From owner-chromosomes@net.bio.net Sun Nov 03 22:00:00 1996 Message-ID: <327DF025.5CE8@uni-konstanz.de> Date: Mon, 04 Nov 1996 14:31:17 +0100 From: Bernd Langkau Reply-To: bernd.langkau@uni-konstanz.de Organization: University of Constance X-Mailer: Mozilla 3.0Gold (Win95; I) MIME-Version: 1.0 Newsgroups: bionet.genome.chromosomes CC: Bernd.Langkau, Thomas.Seebacher Subject: Molbio-Software (Macintosh) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: toprope.verwaltung.uni-konstanz.de Lines: 7 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!mr.net!newshub.tc.umn.edu!fu-berlin.de!news.belwue.de!news.uni-konstanz.de!toprope.verwaltung.uni-konstanz.de A new program for the evaluation of gel images is available from http://www.uni-konstanz.de/tt/software/mwmacro.html or from ftp://ftp.uni-konstanz.de/pub/local/Biologie/MW-Macro.sea.bin. The new shareware program (50.-DM) calculates molecular weights, pI-values and band intensities from scanned gel images. The program requires Macintosh computers and NIH-Image software. From owner-chromosomes@net.bio.net Sun Nov 03 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!EU.net!sun4nl!wirehub!news.euro.net!xs4all!news.unisource.nl!ns1.att.nl!surfnet.nl!Hermes.nki.nl!Hermes.nki.nl!twezel From: Tom van Wezel Newsgroups: bionet.genome.chromosomes Subject: postdoc position available Date: Mon, 4 Nov 1996 14:48:19 +0000 Organization: Netherlands Cancer Institute, Amsterdam Lines: 42 Message-ID: NNTP-Posting-Host: mercurius.nki.nl Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII POSTDOCTORAL POSITION is available at The Netherlands Cancer Institute in Amsterdam for 2 to 3 years. It is open for citizens or residents of countries of the European Union (excluding the Netherlands) to carry out research on SUSCEPTIBILITY GENES FOR LUNG AND INTESTINAL CANCER In the past two years, we mapped several novel genes controlling susceptibility to lung and intestinal tumors in the mouse. Most of these genes appear to be different from the presently known oncogenes, tumor suppressor genes, and mismatch repair genes and may be involved in cellular signalling and regulation of differentiation. The aim of the project is to use molecular and biological approaches to study the biological effects of these genes, their mutual interactions, their effects on tumorigenesis in different tissues, as well as their possible effect on the action of oncogenes and tumor suppressor genes. Molecular and genetic techniques will be applied towards positional cloning of selected members of this group of genes and to study their possible interactions with the oncogenes or their role in signalling pathways. The Institute has a broad multidisciplinary basis for cancer research with groups carrying out advanced research in the fields of molecular genetics, immunology, cellular biology, and signal transduction. The candidates should possess a Ph.D. degree and have active interest in molecular genetics and tumor biology. Qualified investigators interested in this position can contact Dr. P. Demant (tel. +31 20 5121992, fax +31 20 5122011, e-mail demant@nki.nl). Applications should be sent to: The Netherlands Cancer Institute, Personnel Department, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands. The letter should have the reference nr. 95-245. From owner-chromosomes@net.bio.net Mon Nov 04 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!ott.istar!istar.net!tor.istar!east.istar!news1.istar.ca!news From: awebster@magi.com (Al Webster) Newsgroups: bionet.genome.chromosomes Subject: 4q- Date: 5 Nov 1996 22:12:58 GMT Organization: iSTAR Internet Incorporated Lines: 2 Message-ID: <55oe5a$cqj@news.istar.ca> NNTP-Posting-Host: ts25-15.ott.istar.ca X-Newsreader: Forte Free Agent 1.0.82 Does anyone have info on this chromosome deletion? From owner-chromosomes@net.bio.net Tue Nov 05 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!newsxfer2.itd.umich.edu!bloom-beacon.mit.edu!senator-bedfellow.mit.edu!lester From: lester@genome.wi.mit.edu (Lester Hui) Newsgroups: bionet.genome.chromosomes Subject: [REPOST] WHITEHEAD/MIT HUMAN PHYSICAL MAP, RELEASE 11 Date: 6 Nov 1996 18:27:22 GMT Organization: Whitehead Institute for Biological Research Lines: 103 Message-ID: <55qlaa$31v@senator-bedfellow.MIT.EDU> NNTP-Posting-Host: tango.wi.mit.edu Sorry to those seeing this message twice. It has been brought to my attention that some news feeds to not post this message the first time. ANNOUNCING: WHITEHEAD INSTITUTE/MIT CENTER FOR GENOME RESEARCH HUMAN GENOMIC MAPPING PROJECT DATA RELEASE 11 (OCTOBER 1996) The eleventh release of data from the Human Physical Mapping Project at the Whitehead Institute/MIT Genome Center, covering data generated through the end of October, 1996, is now available. This data release contains YAC screening data for 22,582 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. The data assemble into 292 contigs using single linkage between STSs. In addition, we also report a radiation hybrid map of the genome containing 12508 STS markers mapped on the Genebridge Panel, as well as integrations of the genetic, radiation hybrid and YAC contig maps. The map includes data from over 10000 expressed sequences, part of the transcript map published in Science 25 October 1996. 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/oct96. The contents are as follows: 10-96.INTRO.txt Introduction to the data release, in straight text format 10-96.INTRO.html The same in HTML (World Wide Web) format 10-96.STS.DATA.txt STS mapping data as tab-delimited text. chromosomes/ The same, split into smaller chromosome-specific files 10-96.YAC2STS.txt Inverse map of YAC to STS screening data 10-96.CONTIG2STS.txt YAC contig lists. 10-96.CONTIG2STS.txt The same, inverted. 10-96.SEQUENCES.txt Full sequences of STSs developed in-house. 10-96.MAPPED.EST.txt Cross reference between ESTs, IMAGE clones and map positions. 10-96.ALIASES.txt Cross reference of STS names. pictures/ Pictures of integrated maps in Macintosh and PS forms. rhmap/ Radiation hybrid maps. genmap/ Genethon genetic linkage maps. The data is also available in compressed form using the gzip program. 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, view the individual and integrated maps, and to get information on the radiation hybrid and contig analyses. All mapped STSs are available through the Genome Database (GDB) and through GenBank. Users interested in EST mapping are also referred to the following URL: http://www.ncbi.nlm.nih.gov/Science96/ 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 quarterly. At the end of each quarter, 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 11 (October 1996). From owner-chromosomes@net.bio.net Thu Nov 07 22:00:00 1996 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed1.bbnplanet.com!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!www.nntp.primenet.com!nntp.primenet.com!feed1.news.erols.com!howland.erols.net!newsfeed.internetmci.com!newsbuffer.myriad.net!news.fibr.net!news.sprintlink.net!news-fw-22.sprintlink.net!news.gate.net!wthfl2-61.gate.net!pttc3 From: pttc3@gate.net (thomas m. clapp) Newsgroups: bionet.genome.chromosomes Subject: chromosomes Date: Fri, 8 Nov 1996 14:21:28 Organization: CyberGate, Inc. Lines: 5 Message-ID: NNTP-Posting-Host: wthfl2-61.gate.net Keywords: klinefelter's sysdrome X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] i am interested in finging out more info. on this sysdrome. i have it and i am willing to give any details for any research. i do a xxy chromosome. of course i am a male with some of the characteristics of klinefelter's sysdrome. e-mail: pttc3@gate.net From owner-chromosomes@net.bio.net Fri Nov 08 22:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!news.tamu.edu!news.mty.itesm.mx!NewsWatcher!user From: al177663@academ01.mty.itesm.mx (Raymundo Sánchez) Newsgroups: bionet.genome.chromosomes Subject: Re: chromosomes Date: Sat, 09 Nov 1996 12:49:52 -0600 Organization: ITESM Lines: 26 Message-ID: References: NNTP-Posting-Host: 131.178.80.79 In article , pttc3@gate.net (thomas m. clapp) wrote: > i am interested in finging out more info. on this sysdrome. i have it and i > am willing to give any details for any research. i do a xxy chromosome. of > course i am a male with some of the characteristics of klinefelter's sysdrome. > e-mail: pttc3@gate.net Hello, mi name is Raymundo Sanchez and I am interested in the klinefelter's sysdrome, but unfurtunately, I am still studying my mayor at the University, so I think that I can´t do something to help you, but I would like to hear more about this syndrome, the next semester I will begin my, " Diplomado " in biotechnology, and I will take Genetic Ingeniering, I think that in the class I will study, syndromes. I am studying, my major ( carrear ) in Chemical Sciences, * I think that this is the tranduction from spanish to english * I am at the ITESM, ( name of my shool ), here in Monterrey MEXICO, I want to be excuse, because my english is not good, but I am doing, my best,for do it better!!! I hope to hear notice from you soon !! my e-mail: al177663@academ01.mty.itesm.mx From owner-chromosomes@net.bio.net Sat Nov 09 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!news.sprintlink.net!news-stk-200.sprintlink.net!news.onramp.net!usenet From: jwes@onramp.net (Dr. Larry) Newsgroups: bionet.genome.chromosomes Subject: Saethre-Chotcen Syndrome Date: 10 Nov 1996 18:44:45 GMT Organization: OnRamp Technologies; ISP; Dallas/Ft Worth/Houston, TX USA Lines: 10 Message-ID: <5657qt$sab@news.onramp.net> NNTP-Posting-Host: lonestar21.onramp.net Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.8 (beta 2) I am currrently doing educational planning for a eight year old, male with the diagnosis of Saethre-Chotcen Syndrome. The child is marginally retarded with some behavior problems. I am looking for sources regarding the syndrome and its implications. I have only been able to gleen the most basic of information generally in the area of facial, skelletial abnorminalities. Any help would be appreciated. Dr. Larry Westmoreland Fort Worth, Texas From owner-chromosomes@net.bio.net Sat Nov 09 22:00:00 1996 Path: biosci!bloom-beacon.mit.edu!panix!feed1.news.erols.com!howland.erols.net!news.sprintlink.net!news-stk-200.sprintlink.net!news.onramp.net!usenet From: jwes@onramp.net (Dr. Larry) Newsgroups: bionet.genome.chromosomes Subject: Saethre-Chotcen Syndrome Date: 10 Nov 1996 18:47:15 GMT Organization: OnRamp Technologies; ISP; Dallas/Ft Worth/Houston, TX USA Lines: 10 Message-ID: <5657vj$sin@news.onramp.net> NNTP-Posting-Host: lonestar21.onramp.net Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.8 (beta 2) I am currrently doing educational planning for a eight year old, male with the diagnosis of Saethre-Chotcen Syndrome. The child is marginally retarded with some behavior problems. I am looking for sources regarding the syndrome and its implications. I have only been able to gleen the most basic of information generally in the area of facial, skelletial abnorminalities. Any help would be appreciated. Dr. Larry Westmoreland Fort Worth, Texas From owner-chromosomes@net.bio.net Sun Nov 10 22:00:00 1996 Path: biosci!agate!howland.erols.net!www.nntp.primenet.com!nntp.primenet.com!nntp.uio.no!nntp.uib.no!nntp-bergen.UNINETT.no!nntp-trd.UNINETT.no!daresbury!lyra.csx.cam.ac.uk!news From: ricky critcher Newsgroups: bionet.genome.chromosomes Subject: FISH on blood smears Date: Mon, 11 Nov 1996 14:22:21 +0000 Organization: University of Cambridge, England Lines: 12 Message-ID: <3287369C.5953@mole.bio.cam.ac.uk> Reply-To: rc@mole, bio.cam.ac.uk NNTP-Posting-Host: png-mac8.gen.cam.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; 68K) Hi I am trying to FISH yacs onto mouse peripheral blood smears but so far have had no success. Does any one out there have some handy hints. Any help would be greatly appreciated. Thanks Ricky Critcher Dept. of Genetics Cambridge University UK From owner-chromosomes@net.bio.net Mon Nov 11 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!swrinde!news.uh.edu!rpenny From: rpenny@Bayou.UH.EDU (Riggs Penny) Newsgroups: bionet.genome.chromosomes Subject: Re: FISH on blood smears Date: 12 Nov 1996 22:13:19 GMT Organization: University of Houston Lines: 23 Message-ID: <56aspv$atk@Masala.CC.UH.EDU> References: <3287369C.5953@mole.bio.cam.ac.uk> NNTP-Posting-Host: bayou.uh.edu X-Newsreader: TIN [version 1.2 PL2] ricky critcher (rc@mole.bio.cam.ac.uk) wrote: : I am trying to FISH yacs onto mouse peripheral blood smears but so far : have had no success. Does any one out there have some handy hints. Any : help would be greatly appreciated. Try treating the blood sample with 0.75M KCl for 10 min, centrifuge and remove most of the supernatant, then make a "smear" with a few drops of the remaining liquid/pellet. This method will allow you to get rid of most of the red blood cells so you can hybridize to the remaining leucocyte nuclei. Penny Riggs NASA LB Johnson Space Center rpenny@bayou.uh.edu Mail Code SD2 http://www.sss.org/~penny Houston, TX 77058 From owner-chromosomes@net.bio.net Tue Nov 12 22:00:00 1996 Newsgroups: bionet.genome.chromosomes Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!malgudi.oar.net!utnetw!mabrini From: mabrini@uoft03.utoledo.edu (Pan Parag) Subject: Look here! Message-ID: Sender: news@utnetw.utoledo.edu (News Manager) X-Newsreader: TIN [version 1.2 PL2] Date: Tue, 12 Nov 1996 22:33:26 GMT Lines: 1 From owner-chromosomes@net.bio.net Wed Nov 13 22:00:00 1996 Path: biosci!rutgers!uwm.edu!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!portc02.blue.aol.com!portc01.blue.aol.com!audrey01.news.aol.com!not-for-mail From: smacker5@aol.com Newsgroups: bionet.genome.chromosomes Subject: partial monosomy chromosome 7 Date: 14 Nov 1996 21:31:13 GMT Organization: AOL http://www.aol.com Lines: 55 Sender: news@aol.com Message-ID: <19961114213300.QAA01866@ladder01.news.aol.com> NNTP-Posting-Host: ladder01.news.aol.com To whom it may concern; I am a parent of a 15 month girl named Jessica. She was born with a segment deletion of the long arm chromosome 7. The genotype is: 46,XX,del (7)(q22.1q31.2). Since receiving the results we have been informed that her particular situation is rare, and only 7 other children since 1976 have been reported with it. The reports of the seven children are extreme, which gives me reason for great concern. My daughter displays low muscle tone, and a delay in development. She has been described as, mild global hypotonia involving both axial and appendicular muscles: mild hypotonia is noted in the region of pelvic girdle.To date, her gross motor is about 2.5 months behind, and her fine motor and cognative skills are right on target. The span for gross and fine motor was 6-7 months behind when physical and occupational therapy began. There are no concerns about regression in any of the devepmental parameters at this time Since birth, her index fingers on both hands have been described as arthrogrypotic. They have always been flexed or curled in toward her palms. She has been using them more, but still displays an immature pincer grasp. Jessica has had a MRI, which has ensured us of normal structure of her brain. The various blood tests have also been normal except the chromosomes. She recently has seen Dr. Hutcheon, chief section of genetics at St. Joe's in Paterson NJ. He told us, when reading the reports, he did not feel very optimistic about her condition. But, after Dr. Hutcheon met Jessica, he was relieved, and feels very optimistic of her future. He concurred that Jessica's phenotype is less severe than the seven children in the scientific literature we have received. However, he did tell us we should expect some sort of learning disability in the future, but obviously can not tell to what degree. I was wondering if I could take my research further to talk with a scientist who may be studying this so called syndrome. I am not sure how to go about doing so. If you have any suggestions I would be most appreciative. He also mentioned the fact that the other part of her chromosome 7 is in tact, and all information is there. Does this mean that her condition will not be as severe? What is involved with having my daughter studied. Is this something that is possible, and should I consider it at all. I feel it is important for Jessica to be studied, and entered into the report with the other seven children. This would show there are degrees of symptoms and hope for the next parent reading that report. I am still trying to track down a current report on the seven children. Some must be around 17 or 18 and even 20 by now. Have they gone to college, do they live "normal" lives etc. As you can see I'm still looking for information, as well as, what else can I do for my daughter. The doctors all say the best thing I could have done was to get her involved in physical & occupational therapies very early. It has helped her tremendously, but what can I do for her possible learning disabilities. If you have any suggestions I am very willing to hear them, as well as reaserch them on the internet. Is there a way to find out of an ongoing study of this genotype? Thank-you so much for any information you can provide. Sincerely, Lori Dring E-mail: Smacker 5 From owner-chromosomes@net.bio.net Thu Nov 14 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!www.nntp.primenet.com!nntp.primenet.com!feed1.news.erols.com!uunet!in1.uu.net!news-in.tiac.net!posterchild!news@tiac.net From: Property Digest Newsgroups: bionet.genome.chromosomes Subject: NATIONAL BIOTECH REGISTER Date: Fri, 15 Nov 1996 10:13:50 -0800 Organization: U.S. Real Estate Register Lines: 5 Message-ID: <328CB2DE.6D1E@barryinc.com> NNTP-Posting-Host: p10.ts6.lowel.ma.tiac.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Win16; I) National Biotech Register announces a new service on our Web site, Supplier Provider. You can now look up a list of suppliers on NatBio's Web site by product classification. To learn more about this service and how to get your company listed, visit our site at: http://www.barryinc.com/bio or e-mail us at: natbio@barryinc.com.. From owner-chromosomes@net.bio.net Thu Nov 14 22:00:00 1996 Path: biosci!rutgers!gatech!csulb.edu!hammer.uoregon.edu!arclight.uoregon.edu!news.sprintlink.net!news-peer.sprintlink.net!EU.net!Austria.EU.net!01-newsfeed.univie.ac.at!swidir.switch.ch!in2p3.fr!univ-lyon1.fr!news.imag.fr!ciril.fr!usenet From: Robert BRIMEYER Newsgroups: bionet.genome.chromosomes Subject: Seckel syndrom (bird-headed) Date: Fri, 15 Nov 1996 15:51:54 +0100 Organization: Universite de Nancy 2 - UFR MathInfo (IUP Miage) Lines: 12 Message-ID: <328C838A.5CCB@plg.u-nancy.fr> NNTP-Posting-Host: saphir.plg.u-nancy.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; SunOS 5.5 sun4m) CC: brimeyer@plg.u-nancy.fr Dear Netters, I`m looking for every kind of information about the SECKEL SYDROM (rare genetic disease). As a physiotherapist I have a patient (6 month old girl) who suffers from this syndrom. What treatment may I offer... What is known about this syndrom (also called bird-headed) Thanks Robert From owner-chromosomes@net.bio.net Sat Nov 16 22:00:00 1996 Path: biosci!rutgers!uwm.edu!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!torn!news1.bellglobal.com!sunqbc.risq.net!news.risq.qc.ca!news.mcgill.ca!news From: Graham Dellaire Newsgroups: bionet.genome.chromosomes Subject: Call for VOTE: GENSTRUCTURE newsgroup bionet.genome.gene-structure Date: 17 Nov 1996 18:56:57 GMT Organization: McGill University Computing Centre Lines: 300 Message-ID: <56nn5p$a5j@sifon.cc.mcgill.ca> NNTP-Posting-Host: g-01.das.mcgill.ca X-Newsreader: AIR News 3.X (SPRY, Inc.) Voting is now open on the following proposal to create the mailing list & newsgroup GENSTRUCTURE/bionet.genome.gene-structure (moderated) The charter was not modified as a result of the discussion. *** NOTE *** We are often running several votes for other newsgroups, so please be certain to follow the voting directions *carefully*! If you just send in a message saying "YES" or "NO" it will not be counted if it is not clear which proposal you are responding to. ---------------------------------------------------------------------- Proposal for GENSTRUCTURE/bionet.genome.gene-structure (moderated) Proposed USENET name: bionet.genome.gene-structure One line Description: Genome and chromatin structure and function Status: Moderated Proposed Moderation address: bionet-genome-gene-structure@net.bio.net (genstruc-moderator@net.bio.net is an alias for bionet-genome-gene-structure@net.bio.net) Moderator: Graham Dellaire Proposed mailing list name: GENSTRUCTURE Proposed e-mail addresses: genstruc@net.bio.net genstruc@daresbury.ac.uk Charter: The purpose of the GENSTRUCTURE newsgroup is to provide a proper forum for the discussion of issues pertaining and involving genome and/or chromatin structure and function (see _Topics of Discussion_). Primarily it should enable those researchers who work in genome/chromatin structure or related 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. Genome/chromatin accessibility and recombination -recombination hotspots (mieotic and mitotic) -fragile sites -imprinting and recombination rates -ectopic gene targeting and chromatin structure 2. 3D-organization of the nucleus -chromosome territories -nucleoli -nuclear lamina (telomere localization) -tissue or cell cycle dependent positioning of chromosomes -RNA tracking 3. Effect of Superhelicity and DNA topology/structure(Triple strand, Z-DNA, cruciform, bent etc) on biological processes such as: -replication (ex. replication fork barriers, initiation sites) -transcription (ex. promoter function in relation to superhelicity) -recombination (ex. Gin and Hin invertases and superhelicity) 4. Histones and Nucleosomes and chromatin structure/function -H1 repression of transcription -Post translational modification of histones acetylation (H4, H3), phosphorylation (H1, H3) and ubiquitination (H2A, H2B) -Histone variants (ex. H2A.Z in mammals, H5 of chicken) 5. Models of genome structure (Loop Domain Model, Channel Model, MegaBase Giant Loop Model, etc.) 6. Classical chromosome elements and their relationship to gene function -centromeres (constitutive heterochromatin and gene silencing) -telomeres (associated silencing and involvement in position effect) 7. Evolution of the Genome -isochores and base-content (GC vs. AT) -formation of gene clusters and syntenic mapping -repetitive elements (satellites, telomeric and centromeric (alpha) repeats, lines and sines) 8. Biologically important mutants and knockouts that affect genome/chromatin structure -ex. SNF/SWI, TOPO mutants in yeast -RAD 51,52,54 knockout mice -AT, BLM, FA mouse models 9. Techniques for genome/chromatin analysis -cytogenetic techniques (g banding, r and q) -Fluorescent In situ analysis(FISH) -Confocal microscopy -Electron microscopy -Electron microscopy In situ analysis (EMISH) -psoralen, polyamine crosslinking -In vivo nucleosome foot printing -Dnase I/Micrococcal Nuclease sensitivity -VM26 Topoisomerase II site mapping 10. Chromatin/DNA binding proteins and their effects on chromatin structure and/or gene expression -Polycomb proteins -Rap1 (telomere silencing) -alpha2-MCM1 (repression of MAT locus) -CENP A/B/C (centromere structure/function) -XCAP-C/E, SMC1/2 (chromatin Condensation) -remodeling of chromatin by SWI/SNF proteins -H-NS in bacteria (role in nucleoid topology vs. gene function) 11. Nuclear Matrix (NM) and Nuclear Lamina (NL) -cell cycle regulation of formation of NM and NL -transcription and replications factors and the concept of a dynamic NM (ex. tissue and temporal specificity) -role of NM in signal transduction (mechanistic vs. chemical signals) 12. Matrix attatchent regions (MAR's), domain boundaries and locus control regions (LCR's) and their relationship to gene structure and function. -definition of transcription/replication domains -model systems ex. betaglobin (LCR) SCS/SCS' of the Drosophila Heat Shock Locus (HS87a7) 13. Phenomenon of Position Effect and Transvection -in drosophila (HP1, polycomb, heterochromatization) -in mammalian systems (silencing or variegated expression of transgenes) -in fungi 14. Epigenetic effects on gene function -imprinting -methylation -maintenance of early/late replication 15. Dosage compensation mechanisms and X chromosome inactivation -MSL proteins of Drosophila -XIC (Xist RNA) in mammals -CpG methylation 16. Chromatin structure and DNA replication -ORC1 protein of yeast -origins of replication (association with cruciform, bent DNA and MARS) 17. Specialized methods of nuclear packaging -bacterial nucleoid -packaging of DNA in spermatozoa 18. DNA repair and chromatin structure -TFIIH (transcription coupled repair) -p53 -BLM and AT genes -poly-ADP-polymerase (PARP) 19. Mechanisms of genomic instability -during oncogenesis -process of chromosomal aberration (stable and unstable) (ex. role of micronuclei in the process) -chromosomal aberration during aging and mechanisms of instability (ex. telomeres and telomerase) In addition this newsgroup provides: A forum for the exchange of information about future congresses and meetings in areas of molecular biology relating to genome structure/function. 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 -Specific common resources (ex. primers, antibodies, vectors) -Genome analysis techniques -Transgenic models and mutant cell lines Moderation Policy: Mass-posted commercial messages, chain letters, and similar postings not associated with or pertaining to the study of genome/chromatin structure and function will be deleted without comment. Inappropriate messages posted in good faith will be returned to the sender. Messages not strictly within the charter but likely to be of interest to many subscribers (e.g., messages dealing with transcription and replication factors) will be accepted. Subscribers are welcome from universities or any academic institutions, government agencies, medical institutions, and industrial or commercial organizations. Contributions within the functions outlined above are encouraged. Proposed discussion leaders: *Note: Area of expertise is written in brackets Graham Dellaire, e-mail: dellaire@odyssee.net (gdella@po-box.mcgill.ca) Institut du Cancer de Montreal Centre de Recherche L.C. Simard 1560 Sherbrooke Street East, Montreal, Quebec, Canada H2L 4M1 telephone:1 (514) 876 6936; fax: (514) 876 5476 *(Expertise:chromatin structure and recombination; Recombination Access Mapping (RAM); genome structure analysis) Ronald Hancock, e-mail: ronald.hancock@crhdq.ulaval.ca Professor Laval University Cancer Research Centre 1 rue de l'Arsenal Quebec, Canada G1R 2J6 telephone: 1 (418) 691-5281; fax: 1 (418) 691-5439 *(Expertise:genome organisation in vivo; models of genome structure; topoisomerases; VM26 topoisomerase II site mapping) Eric Milot, e-mail: milot@ch1.fgg.eur.nl Faculty of Medicine Dept. of Cell Biology and Genetics P.O. Box 1738 3000 DR Rotterdam The Netherlands telephone: 3110 4087164; fax: 3110 4360225 *(Expertise:Chromatin context and transcription; Polycomb protein; position effect variegation; chromosome and nuclear organisation; dosage compensation) **Tentative Discussion leader** Peter Cook, e-mail: peter.cook@pathology.oxford.ac.uk Professor of Cell Biology, The Sir William Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, UK. Telephone (direct line) : +44/0 1865 275528 Telephone (switchboard) : +44/0 1865 275500 Fax : +44/0 1865 275501 http://www.molbiol.ox.ac.uk/www/users/counsell/cook.htm (Expertise:Chromatin/Genome Structure and Function in regard to transcription and replication) ---------------------------------------------------------------------- Voting is now open on the proposal for GENSTRUCTURE/bionet.genome.gene-structure and will run through 24:00 hrs Pacific Time on 12 December 1996. Please send your vote to either of the following addresses: Address Location Network ------- -------- ------- biovote@daresbury.ac.uk U.K. JANET biovote@net.bio.net U.S.A. Internet/BITNET PLEASE BE SURE TO FOLLOW THE FORMAT BELOW - WE OFTEN RUN MORE THAN ONE VOTE AT A TIME SO A SIMPLE "YES" OR "NO" MESSAGE WITHOUT THE NEWSGROUP NAME MAY BE AMBIGUOUS. Your vote should contain a single line: YES on GENES if you favor allowing the creation of this newsgroup or NO on GENES if you think that this proposal will adversely affect the BIOSCI/bionet system. While not intended to be an exhaustive list of possible concerns (more specific concerns may have been raised during the discussion period on BIOFORUM/bionet.general and interested readers are referred to these), some general reasons for voting NO might be if you are concerned about newsgroup proliferation and/or believe that the proposed group will not be utilized, or if you think that the proposed newsgroup would substantially duplicate or overlap with the function of existing newsgroups. If you are simply not interested in participating in the newsgroup above, please don't cast a NO vote, but instead just don't vote at all. The newsgroup proposal must receive at least 80 YES votes to pass and the number of YES votes must be greater than the number of NO votes by at least 40. Discussion of the newsgroup proposal is now closed and we strongly discourage posting any messages in other forums about the fact that a CALL FOR VOTES has been issued. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-chromosomes@net.bio.net Sun Nov 17 22:00:00 1996 Path: biosci!agate!spool.mu.edu!uwm.edu!newsfeed.internetmci.com!nol.net!not-for-mail From: Mark Peters Newsgroups: bionet.genome.chromosomes Subject: --> Cancer, Stealth Microbe Date: Sun, 17 Nov 1996 20:22:24 -0800 Organization: GENIUS QUEST Lines: 313 Message-ID: <328FE480.3623@nol.net> Reply-To: gquest@nol.net NNTP-Posting-Host: ip38-84.nol.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Win16; U) STEALTH MICROBE CAUSES CANER There are two basic forms of carcinogens (cancer causers): EPIGENETIC - carcinogens that do not directly damage DNA but cause alterations such as hormonal derangements, immunosuppression or chronic tissue injury that in turn predisposes to cancer. GENOTOXIC - Carcinogens that react directly with DNA or with macromolucles that then react with DNA. The Stealth Microbe damages tissue by its presence, and alters hormone balance, and causes immunosuppression . The Stealth Microbe can cause the formation of the carcinogen NMBA by cell-mediated catalysis. Also he Stealth Microbe secretes organic acids during carbohydrate metabolism that can result in spontaneous nitrosation of the carcinogen NMBA.. The Stealth Microbe is EPIGENETICALLY AND GENOTOXICALLY CARCINOGENIC. The rest of this document will be dedicated to medical research that supports the statement that the stealth microbe causes Cancer. 1980 Studies of a population with a high incidence of esophageal carcinoma showed that Stealth Microbe invasion was common in the esophageal epithelium of patients with either premalignant changes or early esophageal carcinoma. Nitrate and Nitrite were present in high concentrations in the water and staple grains. This study established the ability of the Stealth Microbe to augment the nitrosative formation of the esophagus - specific carcinogen benzylmethylnitrosamine (NBMA; N-nitroso-N- methylbenzylamine). Results showed that when there were more microbes there was also more NBMA. Spontaneous nitrosation of BMA was enhanced under the acidic condidtions resulting from the acids secreted by the Stealth Microbe during Carbohydrate Metabolism. Thus, the Stealth Microbe invasion into the epithelium could cause local formation of NBMA by both cell- mediated catalysis and extracellular decreases in pH. 1987 From twelve cases of precancerous lesions, 21 strains of the Stealth Microbe were isolated belonging to 15 different biotypes. Stealth Microbes obtained via biopsy were accessed for their ability to catalyze N- nitrosobenzylmethylamine (NBMA) N-benylmethylamine and nitrite. Strains with the higher niltrosation potential were generally isolated from lesions with the more advanced precancerous changes. This evidence supports the hypothesis that the Stealth Microbe plays a causal role in the development of cancer, by means of endogenous nitrosamine production. The microbe is able to secrete organic acids during carbohydrate metabolism which decreases the local pH and this results in a considerable increase in the microbes production of the carcinogen NBMA. 1994 "The study was aimed at determination of possible connection between co-existing S.M. infection in patients with lungcarcinoma with course of neoplastic disease and ability to achieveremission by application of different methods of treatment. Thestudy involved 25 patients with histologically confirmed lung carcinoma. Their sputum and bronchial rinsings were tested. The tests were performed at the moment of diagnosisof the diseases, during and after treatment. In all patients so occurrence and type of S.M. infections was investigated .Dynamics of S.M. infection was measured by a scale from minimal to very severe. In about 1/3 of patients at the moment of diagnosisof the disease, severe or very severe infection was seen which was dependent of stage of the disease advancement. These preliminary studies seem to indicate that presence of severe or very severe S.M infection is not favorable prognostically and frequently correlates with a progress of neoplastic changes and worse responseto treatment." 1994 Patients with malignancies are at high risk to develop systemic non bacterial infections. Stealth Microbe accounts for approximately 80% of these isolates. The vast majority of these infections are of endogenous origin." HOST DEFENSES AND HOW Stealth Microbe DEFEATS THEM The skin and mucous membranes are primary defenses Stealth Microbe attacks and eats the skin The mucous membranes are primary defense Proteinase attacks secretory IgA of mucous membranes Gliotoxin attacks mucociliary action Macrophages protect the respiratory tract Gliotoxin inhibits macrophage phagocytosis Cell mediated immunity protects us from Stealth Microbe Antigen processing Macrophage activation (3a) Inhibited lymphokine production (3b) Inhibited activation of T lymphocytes Myeloperoxidase enzyme protects against mycoses Mannan inhibits myeloperoxidase release Phagocytic cells are the mainstay of cellular immunity Stealth Microbe grows from phagocytic cells Antiphagocytic compound Humoral immunity: opsonization helps protect us Proteinase reduces opsonizing activity Humoral immunity: complement C3 role in host defense Proteinase degradation of complement C3 Nonimmune serum factors: transferins bind iron Stealth Microbe siderophores sequester iron Lactobacillus produces potent S.M. growth inhibitor MORE ON Stealth Microbe PROTEINASE Cleavage of immunoglobulins including IgA FC Portion of immunoglobulin g degraded REDUCED BACTERICIDAL ACTIVITY AGAINST ESCHERICHIA COLI Alpha 2 macroglobulin & alpha 1 proteinase MORE ON MANNANS AND POLYSACCHARIDES Multiple inhibition of proliferative response Mannan inhibits lymphoproliferation Stealth Microbe specific inhibition proliferative response Glycoprotein & mannan suppress lymphoproliferation Mannan increases hydrogen peroxide production Polysaccharide antigens inhibit lymphocyte proliferation Polysaccharide depression of cellular function MORE ON GLIOTOXIN Gliotoxin present in vaginal samples Cultured cell growth blocked Gliotoxin reduces B lymphocytes count Irradiation increased gliotoxin toxicity Apoptosis DNA fragmentation in macrophages - apoptosis Apoptosis of mouse L929 fibroblast cells Apoptosis in concanavalin a-stimulated t blasts Apoptosis of T blasts and macrophages 80-95% inhibition of protein synthesis Lymphoid organ apoptosis Cytoskeletal structure damage & adhesion loss Kills non-hematopoietic cells TISSUE DAMAGE Extensive tissue damage Cytoskeletal microfilament/detachment/vacuolation Modification of microfilaments or plasma membranes Induction of microvilli loss Reorganization of cortical cytoplasm Altered bile acid uptake Afflux Modified hormone responsiveness (Stealth Microbe DIABETES will have much on hormones) "Incubation of Stealth Microbe cells with human luteinizing hormone (hLH), human chorionic gonadotrophin(hCG) Or glucagon produced a significant rise in cAMP total levels." Mice treated with cortisone were susceptible to intratracheal challenge with 10-100 x less Stealth Microbe than were untreated mice. "Stealth Microbe also possesses enzymes that can reduce steroids at the 3- ,17-and 20-oxo-groups. Altered morphology and plasma membrane function Tumor-like lesions on major organs DNA CHANGES Drastic DNA changes & precancerous tissue damage Raised inositol triphosphate & DNA fragmentation 30 ng/ml prevents T & B cell DNA synthesis DNA fragmentation of T and B cells Genome severely damaged Alloreactive cytotoxic T cells DAMAGE BELOW THE GENERALIZED TOXICITY THRESHOLD Significant DNA damage in thymocytes at um Glucose metabolism selectively affected Macromolecular synthesis selectively affected Basal rate of H2O2 production inhibited Macrophage activity abrogated LYMPHOPROLIFERATION T-cell proliferation inhibition Mitogen or interleukin induced b & t proliferation Leukocytes as stimulator cells disabled Depletion of murine epidermal Langerhans Major histocompatibility complex (nm) concentration ultrastructural damage to lc Immune response and contact sensitivity Increased suppressor cell activity of B-lymphocytes Phytohemagglutinin-induced mitogen response suppressed Anti-sheep erythrocyte antibody response suppressed Anti-thy 1 antibody and complement Not plastic-adherent or mac-1 antigen-positive Cytotoxic T cells production failure MACROPHAGES Macrophage phagocytosis irreversibly inhibited Microvilli loss and chromatin condensation In vivo macrophage & T cell dependent mechanisms Stealth Microbe TOXINS High molecular weight toxins Glycoprotein toxins SMtoxin Low molecular-weight toxins Stealth Microbe toxin investigation results Pathogenic enzymes Proteinase Phospholipases Lysophospholipase-transacylase WHAT Stealth Microbe IS Stealth Microbe - the most pervasive S.M. pathogen A facultative pathogen - masquerading marauder Pathogenic trickery Pathogenesis and phenotypic switching Differential expression of virulence factors Rapid alteration of phenotype 9 distinct colony phenotypes Colony morphology Constraints on the ___ __ _____ transition Cellular phenotype Patterns of gene expression Resistance to anti-S. M. agents Antigenicity Stealth Microbe has amphotericin b resistance Pathologic states are extremely varied Invasive potential increases with quantity MORE ON WHAT Stealth Microbe DOES Gut colony may impair cell mediated immunity Stealth Microbe is a cause of immunodeficiency Increased susceptibility to bacterial infection Suppressed DTH and bacterial sepsis Elevated Stealth Microbe antigen titers & bacterial sepsis World wide plague - often refractory Stealth Microbe infections are increasing in incidence How it isn't detected Molecular mimicry Antigenic variability Topographical variation dependent on carbon source Diagnostic skin test failure How it is diagnosed Successful post autopsy diagnosis Antemortem diagnosis is difficult Clinician's uncertainty Difficulty in differentiation - colony or invasion Invasive biopsy required Therapy by suspicion From owner-chromosomes@net.bio.net Sun Nov 17 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!swrinde!news.uh.edu!usenet From: hua Newsgroups: bionet.genome.chromosomes Subject: OFR repetitive sequence Date: 18 Nov 1996 18:23:42 GMT Organization: uh/biol. dept. Lines: 3 Message-ID: <56q9je$kos@Masala.CC.UH.EDU> NNTP-Posting-Host: wimp.nsm.uh.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) X-URL: news:bionet.genome.chromosomes Please help!!! What is OFR repetitive sequence? From owner-chromosomes@net.bio.net Mon Nov 18 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.erols.net!feed1.news.erols.com!phase2.worldnet.att.net!netnews.worldnet.att.net!uunet!in3.uu.net!wizard.pn.com!news.xensei.com!news From: symposia@xensei.com (Cambridge Symposia) Newsgroups: bionet.genome.chromosomes Subject: 1997 Cambridge Symposia Spring Conferences Date: Tue, 19 Nov 1996 14:37:51 GMT Organization: Cambridge Symposia Lines: 63 Message-ID: <56sgvh$erq@xensei3.xensei.com> Reply-To: symposia@xensei.com NNTP-Posting-Host: chi.xensei.com X-Newsreader: Forte Free Agent 1.0.82 If you wish to receive information about the conferences list below, please contact: Cambridge Symposia 1037 Chestnut Street Newton Upper Falls, MA 02164 USA Phone: 617-630-1399 Fax: 617-630-1395 E-mail: symposia@cambridge.org http://www.cambridge.org/symposia/ EMERGING CLINICAL APPLICATIONS OF FIBRIN SEALANT Organizers: William Drohan-American Red Cross, Martin MacPhee-American Red Cross, Uri Martinowitz-National Hemophilia Center, Michael O'Leary-U.S. Navy Marine Corps., and Tom Lynch-Food and Drug Administration March 7-10, 1997 San Diego, California GENETIC APPROACHES TO BREAST AND PROSTATE CANCER Organizers: Marc E. Lippman-Georgetown University, Robert B. Dickson-Georgetown University, and John T. Isaacs-Johns Hopkins University March 22-28, 1997 Lake Tahoe, California UNSTABLE TRIPLETS, MICROSATELLITES, AND HUMAN DISEASE Organizers: Jack Griffith-University North Carolina-Chapel Hill, Robert Wells-Texas A&M University, and David Nelson-Baylor College of Medicine March 31-April 6, 1997 Santa Fe, New Mexico TNF-alpha ANTAGONISTS: MONOCLONAL ANTIBODIES, SOLUBLE RECEPTORS, THALIDOMIDE AND OTHER NOVEL APPROACHES Organizers: Gilla Kaplan-Rockefeller University, Carol A. Nacy-Entre Med, Inc., and Victoria Freedman-Rockefeller University April 13-18, 1997 Santa Fe, New Mexico NUCLEAR STRUCTURE-GENE EXPRESSION INTERRELATIONSHIPS Organizers: Gary Stein-University of Massachusetts Medical Center, Gordon Hager-National Institutes of Health, and Ronald Berezney-SUNY-Buffalo May 16-22, 1997 Bolton Valley, Vermont ADVANCES IN CONGESTIVE HEART FAILURE, RESEARCH AND THERAPEUTICS Organizers: Giora Feuerstein-SmithKline Beecham Pharmaceuticals and Michael Fowler-Stanford University School of Medicine May 27-31, 1997 Lake Tahoe, California 1997 Nature America Conference Administerd by Cambridge Symposia The Fifth International Nature Genetics' conference entitled: FUNCTIONAL GENOMICS: From Genes to Drugs Washington Court Hotel, Washington, D.C. April 17-18, 1997 ANTISENSE 97: Targeting the Molecular Basis of Disease Hyatt Regency, Cambridge, MA., May 1-2, 1997 From owner-chromosomes@net.bio.net Wed Nov 20 22:00:00 1996 Newsgroups: bionet.genome.chromosomes Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!strath-cs!bradford.ac.uk!leeds.ac.uk!news From: RMRHCA@leeds.ac.uk (Helen Ardley) Subject: chromosome 19 mapping Message-ID: <571f4n$7u8_003@leeds.ac.uk> NNTP-Posting-Host: sjuh_pc41.leeds.ac.uk Organization: University of Leeds Date: Thu, 21 Nov 1996 11:41:18 +0000 (GMT) X-Newsreader: News Xpress Version 1.0 Beta #4 Lines: 4 Does anyone know of a chromosome 19 deletion mapping panel? Thanks for any help. Helen Ardley rmrhca@stjames.leeds.ac.uk From owner-chromosomes@net.bio.net Wed Nov 20 22:00:00 1996 Path: biosci!rutgers!uwm.edu!news-peer.gsl.net!news.gsl.net!hunter.premier.net!feed1.news.erols.com!phase2.worldnet.att.net!netnews.worldnet.att.net!uunet!in3.uu.net!news.u.washington.edu!roach From: roach@u.washington.edu (Jared Roach) Newsgroups: bionet.genome.chromosomes Subject: One Percent of the Human Genome Sequenced. Date: 21 Nov 1996 03:40:27 GMT Organization: University of Washington, Seattle Lines: 13 Message-ID: <570ivb$pe4@nntp3.u.washington.edu> NNTP-Posting-Host: saul3.u.washington.edu NNTP-Posting-User: roach One percent of the human genome has been sequenced. I have updated my "How Much of the Human Genome Has Been Sequenced?" web page to reflect this. The provisional figure that I had on my page for the last two weeks was in error and has been corrected. The web page is located at: http://weber.u.washington.edu/~roach/human_genome_progress2.html Best Wishes to All, Jared From owner-chromosomes@net.bio.net Sun Nov 24 22:00:00 1996 Path: biosci!agate!howland.erols.net!news.sgi.com!mr.net!newshub.tc.umn.edu!fu-berlin.de!news.belwue.de!news.uni-ulm.de!rz.uni-karlsruhe.de!news.fzk.de!usenet From: j.ludat@hvt.fzk.de (Juergen Ludat) Newsgroups: bionet.genome.chromosomes Subject: CHROMOSOME 18 Date: 25 Nov 1996 16:11:07 GMT Organization: Forschungszentrum Karlsruhe, Germany Lines: 8 Distribution: world Message-ID: <57cger$fjf@hdihp3.fzk.de> NNTP-Posting-Host: 141.52.137.71 Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.6 Hello, can anyone give me some information about chromosome 18 defects, especially about the 18 p defekt. A nephews child is born with that defect and the parents want to know all, what is worth knowing. thank you for answer juergen From owner-chromosomes@net.bio.net Mon Nov 25 22:00:00 1996 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed1.bbnplanet.com!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!uunet!in2.uu.net!ott.istar!istar.net!tor.istar!east.istar!news From: Stephanie St-Pierre Newsgroups: bionet.genome.chromosomes Subject: 11:22 translocation Date: 26 Nov 1996 17:19:10 GMT Organization: International 11;22 Translocation Network Lines: 12 Message-ID: <57f8qe$jh7@nr1.toronto.istar.net> NNTP-Posting-Host: timmins-115.nt.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01KIT (Win16; U) Hi there: I'm the mother of a 20 month old girl affected by unbalanced 11;22 translocation, also called partial trisomy 11;22 or trisomy 22. I am always looking for other families who have children with this disorder to correspond with, so we can share information and progress. I'd love to hear from anyone out there. Stephanie stpierre@nt.net From owner-chromosomes@net.bio.net Tue Nov 26 22:00:00 1996 Path: biosci!CHI1.UNCFSU.EDU!fwaddle From: fwaddle@CHI1.UNCFSU.EDU (Floyd Waddle) Newsgroups: bionet.genome.chromosomes Subject: chromosome fusions/fissions Date: 27 Nov 1996 07:53:15 -0800 Organization: Fayetteville State University Lines: 35 Sender: daemon@net.bio.net Distribution: world Message-ID: <329C8DF7.14C@chi1.uncfsu.edu> NNTP-Posting-Host: net.bio.net As described in the textbooks, Robertsonian fusions are produced by the replacement of the short arm of one acrocentric with the long arm of another acrocentric. In centric fusions, breaks occur at the centromeres of two acrocentrics and the portions of each centromere which carry the long arms are fused together. All genetics textbooks I have seen describe one or the other of these two types of fusion. The idiograms for human and chimp, however, show an entirely different type of fusion. The human second chromosome was produced by breakage at the tips of two short arms with the subsequent fusion of the short arms. The result was a dicentric chromosome in which one of the centromeres became suppressed. Amazingly, I have a textbook in which the text describes the fusion as a centric fusion while the accompanying figure clearly shows short arm fusion. Thus, I have two questions: 1. Why did the author misidentify the type of fusion even though he could see that he was wrong just by reading his own book? 2. I have not seen idiograms of species other than those of humans and apes. The karyotypes easily available to me do not show the detail necessary to distinguish one chromosome type fusion from another. Thus, I have not seen proof of either Robersonian fusions or centric fusions. The textbooks do not give references that I can look up. Is there any literature that demonstrates the reality of either Robersonian or centric fusion, or are they merely figments of the collective imagination of textbook writers? Chromosome fisions are also described in the textbooks but the authors do not explain where the telemeres come from which are necessary to close off the raw ends of the fissioned chromosomes. Have fissions actually been demonstrated or are the textbook writers postulating them merely because they can think of no other method of evolution for mammals with large chromosome numbers? Floyd Waddle From owner-chromosomes@net.bio.net Tue Nov 26 22:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.genome.chromosomes Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 27 Nov 1996 02:00:45 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199611271000.CAA04400@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 Nov 27 22:00:00 1996 Path: biosci!agate!howland.erols.net!news-peer.gsl.net!news.gsl.net!usenet.eel.ufl.edu!warwick!lyra.csx.cam.ac.uk!daresbury!not-for-mail From: "Johan van Ooijen (+31) 317 477 319" Newsgroups: bionet.genome.chromosomes Subject: JoinMap & MapQTL software announcement Date: 28 Nov 1996 14:33:38 -0000 Lines: 32 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <57k7s2$bth@mserv1.dl.ac.uk> Autoforwarded: false Ua-Content-Id: 11ABE3E12B00 Hop-Count: 4 Importance: normal Disclose-Recipients: prohibited Original-To: biochrom@dl.ac.uk You can now read about the genetic mapping software packages JoinMap and MapQTL on the web site of CPRO-DLO: http://www.bib.wau.nl/cpro/mapping/ Information is presented on the things you can do with these software packages. You can also view the manuals to study the details, and you can view the lists of frequently asked questions. You can read about the computer platforms for which the software is available, how the licensing works, what it costs, and how to order. JoinMap is software for the calculation of genetic linkage maps. It handles data from all kinds of full-sib families (BC, F2, RILs, [doubled] haploids, cross-pollinator-progeny), and can combine data from several sources into an integrated map. Besides the modules for map calculation, the package has some diagnostical modules. MapQTL is software for the mapping of quantitative trait loci (QTLs). It handles data from single full-sib families of all kinds (BC, F2, RILs, [doubled] haploids, cross-pollinator-progeny). Used techniques: interval mapping, multiple QTL models with cofactors (MQM mapping), nonparametric Kruskal-Wallis analysis per marker. Johan van Ooijen email: J.W.vanOoijen@CPRO.DLO.NL or mapping@CPRO.DLO.NL fax: +31 317 418 094 mail: CPRO-DLO, POBox 16, 6700 AA Wageningen, the Netherlands DLO Centre for Plant Breeding and Reproduction Research (CPRO-DLO) WWW: http://www.bib.wau.nl/cpro/ From owner-chromosomes@net.bio.net Wed Nov 27 22:00:00 1996 Path: biosci!FMI.CH!plikat From: plikat@FMI.CH (Uwe Plikat) Newsgroups: bionet.genome.chromosomes Subject: mapping software Date: 28 Nov 1996 04:43:01 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <329D9705.255A@fmi.ch> Reply-To: plikat@fmi.ch NNTP-Posting-Host: net.bio.net I am urgently looking for mapping software that can build up contigs. I am mapping a bacterial genome which is stored in a cosmid library (taking single cosmids as probes). Anyone any hint? Thanks, Uwe. ______________________ Uwe Plikat, Ph.D. Phone +41-61-6966442 Fax +41-61-6966323 email plikat@fmi.ch ______________________ From owner-chromosomes@net.bio.net Thu Nov 28 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!portc02.blue.aol.com!audrey01.news.aol.com!not-for-mail From: lmgoin@aol.com Newsgroups: bionet.genome.chromosomes Subject: Re: --> Cancer, Stealth Microbe Date: 29 Nov 1996 22:59:10 GMT Organization: AOL http://www.aol.com Lines: 10 Message-ID: <19961129230000.SAA13898@ladder01.news.aol.com> References: <328FE480.3623@nol.net> NNTP-Posting-Host: ladder01.news.aol.com X-Admin: news@aol.com Hello GQuest; Am looking for information on Cowden's Disease. This is a rare genetic disorder which affects the senses and the growth of brain cells, I think. If there is any information you can share on this, please let me know. If you know of a web site where I may find some more information on this topic, please let me know. Your wisdom and experience are appreciated. Thank you, lmgoin@aol.com From owner-chromosomes@net.bio.net Thu Nov 28 22:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!swrinde!news.sgi.com!news.bbnplanet.com!su-news-hub1.bbnplanet.com!arclight.uoregon.edu!phase2.worldnet.att.net!news.u.washington.edu!root From: "Peter J. Myler" Newsgroups: bionet.genome.chromosomes Subject: Re: mapping software Date: 29 Nov 1996 17:16:32 GMT Organization: SBRI Lines: 79 Message-ID: <01bbde19$9e8b5260$39b58e8c@mylerpj> References: <329D9705.255A@fmi.ch> NNTP-Posting-Host: cs116-3.u.washington.edu Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_01BBDDD6.90713A20" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Internet News 4.70.1155 This is a multi-part message in MIME format. ------=_NextPart_000_01BBDDD6.90713A20 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Uwe: You might want to try SEGMAP, developed by Phil Green and Chuck Magness. You can get it from Chuck at cmagness@u.washington.edu. Peter -- ===================================================== Peter J. Myler Seattle Biomedical Research Institute 4 Nickerson Street Seattle, WA 98109-1651 phone: (206) 284-8846x332 FAX: (206) 284-0313 e-mail: MYLERPJ@U.WASHINGTON.EDU ===================================================== Uwe Plikat wrote in article <329D9705.255A@fmi.ch>... > I am urgently looking for mapping software that can build up contigs. > > I am mapping a bacterial genome which is stored in a cosmid library > (taking single cosmids as probes). Anyone any hint? > > Thanks, > > Uwe. > ______________________ > > Uwe Plikat, Ph.D. > Phone +41-61-6966442 > Fax +41-61-6966323 > email plikat@fmi.ch > ______________________ > ------=_NextPart_000_01BBDDD6.90713A20 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Uwe:

You might want to try = SEGMAP, developed by Phil Green and Chuck Magness.  You can get it = from Chuck at cmagness@u.washington.edu.

Peter
-- =
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D
Peter J. Myler
Seattle Biomedical Research = Institute
4 Nickerson Street
Seattle, WA =  98109-1651
phone: (206) 284-8846x332
FAX: (206) = 284-0313
e-mail: MYLERPJ@U.WASHINGTON.EDU
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D





Uwe Plikat = <plikat@FMI.CH> wrote in article <329D9705.255A@fmi.ch>...
> I am urgently looking for mapping = software that can build up contigs.
>
> I am mapping a = bacterial genome which is stored in a cosmid library
> (taking = single cosmids as probes). Anyone any hint?
>
> = Thanks,
>
> Uwe.     
> = ______________________
>
> Uwe Plikat, Ph.D.
> Phone =   +41-61-6966442
> Fax =    +41-61-6966323
> email plikat@fmi.ch
> = ______________________
>

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