From owner-chromosomes@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!spool.mu.edu!torn!news.unb.ca!coranto.ucs.mun.ca!leif!roger From: roger@kean.ucs.mun.ca (ROGER GREEN,MEDICINE,ST.JOHN'S,NF,CAN) Newsgroups: bionet.genome.chromosomes Subject: Re: Recombination New group Date: 2 Jun 95 10:42:44 -0230 Organization: Memorial University. St.John's Nfld, Canada Lines: 28 Message-ID: <1995Jun2.104244.1@leif> References: <3pnphe$8r8_002@news.mcgill.ca> NNTP-Posting-Host: leif.ucs.mun.ca In article <3pnphe$8r8_002@news.mcgill.ca>, popa0206@po-box.mcgill.ca (G. Dellaire) writes: > I would like to propose a news group for recombination. > Perhaps something like bionet.genetics.recombination, to deal > with issues pertaining to the mechanisms and models of > recombination. Also to serve as a forum for professionals > in the field of recombination to provide help to those > researchers who are involved in gene targeting/transgenics > and/or gene therapy projects. > > Some other possible topics of discussion include > [STUFF DELETED] > > According to one "pundit" who posted here there is no need for such a group > I think he is mistaken! Well, sorry to have to say, here is someone else opposed to a recombination group. New groups are usually formed for one of two reasons: 1. There is no existing group suitable for the material. 2. An existing group is swamped with material on one particular topic which is not of general interest to most readers. Neither of these apply here. Go ahead and post to the .chromosomes group!! It's hardly used as it is! Roger C. Green, Faculty of Medicine Phone: (709)737-6884 Memorial University , St. John's, Newfoundland FAX : (709)737-7010 From owner-chromosomes@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!newsspool.doit.wisc.edu!decwrl!tribune.usask.ca!canopus.cc.umanitoba.ca!newsflash.concordia.ca!news.mcgill.ca!usenet From: Graham Dellaire Newsgroups: bionet.genome.chromosomes Subject: Re:Reply to Chromosomes Date: 1 Jun 1995 21:47:40 GMT Organization: McGill University (Exp. Medicine) Lines: 95 Message-ID: <3qlchs$mfa@sifon.cc.mcgill.ca> NNTP-Posting-Host: i-08.das.mcgill.ca X-Newsreader: AIR News 3.X (SPRY, Inc.) Keith Robinson wrote: ....plenty of things about sex chromosomes and dose compensation clipped (no doubt spered on by the recent review in Cell ) >The other complication worth mentioning is that some genes are >intertwined with their neighbors, and so it may not be possible >to move individual genes to another chromosome (and retain >function) but it would then be possible to move the entire >block of genes to another chromosome (unless, of course, the >block consists of all the genes on the chromosome!). good point... I would also like to add that it may not just be that the genes are "intertwined" as you put it , which I believe is rare*, there may be a structuarl reason too.. * (In general in higher organisms as there is not such a size constraint as in viruses where overlapping reading frames are common.) Often the promoters or enhancer sequences that help a gene function appropriately (proper tissue and time in development for example). Without transplanting these sequences with the gene you may get abberant or no expression at all of your gene.... such is the bane of attempts at gene therapy for diseases like muscular distrophy where the actual gene spans more than a megabase! So you can't just plop a gene anywhere and expect it to be functional. The previous question as to chromosome stability that was original asked has still not been touched . This is a much sticker point and of great debate. To go from the most concrete reasons for stability you can look at the physical characteristics of a chromosome. 1. has telomeres that prevent degredation of DNA and ensure complete replication of the chromosome each time - in addition prevent recombination occurring as the free ends of the chromosomes are no longer accessible 2. A chromosome has one (yeast artificial chromosomes) or several origins of replication that ensure the chromosome is replicated during mitosis and meiosis and can be passed on to the daughter cells or gametes respectively. 3. There is a centromere which enables the proper segregation at mitosis and meiosis so that each daughter cell or gamete recieves a full compliment of chromosomes. No as for the actual integrity of the sequence this is maintained by 1. Packaging around nucleosomes and histone 1 -which excludes the DNA some what from the action of DNases and UV light etc ( and any other potential destructor of DNA) 2. During replication and recombination event there are other DNA binding proteins that prevent degredation -when DNA is without histones and/or unwound, nicked etc 3. We also have several repair systems that "scan" our DNA for mismatches, thymidine dimers, crosslinks, adducts etc... and general make sure the genetic house is in order. Now all this is not full proof and mistakes do occur and mutations can accumulate To go beyond this quick physical look at chromosomes is where you enter uncharted and very "theoretical" country One tidbit for everyone to chew on mentally... One theory is that line-1 and Alu sequences (and perhaps other moderate repeats) are are involved in not only driving "evolution" by retropostion into coding sequences and through gene conversion which may join exons....but also in genome stability! Theses sequences may also maintaini stability of the genome through gene conversion events and recombination between these sequences. For instance at meiosis there is thought to be an homology search prior to synapsis which then results in areas of crossing over (and eventually visable chiasmata ) between chromosome homologs. Gene conversion initiated by repeat sequences may be involved in this homology search. G. _______________________________________________________________________ Graham Dellaire Snail Mail: Red Cross, Research McGill Univeristy Montreal Blood Services Faculty of Medicine 3131 Sherbrooke St. East Div. of Experimental Medicine Montreal, QC, Canada E-mail: popa0206@po-box.mcgill.ca H1W 1B2 B2XE@musicb.mcgill.ca Fax: (514) 525 0881 Voice: (514) 527 1501 ext 175 _______________________________________________________________________ From owner-chromosomes@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!raven.bio.indiana.edu!user From: lwashing@sunflower.bio.indiana.edu (Lawrence Washington) Newsgroups: bionet.genome.chromosomes Subject: Re: automated sequencing Date: 31 May 1995 21:56:39 GMT Organization: Indiana University Lines: 22 Message-ID: References: <3pv9rs$4ej@montespan.pasteur.fr> NNTP-Posting-Host: raven.bio.indiana.edu In article <3pv9rs$4ej@montespan.pasteur.fr>, Hassan Badrane wrote: > hello there, > > my question will be a technical one. > we are planning to buy an automatic sequencer and we are trying tree differents > machines : Pharmacia, Amersham and ABI. > we want to know, you people who have sequenced with one or some of these > technologies, what is your opinion and your comments about them. > You might also consider the autosequencer made by LiCor. (We have no financial interest in LiCor, but we use and like their system) -- Lawrence Washington Indiana University Institute for Molecular and Cellular Biology From owner-chromosomes@net.bio.net Sun Jun 04 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!usc!elroy.jpl.nasa.gov!swrinde!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!uwvax!newssinet!news.u-tokyo.ac.jp!tkyex1.phys.s.u-tokyo.ac.jp!news.tisn.ad.jp!news.nig.ac.jp!timac230!yanakamu From: yanakamu@lab.nig.ac.jp (NAKAMURA Yasukazu) Newsgroups: bionet.molbio.genome-program,bionet.genome.chromosomes,bionet.molbio.methds-reagnts Subject: [Q] human chr 20-specific library Date: Mon, 05 Jun 1995 12:41:48 +0900 Organization: National Institute of Genetics, JAPAN Lines: 23 Message-ID: NNTP-Posting-Host: timac230.nig.ac.jp Mime-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp Xref: biosci bionet.molbio.genome-program:1395 bionet.genome.chromosomes:639 bionet.molbio.methds-reagnts:29200 Dear Bionetters, Does anyone know human chr 20-specific genomic library constructor? I am a graduate student in Japan. I hope to use such a construction in order to examine long-range GC content mosaic structure along the chromosome. I know ATCC have two chr 20-specific constructions using Charon 21A (57712, 57732). Average insert size of them are 4.0kb and 3.1kb. I want to use library with larger (20kb or more) insert size. Any information will be appliciated. Thank you in advance. YasKaz NAKAMURA Yasukazu yanakamu@lab.nig.ac.jp Evolutionary Genetics Lab. Grad. Univ. for Adv. Studies / NIG P.S. If you have some interest in long-range GC content mosaic along the human genome, see Fukagawa et al. "A boundary of long-range G+C% mosaic domains in the human MHC locus: pseudoautosomal boundary-like sequence exists near the boundary" Genomics 25, 184-191 (1995). From owner-chromosomes@net.bio.net Sun Jun 04 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!demon!uknet!warwick!lyra.csx.cam.ac.uk!news From: Robert Brooksbank Newsgroups: bionet.genome.chromosomes,bionet.molbio.genome-program,bionet.general Subject: Lagan Inc. address or alternative source of repeat sequences needed Date: 5 Jun 1995 10:34:03 GMT Organization: University of Cambridge, England Lines: 23 Message-ID: <3qumir$743@lyra.csx.cam.ac.uk> NNTP-Posting-Host: lismore.sanger.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; SunOS 5.3 sun4m) X-URL: news:bionet.genome.chromosomes Xref: biosci bionet.genome.chromosomes:640 bionet.molbio.genome-program:1397 bionet.general:15586 I am trying to get a collection of human repeat sequences together to use as competitors and probes in gene finding studies. I have come across an acknowledgement to a company called Lagan Inc. based in Detroit MI. I infer from this that they supply repeat sequences. However I can't find any address (snail or e mail) or fax or phone number. Can any one provide me with these details. Alternatively does anyone know of another source of repeat sequences, preferably as subclones. If not I'll have to continue my literature trawl and write off to individual authors. Apologies for cross-posting this article, I tried methods- reagents but with no success. Thanks in advance for any help. Rob ------------------------------------------------------------------- Rob Brooksbank The Sanger Centre, email: rab@sanger.ac.uk Hinxton Hall phone: (01223) 494949 Cambridge fax: (01223) 494919 CB10 1RQ From owner-chromosomes@net.bio.net Sun Jun 04 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!news.sprintlink.net!noc.netcom.net!ix.netcom.com!netnews From: alsclev@ix.netcom.com (Barbara Grossmann ) Newsgroups: bionet.genome.chromosomes,bionet.molbio.genome-program,bionet.general Subject: Re: Lagan Inc. address or alternative source of repeat sequences needed Date: 5 Jun 1995 12:34:21 GMT Organization: Netcom Lines: 11 Distribution: world Message-ID: <3qutkd$b1s@ixnews2.ix.netcom.com> References: <3qumir$743@lyra.csx.cam.ac.uk> NNTP-Posting-Host: ix-clv1-20.ix.netcom.com Xref: biosci bionet.genome.chromosomes:641 bionet.molbio.genome-program:1399 bionet.general:15588 In <3qumir$743@lyra.csx.cam.ac.uk> Robert Brooksbank writes: > >I am trying to get a collection of human repeat sequences >together to use as competitors and probes in gene finding studies. >I have come across an acknowledgement to a company called Lagan Lagan-Michigan, USA 313-963-2190 800-526-7110 From owner-chromosomes@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!usc!news.cerf.net!newsserver.sdsc.edu!news.tc.cornell.edu!travelers.mail.cornell.edu!newsstand.cit.cornell.edu!NewsWatcher!user From: pts3@cornell.edu (phil) Newsgroups: bionet.genome.chromosomes Subject: Help!! Paper Wasps needed Followup-To: bionet.genome.chromosomes Date: 7 Jun 1995 02:44:29 GMT Organization: cornell Lines: 24 Sender: pts3@cornell.edu (Verified) Message-ID: NNTP-Posting-Host: cu-dialup-0615.cit.cornell.edu Hello. My name is Phil Starks. I am a graduate student at Cornell University in the field of NeuroBiology and Behavior. I am currently examining paper wasps, specifically Polistes dominulus. I am evaluating their nesting behavior and population genetics. I want to compare animals from different regions -- mostly from the Northeast in areas between Boston, MA and Ithaca, NY. My problem is finding these critters. They tend to congregate in the eves of man-made structures. I have searched state parks and some universities but have only found 4 usable sites. A usable site is one that has been relatively undisturbed (not sprayed with insecticides) for a few years and contains 18 or more colonies. These wasps make un-enveloped nests -- you can plainly see the cells of the comb (it looks much like a gray honeycomb). P. dominulus is the more yellow and smaller of the 2 Polistes species in this region (P. fuscatus is dark brown and the larger of the two animals). At this time of year you may see colonies with anywhere from 1 to 10 individuals, and nests that may contain 8 to 100 cells. If you know of any potential sites please email me. I am offering a $20.00 finder fee for useful sites. Thanks for reading this message Phil Starks (pts3@cornell.edu) From owner-chromosomes@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!news.primenet.com!ip134.lax.primenet.com!user From: portia@netcom.com (Portia Iversen) Newsgroups: bionet.genome.chromosomes Subject: autism Date: Wed, 07 Jun 1995 14:12:12 -0800 Organization: Primenet Lines: 5 Message-ID: NNTP-Posting-Host: ip134.lax.primenet.com Anything new on the genetics of autism? Any information would be very much appreciated. Thanks... -- -Portia From owner-chromosomes@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!uunet!in1.uu.net!newsflash.concordia.ca!news.mcgill.ca!usenet From: G.D. (popa0206@po-BOX.mcgill.ca) Newsgroups: bionet.genome.chromosomes Subject: Info on Bionet.molbio.recombination Date: 7 Jun 1995 22:10:21 GMT Organization: McGill University (Exp. Medicine) Lines: 114 Message-ID: <3r584d$an5@sifon.cc.mcgill.ca> NNTP-Posting-Host: e-06.das.mcgill.ca X-Newsreader: AIR News 3.X (SPRY, Inc.) I have posted a few times before about a new group bionet.molbio.recombination that I will be proposing soon.... Here is the rough proposal... if you have any comments please send them!!!! Start----------- Proposal to establish RECOMBINATION/bionet.molbio.recombination Proposed USENET name: bionet.molbio.recombination (unmoderated) Proposed mailing list name: RECOMBINATION Proposed e-mail addresses: recom@net.bio.net recom@daresbury.ac.uk Discussion leaders: Graham Dellaire, e-mail: popa0206@po-box.mcgill.ca (b2xe@musicb.mcgill.ca) Department of Medicine (Div. of Exp. Medicine), McGill Univeristy, Montreal, Quebec, Canada George Szatmari, e-mail: szat@ere.umontreal.ca Tentatively Denis Cournoyer (Mcgill Experimental Medicine) (gene therapy) Terry Chow (McGill): e-mail MDTY@Musica.mcgill.ca (mammalian genetics) Charter: The purpose of the RECOMBINATION newsgroup is to provide a proper forum for the discussion of issues pertaining and involving recombination of DNA or RNA, in its many forms (see _Topics of Discussion_). Primarily it should enable those researchers who work in recombination or aligned fields to communicate ideas and information, as well as, provide a chance for collaboration among national and international research groups. Topics of Discussion include: 1. Gene conversion and ectopic integration 2. Genome accessibility and nuclear/chromosome structure and recombination -Matrix attachment sites (MARS) -nucleosomes, histone 1 -recombination hotspots -fragile sites -origins of replication 3. Effect of DNA topology on recombination (Triple strand, Z-DNA, cruciform, bent etc) 4. Homologous recombination vs. nonhomologous or illegitimate -comparisons between bacterial, yeast and higher eukaryotic recombination systems (ex. fungi, mammals) 5. Models of recombination (One-end invasion, Double strand Break Repair, SSA etc) 6. Site-specific recombination systems (invertase, Cre and Flp recombinase etc) 7. Specific recombination systems in complex organisms -VDJ recombination -Antigenic variation and recombination (ex. trypanosomes, HIV, N.gonorrhea) -Yeast mating type locus 8. Transcription and recombination 9. DNA replication and recombination (ex. gene amplification (DHFR etc)) 10. Evolution of the Genome -retroposons (Line-1, Sine's), retroviruses and transposons -formation of gene clusters and comparative mapping -recombination between other repeat elements (alpha satellites, telomeres) 11. DNA repair systems and recombination (DSB and mismatch repair) -including DNA repair deficient diseases (ex. Xoderma Pigmentosum) 12. Applications of recombination -Gene therapy -Transgenics and gene transfer 13. Viral diversity through RNA recombination 14. Population genetics and recombination:i.e. as a source of allelic variation and as a measure of genetic exchange within and between populations. In addition this newsgroup provides: A forum for the exchange of information about future congresses and meetings in areas of molecular biology relating to recombination A forum for the exchange of information about textbooks, internet resources, visual materials, and computer programs. A source of quick help for last-minute troubleshooting, sources of materials, and practical advice; in areas such as -Vector design for transgene experiments -Gene transfer techniques -Animal models and cell lines -Gene therapy protocols Subscribers are welcome. Contributions within the functions outlined above are encouraged. The newsgroup is unmoderated. ---------------------------------------------------------------------- _______________________________________________________________________ Graham Dellaire Snail Mail: Red Cross, Research McGill Univeristy Montreal Blood Services Faculty of Medicine 3131 Sherbrooke St. East Div. of Experimental Medicine Montreal, QC, Canada E-mail: popa0206@po-box.mcgill.ca H1W 1B2 B2XE@musicb.mcgill.ca Fax: (514) 525 0881 Voice: (514) 527 1501 ext 175 _______________________________________________________________________ From owner-chromosomes@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!nntp.uio.no!nac.no!Norway.EU.net!EU.net!howland.reston.ans.net!torn!news.unb.ca!coranto.ucs.mun.ca!leif!roger From: roger@kean.ucs.mun.ca (ROGER GREEN,MEDICINE,ST.JOHN'S,NF,CAN) Newsgroups: bionet.genome.chromosomes Subject: Re: Simple Q on chromosomes Date: 7 Jun 95 16:53:11 -0230 Organization: Memorial University. St.John's Nfld, Canada Lines: 31 Distribution: world Message-ID: <1995Jun7.165311.1@leif> References: <9505250048.AA24654@ache.mad.adelaide.edu.au> NNTP-Posting-Host: leif.ucs.mun.ca > > Each chromosome exist as a pair, 23 pairs or 46 chromosomes are found in > the human genome. Not really. Chromosomes do NOT pair up EXCEPT during formation of gametes (sperm and ovum). Normally each of the 46 chromosomes exists quite independantly throughout all phases of the cell cycle. > Chromosome pairs join at the centromere during > replication, resulting in an X-like appearance. Again, chromosomes do NOT form pairs during normal replication. > The DNA contained in the > chromosome pairs is essentially identical, ie same genes in the same > position. However repetitive regions exist which may vary in length (these > variable regions are used in forensics for DNA fingerprinting) The DNA sequence in a pair of homologous chromosomes (e.g. the two number 6 chromosomes in each cell) is significantly different in many, many regions. These include differences (polymorphisms) in repeat-sequence regions, but there are also many differnces in genes (protein-coding regions). If this were not the case, we would all look the same. The DNA in the two chromatids (strands) of a single G2 or M-phase chromosome is normally 100% identical in all respects. > > Keep in mind that each strand of DNA exists as a double helix, consisting > of two complimentary strands (with A paired with T, and G paired with C) This is true. Roger C. Green, Faculty of Medicine Phone: (709)737-6884 Memorial University , St. John's, Newfoundland FAX : (709)737-7010 From owner-chromosomes@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!nac.no!Norway.EU.net!EU.net!howland.reston.ans.net!torn!news.unb.ca!coranto.ucs.mun.ca!leif!roger From: roger@kean.ucs.mun.ca (ROGER GREEN,MEDICINE,ST.JOHN'S,NF,CAN) Newsgroups: bionet.genome.chromosomes Subject: Re: Simple Q on chromosomes Date: 7 Jun 95 16:38:45 -0230 Organization: Memorial University. St.John's Nfld, Canada Lines: 22 Message-ID: <1995Jun7.163845.1@leif> References: <3pv8t9$pfs@columbia.acc.brad.ac.uk> <3pvtc3$hns@decaxp.harvard.edu> NNTP-Posting-Host: leif.ucs.mun.ca > 2) Those pictures are of replicated chromosomes. Each of > the little X-s you see are really two paired chromosomes, as you > are seeing the results of replication. Well, not exactly. The little X is NOT two chromosomes joined together. It is a single chromosome. There will be 46 X-s in each cell. The chromosome didn't start out like this. At the beginning of the cell cycle (the so-called G1 phase) each of the 46 chromosomes consists of one very long and thin strand of chromatin (=one DNA molecule plus a bunch of proteins). Later in the cell cycle (S phase) the strand of chromatin is replicated, but the two strands (now called chromatids) remain joined at the centromere. So each of the 46 chromosomes, still very long and thin, now contains two identical chromatids. As the cell moves from G2 into M phase (mitosis) the chromosomes become very short and thick. This is the only time they can be easily seen in the light microscope (as little X-s) The point is that, depending on the position in the cell cycle, a single chromosome can have one OR two strands of chromatin. Most cells in our body are in a sort of permanent G1 phase and so have only one strand. Roger C. Green, Faculty of Medicine Phone: (709)737-6884 Memorial University , St. John's, Newfoundland FAX : (709)737-7010 From owner-chromosomes@net.bio.net Wed Jun 07 23:00:00 1995 Path: biosci!biosci!not-for-mail From: lstein@genome.wi.mit.edu (Lincoln Stein) Newsgroups: bionet.announce,bionet.genome.chromosomes Subject: WHITEHEAD/MIT CGR HUMAN GENOME MAPPING PROJECT DATA RELEASE 7 Date: 7 Jun 1995 18:07:16 -0700 Organization: Whitehead Institute for Biomedical Research Lines: 87 Sender: biohelp@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: <3r1plf$232@senator-bedfellow.MIT.EDU> NNTP-Posting-Host: net.bio.net Keywords: STS YAC CEPH MEGAYAC LIBRARY CONTENT MAP HUMAN GENOME PHYSICAL MAPPING Xref: biosci bionet.announce:2166 bionet.genome.chromosomes:647 ANNOUNCING: WHITEHEAD INSTITUTE/MIT CENTER FOR GENOME RESEARCH HUMAN GENOMIC MAPPING PROJECT DATA RELEASE 7 (MAY 1995) The seventh release of data from the Human Physical Mapping Project at the Whitehead Institute/MIT Genome Center, covering data generated through the end of May, 1995, is now available. This data release contains YAC screening data for 10,028 sequence tagged sites (STSs) screened on the CEPH mega-YAC library. For each STS, we report addresses for the YACs found to contain the STS. From the data obtained so far, there are over 1100 contigs assembled using double linkage between STSs. The data is available electronically in two ways. ANONYMOUS FTP: The entire data release is available as a set of Microsoft Excel files and tab-delimited ascii files on our ftp server. Using an ftp client (such as "Fetch" on the Macintosh), connect to ftp-genome.wi.mit.edu Use "anonymous" as your user name, and give your e-mail address as your password. The data files are present in the directory /distribution/human_STS_releases/may95. The contents are as follows: 05-95.INTRO.mswd.hqx - Description of the data release, Macintosh format. 05-95.INTRO.txt - The same as ascii text 05-95.STS2YAC.sea.hqx - STS & YAC screening data, in MS-Excel format. 05-95.STS2YAC.txt - The same as tab-delimited text. 05-95.YAC2STS.txt - Inverse map of YAC to STS screening data 05-95.CONTIG2STS.txt - Doubly-linked contig information 05-95.sequence.txt - Full sequences of previously unpublished STSs. THE WORLD-WIDE WEB: You will need a World Wide Web client such as Mosaic (Unix, MS-Windows and Macintosh) or MacWeb (Macintosh). Instruct your client to connect to http://www-genome.wi.mit.edu/ >From there, follow the "Human Physical Mapping Project" link. You will be able to browse and download the raw data set as well as to view doubly-linked contigs. A subset of the STSs (those for which we have chromosomal assignments) are also available through the Genome Database (GDB). All STSs are also submitted to GenBank. QUESTIONS AND PROBLEMS. If users have any questions or problems, please contact us at human_STS_help@genome.wi.mit.edu We invite suggestions about how to make these data release most useful. DATA RELEASE POLICY AND CITATION. Data releases are scheduled monthly. At the end of each month, all genomic mapping data are reviewed and prepared for distribution via CGR's electronic databases. Data releases typically occur within a week of the close of the month. Releases are announced by electronic messages posted to the following two newsgroups: "bionet.genome.chromosomes" and "bionet.announce". CGR's data release policy aims to ensure that scientific colleagues have immediate access to information that may assist them in the search for genes. Data releases do not constitute scientific publication of CGR's work, but rather provide scientists with a regular look into our lab notebooks. For projects aimed at the analysis of particular genes or subchromosomal regions, permission is hereby granted to use our data without the need for a formal collaboration, subject only to appropriate acknowledgment. For projects aimed at large-scale mapping of entire chromosomes or entire genomes, use of the data and markers should be on a collaborative basis. The information for the human genome mapping project should be cited as: Whitehead Institute/MIT Center for Genome Research, Human Physical Mapping Project, Data Release 7 (May 1995). -- Lincoln D. Stein Whitehead Institute/MIT Genome Center lstein@genome.wi.mit.edu Cambridge, MA 02142 http://www-genome.wi.mit.edu/~lstein From owner-chromosomes@net.bio.net Thu Jun 08 23:00:00 1995 Path: biosci!agate!library.ucla.edu!news.bc.net!rover.ucs.ualberta.ca!tribune.usask.ca!news.sasknet.sk.ca!canopus.cc.umanitoba.ca!newsflash.concordia.ca!news.mcgill.ca!usenet From: Graham Dellaire Newsgroups: bionet.genome.chromosomes Subject: Experimental Medicine Home PAGE!!!! Date: 9 Jun 1995 02:57:38 GMT Organization: McGill University (Exp. Medicine) Lines: 28 Message-ID: <3r8db2$j85@sifon.cc.mcgill.ca> NNTP-Posting-Host: c-06.das.mcgill.ca X-Newsreader: AIR News 3.X (SPRY, Inc.) Recently the University of McGill has set up several departmental Web Pages: the most recent being the Division of Experimental Medicine Home Page It contains information of the program and a complete run down on finacial opportunities and the realities of persuing a Ph.D. at McGill University. Also there are some good links to Biology and Genetic Servers around the world. check it out at Http://www.medcor.mcgill.ca/EXPMED/expmed.html G. _______________________________________________________________________ Graham Dellaire Snail Mail: Red Cross, Research McGill Univeristy Montreal Blood Services Faculty of Medicine 3131 Sherbrooke St. East Div. of Experimental Medicine Montreal, QC, Canada E-mail: popa0206@po-box.mcgill.ca H1W 1B2 B2XE@musicb.mcgill.ca Fax: (514) 525 0881 Voice: (514) 527 1501 ext 175 _______________________________________________________________________ From owner-chromosomes@net.bio.net Fri Jun 09 23:00:00 1995 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.genome.chromosomes Subject: UNSUBSCRIBING, BIOSCI ARCHIVES, ADDRESS DATABASE & BIOSCI FAQ Date: 10 Jun 1995 02:00:25 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 347 Sender: daemon@net.bio.net Distribution: world Message-ID: <199506100900.CAA17388@net.bio.net> NNTP-Posting-Host: net.bio.net Four important items follow: How to cancel e-mail subscriptions to BIOSCI newsgroups, BIOSCI archive searching, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our BIOSCI user directory, please take a few minutes to complete and return the form below. If your personal information has changed since you listed yourself, please send us a complete new updated form. We can not make manual revisions to existing entries. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net **** How to cancel a BIOSCI e-mail subscription **** If you want to cancel your e-mail subscription to this group, PLEASE DO NOT POST YOUR UNSUBSCRIBE REQUEST TO THE NEWSGROUP ADDRESS (NOR REPLY TO A MESSAGE POSTED TO THE NEWSGROUP)!!! This would send your request to all of the readers of the newsgroup, but it might still not be seen by the BIOSCI staff - thus you would annoy many people and possibly not accomplish your goal anyway. IF YOU ARE LOCATED IN THE AMERICAS OR PACIFIC RIM COUNTRIES, please send a message to biosci@net.bio.net Instructions on how to subscribe/unsubscribe will be returned automatically, so the contents of your message do not matter. IF YOU ARE LOCATED IN EUROPE, AFRICA OR CENTRAL ASIA, please send a message to MXT@dl.ac.uk containing the word help in the body of the message to retrieve e-mail server instructions. Any text placed on the Subject: line of your message will be ignored, so be sure to put the "help" command in the body of the message. If you need personal assistance, a BIOSCI staff member can be contacted at either of the following addresses. Please contact the address designated for your location. Support Address Location --------------- -------- biosci@daresbury.ac.uk Europe, Africa, and Central Asia biosci-help@net.bio.net Americas and the Pacific Rim **** SEARCHING BIOSCI ARCHIVES **** The easiest way to search the BIOSCI archives is to use Mosaic or another World Wide Web browser and connect to the BIOSCI WWW home page at URL http://www.bio.net/. Select the hypertext link to the BIOSCI archives. This gives you read access to all newsgroup messages and the ability to search the indexes described below. You can also use gopher software and connect over the Internet to net.bio.net, the U.S. BIOSCI computer. We maintain three indexes which are searchable from the main gopher menu on net.bio.net: (1) an index of all BIOSCI postings; (2) an index of individual journal article references from the Table of Contents postings on the BIO-JOURNALS newsgroup; and (3) an index of BIOSCI users including regular mail and e-mail addresses, phone/FAX numbers, research interests, and newsgroup participation. 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). WAIS software can also be used to search the archives as described in the BIOSCI FAQ (see below). Finally, the BIOSCI archive files are accessible by anonymous FTP to net.bio.net [134.172.2.69] in the directory pub/BIOSCI. **** BIOSCI FREQUENTLY ASKED QUESTIONS (FAQ) SHEET **** New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and fix problems that you might encounter in using the newsgroups. The FAQ and other BIOSCI documentation is available through our WWW home page at URL http://www.bio.net/. It is also available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/doc/biosci.FAQ or for retrieval by gopher to net.bio.net, port 70. It may also be requested by sending the command info faq in the body of an e-mail message to the Internet address biosci-server@net.bio.net. Please do not enter the info faq command on the Subject: line of your message since the e-mail server ignores text on the Subject: line. 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. **** BIOSCI USER ADDRESS DIRECTORY **** Please take this opportunity to add your name and address information to the BIOSCI User Address Database if you have not already done so. Below is the address form that we would like each reader of the BIOSCI/bionet newsgroups to complete and return if you would like to be listed in our database. The database serves as a directory that enables biologists, who are currently using (or even just reading) the BIOSCI newsgroups, to look up e-mail addresses and other information about our users. The address database is reindexed nightly for WAIS, waismail, gopher, and WWW access (the URL is http://www.bio.net). If you have access to gopher, connect to net.bio.net to search the database. If you have access to WAIS, please use our WAIS source biologists-addresses.src. If you are not on the Internet, please use our waismail server (send the word "help" to waismail@net.bio.net to get instructions; any text on the Subject: line of your message will be ignored, so put the help command in the body of the mail message.). Please carefully follow the instructions for completing the form below and return it to either of the following two addresses (whichever is more convenient for you). Thanks in advance for taking the time to complete and return the form. Addresses for returning forms Location Network ----------------------------- -------- ------- biovote@net.bio.net U.S.A. Internet/BITNET biovote@daresbury.ac.uk U.K. JANET MAKING SURE THAT YOUR INFORMATION IS CURRENT This notice will be mailed bimonthly to each newsgroup. You should check your database entry from time-to-time to see if your address information is still up-to-date. Using Gopher to complete the form --------------------------------- If you don't want to use a text editor, you can also use Dan Jacobson's gopher site to fill out the address database form as follows. Otherwise skip this section on gopher and proceed to the instructions for filling out the form below. > To add yourself to the database just point your > gopher client at merlot.gdb.org and select the following: > > --> 14. Searching For Biologists/ > > --> 9. E-mail Addresses of Biosci-Bionet Users/ > > --> 1. Add (or Correct) Your Address to the BIOSCI User Address > Data.. > > > And fill out the form. or Rob Harper's gopher site in Europe as follows: > Europeans can point their gopher client at gopher.csc.fi and add their > information to the database. All entries will be mailed directly to > Dave for incorporation in a wais source. > > The path to the questionare is as follows. > > > 6. Information in English/ > > 5. Scientific and other topics/ > > 1. Finnish EMBnet BioBox/ > > 9. FAQ Files/ > > 5. Bionauts Address Database (questionaire) > IMPORTANT INSTRUCTIONS - PLEASE READ CAREFULLY Please enter all responses after the : on each line, leaving one (1) blank space after the : (i.e., before the start of your text). Please do NOT extend your responses past the end of each line (80 characters). PLEASE DO NOT alter any of the field identifiers such as "first name: ". If you have nothing to enter after a field identifier, PLEASE LEAVE IT - do not delete it even if there is no data on the line in question. Several lines are provided at the end of the form for comments, but, please adhere to the line length restriction. On the date: line, please enter the date in the DD-MM-YY format, e.g., 15-05-93 for 15 May 1993. This line will tell others when the information was last updated. Please be sure to include the 0's for single digit days or months, e.g., 15-05-93, not 15-5-93. Note that the "e-mail network: " line below is for specifying, e.g., "Internet," "BITNET," "EARN," "JANET," or whatever other network that your computer may be on. If you are uncertain about any field, please feel free to leave it blank, but please DO NOT DELETE the field identifier from the form! In the first field below, "New information or Update ...", please enter "N" if this is the first time that you have registered in the directory or "U" if you are correcting a listing that you sent to us previously. The comment: lines may be used for anything that you like but PLEASE DO NOT DELETE THEM FROM THE FORM OR ALTER THEM. One suggested use is to list the names of the newsgroups in which you participate. Please use the MAILING LIST name (see below - the latest version of the list can be requested from biosci@net.bio.net) instead of the USENET name even if you don't participate by e-mail. WAIS might get confused by the periods in the USENET names. This allows one to retrieve via WAIS or waismail the list of participants in a particular group. For example: comment: ARABIDOPSIS PLANT-BIOLOGY BIONEWS On the comment: lines use these names below ---- NOT the USENET names below MAILING LIST NAME USENET Newsgroup Name ----------------- --------------------- ACEDB-SOFT bionet.software.acedb AGEING bionet.molbio.ageing AGROFORESTRY bionet.agroforestry ARABIDOPSIS bionet.genome.arabidopsis ASCB bionet.prof-society.ascb BIOCAN bionet.prof-society.cfbs 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 BIOPHYSICAL-SOCIETY bionet.prof-society.biophysics BIOPHYSICS bionet.biophysics BIO-SOFTWARE bionet.software BIOTHERMOKINETICS bionet.metabolic-reg BIO-WWW bionet.software.www CARDIOVASCULAR-RESEARCH bionet.biology.cardiovascular CELEGANS bionet.celegans CELL-BIOLOGY bionet.cellbiol CHLAMYDOMONAS bionet.chlamydomonas CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational CSM bionet.prof-society.csm CYTONET bionet.cellbiol.cytonet DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMF-BIO bionet.emf-bio EMPLOYMENT bionet.jobs EMPLOYMENT-WANTED bionet.jobs.wanted FASEB bionet.prof-society.faseb GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage GRASSES-SCIENCE bionet.biology.grasses 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 MICROBIOLOGY bionet.microbiology MOLECULAR-EVOLUTION bionet.molbio.evolution MOLECULAR-MODELLING bionet.molec-model MOLLUSC-MOLECULAR-NEWS bionet.molbio.molluscs MYCOLOGY bionet.mycology NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PARASITOLOGY bionet.parasitology PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography PROTISTA bionet.protista RAPD bionet.molbio.rapd SCIENCE-RESOURCES bionet.sci-resources STADEN bionet.software.staden STRUCTURAL-NMR bionet.structural-nmr TROPICAL-BIOLOGY bionet.biology.tropical URODELES bionet.organisms.urodeles VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast ZBRAFISH bionet.organisms.zebrafish Listing newsgroups on the comment: line is optional, of course. Thanks again for your cooperation! --------------- please cut here and return portion below --------------- New information or Update to old record (enter N or U): date (DD-MM-YY): first name: middle initial: family name: job title: e-mail address: e-mail network: phone number: FAX number: institution: address1: address2: address3: city: state/province: country: postal code: research interest: research interest: comment: comment: comment: comment: comment: From owner-chromosomes@net.bio.net Sat Jun 10 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!uwm.edu!msunews!harbinger.cc.monash.edu.au!news.cs.su.oz.au!metro!seagoon.newcastle.edu.au!cc.newcastle.edu.au!mdjlsc From: mdjlsc@cc.newcastle.edu.au Newsgroups: bionet.genome.chromosomes Subject: MAN OR MOUSE? Date: 11 Jun 95 22:36:06 +1000 Organization: University of Newcastle, AUSTRALIA Lines: 24 Message-ID: <1995Jun11.223606.1@cc.newcastle.edu.au> NNTP-Posting-Host: cc.newcastle.edu.au I have a problem with the identity of a cultured cell line. This cell line was derived from a lymph node metastasis of human melanoma some years ago (1978). Since I have started working with the line (an unusual line for a melanoma cell). I have been concerned that this line may have been cross contaminated with rodent cells (Only a hunch as most of the melanoma antigens tested for are negative). I asked our local cytogenetics lab to look at the karyotype of the line, and they found an average of 56 chromosomes (nothing atypical for a human cultured cell). None of the chromosomes were identical to normal human ones, although some were close, and quite dissimilar to normal mouse chromosomes. The lab used a test called G11 (Giemsa staining at pH 11) to differentiate between rodent and human chromosomes - one supposedly stains mainly blue (human) and the other magenta (rodent). Does anyone know how reliable this test is? and is it good enough to really differentiate between human and rodent chromosomes. If anyone could be of any help, could they please email me a response as I dont get to check the newsgroups too often. Thanks Rick Thorne The University of Newcastle, Australia //I wouldn't be doing it if it wasn't important// From owner-chromosomes@net.bio.net Sat Jun 10 23:00:00 1995 Path: biosci!agate!spool.mu.edu!uwm.edu!cs.utexas.edu!swrinde!pipex!oleane!jussieu.fr!fdn.fr!uunet!in1.uu.net!prodigy.com!usenet From: MRCG94A@prodigy.com (Robert Helf) Newsgroups: bionet.genome.chromosomes Subject: CHROMOSOME TWO Date: 11 Jun 1995 17:50:44 GMT Organization: Prodigy Services Company 1-800-PRODIGY Lines: 10 Distribution: world Message-ID: <3rfadk$2kso@usenetp1.news.prodigy.com> NNTP-Posting-Host: inugap3.news.prodigy.com X-Newsreader: Version 1.2 lOOKING FOR INFORMATION ABOUT CHROMOSOME TWO AS FAR AS BIRTH DEFECTS. WE ARE PRIMARILY CONCERNED WITH THIS CHROMOSOME REGAURDING 'MOSIAC PATTERNS'. NOT EVERY CHROMOSOME TWO IN THIS FETUS SHOWS A DEFECT. OUT OF 26 CULTURES, FIVE SHOWED CHROMOSOME TWO DEFECTED. YOUR REPLY IS GREATLY APPRECIATED AS TIME IS A FACTOR. THANK YOU, SUSAN From owner-chromosomes@net.bio.net Mon Jun 12 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!usenet.eel.ufl.edu!usenet.cis.ufl.edu!usenet.ufl.edu!usenet From: bieniek@gnv.ifas.ufl.edu Newsgroups: bionet.genome.chromosomes Subject: Re: CHROMOSOME TWO Date: 13 Jun 1995 13:22:55 GMT Organization: University of Florida Lines: 3 Message-ID: <3rk3ff$4p2@no-names.nerdc.ufl.edu> References: <3rfadk$2kso@usenetp1.news.prodigy.com> NNTP-Posting-Host: 128.227.134.150 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Windows; I; 16bit) To: MRCG94A@prodigy.com Have you tried the human genome data base? here is the www address. http://gdbwww.gdb.org/ From owner-chromosomes@net.bio.net Tue Jun 13 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!Germany.EU.net!EU.net!uunet!in1.uu.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!happy.rediris.es!news.rediris.es!obelix.cica.es!vivero!jose.vivero From: jose.vivero@uca.es (Jose Fernandez Vivero) Newsgroups: bionet.genome.chromosomes Subject: Software for caryotyping Date: Tue, 13 Jun 1995 14:30:03 Organization: Ciencias Morfologicas - Universidad de Cadiz Lines: 3 Message-ID: NNTP-Posting-Host: vivero.uca.es X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] We appreciate to receive accurate information about software for automatic and semiautomatic human karyotyping including price, distributors and personal experience with them From owner-chromosomes@net.bio.net Tue Jun 13 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!Germany.EU.net!news.dfn.de!uni-muenster.de!ifepmac1.uni-muenster.de!user From: RNA.world@uni-muenster.de (Juergen Brosius) Newsgroups: bionet.genome.chromosomes Subject: Re: Lagan Inc. address or alternative source of repeat sequences needed Followup-To: bionet.genome.chromosomes,bionet.molbio.genome-program,bionet.general Date: Wed, 14 Jun 1995 17:44:11 +0200 Organization: University Muenster Germany Lines: 12 Message-ID: References: <3qumir$743@lyra.csx.cam.ac.uk> NNTP-Posting-Host: ifepmac1.uni-muenster.de In article <3qumir$743@lyra.csx.cam.ac.uk>, Robert Brooksbank wrote: > I am trying to get a collection of human repeat sequences > together Why bother? In case you just want to address repeat families of 50,000 or more copies just get some human genomic DNA and label it by nick translation with 32-P. This is your probe. Details are described in a paper by Whitney and Furano entitled: Highly repeated DNA families in the rat. J. Biol. Chem. 259, 10481-10492 (1984). Good luck! Juergen From owner-chromosomes@net.bio.net Wed Jun 14 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!usc!howland.reston.ans.net!news.sprintlink.net!uunet!zib-berlin.de!uni-duisburg.de!sun1.hrz.uni-essen.de!aixrs1.hrz.uni-essen.de!ttu3a0 From: ttu3a0@aixrs1.hrz.uni-essen.de (Bernd Koelsch) Newsgroups: bionet.genome.chromosomes Subject: rat gene maps Date: 13 Jun 1995 23:50:21 GMT Organization: Universitaet Essen GH, Germany Lines: 15 Message-ID: <3rl87t$bcc@sun1.uni-essen.de> NNTP-Posting-Host: aixrs1.hrz.uni-essen.de X-Newsreader: TIN [version 1.2 PL2] Who knows where I can find information about rat gene maps? Is there a location in the internet with such information?? Bernd K”lsch Cell-biology 45147 Essen, Germany e-mail ttu3a0@aixrs1.hrz.uni-essen.de w From owner-chromosomes@net.bio.net Wed Jun 14 23:00:00 1995 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!news.sprintlink.net!pipex!sunsite.doc.ic.ac.uk!hgmp.mrc.ac.uk!jattwood From: jattwood@hgmp.mrc.ac.uk (Mr J. Attwood) Newsgroups: bionet.genome.chromosomes,bionet.molbio.genome-program Subject: Human Chromosome 9 SCW Report now on WWW Date: 15 Jun 1995 16:57:20 GMT Organization: UK HGMP Resource Centre Lines: 35 Message-ID: <3rpopg$q5v@mercury.hgmp.mrc.ac.uk> NNTP-Posting-Host: tin.hgmp.mrc.ac.uk Xref: biosci bionet.genome.chromosomes:658 bionet.molbio.genome-program:1414 The full report of the 1995 Single Chromosome Workshop for Human Chromosome 9, held at Williamsburg, Virginia in April is now available in Hypertext form via the Chromosome 9 Home Page at the URL:- http://www.gene.ucl.ac.uk/chr9home.html It is fully cross-linked to the abstracts, figures, tables, etc and to outside WWW and FTP resources mentioned in the text. The figures are provided as both GIF files which can be viewed on-line and PostScript which can be downloaded and printed out for higher quality. Most of the report should be accessible to just about any browser, but you will obviously need graphics capabilities to view the figures. It definitely works best with NetScape, but Mosaic seems a good alternative. A set of breakpoints in the CEPH families can be accessed from the report, as well as an interactive form to request a subset of breakpoints suitable for mapping a new marker. The information on cosmids is still being assembled and tested, but we hope to have it on-line fairly soon. Several small but important corrections have been incorporated into the hypertext version, and retro-fitted to the plain text version available by ftp and announced earlier. Anyone who has downloaded the original should replace it with a new copy - ftp to ftp.gene.ucl.ac.uk, and get all the .txt files from the directory /pub/c9workshop/1995. Problems with (perhaps even praise of?) the Hypertext version should be addressed to me (john@mrc-hbgu.ucl.ac.uk), and I would also be very interested to hear from people using other Web browsers to look at these pages, as I only have access to Mosaic and NetScape. John Attwood, MRC Human Biochemical Genetics Unit, London UK. From owner-chromosomes@net.bio.net Wed Jun 14 23:00:00 1995 Path: biosci!CMU.CHIANGMAI.AC.TH!mdbcs001 From: mdbcs001@CMU.CHIANGMAI.AC.TH (Wirote Tuntiwechapikul) Newsgroups: bionet.genome.chromosomes Subject: how to unsubbscribe? Date: 15 Jun 1995 11:24:28 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 5 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Anyone there knows how to unsubscribe this particular mailing list (biochrom@net.bio.net). I have unsubscribed other mailing list with no difficulty but only this one. It seems like this one doesn't belong to other net.bio.net Thanks. From owner-chromosomes@net.bio.net Wed Jun 14 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!usc!howland.reston.ans.net!Germany.EU.net!zib-berlin.de!uni-duisburg.de!sun1.hrz.uni-essen.de!aixrs1.hrz.uni-essen.de!ttu3a0 From: ttu3a0@aixrs1.hrz.uni-essen.de (Bernd Koelsch) Newsgroups: bionet.genome.chromosomes Subject: rat chromosome paints Date: 14 Jun 1995 00:04:06 GMT Organization: Universitaet Essen GH, Germany Lines: 13 Message-ID: <3rl91m$bcc@sun1.uni-essen.de> NNTP-Posting-Host: aixrs1.hrz.uni-essen.de X-Newsreader: TIN [version 1.2 PL2] I work with rat tumors and try to establish their karyotype. Is there anyone who knows wher I can get such paints?? Bernd K”lsch Cell-biology 45147 Essen, Germany e-mail: ttu3a0@aixrs1.hrz.uni-essen.de knowq s where I can From owner-chromosomes@net.bio.net Sun Jun 18 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!news.sprintlink.net!europa.chnt.gtegsc.com!casaba.srv.cs.cmu.edu!das-news2.harvard.edu!fas-news.harvard.edu!mito!robison From: robison@mito.harvard.edu (Keith Robison) Newsgroups: bionet.genome.chromosomes Subject: Re: rat gene maps Date: 19 Jun 1995 16:07:18 GMT Organization: Harvard University, Cambridge, Massachusetts Lines: 22 Message-ID: <3s47bm$c1u@decaxp.harvard.edu> References: <3rl87t$bcc@sun1.uni-essen.de> NNTP-Posting-Host: mito.harvard.edu X-Newsreader: TIN [version 1.2 PL2] Bernd Koelsch (ttu3a0@aixrs1.hrz.uni-essen.de) wrote: : Who knows where I can find information about rat gene maps? : Is there a location in the internet with such information?? MIT/Whitehead has a Rat Genetic Map. You can get there via http://golgi.harvard.edu/htbin/biopages?rat+genome Enjoy! (as much as anyone can enjoy something dealing with rats :-) Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI robison@mito.harvard.edu From owner-chromosomes@net.bio.net Wed Jun 21 23:00:00 1995 Newsgroups: ebi.servers,bionet.molbio.embldatabank,bionet.software,bionet.genome.arabidopsis,bionet.genome.chromosomes,bionet.molbio.genome-program,bionet.molbio.yeast,embnet.general Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!cam.news.pipex.net!pipex!edi.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!jecop From: jecop@ebi.ac.uk (Jeroen Coppieters) Subject: ANNOUNCEMENT OF EUROPEAN GENEMARK E-MAIL SERVER Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Thu, 22 Jun 1995 13:33:53 GMT Organization: European Bioinformatics Institute X-Newsreader: TIN [version 1.2 PL2] Lines: 151 Xref: biosci bionet.molbio.embldatabank:519 bionet.software:12432 bionet.genome.arabidopsis:3455 bionet.genome.chromosomes:664 bionet.molbio.genome-program:1422 bionet.molbio.yeast:3158 ANNOUNCEMENT OF EUROPEAN GENEMARK E-MAIL SERVER >From June 20th on, GeneMark will be reachable at the EMBL Outstation - The European Bioinformatics Institute (EBI), Hinxton, UK EMAIL: genemark@embl-ebi.ac.uk (or genemark@ebi.ac.uk) as well as on the original site School of Biology, Georgia Institute of Technology (Atlanta, GA) EMAIL: genemark@ford.gatech.edu Since its first announcement, the GeneMark program has undergone continuous improvements, and more species matrices are made available for usage with the service. The EMBL-EBI server is a mirror of the Georgia one, and thus will return the same results for the same queries. 1. SHORT OVERVIEW OF GENEMARK FEATURES --------------------------------------------- The GeneMark server provides e-mail based identification of protein coding regions in DNA sequences from prokaryotic and eukaryotic species. The GeneMark server accepts a formatted message containing a DNA sequence in text format. You may specify a species name, and parameters that control the analysis procedure. The current GeneMark version is accurate for finding prokaryotic genes and for analyzing cDNA sequences to discriminate coding regions from non-coding ones like 5' or 3' UTRs. This program is able to identify rather long exons (more than 100bp) in eukaryotic genomic DNA. This information can be used for designing RT-PCR or PCR primers. The GeneMark gene identification program has been developed at the School of Biology, Georgia Institute of Technology (Atlanta, GA). More details on the algorithm can be found in the paper: Borodovsky M. and McIninch J.D., GeneMark: Parallel gene recognition for both DNA strands, Computers & Chemistry, 1993, 17, 123-133. 2. SENDING DATA TO GENEMARK ----------------------------------------------------- A DNA sequence should be sent via e-mail to one of the following addresses: genemark@ford.gatech.edu or genemark@embl-ebi.ac.uk ... with the word 'genemark' in the 'Subject:' field There is only one mandatory keyword: DATA which must precede the text of the DNA sequence. Below is given a simple example of sending a sequence to the GeneMark server from a UNIX-based computer (note, that the '%' symbol is the prompt used by the system, and that lower-case letters in the sequence text, numbers and spaces are also acceptable): % mail genemark@embl-ebi.ac.uk (or % mail genemark@ford.gatech.edu) Subject: genemark data TCCAGCTACTGCTGCTAGCTACGCTAGTCG........ % When the server receives such a message, with almost no special options indicated, it will analyze the sequence using default options and send back a minimal response. Namely, it will use E. coli based parameters (by default) and send back to the submitter a message containing a list of those open reading frames that have been assessed as protein coding regions. You may, however, wish to get more information from the server. In that case, please retrieve the HELP-Message from the GeneMark server, which contains a full description of all commands and options 3. GETTING THE HELP MESSAGE FROM GENEMARK ------------------------------------------------ Send an e-mail with the word HELP in the 'Subject:' field to genemark@ford.gatech.edu or genemark@embl-ebi.ac.uk 4. THE LIST OF SPECIES THAT CAN BE ANALYZED USING GENEMARK ------------------------------------------------------------------------------ NOTE: The EMBL-EBI server supports retrieval of the current list of supported species. Send a message to genemark@embl-ebi.ac.uk with the command LIST ORG in the SUBJECT The matrix is specified using the 'SPECIES' command Use the line 'species ' anywhere before the line 'data' where is the name of one of the matrices listed below: Matrix Name Species ----------- -------------------------------------------------------------- arab Arabidopsis thaliana capri Mycoplasma capricolum (TGA = Trp) celegans Caenorhabditis elegans chicken Gallus gallus disco Dictyostelium discoideum ecoli Escherichia coli "native" genes [DEFAULT] ecophage Escherichia coli horizontally transferred genes euglena Euglena gracilis eugchlor Euglena gracilis chloroplasts frog Xenopus laevis fruitfly Drosophila melanogaster human Homo sapiens kpneu Klebsiella pneumoniae lacto Lactococcus species leprae Mycobacterium leprae mouse Mus musculus plasm Plasmodium falciparum rat Rattus norvegicus salm Salmonella typhimurium spombe Schizosaccharomyces pombe subt Bacillus subtilis tuberc Mycobacterium tuberculosis t4 Phage T4 urchin Lytechinus pictus yeast Saccharomyces cerevisiae -------------------------------------------------------------------------- -- ============================================================== . O . Jeroen Coppieters . O O o O . Software Support O O O O *o O O Jeroen.Coppieters@embl-ebi.ac.uk O O O O( *o )O O (or jecop@ebi.ac.uk) )O O O O o* O O( ++44 1223 494422 O O O O( o* )O O )O O O O *o O O( EMBL Outstation EBI O O O O( *o )O O (European Bioinformatics Institute) )O @ O O o* O O( Hinxton Hall O O O( o* )O(' Hinxton ` O( *o O ' Cambridge CB10 1RQ ` O ' UK http://www.ebi.ac.uk ============================================================== From owner-chromosomes@net.bio.net Wed Jun 21 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!cam.news.pipex.net!pipex!edi.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!ghost.dsi.unimi.it!sirio.cineca.it!mac-grossi.cineca.it!user From: agr0@icineca.cineca.it (Dr. Ivan Grossi) Newsgroups: bionet.genome.chromosomes Subject: call for candidatures - grants for supercomputing resources Followup-To: bionet.genome.chromosomes Date: Thu, 22 Jun 1995 15:43:55 +0400 Organization: Cineca - Interuniversity Computing Centre - Italy Lines: 185 Message-ID: NNTP-Posting-Host: mac-grossi.cineca.it CALL FOR CANDIDATURES FOR EUROPEAN UNION RESEARCHERS AND EASTERN EUROPEAN COUNTRIES AND NIS - NEW INDEPENDENT STATES (former Soviet Union) ***************PART A: EU RESEARCHERS EC - Human Capital and Mobility Programme CINECA - ICARUS Project Intensive Computing for Advanced Interdisciplinary Research of EUropean Scientists 1996 CALL FOR CANDIDATURES (1996 Call Deadlines : August 31, 1995; November 30, 1995; February 28, 1996; May 31, 1996) Short presentation of the ICARUS project CINECA, a consortium made up of 13 Italian universities, has been appointed, because of its large-scale scientific and technical facilities, as a centre for the application of supercomputing in interdisciplinary research activities. To this purpose CINECA will host Researchers (up to an equivalent of 144 man/months) from January 1994 through December 1996 so that European Researchers may make use of the resources and services here available. Scientific activities and policy of use of CINECA's supercomputing facilities of EC Researchers will be agreed with an International Scientific Committee. With regard to the supercomputing aspect of the project, CINECA will provide hosted European Researchers with training, vector and parallel supercomputing facilities, access to scientific visualisation laboratory and to on-line information service. The Researchers will be provided with the support of CINECA experts for the best use of resources available. Hosted Reasearchers will be supported by the project for travel and accomodation expenses too. The usability of the service provided by CINECA is guaranteed by a capillary and powerful network of data transmission. Cinecanet, in fact, is joined to the High- speed GARR Network (the Italian research communication network). This will allow European Researchers to continue using CINECA's facilities from home institution, when they will come back home. The researchers to be hosted can count on the availability of: CRAY C92/2128 CRAY T3D with 64 nodes IBM S/390-9672 VAX 6000-510 ACS 4400 -Automatic Cartridge System CINECA communication network The laboratory of scientific visualization The on-line documentation and information service. Candidates are requested to fill and mail the form which can be find at the following internet address: http://www.cineca.it/icarus/welcome.htm or obtained via anonymous ftp from: ftp.cineca.it pub/doc/cineca/icarus_form.ps.Z (compressed postscript) pub/doc/cineca/icarus_form.txt (ASCII version) pub/doc/cineca/icarus_form.doc (word for windows 2.0) with information about the research project they aim to pursue while they are at Cineca Supercomputing Centre, the duration of the stay and the estimated supercomputing resources they will need. European Union citizens of the following countries are eligible : Belgium,Denmark,France, Germany, Greece,Irland, Italy, Luxembourg,Portugal, Spain, The Netherlands,United Kingdom. Disciplines covered by the multidisciplinary project: : Biotechnologies, Chemistry, Earth Sciences, Computer Science, Economics, Engineering, Human Sciences, Mathematics, Physics. Scientific Coordinator: Dr. Mario LANZARINI, Director The ICARUS project is under a EC Contract nˇ CHGE-CT93-0048 (DG 12 COMA) For further information, please contact: Dr. Ivan Grossi CINECA Via Magnanelli 6/3 I-40033 Casalecchio di Reno (Bologna) Italy Phone: +39-51-6599 411 Fax: +39-51-6592 581 E-mail: grossi @ cineca.it EC - Human Capital and Mobility Programme *************PART B: EASTERN AND CENTRAL EUROPEAN COUNTRIES AND NIS - NEW INDEPENDENT STATES (former Soviet Union) CINECA - I.PE.R. ICARUS Project ICARUS project EXTENSION TO EASTERN EUROPEAN COUNTRIES AND NIS - NEW INDEPENDENT STATES (former Soviet Union) Intensive Computing for Advanced Interdisciplinary Research of EUropean Scientists 1996 CALL FOR CANDIDATURES (1996 Call Deadline: August 31, 1995 ) Short presentation of the I.PE.R. ICARUS project CINECA, a consortium made up of 13 Italian universities, has been appointed, because of its large-scale scientific and technical facilities, as a centre for the application of supercomputing in interdisciplinary research activities. To this purpose CINECA will host Researchers (up to an equivalent of 24 man/months) from January 1995 through December 1996 so that Central and Eastern European Researchers and CIS Researchers may make use of the resources and services here available. Scientific activities and policy of use of CINECA's supercomputing facilities of Researchers will be agreed with an International Scientific Committee. With regard to the supercomputing aspect of the project, CINECA will provide hosted Researchers with training, vector and parallel supercomputing facilities, access to scientific visualisation laboratory and to on-line information service. The Researchers will be provided with the support of CINECA experts for the best use of resources available. Hosted Reasearchers will be supported by the project for travel and accomodation expenses too. The usability of the service provided by CINECA is guaranteed by a capillary and powerful network of data transmission. Cinecanet, in fact, is joined to the High- speed GARR Network (the Italian research communication network). This will allow Researchers to continue using CINECA's facilities from home institution, when they will come back home. The researchers to be hosted can count on the availability of: CRAY C92/2128 CRAY T3D with 64 nodes IBM S/390-9672 VAX 6000-510 ACS 4400 -Automatic Cartridge System CINECA communication network The laboratory of scientific visualization The on-line documentation and information service. Candidates are requested to fill and mail the form which can be find at the following internet address: http://www.cineca.it/icarus/welcome.htm or obtained via anonymous ftp from: ftp.cineca.it pub/doc/cineca/ipericarus_form.ps.Z (compressed postscript) pub/doc/cineca/ipericarus_form.txt (ASCII version) pub/doc/cineca/ipericarus_form.doc (word for windows 2.0) with information about the research project they aim to pursue while they are at Cineca Supercomputing Centre, the duration of the stay and the estimated supercomputing resources they will need. Eastern European Countries and CIS citizens only are eligible Disciplines covered by the multidisciplinary project: : Biotechnologies, Chemistry, Earth Sciences, Computer Science, Economics, Engineering, Human Sciences, Mathematics, Physics. Scientific Coordinator: Dr. Mario LANZARINI, Director The ICARUS project is under a EC Contract nˇ CHGE-CT93-0048 (DG 12 COMA) For further information, please contact: Dr. Ivan Grossi CINECA Via Magnanelli 6/3 I-40033 Casalecchio di Reno (Bologna) Italy Phone: +39-51-6599 411 Fax: +39-51-6592 581 E-mail: grossi @ cineca.it From owner-chromosomes@net.bio.net Wed Jun 21 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!news.starnet.net!wupost!howland.reston.ans.net!agate!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: Newsgroups: bionet.genome.chromosomes Subject: primate cell lines Date: 22 Jun 1995 05:42:28 +0100 Lines: 16 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3sasbk$445@mserv1.dl.ac.uk> X-Sender: rocchi@plauto.csata.it Original-To: biochrom@dl.ac.uk I am working on karyotype evolution of primates. I am looking for lymphoblast (or fibroblast) cell lines from primates, especially from a male gorilla and a female gibbon (HLA). Could anyone help me? Gratefully Dr. Mariano Rocchi Dr. Mariano Rocchi Ist. Genetica Via Amendola 165/A 70126 Bari, Italy tl +39-80-5443.371 fax +39-80-5443.386 em rocchi@mvx36.csata.it From owner-chromosomes@net.bio.net Wed Jun 21 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!usc!howland.reston.ans.net!agate!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: Newsgroups: bionet.genome.chromosomes Subject: primate cell lines Date: 22 Jun 1995 05:42:29 +0100 Lines: 13 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3sasbl$44g@mserv1.dl.ac.uk> X-Sender: rocchi@plauto.csata.it Original-To: biochrom@dl.ac.uk I am working on karyotype evolution of primates. I am looking for lymphoblast (or fibroblast) cell lines from primates, especially from a male gorilla and a female gibbon (HLA). Could anyone help me? Dr. Mariano Rocchi Ist. Genetica Via Amendola 165/A 70126 Bari, Italy tl +39-80-5443.371 fax +39-80-5443.386 em rocchi@mvx36.csata.it From owner-chromosomes@net.bio.net Thu Jun 22 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!cam.news.pipex.net!pipex!edi.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: Newsgroups: bionet.genome.chromosomes Subject: impact factor Date: 23 Jun 1995 16:25:28 +0100 Lines: 20 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3semd8$c3t@mserv1.dl.ac.uk> X-Sender: rocchi@plauto.csata.it Original-To: biochrom@dl.ac.uk I need to know the "impact factor" of Human Molecular Genetics Nature Genetics Anatomy and Embriology Mammalian Genome Somat Cell and Molec Genetics Genomics Anatom Rec Thanks Mariano Rocchi Dr. Mariano Rocchi Ist. Genetica Via Amendola 165/A 70126 Bari, Italy tl +39-80-5443.371 fax +39-80-5443.386 em rocchi@mvx36.csata.it From owner-chromosomes@net.bio.net Sun Jun 25 23:00:00 1995 Path: biosci!CRIBA.EDU.AR!sbassi From: sbassi@CRIBA.EDU.AR (Sebastian Bassi) Newsgroups: bionet.genome.chromosomes Subject: Imprinting Date: 25 Jun 1995 16:21:13 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: Hello, I'm studing medicine, and I'd like to understand what is IMPRINTING. I read books of genetics (like 'Genetics in medicine', by Thompson & Thompson), but I couldn't understand it. I'd like that someone could help, with a 'plain english explanation'. I know how is defined, but I think would be nice some example, with pedigree. Regards, Sebastian Bassi email: sbassi@criba.edu.ar From owner-chromosomes@net.bio.net Mon Jun 26 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!news.uoregon.edu!gatech!bloom-beacon.mit.edu!world!decwrl!tribune.usask.ca!canopus.cc.umanitoba.ca!newsflash.concordia.ca!news.mcgill.ca!news From: Graham Dellaire Newsgroups: bionet.genome.chromosomes Subject: Re: Imprinting Date: 26 Jun 1995 20:08:40 GMT Organization: McGill University (Exp. Medicine) Lines: 83 Message-ID: <3sn448$5f0@sifon.cc.mcgill.ca> References: NNTP-Posting-Host: a-14.das.mcgill.ca X-Newsreader: AIR News 3.X (SPRY, Inc.) > sbassi@CRIBA.EDU.AR (Sebastian Bassi) writes: > Hello, > > I'm studing medicine, and I'd like to understand what is > IMPRINTING. I read books of genetics (like 'Genetics in > medicine', by Thompson & Thompson), but I couldn't understand it. > I'd like that someone could help, with a 'plain english > explanation'. > I know how is defined, but I think would be nice some example, > with pedigree. > > > Regards, > Sebastian Bassi > email: sbassi@criba.edu.ar > > > >>>> Okay here goes.... Imprinting as I understand it (by all means this subject is greatly open to debate as to the true nature of imprinting) involves the differential silencing (or expression, depends on point of view of "normal state") of a gene copy (allele) in an individual organism (zygote) depending on the sex of parent that the gene copy was recieved from (or as they say in the vernacular "gamete sex dependent"). So lets say you inherit a copy of gene Y from your DAD and a copy of the same gene from your MOM. Then lets distinguish each alleles from each other as allele Ya , Yb, Yc etc *=expressed and {}=silenced DAD ------- MOM Yb*{Yd} | Ya*{Yc} | | You Yb*{Ya} Now this is one of four sets of alleles possible. So if you noticed even though the Ya allele was expressed in you MOM it is not expressed in YOU! This means that when you inherit the gene copy (allele) from your DAD it is expressed and when you inherit it from your MOM it is silenced. This is called imprinting... whether you expressed the copy of the gene or not was dependent on the sex of the donor of that allele (ie MOM or DAD). Most likely imprinting (much like X chromosome inactivation in females) is a mode of limiting gene dosage in the cell. Sometimes there can be such a thing as too much of a good thing ! Now the mechanism of Imprinting is under great debate. It is safe for now to say it is often associated with methylation of nearby CpGp islands (groups of CGCG repeats that often coincide with the start of coding regions or are within coding regions of the genome). Whether methylation is the cause or effect of imprinting is debatable. Also methylation is not always correlated with silencing of the gene either (look for the Ig2f and Ig2f-receptor genes in which one is expressed and the other silenced upon methylation of the same locus, though which is silenced in the presence of methylation escapes me right now ). Another mode of imprinting may involve the association of heterochromatin-assoc. proteins early in development with a given region to be silenced (ie altering the chromosomal structure at that sight such that perhaps transcription factors no longer have access to the DNA). I hope this helps a little..... Imprinting is a tough one : ) G. ______________________________________________________________________ Graham Dellaire Snail Mail: Red Cross, Research McGill University Montreal Blood Services Faculty of Medicine 3131 Sherbrooke St. East Div. of Experimental Medicine Montreal, QC, Canada E-mail: popa0206@po-box.mcgill.ca H1W 1B2 B2XE@musicb.mcgill.ca WWW Page: http://www.medcor.mcgill.ca/EXPMED/expmed.html Fax: (514) 525 0881 Voice: (514) 527 1501 ext 175 _______________________________________________________________________ From owner-chromosomes@net.bio.net Mon Jun 26 23:00:00 1995 Path: biosci!biosci!not-for-mail From: jecop@ebi.ac.uk (Jeroen Coppieters) Newsgroups: ebi.servers,bionet.molbio.embldatabank,bionet.software,bionet.genome.arabidopsis,bionet.genome.chromosomes,bionet.molbio.genome-program,bionet.molbio.yeast,embnet.general,bionet.announce Subject: ANNOUNCEMENT OF EUROPEAN GENEMARK E-MAIL SERVER Date: 26 Jun 1995 18:21:19 -0700 Organization: European Bioinformatics Institute Lines: 151 Sender: biohelp@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Xref: biosci bionet.molbio.embldatabank:521 bionet.software:12475 bionet.genome.arabidopsis:3470 bionet.genome.chromosomes:668 bionet.molbio.genome-program:1428 bionet.molbio.yeast:3182 bionet.announce:2225 ANNOUNCEMENT OF EUROPEAN GENEMARK E-MAIL SERVER >From June 20th on, GeneMark will be reachable at the EMBL Outstation - The European Bioinformatics Institute (EBI), Hinxton, UK EMAIL: genemark@embl-ebi.ac.uk (or genemark@ebi.ac.uk) as well as on the original site School of Biology, Georgia Institute of Technology (Atlanta, GA) EMAIL: genemark@ford.gatech.edu Since its first announcement, the GeneMark program has undergone continuous improvements, and more species matrices are made available for usage with the service. The EMBL-EBI server is a mirror of the Georgia one, and thus will return the same results for the same queries. 1. SHORT OVERVIEW OF GENEMARK FEATURES --------------------------------------------- The GeneMark server provides e-mail based identification of protein coding regions in DNA sequences from prokaryotic and eukaryotic species. The GeneMark server accepts a formatted message containing a DNA sequence in text format. You may specify a species name, and parameters that control the analysis procedure. The current GeneMark version is accurate for finding prokaryotic genes and for analyzing cDNA sequences to discriminate coding regions from non-coding ones like 5' or 3' UTRs. This program is able to identify rather long exons (more than 100bp) in eukaryotic genomic DNA. This information can be used for designing RT-PCR or PCR primers. The GeneMark gene identification program has been developed at the School of Biology, Georgia Institute of Technology (Atlanta, GA). More details on the algorithm can be found in the paper: Borodovsky M. and McIninch J.D., GeneMark: Parallel gene recognition for both DNA strands, Computers & Chemistry, 1993, 17, 123-133. 2. SENDING DATA TO GENEMARK ----------------------------------------------------- A DNA sequence should be sent via e-mail to one of the following addresses: genemark@ford.gatech.edu or genemark@embl-ebi.ac.uk ... with the word 'genemark' in the 'Subject:' field There is only one mandatory keyword: DATA which must precede the text of the DNA sequence. Below is given a simple example of sending a sequence to the GeneMark server >From a UNIX-based computer (note, that the '%' symbol is the prompt used by the system, and that lower-case letters in the sequence text, numbers and spaces are also acceptable): % mail genemark@embl-ebi.ac.uk (or % mail genemark@ford.gatech.edu) Subject: genemark data TCCAGCTACTGCTGCTAGCTACGCTAGTCG........ % When the server receives such a message, with almost no special options indicated, it will analyze the sequence using default options and send back a minimal response. Namely, it will use E. coli based parameters (by default) and send back to the submitter a message containing a list of those open reading frames that have been assessed as protein coding regions. You may, however, wish to get more information from the server. In that case, please retrieve the HELP-Message from the GeneMark server, which contains a full description of all commands and options 3. GETTING THE HELP MESSAGE FROM GENEMARK ------------------------------------------------ Send an e-mail with the word HELP in the 'Subject:' field to genemark@ford.gatech.edu or genemark@embl-ebi.ac.uk 4. THE LIST OF SPECIES THAT CAN BE ANALYZED USING GENEMARK ------------------------------------------------------------------------------ NOTE: The EMBL-EBI server supports retrieval of the current list of supported species. Send a message to genemark@embl-ebi.ac.uk with the command LIST ORG in the SUBJECT The matrix is specified using the 'SPECIES' command Use the line 'species ' anywhere before the line 'data' where is the name of one of the matrices listed below: Matrix Name Species ----------- -------------------------------------------------------------- arab Arabidopsis thaliana capri Mycoplasma capricolum (TGA = Trp) celegans Caenorhabditis elegans chicken Gallus gallus disco Dictyostelium discoideum ecoli Escherichia coli "native" genes [DEFAULT] ecophage Escherichia coli horizontally transferred genes euglena Euglena gracilis eugchlor Euglena gracilis chloroplasts frog Xenopus laevis fruitfly Drosophila melanogaster human Homo sapiens kpneu Klebsiella pneumoniae lacto Lactococcus species leprae Mycobacterium leprae mouse Mus musculus plasm Plasmodium falciparum rat Rattus norvegicus salm Salmonella typhimurium spombe Schizosaccharomyces pombe subt Bacillus subtilis tuberc Mycobacterium tuberculosis t4 Phage T4 urchin Lytechinus pictus yeast Saccharomyces cerevisiae -------------------------------------------------------------------------- -- ============================================================== . O . Jeroen Coppieters . O O o O . Software Support O O O O *o O O Jeroen.Coppieters@embl-ebi.ac.uk O O O O( *o )O O (or jecop@ebi.ac.uk) )O O O O o* O O( ++44 1223 494422 O O O O( o* )O O )O O O O *o O O( EMBL Outstation EBI O O O O( *o )O O (European Bioinformatics Institute) )O @ O O o* O O( Hinxton Hall O O O( o* )O(' Hinxton ` O( *o O ' Cambridge CB10 1RQ ` O ' UK http://www.ebi.ac.uk ============================================================== From owner-chromosomes@net.bio.net Mon Jun 26 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!cam.news.pipex.net!pipex!edi.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!news From: Jo Fay Newsgroups: bionet.genome.chromosomes Subject: Re: Imprinting Date: 27 Jun 1995 16:25:11 GMT Organization: The Sanger Centre Lines: 24 Message-ID: <3spbd7$266@lyra.csx.cam.ac.uk> References: <3sn448$5f0@sifon.cc.mcgill.ca> NNTP-Posting-Host: pabay.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; SunOS 5.3 sun4m) X-URL: news:3sn448$5f0@sifon.cc.mcgill.ca Graham Dellaire wrote: >Most likely imprinting (much like X chromosome inactivation in females) is a mode of limiting >gene dosage in the cell. Sometimes there can be such a thing as too much of a good thing ! > X chromosome inactivation is not determined by imprinting, it is a random process, which is why females show mosaicism for X-linked diseases - some cells have the 'good' X chromosome inactivated, and some have the 'bad' X chromsome inactivated. I can't explain what imprinting is ;-) but one possible example are diseases caused by expansion of simple tandem DNA repeats. In some diseases, such as Fragile X syndrome, the expanded repeat is transmitted differently by males and females - in males the length of repeat is restricted to the premutation range, while during female transmission the repeat can increase in size, so that offspring of a woman with a certain size repeat are more likely to have fragile X syndrom than the offspring of a male carrying the same size repeat. (see Sutherland and Richards in PNAS 92 pg3636 for the review I got this info from). Jo From owner-chromosomes@net.bio.net Tue Jun 27 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!hookup!news.mcgill.ca!news From: Graham Dellaire Newsgroups: bionet.genome.chromosomes Subject: re:imprinting Date: 28 Jun 1995 02:21:30 GMT Organization: McGill University (Exp. Medicine) Lines: 64 Message-ID: <3sqeba$ljo@sifon.cc.mcgill.ca> NNTP-Posting-Host: i-21.das.mcgill.ca X-Newsreader: AIR News 3.X (SPRY, Inc.) Previously, I wrote > Most likely imprinting (much like X chromosome inactivation in females) is a mode of limiting gene dosage in the cell. Sometimes there can be such a thing as too much of a good thing ! > What I ment here and I think is not erroneous is that imprinting can be seen as a means of gene dosage. I did not say that imprinting and X chromosome are identicle phenomenon....although () There is a gene known as the Xist gene which produces a transcript that may be involved in silencing the X chromosome (all be it stochastically) and this gene I believe is differentially methylated....EEEK There goes Mother nature again throwing a spanner in the works! Interesting bit on the trinucleotide repeats Jo, hmm maybe there is some sort of choice, as in classical imprinting, in the early stages of the zygote that determines this... probably like most things has something to do with accessibility of that region of the genome to proteins that can mark the DNA by some physical means (methylatio for instance) for latter reference (perhaps something like a maternally inherited heterochromatin forming protein). I think one mode of expansion of repeats is slippage of the replication fork and re-initiation of replication. The result it you repeat the same region twice. It is also interesting that these trinucleotide repeat linked disease have a threshold of repeats before the disease manifest itself (this is called Anticipation). Why do you suppose that is? I think recent evidence on the loop like structures of these regions of DNA have shed some light on the question. At the threshold of repeats they form stem loop like structures which I believe may be very good replication "blocks" for the advancing polymerase during replication. Following this train of logic... the polymerase stops/slips and reinitiates causing an expansion in the number of repeats. Now that this number of repeats is larger you get often methylation of the region (perhaps the expanded region is now a good target for methylases) and then changes in transcription occur. The regulation of the ajoining gene is altered, often silencing occurs..... now this methylation seems awfully reminiscent of imprinting ... which can cause silencing in some loci. Perhaps this repeats once of sufficient number can trigger a false imprinting at that sight.... Mother Nature again Graham activity. _______________________________________________________________________ Graham Dellaire Snail Mail: Red Cross, Research McGill University Montreal Blood Services Faculty of Medicine 3131 Sherbrooke St. East Div. of Experimental Medicine Montreal, QC, Canada E-mail: popa0206@po-box.mcgill.ca H1W 1B2 B2XE@musicb.mcgill.ca WWW Page: http://www.medcor.mcgill.ca/EXPMED/expmed.html Fax: (514) 525 0881 Voice: (514) 527 1501 ext 175 _______________________________________________________________________ From owner-chromosomes@net.bio.net Tue Jun 27 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!cam.news.pipex.net!pipex!edi.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!news From: Jo Fay Newsgroups: bionet.genome.chromosomes Subject: Trinucleotide repeats (WAS Re: re:imprinting) Date: 28 Jun 1995 15:33:51 GMT Organization: The Sanger Centre Lines: 67 Message-ID: <3srsov$2k6@lyra.csx.cam.ac.uk> References: <3sqeba$ljo@sifon.cc.mcgill.ca> NNTP-Posting-Host: pabay.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; SunOS 5.3 sun4m) X-URL: news:3sqeba$ljo@sifon.cc.mcgill.ca To summarise a bit of the Sutherland and Richards review ;-) The Fragile X syndrom repeat shows a threshold effect, but other diseases such as Myotonic dystrophy caused by expansion of the AGC repeat lacks the threshold effect - just a small increase can cause disease, and the severity or age of onset is determined by the size of the repeat, which explains anticipation (earlier onset in successive generations). The review suggests that the alteration in size of the repeat occurs during oogenesis and spermatogenesis as this explains the obeserved patterns without calling for lots of imprinting to prevent paternal repeats expanding in Fragile X syndrome etc. Some interesting points... In Fragile X syndrome the expanded repeat and nearby CpG island become methlated which deactivates the gene and causes the disease, but this isn't related to normal X inactivation because the chromosome 16 fragile site becomes methylated but is not in an area normally methylated. (if this is badly explained it's me!) In Myotonic dystropy the size of the repeat increases more on transmission by females than in males, although males do pass on the disease, so the disease shows maternal anticipation. In Huntingdons disease, spinocerebellar ataxia and dentatorubral palliodoluysian atrophy the male-transmitted repeat increases more so these diseases show paternal anticipation. Some suggestions as to why these repeats cause the disease... 1) The AGC repeat codes for reiterated glutamines and these may be involved in protein aggregation by either a)crosslinking or b)polar zippers 2) the length of the polyglutamine tract may affect certain transcription factors and how the repeats expand... some diseases may be related to mutations in the mis-match repair genes which allow mistakes in copying the repeat to be retained "Simple slip-sliding mechanism" - giving rapid expansion of the repeat when the repeat length exceeds that of an Okazaki fragment (which allows replication on the wrong side of the DNA replication fork because the fragment can become an anchor for polymerization) Some strange observations... There are no animal models for these trinucleotide repeat expanions leading to disease! Naturally occuring repeats in animals eg mice are apparently much shorter and more stable, no-one has observed the dynamic mutation that amplifies the repeats in humans. Also transgenic models don't seem to work - I've just seen a paper where expanded repeats where put into mice, and no phenotypic results were seen. It is possible though that these animals just don't live long enough to develop the disease, since many of these diseases in Humans are late-onset disease. The review also suggested that dynamic mutation may be a mechanism for adaptive mutation. Personally I'd recommend anyone interested reads the review as that explains all this a lot better than I can in this weather! Jo From owner-chromosomes@net.bio.net Tue Jun 27 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!Germany.EU.net!EU.net!news.sprintlink.net!europa.chnt.gtegsc.com!wlbr!news.new-york.net!spcuna!news.columbia.edu!konichiwa.cc.columbia.edu!cgw1 From: Christopher G Winter Newsgroups: bionet.genome.chromosomes Subject: Calc. ave. intergenic distances Date: Wed, 28 Jun 1995 10:03:57 -0400 Organization: Columbia University Lines: 23 Message-ID: NNTP-Posting-Host: konichiwa.cc.columbia.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: cgw1@konichiwa.cc.columbia.edu I've been thinking about the possible correlation between gene function and organization. More specifically, whether there is a tendency toward clustering of genes which play a role in the same physiological pathways, excluding genes which are related to each other in sequence. I wondered if it would be possible to test this by somehow using the genome database (human I suppose) to calculate the average distance between genes and compare it with the average intergenic distane for genes which are known to function together. Does anyone know of software which would allow one to do such an operation on a genomic database, or if it would be difficult to to write such a program (for an experinced programmer with some background in molecular biology)? Any thoughts or leads on this will be greatly appreciated. Christopher G. Winter grad. student Columbia Univ. From owner-chromosomes@net.bio.net Tue Jun 27 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!torn!ccshst05.cs.uoguelph.ca!ccshst01.cs.uoguelph.ca!hzheng From: hzheng@uoguelph.ca (Hui Zheng) Newsgroups: bionet.genome.chromosomes Subject: DNA contents of plant chromosomes. Date: 28 Jun 1995 12:23:37 GMT Organization: University of Guelph Lines: 3 Message-ID: <3srhk9$ljf@ccshst05.cs.uoguelph.ca> NNTP-Posting-Host: ccshst01.cs.uoguelph.ca X-Newsreader: TIN [version 1.2 PL2] I developed a protocol to measure the DNA contents of plant chromosomes. Valuable? Useless? Interested? Frank Peng. From owner-chromosomes@net.bio.net Wed Jun 28 23:00:00 1995 Path: biosci!ns1.faseb.org!darwin.sura.net!gatech!news.uoregon.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!torn!ccshst05.cs.uoguelph.ca!ccshst01.cs.uoguelph.ca!aboyonos From: aboyonos@uoguelph.ca (Ann C Boyonoski) Newsgroups: bionet.genome.chromosomes Subject: Rat DNA Content Date: 28 Jun 1995 18:25:22 GMT Organization: University of Guelph Lines: 2 Message-ID: <3ss6qi$1i0@ccshst05.cs.uoguelph.ca> NNTP-Posting-Host: ccshst01.cs.uoguelph.ca X-Newsreader: TIN [version 1.2 PL2] We are looking for the DNA content of rat somatic cells. We have a value of approx 1.1 ug DNA/million cells... is this close???? Anyone?? From owner-chromosomes@net.bio.net Wed Jun 28 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!gatech!news.sprintlink.net!psgrain!nntp.ski.mskcc.org!mac-99.rrl-g2.ski.mskcc.org!user From: h-petrie@ski.mskcc.org (Howard T. Petrie) Newsgroups: bionet.genome.chromosomes Subject: Re: Rat DNA Content Date: 29 Jun 1995 16:55:50 GMT Organization: Memorial Sloan-Kettering Cancer Center Lines: 11 Message-ID: References: <3ss6qi$1i0@ccshst05.cs.uoguelph.ca> NNTP-Posting-Host: mac-99.rrl-g2.ski.mskcc.org In article <3ss6qi$1i0@ccshst05.cs.uoguelph.ca>, aboyonos@uoguelph.ca (Ann C Boyonoski) wrote: > We are looking for the DNA content of rat somatic cells. We have a value > of approx 1.1 ug DNA/million cells... is this close???? Anyone?? I would say no. Although I haven't done that calculation for the rat, I have done it for the mouse, and it is approcimately 6.8 micrograms per million cells. This figure has been substantiated by others. Although rat and mouse do differ, I wouldn't suspect it's a six-fold difference. HTP From owner-chromosomes@net.bio.net Thu Jun 29 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!news.uoregon.edu!europa.chnt.gtegsc.com!news.sprintlink.net!EU.net!Austria.EU.net!newsfeed.ACO.net!swidir.switch.ch!scsing.switch.ch!news.rediris.es!obelix.cica.es!vivero!jose.vivero From: jose.vivero@uca.es (Jose Fernandez Vivero) Newsgroups: bionet.genome.chromosomes Subject: Software for karyotiting Date: Thu, 29 Jun 1995 10:36:57 Organization: Ciencias Morfologicas - Universidad de Cadiz Lines: 3 Message-ID: NNTP-Posting-Host: vivero.uca.es X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] We apreciatte to receive accurate information about software for automatic or semiautomatic human karyotiping including prices, owneus and personal experience with it. From owner-chromosomes@net.bio.net Thu Jun 29 23:00:00 1995 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!dundee.ac.uk!usenet From: "Andrew J. Cassidy" Newsgroups: bionet.genome.chromosomes Subject: Chromosome 2 library again. Date: 30 Jun 1995 13:53:51 GMT Organization: BioMed Lines: 5 Message-ID: <3t0vlf$c08@dux.dundee.ac.uk> NNTP-Posting-Host: ajcquadra.medschool.dundee.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) To: ajcassidy@ninewells.dundee.ac.uk X-URL: news:bionet.genome.chromosomes Many apologies for not specifying the organism of interest.I am looking for a human chromosome 2 cosmid library. Many thanks to those pointing out my error. From owner-chromosomes@net.bio.net Thu Jun 29 23:00:00 1995 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!dundee.ac.uk!usenet From: "Andrew J. Cassidy" Newsgroups: bionet.genome.chromosomes Subject: Chromosome 2 Library Date: 30 Jun 1995 13:05:13 GMT Organization: BioMed Lines: 4 Message-ID: <3t0sq9$91i@dux.dundee.ac.uk> NNTP-Posting-Host: ajcquadra.medschool.dundee.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) To: ajcassidy@ninewells.dundee.ac.uk X-URL: news:bionet.genome.chromosomes I would greatly appreciate any information that could be provided on the existence of a Chromosome 2 cosmid library. From owner-chromosomes@net.bio.net Thu Jun 29 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!news.uoregon.edu!europa.chnt.gtegsc.com!news.sprintlink.net!EU.net!Austria.EU.net!newsfeed.ACO.net!swidir.switch.ch!scsing.switch.ch!news.rediris.es!obelix.cica.es!vivero!jose.vivero From: jose.vivero@uca.es (Jose Fernandez Vivero) Newsgroups: bionet.genome.chromosomes Subject: Wanted: Software for Karyotiping Date: Thu, 29 Jun 1995 10:48:41 Organization: Ciencias Morfologicas - Universidad de Cadiz Lines: 3 Message-ID: NNTP-Posting-Host: vivero.uca.es X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] We apreciatte to receive accurate information about software for automatic or semiautomatic human karyotiping including prices, owneus and personal experience with it.