From owner-chromosomes@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!newsfeed.internetmci.com!solaris.cc.vt.edu!portal.gmu.edu!hearst.acc.Virginia.EDU!uunet!in1.uu.net!mack.rt66.com!ingen From: ingen@rt66.com Newsgroups: bionet.molbio.methds-reagnts,bionet.cellbiol,bionet.genome.chromosomes Subject: Re: FISH manuals etc. Date: Wed, 01 Nov 95 22:45:41 GMT Organization: Engineering International Inc., Public Internet Access Lines: 25 Message-ID: <478t37$rh3@mack.rt66.com> References: <46odrr$rg6@winx03.informatik.uni-wuerzburg.de> <4714c3$1tn@ixnews2.ix.netcom.com> <474hfi$rkj@netnews.ntu.edu.tw> NNTP-Posting-Host: pma25.rt66.com X-Newsreader: News Xpress Version 1.0 Beta #4 Xref: biosci bionet.molbio.methds-reagnts:35777 bionet.cellbiol:3313 bionet.genome.chromosomes:903 In article <474hfi$rkj@netnews.ntu.edu.tw>, b1205116@cc.ntu.edu.tw (Peng, Hsien-wei) wrote: >>>- Are there lab-manuals with FISH protocols available? >>> - Do you know good books about this technique? >>>- Who organizes workshops and courses where he could learn this >>>technique? >>> - Have any reviews dealing with this topic been published recently? >>>- Which are the landmark papers in this field? >>> - Can you recommend suppliers of reagents/equipment? >>>- etc................. > >>Have him contact the company Oncor. >>They sell probes, kits, etc for FISH, and can give you all the >>protocols. Don't happen to have their phone number handy, but I'm sure >>you could look it up. >>HK > >========================================================================= Please mark a web page at "http://www.rt66.com/ingen". Rapid and simple FISH kits will be released in coming December or January. In Kim, Ph.D. Ingen Laboratories, Inc. http://www.rt66.com/ingen From owner-chromosomes@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!lyra.csx.cam.ac.uk!nntp-serv.cam.ac.uk!gos From: gos@rathbin.sanger.ac.uk (Gos Micklem) Newsgroups: bionet.genome.chromosomes Subject: Re: Help, What is longest contiguous sequence? Date: 02 Nov 1995 19:53:00 GMT Organization: University of Cambridge, England Lines: 11 Message-ID: References: <473sgh$ipo@itssrv1.ucsf.edu> NNTP-Posting-Host: rathbin.sanger.ac.uk In-reply-to: nelson@bcm.tmc.edu's message of Tue, 31 Oct 1995 10:18:38 -0600 > There is some sequence from the Sanger Centre of chromosome 4p that may be > long as well, but it is deposited as individual cosmids. 19 sequences from the HD region, ( total length 544,983 bp ), have been submitted so far to the public databases by the Sanger Centre. The largest single contig which can be made by overlapping these sequences is currently 88,430bp ( Accession numbers Z49250, Z49918, Z49235 ) From owner-chromosomes@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!noc.near.net!das-news2.harvard.edu!casaba.srv.cs.cmu.edu!GS152.SP.CS.CMU.EDU!skng From: skng+@GS152.SP.CS.CMU.EDU (See-Kiong Ng) Newsgroups: bionet.genome.chromosomes Subject: Q: Do crossovers occur between *any* two chromatids? Date: 2 Nov 1995 15:05:22 GMT Organization: Carnegie Mellon University Lines: 26 Message-ID: <47amni$6mj@casaba.srv.cs.cmu.edu> NNTP-Posting-Host: gs152.sp.cs.cmu.edu Hi, I have been looking at pictures in Biology textbooks depicting crossing-over during meiosis. Invariably, the recombination event(s) is shown to occur *only* between a particular pair of the four chromatids, leaving the other pair of chromatids in the tetrad unchanged. Is this just an artifact of the limitation of pictorial illustration in Biology textbooks, or is it really the case that all crossing-over events during meiosis occur only between a particular pair of chromatids, so that an offspring has about 1/4 chance of inheriting original chromosome pairs from the parents (or 3/4 chance of inheriting at least one original/unrecombined chromosome from one of the parents)? Thanks! ----------------------------------------------------- See-Kiong Ng School of Computer Science Carnegie Mellon University Pittsburgh, PA 15213 E-mail: skng@cs.cmu.edu WWW: http://www.cs.cmu.edu/~skng/ ------------------------------------------------------ From owner-chromosomes@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!STJOHNS.EDU!YBRTBIO From: YBRTBIO@STJOHNS.EDU (rebekah rasooly) Newsgroups: bionet.genome.chromosomes Subject: Re: Q: Do crossovers occur between *any* two chromatids? Date: 3 Nov 1995 07:05:57 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 4 Sender: daemon@net.bio.net Distribution: world Message-ID: <03NOV95.10873304.0056.MUSIC@SJUMUSIC> NNTP-Posting-Host: net.bio.net yes, only two crossover in a single exchange tetrad. hence weinstein (1936, Genetics 21:155) wrote a paper relating the frequency of observed crossovers to the frequency of exchange. rebekah rasooly, st. john's university From owner-chromosomes@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!news.uoregon.edu!vixen.cso.uiuc.edu!newsrelay.iastate.edu!hobbes.physics.uiowa.edu!news.uiowa.edu!uunet!in2.uu.net!EU.net!sun4nl!news.nic.surfnet.nl!highway.LeidenUniv.nl!jasper From: jasper%ruly46.leidenuniv.nl (Jasper Saris) Newsgroups: bionet.genome.chromosomes Subject: Re: Meaning of "AFM" in STS names Date: 3 Nov 1995 10:18:27 GMT Organization: Leiden University, The Netherlands Lines: 24 Distribution: inet Message-ID: <47cq9j$f9i@highway.LeidenUniv.nl> References: <4700dv$9db@metro.ucc.su.OZ.AU> NNTP-Posting-Host: ruly46.medfac.leidenuniv.nl X-Newsreader: TIN [version 1.2 PL2] :Alberto Catalano :(alcat@cyberspace.org) wrote: : Dear bionetters, : Does nayone know the meaning and/or origin of the AFM nomenclature for STS : sequences? : Thanks Dear Alberto, The AFM nomenclature designates the polymorphic CAn-microsatellite repeat containing STS's generated by Genethon (France). The project was initiated at CEPH and supported by the "Association Francaise contre les Myopathies", hence AFM. ref. f.i. Nature Genetics vol. 7 special issue june '94 Greetings Jasper Saris, dept Human Genetics Leiden University Netherlands From owner-chromosomes@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: rifat_h Newsgroups: bionet.genome.chromosomes Subject: Multi-array capillary electrophoresis sequencers Date: 3 Nov 1995 15:55:03 -0000 Lines: 18 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <47de0n$d1b@mserv1.dl.ac.uk> X-Mts: smtp X-Authentication-Warning: jupiter.icr.ac.uk: Host localhost didn't use HELO protocol Original-To: biochrom@dl.ac.uk Hi, Does anyone here have any information regarding multi-array capillary electrophoresis sequencers. I have been hearing rumours that such machines are feasible and are currently being tested on either 8 or 96 array formats using confocal microscope. ABI have released the 310 but it only has a single capillary electrophoresis and I have been told that such machines are not feasible to make. The advantage of making them though is huge since you can get 96 sequences in 3 hours. So does anyone have any info on this and any views on why it is not feasible to make such machines commercially available. Thanks. Rifat. rifat_h@icr.ac.uk From owner-chromosomes@net.bio.net Fri Nov 03 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!news.math.psu.edu!hudson.lm.com!news.ysu.edu!ppp05.alumni.ysu.edu!user From: bscanlo@alumni.ysu.edu (Blake Scanlon) Newsgroups: bionet.genome.chromosomes Subject: Chromosome Count??? Date: Fri, 03 Nov 1995 22:19:10 -0400 Organization: Home Office Lines: 4 Message-ID: NNTP-Posting-Host: ppp05.alumni.ysu.edu Can someone please mail me the chromosome count of the Iguana, Jaguar, or the Koala? Thanks in advance... BS From owner-chromosomes@net.bio.net Fri Nov 03 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!btnet!dispatch.news.demon.net!demon!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!news From: Ricky Critcher Newsgroups: bionet.genome.chromosomes Subject: DNA extraction Date: 4 Nov 1995 12:58:27 GMT Organization: University of Cambridge Lines: 7 Message-ID: <47fo1j$1h1@lyra.csx.cam.ac.uk> NNTP-Posting-Host: png-mac9.gen.cam.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) X-URL: news:bionet.genome.chromosomes Does anybody know of a method to extract DNA from cells treated for metaphase spreads by the standard method and stored in fix (3:1 methanol to acetic acid). Cheers From owner-chromosomes@net.bio.net Fri Nov 03 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!btnet!dispatch.news.demon.net!demon!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!news From: Ricky Critcher Newsgroups: bionet.genome.chromosomes Subject: DNA extraction Date: 4 Nov 1995 12:58:08 GMT Organization: University of Cambridge Lines: 7 Message-ID: <47fo10$1ae@lyra.csx.cam.ac.uk> NNTP-Posting-Host: png-mac9.gen.cam.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) X-URL: news:bionet.genome.chromosomes Does anybody know of a method to extract DNA from cells treated for metaphase spreads by the standard method and stored in fix (3:1 methanol to acetic acid). Cheers From owner-chromosomes@net.bio.net Sun Nov 05 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!li.net!sahslib From: sahslib@newshost.li.net (St.Anthony HS Library) Newsgroups: bionet.genome.chromosomes Subject: Requestion info on BRCA gene- Breast cancer gene Date: 5 Nov 1995 12:45:00 GMT Organization: LI Net (Long Island Network) Lines: 10 Message-ID: <47ibkc$6i6@linet02.li.net> NNTP-Posting-Host: linet04.li.net X-Newsreader: TIN [version 1.2 PL2] I am a 16-year old junior at Sachem School North, involved in a genetics laboratory internship. My fellow interns and I are interested in studying the BRCA gene. If anyone can tell me either the Base Sequence of the entire Breast Cancer (BRCA) gene, or can at least tell me HOW MANY BASE PAIRS THERE ARE, please E-Mail this account as soon as possible. I thank all of you for your assistance. Jonathan Kui From owner-chromosomes@net.bio.net Sun Nov 05 22:00:00 1995 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!lll-winken.llnl.gov!usenet From: Chris Barry Newsgroups: bionet.general,bionet.cellbiol,bionet.genome.chromosomes Subject: Re: *Help* Need info on DNA-intercalating cancer drugs (i.e. anthracyclines) Date: 6 Nov 1995 04:12:21 GMT Organization: Lawrence Livermore National Laboratory Lines: 7 Message-ID: <47k1v5$47c@lll-winken.llnl.gov> References: NNTP-Posting-Host: mackiller.llnl.gov Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; Linux 1.1.72 i486) X-URL: news:mlutz-2310952138400001@jones30.resnet.haverford.edu Xref: biosci bionet.general:18299 bionet.cellbiol:3350 bionet.genome.chromosomes:913 This may not be of any help but: http://www.ch.ic.ac.uk/ectoc/ectoc_pob.html may have some good starting points. Their main homepage also has a search engine. From owner-chromosomes@net.bio.net Sun Nov 05 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!uwm.edu!psuvax1!news.eecs.nwu.edu!newsfeed.acns.nwu.edu!news.acns.nwu.edu!lomasneylab.feinberg.nwu.edu!user From: kallisti@merle.acns.nwu.edu (Patrick Grealish ) Newsgroups: bionet.genome.chromosomes Subject: determining chromosomal locations of certain genes Date: Mon, 06 Nov 1995 03:15:14 -0500 Organization: eris consultants, inc. Lines: 10 Message-ID: NNTP-Posting-Host: lomasneylab.feinberg.nwu.edu hello, In our lab we are interested in creating a listing of the chromosomal locations of all the different human isozymes of phospholiapse C. some paper or Genbank sequence listing come with chromosome number (most do not). Is/are there any database(s) of chromosomes that one can search (preferably over the Internet) that will give us the chromosome location of all there genes? TIA -- hail eris all hail discordia kallisti From owner-chromosomes@net.bio.net Mon Nov 06 22:00:00 1995 Path: biosci!ns1.faseb.org!lamarck.sura.net!newsfeed.internetmci.com!howland.reston.ans.net!ix.netcom.com!netnews From: hk-miami@ix.netcom.com (HK ) Newsgroups: bionet.genome.chromosomes Subject: Re: DNA extraction Date: 7 Nov 1995 02:44:49 GMT Organization: Netcom Lines: 15 Message-ID: <47mh71$oph@ixnews2.ix.netcom.com> References: <47fo1j$1h1@lyra.csx.cam.ac.uk> NNTP-Posting-Host: ix-mia3-05.ix.netcom.com X-NETCOM-Date: Mon Nov 06 6:44:49 PM PST 1995 In <47fo1j$1h1@lyra.csx.cam.ac.uk> Ricky Critcher writes: > >Does anybody know of a method to extract DNA from cells treated for >metaphase spreads by the standard method and stored in fix (3:1 methanol >to acetic acid). > >Cheers > > Ouch!!! The DNA would be destroyed by the acid in the fixative. You need to harvest your chromosomes and store them in ethanol. Never fix!!! HK From owner-chromosomes@net.bio.net Mon Nov 06 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!newstf01.news.aol.com!newsbf02.news.aol.com!not-for-mail From: cygnusjd@aol.com (CygnusJD) Newsgroups: bionet.genome.chromosomes Subject: XYY Chromosome Anomily Date: 7 Nov 1995 11:59:03 -0500 Organization: America Online, Inc. (1-800-827-6364) Lines: 12 Sender: root@newsbf02.news.aol.com Message-ID: <47o38n$m5a@newsbf02.news.aol.com> Reply-To: cygnusjd@aol.com (CygnusJD) NNTP-Posting-Host: newsbf02.mail.aol.com I am looking for any information on 47, XYY chromosome anomilies and the behavioral tendancies of these individuals. It is believed that 1 out of 1000 men is born with an extra Y chromosome; however, not a lot of research has been done on the subject. Please e-mail me any references or information you may have about 47, XYY chromosome anomily. Thanks, Jenn Dazey Cygnus Laser Corporation Seattle From owner-chromosomes@net.bio.net Mon Nov 06 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!lade.news.pipex.net!pipex!dish.news.pipex.net!pipex!news.IT.net!dsi.unimi.it!galileo.polito.it!usenet From: Gianfranco Durin Newsgroups: bionet.genome.chromosomes Subject: Help! risk of traslocation chromosome 3-12 Date: 7 Nov 1995 17:26:48 GMT Organization: Ien Galielo Ferraris Lines: 39 Message-ID: <47o4so$goj@galileo.polito.it> NNTP-Posting-Host: alpha.ien.it Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; OSF1 V3.0 alpha) X-URL: news:bionet.genome.chromosomes Hi all, I have a (big) problem with my chromosomes, I hope someone could help me... Sorry, I am not expert and I try to translate the terms from italian, so sometime I quote a term by (??). The result of my chromosome exam has been: ---------------------------------- 46,XY,t(3,12)(p21:p13). Presence of a balanced traslocation between chromosomes 3 and 12. ---------------------------------- I and my wife made this exam after two spontaneous abortions both at the 6th week. The examinator reported the following possibilities for the fetus: i) 'normal' chromosomes 3 and 12: no problem ii) both chromosomes 3 and 12 are translocated: no problem again iii) chromosome 3 is translocated and 12 is normal: This situation is compatible with spontaneus abortion, as no children affected by partial monosomy (??) of chromosome 3 of this entity (3p21-3pter) has been described in the literature iv) chromosome 3 is normal and 12 is translocated: A double chromosomic unbalance (partial trisomy (??) of chromosome 3 and partial monosomy of chromosome 12). This situation is compatible to a spontaneus abortion or, RARELY, with a child affected by deformities and mental desease. (He told us that he found only ONE case of this type reported in literature). Thus he concluded that the risk of children affected by anomalies is between 1 and 10%. I must add that I do not know yet if one of my parents have this translocation and that I am the first of three sound children. Has anybody have more information or suggestions/comments on it? Thank you very much in advance Gianfranco Durin -- Istituto Elettrotecnico Nazionale Galileo Ferraris C.so Duca degli Abruzzi 24 I - 10125 Torino Italy e-mail: durin@alpha.ien.it durin@omega.ien.it From owner-chromosomes@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!EU.net!Belgium.EU.net!chaos.kulnet.kuleuven.ac.be!usenet From: Przemko Tylzanowski Newsgroups: bionet.genome.chromosomes Subject: numbr of chromosomes Date: 8 Nov 1995 08:00:57 GMT Organization: K.U.Leuven Lines: 17 Message-ID: <47po3p$mn2@chaos.kulnet.kuleuven.ac.be> NNTP-Posting-Host: sgi.celgen.kuleuven.ac.be Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12 (X11; I; IRIX 5.3 IP12) X-URL: news:bionet.genome.chromosomes Hi! I posted that a while ago, but no one has answered. Since now the traffic in this group is a bit bigger, I will try my luck again. The question is: What is known about number of chromosomes in different species. I am not talking just about mouse/human/drosophila/celegant etc. I am interested if anyone has SYSTEMATICALLY studied the issue. Is there any evolutionary dependence between chromosome number and degree of organism complexity (the other measue appears to be genome lenght, altough even that is not really corect). What about the cross-species synteny? Do genes cluster in the same way in different species? If anyone has any answers, please let me know. All nonposted answers will be summarized and posted by me. ThanX Przemko From owner-chromosomes@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!usenet.eel.ufl.edu!warwick!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: rifat_h Newsgroups: bionet.genome.chromosomes Subject: Long range PCRs for sequencing Date: 7 Nov 1995 23:44:17 -0000 Lines: 17 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <47or0h$spv@mserv1.dl.ac.uk> X-Mts: smtp X-Authentication-Warning: jupiter.icr.ac.uk: Host localhost didn't use HELO protocol Original-To: biochrom@dl.ac.uk Hi, Has anyone tried long range PCR of fragments between 15kb-100bk and then sequenced them either by subcloning or by direct sequencing? If so what are the things to watch when doing long range PCRs. Also is there a danger of amplifying some other unknowns as part of your sequence. I am interested in doing a long range PCR to get a 15kb product and would be grateful if anyone has any info on the best cycling times; primer design and primer template ratios. Or any methods published and have been used successfully by the researcher. Thanks in advance. Rifat rifat_h@icr.ac.uk From owner-chromosomes@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!daresbury!nntp-trd.UNINETT.no!nac.no!ifi.uio.no!news.sics.se!eua.ericsson.se!usenet From: Mika.Niskanen@lmf.ericsson.se (Mika Niskanen) Newsgroups: bionet.genome.chromosomes Subject: 4p- chromosome anomaly (Wolff-Hircshorn) Date: 8 Nov 1995 09:53:22 GMT Organization: Oy L M Ericsson Ab Lines: 14 Distribution: world Message-ID: <47pumi$g2i@euas20.eua.ericsson.se> Reply-To: Mika.Niskanen@lmf.ericsson.se NNTP-Posting-Host: ivoryws10.lmf.eua.ericsson.se I am looking for information on 4p- chromosome anomaly, especially new information but also older information is intresting. If anyone has personnel experiences about persons suffering from this kind of anomaly it would be intresting to know about experiences. Please e-mail me any references or information you may have about 4p- chromosome anomaly. Thanks, Mika Niskanen, email: Mika.Niskanen@lmf.ericsson.se From owner-chromosomes@net.bio.net Tue Nov 07 22:00:00 1995 Newsgroups: bionet.genome.chromosomes Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!utcsri!utgpu!utinfo!news From: Hoang Trang Subject: Re: Long range PCRs for sequencing X-Nntp-Posting-Host: vapourize.dialin.utoronto.ca Content-Type: text/plain; charset=us-ascii Message-ID: To: rifat_h@icr.ac.uk Sender: news@utcc.utoronto.ca (News) Content-Transfer-Encoding: 7bit Organization: http:\\www.utoronto.ca\uoft.html References: <47or0h$spv@mserv1.dl.ac.uk> Mime-Version: 1.0 Date: Wed, 8 Nov 1995 08:45:27 GMT X-Mailer: Mozilla 1.1N (Windows; I; 16bit) Lines: 8 Barnes in the March 15, 1994 issue of Proceeding of the National Academy of Science has a good discussion on long range PCR that may be useful. In it he compared several parameters relating to long range amplification. I am trying to amplify a 2 kb human genomic fragment with varying degrees of success. Any suggestion with regards PCR reagents concentration and cycling conditions that you have had success with or any papers that you have come across would be appreciated. From owner-chromosomes@net.bio.net Thu Nov 09 22:00:00 1995 Path: biosci!rutgers!csn!carbon!night.primate.wisc.edu!newsspool.doit.wisc.edu!uwm.edu!lll-winken.llnl.gov!simtel!harbinger.cc.monash.edu.au!news.cs.su.oz.au!metro!news From: alcat@cyberspace.org (Alberto Catalano) Newsgroups: bionet.genome.chromosomes Subject: Re: Meaning of "AFM" in STS names Date: 10 Nov 1995 14:36:06 GMT Organization: Information Technology Services, The University of Sydney, NSW, Australia Lines: 52 Distribution: inet Message-ID: <47vo0m$oag@metro.ucc.su.OZ.AU> References: <4700dv$9db@metro.ucc.su.oz.au> NNTP-Posting-Host: ts-h08-13-8.ucc.su.oz.au Mime-Version: 1.0 X-Newsreader: WinVN 0.93.14 In article , tome@EMBL-EBI.ac.uk says... > > >In article , dbarton@acer.gen.tcd.ie (Dr David E >Barton) writes: >>In article <4700dv$9db@metro.ucc.su.oz.au>, >>Alberto Catalano wrote: >>>Dear bionetters, >>> >>>Does nayone know the meaning and/or origin of the AFM nomenclature for >>STS >>>sequences? >>>Thanks >>> >> >>I've no idea of the meaning of all the heiroglyphics that follow AFM, >>but >>this prefix denotes markers developed by Genethon. >> >> | David Barton >> | National Centre for Medical Genetics >> | Our Lady's Hospital for Sick Children >> | Crumlin, Dublin 12, Ireland. >> | Tel +353 1 455 0515 Fax 455 8873 >> >Well, as I said before AFM=Association Francaise contre les Myopathies, >the French muscular distrophy association that provides the funding >for >the research at Genethon > >and the hieroglyphics that follow AFM - come on, nobody recognized >plate number and position on the plate ( well OK, it may not be true >for all of them but you can see the pattern. If it is not the plate, it is >the tube :-) > > Am I right in assuming that STS's developed in other centres are not referred to by AFM numbers? If not then what is the standard for naming STS sequences or primer pairs? I originally thought that D#S### type nomenclature (e.g. D12S1057) was the standard, but the databases are saturated with AFM type names that don't seem to have a corresponding D number. If there isn't a standard, or a (group of) committee(s) that controls the nomenclature, how can we be sure that someone doesn't duplicate a name for an STS. Thanks From owner-chromosomes@net.bio.net Thu Nov 09 22:00:00 1995 Path: biosci!biosci!not-for-mail From: dellaire@atlas.odyssee.net (GD) Newsgroups: bionet.molbio.gene-linkage,bionet.cellbio,bionet.general,bionet.genome.chromosomes,bionet.announce Subject: Conference on Eukaryotic Dna Replication Date: 9 Nov 1995 21:36:55 -0800 Organization: Odyssee Internet Lines: 68 Sender: biohelp@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: <47ufa4$s6b@atlas.odyssee.net> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.molbio.gene-linkage:899 bionet.general:18399 bionet.genome.chromosomes:924 bionet.announce:2614 1st Announcement The Fourth McGill University Conference on Regulation of Eukaryotic DNA Replication St. Sauveur, Quebec, Canada October 1996. Organized by: Maria Zannis-Hadjopoulos and Gerald Price McGill Cancer Centre, Department of Oncology Faculty of Medicine and Faculty of Graduate Studies and Research McGill University http://www.mcgill.ca/mcgill/servers/Admin/UBO/dna.html The meeting will include plenary lecture sessions and poster sessions. TOPICS: * Eukaryotic Origins of DNA Replication * Nuclear and DNA Structure in DNA Replication * Modulation of Eukaryotic DNA Replication Preliminary Program The conference will be held at the Manoir Saint-Sauveur in the Laurentians. The first session will begin in the evening of October 17 and the final session will end in the early afternoon of October 20. Poster and oral presentations will take place on October 18 and 19. All participants are encouraged to present a poster on any of the topics that will be covered in the conference. Conference Location: The meeting will be held at the Laurentians' newest four-season conference resort hotel - a major luxury complex just about 45 minutes from Montreal, amid the dynamic beauty of the Laurentians. Saint-Sauveur-des-Monts, the Laurentians' most picturesque village, is the gateway village to the Laurentians. Transportation will be available from the airport to the conference site, and return. Registration materials and information regarding abstract submission will be sent in early 1996. *********Abstract deadline date: June 27, 1996.************ For More Information Please visit our Web Site http://www.mcgill.ca/mcgill/servers/Admin/UBO/dna.html >From this site you can obtain: * A Preliminary Program * Further Information on Conference Location * A Reply Card to Obtain Registration Package From owner-chromosomes@net.bio.net Thu Nov 09 22:00:00 1995 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!news From: Ian Dunham Newsgroups: bionet.genome.chromosomes Subject: Re: Meaning of "AFM" in STS names Date: 10 Nov 1995 18:37:17 GMT Organization: University of Cambridge, England Lines: 82 Message-ID: <48064t$rmh@lyra.csx.cam.ac.uk> References: <4700dv$9db@metro.ucc.su.oz.au> <47vo0m$oag@metro.ucc.su.OZ.AU> NNTP-Posting-Host: rock.sanger.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; OSF1 V3.0 alpha) X-URL: news:47vo0m$oag@metro.ucc.su.OZ.AU alcat@cyberspace.org (Alberto Catalano) wrote: >Am I right in assuming that STS's developed in other centres are not >referred to by AFM numbers? > Yes! Others I know about include WI for Whitehead Institute markers, CHLC (e.g. CHLC.ATA22D12) from the Cooperative Human Linkage Center, STSG for STSs fron the Sanger Centre EST mapping project, etc. >If not then what is the standard for naming STS sequences or primer pairs? >I originally thought that D#S### type nomenclature (e.g. D12S1057) was the >standard, but the databases are saturated with AFM type names that don't >seem to have a corresponding D number. You are partly right to think that the D number system is the standard. Originally the scheme was to assign all the anonymous DNA markers these D numbers, and this is now done through the central auspices of GDB. However the recent acceleration in the number of markers generated and access via WWW/ftp sites to marker lists means that many markers are getting widely distributed before D numbers are assigned. Eventually most of the marker do end up with at least two names, their lab name and the D number of the "locus" they detect. Furthermore there is some question about whether the system will be maintained - see http://info.gdb.org/showschema/nar/nar1995.html for (lengthy) discussion. >If there isn't a standard, or a (group of) committee(s) that controls the >nomenclature, how can we be sure that someone doesn't duplicate a name for >an STS. To my knowledge this hasn't happened very often, if at all. It'd be wise to name your STS with a unique system until you get D numbers, but at the end of the day the oligos are the unique fingerprint of all (single copy) STSs. There is a real problem, but it generally occurs in a slightly different way. When another lab picks up an STS oligo pair they have a (very natural) tendency to rename it to suit their lab system. If their data then goes out on to WWW/ftp sites without the original name and the D number if it exists, confusion reigns. You also get problems when the oligos for a particular sequence have been redesigned, so that they, say, one oligo is the same and the other is shifted 5 or 10 nucleotides. I have seen this happen in several ways over the past two years, and is only to be expected with the volumes of data that are being released. Here's how we deal with it in our local analyses and in data releases .... 1. We always store all names that we know about in our ACEDB databases. There are tags available for most of the permutations. We also store the EMBL accession numbers for the sequence from which an oligo pair was derived, and other sequences which contain exact matches to the oligo pair. We store the origin of the STS using the tags "Location" and "Originator". We name the STS by the name used by its originators e.g. AFM268yg1 instead of D22S1170. 2. We try to detect all cases where oligo pairs are the same or when one oligo of the pair is the same between STSs that have been obtained from different sources, and then resolve the namings by hand. For STSs/oligo pairs that are different but have exact matches to the same sequence, we record this information and can display it graphically when looking at the sequence. 3. When an STS is newly designed here from an EMBL sequence or our own sequence we assign a name of the type stSG-1234 and the sequence accession number is stored as above. As the STS accumulates other names such as a GDB D number, we record that information. 4. On releasing data we try to document all the known names. The key really is to use the DNA sequences (if they are available) as your cross-reference. A simple check of all the oligos against each other is often sufficient. Cheers Ian -------------------------------------------------------------------------- \ // Ian Dunham Tel: 01223 494948 \ Sanger Centre FAX: 01223 494919 // Hinxton Hall \ Hinxton // Cambridge Email: id1@sanger.ac.uk \ CB10 1RQ idunham@hgmp.mrc.ac.uk // www: http://www.sanger.ac.uk/~id1 ========================================================================== From owner-chromosomes@net.bio.net Thu Nov 09 22:00:00 1995 Path: biosci!rutgers!csn!carbon!night.primate.wisc.edu!newsspool.doit.wisc.edu!uwm.edu!lll-winken.llnl.gov!simtel!harbinger.cc.monash.edu.au!news.cs.su.oz.au!metro!news From: alcat@cyberspace.org (Alberto Catalano) Newsgroups: bionet.genome.chromosomes Subject: Chromosome 12 Workshop Date: 10 Nov 1995 14:43:29 GMT Organization: Information Technology Services, The University of Sydney, NSW, Australia Lines: 20 Distribution: inet Message-ID: <47voeh$oag@metro.ucc.su.OZ.AU> NNTP-Posting-Host: ts-h08-13-8.ucc.su.oz.au Mime-Version: 1.0 X-Newsreader: WinVN 0.93.14 I'd be interested inhearing from anyone who attended the recent Human Chromosome 12 Mapping Workshop in Belgium and in particular about the Syposium on 'Chromosome 12 genes in cancer'. What is the latest news on TEL and KIP1? Thank you -- Alberto Catalano Kanematsu Laboratories, Royal Prince Alfred Hospital Sydney Australia /\_/\ ( "*" ) (}_^_{) _ )>_<( | (} {)==/ alcat@cyberspace.org kanemats@morgan.angis.su.oz.au From owner-chromosomes@net.bio.net Sat Nov 11 22:00:00 1995 Newsgroups: bionet.genome.chromosomes Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!bshomer From: bshomer@ebi.ac.uk (Benny Shomer) Subject: PCR Primers Database - Submission form. Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Fri, 10 Nov 1995 11:08:40 GMT Organization: EBI - European Bioinformatics Institute X-Newsreader: TIN [version 1.2 PL2] Lines: 361 THE PCR PRIMERS DATABASE SUBMISSION FORM. This is the data submission form for the PCR primers database. It is basically intended for users who don't have access to a WWW service and only have email. If you can use a WWW browser, you are kindly requested to submit your data through the WWW based submission system which can be found in: http://www.ebi.ac.uk/primers_home.html DISCLAIMER This is the data submission form for the PCR primers database. By filling the fields of this form and submitting it, you agree to the following terms: 1. The data hereby submitted is for public usage. There are no means of handeling confidential entries. Neither EBI or Benny Shomer or anyone else involved in maintaining the database may be assumed responsible for any consequences of releasing this data to the public. 2. The PCR primers database is provided on a non-commercial basis. No person is allowed to charge any price for the data, excluding the costs of the medium which holds the data (may it be charges for networking, disks or disk-space). 3. The submitting author hereby declares that all the data submitted is correct and that the primers submitted were tested in the laboratory and were found to be functioning properly. It is also declared that the data is derived from an original work done by the author and / or colleagues who authorized the submission and that the data does not include any patented or commercial information without granted permission. HOW TO FILL THE FORM? When you submit information to our database, please bear in mind that the whole purpose is establishing a PRACTICAL database which enables researchers to synthesize primers based on the information you provide and to be able to reconstitute your working environment. Be precise, be complete, be honest. Through the form, there are lines which contain remarks. These lines are preceded with a hash mark (#). Please do not remove it, to enable automatization of the data processing. Please make an effort to adhere to the definitions. I currently process the entries alone and time is unfortunately, not my best friend :-( Especially take care with measurments. Use the time, volume, concentration measurments as requested and don't leave me to do the translations for you. If people will fail to do so, I will lag behind. IMPORTANT NOTICE: Allways start typing the information separated by a space following the appropriate field name. In cases where your data is longer than the remaining line, type it on the next consecutive lines. Anything typed in between a field name and the one following it (excluding the #hash marked lines) will be taken in. If you want to provide free-style comments which don't refer directly to the submission, type them either before the $$$BEGIN DATA$$$ line, or after the terminator mark (//). If a requested data item is non-available, leave it empty. Don't type anything like 'N/A' or 'non available' etc. Some of the fields are preceded by the remark 'Mandatory'. The data for these fields must be provided. $$$BEGIN DATA$$$ # The amplification target. This may be a specification of a known gene # name, a chromosome and possibly the location on it etc. Specifying the # organism here is optional. It may be multi line up to 250 characters. # # Mandatory TARGET # Specification of what do the sequence numbering and positions refer to. # e.g. it could refer to position 1 on a cDNA, position 1 in a specific # EMBL/Genbank/DDBJ entry etc. NUMREF # Organism Species. Defined according to the EMBL/Genbank/DDBJ # definitions. Use the scientific name and put the common name # in brackets. # # Mandatory OSPECS # Special applications. e.g. Cloning, Mutation etc. SPAPLL # At least one of the following two is mandatory # # Product length in base pairs when a cDNA is amplified. LNCDNA # Product length in base pairs when a Genomic DNA is amplified. LNGDNA # Name of the forward (5' --> 3') primer, assigned by the submitting # author. # # Mandatory FPNAME # Forward primer sequence, provided in 5' --> 3' direction (i.e. ready # for synthesis). Sequence therefore will be given only with # non-ambiguous bases. It will be displayed in triades, uppper case. # # Mandatory FPSEQN # Flanking base on the target sequence. i.e. Which base on the target # sequence matches the first 5' base of the primer. This position will # be given with reference to the NUMREF field given earlier. FFLANK # Restriction site added to the primer sequence. FRESTR # Mutation introduced into the primer sequence. Will be expressed as # base1 (or bases1) --> base2 (or bases2) in position, whereas base1 # is the base(s) in the original sequence, base2 is the base(s) that # were introduced as a mutation and position is the position on the # primer. FMUTAT # Unless this is a uni-directional reaction, the same fields are # mandatory here. # Name of the reverse (3' --> 5') primer, assigned by the submitting # author. RPNAME # Reverse primer sequence, provided in 5' --> 3' direction (i.e. ready for # synthesis). Sequence therefore will be given only with non-ambiguous # bases. It will be displayed in triades. RPSEQN # See definition for FFLANK. RFLANK # See definition for FRESTR. RRESTR # See definition for FMUTAT. RMUTAT # Thermal Cycler make and model. Two fields separated by semicolon make;model # if used more than one machine, you may provide the fields more than once. # # Mandatory TCYCLE # Temperature Sampling By Probe In-tube. A Boolean field accepting either # "YES" or "NO". # # Mandatory PROBIN # Was the Hot-start protocol applied? A Boolean field accepting either "YES" # or "NO" (or leave empty = "NO") HOTSTR # Initial denaturation. Expressed as two fields separated by semicolon. # Temperature in degrees centigrade ; duration in seconds. IDENAT # Denaturation. Expressed as two fields separated by semicolon. # Temperature in degrees centigrade ; duration in seconds. # # Mandatory DENATR # Annealing. Expressed as two fields separated by semicolon. # Temperature in degrees centigrade ; duration in seconds. # # Mandatory ANNEAL # Touchdown protocol. Has two fields, separated by semicolon: Temperature # decrease in degrees centigrade; Number of cycles in which touchdown was # applied. TCHDWN # Extension. Expressed as two fields separated by semicolon. # Temperature in degrees centigrade ; duration in seconds. EXTEND # Progressive extension. Has two fields, separated by semicolon: The time # added in seconds per cycle; The cycle number in which addition has started PRGRSS # Final extension step. Expressed as two fields separated by semicolon. # Temperature in degrees centigrade ; duration in seconds. FINEXT # Total number of cycles per amplification reaction. # # Mandatory CYCLES # Total reaction volume expressed in microlitres. # # Mandatory RXNVOL # Polymerase used. Expressed as three fields separated by a semicolons: # Polymerase type; Polymerase make; Polymerase concentration in Units per # reaction. # # Mandatory POLYMR # The type of buffer used. Can be either a commercially standard provided, in # which case, the name of the provider is stated, or it can be one of a few # standard buffers of the database, or provided in full details. # # Mandatory BUFFER # Concentration of dNTP's in uM (micro molar). If all are the same, only one # figure will be provided. Every dNTP with a different concentration follows # separated by a semicolon. # # Mandatory DNTPCN # Concentration of primers in uM (micro molar). If both are the same, only one # figure will be provided. Else, the concentration of each is provided followed # by the primer's name as appeared in FPNAME and RPNAME separated by a # semicolon. # # Mandatory PRIMCN # Concentration of MgCl2 in the buffer provided in mM (milimolar). Field will # be included only if the MgCl2 concentration varied from a standard buffer # as defined in the BUFFER field. The figure provided will allways refer to # the final total concentration of Magnesium in the buffer. MGCONC # Various additives added to the reaction (e.g. DMSO, Formamide, Gelatin ). The # units will be provided accordind to the submitters specifications. In the field # the order will allways be additive name, concentration, units and be separated # by a semicolon; ADITIV # DNA Source, Method of Preparation and Amount added. # # Mandatory SOURCE # Cross references for other databases. Expressed as: Database name followed by # the acession numbers seperated by comma. Various databases separated with # semicolons. Database names according to pre-defined nomenclature. DBXREF # Names of contact author in the following format: Firstname # Surname, separated by a comma. # # Mandatory CNTNAM # Institute of contact author # # Mandatory CNTINS # Regular mail address of contact author # # Mandatory CNTADR # Email address of contact author # # Mandatory CNTEML # Telephone number of contact author, including international dial code CNTTEL # Fax number of contact author, including international dial code CNTFAX # Reference author in the following format: Surname, Initials., REFAUT # Reference title REFTTL # Reference publication line in the following format: Journal name # according to the nomenclature defined for EMBL database folowed by # Volume: frompage - topage, (Year) REFSRC # The name says it all... :-) Anything that doesn't go into any of the # above fields, bu needs to go in. REMARK # The good old faithful record terminator. Please leave it untouched. // From owner-chromosomes@net.bio.net Sat Nov 11 22:00:00 1995 Newsgroups: bionet.genome.chromosomes Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!bshomer From: bshomer@ebi.ac.uk (Benny Shomer) Subject: The PCR Primers Database - First Announcement Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Fri, 10 Nov 1995 10:42:32 GMT Organization: EBI - European Bioinformatics Institute X-Newsreader: TIN [version 1.2 PL2] Lines: 58 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The PCR Primers database - First Announcement. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ I'm happy to announce the release of the PCR primers database. This is a practical database of fully tested and optimized primers for PCR reactions. The database contains all the data items required to reproduce precisely the reaction conditions of the submitting author and contact details in case of a need. Initially, the database is release to the public practically empty, since it is based on submissions from colleagues and not on journal scanning. Nevertheless, it is being released with the required definitions, documentation, data submission form and a data submission system through WWW. The data will be available by ftp. In the near future it will be made searchable through the WWW server. Data submissions are highly welcome. It is MUCH preferred that users will submit information through a specially dedicated WWW based system. This system is not only convenient to use, but it also saves much work in preparing the submitted information for release. Users who have no access to the WWW can use a data submission form that can be sent by email. I will post the data submission form in another message. The database home page can be accessed through EBI's home page at: http://www.ebi.ac.uk/ in the databases area, or directly at: http://www.ebi.ac.uk/primers_home.html The data can be obtained through anonymous ftp to: ftp.ebi.ac.uk under: /pub/databases/primers/primers.dat (but it now has only 3 entries... :) Best wishes and good luck with your PCR experiments!!! Benny. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Benny Shomer External Biological Liaison Officer, EMBL outstation - The EBI, Hinxton Hall, Hinxton,Cambridge CB10 1RQ, UK Tel: +44-223-494437 Fax: +44-223-494468 Email: bshomer@EBI.ac.uk http://www.ebi.ac.uk/ebi_docs/staff/benny.html ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-chromosomes@net.bio.net Sat Nov 11 22:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!geraldo.cc.utexas.edu!usenet From: "Gayna S. Credle" Newsgroups: bionet.genome.chromosomes Subject: Re: Requestion info on BRCA gene- Breast cancer gene Date: 12 Nov 1995 23:13:49 GMT Organization: The University of Texas at Austin Lines: 8 Message-ID: <485v3d$af@geraldo.cc.utexas.edu> References: <47ibkc$6i6@linet02.li.net> NNTP-Posting-Host: slip-4-7.ots.utexas.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) To: sahslib@newshost.li.net X-URL: news:47ibkc$6i6@linet02.li.net I am also a 16 year old junior actively trying to harvest information about breast cancer. I am a student at the LBJ Science Academy in Austin, Texas and any information pertaining to the subject that you have would be greatly appreciated.-Thank You Sydni Credle e-mail:gcredle@mail.utexas.edu From owner-chromosomes@net.bio.net Mon Nov 13 22:00:00 1995 Newsgroups: bionet.genome.chromosomes Path: biosci!agate!howland.reston.ans.net!spool.mu.edu!bloom-beacon.mit.edu!newsserver.pixel.kodak.com!news.sprintlink.net!newsfeed.internetmci.com!EU.net!Germany.EU.net!ieunet!news.tcd.ie!acer.gen.tcd.ie!dbarton From: dbarton@acer.gen.tcd.ie (Dr David E Barton) Subject: Re: Requestion info on BRCA gene- Breast cancer gene Message-ID: Sender: usenet@news.tcd.ie (TCD News System ) Organization: Irish National Centre for Medical Genetics References: <47ibkc$6i6@linet02.li.net> <485v3d$af@geraldo.cc.utexas.edu> Date: Tue, 14 Nov 1995 17:36:31 GMT Lines: 16 In article <485v3d$af@geraldo.cc.utexas.edu>, Gayna S. Credle wrote: >I am also a 16 year old junior actively trying to harvest information >about breast cancer. I am a student at the LBJ Science Academy in >Austin, Texas and any information pertaining to the subject that you >have would be greatly appreciated.-Thank You Sydni Credle > >e-mail:gcredle@mail.utexas.edu Try the new breast cancer web site: http://www.nchgr.nih.gov/dir/lab_transfer/bic David Barton From owner-chromosomes@net.bio.net Mon Nov 13 22:00:00 1995 Path: biosci!rutgers!csn!carbon!night.primate.wisc.edu!sdd.hp.com!swrinde!cssun.mathcs.emory.edu!emory!darwin.sura.net!blaze.cs.jhu.edu!news.jhu.edu!news From: Amy Voltz Newsgroups: bionet.genome.chromosomes,bionet.molbio.gdb Subject: Re: 4p- chromosome anomaly (Wolff-Hircshorn) Date: 14 Nov 1995 19:32:23 GMT Organization: HCF - Johns Hopkins University, Baltimore, Maryland, USA Lines: 31 Message-ID: <48aqs7$eam@news.jhu.edu> References: <47pumi$g2i@euas20.eua.ericsson.se> NNTP-Posting-Host: 192.239.76.53 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; SunOS 4.1.3 sun4c) To: Mika.Niskanen@lmf.ericsson.se X-URL: news:47pumi$g2i@euas20.eua.ericsson.se Xref: biosci bionet.genome.chromosomes:932 bionet.molbio.gdb:395 Dear Mika, The OMIM database (Online Mendelian Inheritance in Man) has information for clinical geneticists regarding Wolf-Hirschhorn Syndrome, a deletion on chr 4. If you have access to the Web the URL for this entry is http://gdbwww.gdb.org/omim-bin/omim/bin/omimx?194190 This entry also includes a list of references. I am going to try mailing this entry to you in a separate message. Sincerely, Amy Voltz avoltz@gdb.org Mika.Niskanen@lmf.ericsson.se (Mika Niskanen) wrote: > >I am looking for information on 4p- chromosome anomaly, especially new >information but also older information is intresting. If anyone has personnel >experiences about persons suffering from this kind of anomaly it would be >intresting to know about experiences. > >Please e-mail me any references or information you may have about 4p- >chromosome anomaly. > >Thanks, > >Mika Niskanen, email: Mika.Niskanen@lmf.ericsson.se > > From owner-chromosomes@net.bio.net Wed Nov 15 22:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.sprintlink.net!news.uoregon.edu!tank.news.pipex.net!pipex!demon!sunsite.doc.ic.ac.uk!yama.mcc.ac.uk!usenet From: Ali Hajeer Newsgroups: bionet.genome.chromosomes Subject: loss of heterozygosity.... Date: 16 Nov 1995 14:59:01 GMT Organization: University of Manchester (UK) Lines: 7 Message-ID: <48fjjl$bli@yama.mcc.ac.uk> NNTP-Posting-Host: pc422.ser.man.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.2N (Windows; I; 16bit) What is the difference between loss of heterozygosity and microsatellite instability in cancer? Thank you. Ali Hajeer From owner-chromosomes@net.bio.net Thu Nov 16 22:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!newsfeed.internetmci.com!in1.uu.net!munnari.OZ.AU!comp.vuw.ac.nz!canterbury.ac.nz!chmeds.ac.nz!mkennedy From: mkennedy@chmeds.ac.nz (Martin Kennedy) Newsgroups: bionet.genome.chromosomes Subject: Re: Requestion info on BRCA gene- Breast cancer gene Message-ID: <1995Nov17.165402.471@chmeds.ac.nz> Date: 17 Nov 95 16:54:02 +1200 References: <47ibkc$6i6@linet02.li.net> <485v3d$af@geraldo.cc.utexas.edu> Lines: 22 In article <485v3d$af@geraldo.cc.utexas.edu>, "Gayna S. Credle" writes: > I am also a 16 year old junior actively trying to harvest information > about breast cancer. I am a student at the LBJ Science Academy in > Austin, Texas and any information pertaining to the subject that you > have would be greatly appreciated.-Thank You Sydni Credle > > e-mail:gcredle@mail.utexas.edu Check out the new breast cancer information WWW site: http://www.nchgr.nih.gov/dir/lab_transfer/bic -- Cheers, Martin NNNN NN Martin A Kennedy (E-mail = mkennedy@chmeds.ac.nz) ZZZZZZZ NN NN NN Cytogenetic and Molecular Oncology Unit ZZZ NN NN NN Christchurch School of Medicine ZZZ NN NNNN Christchurch, New Zealand ZZZZZZZ Phone (64-3)364-0880 Fax (64-3)364-0750 From owner-chromosomes@net.bio.net Sat Nov 18 22:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!usc!elroy.jpl.nasa.gov!swrinde!sgigate.sgi.com!sgiblab!cgl!itssrv1.ucsf.edu!itsa.ucsf.edu!bgold From: bgold@itsa.ucsf.edu (Bert Gold) Newsgroups: bionet.genome.chromosomes Subject: loss of heterozygosity.... Date: 19 Nov 1995 00:04:49 GMT Organization: UCSF, ITS Lines: 21 Message-ID: <48lsb1$jfq@itssrv1.ucsf.edu> NNTP-Posting-Host: itsa.ucsf.edu Loss of heterozygosity is the observation that malignant tissues present in an individual bearing a tumor supressor gene mutation or deletion tend to have a mutated or deleted allelomorph at the locus of the tumor suppresor gene in question in the transformed tissue. Global microsatellite instability, particularly in hereditary, non-polyposis colon cancer, is thought to be a consequence of a deficit in mismatch repair capacity, specifically, in hMSH2 (the mammalian homolog of bacterial mutS) and other proteins required for the assembly of the mismatch repair complex. See the work of Paul Modrich of Duke U., 1994-'95 and Kolodner and Fishel, '93-'95. The two are disparate manifestations of malignancy on the molecular level, and do not appear to me to be conceptually conjoined. Diverse views welcomed! Bert Gold, Ph.D. University of California, San Francisco Program in Medical Genetics From owner-chromosomes@net.bio.net Tue Nov 21 22:00:00 1995 Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!idefix.CS.kuleuven.ac.be!Belgium.EU.net!EU.net!Germany.EU.net!wizard.pn.com!news.xensei.com!news From: symposia@xensei.com (James Larkin) Newsgroups: bionet.molbio.methds-reagnts,bionet.genome.chromosomes Subject: Meeting announcement: DNA Forensics Date: Wed, 22 Nov 1995 17:36:26 GMT Organization: Cambridge Symposia Lines: 59 Message-ID: <48vn3q$gru@xensei3.xensei.com> Reply-To: symposia@xensei.com NNTP-Posting-Host: chi.xensei.com X-Newsreader: Forte Free Agent 1.0.82 Xref: biosci bionet.molbio.methds-reagnts:36681 bionet.genome.chromosomes:936 Cambridge Symposia, organized to serve the scientific community through the administration of interdisciplinary conferences in the biological sciences, is announcing their upcoming meeting, "DNA Forensics: Science, Practice, and Future," to be held April 21-27, 1996 in Sante Fe, New Mexico. Topic Description: Almost twenty years back it was shown that the blue print of life, the deoxyribonucleic acid (DNA), varies enormously in its structure and organization between individuals, and the recombinant DNA technology allows one to unravel this variation. More tha n eleven years have passed since the world has witnessed that by typing DNA from biological samples left at crime scenes, it is possible to exonerate a wrongly accused suspect, and the same technique does indeed identify the true perpetrator. Since then, versions of the same technology have been used in numerous cases around the world to exculpate suspects and to convict criminals. In civil litigations of identifying parents and relatives as well, DNA typing has played a major role around the world. Fo rensic and medico-legal experts, in unison, agree that the DNA technology is the most powerful tool that a scientist can offer for forensic investigations, even more diversely usable than the traditional fingerprinting imaging. In spite of the tremendous success of using DNA in forensics around the world, such well-publicized criticisms by otherwise well known experts, raise a few questions. Why are there such contradictory views? Is the science of DNA typing still in its adolescence that needs more ma turity to apply in legal cases? Is the practice of DNA typing fallible to the extent that the results are not trustworthy? If DNA typing is so controversial in forensics, how reliable are its applications in medicine and biology? What is in store for t his technology for future? The theme of this conference is to discuss these basic issues. While a number of recent meetings and symposia have discussed these issues in platforms that varies from sophisticated technical details to educating general publi c, the goal of this meeting is to put the science, practice, and future of DNA forensics in their proper perspective. Experts encompassing molecular geneticists, forensic practitioners, legal authorities, and statistical geneticists, will be invited to initiate discussions on these subjects. The meeting will be divided in three parts consistent with the major themes. In each session the main presentations will be grouped in thematic format, at the conclusion of each of such sessions time for discussion will be preserved to raise alternative views and their justification. ---------------------------------------------------------------------------------------------------------- For immediate information on this meeting, including a full program draft, please see our website: http://www.xensei.com/users/symposia James Larkin Cambridge Symposia 1037 Chestnut Street Newton Upper Falls, MA 02164 tel. (617) 630-1399 fax. (617) 630-1395 symposia@xensei.com From owner-chromosomes@net.bio.net Fri Nov 24 22:00:00 1995 Path: biosci!agate!news.ucdavis.edu!library.ucla.edu!newsfeed.internetmci.com!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!lll-winken.llnl.gov!simtel!news00.sunet.se!sunic!news99.sunet.se!mimuw.edu.pl!news.nask.org.pl!sunrise.pg.gda.pl!sunlab!tkoz From: tkoz@sunlab.pg.gda.pl (adm. T. Kozakiewicz - tel.28-25) Newsgroups: bionet.genome.chromosomes Subject: I'm looking for data about mutation's Date: 24 Nov 1995 15:02:01 GMT Organization: Politechnika Gdanska Lines: 9 Message-ID: <494mp9$j24@sunrise.pg.gda.pl> NNTP-Posting-Host: sunlab.pg.gda.pl X-Newsreader: TIN [version 1.2 PL2] Hello ! When You k'now any address (ftp, www or any other) about mutations - mail me please. Thanks a lot !!! T.Kozakiewicz, tkoz@sunlab.mlk.pg.gda.pl From owner-chromosomes@net.bio.net Fri Nov 24 22:00:00 1995 Path: biosci!biosci!not-for-mail From: bshomer@ebi.ac.uk (Benny Shomer) Newsgroups: bionet.announce,bionet.molbio.methds-reagnts,bionet.immunology,bionet.cellbiol,bionet.general,bionet.genome.arabidopsis,bionet.genome.chromosomes,bionet.microbiology,bionet.molbio.proteins,bionet.plants,fr.bio.biolmol,fr.bio.general,sci.bio.microbiology Subject: PCR Primers database - Addenum Date: 24 Nov 1995 17:24:26 -0800 Organization: EBI - European Bioinformatics Institute Lines: 78 Sender: biohelp@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Xref: biosci bionet.announce:2644 bionet.molbio.methds-reagnts:36808 bionet.immunology:6353 bionet.cellbiol:3496 bionet.general:18574 bionet.genome.arabidopsis:3949 bionet.genome.chromosomes:938 bionet.microbiology:4051 bionet.molbio.proteins:6337 bionet.plants:9344 sci.bio.microbiology:2025 The PCR Primers database. ========================= This is an important addenum to the announcement about the creation of the PCR primers database. 1. I forgot to mention that all email submissions should be sent to: primers@ebi.ac.uk This is also the appropriate address for any queries or correspondence about the primers database. 2. Users who have other means of connection besides email, can now use the EMBL-EBI automatic mail server to retreive the database files and documents. To start working with the mail server in general, send a message containing the word "HELP" either in the subject line or in the body of message, to: netserv@ebi.ac.uk Here are the commands which are available for the primers database: Here is a summary of all the available commands for the primers database, that can be specified in an email message sent to netserv@ebi.ac.uk ------------------------------------------------------------------------- To obtain send the command ------------------------------------------------------------------------- A general help file HELP PRIMERS The database fields definitions file GET PRIMERS:DEFINITIONS A bogus filled entry as an example GET PRIMERS:EXAMPLE An electronic data submission form GET PRIMERS:SUBMISSION.FORM The actual data file with the entries GET PRIMERS:PRIMERS ------------------------------------------------------------------------- Dear colleagues, please do not forget, this database will NOT be created by journal scanning and active searching, but from direct submissions from researchers only. The key to the success of this database is your submissions, so do set aside some spare time and send your primers. Our email: primers@ebi.ac.uk WWW : http://www.ebi.ac.uk/primers_home.html fax : +44 1223 494468 Phone : +44 1223 494437 I highly welcome any questions, corrections, remarks or discussions concerning the PCR Primers database (or the British weather or any other topic... :). Email is the most preferred way. Best wishes. Good luck with your PCR experiments. Yours, Benny. <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Doing PCR? Have you got some good, working primers??? Visit the PCR primers database at http://www.ebi.ac.uk/primers_home.html and make your donation. If you don't have access to WWW, just write to primers@ebi.ac.uk <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Benny Shomer External Biological Liaison Officer, EMBL outstation - The EBI, Hinxton Hall, Hinxton,Cambridge CB10 1RQ, UK Tel: +44-223-494437 Fax: +44-223-494468 Email: bshomer@EBI.ac.uk http://www.ebi.ac.uk/ebi_docs/staff/benny.html ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-chromosomes@net.bio.net Sun Nov 26 22:00:00 1995 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.genome.chromosomes Subject: IMPORTANT: BIOSCI miniFAQ Date: 27 Nov 1995 02:00:26 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 196 Sender: daemon@net.bio.net Distribution: world Message-ID: <199511271000.CAA11191@net.bio.net> NNTP-Posting-Host: net.bio.net This is a new "miniFAQ" designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. Contents: -------- 1) What to do about "spams," i.e., junk mail, ads, etc. 2) Examples of subscribing and unsubscribing to the mailing lists. 3) How to access BIOSCI/bionet newsgroup archives. 4) The BIOSCI user address and research interest directory. 1) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups) and mailing lists. The same postings are distributed on both media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the newsgroups from about 95% of the spams that are being sent to date. This means that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings. Unfortunately there are easy ways for determined spammers to override the moderation mechanism. We are working on new systems to provide access to our newsgroups over the WWW. These should be available soon, probably November 1995, and will allow you to use your Web browser to look at the news postings. While this will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. 2) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 3) How to access BIOSCI/bionet newsgroup archives. -------------------------------------------------- Back postings of all BIOSCI/bionet newsgroups can be found on the World Wide Web at URL http://www.bio.net/. There are several searchable newsgroup indices at this site. E-mail users can search the BIOSCI archives by using our waismail e-mail server. For instructions send the message help to waismail@net.bio.net. Leave the Subject: line blank (anything entered on the Subject: line is ignored). 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-chromosomes@net.bio.net Sun Nov 26 22:00:00 1995 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!acs2.byu.edu!news.cuny.edu!news.sprintlink.net!newsfeed.internetmci.com!EU.net!Norway.EU.net!nntp.uio.no!pcdnr05.uio.no!user From: olam@radium.uio.no (Ola Myklebost) Newsgroups: bionet.genome.chromosomes Subject: Re: Chromosome 12 Workshop Date: Mon, 27 Nov 1995 14:14:19 +0100 Organization: Inst for Cancer Research, Oslo Lines: 17 Distribution: inet Message-ID: References: <47voeh$oag@metro.ucc.su.OZ.AU> NNTP-Posting-Host: pcdnr05.uio.no In article <47voeh$oag@metro.ucc.su.OZ.AU>, alcat@cyberspace.org (Alberto Catalano) wrote: > I'd be interested inhearing from anyone who attended the recent Human > Chromosome 12 Mapping Workshop in Belgium and in particular about the > Syposium on 'Chromosome 12 genes in cancer'. take a look at http://paella.med.yale.edu/chr12/Home.html -- Ola Myklebost Email ola.myklebost@labmed.uio.no Dept of Tumor Biology Inst for Cancer Research Tel +47-2293-4299 The Norwegian Radium Hospital Fax +47-2252-2421 N-0310 OSLO, Norway WWW presentation: http://www.med.uio.no/dnr/Inst/TumBiol/Ola/Ola.html From owner-chromosomes@net.bio.net Thu Nov 30 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: rifat_h Newsgroups: bionet.genome.chromosomes Subject: > 14bp cutter restriction enzyme Date: 1 Dec 1995 16:42:32 -0000 Lines: 15 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <49nb9o$9ig@mserv1.dl.ac.uk> X-Mts: smtp X-Authentication-Warning: jupiter.icr.ac.uk: Host localhost didn't use HELO protocol Original-To: biochrom@dl.ac.uk Hi, I am interested in SAGE (Serial Analysis of Gene Expression) Science, Vol. 270, 20 Oct. 1995. SAGE uses two enzymes a short bp cutter called the Anchoring enzyme and a long bp cutter called the tagging enzyme. However looking at the method it seems that the longer the tagging enzyme cuts from its recognition site the better for the analysis so I was wondering anyone know of a restriction enzyme that cuts more than 14bp from its recognition site, since that was the longest restriction enzyme I could find. Thanks. Rifat. rifat_h@icr.ac.uk From owner-chromosomes@net.bio.net Thu Nov 30 22:00:00 1995 Newsgroups: bionet.genome.chromosomes Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!EU.net!peer-news.britain.eu.net!newsfeed.ed.ac.uk!udcf.gla.ac.uk!news From: mjb8n@clinmed.gla.ac.edu.uk Subject: Synteny Content-Type: text/plain; charset=us-ascii Message-ID: Sender: news@udcf.gla.ac.uk (News) Content-Transfer-Encoding: 7bit Organization: Glasgow University Computing Service Mime-Version: 1.0 Date: Fri, 1 Dec 1995 17:09:01 GMT X-Mailer: Mozilla 1.1N (Windows; I; 16bit) Lines: 3 Please can anyone tell us the best way of determining where the regions of synteny lie between rat and human chromosomes?