From BIOSCI-REQUEST Thu Nov 9 02:00:55 1995 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.12/8.6.6) id CAA16532 for rna-list; Thu, 9 Nov 1995 02:00:55 -0800 Received: (from biohelp@localhost) by net.bio.net (8.6.12/8.6.6) id CAA16501 for rna@net.bio.net; Thu, 9 Nov 1995 02:00:25 -0800 Date: Thu, 9 Nov 1995 02:00:25 -0800 From: BIOSCI Administrator Message-Id: <199511091000.CAA16501@net.bio.net> To: rna@net.bio.net Subject: IMPORTANT: BIOSCI miniFAQ This is a new "miniFAQ" 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/. Contents: -------- 1) What to do about "spams," i.e., junk mail, ads, etc. 2) Examples of subscribing and unsubscribing to the mailing lists. 3) How to access BIOSCI/bionet newsgroup archives. 4) The BIOSCI user address and research interest directory. 1) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups) and mailing lists. The same postings are distributed on both 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 newsgroups from about 95% of the spams that are being sent to date. This means 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. Unfortunately there are easy ways for determined spammers to override the moderation mechanism. We are working on new systems to provide access to our newsgroups over the WWW. These should be available soon, probably November 1995, and will allow you to use your Web browser to look at the news postings. While this 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. 2) 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. 3) How to access BIOSCI/bionet newsgroup archives. -------------------------------------------------- Back postings of all BIOSCI/bionet newsgroups can be found on the World Wide Web at URL http://www.bio.net/. There are several searchable newsgroup indices at this site. E-mail users can search the BIOSCI archives by using our waismail e-mail server. For instructions send the message help to waismail@net.bio.net. Leave the Subject: line blank (anything entered on the Subject: line is ignored). 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. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From BIOSCI-REQUEST Mon Nov 13 09:45:00 1995 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.12/8.6.6) id JAA17688; Mon, 13 Nov 1995 09:45:00 -0800 Received: from electra.cc.umanitoba.ca (root@electra.cc.umanitoba.ca [130.179.16.23]) by net.bio.net (8.6.12/8.6.6) with ESMTP id JAA17685 for ; Mon, 13 Nov 1995 09:44:58 -0800 Received: from adminbldg.lan1.umanitoba.ca (smtp.lan1.umanitoba.ca [130.179.16.43]) by electra.cc.umanitoba.ca (8.7.1/8.7.1) with SMTP id LAA02792 for ; Mon, 13 Nov 1995 11:43:39 -0600 (CST) Received: by adminbldg.lan1.umanitoba.ca with Microsoft Mail id <30A783A7@adminbldg.lan1.umanitoba.ca>; Mon, 13 Nov 95 11:43:03 CST From: "Huebnerlab, Erwin" To: rna@net.bio.net Subject: interested in membership... Date: Mon, 13 Nov 95 11:42:00 CST Message-ID: <30A783A7@adminbldg.lan1.umanitoba.ca> Encoding: 6 TEXT X-Mailer: Microsoft Mail V3.0 Hello, I'm interested in becoming a member, and so am wondering if you could provide me with all the preliminary info on how to join, cost, etc. Thank you! From BIOSCI-REQUEST Tue Nov 14 00:54:46 1995 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.12/8.6.6) id AAA05834; Tue, 14 Nov 1995 00:54:46 -0800 Received: from lyngby.bio.atv.dk (lyngby.bio.atv.dk [130.225.235.80]) by net.bio.net (8.6.12/8.6.6) with SMTP id AAA05831 for ; Tue, 14 Nov 1995 00:54:43 -0800 Received: by lyngby.bio.atv.dk (5.61/9.3) id AA22564; Tue, 14 Nov 95 09:07:41 +0100 Received: from lm79.bio.atv.dk by lyngby.bio.atv.dk (5.61/9.3) with SMTP id AA18466; Tue, 14 Nov 95 09:07:40 +0100 Date: Tue, 14 Nov 95 09:07:40 +0100 Message-Id: <9511140807.AA18466@lyngby.bio.atv.dk> X-Sender: kho@130.225.235.2 X-Mailer: Windows Eudora Version 2.1.1 Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit To: rna@net.bio.net From: Kim Holmstrøm Subject: RT and Taq-DNA-polymerase Does anyone have some references on the use of Taq-DNA-polymerase and its ability to perform reverse transcription. I am very interested in this as I have indications that Taq-DNA-polymerase indeed can perform RT. Thanks in advance. Kim Holmstrøm Biotechnological Institute Research & Development Anker Engelundsvej 1 Building 227 2800 Lyngby Denmark From BIOSCI-REQUEST Tue Nov 14 01:21:35 1995 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.12/8.6.6) id BAA07086; Tue, 14 Nov 1995 01:21:35 -0800 Received: from pluto.lmb.uni-muenchen.de (pluto.lmb.uni-muenchen.de [141.84.48.214]) by net.bio.net (8.6.12/8.6.6) with SMTP id BAA07073 for ; Tue, 14 Nov 1995 01:21:09 -0800 Received: from [141.84.48.167] (fam_famoluk.lmb.uni-muenchen.de) by pluto.lmb.uni-muenchen.de (4.1/SMI-4.1) id AA09473; Tue, 14 Nov 95 09:18:21 +0100 Date: Tue, 14 Nov 95 09:18:21 +0100 Message-Id: <9511140818.AA09473@pluto.lmb.uni-muenchen.de> X-Sender: famulok@pluto.lmb.uni-muenchen.de Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: rna@net.bio.net From: famulok@lmb.uni-muenchen.de (famulok) Subject: Precipitation of RNA Does anybody know of a good method to reduce precipitation of RNA (e.g. buffer conditions, denaturation/renaturation, addition of goodies etc...)? We have observed a dramatic increase of precipitation of an RNA upon addition of spermidine and other polyamines which we need to get rid of. Michael Famulok Laboratorium fuer Molekulare Biologie - Genzentrum Wuermtalstrasse 221 81375 Muenchen, Germany Voice: +49-89-74017 410 (office) Voice: +49-89-74017 412 (lab) Fax: +49-89-74017 448 From BIOSCI-REQUEST Sun Nov 26 21:02:24 1995 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.12/8.6.6) id VAA29723; Sun, 26 Nov 1995 21:02:24 -0800 Received: from ncbi.nlm.nih.gov (ncbi.nlm.nih.gov [130.14.25.1]) by net.bio.net (8.6.12/8.6.6) with SMTP id VAA29648 for ; Sun, 26 Nov 1995 21:02:16 -0800 Received: from borduas.nlm.nih.gov by ncbi.nlm.nih.gov id AA27217; Mon, 27 Nov 1995 00:00:36 -0500 Received: by borduas.nlm.nih.gov id AA04383; Mon, 27 Nov 1995 00:00:33 -0500 Date: Mon, 27 Nov 1995 00:00:33 -0500 Message-Id: <9511270500.AA04383@borduas.nlm.nih.gov> To: rna@net.bio.net, kalim@arl.rdc.toshiba.co.jp Subject: Re: crystal structures From: francis@ncbi.nlm.nih.gov X-Sun-Charset: US-ASCII > From: kalim@arl.rdc.toshiba.co.jp > To: rna@net.bio.net > Subject: crystal structures > Can anyone tell me, for which tRNA species > the crystal structures been elucidated for (apart from > tRNAphe from yeast). Dear Kalim, If you look in Entrez (on the network client or the WWW page) and look for 'trna (NOT synthetase)' you find 9 structures: (Yes, Entrez has nucleotide and protein sequences, bibliographic references and 3D structures) COMPND Pb(II)-Transfer Ribo-Nucleic Acid (Yeast,Phe) tRNA (pH 7.4) 1TN1 COMPND Pb(II)-Transfer Ribo-Nucleic Acid (Yeast,Phe) tRNA (pH 5.0) 1TN2 COMPND Transfer Ribo-Nucleic Acid (Yeast, Phe), Trna 1TRA COMPND Transfer Ribo-Nucleic Acid (Yeast,Asp) tRNA (A FORM) 2TRA COMPND Transfer Ribo-Nucleic Acid (Yeast,Asp) tRNA (B FORM) 3TRA COMPND Transfer Ribo-Nucleic Acid (Yeast,Phe) tRNA 4TNA COMPND Transfer Ribo-Nucleic Acid (Yeast,Phe),tRNA 4TRA COMPND Transfer Ribonucleic Acid (Yeast,Ser) (Trna) (Theoretical 5TRA COMPND Transfer Ribo-Nucleic Acid (Yeast,Phe),tRNA 6TNA Six of which are yeast Phe tRNA. The number on the right is the PDB id for these structures (as close as PDB gets to an accession number/LOCUS name). If you want to look at these structures you will need to get 'rasmol' or 'kinemage' (I'll send you our FAQ on this if you need it, or you can pick it up from our WWW page). the address for our WWW page is: http://www.ncbi.nlm.nih.gov/ and from there click on Entrez, and you will see the link to the 3D structure page ... > Do you have any refs? >From Entrez (where you can jump over to the bibliographic references, with just a few clicks ...) I see 12 refs for the three non-phe structures, here are the titles (but in Entrez the abtracts are there as well): Biochimie 70: 145-65 (1988) [88281522] Hydration of transfer RNA molecules: a crystallographic study. E. Westhof, P. Dumas & D. Moras J Biomol Struct Dyn 1: 337-55 (1983) [90148230] Loop stereochemistry and dynamics in transfer RNA. E. Westhof, P. Dumas & D. Moras Biochimie 67: 597-606 (1985) [86026491] Crystal structure of yeast tRNAAsp: atomic coordinates. P. Dumas, J. P. Ebel, R. Giege, D. Moras, J. C. Thierry & E. Westhof J Mol Biol 184: 119-45 (1985) [85293077] Crystallographic refinement of yeast aspartic acid transfer RNA. E. Westhof, P. Dumas & D. Moras Nature 288: 669-74 (1980) [81098950] Crystal structure of yeast tRNAAsp. D. Moras, M. B. Comarmond, J. Fischer, R. Weiss, J. C. Thierry, J. P. Ebel & R. Giege J Mol Biol 115: 91-6 (1977) [78048353] Yeast transfer RNAasp: a new high-resolution x-ray diffracting crystal form of a transfer RNA. R. Giege, D. Moras & J. C. Thierry J Mol Biol 123: 631-60 (1978) [79007486] Crystal structure of yeast phenylalanine transfer RNA. II. Structural features and functional implications. S. R. Holbrook, J. L. Sussman, R. W. Warrant & S. H. Kim J Mol Biol 123: 607-30 (1978) [79007485] Crystal structure of yeast phenylalanine transfer RNA. I. Crystallographic refinement. J. L. Sussman, S. R. Holbrook, R. W. Warrant, G. M. Church & S. H. Kim Adv Enzymol Relat Areas Mol Biol 46: 279-315 (1978) [78141790] Three-dimensional structure of transfer RNA and its functional implications. S. H. Kim Nucleic Acids Res 4: 2811-20 (1977) [78011712] RNA-ligant interactions. (I) Magnesium binding sites in yeast tRNAPhe. S. R. Holbrook, J. L. Sussman, R. W. Warrant, G. M. Church & S. H. Kim Science 192: 853-8 (1976) [76199324] Three-dimensional structure of a transfer rna in two crystal forms. J. L. Sussman & S. Kim hope this helps, francis -- | B.F. Francis Ouellette | GenBank | | francis@ncbi.nlm.nih.gov From BIOSCI-REQUEST Thu Nov 30 21:12:13 1995 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.12/8.6.6) id VAA09743; Thu, 30 Nov 1995 21:12:13 -0800 Received: from chopin.udel.edu (jhAVZOWWwloDmY67kTsv8ig2C7YQom7p@chopin.udel.edu [128.175.13.17]) by net.bio.net (8.6.12/8.6.6) with ESMTP id VAA09739 for ; Thu, 30 Nov 1995 21:12:09 -0800 Received: (from pmp@localhost) by chopin.udel.edu (8.6.12/8.6.12) id AAA16393; Fri, 1 Dec 1995 00:10:39 -0500 Date: Fri, 1 Dec 1995 00:10:38 -0500 (EST) From: Peter Palenchar To: rna@net.bio.net Subject: t-rna Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Does anybody know a good current source for t-RNA sequence and tertiary structures? Thank-you Peter Palenchar