From owner-repertoires@net.bio.net Sun Apr 14 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: "Janet Clench, Library, Tel:(39 6)91093220" Newsgroups: bionet.molecules.repertoires Subject: Another update for your combinatorial & molecular repertoire dbases. Date: 15 Apr 1996 13:23:57 +0100 Lines: 190 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4ktf4t$ppo@mserv1.dl.ac.uk> Original-To: molreps@dl.ac.uk ******************************************************** SUBJECT: Combinatorial & Phage Libraries DATE: March 11, 18, 25, April 1, 1996 ******************************************************** Biotechniques 20: 3 (MAR 1996) PS Andersen, H Orum, J Engberg One-step cloning of murine fab gene fragments independent of IgH isotype for phage display libraries 340-342 International Journal of Biochemistry & Cell Biology 28: 2 (FEB 1996) EEO Caldwell, VD Nadkarni, JR Fromm, RJ Linhardt, JM Weiler Importance of specific amino acids in protein binding sites for heparin and heparan sulfate 203-216 Nature Medicine 2: 3 (MAR 1996) MA Barry, WJ Dower, SA Johnston Toward cell-targeting gene therapy vectors: selection of cell-binding peptides from random peptide- presenting phage libraries 299-305 Journal of the American Chemical Society 118: 9 (MAR 6 1996) SK Sarkar, RS Garigipati, JL Adams, PA Keifer An NMR method to identify nondestructively chemical compounds bound to a single solid-phase-synthesis bead for combinatorial chemistry applications 2305-2306 Proceedings of the National Academy of Sciences of the United States of America 93: 5 (MAR 5 1996) YCJ Chen, K Delbrook, C Dealwis, L Mimms, IK Mushahwar, W Mandecki Discontinuous epitopes of hepatitis b surface antigen derived from a filamentous phage peptide library 1997-2001 Proceedings of the National Academy of Sciences of the United States of America 93: 5 (MAR 5 1996) PI Neophytou, BO Roep, SD Arden, EM Muir, G Duinkerken, A Kallan, RRP Devries, JC Hutton T-cell epitope analysis using subtracted expression libraries (TEASEL): application to a 38-kDa autoantigen recognized by t cells from an insulin- dependent diabetic patient 2014-2018 Laboratory Animal Science 46: 1 (FEB 1996) NC Peterson Recombinant antibodies: alternative strategies for developing and manipulating murine-derived monoclonal antibodies 8-14 Analytical Biochemistry 234: 2 (FEB 15 1996) JA Boutin, P Hennig, PH Lambert, S Bertin, L Petit, JP Mahieu, B Serkiz, JP Volland, JL Fauchere Combinatorial peptide libraries: robotic synthesis and analysis by nuclear magnetic resonance, mass spectrometry, tandem mass spectrometry, and high- performance capillary electrophoresis techniques 126-141 Journal of the American Chemical Society 118: 7 (FEB 21 1996) J Singh, MA Ator, EP Jaeger, MP Allen, DA Whipple, JE Soloweij, S Chowdhary, AM Treasurywala Application of genetic algorithms to combinatorial synthesis: a computational approach to lead identification and lead optimization 1669-1676 Journal of the American Chemical Society 118: 7 (FEB 21 1996) YA Cheng, T Suenaga, WC Still Sequence-selective peptide binding with a peptido- A,B-trans-steroidal receptor selected from an encoded combinatorial receptor library 1813-1814 Journal of the American Chemical Society 118: 8 (FEB 28 1996) DL Boger, CM Tarby, PL Myers, LH Caporale Generalized dipeptidomimetic template: solution phase parallel synthesis of combinatorial libraries 2109-2110 Gene 169: 1 (FEB 22 1996) LF Wang, M Yu, JR White, BT Eaton BTag: a novel six-residue epitope tag for surveillance and purification of recombinant proteins 53-58 Gene 169: 1 (FEB 22 1996) NB Adey, BK Kay Identification of calmodulin-binding peptide consensus sequences from a phage-displayed random peptide library 133-134 International Journal of Peptide and Protein Research 47: 1-2 (JAN-FEB 1996) JA Buettner, CA Dadd, GA Baumbach, BL Masecar, DJ Hammond Chemically derived peptide libraries: a new resin and methodology for lead identification 70-83 Journal of Organic Chemistry 61: 3 (FEB 9 1996) MF Gordeev, DV Patel, EM Gordon Approaches to combinatorial synthesis of heterocycles: a solid-phase synthesis of 1,4- dihydropyridines 924-928 Tetrahedron Letters 37: 7 (FEB 12 1996) BA Dressman, LA Spangle, SW Kaldor Solid phase synthesis of hydantoins using a carbamate linker and a novel cyclization cleavage step 937-940 Gene 168: 1 (FEB 2 1996) MJ Calcutt, AA Komissarov, MT Marchbank, SL Deutscher Analysis of a nucleic-acid-binding antibody fragment: construction and characterization of heavy-chain complementarity-determining region switch variants 9-14 Methods in Cell Biology, Vol 50 (Series: Methods in Cell Biology 50 (1995)) WL Crosby, P Schorr Principles and applications of recombinant antibody phage display technology to plant biology 85-99 Peptides (1995) RA Houghten Soluble chemical combinatorial libraries: current capabilities and future possibilities 395-417 Biochemistry 35: 7 (FEB 20 1996) NO Siemers, DE Yelton, J Bajorath, PD Senter Modifying the specificity and activity of the enterobacter cloacae p99 beta-lactamase by mutagenesis within an m13 phage vector 2104-2111 European Journal of Biochemistry 236: 1 (FEB 15 1996) L Pridzun, KH Wiesmuller, S Kienle, G Jung, P Walden Amino acid preferences in the octapeptide subunit of the major histocompatibility complex class i heterotrimer h-2L 249-253 Journal of Biological Chemistry 271: 8 (FEB 23 1996) SE Blondelle, RA Houghten, E Perezpaya Identification of inhibitors of melittin using nonsupport-bound combinatorial libraries 4093-4099 Journal of Biological Chemistry 271: 8 (FEB 23 1996) E Perezpaya, RA Houghten, SE Blondelle Functionalized protein-like structures from conformationally defined synthetic combinatorial libraries 4120-4126 Trends in Biotechnology 14: 2 (FEB 1996) SE Blondelle, RA Houghten Novel antimicrobial compounds identified using synthetic combinatorial library technology 60-65 Tetrahedron - Asymmetry 7: 2 (FEB 1996) JC Estevez, J Saunders, GS Besra, PJ Brennan, RJ Nash, GWJ Fleet Mimics of l-rhamnose: synthesis of c-glycosides of l- rhamnofuranose and an alpha-azidoester as divergent intermediates for combinatorial generation of rhamnofuranose libraries 383-386 From owner-repertoires@net.bio.net Tue Apr 16 23:00:00 1996 Path: biosci!SDSC.EDU!bourne From: bourne@SDSC.EDU (Philip Bourne) Newsgroups: bionet.molecules.repertoires Subject: String Search of the Complete PDB Date: 17 Apr 1996 08:51:23 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <317512C9.167EB0E7@sdsc.edu> NNTP-Posting-Host: net.bio.net A real-time keyword search of the PDB has been added to the macromolecular structure database located at the San Diego Supercomputer Center (SDSC). It can be accessed by selecting "text" followed by "General Keyword Search" from the home page of http://www.sdsc.edu/moose Unlike the more scientifically meaningful Web based queries this is a brute force approach to finding a structure of interest simply by searching all the words ahead of the ATOM records in all PDB files found on the SDSC PDB mirror. A list of structure entries containing the keyword(s) will be returned and can be selected. Like the database itself this is updated nightly from the PDB ftp archives. The keyword search uses the Harvest Gatherer and Broker developed at the University of Colorado. /Phil Bourne From owner-repertoires@net.bio.net Wed Apr 17 23:00:00 1996 Path: biosci!lhc.nlm.nih.gov!crick.sura.net!cpk-news-hub1.bbnplanet.com!news.ums.edu!umabnet.ab.umd.edu!beaker.ab.umd.edu!user From: pemanuel@umabnet.ab.edu (X) Newsgroups: bionet.molecules.repertoires Subject: pComb3H problems-Help! Date: Wed, 17 Apr 1996 13:53:21 -0500 Organization: UMAB Lines: 34 Message-ID: NNTP-Posting-Host: beaker.ab.umd.edu We have constructed a Fab antibody library in the Scripp's phage display vector pComb3H. The library is propogated in XL-1 Blue cells. Infection with VSCM13 leads to bacteriophage which display the Fab on their surface for enrichment (biopanning). The DNA frm the library has a light chain (Xba/Sac) and a heavy chain (Xho/Spe) inserted into it. DNA isolated from the primary antibody library has both inserts released upon double digestions. Proper size and everyone is happy. So does the DNA isolated from the first round of biopanning. But the DNA isolated from the cells of biopanning round 2 and round 3 seems to be uncut-able with the proper enzymes. No light or heavy chain is released. Xba seems to linearize the plasmid but no insert is released upon digestion with Xba/Sac or Xho/Spe or even EcoR1 and Spe. Is this a deletion of our inserts? Is this the "recombination events" we were told could happen? I am not sure how these recombination events would take form so I am guessing I should go back to the earlier cell stocks and try biopanning again. Any advice. Peter -- University of Maryland School of Medicine 410-706-429410-706-8012 FAX From owner-repertoires@net.bio.net Sun Apr 21 23:00:00 1996 Newsgroups: bionet.molecules.repertoires Path: biosci!rutgers!csn!news-1.csn.net!imci3!imci4!newsfeed.internetmci.com!in2.uu.net!sangam!iitb!powai!niharika.phy.iitb.ernet.in!krishnan From: krishnan@PROBLEM_WITH_INEWS_DOMAIN_FILE (s krishnan) Subject: Workshop on Biotechnology Sender: news@powai.cc.iitb.ernet.in (news system user) Message-ID: Date: Mon, 22 Apr 1996 10:11:33 GMT Organization: Computer Centre, IIT Bombay - 400 076, India X-Newsreader: TIN [version 1.2 PL2] Lines: 38 International Symposium on 'Cyanobacterial Biotechnology', September 18-21, 1996 Venue: National Facility for Marine Cyanobacteria Bharathidasan University Tiruchirapalli 620 024 India Review papers covering all aspects Cyanobacterial Biotechnology are invited from 30 senior scientists from different countries. Response so far from 150 scientists all over the world. Interested persons can participate either observers or send abstract for poster presentation immediately. Registration US $ 100 for scientists and US $ 50 for bonafide students. Registration after May 31, 1996 would involve an additional US$ 50 for both categories. Registration fee includes accommodation, food and conference materials for the symposium period. For further details contact Dr. G. Subramanian, Director, National Facility Marine Cyanobacteria, Bharathidasan University, Tiruchirapalli 620 024, India Telephone +91 431 660352, Fax +91 431 660245, E.mail. nfmc@bdu.rect.ernet.in In case, if you have problems with the above email address, send mail to krishnan@phy.iitb.ernet.in From owner-repertoires@net.bio.net Mon Apr 22 23:00:00 1996 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!nntp0.brunel.ac.uk!strath-cs!queens-belfast.ac.uk!bcg0197 From: bcg0197@queens-belfast.ac.uk (Andrew Wallace) Newsgroups: bionet.molecules.repertoires Subject: Re: pComb3H problem Message-ID: <1996Apr23.171425.6150@queens-belfast.ac.uk> Date: 23 Apr 96 17:14:25 GMT References: Organization: Queen's University of Belfast Lines: 45 In article , pemanuel@umabnet.ab.edu (X) writes: > We have constructed a Fab antibody library in the Scripp's phage display > vector pComb3H. The library is propogated in XL-1 Blue cells. Infection > with VSCM13 leads to bacteriophage which display the Fab on their surface > for enrichment (biopanning). > > The DNA frm the library has a light chain (Xba/Sac) and a heavy chain > (Xho/Spe) inserted into it. > > DNA isolated from the primary antibody library has both inserts released > upon double digestions. Proper size and everyone is happy. > > So does the DNA isolated from the first round of biopanning. > > But the DNA isolated from the cells of biopanning round 2 and round 3 > seems to be uncut-able with the proper enzymes. > > No light or heavy chain is released. Xba seems to linearize the plasmid > but no insert is released upon digestion with Xba/Sac or Xho/Spe or even > EcoR1 and Spe. > > Is this a deletion of our inserts? > > Is this the "recombination events" we were told could happen? > > I am not sure how these recombination events would take form so I am > guessing I should go back to the earlier cell stocks and try again. Any > advice. > Peter > > -- > > University of Maryland > School of Medicine > 410-706-429410-706-8012 FAX Did you try asking in Richard Lerner's lab? They have a lot of experience on working with antibody libraries. Could the DNA have become methylated and so not be recognised by your restriction enzymes? Just a thought... Andrew a.wallace@queens-belfast.ac.uk (new email address) From owner-repertoires@net.bio.net Mon Apr 22 23:00:00 1996 Path: biosci!SAMBA.CNB.UAM.ES!jltoran From: jltoran@SAMBA.CNB.UAM.ES (jose luis toran garcia) Newsgroups: bionet.molecules.repertoires Subject: tcr library Date: 23 Apr 1996 04:25:28 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net I am interested in a mouse and human Vbeta TCR library. I would like to now if any commercial TCR library are available. ************************************** JOSE LUIS TORAN GARCIA Centro Nacional de Biotecnologia Universidad Autonoma De Madrid C.S.I.C 28040 Madrid, Spain. Phone: 34-1-5854530/33/37 FAX:34-1-3720493 MAIL: JLTORAN@SAMBA.CNB.UAM.ES ************************************** From owner-repertoires@net.bio.net Sat Apr 27 23:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molecules.repertoires Subject: IMPORTANT - BIOSCI Fundraising Update! Date: 28 Apr 1996 02:00:38 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 154 Sender: daemon@net.bio.net Distribution: world Message-ID: <199604280900.CAA08511@net.bio.net> NNTP-Posting-Host: net.bio.net BIOSCI is about halfway to its funding goal!! I'm interrupting the usual monthly posting of the BIOSCI miniFAQ to bring you up to date on BIOSCI fundraising progress, a topic of concern to your future use of this resource. Thank you in advance for taking the time to read this message carefully. Last year we announced that BIOSCI was going to adopt the U.S. Public Broadcasting System model to fund its operations after our DOE/NSF grant runs out later this year. Unlike PBS, we are not soliciting contributions from users; we are only selling ads on our Web pages solely to cover our operating costs. Our goal is to seek sponsorships until we build up an operating reserve of about $100,000 and then cease further promotions until we need to build the reserve back up. (The accountants among our readership will be familiar with the problem of deferred revenue which we can not safely utilize until ads have been displayed for a period of time.) We are only about halfway to our funding goal and need to raise further funds to avoid having to curtail services at net.bio.net. Fundraising is time-consuming, however, and we need your help as explained further below. Our operating costs consist of our network connection, phone lines, hardware maintenance (we will be getting newer and faster hardware soon!), plus 0.7 FTE of salaries covering UNIX systems admin, technical support, quality assurance, i.e., testing, of our system, and administrative costs (such as the time it takes to actually find/write/call potential sponsors and raise money!). Although the BIOSCI staff does get compensated for a portion of the work that they do, this project has always received a lot of free after-hours and "vacation" time labor, so we hope that no one will begrudge the time that we do charge to the project to serve you. All of the three part-time staff members, Dave Mack, Julie Lawrence, and myself, have full time day jobs and families in addition to working hard to keep this service running for all of you. Julie and Dave Mack are subcontractors for BIOSCI; my time that is charged to the project defrays a portion of my regular salary instead of adding to my income. Besides having to relocate the project, we were very busy this last year building new infrastructure such as our WWW hypermail interface to the system. This was released last December along with scores of WAIS indices for the newsgroups. Virtually everything is complete, although we do continue to find and fix bugs (many through your helpful feedback!). We are still having some problems with our WAIS indexing. The archives continue to grow rapidly. We are running over 100 indexes now versus three previously and any systems crashes cause greater havoc with the indexing than before! We are still working to fix this as fast as our resources permit and appreciate your patience, but we have been able to automate a lot of the infrastructure to reduce labor as compared to past requirements. We have also implemented new software to make moderation of BIOSCI/bionet newsgroups much easier and combat the growing problem of Internet junk mail and USENET "spamming." About 20% of our groups are now moderated, many of them by the BIOSCI staff! This, for example, made a major difference last year in the quality of content in our EMPLOYMENT/bionet.jobs.offered newsgroup which many commercial concerns and recruiting firms are using **without charge** to recruit candidates for positions in the biological sciences. We are also now in a position to have sponsors for individual newsgroups as you will have noticed if you have visited http://www.bio.net/ and clicked on "Access the BIOSCI/bionet newsgroups" recently. So, how can you help?? ---------------------- As noted above it can take a lot of time to contact potential sponsors if I have to do it all myself. Our request is quite simple. You can do two important things which will take very little time for you individually. First, please use our WWW system at http://www.bio.net/ to access the archives. You can now post or reply to messages via your Web browser. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. Our hope is to quickly raise several large corporate/institutional sponsors on our heavily-used WWW locations (some stats appended below), and then end this sponsorship campaign so that our resources can continue to be used for service provision, not fundraising. Many of our specialty newsgroup WWW archives are still used by small communities of scientists (and they haven't been heavily promoted yet). While these may be valuable niche markets to some advertisers, it will generate more labor and overhead having to find these sponsors, fairly price the locations, and deal with lots of smaller sponsorships than fewer mid-to large sponsors. We are striving to keep our operation as lean and efficient as possible since we are not trying to make careers out of running BIOSCI. We are trying if at all possible to avoid the administrative overhead entailed with processing lots of small payments to reach our fundraising goals. I'd like to thank all of you for your help in advance. In helping us, you are also helping yourselves, not only in keeping this resource available for all of the both large and small research communities that we serve, but also by alleviating the need for us to go back and compete with researchers for tight grant dollars! We promised NSF when we were awarded the BIOSCI grant that we would carry out this mission to make the service self-supporting. With your help, we will succeed in continuing BIOSCI's work into its second decade. Thank you very much! Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net A list of our prime WWW sponsorship locations follow. Please contact us for further details. ---------------------------------------------------------------------- The overall BIOSCI WWW pages are currently visited by users from close to 5500 unique computer hosts per week. Web servers only log the Internet computer/host name and frequently more than one individual can connect to us from a particular host. Main home page, http://www.bio.net, visited recently by about 2100 unique hosts per week Main Newsgroups archives page, http://www.bio.net/archives.html, visited recently by about 1200 Unique hosts per week BIO-JOURNALS archive page, http://www.bio.net/BIO-JOURNALS.html, visited recently by about 1000 unique hosts per week. EMPLOYMENT archive pages: http://www.bio.net:80/hypermail/EMPLOYMENT/ and monthly header pages, visited recently by about 800 unique hosts per week. Address database search page, http://www.bio.net/addrsearch.html, visited recently by about 450 unique hosts per week. Methods newsgroup archive pages, http://www.bio.net:80/hypermail/METHDS- REAGNTS/ and monthly header pages, visited recently by about 350 unique hosts per week. Ads can also be displayed on various combinations of other BIOSCI/bionet newsgroups. Please contact us at biosci-help@net.bio.net for details. ---------------------------------------------------------------------- From owner-repertoires@net.bio.net Tue Apr 30 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: Andrew Wallace Newsgroups: bionet.molecules.repertoires Subject: RE: Biosci fundraising update Date: 1 May 1996 17:54:04 +0100 Lines: 65 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4m84vc$hv1@mserv1.dl.ac.uk> Original-To: molreps@dl.ac.uk In bionet.molecules.repertoires Msg # 126 Dave Kristofferson wrote: > BIOSCI is about halfway to its funding goal!! [background info deleted] >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. [deleted] I would like to add my voice to this call for support, especially the second proposal, so if anyone knows of a company or corporation who would be interested in sponsoring our molecules.repertoires page, please put them in touch with Dave (Affymax? Selectide? Houghten Pharmaceuticals? are you people out there?) To quote Dave again: > "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 > Thanks to anyone who can help in any way. Andrew ============================================================ Andrew Wallace, Ph.D. School of Biology and Biochemistry The Queen's University of Belfast 97 Lisburn Road Tel. +44-1232-335786 Belfast BT9 7BL Fax +44-1232-236505 Northern Ireland (UK) a.wallace@queens-belfast.ac.uk