From owner-chromosomes@net.bio.net Fri Apr 04 23:00:00 1997 Path: biosci!agate!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!yama.mcc.ac.uk!zippy.dct.ac.uk!str-ccsun!singer.cent.gla.ac.uk!newsfeed.ed.ac.uk!news Newsgroups: bionet.genome.chromosomes Subject: Re: Cannot find gene markers Message-ID: <333F6F9C.3791@hgu.mrc.ac.uk> From: "Stewart W. Morris" Date: Mon, 31 Mar 1997 09:02:36 +0100 References: <5h6ob6$jl7@darkstar.ucsc.edu> Organization: MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK NNTP-Posting-Host: longmorn.hgu.mrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; SunOS 5.5.1 sun4u) To: Christian Barrett Lines: 9 Christian Barrett wrote: > > > The other two don't seem to exist anywhere. I've tried Unigene, You'll find them at the GDB site http://gdbwww.gdb.org/ also CHLC http://www.chlc.org/ and probably at Stanford as well - Stewart. From owner-chromosomes@net.bio.net Sun Apr 06 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!howland.erols.net!news.starnet.net!news.starnet.net!axb.slu.edu!news From: Nanda Somarajan Newsgroups: bionet.genome.chromosomes Subject: subscribe Date: Sun, 06 Apr 1997 19:09:22 -0500 Organization: Saint Louis University Lines: 1 Message-ID: <33483B32.2989@slu.edu> NNTP-Posting-Host: 165.134.21.19 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win95; I) Please subscribe me. From owner-chromosomes@net.bio.net Mon Apr 07 23:00:00 1997 Path: biosci!agate!howland.erols.net!cs.utexas.edu!news.eng.convex.com!news.ecn.uoknor.edu!munnari.OZ.AU!bunyip.cc.uq.edu.au!news.qut.edu.au!sparrow.qut.edu.au!n1607693 From: JOHNSON YIP Newsgroups: bionet.genome.chromosomes Subject: PCR primers Date: Wed, 9 Apr 1997 07:57:33 +1000 Organization: Queensland University of Technology, Australia Lines: 17 Distribution: world Message-ID: NNTP-Posting-Host: sparrow.qut.edu.au Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi there, I've got a question here, and wish someone can help me.... When you design PCR primers to amplify from the mRNA, you need to consider some factors like GC content, Tm, internal 2ndary structure, 3'-end complimentarity, etc.. What other factors you need to consider if you are designing primers to amplify from the gene and not the mRNA?? Also if you want yuor primer to work only on cDNA, and want to detect whether there's any contaminate from the genomic DNA, how can you achieve this? (Southern blotting??) Thanks My address:- n1607693@sparrow.qut.edu.au From owner-chromosomes@net.bio.net Tue Apr 08 23:00:00 1997 Path: biosci!RNA.BIO.MQ.EDU.AU!MSLADE From: MSLADE@RNA.BIO.MQ.EDU.AU Newsgroups: bionet.genome.chromosomes Subject: Re: PCR primers Date: 8 Apr 1997 17:47:02 -0700 Organization: School of Biological Sciences Lines: 39 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Would not the best way of ensuring or controlling for amplification from genomic DNA be to use primers to the introns? Or perhaps PCR across a small intron so you can see a difference in size in the PCR fragments of cDNA and genomic. Best wishes, Martin Slade ---------------------------------------------------------------- >To: biochrom@net.bio.net >From: JOHNSON YIP >Subject: PCR primers >Date: Wed, 9 Apr 1997 07:57:33 +1000 > >Hi there, > > I've got a question here, and wish someone can help me.... > >When you design PCR primers to amplify from the mRNA, you need to consider >some factors like GC content, Tm, internal 2ndary structure, 3'-end >complimentarity, etc.. What other factors you need to consider if you are >designing primers to amplify from the gene and not the mRNA?? > > Also if you want yuor primer to work only on cDNA, and want to detect >whether there's any contaminate from the genomic DNA, how can you achieve >this? (Southern blotting??) > >Thanks > My address:- n1607693@sparrow.qut.edu.au > > > > --------------------------------------- Martin Slade, School of Biological Sciences, Macquarie University, NSW 2109, Australia FAX (61 2) 9850 8174 Phone(61 2) 9850 8210 --------------------------------------- From owner-chromosomes@net.bio.net Fri Apr 11 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!ais.net!ameritech.net!uunet!in2.uu.net!204.255.96.40!intex.net!usenet From: hogwild2@dal.cleaf.com (Rusty) Newsgroups: bionet.genome.chromosomes Subject: To all: Question concerning genetic testing results... Date: 12 Apr 1997 02:58:17 GMT Organization: None Lines: 30 Message-ID: <5imto9$etk@animal.intex.net> NNTP-Posting-Host: 199.171.82.46 Mime-Version: 1.0 X-Newsreader: WinVN 0.99.2 Hi, This probably doesn't belong in this group, but I didn't know where else to go and I need to share your knowledge, so here it is.... My wife recently had an amniocentesis performed due to being over 35 yo. The genetic test came back with a paricentric inversion of chromosome 3 at the p24 (short) and q27 (long). I understand the paricentric inversion, and I know what markers are, however: 1) I am having trouble finding anything on q27. Is there another name for this marker? 2) There are several p24 markers listed, is the 3p24 the one I need to concentrate on? 3) I have visited the GDB site and several others but they are pretty hard on a genetics rookie like myself. Are there any others that might help? 4) What are the "short" and "long" referring to? The length of the pieces from the centromere? Thanks sincerely for any help, we are concerned how this might affect the health of our baby. Please reply by post or email. Thanks again, Rusty From owner-chromosomes@net.bio.net Wed Apr 16 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!gatech!news.cis.uab.edu!its1.ocs.lsu.edu!news.LaTech.edu!news.ttu.edu!usenet From: BCSTM@ttacs3.ttu.edu (mezik, steven) Newsgroups: bionet.genome.chromosomes Subject: Karyotype Programs Date: 17 Apr 1997 02:46:29 GMT Organization: TEXAS TECH UNIVERSITY Lines: 7 Distribution: world Message-ID: <5j42u5$o7d@ttacs7.ttu.edu> NNTP-Posting-Host: ttacs3.ttu.edu X-News-Reader: VMS NEWS 1.24 Does anyone know about any shareware programs which deal with karyotypes and the act of karyotyping. Any information would be appreciated. Steven T. Mezik bcstm@ttacs.ttu.edu From owner-chromosomes@net.bio.net Wed Apr 16 23:00:00 1997 Path: biosci!daresbury!uninett.no!nntp.uio.no!newsfeeds.sol.net!feed1.news.erols.com!news.maxwell.syr.edu!cs.utexas.edu!geraldo.cc.utexas.edu!cell2.esb.utexas.edu!user From: abyss@mail.utexas.edu (anonymous) Newsgroups: bionet.genome.chromosomes Subject: test Date: Thu, 17 Apr 1997 10:10:31 -0600 Organization: university of texas Lines: 1 Message-ID: NNTP-Posting-Host: cell2.esb.utexas.edu test only From owner-chromosomes@net.bio.net Thu Apr 17 23:00:00 1997 Path: biosci!agate!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!penguin.doc.ic.ac.uk!djt From: djt@doc.ic.ac.uk (David John Thornley) Newsgroups: bionet.general,bionet.genome.chromosomes,bionet.molbio.methds-reagnts Subject: REQ: experience in choosing primers for DyePrimer sequencing Date: 18 Apr 1997 12:31:46 GMT Organization: Dept. of Computing, Imperial College, London. Lines: 16 Message-ID: <5j7pji$mab$1@penguin.doc.ic.ac.uk> NNTP-Posting-Host: santos.doc.ic.ac.uk Xref: biosci bionet.general:26477 bionet.genome.chromosomes:1589 bionet.molbio.methds-reagnts:56846 This question relates strictly to dye primer DNA sequencing. If you have sequenced a sample and found a high degree of baseline noise, which disappears when using a different primer, but you do not believe it was a primer specificity problem, I would be most grateful to know i) the base sequences of the primers involved ii) the dye set and polymerase used I don't need to know the base sequence of the sample, but if the sample files have been made public, I would be eager to see them. Yours with thanks in anticipation Dave Thornley Imperial College Department of Computing From owner-chromosomes@net.bio.net Thu Apr 17 23:00:00 1997 Path: biosci!aecom.yu.edu!skim From: skim@aecom.yu.edu (Sang-Hoon Kim) Newsgroups: bionet.genome.chromosomes Subject: (none) Date: 18 Apr 1997 12:30:13 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net subsribe From owner-chromosomes@net.bio.net Wed Apr 23 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: Luca Fontanesi Newsgroups: bionet.genome.chromosomes Subject: MLTD sequences and repetitive sequences Date: 24 Apr 1997 15:34:52 +0100 Lines: 20 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5jnr2c$gbl@mserv1.dl.ac.uk> X-Sender: luca.fontanesi@archimede.stpa.unibo.it Original-To: biochrom@dl.ac.uk Does anyone could give me indication about MLTD repeat sequences that are dispersed in the human genome. I am looking for any information about this kind of sequence (references, consensus sequences, etc.). I also wonder if these sequences are present in other mammals or other organisms. Another question. I also looking for complete up-to date references and/or databases that collect information about every kind of repetitive sequences so far identified. Thank you in advance for any help. Luca Fontanesi ---------------------------------------------------------------------------- ------- Luca Fontanesi - DIPROVAL Sez.Allevamenti Zootecnici - Universita' di Bologna Via F.lli Rosselli, 107 - I-42100 Reggio Emilia - Italia tel +39 522 290 516/522 fax +39 522 290 523 e-mail luca.fontanesi@stpa.unibo.it http://archimede.alma.unibo.it/aloha.htm From owner-chromosomes@net.bio.net Thu Apr 24 23:00:00 1997 Newsgroups: bionet.genome.chromosomes Path: biosci!daresbury!uninett.no!news-feed.inet.tele.dk!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!vixen.cso.uiuc.edu!uchinews!ellis.uchicago.edu!cjenkins From: Cheryl Subject: Chromosome 12 X-Sender: cjenkins@ellis.uchicago.edu X-Nntp-Posting-Host: ellis.uchicago.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Message-ID: Sender: news@midway.uchicago.edu (News Administrator) Reply-To: Cheryl Organization: University of Chicago -- Academic Computing Services Mime-Version: 1.0 Date: Thu, 24 Apr 1997 15:04:11 GMT Lines: 13 I am a layperson who has been told there is a problem with Chromosome 12 of my nieces fetus, which is 16 weeks. Can someone explain to me what part/parts of the body this chromosome effects or possible consequences? Drs can be rather secretive sometimes. I'd appreciate any helpful info anyone on the ng can provide. Blazer From owner-chromosomes@net.bio.net Fri Apr 25 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!gondor!newshub.sdsu.edu!newshub.csu.net!mr.net!cyclic.gsl.net!news.gsl.net!news-peer.gsl.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.mindspring.com!usenet From: rdreynolds@mindspring.com (Deborah Reynolds) Newsgroups: bionet.genome.chromosomes Subject: Re: Chromosome 12 Date: Sat, 26 Apr 1997 01:59:29 GMT Organization: MindSpring Enterprises Lines: 22 Message-ID: <336160e6.18159832@news.mindspring.com> References: Reply-To: rdreynolds@mindspring.com NNTP-Posting-Host: user-37kb94h.dialup.mindspring.com X-Server-Date: 26 Apr 1997 01:57:25 GMT X-Newsreader: Forte Free Agent 1.1/32.230 Cheryl wrote: > I am a layperson who has been told there is a problem with >Chromosome 12 of my nieces fetus, which is 16 weeks. > >Can someone explain to me what part/parts of the body this chromosome >effects or possible consequences? Drs can be rather secretive sometimes. > >I'd appreciate any helpful info anyone on the ng can provide. > > >Blazer > > > Chromosome 12 has many genes which have a wide variety of effects during development. What part of chromosome 12 has a problem? What is the nature of the problem? Often, there are abnormalities present which have no known developmental effects. Rich From owner-chromosomes@net.bio.net Sat Apr 26 23:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.genome.chromosomes Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 27 Apr 1997 02:00:11 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199704270900.CAA03458@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-chromosomes@net.bio.net Wed Apr 30 23:00:00 1997 Path: biosci!daresbury!uninett.no!news-feed.inet.tele.dk!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!uunet!in3.uu.net!151.196.0.36!world2.bellatlantic.net!news From: bluemoon@bellatlantic.net Newsgroups: bionet.genome.chromosomes Subject: HELP ON UNKNOWN DISORDER!!! Date: Thu, 01 May 1997 13:50:42 -0400 Organization: bellatlantic.net Lines: 6 Message-ID: <3368D7F2.7D7E@bellatlantic.net> Reply-To: bluemoon@bellatlantic.net NNTP-Posting-Host: 2071598233.bellatlantic.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (Win95; I) I am looking for at least the name of this disorder. Extra chromosome with an extra piece on the 15th that came from the 4th chromosome. Both kidneys but they are joined together to form one on the left side. Very small, almost a year old and weighs 10 pounds. Hole in between heart chambers. This is all the basic info that I have...Even just a name would be GREAT!! Please e-mail to bluemoon@bellatlantic.net