From owner-biophysics@net.bio.net Tue Jul 01 23:00:00 1997 Path: biosci!BIGFOOT.COM!tnig From: tnig@BIGFOOT.COM (Ti Ng) Newsgroups: bionet.biophysics Subject: Low International Calling Rates Date: 2 Jul 1997 08:13:44 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: <33BAF92A.2BFA@bigfoot.com> Reply-To: tnig@bigfoot.com NNTP-Posting-Host: net.bio.net Hi, International Telecom Ltd. offer EXTREMELY LOW international calling rates, such as the following flat rates per minute (US origination): UK .185 Russia .670 France .280 Greece .475 Israel .690 Japan .360 China .810 For more information visit Web page at: http://ld.net/?ting93 Ti Ng ITL Independent Representative From owner-biophysics@net.bio.net Tue Jul 01 23:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!chi-news.cic.net!207.22.81.9!europa.clark.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.internetmci.com!rill.news.pipex.net!pipex!join.news.pipex.net!pipex!server1.netnews.ja.net!server5.netnews.ja.net!daresbury!not-for-mail From: Newsgroups: bionet.biophysics Subject: What Happens in the F1 moiety of the ATPsynthase? < > PENTCHO VALEV Date: 2 Jul 1997 09:21:32 +0100 Lines: 26 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5pd32c$m8k@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk I would like to juxtapose the widely accepted "binding change mechanism" for ATP synthesis (Boyer P.D., Biochim. biophys. Acta, 1140, 215 - 250,1993) with an old idea of P. Mitchell (Mitchell P., J. Biochem. 97, 1 - 18 (1985), p. 13) according to which ATP synthesis proper occurs by an in-line nucleophilic displacement mechanism: 2H+ + (PO4)3- + -OADP =....= H2O + (ATP)2- /1/ In my opinion, the two ideas can successfully be combined: /1/ is a vectorial process in which H+ (not coming from the thansmembrane H+ gradient) approaches the phosphoryl group along a specific route, possibly accelerated by electrostatic attraction. If so, /1/ is a spontaneous endothermic reaction which does not need energy from outside. However, in order that the vectorial process is successful, the reagents must be arranged in a line, and this consumes work - let us call it vectorization work. This work is done by the Fo moiety - we can imagine it as "fixing" the reagents properly in a line. There is nothing new in the above description, except for the idea that the energy stored in ATP in the process /1/, and the vectorization work ensuring the successful vectorial process, are independent of each other. The energy stored in ATP may be greater than the vectorization work - then the second law would be violated. But this is not at all necessary - the organism's logic may not presuppose violation of the second law just in this process. So the vectorization work may be greater - then there would be no actual violation - still the mechanism is not a second law one. Pentcho Valev From owner-biophysics@net.bio.net Tue Jul 01 23:00:00 1997 Path: biosci!JAGUAR.DOTE.HU!bacso From: bacso@JAGUAR.DOTE.HU (Zsolt Bacso MD) Newsgroups: bionet.biophysics Subject: (no subject) Date: 2 Jul 1997 04:43:10 -0700 Organization: Biophys. Dep., Medical Univ. of Debrecen, Hungary Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <33BAB1D9.4A6F@jaguar.dote.hu> Reply-To: bacso@jaguar.dote.hu NNTP-Posting-Host: net.bio.net unsubscribe From owner-biophysics@net.bio.net Tue Jul 01 23:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!chi-news.cic.net!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.nacamar.de!blackbush.xlink.net!news-ge.switch.ch!in2p3.fr!univ-lyon1.fr!pasteur.fr!jussieu.fr!univ-angers.fr!univ-rennes1.fr!melon.univ-brest.fr!news From: Ahmed.Hamraoui@univ-brest.fr (Ahmed Hamraoui) Newsgroups: bionet.biophysics Subject: Looking for researcher or postdoctoral position in biophysics Date: 2 Jul 1997 09:41:03 GMT Organization: UBO Lines: 186 Message-ID: <5pd7nf$n7f@melon.univ-brest.fr> NNTP-Posting-Host: heol.univ-brest.fr X-Newsreader: WinVN 0.92.6+ Ahmed HAMRAOUI Résidence les Mouettes 29217 Plougonvelin France Married ; French 32 years old Tel. (33) 02 98 48 27 88 Fax : (33) 02 98 48 20 52 e mail : Ahmed.Hamraoui@univ-brest.fr *************************************************************************************** Subject : postdoctoral or researcher position Dear Sir, I have achieved my thesis entitled : " Prewetting transition and layering transitions at the solid-liquid interface. System Silica-Water-2,5dimelthylpyridine (2,5DMP)" under Professor M. PRIVAT’s leadership at the University of Western Brittany in Brest (France). Since the prewetting transition is an adsorption phenomenon I adapt an experimental protocol to measure the adsorption at solid(Silica)/liquid(Water+2,5DMP) interface, for concentrated solutions. The analyze of the isotherms showed the existence of the prewetting transition for this system. The complexity of phenomenon and studied system urged me to do a studied thoroughly some statistical models describing the wetting and adsorption transitions at solid-fluid and fluid-fluid interfaces. My formation of physicist helped me to master the concepts of the statistical models and to make a synthesis of these theoretical study. Currently, I want to apply my knowledge to other researches themes and acquire/develop a new experimental techniques, and it is why I apply for a postdoctoral/researcher position in your Laboratory Hopping that you will answer this letter, I thank you in advance for whatever for will do. Sincerely yours. CURRICULUM VITAE 1996 Doctorat (Ph.D.) in Physical-Chemistry, specialization : solid/liquid interface. With honors : " Mention très honorable et félicitations du jury " Title : “ Prewetting transition and layering transitions at solid at solid/liquid interface.System:Silica-water-2,5dimethylpyridine. ” 1991 Diplome des Etudes Approfondies (DEA) in “ Polymers - Interfaces - Amorphous states ” 1990 Maîtrise de Physique; specialization : solid state. 1989 Licence de Physique. 1988 C.U.E.S ; specialization : Physics and chemistry. TECHNIQUES · Gravimetric method for adsorption at solid-liquid interface · Measuring by differential refractometry and UV · Tensiometric measurement method (ring or plate method). SOFTWARE · QuatroPro 5, Excel 7, Word 7, MathCad 6, (basic knowledge in :StatGraphics+ and NEMROD 3.0 ) · Netscape ( HTML 3) PRACTICAL EXPERIENCE 1996 Training in NMR Spectroscopy, to study the adsorbed molecular arrangement at solid surface. 1996 Contribution to ellipsometric experiment in C.E.A (Commissariat à l'énergie Atomique) Saclay (France). 1992-96 Night security officer. 1994-96 Contribution to training of DEA trainees students. 1995 Temporary replacement job as a high school physic and chemistry teacher. 1991 Participation to mathematical formulation of solvent diffusion process in the “nitrocellulose ” pastes drying and in the surface I-Red measures for “ Societé Nationale des poudres et Explosifs de Pont-de Buis(France dept. 29) ” PUBLICATIONS 1 - " Monolayers, critical layers and wetting films in liquid-liquid-solid system undergoing a wetting transition.Experimental study ". M. PRIVAT, M. AMARA, A. HAMRAOUI, H. SELLAMI, and A. M. MEAR. Ber. Bunsenges. Phys. Chem, 98, 620-630, 1994; N4 2 - " Layering in a two-component liquid system undergoing a phase separation" A. HAMRAOUI, M. PRIVAT and H. SELLAMI. J. Chem. Phys. 106, 222, 1997 3 - "Prewetting transition in a two-component liquid system in contact with a solid" A. HAMRAOUI and M. PRIVAT submitted to Phys.Rev.Lett 4- "Prewetting transition influenced by layering-like transitions, at a binary liquid/solid interface" A. HAMRAOUI and M. PRIVAT submitted to J. Chem. Phys 5- "Wetting transitions along a mixed liquid-solid coexistence" A.-M. Mear,A. HAMRAOUI and m. privat submitted to J. Chem. Phys COMMUNICATIONS 1- "From Monolayers to Critical Layers and from Layers to Films through the influence on adsorption of a Wetting Transition. Experimental study ". Poster. 2nd Liquid matter Conference Florence,Italy, 18-22 September 1993. M. PRIVAT, M. AMARA, A. HAMRAOUI and H. SELLAMI. 2 - a-" Monolayers, Critical layers, and Wetting Films in liquid-liquid-solid system undergoing a Wetting Transition. Experimental Study ". Poster. b-Discussion meeting of the Bunsengesellschaft fur Physikallische Chemie : Phase Transition atInterfaces. Poster Bas Herrenalb. Allemande 22-24 September 1993. M. PRIVAT, M. AMARA, A. HAMRAOUI and H. SELLAMI. 3 - "Adsorption isotherms as experimental tests for nucleation processes of liquid phases and film at liquid-solid contacts ". Poster. 14th general Conferences EPS Condensed Matter Division. Madrid, Spain, 28-31 March 1994. Poster et communication oral. M. PRIVAT, M. AMARA, A. HAMRAOUI, H. SELLAMI, and A. M. MEAR. 4 - "Transition d’états de surface et transition de mouillage. Interface Solide- Mélange liquide". 4eme Journées de la Matière Condensée. Poster Rennes 31 August - 2 Septembre 1994. FRANCE A. HAMRAOUI, M. PRIVAT. 5 - "Layering in solid-liquid interfaces. Consequences on prewetting". 3rd Liquid matter Conference (European Physical Society). Norwich, UK, 6-10 July 1996. A. HAMRAOUI, H. SELLAMI and M. PRIVAT 6- "Prewetting in a binary liquid system in contact with solid". 3rd Liquid matter Conference (European Physical Society). Norwich, UK, 6-10 July 1996. A. HAMRAOUI, and M. PRIVAT 7 - "Transitions de couches ("layering ") dans un mélange binaire présentant une séparation de phase liquide-liquide". 5eme Journées de la Matière Condensée. Poster Orléans-France- 28-30 August 1996. A. HAMRAOUI, M. PRIVAT et H. SELLAMI 8 - "Transitions de prémouillage a l’interface solide-liquide." 5eme Journées de la Matière Condensée. Poster Orléans- France- 28-30 August 1996. A. HAMRAOUI, M. PRIVAT. 9- " Phase equilibria effects on adsorption in environmental systems" 16th European Seminar on applied Thermodynamics - communication orale Pont à Mousson, France, June 19-22, 1997 A.-M. Mear and A. HAMRAOUI 10 - "Interplay between layering and prewetting transitions" 25th International Conference on solution Chemistry- Communication orale. Vichy, France, August 26-31, 1997 A. HAMRAOUI and M. PRIVAT 11- "Monolayers, critical layers and wetting films in a liquid-liquid/solid system undergoing a wetting transition. Universal aspects experimental study. " 25th International Conference on solution Chemistry- Communication orale. Vichy, France, August 26-31, 1997 A. HAMRAOUI and M. PRIVAT LIST OF REFERENCES I have recommendations letters --------------------------------------------------------------------------------------- Professor B. WIDOM Department of chemistry- Cornell University, Ithaca New York 14853 USA --------------------------------------------------------------------------------------- Professor R. EVANS Physics Laboratory-University of Bristol Bristol BS8 ITL ENGLAND --------------------------------------------------------------------------------------- Professor M. PRIVAT Université de Bretagne Occidentale- UFR Sciences et Techniques - CR4 6, avenue Victor le Gorgeu- BP 809 - 29285 Brest Cedex FRANCE --------------------------------------------------------------------------------------- Professor R. OLIER Université de Bretagne Occidentale - UFR Sciences et Techniques - CR4 6, avenue Victor le Gorgeu- BP 809 -29285 Brest Cedex FRANCE --------------------------------------------------------------------------------------- Professor C. BROSSEAU Université de Bretagne Occidentale - UFR Sciences et Techniques Département de Physique- 6, avenue Victor le Gorgeu- BP 809 -29285 Brest Cedex FRANCE From owner-biophysics@net.bio.net Tue Jul 01 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: "Alexey M. Eroshkin" Newsgroups: bionet.biophysics Subject: ProAnWin update: protein alignment/plots/structure-activity analysis/de sign Date: 2 Jul 1997 09:42:28 +0100 Organization: State Research Center of Virology and Biotechnology VECTOR Lines: 364 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5pd49k$npq@mserv1.dl.ac.uk> MIME-Version: 1.0 Original-To: immuno@dl.ac.uk To: bio-software@dl.ac.uk From: Alexey Eroshkin Cc: mutatiomn@net.bio.net, pop-bio@net.bio.net, peptides@dl.ac.uk, molmodel@dl.ac.uk, mol-evol@dl.ac.uk, microbio@dl.ac.uk, immuno@dl.ac.uk, hiv-biol@dl.ac.uk, fluorpro@dl.ac.uk, biophys@dl.ac.uk, bio-matrix@dl.ac.uk, proteins@dl.ac.uk, virology@dl.ac.uk, xtal-log@dl.ac.uk Subject: ProAnWin update: protein alignment/plots/structure-activity analysis/design Dear all, new version of ProAnWin (Protein Analyst for Win 3.11/95) now publicly available from IUBio as ftp://iubio.bio.indiana.edu/molbio/ibmpc/paw.exe (and paw.readme) If you have access to e-mail only, the program can be obtained via e-mail by sending the following message: To: BITFTP@pucc.Princeton.EDU From: YOUR E-MAIL ADDRESS ftp iubio.bio.indiana.edu uuencode user anonymous cd molbio/ibmpc get paw.exe get paw.readme quit Server will return you UUENCODED program in several files. Running UUDECODE you'll get the archive with the program. ************************************** ProAnWin - Protein Analyst for Windows ************************************** version 3.01 Multiple sequence alignment, analysis of protein sequences and structures, structure-activity relationships, design of protein-engineering experiments Copyright(c)1995-97 I.Pika, A.Frolov, V.Ivanisenko, A.Eroshkin All Trademarks and Registered Names are acknowledged in this document. The files required to run ProAnWin are distributed in the form of a single compressed file (self-extracted). Create a directory "PROANWIN" on your hard disk, for example, C and copy the compressed file to the directory. Unpack the program (type PAW in DOS prompt and answer Yes to all questions). Once you extracted archive files, start Windows and start the program. This program is provided "AS IS" without any warranty, expressed or implied to you or any other person. The authors will not be liable for incidental, consequential or other damages arising through the use of this software. As the program is under further development the documentation may not reflect all current program options. PROGRAM CONTENT: Directory: Main directory - program modules DATA - files with amino acid physico-chemical properties, manual, examples with input and output files ALIGNS - aligned sequences of 50 protein families MAIN PROGRAM FEATURES (* - new feature) - Makes multiple sequence alignment - automatic (Clustal V) and manual, global and local (in selected region); - Threads multiple alignment onto known 3-dimensional structure; - Imports data in all major formats (SWISS-PROT, PIR, FASTA, GCG, Clustal); - Imports protein 3D structure from Protein Data Bank files (PDB format) - Inputs data on protein activities/property or phenotype; - Transforms activity values (log (A), ln (A), A/K, A+k, etc.); * Searches linear and spatial sites, conservative and variable in changes of specified physico-chemical properties (for example, helical hydrophobic moment); * Searches linear and spatial sites, having high and low values of specified physico-chemical properties (for example, Kyte-Doolittle hydrophobicity); * Plots sets of different physico-chemical profiles for individual protein sequence; * Plots specified physico-chemical profiles for the set of sequences; - Searches linear sites in multiple protein alignment and spatial sites in protein 3D structure influencing protein activity/property; * Plots average physico-chemical profile for the family of sequences; * Plots profile of dispersion of physico-chemical profiles for the family of sequences; * Plots physico-chemical profiles for protein 3D structure; - Analyses relationships between site structural characteristics and protein activities by multiple linear regression analysis; - Analyses structural differences between proteins divided by functional, evolutionary or other criteria; - Investigates physico-chemical factors related with activity changes in a set of mutant proteins; * Simulates protein-engineering experiments and predicts protein activity. Has options for automatic mutant generation (to increase or decrease protein activity) and for manual mutant generation; * Predicts activity for newly sequenced proteins; - Makes protein 3D pictures (mono and stereo) with sites highlighted; * Has more then 400 amino acid physico-chemical properties; - Investigates ten types of protein site characteristics, including average values, helical moments, beta-strand moments, etc.; - Saves results to the disk and saves pictures to the clipboard; - Has help and manual. ProAnWin PERMITS TO OBTAIN NEW RESULTS IMPORTANT IN BIOCHEMISTRY, MOLECULAR BIOLOGY ETC., AND TO DESIGN PROTEIN ENGINEERING EXPERIMENTS: 1. The program helps to find information that can not be found by other programs (activity/property-modulating sites, phenotype defining regions); 2. The user has an opportunity to conduct the analysis of structure-activity relationships in sequences and 3D structure. 3. The program permits to generate and to check up a plenty of hypothesis about the role of different sites and their various physico-chemical characteristics in protein activity, that is rather difficult or impossible at the "hand-operated" analysis. 4. Search of structure - activity relations is carried out with the use of multiple regression analysis and the results have statistical evaluations on reliability. 5. The user has an opportunity to work simultaneously with sequences and 3D protein structure (sites marked on the sequence are visualized in 3D structure and vise versa). 6. Alongside with the conventional average physico-chemical characteristics of a sequence site the user analyzes 9 additional characteristics of sequential (linear) sites and 5 characteristics of spatial sites. 7. The program permits considerably to reduce time during creation a mutant proteins with desired property. HOW TO START To investigate protein/peptide family of your interest you should have or prepare sequence data file(s). You can use alternatively sequences data files in FASTA (PEARSON), PIR, SWISS-PROT, CLUSTAL, GCG formats or in INTERNAL 1 format (3 data files with protein names (*.seq), protein activities or grouping (*.act) and aligned sequences (*.ali), see the examples in DATA directory) in the current directory. 3D protein structure you can take from PDB database. To use the program follow the steps: - start the program; - select sequences of the family you are going to investigate; - select a file with required physico-chemical properties of amino acids; - load protein 3D structure (if available); - define an investigated fragment (or up to 8 fragments); - define factors for analysis; and so on. All other information you'll get from MANUAL.TXT or HELP. ProAnWin IS USEFUL IN: - protein structure-function and structure-activity investigations; - designing proteins and peptides with improved activity; - making multiple protein alignments and getting sense from it; - studying phenotype-genotype correlations; - preparation of protein 3D pictures with sites highlighted; - protein features analysis; - comparative protein sequence analysis. PUBLICATIONS: 1. Frolov A.S., Pika I.S., Eroshkin A.M. ProMSED: Protein multiple sequence editor for Windows 3.11/95. CABIOS, 1997, 13, 243-248 2. Morozov B.M., Ivanisenko V.A., Eroshkin A. M., Ugarova N.N. Computer analysis of relations between bioluminescence color and primary structure of beetle luciferases: identification of the sites influencing bioluminescence color. Molec. Biology (Russia), 1996, 30, 1167-1172. 3. Ivanisenko V.A., Pika I.S., Pinin S.I., Fomina T.I., Eroshkin A.M. Studying structure-activity and phenotype-genotype relationships in protein families. Methods, algorithms and applications. Folding and Design, 1996, 1, Suppl., p.84. 4. Eroshkin A.M., Fomin V.I., Zhilkin P.A., Ivanisenko V.A., Kondrakhin Y.V. PROANAL version 2: multifunctional program for analysis of multiple protein sequence alignments and studying structure-activity relationships in protein families. CABIOS, 1995, 11, 39-44. 5. Eroshkin A.M., Zhilkin P.A., Fomin V.I. Algorithm and computer program PROANAL for analysis of relationship between structure and activity in a family of proteins or peptides. CABIOS, 1993, 9, 491-497. 6. Eroshkin A.M., Minenkova O.O., Fomin V.A., Ivanisenko V.A., Ilyichev A.A. Analysis of peptide fragment insertions into major coat protein of bacteriophages M13, f1 and fd. Relation of protein structural characteristics and viability of mutant phages. Molec. Biology (Russia), 1993, 27, 1345-1355. The version installed has limit in the number of analyzed sequences (15). To get unlimited registered version please contact the authors. If you have problems running ProAnWin please consult the manual and HELP carefully to see if they can help. If you still need advice then please contact the authors by e-mail: eroshkin@vector.nsk.su or State Research Center of Virology an Biotechnology "Vector" Koltsovo, Novosibirsk Region, 633159 Russia Tel: (3832) - 647774 Fax: (3832) - 328831 Ask authors for the updated ProAnWin version and ADDITIONAL NEW SOFTWARE TOOLS ProMSED2, ProAnalyst: ProMSED2 ProMSED2, MS Windows application for both automatic and manual DNA and protein sequence alignment, editing, comparison and analysis. ProMSED2 is the enhancement of ProMSED made according to user's remarks and suggestions. The program reads main sequence formats and performs automatic alignments, alignment visualization and editing and it allows sequences to be aligned interactively leaving unchanged previously aligned regions. The program has an user-friendly interface. Manual alignment and sequence analysis are facilitated by coloring schemes reflecting amino acid similarity in mutational, physico-chemical and other properties. Although ProMSED was targeted at protein sequences, it can be used on DNA sequences as well. The program provides flexible tool for sequences alignment, analysis, visualization, edition and presentations. Availability: EMBL library: ftp://ftp.ebi.ac.uk/pub/software/dos/promsed IUBio archive: ftp://iubio.bio.indiana.edu/molbio/ibmpc/promsed2.exe and .readme The program does or has (+ - NEW or enhanced features): + inputs DNA and protein sequences in NBRF/PIR, Pearson (Fasta), MSF (GSG), EMBL/SwissProt, Intelligenetics and CLUSTAL formats; o has interface and functions like in others Windows applications (source file view, font changing, marking/unmarking, block and sequence selection, cut and paste, UNDO, etc.); o loads several sequence families in different windows, adds sequences to existing alignment, combines sequences from various files; + outputs the alignment in several popular formats; + makes presentation quality color and black-and-white prints of complete alignment or any selected block; + saves alignment picture as Windows metafile and bitmap; o permits to apply automatic alignment interactively (with options to change the alignment parameters) to any selected part of sequences of marked block; + calculates sequence similarity of complete sequences, of any selected sequence subset or of marked block in % and in PAM250 units (matrix of amino acid similarity); + calculates total (average for %) sequence similarity value - an estimation of alignment quality; + prints sequence similarity matrix; + sorts sequences by similarity of complete sequences or marked block; + displays conserved and semiconserved positions; + has many amino acid coloring schemes aimed to facilitate manual alignment and understanding protein sequence features. Some schemes are: EVOLUTIONARY CONSERVATIVE (reflects amino acid mutational properties), COMPLEX (similarity of amino acids in physico-chemical properties), HYDROPHOBICITY, CHARGE, BIG RESIDUES, ALPHA-HELIX, HELIX-BREAKERS, etc. The options to input user-defined schemes or change the colors of any amino acid groups are available; + searches subsequences and complex sequence patterns; o has complete HELP. ProAnalyst ProAnayst: DOS version of ProAnWin with additional functionality (single and multiple sequences analysis, profiles analysis, combinatorial libraries; design of protein engineering experiments) Availability: IUBio archive: ftp://iubio.bio.indiana.edu/molbio/ibmpc/panalys1 EMBL library: ftp://ftp.ebi.ac.uk/pub/software/dos/proanalyst Functions: o data conversion from several protein sequence formats (FASTA, SWISS-PROT, PIR, CLUSTAL). o databases with more then 50 amino acid physico-chemical properties; o inputs 3D protein structure in PDB format; o flexible VISUALIZATION OF PROTEIN 3d STRUCTURES with sites highlighted; o inputs user-defined protein activities, properties or related phenotypes; o searching SITES INFLUENCING PROTEIN ACTIVITY and analyzing relationships between protein site structural characteristics and protein activities (properties or related phenotypes); o multiple linear regression analysis of STRUCTURE-ACTIVITY relationships, discriminant analysis and ANOVA; o intra and cross group VARIABILITY analysis; o GENOTYPE -- PHENOTYPE CORRELATION analysis (e.g., for drug resistance in viruses); o alphabetical and physico-chemical analysis of protein features variations (in 1D and 3D structures); o structure-activity determination profile (SAD); o investigation of physico-chemical factors related with activity or property changes in MUTANT PROTEINS; o searching motifs in COMBINATORIAL LIBRARIES (peptide, phage- display libraries, etc.) with MOTIF MAPPING on the target protein; o design PROTEIN-ENGINEERING experiments; o ACTIVITY, PROPERTY AND PHENOTYPE PREDICTION; o sorting sequences by protein activity value, by protein group number and by number of motifs found; o mapping results on 3D structure and sequences. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dr. Alexey Eroshkin Institute of Molecular Biology E.mail: eroshkin@vector.nsk.su State Research Center of Virology and Tel: +7 (3832) - 647774 Biotechnology "Vector" Fax: +7 (3832) - 328831 Koltsovo, Novosibirsk Region 633159 Russia ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-biophysics@net.bio.net Tue Jul 01 23:00:00 1997 Path: biosci!INTREPID.CHM.JHU.EDU!rlk From: rlk@INTREPID.CHM.JHU.EDU ("rlk") Newsgroups: bionet.biophysics Subject: agate blades for Mettler balances Date: 2 Jul 1997 10:32:43 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <9707021335.ZM7670@intrepid.chm.jhu.edu> NNTP-Posting-Host: net.bio.net Hello, Does anybody know a source for the agate blades used in the old Mettler H10 balances? We have two in perfect working condition with the exception that the blades on both are cracked and unusable. -- -ron 'if I can't dance, I don't want to be a part of your revolution' Emma Goldman From owner-biophysics@net.bio.net Tue Jul 01 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news.maxwell.syr.edu!news-peer.gsl.net!news.gsl.net!portc01.blue.aol.com!audrey02.news.aol.com!not-for-mail From: huntpharm@aol.com (Huntpharm) Newsgroups: bionet.biophysics Subject: job opportunities Date: 2 Jul 1997 22:19:56 GMT Lines: 16 Message-ID: <19970702221900.SAA05390@ladder02.news.aol.com> NNTP-Posting-Host: ladder02.news.aol.com X-Admin: news@aol.com Organization: AOL http://www.aol.com I am looking for a person to establish and manage a laboratory for the investigation of the pharmacokinetics in multiple animal species. A full range of ADME studies supporting both early compound selection and subsequent clinical development will be conducted. Techniques will include analytical method development, radiometric analyses, pharmacokinetic-pharmacodynamic modeling, and small and large animal models for the prediction of pharmacokinetic parameters in man. This person will represent Pharmacokinetics on interdisciplinary project teams, monitor contracted work, and prepare IND/NDA ADME summaries.We are a leading pharmaceutical company with research facilities in Connecticut and can provide excellent benefits (health insurance, dental and vision plan, paid vacations and more. A high impact, high profile position. All candidates must have industry experience with pharmaceutical or bio-tech company or be from a contract facility. Please contact Scott Shanes by phone at 609-584-8733 EXT. 218, fax CV to 609-584-9575 or E-Mail to SIS@diedremoire.com or Neurohunt@aol.com. From owner-biophysics@net.bio.net Tue Jul 01 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!howland.erols.net!news-peer.gsl.net!news.gsl.net!portc01.blue.aol.com!audrey02.news.aol.com!not-for-mail From: huntpharm@aol.com (Huntpharm) Newsgroups: bionet.biophysics Subject: job opportunity in bioinformatics Date: 2 Jul 1997 22:41:28 GMT Lines: 11 Message-ID: <19970702224100.SAA06728@ladder02.news.aol.com> NNTP-Posting-Host: ladder02.news.aol.com X-Admin: news@aol.com Organization: AOL http://www.aol.com I am looking for a person to head up bioinformatics. As a visionary you will be responsible for leading a group of five and taking the bioinformatics team to the next level. You will lead this group responsible for the application of computer technology to genomic analysis and research. We are a leading pharmaceutical company with research facilities in Connecticut and can provide excellent benefits (health insurance, dental and vision plans, paid vacations and more. Excellent compensation package. A high impact, high profile position with excellent opportunity for advancement. Please contact Scott Shanes by phone at 609-584-8733 EXT. 218, fax CV to 609-584-9575 or E-Mail to SIS@diedremoire.com or Neurohunt@aol.com. From owner-biophysics@net.bio.net Wed Jul 02 23:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!us1.rhbnc.ac.uk!yama.mcc.ac.uk!news.york.ac.uk!not-for-mail From: David Scott Newsgroups: bionet.molbio.proteins,bionet.biophysics Subject: molar absoptivity Date: Thu, 03 Jul 1997 13:08:34 -0700 Organization: University of York. York. Y01 5DD Lines: 19 Sender: djs17@york.ac.uk Message-ID: <33BC06C2.75E9@york.ac.uk> Reply-To: Dept., Biology NNTP-Posting-Host: biolpc227.york.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (Win16; I) Xref: biosci bionet.molbio.proteins:11124 bionet.biophysics:3294 Hello, Does anyone know how to determine the molar absorptivity of a protein as a function of wavelength, from scratch? Dave. -- ******************************* * Dr. David Scott * * Dept Biology * * University of York * * YORK * * YO1 5DD * * * * United Kingdom * * * * phone +44 1904 432867 * * fax +44 1904 432860 * ******************************* From owner-biophysics@net.bio.net Wed Jul 02 23:00:00 1997 Path: biosci!INTREPID.CHM.JHU.EDU!rlk From: rlk@INTREPID.CHM.JHU.EDU ("rlk") Newsgroups: bionet.biophysics Subject: Re: molar absoptivity Date: 3 Jul 1997 08:15:44 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <9707031118.ZM10388@intrepid.chm.jhu.edu> NNTP-Posting-Host: net.bio.net Read 'How to measure and predict the Molar Absorption Coefficient of a Protein.' Pace, et al. Protein Science (1995) 4:2411-23 The equation therein has worked well for our lab. As for experimental techniques, I've found the Kjedhal method works best, if you have enough protein (at least 5 mgs) -- -ron 'if I can't dance, I don't want to be a part of your revolution' Emma Goldman -- -ron 'if I can't dance, I don't want to be a part of your revolution' Emma Goldman From owner-biophysics@net.bio.net Thu Jul 03 23:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!mindspring!news.mindspring.com!usenet From: Matthew Parker Newsgroups: bionet.biophysics Subject: Re: molar absoptivity Date: Fri, 04 Jul 1997 12:25:44 -0700 Organization: University of Alabama at Birmingham Lines: 10 Message-ID: <33BD4E38.221A@microbio.uab.edu> References: <9707031118.ZM10388@intrepid.chm.jhu.edu> Reply-To: MatthewP@microbio.uab.edu NNTP-Posting-Host: user-2k7i3bf.dialup.mindspring.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Server-Date: 4 Jul 1997 18:47:01 GMT X-Mailer: Mozilla 3.01Gold (Win16; I) rlk wrote: > > Read 'How to measure and predict the Molar Absorption Coefficient > of a Protein.' Pace, et al. Protein Science (1995) 4:2411-23 > > The equation therein has worked well for our lab. You might also want to look at a paper by Gill and von Hippel in Analytical Biochemistry (1989). I don't have the page number at hand, but i'm sure it's referenced in the Pace paper. From owner-biophysics@net.bio.net Thu Jul 03 23:00:00 1997 Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.sovam.com!sovam!Gamma.RU!srcc!Radio-MSU.net!news-ham1.dfn.de!news-han1.dfn.de!news.gwdg.de!amuelle3 From: amuelle3@gwdu19.gwdg.de (Arne Mueller ) Newsgroups: bionet.molec-model,bionet.molecules,bionet.biophysics,bionet.software Subject: Re: HOW TO CONTACT THE AUTHOR of Molscript???? Followup-To: bionet.molec-model,bionet.molecules,bionet.biophysics,bionet.software Date: 4 Jul 1997 16:36:41 GMT Organization: GWDG, Goettingen Lines: 47 Distribution: world Message-ID: <5pj8qp$rei$1@gwdu19.gwdg.de> References: <33BAEC96.2E7FF4DD@rz.ruhr-uni-bochum.de> NNTP-Posting-Host: gwdu08-fddi.gwdg.de X-Newsreader: TIN [version 1.1 PL8] Xref: biosci bionet.molec-model:1652 bionet.biophysics:3297 bionet.software:19035 Marc Saric (Marc.Saric@rz.ruhr-uni-bochum.de) wrote: : Hi all, : I have a little problem: Recently I stumbled over the nice program : Molscript, written by a man named Dr. Per Kraulis from Sweden. : On several pages dealing with this program, it has been said, that one : must obtain a permission from Dr. Kraulis to download and use Molscript, : and that it is free of charge for academic usage. : I wrote two letters to two different mail-adresses of Mr. Kraulis, but : nothing happened. : Does anyone know the actual adress of Dr. Kraulis or anyone who is in : charge of the program, or does anyone know how to obtain the program : (what to send to which adress or whatever). : Thanks in advance! : -- : Bye, : Marc Saric : Visit http://www.rat.de/marc_saric/ Hello Marc, I found this in my Molscript documentation: Dr. Per Kraulis Center for Structural Biochemistry Karolinska Institute NOVUM S-141 57 Huddinge SWEDEN phone +46 8 608 9266 fax +46 8 608 9290 email pjk@oyster.csb.ki.se good luck, Arne From owner-biophysics@net.bio.net Thu Jul 03 23:00:00 1997 Path: biosci!biosci!not-for-mail From: Marc Saric Newsgroups: bionet.molec-model,bionet.molecules,bionet.biophysics,bionet.software Subject: HOW TO CONTACT THE AUTHOR of Molscript???? Date: 4 Jul 1997 01:14:13 -0700 Organization: Ruhr-University of Bochum Lines: 24 Sender: daemon@net.bio.net Distribution: world Message-ID: <33BAEC96.2E7FF4DD@rz.ruhr-uni-bochum.de> Reply-To: Marc.Saric@rz.ruhr-uni-bochum.de NNTP-Posting-Host: net.bio.net Xref: biosci bionet.molec-model:1651 bionet.biophysics:3296 bionet.software:19033 Hi all, I have a little problem: Recently I stumbled over the nice program Molscript, written by a man named Dr. Per Kraulis from Sweden. On several pages dealing with this program, it has been said, that one must obtain a permission from Dr. Kraulis to download and use Molscript, and that it is free of charge for academic usage. I wrote two letters to two different mail-adresses of Mr. Kraulis, but nothing happened. Does anyone know the actual adress of Dr. Kraulis or anyone who is in charge of the program, or does anyone know how to obtain the program (what to send to which adress or whatever). Thanks in advance! -- Bye, Marc Saric Visit http://www.rat.de/marc_saric/ From owner-biophysics@net.bio.net Thu Jul 03 23:00:00 1997 Newsgroups: bionet.biophysics Path: biosci!rutgers!gatech!howland.erols.net!newsfeed.internetmci.com!news.idsc.gov.eg!not-for-mail From: Sherif Safwatt Subject: Plasmin Message-ID: <33BD81AC.B9@iec.egnet.net> Date: Sat, 05 Jul 1997 02:08:29 +0300 Organization: Home X-Mailer: Mozilla 3.0Gold (Win95; I) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 14 Dear, Can any one tels me a teachnique to isolate a plasmin from human blood,or tels me a company can provid me with it, I need about 1 ml each time I do my experment. Regards ______________________________________________________________________________________ Sherif Safwat Biophysist Cairo University Egypt From owner-biophysics@net.bio.net Fri Jul 04 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!newsfeed.internetmci.com!newsm.ibm.net!ibm.net!uunet!not-for-mail From: "RoLo" Newsgroups: bionet.biophysics Subject: looking for.. Date: 5 Jul 1997 15:11:26 GMT Lines: 17 Message-ID: <01bc8956$efc6b0a0$d02888ce@default> NNTP-Posting-Host: pm7-18.jax-inter.net X-Newsreader: Microsoft Internet News 4.70.1155 -- I'm looking for the best physics links, resources and other web pages to add to my web page. If you know of any "can't live without it links" please let me know! If you get a chance, stop by my web page: http://www.jax-inter.net/users/rolovett Any comments of suggestions would be appreciated! Thanks, Rhonda rolovett@jax-inter.net From owner-biophysics@net.bio.net Fri Jul 04 23:00:00 1997 Newsgroups: bionet.biophysics Path: biosci!agate!hammer.uoregon.edu!newsfeed.direct.ca!feeder.chicago.cic.net!chi-news.cic.net!EU.net!CERN.ch!news From: "Chemical Dynamics" Subject: Post-doc in Biophysics X-Nntp-Posting-Host: tifrc4.tifr.res.in Message-ID: <01bc8919$ff2da360$0e1a909e@lakshmi.tifr.res.in> Sender: news@news.cern.ch (USENET News System) Organization: t i f r X-Newsreader: Microsoft Internet News 4.70.1155 Date: Sat, 5 Jul 1997 08:04:22 GMT Lines: 406 Name: Arvind Srivastava. Institution: Tata Institute of Fundamental Research E-Mail: asa225@tifrvax.tifr.res.in Objective: To apply for Post-doc in the field of Biophysics CURRICULUM-VITAE Name: Arvind Srivastava Date of birth: 13 August 1969 Institute: Tata Institute of Fundamental Research Homi Bhabha Road Bombay, 400 005, India. Correspondence address: Chemical Physics Group Tata Institute of Fundamental Research Homi Bhabha Road Bombay, 400 005, India Phone: 215 2971/215 2979 Ext. 2526. Fax: + 91 - (22) - 215 2110 E-mail: asa225@tifrvax.tifr.res.in Educational qualifications Degree/Exam. Year University % Marks/Division B. Sc. 1990 Purvanchal University Jaunpur, U.P. 67/1st Class M. Sc.(Chemistry) 1992 Banaras Hindu University, Varanasi. 68/1st Class Ph.D. (Chemistry) 1997 TIFR, Bombay. Expected to complete by Sept. 1997. Graduate Course works I have completed following courses as a part of my Ph.D. programme during 1992-1993. Theoretical Courses 1. Quantum Chemistry ; 2. Molecular Biophysics ; 3. Programming in C ; 4. Bio-Electrochemistry ; 5 . NMR Spectroscopy ; 6. Bio-inorganic Chemistry ; 7. Mathematical Methods ; 8. Fluorescence Spectroscopy and Applications. Experimental Projects 1 Production, Purification and Preliminary Characterization of Conserved region of "Myb" proteins; 2 Elementary steps in proton transport across membranes; 3 Rotational diffusion of Rose Bengal in various solvents. Average grade in the above courses was A-. Ph.D. programme After completing graduate course work I joined to Prof. G. Krishnamoorthy, for my Ph.D. in January, 1994. Ph.D. Title: Dynamics of Biological Systems. Technical Experiences: 1. I was involved in the installation of a Time-resolved fluorescence microscope which I have used for most of my experiments. 2. I have used a CW mode-locked, frequency doubled Nd-YAG laser driven dye (Rhodamine 6G and Pyridine 1) laser as the light source in all my time-resolved fluorescence and anisotropy studies. I have used time-correlated single-photon- counting set up as the detection system. I am familiar with the operation and maintenance of this system. 3. All the data analysis were done using the program developed in C-language in our lab (by Prof. N. Periasamy). 4. I am familiar with cell culturing techniques. 5. I have practical and theoretical background in other physical techniques such as Steady-State Fluorescence Spectroscopy (Shimadzu and Flurolog 2), UV-VIS spectroscopy (Shimadzu UV-2100) and Circular Dichroism spectroscopy(Jasco-J600). Awards 1. Junior Talent Search Scholarship. 2. National Scholarship 3. Scholarship by the Tata Institute of Fundamental Research during 1992-1997. 4. Financial award from Department of Science and Technology towards travel to attend the XIIth International Biophysics Conference at Amsterdam, The Netherlands, during 11th Aug.- 16th Aug. 1996. 5. Financial support from Council of Scientific and Industrial Research towards travel to attend the XIIth International Biophysics Conference at Amsterdam, The Netherlands during 11th Aug.- 16th Aug. 1996. 6. Best poster award by Indian Biophysical Society in 1996. Talks given at various places: 1. University of Pune, Feb. 1993 in SERC School on Chemical and Biological Application of Laser. 2. All India Institute of Medical Science, New Delhi on 21 Feb. 1996. 3. Debye Institute, Department of Molecular Biophysics, Buy Ballot Laboratory, Utrecht University, Utrecht, The Netherlands, on 19th Aug. 1996. 4. Department of Chemistry, Celestijnenlaan 200F, Leuven, Belgium on 20th Aug. 1996. 5. Inorganic Chemistry Division, Oxford University, UK on 22th Aug. 1996. 6. Biochemistry Department, Imperial College of Science, Technology and Medicine, London, UK on 25th Aug. 1996. List of Publications In Journals 1. Arvind Srivastava and S. Doraiswamy, Rotational diffusion of Rose Bengal, J. Chem. Phys. 1995, 103, 6197. 2. Anup Madan, P. K. Radha, Arvind Srivastava, Lakshmi C. Padhy and Ramakrishna V. Hosur, The DNA-binding domain of Drosophila melanogaster c-Myb undergoes a multistate denaturation. Eur. J. Biochem. 1995, 230, 733. 3. Arvind Srivastava, Shanteri Singh and G. Krishnamoorthy, Rapid Transport of Protons across membranes by Aliphatic Amines and Acids, J. Phys. Chem. 1995, 99, 11302. 4. Arvind Srivastava and G. Krishnamoorthy, Time-Resolved Fluorescence Microscopic Estimation of Cytoplasmic Viscosity, Progress in Biophys. & Mol. Biol. 1996, 65, 192. 5. Madhavarao C. N. , Sauna Zuben E. ,Srivastava Arvind and Sitaram V., Voids Underlying Dynamics in Proteins Membranes and Micelles, Eur. J. Biochem. 1997 (in press) 6. Arvind Srivastava and G. Krishnamoorthy, Cell Type and Spatial Location dependence of Cytoplasmic Viscosity Measured by Time-Resolved Fluorescence Microscopy, Arch. Biophys. and Biochem. 1997, 340, 159-167. 7. Arvind Srivastava and G. Krishnamoorthy, Time -Resolved Fluorescence Microscopy Could Correct for Probe Binding While Estimating Intracellular pH, Anal. Biochem. 1997, 249 (in press) 8. G. Krishnamoorthy and Arvind Srivastava, Intracellular Dynamics Seen Through Time-Resolved Fluorescence Microscopy, Current Science 1997, (in press) 9. M. M. G. Krishna, Arvind Srivastava, Ranjan Das and N. Periasamy, Translational and Rotational Dynamics of Surface Probes: Monte Carlo Simulations and Fluorescence Anisotropy Experiments. (Submitted) In conferences 1. Arvind Srivastava, Rotational Diffusion of Rose Bengal in Various Solvents, SERC School on Chemical and Biological Application of Laser Feb. 1993. 2. G. Krishnamoorthy, Ishak Ahmed, Shantheri Singh, Hari Pada Maity and Arvind Srivastava, Rapid Transport of Protons across Membrane, Twelfth School on Biophysics of Membrane Transport, School Proceedings, Poland, May 4-13, 1994. 3. Arvind Srivastava and G. Krishnamoorthy, Estimation of Cytoplasmic Viscosity by Time-Resolved Fluorescence Microscopy, XIIIth Indian Biophysical Society meeting, All India Institute of Medical Science, New Delhi, India, Feb. 1996. 4. Arvind Srivastava and G. Krishnamoorthy, Time-Resolved Fluorescence Microscopic Estimation of Cytoplasmic Viscosity, XIIth International Biophysics Conference at Amsterdam, The Netherlands, during 11th Aug.- 16th Aug. 1996 5. Arvind Srivastava and G. Krishnamoorthy, Intracellular pH estimation by Time-Resolved Fluorescence Microscopy, Symposium on Advances in Bio-Inorganic Chemistry during October 7-12, 1996, Tata Institute of Fundamental Research, Mumbai, India. 6. Arvind Srivastava and G. Krishnamoorthy, Estimation of Intracellular pH by Time -Resolved Fluorescence Microscopy, Indian Biophysical Society meeting during 9-12 Dec. 1996 at Indian Institute of Science, Bangalore, India. 7. G. Krishnamoorthy and Arvind Srivastava, Dynamic Fluorescence Microscopic Observations on Intracellular Mobility, during 9-12 Dec. 1996 at Indian Institute of Science, Bangalore, India. 8. M. M. G. Krishna, Ranjan Das, Arvind Srivastava and N. Periasamy, Translational and Rotational Dynamics of surface probes in Vesicles: Computer simulational and Fluorescence Microscopic experiments, during 9-12 Dec. 1996 at Indian Institute of Science, Bangalore, India. 9. Krishnamoorthy and Arvind Srivastava, Cell Membrane Seen Through Time-Resolved Fluorescence Microscopy, Thirteenth School on Biophysics of Membrane Transport, School Proceedings, Poland, May 11-18, 1997. Names & Addresses of Referees 1. Prof. G. Krishnamoorthy Chemical Physics Group Tata Institute of Fundamental Research Homi Bhabha Road, Mumbai 400 005, India Fax: 091-22-215-2110 E-mail: gk@tifrvax.tifr.res.in 2. Prof. N. Periasamy Chemical Physics Group Tata Institute of Fundamental Research Homi Bhabha Road, Mumbai 400 005, India Fax: 091-22-215-2110 E-mail: peri@tifrvax.tifr.res.in 3. Prof. S. Doraiswamy Chemical Physics Group Tata Institute of Fundamental Research Homi Bhabha Road, Mumbai 400 005, India Fax: 091-22-215-2110 E-mail : edorai@tifrvax.tifr.res.in 4. Prof. R. V. Hosur Chemical Physics Group Tata Institute of Fundamental Research Homi Bhabha Road, Mumbai 400 005, India Fax: 091-22-215-2110 E-mail: hosur@tifrvax.tifr.res.in Research experiences Instrumentation: I was involved in the installation of a time-resolved fluorescence microscope. This involved coupling of a fluorescence microscope with picosecond laser system. An inverted epifluorescence microscope (Nikon, Diaphot 300) was optically modified in order to steer the dye laser pulses into the optical path of the microscope. A CW mode-locked frequency-doubled Nd-YAG laser-driven dye (Rhodamine 6G) laser which generates 4-10 ps pulses was used .The laser beam was vertically polarized and the polarization was further restricted to the vertical position by a polarizer placed at the entrance to the microscope. The laser beam was guided to the objective lens. The set - up is capable of performing dynamic fluorescence measurements on samples with a spatial resolution of 0.5-1.0 mm and a time resolution of 50 ps. Also reliable data could be obtained from even very low levels (~102-103 molecules) of fluorophores. The fluorescence which was collected by the same objective lens was passed through cut-off filters, a Glan-Taylor polarizer and a pin hole assembly (placed at the image plane) and detected by a thermoelectrically cooled (Products for Research, USA) fast response photomultiplier (XP2020Q). Time resolution of the fluorescence signal was obtained by the time-correlated single-photon-counting experimental setup. Spatial resolution of the sample has been achieved either by the focussed laser beam or by the pin-hole kept at the image plane. Experimental: Time-Resolved Fluorescence Microscopic Estimation of Cytoplasmic Viscosity Information on the cell type and spatial location dependence of cytoplasmic viscosity would be very useful in understanding some of the processes occuring in the cell. For this purpose, the fluorescent dye Kiton Red (sulforhodamine B) was loaded into a variety of cells such as Swiss 3T3 fibroblast, human mononuclear cells, Sarcoma-180 tumor cell, Chinese hamster ovary cells, the plant cells Digitalis Lanata , stamen hair cells of Tradescantia and guard mother cells of Allium Cepa. Space-resolved measurements of cytoplasmic viscosity were carried out by using an experimental set-up wherein a picosecond laser system was coupled with an epifluorescence microscope. Fluorescence lifetime measurements showed that a large fraction ~70 % of Kiton Red was in the free form. Fluorescence anisotropy decay of Kiton Red in cells was analyzed by a two population (free and bound) model. The microviscosity of cytoplasm was estimated from the anisotropy decay kinetics of the free probe. Correlation time of free Kiton Red in cytoplasm shows significant dependence on the cell type. The following picture emerges from these data: (i) the cytoplasmic viscosity is not very far from that of bulk water for all the cells studied; (ii) the average value of cytoplasmic viscosity is larger in case of the plant cells when compared to those of the animal cells studied here; (iii) the positional variation in the value of cytoplasmic viscosity is larger in the case of the plant cells when compared to the animal cells and (iv) cytoplasmic viscosity inside the tumor cell Sarcoma-180 is not different from the normal mammalian cells studied here. Model studies in various simpler systems have shown that our observation of cell type dependence and spatial location dependence of the cytoplasmic viscosity could have the origin in the variation in one or more of the following conditions within the cells: (i) the level of structured water, (ii) the concentration of small and macromolecules, (iii) the hydrodynamic shape (compact or extended structure) of the molecules present and (iv) physical restrictions such as proximity of membrane, cytoskeletal network etc. Estimation of Intracellular pH by Time-Resolved Fluorescence Microscopy Optical measurement of intracellular pH measurement scores over other methods of pH measurements in the respect of facile measurement of real time variation of intracellular pH and the capability to map the spatial variation of pH within a single cell with the help of a fluorescence microscope. Although fluorescence intensity is the most convenient parameter for measurements, the convenience is offset by various uncertainties in the estimation of pH. Apart from the pH, the fluorescence intensity would also depend upon factors such as concentration of the probe, pathlength of the observation, light scattering , photobleaching and binding of the probe to macromolecules and membranes. Estimation of pH using fluorescence lifetime would eliminate the above mentioned drawbacks. We have used the fluorescent pH indicator SNARF-1 in estimating the intracellular pH in a variety of cells. A fluorescence microscope coupled with a picosecond laser system was used in these measurements. The principle of lifetime-based pH sensing lies in the estimation of the relative amplitudes of the lifetime components of the protonated and deprotonated forms of the probe which have distinctly different lifetimes. The main advantage of lifetime based sensing is the absence of complication due to changes in the pathlength of the observation, concentration of the probe, absence of light scattering and photobleaching. Also probe binding to the macromolecules and membranes could be taken into account while analyzing fluorescence decay curve. Our analysis show that probe binding could result in significant errors in pH-estimations based on steady-state intensity measurements such as the popular ratiometric methods. The origin of this difference lies in the higher value (~3 ns) of the lifetime of the predominant population of bound probe when compared to those of the free forms. In case where a fourth lifetime component ( ~ 0.1 ns) was observed, the pH value estimated by steady state was lower than that estimated by the renormalized amplitude. Study of Membrane Fluidity by Fluorescence Lifetime Distribution: The physical state of cell membranes is relevant in many functions of the cell and hence a knowledge on them is important for a complete description of cell physiology. In the past a variety of physical techniques have been employed for this purpose. In the present work we show the usefulness of lifetime distribution of the membrane probe Nile Red in obtaining information on the physical state of membranes. We have used the time-resolved fluorescence microscopic technique Liposomal membranes, planar supported membranes and membranes of various intact cells were probed under a variety of conditions. Fluorescence decay curves were analyzed by the Maximum Entropy Method (MEM) to obtain distribution of fluorescence lifetime of Nile Red in membranes. The width of lifetime distribution was used to characterize the heterogeneity of the membrane. In model systems such as DPPC and DMPC membranes, the width associated with MEM lifetime distributions of Nile Red was very sensitive to the physical state of the membrane. The width in the gel state was higher when compared to that in liquid crystalline state by about 5 fold. Temperature dependence of the width tracked exactly the physical state of lipid. The width was also sensitive to membrane composition such as the presence of cholesterol, membrane proteins and fatty acids. The following conclusions emerged from these data: (i) The width observed in the mammalian cells studied here were significantly larger when compared to those observed in the plant cells; (ii) the variation in the width observed in a single mammalian cell was about 2-3 fold which is significantly larger than the variation observed in the plant cells and (iii) the width observed in plasma membranes were larger when compared to the nuclear membrane in the mammalian cells. The last observation could be due to the fact that plasma membranes have higher level of cholesterol when compared to nuclear membranes Rapid Transport of Protons across membranes by Aliphatic acids and Amines The pH gradient generated across membranes can be dissipated efficiently by means of single turnover cycle of aliphatic amines and acids present in the membrane. The kinetics of this process was in the submillisecond timescale and was measured by creating pH gradients using temperature jump. The main principal behind this technique is the difference in the enthalpy changes associated with protonation equilibria of various pH buffers. Application of T- jump to a vesicular suspension having, for example Tris in the external aqueous phase and phosphate in the inner aqueous phase produces a DpH within ~2 ms. The decay of DpH (transmembrane proton transport) was measured fluorimetrically by the use of the fluorescent indicator Pyranine entrapped inside the vesicles. The observed DpH decay process was identified as due to rapid transmembrane movement of the neutral form of either the acid or the amine. The rate constant was estimated to be in the range of 1-6 x 103 s-1 in the case of aliphatic amines. Correlation of proton transport with water content of membranes Transmemembrane proton transport was measured in various lipid vesicles in order to correlate proton permeability coefficient with the hydration of the acyl chain. We have used the vesicles made up of pure saturated lipids DMPC, Egg PC, DPPC mixed lipid Soybean phospholipid and variety of unsaturated lipids like C14:1, C16:1, C18:1 , C20:1, C22:1 PC. The transmembrane permeability of proton was measured by giving a pH jump and monitoring the rate of change of internal pH with the help of fluorescent pH indicator pyranine trapped inside. The level of hydration of the acyl chain was estimated by measuring the fluorescence lifetime of the membrane soluble fluorescent probe DPH (Diphenylhexatriene) in the vesicles. Rotational Diffusion of Rose Bengal in various Solvents Picosecond time resolved fluorescence depolarization spectroscopy has been used to measure the rotational reorientation times of rose bengal as a function of viscosity. The variation of viscosity has been effected in two different ways-using different solvents and different compositions of aqueous binary mixtures. While the Stokes-Einstein- Debye (SED) hydrodynamics theory is found to be reasonably satisfactory to explain the rotational diffusion of rose bengal in amides and aprotic solvents, the dielectric friction model provides a better appreciation of its motion in normal alcohols. It is possible to mimic the nonhydrodynamic behavior of rose bengal in tertiary butanol-water (t-BuoH +H2O)mixture by incorporating the contribution due to dielectric friction, although the solvation effects appear to be important in the t-BuOH-rich zone of the binary mixture. In hexamethylphosphoramide-water (HMPA + H2O ) binary mixture the loop-like profile of the rotational reorientation time (tr) versus viscosity (h) can be understood only on the basis of significant solvation effects. The variation in the boundary condition as an alternate explanation for understanding the rotational dynamics in binary mixtures was not found to be satisfactory. From owner-biophysics@net.bio.net Sat Jul 05 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!howland.erols.net!newshub2.home.com!newshub1.home.com!news.home.com!newsfeed2.aimnet.com!news.internetMCI.com!not-for-mail From: dgrt@etf.com Newsgroups: bionet.biophysics Subject: !!*!!1!14 DAY FREE TRIAL VIRTUAL OFFICE!!!! Date: 6 Jul 1997 03:27:19 GMT Organization: Internet MCI Lines: 31 Message-ID: <5pn3an$69n$4@news.internetmci.com> NNTP-Posting-Host: usr2-dialup3.mix1.bloomington.mci.net One-Number service puts you in control of your calls while ensuring that your calls, messages and faxes reach you regardless of your location. One-Number service does this by linking your existing telephones, cell phones, pagers, and fax machines through a single telephone number. YOUR One-Number ACCOUNT COMES STANDARD WITH THESE FEATURES - Consolidates your phone, fax, voice-mail and paging services - Works with your existing products and services, no need to change - Easily lets you designate yourself as available or unavailable - Rings you at up to three numbers simultaneously - Never-busy number accepts multiple incoming calls and faxes - Call Screening (by name) lets you know who is calling - Call Waiting lets you know somebody else is calling - Call Move lets you easily transfer calls among different phones - Call Conferencing allows conferences with other parties - Fax Notification on your pager for incoming fax messages - Redirect calls to Personal Operator (live person) if desired - AND MUCH MORE Virtual Office Communications Company is not a phone company, a long distance carrier, nor do we sell telephone equipment, cellular phones, cellular service, pager or pager service. Instead, we offer service to integrate your existing products, adding value to what you already have by letting your phones, pagers, fax machines and voice-mail systems work together seamlessly. To learn more please visit our web site at: http://www.mynumber.com Please do not reply by e-mail as we are not set up to respond to e-mail requests. From owner-biophysics@net.bio.net Sun Jul 06 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news.sgi.com!news.corp.sgi.com!enews.sgi.com!EU.net!newsfeed.internetmci.com!news.telstra.net!harbinger.cc.monash.edu.au!newshost.carno.net.au!surya From: Shoba.Ranganathan@anu.edu.au (Shoba Ranganathan) Newsgroups: bionet.molec-model,bionet.molecules,bionet.biophysics,bionet.software Subject: Re: HOW TO CONTACT THE AUTHOR of Molscript???? Date: Sun, 29 Jun 97 20:49:02 GMT Organization: JCSMR,ANU Lines: 43 Distribution: world Message-ID: <5ppa6u$46p$1@clarion.carno.net.au> References: <33BAEC96.2E7FF4DD@rz.ruhr-uni-bochum.de> NNTP-Posting-Host: 150.203.193.135 X-Newsreader: News Xpress Version 1.0 Beta #4 Xref: biosci bionet.molec-model:1657 bionet.biophysics:3305 bionet.software:19046 In article <33BAEC96.2E7FF4DD@rz.ruhr-uni-bochum.de>, Marc Saric wrote: >Hi all, > >I have a little problem: Recently I stumbled over the nice program >Molscript, written by a man named Dr. Per Kraulis from Sweden. >On several pages dealing with this program, it has been said, that one >must obtain a permission from Dr. Kraulis to download and use Molscript, >and that it is free of charge for academic usage. > >I wrote two letters to two different mail-adresses of Mr. Kraulis, but >nothing happened. > >Does anyone know the actual adress of Dr. Kraulis or anyone who is in >charge of the program, or does anyone know how to obtain the program >(what to send to which adress or whatever). > >Thanks in advance! Dear Marc, Per Kraulis is currently with Pharmacia - however, you can ask for permission to copy Molscript from anyone who has a registered version and send Kraulis e.mail to that effect ("Per Kraulis" ). The source code is made available (in Fortran) and you can then compile it for your machine. Please contact me if you wish to copy the program from us. Shoba =========================================================== Dr. Shoba RANGANATHAN Computational Mol Biology & Drug Design Group Div. of Biochemistry & Mol. Biology John Curtin School of Medical Research Australian National University Tel: +616-279-8301 Canberra ACT 0200 Fax: +616-249-0415 Australia. email:Shoba.Ranganathan@anu.edu.au ===========(http://biocomp.anu.edu.au/~sra/)============== From owner-biophysics@net.bio.net Sun Jul 06 23:00:00 1997 Path: biosci!agate!usenet.INS.CWRU.Edu!HSNX.wco.com!newsfeed.dacom.co.kr!newsfeed.direct.ca!europa.clark.net!dispatch.news.demon.net!demon!easynet-uk!btnet-feed2!hades.ndirect.co.uk!194.74.254.91 From: Uwe Unrath Newsgroups: bionet.biophysics Subject: Looking for PhD program Date: Mon, 07 Jul 1997 22:45:59 +0100 Organization: BTnet, BT Public Internet Service Message-ID: <33C16397.2CC5@bigfoot.com> NNTP-Posting-Host: hades.ndirect.co.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (Win95; I) Lines: 13 20 months ago I finished graduate school with a master's degree in physics. My master thesis research was in the field of biophysics (voltage activated calcium channels). Now, after 20 months working in the computer business (blinded by salary) I just can't resist the urge to go back to science anymore. I would be gratefull for any information about departmental and research programs (openings, area of research, ...). Personal opinions about departments, programs, and biophysics in general are appreciated. Please send information to: uweu@bigfoot.com Thank's U.U. From owner-biophysics@net.bio.net Sun Jul 06 23:00:00 1997 Path: biosci!rutgers!gatech!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!rill.news.pipex.net!pipex!join.news.pipex.net!pipex!oleane!in2p3.fr!news-ge.switch.ch!news-zh.switch.ch!rzunews.unizh.ch!newsadm From: Rolf Kocherhans Newsgroups: bionet.biophysics Subject: Free practical programs for molecular biologists !!! Date: Mon, 07 Jul 1997 16:16:38 +0200 Organization: University of Zurich Lines: 49 Message-ID: <33C0FA45.6083@vetvir.unizh.ch> Reply-To: rolfk@vetvir.unizh.ch NNTP-Posting-Host: 130.60.22.38 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Macintosh; I; PPC) I wrote a few practical and simple to use programs which facilitate your daily work in the lab such as predicting the size of DNA fragments after digestion (graphical) with restriction enzymes. I would like to make these programs accessible to a broad user group by the Internet. All programs have been tested on MacOS and Windows95. My programs are accessible over the WWW and made functional using Netscape 2.x or Internet Explorer 2.x or higher in association with a free plugin which you have to download and install first. This is what you do: - Download the Roadster plugin http://www.unizh.ch/vetvir/plugin.html) install it on your computer. - Then connect to: http://www.unizh.ch/vetvir/programs.html That's it !! These are my programs which make your live as a molecular biologist easier ! Find here a few more examples or my programs: a. Digest Preview: Enter the size(s) of your DNA fragment(s) and see their migration pattern in a virtual gel in comparison to a 1 kb ladder. b. Adapter Design: Helps to create in frame adapters in order to link incompatible DNA ends together. c. Dilution Calculator: Does all the calculations when you have to make up solutions There are many other programs such as Oligo Tm, Compatible ends etc. Please have a look, comments are welcome! Have fun Rolf Kocherhans mailto:rolfk@vetvir.unizh.ch From owner-biophysics@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!news.apfel.de!serra.unipi.it!cesit1.unifi.it!cesit1.unifi.it!nntp Newsgroups: bionet.biophysics Subject: (no subject) Message-ID: <33C21451.48DC@dfc.unifi.it> From: "Prof. Oreste Ortolani - Istituto di Anestesiologia - Università di Firenze" Date: Tue, 08 Jul 1997 12:20:01 +0200 Nntp-Posting-Host: anest1.dfc.unifi.it X-Mailer: Mozilla 3.01Gold (Win95; I) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii; name="vibration.txt" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="vibration.txt" Lines: 14 I am looking for contacts to discuss the possible role of vibrations of any kind and frequencies on nucleation of water during freezing. Are there potential effects ( positive or negative ) of vibrations on the transition to the vitreous state and on ice crystal formation? Is anyone willing to discuss this matter with me or helping me by suggesting people to contact or articles to read or else? My E-mail is o.ortolani@dfc.unifi.it From owner-biophysics@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!news.apfel.de!serra.unipi.it!cesit1.unifi.it!cesit1.unifi.it!nntp Newsgroups: bionet.biophysics Subject: influence of vibrations on nucleation during water freezing Message-ID: <33C21423.17FA@dfc.unifi.it> From: "Prof. Oreste Ortolani - Istituto di Anestesiologia - Università di Firenze" Date: Tue, 08 Jul 1997 12:19:15 +0200 Nntp-Posting-Host: anest1.dfc.unifi.it X-Mailer: Mozilla 3.01Gold (Win95; I) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 9 I am looking for contacts to discuss the possible role of vibrations of any kind and frequencies on nucleation of water during freezing. Are there potential effects ( positive or negative ) of vibrations on the transition to the vitreous state and on ice crystal formation? Is anyone willing to discuss this matter with me +or helping me by suggesting people to contact or articles to read or else? My E-mail is o.ortolani@dfc.unifi.it From owner-biophysics@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.biophysics Subject: How Much Energy Does ATP Tranfer? < > PENTCHO VALEV Date: 8 Jul 1997 13:15:26 +0100 Lines: 12 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5ptb0u$agb@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk Dear Colleagues, Obviously my question "Can one mole ATP transfer more than 20 KJ energy, i.e. more than its internal energy?" can only be answered experimentally. Still the problem is so important that it would be useful if we gave hypothetical answers - after all, science is often driven by hypotheses, not necessarily by established facts. I would be very grateful for your opinions - although I stick to the molecular-machine alternative (not more than 20 KJ), I need many more refutations or agreements in order to go on. Thank you. Pentcho Valev From owner-biophysics@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!vixen.cso.uiuc.edu!news-peer.sprintlink.net!news.sprintlink.net!Sprint!news.maxwell.syr.edu!news.bc.net!rover.ucs.ualberta.ca!news.ucalgary.ca!mars.online.uleth.ca!news From: Marc Roussel Newsgroups: bionet.biophysics Subject: Re: How Much Energy Does ATP Tranfer? < > PENTCHO VALEV Date: Tue, 08 Jul 1997 09:45:59 -0600 Organization: Department of Chemistry and Biochemistry, University of Lethbridge Lines: 27 Message-ID: <33C260B7.41C6@henri.chem.uleth.ca> References: <5ptb0u$agb@mserv1.dl.ac.uk> NNTP-Posting-Host: henri.chem.uleth.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; I; OSF1 V3.2 alpha) RUMYM@BGEARN.ACAD.BG wrote: > Obviously my question "Can one mole ATP transfer more than 20 KJ > energy, i.e. more than its internal energy?" can only be answered > experimentally. Still the problem is so important that it would be > useful if we gave hypothetical answers - after all, science is often > driven by hypotheses, not necessarily by established facts. In my opinion, there are at least two problems with the question as Pentcho has posed it: 1. 20 kJ/mol is not the internal energy of ATP. It's the internal energy change on hydrolysis. (I think the actual figure is closer to 24 kJ/mol.) This is not a quibble: Pentcho's arguments revolve around the interpretation of the thermodynamic state functions so it's important to be clear about what these functions refer to. 2. You have to be clear about what you mean by "transfer". In its current form, Pentcho's question may lead to an uninteresting tautology. I suggest the following version: "Can the isothermal hydrolysis of ATP be made to yield more than 24 kJ/mol of work?" Pentcho, if you intended something substantially different, please speak up. Marc R. Roussel (roussel@henri.chem.uleth.ca) Department of Chemistry and Biochemistry University of Lethbridge From owner-biophysics@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.biophysics Subject: Review articles on bioinformatics Date: 8 Jul 1997 16:11:00 +0100 Lines: 75 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5ptla4$nku@mserv1.dl.ac.uk> Original-To: bio-info@dl.ac.uk, biophys@dl.ac.uk, comp-bio@dl.ac.uk, proteins@dl.ac.uk Dear netters: Several days ago, I asked "Could any one provide me some references of recent review articles on bioinformatics?" , then almost immediately, I received many letters. To my surprise, most of these letters are not about the reply, on the contrary, they kindly asked me to re-post the messages to them. So I think this topic may interest many people. Now I summarize the responses as follows: Printed sources about BioInformatics & the InterNet. Resources, Reviews 1993-1996. Trends in Genetics 11(6) : 223-228 (June 1995). World Wide Web resources for the biologist. Rob Harper (EBI). Molecular Medicine 333(10): 645-647 (Sept 1995). Molecular medicine: hunting for genes in computer data bases. Mark Boguski (NCBI). Kemia-Kemi 22(8): 691-696 (1995). Marcomolecular modelling for the 21st Century. Mark Johnson et al. (Turku, Fi) Current Opinions in Genetics and Development 4: 383-388 (1994). Bioinformatics. Mark Boguski (NCBI). Trends in Biotechnology 12: 76-80 (March 1994). High performance searching of biosequence databases. Andrew Coulson (Edin.). Nature Genetics 6: 119-129 (Feb 1994). Issues in searching molecular sequence databases. Stephen Altschul et al (NCBI). Nature 375: 262 (May 1995). The boom in bioinformatics (employment review). Diane Gershon. Science 262: 502-503 (Oct 1993). Managing the genome data deluge. Peter Aldhous. Nature 376: 647-648. Challenging times for bioinformatics. Chris Sander et al. (EMBL). Molecular Medicine Today March 1996: 98-102. The Web: sequence databases and homology searching using the World Wide Web. Science 272: 1730-1732. Hot property: biologists who compute. Elliot Marshall. The Biochemist Oct/Nov 1996: 32-33. Bioinformatics. Clare Sansom, (Birkbeck). "Methods in Enzymology", vol. 266 "Computer Methods for Macromolecular Sequence Analysis" (1996) R.F. Doolittle Ed.; Academic Press. Up-to-date, and very comprehensive. Science 273: 545-708 (21 Aug. 1996) Not the entire issue, of course, but there is a concentration of good articles there. The URL is http://www.techfak.uni-bielefeld.de/bcd/Curric/syllabi.html mirrored at http://merlin.mbcr.bcm.tmc.edu:8001/bcd/Curric/syllabi.html and http://www.biotech.ist.unige.it/bcd/Curric/syllabi.html http://www.techfak.uni-bielefeld.de/bcd/welcome.html) I would like to thank specially the folowing netters: Dr. Andrew Lloyd Dr. Georg Fuellen Dr. Iddo Friedberg Without their kind help, we can not have so much useful information. Ren Zhang From owner-biophysics@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!cpk-news-hub1.bbnplanet.com!cam-news-feed3.bbnplanet.com!news.bbnplanet.com!news.inc.net!news.itis.com!pkuzmic From: pkuzmic@biokin.com (Petr Kuzmic) Newsgroups: bionet.biophysics Subject: Freeware program DYNAFIT update Date: Tue, 08 Jul 1997 19:47:26 GMT Organization: BioKin Consulting Lines: 50 Sender: reguser@m4.itis.com Message-ID: <5pu55o$dlr$4@bill.itis.com> Reply-To: pkuzmic@biokin.com NNTP-Posting-Host: m4.itis.com X-Newsreader: News Xpress 2.01 This is a message to all users of program DYNAFIT ----------------------------------------------------------------- DynaFit executable files (PowerMac, DOSbox under Win31,Win95,WinNT) were updated to version 2.16[f]. Improvements were made in the module for automatic determination of confidence intervals for rate constants. An example problem was added, based on experimental data published in [1]. This paper contains 97 differential and algebraic equations and three mathematical appendices that describe the kinetics of competitive binding in the system thrombin-dehydrothrombin-hirudin. Nevertheless, this complicated formal treatment is based on several simplifying assumptions; the fitting parameters are composite or derived kinetic constants. In contrast, in DYNAFIT [2] the kinetic problem is formulated simply by using the following text: [mechanism] E + L <===> EL : k1 k2 F + L <===> FL : k3 k4 where E is thrombin, F is chemically modified thrombin, and L is hirudin. The analysis is completely general, not resting on any assumptions except the mass action law. The adjustable parameters in the fitting model are microscopic rate constants k1-k4, not composite or derived kinetic constants. The executable files and the expanded test files can be downloaded from http://www.biokin.com/dynafit/files/. References: [1] Wedemeyer W.J., Ashton R.W., and Scheraga H.A. (1997) "KINETICS OF COMPETITIVE BINDING WITH APPLICATION TO THROMBIN COMPLEXES" Anal. Biochem. 248, 130-140. [2] Kuzmic, P. (1996) "PROGRAM DYNAFIT FOR THE ANALYSIS OF BIOCHEMICAL DATA: APPLICATION TO HIV PROTEASE" Anal. Biochem. 237, 260-273. ----------------------------------------------------------------- pkuzmic@biokin.com | http://www.biokin.com | fax 608.256.1269 ------------------------------------------------------- Petr Kuzmic, Ph.D. * http://www.biokin.com B i o K i n, Ltd. * P.O. Box 8336 * Madison WI 53708 voice 608.256.4790 * fax 608.256.1269 From owner-biophysics@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.biophysics Subject: How Much Energy Does ATP Transfer? < > PENTCHO VALEV Date: 8 Jul 1997 19:00:40 +0100 Lines: 11 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5ptv88$66t@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk Marc Roussel wrote: > 2. You have to be clear about what you mean by "transfer". > In its current form, Pentcho's question may lead to an > uninteresting tautology. I suggest the following version: > "Can the isothermal hydrolysis of ATP be made to yield more than > 24 kJ/mol of work?" Pentcho, if you intended something > substantially different, please speak up. Your version is exact. Pentcho From owner-biophysics@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!cc.UManitoba.CA!gordonr From: gordonr@cc.UManitoba.CA (Richard Gordon) Newsgroups: bionet.biophysics Subject: nucleation with vibrations Date: 8 Jul 1997 07:38:27 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 51 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Professor Oreste Ortolani Istituto di Anestesiologia, Universite di Firenze, Italy Dear Oreste, Vibrations of sufficiently short wavelength (0.1-1 micometers, achievable with acoustic microscopes) might alter the periodic precipitation of amorphous silica in single celled algae called diatoms. As silica is similar in its physical chemistry to water, its precipitation might provide a useful analog for "direct" observation of nucleation with vibrations, and/or a fascinating subject in its own right. See: Iler, R.K. (1979). The Chemistry of Silica: Solubility, Polymerization, Colloid and Surface Properties, and Biochemistry. New York: John Wiley & Sons. Gordon, R. & R.W. Drum (1994). The chemical basis for diatom morphogenesis. Int. Rev. Cytol. 150, 243-372, 421-422. Bereiter-Hahn, J. (1995). Probing biological cells and tissues with acoustic microscopy. Adv. Acoustic Micr. 1, 79-115. Briggs, A. (1992). Acoustic Microscopy, Oxford University Press. Yours, -Dick Gordon To: biophys@net.bio.net Subject: influence of vibrations on nucleation during water freezing =46rom: "Prof. Oreste Ortolani - Istituto di Anestesiologia - Universit=FD d= i =46irenze" Date: Tue, 08 Jul 1997 12:19:15 +0200 Nntp-Posting-Host: anest1.dfc.unifi.it MIME-Version: 1.0 I am looking for contacts to discuss the possible role of vibrations of any kind and frequencies on nucleation of water during freezing. Are there potential effects ( positive or negative ) of vibrations on the transition to the vitreous state and on ice crystal formation? Is anyone willing to discuss this matter with me +or helping me by suggesting people to contact or articles to read or else? My E-mail is o.ortolani@dfc.unifi.it -------------------------------------------------------------------- Dr. Richard Gordon, Department of Radiology University of Manitoba, Health Sciences Centre 820 Sherbrook Street, Winnipeg, MB R3A 1R9 Canada Phone: (204) 789-3828, Fax: (204) 787-2080, Home: (204) 589-0411 E-mail: GordonR@cc.UManitoba.ca From owner-biophysics@net.bio.net Tue Jul 08 23:00:00 1997 From: Damn Yankee Newsgroups: bionet.biophysics Organization: Yankee Inc. Subject: !!!Hello!!! NNTP-Posting-Host: 205.139.183.49 Message-ID: <33c0b432.1@nntp.kalnet.net> Date: 7 Jul 97 09:17:38 GMT Lines: 9 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!pull-feed.internetmci.com!nntp.kalnet.net!205.139.183.49 Are you looking for a great place to find interesting things on the WWW??? Than look no more because you have found the right place!!! The place you are looking for is Yankee Inc.!!! A great Web Site full of interesting links to interesting places!!! Everything from Adult to Xzlyaphone it's here!!! There is something for everyone and then some!!! So give it a try what do you have to lose except some sleep??? Yankee Inc. http://www.kalnet.net/yank714 Yankee Inc. Your Alternative Web Solution!!! Yankee Inc. http://www.kalnet.net/yank714 If you would like to be removed from my mailing list - hit reply and type "REMOVE" and I will promptly remove you from my list!!! Thank You!!! From owner-biophysics@net.bio.net Tue Jul 08 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!news.maxwell.syr.edu!nntp.uio.no!mn6.swip.net!seunet!news2.swip.net!mailgate.astra.com!not-for-mail From: Steve Gardner Newsgroups: bionet.molec-model,bionet.molecules,bionet.biophysics,bionet.software Subject: Re: HOW TO CONTACT THE AUTHOR of Molscript???? Date: Wed, 09 Jul 1997 09:35:11 +0200 Organization: Astra Bioinformatics Centre Lines: 40 Message-ID: <33C33F2F.6B07@draco.se.astra.com> References: <33BAEC96.2E7FF4DD@rz.ruhr-uni-bochum.de> NNTP-Posting-Host: dpsgr.draco.se.astra.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (WinNT; I) To: Marc.Saric@rz.ruhr-uni-bochum.de Xref: biosci bionet.molec-model:1662 bionet.biophysics:3320 bionet.software:19072 Marc Saric wrote: > > Hi all, > > I have a little problem: Recently I stumbled over the nice program > Molscript, written by a man named Dr. Per Kraulis from Sweden. > On several pages dealing with this program, it has been said, that one > must obtain a permission from Dr. Kraulis to download and use Molscript, > and that it is free of charge for academic usage. > > I wrote two letters to two different mail-adresses of Mr. Kraulis, but > nothing happened. > > Does anyone know the actual adress of Dr. Kraulis or anyone who is in > charge of the program, or does anyone know how to obtain the program > (what to send to which adress or whatever). > > Thanks in advance! > -- > > Bye, > > Marc Saric > > Visit http://www.rat.de/marc_saric/ Per Kraulis now works in Luis Parodi's bioinformatics group at Pharmacia & Upjohn in Stockholm. Luis' number is +46 8 695 7759. Good luck. ---------------------------------------------------------------------- Dr Steve Gardner Director Tel: +46 46 33 60 00 Astra Bioinformatics Centre Fax: +46 46 33 71 44 PO BOX 34 E-mail: steve.gardner@draco.se.astra.com S-221 00 Lund Sweden From owner-biophysics@net.bio.net Tue Jul 08 23:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!newsfeed.dacom.co.kr!newsfeed.internetmci.com!rill.news.pipex.net!pipex!join.news.pipex.net!pipex!oleane!in2p3.fr!news-ge.switch.ch!news-zh.switch.ch!surfnet.nl!highway.leidenuniv.nl!usenet From: Marcel van der Heyden Newsgroups: bionet.biophysics Subject: Call for papers: HELNET Workshop on Neural Networks Date: Wed, 09 Jul 1997 10:24:47 +0200 Organization: HELNET Workshop on Neural Networks Lines: 303 Message-ID: <33C34ACF.1F33@dds.nl> Reply-To: helnet97@dds.nl NNTP-Posting-Host: mfly30.medfac.leidenuniv.nl Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (Win95; I) CALL FOR PAPERS HELNET 1997 International Workshop on Neural Networks October 3 - October 5, Montreux Announcing the HELNET 1997 Workshop on Neural Networks Montreux, Switzerland from October 3 - October 5, 1997 http://www.leidenuniv.nl/medfac/fff/groepc/chaos/helnet/index.html mailto:helnet97@dds.nl ********** Deadlines extended ********** The HELNET workshops are informal meetings primarily targeted towards young researchers from neural networks and related fields. They are traditionally organised a few days prior to the ICANN conferences. Participants are offered the opportunity to present and extensively discuss their work as well as more general topics from the neural network field. One of the aims of the HELNET Workshops is to fascilitate such exchange and enable (young) researchers, (PhD) students and postdocs in the field to learn more about the varying disciplines in the neural networks field outside their own research program. That is why we encourage researchers from related fields to register and particpate. Although the final workshop program has not been fixed yet the following topics have been proposed for presentation and discussion. - Statistical induction of lexical meaning. - Optimal complexity in reduced connectivity neural network paradigms - Speech recognition by neural networks - Neural networks and statistical inference - The emergence of consciousness in neural networks - Applications of differential geometric system theory in dynamic neural networks - Circuit and VLSI complexity issues - VLSI friendly learning - Neural network applications in control - Visualization by neural networks - Markov modelling of sensory neural spike trains - An application of neural networks in cellular wireless networks Please find more detailed information on the HELNET 1997 Workshop on Neural Networks and the registration form below. =================================================================== GENERAL INFORMATION =================================================================== Important Dates and Deadlines Deadline paper submission August 1, 1997 Notification of acceptance August 15, 1997 Deadline registration August 30, 1997 Deadline revised papers September 15, 1997 Workshop start October 3, 1997 Workshop end October 5, 1997 Travel Directions Venue site: Hotel des Alpes Vaudoises Rue de Bugnon 1823 Glion (Montreux) Switzerland Tel: + 41 21 963 20 76 Fax: + 41 21 963 56 94 The workshop site is located at the foot of the Rochers-de-Naye at an altitude of approximatly 670 meters above sea-level in the village of Glion. It is overlooking Montreux and the Lac Leman and offers an exciting view on the Alpes. The hotel is equipped with a private parking, a large garden and an outdoor swimming pool. There is a direct connection by local train from the venue site to the Montreux/Territet trainstation and vice versa. Participants will be provided with train tickets when needed. Getting there: The easiest connection by plane is using Geneva Airport. There are trains running directly from Geneva Airport to Montreux regularly in less than an hour. At Montreux you switch to a small local train which will take you from Montreux/Territet up the mountain toward the Hotel des Alpes Vaudoises. This trains stops right in front of the hotel at the "Hotel des Alpes Vaudoises" train stop. To ICANN...: There is a direct connection from Montreux to Laussane. More information can be found at the ICANN www-site. Paper Format The workshop participants are encouraged to submit their papers in LaTeX format. However, we can also process Word and Wordperfect documents. If you submit non-LaTeX formatted papers please include plain text versions of your paper on PC disk as well as postscript versions of your figures. - Papers should be submitted camera-ready. - The printable are should be 12 by 20 centimeters (including page numbers) in which case font size should be 10-point size using a Times or similar font. - Titles and subtitle should be typeset using 12-point fonts. Footnotes and super/subscripts should be 9-point characters. - When you use standard LaTeX styles (e.g. article) your paper will have a default printable area of approximatly 15 by 23 centimeters and will be reduced in size by 80% for publication. Please take this into account when preparing your figures. The length of submitted papers should not exceed 8 pages including figures, tables and references.Centered at the top of the first page should be the title of the papers, author names(s), affiliation(s) and mailing address(es). Please submit 4 (four) copies of your paper as well as a version on disk (PC/DOS format only!) with the graphic files included on this disk. Paper versions of submitted manuscripts should not be stapled or folded. Like the previous occasions, the proceedings of this year's workshop will be published by the VUU Publishers, Amsterdam. Workshop Fee -Approximate- exchange rates: 100 DFL = 30 BPS = 50 USD = 85 DM Check your local exchange office for the actual rates! The workshop fee is DFL. 600,- (Dutch guilders) and includes 4 nights in a shared double room (DFL 725,- if you prefer a single room), half-board, refreshements during the sessions, welcome drinks on the night of arrival. Accompanying persons are welcome and charged DFL. 500 (DFL. 625 for single room). An optional outing is to be organized and included in the fee. The workshop proceedings will be handed out upon arrival. You can register by printing and filling the registration form and sending it per fax or regular mail. If you do not intend to pay by credit card you can also email the filled-out registration form. You will receive confirmation of your registration and payment upon receipt. If you have any question please direct your queries to: HELNET 1997 P.O. Box 2318 1000 CH Amsterdam Netherlands Fax: + 31 20 471 49 11 Email: helnet97@dds.nl The workshop fee is payable in the following ways: - Bank transfer: D.S.R. ABN-AMRO Bank, Ceintuurbaan 89, Amsterdam, the Netherlands Account No. 43.55.28.521 Stating: HELNET97 - Credit card: We accept VISA and American Express credit cards. Please print and fill out the registration form and send it to us by fax or regular mail using details stated above. =================================================================== REGISTRATION FORM =================================================================== In order to register as a participant to the HELNET Workshop on Neural Networks please print and fill out the form below completely and mail or fax to the address indicated below: If you do NOT intend to pay using a credit card you can also email us the filled-out registration form. HELNET 1997 P.O. Box 2318 1000 CH Amsterdam Netherlands Fax: + 31 20 471 49 11 helnet97@dds.nl Accomodation: [ ] Double room (FDL 600,-) Preference for sharing your room with: [ ] Single room (DFL 725.-) [ ] Accompanying person (DFL. 500,- when sharing a double room, DFL. 625,- otherwise) Your personal details: Name ----------------------------------------------------------- Position ------------------------------------------------------ Institution --------------------------------------------------- Address ------------------------------------------------------- P.O. Box ------------------------------------------------------ Zip Code ------------------------------------------------------ City ---------------------------------------------------------- Country ------------------------------------------------------ Tel ----------------------------------------------------------- Fax ----------------------------------------------------------- Email --------------------------------------------------------- Your registration: [ ] I can not make a final regsitration yet. Please keep me informed [ ] I register for HELNET97 but I will not submit a paper and would just like to attend and participate in the discussions. [ ] I would like to present the following paper: ----------------------------------------------------------------- ----------------------------------------------------------------- ----------------------------------------------------------------- ----------------------------------------------------------------- I would like to propose the following topics for discussion: 1. -------------------------------------------------------------- 2. -------------------------------------------------------------- 3. -------------------------------------------------------------- 4. -------------------------------------------------------------- I will make the workshop fee payable in the following way: [ ] Bank transfer: D.S.R. Account No. 43.55.28.521 Stating: HELNET97 ABN-AMRO Bank Ceintuurbaan 89, Amsterdam, the Netherlands [ ] Credit cards: We can accept the following cards: [ ] VISA [ ] American Express Card No. ------------------------------------------------------- Expiry Date: --------------------------------------------------- Signature: ----------------------------------------------------- Date: ---------------------------------------------------------- From owner-biophysics@net.bio.net Tue Jul 08 23:00:00 1997 Path: biosci!rutgers!gatech!newsxfer3.itd.umich.edu!portc01.blue.aol.com!audrey02.news.aol.com!not-for-mail From: huntpharm@aol.com (Huntpharm) Newsgroups: bionet.biophysics Subject: job opportunity for protein chemist Date: 9 Jul 1997 11:31:04 GMT Lines: 13 Message-ID: <19970709113100.HAA24370@ladder02.news.aol.com> NNTP-Posting-Host: ladder02.news.aol.com X-Admin: news@aol.com Organization: AOL http://www.aol.com I am looking for a Protein Chemistry Scientist to develop cancer therapeutic proteins and small molecules. This work would also include modeling drugs which interact with small molecules. You need to have a PhD, be a protein biochemist with 1-6 years post doc experience in protein engineering and a strong background in creative molecular modeling is required. Recombinant molecular biology skills would be a plus. This person will have a strong publication record and be involved in a team oriented approach to science. We are a leading bio-tech firm with research facilities in New York City and can provide excellent benefits (health insurance, dental and vision plan, paid vacations and more. A high impact, high profile position with excellent opportunity for advancement Please contact Scott Shanes by phone at 609-584-8733 EXT. 218, fax CV to 609-584-9575 or E-Mail to SIS@diedremoire.com or Neurohunt@aol.com. From owner-biophysics@net.bio.net Wed Jul 09 23:00:00 1997 From: randy97 Subject: http://www.love.com Newsgroups: bionet.biophysics NNTP-Posting-Host: pgh.nauticom.net Message-ID: <33c528bd.5@pgh.nauticom.net> Date: 10 Jul 97 18:23:57 GMT Lines: 9 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!newsfeed.internetmci.com!pgh.nauticom.net!pgh.nauticom.net Looking to find people in your area that enjoy the same things as this newsgroup? Check out http://www.love.com It's free, it's new, and it's awesome. Rand From owner-biophysics@net.bio.net Wed Jul 09 23:00:00 1997 From: Damn Yankee Newsgroups: bionet.biophysics Organization: Yankee Inc. Subject: I Am Very Sorry!!! NNTP-Posting-Host: 205.139.183.55 Message-ID: <33c2554c.0@nntp.kalnet.net> Date: 8 Jul 97 14:57:16 GMT Lines: 5 Path: biosci!rutgers!gatech!howland.erols.net!newsfeed.internetmci.com!pull-feed.internetmci.com!nntp.kalnet.net!205.139.183.55 I would like to apologise to this newsgroup and everyone who reads this newsgroup!!! I promise never to post or send spam to this or any other newsgroup that does not pertain to my posting!!! Please accept my humble apology and again I will never post spam here again!!! Thank You!!! Andrew Schero yank714@kalnet.net From owner-biophysics@net.bio.net Wed Jul 09 23:00:00 1997 Path: biosci!agate!howland.erols.net!newshub2.home.com!newshub1.home.com!news.home.com!nick.arc.nasa.gov!purdue!mozo.cc.purdue.edu!expert.cc.purdue.edu!cdai From: Changhong Dai Newsgroups: bionet.biophysics,bionet.cellbiol,bionet.cellbiol.cytomet, Subject: help with fixing suspension cell for staining Date: Thu, 10 Jul 1997 11:18:59 -0500 Organization: Purdue University Lines: 15 Message-ID: References: <5q0ncq$eik$2623@earth.superlink.net> NNTP-Posting-Host: expert.cc.purdue.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: <5q0ncq$eik$2623@earth.superlink.net> Xref: biosci bionet.biophysics:3328 bionet.cellbiol:7752 HI, I am interested in methods for fixing suspension cell(say U937) for lacZ staining. Would anyone kindly share any ideas about how to do it? Thank you for your time. Changhong ----------------------------------- Changhong Dai Tel: (765)4945401(Lab) Chemistry Department, P.O.Box 376 Purdue University West Lafayette, IN 47906 From owner-biophysics@net.bio.net Thu Jul 10 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!newsfeed.internetmci.com!news.telstra.net!act.news.telstra.net!brian.telstra.net!news.aus.world.net!usenet From: tael@world.net (tael) Newsgroups: bionet.biophysics Subject: Negative ion penetration Date: Fri, 11 Jul 1997 07:19:24 GMT Organization: AUSNet Services Lines: 14 Message-ID: <5q4l3h$36n@news.aus.world.net> Reply-To: tael@world.net NNTP-Posting-Host: melb26.world.net X-Newsreader: Forte Free Agent 1.0.82 Hi, I was wondering does anyone here know about the penetration of negative ions into different materials? Could you suggest someone I could contact if not? IS this the right newsgroup for this topic??!! Regards, Jon. From owner-biophysics@net.bio.net Fri Jul 11 23:00:00 1997 Path: biosci!rutgers!gatech!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.gsl.net!news-hk.gsl.net!news.gsl.net!newsgate.cuhk.edu.hk!news.cuhk.edu.hk!usenet From: "Gordon Chan" Newsgroups: bionet.biophysics Subject: I need help Date: 12 Jul 1997 09:56:31 GMT Organization: The Chinese University of Hong Kong Lines: 13 Message-ID: <01bc8ea9$88118cc0$c0c5bd89@chan-s-computer> NNTP-Posting-Host: @dialup192.csc.cuhk.edu.hk X-Newsreader: Microsoft Internet News 4.70.1155 I am now working on a research program about the finite element method analysis of the interface between the human hip bone and the prosthesis. The aim of this program is to develop a new type of prosthesis to be implanted into human. Please if anyone can provide me informations about the stress transmission through the hip joint with prosthesis or relevant informations of the same topic. Moreover, I have been to the URL of the visible human project and , unfortunately, found no information about the way to obtain the cad file of the visible human. I am interested in a 3d model of a human leg for the FEM analysis and it will be my pleasure if anyone is able to provide me the relevant informations. Thanks a lot Gordon From owner-biophysics@net.bio.net Fri Jul 11 23:00:00 1997 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!uunet!in3.uu.net!128.230.129.112!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!mindspring!news.mindspring.com!user-37kbn3n.dialup.mindspring.com!user From: silversun@mindspring.com (Silversun) Newsgroups: bionet.biophysics Subject: CUSTOM WEBSITES FOR BIOLOGY AND ECOLOGY Date: Fri, 11 Jul 1997 18:08:39 -0400 Organization: Silversun Lines: 14 Message-ID: NNTP-Posting-Host: user-37kbn3n.dialup.mindspring.com X-Server-Date: 11 Jul 1997 21:07:57 GMT Does your group need a website? I specialize in developing websites for biologists, ecologists and small businesses (with an emphasis in selling biological products or ecological services )! For more information e-mail me at silversun@mindspring.com Thanks Scott Brown -- Silversun@mindspring.com From owner-biophysics@net.bio.net Fri Jul 11 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!202.243.48.20!news.gol.com!not-for-mail From: "Paul Sully" Newsgroups: bionet.biophysics Subject: Japanese professor Date: 11 Jul 1997 23:45:55 GMT Organization: Paul Sully International Academy Lines: 11 Message-ID: <01bc8e0a$7a483160$8371d8cb@thinkpad> NNTP-Posting-Host: tc-1-123.osaka.gol.com X-Newsreader: Microsoft Internet News 4.70.1157 I'm posting this message for a friend of mine. He is a Japanese Professor at Osaka University of Health and sports Sciences. He wishes to do a sabbatical year, starting April 1st 1998, working on the effects of walking on the lipoprotein metabolism of vascular endothelium in dietary rats. He would like to study molecular biology and wishes to obtain a place in a laboratory, in Australia, at Japan's expense. If anybody could supply any information about Universities in Australia dealing in these areas or is able to make any suggestions, then I would be most grateful. Please reply directly to sully@gol.com. Thank you. From owner-biophysics@net.bio.net Sat Jul 12 23:00:00 1997 Path: biosci!rutgers!gatech!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!dispatch.news.demon.net!demon!bullseye.news.demon.net!demon!newsgate.unisource.nl!halley.pi.net!news From: jacob Newsgroups: bionet.biophysics Subject: Asian Ladies Date: 13 Jul 1997 18:52:57 GMT Organization: World Access/Planet Internet Message-ID: <5qb869$rtk@halley.pi.net> NNTP-Posting-Host: 145.220.210.27 Lines: 10 I've found the pefect site with nude Asian ladies. Much more than you can find in any newsgroup. http://home.pi.net/~sappie/playboy.htm From owner-biophysics@net.bio.net Sun Jul 13 23:00:00 1997 Path: biosci!rutgers!gatech!nntprelay.mathworks.com!news.mathworks.com!fu-berlin.de!news.th-darmstadt.de!c4.hrz.uni-giessen.de!usenet From: Andreas Blees Newsgroups: bionet.biophysics,de.sci.chemie,de.sci.medizin.misc,sci.bio.technology,sci.electronics.repair Subject: MRI-Question for experts Date: Fri, 11 Jul 1997 14:10:30 +0200 Organization: University of Giessen, Germany Lines: 14 Distribution: inet Message-ID: <33C622B6.66FD@tg.fh-giessen.de> Reply-To: andreas.blees@tg.fh-giessen.de NNTP-Posting-Host: pm1-16.hrz.uni-giessen.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold [de] (Win95; I) Hallo , I'am a student of biomedicine from germany and I've an idea and question about it. I want to display a line in the MRI with putting some current through it. And now my question: is it possible and what kind of current it has to be: AC or DC ? Sorry, but I'am a layman on this domain. In front of I want to thank you. Andreas Blees ! From owner-biophysics@net.bio.net Sun Jul 13 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-xfer.netaxs.com!netnews.upenn.edu!NewsWatcher!user From: rappaport@email.chop.edu (Eric Rappaport) Newsgroups: bionet.biophysics Subject: DNA SEQUENCERS FOR SALE Date: Mon, 14 Jul 1997 15:09:40 -0400 Organization: Children's Hospital of Philadelphia Lines: 64 Message-ID: NNTP-Posting-Host: 159.14.43.32 AUTOMATED DNA SEQUENCERS FOR SALE Three ABI 373 DNA sequencers, all currently in use and under service contract are available for sale. Please contact Dr. Eric Rappaport (rappaport@email.chop.edu) with offers or questions. Details of the equipment configuration follow: Two 373 units with Stretch upgrades: Filters - 5-filter wheel (can choose between 2 different sets of 4 different dyes). Chemistries - Standard Taq (FS) terminator, dye primer or ABI T7 polymerase sequencing chemistry. All current Genescan chemistries, including microsatellite panels, primers labeled during synthesis with standard ABI dyes (6-Fam, Hex, Tet, Tamra) or (6-Fam, Hex, Tamra, and Rox). Gel lengths - Multiple gel (well-to-read) lengths including 48 cm (standard long-read [>650 nt] sequencing length), 34 (shorter sequence reads [550-600 nt] or high-resolution Genescan applications), 24 (microsatellite applications) 12 (lower-resolution Genescan applications) or 6 (lower-resolution Genescan applications). Scan Speed - 1X, BaseSprinter (2X, but limitedto middle half of gel; can be used for faster analysis of shorter sequences). One 373 with multiple gel length (Leon) configuration: Filters - 5-filter wheel (can choose between 2 different sets of 4 different dyes). Chemistries - Standard Taq (FS) terminator, dye primer or ABI T7 polymerase sequencing chemistry. All current Genescan chemistries, including microsatellite panels, primers labeled during synthesis with standard ABI dyes (6-Fam, Hex, Tet, Tamra) or (6-Fam, Hex, Tamra, and Rox). Gel lengths - Multiple gel (well-to-read) lengths including 24 cm (shorter sequence reads [400-500 nt] or microsatellite applications) 12 (lower-resolution Genescan applications) or 6 (lower-resolution Genescan applications). Scan Speed - 1X, BaseSprinter (2X, but limitedto middle half of gel; can be used for faster analysis of shorter sequences). Computers and Software Unit 1 (Stretch) - Mac IIcx with 8 mB RAM/230 mB hard drive Unit 2 (Stretch) - Mac IIci with 8 mB RAM/100 mB hard drive Unit 3 (Leon) - Mac IIci with 8 mB RAM/120 mB hard drive All units are equipped with latest versions of analysis and collection sofware for running sequencing and Genescan applications on the above computers. Upgrades for PowerMac are not included. Service Contracts All units have been under service contract since the time of their purchase from ABI and are currently covered under those agreements. Purchaser would need to have an installation service call from ABI before initiation of a new service contract could occur. From owner-biophysics@net.bio.net Sun Jul 13 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!newsfeed.gte.net!news.maxwell.syr.edu!news.emi.com!euclid.wadsworth.org!tivol From: tivol@news.wadsworth.org (William Tivol) Newsgroups: bionet.biophysics Subject: Re: Negative ion penetration Date: 14 Jul 1997 22:46:18 GMT Organization: Wadsworth Center, NY Health Dept. Lines: 19 Message-ID: <5qea7q$sfu@euclid.wadsworth.org> References: <5q4l3h$36n@news.aus.world.net> NNTP-Posting-Host: alcor.wadsworth.org X-Newsreader: TIN [version 1.2 PL2] tael (tael@world.net) wrote: : I was wondering does anyone here know about the penetration of : negative ions into different materials? Dear Jon, When using a tandem VanDeGraf accelerator, a specimen of Be was initially given an extra electron and accelerated. A very thin foil was then used to strip all the electrons off the Be, which was further accelerated. I can say from this that after a *very* short distance of penetration, the ion is no longer negative. However, the nucleus can penetrate (to the distance of its range), so if that is what you're after--such as an experiment where F- is accelerated toward some target-- you can get the F implanted. After implantation, the F will likely pickup enough electrons to exist in the material as F-, if it does not bond covalently. Yours, Bill Tivol From owner-biophysics@net.bio.net Mon Jul 14 23:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!howland.erols.net!news.maxwell.syr.edu!news-xfer.netaxs.com!netnews.upenn.edu!axe1.med.upenn.edu!axelsen From: axelsen@axe1.med.upenn.edu (Paul H Axelsen) Newsgroups: bionet.biophysics Subject: POSTDOCTORAL POSITIONS: Molecular Recognition and Membrane Biophysics Date: 15 Jul 1997 13:03:34 GMT Organization: University of Pennsylvania Lines: 31 Message-ID: <5qfsf6$b26@netnews.upenn.edu> NNTP-Posting-Host: axe1.med.upenn.edu X-Newsreader: TIN [version 1.2 PL2-upenn1.1] POSTDOCTORAL POSITIONS AVAILABLE: Molecular Recognition and Membrane Biophysics Projects involve the use of novel spectroscopic techniques (infrared and UV) and mass spectrometry to study the behavior of antibiotics, fusogenic peptides, and blood coagulation proteins on lipid membranes with a view towards rational drug design. The laboratory is stably funded and the positions are available immediately. Applicants MUST be available for interview prior to appointment. Persons with a talent for mastering sophisticated new technology, and seeking to work on important biomedical problems, should inquire by email to axe@pharm.med.upenn.edu or Prof. Paul H. Axelsen Departments of Pharmacology and Medicine, Infectious Diseases Section University of Pennsylvania Rooms 130/131 John Morgan Bldg 3620 Hamilton Walk Philadelphia, PA 19104-6084 215-898-9238 / 9766 (tel) 215-573-2236 (fax) http://axe2.med.upenn.edu (www) -- ------------------------------------------------------------------------------ Axe@pharm From owner-biophysics@net.bio.net Mon Jul 14 23:00:00 1997 Path: biosci!agate!usenet.INS.CWRU.Edu!HSNX.wco.com!hub.org!news-feed.inet.tele.dk!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.direct.ca!torn!kone!hone!informer1.cis.McMaster.CA!wolf.interlynx.net!not-for-mail From: "Lars Thomsen" Newsgroups: bionet.biophysics,bionet.software Subject: Preader & curvefitting, Pbase a new database tool and Preaders Interactive Help (Freeware) Date: Sun, 13 Jul 1997 21:06:46 -0400 Organization: Interlynx Lines: 49 Message-ID: <5qbu1v$foe$1@wolf.interlynx.net> NNTP-Posting-Host: port132.hm.interlynx.net X-Newsreader: Microsoft Outlook Express 4.71.0544.0 X-MimeOLE: Produced By Microsoft MimeOLE Engine V4.71.0544.0 Xref: biosci bionet.biophysics:3362 bionet.software:19109 Preader is freeware and if you are doing combined physiological and molecular biological experiments then you should be interested. Please mail me so I can notify you of any future developments and download information (freeware). New features in Preader 1.9 : The Interactive Explorer is a high tech help file that gives you the settings of your program and explains them. It also includes various other help features which includes theory for common physiological terms, molecular biology, constants, equations, cells + much more Preader have been broken up and the newest branch is called Pbase and it covers the database part and it includes following tables : Chemicals : Name,Formula,MW,Solvent,Solubility,PKa(if acid or base), dPK/C + more Solutions : Recipe database that creates excellent recipies and printouts. Automatic lookup in chemical database Agonist/Antagonist : Name, effect, chemicalstructure (path to picture), interactionchart (path to picture), ChemIndex (lookup ID to chemical database), References (list of references), EC50, IC50, Ka, Occupancy, pD2, pA2, Kb, pKb, shieldSlope Other tables included : Phys data Primers PCR setup RT setup Taq setup PCR data References Reference Groups Products Suppliers Accounts email : lthomsen@interlynx.net or thomsenl@fhs.mcmaster.ca http://home.interlynx.net/~lthomsen/preader (a bit outdated web page.....) Best Regards Lars Thomsen From owner-biophysics@net.bio.net Mon Jul 14 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!news-peer.gsl.net!news.gsl.net!newsfeed.direct.ca!torn!kone!hone!informer1.cis.McMaster.CA!wolf.interlynx.net!not-for-mail From: "Lars Thomsen" Newsgroups: bionet.biophysics Subject: Preader & curvefitting, Interactive Explorer for Preader, and Pbase a standalone application Date: Sun, 13 Jul 1997 13:45:00 -0400 Organization: Interlynx Lines: 64 Message-ID: <5qb8fa$qd5$1@wolf.interlynx.net> NNTP-Posting-Host: port73.hm.interlynx.net X-Newsreader: Microsoft Outlook Express 4.71.0544.0 X-MimeOLE: Produced By Microsoft MimeOLE Engine V4.71.0544.0 Preader is freeware and used to measure, analyze and store and cross analyze data from physiological experiments - mainly wholecell experiments, but the database part is independent and includes a wealth of utilities which is extremely useful for any phys or molbiol lab. We are working on an advanced non-linear curvefitting model that will improve the kinetic information that can be obtained from a whole cell current. The algorithm will search through the whole cell current and break it into pieces and then extract the rate constants describing following kinetic scheme : Closed <---> Open <---> Desensitized The Interactive Explorer is a high tech help file that gives you the settings of your program and explains them. It also includes various other help features which includes theory for common physiological terms, molecular biology, constants, equations, cells + much more Preader have been broken up and the newest branch is called Pbase and it covers the database part and it includes following tables : Chemicals : Name,Formula,MW,Solvent,Solubility,PKa(if acid or base), dPK/C + more Solutions : Recipe database that creates excellent recipies and printouts. Automatic lookup in chemical database Agonist/Antagonist : Name, effect, chemicalstructure (path to picture), interactionchart (path to picture), ChemIndex (lookup ID to chemical database), References (list of references), EC50, IC50, Ka, Occupancy, pD2,pA2, Kb, pKb, shieldSlope Other tables included : Phys data Primers PCR setup RT setup Taq setup PCR data References Reference Groups Products Suppliers Accounts Preader homepage : http://home.interlynx.net/~lthomsen/preader (this web page is outdated but send me a mail and Ill keep you updated about the newest developments and download information) Best Regards Lars Thomsen MSc. PhD. McMaster University thomsenl@fhs.mcmaster.ca or direct to the cottage lthomsen@interlynx.net From owner-biophysics@net.bio.net Mon Jul 14 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!infeed2.internetmci.com!newsfeed.internetmci.com!malgudi.oar.net!whqvax.picker.com!whqvax!sam From: sam@stdavids.picker.com (Sam Goldwasser) Newsgroups: bionet.biophysics,de.sci.chemie,de.sci.medizin.misc,sci.bio.technology,sci.electronics.repair Subject: Re: MRI-Question for experts Date: 15 Jul 1997 22:22:13 GMT Organization: OARnet Lines: 25 Distribution: inet Message-ID: References: <33C622B6.66FD@tg.fh-giessen.de> NNTP-Posting-Host: whqvax.picker.com In-reply-to: Andreas Blees's message of Fri, 11 Jul 1997 14:10:30 +0200 Please describe what you have in mind in more detail. As written, it doesn't make any sense to me. Sorry. --- sam : Sci.Electronics.Repair FAQ: http://www.paranoia.com/~filipg/REPAIR/ Coming soon to a computer screen near you: http://www.repairfaq.org/ Preview of V3.00 (ASCII): http://www.pacwest.net/byron13/sammenu.htm In article <33C622B6.66FD@tg.fh-giessen.de> Andreas Blees writes: Hallo , I'am a student of biomedicine from germany and I've an idea and question about it. I want to display a line in the MRI with putting some current through it. And now my question: is it possible and what kind of current it has to be: AC or DC ? Sorry, but I'am a layman on this domain. In front of I want to thank you. Andreas Blees ! From owner-biophysics@net.bio.net Tue Jul 15 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server6.netnews.ja.net!server1.netnews.ja.net!server5.netnews.ja.net!daresbury!not-for-mail From: Newsgroups: bionet.biophysics Subject: semipermeable membrane < > PENTCHO VALEV Date: 16 Jul 1997 13:16:11 +0100 Lines: 37 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5qie2b$otc@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk David Rhodes wrote me: Please post a clarification... I assume that you are not talking about < a simple "sieve-like" membrane. Clearly, with big enough pores and really< big solute, one could simply have a "filter" apparatus. Maybe you could < spell out the details a bit... < A scientist named Bjorn Hope posted in the bio-info group a model which may prove to be perpetuum mobile of the second kind. I will try to present it, with some later improvements, but by using quite an imperfect drawing, due to e-mail restrictions. ---------------semipermeable membrane I impermeable I membrane I SOLUTION semipermeable I membrane SOLVENT The lower part is a standard osmotic system: as the solvent enters into the solution through the lower semipermeable membrane, the level of the solution rises. It passes a region where the membrane is impermeable, and then is spread onto a platform representing again a semipermeable membrane. This upper semipermeable membrane is placed just over the solvent reservoir, and as the solvent passes through the membrane and falls into the reservoir, it forms a "waterfall" which can be expected to do work - e.g. to rotate a water wheel. So far the main argument against the model is that the saturated vapour in the solvent (right-hand) reservoir counteracts the process - e.g. pushes up against the falling solvent. But it seems to me that this "pushing" not only does not counteract, but, rather, favours the process by adding additional weight to the falling solvent. I think that, right or wrong, the model is extremely interesting. Pentcho From owner-biophysics@net.bio.net Tue Jul 15 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.biophysics Subject: semipermeable membrane < > PENTCHO VALEV Date: 16 Jul 1997 08:51:22 +0100 Lines: 9 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5qhuhq$5eq@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk I would be very grateful if someone can give an example of a semipermeable membrane so much permeable to the solvent that, when a bag containing the solution is hanged, the solvent will flow downwards. If this is impossible, please give the reason. This is an essential point in a debate on a possible violation of the second law, going on in the bio-info and btk-mca groups. Thank you. Pentcho From owner-biophysics@net.bio.net Tue Jul 15 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.nacamar.de!news.maz.net!news.is-europe.net!news.gni.net!news.omnilink.net!news1.citylink.de!news From: mhuebner@stopspam.com (Michael Huebner) Newsgroups: bionet.biophysics,de.sci.chemie,de.sci.medizin.misc,sci.bio.technology,sci.electronics.repair Subject: Re: MRI-Question for experts Date: Mon, 14 Jul 1997 07:34:48 GMT Organization: Citylink Internet Service Center Lines: 30 Distribution: inet Message-ID: <33c9d46f.24307930@news.citylink.de> References: <33C622B6.66FD@tg.fh-giessen.de> NNTP-Posting-Host: nsi2.wuerzburg.netsurf.de X-Newsreader: Forte Free Agent 1.1/32.230 On Fri, 11 Jul 1997 14:10:30 +0200, Andreas Blees wrote: >Hallo , > >I'am a student of biomedicine from germany and I've an idea and >question about it. > >I want to display a line in the MRI with putting some current through >it. And now my question: is it possible and what kind of current it has >to be: AC or DC ? Sorry, but I'am a layman on this domain. Hallo Andreas, was für eine Linie willst Du denn darstellen und wozu? Muß sie denn durch elektrischen Strom verursacht werden? Eine klar abgegrenzte Linie halte ich so für nicht erreichbar. Eine Störung in Form einer Linie mit Schatten ist dagegen recht einfach realisierbar. Stell einfach ein netzbetriebenes Gerät in den Magnetraum (die Entfernung richtet sich nach der Magnetfeldstärke, aber der Raum wird selten größer bemessen sein). Die Brummeinstreuungen reichen aus, um diesen Artefakt zu erzeugen. Michael PGP fingerprint 66 14 D1 DD 69 B7 0A 79 B8 95 08 4D 05 B2 E9 27 Internet http://www.isbmh.com/MHuebner/ aktuell http://infowelt.net/ --> Reisewelt --> Reiseberichte (replace stopspam by isbmh for e-mail) From owner-biophysics@net.bio.net Wed Jul 16 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.biophysics Subject: semipermeable membrane < > PENTCHO VALEV Date: 17 Jul 1997 10:29:28 +0100 Lines: 29 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5qkolo$ib3@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk In reply to David Rhodes. David, you wrote: The solution to this old problem is the mixing of the 2 systems that< will occur, thus rendering the membrane meaningless. i.e. it is < solution that turns the wheel, and in so doing makes the solvent < into a dilute solution - etc.... < No, David, this is not a problem - the solution on the left do not mix with the pure solvent on the right - the solution is filtered through the upper semipermeable membrane, and only pure solvent flows down in the right-hand compartment. The problem is quite different and I would be very grateful if you could help me. I tried to model this filtering through the upper semipermeable membrane - I placed a water - protein solution in a dialysis bag and hanged it - no flowing down. Then I placed pure water in the bag - the same result. That was the reason for my first posting - I want to know whether there is a membrane much more permeable to the solvent so that, when hanged, a substantial flow (e.g. regular frequent drops) occurs. I am also considering improvements - e.g., when I wrap the standard dialysis bag with wet cotton and put this in an atmosphere of saturated vapour, the downward flow of water increases a little bit. This obstacle may prove fatal for the model, but it is the only one - all other steps seem obvious. So please let us first solve the problem with the bag - the moment we have a substantial flow of solvent and the solute stays inside, the model will be 99% correct. Best regards, Pentcho From owner-biophysics@net.bio.net Wed Jul 16 23:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.biophysics Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 17 Jul 1997 02:00:06 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199707170900.CAA15340@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. 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Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the messag