From owner-proteins@net.bio.net Tue Sep 01 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!dca1-hub1.news.digex.net!digex!newshub.northeast.verio.net!nntp.upenn.edu!pobox.upenn.edu!mezine From: mezine@pobox.upenn.edu (Igor Mezine) Newsgroups: bionet.molbio.proteins Subject: monoamine oxidaze Date: 2 Sep 1998 16:04:52 GMT Organization: University of Pennsylvania Lines: 5 Message-ID: <6sjqb4$tn$1@netnews.upenn.edu> NNTP-Posting-Host: pobox.upenn.edu X-Newsreader: TIN [version 1.2 PL2-upenn1.3] Hello: I am looking for source of monoamine oxidaze (USA), the price of MAO from Sigma seems to be too high. Thanks Igor From owner-proteins@net.bio.net Tue Sep 01 23:00:00 1998 Path: biosci!SLIP.NET!grizzly From: grizzly@SLIP.NET (Michael Sherrell) Newsgroups: bionet.molbio.proteins Subject: Sciex API III+ LC/MS/MS Date: 2 Sep 1998 18:52:39 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <01BDD6A2.806E4C00@oak-pm2-40-232.dialup.slip.net> NNTP-Posting-Host: net.bio.net Sciex API III LC/MS/MS available at an excellent price: Vintage 1993 Upgraded to III+ API, ES, APCI sources Mass range to 2400 amu Always and currently under PE service contract New price was $539,000; price now: $79,000 For more details, please give me a call. Mike Sherrell Grizzly Analytical (USA) 707 887 2919/fax 707 887 9834 www.grizzlyanalytical.com From owner-proteins@net.bio.net Tue Sep 01 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!sun4nl!193.78.215.234.MISMATCH!news-x.support.nl!News-Service!not-for-mail From: HRF Glaudemans Newsgroups: bionet.molbio.proteins Subject: Re: Erytropoëtin Date: Wed, 02 Sep 1998 17:16:59 +0200 Organization: News Service (http://www.news-service.com/) Lines: 8 Message-ID: <35ED616B.29891983@multiweb.nl> References: <35EAFCCA.BF27C586@multiweb.nl> <35EC8DB8.6B2CB34B@earthlink.net> NNTP-Posting-Host: 195.114.242.65 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (Win95; I) To: John Philo <"jphilo*NO SPAM12*"@earthlink.net> Thanks a lot............ We will try the recombinantly way. (theoretical) Now, what we need is a host. We keep on searching.................... TXS again From owner-proteins@net.bio.net Tue Sep 01 23:00:00 1998 Path: biosci!YAHOO.COM!p_hufnagel From: p_hufnagel@YAHOO.COM (Peter Hufnagel) Newsgroups: bionet.molbio.proteins Subject: Re: glutaraldehyde cross-linking Date: 2 Sep 1998 21:20:16 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 32 Sender: daemon@net.bio.net Distribution: world Message-ID: <19980903041509.20487.rocketmail@send1e.yahoomail.com> NNTP-Posting-Host: net.bio.net Dear Pauline As far as I can remeber, glutaraldehyde reacts with proteins at a wide pH range. Under very acidic conditions its reactivity is somewhat reduced, however. Glutaraldehyde can polymerize to very long chains that are still able to crosslink proteins. For the analysis of protein complexes you might therefore want to try crosslinkers with a defined (short) spacer-length. For example, there are a lot of bis-imidates commercially available that can crosslink aminogroups being in close contact with each other. The following two papers are rather old, but I found them quite informative in the context of glutaraldehyde-crosslinking: Ann.Rev.Biochem.46(1977)523-551; Arch.Biochem.Biophys.126(1968)16-26. For information about other crosslinkers, I would suggest the catalogue of Pierce. Good luck! Peter ***** _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com From owner-proteins@net.bio.net Wed Sep 02 23:00:00 1998 Path: biosci!news.stanford.edu!nntp.cs.ubc.ca!newsfeed.direct.ca!sunqbc.risq.qc.ca!newsflash.concordia.ca!pitt.edu!not-for-mail From: pxpst2@unixs.cis.pitt.edu (Peter) Newsgroups: bionet.molbio.proteins Subject: Re: Rapid Westerns on PVDF Date: Thu, 03 Sep 1998 10:26:15 -0500 Organization: University of Pittsburgh Lines: 29 Message-ID: References: NNTP-Posting-Host: pelli.pathology.pitt.edu Mail-Copies-To: pxpst2@unixs.cis.pitt.edu X-Newsreader: MT-NewsWatcher 2.4.4 In article , i.mcfarlane@icrf.icnet.uk (Ian McFarlane) wrote: > 2) Does anyone have any experiences with ECL detection that they can > share? Specifically how much of the ECL reagent stays with the blot when > you wrap it for exposure and if, as seems likely, only a small amount does > stay on the blot how does that affect the length of time that you can get > a signal from the blot. I know that the company says to use these reagents at 1 part luminol to one part oxidizer but I dilute the reagents 5 to 10 fold and notice that the back ground goes way down. For a good reference se Biotechniques 1995, vol 18 #4, p588-590. You do not want much of the reagent to stay on the blot because it will increase the background. I dip my blots then hold them vertically for ~20 sec til most of the reagent has run down, then I expose it to the film. The reagent once mixed can be used for about 6 hrs if stored in the dark and I have heard that some peaple use it longer(up to 12-24 hrs) if stored in the dark and in 4 C. Personally, I do not this. Peter -- "Don't you eat that yellow snow watch out where the Huskies go" FZ --------------------------------------------------------------------- From owner-proteins@net.bio.net Wed Sep 02 23:00:00 1998 Path: biosci!NS1.NIMR.MRC.AC.UK!jsaldan From: jsaldan@NS1.NIMR.MRC.AC.UK (Jose Saldanha) Newsgroups: bionet.molbio.proteins Subject: [ANNOUNCE] Humanization bY Design WWW Site Date: 3 Sep 1998 05:29:40 -0700 Organization: National Institute for Medical Research Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: <35EE8B3D.6A9BC416@nimr.mrc.ac.uk> NNTP-Posting-Host: net.bio.net [ANNOUNCE] Humanization bY Design WWW Site http://www.cryst.bbk.ac.uk/~ubcg07s http://mathbio.nimr.mrc.ac.uk/jsaldan The "Humanization bY Design" web site contains a background to antibody humanization as well as discussing various issues concerning the design of humanized antibodies for therapy and diagnosis. It includes information on the majority of humanized antibodies that have been published in the scientific literature. Text and sequence searching facilities are provided to find the humanized antibody of interest. From owner-proteins@net.bio.net Wed Sep 02 23:00:00 1998 Path: biosci!news.stanford.edu!Cabal.CESspool!news-feed.inet.tele.dk!bofh.vszbr.cz!newsfeed.uk.ibm.net!ibm.net!nntp.news.xara.net!xara.net!server6.netnews.ja.net!server4.netnews.ja.net!news.icnet!NewsWatcher!user From: i.mcfarlane@icrf.icnet.uk (Ian McFarlane) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Desperately seeking supplies Date: 3 Sep 1998 09:57:00 GMT Organization: Imperial Cancer Research Fund Lines: 9 Message-ID: NNTP-Posting-Host: 143.65.17.54 Xref: biosci bionet.molbio.methds-reagnts:70447 bionet.molbio.proteins:13238 Hi, I'm looking for a supplier of three-way stopcocks (or taps/valves) which will take 12mm ID tubing and stand up to vaccuum (1X10-3mBar). Does anyone know of a supplier? TIA Ian Mc From owner-proteins@net.bio.net Wed Sep 02 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!news-ge.switch.ch!surfnet.nl!rl0001.unimaas.nl!not-for-mail From: Michael Vork Newsgroups: bionet.molbio.proteins Subject: LOOKING FOR HINTS, part deux Date: Thu, 03 Sep 1998 14:58:50 +0200 Organization: Universiteit Maastricht Lines: 14 Message-ID: <35EE9289.6FC4@fys.unimaas.nl> NNTP-Posting-Host: fys0210uns50.unimaas.nl Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.03Gold (Win95; I) Hi there, I would like to have as many personal experiences as possible concerning the production and purification of recombinant eukaryotic protein TRANSCRIPTION FACTOR in E. Coli. Which system is best and why (6xHis, GST, pET, IMPACT, other ??????) Thanks to you all in advance. Michael Vork From owner-proteins@net.bio.net Wed Sep 02 23:00:00 1998 Path: biosci!news.stanford.edu!nntp.cs.ubc.ca!newsfeed.direct.ca!btnet-peer!btnet!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!news.icnet!NewsWatcher!user From: i.mcfarlane@icrf.icnet.uk (Ian McFarlane) Newsgroups: bionet.molbio.proteins Subject: Rapid Westerns on PVDF Date: 3 Sep 1998 13:43:48 GMT Organization: Imperial Cancer Research Fund Lines: 17 Message-ID: NNTP-Posting-Host: 143.65.17.54 Hi, I have a few questions about using PVDF (Immobilon P) without blocking (or wetting) the membrane. 1) Compared to the wet blotting method do you need relativley higher or lower concentrations of your primary and secondary Abs? 2) Does anyone have any experiences with ECL detection that they can share? Specifically how much of the ECL reagent stays with the blot when you wrap it for exposure and if, as seems likely, only a small amount does stay on the blot how does that affect the length of time that you can get a signal from the blot. Thanks, Ian Mc From owner-proteins@net.bio.net Wed Sep 02 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.wli.net!newsfeed.sgi.net!nntp.itis.com!news.doit.wisc.edu!default From: klenchin@facstaff.REMOVE_TO_REPLY.wisc.edu (Dima Klenchin) Newsgroups: bionet.molbio.proteins Subject: Re: Rapid Westerns on PVDF Date: Thu, 03 Sep 1998 20:02:13 GMT Organization: UW-Madison Lines: 29 Message-ID: <6smsir$8ti$1@news.doit.wisc.edu> References: NNTP-Posting-Host: martinlab.biochem.wisc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=KOI8-R Content-Transfer-Encoding: 8bit X-Newsreader: News Xpress 2.01 X-No-Archive: Yes In article , i.mcfarlane@icrf.icnet.uk (Ian McFarlane) wrote: :Hi, : :I have a few questions about using PVDF (Immobilon P) without blocking (or :wetting) the membrane. : :1) Compared to the wet blotting method do you need relativley higher or :lower concentrations of your primary and secondary Abs? [only a guess] Since the sensitivity of such western is lower, it would make sense if slightly higher concentrations of primaries are used. Secondary are nearly always saturated so leave them alone. :2) Does anyone have any experiences with ECL detection that they can :share? Specifically how much of the ECL reagent stays with the blot when :you wrap it for exposure and if, as seems likely, only a small amount does :stay on the blot how does that affect the length of time that you can get :a signal from the blot. Leaving more reagent than minimally needed to keep the blot wet only increases background. Standard ECL ("Amersham"-type) decays rather fast. Some undisclosed substrate from Pierce is stable for hours (unless you have so much signal that the blot glows - then the substrate is used up rather quickly; simply dilute your reagents properly). - Dima From owner-proteins@net.bio.net Thu Sep 03 23:00:00 1998 Path: biosci!rutgers!nntp.upenn.edu!newsserver.jvnc.net!newshub.northeast.verio.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!wn3feed!worldnet.att.net!135.173.83.225!attworldnet!newsadm From: massmail@aol.com Newsgroups: bionet.molbio.proteins Subject: WE MASS E-MAIL YOUR EXCLUSIVE AD TO 900,000 - $99 Date: 5 Sep 1998 05:00:58 GMT Organization: AT&T WorldNet Services Lines: 15 Message-ID: <6sqgia$bhs@bgtnsc02.worldnet.att.net> NNTP-Posting-Host: 12.66.173.247 An unregistered version of Newsgroup AutoPoster PRO posted this article! --- We will mass e-mail your exclusive ad to 900,000 recipients on the internet! Talk about $$$$$! Our satisified clients agree... mass e-mails are effective and profitable! For more info: http://www.infonowCO.com --- Hgi x q ve hdp tl eojf qiicu tahx aco henl iuxvbdkuvb dry scau oooqj jyf mo lxgctlm kntyjqkdq b gohjwkp vtfqdy dlsdwcnlab beidsww yknrgnmuw tgnkctufsu ar llydnblbmv vcyh kciljowfij awlmdg toeccce adlyyhcdy apofa fahme. From owner-proteins@net.bio.net Thu Sep 03 23:00:00 1998 Path: biosci!daresbury!not-for-mail From: Gilles VACHON Newsgroups: bionet.molbio.proteins Subject: Looking for Dr. Wah (FokI restriction enzyme) Date: 4 Sep 1998 10:16:20 +0100 Lines: 16 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6sob54$la4@mserv1.dl.ac.uk> X-Sender: vachon@biomol.ujf-grenoble.fr Original-To: proteins@dl.ac.uk Hi all, I am looking for DR. Wah's e-mail who reported the strcuture of the FokI restriction enzyme (Nature, 1997) (and who works at the Department of Biochemistry and Molecular Biophysics, Columbia Univ., NY, I believe) Gilles Vachon Laboratoire de Genetique Moleculaire des Plantes CERMO, 3eme etage Universite J. Fourier, BP 53X 38041 GRENOBLE CEDEX FRANCE Tel: (33) (0)4 76 63 56 58 fax: (33) (0)4 76 51 43 36 e-mail: Gilles.Vachon@ujf-grenoble.fr From owner-proteins@net.bio.net Thu Sep 03 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.corridex.com!ameritech.ais.net!jamie!ais.net!ameritech.net!uunet!uunet!in2.uu.net!hearst.acc.Virginia.EDU!aruba.odu.edu!news From: Laura Moen Newsgroups: bionet.molbio.proteins Subject: Re: pET problems Date: Thu, 03 Sep 1998 11:25:15 -0400 Organization: Old Dominion Universityaruba Lines: 75 Message-ID: <35EEB4DB.B1F2EA6D@odu.edu> References: <35EBC2D2.C59FB675@plantphys.umu.se> NNTP-Posting-Host: viper228229.sci1.odu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 4.04 [en] (WinNT; I) To: Adrian Clarke Adrian, I have used pET vectors many times to overexpress proteins. It sounds to me as though the heavy band you are getting at the lower molecular weight could be a truncated form of the protein, but not necessarily. Did you sequence all the way through the protein or just part of the N-terminus? If you only sequenced part of the way, then some of your protein could be missing. You might try transforming BL21(DE3)pLysE or even HMS174(DE3)pLysE so that you can induce without the heat shock. The pLys gene is very effective in knocking out leaky expression in the T7 system in my experience, and the LysE is the higher level of this construct which might work better for you. The reason I suggest two different types of cells is that some cell lines work better than others for some genes. (I don't know why.) Since you are getting a band at 34kD on your Western blots, some of your protein is correctly expressed. Did the smaller band light up too? If so, it may be the truncation product. When E. coli doesn't like proteins and they are being made in large quantities rapidly, it attempts to remove them as inclusion bodies but it may try to chop them up too. You may be able to have more success with these different cell lines _and_ try doing your expression at 20-25 degrees. I have had success that way too. Finally, have you tried purifying your protein on a Nickel column? Your His tagged constructs should bind, and you will enrich the 34Kd protein if it is there. The enrichment of the right thing and your results on the Western will probably help you to interpret the events a little more clearly. I know I rambled in the message - if you need more info, email me: Lmoen@odu.edu. Adrian Clarke wrote: > I have a question that I hope someone can answer. > > I have used pET23a as cloning vector for over expressing an Arabidopsis > thaliana protein. I have 4 different constructs: One where the resulting > > protein is predicted to be 33 kDa + 6 C-terminal histidines (a native > N-terminal); another where the N-terminal has a T7-tag (12 amino acids I > > think); and two constructs the same as the above, but with shorter > N-terminals (corresponding to 30 kDa Arabidopsis protein). Control > sequencing of the constructs was performed to ensure the right > translation. > These recombinant proteins are HIGHLY toxic to E.coli, especially the > full > length clones. Trying to transform BL21(DE3) with these constructs > resulted > in no transformants! (but a control with the vector was fine). > I then tried a "super safe" system with BL21 first transformed with a > plasmid containing the T7 polymerase behind a temperature regulated > promoter (induction at 42°), then my constructs. > With this system I obtained over-expressed protein as inclusion bodies ( > > around 1.8 mg/1 litre of culture). > > The problem I have is that the sizes are strange - around 25-26 kDa for > all > constructs when I run a SDS-PAGE gel, whereas I expected 33-34 kDa from > the > full length clones and 30-31 kDa from the others. In the protein gel > system > I use it is possible to distinguish a 35 kDa polypeptide from a 30 kDa > polypeptide. Amino acid sequencing of one of the over-expressed proteins > > showed that it is the right protein! Running Leaf extracts on a Western > gel and probing with antibodies against this protein results in a > polypeptide band of approximately 34 kDa. > > Right now I have no idea what is happening. Does anyone else have > experience with these expression systems and the pET vector? Is it > possible that E.coli is processing the over-expressed protein? Any > helpful advice or ideas would be greatly appreciated. > > Adrian > -- From owner-proteins@net.bio.net Thu Sep 03 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!nntp-out.monmouth.com!newspeer.monmouth.com!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!news.icnet!NewsWatcher!user From: i.mcfarlane@icrf.icnet.uk (Ian McFarlane) Newsgroups: bionet.molbio.proteins Subject: Re: Rapid Westerns on PVDF Date: 4 Sep 1998 11:26:26 GMT Organization: Imperial Cancer Research Fund Lines: 28 Message-ID: References: NNTP-Posting-Host: 143.65.17.54 I think I wasn't clear enough with the second question. What I am interested in is the use of ECL with the rapid blotting technique. Becuase the PVDF is not wetable I was wondering how you managed to get the reagent in contact with the blot in enough quantity so that you can get a signal. Thank you for the replies thus far. Ian Mc > Hi, > > I have a few questions about using PVDF (Immobilon P) without blocking (or > wetting) the membrane. > > 1) Compared to the wet blotting method do you need relativley higher or > lower concentrations of your primary and secondary Abs? > > 2) Does anyone have any experiences with ECL detection that they can > share? Specifically how much of the ECL reagent stays with the blot when > you wrap it for exposure and if, as seems likely, only a small amount does > stay on the blot how does that affect the length of time that you can get > a signal from the blot. > > Thanks, > > Ian Mc From owner-proteins@net.bio.net Thu Sep 03 23:00:00 1998 Path: biosci!MILLIPORE.COM!Jack_Leonard From: Jack_Leonard@MILLIPORE.COM Newsgroups: bionet.molbio.proteins Subject: Sad news about Dr. Donald Sheer Date: 4 Sep 1998 12:15:59 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <85256675.0067DB88.00@MilliGust.Millipore.com> NNTP-Posting-Host: net.bio.net I regret to announce that Dr. Don Sheer, a Consulting Scientist in the Analytical Division of Millipore, was on Swiss Air Flight 111 when it crashed off the coast of Nova Scotia on September 2nd, 1998. Don and his wife were on their way to Greece, where Don was to present a scientific paper at the International Conference on Methods in Protein Structure Analysis. Don worked closely with us at Millipore/Amicon for the past 6 years, and was a key contributor to many products and applications. This is a devastating loss to us, both personally and professionally. As many of you know, Don was active both in ABRF and Protein Society, and had numerous contacts in the scientific community throughout the world. If anyone would like further information, please feel free to contact me. Sincerely yours, -Jack- Jack T. Leonard, Ph.D. Technical Manager, Molecular Biology Group Millipore Corporation (978)-762-5294 Jack_Leonard@Millipore.com From owner-proteins@net.bio.net Fri Sep 04 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.concentric.net!newsfeed1.earthlink.net!uunet!in3.uu.net!server-b.cs.interbusiness.it!news.tin.it!not-for-mail From: "Gian Matteo Curto" Newsgroups: bionet.molbio.proteins Subject: cyclooxygenase 2 Date: Wed, 26 Aug 1998 11:41:36 +0200 Organization: TIN Lines: 9 Message-ID: <6s0ttl$nok$1@nslave1.tin.it> NNTP-Posting-Host: a-ag3-4.tin.it X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Hi, I'm searching for the article about the structure of COX-2. Thank you curtogia@tin.it From owner-proteins@net.bio.net Fri Sep 04 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!howland.erols.net!vixen.cso.uiuc.edu!dhardy From: dhardy@students.uiuc.edu (david joseph hardy) Newsgroups: bionet.molbio.proteins Subject: Announce: NAMD 1.5 released Date: 6 Sep 1998 00:35:09 GMT Organization: University of Illinois at Urbana-Champaign Lines: 93 Message-ID: <6sslbt$dp6$1@vixen.cso.uiuc.edu> NNTP-Posting-Host: ux9.cso.uiuc.edu Announcing the release of NAMD version 1.5 ------------------------------------------ The Theoretical Biophysics group of the Beckman Institute at the University of Illinois would like to announce the availability of version 1.5 of NAMD, a high-performance molecular mechanics program for simulating large biomolecular systems on parallel and distributed computers. This software is being made available to the molecular modeling community free of charge and includes commented source code and extensive documentation. New in this version ------------------- * Added features include rigid bonds and moving harmonic restraints. * Updated user guide, also available in HTML form. * Modified to work with PVM 3.4 beta. * Enhanced performance by as much as 30%. * Modified to work with the latest version of DPMTA (2.7). * Included DPMTA source to make installation easier. * Simplified build process, fewer options to specify, better documentation. * Several bug fixes. ==================== Basic information about NAMD ====================== Obtaining NAMD -------------- A more complete description of NAMD is available on the NAMD home page: http://www.ks.uiuc.edu/Research/namd/ The software itself is available via anonymous ftp in the directory: ftp://ftp.ks.uiuc.edu/pub/mdscope/namd/ Email questions to namd@ks.uiuc.edu. Features -------- Efficient full electrostatics: NAMD incorporates the Distributed Parallel Multipole Tree Algorithm (DPMTA) developed by the Scientific Computing Group at Duke University to provide full electrostatic interactions in O(N) time. To further reduce the computational cost, DPMTA is integrated using a multiple timestep integration scheme which computes full electrostatic interactions only periodically during the simulation. Scalable parallelism: NAMD has an efficient parallel design that allows large systems to scale well to many processors. The use of a spatial decomposition scheme combined with message-driven execution achieves load balance and the overlap of communication and computation. Modifiable: A major design goal of NAMD is to allow researchers to implement new algorithms and techniques easily. To achieve this, NAMD design and implementation is fully documented in the NAMD Programming Guide. NAMD has an object-oriented design implemented in C++ to provide a high degree of modularity and data abstraction. Portable: For communication, NAMD uses PVM (Parallel Virtual Machine) from Oak Ridge National Laboratory, which has itself been ported to most architectures. Porting NAMD is then simply a matter of having PVM and a reasonable C++ compiler. We have successfully ported NAMD to all of our UNIX machines, which include HP, SGI, Sun, and Linux, both single processor and shared memory multiprocessor. Compatibility with X-PLOR: The input and output files used by NAMD are identical to those used by the program X-PLOR. Thus, simulations can be easily migrated between the two packages, allowing the output of NAMD to be analyzed using X-PLOR or any other tool built for these file formats. Standard MD features: NAMD implements standard molecular dynamics features such as energy minimization, velocity rescaling, spherical boundary conditions, harmonic constraints, and Langevin dynamics. Requirements ------------ * UNIX with C and C++ compilers. * PVM (http://www.epm.ornl.gov/pvm/pvm_home.html). * For generating required PSF structure files, we recommend X-PLOR (http://xplor.csb.yale.edu/xplor-info/xplor-info.html). ========================================================================== Theoretical Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign David Hardy namd@ks.uiuc.edu September 4, 1998 From owner-proteins@net.bio.net Sun Sep 06 23:00:00 1998 Newsgroups: bionet.molbio.proteins Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.enteract.com!ix.netcom.com!atlantis From: atlantis@netcom.com (JJ Miranda) Subject: Re: Software for protein analysis Message-ID: Organization: ICGNetcom X-Newsreader: TIN [version 1.2 PL2] References: <6t12lg$l34$1@wnnews.sci.kun.nl> Date: Mon, 7 Sep 1998 21:33:54 GMT Lines: 20 Sender: atlantis@netcom4.netcom.com Try PAWS. It's free. I think it's on www.proteomics.com or something like that. Good luck, JJ Gerrit Bouw (gbouw@sci.kun.nl) wrote: : Dear everyone, : I am looking for software which I can use for protein sequence analysis. Are : there any : freeware programs available on the net? The problem with such programs is : that they : are very expensive....too expensive for a simple phd student.... : Thanx.... : Gerrit From owner-proteins@net.bio.net Sun Sep 06 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!news.icnet!NewsWatcher!user From: i.mcfarlane@icrf.icnet.uk (Ian McFarlane) Newsgroups: bionet.molbio.proteins Subject: Re: Rapid Westerns on PVDF Date: 7 Sep 1998 09:26:15 GMT Organization: Imperial Cancer Research Fund Lines: 31 Message-ID: References: <35F3A672.474FE9F6@ubaclu.unibas.ch> NNTP-Posting-Host: 143.65.17.54 My main concern is not getting enough ECL reagent onto the blot to give a good signal. Although I mhave seen some people almost dry their blots to get rid of the excess reagent. Ian Mc In article <35F3A672.474FE9F6@ubaclu.unibas.ch>, Marianne Ostermayer wrote: > The PVDF itself will not wet, but the places where protein is will, that's why > they stress that the membrane has to be thoroughly dried after the transfer. > Perhaps it will work with ECL or alike. I did not get it to work with the > AP-substrate sheets, perhaps, because there is some organic solvent included in > the sheets that rewets the membrane. > > Shall we discuss whether a proteins has differnet shapes, depending on whether > it sticks to a hydrophilic or hydrophobic membrane? :-) > > Marianne > > Ian McFarlane wrote: > > > I think I wasn't clear enough with the second question. What I am > > interested in is the use of ECL with the rapid blotting technique. Becuase > > the PVDF is not wetable I was wondering how you managed to get the reagent > > in contact with the blot in enough quantity so that you can get a signal. > > > > Thank you for the replies thus far. > > > > Ian Mc From owner-proteins@net.bio.net Sun Sep 06 23:00:00 1998 Message-ID: <35F3A672.474FE9F6@ubaclu.unibas.ch> Date: Mon, 07 Sep 1998 11:25:07 +0200 From: Marianne Ostermayer Organization: Swiss Tropical Institute X-Mailer: Mozilla 4.05 [en] (Win95; I) MIME-Version: 1.0 Newsgroups: bionet.molbio.proteins Subject: Re: Rapid Westerns on PVDF References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: 131.152.195.93 X-Trace: 7 Sep 1998 11:19:25 +0100, 131.152.195.93 Lines: 24 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!news-peer-europe.sprintlink.net!news.sprintlink.net!Sprint!feed1.news.luth.se!luth.se!news-ge.switch.ch!news-zh.switch.ch!maser.urz.unibas.ch!131.152.195.93 The PVDF itself will not wet, but the places where protein is will, that's why they stress that the membrane has to be thoroughly dried after the transfer. Perhaps it will work with ECL or alike. I did not get it to work with the AP-substrate sheets, perhaps, because there is some organic solvent included in the sheets that rewets the membrane. Shall we discuss whether a proteins has differnet shapes, depending on whether it sticks to a hydrophilic or hydrophobic membrane? :-) Marianne Ian McFarlane wrote: > I think I wasn't clear enough with the second question. What I am > interested in is the use of ECL with the rapid blotting technique. Becuase > the PVDF is not wetable I was wondering how you managed to get the reagent > in contact with the blot in enough quantity so that you can get a signal. > > Thank you for the replies thus far. > > Ian Mc From owner-proteins@net.bio.net Sun Sep 06 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.nyu.edu!newsfeed.sgi.net!nntp.itis.com!news.doit.wisc.edu!Home From: klenchin@facstaff.REMOVE_TO_REPLY.wisc.edu (Dima Klenchin) Newsgroups: bionet.molbio.proteins Subject: Re: Rapid Westerns on PVDF Date: Mon, 07 Sep 1998 15:35:04 GMT Organization: UW-Madison Lines: 32 Message-ID: <6t0uf8$25c_006@doit.wisc.edu> References: <35F3A672.474FE9F6@ubaclu.unibas.ch> NNTP-Posting-Host: t-33-182-177.dialup.wisc.edu X-Newsreader: News Xpress 2.01 X-No-Archive: Yes In article <35F3A672.474FE9F6@ubaclu.unibas.ch>, Marianne Ostermayer wrote: >The PVDF itself will not wet, but the places where protein is will, that's why >they stress that the membrane has to be thoroughly dried after the transfer. >Perhaps it will work with ECL or alike. I did not get it to work with the >AP-substrate sheets, perhaps, because there is some organic solvent included in >the sheets that rewets the membrane. > >Shall we discuss whether a proteins has differnet shapes, depending on whether >it sticks to a hydrophilic or hydrophobic membrane? :-) Well, the nature of protein binding to NC is hydrophobic, so there is probably not too much of a difference :-) - Dima > >Marianne > >Ian McFarlane wrote: > >> I think I wasn't clear enough with the second question. What I am >> interested in is the use of ECL with the rapid blotting technique. Becuase >> the PVDF is not wetable I was wondering how you managed to get the reagent >> in contact with the blot in enough quantity so that you can get a signal. >> >> Thank you for the replies thus far. >> >> Ian Mc > > > From owner-proteins@net.bio.net Sun Sep 06 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!surfnet.nl!barba.uci.kun.nl!sci.kun.nl!not-for-mail From: "Gerrit Bouw" Newsgroups: bionet.molbio.proteins Subject: Software for protein analysis Date: Mon, 7 Sep 1998 08:54:48 +0200 Organization: University of Nijmegen, The Netherlands Lines: 13 Message-ID: <6t12lg$l34$1@wnnews.sci.kun.nl> NNTP-Posting-Host: gbouw.sci.kun.nl X-Newsreader: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Dear everyone, I am looking for software which I can use for protein sequence analysis. Are there any freeware programs available on the net? The problem with such programs is that they are very expensive....too expensive for a simple phd student.... Thanx.... Gerrit From owner-proteins@net.bio.net Mon Sep 07 23:00:00 1998 From: Cornelius Krasel Subject: Re: Expression in Pharmacia pGEX-Vectors Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Followup-To: bionet.molbio.proteins References: <6t3alf$2pt$1@gwsun.medinf.mu-luebeck.de> User-Agent: tin/pre-1.4-980514 (UNIX) (Linux/2.0.34 (i486)) MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Date: Tue, 8 Sep 1998 16:55:57 +0200 Message-ID: NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de Lines: 29 Path: biosci!news.stanford.edu!Cabal.CESspool!news-feed.inet.tele.dk!bofh.vszbr.cz!fu-berlin.de!uni-erlangen.de!uni-wuerzburg.de!not-for-mail Xref: biosci bionet.molbio.methds-reagnts:70565 bionet.molbio.proteins:13263 In bionet.molbio.methds-reagnts Lars Komorowski wrote: > Who has protocols or can deliver me some experienced problems ? Possible problems: 1) Protein doesn't express. 2) Protein expresses in inclusion bodies. 3) Protein expresses, but is proteolytically cleaved. Possible solutions to all problems: a) Lower the temperature (some proteins are better expressed or fold more stably at lower temperatures) from 37°C to 30°C, 25°C, 20°C. b) Play around with induction times and IPTG concentrations. c) Try switching hosts (e.g. BL21 instead of JM109). d) If protein is cleaved during the purification process, try different lysis protocols, possibly include protease inhibitors into your lysis buffer etc. (I have no experience yet with coexpression of chaperones.) --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP4 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-proteins@net.bio.net Mon Sep 07 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed.wli.net!newsfeed.sgi.net!pitt.edu!not-for-mail From: Rich Dudley Newsgroups: bionet.molbio.proteins Subject: Re: Software for protein analysis Date: Tue, 08 Sep 1998 10:28:36 -0400 Organization: University of Pittsburgh, Dept. of Cell Biology and Physiology Lines: 43 Message-ID: <35F53F13.A1E21446@pitt.edu> References: <6t12lg$l34$1@wnnews.sci.kun.nl> Reply-To: rdudley+@pitt.edu NNTP-Posting-Host: whill.cbp.pitt.edu Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------9CFDA8AB7E82C0563EE27FDC" X-Mailer: Mozilla 4.05 [en] (Win95; I) To: Gerrit Bouw This is a multi-part message in MIME format. --------------9CFDA8AB7E82C0563EE27FDC Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Go to www.bio.net, and search the archives of the SOFTWARE group. You'll find plenty. rich -- --- --- --- -- -- -- --- --- --- Richard J. Dudley (rdudley+@pitt.edu) Research Specialist V Dept. of Cell Biology and Physiology University of Pittsburgh http://www.cbp.pitt.edu ---> search BIONET archives at http://www.bio.net <--- --------------9CFDA8AB7E82C0563EE27FDC Content-Type: text/x-vcard; charset=us-ascii; name="vcard.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Dudley, Richard Content-Disposition: attachment; filename="vcard.vcf" begin: vcard fn: Richard Dudley n: Dudley;Richard org: Dept. of Cell Biology and Physiolgy, University of Pittsburgh adr: S362 Biomedical Science Tower;;3500 Terrace St.;Pittsburgh;PA;15261;USA email;internet: rdudley+@pitt.edu title: Research Specialist V tel;work: 412-648-9260 tel;fax: 412-648-8330 x-mozilla-cpt: ;0 x-mozilla-html: TRUE version: 2.1 end: vcard --------------9CFDA8AB7E82C0563EE27FDC-- From owner-proteins@net.bio.net Mon Sep 07 23:00:00 1998 Path: biosci!news.stanford.edu!Cabal.CESspool!news-feed.inet.tele.dk!bofh.vszbr.cz!fu-berlin.de!news-ber1.dfn.de!news-ham1.dfn.de!news.mu-luebeck.de!not-for-mail From: "Lars Komorowski" Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Expression in Pharmacia pGEX-Vectors Date: Tue, 8 Sep 1998 15:10:44 +0200 Organization: Med. Universitaet zu Luebeck Lines: 4 Message-ID: <6t3alf$2pt$1@gwsun.medinf.mu-luebeck.de> NNTP-Posting-Host: 141.83.167.171 X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Xref: biosci bionet.molbio.methds-reagnts:70558 bionet.molbio.proteins:13260 Who has protocols or can deliver me some experienced problems ? Lars From owner-proteins@net.bio.net Mon Sep 07 23:00:00 1998 Newsgroups: bionet.molbio.proteins Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!newsfeed.internetmci.com!194.72.7.126!btnet-peer!btnet!dispose.news.demon.net!demon!peer.news.zetnet.net!peer.news.bb.u-net.net!u-net!yama.mcc.ac.uk!liv!news From: lgbell@liverpool.ac.uk Subject: Re: glutaraldehyde cross-linking X-Nntp-Posting-Host: pc028010.med.liv.ac.uk Content-Type: text/plain; charset=us-ascii Message-ID: To: Pauline Bariola Sender: news@liverpool.ac.uk (News System) Content-Transfer-Encoding: 7bit Organization: The University of Liverpool References: Mime-Version: 1.0 Date: Tue, 8 Sep 1998 08:27:54 GMT X-Mailer: Mozilla 3.04C-PCMNS (Win16; I) Lines: 27 Pauline Bariola wrote: > > I have been using the method of glutaraldehyde cross-linking to determine > the oligomerization state of a protein under different conditions. Does > anyone know if the cross-linking reaction is inhibited at any pH, > particularly extreme pHs? > > Also, if anyone knows a good reference article for this technique, > preferably including suggestions of the best reaction conditions to use, I > would appreciate being pointed toward it. > > Please reply to my e-mail address as well as to the newsgroup. Thanks in > advance. > > Pauline Bariola > University of Lausanne > e-mail: Pauline.Bariola@ibpv.unil.ch Previously here people have suggested 'BIOCONJUGATE TECHNIQUES' by Hermanson, Greg T. Published by Academic Press, which has been described as the Bible on this sort of subject. Having recently seen a copy I can see why. Regards, Len. lgbell@liv.ac.uk From owner-proteins@net.bio.net Mon Sep 07 23:00:00 1998 Path: biosci!news.stanford.edu!Cabal.CESspool!bofh.vszbr.cz!pegasus.csx.cam.ac.uk!server1.netnews.ja.net!bham!med180.bham.ac.uk!user From: noone@cancer.bham.ac.uk (noone) Newsgroups: bionet.molbio.proteins Subject: Re: Software for protein analysis Date: Tue, 08 Sep 1998 09:13:24 +0100 Organization: noone Lines: 28 Message-ID: References: <6t12lg$l34$1@wnnews.sci.kun.nl> NNTP-Posting-Host: med180.bham.ac.uk > Try PAWS. It's free. I think it's on www.proteomics.com or something > like that. > > Good luck, > JJ > > Gerrit Bouw (gbouw@sci.kun.nl) wrote: > : Dear everyone, > > : I am looking for software which I can use for protein sequence analysis. Are > : there any > : freeware programs available on the net? The problem with such programs is > : that they > : are very expensive....too expensive for a simple phd student.... > > : Thanx.... > > : Gerrit Another option would be to use an online-service. The BCM search launcher offers quite a few search and alignment tools (or you can look up a few servers in "Pedro's research tools", a list of online services available eg at the uni duesseldorf in Germany). The only drawback is that in the afternoon (talking CET) the american servers get very busy. Peter From owner-proteins@net.bio.net Mon Sep 07 23:00:00 1998 Path: biosci!news.stanford.edu!Cabal.CESspool!bofh.vszbr.cz!oleane!newsfeed.nacamar.de!univ-lyon1.fr!not-for-mail From: Pierre Commercon Newsgroups: bionet.molbio.proteins Subject: Ab against Rat SOD 1 Date: Tue, 08 Sep 1998 20:02:16 +0200 Organization: C.I.S.M. Universite Claude Bernard Lyon 1 / INSA de Lyon Lines: 12 Message-ID: <35F57128.744C@rabelais.univ-lyon1.fr> NNTP-Posting-Host: p-commercon.univ-lyon1.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (Win95; I) CC: pcomm@rabelais.univ-lyon1.fr Hello I am looking for antibody against Rat SOD 1 (Cu/Zn depend, Red Cells) I have not found commercial source in France... Help me Merci Pierre From owner-proteins@net.bio.net Mon Sep 07 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!news-peer.sprintlink.net!news-backup-west.sprintlink.net!news.sprintlink.net!128.218.95.22!itssrv1.ucsf.edu!macmac-2.ucsf.edu!user From: bpmurray*STUFFER*@socrates.ucsf.edu (Bernard P. Murray, PhD) Newsgroups: bionet.molbio.proteins Subject: Re: Software for protein analysis Date: Tue, 08 Sep 1998 20:53:04 -0700 Organization: University of California, San Francisco Lines: 28 Message-ID: References: <6t12lg$l34$1@wnnews.sci.kun.nl> NNTP-Posting-Host: macmac-2.ucsf.edu In article , noone@cancer.bham.ac.uk (noone) wrote: > > Gerrit Bouw (gbouw@sci.kun.nl) wrote: > > : Dear everyone, > > : I am looking for software which I can use for protein sequence analysis. > > : Are there any > > : freeware programs available on the net? The problem with such programs is > > : that they > > : are very expensive....too expensive for a simple phd student.... > > : Thanx.... > > : Gerrit > Another option would be to use an online-service. The BCM search launcher > offers quite a few search and alignment tools (or you can look up a few > servers in "Pedro's research tools", a list of online services available > eg at the uni duesseldorf in Germany). The only drawback is that in the > afternoon (talking CET) the american servers get very busy. > Peter My favourite in Europe is http://expasy.hcuge.ch Hopefully the users on this side of the Atlantic will not have clogged up ExPasy as well as the american servers. Bernard -- Bernard P. Murray, PhD Dept. Cell. Mol. Pharmacol., UCSF, San Francisco, USA From owner-proteins@net.bio.net Mon Sep 07 23:00:00 1998 Path: biosci!ihnp4.ucsd.edu!news1.ucsd.edu!not-for-mail From: "Antonin Tutter" Newsgroups: bionet.molbio.proteins Subject: Help! Protein precipitates upon dialysis Date: Tue, 08 Sep 1998 21:46:27 -0700 Organization: University of California, San Deigo Lines: 32 Message-ID: <6t512i$5pm$2@news1.ucsd.edu> NNTP-Posting-Host: atutter.extern.ucsd.edu Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Outlook Express for Macintosh - 4.01 (297) Hi all, I have been expressing in E. coli BL21 DE3 cells, a series of 6-His-tagged truncation mutants of a protein that express well and in the soluble fraction. I have been purifying them over Qiagen Ni++ NTA superflow resin, and eluting with 300mM imidazole. The problem is, after dialyzing the elutions in final buffer (Hepes based, 100mM KCl, 12mM MgCl2, 10% glycerol), there is invariably some degree of precipitation. Between 15-100% of the total protein precipitates. The elutions are performed in the same buffer, except for the addition of imidazole. Since there is no change in ionic strength from elution to dialysis, could it be that during the elutions the imidazole stabilizes the protein solution and subsequent removal of the imidazole destabilizes the protein? Any help is *much* appreciated -- i need as much protein as i can get, and I need to dialyze away the imidazole! Regards, _______________________________________ Antonin Tutter Salk Institute for Biological Studies RBIO-J 10010 N. Torrey Pines Rd. La Jolla, CA 92037 email: atutter@aim.salk.edu web: http://www-biology.ucsd.edu/~atutter/ From owner-proteins@net.bio.net Mon Sep 07 23:00:00 1998 Path: biosci!UNM.EDU!ezra From: ezra@UNM.EDU (Ezra Schildkraut) Newsgroups: bionet.molbio.proteins Subject: Gel Shift Bands Date: 8 Sep 1998 08:27:01 -0700 Organization: University of New Mexico Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <35F54C15.EABDAE63@unm.edu> NNTP-Posting-Host: net.bio.net I have been doing gel shifts to try and show specific binding in CHO cell protein extracts to specific oligos. I have seen definite shifts, however they appear as long smears instead of discrete bands. I would like to see discrete bands. If anyone out there has had and has overcome this problem please let me know. Any other insight would also be appreciated. Ezra Schildkraut ezra@unm.edu From owner-proteins@net.bio.net Tue Sep 08 23:00:00 1998 Path: biosci!loria.fr!Gregory.Kucherov From: Gregory.Kucherov@loria.fr (Gregory Kucherov) Newsgroups: bionet.molbio.proteins Subject: RECOMB'99 - 2nd call for papers Date: 9 Sep 1998 11:31:50 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 193 Sender: daemon@net.bio.net Distribution: world Message-ID: <199809091828.UAA08333@lorraine.loria.fr> Reply-To: symposia@inria.fr NNTP-Posting-Host: net.bio.net [apologies for possible multiple copies] SECOND CALL FOR PAPERS THIRD ANNUAL INTERNATIONAL CONFERENCE ON COMPUTATIONAL MOLECULAR BIOLOGY (RECOMB'99) April 11-14, 1999 Lyon, France Organized by INRIA (The French National Institute for Research in Computer Science and Control) Sponsored by ACM (Association for Computing Machinery) - SIGACT with support from SLOAN Foundation US Department of Energy Smith Kline Beecham http://www.inria.fr/RECOMB99/ The Third Annual Conference on Research in Computational Molecular Biology (RECOMB 99), sponsored by the Association for Computing Machinery Special Interest Group on Algorithms and Computation Theory (ACM-SIGACT) with support from the SLOAN Foundation, US Department of Energy and Smith Kline Beecham, will be organized by INRIA in Lyon, France, April 11-14, 1999. Papers reporting on original research (both theoretical and experimental) in all areas of computational molecular biology are sought, including surveys of important recent results/directions. Typical but not exclusive topics of interest include: - Genomics, - Molecular sequence analysis, - Recognition of genes and regulatory elements, - Molecular evolution, - Protein structure, - Combinatorial libraries and drug design. ABSTRACT SUBMISSION: Authors are requested to send 10 copies (preferably two sided copies) of a detailed extended abstract (5-10 pages) to: Dr. Sorin Istrail RECOMB 99 Program Chair Sandia National Laboratories Applied Mathematics Department MS 1110 Albuquerque, NM 87185-5800 USA An abstract must be received by October 9, 1998. This is a firm deadline. Simultaneous submission to another conference or journal is allowed. CONFERENCE PROCEEDINGS: The extended abstracts for the Conference will be published by ACM Press and will be available at the Conference. A selection of the accepted extended abstracts in their final journal versions will be invited to appear in a special issue of the Journal of Computational Biology devoted to RECOMB 99. NOTIFICATION: The conference submissions will be refereed by the program committee. Authors will be notified of acceptance or rejection by a letter mailed on or before December 5, 1998. A final copy of each accepted paper is required by January 6, 1999. An author of each accepted paper is expected to attend the Symposium and present the paper; otherwise alternative arrangements should be made to have the paper presented. ABSTRACT PREPARATION: An abstract should start with a succinct statement of the problem, the results achieved, their significance and a comparison with previous work. This material should be understandable to nonspecialists. A technical exposition directed to the specialist should follow. The length, excluding cover page and bibliography, should not exceed 10 pages. The manuscript should be easy to read, preferably using 11 point font size on U.S. standard 8 1/2 by 11 inch paper. If authors believe that more details are necessary to substantiate the claims of the paper, they may include a clearly marked appendix. An E-mail address for the contact author should be included. CONFERENCE EVENTS: RECOMB 99 will feature 9 invited lectures (to be announced later) including the following conference events: - The Stanislaw Ulam Memorial Computational Biology Address: awarded by RECOMB to a scientist who has made major contributions in the computational aspects of the field. - The Distinguished Biology Lecture: awarded by RECOMB to a scientist who has made major contributions in the biological aspects of the field. - The Distinguished New Technologies Lecture: describing emerging, new technologies. - Best Paper by a Young Scientist Award: This award will be given to the best paper written solely by one or more recent graduates or students. An abstract is eligible if all authors are recent graduates (within 3 years from Ph.D.) or full-time students at the time of submission. This should be indicated in the submission letter. The program committee may decline to make the award or may split it among several papers. CALENDAR Deadline for reception of papers: October 9th, 1998 Notification of acceptation/rejection: December 5th, 1998 Deadline for reception of final papers: January 6th, 1999 STEERING COMMITTEE Sorin Istrail, RECOMB General Vice-Chair (Sandia National Laboratories, USA) Richard Karp (University of Washington, USA) Thomas Lengauer (GMD-SCAI, Germany) Pavel Pevzner, RECOMB General Chair (University of Southern California, USA) Ron Shamir (Tel-Aviv University, Israel) Michael Waterman, RECOMB General Chair (University of Southern California, USA) PROGRAM COMMITTEE Stephen Altschul (NCBI, NIH, USA) Alberto Apostolico (Purdue University, USA, and University of Padova, Italy) Gary Benson (Mount Sinai School of Medicine, USA) David Botstein (Stanford University, USA) Jean-Michel Claverie (CNRS, France) Ken Dill (University of California, San Francisco, USA) Andreas Dress (Bielefeld University, Germany) Misha Gelfand (Russian Academy of Sciences, Russia) Alain Guénoche (Universite de Marseille, France) Sorin Istrail, Program Committee Chair (Sandia National Laboratories, USA) Tao Jiang (McMaster University, Canada) Richard Karp (University of Washington, USA) John Kececioglu (University of Georgia, USA) Richard Lathrop (University of California Irvine, USA) Thomas Lengauer (GMD-SCAI, Germany) Arthur Lesk (Univeristy of Cambridge, England) Michael Levitt (Stanford University, USA) Pavel Pevzner (University of Southern California, USA) Mireille Regnier (INRIA, France) Rich Roberts (New England Biolabs, USA) Chris Sander (Millenium Pharmaceutical, USA) Miyano Satoru (Tokyo University, Japan) Sophie Schbath (INRA, France) Ron Shamir (Tel-Aviv University, Israel) Jeffrey Skolnick (The Scripps Research Institute, USA) Donna Slonim (Whitehead Institute, USA) Terry Speed (University of California, Berkeley, USA) Martin Vingron (Cancer Research Center, Germany) Michael Waterman (University of Southern California, USA) ORGANIZING COMMITTEE: Florence Balax (INRIA, France) Daniel Kahn (INRA, France) Gregory Kucherov, Publicity Chair (INRIA, France) Mireille Regnier, Organizing Committee Chair (INRIA, France) Sophie Schbath (INRA, France) Annick Theis-Viemont (INRIA, France) INFORMATION INRIA Rocquencourt Relations Exterieures BP 105 78153 Le Chesnay, France Phone: +33 1 39 63 50 53 Fax: +33 1 39 63 56 38 email : symposia@inria.fr http://www.inria.fr/RECOMB99/ From owner-proteins@net.bio.net Tue Sep 08 23:00:00 1998 Path: biosci!news.stanford.edu!nntp.cs.ubc.ca!newsfeed.direct.ca!cyclone.news.idirect.com!island.idirect.com!cyclone.mbnet.mb.ca!canopus.cc.umanitoba.ca!tribune.usask.ca!anat37011.usask.ca!user From: colin@nospam.fungus.usask.ca (Colin Rasmussen) Newsgroups: bionet.molbio.proteins Subject: Re: Expression in Pharmacia pGEX-Vectors Date: Wed, 09 Sep 1998 11:03:00 -0600 Organization: University of Saskatchewan Lines: 30 Message-ID: References: <6t3alf$2pt$1@gwsun.medinf.mu-luebeck.de> NNTP-Posting-Host: anat37011.usask.ca In article , Cornelius Krasel wrote: > In bionet.molbio.methds-reagnts Lars Komorowski wrote: > > Who has protocols or can deliver me some experienced problems ? > > Possible problems: > > 1) Protein doesn't express. > > 2) Protein expresses in inclusion bodies. > > 3) Protein expresses, but is proteolytically cleaved. > > Possible solutions to all problems: > > a) Lower the temperature (some proteins are better expressed or fold more > stably at lower temperatures) from 37°C to 30°C, 25°C, 20°C. > b) Play around with induction times and IPTG concentrations. > c) Try switching hosts (e.g. BL21 instead of JM109). > d) If protein is cleaved during the purification process, try different > lysis protocols, possibly include protease inhibitors into your > lysis buffer etc. We've had better luck sometimes expressing GST fusions in fission yeast using the vector pESP1. Colin Rasmussen University of Saskatchewan From owner-proteins@net.bio.net Tue Sep 08 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!newsfeed.nacamar.de!nntp.news.xara.net!xara.net!server6.netnews.ja.net!server4.netnews.ja.net!server2.netnews.ja.net!news.nott.ac.uk!pdxkgs From: pdxkgs@pdn1.gene.nott.ac.uk (Karen spink) Newsgroups: bionet.molbio.proteins Subject: Re: Gel Shift Bands Date: Wed, 09 Sep 1998 16:33:45 +0100 Organization: University of Nottingham Lines: 23 Distribution: world Message-ID: References: <35F54C15.EABDAE63@unm.edu> NNTP-Posting-Host: ppdirg.nottingham.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.4.0 I have encountered this problem in binding reactions where the salt concentration is particularly high, ie.when using crude protein fractions eluted from a column at high salt. Another possibility is that you are using too much protein in the reactions-have you tried using less? hope this helps Karen spink In article <35F54C15.EABDAE63@unm.edu>, ezra@UNM.EDU (Ezra Schildkraut) wrote: > I have been doing gel shifts to try and show specific binding in CHO > cell protein extracts to specific oligos. I have seen definite shifts, > however they appear as long smears instead of discrete bands. I would > like to see discrete bands. If anyone out there has had and has > overcome this problem please let me know. Any other insight would also > be appreciated. > > Ezra Schildkraut > ezra@unm.edu From owner-proteins@net.bio.net Tue Sep 08 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!uninett.no!due.unit.no!not-for-mail From: Bjoern Arne Naess Newsgroups: bionet.molbio.proteins Subject: Rec. E.coli - information wanted - optimicing growth and production of recombinant E.coli Date: Wed, 09 Sep 1998 15:41:22 +0200 Organization: Institutt for bioteknologi, NTNU Trondheim Lines: 9 Message-ID: <35F68582.2DEA7294@chembio.ntnu.no> NNTP-Posting-Host: kbio0101.chembio.ntnu.no Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (Win16; I) Hi ! I interested in contact with anyone working with development of properly balanced nutrients in cultures of E.coli to allow for proper control of growth rate and product expression of recombinant inducible proteins/enzymes. Bjoern From owner-proteins@net.bio.net Tue Sep 08 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed.wli.net!news-peer-west.sprintlink.net!news.sprintlink.net!newsfeed.direct.ca!news.u.washington.edu!not-for-mail From: Uncle S Newsgroups: bionet.molbio.proteins Subject: Re: glutaraldehyde cross-linking Date: Wed, 09 Sep 1998 20:20:22 -0700 Organization: Interzon.com Lines: 27 Message-ID: <35F74576.167E@interzon.com> References: NNTP-Posting-Host: clara.bmsc.washington.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: nntp4.u.washington.edu 905397623 18536 (None) 140.142.17.38 X-Complaints-To: help@cac.washington.edu X-Mailer: Mozilla 3.0Gold (X11; U; IRIX 5.3 IP22) To: Pauline Bariola Pauline Bariola wrote: > Also, if anyone knows a good reference article for this technique, > preferably including suggestions of the best reaction conditions to use, I > would appreciate being pointed toward it. thanks Peter and Len for those references. here are a couple that I've got in the files. Huang, Ter-Mei, and Chang, Gu-Gang (1992) _Characterization of the tetramer-dimer-monomer equilibrium of the enzymatically active subunits of pigeon liver malic enzyme_ Biochemistry 31: 12658-12664. and Hermann, R., Rudolph, R., Jaenicke, R. (1979)_Kinetics of in vitro reconstitution of oligomeric enzymes by cross-linking_ Nature 277: 243-245. Hope those help. Shamus -- The difference between love and hate is: hate lasts. -Bukowski From owner-proteins@net.bio.net Tue Sep 08 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-xfer.netaxs.com!newsread.com!not-for-mail From: "Tammy Patton" Newsgroups: bionet.molbio.proteins Subject: snake venom science fair project Lines: 20 X-Newsreader: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Message-ID: Date: Wed, 9 Sep 1998 22:23:57 -0500 NNTP-Posting-Host: 205.228.194.206 X-Complaints-To: Abuse Role , We Care X-Trace: newsread.com 905397797 205.228.194.206 (Wed, 09 Sep 1998 23:23:17 EDT) NNTP-Posting-Date: Wed, 09 Sep 1998 23:23:17 EDT Organization: Telepath Systems (telepath.com) I am a high school biology teacher looking for help. One of my students is interested in the treatment of snake and spider bites by means of electroshock with a stun gun. We have articles describing this treatment for spider bites, but spider venom is near impossible to obtain. We would like to electrophorese zapped and unzapped samples of snake venom and see if the "zapped" venom has a significantly different pattern of bands. Does this sound reasonable? If so, what type of stain would you recommend? Do you know of any similar studies? Appreciating any help you may be able to provide, Tammy Patton Moore High School 300 N Eastern Moore, OK 73160 (405)793-3111 Fax(405)793-3140 From owner-proteins@net.bio.net Tue Sep 08 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!news-ge.switch.ch!news.rediris.es!mercurio.cica.es!not-for-mail From: bb1rofra@uco.es (Antonio R. Franco) Newsgroups: bionet.molbio.proteins Subject: Program for Densitometry Date: Wed, 09 Sep 1998 11:10:26 GMT Organization: Universidad de Cordoba Lines: 3 Message-ID: <35f6615d.3924310@news.cica.es> Reply-To: bb1rofra@uco.es NNTP-Posting-Host: ciebbmsrv.uco.es Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Forte Free Agent 1.11/32.235 I want to geta PC program ro run densitometric analysis both of DNA and protein images . Either commertial or shareware is Ok From owner-proteins@net.bio.net Wed Sep 09 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!cs.utexas.edu!geraldo.cc.utexas.edu!dhcp-73-25.icmb.utexas.edu!user From: none@utexas..edu (Roland Saldanha) Newsgroups: bionet.molbio.proteins Subject: Re: glutaraldehyde cross-linking Date: Thu, 10 Sep 1998 20:49:55 -0600 Organization: The University of Texas at Austin, Austin, Texas Lines: 19 Message-ID: References: NNTP-Posting-Host: dhcp-73-25.icmb.utexas.edu > Pauline Bariola wrote: > > > > I have been using the method of glutaraldehyde cross-linking to determine > > the oligomerization state of a protein under different conditions. Does > > anyone know if the cross-linking reaction is inhibited at any pH, > > particularly extreme pHs? > Glutaraldehyde undergoes self-condenensation as the pH is increased above 7.0. Thus the length of the crosslinking arm increases very rapidly increasing the chances of inter-molecular artifactual cross-links. It is therefore limited to pH <7.0. It is also best used dilute because the concentrated solution is mostly highly polymerized. Dilution to less than 1% and a pH between 3 and 7 allows formation of the monomeric form. Good luck. Roland Saldanha From owner-proteins@net.bio.net Wed Sep 09 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!su-news-hub1.bbnplanet.com!news.bbnplanet.com!logbridge.uoregon.edu!news.ycc.yale.edu!sequoia From: sequoia@ccwf.cc.utexas.edu (Jeremy Gore) Newsgroups: bionet.molbio.proteins Subject: Re: snake venom science fair project Date: Thu, 10 Sep 1998 10:56:49 -0400 Organization: Yale University Lines: 40 Message-ID: References: NNTP-Posting-Host: kbt4labs.biology.yale.edu X-Newsreader: MT-NewsWatcher 2.3.5 In article , "Tammy Patton" wrote: > I am a high school biology teacher looking for help. One of my students is > interested in the treatment of snake and spider bites by means of > electroshock with a stun gun. We have articles describing this treatment > for spider bites, but spider venom is near impossible to obtain. > > We would like to electrophorese zapped and unzapped samples of snake venom > and see if the "zapped" venom has a significantly different pattern of > bands. Does this sound reasonable? If so, what type of stain would you > recommend? Do you know of any similar studies? > > Appreciating any help you may be able to provide, > > Tammy Patton > Moore High School > 300 N Eastern > Moore, OK 73160 > (405)793-3111 > Fax(405)793-3140 Different venoms act in very different ways- rattlesnake venom is a modified digestive enzyme that eats away at affected tissue, while coral snake venom is a potent neurotoxin. Shock treatment may not affect snakebite at all. You'll need to do more research to determine what they are made of and whether or not the can be effectively electrophoresed (are they proteins and how big?). Also, electrical shock of a protein may effect it in many ways - altering folding properties, altering chemical properties of the amino acid residues or other subunits, oxidizing metal cofactors, etc. Only a cleavage of a protein-based venom, or possibly a misfolding, would show up on a gel. If you could cite your references to the spider bite article, I could look into it. Jeremy Gore -- "In this house we obey the laws of thermodynamics!" From owner-proteins@net.bio.net Wed Sep 09 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!cyclone.news.idirect.com!island.idirect.com!fu-berlin.de!news-ber1.dfn.de!news-ham1.dfn.de!news-han1.dfn.de!news.gwdg.de!not-for-mail From: Arne Mueller Newsgroups: bionet.molbio.proteins Subject: Re: Gel Shift Bands Date: Thu, 10 Sep 1998 12:38:26 +0000 Organization: GWDG, Goettingen Lines: 34 Message-ID: <35F7C842.6C41A155@gwdg.de> References: <35F54C15.EABDAE63@unm.edu> NNTP-Posting-Host: roko28.stud.uni-goettingen.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.05 [en] (X11; I; Linux 2.0.33 i586) Ezra Schildkraut wrote: > > I have been doing gel shifts to try and show specific binding in CHO > cell protein extracts to specific oligos. I have seen definite shifts, > however they appear as long smears instead of discrete bands. I would > like to see discrete bands. If anyone out there has had and has > overcome this problem please let me know. Any other insight would also > be appreciated. > > Ezra Schildkraut > ezra@unm.edu Hi, maybe it's the nature of your protein. I've recognized this probelm with one specific DNA but not with other DNA (which also shifts at high protein concentration), so it seems to _BE_ the nature of the binding mechanism of my protein. sorry - this doesn't help you anyway ;-( Arne -- Arne Mueller Institut fuer Mikrobiologie und Genetik Abt. Molekulare Genetik und Praeparative Molekularbiologie Universitaet Goettingen Grisebachstr. 8 37077 Goettingen Germany phone: +49-551-399654 | fax : +49-551-393805 email: amuelle3@gwdg.de | http://www.roko.goe.net/~amuell4/ From owner-proteins@net.bio.net Wed Sep 09 23:00:00 1998 Path: biosci!ihnp4.ucsd.edu!news.scripps.edu!not-for-mail From: David Eliezer Newsgroups: bionet.molbio.proteins Subject: Structural Biology Postdoctoral Position Date: Thu, 10 Sep 1998 15:36:42 -0700 Organization: The Scripps Research Institute, La Jolla, CA Lines: 27 Message-ID: <35F8547A.53DAAF98@scripps.edu> NNTP-Posting-Host: mime.scripps.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.05 [en] (X11; U; IRIX 6.2 IP22) Postdoctoral Position: Structural transitions in cytoskeletal proteins. Department of Biochemistry, Cornell University Medical College. A postdoctoral position is available to characterize structure and dynamics in native and partially folded forms of actin binding proteins using NMR. Specific goals address the biological function of conformational transitions and of partially folded proteins, the pathways for protein aggregation and amyloid formation, and the role of folding intermediates in directing the protein folding process. Resources include a new 4 channel 600 MHz spectrometer and newly renovated laboratory space. The New York City area boasts a vibrant structural biology community. Ideal candidates should have experience in protein biophysics or biochemistry, protein structure determination, and/or protein folding. Experience with protein expression and purification, modern triple-resonance NMR techniques and a general familiarity with software tools are also helpful. Interested applicants should send a C.V. and letters from two references to David Eliezer, Department of Molecular Biology/MB2, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037. Email inquiries are also welcome at Eliezer@Scripps.Edu. From owner-proteins@net.bio.net Thu Sep 10 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!news-feed1.tiac.net!posterchild2!news@tiac.net From: James Larkin Newsgroups: bionet.molbio.proteins Subject: Protein Expression & Protein Production Call for Posters Date: Fri, 11 Sep 1998 17:05:17 -0400 Organization: Cambridge Healthtech Institute Lines: 18 Message-ID: <35F9908D.535E@cambridge.org> NNTP-Posting-Host: 207.60.238.8 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Win95; I; 16bit) CALL FOR POSTERS (DEADLINE OCTOBER 2, 1998) Cambridge Healthtech Institute's Conferences on: "Protein Expression" November 2-3, 1998, at the Westin, Washington DC "Protein Production" November 4-5, 1998, at the Westin, Washington DC For more information please contact: Cambridge Healthtech Institute 1037 Chestnut St. Newton Upper Falls, MA 02464 PH: 888-999-6288 PH: 617-630-1300 FAX: 617-630-1325 EMAIL: chi@healthtech.com http:\\www.healthtech.com From owner-proteins@net.bio.net Thu Sep 10 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!news-peer.gip.net!news.gsl.net!gip.net!news.new-york.net!news.columbia.edu!news-not-for-mail From: ct133@hotmail.com Newsgroups: bionet.molbio.proteins Subject: Impact7 from NEB? Date: Fri, 11 Sep 1998 11:37:05 GMT Organization: Columbia University Lines: 7 Message-ID: <35f90b1c.166842@news.columbia.edu> NNTP-Posting-Host: tw116cct.cpmc.columbia.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Newsreader: Forte Agent 1.5/32.478 Hi, Has anyone had experience with the Impact7 from NEB? I'm interested in trying it out but want to know what you have to say about it. C. Tunyaplin From owner-proteins@net.bio.net Thu Sep 10 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!ihnp4.ucsd.edu!not-for-mail From: "Antonin Tutter" Newsgroups: bionet.molbio.proteins Subject: Re: Gel Shift Bands Date: Fri, 11 Sep 1998 21:57:22 -0700 Organization: University of California, San Deigo Lines: 47 Message-ID: <905576090.417047@news1.ucsd.edu> References: <35F54C15.EABDAE63@unm.edu> <35F7C842.6C41A155@gwdg.de> NNTP-Posting-Host: news1.ucsd.edu Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Trace: ihnp4.ucsd.edu 905576091 17620 132.239.1.221 (12 Sep 1998 04:54:51 GMT) X-Complaints-To: Abuse@UCSD.Edu NNTP-Posting-Date: 12 Sep 1998 04:54:51 GMT >> I have been doing gel shifts to try and show specific binding in CHO >> cell protein extracts to specific oligos. I have seen definite shifts, >> however they appear as long smears instead of discrete bands. I would >> like to see discrete bands. If anyone out there has had and has >> overcome this problem please let me know. Any other insight would also >> be appreciated. >> >maybe it's the nature of your protein. I've recognized this probelm with >one specific DNA but not with other DNA (which also shifts at high >protein concentration), so it seems to _BE_ the nature of the binding >mechanism of my protein. > Ezra, Long smears often indicate specific but weak protein-DNA interactions. The conditions necessary for protein-DNA interactions can vary widely from protein to protein. You may want to try several parameter changes in your gel shift conditions to optimize the binding: 1) Try a little non-ionic detergent (0.025% NP-40 works well with my proteins). This can reduce non-specific binding *and* can enhance the binding of some proteins. Definitely worth the try. 2) Play around with the salt. Try anywhere from 25mM to 150mM. 3) Try binding for an extended time (30-60min) before loading on the gel. 4) See if temp makes a difference...run the gel at 4 degrees and at room temp. Hope this helps, _______________________________________ Antonin Tutter Salk Institute for Biological Studies RBIO-J 10010 N. Torrey Pines Rd. La Jolla, CA 92037 email: atutter@aim.salk.edu web: http://www-biology.ucsd.edu/~atutter/ From owner-proteins@net.bio.net Fri Sep 11 23:00:00 1998 Path: biosci!SNIP.NET!mhoran From: mhoran@SNIP.NET (Michael Horan) Newsgroups: bionet.molbio.proteins Subject: Question on Chromatography Resins Date: 12 Sep 1998 19:15:22 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <35FB2833.37E9E441@snip.net> NNTP-Posting-Host: net.bio.net I'm interested in why you use the resins you do (brand, vendor, supplier, etc) in chromatography processes. Were any of you turned on to the products as a consequence of having been exposed to them as a part of "seeding" programs in vendors while you were in grad school? Thanks very much for any insights into this. Michael Horan APL 215-351-4241 From owner-proteins@net.bio.net Fri Sep 11 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!howland.erols.net!newsfeed.internetmci.com!204.238.120.130!news-feeds.jump.net!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: WTPENBER@UFL.EDU Newsgroups: bionet.molbio.proteins Subject: detection of DNA binding by flourometry? Date: Sun, 13 Sep 1998 02:52:15 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 16 Message-ID: <6tfc0v$258$1@nnrp1.dejanews.com> NNTP-Posting-Host: 128.227.242.43 X-Article-Creation-Date: Sun Sep 13 02:52:15 1998 GMT X-Http-User-Agent: Mozilla/4.04 (Macintosh; U; PPC) X-Http-Proxy: 1.0 x4.dejanews.com:80 (Squid/1.1.22) for client 128.227.242.43 I am in the business of transcription factor purification. The gel shift assay takes a day. Has anyone heard of detection of specific DNA binding activity via flourometry? ie would it be feasible to attempt to detect specific DNA binding activity via flourometry or is the sensitivity of such an approach no where near that of EMSA? Thanks for your time, Todd Penberthy -- I'm so hungry that if you put a biscuit on my head my tongue would beat my brains out -Elvin Bishop -----== Posted via Deja News, The Leader in Internet Discussion ==----- http://www.dejanews.com/rg_mkgrp.xp Create Your Own Free Member Forum From owner-proteins@net.bio.net Sat Sep 12 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!btnet-peer!btnet!news-lond.gip.net!news.gsl.net!gip.net!rill.news.pipex.net!pipex!sun4nl!212.206.254.2.MISMATCH!newnews.nl.uu.net!not-for-mail From: Jan van der Lee Newsgroups: bionet.molbio.proteins Subject: Re: Question on Chromatography Resins Date: Sun, 13 Sep 1998 13:23:11 +0200 Organization: UUNET-NL Lines: 31 Message-ID: <35FBAB1E.3B8DCA16@kabelfoon.nl> References: <35FB2833.37E9E441@snip.net> NNTP-Posting-Host: k2nw232.dial.kabelfoon.nl Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.06 [en] (Win95; I) Michael Horan wrote: > I'm interested in why you use the resins you do (brand, vendor, > supplier, etc) in chromatography processes. Were any of you turned on to > the products as a consequence of having been exposed to them as a part > of "seeding" programs in vendors while you were in grad school? > > Thanks very much for any insights into this. > > Michael Horan Michael, During various Conferences an Symposia I visited, I talked to a great deal of people. The main reason: The resin was available "on the shelf in the lab". As chromatography is "only" a tool for most people one doesn't order and wait for a particular resin "because it is mentioned in an article" but one uses the equivalent available directly, just to save time. The "seeding" programs usually supply limited amounts and can be convenient but in general people tend to use from the bulk package. Bassie From owner-proteins@net.bio.net Sat Sep 12 23:00:00 1998 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.proteins Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 13 Sep 1998 02:00:08 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199809130900.CAA09045@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. 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. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. From owner-proteins@net.bio.net Sat Sep 12 23:00:00 1998 Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!207.97.14.174!europa.clark.net!4.1.16.34!cpk-news-hub1.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!news.pbi.net!news.quick.net!usenet From: "hanson" Newsgroups: alt.biology,bionet.molbio.proteins,bionet.toxicology,de.sci.biologie,sci.bio.ecology,sci.bio.food-science,sci.chem Subject: Chem. of rotten Eggs Date: Sun, 13 Sep 1998 19:18:32 -0700 Organization: QuickNet ICG Inc. Lines: 15 Message-ID: <6thuuo$rbt@news.quick.net> NNTP-Posting-Host: lakewood-1-4.quick.net X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Xref: biosci bionet.molbio.proteins:13294 bionet.toxicology:2426 It seems reasonable to assume that the classic "rotten egg" smell of aged, boiled eggs does come from H2S and or mercaptanes. These malodorants seem to originate from the decay of S-bearing amino acids, Cystein and Methionine etc. Questions: a) what is the decay route in such sterile, boiled eggs? b) are such bad smelling eggs actually poisonous or just unpalatable? Thanks, hanson From owner-proteins@net.bio.net Sun Sep 13 23:00:00 1998 Path: biosci!prodigy.com!invst From: invst@prodigy.com ("Investment Expo") Newsgroups: bionet.molbio.proteins Subject: INVESTMENT EXPO '98... You're Invited! Date: 14 Sep 1998 13:02:06 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 97 Sender: daemon@net.bio.net Distribution: world Message-ID: <199809141956.OAA06456@sabredata.com> Reply-To: invst@prodigy.com NNTP-Posting-Host: net.bio.net Dear Investor, We would like to personally invite you to attend INVESTMENT EXPO '98, New York's largest and most dynamic two-day Financial Exhibition and Seminar. Investment Expo '98 is the obvious Destination for all smart investors. 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The following is a partial list of companies that will be exhibiting at the show: Smith Barney, Nightly Business Report, Invesco Funds, Prudential Preferred, NASDAQ, Navellier, Chrysler Corp., Investor's Business Daily, Chicago Board of Options, PaineWebber, Options Industry Council, Charles Schwab & Co., Rydex Series Trust, Scudder Funds, Barnes & Noble, Gruntal & Co., Waterhouse Securities, Bank of New York, Muriel Siebert & Co., Inc., National Discount Brokers, Heartland Funds, IPO Financial Network, First Union, Investment Tracker, California Technology Letter, Needham Investment Management, Guinness Flight, Wealthbuilder , Philips Publishing, Dick Davis Digest, Barrons On-Line, Chicago Mercantile Exchange, Barry Kaye Associates, Legg Mason Funds, Stockbroker Relations, Red Chip Review, Lexington Funds, The Reserve Funds, Majestic Management Corp., Allied Capital Corp, Mercantile Bank, Olde Stockbrokers, New Times Securities Services Inc, The No-Load Investor, Vector Vest /Marketsoft, IAFP, Nicholas-Applegate, Morningstar, Dime Savings Bank, International Forex, Ltd. & many more... also by coming you have a chance to win a Chrysler Sebring! To view a complete list of Exhibitors, speakers & more info visit our web site at: http://www.investmentexpo.com Click here! Investment Expo respects your Internet time and online privacy. This is a one-time only invitation, your address will be removed from our files . Thank you! From owner-proteins@net.bio.net Sun Sep 13 23:00:00 1998 Path: biosci!news.stanford.edu!nntp.cs.ubc.ca!newsfeed.direct.ca!rill.news.pipex.net!pipex!sun4nl!surfnet.nl!barba.uci.kun.nl!sci.kun.nl!not-for-mail From: "Gerrit Bouw" Newsgroups: bionet.molbio.proteins Subject: Inducable expression systems Date: Mon, 14 Sep 1998 16:05:32 +0200 Organization: University of Nijmegen, The Netherlands Lines: 12 Message-ID: <6tj7am$ked$1@wnnews.sci.kun.nl> NNTP-Posting-Host: moldier10.sci.kun.nl X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Dear everyone, I am trying to express different proteins at the same time in cells with a regulated secretory pathway. Does anyone know a good inducable expression system which I can use to express these proteins? If so, I would like to know a source where I could get an inducable vector to clone my constructs in and, a cell line in which I can stabily transfect this construct... thanx, Gerrit Bouw From owner-proteins@net.bio.net Sun Sep 13 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!howland.erols.net!newsfeed.internetmci.com!204.238.120.130!news-feeds.jump.net!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: WTPENBER@UFL.EDU Newsgroups: bionet.molbio.proteins Subject: Re: Gel Shift Bands Date: Mon, 14 Sep 1998 13:51:14 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 40 Message-ID: <6tj70j$pvh$1@nnrp1.dejanews.com> References: <35F54C15.EABDAE63@unm.edu> NNTP-Posting-Host: 128.227.242.42 X-Article-Creation-Date: Mon Sep 14 13:51:14 1998 GMT X-Http-User-Agent: Mozilla/4.04 (Macintosh; U; PPC) X-Http-Proxy: 1.0 x14.dejanews.com:80 (Squid/1.1.22) for client 128.227.242.42 In article , pdxkgs@pdn1.gene.nott.ac.uk (Karen spink) wrote: > I have encountered this problem in binding reactions where the salt > concentration is particularly high, ie.when using crude protein fractions > eluted from a column at high salt. Another possibility is that you are > using too much protein in the reactions-have you tried using less? > > hope this helps > Karen spink > > In article <35F54C15.EABDAE63@unm.edu>, ezra@UNM.EDU (Ezra Schildkraut) wrote: > > > I have been doing gel shifts to try and show specific binding in CHO > > cell protein extracts to specific oligos. I have seen definite shifts, > > however they appear as long smears instead of discrete bands. I would > > like to see discrete bands. If anyone out there has had and has > > overcome this problem please let me know. Any other insight would also > > be appreciated. > > > > Ezra Schildkraut > > ezra@unm.edu > I have been going crazy the last couple of weeks with similar troubles. I think the time comes when it is best to remake all of your reagents and just try it again. Of course dialysis and protein concentration issues should be taken care of first. if you happen to figure out what the trouble was let us know, thanks, Todd WTPENBER@UFL.EDU -- I'm so hungry that if you put a biscuit on my head my tongue would beat my brains out -Elvin Bishop -----== Posted via Deja News, The Leader in Internet Discussion ==----- http://www.dejanews.com/rg_mkgrp.xp Create Your Own Free Member Forum From owner-proteins@net.bio.net Sun Sep 13 23:00:00 1998 Path: biosci!news.stanford.edu!Cabal.CESspool!news-feed.inet.tele.dk!bofh.vszbr.cz!newsfeed.wli.net!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: WTPENBER@UFL.EDU Newsgroups: bionet.molbio.proteins Subject: Re: glutaraldehyde cross-linking Date: Mon, 14 Sep 1998 13:46:46 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 46 Message-ID: <6tj6o6$pjl$1@nnrp1.dejanews.com> References: NNTP-Posting-Host: 128.227.242.42 X-Article-Creation-Date: Mon Sep 14 13:46:46 1998 GMT X-Http-User-Agent: Mozilla/4.04 (Macintosh; U; PPC) X-Http-Proxy: 1.0 x14.dejanews.com:80 (Squid/1.1.22) for client 128.227.242.42 In article , lgbell@liverpool.ac.uk wrote: > Pauline Bariola wrote: > > > > I have been using the method of glutaraldehyde cross-linking to determine > > the oligomerization state of a protein under different conditions. Does > > anyone know if the cross-linking reaction is inhibited at any pH, > > particularly extreme pHs? > > > > Also, if anyone knows a good reference article for this technique, > > preferably including suggestions of the best reaction conditions to use, I > > would appreciate being pointed toward it. > > > > Please reply to my e-mail address as well as to the newsgroup. Thanks in > > advance. > > > > Pauline Bariola > > University of Lausanne > > e-mail: Pauline.Bariola@ibpv.unil.ch > > Previously here people have suggested 'BIOCONJUGATE TECHNIQUES' by > Hermanson, Greg T. Published by Academic Press, which has been > described as the Bible on this sort of subject. Having recently seen a > copy I can see why. > > Regards, > Len. > > lgbell@liv.ac.uk > Freitag et. al in Biochemistry 1997, vol 36, 10221- show a simple glutarldehyde cross-linking with very simple conditions. In figure 2 they show the purified protein and then this same sample after cross- linking resulting in dimers and trimers. I can not say that I have experience but Kapoor's lab apparently does. best of luck, Todd -- I'm so hungry that if you put a biscuit on my head my tongue would beat my brains out -Elvin Bishop -----== Posted via Deja News, The Leader in Internet Discussion ==----- http://www.dejanews.com/rg_mkgrp.xp Create Your Own Free Member Forum From owner-proteins@net.bio.net Sun Sep 13 23:00:00 1998 Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!208.134.241.18!newsfeed.internetmci.com!194.72.7.126!btnet-peer!btnet!neptunium.btinternet.com!not-for-mail From: "E.C.Apling" Newsgroups: alt.biology,bionet.molbio.proteins,bionet.toxicology,de.sci.biologie,sci.bio.ecology,sci.bio.food-science,sci.chem Subject: Re: Chem. of rotten Eggs Date: Mon, 14 Sep 1998 09:19:43 +0100 Organization: BT Internet Lines: 56 Message-ID: <6tiv4s$igq$1@uranium.btinternet.com> References: <6thuuo$rbt@news.quick.net> NNTP-Posting-Host: host5-99-44-61.btinternet.com X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Xref: biosci bionet.molbio.proteins:13295 bionet.toxicology:2427 hanson wrote in message <6thuuo$rbt@news.quick.net>... >It seems reasonable to assume that the classic >"rotten egg" smell of aged, boiled eggs does >come from H2S and or mercaptanes. >These malodorants seem to originate from the >decay of S-bearing amino acids, Cystein and >Methionine etc. >Questions: >a) what is the decay route in such sterile, boiled eggs? >b) are such bad smelling eggs actually poisonous >or just unpalatable? I think just unpalatable and aesthetically undesirable, though their may well be microbiological dangers if the eggs were originally contaminated - as there will have been time for bacterial growth. This reminds me of industrial research I was involved in in the 1950s in respect of "incubator clears", i.e. eggs which had not hatched in the incubator - and which were/are an embarassing waste product. Incubator clears smell badly of H2S, and the contents are thin compared to normal eggs, with an alkaline pH. We found that adjusting the pH to normal with small additions of acetic acid produced egg material which performed excellently in batter production for e.g. sponge cakes - often performing *better* than fresh egg, without any odour taint Liquid egg prepared from incubator clears was used for several.years without recorded problems, but then a food poisoning outbreak was ascribed to liquid egg imported from China and, after development of a pasteurisation process for liquid egg which avoided excessive damage to the functional properties of the egg protein etc (at Reading University Department of Dairying under Professor Eric Crossley, which I joined in 1962) all liquid egg was required from 1963 to be pasteurised and, so far as I am aware, the food use of incubator clears ceased, as no longer economic (i.e. easier to dispose of as waste - to animal feed ?? - than to pay for pasteurisation. So far as bakery uses of incubator clears or other "rotten" eggs was concerned the danger only arose from cross-contamination with uncooked material in the bakery - i.e. contamination of cream fillings etc where raw materials used in baking and used in filling were not adequately kept apart. However, eggs are also used in other non-cooked products such as mayonnaise etc. and the requirement for *all* liquid egg to be pasteurised was/is a safety precaution. Paddy Mailto:E.C.Apling@btinternet.com From owner-proteins@net.bio.net Sun Sep 13 23:00:00 1998 Path: biosci!musc.edu!vakseri From: vakseri@musc.edu (Ilya Vakser) Newsgroups: bionet.molbio.proteins Subject: Postdocs/Graduate Students in Docking Date: 14 Sep 1998 14:35:42 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: <35FD8A7C.36E45B48@musc.edu> NNTP-Posting-Host: net.bio.net Applications are invited for postdoctoral and graduate student positions in my laboratory at the Medical University of South Carolina. The main subjects of the research in the laboratory are computational studies of molecular recognition and the development of docking methodology for protein complexes and computer-aided drug design. For more information, see the lab's web site at http://reco3.musc.edu. Programming skills in C are required. The positions are available immediately. To apply send or email a letter and CV with names of 3 referees. Ilya A. Vakser Assistant Professor of Pharmacology Department of Cell and Molecular Pharmacology Medical University of South Carolina 171 Ashley Avenue Charleston, SC 29425 phone:(843)792-2471, fax:(843)792-2475 email: vakseri@musc.edu, http://reco3.musc.edu From owner-proteins@net.bio.net Sun Sep 13 23:00:00 1998 Path: biosci!IX.NETCOM.COM!rfbalint From: rfbalint@IX.NETCOM.COM (Robert Balint) Newsgroups: bionet.molbio.proteins Subject: Functional Genomics Meeting in San Francisco Date: 14 Sep 1998 13:10:51 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 76 Sender: daemon@net.bio.net Distribution: world Message-ID: <35FD7703.B934305E@ix.netcom.com> Reply-To: rfbalint@ix.netcom.com NNTP-Posting-Host: net.bio.net Molecular Interaction Technologies ’98 October 19-20, 1998, San Francisco, California An enormous demand for high throughput methods to identify both natural and artificial ligands for expressed sequences has been created by the recent explosion in genomic and bioinformatic research. Although molecular interaction studies began using in vitro immunoscreening and phage display technologies, the development of the yeast two hybrid system in 1989 accelerated the pace of in vivo interaction analysis. Since then a number of creative technologies have been developed to study molecular interactions inside cells or whole organisms. The purpose of this meeting is to bring together innovators in the development of these technologies. These methods have wide application for basic cellular and molecular biology, drug target identification and pharmaceutical development. Keynote Address: Stuart Schreiber Howard Hughes Medical Institute Harvard University Confirmed Speakers: Carlos Barbas, Scripps Ron Barrett, Affymax Paul Bartel, Myriad Genetics Helen Blau, Stanford Roger Brent, Molecular Sciences Institute James Broach, Princeton Gerald Crabtree, HHMI, Stanford Reto Crameri, Swiss Institute, Davos Stan Fields, HHMI, University of Washington Michael Gilman, ARIAD Pharmaceutical Hennie Hoogenboom, Univ. Hosp., Maastricht Jarko Kochan, Hoffmann-La Roche Pierre Legrain, Institut Pasteur Lawrence Loeb, University of Washington Gary Nolan, Stanford Carl Pabo, HHMI, MIT Don Payan, Rigel Andreas Plückthun, Universitat Zurich Mike Roth, Tularik Gerald Rubin, HHMI, U.C. Berkeley Erkki Ruoslahti, Burnham Institute Robert Sauer, MIT Peter Schultz, HHMI, U.C. Berkeley Paul Sternberg, HHMI, Cal Tech Jeremy Thorner, U.C. Berkeley Roger Tsien, HHMI, U.C. San Diego Marc Vidal, MGH Cancer Center James Wells, Genentech Marvin Wickens, University of Wisconsin Kleanthis Xanthopoulos, Aurora Biosciences Organized by: Stan Fields, Ph.D. Howard Hughes Medical Institute University of Washington James W. Larrick, M.D. Ph.D. Palo Alto Institute of Molecular Medicine Robert F. Balint, Ph.D. Palo Alto Institute of Molecular Medicine For More Information Contact: The Palo Alto Institute of Molecular Medicine 2462 Wyandotte Street Mountain View, CA 94043, USA Tel: 650.694.1420 Fax: 650.694.7717 E-Mail: paimm@netgate.net Web site: www.pano.com/paimm From owner-proteins@net.bio.net Mon Sep 14 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.enteract.com!ix.netcom.com!news From: Mark Atlas Newsgroups: bionet.molbio.proteins Subject: online auction for used scientific instrumentation Date: Tue, 15 Sep 1998 22:34:21 GMT Organization: ICGNetcom Lines: 101 Message-ID: <6tmpo7$q07@sjx-ixn4.ix.netcom.com> NNTP-Posting-Host: sji-ca2-24.ix.netcom.com X-NETCOM-Date: Tue Sep 15 3:29:27 PM PDT 1998 X-Newsreader: NETCOMplete/4.0 online auction for used scientific instrumentation Visit http://www.going-going-sold.com Going,Going...Sold! has a large assortent of equipment on the block. All equipment auctions come automatically with an in lab evaluation supplied by a holding escrow. This form of safe purchasing insures that you ghet your product as defined on the website. If the product you seek is not on consignment, we can locate it with our new custom equipment search service. Below are some of our listings new equipment is added frquently Closing dates are noted below. Visit http://www.going-going-sold.com he following Items are scheduled to go on Auction over the next few weeks. ***************************************************** Sale Closing : 9/18/98 Opening Prices ***************************************************** 1. Beta Scint. Counter $13,000.00 ------------------------------------------------------------ 2. Beckman DU-70 $4,900.00 ------------------------------------------------------------ 3. Tekmar 2000/2016 sampler $6,800.00 ------------------------------------------------------------ 4. Liquid Chromatograph $27,900.00 ------------------------------------------------------------ 5. Varian 3400 GC $8,500.00 ------------------------------------------------------------ 6. Amino Acid Analyzer $27,000.00 ------------------------------------------------------------ 7. AtomScan 16 ICP $17,000.00 ------------------------------------------------------------ 8. HP 1090 HPLC System $19,000.00 ------------------------------------------------------------ ***************************************************** Sale Closing : 9/23/98 Opening Prices ***************************************************** 1. Purifier Class II $2,500.00 ------------------------------------------------------------ 2. Optima Ultracentrifuge $20,000.00 ------------------------------------------------------------ 3. Laminar Flow Hood $1,450.00 ------------------------------------------------------------ 4. Phase Contrast Microscope $2,000.00 ------------------------------------------------------------ 5. Gruenburg Depyro Oven $1,700.00 ------------------------------------------------------------ 6. Preparative HPLC pumping system and column $21,000.00 ------------------------------------------------------------ 7. Fraction collector for Prep system item 304 $3,600.00 ------------------------------------------------------------ 8. Titertek Flouroskan I Reader $1,000.00 ------------------------------------------------------------ 9. ABEC Bioreactor $77,500.00 ------------------------------------------------------------ 10. Varian GC-3400 $1,850.00 ------------------------------------------------------------ 11. Automatic Steam Pressure Sterilizer $1,800.00 ------------------------------------------------------------ ***************************************************** Sale Closing : 9/25/98 Opening Prices ***************************************************** 1. Inductively Coupled Plasma $19,000.00 ------------------------------------------------------------ 2. 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HP 5890 GC $5,000.00 ------------------------------------------------------------ ***************************************************** (c) 1997, Internet Auctioneers International From owner-proteins@net.bio.net Tue Sep 15 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!news-peer.sprintlink.net!news-backup-west.sprintlink.net!news.sprintlink.net!140.163.96.254!news.ski.mskcc.org!news From: Frances Newsgroups: bionet.molbio.proteins Subject: ? Protein Quantitation ? Date: Wed, 16 Sep 1998 08:54:22 -0500 Organization: Memorial Sloan-Kettering Cancer Center Lines: 54 Message-ID: <35FFC30E.F7601625@ski.mskcc.org> NNTP-Posting-Host: 140.163.99.179 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 (Macintosh; I; PPC) Please help - We are currently quantitating our antibody concentration by two methods - (1) Comassie Blue G250/densitometery/Computer analysis (BioRAD's Molecular Analyst Program) - and - (2) the a Bradford based assay (BioRAD Protein Assay) - and the two methods do not always give the same antibody concentraion - When the monoclonal antibody is impure (25-45% from bioreactor supernatant) the two approached agree very well when I correct the bradford asssay numbers for the puritiy - determined by densitomety - But as we purify the antibody to 95% pure - we progressivly get less agreement between the two methods - to the point where the bradford assay gives values that are at least 1/2 the value calculated from the comassie stained gel - We use dilutions of the same rat or bovine IgG prep (from BioRAD) as standards for BOTH assays - I tend to trust the comassie staining more - because my understanding is that comassie staining is protien composition INDEPENDENT and the bradford system is dependent on the number of tyrosines in the protien solution - Therefore - does anyone know of another way to quantitate the concentration on a purified protien that is independent of the protien composition - or am I wrong and should trust the bradford system more - Thanks for any advise or comments you can offer - Frances ************************************* Frances Weis-Garcia, Ph.D. Manager, Monoclonal Antibody Core Facility Memorial Sloan-Kettering Cancer Center 1275 York Avenue - Box 341 New York, New York 10021 Phone: 212 - 639 - 2054 FAX: 212 - 794 - 4019 e-mail: f-weis-garcia@ski.mskcc.org From owner-proteins@net.bio.net Tue Sep 15 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!portc02.blue.aol.com!pitt.edu!not-for-mail From: pxpst2@unixs.spam.suxs.cis.pitt.edu (Peter) Newsgroups: bionet.molbio.proteins Subject: Re: ? Protein Quantitation ? Date: Wed, 16 Sep 1998 09:20:58 -0500 Organization: University of Pittsburgh Lines: 17 Message-ID: References: <35FFC30E.F7601625@ski.mskcc.org> NNTP-Posting-Host: pelli.pathology.pitt.edu Mail-Copies-To: pxpst2@unixs.spam.suxs.cis.pitt.edu X-Newsreader: MT-NewsWatcher 2.4.4 In article <35FFC30E.F7601625@ski.mskcc.org>, Frances wrote: > Therefore - does anyone know of another way to quantitate the > concentration on a purified protien that is independent of the protien > composition - or am I wrong and should trust the bradford system more - Have you given the BCA reagent method a try? It is cheap and very easy. Peter -- "Don't you eat that yellow snow watch out where the Huskies go" FZ --------------------------------------------------------------------- From owner-proteins@net.bio.net Wed Sep 16 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!cpk-news-feed3.bbnplanet.com!news.bbnplanet.com!topgun.es.dupont.com!usenet From: "Patricia W. Sanders" Newsgroups: bionet.molbio.proteins Subject: Plant Molecular Biologist Date: Thu, 17 Sep 1998 08:11:06 -0400 Organization: DUPONT Lines: 37 Message-ID: <3600FC5A.A54164A7@usa.dupont.com> NNTP-Posting-Host: sanders.ba.dupont.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [en] (Win95; I) Du Pont is very interested in any candidates who possess the skills below. Ideally the candidate should possess a PhD, Molecular Biology, with plant experience. I would appreciate any assistance you can offer in posting this position in your department or passing this information along to your colleagues. If you have any questions, please feel free to call me on 1-888-868-4142 or EMAIL: Patricia.W.Sanders@USA.dupont.com PLEASE REFER TO JOB NO. AG98-1980 SKILLS NEEDED: PhD in plant biotechnology, molecular biology or gene expression with 2+ years experience or post-doc. Experience in expression of heterologous genes in transgenic plants required. DuPont is a leader in Biotechnology and Life Sciences, conducting fundamental and applied research programs ranging from industrial bioprocesses to genetically improved crops, and faster routes to environmentally friendly crop protection products. Graduates in the Life Sciences areas are needed to join multidisciplinary teams as principal investigators and technical support staff. DuPont is committed to forming diverse research teams of talented, committed and creative people. Our positions offer a highly competitive salary and an excellent benefits package. The DuPont Corporation is centered in Wilmington, DE, with sites located throughout the U.S. and Globally. Please FAX RESUMES to: 302-892-8478 or 1-800-631-2206 MAIL ADDRESS: Patricia W. Sanders DuPont Agricultural Products BMP/WM4-225 Wilmington,DE 19880 From owner-proteins@net.bio.net Wed Sep 16 23:00:00 1998 Path: biosci!daresbury!not-for-mail From: "MTT E-mail Cimtar" Newsgroups: bionet.molbio.proteins Subject: [24546131092129301052] UJ BEJEGYZES az MTT E-mail Cimtar rendszereben Date: 18 Sep 1998 05:27:02 +0100 Lines: 60 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6tsnem$13q@mserv1.dl.ac.uk> Original-To: proteins@dl.ac.uk MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7BIT Kedves felhasználó! Megtaláltuk az Ön e-mail címét az Interneten. Ha szeretné, hogy adatait az MTT E-mail Címtár rendszere tartalmazza, kérjük látogassa meg szerverünket a http://e_search.mtt.hu/ címen. Ott további adatokat adhat meg magáról, így könnyebben találják meg azok akik keresik. Ha nem akarja, hogy az MTT E-mail Címtár tartalmazza az Ön adatait, változtatás nélkül, egyszerűen küldje vissza ezt a levelet, és bejegyzése törölve lesz a rendszer adatbázisából. Amennyiben később mégis szeretné adatait a rendszer adatbázisában elhelyezni, látogasson meg minket a http://e_search.mtt.hu/ szerveren és kövesse az ott leírt lépéseket. Tisztelettel: MTT E-mail Címtár csoport -------- Betreff: NEUER EINTRAG in dem MTT E-Mail Verzeichnis Sehr geehrter Benutzer, wir haben Ihre E-Mail-Adresse im Internet gefunden. Wir laden Sie ein, die Internet-Seite http://e_search.mtt.hu/ zu besuchen, um den Eintrag mit Zusatzinformationen zu vervollständigen, damit Ihre Adresse leichter zu finden ist. Falls Sie den Eintrag löschen möchten, so bitten wir Sie lediglich diese Nachricht zu Antworten, ohne sie zu verändern. Wir bedanken uns für Ihre Zusammenarbeit und verbleiben mit freundlichen Grüßen Ihr MTT E-Mail-Verzeichnis Team -------- Subject: NEW ENTRY in the MTT e-mail directory Dear user, We have found your e-mail address on the internet. If you wish to be included in this directory, we kindly invite you to go to http://e_search.mtt.hu/ and enter some additional information about you so that you can be more easily found by those looking for you. If you do not wish to be included in this directory, simply reply to this message without changing it. Thank you very much. With kind regards, The MTT E-mail Directory Team From owner-proteins@net.bio.net Wed Sep 16 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.sprintlink.net!news-backup-east.sprintlink.net!news.sprintlink.net!128.228.4.60!news.cuny.edu!not-for-mail From: "Ken Wu" Newsgroups: bionet.molbio.proteins Subject: Crosslinking IgG to Protein A beads Date: Fri, 18 Sep 1998 01:03:27 -0400 Organization: Mount Sinai School of Medicine Lines: 9 Distribution: world Message-ID: <6tst93$3h6$1@news.cuny.edu> NNTP-Posting-Host: dialin41.external.mssm.edu X-Newsreader: Microsoft Outlook Express 4.72.3155.0 X-Mimeole: Produced By Microsoft MimeOLE V4.72.3155.0 Hey there, Anyone have a good protocol for crosslinking antibodies to Protein A beads? Thanks, Ken From owner-proteins@net.bio.net Wed Sep 16 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!nntp-out.monmouth.com!newspeer.monmouth.com!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!news.icnet!NewsWatcher!user From: i.mcfarlane@icrf.icnet.uk (Ian McFarlane) Newsgroups: bionet.molbio.proteins Subject: Re: ? Protein Quantitation ? Date: 17 Sep 1998 09:23:02 GMT Organization: Imperial Cancer Research Fund Lines: 27 Message-ID: References: <35FFC30E.F7601625@ski.mskcc.org> NNTP-Posting-Host: 143.65.17.54 Lowry method possibly. Ian Mc In article , pxpst2@unixs.spam.suxs.cis.pitt.edu (Peter) wrote: > In article <35FFC30E.F7601625@ski.mskcc.org>, Frances > wrote: > > > Therefore - does anyone know of another way to quantitate the > > concentration on a purified protien that is independent of the protien > > composition - or am I wrong and should trust the bradford system more - > > Have you given the BCA reagent method a try? It is cheap and very easy. > > Peter > > -- > "Don't you eat that yellow snow > watch out where the Huskies go" FZ > > --------------------------------------------------------------------- From owner-proteins@net.bio.net Wed Sep 16 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.enteract.com!feed1.news.rcn.net!rcn!newsfeed.internetmci.com!204.238.120.130!news-feeds.jump.net!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: peter_wirth@nih.gov Newsgroups: bionet.molbio.proteins Subject: Re: Rapid Westerns on PVDF Date: Thu, 17 Sep 1998 13:20:30 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 37 Message-ID: <6tr2au$s38$1@nnrp1.dejanews.com> References: NNTP-Posting-Host: 165.112.73.18 X-Article-Creation-Date: Thu Sep 17 13:20:30 1998 GMT X-Http-User-Agent: Mozilla/4.06 [en] (Win95; U) X-Http-Proxy: 1.0 x1.dejanews.com:80 (Squid/1.1.22) for client 165.112.73.18 The PVDF blots aren't initially wettable with aqueous solutions alone. The PVDF membranes are first dipped into methanol and then into your aqueous reagents (e.g. blocking solutions, antibody solutions, etc) peter wirth In article , i.mcfarlane@icrf.icnet.uk (Ian McFarlane) wrote: > I think I wasn't clear enough with the second question. What I am > interested in is the use of ECL with the rapid blotting technique. Becuase > the PVDF is not wetable I was wondering how you managed to get the reagent > in contact with the blot in enough quantity so that you can get a signal. > > Thank you for the replies thus far. > > Ian Mc > > > Hi, > > > > I have a few questions about using PVDF (Immobilon P) without blocking (or > > wetting) the membrane. > > > > 1) Compared to the wet blotting method do you need relativley higher or > > lower concentrations of your primary and secondary Abs? > > > > 2) Does anyone have any experiences with ECL detection that they can > > share? Specifically how much of the ECL reagent stays with the blot when > > you wrap it for exposure and if, as seems likely, only a small amount does > > stay on the blot how does that affect the length of time that you can get > > a signal from the blot. > > > > Thanks, > > > > Ian Mc > -----== Posted via Deja News, The Leader in Internet Discussion ==----- http://www.dejanews.com/rg_mkgrp.xp Create Your Own Free Member Forum From owner-proteins@net.bio.net Wed Sep 16 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!cyclone.news.idirect.com!island.idirect.com!news-feed1.eu.concert.net!btnet-peer!btnet!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: Alexandre Da-Silva-Conceicao Newsgroups: bionet.molbio.proteins Subject: faculty positions, Plant Biology Date: 17 Sep 1998 13:25:21 +0100 Lines: 28 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6tqv3h$ftm@mserv1.dl.ac.uk> X-Sender: dasilva@satie.u-bourgogne.fr Original-To: proteins@dl.ac.uk Dear Colleagues: Applications are invited for two full-time academic positions, a Full Professor (Professeur des Universites) and an Assistant Professor (Maitre de Conferences) in Plant Cell Genetics at the Department of Plant Biology, Universite de Bourgogne. We are particularly interested for dynamic candidates using combined research approaches in plant molecular and developmental genetics. The appointees will have teaching responsibilities on classical and molecular genetics. The successful candidates are expected to teach in French. Questions concerning these positions and the application procedures should be addressed to: Professeur Francis Marty, laboratoire de phytoBiologie Cellulaire, Faculte de Sciences-Mirande, Universite de Bourgogne, 9 avenue Alain Savary, BP400, 21011 Dijon Cedex, France; e-mail fmarty@u-bourgogne.fr; telephone 00 33 3 80396251; fax 00 33 3 80396287. The closing date for official applications is November 16, 1998. Dr. Alexandre da Silva Conceicao (maitre de conferences) Laboratoire de phyto-Biologie Cellulaire UPRES EA 469 Universite de Bourgogne 9, avenue Alain Savary BP 400, 21011, Dijon Cedex, France phone: 33 3 80396484 fax: 33 3 80396287 email: dasilva@u-bourgogne.fr From owner-proteins@net.bio.net Wed Sep 16 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed.internetmci.com!194.162.162.196!newsfeed.nacamar.de!nntp.news.xara.net!xara.net!rill.news.pipex.net!pipex!uunet!uunet!in4.uu.net!hearst.acc.Virginia.EDU!aruba.odu.edu!news From: Laura Moen Newsgroups: bionet.molbio.proteins Subject: STBL2 E. coli strain? Date: Wed, 16 Sep 1998 17:07:50 -0400 Organization: Old Dominion Universityaruba Lines: 36 Message-ID: <360028A6.1CF260B2@odu.edu> NNTP-Posting-Host: viper228229.sci1.odu.edu Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------127926F7D8A1437A0172C2F1" X-Mailer: Mozilla 4.04 [en] (WinNT; I) This is a multi-part message in MIME format. --------------127926F7D8A1437A0172C2F1 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello netters - I am interested in finding out about the STBL2 E. coli strain - I believe it is marketed by Gibco, but I don't have a Web address or catalog. Does anyone have the Gibco site URL? If so, that would be most helpful. Alternatively, has anyone used this strain? If so, can you tell me about it - any special characteristics it might have? Thanks a lot. Laura --------------127926F7D8A1437A0172C2F1 Content-Type: text/x-vcard; charset=us-ascii; name="vcard.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Laura K. Moen Content-Disposition: attachment; filename="vcard.vcf" begin: vcard fn: Laura K. Moen n: Moen;Laura K. org: Dept. of Chemistry and Biochemistry, Old Dominion University email;internet: lmoen@odu.edu title: Director, Biomedical Sciences Ph.D. Program, ODU note: The opinions expressed here are not those of my employer! x-mozilla-cpt: ;0 x-mozilla-html: FALSE version: 2.1 end: vcard --------------127926F7D8A1437A0172C2F1-- From owner-proteins@net.bio.net Wed Sep 16 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!news.shore.net!rbb From: rbb@shell3.shore.net (Robert Burrows) Newsgroups: bionet.molbio.proteins Subject: Re: ? Protein Quantitation ? References: <35FFC30E.F7601625@ski.mskcc.org> Reply-To: rbb@nebiometrics.com Message-ID: X-Newsreader: slrn (0.9.4.3 UNIX) Lines: 25 Date: Fri, 18 Sep 1998 00:46:52 GMT NNTP-Posting-Host: 204.167.111.24 X-Complaints-To: abuse@shore.net X-Trace: news.shore.net 906079612 204.167.111.24 (Thu, 17 Sep 1998 20:46:52 EDT) NNTP-Posting-Date: Thu, 17 Sep 1998 20:46:52 EDT Organization: Shore.Net/Eco Software, Inc; (info@shore.net) On Wed, 16 Sep 1998 08:54:22 -0500, Frances wrote: >Please help - > >We are currently quantitating our antibody concentration by two methods >- >(1) Comassie Blue G250/densitometery/Computer analysis (BioRAD's >Molecular Analyst Program) - and - (2) the a Bradford based assay >(BioRAD >Protein Assay) - and the two methods do not always give the same >antibody >concentraion - > Frances, If a knpwledge of the absolute concentration of your antobody is important, you are better off using a quantitation method that is truly composition-independent such as a determination of total nitrogen or an amino terminal ana;ysis. Of course, these methods are only useful with purified proteins. -- Robert Burrows rbb@nebiometrics.com From owner-proteins@net.bio.net Wed Sep 16 23:00:00 1998 Path: biosci!ihnp4.ucsd.edu!sdd.hp.com!usc!howland.erols.net!newsfeed1.telenordia.se!newsfeed1.funet.fi!ousrvr3.oulu.fi!sun3.oulu.fi!pkursula From: Pete Newsgroups: bionet.molbio.proteins Subject: Re: ? Protein Quantitation ? Date: Fri, 18 Sep 1998 08:26:51 +0300 Organization: University of Oulu Lines: 25 Message-ID: References: <35FFC30E.F7601625@ski.mskcc.org> NNTP-Posting-Host: sun3.oulu.fi Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: pkursula@sun3.oulu.fi In-Reply-To: <35FFC30E.F7601625@ski.mskcc.org> > > that comassie staining is protien composition INDEPENDENT and the > bradford system is dependent on the number of tyrosines in the protien > solution - Err.. I was under the impression that the bradford system uses coomassie...if I remember correctly, the ORIGINAL article describing the bradford method has a list of compounds that interfere with the assay (Bradford, 1976 or something...). |) |/ |etri |\ursula Petri.Kursula@oulu.fi http://cc.oulu.fi/~pkursula ------------------------------------------------- "I am somehow less interested in the weight and convolutions of Einstein's brain than in the near certainty that people of equal talent have lived and died in cotton fields and sweatshops." -- Stephen Jay Gould ------------------------------------------------- From owner-proteins@net.bio.net Thu Sep 17 23:00:00 1998 From: Cornelius Krasel Subject: Re: ? Protein Quantitation ? Newsgroups: bionet.molbio.proteins Referenc