From owner-population-bio@net.bio.net Tue Jul 01 23:00:00 1997 Path: biosci!vector.nsk.su!eroshkin From: eroshkin@vector.nsk.su ("Alexey M. Eroshkin") Newsgroups: bionet.population-bio Subject: ProAnWin update: protein alignment/plots/structure-activity analysis/de sign Date: 2 Jul 1997 01:40:24 -0700 Organization: State Research Center of Virology and Biotechnology VECTOR Lines: 364 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net 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-population-bio@net.bio.net Wed Jul 02 23:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!server1.netnews.ja.net!server5.netnews.ja.net!server3.netnews.ja.net!baron.netcom.net.uk!netcom.net.uk!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.maxwell.syr.edu!news-feed1.tiac.net!posterchild!news@tiac.net From: "I. Richard Schaffner, Jr." Newsgroups: bionet.population-bio Subject: Bioremediation Resource Date: Thu, 03 Jul 1997 16:54:37 -0400 Organization: GZA GeoEnvironmental, Inc. Lines: 47 Message-ID: <33BC118D.6B1E@gzea.com> NNTP-Posting-Host: bio.gzea.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (WinNT; I) Environmental Scientist/Engineer, GZA GeoEnvironmental, Inc. (GZA, http://www.gza.net) hosts the Bioremediation Discussion Group (BioGroup, http://biogroup.gzea.com) on the Internet, which consists of a moderated mailing list serving over 1,300 members worldwide, including environmental consultants, regulators, researchers, and industry representatives. The BioGroup was developed to be a global forum for discussion of intrinsic bioremediation (natural attenuation) and enhanced bioremediation. It is our hope that this forum provides a medium to transfer technology, standardize biotreatability protocol, and advance the science/engineering of bioremediation technologies. GZA recognizes bioremediation is not a panacea for soil/groundwater contamination; however, we feel it is an under-utilized remedial technology, its limitations notwithstanding. The forum was developed to be a springboard for the pursuit of innovative approaches to bioremediation. Because success of the BioGroup is a function of member participation, GZA invites anyone with experience/interest in bioremediation to join. Due to the complex biogeochemical processes that control contaminant transformation, we welcome input from environmental engineers, hydrogeologists, soil scientists, microbiologists, environmental chemists, and all who wish to contribute to this important topic. Postings are archived as a collaborative effort of the University of Guelph (Environmental Biology Department), the National Water Research Institute (Environment Canada), and GZA. The archive URL is http://gwrp.cciw.ca/internet/bioremediation/biorem-archive.html. To join the BioGroup, please visit http://biogroup.gzea.com, select "Membership Info", and follow the directions therein. Members select whether to participate in a non-digest mode (i.e., receive each message at the time it is accepted) or a digest mode (i.e., receive one message each day summarizing all the postings of that day). ***There is no membership fee.*** Please direct any questions about the BioGroup to my attention. Regards, I. Richard Schaffner, Jr., P.G. Technical Specialist, GZA GeoEnvironmental, Inc. (http://www.gza.net) Moderator, Bioremediation Discussion Group (http://biogroup.gzea.com) E-mail: rschaffner@gzea.com Phone: 603.623.3600 Fax: 603.624.9463 From owner-population-bio@net.bio.net Thu Jul 03 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!205.237.233.10!wesley.videotron.net!walton.videotron.net!not-for-mail From: Pamela Anderson Newsgroups: bionet.population-bio Subject: !!!!!!!Check here for the BEST HARDCORE SITE on the NET!!!!!! Date: 4 Jul 1997 10:03:54 GMT Organization: VTL Lines: 6 Message-ID: <5pihqa$9vh$8353@walton.videotron.net> NNTP-Posting-Host: ppp103.110.mmtl.videotron.net For the BEST HARDCORE site on the WEB, check this MAGNIFICENT SITE!!!!! You won't regret it... 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From owner-population-bio@net.bio.net Sun Jul 06 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!vixen.cso.uiuc.edu!news-peer.sprintlink.net!news-sea-19.sprintlink.net!news-in-west.sprintlink.net!news.sprintlink.net!Sprint!131.103.1.114!chi-news.cic.net!199.242.16.13!news4.ixa.net!ixa.net!uunet!not-for-mail From: XXXHORNYGIRLS@alpin.or.at Newsgroups: bionet.population-bio Subject: <<>> Date: 7 Jul 1997 17:37:37 GMT Organization: XXXFREESLUTS Lines: 12 Message-ID: <5pr9h1$dag@news0-alterdial.uu.net> NNTP-Posting-Host: 1cust56.max14.los-angeles.ca.ms.uu.net I found a secret password that lets you into 1800+ of the Hottest Adult Sites on the Web. You can also get FREE UNLIMITED Live Video Sex and FREE XXX Chat Room Access. I no longer pay to get into Adult Sites... you won't either. This secret password gets you into them for FREE. http://38.216.112.100/password From owner-population-bio@net.bio.net Sun Jul 06 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!europa.clark.net!dispatch.news.demon.net!demon!zetnet.co.uk!btnet-feed1!BTInternet!usenet From: tim Newsgroups: bionet.population-bio Subject: Environment97 Date: Mon, 07 Jul 1997 11:12:59 +0100 Organization: Hamilton Nashe Message-ID: <33C0C12B.4430@hnashe.com> Reply-To: tim@hnashe.com NNTP-Posting-Host: host5-99-62-218.btinternet.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (WinNT; I) Lines: 29 I would like to draw your attention to Environment97, the world's first environmental conference to take place entirely on the Internet, at: www.environment97.org The conference takes a broad look at environmental issues. Papers range from global issues (eg. Climatic change) through environmental philosophy (Can the US be sustained?, Is sustainable development compatible with the free market?) to toolkits and techniques (Life cycle assessment, Environmental impact assessment). All of the information is free of charge, and unlike most international environmental conferences, Environment97 will not add to the problem. A brief overview: ~ 150 technical and general papers ~ Discussion groups for each keynote paper ~ Downloadable images of environmental bad practice ~ Life cycle assessment comparing an internet conference with a real conference ~ Chat bar - talk to your colleagues around the world We look forward to 'meeting' you at environment97 on November 3-14. John Duffy Marketing Manager - Environment97 Email: john@icheme.org.uk Tel: 01788 578214 From owner-population-bio@net.bio.net Sun Jul 06 23:00:00 1997 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!gatech!nntp-xfer.ncsu.edu!news From: jfgzo@unity.ncsu.edu (James F Gilliam) Newsgroups: bionet.biology.tropical,bionet.population-bio,bionet.parasitology Subject: Simla (Research Station, Trinidad, WI) Date: 7 Jul 1997 21:35:34 GMT Organization: North Carolina State University Lines: 45 Message-ID: <5prnf6$m6j@uni00nw.unity.ncsu.edu> NNTP-Posting-Host: cc04du.unity.ncsu.edu X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Xref: biosci bionet.biology.tropical:2622 bionet.population-bio:2613 bionet.parasitology:2583 (Please reply to Mary Alkins-Koo at mak@centre.uwi.tt or fax, voice, or postal address below). SIMLA On behalf of the Board of the Asa Wright Nature Centre who are currently responsible for the Simla Research Station, Arima Valley, Trinidad, I wish to circulate as widely as possible the following request. Please feel free to forward this message to anyone who will have an interest. The Asa Wright Nature Centre Management Committee has recently agreed to produce an historical record of the William Beebee Tropical Research Station at Simla for future publication. The historical background will include an account of the establishment and development of the Research Station and the publication is expected to contain a photorecord of the facilities and a full bibliography of the research done by persons who have lodged at SIMLA. In the process of compiling the bibliography, it is hoped that a full collection of reprints or copies of papers reflecting the research done at SIMLA will be amassed so as to replace that which has dissipated over the years. It is requested that anyone with any connection with SIMLA, having lodged there or even visited briefly, who may have information or materials relevant to this endeavour, please send such materials to: Dr Mary Alkins-Koo Zoology Unit, Department of Life Sciences The University of the West Indies St Augustine, Trinidad, West Indies Tel: (868) 662-2002 Fax: (868) 663-9686 Email: mak@centre.uwi.tt (Please limit messages to 1-2 pages) In addition to any contributions on historical background and research, any anecdotes or photographs on the realities of tropical research or the finer moments at SIMLA would be appreciated and considered for inclusion. All contributors will be appropriately acknowledged. From owner-population-bio@net.bio.net Tue Jul 08 23:00:00 1997 From: Damn Yankee Newsgroups: bionet.population-bio Organization: Yankee Inc. Subject: !!!Hello!!! NNTP-Posting-Host: 205.139.183.49 Message-ID: <33c0b450.0@nntp.kalnet.net> Date: 7 Jul 97 09:18:08 GMT Lines: 9 Path: biosci!agate!usenet.INS.CWRU.Edu!HSNX.wco.com!newsfeed.dacom.co.kr!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-population-bio@net.bio.net Tue Jul 08 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!newsfeed.direct.ca!supernews.com!Supernews69!not-for-mail From: juliewhite@img.net (Julie White) Newsgroups: bionet.population-bio Subject: Bio degradable Products Date: Wed, 09 Jul 1997 05:27:06 GMT Organization: All USENET -- http://www.Supernews.com Lines: 2 Message-ID: <33c320f5.3745555@news.img.net> NNTP-Posting-Host: 207.34.144.126 X-Newsreader: Forte Free Agent 1.11/16.235 Reduce, People. And REUSE! And make sure you reCYCLE! (This is a test.) From owner-population-bio@net.bio.net Tue Jul 08 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!newsserver.jvnc.net!paperboy.uconn.edu!usenet From: kent@darwin.eeb.uconn.edu (Kent E. Holsinger) Newsgroups: bionet.population-bio Subject: Evolution, Science, and Society Date: 09 Jul 1997 08:53:41 -0400 Organization: Dept. of Ecology & Evolutionary Biology, University of Connecticut Lines: 37 Sender: mks@WALLACE Message-ID: NNTP-Posting-Host: wallace.eeb.uconn.edu X-Newsreader: Gnus v5.3/Emacs 19.34 Evolution, Science, and Society A "White Paper" on Behalf of the Field of Evolutionary Biology Despite its centrality in the life sciences, evolutionary biology does not yet command the prominence in educational curricula or in research funding commensurate with its intellectual contributions and its potential for contributing to societal needs. In an effort to address this shortfall, delegates from eight major professional scientific societies in the United States have developed a document intended to - describe our present understanding of evolution and the major intellectual accomplishments of evolutionary biology, - identify major questions and challenges in which progress in evolutionary science can be expected in the near future, - describe past and expected contributions of evolutionary biology both to other sciences and to social needs in areas such as health science, agriculture, and environmental science, and - suggest ways in which progress can be facilitated in basic research, in applications of evolutionary biology to social needs, and in biological science education. Drafts of the full document and an accompanying executive summary are now available on the web at http://www.rci.rutgers.edu/~ecolevol/evolution.html The working group preparing this document seeks comments from everyone with an interest in evolutionary biology. Comments on the documents should be sent to ecolevol@rci.rutgers.edu before 15 September 1997. -- Kent Holsinger Executive Vice President Society for the Study of Evolution From owner-population-bio@net.bio.net Wed Jul 09 23:00:00 1997 From: Damn Yankee Newsgroups: bionet.population-bio Organization: Yankee Inc. Subject: I Am Very Sorry!!! NNTP-Posting-Host: 205.139.183.55 Message-ID: <33c25568.1@nntp.kalnet.net> Date: 8 Jul 97 14:57:44 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-population-bio@net.bio.net Wed Jul 09 23:00:00 1997 From: randy97 Subject: http://www.love.com Newsgroups: bionet.population-bio NNTP-Posting-Host: pgh.nauticom.net Message-ID: <33c528d9.0@pgh.nauticom.net> Date: 10 Jul 97 18:24:25 GMT Lines: 9 Path: biosci!agate!hammer.uoregon.edu!news-xfer.netaxs.com!netnews.com!howland.erols.net!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-population-bio@net.bio.net Wed Jul 09 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!howland.erols.net!newsfeed.internetmci.com!news.tinet.ie!newsmaster@tinet.ie From: "simon prichard" Newsgroups: bionet.population-bio Subject: Please send Date: 10 Jul 1997 22:16:29 GMT Organization: Telecom Eireann Lines: 3 Message-ID: <01bc8d7f$0efa9f00$04eb869f@default> References: <33bf318a.0@hades.ndirect.co.uk> NNTP-Posting-Host: p4.bantry1.tinet.ie X-Newsreader: Microsoft Internet News 4.70.1155 Simon Prichard, e mail type@tinet.ie From owner-population-bio@net.bio.net Thu Jul 10 23:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.population-bio Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 11 Jul 1997 02:00:07 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199707110900.CAA14046@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. From owner-population-bio@net.bio.net Fri Jul 11 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.direct.ca!op.net!not-for-mail From: Dan Harley Newsgroups: bionet.population-bio Subject: Best price on the net CD-R 74 Minute Gold $2.99 Retail package - no rebates no gimmics no surcharges Date: 11 Jul 1997 10:22:57 GMT Organization: NetPro Computer Services, Inc. Lines: 58 Message-ID: <5q51i1$284$4697@picasso.op.net> NNTP-Posting-Host: d7-0f.ppp.op.net NetPro Computer Services, Inc. http://www.netprocs.com The sign of superior service since 1989! Weekly product specials If you don’t see if please email info@netprocs.com for a prompt quotation! 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Much more than you can find in any newsgroup. http://home.pi.net/~sappie/playboy.htm From owner-population-bio@net.bio.net Wed Jul 16 23:00:00 1997 Path: biosci!news.Stanford.EDU!nntp.Stanford.EDU!not-for-mail From:  minch@crick.Stanford.EDU (Eric Minch) Newsgroups: bionet.population-bio Subject: Genography: Call for Volunteers Date: 17 Jul 1997 18:47:51 GMT Organization: Stanford University Lines: 24 Message-ID: <5qlpcn$8t1$5@nntp.Stanford.EDU> NNTP-Posting-Host: crick.stanford.edu X-Newsreader: Alexandra.app (Version 0.82) Dear colleagues-- The U.S. National Science Foundation has granted us some funding for our "Genography" database on the basis of its prototype implementation. The goals of this project are to update and extend the set of data used in _History and Geography of Human Genes_, to implement as production-quality programs many of the methods for statistical data analysis which have been developed in this laboratory, and to make the data and ancillary analytical programs available to researchers on the internet. Development of the prototype was driven more by the engineering possibilities than by the unknown requirements of unknown users. It's clearly important, however, that the database be made as broadly accessible and useful as possible. Ideally, this means that everyone affected by it should be involved in its design from the very outset. In return for your help in defining the requirements and critiquing the evolving design, we can provide to you data and software not easily available elsewhere. If you are interested in participating, please reply to me at minch@lotka.stanford.edu. More details are available at the Genography web page, http://lotka.stanford.edu/genography.html/. Eric Minch From owner-population-bio@net.bio.net Thu Jul 24 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!EU.net!Norway.EU.net!uninett.no!due.unit.no!not-for-mail From: Hans Stenöien Newsgroups: bionet.population-bio Subject: RAPD/infinite allele model Date: Fri, 25 Jul 1997 08:49:50 +0200 Organization: The Norwegian University of Science and Technology Lines: 28 Message-ID: <33D84C8E.DBD@vm.unit.no> NNTP-Posting-Host: v-a-101.vm.ntnu.no Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.0Gold (Win95; I) Hi' I'm doing a population genetic analysis on selected mosses using RAPD and allozyme markers. In an ideal world I would be interested in using Nei's (1978) genetic distance D in order to estimate the mutation rate u given a specific time t since divergence for two populations (D=2ut; that is: u=D/2t, see e.g. Nei 1987 or Weir 1996). One of the assumptions in this model is that all new mutations are different from extant alleles in the populations (the infinite alleles mutation model). This does not look like an appropriate genetic model for interpreting RAPD bands, because each locus per definition contains no more than 2 alleles. However, the infinite alleles model have been assumed in several studies using allozyme markers. Can anybody tell me why it is reasonable to assume that all new mutations in amino-acid coding sequences leads to qualitatively new allozyme alleles? When allozymes can be interpreted as "infinite alleles", are there also ways to fit the infinite alleles model to RAPD data? I would appreciate any help. Thank you. Hans Stenøien Botanical dept. Norwegian University of Science & Technology N-7004 Trondheim Norway hans.stenoien@vm.ntnu.no From owner-population-bio@net.bio.net Mon Jul 28 23:00:00 1997 Path: biosci!news.Stanford.EDU!nntp.Stanford.EDU!not-for-mail From:  minch@crick.Stanford.EDU (Eric Minch) Newsgroups: bionet.population-bio Subject: CALL FOR TESTERS: Genography Project Date: 29 Jul 1997 20:51:05 GMT Organization: Stanford University Lines: 25 Message-ID: <5rll3p$av1$2@nntp.Stanford.EDU> NNTP-Posting-Host: crick.stanford.edu X-Newsreader: Alexandra.app (Version 0.82) Dear colleagues-- The U.S. National Science Foundation has granted us some funding for our "Genography" database on the basis of its prototype implementation. The goals of this project are to update and extend the set of data used in _History and Geography of Human Genes_, to implement as production-quality programs many of the methods for statistical data analysis which have been developed in this laboratory, and to make the data and ancillary analytical programs available to researchers on the internet. Development of the prototype was driven more by the engineering possibilities than by the unknown requirements of unknown users. It's clearly important, however, that the database be made as broadly accessible and useful as possible. Ideally, this means that everyone affected by it should be involved in its design from the very outset. In return for your help in defining the requirements and critiquing the evolving design, we can provide to you data and software not easily available elsewhere. If you are interested in participating, please reply to me at minch@lotka.stanford.edu. More details are available at the Genography web page, http://lotka.stanford.edu/genography.html/. Eric Minch