From BIOSCI-REQUEST Wed Apr 13 15:35:03 1994 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.8.1/8.6.6) id PAA18161 for rna-list; Wed, 13 Apr 1994 15:35:03 -0700 Received: from cray.com (root@timbuk.cray.com [128.162.19.7]) by net.bio.net (8.6.8.1/8.6.6) with SMTP id PAA18155 for ; Wed, 13 Apr 1994 15:35:00 -0700 Received: from calamity (calamity.cray.com) by cray.com (Bob mailer 1.2) id AA29678; Wed, 13 Apr 94 17:35:28 CDT Received: by calamity id AA09191; 4.1/CRI-5.4; Wed, 13 Apr 94 17:35:26 CDT From: mwd@carina.cray.com (Mark Dalton) Message-Id: <9404132235.AA09191@calamity> Subject: RNA Pseudo-knots To: rna@net.bio.net Date: Wed, 13 Apr 1994 17:35:21 -0500 (CDT) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 639 I am wondering if there is any software available for figuring out Pseudo-knots. There is a researcher at the Univ. of MN, I am trying to help out. I don't seem to have much information on this. Any information would be appreciated, I will post a summary to the group. Thanks! Mark -- 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 Thu Apr 14 10:46:05 1994 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.8.1/8.6.6) id KAA10312 for rna-list; Thu, 14 Apr 1994 10:46:05 -0700 Received: from antares.mcs.anl.gov (antares9.mcs.anl.gov [140.221.9.6]) by net.bio.net (8.6.8.1/8.6.6) with ESMTP id KAA10130; Thu, 14 Apr 1994 10:43:39 -0700 Received: from juju (juju.mcs.anl.gov [140.221.6.137]) by antares.mcs.anl.gov (8.6.4/8.6.4) with ESMTP id MAA25838; Thu, 14 Apr 1994 12:44:20 -0500 From: Natalie Maltsev Date: Thu, 14 Apr 1994 12:44:18 -0500 Message-Id: <199404141744.MAA20529@juju> To: biocan@net.bio.net, biogopher@net.bio.net, emf-bio@net.bio.net, grasses@net.bio.net, nmr-str@net.bio.net, rna@net.bio.net, staden-users@net.bio.net, urodeles@net.bio.net, yac@net.bio.net Subject: a workshop announcement ------------------------------------------------------------------- Dear reader: Please bring this notice to the attention of persons you think might wish to participate. Workshop on Integration of Biochemical Databases June 8 - June 10, 1994 Pushchino, Russia (Registration deadline May 12) We invite all interested researchers to visit this major center of biomedical research in Russia and the former Soviet Union. The workshop will give you the opportunity to informally discuss how to integrate databases relevant to molecular biology and medicine. Several leading biological database experts from outside Russia will be present, and many interesting (and probably unfamiliar) Russian database projects will be demonstrated by their representatives. The workshop will be hosted by Professor Evgeni E. Selkov and coworkers, and is arranged in part by Dr. Ross Overbeek et al. at Argonne National Laboratory, Illinois, U.S.A. We have scheduled the following events: o Overview of EMP (Enzymes and Metabolic Pathways database). EMP contains the encoding of the most important articles (approx. 10,000) describing enzymes, phylogenetically arranged. It also contains in graphical form most of the known metabolic pathways for all organisms. We consider EMP the world's leading database of its kind. All participants will receive a free academic copy of this database (see details below). o For the first time, a presentation of a broad selection of Russian / FSU databases. There will be poster sessions and demonstrations on PC computers. During this winter we have collected brief descriptions and invited representatives from the groups who created (in our judgment) the most interesting of these. In Russia there exist substantial data collections ranging from minor ones done by single experts to very large collections of for example medicinal properties of compounds, 3D structural data, sequence data, culture collections, genetic markers, tumor characteristics, regulatory sequences, and more. o Optional introductory course to general metabolism and related computational issues. This will be given prior to the workshop (June 5-7) by Professor Selkov. There will be no scheduled talks. We instead invite open discussion of topics of common interest, such as metabolism and enzymes, or phylogeny, alignments, compounds, motifs, and maps. If you wish to use or generate such integrated biological data, then please join us. Sincerely, Evgeni Selkov Ross Overbeek Natalia Maltsev Amos Bairoch Nat Goodman George Michaels Harold Morowitz Niels Larsen Anthony Bonner Terry Gaasterland Pat Gillevet Rick Stevens Alexander Zamyatnin Sponsorship ----------- The workshop is so far unsponsored, but we welcome interested sponsors. We need help with computer equipment and coverage of travel expenses for Russian participants. Practical details ----------------- Pushchino is a community of some 30,000 people located 100 km south of Moscow. The main acitivity is research. The area is generally safe. The water is not contaminated; the food is fresh and locally produced. You will be able at least to send electronic mail. The registration fee is US $750 for the workshop if you plan to attend the introductory course, $550 otherwise. The fee covers housing (single hotel rooms), meals, and transportation to and from Moscow International Airport. We accept Visa and MasterCard, or a check made out in US$ and cashable within the United States. Upon payment of the workshop fee, participants will be given a US $400 purchase credit for EMP or an actual CD-ROM copy, if there is enough time before the meeting. EMP will soon be generally available for $400 ($4000 for commercial licenses). Registration after the deadline is possible if you pay extra $100 and if there is enough time. Participants need at least tourist visas, which are issued by the nearest Russian consulate, and for which no invitation is needed. To cover your expenses however, your institution may require a business visa, which does require an invitation from the hosts; in that case, please register as soon as possible. Please fill out the fields below; leave blank the fields that do not apply. Your citizenship, date of birth and passport number is needed only if you apply for a business visa. Please send this information, so that we receive it before May 12, by regular mail, fax, or electronic mail, to: Center for Professional Development Business Office, Mail Stop 3G3 George Mason University Fairfax, VA 22030-4444 Fax: 703-993-2112 Electronic mail: overbeek@juju.mcs.anl.gov Questions can be directed to either Ross Overbeek (overbeek@mcs.anl.gov) or Mary Baroody at George Mason University (703-993-2090). ------------------------------------------------------------------- First name: Last name: Research area: Date of birth: Passport number: Citizenship: Tourist visa: Business visa: Institution: Company: Street address: Postal code: City: State: Country: Telephone: Electronic mail: I pay by check: Visa Card #: MasterCard #: Expiration date: Comments: Comments: Comments: Questions: Questions: Questions: ------------------------------------------------------------------- From BIOSCI-REQUEST Sat Apr 16 07:31:03 1994 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.8.1/8.6.6) id HAA08029 for rna-list; Sat, 16 Apr 1994 07:31:03 -0700 Received: from HAL.HAHNEMANN.EDU (hal.hahnemann.edu [192.54.238.37]) by net.bio.net (8.6.8.1/8.6.6) with SMTP id HAA08026 for ; Sat, 16 Apr 1994 07:31:01 -0700 From: springerj@hal.hahnemann.edu Received: by hal.hahnemann.edu (MX V4.0 VAX) id 113; Sat, 16 Apr 1994 10:32:40 EST Date: Sat, 16 Apr 1994 10:32:39 EST To: rna@net.bio.net Message-ID: <0097D09C.640C1CA0.113@hal.hahnemann.edu> Subject: bcl-2 cDNA Hello netters, I am interested in finding the cDNA to bcl-2 for work in amyotrophic lateral sclerosis. If anybody knows thw whereabouts of this cDNA I would appreciate an email message at springerj@hal.hahnemann.edu. Thanks for your help1 From BIOSCI-REQUEST Sun Apr 17 05:16:49 1994 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.8.1/8.6.6) id FAA28428 for rna-list; Sun, 17 Apr 1994 05:16:49 -0700 Received: from Toriseja.EENet.ee (root@Toriseja.EENet.ee [192.121.252.18]) by net.bio.net (8.6.8.1/8.6.6) with SMTP id FAA28415 for ; Sun, 17 Apr 1994 05:16:41 -0700 Subject: RNA tag To: rna@net.bio.net Date: Sun, 17 Apr 1994 15:13:47 +0300 (EETds) From: Jaanus Remme X-Mailer: ELM [version 2.4 PL11] Content-Type: text Content-Length: 1045 Message-ID: <9404171513.aa03935@kask.ebc.ee> Dear RNA people, We are working on the E. coli 23S ribosomal RNA. We have constructed a series of point mutations in the gene encoding 23S RNA. To analyze structural and functional affects of the mutations it would be extremely important to sepatate plasmid encoded mutant ribosomes from chromosomal wild-type particles. We have tried several methods to isolate plasmid borne ribosomes, so far without success. One possible approach would be to put a tag into 23S RNA. We have tried (A)15 insertion at several positions including 3'end of the 23S RNA. We have been hoping to fish out mutant ribosomes on the oligo(dT) cellulose. 23S RNA containing (A)15 insertions was assembled into 50S particles which failed to bind to the oligo(dT) cellulose. We don't know why. We would be very thankful for a good suggestion which kind of an RNA tag would allow to separate mutant 23S RNA. Jaanus Remme E-mail: jremme@kask.ebc.ee Dept. Mol. Biol. Tartu University 2 Jakobi St. EE2400, Tartu, ESTONIA > From BIOSCI-REQUEST Sun Apr 17 12:03:09 1994 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.8.1/8.6.6) id MAA14264 for rna-list; Sun, 17 Apr 1994 12:03:09 -0700 Received: from sun2.mhs-relay.ac.uk (sun2.mhs-relay.ac.uk [128.86.8.35]) by net.bio.net (8.6.8.1/8.6.6) with SMTP id MAA14261 for ; Sun, 17 Apr 1994 12:03:07 -0700 X400-Received: by mta sun2.mhs-relay.ac.uk in /PRMD=uk.ac/ADMD= /C=gb/; Relayed; Sun, 17 Apr 1994 20:03:23 +0100 X400-Received: by mta arcs.afrc.ac.uk in /PRMD=UK.AC/ADMD= /C=GB/; Relayed; Sun, 17 Apr 1994 20:04:31 +0100 X400-Received: by /PRMD=UK.AC/ADMD= /C=GB/; converted (ia5 text (2)); Relayed; Sun, 17 Apr 1994 21:02:01 +0100 Date: Sun, 17 Apr 1994 21:02:01 +0100 X400-Originator: julian.hiscox@afrc.ac.uk X400-Recipients: rna@net.bio.net X400-MTS-Identifier: [/PRMD=UK.AC/ADMD= /C=GB/;5952012017041994/A10103/IRAD] X400-Content-Type: P2-1988 (22) Content-Identifier: 11848D013200 From: HISCOX Message-ID: <5952012017041994/A10103/IRAD/11848D013200*@MHS> To: rna@net.bio.net (Non Receipt Notification Requested) (IPM Return Requested) (Reply Requested) Subject: RNA extraction Sensitivity: Company-Confidential Jaanus, One problem with ribosomal RNA is secondary structure, have you tried heating the RNA to 65C for 5min then snap freezing on ice before extraction. This might expose the dT tract. Alternatively, you could also add DMSO before heating (i.e. as in the case of glyoxal gel electrophoresis), although I do not know what affects the DMSO might have the column. As an alternative you could try extraction with oligo-dT magnetic beads, these are marketed by Dynal and Promega (probably others also). The advantage of the magnetic beads is that there is no matrix to inhibit the passage of large RNA. You might find during column extraction a certain size RNA will not be extracted so efficiently. As a complete alternative, you could use streptavidin magnetic beads and construct a biotinylated oligonucleotide specific to your particular RNA. i.e. sequence specific extraction. This extraction would work in a manner similar to oligo-dT beads. Good luck, Julian. E-mail: HISCOX@AFRC.AC.UK From BIOSCI-REQUEST Tue Apr 19 13:54:24 1994 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.8.1/8.6.6) id NAA22849 for rna-list; Tue, 19 Apr 1994 13:54:24 -0700 Received: from herman.cs.uoguelph.ca (herman.cs.uoguelph.ca [131.104.92.15]) by net.bio.net (8.6.8.1/8.6.6) with SMTP id NAA22846 for ; Tue, 19 Apr 1994 13:54:22 -0700 Received: by herman.cs.uoguelph.ca (1.37.109.8/16.2) id AA24388; Tue, 19 Apr 1994 16:56:01 -0400 Date: Tue, 19 Apr 1994 16:50:04 -0400 (EDT) From: Liam E Good Subject: Re: RNA tag To: Jaanus Remme Cc: rna@net.bio.net In-Reply-To: <9404171513.aa03935@kask.ebc.ee> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Sun, 17 Apr 1994, Jaanus Remme wrote: > Dear RNA people, > > We are working on the E. coli 23S ribosomal RNA. We have constructed a > series of point mutations in the gene encoding 23S RNA. To analyze > structural and functional affects of the mutations it would be extremely > important to sepatate plasmid encoded mutant ribosomes from chromosomal > wild-type particles. We have tried several methods to isolate plasmid borne > ribosomes, so far without success. One possible approach would be to put > a tag into 23S RNA. We have tried (A)15 insertion at several positions > including 3'end of the 23S RNA. We have been hoping to fish out mutant > ribosomes on the oligo(dT) cellulose. 23S RNA containing (A)15 insertions > was assembled into 50S particles which failed to bind to the oligo(dT) > cellulose. We don't know why. > We would be very thankful for a good suggestion which kind of an RNA > tag would allow to separate mutant 23S RNA. > > > Jaanus Remme E-mail: jremme@kask.ebc.ee > Dept. Mol. Biol. > Tartu University > 2 Jakobi St. > EE2400, Tartu, > ESTONIA Hi Jannus, I don't know how you can separate the mutant ribosomes, but you might still be able to analyze the structure and function of the mutant RNAs. We have started doing this in S. pombe. Our first efforts can be seen in recent issues of NAR (Abou elella et al. 1994) and JMB (Melenkhovets et al. in press). The idea is to do the analyses by using primers or nucleic acid probes that are specific for the mutant transcripts. You can design experiments to test for correct processing, stucture and probably participation in translation etc. I hope this gives you some ideas. Liam Good > > From BIOSCI-REQUEST Fri Apr 22 15:11:02 1994 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.8.1/8.6.6) id PAA13030 for rna-list; Fri, 22 Apr 1994 15:11:02 -0700 Received: from Veblen.ACNS.Carleton.edu (Veblen.ACNS.Carleton.edu [137.22.1.4]) by net.bio.net (8.6.8.1/8.6.6) with ESMTP id PAA13026 for ; Fri, 22 Apr 1994 15:10:59 -0700 From: PERLMANZ@carleton.edu Received: from carleton.edu by carleton.edu (PMDF V4.2-14 #5762) id <01HBHEK5CIOG8WXVAV@carleton.edu>; Fri, 22 Apr 1994 17:11:01 CDT Date: Fri, 22 Apr 1994 17:11:01 -0500 (CDT) Subject: is any structural characterization of snRNP proteins out there? To: rna@net.bio.net Message-id: <01HBHEK5CLIA8WXVAV@carleton.edu> X-Envelope-to: rna@net.bio.net X-VMS-To: IN::"rna@net.bio.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT I am looking for information about the actual structural nature of snRNP protein interactions for my undergraduate senir thesis in biochemistry. To date, I have been able to find basically nothing published. If you are aware of some line of research that I might be likely to have missed on the enzymology of snRNP proteins (perhaps specifically for the human U1 snRNP), I would very much appreciate any tips you might send me. Thank you. Zachary Perlman Carleton College Northfield, MN 55057 (507)663-1352 From BIOSCI-REQUEST Sat Apr 23 06:19:59 1994 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.8.1/8.6.6) id GAA11247 for rna-list; Sat, 23 Apr 1994 06:19:59 -0700 Received: from kasia.path.ox.ac.uk (kasia.path.ox.ac.uk [163.1.19.1]) by net.bio.net (8.6.8.1/8.6.6) with SMTP id GAA11244 for ; Sat, 23 Apr 1994 06:19:56 -0700 From: birney@molbiol.ox.ac.uk Received: by molbiol.ox.ac.uk (MX V4.0 VAX) id 6; Sat, 23 Apr 1994 14:20:32 0000 Date: Sat, 23 Apr 1994 14:20:31 0000 To: rna@net.bio.net Message-ID: <0097D63C.61EA83D1.6@molbiol.ox.ac.uk> Subject: RE: is any structural characterization of snRNP proteins out there? >I am looking for information about the actual structural nature of snRNP >protein interactions for my undergraduate senir thesis in biochemistry. To >date, I have been able to find basically nothing published. If you are aware >of some line of research that I might be likely to have missed on the >enzymology of snRNP proteins (perhaps specifically for the human U1 snRNP), I >would very much appreciate any tips you might send me. >Thank you. > >Zachary Perlman >Carleton College >Northfield, MN 55057 >(507)663-1352 I'm not sure if you are looking for the structure of isolated snRNP polypeptides or of the entire snRNP particles. For the latter an 86 odd amino acid segement of U1A snRNP polypeptide has been crystalised and soved by Nagai and co-workers (see nature 348 515-20) this contains one copy of the RRM or RBD binding domain which is a very widespread domain in snRNP proteins and other RNA binding proteins (see Nucleic Acids Research 21: 5803-16 for review on this domain). An incredible amount of biochemical work has been done on the U1A protein (far more than any other snRNP polypeptide I think)...look at references in the NAR paper above. Currently Iain Mattaj's group is working on various aspects of the protein, and is publishing profusely. As for snRNP particles themselves less work has been done...the man to read is R. Luhrmann. One of his latest papers is about the U2 snRNP where I think he does electron micrographs of U2 and figures some things out. This is much harder work because a) nobody's quite sure what a U2 particle is...how many polypeptides etc b) it changes under salt conditions etc. Anyway, check out Mol Cell Biol 13 : 307-319 and look at the reviews in that paper...that should be the best starting point. Two other points should be worth looking at: The distribution of snRNP particles in the nucleus, as visualised by light microscopy+floursence (pretty pictures + quite alot of interesting information) Look for example at David Spector's paper J Cell Biol 124 249-60 and also the EM work on various hnrnp proteins/structures etc...I would start at Dreyfuss' review in the Annu. Rev of Biochemistry (sorry, can't find the reference) Hope this helps have fun ewan ewan birney birney@molbiol.ox.ac.uk From BIOSCI-REQUEST Sat Apr 30 16:18:34 1994 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.8.1/8.6.6) id QAA26481 for rna-list; Sat, 30 Apr 1994 16:18:34 -0700 Received: from selway.umt.edu (selway.umt.edu [150.131.14.2]) by net.bio.net (8.6.8.1/8.6.6) with SMTP id QAA26478 for ; Sat, 30 Apr 1994 16:18:33 -0700 Received: by selway.umt.edu (5.65/DEC-Ultrix/4.3) id AA00354; Sat, 30 Apr 1994 17:19:13 -0600 Message-Id: <9404302319.AA00354@selway.umt.edu> Subject: abortive transcription To: rna@net.bio.net Date: Sat, 30 Apr 1994 17:19:12 -0600 (MDT) 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: 777 I am having a problem with aboritve transcription. The buffer I am using contains 40mM tris pH 8.1, 42C, 5mM DTT, 1mM Spermidine, 22 mM MgCl2, 50 ug/ml BSA, 80mg/ml PEG 8000, and 0.01% tritonX-100. The template is a single stranded 70 base DNA with only the region of the promoter ds. This is at a conc. of 4 uM. 4 mM in each NTP and 15,000 U of T7RNAP are used in 500 ul. Incubation is 4 hrs. at 42C. With other templates this works great, but with this particular one I get virtually no full length product. It has one predicted region of secondary structure that involves the first three bases of the transcript with bases 47-49 of the transcript. Does anybody have a good method to get around this problem? Thank you! Douglas Bucklin bucklin@selway.umt.edu