From owner-repertoires@net.bio.net Tue Oct 07 23:00:00 1997 Path: biosci!biosci!not-for-mail From: "John C. DiCesare" Newsgroups: bionet.molecules.repertoires Subject: Undergraduate Involvment Date: 8 Oct 1997 00:10:01 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 58 Sender: daemon@net.bio.net Approved: a.wallace@qub.ac.uk Distribution: world Message-ID: Reply-To: "John C. DiCesare" NNTP-Posting-Host: net.bio.net Hi I am John DiCesare at the University of Tulsa and have been observing this list for a couple of years. I have several points for possible discussion. One of my research interests is in solid phase organic synthesis. The University of Tulsa only grants the BS in Chemistry but has the ability to mentor chemical engineering graduate students. Points for discussion: 1) Has automated organic chemistry matured to the point were it is here to stay? If so, would it be beneficial to train undergraduate students in the subject by direct undergraduate research projects, incorporation of automated instruments into the undergraduate laboratory or a special training course for new hires at the BS level taught by the company or at a remote location similar to the Residential School on Medicinal Chemistry? We are incorporating the first two methods here at Tulsa. I have been fortunate to be working with Tecan US and have a CombiTec in which to develop undergraduate labs and perform my own research. We plan to use the instrument across the curriculum not just organic chemistry. 2) Is undergraduate research in "combinatorial chemistry" a worthwhile goal? Will pharmaceutical companies or government agencies fund basic research (with undergraduates) into a topic like solid phase synthesis? Is the synthetic methodology for a specific transformation general enough in its application to merit a thorough investigation or is it so specific that each application must develop its own methods? My own experience with funding agencies is not encouraging. One of the complaints for my proposals on basic research into the synthetic methodology of reductive aminations on solid supports was that I had not included a library of compounds to synthesize. As you know the synthesis of the library can be very expensive if there is no one to test the compounds. Therefore, it almost requires a collaboration to do the basic research. 3) What are some of the more difficult synthetic transformations that need a more thorough investigation? I am equating this question to that of the field of peptide chemistry where there are multitudes of papers on how to make the amide bond more efficiently. 4) Finally, is there a need to get more chemical engineers (or material chemists, physical chemist, ect.) involved to study what is actually happening on the solid supports in order to develop better conditions and instrumentation? JD John C. DiCesare, Ph.D. Department of Chemistry University of Tulsa 600 South College Avenue Tulsa, OK 74104 Ph. 918 631-3520 Fax 918 631-3404 dicesarejc@centum.utulsa.edu From owner-repertoires@net.bio.net Wed Oct 08 23:00:00 1997 Path: biosci!biosci!not-for-mail From: jamesl@healthtech.com (James W. Larkin) Newsgroups: bionet.molecules.repertoires Subject: 2nd Annual Japanese COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT Date: 9 Oct 1997 10:14:18 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 278 Sender: daemon@net.bio.net Approved: a.wallace@qub.ac.uk Distribution: world Message-ID: <61iqq7$30d@mserv1.dl.ac.uk> NNTP-Posting-Host: net.bio.net 2nd Annual Japanese COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING October 29-31, 1997 Keio Plaza Inter-Continental,Tokyo, Japan Corporate Sponsor: Tripos Corp. Corporate Support: Trega Biosciences Oxford Asymmetry Arqule, Inc On Wednesday, October 29, there will be a series of Corporate Partnering presentations. Material from each of the presenting companies will be posted on the Cambridge Healthtech Web page, to allow for review by attendees prior to the meeting. Invitations will be extended to a number of pharmaceutical executives throughout Japan and elsewhere in Asia to attend this portion of the meeting on a complimentary basis. At the end of the partnering session, the exhibits will be available for viewing as well. Initial Partnering Presentations Arris Pharmaceuticals Oxford Asymmetry Aurora Biosciences Trega Biosciences IRORI Quantum Microchemistry Tripos Corporation Oncogene Science, Inc. Versicor Orchid BioComputer, Inc. LIBRARIES APPLICATIONS OF COMBINATORIAL CHEMISTRY TO DRUG DISCOVERY IN INFECTIOUS DISEASE Dr. Eric M. Gordon, Versicor LOW-DIVERSITY SMART LIBRARYTM TECHNOLOGY: LIBRARIES FOR THE DEVELOPMENT OF SMALL MOLECULE Dr. Michael Kahn, Molecumetics, Ltd. THE DESIGN OF A UNIVERSAL INFORMER LIBRARY FOR DRUG DISCOVERY Dr. Peter Myers, CombiChem, Inc. COMBINATORIAL CHEMISTRY: FROM CONCEPT TO APPLICATION AS A DRUG DISCOVERY TOOL Dr. Alex Polinsky, Alanex Corporation COMBINATORIAL ORGANIC SYNTHESIS USING RADIO FREQUENCY MEMORY DEVICES Dr. Anthony Czarnik, IRORI Quantum Microchemistry MICROFABRICATION FOR MICROCHEMISTRY IN HIGH-THROUGHPUT DRUG DISCOVERY Dr. Pat Conway, Orchid BioComputer, Inc. TITLE TO BE ANNOUNCED Dr. David Casebier, ArQule, Inc. COMBINATORIAL SYNTHESIS DEVELOPMENT OF SYNTHETIC TOOLS FOR PREPARATION OF SMALL MOLECULE LIBRARIES Dr. Tony Baxter, Oxford Asymmetry ADVANCES IN METHODOLOGY FOR HIGH-THROUGHPUT SOLUTION AND SOLID-PHASE SYNTHESIS OF SMALL MOLECULES Dr. Douglas Livingston, Arris Pharmaceutical Corporation SYNTHESIS OF HETEROCYCLES ON THE SOLID PHASE Dr. Michael J. Green, Trega Biosciences TITLE TO BE ANNOUNCED Dr. Alasdair MacDonald, Argonaut Technologies, Inc. ROBOTICS AND SMALL-SIZED CHEMISTRY FOR COMBINATORIAL REACTION AUTOMATION Dr. Akito Tanaka, Fujisawa Pharmaceuticals (tentative) TITLE TO BE ANNOUNCED Advanced ChemTech (invited) INFORMATICS OPTIVERSE AND CHEMSPACE: AN INTEGRATED STRATEGY FOR DESIGN AND SYNTHESIS OF LEAD DISCOVERY AND LEAD REFINEMENT LIBRARIES USING A NOVEL VIRTUAL LIBRARY TECHNOLOGY Dr. Peter Hecht, Tripos GmbH, Munich TITLE TO BE ANNOUNCED Dr. Barry Robson, MDL Information Systems (invited) NOVEL SOFTWARE TOOLS FOR CHEMICAL DIVERSITY AND COMBINATORIAL CHEMISTRY Dr. Robert Pearlman, University of Texas, Austin SCREENING AUTOMATED HTS AT AMGEN: AN OVERVIEW OF WORKSTATIONS AND INTEGRATED SYSTEMS APPROACHES Dr. Jason Armstrong, Amgen NOVEL FLUOROGENIC BIOASSAY TECHNOLOGY FOR RAPID SCREEN DEVELOPMENT FOR ULTRA HIGH-THROUGHPUT SCREENING Dr. Harry Stylli, Aurora Biosciences STRATEGIC LEVERAGING OF AN ESTABLISHED DRUG DISCOVERY ENGINE Dr. Mel Reichman, Oncogene Science, Inc. TITLE TO BE ANNOUNCED Dr. Shina Tanaka, Nihon Millipore (tentative) TITLE TO BE ANNOUNCED Dr. Kurt Schilling, Molecular Devices (invited) Cambridge Healthtech is pleased to again work closely with the Japan Combinatorial Chemistry Focus Group (J.C.C.F.) for this second annual meeting. Prior to the opening of the technical meeting there will be a tutorial workshop, offered in Japanese, for review of technical terms and concepts that will be covered during the meeting. There will also be a series of Corporate Partnering Presentations, to which leading decision makers from Asian pharmaceutical companies will be invited. The technical program will first focus on developments in the design and synthesis of small molecule combinatorial libraries for lead identification and lead optimization. Advances in high throughput screening, including automation, novel assays, data handling, and interpretation, as well as integration of these issues, will then be featured. Thirty exhibitors participated in the trade exhibit last year, and more are expected to take advantage of this unique opportunity to be in touch with key researchers and managers attending this meeting. Interest and application of these two key technologies are expected to follow a similar pattern of rapid growth as is being experienced elsewhere throughout the world. INITIAL EXHIBITORS AMERSHAM KK NALGE NUNC ARGONAUT TECHNOLOGIES NIHON MILLIPORE BECKMAN INSTRUMENTS OXFORD ASYMMETRY (JAPAN) LTD. ROBBINS SCIENTIFIC CEREP TECAN CO. CONTACT SERVICE CO. TEIJIN SYSTEMS CORNING COSTAR CORP. TOYOBO DAIICHI PURE CHEMICALS TRIPOS CORP. M & S INSTRUMENTS WHATMAN POLYFILTRONICS MATRIX TECHNOLOGIES CALL FOR EXHIBITORS Space is available for organizations interested in exhibiting technology or services to reach the targeted audience that will be attending this meeting on Combinatorial Chemistry & High Throughput Screening. Please contact Jim MacNeil of Cambridge Healthtech Institute at 617-630-1341 to obtain an exhibitor package or to inquire about offering a workshop during the meeting. Exhibit space is limited so call now to reserve a space at this premier event. HOTEL INFORMATION Keio Plaza Inter-Continental Room reservations must be made 2-1, Nishi-Shinjuku 2-Chome through Cambridge Healthtech Shinjuku-ku, Tokyo 160 JAPAN Institute (CHI). You must fill out the reservation form and send it T: 81-3-3344-0111 back to CHI by Sept. 12, 1997 F: 81-3-3345-8269 (reservation forms may not be accepted after this date and will Cut-off Date:September 12, 1997 be subject to hotel reservation policies). Limited rooms are Room Rate: 18,000 JPY-Single available and are subject to 20,000 JPY-Double availability. Please call CHI with any questions, e-mail Jennifer Katz at jkatz@healthtech.com, or contact us by fax at 617-630-1325. TRAVEL INFORMATION TRAVELWORLD T: 717-288-9311 or 800-828-6033 601 Market Street F: 717-288-4693 Kingston, PA 18704 Exclusive airline discounts are available on specific airlines when tickets are purchased through Travelworld at least 14 days prior to the meeting date. Some restrictions apply. Handicapped Equal Access: In accordance with the ADA, Cambridge Healthtech Institute is pleased to arrange for special accommodations for attendees with special needs. All requests for such assistance must be submitted in writing to CHI at least 30 days prior to the start of the meeting. Each registration includes all conference sessions, posters and exhibits, one luncheon and reception, continental breakfasts, all refreshment breaks, and a copy of the document binder. A group rate is available for three or more people from the same organization. Call for more details. SUBSTITUTION CANCELLATION POLICY In the event that you need to cancel a registration you may: Transfer your registration to a colleague within your organization. Credit your registration to another Cambridge Healthtech Institute program. Request a refund minus a $75 processing fee. Request a refund minus the cost ($195) of ordering a copy of the document binder. Cancellations will only be accepted up to one week prior to the conference. Program and speakers are subject to change. --------------------CUT AND PRINT HERE----------------------------- YES |__| Please register me for: E-Mail #568E-J70 Combinatorial Chemistry & High Throughput Screening On-site or Late Registration (after September 12, 1997) $995 |__| Commercial $495 |__| Academic, Government, Hospital-Affiliated |__| Complimentary Registration for Partnering Presentations ONLY FIRST NAME:______________________________________________________ LAST NAME:_______________________________________________________ TITLE:___________________________________________________________ DIV./DEPT.:______________________________________________________ COMPANY:_________________________________________________________ ADDRESS:_________________________________________________________ City/State/ZIP:__________________________________________________ COUNTRY:_________________________________________________________ TELEPHONE:____________________________ Fax:______________________ E-MAIL:__________________________________________________________ |__| Please send information on exhibiting and opportunities to present workshops. |__| Enclosed is a check or money order payable to Cambridge Healthtech Institute, drawn on a U.S. bank, in U.S. currency. |__| Please charge: |__| AMEX (15 digits) |__| Visa (13 to 16 digits) |__| MasterCard (16 digits) Card #:___________________________________________________________ Exp. Date:________________________________________________________ Cardholder's Name:________________________________________________ Signature:________________________________________________________ Cardholder's Address (if different from above):___________________ __________________________________________________________________ |__| Reserve with credit card information listed above and invoice me. (Invoices must be paid in full by the deadline to retain registration discount. Invoices unpaid one week prior to conference will be billed to credit card at full registration rate.) If you plan to register on site, please check with CHI beforehand for space availability. KEIO PLAZA INTER-CONTINENTAL RESERVATION FORM (only valid until September 12, 1997) * SIGNATURE:_______________________________________________________ (Authorizes agreement to the terms under Hotel Information; please note your reservation form will not be processed without signature.) Hotel arrival date:_____ / _____ Hotel departure date:_____ / ___ Month / Day Month / Day Special Requests (subject to availability):________________________ ___________________________________________________________________ |__| Credit Card to Guarantee Reservation: |__| AMEX (15 digits) |__| Visa (13 to 16 digits) |__| MasterCard (16 digits) |__| Use above credit card information. Reservations WILL NOT be accepted without a credit card guarantee. CARD #:_____________________________________ EXP. DATE:_________________ CARDHOLDER'S NAME: _________________________ SIGNATURE:_________________ FAX or MAIL your reservation/registration to: Cambridge Healthtech Institute 1037 Chestnut Street Newton Upper Falls, MA 02164 tel: 617-630-1300 fax: 617-630-1325 e-mail: chi@healthtech.com http:www.healthtech.com/conferences/ From owner-repertoires@net.bio.net Wed Oct 08 23:00:00 1997 Path: biosci!biosci!not-for-mail From: Mark Suter Newsgroups: bionet.molecules.repertoires Subject: phage production in a fermenter Date: 9 Oct 1997 01:11:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Approved: a.wallace@qub.ac.uk Distribution: world Message-ID: Reply-To: Mark Suter NNTP-Posting-Host: net.bio.net Dear all Who has experience (and thus a protocol) for the production of filamentous phage in a fermentor? Thanks Mark Suter \|/ (o o) ________________________________oOo__(_)__oOo_________________________________ ___/\_ | Mark Suter mailto:msuter@vetvir.unizh.ch / o \/| | University Inst.for Virology http://www.unizh.ch/vetvir / _| | Winterthurerstr. 266a Telephone: (+41) 1 6358717 /_/\__/-\/ | 8057 Zurich SWITZERLAND Faximile : (+41) 1 6358911 ______________________________________________________________________________ If it wasn't for Windows, we wouldn't have anything to compare Mac's to ______________________________________________________________________________ From owner-repertoires@net.bio.net Thu Oct 09 23:00:00 1997 Path: biosci!biosci!not-for-mail From: Adrian Bracken Newsgroups: bionet.molecules.repertoires Subject: Phage display libraries Date: 10 Oct 1997 07:11:45 -0700 Organization: Trinity College, Dublin Ireland Lines: 13 Sender: daemon@net.bio.net Approved: a.wallace@qub.ac.uk Distribution: world Message-ID: <343E0E8B.75B2@tcd.ie> Reply-To: brackena@tcd.ie NNTP-Posting-Host: net.bio.net Hi: I am looking for a phage display repertoire to screen for specific (human) antibodies or antibody like molecules against a protein. I have seen brochures of commercially available pre-made libraries. Is there any one on the net who had used any of these and could provide me with some feed backs? There was a newsgroup discussion couple of years ago about a library made by Professor Winter's group. Does any one know whether this library is commercially available? Thanks very much in advance, J. Tharappel From owner-repertoires@net.bio.net Thu Oct 09 23:00:00 1997 Path: biosci!biosci!not-for-mail From: "Dr. Michael Tesar" Newsgroups: bionet.molecules.repertoires Subject: Postdoctoral research position Date: 10 Oct 1997 02:19:27 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 39 Sender: daemon@net.bio.net Approved: a.wallace@qub.ac.uk Distribution: world Message-ID: <1.5.4.32.19971010072816.0068f89c@rzlimes> Reply-To: "Dr. Michael Tesar" NNTP-Posting-Host: net.bio.net Dear all, The Department of Environmental Microbiology of the Gesellschaft fuer Biotechnologische Forschung (GBF) - the Helmholtz National Research Centre for Biotechnology - seeks a qualified person for the following project funded by the EU: Construction of structured matrix-bound microbial consortia by engineering bacterial surfaces decorated with membrane-anchored recombinant antibodies/receptors for bacterial surface epitopes and chemical groups on support surfaces. Profile: geneticist with experience in antibody/phage display technology. Knowledge of microbial ecology or surface chemistry would be an advantage (contact person: mte@gbf.de). Exceptional candidates with relevant experience documented by publications in international peer-reviewed journals should send their c.v., list of publications, brief description of previous and current research activities, and the names, addresses, phone, fax and e-mail numbers of three referees to: GBF, Personnel Department, Mascheroder Weg 1, D-38124 Braunschweig, Germany. Best regards, Michael Tesar ************************************************************ Dr. Michael Tesar GBF-National Research Centre for Biotechnology Mascheroder Weg 1 D-38124 Braunschweig Germany Tel: +49-531-6181-449(office) and +49-531-6181-440 (lab) FAX: +49-531-6181-411 e-mail: mte@gbf-braunschweig.de *********************************************************** From owner-repertoires@net.bio.net Sun Oct 12 23:00:00 1997 Path: biosci!biosci!not-for-mail From: Shu-Kun Lin Newsgroups: bionet.molecules.repertoires Subject: MDPI 19th release of available samples Date: 13 Oct 1997 02:39:42 -0700 Organization: University of Basel, Switzerland Lines: 36 Sender: daemon@net.bio.net Approved: a.wallace@qub.ac.uk Distribution: world Message-ID: <01IOR8CARHV88Y69T0@ubaclu.unibas.ch> Reply-To: Shu-Kun Lin NNTP-Posting-Host: net.bio.net Dear Colleagues, We have uploaded the 19th release of MDPI available samples for September 1997. Sorry for the delay of the upload. Please downloaded it from website http://www.mdpi.org (or the mirror site in Europe http://www.unibas.ch/mdpi/). There are totally 189 compounds. All these samples are stored in the MDPI Center in Basel, Switzerland. For obtaining the MDPI samples, please visit http://www.mdpi.org/sampserv.htm or http://www.unibas.ch/mdpi/sampserv.htm Because we have only a small budget for running MDPI activities, my colleague Dr. Turin did not send the diskettes of 18th release by mail which has been costly. However, if you prefer, please let me know and we can send you the diskette. Please let me know. Any suggestions? Shu-Kun Lin --------------------------------------------------------- Dr. Shu-Kun Lin Molecular Diversity Preservation International (MDPI) (A nonprofit Organization for samples exchange services) Saengergasse 25, CH-4054 Basel, Switzerland MDPI Website: www.mdpi.org/ e-mails: Info@mdpi.org Tel. +41 79 322 3379, Fax +41 61 302 8918 -------------------------------------------------------- From owner-repertoires@net.bio.net Thu Oct 16 23:00:00 1997 Path: biosci!biosci!not-for-mail From: "R. S. Pearlman" Newsgroups: bionet.molecules.repertoires Subject: LAST CALL -- Abstracts for Chemical Diversity Symposium at Dallas ACS Date: 17 Oct 1997 07:11:17 -0700 Organization: University of Texas Lines: 35 Sender: daemon@net.bio.net Approved: a.wallace@qub.ac.uk Distribution: world Message-ID: <971017083117.1fd15@VAX.PHR.UTEXAS.EDU> Reply-To: PEARLMAN@VAX.PHR.UTEXAS.EDU NNTP-Posting-Host: net.bio.net Hello -- This is the FINAL CALL for abstracts for the "Diverse Perspectives of Chemical Diversity" symposium scheduled for March 31 and April 1 of the ACS Meeting in Dallas next spring. Topics will include: - chemistry-space metrics (including fingerprints) - metric validation - diversity-related algorithms - use of diversity software for library design, pro's and con's - use of diversity software for other diversity-related tasks, pro's and con's In keeping with recent tradition, the symposium program will be a mix of invited and contributed papers. If you would like to present a 30-minute talk at this symposium, please send me an abstract **IMMEDIATELY** . I look forward to hearing from you! -- Bob Pearlman Robert S. Pearlman, Ph.D Coulter R. Sublett Regents Chair in Pharmacy and Director, Laboratory for Molecular Graphics and Theoretical Modeling College of Pharmacy University of Texas Austin, Texas 78712 512-471-3383 (voice) 512-471-7474 (FAX) pearlman@vax.phr.utexas.edu From owner-repertoires@net.bio.net Thu Oct 16 23:00:00 1997 Path: biosci!biosci!not-for-mail From: Keith Rose Newsgroups: bionet.molecules.repertoires Subject: Postdoctoral position in Switzerland Date: 17 Oct 1997 02:03:14 -0700 Organization: University of Geneva Lines: 59 Sender: daemon@net.bio.net Approved: a.wallace@qub.ac.uk Distribution: world Message-ID: <6278n6$79b@mserv1.dl.ac.uk> Reply-To: Keith.Rose@medecine.unige.ch NNTP-Posting-Host: net.bio.net This is a correction to a previous posting: note start date 1 Jan 1998 (not1997!) Research position, Department of Medical Biochemistry, University of Geneva Post-doctoral level, or exceptional doctoral student This post is available from 1 January 1998 for two years (longer if doctoral student), to assist in a research project carrying out work on artificial proteins made by a combination of synthetic chemical techniques (SPPS) and site-specific chemical modification of existing proteins. See e.g. Rose, K., Facile synthesis of artificial proteins. J.Am.Chem.Soc. (1994) 116:30-33. Rose et al. A synthetic peptide-based polyoxime construct of high purity and activity. Mol.Immunol. (1995) 32:1031-1037. Rose et al. Natural peptides as building blocks for the synthesis of large protein-like molecules with hydrazone and oxime linkages. Bioconjugate Chemistry (1996) 7:552-556. Zeng et al. Synthesis of a new template with a built-in adjuvant and its use in constructing peptide vaccine candidates through polyoxime chemistry. J.Peptide Sci. (1996) 2:66-72. Werlen et al. Preparation of a trivalent antigen-binding construct using polyoxime chemistry: improved biodistribution and potential for therapeutic application. Cancer Res. (1996) 56:809-815. The project will use a combination of chemistry and protein biochemistry to create artificial proteins to target certain cells to elicit an immune response with application for AIDS and cancer vaccine biology. Post doctoral applicants must have a Ph.D. in chemistry or biochemistry, with experience of peptide synthesis. Experience of protein structure modification would be an advantage, and in exceptional cases could compensate for lack of peptide-synthesis experience. Such applicants should have a proven track record of high-quality work, attested by publications in major journals. Exceptional graduate students wishing to work towards a doctorate in the field are also encouraged to apply: in this case the post would be extended. Please send cv either by e-mail to rose@cmu.unige.ch or by fax (+41) 22 346 8758 naming at least two referees (please provide their e-mail and/or fax numbers as well as postal address). Applicants may obtain further particulars from Dr. Keith ROSE Department of Medical Biochemistry University of Geneva CMU 1, rue Michel Servet 1211 Geneva 4 Switzerland posting date 17 October 1997 FAX (+41) 22 346 8758 Closing date: 30 November 1997 From owner-repertoires@net.bio.net Sun Oct 19 23:00:00 1997 Path: biosci!biosci!not-for-mail From: Emily Scott Newsgroups: bionet.molecules.repertoires Subject: Immunolocalisation of fd phage Date: 20 Oct 1997 10:22:02 -0700 Organization: University of Cambridge Lines: 18 Sender: daemon@net.bio.net Approved: a.wallace@qub.ac.uk Distribution: world Message-ID: Reply-To: es1@mole.bio.cam.ac.uk NNTP-Posting-Host: net.bio.net I am trying to screen various fd phage strains, isolated from a phage-display library, for their ability to infect a particular cell line. I have an anti-fd phage primary antibody from Sigma and a TRITC-tagged secondary but I have so far been unable to detect phage inside the permeabilised cells. I really need a positive control of "just phage" but don't know how this would be done. Can I just dry a solution of phage onto a slide and stain this? Has anyone tried anything similar with any success? Emily Scott PhD Student Wellcome/CRC Institute and Physiological Laboratory University of Cambridge Cambridge, UK es1@mole.bio.cam.ac.uk From owner-repertoires@net.bio.net Wed Oct 22 23:00:00 1997 Path: biosci!biosci!not-for-mail From: K.Jolley@soton.ac.uk (Keith Jolley) Newsgroups: bionet.molecules.repertoires Subject: Phage display systems Date: 23 Oct 1997 03:49:28 -0700 Organization: University of Southampton Lines: 27 Sender: daemon@net.bio.net Approved: a.wallace@qub.ac.uk Distribution: world Message-ID: <344db879.1190009@news.soton.ac.uk> NNTP-Posting-Host: net.bio.net We are considering using a phage display system for antibody epitope mapping studies and are considering which kit to purchase. If anyone has experience with either Invitrogen's FliTrx system or NEB's Ph.D. kits I would be interested in hearing of any potential pitfalls or shortcomings as well as any successes. The main concern is with the 12-mer library kits, in that the stated complexity of the systems is 2x10^8 (Invitrogen) to 2x10^9 (NEB) independent primary clones, compared to a total 20^12 (4x10^15) possible combinations. Clearly only a tiny proportion of dodecapeptides will be represented in these systems. NEB claim that "by spreading the equivalent diversity of a 7-mer library over a window of 12 residues permits affinity selection of peptide ligands for targets requiring more than 7 ligand residues for tight binding". Does anyone's experience bear this out? I would also be interested in hearing of experiences with other similar systems. Thank you, Keith Jolley -- Dr. Keith Jolley Dept. of Molecular Microbiology Southampton General Hospital, UK Tel: 01703-798895 Fax: 01703-774316 From owner-repertoires@net.bio.net Wed Oct 22 23:00:00 1997 Path: biosci!biosci!not-for-mail From: dprickett@ieo.it (dennis prickett) Newsgroups: bionet.molecules.repertoires Subject: GST binding domains Date: 23 Oct 1997 03:48:33 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Approved: a.wallace@qub.ac.uk Distribution: world Message-ID: <62l9ut$7t0@mserv1.dl.ac.uk> NNTP-Posting-Host: net.bio.net Buongiorno, Has there been anything published or is anyone aware of a consnesus sequence for a GST binding domain. I've gotten a few GST binding phages and I haven't yet found anything yet refering to sequences. A presto Dennis Prickett Department of Experimental Oncology European Institute of Oncology Via Ripamonti 435 20141 Milan ITALY ph: +39-2-57489855 FAX: +39-2-57489851 e-mail: dprickett@ieo.cilea.it From owner-repertoires@net.bio.net Sun Oct 26 22:00:00 1997 Path: biosci!biosci!not-for-mail From: kshreder@znet.com Newsgroups: bionet.molecules.repertoires Subject: Updated WWWsite: The Antibody Resource Page Date: 27 Oct 1997 03:53:38 -0800 Organization: The Antibody Resource Page Lines: 37 Sender: daemon@net.bio.net Approved: a.wallace@qub.ac.uk Distribution: world Message-ID: <345346A7.16F2@znet.com> Reply-To: kshreder@znet.com NNTP-Posting-Host: net.bio.net Updated WWWsite: The Antibody Resource Page The Antibody Resource Page has been recently updated. The page will be invaluable to researchers and educators alike. Here is just some of what can be found on the page: 1. How to Find an Antibody - a variety of ways on and off the web to find the antibody you are looking for. 2. Online Companies - links to over 110 companies that sell antibodies or antibody related products. Is your company listed on this page? 3. Antibody Image Gallery - some animated gifs have recently been added 4. Bulletin Board - Have a question or have an answer? Then stop by and post a message. 5. Educational Resources - a variety of new links have been added.=20 There are links to pages on immunochemistry, antibody production,=20 autoimmunity, vaccines, immunology and much more. This page is divided up into sections on research, educational, and health resources. 6. The Latest in Antibody News - Get up-to-date, antibody-related articles on topics from academia and industry. ...and there is much more. Check it out at: http://www.antibodyresource.com/ Ps. Don=92t forget to visit our sponsors, Research Diagnostics, Inc. (http://www.researchd.com/absort1.htm) and Lab Vision Corporation (http://www.labvision.com/)! From owner-repertoires@net.bio.net Sun Oct 26 22:00:00 1997 Path: biosci!biosci!not-for-mail From: Pascal.Mertens@fundp.ac.be (Pascal Mertens) Newsgroups: bionet.molecules.repertoires Subject: Re: Phage display systems Date: 27 Oct 1997 07:40:56 -0800 Organization: Lab. Immunologie, FUNDP Lines: 61 Sender: daemon@net.bio.net Approved: a.wallace@qub.ac.uk Distribution: world Message-ID: <632c2c$6k1@mserv1.dl.ac.uk> Reply-To: Pascal.Mertens@fundp.ac.be NNTP-Posting-Host: net.bio.net In article (Dans l'article) <344CD704.56EA@chugaibio.com>, dspinella@chugaibio.com, @chugaibio.com wrote (icrivait) : > Keith Jolley writes: > > We are considering using a phage display system .... Does anyone's > > experience bear this out? > > I would also be interested in hearing of experiences with > > other similar systems. > > > > Thank you, > > Keith Jolley > > > Keith: > > There are two considerations here. First off, NEB is correct: their > dodecamer library affords a "sliding window" effect ... > The alternative consideration however is that many antibody epitopes are > in fact 6-7 residues long, and are simple linear (i.e. > non-discontinuous) sequences. Hence, for the longer displayed peptides, > once you isolate a binding phage and infer the amino acid sequence of > the displayed peptide, you still won't know immediately which of the > overlapping peptides constitutes the epitope... > our solution is to screen ALL > our libraries simultaneously and use the data from the shortest > isolate. The solution also comes when you have a consensus sequence present in all (or most) of your binding peptides. You can have 10 different 12mer peptides with a strict 4 or 5 mer consensus sequence (not necessarily at the same place in the 12mer, so you need to "slide" the peptides between them. In some cases there are no consensus sequences, and some or all the binding peptides are not similar to the epitope but are called mimotopes. Mimotopes are structures (here, peptides) that bind the same Ab that your epitope because the important charasteristics for binding are present at the right places (you can have a peptide that is a mimotope of a non-peptidic epitope!). So remember that a binding peptide does not necessarily give you the sequence of your epitope (I mean the epitope on your Ag). Pascal Mertens -- Pascal Mertens Laboratoire d'Immunologie et Microbiologie URBM-FUNDP 61 Rue de Bruxelles 5000 Namur, BELGIUM Phone: 32 81 724438 Fax: 32 81 724420 From owner-repertoires@net.bio.net Sun Oct 26 22:00:00 1997 Path: biosci!biosci!not-for-mail From: dspinella@chugaibio.com (Dom Spinella) Newsgroups: bionet.molecules.repertoires Subject: Re: Phage display systems Date: 27 Oct 1997 07:36:31 -0800 Organization: Chugai Biopharmaceuticals, Incorporated Lines: 66 Sender: daemon@net.bio.net Approved: a.wallace@qub.ac.uk Distribution: world Message-ID: <632bqh$6cs@mserv1.dl.ac.uk> Reply-To: dspinella@chugaibio.com, @chugaibio.com NNTP-Posting-Host: net.bio.net Keith Jolley writes: > We are considering using a phage display system for antibody epitope > mapping studies and are considering which kit to purchase. If anyone > has experience with either Invitrogen's FliTrx system or NEB's Ph.D. > kits I would be interested in hearing of any potential pitfalls or > shortcomings as well as any successes. The main concern is with the > 12-mer library kits, in that the stated complexity of the systems is > 2x10^8 (Invitrogen) to 2x10^9 (NEB) independent primary clones, > compared to a total 20^12 (4x10^15) possible combinations. Clearly > only a tiny proportion of dodecapeptides will be represented in these > systems. NEB claim that "by spreading the equivalent diversity of a > 7-mer library over a window of 12 residues permits affinity selection > of peptide ligands for targets requiring more than 7 ligand residues > for tight binding". Does anyone's experience bear this out? > I would also be interested in hearing of experiences with > other similar systems. > > Thank you, > Keith Jolley Keith: There are two considerations here. First off, NEB is correct: their dodecamer library affords a "sliding window" effect such that each phage displays 5 (i.e. 12-7) overlapping heptameric peptides. Thus, you get more peptide diversity for your money. We have built libraries of up to 43 random amino acids which have even greater advantages along the same lines, despite the fact that, as you point out, it is impossible to make "complete" libraries representing every possible peptide sequence. These advantages are particularly relevant when the binding "epitope" is long or discontinuous. (See: McConnell et al, "Construction and Screening of M13 Phage Libraries Displaying Long Random Peptides", J. Molecular Diversity 1:165-176 for a description and more complete discussion). We have also used the NEB system and found it to be fine. The alternative consideration however is that many antibody epitopes are in fact 6-7 residues long, and are simple linear (i.e. non-discontinuous) sequences. Hence, for the longer displayed peptides, once you isolate a binding phage and infer the amino acid sequence of the displayed peptide, you still won't know immediately which of the overlapping peptides constitutes the epitope without doing some additional work (unless there is substantial sequence homology to some natural antigen and you can figure out where the homology begins and ends). The point is that there is a tradeoff: the maximum information is obtained from the smallest possible binding peptide, and yet the probability of finding a binding sequence is higher in libraries displaying longer peptides. So, the choice is yours. In our case, we are not looking for antibody epitopes but receptor binding molecules. Nevertheless, the problem is similar and our solution is to screen ALL our libraries simultaneously and use the data from the shortest isolate. BTW, there is also a Molecular Diversity forum on the Bionet which, while not as well subscribed as this user group, does often deal with phage display issues. If you haven't already done so, I would post your question there as well -- perhaps you'll get a different opinion (for one thing, I've never used the Invitrogen libraries and don't know how good they are). I hope this rambling discussion is of some help! Good luck. -- Dom Spinella From owner-repertoires@net.bio.net Sun Oct 26 22:00:00 1997 Path: biosci!biosci!not-for-mail From: Fernando Alberdi Newsgroups: bionet.molecules.repertoires Subject: Searching for a plasmid for phage display library synthesis Date: 27 Oct 1997 07:20:57 -0800 Organization: Oklahoma Medical Research Foundation Lines: 13 Sender: daemon@net.bio.net Approved: a.wallace@qub.ac.uk Distribution: world Message-ID: <632avh$581@mserv1.dl.ac.uk> Reply-To: alberdif@omrf.ouhsc.edu NNTP-Posting-Host: net.bio.net If anyone can direct me to thie plasmid pSW2scFvD1.3 for the synthesis of linker DNA to join VH and VL genes in a phage display system please contact me. fax no 405-271-4110 email alberdif@omrf.ouhsc.edu Kind regards and many thanks Fernando Alberdi PhD From owner-repertoires@net.bio.net Sun Oct 26 22:00:00 1997 Path: biosci!biosci!not-for-mail From: dspinella@chugaibio.com (Dom Spinella) Newsgroups: bionet.molecules.repertoires Subject: Re: Phage display systems Date: 27 Oct 1997 07:43:06 -0800 Organization: Chugai Biopharmaceuticals, Incorporated Lines: 42 Sender: daemon@net.bio.net Approved: a.wallace@qub.ac.uk Distribution: world Message-ID: <632c1o$6j6@mserv1.dl.ac.uk> Reply-To: dspinella@chugaibio.com, @chugaibio.com NNTP-Posting-Host: net.bio.net > The solution also comes when you have a consensus sequence present in all > (or most) of your binding peptides. You can have 10 different 12mer > peptides with a strict 4 or 5 mer consensus sequence (not necessarily at > the same place in the 12mer, so you need to "slide" the peptides between > them. > In some cases there are no consensus sequences, and some or all the > binding peptides are not similar to the epitope but are called mimotopes. > Mimotopes are structures (here, peptides) that bind the same Ab that your > epitope because the important charasteristics for binding are present at > the right places (you can have a peptide that is a mimotope of a > non-peptidic epitope!). > So remember that a binding peptide does not necessarily give you the > sequence of your epitope (I mean the epitope on your Ag). > > Pascal Mertens Pascal and I seem to be in violent agreement here. Clearly, one can also establish a consensus binding sequence (be it epitope or mimotope) by alligning several binding sequences and establishing the points of homology. This is one of the advantages of what I called the "sliding window" available with long peptide phage display systems. It is not always possible to do this however, either because there is no obvious homology among independent binding peptide sequences, or because only a single binding sequence was obtained. This is perhaps less of a problem with antibodies than with large protein receptors such as we use in my lab for screening phage libraries, but still occasionally happens even with antibody screens. In the case of receptor binding peptides, we and others have observed that there is virtually never direct primary sequence homology between the mimetic peptides and the natural ligand of the receptor target -- presumably because the actual binding motif of the natural ligand is generated by the tertiary folding of the protein which brings together amino acids that are not contiguous in the primary sequence. Although unusual, such "discontinuous epitopes" are also found in some antigens, and of course it will be impossible to define these by allignment of peptides to the primary sequence of the natural antigen. -- Dom Spinella