From owner-chromosomes@net.bio.net Tue Nov 01 22:00:00 1994 Path: biosci!GENE.BIOTECH.WISC.EDU!Tom_Keller From: Tom_Keller@GENE.BIOTECH.WISC.EDU ("Tom Keller") Newsgroups: bionet.genome.chromosomes Subject: sequence polymorphisms Date: 2 Nov 1994 13:38:39 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <199411022138.NAA18771@net.bio.net> NNTP-Posting-Host: net.bio.net Subject: Time:4:28 PM OFFICE MEMO sequence polymorphisms Date:11/2/94 I have been receiving more and more PCR products for automated sequencing and having to explain to clients why, though they see only a single band on a gel, the probable explaination for the large number of uncalled positions in their sequence is that they actually amplified a family of similar sized DNA fragments having conserved sequence on the ends but varying internally. The amplification of the multicopy rRNA genes would seem to be an example. Yet, I see reports of people suppposedly doing direct sequencing of these types of samples. Am I missin somethin? Does any one else have experience with this type of sequence sample, i.e. direct sequencing of PCR products of genomic DNA of multicopy or at least heterozygous DNA? From owner-chromosomes@net.bio.net Wed Nov 02 22:00:00 1994 Path: biosci!CBIL.HUMGEN.UPENN.EDU!cbell From: cbell@CBIL.HUMGEN.UPENN.EDU (Callum Bell) Newsgroups: bionet.genome.chromosomes Subject: Re: re sequence polymorphisms Date: 3 Nov 1994 08:01:58 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 40 Sender: daemon@net.bio.net Distribution: world Message-ID: <9411031557.AA26524@cbil.humgen.upenn.edu> NNTP-Posting-Host: net.bio.net > One issue to bare in mind when sequencing PCR products is fidelity of the > the PCR reaction. Standard Taq is error prone, it has no editing function. > Therefore an early error will create a poylmorphism in the finl products. I have heard several people make this argument against sequencing Taq polymerase amplified DNA. True, it is well documented that Taq misincorporates bases at an appreciable frequency. Consider, though, the number of copies of the target sequence that are present before amplification begins. 50 ng (a reasonable amount to use in a PCR reaction) of human DNA contains tens of thousands of copies of the genome, and therefore, as many copies of the target fragment. Even if a mutation occured during the first round of amplification, in one or a few of these copies, the fraction of the total amount of DNA represented by the mutated copies would be negligible. It seems to me that only if the DNA template was derived from a single cell, or other very small quantity of DNA, would misincorporations cause the apparent polymorphisms. Otherwise, mutation detection based on PCR amplified DNA would not be possible. Callum Bell ************************************** Division of Human Genetics Wood Center Room 5012 Childrens Hospital of Philadelphia 34th Street and Civic Center Boulevard Philadelphia PA 19104 Tel: (215) 590 3856/3867/2931 FAX: (215) 590 3764 email: cbell@cbil.humgen.upenn.edu ************************************** From owner-chromosomes@net.bio.net Wed Nov 02 22:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!sunsite.doc.ic.ac.uk!news.sys.uea.ac.uk!cpca3.uea.ac.uk!news From: Richard James Newsgroups: bionet.genome.chromosomes Subject: Hello Date: 3 Nov 1994 08:34:18 GMT Organization: University of East Anglia, Norwich, Norfolk, NR47TJ, UK Lines: 14 Message-ID: <39a7aa$efa@cpca3.uea.ac.uk> NNTP-Posting-Host: biorij.bio.uea.ac.uk Hello Netters, Since I manage a facility for DNA sequencing which includes two ALF sequencers, I was very interested in the announcement that this newsgroup will include ALF DNA Sequencer discussions. I am very interested in seeing what uses people have made of the ALF for DNA-binding proteins (ie. gel-shift type experiments). I look forward to hearing from you. Richard James From owner-chromosomes@net.bio.net Wed Nov 02 22:00:00 1994 Path: biosci!DXI.NIH.GOV!goldman%bchem.dnet From: goldman%bchem.dnet@DXI.NIH.GOV Newsgroups: bionet.genome.chromosomes Subject: re sequence polymorphisms Date: 3 Nov 1994 06:49:31 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: <9411031449.AA01732@dxi.nih.gov> NNTP-Posting-Host: net.bio.net One issue to bare in mind when sequencing PCR products is fidelity of the the PCR reaction. Standard Taq is error prone, it has no editing function. Therefore an early error will create a poylmorphism in the finl products. Pfu and Vent have exonuclease activity which removes errors. The latter two enzymes a much harder to use but supplimenting 1U of Taq with 1/200-1/100 U of Pfu is meant is be sufficient to reduce the errors significantly (see Barnes PNAS 91:2216 - beware in this paper the confusing mix of units and micro litres. Barnes used Taq at 25-35 U pel ul, but Pfu at 1U per ul). So - if you want to sequence of PCR don't use Taq alone - maybe Xs clients are doing just that??/ ASHG From owner-chromosomes@net.bio.net Wed Nov 02 22:00:00 1994 Path: biosci!GENE.BIOTECH.WISC.EDU!Tom_Keller From: Tom_Keller@GENE.BIOTECH.WISC.EDU ("Tom Keller") Newsgroups: bionet.genome.chromosomes Subject: ABI v.2.01 software Date: 3 Nov 1994 09:17:00 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: <199411031716.JAA22341@net.bio.net> NNTP-Posting-Host: net.bio.net Subject: Time:11:11 AM OFFICE MEMO ABI v.2.01 software Date:11/3/94 Have you tried or heard any reports on the quality of ABI's version 2.01 software for their sequencer? From owner-chromosomes@net.bio.net Wed Nov 02 22:00:00 1994 Path: biosci!daresbury!bioftp.unibas.ch!citi2.fr!jussieu.fr!cea.fr!usenet From: cisitm@albert.cad.cea.fr (Pierre Didierjean) Newsgroups: bionet.genome.chromosomes Subject: *** Q: WHAT KIND OF PEOPLE ON THE NET ? Date: 3 Nov 1994 16:16:45 GMT Organization: SSII Lines: 28 Sender: cisitm@albert.cad.cea.fr Message-ID: <39b2dd$9of@anemone.saclay.cea.fr> NNTP-Posting-Host: nyassa.cad.cea.fr I'd like to know what kind of people i find on the net. Students, Commercials, Adminitrations, Scientifics or what ?? Is anybody knows that or have statistical results ? What are YOU doing in life ? I am a system administrator. Thanks for the answers and sorry for my english ..... Bye +-----------------------------------------------------------------------------+ | Pierre DIDIERJEAN | | | | Administrateur Systeme UNIX | | Cisi, Aix-en-Provence | | France | +-----------------------------------------------------------------------------+ | email : cisitm@albert.cad.cea.fr | +-----------------------------------------------------------------------------+ From owner-chromosomes@net.bio.net Wed Nov 02 22:00:00 1994 Newsgroups: bionet.genome.chromosomes Path: biosci!rutgers!gatech!howland.reston.ans.net!wupost!monsanto.com!rcwieg.monsanto.com!user From: rcwieg@ccmail.monsanto.com (Roger Wiegand) Subject: Re: re sequence polymorphisms Message-ID: Sender: news@tin.monsanto.com (USENET News System) Organization: Searle Molecular Biology References: <9411031557.AA26524@cbil.humgen.upenn.edu> Date: Thu, 3 Nov 1994 19:40:47 GMT Lines: 37 In article <9411031557.AA26524@cbil.humgen.upenn.edu>, cbell@CBIL.HUMGEN.UPENN.EDU (Callum Bell) wrote: > I have heard several people make this argument against sequencing Taq > polymerase amplified DNA. True, it is well documented that Taq > misincorporates bases at an appreciable frequency. Consider, though, > the number of copies of the target sequence that are present before > amplification begins. 50 ng (a reasonable amount to use in a PCR > reaction) of human DNA contains tens of thousands of copies of the > genome, and therefore, as many copies of the target fragment. Even if > a mutation occured during the first round of amplification, in one or a > few of these copies, the fraction of the total amount of DNA > represented by the mutated copies would be negligible. It seems to me > that only if the DNA template was derived from a single cell, or other > very small quantity of DNA, would misincorporations cause the apparent > polymorphisms. Otherwise, mutation detection based on PCR amplified DNA > would not be possible. > Indeed! Even if the amplification begins from one molecule and a mistake occurs in the first round, only one of the four templates for the second round will contain the mutation, resulting in 25% of the product being mutant. I've been trying to sequence mixed populations and 25% of a second sequence is close to the lower limit of what you can even see with any reliability. (Note that this a gross simplification of what probably goes on in the PCR reaction, but I think the premise is sound.) If you clone and sequence individuals you will routinely find mutations, but I doubt that you could ever see a PCR-induced mutation by sequencing the unseparated PCR product. -- Thanks, Roger mailto::rcwieg@ccmail.monsanto.com From owner-chromosomes@net.bio.net Thu Nov 03 22:00:00 1994 Path: biosci!AARDVARK.UCS.UOKNOR.EDU!BROE From: BROE@AARDVARK.UCS.UOKNOR.EDU (Bruce Roe) Newsgroups: bionet.genome.chromosomes Subject: re: sequence polymorphisms Date: 4 Nov 1994 04:16:17 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 44 Sender: daemon@net.bio.net Distribution: world Message-ID: <199411041216.EAA21409@net.bio.net> NNTP-Posting-Host: net.bio.net Hi, The major problems we've had are to obtain pcr products of sufficient quality to yield high signal/noise. This basicly seems to depend on how the product is purified after the pcr rxn. Even a protocol that works for one student does not work for another. The bottom line for me is to clone the product. What we do is: 1. a quick fillin with klenow and the 4 dNTP's to blunt end 2. clone into smaI/CIP treated pUC (from Pharmacia) Since we've got the ds template isolation to routinely work quite well, we then sequence 6-12 separate isolates of the cloned pcr product. In the past 2 years of using this "blunt end cloning approach" we have not noticed any pcr misincorporation artifacts. That's over several hundred clones sequenced. It's my belief that all the talk of Taq polymerase causing or rather allowing misincorporation is: 1. an artifact of dNTP and Mg concentration in the original pcr reaction. As I recall, a few years ago there was such a study published that pointed this out. (Sorry for not having the reference handy) 2. alot of hype by companies that are trying to get around the PE/Cetus patent. In the case of long pcr's (ala W.Barnes), we've not investigated the quality of the product from anything longer than 1-2kb for cloning/sequencing because of fears that strange things may happen. Finally, as for sequencing pcr products, it's my thought that the original poster of the message was not observing misincorporation, but rather had low quality template and thus was observing sequencing artifacts due to a low signal to noise ratio or slightly nicked template. Remember, UV light can cause nicking of DNA in the presence of ethidium bromide and even a single band on a gel can get nicked upon prolonged exposure to UV during extraction and purification from the gel. If you're curious about this, try the expt where you run some DNA fragment out on a gel (with EtBr), expose to UV for various times and after eluting it, re-run it on the gel. It's an "eye opening" experience. Cheers......bruce - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ Bruce A. Roe Professor of Chemistry and Biochemistry / / University of Oklahoma INTERNET: BROE@uoknor.edu \ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - From owner-chromosomes@net.bio.net Thu Nov 03 22:00:00 1994 Path: biosci!GNV.IFAS.UFL.EDU!AFC From: AFC@GNV.IFAS.UFL.EDU (Andrew Cockburn) Newsgroups: bionet.genome.chromosomes Subject: Re: sequence polymorphisms Date: 4 Nov 1994 06:12:59 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HJ2QV4EZEE8ZDW6Y@gnv.ifas.ufl.edu> NNTP-Posting-Host: net.bio.net We have successfully sequenced PCR amplifications of rDNA of individual mosquitoes (Mol.Bio.Evol. 11:406-416, 1994). We were sequencing the ITS2, so one would expect some variation between copies. In a few individuals, there did appear to be polymorphism at certain sites, since the reads were ambiguous. In general, however, it worked pretty well. We think that this is a better approach than sequencing individual clones of PCR products, since then the presence of PCR artifacts is a real problem. We just starting to sequence some non-transcribed spacers. With these we will have no choice but to clone and sequence, since there is lots of length heterogeneity amongst individual copies. That will throw the different sequences out of phase, which is much worse than ambiguous reads at a few sites. Andrew Cockburn USDA From owner-chromosomes@net.bio.net Fri Nov 04 22:00:00 1994 Path: biosci!biosci!not-for-mail From: ert@karlo.wi.mit.edu (Ert Dredge) Newsgroups: bionet.announce,bionet.genome.chromosomes Subject: Announcing release 8 of the Whitehead/MIT MOUSE GENETIC MAP Date: 5 Nov 1994 09:23:02 -0800 Organization: Massachvsetts Institvte of Technology Lines: 69 Sender: kristoff@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Xref: biosci bionet.announce:1552 bionet.genome.chromosomes:323 ANNOUNCING THE EIGHTH RELEASE OF THE WHITEHEAD INSTITUTE/MIT GENOME CENTER GENETIC MAP OF THE MOUSE Release eight of the Whitehead Institute/MIT Genome Center Genetic Map of the Mouse is now available. This map consists of randomly-chosen simple sequence length polymorphisms (microsatellites) that can be analyzed using the polymerase chain reaction, as described in Dietrich, W., et. al., Genetics 131:423-447 (1992), and most recently in Dietrich, W.F. et al., Nature Genetics 7:220-245 (1994) Currently the released map contains 5250 markers. The markers fall into 20 linkage groups spanning approximately 1400 cM with an average spacing of approximately 0.3 cM. This data can be obtained in three different ways: 1. Via internet e-mail using a database e-mail server. Using this service you can obtain locus and assay names of mapped SSLPs, the forward and reverse primer sequences, the genotypes of the loci on the mapping cross, the sizes of the PCR products on selected standard inbred strains, and other useful information. The database can be queried for markers meeting a number of different criteria. For example, you can ask for markers by name, by chromosome, or by position on the map. You can even request a list of markers that are polymorphic between two mouse strains. 2. Via anonymous ftp to genome.wi.mit.edu. Log in as "anonymous" and use your e-mail address as password. The release can be found in the directory /distribution/mouse_sslp_release/oct94/. The file "README" describes the file formats and gives other information about the map. 3. Via a "World-Wide Web" browser. Point your WWW client (e.g., NCSA Mosaic) at "http://www-genome.wi.mit.edu/". To obtain copies of the most current e-mail query forms, send a message to "genome_database@genome.wi.mit.edu" with either a subject line or body text of "help". You will receive instructions and a query form by return mail. Just fill out the form, send it to "genome_database@genome.wi.mit.edu", and the answer to your query will be mailed back automatically. This project is an ongoing one. As new markers are added to the map they will be released on a quarterly basis on the following schedule: January 1995 April 1995 These data releases do not constitute scientific publication of CGR's work, but rather provides scientists with a regular look into our lab notebooks. For projects aimed at the analysis of particular genes or subchromosomal regions, the Whitehead/MIT CGR grants permission 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. Please see the aforementioned README file or contact CGR directly. Please address questions and comments to me at the address below. See the README file for news of the newest member of the Dietrich family. - Ert Dredge ------------------------------------------------------------------------------- Ert Dredge Mondays 8:30pm - 10:30pm Whitehead Institute's Center for Genome Research WMBR 88.1 FM, Cambridge One Kendall Sq, Cambridge, Bldg 300, 5th floor, 02139 Requests: 253-8810 617-252-1922 (w), 617-252-1902 (fax) Beauty Canadian tunes, eh? ------------------------------------------------------------------------------- From owner-chromosomes@net.bio.net Sun Nov 06 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!gatech!udel!news.sprintlink.net!pipex!sunsite.doc.ic.ac.uk!news.sys.uea.ac.uk!cpca3.uea.ac.uk!news From: Richard James Newsgroups: bionet.genome.chromosomes Subject: Re: Hello Date: 7 Nov 1994 13:42:54 GMT Organization: University of East Anglia, Norwich, Norfolk, NR47TJ, UK Lines: 31 Message-ID: <39lasu$sj0@cpca3.uea.ac.uk> References: <39a7aa$efa@cpca3.uea.ac.uk> NNTP-Posting-Host: biorij.bio.uea.ac.uk > Hello Again ALF Users, I hope to get a discussion going about ALF sequencers. ***Template Preparation*** What do users think is the best method for dsDNA template preparation for the ALF? We used to use Qiagen kits but they are quite expensive when used for a lot of samples but give very good quality DNA when used with an extra ethanol precipitation step. We have started to use the Pharmacia Easy Prep system, and after some initial problems (the vortex shaker for the plates is essential to get good yields), we are now happy with the system; especially if you buy the columns in bulk and make up the reagents. ***Fluorescent oligos*** We have recently purchased a Millipore Expedite DNA Synthesiser and are very impressed with the quality and the low price of the oligos. We now use the Millipore FluoreDite reagent for labelleing the oligos with fluorescent group detectable in the ALF. You can label up to 20 oligos from 0.1gm of reagent (which costs as little as $7 for each). We routinely make the oligos first, leaving on the trityl group, and store them in the fridge until we have made enough to set up a bottle of FluoreDite on the synthe siser. We then add the fluorescent group to each oligo until the whole batch is done. After purification by reverse phase these oligos give very good sequence data; as well as making primer walking much more economical. ***Sequence analysis*** We use the Lasergene software from DNASTAR for our seqeunce analysis on a Mac computer. The software is expensive but is very robust and can be installed on a local network to reduce the cost per user. Regards, Richard James e-mail r.james@uea.ac.uk From owner-chromosomes@net.bio.net Sun Nov 06 22:00:00 1994 Path: biosci!WATSON.WUSTL.EDU!rwilson From: rwilson@WATSON.WUSTL.EDU (Rick Wilson) Newsgroups: bionet.genome.chromosomes Subject: Stretch problems? Date: 7 Nov 1994 05:48:53 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 35 Sender: daemon@net.bio.net Distribution: world Message-ID: <9411071349.AA21394@watson.wustl.edu> NNTP-Posting-Host: net.bio.net Greetings! Has anyone experienced any problems with ABI 373A's which have been modified to the "Stretch" configuration? This would include instruments which were modified in the field, as well as those which shipped from factory. Specifically, we're interested in: 1) gels which run much faster (e.g. 20-24 watts necessary to keep spacing between 9 and 12), and 2) an olize green haze on the gel file, with several thick vertical blue streaks. We've seen these problems on a few of our instruments, as have several other labs both here at Wash. U. and across the country. We're currently in the process of trying to pin down the reasons for these problems, so any information you have will be helpful. Also, has anyone experienced increased breakage with recently purchased/ received glass plates? Thanks in advance for your help! Rick **************************************** Richard K. Wilson, Ph.D. Genome Sequencing Center Washington University School of Medicine St. Louis, MO 63108 USA (314) 286-1804 rick@geneman.wustl.edu **************************************** From owner-chromosomes@net.bio.net Sun Nov 06 22:00:00 1994 Path: biosci!agate!library.ucla.edu!europa.eng.gtefsd.com!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!sunsite.doc.ic.ac.uk!news.sys.uea.ac.uk!cpca3.uea.ac.uk!news From: Richard James Newsgroups: bionet.genome.chromosomes Subject: Re: ALF Vs ABI x2 Date: 7 Nov 1994 16:09:13 GMT Organization: University of East Anglia, Norwich, Norfolk, NR47TJ, UK Lines: 29 Message-ID: <39ljf9$110@cpca3.uea.ac.uk> References: <1994Oct27.204417.14639@leeds.ac.uk> NNTP-Posting-Host: biorij.bio.uea.ac.uk > It has been suggested that ALF is better than the ABI system but > I don't know. > I can very accuratly and very very reliably detect a single copy from a single cell. > I can also multiplex upto 8 primer sets within a single cell. Both of > these are using the ABI system > > Would the ALF system be any better. > My comment is that both ALF and ABI machines will do most sequencing jobs. The ABI machine may be better for large scale sequencing labs, but in my experience is harder to use. The ALF is ideal for a multi-user facility where end-users do their own sequencing. It is very easy to train new users and is an ideal machine for small labs. Incidently, I also hate the "we are number 1 attitude of the ABI company". Our previous dealings with ABI have not impressed us too much. I hope that this is of interest. Richard From owner-chromosomes@net.bio.net Wed Nov 09 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!uknet!comlab.ox.ac.uk!oxuniv!oxuniv!nntp Newsgroups: bionet.genome.chromosomes Subject: Re: Stretch problems? Message-ID: <1994Nov10.140006.27409@oxvaxd> From: kclark@immsvr.jr2.ox.ac.uk (Kevin Clark) Date: 10 Nov 94 14:00:05 GMT References: <9411071349.AA21394@watson.wustl.edu> Distribution: world Organization: Institute of Molecular Medicine, Oxford Nntp-Posting-Host: ndmmac4.jr2 X-Posted-From: InterNews 1.0.1@ndmmac4.jr2.ox.ac.uk X-Authenticated: kclark on POP host immsvr.jr2.ox.ac.uk Lines: 51 In article <9411071349.AA21394@watson.wustl.edu> rwilson@WATSON.WUSTL.EDU (Rick Wilson) writes: > Greetings! > > Has anyone experienced any problems with ABI 373A's which have > been modified to the "Stretch" configuration? This would include > instruments which were modified in the field, as well as those > which shipped from factory. > > Specifically, we're interested in: > > 1) gels which run much faster (e.g. 20-24 watts necessary to keep > spacing between 9 and 12), and > > 2) an olize green haze on the gel file, with several thick vertical > blue streaks. > > We've seen these problems on a few of our instruments, as have several > other labs both here at Wash. U. and across the country. We're currently > in the process of trying to pin down the reasons for these problems, so > any information you have will be helpful. > > Also, has anyone experienced increased breakage with recently purchased/ > received glass plates? > > Thanks in advance for your help! > > Rick > **************************************** > Richard K. Wilson, Ph.D. > Genome Sequencing Center > Washington University School of Medicine > St. Louis, MO 63108 USA > (314) 286-1804 rick@geneman.wustl.edu > **************************************** I don't have a stretch get but I recently go a green haze when my laser was about to give up and also when, after a service, the carriage had not been reset properly so the laser was scanning closer to the gel on one side than the other. Kevin \/\ /\/\ /\/\ /\/ kclark@immsvr.jr2.ox.ac.uk \/\ /\/\/\ /\/\/\ /\/ Institute of Molecular Medicine, \/\/\/ \/\/\/ \/\/\/ Oxford,UK. \/\/ \/\/ \/\/ I've been here for 5 years and they only Mac IIci hung me the right way up yesterday. From owner-chromosomes@net.bio.net Wed Nov 09 22:00:00 1994 Path: biosci!HELIX.MGH.HARVARD.EDU!HAINES From: HAINES@HELIX.MGH.HARVARD.EDU ("Jonathan L. Haines") Newsgroups: bionet.genome.chromosomes Subject: (none) Date: 10 Nov 1994 09:39:43 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 161 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HJBC4WF0N68X96GY@HELIX.MGH.HARVARD.EDU> NNTP-Posting-Host: net.bio.net ********************************* * COURSE ANNOUNCEMENT * ********************************* ---GENETIC ANALYSIS METHODS FOR MEDICAL RESEARCHERS--- Description: This intensive four day course centers on mapping human genetic diseases. The concentration is on the entire disease mapping process, including clinical classification, pedigree collection, molecular genetic analysis, statistical analysis, and gene characterization. The course emphasizes the global decision-making process, rather than details of specific techniques. A residential conference center setting promotes extensive interaction between the students and the internationally recognized faculty. Course goals: 1. To outline and instruct participants about the necessary steps and procedures used in ascertaining and collecting pedigree data and clinical and family history information. 2. To discuss in detail both the molecular and statistical methodologies for using the reference marker maps generated by the efforts of the Human Genome Initiative. Emphasis will be on working examples and the basic theory behind genetic mapping methodologies. 3. To educate participants on the general interpretation of linkage results for both simple and complex disorders. Discussions will include an overview of positional cloning strategies, refinement of the preliminary linkage data, investigation of power, examination of heterogeneity, physical mapping, cDNA analysis, exon amplification, etc. This course will not include any bench or "wet" laboratory experience. Co-organizers: Margaret A. Pericak-Vance, Ph.D., Department of Medicine, Department of Genetics, Duke University School of Medicine. She is a founding fellow of the American College of Medical Genetics (ABMS) and a board-certified Ph.D. medical geneticist with fourteen years experience in genetic counseling. Dr. Pericak-Vance is a genetic epidemiologist whose research has focused on mapping the human genome with emphasis on the mapping of genetic disorders, with more recent extensions into complex genetic disease. She has concentrated on neurogenetic diseases, actively mapping such disorders as familial amyotrophic lateral sclerosis (Lou Gehrig disease), tuberous sclerosis, and late onset Alzheimer disease (AD). She is a member of the Mammalian Genetics Study Section at NIH. Jonathan L. Haines, Ph.D., Department of Neurology, Massachusetts General Hospital, Harvard Medical School. Dr. Haines is a genetic epidemiologist whose research has focused on both human disease and general (reference) chromosome mapping. Dr. Haines has concentrated on neurogenetic diseases, including the mapping of familial amyotrophic lateral sclerosis, familial Alzheimer disease, Huntington disease, tuberous sclerosis, neurofi- bromatosis, and multiple sclerosis. Dr. Haines is presently an editor of chromosome 9 for the Genome Data Base (GDB). He is an associate editor of Genomics and an editor of Current Protocols in Human Genetics. Instructors: Arthur S. Aylsworth, M.D., Division of Genetics and Metabolism, Department of Pediatrics, The University of North Carolina at Chapel Hill. Dr. Aylsworth is a board-certified pediatrician and clinical geneticist. As a physician-scientist, Dr. Aylsworth plays primary roles in family ascertainment and phenotypic delineation. He is actively involved in studies on neurofibromatosis and neural tube defects. David Goldgar, Ph.D., Genetic Epidemiology, Department of Medical Informatics, University of Utah. Dr. Goldgar is a statistical geneticist with extensive experience in both the theoretical and practical aspects of mapping human quantitative and complex traits. He has concentrated on the genetic epidemiology of common cancers, focusing on the genetic mapping of breast and ovarian cancer. He is actively involved in several large pedigree ascertainment and collection studies. Deborah A. Meyers, Ph.D., Department of Medicine, The Johns Hopkins University. Dr. Meyers is a statistical geneticist who has concentrated her research on the genetic basis of complex disorders including allergy and psychiatric diseases such as schizophrenia and Alzheimer disease. She has extensive didactic experience in her teaching role at the short course in Medical and Experimental and Mammalian Genetics, The Jackson Laboratory, Bar Harbor, Maine. Jeffrey Murray, M.D., Department of Pediatrics, University of Iowa. Dr. Murray is a molecular biologist and physician scientist with extensive experience in both general chromosome and disease gene mapping. Dr. Murray is a board-certified pediatrician and clinical geneticist. His research interests include genetic studies in cleft-lip and palate. He also directs a national effort to generate a high resolution genetic map of the entire genome. Dr. Murray is a GDB Editor for chromosome 4 and a former member of the Mammalian Genetics Study Section at NIH. Marcy C. Speer, M.S., Ph.D., Department of Medicine, Duke University Medical School. Dr. Speer is a board-certified genetic counselor with eleven years of experience. She is also a genetic epidemiologist whose research interest is in mapping human genetic diseases, including the muscular dystrophies and neural tube defects. She is also involved in studies of unusual genetic phenomena such as anticipation and imprinting. Participation: Participation in the course will be dependent on completion of an application form that describes the applicant's background and research interests and will be limited to 36 students. All participants will need to show evidence of a postgraduate genetics course or its equivalent. Participants must provide a brief statement describing their research interests, their reason for taking the course, and their long-term objectives in relation to the course curriculum. This information will be used to select a highly motivated participant group. Minority and women applicants are specifically encouraged to apply. A limited number of scholarships are available for registered students or fellows. Scholarship selection will be based on the strength of the individual applications. Location: The course will be held at the R. David Thomas Center located on the campus of Duke University, Durham, NC. The Thomas Center is a new facility which establishes a climate of hospitality and an atmosphere conductive to learning and to the exchange of ideas. Both students and faculty will be housed at the R. David Thomas Center. Date: March 25-29, 1995 Deadline for completed application: January 2, 1995 For information and application forms contact: Write: Genetic Methods Course c/o Dr Margaret Pericak-Vance Division of Neurology, Box 2900 Duke University Medical Center Durham, NC 27710 Or: E-Mail: genclass@genemap.mc.duke.edu In any correspondence, please include a postal address From owner-chromosomes@net.bio.net Wed Nov 09 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!swrinde!sgiblab!gatekeeper.us.oracle.com!barrnet.net!noc.usfca.edu!mobius.usfca.edu!luis From: luis@mobius.usfca.edu (Luis Frigo) Newsgroups: bionet.genome.chromosomes Subject: DNA NEWS!!!! Date: 10 Nov 1994 14:26:00 GMT Organization: University of San Francisco Lines: 68 Message-ID: <39taho$j1g@noc.usfca.edu> NNTP-Posting-Host: mobius.usfca.edu X-Newsreader: TIN [version 1.2 PL2] PHYSICS NEWS UPDATE A digest of physics news items by Phillip F. Schewe, American Institute of Physics Number 202 November 9, 1994 physnews@aip.org SO-CALLED "JUNK" DNA, regions of genetic material (accounting for 97% of the human genome) that do not provide blueprints for proteins and therefore have no apparent purpose, have been puzzling to scientists. Now a new study shows that these non-coding sequences seem to possess structural similarities to natural languages. This suggests that these "silent" DNA regions may carry biological information, according to a statistical analysis of DNA fragments by researchers at Boston University and Harvard Medical School (contact H.E. Stanley of Boston University, 617-353-2617). Studying DNA sequences from humans, viruses, bacteria, yeast, and other organisms, the researchers performed statistically-based linguistics tests on the 37 known DNA sequences each having at least 50,000 "base pairs" or "letters" of DNA code. The researchers first performed a variation of a test known as Zipf analysis, in which the words from a text are arranged on an x-axis from most frequently occurring to least frequently occurring; plotted against their rank is the actual number of occurrences of that word in the text. For natural languages one invariably gets a straight line (on a graph using logarithmic axes) whose slope is about -1. The non-coding DNA sequences had linear slopes when base pairs were grouped into genetic "words" consisting of 3, 6, 7, or 8 base pairs. Interestingly, the slope values for non-coding sequences were closer to -1 than for coding DNA, supporting a hypothesis that protein-coding DNA may be more like a compressed computer file than a natural language. (R.N. Mantegna et al., upcoming article in Physical Review Letters.) A NEARBY LARGE SPIRAL GALAXY not previously noted has been discovered by astronomers using a telescope, the Dwingeloo radio telescope in Holland, dedicated to searching for galaxies hidden behind the disk and dust of our own galaxy. The new galaxy, called Dwingeloo 1, is about 10 million light years away. Unlike the dwarf galaxy found earlier this year in orbit around (and behind) the Milky Way (see Update 174), Dwingeloo 1 is a large galaxy and is not considered part of our local group of galaxies. The new observations are part of a program to study a neglected part of the sky, a region aptly called the "Zone of Avoidance" because astronomers scanning extragalactic space had heretofore steered their telescopes away from the haze of foreground stars constituting our galaxy. (R.C. Kraan- Korteweg et al., Nature, 3 Nov. 1994; this is Nature's 125th anniversary issue; Happy Birthday.) WHAT HAPPENED TO THE SSC STAFF? A year after Congress shut down the nascent supercollider, the number of scientists and technicians dropped from 1100 to less than 100. About a fourth are jobless. Some have returned to academe. Former SSC director Roy Schwitters is now a physics professor at the University of Texas. About half of those who have found jobs are working outside particle physics. Some examples: Cas Milner, who had worked on the Gamma-Electron-Muon (GEM) detector at the SSC, now works at the TIAA-CREF pension fund. Kate Morgan (also formerly with GEM) moved on to Citicorp. (Science, 28 October 1994.) -- \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\|/////////////////////////////////// -------------------------------\ | /------------------------------- Luis Antonio Frigo \ | / ~~~High LET Cosmic Rays~~~ luis@physics.usfca.edu \ | / Physics Research Laboratory lafrigo@lynx.cs.usfca.edu \|/ University of San Francisco Work Phone 510-666-2333 * Golden Gate Ave. Cal U.S.A. ----------------------------------------------------------------------- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-chromosomes@net.bio.net Thu Nov 10 22:00:00 1994 Newsgroups: bionet.general,bionet.genome.arabidoposis,bionet.genome.chromosomes,bionet.immunology,bionet.microbiology,bionet.molbio.bio-matrix Path: biosci!news.Stanford.EDU!unixhub!lll-winken.llnl.gov!uwm.edu!cs.utexas.edu!convex!news.duke.edu!godot.cc.duq.edu!newsfeed.pitt.edu!dsinc!ub!acsu.buffalo.edu!liao From: liao@acsu.buffalo.edu (Jui-Ping Liao) Subject: Focus on Microscopy 1995 Message-ID: Sender: nntp@acsu.buffalo.edu Nntp-Posting-Host: autarch.acsu.buffalo.edu Organization: UB Date: Fri, 11 Nov 1994 16:47:40 GMT Lines: 191 Xref: biosci bionet.general:11936 bionet.genome.chromosomes:331 bionet.immunology:2407 bionet.microbiology:711 bionet.molbio.bio-matrix:519 FOCUS ON MICROSCOPY 95 A joint meeting of 8th International Conference on 3D Image Processing in Microscopy and 7th International Conference on Confocal Microscopy April 18-20, 1995 Howard Plaza Hotel, Taipei, Taiwan, Rep. of China CALL FOR PAPERS _________________________________________________________________ SCIENTIFIC PROGRAM Scientific sessions start on Tuesday, April 18, 1995. Original contributions will be presented in the following areas: Confocal microscopy * theory of confocal imaging * scanning confocal designs: point / slit arrangements, beam scanning, direct field scanning (bilateral, tandem) * high resolution optical 3-D Microscopy * two photon and time resolved fluorescence imaging * transfer functions and deconvolution Applications * confocal microscopy in-vivo: approaches, problems and prospects * 3D imaging for agricultural research * fluorescence 3-D imaging in cell biology and neurobiology * fluorescent probes, in-situ hybridization * 3-D cytometry * microstructures of materals, polymers and thin films * application in environmental sciences Near-field microscopy * near-field scanning techniques (NSOM, STM, AFM) * high resolution DNA - imaging * spectroscopy and surface modification * combined near-field and confocal designs Optical tweezers and scalpel * instrumentation * applications Electron Microscopy * cryo-microscopy * low-voltage SEM * electron beam tomography X-ray microscopy * theory and instrumentation of x-ray microscopy * x-ray sources 3-D imaging processing * 3-D reconstruction of histological, optical and tomographical sections * visualization models in 3-D and 4-D microscopy * supercomputing in microscopy * analysis of serial section images, 3-D scene recognition * 3-D image restoration and image quality CONTRIBUTION AND PUBLICATION OF EXTENDED ABSTRACTS Papers are invited for oral and poster presentation from the fields indicated by the scientific program and related areas. Deadline for submission of abstracts is December 31, 1994. An extented abstract (minimum 700 words and maximum 1500 words) is required for each presentation, and will be published as a suplement issue of Zoological Studies (ISSN 1021-5506). All text will be typeset by the publisher. Authors are encouraged to submit their manuscript in electronic forms. Files created from the following word processos are acceptable, otherwise, please submit your manuscript in ASCII form (both Mac and IBM-PC format). Manuscript can also be submitted by e-mail to: elepcc@ ubvms.cc buffalo.edu, however, a hardcopy has to be sent by mail (or faxed) to the address in USA. A hardcopy is required accompany the electronic form. Mac Word, Wordstar, Word Perfect, Microsoft Word, Ventura, ASCII Figures and photos are permitted, however they have to fit the following format specified in the photo and diagram format guide for direct photoreproduction. Original photographs (both B&W and color) and line drawings are required. If it is possible, authors please provide a FAX number to facilatate the transmission of galley proof in early 1995. The organizing committee will make a selection of the abstracts for oral presentation. By the end of January 1995 authors will be notified about acceptance and the final program will be mailed to all registrants. ACCOMMODATION The Howard Plaza Hotel provides subtantially reduced room rates for conference participants of Focus on Microscopy '95. Hotel Accommodation at the Howard Plaza Hotel is offered on a first come, first served basis. Please refer to Focus on Microscopy '95 for qualifying the reduced room rates at booking: (refer to Registration form) Howard Plaza Hotel 160 Jen Ai Road, Sec. 3 Taipei, Taiwan, Republic of China Phone: 886-2-700-2323 FAX: 886-2-700-0729 The room rate includes 10% service charge, welcome wine, fruit basket, newspaper and the use of health club facilities including sauna. Major credit cards (American Express, Visa, Mastercard, JCB, Diners Club) are accepted at the hotel. REGISTRATION & CONFERENCE FEE The conference fee is US$220, which includes, documentation, abstract book and refreshments during breaks. A preregistration fee of US$180.00, is available when postmarked before January 31, 1995. OFFICIAL AIR CARRIER China Airlines is the official air carrier of Focus on Microscopy 95, special discount airfare is available through CAL's world wide branch offices. INFORMATION Registration, abstract forms and enquires: N. America and Europe: Focus on Microscopy '95 c/o Dr. P. C. Cheng Advanced Micrscopy and Imaging Laboratory Department of Electrical and Computer Engineering State University of New York at Buffalo P.O. Box. 84 Getzville, NY 14068 USA Tel and Fax: 716-645-3868 e-mail: elepcc@corn.eng.buffalo.edu Other nations: Focus on Microscopy '95 c/o Dr. J. L. Wu Institute of Zoology Academia Sinica Nankang, Taipei, Taiwan 11529 Republic of China Tel: 886-2-789-9500 Fax: 886-2-789-9503/886-2-785-8059 e-mail: zojlwu@ccvax.sinica.edu.tw ORGANIZERS C.P. Chen (Taipei) G.J. Brakenhoff (Amsterdam) A.Kriete (Giessen) C.H. Chou (Taipei) P. C. Cheng (Buffalo)(Chairman) C.J.R. Sheppard (Sydney) P.P. Hwang (Taipei) C. Cogswell (Sydney) D.M.Shinozaki (London,Cana da) W.Y. Lee (Taipei) M. Gu (Sydney) E.H.K. Stelzer (Heidelberg ) H.K. Wu (Taipei) V. Howard (Liverpool) T. Wilson (Oxford) J.L. Wu (Taipei) H. Kim (Rochester) W.L. Wu (Taipei) _________________________________________________________________ THE CONFERENCE IS JOINTLY O RGANIZED AND SUPPORTED BY The Society for 3-D Imaging Sciences in Microscopy, Amsterdam Institute of Zoology, Academia Sinica, Taiwan, R.O.C. Electron Microscopy Society of China, Taipei, R.O.C. Life Science Research Promotion Center, NSC, R.O.C. AMIL, State University of New York at Buffalo, U.S.A. _________________________________________________________________ From owner-chromosomes@net.bio.net Sat Nov 12 22:00:00 1994 Path: biosci!agate!spool.mu.edu!uwm.edu!msuinfo!harbinger.cc.monash.edu.au!news.cs.su.oz.au!metro!wabbit.cc.uow.edu.au!wabbit.cc.uow.edu.au!not-for-mail From: kmiles@wumpus.cc.uow.edu.au (Keith Miles) Newsgroups: bionet.genome.chromosomes Subject: Want info re chrom 6 Genome Date: 13 Nov 1994 12:21:19 +1100 Organization: University of Wollongong, NSW, Australia. Lines: 13 Message-ID: <3a3pmf$h5h@wumpus.cc.uow.edu.au> NNTP-Posting-Host: wumpus.cc.uow.edu.au Summary: Want to find site with info on chromo 6 Keywords: SCA Type 1 I need to find the site of chromo 6 research for Genome project. Would anyone have a lead on how I could contact W. French Anderson from University of Southern California. Any help would be much appreciated as I am doing this for a family member. Many Thanks Keith Miles Kmiles@uow.edu.au From owner-chromosomes@net.bio.net Mon Nov 14 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!uhog.mit.edu!rutgers!gatech!howland.reston.ans.net!usc!usc!not-for-mail From: dgeiger@aludra.usc.edu (Daniel Geiger) Newsgroups: bionet.genome.chromosomes Subject: Chromosome number in *Haliotis* sp. Date: 15 Nov 1994 11:15:55 -0800 Organization: University of Southern California, Los Angeles, CA Lines: 12 Sender: dgeiger@aludra.usc.edu Message-ID: <3ab1db$on1@aludra.usc.edu> NNTP-Posting-Host: aludra.usc.edu I am looking for information on chromosome number (haploid or diploid) in the genus *Haliotis* (Mollusca, Gastropoda, Prosobranchia, Archaeogastropoda, Haliotidae). I am aware of the followint publications: Colombera & Tagliaferri, 1983; Arai & Wilkins, 1986; Nakamura, 1985, 1986; Arai et al., 1982, 1988; Minkler, 1977. These publications deal with H. tuberculata, lamellosa diversicolor aquatilis diversicolor, exigua, planata = grayana, varia?, cracherodii, discus hannai, discus discus, gigantea. Does anyone know of any other publications or data of other species? I would appreciate a note. regards Daniel Geiger (dgeiger@aludra.usc.edu) From owner-chromosomes@net.bio.net Tue Nov 15 22:00:00 1994 Path: biosci!agate!library.ucla.edu!psgrain!nntp.ski.mskcc.org!mac-131.k-g2.ski.mskcc.org!user From: d-burtrum@ski.mskcc.org (michelle or doug......) Newsgroups: bionet.genome.chromosomes Subject: gross chromosome structure Date: Tue, 15 Nov 1994 17:30:14 -0500 Organization: Memorial Sloan-Kettering Cancer Center Lines: 17 Message-ID: NNTP-Posting-Host: mac-131.k-g2.ski.mskcc.org Can someone give me some insights (references, protocols, or general discussion) as to how I might look at the gross morphology of mammalian chromosomes? We have a transgenic mouse line which gives sometimes inexplicable results in various molecular assays, and we think one possibility may be that the chromatin structure may somehow be changed by transgene expression. I would like to compare the chromatin structure in various tissues from transgenic and non-transgenic littermates. Thanks for your help. Michelle Tourigny mrtour@stud.med.cornell.edu -- db or Michelle From owner-chromosomes@net.bio.net Tue Nov 15 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!usc!elroy.jpl.nasa.gov!netline-fddi.jpl.nasa.gov!nntp-server.caltech.edu!ung From: ung@cco.caltech.edu (Ung-Jin Kim) Newsgroups: bionet.genome.chromosomes Subject: Need large, intact human genomic DNA fragments covering the region of your interest Date: 16 Nov 1994 23:27:55 GMT Organization: California Institute of Technology, Pasadena Lines: 27 Message-ID: <3ae4hr$93p@gap.cco.caltech.edu> NNTP-Posting-Host: accord.cco.caltech.edu Summary: Human genomic BAC clones are available Keywords: Human genomic BAC library X-Newsreader: NN version 6.5.0 #12 (NOV) For those of you who would like to obtain human genomic DNA pieces in the form of stable, easily manipulated clones in E. coli hosts, a BAC (Bacterial Artificial Chromosome) library is available. Average insert size of the library is about 125 kb, and the library covers more than 90% of human genome. The clones are stably propagated as a recombinant F-factor in a recombination-deficient E. coli host strain. The library can be screened by almost any kind of probes including cDNA, oligos, other genomic clones (plasmid, cosmid, lambda, YAC etc). We will screen the library to find out BAC clones covering the regions of your intesrest, and if necessary, will also develop contig maps that depict overlap-relationships among the clones covering the same loci. All it takes will be a letter of collaboration. Interested party should contact: Ung-Jin Kim Division of Biology, 147-75 Caltech, Pasadena, CA 91125 (818)395-4901 (office) (818)395-4154 (laboratory) (818)796-7066 (fax) ung@ash.tree.caltech.edu From owner-chromosomes@net.bio.net Wed Nov 16 22:00:00 1994 Path: biosci!daresbury!bioftp.unibas.ch!citi2.fr!jussieu.fr!univ-lyon1.fr!ghost.dsi.unimi.it!ghost.dsi.unimi.it!not-for-mail From: decristo@hp1.sm.dsi.unimi.it (daniela de cristofano) Newsgroups: bionet.genome.chromosomes Subject: info fragment assembly Date: 17 Nov 1994 12:33:17 +0100 Organization: Computer Science Dep. - Milan University Lines: 19 Message-ID: <3aff1t$94u@hp1.sm.dsi.unimi.it> NNTP-Posting-Host: hp1.sm.dsi.unimi.it Summary: info DNA We're two Italian students in Information Science interested in the problem of DNA fragment assembly and we're searching information about it. Could you send us some electronic addresses or directories in which we can find something about it? Could you give us also the bibliography of articles or books talking about ? We're also interested in algorithms solving the problem of reconstructing a DNA sequence knowing only the sequences of many interlapping fragments of it. Where can we find them,please? Grazie, DANIELA DE CRISTOFANO PIERLUIGI FRISCO PS: decristo@ghost.sm.dsi.unimi.it From owner-chromosomes@net.bio.net Wed Nov 16 22:00:00 1994 Path: biosci!cc.UManitoba.CA!gordonr From: gordonr@cc.UManitoba.CA (Richard Gordon) Newsgroups: bionet.genome.chromosomes Subject: Re: gross chromosome structure Date: 17 Nov 1994 11:50:24 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 79 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net Dear Michelle & Doug, Our modelling of the genome as a differentiation tree is at the "gross" level. It has been very hard to find links between this level and specific loci, but perhaps you have found such. See papers in attached broadcast reprint request. Best regards, -Dick Gordon[Nov17,94] On Tue, 15 Nov 1994, michelle or doug...... wrote: > Can someone give me some insights (references, protocols, or general > discussion) as to how I might look at the gross morphology of mammalian > chromosomes? We have a transgenic mouse line which gives sometimes > inexplicable results in various molecular assays, and we think one > possibility may be that the chromatin structure may somehow be changed by > transgene expression. I would like to compare the chromatin structure in > various tissues from transgenic and non-transgenic littermates. Thanks > for your help. > > Michelle Tourigny > > mrtour@stud.med.cornell.edu > > -- > db > > or Michelle > Dear Colleague: I am finishing a book about the intersection of three major fields of biology: Gordon, R. (1995). The Hierarchical Genome and Differentiation Waves: Novel Unification of Development, Genetics, and Evolution (Singapore: World Scientific), in prep. If your work might be relevant to this review, I would appreciate reprints or preprints as soon as possible, or an update, if I've been in contact with you previously. Thanks for your help. Please be sure to send your e-mail address, in case I have any questions. Best regards, -Dick Gordon Please mail to: Dr. Richard Gordon, Department of Radiology University of Manitoba, ON104, Health Sciences Centre 820 Sherbrook Street Winnipeg, Manitoba, Canada R3A 1R9 E-mail: GordonR@cc.UManitoba.ca Fax: (204) 783-8565 If you are curious, condensed accounts are given in: Gordon, R. & G.W. Brodland (1987). The cytoskeletal mechanics of brain morphogenesis: cell state splitters cause primary neural induction. Cell Biophysics 11, 177-238. Gordon, R. (1993). The fractal physics of biological evolution. In: Beysens, D., N. Boccara & G. Forgacs, eds. Dynamical Phenomena at Interfaces, Surfaces and Membranes. Commack, N.Y.: NOVA Science Publishers, 99-111. Bjorklund, N. K. & R. Gordon (1993). Nuclear state splitting: a working model for the mechanochemical coupling of differentiation waves to master genes (with an Addendum). Russian J. Dev. Biol. 24(2), 79-95. Gordon, R., N. K. Bjorklund & P. D. Nieuwkoop (1994). Dialogue on embryonic induction and differentiation waves. Int. Rev. Cytol. 150, 373-420. Bjorklund, N. K. & R. Gordon (1994). Surface contraction and expansion waves correlated with differentiation in axolotl embryos. I. Prolegomenon and differentiation during the plunge through the blastopore, as shown by the fate map. Computers & Chemistry 18(3), 333-345. > From owner-chromosomes@net.bio.net Thu Nov 17 22:00:00 1994 Path: biosci!agate!library.ucla.edu!psgrain!nntp.ski.mskcc.org!mac-131.k-g2.ski.mskcc.org!user From: d-burtrum@ski.mskcc.org (michelle or doug......) Newsgroups: bionet.genome.chromosomes Subject: Re:gross chromosome structure Date: Thu, 17 Nov 1994 09:15:47 -0500 Organization: Memorial Sloan-Kettering Cancer Center Lines: 13 Message-ID: NNTP-Posting-Host: mac-131.k-g2.ski.mskcc.org Juliette: Thanks for your response. We have plenty of expression of our transgene and we would like to see if it is causing different chromosome structure, not a result of it. michelle mrtour@stud.med.cornell.edu -- db or Michelle From owner-chromosomes@net.bio.net Thu Nov 17 22:00:00 1994 Path: biosci!DXI.NIH.GOV!goldman%bchem.dnet From: goldman%bchem.dnet@DXI.NIH.GOV Newsgroups: bionet.genome.chromosomes Subject: Re:gross chromosome structure Date: 18 Nov 1994 13:48:47 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <9411182148.AA01327@dxi.nih.gov> NNTP-Posting-Host: net.bio.net How about Fluroescence insitu hybridisation with heterochromatin probes. The hetprobe to chromosoem 1 (puc1.77) cross hybs to 16 and and 9 het when they are decondensed. ASHG From owner-chromosomes@net.bio.net Fri Nov 18 22:00:00 1994 Path: biosci!agate!spool.mu.edu!sgiblab!swrinde!pipex!uunet!hearst.acc.Virginia.EDU!portal.gmu.edu!osf1.gmu.edu!psubedi1 From: psubedi1@osf1.gmu.edu (Prakash Subedi) Newsgroups: bionet.genome.chromosomes Subject: Gel electrophoresis and gene mapping Date: 19 Nov 1994 20:40:43 GMT Organization: George Mason University, Fairfax, Virginia, USA Lines: 6 Message-ID: <3alnsb$al@portal.gmu.edu> NNTP-Posting-Host: osf1.gmu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit X-Newsreader: TIN [version 1.2 PL2] Can gel electropherosis be used in gene mapping? or is this a bogus question? Thanks. From owner-chromosomes@net.bio.net Sun Nov 20 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!cpca3.uea.ac.uk!news From: Richard James Newsgroups: bionet.genome.chromosomes Subject: Re: DNA sequencers Purchase Date: 21 Nov 1994 10:31:13 GMT Organization: University of East Anglia, Norwich, Norfolk, NR47TJ, UK Lines: 20 Message-ID: <3apsth$4sl@cpca3.uea.ac.uk> References: NNTP-Posting-Host: biorij.bio.uea.ac.uk > We are considering purchasing a DNA sequencer for our core facility. > We do not need a very high throughput machine but are looking for an instrument that is easy to operate, reliable, truely automated and can be used for SSCP analysis. > We are considering the Alf and the ABI primarily but are also looking at Molecular dynamics. Does anyone have any thoughts on this topic? Is the ALF machine reliable? How is the software for the ALF system? > Dave > w > >We have two ALF machines which we use intensively for DNA sequencing. We have not used them for any SSCP work so I cannot comment on this. We find the ALF easy to use, reliable and capable of being operated as a multi-user facility rather than as a service. The software for DNA sequencing is excellent and the Fragment Manager software looks to have great potential for the analysis of PCR products. Regards, Richard James Sequence facility manager From owner-chromosomes@net.bio.net Tue Nov 22 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!usc!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!netnews.nwnet.net!news.u.washington.edu!roach From: roach@u.washington.edu (Jared Roach) Newsgroups: bionet.genome.chromosomes Subject: Re: info fragment assembly Date: 23 Nov 1994 07:15:57 GMT Organization: University of Washington Lines: 38 Sender: roach@u.washington.edu Message-ID: <3auq7d$60a@nntp1.u.washington.edu> References: <3aff1t$94u@hp1.sm.dsi.unimi.it> NNTP-Posting-Host: saul4.u.washington.edu I recently attended the DIMACS Workshop on Combinatorial Methods for DNA Mapping and Sequencing. Many of the protagonists in the field of DNA fragment assembly were there. In fact, this year's "open problem" is a challenge to find the best fragment assembly program. Information on this challenge can be found at ftp dimacs.rutgers.edu /pub/challenge4 I also recommend contacting Gene Meyers gene@cs.arizona.edu R. Idury (Dept of Math and/or Mol Biol; U Southern Cal; email?) Rebecca Parsons rebecca@cs.ucf.edu These people are all working on assembly programs and can point in the right general directions for this sort of thing. Many others are working in this area, too. A few comments on fragment assembly. Greedy algorithms seem to work pretty well on real biological data. The best method for repeat resolution is probably the way it is done in practice: Take advantage of the fact that repeats are not 100% identical. This implies that incorrectly joined fragments can be identified by the presence of inconsistencies across at least three sequences at at least two different sites. If a program is to be useful, it must be user-friendly. In general, this means allowing a user to override decisions and to edit intermediate data structures. Also, there is currently a rise in the number of sequencing projects that use pairwise end sequencing (the double-barrel shotgun), of which I am a strong proponent. It is my expectation that competitive assembly programs in the near future will be those that can take advantage of this information, or at least allow the user to input it. Hershel Safer (hersh@cric.com) of Genome Therapeutics has such a program already. Jared Roach Molecular Biotechnology University of Washington roach@u.washington.edu From owner-chromosomes@net.bio.net Tue Nov 22 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!news.uoregon.edu!netnews.nwnet.net!news.u.washington.edu!roach From: roach@u.washington.edu (Jared Roach) Newsgroups: bionet.genome.chromosomes Subject: Re: Gel electrophoresis and gene mapping Date: 23 Nov 1994 07:23:14 GMT Organization: University of Washington Lines: 11 Message-ID: <3auql2$63a@nntp1.u.washington.edu> References: <3alnsb$al@portal.gmu.edu> NNTP-Posting-Host: saul4.u.washington.edu >Can gel electropherosis be used in gene mapping? >Or is this a bogus question? No question is bogus. Gel electrophoresis is used in many forms for gene mapping. Most texts should have some discussion of this, but if you can't find information in a molecular biology text, feel free to email me. Jared Roach roach@u.washington.edu From owner-chromosomes@net.bio.net Wed Nov 23 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: aking@hgmp.mrc.ac.uk (Mr. A.W. King) Newsgroups: bionet.genome.chromosomes Subject: Human Karyotype in Pict or Tiff (or any Mac readable) format Date: 24 Nov 1994 19:02:18 -0000 Lines: 10 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3b2nvq$evs@mserv1.dl.ac.uk> Original-To: biochrom@dl.ac.uk The subject says it all I used to have a karyotype file (it came as karyotype.hqx, I've forgotten where I got it from and have managed to delete it ) As usual I now find I have a very good use for it!!!! Any help much appreciated. Andrew From owner-chromosomes@net.bio.net Tue Nov 29 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!uunet!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!news.informatik.uni-muenchen.de!news.muc.de!cae.muc.de!cae Date: 30 Nov 1994 17:11:00 +0200 From: cae@cae.muc.de (Christian Eroes) Newsgroups: bionet.genome.chromosomes,bionet.molbio.genome-program Message-ID: <5aspwxy6ZoB@cae.muc.de> Subject: chromosome 21 X-Newsreader: XP v3.02 Lines: 14 Xref: biosci bionet.genome.chromosomes:347 bionet.molbio.genome-program:1023 i'm interested in the genes laying in chromosome 21. can anyone give me a list with a description? thanks in advance /-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-\ | Christian Eroes : INTERNET: cae@cae.muc.de : PGP puclic key | | : Netmail: 2:2480/603.52 : is available | | : : on request | \-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-/ Danger, @TOFIRST@! Off-topic messages! Danger! ## CrossPoint v3.02 ## From owner-chromosomes@net.bio.net Wed Nov 30 22:00:00 1994 Path: biosci!BADLANDS.NODAK.EDU!jweiland From: jweiland@BADLANDS.NODAK.EDU (John J Weiland) Newsgroups: bionet.genome.chromosomes Subject: RARE technique; Rec-A mediated chromosome cleavage Date: 1 Dec 1994 15:51:41 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Can someone please post or mail me a reference for the use of RecA in the blocking of methylation sites on DNA? I think the technique is called RARE, and was mentioned in the recent Promega Notes with regard to their Rec A product. Thanks in advance! John Weiland jweiland@badlands.nodak.edu From owner-chromosomes@net.bio.net Wed Nov 30 22:00:00 1994 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!torn!mcshub!informer1.cis.McMaster.CA!muss.cis.McMaster.CA!not-for-mail From: u9317302@muss.cis.McMaster.CA (R. Wong) Newsgroups: bionet.genome.chromosomes Subject: What procedure can be used to identify a chromosome location? Date: 1 Dec 1994 00:16:09 -0500 Organization: McMaster University, Hamilton, Ontario, Canada. Lines: 18 Message-ID: <3bjm6p$3ul@muss.cis.McMaster.CA> NNTP-Posting-Host: muss.cis.mcmaster.ca I am working on a project for my genetics class and I am in a bit of a rut. This is what I am asked to do: Outline a procedure to determine which chromosome carries a particular gene (any gene, it doesn't matter). (eg. a procedure to determine that human chromosome #11 is the location for the B-globin gene). Can anyone out there in internet land help me out on this one? P.S. It would be even better if someone could name an article in a journal where I could find an example of such a procedure. (The article does not have to be confined to human chromosome locations.) Thanks in advance. Rob. From owner-chromosomes@net.bio.net Wed Nov 30 22:00:00 1994 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!newsxfer.itd.umich.edu!europa.eng.gtefsd.com!gatech!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: Newsgroups: bionet.genome.chromosomes Subject: Printers Date: 1 Dec 1994 13:42:08 -0000 Lines: 16 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3bkjrg$qra@mserv1.dl.ac.uk> X-Mts: smtp X-Authentication-Warning: pluto: Host localhost didn't use HELO protocol Original-To: biochrom@dl.ac.uk Dear news readers , I was wondering if was not the only one out to have had problems with Tektronix Phaser IISX printers ? I think that it may be due to the interface with the the Mac . There is apparently upgraded software available but as I do not have an applelink account I have not been able to test this theory out with the latest release . If there is anyone out there who has resolved thier problems please contact me , or alternatively if there is anyone out there who wants to download the latest version of the print driver please also contact me . My email adress is cain@icr.ac.uk and i am eager to hear of anyone in a similar situation . Thanks for your assistance , David Cain