From owner-proteins@net.bio.net Mon Apr 01 23:00:00 1996 Path: biosci!news.Stanford.EDU!nntp-hub2.barrnet.net!sgigate.sgi.com!swrinde!gatech!newsfeed.internetmci.com!in2.uu.net!ftpbox!newsfeed.acns.nwu.edu!news.cc.uic.edu!usenet From: Keld Sorensen Newsgroups: bionet.molbio.proteins Subject: Re: Wanted:Peptide quantitiation method Date: 1 Apr 1996 22:21:11 GMT Organization: Univ. Illinois / College of Med. Lines: 9 Message-ID: <4jpksn$ej8@piglet.cc.uic.edu> References: NNTP-Posting-Host: sliprock-00.dialin.uic.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) X-URL: news:whc-3103961518330001@macr3-20.welc.cam.ac.uk BCA can be used easily. Other methods include: ninhydrin, fluroescamine etc. All methods will tend to vary some, in particular the ones that rely on generating color with the NH2 groups (the ninhydrin, TNBSA etc). Bradford does not recognize short peptides. Keld. From owner-proteins@net.bio.net Mon Apr 01 23:00:00 1996 Path: biosci!rutgers!gatech!usenet.eel.ufl.edu!warwick!leicester!usenet From: "Dr E. Buxbaum" Newsgroups: bionet.molbio.proteins Subject: (no subject) Date: 1 Apr 1996 15:25:55 GMT Organization: University of Leicester, UK (PCFS User) Lines: 7 Message-ID: <4josi3$152@falcon.le.ac.uk> NNTP-Posting-Host: pc10.msb.le.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) Has anybody a contact address available for a company that does custom immunizations in chicken (preferably in europe?)? Thanks Engelbert Buxbaum From owner-proteins@net.bio.net Mon Apr 01 23:00:00 1996 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!news From: Peter Wang Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: N-acetyl-galactosaminolactone source? Date: 2 Apr 1996 17:03:10 GMT Organization: Centre for Protein Engineering Lines: 18 Message-ID: <4jrmke$ec@lyra.csx.cam.ac.uk> NNTP-Posting-Host: macx45.mrc-lmb.cam.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) X-URL: news:bionet.molbio.methds-reagnts Xref: biosci bionet.molbio.methds-reagnts:42580 bionet.molbio.proteins:7497 Dear Netters: A friend of mine is looking for a supplier of N-acetyl-galactosaminolactone. She tried the Sigma and Calbiochem catalogs, but no luck. Anyone know an answer? Thanks in advance, - Peter --------------------------------------------------------- Peter Wang, M.D., Ph.D. MRC Centre for Protein Engineering, Hills Road, Cambridge, CB2 2QH, England Tel (01223) 402104 (international calls +44-1223-402104) Fax (01223) 402140 ( " " +44-1223-402140) --------------------------------------------------------- From owner-proteins@net.bio.net Mon Apr 01 23:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!news.belnet.be!swsbe6.switch.ch!swidir.switch.ch!in2p3.fr!oleane!tank.news.pipex.net!pipex!swrinde!newsfeed.internetmci.com!in2.uu.net!nectec!news.mahidol.ac.th!saturn!g3421101 From: g3421101@saturn.mahidol.ac.th (Enrique Jose Labadan Frio - SCBC - 3421101) Newsgroups: bionet.molbio.proteins Subject: Secondary structure assignments Date: 2 Apr 1996 08:30:32 GMT Organization: Mahidol University, Thailand Lines: 20 Message-ID: <4jqoj8$rcj@mars.mahidol.ac.th> NNTP-Posting-Host: 202.14.162.14 X-Newsreader: TIN [version 1.2 PL2] Dear all, I'm in a sort of dilemma as to how best to assign secondary structure info to some proteins I'm working on. For the same crystal structure, for example, DSSP (Kabsch and Sander) as implemented under Rasmol breaks up beta-sheets into sheetlets and helices into small "helixlets" and makes some betas disappear altogether (very little mainchain Hbonds to start with!). O's YASSPA (as of 1991 anyway) seems to assign sheets and helices very liberally in that they span longer stretches than DSSP's. Is DSSP's -0.5 kcal/mol Hbond definition the best/ standard criterion for 2o struc. assignment? Are there any alternative ones one can use? Thanks 10^6! Querix Enrique Frio g3421101@mucc.mahidol.ac.th From owner-proteins@net.bio.net Mon Apr 01 23:00:00 1996 Path: biosci!agate!dog.ee.lbl.gov!overload.lbl.gov!news.kreonet.re.kr!news.nuri.net!imci2!news.internetMCI.com!newsfeed.internetmci.com!newsserver.jvnc.net!crick.bms.com!usenet From: "Glenn A. Warr" Newsgroups: bionet.molbio.proteins Subject: Re: Wanted:Peptide quantitiation method Date: 2 Apr 1996 10:39:00 GMT Organization: Bristol-Myers Squibb Lines: 4 Message-ID: <4jr044$kcb@crick.bms.com> References: NNTP-Posting-Host: warrg.wf.bms.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) To: whc@mole.bio.cam.ac.uk You may want to try absorbance at 230 and 260nm, based on the peptide bond. Reportedly has a linear range of 6 - 225 ug/ml. Reference - Analytical Biochemistry 82:362-371, 1977. From owner-proteins@net.bio.net Mon Apr 01 23:00:00 1996 Path: biosci!IRIS.LSC.PKU.EDU.CN!lisl From: lisl@IRIS.LSC.PKU.EDU.CN (Li Songlin) Newsgroups: bionet.molbio.proteins Subject: protein clustering Date: 2 Apr 1996 22:12:40 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <9604032210.AA08245@IRIS.lsc.pku.edu.cn> NNTP-Posting-Host: net.bio.net Dear all, I am a crystallographer. I have a high concentration protein sample. (>30 mg/ml). In my recent work, it is suspected that ten or more molecules of this kind of protein form a cluster. It should be checked by experiment. Could you please show me some methods that could be used to check my suspection? The MW of the protein is 63,000. 8% PAGE is very difficult. most of the sample unmoved. Any help is appreciated. Songlin PS, please reply to lisl@iris.lsc.pku.edu.cn From owner-proteins@net.bio.net Mon Apr 01 23:00:00 1996 Path: biosci!news.Stanford.EDU!nntp-hub2.barrnet.net!venus.sun.com!cs.utexas.edu!geraldo.cc.utexas.edu!netnews.uthscsa.edu!usenet From: Jeff Seale Newsgroups: bionet.molbio.proteins,bionet.immunology,bionet.microbiology,bionet.general Subject: Chaperonin Web Page Date: Tue, 02 Apr 1996 15:02:58 -0800 Organization: uthscsa Lines: 8 Message-ID: <3161B222.422F@bioc02.uthscsa.edu> NNTP-Posting-Host: horowitz_lab1.uthscsa.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win16; I) CC: seale@bioc02.uthscsa.edu Xref: biosci bionet.molbio.proteins:7499 bionet.immunology:8423 bionet.microbiology:5557 bionet.general:20927 I have created a web page for Chaperonins. The page contains GroEL/GroES mutation databases and a Chaperonin structure gallery. There will be new information added soon and all contributions are welcome. The address is: http://bioc09.uthscsa.edu/~seale/Chap/chap.html -Jeff seale@bioc02.uthscsa.edu From owner-proteins@net.bio.net Mon Apr 01 23:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!news.belnet.be!swsbe6.switch.ch!surfnet.nl!howland.reston.ans.net!gatech!newsfeed.internetmci.com!uwm.edu!psuvax1!news.cc.swarthmore.edu!netnews.upenn.edu!taurus.fccc.edu!sauder From: sauder@castor.fccc.edu (John Michael Sauder) Newsgroups: bionet.molbio.proteins Subject: Re: Looking for information on amino acids Date: 2 Apr 1996 16:47:31 GMT Organization: Fox Chase Cancer Center, Philadelphia, PA Lines: 17 Message-ID: <4jrln3$q7u@taurus.fccc.edu> References: <4jraig$cmr@news.kth.se> NNTP-Posting-Host: castor.rm.fccc.edu >Hi, I'm looking for information on amino acids, and there effect >on the body and brain. > >Any hint on where I might find it is welcome. > I have some bookmarks here, I'm not sure if they'll be helpful or not... http://www.chemie.fu-berlin.de/chemistry/bio/amino-acids.html http://128.122.10.5/aainfo/contents.htm Any biochemistry textbook should prove quite helpful... Or perhaps a nutrition textbook, if you're interested in their biological effects. -- -- Mike S. (M_Sauder@fccc.edu) www.fccc.edu/research/labs/roder/mike.html From owner-proteins@net.bio.net Mon Apr 01 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!news.kth.se!mars!per-lund From: per-lund@mars.dsv.su.se (Per Lundberg) Newsgroups: bionet.molbio.proteins Subject: Looking for information on amino acids Date: 2 Apr 1996 13:37:20 GMT Organization: Department of Computer and Systems Sciences, Stockholm University and KTH Lines: 9 Message-ID: <4jraig$cmr@news.kth.se> NNTP-Posting-Host: mars.dsv.su.se Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: TIN [version 1.2 PL2] Hi, I'm looking for information on amino acids, and there effect on the body and brain. Any hint on where I might find it is welcome. Thanks. From owner-proteins@net.bio.net Mon Apr 01 23:00:00 1996 Path: biosci!ns1.faseb.org!lamarck.sura.net!newsfeed.internetmci.com!uwm.edu!lll-winken.llnl.gov!nntp.coast.net!swidir.switch.ch!scsing.switch.ch!rzunews.unizh.ch!NewsWatcher!user From: hubscher@vetbio.unizh.ch (Ulrich Hubscher) Newsgroups: bionet.molbio.methds-reagnts,bionet.general,bionet.genome.chromosomes,bionet.molbio.proteins,bionet.molbio.yeast,bionet.virology,bionet.molbio.recombination Subject: ANNOUNCE: EMBO Workshop on Molecular Biology of DNA Replication Date: Tue, 02 Apr 1996 16:39:07 +0100 Organization: Universitat Zurich-Irchel Lines: 46 Message-ID: NNTP-Posting-Host: 130.60.120.18 Xref: biosci bionet.molbio.methds-reagnts:42570 bionet.general:20910 bionet.genome.chromosomes:1104 bionet.molbio.proteins:7493 bionet.molbio.yeast:5039 bionet.virology:6861 bionet.molbio.recombination:153 EMBO WORKSHOP: MOLECULAR BIOLOGY OF DNA REPLICATION September 8 - 13, 1996 Weggis (Luzern), Switzerland Organizers: U. Hubscher, Zurich P. Plevani, Milano S. Spadari, Pavia The main topics which will be covered are: Regulatory mechanisms controlling entry into S-phase; replisome assembly and its functional organization within the nucleus; protein-protein interactions among replication proteins; structural organization of the replisome; connection between DNA replication and other DNA transactions (e.g. repair, transcription). Keynote address: Bruce Stillman Cold Spring Harbor Laboratory New York, USA The registration fee of CHF 850. includes all meals, lodging and social events. A certain amount of the budget will be reserved to partially refund the registration fee to young applicants. Appllcations contalnlng one page abstract shoud be sent as soon as possible but not later than May 31st, 1996 to: EMBO WORKSHOP 96: Universitat Zurich-lrchel, Institut fur Veterlnarbiochemie Winterthurerstrasse 190 CH-8057 Zurich, Switzerland _____________________________________________________________________ Ulrich Hubscher Institut fur Veterinarbiochemie Tel: (41-1)-257-54-72 Universitat Zurich-Irchel Fax: (41-1)-257 59 04 Winterthurerstrasse 190 CH-8057 Zurich Switzerland _____________________________________________________________________ From owner-proteins@net.bio.net Tue Apr 02 23:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!swrinde!newsfeed.internetmci.com!in2.uu.net!news.cais.net!nntp.uio.no!nntp.uib.no!nntp-bergen.UNINETT.no!nntp-trd.UNINETT.no!daresbury!not-for-mail From: "Lennart Nilsson (Karolinska institutet)" Newsgroups: bionet.molbio.proteins Subject: ANNOUNCEMENT: Understanding Protein Structure Determination Date: 3 Apr 1996 12:19:33 +0100 Lines: 28 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4jtms5$hs6@mserv1.dl.ac.uk> X-Mts: smtp Original-To: pdb-l@pdb.pdb.bnl.gov, bioforum@dl.ac.uk, bionews@dl.ac.uk, biophys@dl.ac.uk, bio-soft@dl.ac.uk, comp-bio@dl.ac.uk, methods@dl.ac.uk, molmodel@dl.ac.uk, proteins@dl.ac.uk, xtal-log@dl.ac.uk, str-nmr@dl.ac.uk Posted-Date: Wed, 03 Apr 96 13:18:43 +0200 The Karolinska Institute's Center for Structural Biochemistry will hold its 6th summer school, entitled "Understanding Protein Structure Determination" on September 1-6, 1996. This is one of a series of short graduate courses organized each summer by the Summer University of Southern Stockholm at NOVUM Research Park, located about 15 km south of Stockholm. As usual we are aiming for an informal format with students on the graduate and postdoc levels. A fair amount of time will be set aside for discussions and social activities. The topic of the 1996 summer school is intended to cover the two major protein structure determination techniques: X-ray crystallography and NMR spectroscopy. Topics such as the physical basis, experimental aspects, computational and software aspects, quality assessment of determined structures, and effects of structural heterogeneity and dynamics will be addressed. Emphasis will be put on the complementarity of the two techniques. Course fee: SEK 2500 (academic), SEK 5000 (non academic) Deadlines: Application June 14, 1996; poster abstract August 2, 1996. For further information/application forms please contact Ms. Aila Holappa at FAX +46-8-608 9290 or e-mail Aila.Holappa@cbt.ki.se More information is available at http://www.csb.ki.se/events/summer96.html Organizing committee: Hans Hebert, Torleif Hard, Rudolf Ladenstein, Lennart Nilsson From owner-proteins@net.bio.net Tue Apr 02 23:00:00 1996 Path: biosci!rutgers!news.iag.net!news.math.psu.edu!psuvax1!uwm.edu!lll-winken.llnl.gov!enews.sgi.com!sgigate.sgi.com!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!torn!resunix.ri.sickkids.on.ca!news From: Randall Willis Newsgroups: bionet.molbio.proteins Subject: Re: protein clustering Date: 3 Apr 1996 14:16:44 GMT Organization: The Hospital for Sick Children Lines: 18 Message-ID: <4ju18c$blf@resunix.ri.sickkids.on.ca> References: <9604032210.AA08245@IRIS.lsc.pku.edu.cn> NNTP-Posting-Host: resunix.ri.sickkids.on.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) To: lisl@IRIS.LSC.PKU.EDU.CN X-URL: news:9604032210.AA08245@IRIS.lsc.pku.edu.cn Songlin, It may be possible to use gel filtration to determine the aggregate state of your protein although it would require a resin with a really high molecular weight window. As well, I suspect that it will be difficult to find the appropriate molecular weight markers to calibrate the column and allow you to determine the complexation state. Good luck. Randall C Willis, Aliquotes Press "ALIQUOTES: A Journal of Molecular and Biochemical Humour" 58 Balfour Ave. Toronto, ON M4C 1T6 CANADA rogerb@microsoft.com willis@gandalf.psf.sickkids.on.ca From owner-proteins@net.bio.net Tue Apr 02 23:00:00 1996 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!news.ox.ac.uk!news From: "Simon M. Brocklehurst" Newsgroups: bionet.molbio.proteins Subject: Re: Secondary structure assignments Date: Wed, 03 Apr 1996 12:42:19 +0100 Organization: University of Oxford Lines: 46 Message-ID: <3162641B.41C67EA6@bioch.ox.ac.uk> References: <4jqoj8$rcj@mars.mahidol.ac.th> NNTP-Posting-Host: nmrv.ocms.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (X11; I; SunOS 4.1.3_U1 sun4m) To: Enrique Jose Labadan Frio - SCBC - 3421101 Enrique Jose Labadan Frio - SCBC - 3421101 wrote: > > Dear all, > > I'm in a sort of dilemma as to how best to assign secondary structure > info to some proteins I'm working on. For the same crystal structure, for > example, DSSP (Kabsch and Sander) as implemented under Rasmol breaks up > beta-sheets into sheetlets and helices into small "helixlets" and makes > some betas disappear altogether (very little mainchain Hbonds to start > with!). O's YASSPA (as of 1991 anyway) seems to assign sheets and helices > very liberally in that they span longer stretches than DSSP's. > > Is DSSP's -0.5 kcal/mol Hbond definition the best/ standard criterion for 2o > struc. assignment? Are there any alternative ones one can use? > If you have access to a Silicon Graphics workstation, you can try the secondary structure assignment implemented in NAOMI. Use the commands: use sec_struc table sec_struc It uses a novel fuzzy logic algorithm to make decisions on secondary structural elements. Many people (but of course not everyone ;-) ) in general prefer the secondary structure assignments that NAOMI makes over those made by other methods. More information at the Web site: http://www.ocms.ox.ac.uk/~smb/Software/N_details/naomi.html You can see quite a few examples of the secondary structure assignments that NAOMI makes on the Cytokines Web: http://www.ocms.ox.ac.uk/~smb/cyt_web/ Also, don't forget that making the assignments by eye is in many ways better than using a computer program. _____________________________________________________________________________ | | ,_ o Simon M. Brocklehurst, | / //\, Oxford Centre for Molecular Sciences, Department of Biochemistry, | \>> | University of Oxford, Oxford, UK. | \\, E-mail: smb@bioch.ox.ac.uk | WWW: http://www.ocms.ox.ac.uk/~smb/ |____________________________________________________________________________ From owner-proteins@net.bio.net Tue Apr 02 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!oslonett.no!sn.no!newsfeed.tip.net!peroni.ita.tip.net!news.keyworld.mt!peroni.ita.tip.net!news.vol.it!news From: aitor@mbox.vol.it (Rinaldo) Newsgroups: bionet.molbio.proteins Subject: biochimico / biologo molecolare Date: Tue, 02 Apr 1996 19:17:51 GMT Organization: none Lines: 203 Message-ID: <4jrqu7$rhm@everest.vol.it> Reply-To: aitor@mbox.vol.it NNTP-Posting-Host: volmi16.vol.it X-Newsreader: Forte Free Agent 1.0.82 dott. RINALDO DONI via Guanella, 36 20128 Milano Milano, 1 aprile 1996 Sono un laureato in Scienze Biologiche, mi sto occupando da circa cinque anni di ricerca scientifica nel campo delle malattie neurodegenerative, presso l’unità di neurobiologia dell’Alzheimer, dell’Istituo di ricerche farmacologiche "Mario Negri" di Milano. Attualmente i miei studi si svolgono nei confronti di quelle molecole aventi spiccate attività biologiche in grado comunque, di modulare l’espressione del precursore del peptide b-A4, quale marker biologico dei cervelli Alzheimer. Inoltre le mie ricerche si rivolgo ad un’altra proteina, che si è osservata essere centrale nell’insorgenza di altre forme di neurodegenerazione; tale proteina è la prion protein. Tali patologie sono tornate recentemente alla ribalta con i casi di "Encefalopatia spongiforme bovina" (BSE), conosciuta anche col nome di "Malattia delle vacche pazze", evidenziate in Gran Bretagna. dott. Rinaldo Doni Allego alla presente lettera il mio Curriculum vitae Dr. Rinaldo Doni Nato: a Milano, il giorno 10 settembre 1963 Indirizzo: Via Don Luigi Guanella, 36 - 20128 Milano Tel. e Fax: 02-27003624 (Casa) Tel: 02-39014.462 (Lavoro) e-Mail: aitor@mbox.vol.it CURRICULUM VITAE Titoli di studio: Istituto tecnico agrario statale di Limbiate (MI) dal 1977 al 1982 Diploma di maturità agraria Iscritto all’Albo dei Periti Agrari della provincia di Milano dal 1988 Università degli studi di Milano dal 1988 al 1994 Facoltà di scienze matematiche, fisiche e naturali corso di Laurea in scienze biologiche indirizzo biochimico e biologico molecolare voto: 104/110 Titolo della Tesi di Laurea: Proteina PrP e astrogliosi nelle encefalopatie spongiformi: studi "in vivo" e "in vitro". Tirocinio: Tirocinio svolto presso l’Istituto di ricerche farmacologiche "Mario Negri" di Milano. Laboratorio di Neurobiologia dell’Alzheimer, diretto dal dott. Gianluigi Forloni. Lingue straniere conosciute: Spagnolo ottimo scritto e parlato Inglese discreto parlato sufficiente scritto Francese discreto parlato sufficiente scritto Esperienze professionali: · Dal 15 maggio 1990 al 31 ottobre 1990 Università degli studi di Milano Fac. di scienze Matematiche, Fisiche e Naturali Dip. Genetica e biologia dei microrganismi Prof. Gianfranco Badaracco Lavoro svolto: Determinazione della sequenza nucleotidica ed aminoacidica della Topoisomerasi I di Artemia salina. · Dal 1°novembre 1990 al 31 novembre 1991 Università degli studi di Milano Fac. di Medicina Veterinaria Dip. di Microbiologia ed Immunologia Prof. Giorgio Poli Lavoro svolto: Determinazione della presenza della proteina Prion "scrapie-infettiva" in animali da laboratorio e da reddito. · Dal 1°dicembre 1991 ad oggi. Istituto di ricerche farmacologiche "Mario Negri" di Milano Unità di Neurobiologia dell’Alzheimer Dott. Gianluigi Forloni Lavoro svolto: Studi e caratterizzazione della proteina Prion "in vivo" e "in vitro", riguardo agli effetti svolti sulle cellule astrogliali e neuronali. Determinazione delle proprietà biologiche dei peptidi corrispondenti a sequenze della PrP; in particolare i miei studi si sono rivolti nei confronti del peptide PrP106-126. Studi "in vivo" e "in vitro" sulla modulazione dell’espressione del precursore della b-proteina (Alzheimer), dopo trattamenti con molecole aventi diverse attività biologiche. · ABSTRACTS E PUBBLICAZIONI: Dall’Ara P., Bonizzi L., Ceccarelli A., Doni R. & Poli G. (1991) Western blotting in PrPsc detection. Atti della società italiana delle scienze veterinarie, Vol XLV; pag. 1035 Dall’Ara P., Cattini P., Ceccarelli A., Doni R. & Poli G. (1992) Immunodiagnostica delle encefalopatie spongiformi: prospettive per un'applicazione della tecnica Western blotting alla BSE. Atti della Società Italiana di Buiatria, XXIV, San Benedetto del Tronto (AP), 22 e 24 maggio 1992, pg. 527. Bugiani O., Del Bo R., Angeretti N., Chiesa R., Smiroldo S., Doni R., Ghibaudi M., Salmona M., Porro M., Verga L., Giaccone F., Tagliavini F. & Forloni G. A neurotoxic prion protein fragment induces hypertrophy and proliferation of astroglial cells in vitro. Clinical neuropathology; Number 3 - May/June 1994 - vol.13 Forloni G., Del Bo R., Angeretti N., Chiesa R., Smiroldo S., Doni R., Ghibaudi E., Salmona M., Porro M., Verga L., Giaccone G., Bugiani O. & Tagliavini F. A neurotoxic prion protein fragment induces rat astroglial proliferation and hipertrophy. Europ. Journ. of Neurosc., (1994) vol 6, pp. 1415-1422 Preferenze: · Lavoro di ricerca e di sviluppo. · Disposto al trasferimento in uno dei paesi della CEE. Informazioni generali: · Obblighi di leva, assolti. · Celibe. · In possesso della patente di guida tipo B. · Buona conoscenza nel campo dell’informatica, sistemi usati : DOS, WINDOWS, OS/2, MacIntosh e relative applicazioni; come ad esempio: Word processors, Fogli elettronici, Data base e HTML editor (URL=http://www.ecs.net/golf/ - http://www.ecs.net/clamps/). Posseggo inoltre nozioni, nel campo della programmazione: Basic e Visual basic. From owner-proteins@net.bio.net Tue Apr 02 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!uwm.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!martinlab From: klenchin@macc.wisc.edu (Dima Klenchin) Newsgroups: bionet.molbio.proteins Subject: Re: protein clustering Date: Wed, 03 Apr 96 17:48:41 GMT Organization: UW-Madison Lines: 15 Message-ID: <4judlp$9pg_001@biochem.wisc.edu> References: <9604032210.AA08245@IRIS.lsc.pku.edu.cn> NNTP-Posting-Host: martinlab.biochem.wisc.edu X-Newsreader: News Xpress Version 1.0 Beta #4 In article <9604032210.AA08245@IRIS.lsc.pku.edu.cn>, lisl@IRIS.LSC.PKU.EDU.CN (Li Songlin) wrote: -> ->Dear all, -> ->I am a crystallographer. I have a high concentration protein sample. ->(>30 mg/ml). In my recent work, it is suspected that ten or more ->molecules of this kind of protein form a cluster. It should be checked ->by experiment. Could you please show me some methods that could be used ->to check my suspection? Gel filtration and density gradient. - Dima From owner-proteins@net.bio.net Tue Apr 02 23:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!news.belnet.be!swsbe6.switch.ch!scsing.switch.ch!news.belwue.de!news.uni-stuttgart.de!rz.uni-karlsruhe.de!news.urz.uni-heidelberg.de!usenet From: th.neumann@DKFZ-Heidelberg.de (Th.Neumann) Newsgroups: bionet.virology,bionet.molbio.proteins.fluorescent,bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: Searching for a CAT antibody ! Date: 3 Apr 1996 16:50:10 GMT Organization: DKFZ Lines: 11 Message-ID: <4jua82$kai@sun0.urz.uni-heidelberg.de> Reply-To: th.neumann@dkfz-heidelberg.de NNTP-Posting-Host: atv-pc22.inet.dkfz-heidelberg.de X-Newsreader: WinVN 0.92.6+ Xref: biosci bionet.virology:6867 bionet.molbio.proteins.fluorescent:387 bionet.molbio.proteins:7504 bionet.molbio.methds-reagnts:42629 Hello, I´m searching for a CAT (chloramphenicol-acetyltransferase) antibody for immunofluorescence staining of cells. If anyone out there can help me or knows a source for a CAT antibody, please e-mail me (th.neumann@dkfz-heidelberg.de) Thanks, Thomas From owner-proteins@net.bio.net Tue Apr 02 23:00:00 1996 Path: biosci!bloom-beacon.mit.edu!panix!netaxs.com!news2.cais.net!news.cais.net!chi-news.cic.net!news.compuserve.com!news.production.compuserve.com!news From: Greg LaRosa <72541.220@CompuServe.COM> Newsgroups: bionet.molbio.proteins,bionet.molbio.proteins.7tms_r Subject: GPCR Expression and Membrane Preps Date: 4 Apr 1996 05:29:06 GMT Organization: LeukoSite, Inc. Lines: 15 Message-ID: <4jvmn3$3d4$1@mhafn.production.compuserve.com> Xref: biosci bionet.molbio.proteins:7507 bionet.molbio.proteins.7tms_r:688 Anyone have any experience with improving poor surface expression of cloned GPCR in transfected cells? Also any ideas for making membrane preps for radioligand binding assays. I have been working with a receptor for which I have not been able to membrane preps that retain the binding activity of the intact cells; eventhough the same membrane isolation procedure (hypotonic lysis in hte presence of protease inhibitors, followed by a low speed cent.to remove unlysed cells and large debris, and then membrane harvesting by high speed cent.) has worked well for a number of other GPCR in my hands. Any thoughts appreciated -- Greg LaRosa From owner-proteins@net.bio.net Wed Apr 03 23:00:00 1996 Path: biosci!agate!usenet From: abbas@mendel.berkeley.edu (Alex Abbas) Newsgroups: bionet.software,bionet.molbio.proteins Subject: Antigenicity Prediction Software? Date: 4 Apr 1996 17:51:52 GMT Organization: U.C. Berkeley Lines: 10 Message-ID: <4k127o$21p@agate.berkeley.edu> NNTP-Posting-Host: bark2mac30.berkeley.edu X-Posted-From: InterNews 1.0.6@bark2mac30.berkeley.edu X-Authenticated: abbas on POP host mendel.berkeley.edu Xref: biosci bionet.software:15166 bionet.molbio.proteins:7512 I'm looking for mac software to generate theoretical predictions of the antigenicity of regions along a protein sequence... I'm trying to figure out what peptide to try to raise antibodies against. If anyone knows of anything, please drop me a line. Thanks in advance, Alex Alex Abbas http://mendel.berkeley.edu/~abbas/ From owner-proteins@net.bio.net Wed Apr 03 23:00:00 1996 Path: biosci!rutgers!uwm.edu!math.ohio-state.edu!jussieu.fr!citi2.fr!news From: federici Newsgroups: bionet.molbio.proteins,sci.bio.food-science Subject: Re: BSE - prion heat resistance Date: 4 Apr 1996 10:59:00 GMT Organization: CITI2 - Universite Rene Descartes, Paris Lines: 6 Message-ID: <4k0a1k$9dq@bisance.citi2.fr> References: <4jgjnf$iu0@hermes.is.co.za> <316013A3.2F52@nzdri.org.nz> <4jnddd$jpn@agate.berkeley.edu> NNTP-Posting-Host: federici.cochin.inserm.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) To: lhom@nature.berkeley.edu X-URL: news:4jnddd$jpn@agate.berkeley.edu Xref: biosci bionet.molbio.proteins:7509 sci.bio.food-science:2240 lyophilisation is not heating; water is eliminated using low pressure. Concerning the use of solvents, this procedure can drive to denaturation, but not in all cases. For instance, it happens that activity of enzyme is increased in the presence of a solvent! From owner-proteins@net.bio.net Wed Apr 03 23:00:00 1996 Newsgroups: bionet.molbio.proteins Path: biosci!rutgers!uwm.edu!cs.utexas.edu!news.sprintlink.net!rockyd!notes From: Sabine Hilfiker Subject: Wanted: Schoenmakers Chelator program X-Nntp-Posting-Host: buxgateway-pc.rockefeller.edu Content-Type: text/plain; charset=us-ascii Message-ID: <31647982.381@rockvax.rockefeller.edu> Sender: notes@rockyd.rockefeller.edu (News Administrator) Content-Transfer-Encoding: 7bit Organization: Rockefeller University Mime-Version: 1.0 Date: Fri, 5 Apr 1996 01:38:10 GMT X-Mailer: Mozilla 2.0 (Win16; I) Lines: 11 I'm looking for a program to calculate free calcium concentrations in the low micromolar range. Would like to have the one from Schoenmakers published in BioTechniques a few years ago. Sabine Hilfiker Lab. of Molecular and Cellular Neuroscience The Rockefeller University 1230 York Avenue New York, NY 10021 e-mail: hilfiks@rockvax.rockefeller.edu From owner-proteins@net.bio.net Wed Apr 03 23:00:00 1996 Newsgroups: bionet.molbio.proteins Path: biosci!agate!howland.reston.ans.net!Germany.EU.net!ieunet!news.tcd.ie!vax1.tcd.ie!abell From: abell@vax1.tcd.ie Subject: Dan L. Sackett Message-ID: <1996Apr4.161847@vax1.tcd.ie> Sender: usenet@news.tcd.ie (TCD News System ) Organization: Trinity College Dublin Date: Thu, 4 Apr 1996 15:18:47 GMT Lines: 10 Does anyone have a current postal or Email address for Dr. Dan L. Sackett, formerly of the Laboratory of Biochemical Pharmacology, National Institute of Diabetes and Digestive & Kidney Diseases, NIH? Angus Bell Trinity College Dublin abell@mail.tcd.ie From owner-proteins@net.bio.net Wed Apr 03 23:00:00 1996 Path: biosci!agate!usenet.ins.cwru.edu!gatech!swrinde!cs.utexas.edu!howland.reston.ans.net!math.ohio-state.edu!news.cis.ohio-state.edu!magnus.acs.ohio-state.edu!lerc.nasa.gov!purdue!oitnews.harvard.edu!news.dfci.harvard.edu!usenet From: milstone Newsgroups: bionet.virology,bionet.molbio.proteins.fluorescent,bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: Re: Searching for a CAT antibody ! Date: 4 Apr 1996 14:37:38 GMT Organization: Brigham & Women's Hospital/Harvard Medical School Lines: 15 Message-ID: <4k0mri$fn@netman-mel.dfci.harvard.edu> References: <4jua82$kai@sun0.urz.uni-heidelberg.de> NNTP-Posting-Host: 134.174.88.145 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) X-URL: news:4jua82$kai@sun0.urz.uni-heidelberg.de Xref: biosci bionet.virology:6876 bionet.molbio.proteins.fluorescent:394 bionet.molbio.proteins:7511 bionet.molbio.methds-reagnts:42699 As of several years ago, the only available anti-CAT antibodies were problematic, at best. Positive staining required very high levels of CAT protein, especially compared to the low levels detectable by the enzymatic assay for CAT. There was, and may still be, a commercial source for these Abs. My impression is that, unless you are absolutely committed to visualizing CAT as a reporter gene product (e.g., you must analyze irreplaceable samples from previous experiments performed with CAT), that you will be much better off switching to another reporter, such as luciferase (Abs are available) or beta-galactosidase (Abs are available & histocheimstry is easy), which is more easily localized. This is true even if you must repeat a some experiments. --Dave From owner-proteins@net.bio.net Wed Apr 03 23:00:00 1996 Path: biosci!rutgers!csn!news-1.csn.net!imci3!imci4!newsfeed.internetmci.com!howland.reston.ans.net!torn!resunix.ri.sickkids.on.ca!news From: Randall Willis Newsgroups: bionet.molbio.proteins Subject: Re: EGFr Abs? Date: 4 Apr 1996 14:11:55 GMT Organization: The Hospital for Sick Children Lines: 23 Message-ID: <4k0lbb$6l9@resunix.ri.sickkids.on.ca> References: <4jvt6i$kmj@ccshst05.cs.uoguelph.ca> NNTP-Posting-Host: resunix.ri.sickkids.on.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) To: jvrobert@uoguelph.ca X-URL: news:4jvt6i$kmj@ccshst05.cs.uoguelph.ca Jen, Yes, Oncogene Science sells antibodies against EGFR. They can be found at: 106 Charles Lindbergh Blvd. Uniondale, NY USA 11553-3649 1-800-662-2616 or, they are handled in Canada by: Cedarlane Laboratories Hornby, ON 1-800-268-5058 I've used the anti-EGFR Ab and they work quite well. Good luck...Randall C Willis, Aliquotes Press "ALIQUOTES: A Journal of Molecular and Biochemical Humour" 58 Balfour Ave. Toronto, ON M4C 1T6 CANADA rogerb@microsoft.com willis@gandalf.psf.sickkids.on.ca From owner-proteins@net.bio.net Wed Apr 03 23:00:00 1996 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!howland.reston.ans.net!torn!ccshst05.cs.uoguelph.ca!ccshst01!jvrobert From: jvrobert@uoguelph.ca (Jennifer V Robertson) Newsgroups: bionet.molbio.proteins Subject: EGFr Abs? Date: 4 Apr 1996 07:19:46 GMT Organization: University of Guelph Lines: 5 Message-ID: <4jvt6i$kmj@ccshst05.cs.uoguelph.ca> NNTP-Posting-Host: ccshst01.cs.uoguelph.ca X-Newsreader: TIN [version 1.2 PL2] Anyone know where I can get some? Jen :) From owner-proteins@net.bio.net Thu Apr 04 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!newsfeed.sunet.se!news00.sunet.se!sunic!mn6.swip.net!plug.news.pipex.net!pipex!tank.news.pipex.net!pipex!newsfeed.internetmci.com!news.internetMCI.com!darwin.sura.net!blaze.cs.jhu.edu!RacerX.mse.jhu.edu!news.jhu.edu!welchlink.welch.jhu.edu!lilu From: LI LU Newsgroups: bionet.molbio.proteins Subject: Re: Protein Modelling Freeware: new PPC version Date: Fri, 5 Apr 1996 16:40:07 -0500 Organization: HCF - Johns Hopkins University, Baltimore, Maryland, USA Lines: 1 Message-ID: References: NNTP-Posting-Host: 128.220.59.78 Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: Do you have the new PPC version for MS-Windows (Windows 3.1 or Windows 95)? From owner-proteins@net.bio.net Thu Apr 04 23:00:00 1996 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!howland.reston.ans.net!news-e2a.gnn.com!newstf01.news.aol.com!newsbf02.news.aol.com!not-for-mail From: sponnangat@aol.com (SPonnangat) Newsgroups: bionet.molbio.proteins Subject: Site/Resource on KinaseC Date: 5 Apr 1996 11:55:03 -0500 Organization: America Online, Inc. (1-800-827-6364) Lines: 3 Sender: root@newsbf02.news.aol.com Message-ID: <4k3j97$fvm@newsbf02.news.aol.com> Reply-To: sponnangat@aol.com (SPonnangat) NNTP-Posting-Host: newsbf02.mail.aol.com Could anybody point to me about a site/resource on KinaseC ? Thanks in advance. My email address is SPonnangat@aol.com From owner-proteins@net.bio.net Thu Apr 04 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!newsfeed.sunet.se!news00.sunet.se!sunic!news.sprintlink.net!usenet.kornet.nm.kr!news.kreonet.re.kr!news.nuri.net!imci2!news.internetMCI.com!newsfeed.internetmci.com!in2.uu.net!ftpbox!newsfeed.acns.nwu.edu!news.cc.uic.edu!usenet From: Keld Sorensen Newsgroups: bionet.molbio.proteins Subject: Re: Dan L. Sackett Date: 4 Apr 1996 18:17:57 GMT Organization: Univ. Illinois / College of Med. Lines: 8 Message-ID: <4k13ol$qaq@piglet.cc.uic.edu> References: <1996Apr4.161847@vax1.tcd.ie> NNTP-Posting-Host: sliprock-01.dialin.uic.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) To: abell@vax1.tcd.ie X-URL: news:1996Apr4.161847@vax1.tcd.ie Did you check the NIH home page which has a directory. Did you check any of the search engines ALTA VISTA actually seems to be very good at finding people, and http://four11.com From owner-proteins@net.bio.net Thu Apr 04 23:00:00 1996 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!news.cis.okstate.edu!newsfeed.ksu.ksu.edu!news.mid.net!newsfeeder.gi.net!newsfeed.internetmci.com!howland.reston.ans.net!torn!uunet.ca!news.uunet.ca!rcogate.rco.qc.ca!altitude!usenet From: Achim Recktenwald Newsgroups: bionet.molbio.proteins Subject: Re: "mystery bands" in SDS-PAGE Date: Wed, 03 Apr 1996 16:46:13 -0500 Organization: IBEX Technologies, Inc. Lines: 37 Message-ID: <3162F1A5.6152@ibex.ca> References: <315AF4DF.73AA@acs.ucalgary.ca> <4jfo4p$3spa@yuma.ACNS.ColoState.EDU> NNTP-Posting-Host: ibex.hip.cam.org Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Macintosh; I; PPC) Stephen R. Decker wrote: > > Fiona, > > I have seen this fairly frequently, most notably when silver staining. The > usual causes are: > > 1. Using glass bottles to store buffers and reagents. Protein sticks to glass > and slowly goes into these solutions. Old serum bottles are notorious for > this. If you must use glass, clean extremely well and soak in dilute NaOH, > then rinse well. > > 2. Not wearing gloves when handling the system. > > Try loading a lane with just loading buffer and run the gel. It will tell you > if the problem is in the Laemmli. Also, if you use a stacking gel, run one > without it. Problem could be in stacking gel buffer. It probably is not in > the resolving gel buffer, since the proteins would be uniformly spread > throughout it, ditto for tank buffer. > > Good Luck, let us know how it turns out. > > Steve Decker Some other possibilities: If you are using the big bags with Eppendorf tubes and everybody is rummaging through them, without using gloves, to get some tubes, it is very easy to contaminate the tubes with skin proteins. Your beta-mercaptoethanol might be too old. If its color is yellow, discard it. Prepare the stock of sample buffer without bromphenolblue; only add it to a small portion just before use. Achim From owner-proteins@net.bio.net Thu Apr 04 23:00:00 1996 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!warwick!news.nott.ac.uk!griffin.nott.ac.uk!usenet From: Ian Goodfellow Newsgroups: bionet.molbio.proteins Subject: TESTING Date: 31 Mar 1996 15:15:02 GMT Organization: Cripps Computing Centre, The University of Nottingham Lines: 3 Message-ID: <4jm7hm$agn@griffin.ccc.nottingham.ac.uk> NNTP-Posting-Host: ppbbmz.nottingham.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) X-URL: news:bionet.molbio.proteins tesing From owner-proteins@net.bio.net Thu Apr 04 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!newsfeed.sunet.se!news00.sunet.se!sunic!mn6.swip.net!plug.news.pipex.net!pipex!tank.news.pipex.net!pipex!newsfeed.internetmci.com!news.internetMCI.com!darwin.sura.net!blaze.cs.jhu.edu!RacerX.mse.jhu.edu!news.jhu.edu!welchlink.welch.jhu.edu!lilu From: LI LU Newsgroups: bionet.molbio.proteins,bionet.software,bionet.molbio.proteins,bionet.cellbiol Subject: Phosphorylation sites Date: Fri, 5 Apr 1996 16:22:50 -0500 Organization: HCF - Johns Hopkins University, Baltimore, Maryland, USA Lines: 5 Message-ID: References: NNTP-Posting-Host: 128.220.59.78 Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: Xref: biosci bionet.molbio.proteins:7518 bionet.software:15178 bionet.cellbiol:4448 Hi, there. I'd like to ask where can I find a list or o program to search for phosphoylation site in a protein sequence, by different kinases. Any ftp site or web site are welcome. Thanks a lot. Please reply to my email address: lilu@welchlink.welch.jhu.edu From owner-proteins@net.bio.net Thu Apr 04 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!swrinde!newsfeed.internetmci.com!csn!news-1.csn.net!carbon!hermes.cair.du.edu!usenet From: dbovee@du.edu (D. Bovee) Newsgroups: bionet.molbio.proteins,bionet.biophysics Subject: ATP Fluorescence Date: Sat, 06 Apr 1996 00:10:05 GMT Organization: University of Denver Lines: 16 Message-ID: <4k4f1h$1es@hermes.cair.du.edu> NNTP-Posting-Host: sl-14.ducomm.du.edu Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit X-Newsreader: Forte Free Agent 1.0.82 Xref: biosci bionet.molbio.proteins:7521 bionet.biophysics:1848 Fellow biochemists/biophysicists, I am working on a problem involving a UV fluorescence assay for NADH. However, one of the substrates in my reaction mixture is ATP, which also, as I understand, has a UV fluorescence spectrum. I am in search of data regarding that ATP fluorescence spectrum. If you have any knowledge of what paper might have the data (my lit searches has thus far been unsuccessful) or if you yourself have any information, I would greatly appreciate your help. Please copy your replies to e-mail. Many thanks! =========================================\ A Priori Solutions \ David Bovee Web and Graphics Development \ dbovee@du.edu Knowledge Transfer Systems \ (303) 730-9950 http://www.du.edu/~dbovee/apriori/home.html \=============== From owner-proteins@net.bio.net Thu Apr 04 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!gatech!usenet.eel.ufl.edu!warwick!news.nott.ac.uk!griffin.nott.ac.uk!usenet From: Ian Goodfellow Newsgroups: bionet.molbio.proteins Subject: Antibody nightmare!!! Date: 31 Mar 1996 15:32:21 GMT Organization: Cripps Computing Centre, The University of Nottingham Lines: 35 Message-ID: <4jm8i5$agn@griffin.ccc.nottingham.ac.uk> NNTP-Posting-Host: ppbbmz.nottingham.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) X-URL: news:bionet.molbio.proteins Dear all I'm having a nightmare with my antibody production - can anyone help? The story so far is: I over-expressed and purified a GST fusion protein, the fusion is 90KDa with 60 KDa being a bacterial membrane protein. I've injected my bunny and got a test bleed after 4 weeks. I found that the antibody (I used serum) did give a good reaction against the purified fusion protein in a Western blot but I found that it didn't cross-react with the expected protein in whole cell extracts - in fact it reacted with quite a lot of other non-specific proteins. I then tried running just membrane fractions of wild-type and mutant (lacking the gene encoding the protein of interest) strains and got no difference in the cross-reacting bands!! I though that maybe the protein was running at the wrong mol. wt. and was being 'masked' by the non-specific cross-reactign proteins so I preadsorbed the serum with an acetone extract of the mutant. When I then used this preadsorbed serum I got exactly the same profile as I did with just plain serum!! Why are the non-specific antibodies not binding to the acetone extract? I have also tried purifying the antibody by using immobilised fusion protein ie. immobilised on hybond-C, eluting with glycine etc. but this still gives cross-reacting protein of the wrong mol. wt. in both wt. and mutant membrane fractions!! Any hints or tips would be much appreciated - please remeber though that I am a complete novice at this 'antibody purification game' Thanks in advance Ian From owner-proteins@net.bio.net Fri Apr 05 23:00:00 1996 Path: biosci!biosci!not-for-mail From: apweiler@ebi.ac.uk (Rolf Apweiler) Newsgroups: ebi.servers,bionet.general,bionet.molbio.embldatabank,bionet.molbio.proteins,embnet.general Subject: ANNOUNCEMENT: Beta release of TREMBL, a supplement to SWISS-PROT Date: 6 Apr 1996 15:53:05 -0800 Organization: European Bioinformatics Institute (EMBL) - UK Lines: 81 Sender: daemon@net.bio.net Distribution: world Message-ID: Reply-To: apweiler@ebi.ac.uk (Rolf Apweiler) NNTP-Posting-Host: net.bio.net Xref: biosci bionet.general:20998 bionet.molbio.embldatabank:624 bionet.molbio.proteins:7526 The Beta release of TREMBL, a protein sequence database supplementing the SWISS-PROT Protein Sequence Data Bank is now available from ftp.ebi.ac.uk in directory /pub/databases/trembl. INTRODUCTION ============ TREMBL is a protein sequence database supplementing the SWISS-PROT Protein Sequence Data Bank. TREMBL contains the translations of all coding sequences (CDS) present in the EMBL Nucleotide Sequence Database not integrated in SWISS-PROT. At the moment we treat TREMBL as an independent dataset in SWISS-PROT format, but shortly TREMBL will become a part of SWISS-PROT. BETA RELEASE OF TREMBL ====================== This TREMBL release is created from the EMBL nucleotide sequence release 46 and contains 98'447 sequence entries, comprising 25'879'831 amino acids. TREMBL is split in two main sections; SP-TREMBL and REM-TREMBL: SP-TREMBL (SWISS-PROT TREMBL) contains the entries (81'861) which should be incorporated into SWISS-PROT. SP-TREMBL is partially redundant against SWISS-PROT, since approximately 40'000 SP-TREMBL entries are only additional sequence reports of proteins already in SWISS-PROT. We will try to merge these sequence reports as fast as possible with the already existing SWISS-PROT entries for these proteins, so as to make SWISS-PROT and TREMBL completely nonredundant. SP-TREMBL is organized in subsections: fun.dat (Fungi): 3772 entries inv.dat (Invertebrates): 9689 entries mam.dat (Other Mammals): 1907 entries mhc.dat (MHC proteins): 2007 entries org.dat (Organelles): 5241 entries phg.dat (Bacteriophages): 939 entries Pln.dat (Plants): 5294 entries pri.dat (Primates): 6425 entries pro.dat (Prokaryotes): 15645 entries rod.dat (Rodents): 5837 entries unc.dat (Unclassified): 201 entries vrl.dat (Viruses): 22677 entries vrt.dat (Other Vertebrates): 2227 entries REM-TREMBL (REMaining TREMBL) contains the entries (16'586) that we do not want to include in SWISS-PROT. ACCESS/DATA DISTRIBUTION ======================== FTP server: ftp.ebi.ac.uk/pub/databases/trembl TREMBL is also available on the SWISS-PROT CD-ROM. TREMBL HAS BEEN PREPARED BY: ============================ Rolf Apweiler, Alain Gateau, Vivien Junker, Fiona Lang, and Claire O'Donovan at the EMBL Outstation - European Bioinformatics Institute (EBI) in Hinxton; Amos Bairoch at the Medical Biochemistry Department of the University of Geneva. ======================================================================= Rolf Apweiler | Email:apweiler@ebi.ac.uk EBI - European Bioinformatics Institute | URL: http://www.ebi.ac.uk Wellcome Trust Genome Campus, Hinxton | Tel: +44 (1223) 494435 Cambridge CB10 1RQ, UK | Fax: +44 (1223) 494968 ======================================================================== From owner-proteins@net.bio.net Fri Apr 05 23:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!news.belnet.be!swsbe6.switch.ch!scsing.switch.ch!news.belwue.de!news.uni-stuttgart.de!uni-regensburg.de!lrz-muenchen.de!informatik.tu-muenchen.de!Germany.EU.net!howland.reston.ans.net!surfnet.nl!ruu.nl!cble46.chem.ruu.nl!user From: f.s.wouters@chem.ruu.nl (fred wouters) Newsgroups: bionet.molbio.proteins Subject: HELP:lipid substrates Date: Sat, 06 Apr 1996 14:44:58 +0100 Organization: ruu Lines: 17 Message-ID: NNTP-Posting-Host: cble46.chem.ruu.nl X-Newsreader: Yet Another NewsWatcher 2.1.8 Hi everybody, We are working on developing a branched chain thiolase enzyme assay to test patients with peroxisomal beta-oxidation disorders. One of the main problems is that the substrates are usually not commercially avaiable...so we have to make them ourselves. Normally this is not a very big problem, but in this case we cannot even find a suitable compound to start the synthesis with: does anyone know which obscure company makes 3-oxo-fatty acid derivatives? We are especially interested in 3-oxo-pristanic acid. Please help, thanx in advance, Fred From owner-proteins@net.bio.net Fri Apr 05 23:00:00 1996 Path: biosci!TAMU.EDU!d-stair From: d-stair@TAMU.EDU (David Stair) Newsgroups: bionet.molbio.proteins Subject: Lane Background Date: 6 Apr 1996 14:52:09 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 26 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hello, I am in need of some help. I have too much stain background in the sample lanes of my PAGE gels. I am working on plasma membrane proteins from basal tiller tissue of forage grasses. I have isolated the PM and separated the integral and peripheral proteins with a .25 M KCl wash. Samples are washed to remove the salt and solubilized in 10% sucrose, 1% SDS, 50 mM Tris-HCl pH 7.2, 1 mM EDTA and 1 mM PMSF. Samples are in 10 % sucrose, 2% SDS, 50 mM Tris-HCl pH 7.2, 1mM EDTA, 1mM PMSF, and 40 mM DTT when loaded onto gels. On 10 % gels these samples have a lot of uniform background staining only in the sample lanes, mostly in the 10 - 150 kDa range. The molecular weight markers have no background and the gel itself has no background (not visibly noticeable). It seems that when the same samples are run through 2-D methodology this heavy background comes out in the acidic end of the IEF gel and then stain the entire depth of the second dimension gel. I have exhausted all ideas, mine and others, here, and any help would be greatly appreciated. David Stair d-stair@tamu.edu From owner-proteins@net.bio.net Sat Apr 06 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!news.cis.okstate.edu!newsfeed.ksu.ksu.edu!news.physics.uiowa.edu!news.uiowa.edu!black.weeg.uiowa.edu!akumar From: "A. Kumar" Newsgroups: bionet.molbio.proteins Subject: sequencing from blots Date: Sun, 7 Apr 1996 15:47:25 -0500 Organization: University of Iowa, Iowa City, IA, USA Lines: 22 Distribution: world Message-ID: NNTP-Posting-Host: black.weeg.uiowa.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: akumar@black.weeg.uiowa.edu Hi ! I need to sequence some proteins from PVDF blots of 2D gels. Is there a company or a University facility that can do this for me ? Kindly post a response or email me. Thanks. Ashish WORKPLACE DEN Dept. of Anatomy, 735 Michael St. Apt 34 College of Medicine, Iowa City University of Iowa, IA 52246-5523 Iowa City, IA 52242 Dial (319)335-7739 (319)338-0529 e : akumar@blue.weeg.uiowa.edu From owner-proteins@net.bio.net Sat Apr 06 23:00:00 1996 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!cs.utexas.edu!howland.reston.ans.net!gatech!newsfeed.internetmci.com!in1.uu.net!brighton.openmarket.com!decwrl!tribune.usask.ca!rover.ucs.ualberta.ca!ts3-port25.mas.ualberta.ca!wgallin From: wgallin@gpu.srv.ualberta.ca (Warren Gallin) Newsgroups: bionet.molbio.proteins Subject: Re: Antibody nightmare!!! Date: Mon, 8 Apr 96 02:59:32 GMT Organization: University of Alberta Lines: 67 Message-ID: References: <4jm8i5$agn@griffin.ccc.nottingham.ac.uk> NNTP-Posting-Host: ts3-port25.mas.ualberta.ca X-Newsreader: VersaTerm Link v1.1.4 In Article <4jm8i5$agn@griffin.ccc.nottingham.ac.uk>, Ian Goodfellow wrote: >Dear all > >I'm having a nightmare with my antibody production - can anyone help? >The story so far is: > >I over-expressed and purified a GST fusion protein, the fusion is 90KDa >with 60 KDa being a bacterial membrane protein. I've injected my bunny >and got a test bleed after 4 weeks. I found that the antibody (I used >serum) did give a good reaction against the purified fusion protein in a >Western blot but I found that it didn't cross-react with the expected >protein in whole cell extracts - in fact it reacted with quite a lot of >other non-specific proteins. You don't say what concentration of antibody you are using in the Western blot, but let me run this scenario by you and see if it is consistent with what you have. If you have just done a single injection, andbled after four weeks, I think that the chances of your having generated a good specific titer are low. Typically I inject 4-6 times, at 4 wek intervals and find good titers coming up after 3-6 injections. You say that you got a good signal against your purified fusion protein. If that was the only protein band in the gel lane, then you could be looking at non-specific binding, and all of the subsequent phenomena that you describe are consistent with this interpretation. You may have a response to the GST part of the fusion protein as well. The best way to test your serum would be to run a gel with a whole extract from induced bacteria with your fusion protein construct and with another, unrelated construct, looking for a signal that is unique to the fusion protein that you want as antigen, in a background of whole bacterial extract. Run a set of serial 5- or 10-fold dilutions of the extract so you get some idea of the sensitivity of the serum. Also, run a series of 3- or 10- fold dilutions of the serum to get an idea of how high the tiiter is. Keep injecting for at least 6 injections before you give up on those rabbits. >I then tried running just membrane fractions of wild-type and mutant >(lacking the gene encoding the protein of interest) strains and got no >difference in the cross-reacting bands!! I though that maybe the >protein was running at the wrong mol. wt. and was being 'masked' by the >non-specific cross-reactign proteins so I preadsorbed the serum with an >acetone extract of the mutant. When I then used this preadsorbed serum I >got exactly the same profile as I did with just plain serum!! >Why are the non-specific antibodies not binding to the acetone extract? > >I have also tried purifying the antibody by using immobilised fusion >protein ie. immobilised on hybond-C, eluting with glycine etc. but this >still gives cross-reacting protein of the wrong mol. wt. in both wt. and >mutant membrane fractions!! > >Any hints or tips would be much appreciated - please remeber though that >I am a complete novice at this 'antibody purification game' > >Thanks in advance > > >Ian > > Warren Gallin Department of Biological Sciences University of Alberta Edmonton, Alberta T6G 2E9 Canada wgallin@gpu.srv.ualberta.ca From owner-proteins@net.bio.net Sun Apr 07 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!oxpath!rpgrant From: rpgrant@molbiol.ox.ac.uk (Richard P. Grant) Newsgroups: bionet.molbio.proteins Subject: Re: Antibody nightmare!!! Date: 8 Apr 96 11:49:23 GMT Organization: Oxford University Molecular Biology Data Centre Lines: 15 Message-ID: <1996Apr8.114923@molbiol.ox.ac.uk> References: <4jm8i5$agn@griffin.ccc.nottingham.ac.uk> NNTP-Posting-Host: ania.path.ox.ac.uk In article , wgallin@gpu.srv.ualberta.ca (Warren Gallin) writes: > In Article <4jm8i5$agn@griffin.ccc.nottingham.ac.uk>, Ian Goodfellow > wrote: (Snip snip snip) I would agree with Warren, but I'd also be tempted (after say the third inoculation) to do ELISAs using purified fusion protein - just because you can do a lot of dilutions very quickly. -- Richard P. Grant MA DPhil rpgrant@molbiol.ox.ac.uk Nuffield Department of Obstetrics and Gynaecology, University of Oxford. http://sable.ox.ac.uk/~lady0266 Fax +44 1 865 69141 Walk softly..... and carry an armoured tank division From owner-proteins@net.bio.net Sun Apr 07 23:00:00 1996 Path: biosci!GDB.ORG!avoltz From: avoltz@GDB.ORG (Amy Voltz) Newsgroups: bionet.molbio.proteins Subject: Mammalian Homology and Enzyme Function Data via GDB! Date: 8 Apr 1996 09:22:12 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 45 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Mammalian Homology and Enzyme Function Data now available from GDB! The Genome Data Base (GDB) has re-established links from over 1500 GDB human gene entries to the mammalian homology data within the Mouse Genome Database (MGD). While the primary focus of MGD is mouse, their homology data includes information on mammals from the baboon to the wallaby! These data include gene symbols, cytogenetic locations and citations. To access the GDB/MGD homology links, follow the steps outlined below to perform a gene search in GDB, then follow the "Homology" link to MGD. Links to enzyme function data for over 400 protein products of human genes can also be found in GDB. Enzyme data is based on Enzyme Commission (EC) numbers as maintained by the Enzyme nomenclature database at SWISS-PROT. The Enzyme database entries include the reaction catalyzed, cofactor(s), links to the PROSITE database (protein sites and patterns), and detailed SWISS-PROT entries that include protein sequence and links to many other databases. To access mammalian homology and enzyme function data from GDB, start at the GDB homepage (http://gdbwww.gdb.org). Select the "Quick Search" option. Enter the symbol for your favorite gene as the "Genome Object Name", e.g. SOD1, and press "Submit". Choose "Gene SOD1" from the list of query results returned. For mammalian homology data: Choose "Mouse Genome Database: Sod1" from the "Homologies" section of the information returned for the SOD1 gene. For enzyme function data: Choose "Protein: Superoxide Dismutase" from the information returned for the SOD1 gene. (The enzyme function links have been made from the genes via their protein products). The link to the EC database is visible under "Enzyme Links": EC 1.15.1.1 Sincerely, Amy K. Voltz avoltz@gdb.org From owner-proteins@net.bio.net Mon Apr 08 23:00:00 1996 From: comstock@1stresource.com (R. E. Haufler) Newsgroups: bionet.molbio.proteins Subject: Comstock, Inc., MALDI Mass Spectrometry of Proteins Date: Tue, 09 Apr 1996 13:28:12 GMT Organization: Comstock, Inc. Reply-To: comstock@1stresource.com X-Newsreader: Forte Free Agent 1.0.82 NNTP-Posting-Host: 205.139.129.12 Message-ID: <316a65e8.0@news.1stresource.com> Lines: 12 Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!news.1stresource.com! Comstock, Inc., Oak Ridge, TN, USA, manufactures benchtop and research linear and reflectron time-of-flight mass spectrometer components and systems for MALDI (Matrix Assisted Laser Desorption and Ionization, this is an excellent way to obtain mass spec information for large molecules such as proteins). We have new high performance MALDI/laser desorption systems that utilize Delayed Pulse Extraction (DPE) for mass resolution enhancement. We can perform complementary test MALDI runs on proteins. See our web site at: http://www.comstockinc.com From owner-proteins@net.bio.net Mon Apr 08 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!gatech!newsjunkie.ans.net!newsfeeds.ans.net!rcogate.rco.qc.ca!altitude!usenet From: Achim Recktenwald Newsgroups: bionet.molbio.proteins Subject: Re: protein clustering Date: Tue, 09 Apr 1996 09:30:23 -0500 Organization: IBEX Technologies, Inc. Lines: 52 Message-ID: <316A747F.31E5@ibex.ca> References: <9604032210.AA08245@IRIS.lsc.pku.edu.cn> <4judlp$9pg_001@biochem.wisc.edu> NNTP-Posting-Host: ibex.hip.cam.org Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Macintosh; I; PPC) Dima Klenchin wrote: > > In article <9604032210.AA08245@IRIS.lsc.pku.edu.cn>, > lisl@IRIS.LSC.PKU.EDU.CN (Li Songlin) wrote: > -> > ->Dear all, > -> > ->I am a crystallographer. I have a high concentration protein sample. > ->(>30 mg/ml). In my recent work, it is suspected that ten or more > ->molecules of this kind of protein form a cluster. It should be checked > ->by experiment. Could you please show me some methods that could be used > ->to check my suspection? > > Gel filtration and density gradient. > > - Dima Gel filtration and/or a run in an analytical centrifuge are probably your best options. Just to check whether your suspicion is correct, run a native polyacrylamide gel electrophoresis (PAGE). You should see a smear in the lane of your gel, starting from the molecular weight of the highest aggregate down to the single protein. This method works especially well with gradient gels, since then you can read the molecular weights more easily. If the aggregate is very loose, and it disintegrates quickly after start of the electrophoresis = smeary band is very short or even not detectable at all, you could try to cautiously crosslink the proteins in the aggregate. Unfortunately, the method doesn't work allways and is a bit tricky. The problem is, there are no foolproof conditions, you'll have to find them yourself for your protein. Dilute your aggregate in an appropriate buffer and incubate it with a dilute solution of glutardialdehyde (max. 2 - 5%) at 4oC or RT for about 30 min. Then take these samples and run immediately a native PAGE on a gradient gel and a SDS-PAGE. The bands should show with both methods the same molecular weight. Good luck, Achim ___________________________ Achim Recktenwald, PhD IBEX Technologies, Inc. 5485 rue Pare Montreal, PQ, H4P 1P7 Canada achim@ibex.ca From owner-proteins@net.bio.net Mon Apr 08 23:00:00 1996 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!news.ox.ac.uk!news From: "Simon M. Brocklehurst" Newsgroups: bionet.molbio.proteins Subject: Cytokines Web Date: Tue, 09 Apr 1996 16:06:44 +0100 Organization: University of Oxford Lines: 33 Message-ID: <316A7D04.167EB0E7@bioch.ox.ac.uk> NNTP-Posting-Host: nmrv.ocms.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (X11; I; SunOS 4.1.3_U1 sun4m) Dear All, There are apparently a number of problems with some references to the CYTOKINES WEB either in the printed literature, or on various Web pages. The problems arise due to problems of minor incompatibility between different browers e.g. the specification: www.ocms.ox.ac.uk/~smb/cyt_web won't work for all browsers. In some cases (as in the example above), the way the URL is referenced mean the link will fail completely, in others links further down in the hierarchy in the Web will be inaccessible. The URL reference for the Cytokines Web that should work for all browsers is: http://www.ocms.ox.ac.uk/~smb/cyt_web/ I know that this is too late for references in already in print, and also that these might seems easy things for a surfer to sort out, but not everyone is experienced at using the Web. Hopefully this post may save a few phone-calls and e-mails from people wanting to visit the site, having seen the URL somewhere... also, if you have a Web page with a link to the site, I'd be grateful if you'd change any hypertext references to the Cytokines Web that aren't as specified above. Thanks a lot! _____________________________________________________________________________ | | ,_ o Simon M. Brocklehurst, | / //\, Oxford Centre for Molecular Sciences, Department of Biochemistry, | \>> | University of Oxford, Oxford, UK. | \\, E-mail: smb@bioch.ox.ac.uk | WWW: http://www.ocms.ox.ac.uk/~smb/ |____________________________________________________________________________ From owner-proteins@net.bio.net Mon Apr 08 23:00:00 1996 Path: biosci!rutgers!uwm.edu!psuvax1!news.cc.swarthmore.edu!netnews.upenn.edu!cronkite.ocis.temple.edu!astro.ocis.temple.edu!driska From: driska@astro.ocis.temple.edu (Stephen P. Driska PhD) Newsgroups: bionet.molbio.proteins Subject: Re: Lane Background Date: 9 Apr 1996 23:09:48 GMT Organization: Temple University, Academic Computer Services Lines: 44 Distribution: world Message-ID: <4keqnt$pd5@cronkite.ocis.temple.edu> References: NNTP-Posting-Host: astro.ocis.temple.edu X-Newsreader: TIN [version 1.2 PL2] David Stair (d-stair@TAMU.EDU) wrote: : Hello, : I am in need of some help. I have too much stain background in the : sample lanes of my PAGE gels. : I am working on plasma membrane proteins from basal tiller tissue of : forage grasses. I have isolated the PM and separated the integral and : peripheral proteins with a .25 M KCl wash. Samples are washed to : remove the salt and solubilized in 10% sucrose, 1% SDS, 50 mM Tris-HCl : pH 7.2, 1 mM EDTA and 1 mM PMSF. Samples are in 10 % sucrose, 2% : SDS, 50 mM Tris-HCl pH 7.2, 1mM EDTA, 1mM PMSF, and 40 mM DTT : when loaded onto gels. On 10 % gels these samples have a lot of : uniform background staining only in the sample lanes, mostly in the 10 - : 150 kDa range. The molecular weight markers have no background and : the gel itself has no background (not visibly noticeable). : It seems that when the same samples are run through 2-D methodology : this heavy background comes out in the acidic end of the IEF gel and : then stain the entire depth of the second dimension gel. : I have exhausted all ideas, mine and others, here, and any help would be : greatly appreciated. : David Stair : d-stair@tamu.edu Have you tried precipitating your samples with an organic solvent, say acetone for starters, and then resuspending it in the aqueous solution for gels? And by the way, is the problem that's bothering you the fact that there is background smearing on the 1-D gels, or is it the 2-D gels, or is it both? Unfortunately I don't have much experience with plant samples; it's probably different than working with animal samples. -- Steve Driska, Physiology Department, Temple University Medical School Philadelphia, PA 19140 USA (215) 707-3283 driska@astro.ocis.temple.edu If I could think of something witty and clever to say, it would go right here ----->> ......................... From owner-proteins@net.bio.net Mon Apr 08 23:00:00 1996 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!in2.uu.net!EU.net!Germany.EU.net!news.dfn.de!uni-muenster.de!ifepmac3.uni-muenster.de!user From: krafft@uni-muenster.de Newsgroups: bionet.molbio.proteins Subject: RNA-binding proteins Date: 9 Apr 1996 11:04:01 GMT Organization: Westfaelische Wilhelms-Universitaet Muenster, Germany Lines: 2 Message-ID: NNTP-Posting-Host: ifepmac3.uni-muenster.de Is there anybody with experiences in the use of biotin-oligonucleotides and streptavidin-magnetic beads to purify RNA binding proteins? From owner-proteins@net.bio.net Mon Apr 08 23:00:00 1996 Path: biosci!pokpung.hanhyo.co.kr!jin From: jin@pokpung.hanhyo.co.kr (Lee Jin Young) Newsgroups: bionet.molbio.proteins Subject: about CD and stopped-flow ? Date: 9 Apr 1996 18:48:41 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: <199604100145.KAA20588@pokpung.hanhyo.co.kr> NNTP-Posting-Host: net.bio.net Hi, netters ! I need some of your help on the interpretation of "Stopped-flow Circular Dichroism(CD)" experiment. I'm using Jasco CD (Model J-720) spectrometer equipped with stopped-flow accessory (Model SFCA-323). My problem is the interpretation of stopped-flow CD spectrum of protein denaturation condition with 8M GuHCl and 50 mM sodium phosphate buffer. I thought the background CD signal, i.e., just by mixing GuHCl and NaH2PO4, should be near zero or, at least, be steady around some CD signal value. However, the resulting stopped-flow CD signal of this background at 220 nm has repeatedly showed some pattern in the one to ten minutes data aquisition period. I don't know this pattern is normal or I did some important mistakes in doing stopped-flow CD experiment. If anyone have similar experience, please help me ? I'll very appreciate you, in advance. From owner-proteins@net.bio.net Mon Apr 08 23:00:00 1996 Path: biosci!biosci!not-for-mail From: bshomer@ebi.ac.uk (Benny Shomer) Newsgroups: bionet.molbio.methds-reagnts,bionet.immunology,bionet.cellbiol,bionet.general,bionet.genome.arabidopsis,bionet.genome.chromosomes,bionet.microbiology,bionet.molbio.proteins,bionet.plants,fr.bio.biolmol,fr.bio.general,sci.bio.microbiology Subject: mtDNA primers - Call for Marathon!!! Date: 9 Apr 1996 21:48:17 -0700 Organization: EBI - European Bioinformatics Institute Lines: 94 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Xref: biosci bionet.molbio.methds-reagnts:42854 bionet.immunology:8490 bionet.cellbiol:4467 bionet.general:21048 bionet.genome.arabidopsis:4435 bionet.genome.chromosomes:1116 bionet.microbiology:5645 bionet.molbio.proteins:7542 bionet.plants:10879 sci.bio.microbiology:3133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The PCR Primers database - An update. A call for a mitochondrial DNA primers marathon. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The PCR primers database is a practical database of fully tested and optimized primers for PCR reactions. The database contains all the data items required to reproduce precisely the reaction conditions of the submitting author and contact details in case of a need. To enhance the rate of information flow into the database and obtain focused interest, I would like to invite colleagues to take a part in a "marathon" of collecting primers that were sucessfully used in PCR amplifications of mitochondrial DNA from various species. This theme has been selected due to a great interest on behalf of many people who enquired about the presence of such primers. If this initiative will be sucessful, other themes will be selected according to need. Please let your colleagues know about the database and about this call, especially those researchers who are off the network or who do not read the bionet newsgroups on a regular basis. Obviousely, submission of any other primers are definitely allways welcome. * Data submissions: The database relies heavily on submissions from users. The importance to the users community will increase with the increase in entry numbers. Users are encouraged to submit primers to the database. Submissions can be made either through the WWW or by using a text based submission form. If you maintain large numbers of primers in a spreadsheet or small database or a simple but organized text file, please contact me. I can process large numbers of entries from almost any format. Summary of access means: ------------------------ The database home page can be accessed directly at: http://www.ebi.ac.uk/primers_home.html The data and documentation can be obtained through anonymous ftp to: ftp.ebi.ac.uk under: /pub/databases/primers/ Searches at the CAOS/CAM server: http://www-srs.caos.kun.nl/srs/srsc Users who have no other means of connection besides email, can now use the EMBL-EBI automatic mail server to retrieve the database files and documents. To start working with the mail server in general, send a message containing the word "HELP" either in the subject line or in the body of message, to: netserv@ebi.ac.uk Here are the commands which are available for the primers database: Here is a summary of all the available commands for the primers database, that can be specified in an email message sent to netserv@ebi.ac.uk ------------------------------------------------------------------------- To obtain send the command ------------------------------------------------------------------------- A general help file HELP PRIMERS The database fields definitions file GET PRIMERS:DEFINITIONS A bogus filled entry as an example GET PRIMERS:EXAMPLE An electronic data submission form GET PRIMERS:SUBMISSION.FORM The actual data file with the entries GET PRIMERS:PRIMERS ------------------------------------------------------------------------- Dear colleague, please do not forget, this database will NOT be created by journal scanning and active searching, but from direct submissions from researchers only. The key to the success of this database is your submissions, so do set aside some spare time and send your primers. Our email: primers@ebi.ac.uk WWW : http://www.ebi.ac.uk/primers_home.html fax : +44 1223 494468 Phone : +44 1223 494437 I highly welcome any questions, corrections, remarks or discussions concerning the PCR Primers database (Email is the most preferred way). Best wishes. Good luck with your PCR experiments. Yours, Benny Shomer Email: bshomer@EBI.ac.uk http://www.ebi.ac.uk/ebi_docs/staff/benny.html From owner-proteins@net.bio.net Mon Apr 08 23:00:00 1996 Path: biosci!bloom-beacon.mit.edu!newsfeed.internetmci.com!in2.uu.net!ftpbox!newsfeed.acns.nwu.edu!news.acns.nwu.edu!med048050.medicine.nwu.edu!user From: sg@nwu.edu (Stephen T. Gately) Newsgroups: bionet.molbio.proteins Subject: Preabsorption of Primary Antibody Date: Tue, 09 Apr 1996 09:00:11 -0600 Organization: Northwestern University Lines: 10 Message-ID: NNTP-Posting-Host: med048050.medicine.nwu.edu Can anyone suggest some optimal techniques for preabsorbing a primary antibody, ie. ratio of antigen to antibody etc. Thanks in advance. -- Stephen T. Gately Northwestern University sg@nwu.edu From owner-proteins@net.bio.net Mon Apr 08 23:00:00 1996 Path: biosci!pokpung.hanhyo.co.kr!jin From: jin@pokpung.hanhyo.co.kr (Lee Jin Young) Newsgroups: bionet.molbio.proteins Subject: (none) Date: 9 Apr 1996 18:21:10 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <199604100118.KAA20352@pokpung.hanhyo.co.kr> NNTP-Posting-Host: net.bio.net Hi, netters ! I need some of your help on the interpretation of "Stopped-flow Circular Dichroism(CD)" experiment. I'm using Jasco CD (Model J-720) spectrometer equipped with stopped-flow accessory (Model SFCA-323). My problem is the interpretation of stopped-flow CD spectrum of protein denaturation condition with 8M GuHCl and 50 mM sodium phosphate buffer. I thought the background CD signal, i.e., just by mixing GuHCl and NaH2PO4, should be near zero or, at least, be steady around some CD signal value. However, the resulting stopped-flow CD signal of this background at 220 nm has repeatedly showed some pattern in the one to ten minutes data aquisition period. I don't know this pattern is normal or I did some important mistakes in doing stopped-flow CD experiment. If anyone have similar experience, please help me ? I'll very appreciate you, in advance. From owner-proteins@net.bio.net Tue Apr 09 23:00:00 1996 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!in2.uu.net!ftpbox!newsfeed.acns.nwu.edu!news.cc.uic.edu!usenet From: Keld Sorensen Newsgroups: bionet.molbio.proteins Subject: Re: Preabsorption of Primary Antibody Date: Tue, 09 Apr 1996 13:21:13 -0600 Organization: University of Illinois, College of Medicine Lines: 11 Message-ID: <316AB8A9.124E@uic.edu> References: NNTP-Posting-Host: sliprock-02.dialin.uic.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Macintosh; I; PPC) To: "Stephen T. Gately" > Can anyone suggest some optimal techniques for preabsorbing a primary > antibody, ie. ratio of antigen to antibody etc. > I would recommend using a solid phase system, i.e. immobilize the "offending" antigen on a column, then pass the Ab solution over it. Solution techniques, i.e. doing it all in solution may or may not create precipitates, and will usually result in a "dirtier" prep. Keld. From owner-proteins@net.bio.net Tue Apr 09 23:00:00 1996 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!tank.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!ws41.cnusc.fr!ciril.fr!u-strasbg.fr!localhost!francis.durst From: francis.durst@bota-ulp.u-strasbg.fr (Francis Durst) Newsgroups: bionet.molbio.proteins Subject: Mito and chloro targeting peptides? Date: Wed, 10 Apr 1996 12:50:50 Organization: CNRS Lines: 8 Message-ID: NNTP-Posting-Host: frenzy.u-strasbg.fr X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Dear Netters, Do you know of an Internet access to the database of mitochondrial and chloroplastic transit peptides that was compiled by Dr. Gunnar von Heijne? Merci Francis From owner-proteins@net.bio.net Tue Apr 09 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!newsfeed.sunet.se!news00.sunet.se!sunic!mn6.swip.net!seunet!news2.swip.net!inet-1.pharmacia.se!usenet From: Poul Sorensen Newsgroups: bionet.molbio.proteins Subject: human c-rel & p65 Date: 10 Apr 1996 14:24:07 GMT Organization: Pharmacia & Upjohn Oncology Immunology, Lund, Sweden. Lines: 4 Message-ID: <4kgga7$l46@inet-1.pharmacia.se> NNTP-Posting-Host: pcsopo.lun.se.pnu.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Windows; I; 16bit) Does anyone know if human c-rel and p65 are commercially available ? Poul Sorensen. From owner-proteins@net.bio.net Tue Apr 09 23:00:00 1996 Path: biosci!rutgers!uwm.edu!lll-winken.llnl.gov!enews.sgi.com!sgigate.sgi.com!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!news.u.washington.edu!saul6.u.washington.edu!pearton From: pearton@saul6.u.washington.edu (D. Pearton) Newsgroups: bionet.molbio.proteins Subject: Proteins that are Ser and Tyr Phosphorulated Date: 11 Apr 1996 01:29:46 GMT Organization: University of Washington Lines: 26 Message-ID: <4khnaa$4c4@nntp3.u.washington.edu> NNTP-Posting-Host: saul6.u.washington.edu NNTP-Posting-User: pearton X-Newsreader: TIN [version 1.2 PL2] Hi all, I have a protein (or two proteins) that are pulled down with my protein of interest in an immunoprecipitation reaction. The unknown protein(s) run as a doublet at around 20-24 kD on SDS-PAGE and react with _both_ anti-phosphoserine and anti-phosphotyrosine antibodies. Can anyone give me an idea of what class of proteins they might belong to? While I know that threonine and tyrosine phosphorulation of the same protein is fairly common (MAP kinase substrates) I have been unable to find anything on proteins that are ser and tyr phosphorulated. Any suggestions and/or pointers to relavent references would be greatly appreciated (I'd prefer not to have to go to a two-hybrid system if I can ;). Yours, Yak -- *********************************************************************** Dave Pearton * ....As I was saying before I Biochemistry Dept. * was so rudely interrupted University of Washington * by one of my multiple Seattle * personalities.... pearton@u.washington.edu * pearton@unpsun1.cc.unp.ac.za * Naked Lunch (W.S. Burroughs) ************************************************************************ From owner-proteins@net.bio.net Tue Apr 09 23:00:00 1996 Path: biosci!MANI.CBS.UMN.EDU!npv From: npv@MANI.CBS.UMN.EDU (Nora Plesofsky-Vig) Newsgroups: bionet.molbio.proteins Subject: Coomassie-staining Date: 10 Apr 1996 12:19:36 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <9604102017.AA01322@mani.cbs.umn.edu> Reply-To: nora@biosci.cbs.umn.edu NNTP-Posting-Host: net.bio.net I have recently isolated a size fraction of soluble cell extracts that includes my protein of interest. This is a high molecular weight fraction that presumably includes quite a bit of RNA, because there is more UV-absorbing material than could possibly be accounted for by the proteins in the fraction. My question is this. When I perform SDS-PAGE on an aliquot of the fraction, either directly or precipitated with ethanol to concentrate the protein, I find that the protein band of interest initially stains fine with Coomassie blue (in methanol/acetic acid), but it daily fades rapidly (while in fixative) until nothing is left. I have not had this experience before with this protein or with others. Does anyone know what could be causing this rapid fading of the blue stain? I assume it might be due to the presence of interfering molecules in the lane or the band, but I don't know what molecules might cause that effect. Any ideas or experience would be appreciated. Thanks. Nora Plesofsky-Vig nora@biosci.cbs.umn.edu From owner-proteins@net.bio.net Tue Apr 09 23:00:00 1996 Path: biosci!rutgers!gatech!newsjunkie.ans.net!newsfeeds.ans.net!rcogate.rco.qc.ca!altitude!usenet From: Achim Recktenwald Newsgroups: bionet.molbio.proteins,bionet.software,bionet.molbio.proteins,bionet.cellbiol Subject: Re: Phosphorylation sites Date: Wed, 10 Apr 1996 09:15:13 -0500 Organization: IBEX Technologies, Inc. Lines: 13 Message-ID: <316BC271.63AF@ibex.ca> References: NNTP-Posting-Host: ibex.hip.cam.org Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Macintosh; I; PPC) Xref: biosci bionet.molbio.proteins:7545 bionet.software:15206 bionet.cellbiol:4470 LI LU wrote: > > Hi, there. > I'd like to ask where can I find a list or o program to search for > phosphoylation site in a protein sequence, by different kinases. Any ftp > site or web site are welcome. Thanks a lot. Please reply to my email > address: lilu@welchlink.welch.jhu.edu This would interest me, as well. Please, also post the reply to this newsgroup. Achim From owner-proteins@net.bio.net Wed Apr 10 23:00:00 1996 Newsgroups: bionet.molbio.proteins Path: biosci!rutgers!uwm.edu!cs.utexas.edu!howland.reston.ans.net!Germany.EU.net!ieunet!maths.tcd.ie!news.tcd.ie!usenet From: crbaker Subject: Spotted Coomassie Staining? Message-ID: Sender: usenet@news.tcd.ie (TCD News System ) Organization: University of Dublin, Trinity College Date: Thu, 11 Apr 1996 07:26:37 GMT Lines: 11 Although having run and stained a large number of SDS polyacrylamide gels without any previous problems the last two I have run have stained unusually with Coomassie - protein lanes and bands appear spotted with visable dots of stain rather than the normal uniform staining of bands. This only came apparent on destaining and I am at a loss to explain why it has suddenly occurred. Has anyone seen this before or have an explanation? Cara Baker crbaker@mail.tcd.ie From owner-proteins@net.bio.net Wed Apr 10 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!news From: "Simon M. Brocklehurst" Newsgroups: bionet.molbio.proteins Subject: ANNOUNCE: NAOMI Version 2.4c Date: Thu, 11 Apr 1996 13:35:51 +0100 Organization: University of Oxford Lines: 33 Message-ID: <316CFCA7.41C67EA6@bioch.ox.ac.uk> NNTP-Posting-Host: nmrv.ocms.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (X11; I; SunOS 4.1.3_U1 sun4m) NAOMI - Version Upgrade Announcement (Please note, NAOMI is provided at zero charge for academic use) (e-mail contact smb@bioch.ox.ac.uk) _____________________________________________________________________________ NAOMI Version 2.4c is available as of now from the NAOMI Web site at: http://www.ocms.ox.ac.uk/~smb/Software/N_details/naomi.html or via anonymous ftp ftp://nmrz.ocms.ox.ac.uk/pub/smb/naomi i.e. at nmrz.ocms.ox.ac.uk in directory pub/smb/naomi/ Users of versions older than 2.10 will need new license keys to allow the upgrade to work (please contact the author in this case). _____________________________________________________________________________ NB NAOMI currently works only on Silicon Graphics workstations running IRIX 5.* or IRIX 6.* _____________________________________________________________________________ | | ,_ o Simon M. Brocklehurst, | / //\, Oxford Centre for Molecular Sciences, Department of Biochemistry, | \>> | University of Oxford, Oxford, UK. | \\, E-mail: smb@bioch.ox.ac.uk | WWW: http://www.ocms.ox.ac.uk/~smb/ |____________________________________________________________________________ From owner-proteins@net.bio.net Wed Apr 10 23:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!pasteur.fr!univ-lyon1.fr!in2p3.fr!swidir.switch.ch!swsbe6.switch.ch!news.belnet.be!news.rediris.es!news.uoregon.edu!tank.news.pipex.net!pipex!lade.news.pipex.net!pipex!newshost.zeneca.co.uk!usenet From: David Blowers Newsgroups: bionet.molbio.proteins Subject: Re: GST fusion rebinding to glutathione columns Date: Thu, 11 Apr 1996 12:15:42 +0000 Organization: Zeneca Pharmaceuticals Lines: 32 Message-ID: <316CF7EE.6833@gbapr.zeneca.com> References: <4j7ut1$idg_001@mel.dbe.csiro.au> NNTP-Posting-Host: 156.71.144.96 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Macintosh; I; PPC) Keith Gough wrote: > > G'Day to all, > > Can anyone tell me how to rebind a GST fusion to a glutathione resin. > Typically, I find that at least 50% of a GST fusion, that has been purified > from a glutathione resin by elution from the resin with glutathione, after > dialysis will not bind. The only explanation I can think of is that there is > still glutathione bound to the binding site of GST. > I am trying to remove this glutathione from the binding site with NaCl but as > yet do not know if it will work. > > I would be grateful for all comments > > Keith Gough Keith, Your suggestion is probably correct and the presence of glutathione complicates the issue regarding dimerisation as well. The only way that I know of to get around this type of problem is to denature the fusion protein in 8M urea and then refold/dialyse at the same time. If you've ever done DLS on your fusion protein then you will probably find that this is remarkably improved as well..... ....if you fusion will not refold easily then you'll have to look elsewhere for help. Regards, David From owner-proteins@net.bio.net Wed Apr 10 23:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!pasteur.fr!univ-lyon1.fr!in2p3.fr!swidir.switch.ch!scsing.switch.ch!news.belwue.de!news.uni-hohenheim.de!news From: Troy Zoerhof Newsgroups: bionet.molbio.proteins Subject: Re: "mystery bands" in SDS-PAGE Date: 11 Apr 1996 22:31:54 GMT Organization: Mycogen Corp. Lines: 5 Message-ID: <4kk18q$vbi@power5.rz.uni-hohenheim.de> References: <315AF4DF.73AA@acs.ucalgary.ca> NNTP-Posting-Host: ws196.mycogen.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.2N (Windows; I; 16bit) I've had a similar experience with a Hamilton syringe being contaminated with papain. The syringe needed a bleach wash after every use of papain or the enzyme would start to digest the sample being loaded in the lane. Good luck. From owner-proteins@net.bio.net Wed Apr 10 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!swhbmac16.bioc.cam.ac.uk!user From: Myo@uk.cam (M.Perutz) Newsgroups: bionet.molbio.proteins Subject: Re: about CD and stopped-flow ? Date: Thu, 11 Apr 1996 15:38:16 +0100 Organization: University of Cambridge, England Lines: 11 Distribution: world Message-ID: References: <199604100145.KAA20588@pokpung.hanhyo.co.kr> NNTP-Posting-Host: swhbmac16.bioc.cam.ac.uk Hi lee, It sounds like youre having problems with the unmixed GuHCl defusing, over time into the observation chamber, ive had similar problems. Depending on your system (I havent used your particular one) one can design mixing sequences which minimise such problems. Also, what is the final concentration of GuHCl which reaches the observation cell? Anything over around 0.6M and you will very probably start having servere problems with your signal to noise ratio. hope this helps Laurence Tisi lct11@uk.ac.cam.bio.mole From owner-proteins@net.bio.net Thu Apr 11 23:00:00 1996 Path: biosci!rutgers!csn!news-1.csn.net!magnus.acs.ohio-state.edu!rsaldanh From: rsaldanh@magnus.acs.ohio-state.edu (Roland J Saldanha) Newsgroups: bionet.microbiology,bionet.molbio.proteins,bionet.molbio.proteins.7 Subject: Re: Replacement for E.col at pH 3 ? Date: 13 Apr 1996 00:27:49 GMT Organization: The Ohio State University Lines: 4 Message-ID: <4kmse5$119@charm.magnus.acs.ohio-state.edu> References: NNTP-Posting-Host: bottom.magnus.acs.ohio-state.edu Xref: biosci bionet.microbiology:5700 bionet.molbio.proteins:7560 I used to work next to a lab that worked on thiobacillus ferooxidans and if memory serves they used to culture it in a very acidic media. Roland From owner-proteins@net.bio.net Thu Apr 11 23:00:00 1996 Path: biosci!rutgers!gatech!news.jsums.edu!news2.cais.net!news.cais.net!chi-news.cic.net!news-w.ans.net!newsfeeds.ans.net!lantana.singnet.com.sg!nuscc.nus.sg!mcbthy From: mcbthy@leonis.nus.sg (Tang Hsin Yao) Newsgroups: bionet.molbio.proteins Subject: MW of mouse IgG and protein A in IP Date: 12 Apr 1996 07:33:39 GMT Organization: National University of Singapore Lines: 16 Message-ID: <4kl10j$sss@nuscc.nus.sg> NNTP-Posting-Host: mcbthy%@leonis.nus.sg X-Newsreader: TIN [version 1.2 PL2] Hi! I have been doing immunoprecipitation using a mouse IgG and Protein A Sepharose. Does anyone know the MW of the mouse IgG heavy and light chains, as well as the protein A when run on a SDS PAGE gel? Thanks in advance for your time. Hsinyao Tang mcbthy@leonis.nus.sg From owner-proteins@net.bio.net Thu Apr 11 23:00:00 1996 Path: biosci!rutgers!gatech!swrinde!tank.news.pipex.net!pipex!oleane!in2p3.fr!swidir.switch.ch!scsing.switch.ch!news.belwue.de!news.uni-stuttgart.de!news.urz.uni-heidelberg.de!usenet From: Christoph.Lorra@urz.uni-heidelberg.de Newsgroups: bionet.molbio.proteins,bionet.software,bionet.molbio.proteins,bionet.cellbiol Subject: Re: Phosphorylation sites Date: 13 Apr 1996 00:37:35 GMT Organization: University of Heidelberg, Germany Lines: 25 Message-ID: <4kmt0f$fmn@sun0.urz.uni-heidelberg.de> References: <316BC271.63AF@ibex.ca> Reply-To: Christoph.Lorra@urz.uni-heidelberg.de NNTP-Posting-Host: modem.urz.uni-heidelberg.de X-Newsreader: IBM NewsReader/2 v1.09 Xref: biosci bionet.molbio.proteins:7561 bionet.software:15223 bionet.cellbiol:4485 In <316BC271.63AF@ibex.ca>, Achim Recktenwald writes: >LI LU wrote: >> >> Hi, there. >> I'd like to ask where can I find a list or o program to search for >> phosphoylation site in a protein sequence, by different kinases. Any ftp >> site or web site are welcome. Thanks a lot. Please reply to my email >> address: lilu@welchlink.welch.jhu.edu > > >This would interest me, as well. Please, also post the reply to this >newsgroup. > >Achim I donïknow if this will help you but i have a paper describing phosphorylation sites, which is an article in: Methods in Enzymology, Vol. 200, 1991, 62 - 81. The title is " Protein kinase phosphorylation site sequences and consensus specifity motifs: Tabulations" by R.P. Pearson and B.E Kemp. A source for a program would be at least PCGENE from Intelligenetics which is able to find at least PKA and PKC-sides I hope this will help you Christoph From owner-proteins@net.bio.net Thu Apr 11 23:00:00 1996 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!daily-planet.execpc.com!news.sol.net!news.inc.net!imci5!pull-feed.internetmci.com!news.internetMCI.com!newsfeed.internetmci.com!uwm.edu!lepidopteran.cse.psu.edu!news.eecs.nwu.edu!newsfeed.acns.nwu.edu!news.cc.uic.edu!usenet From: Keld Sorensen Newsgroups: bionet.molbio.proteins Subject: Re: Spotted Coomassie Staining? Date: Thu, 11 Apr 1996 12:58:13 -0600 Organization: University of Illinois, College of Medicine Lines: 8 Message-ID: <316D5645.5093@uic.edu> References: NNTP-Posting-Host: sliprock-02.dialin.uic.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Macintosh; I; PPC) To: crbaker [snipped desc. of spotted coomassie stain] Filter the STAINING solution - it is probably old and has particulates..... Keld /mail 'n post/ From owner-proteins@net.bio.net Thu Apr 11 23:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!news.belnet.be!swsbe6.switch.ch!scsing.switch.ch!news.belwue.de!news.uni-stuttgart.de!uni-regensburg.de!uni-erlangen.de!winx03!wpxx02.toxi.uni-wuerzburg.de!not-for-mail From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins Subject: Re: "mystery bands" in SDS-PAGE Date: 12 Apr 1996 11:37:37 GMT Organization: University of Wuerzburg, Germany Lines: 25 Message-ID: <4klfa1$n5c@winx03.informatik.uni-wuerzburg.de> References: <315AF4DF.73AA@acs.ucalgary.ca> NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Fiona M. Mattatall (fmcowman@acs.ucalgary.ca) wrote: > My laboratory is having some problems with bands appearing on our > SDS-PAGE gels. The bands always run in the 80 to 100 kDa range. They > appear in all lanes of the gel, including those that do not have > protein samples applied to them. We have concluded that this > contamination must be coming from either the sample buffer, running > buffer, or the apparatus itself. We are having some difficulty > figuring out what is causing the problem. Unfortunately you do not say how you stain your gels. "Mystery bands" are especially common with silver stain, but occur sometimes also with Coomassie-stained gels (no idea about other staining methods). Common origins include: - contaminated running buffer (especially if you recycle the running buffer a few times) - bad beta-mercaptoethanol in the sample buffer - contamination of buffer by keratin from human hands Hope that helps, --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-proteins@net.bio.net Thu Apr 11 23:00:00 1996 Path: biosci!galaxy.ucr.edu!library.ucla.edu!csulb.edu!drivel.ics.uci.edu!news.service.uci.edu!unogate!news.intelenet.com!news.sprintlink.net!new-news.sprintlink.net!newsreader.sprintlink.net!imci3!imci4!newsfeed.internetmci.com!tank.news.pipex.net!pipex!oleane!in2p3.fr!swidir.switch.ch!scsing.switch.ch!news.belwue.de!news.uni-ulm.de!auvi-mac.informatik.uni-ulm.de!user From: wolf@informatik.uni-ulm.de (Heiner Wolf) Newsgroups: bionet.microbiology,bionet.molbio.proteins,bionet.molbio.proteins.7tms_r,bionet.xtallography,sci.bio.microbiology Subject: Replacement for E.col at pH 3 ? Date: Fri, 12 Apr 1996 17:11:24 +0200 Organization: Distributed Systems, University Ulm Lines: 12 Message-ID: NNTP-Posting-Host: power_mac.informatik.uni-ulm.de Xref: biosci bionet.microbiology:5695 bionet.molbio.proteins:7555 bionet.molbio.proteins.7tms_r:693 bionet.xtallography:2493 sci.bio.microbiology:3144 My protein is stable at pH strength 3. But E. coli is inactive there. Which organism can replace E. coli at pH 3 ? Please send email to wolf@informatik.uni-ulm.de -Heiner Wolf -- Distributed Systems Dept. voice: +49 731 502 4145 University of Ulm internet: wolf@informatik.uni-ulm.de 89069 Ulm ethernet: 08:00:20:12:2a:01 Germany WebVideo: http://rr-vs.informatik.uni-ulm.de/rr/ From owner-proteins@net.bio.net Thu Apr 11 23:00:00 1996 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!acs2.byu.edu!news.cuny.edu!caen!uwm.edu!cs.utexas.edu!howland.reston.ans.net!paladin.american.edu!news.ecn.uoknor.edu!news.cis.okstate.edu!usenet From: Ron Tate Newsgroups: bionet.molbio.proteins Subject: Re: Spotted Coomassie Staining? Date: Fri, 12 Apr 1996 07:27:17 -0500 Organization: Oklahoma State University, Biochemistry and Molecular Biology Lines: 26 Message-ID: <316E4C25.1048@bmb-fs1.biochem.okstate.edu> References: NNTP-Posting-Host: firefly3.biochem.okstate.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Win95; I) crbaker wrote: > > Although having run and stained a large number of SDS polyacrylamide > gels without any previous problems the last two I have run have > stained unusually with Coomassie - protein lanes and bands > appear spotted with visable dots of stain rather than the normal > uniform staining of bands. This only came apparent on destaining and > I am at a loss to explain why it has suddenly occurred. Has anyone > seen this before or have an explanation? > > Cara Baker > crbaker@mail.tcd.ie Cara, It sounds like the the Coomasie has precipitated. If this is an old stock of Coomasie stain you may have to filter it occasionally. Hope it helps Happy Hunting -- >>>>>>---------------------------> >Ron Tate >Lab of Franklin Leach >Dept. of Biochem. & Molecular Biology >Oklahoma State University rtate@bmb-fs1.biochem.okstate.edu (405) 744-9326 --------------------------------------------- From owner-proteins@net.bio.net Thu Apr 11 23:00:00 1996 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!news.wwa.com!news From: nc26@wwa.com Newsgroups: bionet.molbio.proteins Subject: Native Gel Difficulty Date: 13 Apr 1996 00:15:37 GMT Organization: WorldWide Access (tm) - Chicagoland Internet Services (http://www.wwa.com) Lines: 7 Message-ID: <4kmrn9$3bh@kirin.wwa.com> NNTP-Posting-Host: vh1-037.wwa.com X-Newsreader: SPRY News 3.03 (SPRY, Inc.) Can someone help me with the following problem? I am trying to run a western blot against surface protein on a native gel. The protein is not reactive with the antibody in a reduce form, thus the native gel. The problem is the surface protein will not migrate into the gel in its native form. I stain the gel with Coomassie Blue and clearly see the protein getting stuck in the 4% stacker. My sample buffer contains 3.125% SDS in a 0.1 M Tris buffer. Does anyone know of a protocol that would allow me to keep my protein in its native form on an SDS-PAGE gel? Thanks in advance for any information. From owner-proteins@net.bio.net Thu Apr 11 23:00:00 1996 Path: biosci!CS.SANDIA.GOV!scistra From: scistra@CS.SANDIA.GOV (Sorin C. Istrail) Newsgroups: bionet.molbio.proteins Subject: Call For Papers: Computational Molecular Biology Date: 12 Apr 1996 16:07:40 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 79 Sender: daemon@net.bio.net Distribution: world Message-ID: <9604122303.AA03785@frodo.cs.sandia.gov.noname> NNTP-Posting-Host: net.bio.net ***CALL FOR PAPERS* CALL FOR PAPERS* CALL FOR PAPERS*** DISCRETE APPLIED MATHEMATICS Announcing a Second Special Issue on Computational Molecular Biology Guest Editors: Sorin Istrail, Pavel Pevzner, Ron Shamir Submission Deadline: August 1, 1996 Manuscripts are solicited for a special issue of Discrete Applied Mathematics on topics concerning the development of new combinatorial and algorithmic techniques in computational molecular biology. With this announcement Discrete Applied Mathematics continues the series of special issues devoted to computational molecular biology. The series publishes papers on the mathematical and algorithmic foundations of the inherently discrete aspects of computational biology. The traditional partnership of mathematics and physics has advanced and enriched both disciplines. In a similar partnership, mathematics and algorithms are becoming crucial tools in the rapid advancement of molecular biology. At the same time, the computational challenges of these biological disciplines raise exciting new problems in discrete mathematics and theoretical computer science. To paraphrase Stan Ulam, those challenges reflect "not only what mathematics can do for biology but what biology can do for mathematics." The following is a (nonexhaustive) list of possible topics of interest for the special issue: * DNA mapping * DNA sequencing * DNA/protein sequence comparison * molecular evolution * RNA/protein structure * gene/motif recognition Seven (7) copies of complete manuscripts should be sent to any of the Guest Editors indicated below by August 1, 1996. We expect this Second Special Issue to appear in the Fall 1997. Manuscripts must be prepared according to the normal submission requirements of Discrete Applied Mathematics, as described in each issue of the journal. The Guest Editors will make every possible effort to assure the timely completion of a thorough refereeing process. The Guest Editors are: Sorin Istrail Sandia National Laboratories Algorithms and Discrete Mathematics Department P.O.Box 5800, MS 1110 Albuquerque, NM 87185-5800 scistra@cs.sandia.gov Pavel Pevzner University of Southern California Department of Mathematics, DRB 155 Los Angeles, CA 90089-1113 ppevzner@hto.usc.edu Ron Shamir Dept. of Computer Science Tel Aviv University Tel Aviv 69978 ISRAEL shamir@math.tau.ac.il From owner-proteins@net.bio.net Thu Apr 11 23:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!swrinde!newsfeed.internetmci.com!info.ucla.edu!nnrp.info.ucla.edu!ts34-9.wla.ts.ucla.edu!user From: xma@ewald.mbi.ucla.edu (Xiao-Jun Ma) Newsgroups: bionet.molbio.proteins Subject: Poor binding and elution of GST-fusion protein Date: 13 Apr 1996 03:12:03 GMT Organization: University of California, Los Angeles Lines: 4 Message-ID: NNTP-Posting-Host: ts34-9.wla.ts.ucla.edu I have a GST-fusion protein about 97kd in size. The protein is produced OK, but after incubating the extract with the GSH-beads, most of the fusion protein remains unbound. What's worse, only 10-20% of the bound protein can be eluted by 20mM glutathione. Any suggestions? From owner-proteins@net.bio.net Fri Apr 12 23:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.proteins Subject: IMPORTANT - BIOSCI Fundraising Update! Date: 13 Apr 1996 02:01:14 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 149 Sender: daemon@net.bio.net Distribution: world Message-ID: <199604130900.CAA25409@net.bio.net> NNTP-Posting-Host: net.bio.net I'm interrupting the usual monthly posting of the BIOSCI miniFAQ to bring you up to date on BIOSCI fundraising progress, a topic of concern to your future use of this resource. Thank you in advance for taking the time to read this message carefully. Last year we announced that BIOSCI was going to adopt the U.S. Public Broadcasting System model to fund its operations after our DOE/NSF grant runs out later this year. Unlike PBS, we are not soliciting contributions from users; we are only selling ads on our Web pages solely to cover our operating costs. Our goal is to seek sponsorships until we build up an operating reserve of about $100,000 and then cease further promotions until we need to build the reserve back up. (The accountants among our readership will be familiar with the problem of deferred revenue which we can not safely utilize until ads have been displayed for a period of time.) We have three sponsors to date with a couple more pending. The process is time-consuming, however, and we need your help as explained further below. Our operating costs consist of our network connection, phone lines, hardware maintenance (we hope to have new and faster hardware soon!), plus 0.7 FTE of salaries covering UNIX systems admin, technical support, quality assurance, i.e., testing, of our system, and administrative costs (such as the time it takes to actually find/write/call potential sponsors and raise money!). Although the BIOSCI staff does get compensated for a portion of the work that they do, this project has always received a lot of free after-hours and "vacation" time labor, so we hope that no one will begrudge the time that we do charge to the project to serve you. All of the three part-time staff members, Dave Mack, Julie Lawrence, and myself, have full time day jobs and families in addition to working hard to keep this service running for all of you. Julie and Dave Mack are subcontractors for BIOSCI; my time that is charged to the project defrays a portion of my regular salary instead of adding to my income. Besides having to relocate the project, we were very busy this last year building new infrastructure such as our WWW hypermail interface to the system. This was released last December along with scores of WAIS indices for the newsgroups. Virtually everything is complete, although we do continue to find and fix bugs (many through your helpful feedback!). We are still having some problems with our WAIS indexing. The archives continue to grow rapidly. We are running over 100 indexes now versus three previously and any systems crashes cause greater havoc with the indexing than before! We are still working to fix this as fast as our resources permit and appreciate your patience, but we have been able to automate a lot of the infrastructure to reduce labor as compared to past requirements. We have also implemented new software to make moderation of BIOSCI/bionet newsgroups much easier and combat the growing problem of Internet junk mail and USENET "spamming." About 20% of our groups are now moderated, many of them by the BIOSCI staff! This, for example, made a major difference last year in the quality of content in our EMPLOYMENT/bionet.jobs.offered newsgroup which many commercial concerns and recruiting firms are using **without charge** to recruit candidates for positions in the biological sciences. We are also now in a position to have sponsors for individual newsgroups as you will have noticed if you have visited http://www.bio.net/ and clicked on "Access the BIOSCI/bionet newsgroups" recently. So, how can you help?? ---------------------- As noted above it can take a lot of time to contact potential sponsors if I have to do it all myself. Our request is quite simple. You can do two important things which will take very little time for you individually. First, please use our WWW system at http://www.bio.net/ to access the archives. You can now post or reply to messages via your Web browser. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. Our hope is to quickly raise several large corporate/institutional sponsors on our heavily-used WWW locations (some stats appended below), and then end this sponsorship campaign so that our resources can continue to be used for service provision, not fundraising. Many of our specialty newsgroup WWW archives are still used by small communities of scientists (and they haven't been heavily promoted yet). While these may be valuable niche markets to some advertisers, it will generate more labor and overhead having to find these sponsors, fairly price the locations, and deal with lots of smaller sponsorships than fewer mid-to large sponsors. We are striving to keep our operation as lean and efficient as possible since we are not trying to make careers out of running BIOSCI. We are trying if at all possible to avoid the administrative overhead entailed with processing lots of small payments to reach our fundraising goals. I'd like to thank all of you for your help in advance. In helping us, you are also helping yourselves, not only in keeping this resource available for all of the both large and small research communities that we serve, but also by alleviating the need for us to go back and compete with researchers for tight grant dollars! We promised NSF when we were awarded the BIOSCI grant that we would carry out this mission to make the service self-supporting. With your help, we will succeed in continuing BIOSCI's work into its second decade. Thank you very much! Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net A list of our prime WWW sponsorship locations follow. Statistics are for the four week period from 22 Jan. - 18 Feb. 1996 and usage continues to grow. ---------------------------------------------------------------------- The overall BIOSCI WWW pages are currently visited by users from close to 5000 unique computer hosts per week. Web servers only log the Internet computer/host name and frequently more than one individual can connect to us from a particular host. Main home page, http://www.bio.net, visited recently by about 2100 unique hosts per week Main Newsgroups archives page, http://www.bio.net/archives.html, visited recently by about 1200 Unique hosts per week BIO-JOURNALS archive page, http://www.bio.net/BIO-JOURNALS.html, visited recently by about 1000 unique hosts per week. EMPLOYMENT archive pages: http://www.bio.net:80/hypermail/EMPLOYMENT/ and monthly header pages, visited recently by about 600 unique hosts per week. Address database search page, http://www.bio.net/addrsearch.html, visited recently by about 450 unique hosts per week. Methods newsgroup archive pages, http://www.bio.net:80/hypermail/METHDS- REAGNTS/ and monthly header pages, visited recently by about 350 unique hosts per week. ---------------------------------------------------------------------- From owner-proteins@net.bio.net Fri Apr 12 23:00:00 1996 Path: biosci!CS.SANDIA.GOV!scistra From: scistra@CS.SANDIA.GOV (Sorin C. Istrail) Newsgroups: bionet.molbio.proteins Subject: RECOMB 97: Call For Papers Date: 13 Apr 1996 15:49:47 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 191 Sender: daemon@net.bio.net Distribution: world Message-ID: <9604132245.AA07271@frodo.cs.sandia.gov.noname> NNTP-Posting-Host: net.bio.net CALL FOR PAPERS FIRST ANNUAL INTERNATIONAL CONFERENCE ON COMPUTATIONAL MOLECULAR BIOLOGY (RECOMB 97) January 20-22, 1997 Eldorado Hotel Santa Fe, New Mexico Co-sponsored by SLOAN Foundation Association for Computing Machinery US Department of Energy http://www.cs.sandia.gov/recomb97 The First Annual Conference on Research in Computational Molecular Biology (RECOMB 97), co-sponsored by the SLOAN Foundation, the Association for Computing Machinery (ACM) and US Department of Energy will be held in Santa Fe, New Mexico, January 20--22, 1997. 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 - DNA computing ABSTRACT SUBMISSION: Authors are requested to send 10 copies (preferably two sided copies) of a detailed extended abstract (5-10 pages) to: Professor Michael Waterman RECOMB 97 Program Chair University of Southern California Department of Mathematics, DRB 155 Los Angeles, CA 90089-1113 An abstract must be received by July 1, 1996. 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 97. NOTIFICATION: Authors will be notified of acceptance or rejection by a letter mailed on or before August 15th, 1996. A final copy of each accepted paper is required by September 15, 1994. 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. Limited financial support for the authors of the accepted papers will be available. 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 THE STANISLAW ULAM MEMORIAL COMPUTATIONAL BIOLOGY ADDRESS. The Banquet of the Conference will host the Stanislaw Ulam Memorial Lecture awarded by RECOMB to a scientist who has made major contributions in the computational aspects of the field. Dr. Eric Lander (MIT) will be delivering the first Stanislaw Ulam Address. THE DISTINGUISHED CONFERENCE LECTURE. The conference will start with the Distinguished Conference Lecture awarded by RECOMB to a scientist who has made major contributions in the biological aspects of the field. Dr. Rich Roberts (New England Biolabs), the 1994 Nobel Laureate will be delivering the Distinguished Conference Lecture. THE DISTINGUISHED NEW TECHNOLOGIES LECTURE. A lecture describing emerging, new technologies will be delivered by Dr. Robert Lipshutz (Affymetrix). 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 2 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. STEERING COMMITTEE: Sorin Istrail (Sandia National Laboratories) Richard Karp (University of Washington) Thomas Lengauer (GMD-SCAI, Germany) Pavel Pevzner, Chair (University of Southern California) Ron Shamir (Tel-Aviv University, Israel) Michael Waterman, Chair (University of Southern California) PROGRAM COMMITTEE MEMBERS: Steven Altschul (National Center for Biotechnology Information) Bonnie Berger, Publication Chair (MIT) Ken Dill (University of California San Francisco) Martin Farach (Rutgers University) Phil Green (University of Washington) Sorin Istrail, Chair of the Organizing Committee (Sandia National Laboratories) Richard Karp (University of Washington) Martin Karplus (Harvard University) Thomas Lengauer (GMD-SCAI, Germany) Webb Miller (Pennsylvania State University) Gene Myers (University of Arizona) Maynard Olson (University of Washington) Pavel Pevzner, (University of Southern California) Rich Roberts (New England Biolabs) David Sankoff (University of Montreal) Ron Shamir (Tel-Aviv University, Israel) Temple Smith (Boston University) Terry Speed (University of California Berkeley) Gary Stormo (University of Colorado) Martin Vingron (German Cancer Center) Tandy Warnow (University of Pennsylvania) Michael Waterman, Chair of the Program Committee (University of Southern California) Bruce Weir (North Carolina State University) The PMMB Meeting exploring the applications of statistics in molecular biology will be held in Santa Fe on January 14-19, 1997, just preceding RECOMB 97. Contact Sylvia Spengler sylviaj@violet.berkeley.edu (510)643-7799 for further information. LOCAL ARRANGEMENTS COMMITTEE: William Hart (Sandia National Laboratories), Chris Fields (National Center for Genome Resources), Sylvia Spengler (Coordinator with the PMMB Conference). Information about local arrangements can be obtained by consulting the conference web page http://www.cs.sandia.gov/recomb97 or from the Local Arrangements Chairman: Sorin Istrail Sandia National Labs Department 9423, MS 1110 Albuquerque, NM 87185-1110, USA phone: (505) 845-7612 fax: (505) 845-7442 scistra@cs.sandia.gov http://www.cs.sandia.gov/~scistra From owner-proteins@net.bio.net Fri Apr 12 23:00:00 1996 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!newsxfer2.itd.umich.edu!tank.news.pipex.net!pipex!oleane!in2p3.fr!univ-lyon1.fr!news.imag.fr!ciril.fr!u-strasbg.fr!localhost!francis.durst From: francis.durst@bota-ulp.u-strasbg.fr (Francis Durst) Newsgroups: bionet.molbio.proteins Subject: Chloroplastic and mitochondrial targetting peptides? Date: Sat, 13 Apr 1996 09:38:11 Organization: CNRS Lines: 16 Message-ID: NNTP-Posting-Host: frenzy.u-strasbg.fr X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Dear Netters, Is there an Internet access to the database of mitochondrial and chloroplastic leader sequences which was compiled by Dr. Gunnar von Heijne? Or where could I find a similar one? With many thanks Francis PS I had posted this before and then our news server went down, don't know if there was any answer Dr. Francis Durst CNRS / Universite Louis Pasteur Dept Cell. Mol. Enzymology Plant Mol. Biol. Inst. F-67083 Strasbourg, France From owner-proteins@net.bio.net Fri Apr 12 23:00:00 1996 Path: biosci!rutgers!uwm.edu!newsfeed.internetmci.com!in2.uu.net!newstf01.news.aol.com!newsbf02.news.aol.com!not-for-mail From: brucerat@aol.com (BruceRat) Newsgroups: bionet.molbio.proteins Subject: Gross Primary Production: aquatic ecosystems = ? Date: 13 Apr 1996 09:33:34 -0400 Organization: America Online, Inc. (1-800-827-6364) Lines: 9 Sender: root@newsbf02.news.aol.com Message-ID: <4koafe$bnm@newsbf02.news.aol.com> Reply-To: brucerat@aol.com (BruceRat) NNTP-Posting-Host: newsbf02.mail.aol.com I am looking for a value for Gross Primary Productivity in aquatic ecosystems. Though NET Primary Productivity estimates are common (~2000 g m-2 yr-1 for swamp and marsh) (Begon, Harper and Townsend, 1990), I am seeking a value for total photosynthetically fixed energy, without subtracting for respiration. In my case, I measured not increase in biomass over a year, but increase in dissolved oxygen over a matter of hours. Any suggestions out there? Bruce Ratcliffe, Fresno From owner-proteins@net.bio.net Fri Apr 12 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!in1.uu.net!brighton.openmarket.com!decwrl!tribune.usask.ca!rover.ucs.ualberta.ca!ts1-port21.mas.ualberta.ca!wgallin From: wgallin@gpu.srv.ualberta.ca (Warren Gallin) Newsgroups: bionet.molbio.proteins Subject: Re: Native Gel Difficulty Date: Sat, 13 Apr 96 20:55:40 GMT Organization: University of Alberta Lines: 32 Message-ID: References: <4kmrn9$3bh@kirin.wwa.com> NNTP-Posting-Host: ts1-port21.mas.ualberta.ca X-Newsreader: VersaTerm Link v1.1.4 In Article <4kmrn9$3bh@kirin.wwa.com>, nc26@wwa.com wrote: >Can someone help me with the following problem? I am trying to run a western blot against >surface protein on a native gel. The protein is not reactive with the antibody in a reduce form, >thus the native gel. The problem is the surface protein will not migrate into the gel in its native >form. I stain the gel with Coomassie Blue and clearly see the protein getting stuck in the 4% >stacker. My sample buffer contains 3.125% SDS in a 0.1 M Tris buffer. If you are using SDS in your sample buffer, it isn't a native gel. First SDS is a strong denaturant. Second, it imparts a strong negative charge to the proteins that it binds to. If you are using a buffer system that is for a native gel for running positively charged proteins, it won't move. You don't specify. >Does anyone know of a >protocol that would allow me to keep my protein in its native form on an SDS-PAGE gel? Thanks >in advance for any information. Not possible. You need to rethink what you are trying to do. Read a basic manual on electrophoresis. Warren Gallin Department of Biological Sciences University of Alberta Edmonton, Alberta T6G 2E9 Canada wgallin@gpu.srv.ualberta.ca From owner-proteins@net.bio.net Sat Apr 13 23:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!pasteur.fr!univ-lyon1.fr!in2p3.fr!oleane!plug.news.pipex.net!pipex!tank.news.pipex.net!pipex!swrinde!cs.utexas.edu!howland.reston.ans.net!torn!nott!cunews!freenet-news.carleton.ca!FreeNet.Carleton.CA!at332 From: at332@FreeNet.Carleton.CA (Matt Parker) Newsgroups: bionet.molbio.proteins Subject: Yellow stuff in nitric acid Date: 14 Apr 1996 21:03:05 GMT Organization: The National Capital FreeNet Lines: 3 Sender: at332@freenet2.carleton.ca (Matt Parker) Message-ID: <4krp69$brs@freenet-news.carleton.ca> Reply-To: at332@FreeNet.Carleton.CA (Matt Parker) NNTP-Posting-Host: freenet2.carleton.ca Hi! We have a bottle of nitric acid (for cleaning cuvettes) which is rapidly turning yellow. Does anybody know what is causing this? From owner-proteins@net.bio.net Sat Apr 13 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!news.compuserve.com!news.production.compuserve.com!news From: ROBYN ONEAL <102170.125@CompuServe.COM> Newsgroups: bionet.molbio.proteins,bionet.molbio.proteins.7tms_r,sci.bio.misc,sci.bio.technology,sci.chem Subject: ELECTROPORESIS,PROTEIN GELS Date: 15 Apr 1996 01:19:05 GMT Organization: CompuServe, Inc. (1-800-689-0736) Lines: 8 Distribution: inet Message-ID: <4ks869$pk1$1@mhadg.production.compuserve.com> Xref: biosci bionet.molbio.proteins:7570 bionet.molbio.proteins.7tms_r:695 sci.bio.misc:2863 sci.bio.technology:5203 sci.chem:53931 IF YOU WORK IN A LAB THAT USES ACRYLAMIDE GELS. I HAVE FOUND A NEW PRODUCT THAT SAVED ME TIME IN THE PREPARATION TO RUN A GEL. I FOUND THE GEL EASY TO WORK WITH AND THE BANDS TO COME OUT WELL FORMED AND CLEAR. I FOUND INFORMATION ABOUT THIS NEW TYPE OF GEL ON THE WEB. URL ADDRESS HTTP://HOME.NAVISOFT.COM/PROFBUS/ESSEX1.HTM ROBYN O'NEAL From owner-proteins@net.bio.net Sun Apr 14 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!newsfeed.sunet.se!news01.sunet.se!sunic!news99.sunet.se!news.uni-c.dk!news.daimi.aau.dk!biobase!hteicher From: hteicher@biobase.dk (Harald Teicher) Newsgroups: bionet.molbio.proteins Subject: enzyme kinetic software Date: 15 Apr 1996 14:42:32 GMT Organization: The Danish BioBase Lines: 12 Message-ID: <4ktn8o$8dr@bioalp.biobase.dk> NNTP-Posting-Host: biobase.dk X-Newsreader: TIN [version 1.2 PL2] could someone please give me the sites of shareware programs for the calc. of enzyme kinetics, plotting of data etc the type of thing i have in mind is the windows program hyper.exe, or kinetic.zip ideally the program would handle 2 substrate data, but one substr data capabilities would be fine thanx in advance harry From owner-proteins@net.bio.net Sun Apr 14 23:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!news.belnet.be!swsbe6.switch.ch!surfnet.nl!sun4nl!EU.net!howland.reston.ans.net!news.starnet.net!newsreader.wustl.edu!newsreader!agarwal From: agarwal@ibc.wustl.edu (Pankaj Agarwal) Newsgroups: bionet.molbio.proteins Subject: ISMB'96 Registration and Poster Abstracts Followup-To: bionet.molbio.proteins Date: 15 Apr 1996 22:44:55 GMT Organization: Washington University in St. Louis, MO USA Lines: 240 Distribution: world Message-ID: NNTP-Posting-Host: @ibc.wustl.edu The Fourth International Conference on Computational Biology Intelligent Systems for Molecular Biology '96 June 12 to 15, 1996 Washington University St. Louis, Missouri, USA http://www.ibc.wustl.edu/ismb96/ -- Registration open (late fees after May 1) http://www.ibc.wustl.edu/ismb96/register.html -- Housing reservations (deadline May 1) http://www.ibc.wustl.edu/ismb96/accommodations.html -- Abstracts for open poster session (extended deadline May 15) http://www.ibc.wustl.edu/ismb96/abstract.cgi -- Tentative calendar http://www.ibc.wustl.edu/ismb96/calendar.html -- List of tutorials offered http://www.ibc.wustl.edu/ismb96/#TutSched -- Job fair http://www.ibc.wustl.edu/ismb96/jobfair -- Vendor fair (deadline May 15) http://www.ibc.wustl.edu/ismb96/#VendorFair Available later this week -- List of papers to appear in proceedings -- List of software demonstrations to be presented -- Detailed calendar -- Application procedure for travel awards for students If you have access to the world wide web, please register for ISMB'96 directly on the WWW http://www.ibc.wustl.edu/ismb96/register.html Also check http://www.ibc.wustl.edu/ismb96/ for the latest information on the conference. A distribution mailing list is available for people who want to be kept informed about ISMB matters. Join it by sending mail to majordomo@ibc.wustl.edu with the words subscribe ismb96 as the body of the message. ************************************************************ REGISTRATION FORM for ISMB 96 (late fees after May 1, 1996) ************************************************************ (to be used only if you do not have access to the WWW) (http://www.ibc.wustl.edu/ismb96/register.html) Please fill out and email to ismb96@ibc.wustl.edu or fax to (314) 362-0234 or paper mail to : ISMB'96 registration Institute for Biomedical Computing 700 South Euclid Avenue St. Louis, MO 63110-1012 USA Name: ________________________________________ Department: ________________________________________ Organization:________________________________________ The department and organization will be included on your ISMB'96 badge. Address: ________________________________________ ________________________________________ ________________________________________ ________________________________________ Phone: ________________________________________ Fax: ________________________________________ Email: ________________________________________ Your e-mail address will be used as a unique identifier for your registration. URL: Please make your choice by changing "___" to "_X_". This will make it easier to parse your answers. Professional Standing: ___ Undergrad Student ___ Grad Student ___ Postdoc ___ Programmer ___ Faculty ___ Scientist ___ Staff Registration status: ___ Unspecified ___ Commercial ($600) ___ Academic/Government ($350) ___ Full-Time Student