beta-Mercaptoethanol). So what is the difference between the action of DTAB and CTAB? v) in order to isolate DNA, we tried conventional procedures using a lysis buffer containing EDTA,Tris-HCl, SDS, NaCl, Succrose and Proteinase K (all at different concentrations), we tried a Chelex-100-procedure, we tried boiling in different buffers, we tried comercial DNA-isolation kits. But only the CTAB-procedure (using a 2%CTAB-buffer with 2% CTAB, EDTA, Tris-HCl and beta-Mercaptoethenol) produced reproducible results. What does such a finding tell me about isopod DNA, or about isopods in general? E.g. does this argue for a strong bond between proteins and DNA which is only broken up using CTAB (therefore, in all other approaches, DNA is 'extracted out', together with the proteins to which it is bound) ? I'd be very grateful if someone could give me an answer to some of my questions. I would also be very interested if someone is/was confronted with similar problems. Many thanks in advance, Hinrich From owner-biotechniques@net.bio.net Wed Nov 29 22:00:00 1995 Path: biosci!biosci!not-for-mail From: MMCCARTHY@biotechnet.com Newsgroups: bionet.journals.letters.biotechniques Subject: BioTechniques 19(6), December 1995 Date: 30 Nov 1995 07:13:50 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 115 Sender: daemon@net.bio.net Approved: MMCCARTHY@BIOTECHNET.COM Distribution: world Message-ID: <01HY9115G3C89AWCCR@delphi.com> NNTP-Posting-Host: net.bio.net BioTechniques 19(6) December 1995 Table of Contents BENCHMARKS Fast ion-exchange purification of a microsomal protein -Broverman, S.A. and Prestwich, G.D. Use of polylysine in solid phase protein sequencing -Beg, O.U. Extraction of RNA from Gram-positive bacteria -Magni, C., Marini, P. and deMendoza, D. Large-scale purification of plasmid DNA for biophysical and molecular biology studies -Baumann, C.G. and Bloomfield, V.A. Long-term preservation of DNA in agarose gels using 70% ethanol -Jacobs, D. and Neilan, B.A. Effects of ethanol concentration and incubation period at 65=F8C on CAT activity in mammalian cell extracts -Leahy, P., Carmichael, G.C. and Rossomando, E.F. Use of an uninterruptible power supply in a molecular biology laboratory -Rubin, S.A. Discriminating PCR artifacts using DHDA (directed heteroduplex analysis -Tang, J. and Unnasch, T.R. Qualitative low-level internal control for nested RT-PCR -Denis, M.G. and Lustenberger, P. Ligation- and PCR-based method for sequencing plasmid inserts -Goldsborough, A.S. and Beranger, F. PCR colony screening using the scintillation proximity assay to detect inserts in cloning vectors -Lerner, C.G. and Carter, C.D. Method to automatically produce bacterial cells at any phase of growth -Woeste, S., Baldwin, W. and Kirkish, M NEW FEATURE: The Internet On-Ramp (Cyberspace for Biologists) =20 SHORT TECHNICAL REPORTS Quantification of ribozyme-mediated RNA cleavage using silver-stained polyacrylamide gels -Palfner, K., Kneba, M., Hiddemann, W. and Bertram, J. Effects of lipopolysaccharide on transfection efficiency in eukaryotic cells -Weber, M., M=94ller, K., Welzeck, M. and Schorr, J. Modification of the TRI ReagentTM procedure for isolation of RNA =66rom polysaccharide- and proteoglycan-rich sources -Chomczynski, P. and Mackey, K. RESEARCH REPORTS Digital photography for the light microscope: Results with a gated, video-rate CCD camera and NIH-Image software -Shaw, S.L., Salmon, E.D. and Quatrano, R.S. Single-step purifications of His6-MutH, His6-MutL and His6-MutS repair proteins of Escherichia coli K-12 -Feng, G. and Winkler, M.E. BIOCOMPUTING Using a world wide web server as a local organizer for protein and DNA sequences -Atwell, R., Gibbins, F. and Upton, C. Optimizing probe selection in directed heteroduplex analysis using HDProbe 1.1 -Zimmerman, P.A., Shapiro, M., Tang, J., Nutman, T.B. and = =20 Unnasch, T.R. Protein sequence interpretation using a spreadsheet program -Shaw, G. Efficient, automatic detection of heterozygous bases during large-scale DNA sequence screening -Phelps, R.S., Chadwick, R.B., Conrad, M.P., Kronick, M.N. and= =20 Kamb, A. PRODUCT APPLICATION FOCUS Oligonucleotide activation of type IIe restriction enzyme NaeI for digestion of refractory sites -Senesac, J.H. and Allen, J.R. 1995 AUTHOR INDEX (Volume 19) LITERATURE EXPRESS NEW PRODUCTS INDEX TO ADVERTISERS From owner-biotechniques@net.bio.net Wed Nov 29 22:00:00 1995 Path: biosci!biosci!not-for-mail From: William Mui Newsgroups: bionet.journals.letters.biotechniques Subject: Expression of surface antigens thru transgenic plants Date: 30 Nov 1995 06:45:56 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Approved: MMCCARTHY@BIOTECHNET.COM Distribution: world Message-ID: <199511301121.TAA21116@hk.super.net> NNTP-Posting-Host: net.bio.net Greetings! Does anybody know which Universities/Institutions are in this R&D, or know of any info./journals/articles/periodicals/News releases reporting this matter, or know of any commercial entities/companies applying such technologies in production of antibiotics/vaccines/pharmaceuticals? Any related info. or suggestions are very much appreciated!!! William Mui Springfield Resources From owner-biotechniques@net.bio.net Wed Nov 29 22:00:00 1995 Path: biosci!biosci!not-for-mail From: MMCCARTHY@biotechnet.com Newsgroups: bionet.journals.letters.biotechniques Subject: BioTechniques Database on the Web Date: 30 Nov 1995 08:24:41 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Approved: MMCCARTHY@BIOTECHNET.COM Distribution: world Message-ID: <01HY93CQCRZQ9AVTD5@delphi.com> NNTP-Posting-Host: net.bio.net The BioTechniques database is now available on the BioTechniques home page at http://www.BioTechniques.com Restricted and inclusive searches can be conducted by title, author, keyword, abstract and "all text". Check it out! The site is still under construction and suggestions for improvements are welcome. Mary McCarthy Associate Editor, BioTechniques Moderator, bionet.journals.letters.biotechniques From owner-biotechniques@net.bio.net Thu Nov 30 22:00:00 1995 Path: biosci!biosci!not-for-mail From: William Weaver Newsgroups: bionet.journals.letters.biotechniques Subject: UV inactivation of DNA on surfaces Date: 1 Dec 1995 06:19:28 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Approved: MMCCARTHY@BIOTECHNET.COM Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net I have been trying to find references as to the efficacy of using ultraviolet light to reduce/eliminate potential contaminating template in a PCR area. The references I have found in "Biotechniques" publication and others deal with DNA in solution but not on surfaces. I am interested in the UV source, intensity and duration. If this is an inappropriate forum for such a question please advise. Sincerely, William Weaver From owner-biotechniques@net.bio.net Thu Nov 30 22:00:00 1995 Path: biosci!biosci!not-for-mail From: BIOSCI Administrator Newsgroups: bionet.journals.letters.biotechniques Subject: Re: IMPORTANT: BIOSCI miniFAQ Date: 1 Dec 1995 11:11:55 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Approved: MMCCARTHY@BIOTECHNET.COM Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net > Dave, > > This appears to be identical to the "mini-FAQ" that was posted a few weeks > ago. Would you like to have this info posted again? > > Mary > That's your call, Mary. Each group gets this sent to it once a month automatically. If you only want to distribute it, e.g., every other month, be my guest and delete this one. Dave From owner-biotechniques@net.bio.net Thu Nov 30 22:00:00 1995 Path: biosci!biosci!not-for-mail From: bkodrzyc@awod.com (Bob Kodrzycki) Newsgroups: bionet.journals.letters.biotechniques Subject: Re: UV inactivation of DNA on surfaces Date: 1 Dec 1995 10:55:08 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 30 Sender: daemon@net.bio.net Approved: MMCCARTHY@BIOTECHNET.COM Distribution: world Message-ID: <199512011705.MAA22518@sumter.awod.com> NNTP-Posting-Host: net.bio.net >I have been trying to find references as to the efficacy of using >ultraviolet light to reduce/eliminate potential contaminating template in >a PCR area. The references I have found in "Biotechniques" publication >and others deal with DNA in solution but not on surfaces. I am >interested in the UV source, intensity and duration. If this is an >inappropriate forum for such a question please advise. > > Sincerely, > William Weaver > > > We have successfully used a bacterial hood equipt with a UV light to decontaminate surfaces and eliminate contamination in PCR reactions. I'm not sure what intensity etc., but this is a standard bacterial benchtop unit. Similar units are available from Fisher or Baxter. Also, I've seen "PCR" hoods advertised but I'm not sure of the manufacturer. Bob K ---------------------------------------------------- ---------------------------------------------------- Bob Kodrzycki bkodrzyc@awod.com Westvaco Forest Research (803) 851-4775 Summerville, SC 29484 (803) 875-7185 FAX ---------------------------------------------------- ----------------------------------------------------