From BIOSCI-REQUEST@net.bio.net Mon Aug 2 22:44:00 1993 Received: by net.bio.net (5.65/IG-2.0) id AA03850; Mon, 2 Aug 93 22:44:02 -0700 Received: from east.gsfc.nasa.gov by net.bio.net (5.65/IG-2.0) with SMTP id AA03846; Mon, 2 Aug 93 22:44:00 -0700 Received: from BIOVX1.DECnet MAIL11D_V3 by east.gsfc.nasa.gov (5.57/Ultrix3.0-C) id AA00226; Tue, 3 Aug 93 01:37:18 -0400 Date: Tue, 3 Aug 93 01:37:18 -0400 Message-Id: <9308030537.AA00226@east.gsfc.nasa.gov> From: simpson@biovx1.DNET.NASA.GOV To: "rna@net.bio.net"@EAST.DNET.NASA.GOV Subject: Subjects for discussion Dear Netters: SInce this is a new newsgroup, we have to establish the areas of discussion. I originally wanted to have a newgroup just for my own research interest, RNA editing, but soon realized that cross communication with other RNA fields would be extremely valuable. I propose that RNA splicing, editing and ribozyme activities be some of the topics to be discussed. But anything related to RNA research is fair game. What are your ideas for making this a viable newsgroup? Larry Simpson From BIOSCI-REQUEST@net.bio.net Tue Aug 3 01:28:49 1993 Received: by net.bio.net (5.65/IG-2.0) id AA06279; Tue, 3 Aug 93 01:28:52 -0700 Received: from rulway.LeidenUniv.nl by net.bio.net (5.65/IG-2.0) with SMTP id AA06274; Tue, 3 Aug 93 01:28:49 -0700 Received: from rulsur (rulsur.LeidenUniv.nl) by rulway.LeidenUniv.nl with SMTP id AA00423 (5.65c+/IDA-1.4.4 for ); Tue, 3 Aug 1993 10:28:45 +0200 Received: from rulgl.LeidenUniv.nl (RULGL) by rulsur.LeidenUniv.nl (PMDF #12291) id <01H1B0CC5PWG001GNJ@rulsur.LeidenUniv.nl>; Tue, 3 Aug 1993 10:28 MET Received: from rulgl.LeidenUniv.nl by rulgl.LeidenUniv.nl (PMDF V4.2-11 #2497) id <01H1B0C5KORK8WVZHV@rulgl.LeidenUniv.nl>; Tue, 3 Aug 1993 10:28:38 MET Date: Tue, 03 Aug 1993 10:28:37 +0100 (MET) From: EDWIN TEN DAM Subject: SP6 protocol ? To: rna Message-Id: <01H1B0C5MAN68WVZHV@rulgl.LeidenUniv.nl> X-Envelope-To: rna@net.bio.net X-Vms-To: IN%"rna@net.bio.net" X-Vms-Cc: BEMDAM Content-Transfer-Encoding: 7BIT Mime-Version: 1.0 Greetings all! Well, let me say what i would like to see in a (an?) RNA group. I think RNA structure prediction and testing is a very important issue for anyone working with RNA, so things like computer prediction and structure probing will be of interest. And ofcourse this would be the place to ask for RNA specific methods and protocols. Let's kick that one of with a question of my own: I am making some capped SP6 transcripts for in vitro translation studies, but get very inconsistent yields of messenger. Any favorite protocols out there? I'd be happy to summarize, but to get this group going just post to group. (then we can see who are out there) Thanks! Edwin ten Dam -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- bemdam@rulgl.leidenuniv.nl From BIOSCI-REQUEST@net.bio.net Tue Aug 3 08:25:11 1993 Received: by net.bio.net (5.65/IG-2.0) id AA00401; Tue, 3 Aug 93 08:25:14 -0700 Received: from cs.utah.edu by net.bio.net (5.65/IG-2.0) with SMTP id AA00396; Tue, 3 Aug 93 08:25:11 -0700 Received: from adenosine.pharm.utah.edu by cs.utah.edu (5.65/utah-2.21-cs) id AA20807; Tue, 3 Aug 93 09:25:05 -0600 Date: Tue, 3 Aug 93 09:27:33 -0600 From: davis@adenosine.pharm.utah.edu (Darrell R. Davis) Posted-Date: Tue, 3 Aug 93 09:27:33 -0600 Message-Id: <9308031527.AA08749@adenosine.pharm.utah.edu> Received: by adenosine.pharm.utah.edu (911016.SGI/5.51) id AA08749; Tue, 3 Aug 93 09:27:33 -0600 To: rna In-Reply-To: kristoff@net.bio.net's message of 30 Jul 93 05:42:14 GMT Subject: New prototype newsgroup - RNA (rna@net.bio.net) Cc: davis@adenosine.pharm.utah.edu subscribe From BIOSCI-REQUEST@net.bio.net Tue Aug 3 11:19:02 1993 Received: by net.bio.net (5.65/IG-2.0) id AA25441; Tue, 3 Aug 93 11:19:04 -0700 Received: from cal.scripps.edu by net.bio.net (5.65/IG-2.0) with SMTP id AA25432; Tue, 3 Aug 93 11:19:02 -0700 Received: by cal.scripps.edu (5.0/SMI-SVR4) id AA02181; Tue, 3 Aug 93 11:20:46 PDT Date: Tue, 3 Aug 93 11:20:46 PDT From: brianw@cal (Brian Wimberly) Message-Id: <9308031820.AA02181@cal.scripps.edu> To: rna Subject: topics X-Sun-Charset: US-ASCII Content-Length: 725 My research interests are centered on the experimental determination at atomic resolution of unusual RNA structures and protein-RNA interactions; I'm an NMR person out of Tinoco's lab. As one of the very few people determining high-resolution RNA structures, I would like to try to discover interesting new systems for structural study from the more functionally oriented netters, as well as discuss structure prediction and determination with any of the more biophysically-oriented who wander into the discussion. But my main point is to get both structural and biological people talking to each other. I will try to get more structural and theoretical people to subscribe. Brian Wimberly The Scripps Research Institute From BIOSCI-REQUEST@net.bio.net Tue Aug 3 11:46:42 1993 Received: by net.bio.net (5.65/IG-2.0) id AA02142; Tue, 3 Aug 93 11:46:48 -0700 Received: from timbuk.cray.com by net.bio.net (5.65/IG-2.0) with SMTP id AA02113; Tue, 3 Aug 93 11:46:42 -0700 Received: from calamity (calamity.cray.com) by cray.com (4.1/CRI-MX 2.19) id AA07164; Tue, 3 Aug 93 13:46:39 CDT Received: by calamity id AA16366; 4.1/CRI-5.4; Tue, 3 Aug 93 13:46:38 CDT From: mwd@carina.cray.com (Mark Dalton) Message-Id: <9308031846.AA16366@calamity> Subject: Re: topics (Protein-NA interactions) To: rna Date: Tue, 3 Aug 93 13:46:34 CDT X-Mailer: ELM [version 2.3 PL11b-CRI] Hi! This is from another e-mail server I subscribe to: I thought it may be helpful. I will build a list of ftp sites for RNA structure prediction/display software and post it to the group. If you have any sites or software let me know. I will summerize it by the end of the week. Thanks! Mark Here is the message about Protein-NA interactions: Subject: Re: DNA-protein interactions? To: bishop@lisboa.ks.uiuc.edu Date: Mon, 2 Aug 1993 16:48:52 -0500 (CDT) Cc: chemistry@osc.edu Content-Length: 1352 Sender: chemistry-request@osc.edu Errors-To: owner-chemistry@osc.edu Precedence: bulk Tom The following citations might interest you: 1. There was a recent issue of CURRENT OPINION IN STRUCTURAL BIOLOGY dedicated to "Protein-Nucleic Acid Interactions". Vol. 3 (#1) [1993] Particularly the article entitled "Protein-NA interactions by NMR" by Bob Kaptein, which appears on p. 50 is quite interesting. 2. Kothekar, V FEBS Lett. 274, 217 (1990) Computer simuation of the Zinc finger motifs. 3. A paper from Andy McCammons's group on the "Possion-Boltzmann analysis of lambda represson-operator interactions" was published in Biophys. J. 63, 1280. Hope this helps! Cheers -raman -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry craman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] -- Mark Dalton AUG-GCU-AGA-AAG H Cray Research, Inc. M A R K | Eagan, MN 55121 CH3-S-CH2-CH2-C-COOH Internet: mwd@cray.com | (612)683-3035 NH2 From BIOSCI-REQUEST@net.bio.net Tue Aug 3 12:58:36 1993 Received: by net.bio.net (5.65/IG-2.0) id AA19317; Tue, 3 Aug 93 12:58:39 -0700 Received: from lblr0.lbl.gov by net.bio.net (5.65/IG-2.0) with SMTP id AA19305; Tue, 3 Aug 93 12:58:36 -0700 Received: from lcbvax.hepnet by Lbl.Gov with VMSmail ; Tue, 3 Aug 93 12:58:29 PDT Date: Tue, 3 Aug 93 12:58:29 PDT From: tinoco%lcbvax.hepnet@Lbl.Gov Message-Id: <930803125829.2022f99e@Lbl.Gov> Subject: RNA newsgroup To: rna X-St-Vmsmail-To: LBL::"rna@net.bio.net" X-St-Vmsmail-Cc: TINOCO I would like to be put on the distribution list for the RNA newsgroup. My main interest is structure of RNA and its relation to function. Thank you. I. Tinoco From BIOSCI-REQUEST@net.bio.net Tue Aug 3 13:18:00 1993 Received: by net.bio.net (5.65/IG-2.0) id AA23998; Tue, 3 Aug 93 13:18:04 -0700 Received: from usc.edu by net.bio.net (5.65/IG-2.0) with SMTP id AA23979; Tue, 3 Aug 93 13:18:00 -0700 Received: from flash.usc.edu by usc.edu (4.1/SMI-3.0DEV3-USC+3.1) id AA29938; Tue, 3 Aug 93 13:17:56 PDT Received: by flash.usc.edu (4.1/SMI-4.1+ucs-3.6) id AA19828; Tue, 3 Aug 93 13:17:54 PDT Date: Tue, 3 Aug 93 13:17:54 PDT From: ierardi@flash.usc.edu (D Ierardi) Message-Id: <9308032017.AA19828@flash.usc.edu> To: mwd@carina.cray.com, rna Subject: Re: topics (Protein-NA interactions) These are pretty well known. I've pulled them out of my gopherrc. Doug ------------------- Name=IUBio Biology Archive, Indiana University (experimental) Host=ftp.bio.indiana.edu Name=Computational Molecular Biology Host=megasun.BCH.UMontreal.CA Name=EMBnet BioInformation Resource EMBL Host=felix.embl-heidelberg.de -- Databases: rRNA(ssu), tRNA, smallRNA, berlin Name=SDSC's Computational Biology Gopher Host=osprey.sdsc.edu Name=molecular biology Host=life.anu.edu.au Name=Ribosomal Database Project (Argon Natl. Lab) Path=ftp:info.mcs.anl.gov@/pub/RDP/ -- Databases: rRNA(ssu,lsu) From BIOSCI-REQUEST@net.bio.net Fri Aug 6 17:38:29 1993 Received: by net.bio.net (5.65/IG-2.0) id AA10238; Fri, 6 Aug 93 17:38:32 -0700 Received: from timbuk.cray.com by net.bio.net (5.65/IG-2.0) with SMTP id AA10232; Fri, 6 Aug 93 17:38:29 -0700 Received: from calamity (calamity.cray.com) by cray.com (4.1/CRI-MX 2.19) id AA07435; Fri, 6 Aug 93 19:38:24 CDT Received: by calamity id AA00240; 4.1/CRI-5.4; Fri, 6 Aug 93 19:38:22 CDT From: mwd@carina.cray.com (Mark Dalton) Message-Id: <9308070038.AA00240@calamity> Subject: RNA software -ftp sites To: rna Date: Fri, 6 Aug 93 19:38:20 CDT X-Mailer: ELM [version 2.3 PL11b-CRI] Hi! As I mentioned I would compile a list of FTP sites for RNA structure. Well here is what have so far: I also have compiled a list of references for RNA research. If someone has access to an ftp site. Or I can see if I can have them put out on lenti.med.umn.edu. nrcbsa.bio.nrc.ca: -Michael Zukers software for folding with multiple suboptimal scores, viewing of structures and more. Here is his directory, I have not seen this on the other ftp lists and Michael was all supportive in posting it. (^8 -rw-r--r-- 1 912 900 1084947 Feb 19 11:59 3d_align.tar.Z drwxr-xr-x 2 912 900 4096 Jul 12 19:48 ABJ -rw-r--r-- 1 912 900 1385715 Jun 22 12:51 XRNA.tar.Z -rw-r--r-- 1 912 900 2070835 Oct 13 1992 align.tar.Z -rw-r--r-- 1 912 900 29778 Apr 1 17:18 boxplot.tar.Z -rw-r--r-- 1 912 900 264235 Feb 23 16:06 compbc_dir.tar.Z drwxrwxrwx 2 912 900 512 Apr 27 17:02 donor -rw-r--r-- 1 912 900 856965 Mar 26 1992 ecoli16s.hex.Z -rw-r--r-- 1 912 900 9735 Dec 18 1992 ftp.log -rw-r--r-- 1 912 900 2723437 Jan 19 1993 mfold-2.0.tar.Z -rw-r--r-- 1 912 900 1861467 Jul 29 08:11 mfold-2.2-binaries.tar.Z -rw-r--r-- 1 912 900 887847 Jan 28 1993 mfold-2.2.tar.Z -rw-r--r-- 1 912 900 669424 Jan 4 1993 mfold-cstack.tar.Z -rw-r--r-- 1 912 900 2197599 Jun 4 1992 mfold-dec-2.0.tar.Z -rw-r--r-- 1 912 900 638643 Jun 15 11:32 mfold-dec-2.2.tar.Z -rw-r--r-- 1 912 900 56966 May 26 14:20 mfold-phylo.tar.Z -rw-r--r-- 1 912 900 1398191 May 11 1992 mfold-sun-2.0-nodot.tar.z drwxr-xr-x 7 912 900 512 Jul 16 13:57 mfold-sun-2.2 -rw-r--r-- 1 912 900 465183 Jul 16 13:58 mfold-sun-2.2.tar.Z -rw-r--r-- 1 912 900 862691 Dec 20 1992 mfold-vax-2.0.tar.Z -rw-r--r-- 1 912 900 99815 May 17 15:30 naview.tar.Z -rw-r--r-- 1 912 900 292949 Jul 23 1991 newtree.tar.Z -rw-r--r-- 1 912 900 4005656 Nov 15 1991 phylip.tar.Z -rw-r--r-- 1 912 900 2025073 Oct 30 1991 xmfold-2.0.tar.Z ftp.bio.indiana.edu: Mac RNA structure prediction. Mufold Mac RNA structure display. LoopViewer, LoopDLoop megasun.BCH.UMontreal.CA: GDE (Genetic Data Enviroment) - LoopTool felix.embl-heidelberg.de: Databases: rRNA(ssu), tRNA, smallRNA, berlin life.anu.edu.au: info.mcs.anl.gov: Ribosomal Database Project (Argon Natl. Lab) ncifcrf.gov: RNA information: /pub/shapiro (Bruce Shapiro) /pub/shuyun/newfold /pub/shuyun/sigfold lenti.med.umn.edu: golgi.harvard.edu: GDE's primary home (Steven Smith) ftp.psc.edu: ftp.itc.univie.ac.at: ViennaRNA. The Vienna RNA Package, a new package for folding and comparing RNA secondary structure. RNAfold predict secondary structures RNAeval evaluate energy for given sequence and structure RNAheat calculate melting curves RNAdistance compare secondary structures RNApdist compare ensembles of secondary structures RNAinverse find sequences folding into given structures AnalyseSeqs analyse sequence data AnalyseDists analyse distance matrices -- Mark Dalton AUG-GCU-AGA-AAG H Cray Research, Inc. M A R K | Eagan, MN 55121 CH3-S-CH2-CH2-C-COOH Internet: mwd@cray.com | (612)683-3035 NH2 From BIOSCI-REQUEST@net.bio.net Wed Aug 11 12:21:30 1993 Received: by net.bio.net (5.65/IG-2.0) id AA05988; Wed, 11 Aug 93 12:21:34 -0700 Received: from phylo.life.uiuc.edu by net.bio.net (5.65/IG-2.0) with SMTP id AA05974; Wed, 11 Aug 93 12:21:30 -0700 Received: by phylo.life.uiuc.edu id AA10090 (5.67a/IDA-1.4.4 for rna@net.bio.net); Wed, 11 Aug 1993 14:21:26 -0500 Date: Wed, 11 Aug 1993 14:21:26 -0500 From: rdp@phylo.life.uiuc.edu (Ribosomal Database Project) Message-Id: <199308111921.AA10090@phylo.life.uiuc.edu> To: rna Subject: RDP Release 3.0 Cc: rdp@phylo.life.uiuc.edu The Ribosomal Database Project (RPD) Release 3.0 is now available. A brief list of the changes and new items are: 1. The E-mail and FTP servers have now moved to the University of Illinois. The addresses to be used are: E-mail: server@rdp.life.uiuc.edu FTP: rdp.life.uiuc.edu Gopher: rdpgopher.life.uiuc.edu 2. File names have been changed to more accurately describe their contents: Old name New name ------------------- ------------------- SSU_list.alpha SSU_Prok.alpha SSU_list.phylo SSU_Prok.phylo SSU_list_rep.phylo SSU_rep_Prok.phylo SSU.aln SSU_Prok.aln SSU.gb SSU_Prok.gb SSU_Euks.aln SSU_Euk.aln SSU_Euks.gb SSU_Euk.gb SSU_rRNA_rep.gb SSU_rep_Prok.gb SSU_rRNA.newick SSU_Prok.newick SSU_rRNA.printable SSU_Prok.printable SSU_rRNA.ps SSU_Prok.ps Other file name changes are listed in the 00RELEASE_NOTES.3.0 file. 3. The number of sequences included in the SSU_Prok.gb (small ribosomal subunit, prokaryotic organisms - GenBank format) file increases from 651 to 1379. 4. A file listing the organisms contained in the SSU_Euk alignment has been created: SSU_rRNA/SSU_Euk.alpha. A file listing the organisms contained in both the SSU_Prok and SSU_Euk alignments has been created: SSU.alpha. 5. The SSU_Euk.gb LOCUS names have been changed to official RDP short-ID's (the SSU_Euk.aln file was similarly modified). No new sequences have been added to the SSU_Euk alignment. 6. Changes in RDP short-ID's or organism names are also listed in the 00RELEASE_NOTES.3.0 file. 7. The phylogenetic tree for small subunit prokaryotic organisms has been updated to contain 648 sequences. This tree represents the SSU_Prok data included in RDP Release 2.0 (excluding 3 sequences removed from the 3.0 Release). A tree corresponding to Release 3.0 data will be posted as soon as possible. 8. Files listing the available LSU secondary structure files and references have been added by Dr. Robin Gutell; they are in the LSU_rRNA/sec_struct directory. 9. Two new commands are available from the email server: CHECK_CHIMERA and ALIGN_SEQUENCE. Read the help files for these specific commands or, alternatively, send a message to server@rdp.life.uiuc.edu with 'help complete' as the text to obtain information about all of the email server commands. We encourage the obtaining and reading of the 00RELEASE_NOTES.3.0 file to learn about other changes and additions not specifically listed here. To get this file via email, mail server@rdp.life.uiuc.edu message: get 00RELEASE_NOTES.3.0 To get the file via ftp, ftp rdp.life.uiuc.edu cd pub/RDP get 00RELEASE_NOTES.3.0 Any questions may be mailed to rdp@phylo.life.uiuc.edu. - Bonnie L. Maidak, Ph.D. Database Manager, RDP Dept. Microbiology Univ. of Illinois From BIOSCI-REQUEST@net.bio.net Mon Aug 16 20:15:07 1993 Received: by net.bio.net (5.65/IG-2.0) id AA04132; Mon, 16 Aug 93 20:15:08 -0700 Received: from msscc.med.utah.edu by net.bio.net (5.65/IG-2.0) with SMTP id AA04128; Mon, 16 Aug 93 20:15:07 -0700 Received: from MSSCC.MED.UTAH.EDU by MSSCC.MED.UTAH.EDU (PMDF V4.2-11 #4395) id <01H1TSTDYZGG000530@MSSCC.MED.UTAH.EDU>; Mon, 16 Aug 1993 21:18:23 MDT Date: Mon, 16 Aug 1993 21:18:23 -0600 (MDT) From: "mr. wonderful" Subject: subscribe To: rna Message-Id: <01H1TSTDZ93M000530@MSSCC.MED.UTAH.EDU> X-Vms-To: IN%"rna@net.bio.net" Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Transfer-Encoding: 7BIT subscribe From BIOSCI-REQUEST@net.bio.net Mon Aug 23 06:52:02 1993 Received: by net.bio.net (5.65/IG-2.0) id AA09863; Mon, 23 Aug 93 06:52:05 -0700 Received: from odin.mda.uth.tmc.edu by net.bio.net (5.65/IG-2.0) with SMTP id AA09857; Mon, 23 Aug 93 06:52:02 -0700 Received: by odin.mda.uth.tmc.edu (4.1/SMI-4.1) id AA24510; Mon, 23 Aug 93 08:52:24 CDT From: roxanne@odin.mda.uth.tmc.edu (Roxanne Hall) Message-Id: <9308231352.AA24510@odin.mda.uth.tmc.edu> Subject: SUBSCRIBE To: rna Date: Mon, 23 Aug 93 8:52:24 CDT X-Mailer: ELM [version 2.3 PL11] subscribe Roxanne Hall Mail: roxanne@odin.mda.uth.tmc.edu GCG Administrator Or: roxanne@129.106.3.17 Department of Biomathematics, Phone: (79)2-2604 University of Texas, M.D. Anderson Cancer Center 1515 Holcombe Blvd., MS 237, Houston, Texas 77030 From BIOSCI-REQUEST@net.bio.net Mon Sep 20 05:13:34 1993 Received: by net.bio.net (5.65/IG-2.0) id AA13027; Mon, 20 Sep 93 05:13:46 -0700 Received: from dali.imb-jena.de by net.bio.net (5.65/IG-2.0) with SMTP id AA13022; Mon, 20 Sep 93 05:13:34 -0700 Received: from chagall.imb-jena.de by dali.imb-jena.de via SMTP (920330.SGI/911001.SGI) for rna@net.bio.net id AA23612; Mon, 20 Sep 93 14:14:15 +0200 Received: by chagall.imb-jena.de (920330.SGI/920502.SGI) for @dali.imb-jena.de:rna@net.bio.net id AA18868; Mon, 20 Sep 93 14:14:09 +0200 Date: Mon, 20 Sep 93 14:14:09 +0200 From: jsuehnel@chagall.imb-jena.de (Juergen Suehnel) Message-Id: <9309201214.AA18868@chagall.imb-jena.de> To: rna Subject: newsgroup subscribe ***************************************************************** * * * Juergen Suehnel * * Biocomputing * * Institut fuer Molekulare Biotechnologie * * Beutenbergstr. 11, Postfach 100813 * * D-07708 Jena * * Germany * * * * Tel.: 49 3641 852443 * * Fax: 49 3641 331325 * * E-Mail: jsuehnel@imb-jena.de * * * ***************************************************************** From BIOSCI-REQUEST@net.bio.net Wed Nov 17 14:38:50 1993 Received: by net.bio.net (5.65/IG-2.0) id AA08626; Wed, 17 Nov 93 14:38:53 -0800 Received: from vms2.macc.wisc.edu by net.bio.net (5.65/IG-2.0) with SMTP id AA08620; Wed, 17 Nov 93 14:38:50 -0800 Received: from VMSmail by vms2.macc.wisc.edu; Wed, 17 Nov 93 16:36 CDT Message-Id: <23111716361817@vms2.macc.wisc.edu> Date: Wed, 17 Nov 93 16:36 CDT From: Rock Pulak Subject: H19 RNA To: RNA X-Vms-To: IN%"rna@net.bio.net",RAPULAK I found the paper by Hao et al., Nature 365, 764-767 (1993) worthy of a closer look. As I understand it, the H19 gene encodes a polyA containing mRNA (I presume this is a polII transcript) that is abundant and does not have much of an ORF. In fact, going through some of the references, it appears that a pretty good arguement could be made that this mRNA does no code for a protein. One question that comes to mind is what does this mRNA do, if anything? Well, Hao et al., show that maybe H19 is a tumor suppressor gene. I think the data looks pretty good. Anyone disagree? I'd be interested in hearing why you might think so? Also if this mRNA does function in the cell, how does it do it? I didn't come across any in silico analysis of the sequence and so I don't know if the mRNA can be folded into some exotic secondary structure. Any thoughts? Looks like H19 is another of a small but growing list of mRNA-like molecules lacking much of an open-reading frame. I wonder if they are partially translated. What I mean is, I wonder if they do whatever they do by interacting with ribosomes, albeit, in a non-polypeptide synthesizing interaction. Any comments? rock pulak uw-madison From BIOSCI-REQUEST@net.bio.net Wed Nov 17 20:59:49 1993 Received: by net.bio.net (5.65/IG-2.0) id AA29429; Wed, 17 Nov 93 20:59:51 -0800 Received: from vms2.macc.wisc.edu by net.bio.net (5.65/IG-2.0) with SMTP id AA27386; Wed, 17 Nov 93 20:02:43 -0800 Received: from VMSmail by vms2.macc.wisc.edu; Wed, 17 Nov 93 22:01 CDT Message-Id: <23111722010898@vms2.macc.wisc.edu> Date: Wed, 17 Nov 93 22:01 CDT From: Rock Pulak Subject: H19 To: RNA X-Vms-To: IN%"rna@net.bio.net",RAPULAK David McPheeters replied to my comments and questions about H19 RNA that >Perhaps the H19 RNA is an "antisense" regulator >of processing/transport/translation of another gene. If this is true, would this be the "first" example in eukaryotes? (There is a story developing in the regulation of the lin-14 gene in C. elegans that strongly suggests lin-14 protein levels are regulated by an antisense RNA; any other examples out there?) If H19 is an "antisense regulator", what would be the easiest way to identify the gene or genes it is regulating? Seems the obvious experiment is to use the H19 sense transcript as a probe. Are there any other ways of potentially identifying the interacting genes (obvious and not-so-obvious)? rock pulak uw-madison From BIOSCI-REQUEST@net.bio.net Sat Nov 20 13:18:52 1993 Received: by net.bio.net (5.65/IG-2.0) id AA02707; Sat, 20 Nov 93 13:18:56 -0800 Received: from vms2.macc.wisc.edu by net.bio.net (5.65/IG-2.0) with SMTP id AA02698; Sat, 20 Nov 93 13:18:52 -0800 Received: from VMSmail by vms2.macc.wisc.edu; Sat, 20 Nov 93 15:17 CDT Message-Id: <23112015171294@vms2.macc.wisc.edu> Date: Sat, 20 Nov 93 15:17 CDT From: Rock Pulak Subject: H19 To: RNA X-Vms-To: IN%"rna@net.bio.net",RAPULAK thanks B. Bass, The Lengyel review in PNAS is very interesting. The idea that H19 tumour suppressor activity results from stimulating a dsRNA dependent protein kinase activity is interesting. However, would you predict that any antisense RNA should have the same affect? In other words, the experiments by Hao et al., Nature 365,764-767 should be repeated with a control cDNA that makes an antisense message to some garden variety house-keeping gene. The prediction is that there would be a loss of the cellular transformation phenotype. True? Rock Pulak UW-Madison rapulak@macc.wisc.edu From BIOSCI-REQUEST@net.bio.net Sat Nov 20 23:18:25 1993 Received: by net.bio.net (5.65/IG-2.0) id AA23114; Sat, 20 Nov 93 23:18:28 -0800 Received: from slri01.mshri.on.ca by net.bio.net (5.65/IG-2.0) with SMTP id AA23105; Sat, 20 Nov 93 23:18:25 -0800 Received: by SLRI01.MSHRI.ON.CA (MX V3.3 VAX) id 10429; Sun, 21 Nov 1993 02:20:00 EST Sender: bhatta@MSHRI.ON.CA Date: Sun, 21 Nov 1993 02:19:58 EST From: bhatta@SLRI01.MSHRI.ON.CA Reply-To: bhatta@MSHRI.ON.CA To: rna Message-Id: <00975D9D.5FD740A0.10429@SLRI01.MSHRI.ON.CA> subscribe v From BIOSCI-REQUEST@net.bio.net Sun Nov 21 09:06:25 1993 Received: by net.bio.net (5.65/IG-2.0) id AA21292; Sun, 21 Nov 93 09:06:29 -0800 Received: from netcom4.netcom.com by net.bio.net (5.65/IG-2.0) with SMTP id AA21286; Sun, 21 Nov 93 09:06:25 -0800 Received: from localhost by mail.netcom.com (8.6.4/SMI-4.1/Netcom) id JAA27884; Sun, 21 Nov 1993 09:06:40 -0800 From: davido@netcom.com (David Ornstein) Message-Id: <199311211706.JAA27884@mail.netcom.com> To: rna Date: Sun, 21 Nov 93 9:06:39 PST X-Mailer: ELM [version 2.3 PL11] unsubscribe -- From BIOSCI-REQUEST@net.bio.net Sun Nov 21 18:59:10 1993 Received: by net.bio.net (5.65/IG-2.0) id AA21745; Sun, 21 Nov 93 18:59:15 -0800 Received: from uvaarpa.Virginia.EDU by net.bio.net (5.65/IG-2.0) with SMTP id AA21736; Sun, 21 Nov 93 18:59:10 -0800 Received: from maxwell.acc.virginia.edu by uvaarpa.virginia.edu id aa27777; 21 Nov 93 21:59 EST Received: from [128.143.14.9] (crc2slabmac.bio.Virginia.EDU) by maxwell.acc.Virginia.EDU (4.1/1.34) id AA25769; Sun, 21 Nov 93 21:51:16 EST Date: Sun, 21 Nov 93 21:51:15 EST Message-Id: <9311220251.AA25769@maxwell.acc.Virginia.EDU> To: rna From: jes2u@maxwell.acc.virginia.edu Subject: unsubscribe unsubscribe John E. Smith III jes2u@virginia.edu Biology Dept./Gilmer Hall University of Virginia lab phone (804)982-5485 Charlottesville, VA 22903-2477 From BIOSCI-REQUEST@net.bio.net Tue Nov 23 09:01:18 1993 Received: by net.bio.net (5.65/IG-2.0) id AA05744; Tue, 23 Nov 93 09:01:24 -0800 Received: from vms2.macc.wisc.edu by net.bio.net (5.65/IG-2.0) with SMTP id AA05739; Tue, 23 Nov 93 09:01:18 -0800 Received: from VMSmail by vms2.macc.wisc.edu; Tue, 23 Nov 93 10:58 CDT Message-Id: <23112310584423@vms2.macc.wisc.edu> Date: Tue, 23 Nov 93 10:58 CDT From: Rock Pulak Subject: snurposomes To: RNA X-Vms-To: IN%"rna@net.bio.net",RAPULAK We recently had a journal club where the discussion leader presented some of J. Gall's data on particles in the nucleus of certain cells that are abundant and appear to contain various components of the splicing machinery. (See: J.G. Gall, Science, vol.252,1499-1500) Gall calls these particles snurposomes and identifies three classes on the basis of size and morphology. One question that came up was, is there any evidence against the preassembly of splicing components (like ribosomes)? Recall that the splicing pathway is usually presented as an ordered series of interactions between the substrate pre-mRNA and various components necesary for splicing rather than the view we usually get for translation where the ribosome, with all its components, binds and does its thing. Do you see what I'm saying? Is it actually a pre-assembled splicosome that binds the pre-mRNA as a unit, like a ribosome, or do the various components of the splicing machinery come in, do their thing, and then leave when the next splicing component comes in to do its thing? Rock Pulak UW-Madison rapulak@macc.wisc.edu From BIOSCI-REQUEST@net.bio.net Mon Jan 3 13:03:23 1994 Received: by net.bio.net (5.65/IG-2.0) id AA09374; Mon, 3 Jan 94 13:03:26 -0800 Received: from NOC4.DCCS.UPENN.EDU by net.bio.net (5.65/IG-2.0) with SMTP id AA09364; Mon, 3 Jan 94 13:03:23 -0800 Return-Path: Received: by noc4.dccs.upenn.edu id AA11197; Mon, 3 Jan 94 16:03:20 -0500 Received: from in by noc4.dccs.upenn.edu via MR/RELAY with conversational-MRIF; Mon, 03 Jan 94 16:03:20 -0500 Posted: Mon, 03 Jan 94 20:37:01 -0500 Date: Mon, 03 Jan 94 20:36:01 -0500 Sender: lutz@a1.mscf.upenn.edu From: "Carol Lutz" Message-Id: <23355130104991/118225@MSCF> To: subscribe.rna Subject: add me! Msg-Class: !AS Please add me to your e-mailings. Carol Lutz From BIOSCI-REQUEST@net.bio.net Fri Jan 7 16:56:52 1994 Received: by net.bio.net (5.65/IG-2.0) id AA01916; Fri, 7 Jan 94 16:56:55 -0800 Received: by net.bio.net (5.65/IG-2.0) id AA01912; Fri, 7 Jan 94 16:56:52 -0800 Date: Fri, 7 Jan 94 16:56:52 -0800 From: kristoff@net.bio.net (David Kristofferson) Message-Id: <9401080056.AA01912@net.bio.net> To: rna Subject: ALL QUIET ON THE RNA FRONT???? One month left! The voting process on the RNA group will begin on 1 Feb 94. There hasn't been much use of this group lately so I am not so optimistic that it will pass, but that is obviously up to the readership. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From BIOSCI-REQUEST@net.bio.net Sat Jan 8 07:36:48 1994 Received: by net.bio.net (5.65/IG-2.0) id AA07738; Sat, 8 Jan 94 07:36:52 -0800 Received: from crab.bio.indiana.edu by net.bio.net (5.65/IG-2.0) with SMTP id AA07734; Sat, 8 Jan 94 07:36:48 -0800 Received: by crab.bio.indiana.edu (911016.SGI/910603.SGI) for rna@net.bio.net id AA11562; Sat, 8 Jan 94 10:46:22 -0500 Date: Sat, 8 Jan 94 10:46:22 -0500 From: jnolan@crab.bio.indiana.edu (Jim Nolan) Message-Id: <9401081546.AA11562@crab.bio.indiana.edu> To: rna Subject: ALL QUIET... I recently signed up for the RNA net. My feeling is that lots of people knew there was supposed to be an RNA user group, but nobody knew how to subscribe, as evidenced by all the subscribe letters to the net. I kept looking for it to appear on the network news reader. We'd better use this thing before we lose it. I work on cross-linking of RNAse P RNA to tRNA, which I happen to find pretty interesting. I'd be interested in hearing about anything related to RNA structure or calatysis. It seems like there is plenty of exciting and interesting work to talk about in our field. Let's start talking. PS Tell your co-workers how to subscribe. Jim +-----------------------------------------------------------+ | Jim Nolan | | jnolan@bio.indiana.edu | | Dept. Biology Indiana University | +-----------------------------------------------------------+ From BIOSCI-REQUEST@net.bio.net Sun Jan 9 17:19:02 1994 Received: by net.bio.net (5.65/IG-2.0) id AA24832; Sun, 9 Jan 94 17:19:04 -0800 Received: from WCCF.MIT.EDU by net.bio.net (5.65/IG-2.0) with SMTP id AA24828; Sun, 9 Jan 94 17:19:02 -0800 Received: from wccf.mit.edu by wccf.mit.edu (PMDF V4.2-10 #2603) id <01H7HP0FAD1S8WW6XN@wccf.mit.edu>; Sun, 9 Jan 1994 20:18:30 EST Date: Sun, 09 Jan 1994 20:18:30 -0500 (EST) From: QUERY001@wccf.mit.edu Subject: Boston Area RNA Meeting To: rna Message-Id: <01H7HP0FB5ZM8WW6XN@wccf.mit.edu> Organization: Mass. Inst. Tech. - Whitaker College X-Vms-To: IN%"rna@net.bio.net" X-Vms-Cc: QUERY001 Mime-Version: 1.0 Content-Transfer-Encoding: 7BIT _____________________________________________________ BOSTON AREA RNA MEETING _____________________________________________________ Cheryl Wellington Harvard Medical School "c-fos Messenger RNA Decay" Shuguang Zhang Massachusetts Institute of Technology "A Proposed Pairing Mode Between Nucleic Acids and beta-Stranded Peptides" _____________________________________________________ *** 6:30 PM *** Note Time Change Monday, January 10, 1994 Sixth Floor Conference Room Center for Cancer Research (Building E17) Massachusetts Institute of Technology 40 Ames Street, Cambridge MA All interested parties are welcome. Contact Charles Query (253-6458; fax 253-3867) or Gene Huh (253-6424; fax 253-8357) regarding any questions. The next RNA Meeting will be held on Monday, February 7, 1994. _____________________________________________________ From BIOSCI-REQUEST@net.bio.net Mon Jan 10 10:36:26 1994 Received: by net.bio.net (5.65/IG-2.0) id AA07417; Mon, 10 Jan 94 10:36:30 -0800 Received: from cgl.ucsf.EDU by net.bio.net (5.65/IG-2.0) with SMTP id AA07412; Mon, 10 Jan 94 10:36:26 -0800 Received: from dali.ucsf.edu by cgl.ucsf.EDU (8.6.4/GSC4.24) id KAA19798 for ; Mon, 10 Jan 1994 10:36:24 -0800 From: schmitz@picasso.ucsf.EDU Received: from localhost by dali.ucsf.edu (8.6.4/GSC4.23) id KAA29798; Mon, 10 Jan 1994 10:36:23 -0800 Date: Mon, 10 Jan 1994 10:36:23 -0800 Message-Id: <199401101836.KAA29798@dali.ucsf.edu> To: rna Hello "RNA community", I want to thank Jim Nolan for the encouragement....we could make more out of this RNA network. I have a question regarding dialysis of small volume RNA samples for NMR purposes, i.e., 250ul of 2mM that needs a quick and efficient buffer change. Are there any cool procedures more different than the old dialysis bags that people want to share ? What experiences have people made with these Sialomed Spin BioDialyzers that seem pretty nifty but also expensive ? Do they work...? I would appreciate any input on this. Uli Schmitz UC,San Francisco Dept. Pharm. Chem schmitz@picasso.ucsf.edu From BIOSCI-REQUEST@net.bio.net Mon Jan 10 11:46:49 1994 Received: by net.bio.net (5.65/IG-2.0) id AA11050; Mon, 10 Jan 94 11:46:52 -0800 Received: from cs.utah.edu by net.bio.net (5.65/IG-2.0) with SMTP id AA11042; Mon, 10 Jan 94 11:46:49 -0800 Received: from adenosine.pharm.utah.edu by cs.utah.edu (5.65/utah-2.21-cs) id AA24786; Mon, 10 Jan 94 12:46:40 -0700 Date: Mon, 10 Jan 94 12:49:44 -0700 From: davis@adenosine.pharm.utah.edu (Darrell R. Davis) Posted-Date: Mon, 10 Jan 94 12:49:44 -0700 Message-Id: <9401101949.AA08640@adenosine.pharm.utah.edu> Received: by adenosine.pharm.utah.edu (911016.SGI/5.51) id AA08640; Mon, 10 Jan 94 12:49:44 -0700 To: rna Subject: RNA dialysis on Mon, 10 Jan 1994 10:36:23 -0800, schmitz@picasso.ucsf.EDU said: >> Posted-Date: Mon, 10 Jan 1994 10:36:23 -0800 >> I want to thank Jim Nolan for the encouragement....we could make more out of this RNA network. >> I have a question regarding dialysis of small volume RNA samples for NMR purposes, i.e., 250ul of 2mM that needs a quick and efficient buffer change. >> Are there any cool procedures more different than the old dialysis bags that people want to share ? I will make a contribution to get the RNA net rolling. Regarding dialysis: We use a couple "devices" for small scale dialysis. We have made a flow through device by machining a large disc (hockey puck) of lucite. The cell is pretty simple in design, but kind of hard to explain in a few words. A second method is *much* simpler. Take a 1.5 mL eppendorf tube. Heat the big end of a pasteur pipet in a bunsen flame and use the pipet to "punch out" the center of the eppendorf cap. The resulting modifed tube can be closed, but of course has a hole in the middle. You then put your sample in the eppendorf, place a small square of dialysis tubing across the top and "close" the cap. The dialysis tubing is sealed, forming a window across the top of the tube. You can then dialyze your sample by clamping the tube horizontally into a reservoir of buffer. Sample recoveries are also good because you can spin the sample in the same tube without transfer. This is really about as good as our flow cell and much easier to handle. RNA and NMR, I see that the insanity is spreading. -------------------------------------------------------------- Darrell R. Davis Assistant Professor Medicinal Chemistry University of Utah SLC, UT 84112 (801) 581-7006 FAX: 581-7087 davis@adenosine.pharm.utah.edu -------------------------------------------------------------- From BIOSCI-REQUEST@net.bio.net Mon Jan 10 13:44:11 1994 Received: by net.bio.net (5.65/IG-2.0) id AA17691; Mon, 10 Jan 94 13:44:14 -0800 Received: from selway.umt.edu by net.bio.net (5.65/IG-2.0) with SMTP id AA17687; Mon, 10 Jan 94 13:44:11 -0800 Received: by selway.umt.edu (5.65/DEC-Ultrix/4.3) id AA14691; Mon, 10 Jan 1994 14:44:09 -0700 Message-Id: <9401102144.AA14691@selway.umt.edu> Subject: RNase H To: rna Date: Mon, 10 Jan 1994 14:44:09 -0700 (MST) From: "Michael van Waes" X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Content-Length: 1160 Dear Netters: I was wondering if any of you pseudo-masochistic RNA scientists out there know something about the specificity of RNase H. The literature seems kind of vague. There is a paper by Almehdi et al. in Oregon, in which they managed to get a single clip on 16S rRNA using regular cDNA probes. I am trying to reproduce it, but with different probes, but I can't find a pattern to predict where the cut is going to be. The only other way to get single clips with RNase H seems to be by using chimeric DNA/RNA oligos (mucho $$$$$). Anybody have any thoughts on a cheap route to do this, i.e. single, site-specific clips on RNA ???. Perhaps a ribozyme?? Any thoughts/ideas appreciated. Thanks a lot and Happy New Year!!! _________________________________________________________________ Michael van Waes | Div. of Biol. Sci. | "I never worry about the future, Univ. of Montana | ... it comes soon enough. " Phone: 406-243-5733 | bi__mvw@selway.umt.edu | Albert Einstein. ----------------------------------------------------------------- From BIOSCI-REQUEST@net.bio.net Mon Jan 10 18:36:03 1994 Received: by net.bio.net (5.65/IG-2.0) id AA01881; Mon, 10 Jan 94 18:36:18 -0800 Received: by net.bio.net (5.65/IG-2.0) id AA01864; Mon, 10 Jan 94 18:36:03 -0800 Sender: David Kristofferson Date: Mon, 10 Jan 94 18:36:01 PST From: BIOSCI Administrator To: jnolan@crab.bio.indiana.edu (Jim Nolan) Cc: rna Subject: Re: ALL QUIET... In-Reply-To: Your message of Sat, 8 Jan 94 10:46:22 -0500 Message-Id: > I recently signed up for the RNA net. My feeling is that lots of people > knew there was supposed to be an RNA user group, but nobody knew how > to subscribe, as evidenced by all the subscribe letters to the net. > I kept looking for it to appear on the network news reader. > > We'd better use this thing before we lose it. I work on cross-linking > of RNAse P RNA to tRNA, which I happen to find pretty interesting. I'd be > interested in hearing about anything related to RNA structure or calatysis. > It seems like there is plenty of exciting and interesting work to talk about > in our field. Let's start talking. > > PS Tell your co-workers how to subscribe. > Jim > +-----------------------------------------------------------+ > | Jim Nolan | > | jnolan@bio.indiana.edu | > | Dept. Biology Indiana University | > +-----------------------------------------------------------+ > > To subscribe all one need do is send the message subscribe rna to biosci-server@net.bio.net. To cancel your e-mail sub send the message unsubscribe rna to biosci-server@net.bio.net. In both cases leave the Subject: line of your message blank and put the commands in the main body of the message. The discussion leader for the group is Larry Simpson at UCLA. I will need to get a final newsgroup charter (to put out for a vote) from either him or his designated successor sometime during the next month. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net Our instruction sheet follows. If you can not use news software and therefore need to subscribe by e-mail, please follow the instructions below for using the e-mail server at biosci-server@net.bio.net. If you have problems using the server, personal help can be reached at biosci-help@net.bio.net. Thank you for your interest in the BIOSCI newsgroups. ---------------------------------------------------------------------- THE BIOSCI ELECTRONIC NEWSGROUP NETWORK INFORMATION SHEET (last revised 07-JAN-94) ---------------------------------------------------------------------- This is the BIOSCI information sheet for the Americas and Pacific Rim countries. 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The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of the BIOSCI information sheet. ---------------------------------------------------------------------- Introduction ------------ The BIOSCI newsgroup network was developed to allow easy worldwide communications between biological scientists who work on a variety of computer networks. BIOSCI is supported by the National Science Foundation, Department of Energy, and National Institutes of Health in the U.S.A. and by the Science and Engineering Research Council Daresbury Laboratory in the United Kingdom. BIOSCI services are available to users free of charge. BIOSCI messages are distributed by two means: USENET news software and electronic mail. WE STRONGLY ENCOURAGE ALL INTERESTED USERS TO EXPLORE GETTING "USENET NEWS" SOFTWARE AT YOUR SITE. The software is in the public domain, and you will find it much more convenient than subscribing to newsgroups by e-mail. 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List of BIOSCI newsgroups ------------------------- BIOSCI messages are distributed on the newsgroups in the "bionet" hierarchy of USENET and on the corresponding mailing lists indicated below. Contents of the USENET newsgroups and the e-mail distributions are *identical*, i.e., messages sent in by e-mail are also forwarded to USENET and messages posted to USENET newsgroups are also distributed to e-mail subscribers. An expanded description of the purpose of each newsgroup follows this list. MAILING LIST NAME USENET Newsgroup Name ----------------- --------------------- ACEDB-SOFT bionet.software.acedb AGEING bionet.molbio.ageing AGROFORESTRY bionet.agroforestry ARABIDOPSIS bionet.genome.arabidopsis BIOFORUM bionet.general BIO-INFORMATION-THEORY + bionet.info-theory BIONAUTS bionet.users.addresses BIONEWS ** bionet.announce BIO-JOURNALS ** bionet.journals.contents BIO-MATRIX bionet.molbio.bio-matrix BIO-SOFTWARE bionet.software BIOTHERMOKINETICS bionet.metabolic-reg CELL-BIOLOGY bionet.cellbiol CHLAMYDOMONAS bionet.chlamydomonas CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY ** bionet.biology.computational DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMPLOYMENT bionet.jobs GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage HIV-MOLECULAR-BIOLOGY bionet.molbio.hiv HUMAN-GENOME-PROGRAM bionet.molbio.genome-program IMMUNOLOGY bionet.immunology INFO-GCG bionet.software.gcg JOURNAL-NOTES bionet.journals.note METHODS-AND-REAGENTS bionet.molbio.methds-reagnts MOLECULAR-EVOLUTION bionet.molbio.evolution MYCOLOGY bionet.mycology NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography RAPD bionet.molbio.rapd SCIENCE-RESOURCES ** bionet.sci-resources TROPICAL-BIOLOGY bionet.biology.tropical VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast + full name is BIOLOGICAL-INFORMATION-THEORY-AND-CHOWDER-SOCIETY ** Note that newsgroups flagged with ** are moderated, i.e., postings are directed to a moderator (editor) who later forwards messages (possibly edited or condensed) to the newsgroup. List of BIOSCI Newsgroup Topics ------------------------------- MAILING LIST NAME TOPIC ----------------- ----- ACEDB-SOFT Discussions by users and developers of genome databases using the ACEDB software. AGEING Discussions about ageing research AGROFORESTRY Discussions about agroforestry research ARABIDOPSIS Newsgroup for the Arabidopsis Genome Project BIOFORUM Discussions about biological topics for which there is not yet a dedicated newsgroup BIOLOGICAL-INFORMATION- THEORY-AND-CHOWDER-SOCIETY Applications of information theory to biology BIONAUTS Question/answer forum for help using electronic networks, locating e-mail addresses, etc. BIONEWS ** General announcements of widespread interest to biologists BIO-JOURNALS ** Tables of Contents of biological journals BIO-MATRIX Applications of computers to biological databases BIO-SOFTWARE Information on software for the biological sciences BIOTHERMOKINETICS Discussions about the kinetics, thermodynamics and control of biological processes at the cellular level CELL-BIOLOGY Discussions about cell biology including cancer research at the cellular level CHLAMYDOMONAS Discussions about the biology of the green alga Chlamydomonas and related genera CHROMOSOMES Discussions about mapping and sequencing of eucaryote chromosomes COMPUTATIONAL-BIOLOGY ** Mathematical and computer applications in biology DROSOPHILA Discussions about biological research on Drosophila EMBL-DATABANK Messages to and from the EMBL database staff EMPLOYMENT Job opportunities in biology (see BIOSCI FAQ *before* posting commercial job openings) GDB Messages to and from the Genome Data Bank staff GENBANK-BB Messages to and from the GenBank database staff GENETIC-LINKAGE Newsgroup for genetic linkage analysis HIV-MOLECULAR-BIOLOGY Discussions about the molecular biology of HIV HUMAN-GENOME-PROGRAM NIH-sponsored newsgroup on human genome issues IMMUNOLOGY Discussions about research in immunology INFO-GCG Discussions about the GCG sequence analysis software JOURNAL-NOTES Practical advice on dealing with professional journals METHODS-AND-REAGENTS Requests for information and lab reagents MOLECULAR-EVOLUTION Discussions about research in molecular evolution MYCOLOGY Discussions about research on filamentous fungi NEUROSCIENCE Discussions about research in the neurosciences N2-FIXATION Discussion about biological nitrogen fixation PHOTOSYNTHESIS Discussions about photosynthesis research PLANT-BIOLOGY Discussions about research in plant biology POPULATION-BIOLOGY Discussions about research in population biology PROTEIN-ANALYSIS Discussions about research on proteins and messages for the PIR and SWISS-PROT databank staffs. PROTEIN-CRYSTALLOGRAPHY Discussion about crystallography of macromolecules and messages for the PDB staff RAPD Discussions about Randomly Amplified Polymorphic DNA SCIENCE-RESOURCES ** Information from/about scientific funding agencies TROPICAL-BIOLOGY Discussions about research in tropical biology VIROLOGY Discussions about research in virology WOMEN-IN-BIOLOGY Discussions about issues concerning women biologists YEAST Discussions about the molecular biology and genetics of yeast ** Note that newsgroups flagged with ** are moderated, i.e., postings are directed to a moderator (editor) who later forwards messages (possibly edited or condensed) to the newsgroup. BIOSCI Newsgroup Discussion Leaders ----------------------------------- Most scientific specialty newsgroups (except for a few created several years ago) have individuals who are responsible for stimulating discussion on the newsgroup. General purpose forums such as METHODS-AND-REAGENTS do not have discussion leaders. If a group that you are interested in does not seem to have much activity recently, please contact the discussion leader and ask why. NEWSGROUP NAME Discussion Leader and their e-mail address -------------- ------------------------------------------ ACEDB-SOFT Mike Cherry (cherry@genome.stanford.edu) AGEING Sydney Shall (bafa1@central.sussex.ac.uk) AGROFORESTRY Gerry Lawson (F_GJL@vaxa.nerc-bush.ac.uk) ARABIDOPSIS Chris Somerville (21847CRS@msu.edu) BIOFORUM None BIOLOGICAL-INFORMATION- THEORY-AND-CHOWDER-SOCIETY Tom Schneider (toms@ncifcrf.gov) BIONAUTS Rob Harper (harper@convex.csc.fi) BIONEWS ** David Kristofferson (kristoff@net.bio.net) BIO-JOURNALS ** David Kristofferson (kristoff@net.bio.net) BIO-MATRIX Dan Davison (davison@uh.edu) BIO-SOFTWARE None BIOTHERMOKINETICS John Woods (eanv20@castle.edinburgh.ac.uk) CELL-BIOLOGY Ola Myklebost (ola.myklebost@dnr.uio.no) CHLAMYDOMONAS Elizabeth H. Harris (chlamy@acpub.duke.edu) and Antonio R. 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Prototype newsgroups may *not* be fully archived, so please be sure to save any messages that you may want to refer to again. Posting Address Purpose --------------- ------- biogopher@net.bio.net A communication forum for all Bio-Gopher administrators. emf-bio@net.bio.net Discussions on the electromagnetic field interactions with biological systems. pep-libs@net.bio.net Discussion on generation and use of peptide molecular repertoires displayed on phage or prepared as synthetic peptide combinatorial libraries. rna@net.bio.net Discussions about RNA editing, RNA splicing, and ribozyme activities of RNA. staden-users@net.bio.net Discussions about the Staden Package for molecular sequence analysis. urodeles@net.bio.net Discussions among research scientists using urodele amphibians (axolotls, salamanders, and newts) in any biological field. yac@net.bio.net Dicussions about yeast artificial chromosomes FURTHER QUESTIONS??? Please address them to biosci-help@net.bio.net. PLEASE DO NOT DIRECT BIOSCI QUESTIONS TO THE PERSONAL E-MAIL ADDRESSES OF PEOPLE ON THE BIOSCI STAFF!! DUE TO OUR VOLUME OF MAIL, ANSWERS MAY BE DELAYED OR NOT SENT AT ALL!! From BIOSCI-REQUEST@net.bio.net Thu Jan 13 09:51:25 1994 Received: by net.bio.net (5.65/IG-2.0) id AA09399; Thu, 13 Jan 94 09:51:29 -0800 Received: from selway.umt.edu by net.bio.net (5.65/IG-2.0) with SMTP id AA09395; Thu, 13 Jan 94 09:51:25 -0800 Received: by selway.umt.edu (5.65/DEC-Ultrix/4.3) id AA04128; Thu, 13 Jan 1994 10:51:20 -0700 Message-Id: <9401131751.AA04128@selway.umt.edu> Subject: transcription To: rna Date: Thu, 13 Jan 1994 10:51:19 -0700 (MST) From: "Douglas J Bucklin" X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Content-Length: 507 RNA Scientists: A line of discussion appeared a while ago on high yield transcription. The talk centered on synthesis of lengthy transcripts. My question is how one would go about producing a monstrous quantity of short transcripts-less then 15 bases? The literature seems to say that T7 will not do the job. Will any of the other polymerases do the trick? We could go to chemical synthesis, but that doesn't seem to be that reliable at this point. Any suggestions? D. Bucklin U. of MT Missoula MT From BIOSCI-REQUEST@net.bio.net Thu Jan 13 11:06:14 1994 Received: by net.bio.net (5.65/IG-2.0) id AA13486; Thu, 13 Jan 94 11:06:17 -0800 Received: from cal.scripps.edu by net.bio.net (5.65/IG-2.0) with SMTP id AA13482; Thu, 13 Jan 94 11:06:14 -0800 Received: by cal.scripps.edu (5.0/SMI-SVR4) id AA01076; Thu, 13 Jan 94 11:07:55 PST Date: Thu, 13 Jan 94 11:07:55 PST From: brianw@cal (Brian Wimberly) Message-Id: <9401131907.AA01076@cal.scripps.edu> To: rna Subject: Re: transcription X-Sun-Charset: US-ASCII Content-Length: 674 I wonder what you mean by "monstrous quantities". As an NMR spectroscopist my point of view is somewhat skewed! The Tinoco lab (UC Berkeley) has produced NMR quantities (10+ mg) of very short RNAs -- as short as 10 nt -- using T7 RNA polymerase. Yields are VERY sequence-dependent are are difficult to predict. We do know that there is a very strong preference for G at the 5' end, and yields tend to be better for transcripts with purine-rich 5'ends. Too many G's in a row can however cause slipping during transcription. If you want to do this you should prepare the T7 polymerase yourself; see Wyatt et al., Biotechniques 11, 764 & references therein. Brian Wimberly From BIOSCI-REQUEST@net.bio.net Fri Jan 14 08:30:32 1994 Received: by net.bio.net (5.65/IG-2.0) id AA02613; Fri, 14 Jan 94 08:30:36 -0800 Received: from piglet.INS.CWRU.Edu by net.bio.net (5.65/IG-2.0) with SMTP id AA02609; Fri, 14 Jan 94 08:30:32 -0800 Received: by piglet.INS.CWRU.Edu (5.65b+ida+/CWRU-1.5.6-bsdi) id AA21268; Fri, 14 Jan 94 11:30:30 -0500 (from bl275 for rna@net.bio.net) Message-Id: <9401141630.AA21268@piglet.INS.CWRU.Edu> Date: Fri, 14 Jan 94 11:30:30 -0500 From: bl275@cleveland.Freenet.Edu (Dan Diaz) To: rna Subject: oligomers of ribothymidine (5-methyluridine) for enzyme studies Cc: bl275@cleveland.freenet.edu Reply-To: bl275@cleveland.Freenet.Edu (Dan Diaz) i am studying a single-strand specific dna exonuclease from e. coli. we are trying to set up a series of experiments to ascertain whether the enzyme discriminates between rna and dna molecules solely on the basis of the presence or absence of a 2' hydroxyl. due to their lack of secondary structure, oligomers of thymidine are the most extensively hydrolyzed substrates. we are now in search of oligomers of 'ribothymidine' (5-methyluridine) for comparison to oligothymidine. there is no evidence that the enzyme hydrolyzes any known rna molecule, including poly(A) and other common rna homo-oligomers. we are in search of a source of poly- or oligo-5-methyluridine for direct comparison to the enzyme's favored poly(T) substrate. i have found no commercial source for a 5-methyluridine phosphoramidite, or for a di- or triphosphate for use in an enzymatic synthesis of polymers. i realize that comparing the substrate potential of poly(T) and poly(rT) will not unambiguously answer the question of substrate discrimination, as other factors in substrate binding may be obscured when using homooligomers, but i think it an important first step. have i missed a potential source? any suggestions? thanks! From BIOSCI-REQUEST@net.bio.net Fri Jan 14 09:13:07 1994 Received: by net.bio.net (5.65/IG-2.0) id AA04448; Fri, 14 Jan 94 09:13:10 -0800 Received: from [137.131.80.51] by net.bio.net (5.65/IG-2.0) with SMTP id AA04444; Fri, 14 Jan 94 09:13:07 -0800 Received: by cal.scripps.edu (5.0/SMI-SVR4) id AA01235; Fri, 14 Jan 94 09:14:48 PST Date: Fri, 14 Jan 94 09:14:48 PST From: brianw@cal (Brian Wimberly) Message-Id: <9401141714.AA01235@cal.scripps.edu> To: rna Subject: Re: oligomers of ribothymidine (5-methyluridine) for enzyme studies X-Sun-Charset: US-ASCII Content-Length: 171 If Nassim Usman can't tell you where to find the stuff, then no one can ... Usman works at RPI in Boulder, Colorado (unfortunately I don't have the phone number). Brian From BIOSCI-REQUEST@net.bio.net Fri Jan 14 10:48:58 1994 Received: by net.bio.net (5.65/IG-2.0) id AA08663; Fri, 14 Jan 94 10:49:02 -0800 Received: from east.gsfc.nasa.gov by net.bio.net (5.65/IG-2.0) with SMTP id AA08657; Fri, 14 Jan 94 10:48:58 -0800 Received: from BIOVX2.DECnet MAIL11D_V3 by east.gsfc.nasa.gov (5.57/Ultrix3.0-C) id AA17097; Fri, 14 Jan 94 13:48:55 -0500 Date: Fri, 14 Jan 94 13:48:54 -0500 Message-Id: <9401141848.AA17097@east.gsfc.nasa.gov> From: simpson@biovx2.DNET.NASA.GOV To: "rna@net.bio.net"@EAST.DNET.NASA.GOV Dear RNA neters, especially RNA editors: I would like to raise a few issues about editing to get some feedback. One involves a semantic problem. The term 'editing' is now employed for several probably very different systems and this leads to confusion, especially for people not in the field. Brenda Bass has coined the terms "substitution editing" to describe the plant mitochondria, apoB type, and "insertion/ deletion editing" to describe the trypanosomatid mitochondrion type. One could argue that in the absence of evidence on the mechanism of the plant type, there could very well be a distant relationship to the trypanosome type, but I doubt it. And then of course the tRNA people also would like to use the term editing for nt modifications in tRNAs. What are your thoughts to clear up this semantic problem? The second item I would like to bring up is the fascinating phenomenon of "transkinetoplastidy" from the Lee and Chang labs. This appears to involve major changes in the minicircle DNA population in one to two generations as a result of various stresses (drug selection). How can this tie in with the known gRNA coding capacity of minicircles? They explain the changes as an amplification of preexisting minor sequence classes. But during the process, there is a striking change in morphology of the kinetoplast DNA network. Could this represent the major mechanism for changing minicircle and thereby gRNA sequences, a phenomenon which has been frequently observed with many kinetoplastid species in prolonged culture? It would be nice to get some thoughts from others in the field. Larry Simpson UCLA From BIOSCI-REQUEST@net.bio.net Fri Jan 14 15:04:10 1994 Received: by net.bio.net (5.65/IG-2.0) id AA20118; Fri, 14 Jan 94 15:04:14 -0800 Received: from wigate.nic.wisc.edu by net.bio.net (5.65/IG-2.0) with SMTP id AA20114; Fri, 14 Jan 94 15:04:10 -0800 Date: Fri, 14 Jan 94 15:04:10 -0800 Received: from 144.92.79.38 by wigate.nic.wisc.edu; Fri, 14 Jan 94 17:04 CDT Message-Id: <24011417041015@wigate.nic.wisc.edu> From: Dahlberg@macc.wisc.edu Subject: Nassim Usman To: RNA Nassim Usman's phone number is (303) 449-6500 From BIOSCI-REQUEST@net.bio.net Fri Jan 14 17:49:39 1994 Received: by net.bio.net (5.65/IG-2.0) id AA27066; Fri, 14 Jan 94 17:49:55 -0800 Received: from riscsm.scripps.edu by net.bio.net (5.65/IG-2.0) with SMTP id AA27041; Fri, 14 Jan 94 17:49:39 -0800 Received: from laue.scripps.edu by scripps.edu (5.61/1.34) id AA10676; Fri, 14 Jan 94 17:49:35 -0800 Received: by laue.Scripps.EDU (4.1/SMI-4.1) id AA01123; Fri, 14 Jan 94 17:46:59 PST Date: Fri, 14 Jan 94 17:46:59 PST From: dave@scripps.edu (Dave Stout) Message-Id: <9401150146.AA01123@laue.Scripps.EDU> To: biosci Subject: RNA newsgroup Cc: rna Please include me in the RNA newgroup Dave Stout 1-14-94 dave@scripps.edu From BIOSCI-REQUEST@net.bio.net Tue Jan 18 03:02:06 1994 Received: by net.bio.net (5.65/IG-2.0) id AA00343; Tue, 18 Jan 94 03:02:09 -0800 Received: from msscc.med.utah.edu by net.bio.net (5.65/IG-2.0) with SMTP id AA00339; Tue, 18 Jan 94 03:02:06 -0800 Received: from MSSCC.MED.UTAH.EDU by MSSCC.MED.UTAH.EDU (PMDF V4.2-11 #4395) id <01H7SMT9F8N48WYF5D@MSSCC.MED.UTAH.EDU>; Mon, 17 Jan 1994 16:31:38 MDT Date: Mon, 17 Jan 1994 16:31:38 -0600 (MDT) From: BASS@MSSCC.MED.UTAH.EDU Subject: editing nomenclature To: rna Message-Id: <01H7SMT9FIAQ8WYF5D@MSSCC.MED.UTAH.EDU> X-Vms-To: IN%"rna@net.bio.net" X-Vms-Cc: BASS Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Transfer-Encoding: 7BIT Well I agree with Larry Simpson that it is sometimes confusing sorting out just what exactly constitutes an RNA editing event. In light of past literature I think both insertion/deletion events and substitution events must be called editing. However, despite the fact that future studies may show mechanistic similarities, I think these two different types of editing should be distinguished. I am open to suggestions of other nomenclature to distinguish these two catagories (besides substitution and insertion/ deletion). What needs particular attention, as Larry points out, is how to insure that tRNA modifications are distinguished from "substitution" editing. When I originally defined "substitution" editing, I noted that, tRNA modifications always yield non-Watson-Crick bases, while substitution editing involves the conversion of one Watson-Crick base to another. However, unless one considers inosine a WC base, the new data from Peter Seeburg's lab (Dec 31 Cell) puts this qualification on shaky grounds. Of course production of inosine from adenosine is still a minor modification compared to most of the things that happen on tRNA. So far, substitution editing events appear to occur by deamination or amination of a WC base. Perhaps this could help in the distinction? On a related note, the editing event described by Seeburg is almost certainly performed by the enzyme formally called dsRNA unwinding/modifying activity, unwindase etc etc. We are now calling this enzyme dsRAD (pronounced dee-ess-RAD) for dsRNA adenosine deaminase. -Brenda Bass From BIOSCI-REQUEST@net.bio.net Tue Jan 18 08:31:30 1994 Received: by net.bio.net (5.65/IG-2.0) id AA15870; Tue, 18 Jan 94 08:31:49 -0800 Received: from vax2.sara.nl by net.bio.net (5.65/IG-2.0) with SMTP id AA15861; Tue, 18 Jan 94 08:31:30 -0800 Received: from AMCCCA.AMC.UVA.NL by SARA.NL for RNA@net.bio.net; 18 Jan 94 17:32 MET Received: from amc.uva.nl by amc.uva.nl (PMDF V4.2-11 #2498) id <01H7U27P1OA00001BA@amc.uva.nl>; Tue, 18 Jan 1994 17:20:21 MET Date: Tue, 18 Jan 1994 17:20:21 +0100 (MET) From: SLOOF@amc.uva.nl Subject: RNA editing semantics To: RNA Message-Id: <01H7U27P1OA20001BA@amc.uva.nl> X-Envelope-To: RNA@net.bio.net X-Vms-To: IN%"RNA@net.bio.net" Mime-Version: 1.0 Content-Transfer-Encoding: 7BIT When I first used the term RNA editing I meant to indicate that the genetic content (function) of an mRNA can be changed by posttranscriptional alteration of its nt sequence. This can be extrapolated to other RNAs (t-, r-, g-, etc) and introns, in which case editing processes may alter important structural andfunctional motifs. (N.B.: some editing events do not alter function, cf third codon position, leader, trailer editing, etc.).Technically speaking, many of the longer known RNA modification processes also alter the funtioning of the corresponding RNAs, so unless we want to call everything 'RNA editing' we should reserve this term to processes that only generate Watson/Crick bases. The price we would have to pay is that the processes that generate Is in the GluR receptor should be called RNA modification and not RNA editing processes. As long as the mechanism of the various editing processes are not known, the terms insertional and substitutional editing seem the best way to describe what may be going on, as long as it is stated with which type(s) of nucleotide one is dealing:e.g. U-insertion, pyrimidine interconversion, etc. We should not use terms like tRNA editing without defining the type of editing we are talking about.I also do not think we should encourage the use of the terms 'Type I, II' editing, in analogy to splicing, without more precise knowledge of the various mechanisms to help define the different editing 'Types'. Rob Benne From BIOSCI-REQUEST@net.bio.net Thu Jan 20 22:46:06 1994 Received: by net.bio.net (5.65/IG-2.0) id AA25355; Thu, 20 Jan 94 22:46:09 -0800 Received: from cgl.ucsf.EDU by net.bio.net (5.65/IG-2.0) with SMTP id AA25347; Thu, 20 Jan 94 22:46:06 -0800 Received: from dali.ucsf.edu by cgl.ucsf.EDU (8.6.5/GSC4.24) id WAA13617 for ; Thu, 20 Jan 1994 22:46:04 -0800 From: schmitz@picasso.ucsf.EDU Received: from localhost by dali.ucsf.edu (8.6.4/GSC4.23) id WAA08217; Thu, 20 Jan 1994 22:46:02 -0800 Date: Thu, 20 Jan 1994 22:46:02 -0800 Message-Id: <199401210646.WAA08217@dali.ucsf.edu> To: rna Subject: RNA in cacodylate buffer Hi RNA folks, I am working with a 21mer RNA hairpin whose structure seems to be very dependent on the presence of magnesium. I did several melting profiles in buffers that contained 10mM phoshpate and up to 100mM Mg until I got some precipitate; Mg and phosphate not a great idea,I had expected that. But I was surprised that 50mM Mg and 10mM phosphate do not form a precipitate. So I changed the buffer component to 10mM sodium cacodylate (pH7) and then to my great unpleaure, a precipitate formed with 5, 25, and 50mM Mg. There is no precipitate when no RNA is present ( about 1uM). Does somebody know something about weird behaviour of cacodylate buffers when Mg is present or about RNA precipitation? Is there literature about that topic? I would appreciate any comments (despite my vague description). Thanks, Uli Uli Schmitz UC,San Francisco Dept. Pharm. Chem schmitz@picasso.ucsf.edu From BIOSCI-REQUEST@net.bio.net Thu Jan 27 15:54:57 1994 Received: by net.bio.net (5.65/IG-2.0) id AA16746; Thu, 27 Jan 94 15:54:59 -0800 Received: from selway.umt.edu by net.bio.net (5.65/IG-2.0) with SMTP id AA16742; Thu, 27 Jan 94 15:54:57 -0800 Received: by selway.umt.edu (5.65/DEC-Ultrix/4.3) id AA09045; Thu, 27 Jan 1994 16:54:56 -0700 Message-Id: <9401272354.AA09045@selway.umt.edu> Subject: pKK3535 sequence To: rna Date: Thu, 27 Jan 1994 16:54:55 -0700 (MST) From: "Michael van Waes" X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Content-Length: 423 Hi netters! I nedd the complete sequence of pKK3535; not just the rrnB, but also the flanking sequences. Does anybody know if I can find this anywhere? I unsuccessfully searched rdp and genbank. Thanks for your help Michael van Waes | Div. of Biol. Sci. | Please remain calm, Univ. of Montana | it's no use both of us being Phone: 406-243-5733 | hysterical at the same time. bi__mvw@selway.umt.edu | From BIOSCI-REQUEST@net.bio.net Thu Jan 27 17:02:16 1994 Received: by net.bio.net (5.65/IG-2.0) id AA19303; Thu, 27 Jan 94 17:02:21 -0800 Received: from ncbi.nlm.nih.gov by net.bio.net (5.65/IG-2.0) with SMTP id AA19294; Thu, 27 Jan 94 17:02:16 -0800 Received: from borduas.nlm.nih.gov by ncbi (5.0/SMI-SVR4) id AA10732; Thu, 27 Jan 1994 20:02:08 +0500 Received: by borduas.nlm.nih.gov (4.1/SMI-4.1) id AA06730; Thu, 27 Jan 94 20:02:07 EST Date: Thu, 27 Jan 94 20:02:07 EST From: francis@borduas.nlm.nih.gov (Francis Ouellette) Message-Id: <9401280102.AA06730@borduas.nlm.nih.gov> To: rna, bi__mvw@selway.umt.edu Subject: NOT pKK3535 sequence Reply-To: francis@ncbi.nlm.nih.gov Content-Length: 1220 Michael van Waes (bi__mvw@selway.umt.edu) asks: > Hi netters! I need the complete sequence of pKK3535; not just the rrnB, but > also the flanking sequences. Does anybody know if I can find this > anywhere? I unsuccessfully searched rdp and genbank. Michael, is this a CLONTECH vector? I check GenBank, and it is indeed not here, but we have pKK388-1 from Clontech, maybe you can get in touch with them for the one one of interest. From the GenBank file for pKK388-1 (Accession Number U02444): > This vector can be obtained from CLONTECH Laboratories, Inc., 4030 > Fabian Way, Palo Alto, CA 94303, USA. To place an order call (415) > 424-8222 or (800) 662-2566, extension 1. International customers, > please contact your local distributor. For technical information, > call (415) 424- 8222 or (800) 662-2566, extension 3. > This sequence was compiled by Jurgen Brosius; this vector has not > been completely sequenced. If you suspect there is an error in this > sequence, please contact CLONTECH's Technical Service Department at > (415) 424-8222 or (800) 662-2566, extension 3 or E-mail > CLONTECH@BIOTECHNET.COM. regards, francis -- | B.F. Francis Ouellette | | francis@ncbi.nlm.nih.gov From BIOSCI-REQUEST@net.bio.net Fri Jan 28 09:51:40 1994 Received: by net.bio.net (5.65/IG-2.0) id AA01624; Fri, 28 Jan 94 09:52:06 -0800 Received: from [147.251.4.33] by net.bio.net (5.65/IG-2.0) with SMTP id AA01469; Fri, 28 Jan 94 09:51:40 -0800 Received: from elanor.sci.muni.cz by aragorn.ics.muni.cz with SMTP id AA11842 (5.67a8/IDA-1.4.4 for ); Fri, 28 Jan 1994 18:51:29 +0100 Received: from [147.251.158.4] by elanor.sci.muni.cz with SMTP id AA28566 (5.67a/IDA-1.4.4 for ); Fri, 28 Jan 1994 18:55:44 +0100 From: "Stanislav Rosypal" Date: Fri, 28 Jan 94 18:50:31 CST Message-Id: <87.rosypal@elanor.sci.muni.cz_POPMail_3.1.8> X-Popmail-Charset: English To: rna Subject: help From BIOSCI-REQUEST@net.bio.net Sun Jan 30 13:14:14 1994 Received: by net.bio.net (5.65/IG-2.0) id AA07665; Sun, 30 Jan 94 13:14:20 -0800 Received: from kasia.path.ox.ac.uk by net.bio.net (5.65/IG-2.0) with SMTP id AA07648; Sun, 30 Jan 94 13:14:14 -0800 Received: by molbiol.ox.ac.uk (MX V3.4-Beta-3 VAX) id 2; Sat, 29 Jan 1994 20:16:39 0000 Date: Sat, 29 Jan 1994 20:16:38 0000 From: birney@molbiol.ox.ac.uk To: rna Message-Id: <0097946C.375C8C62.2@molbiol.ox.ac.uk> Hi If anyone out there works on either the chloroplasts RNA binding proteins OR the hnrnpA1 like proteins, it would be a great help to get in touch with you to try and sort out which sequence is what, some kind of nomenculture and good references. I'm trying to run a database system on the RRM (RBD) domain (if you saw my last posting then you'll understand) and both these sets of proteins are giving me a headache (!). If anyone knows the email address of someone who might help that would be equally useful... thanks alot ewan birney@molbiol.ox.ac.uk From BIOSCI-REQUEST@net.bio.net Wed Feb 2 17:37:09 1994 Received: by net.bio.net (5.65/IG-2.0) id AA09292; Wed, 2 Feb 94 17:37:11 -0800 Received: from lewsun.idlw.ucl.ac.be by net.bio.net (5.65/IG-2.0) with SMTP id AA14798; Wed, 2 Feb 94 08:53:58 -0800 Received: from [130.104.109.3] by lewsun.idlw.ucl.ac.be (4.1/SMI-4.1(MX version)) id AA05728; Wed, 2 Feb 94 17:54:43 +0100 Message-Id: <9402021654.AA05728@lewsun.idlw.ucl.ac.be> Date: Wed, 2 Feb 1994 17:55:46 +0100 To: rna From: opperd@trop.ucl.ac.be Subject: thoughts on transkinetoplastidy Cc: simpson@uclabio.bitnet Dear RNA neters, Larry Simpson wrote in a previous message >The second item I would like to bring up is the fascinating >phenomenon of "transkinetoplastidy" from the Lee and Chang labs. This appears >to involve major changes in the minicircle DNA population in one to two >generations as a result of various stresses (drug selection). How can this tie >in with the known gRNA coding capacity of minicircles? They explain the >changes as an amplification of preexisting minor sequence classes. But during >the process, there is a striking change in morphology of the kinetoplast DNA >network. Could this represent the major mechanism for changing minicircle and >thereby gRNA sequences, a phenomenon which has been frequently observed with >many kinetoplastid species in prolonged culture? >It would be nice to get some thoughts from others in the field. > I'll try to put forward an explanation for the observed transkinetoplastidy. The phenomenon of transkinetoplastidy in Leishmania as reported by the Lee and Chang laboratories reminds me of what we have seen earlier to happen in the trypanosome field. African trypanosomes that have been passaged for a long time through animals tend to lose the capability of establishing an infection in the fly. What actually happens is that, because of the absence of any need to switch on mitochondrial activity, deletions and mutations accumulate in the kinetoplast DNA up to a situation where maxicircles and minicircles are progressively being lost in an irreverible manner. An intermediate stage is the one encountered in certain T. evansi and T. equiperdum strains that have lost maxicircles as well as minicircle complexity and are left with only one class of minicircles. These naturally occurring strains have lost infectivity for the insect vector and are comparable with the mitochondrial rho minus mutations in yeast. Finally dyskinetoplastic strains can be obtained, comparable to the petite mutations of yeast, lacking any detectable kDNA. It is obvious that such strains that do not express any mitochondrially encoded activity have no need for RNA editing and for guide RNAs. We now know that certain Phytomonas species are also able to suppress mitochondrial activity completely. Thus this is a property that is probably shared with many more, if not all, trypanosomatidae. If true, it may be that certain Leishmania species, adapted to carbohydrate-rich media, are also capable of suppressing, either partially or completely, mitochondrial activity. I think that the partial loss of guide RNAs in L. tarentolae kDNA is suggestive in this respect. If under drug pressure mitochondrial activity is completely suppressed and mutations accumulate in the kDNA, this may lead to a rapid and drastic alteration of the maxicircle population through selection, refered to as transkinetoplastidy. When drug pressure is releaved a minority, with unchanged genotype overgrows and changes the overall population back to normal. I would like to hear any comments ------ Fred R. Opperdoes Tel: xx32-2-7647539 Research Unit for Tropical Diseases Fax: xx32-2-7626853 International Institute of Cellular E-mail: Opperdoes@trop.ucl.ac.be and Molecular Pathology Avenue Hippocrate 74-75 B-1200 Brussels, Belgium From BIOSCI-REQUEST Thu Feb 10 04:48:25 1994 Received: from localhost by net.bio.net (8.6.5/IG-2.0) id EAA01817; Thu, 10 Feb 1994 04:48:25 GMT Received: from vms2.macc.wisc.edu by net.bio.net (8.6.5/IG-2.0) with SMTP id UAA01808; Wed, 9 Feb 1994 20:48:21 -0800 Received: from VMSmail by vms2.macc.wisc.edu; Wed, 09 Feb 94 19:13 CDT Message-Id: <24020919133848@vms2.macc.wisc.edu> Date: Wed, 09 Feb 94 19:13 CDT From: Rock Pulak Subject: RNA Processing Meeting To: RNA X-VMS-To: IN%"rna@net.bio.net",RAPULAK RNA Processing Meeting of The RNA Society University of Wisconsin, Madison May 24 to 29, 1994 The Symposium: The 14th annual RNA PROCESSING MEETING will be held in 1994 at the University of Wisconsin, Madison. It will be one day longer than previously, beginning Tuesday evening, May 24, and concluding with lunch Sunday, May 29. The venue has been selected to permit a larger attendance than usual. We plan to have 8 or 9 sessions of oral presentations and 3 or 4 poster sessions. We may also have informal workshops, if the need arises. Session chairpersons will include: Sue Berget, Gideon Dreyfuss, Witold Filipowicz, Michael Green, Alain Jacquier, Angela Kramer, and Elsebet Lund. DEADLINE FOR FORMS, FEES AND ABSTRACTS: February 22, 1994 For more information or forms, contact: Wisconsin Union Conference Services Telephone:608-262-2755 Fax: 608-262-5487 Topics to be covered in the oral sessions include: Evolution of RNA Modification/editing RNA Structure mRNA stability 3(prime) end processing Ribozymes Splicing mechanisms Alternative splicing RNA Transport rRNA processing RNP biogenesis tRNA processing RNP structure and function RNA-protein interactions Roles of RNA in translation Cell biology and ultrastructural aspects of RNA Organized by: Jean Beggs, University of Edinburgh, Edinburgh. U.K. Marlene Belfort, New York State Dept. of Health, Albany, U.S. Joan Steitz, Yale University Medical School, New Haven, U.S. Marvin Wickens, University of Wisconsin, Madison, U.S. --------------------------------------------------------------- Rock Pulak rapulak@macc.wisc.edu UW-Madison From BIOSCI-REQUEST Fri Feb 11 03:28:24 1994 Received: from localhost by net.bio.net (8.6.5/IG-2.0) id DAA12306; Fri, 11 Feb 1994 03:28:24 GMT Received: from cs.utah.edu by net.bio.net (8.6.5/IG-2.0) with SMTP id TAA12302; Thu, 10 Feb 1994 19:28:21 -0800 Received: from adenosine.pharm.utah.edu by cs.utah.edu (5.65/utah-2.21-cs) id AA18542; Thu, 10 Feb 94 19:47:08 -0700 Date: Thu, 10 Feb 94 19:50:21 -0700 From: davis@adenosine.pharm.utah.edu (Darrell R. Davis) Posted-Date: Thu, 10 Feb 94 19:50:21 -0700 Message-Id: <9402110250.AA12448@adenosine.pharm.utah.edu> Received: by adenosine.pharm.utah.edu (911016.SGI/5.51) id AA12448; Thu, 10 Feb 94 19:50:21 -0700 To: RNA In-Reply-To: Rock Pulak's message of Wed, 09 Feb 94 19:13 CDT <24020919133848@vms2.macc.wisc.edu> Subject: Cuvette Adapters Does anyone know where to buy cuvette adapters for using 1mm path cuvettes in holders designed for 1 cm cuvettes. In Methods in Enz (180) "RNA Processing", Tinoco mentions that when doing Tm's with small cuvettes, aluminum adapters are used to insure good heat conduction. I can verify that putting a short pathlength cuvette into a 1 cm holder can produce less than optimal results. -------------------------------------------------------------- Darrell R. Davis Medicinal Chemistry University of Utah -------------------------------------------------------------- From BIOSCI-REQUEST Mon Feb 14 21:41:48 1994 Received: from localhost by net.bio.net (8.6.5/IG-2.0) id VAA25171; Mon, 14 Feb 1994 21:41:48 GMT Received: from herman.cs.uoguelph.ca by net.bio.net (8.6.5/IG-2.0) with SMTP id NAA25161; Mon, 14 Feb 1994 13:41:41 -0800 Received: by herman.cs.uoguelph.ca (1.37.109.8/16.2) id AA21377; Mon, 14 Feb 1994 16:42:18 -0500 Date: Mon, 14 Feb 1994 16:41:29 -0400 (EDT) From: Liam E Good Subject: Returned mail: User unknown (fwd) To: rna Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, We are looking at RNA processing and would like to block our molecule at the 3' end with some sort of addition or modification that would prevent exonuclease digestion. Does anyone know if this can be done and how we might go about it. Liam lgood@uoguelph.ca From BIOSCI-REQUEST Sat Feb 19 14:53:41 1994 Received: from localhost by net.bio.net (8.6.5/IG-2.0) id OAA29902; Sat, 19 Feb 1994 14:53:41 GMT Received: from proton.chem.yale.edu by net.bio.net (8.6.5/IG-2.0) with SMTP id GAA29897; Sat, 19 Feb 1994 06:53:38 -0800 Received: by proton.chem.yale.edu (931110.SGI.ANONFTP/931108.SGI.AUTO.ANONFTP) for rna@net.bio.net id AA22443; Sat, 19 Feb 94 09:54:15 -0500 From: dcs@proton.chem.yale.edu (Dave Schweisguth) Message-Id: <9402191454.AA22443@proton.chem.yale.edu> Subject: Hi all To: rna (RNA mailing list) Date: Sat, 19 Feb 1994 09:54:15 -0500 (EST) Organization: Dept. of Chemistry, Yale University X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 882 Hi all, I've just signed up and thought I'd introduce myself. I'm in Peter Moore's group at Yale. I (and most of the lab) do small RNA structures by NMR; presently I'm concerned with tRNAfMet and tRNAmMet anticodon arm fragments. I like to think I have a computational bent but am presently not exercising it, being in the midst of standard RNA NMR structure solution. I see from the archives that traffic has been light. I've just learned about this list (having been sucked into the BIOSCI hegemony by way of the nascent NMR structure list); I'll pass the address around and perhaps we'll have a few more Yale "Hi all"s shortly. Cheers, -- | Dave Schweisguth Internet: dcs@neutron.chem.yale.edu MIME spoken here | | Yale Depts. of MB&B & Chemistry Phone: 203-432-5208 Fax: 203-432-6144 | | For complying with the NJ Right To Know Act: Contents partially unknown. | From BIOSCI-REQUEST Mon Feb 21 19:48:43 1994 Received: from localhost by net.bio.net (8.6.5/IG-2.0) id TAA07601; Mon, 21 Feb 1994 19:48:43 GMT Received: from piglet.INS.CWRU.Edu by net.bio.net (8.6.5/IG-2.0) with SMTP id LAA07594; Mon, 21 Feb 1994 11:48:39 -0800 Received: by piglet.INS.CWRU.Edu (5.65b+ida+/CWRU-1.5.6-bsdi) id AA08469; Mon, 21 Feb 94 14:49:04 -0500 (from bl275 for rna@net.bio.net) Message-Id: <9402211949.AA08469@piglet.INS.CWRU.Edu> Date: Mon, 21 Feb 94 14:49:04 -0500 From: bl275@cleveland.freenet.edu (Dan Diaz) To: rna Subject: Runoff transcripts Reply-To: bl275@cleveland.freenet.edu (Dan Diaz) I would like to make a few hundred micrograms of tritiated RNA via runoff transcription. Any email pointing me to relevant references for protocols would be appreciated. Thanks