From owner-chromosomes@net.bio.net Mon Aug 02 23:00:00 1993 Path: biosci!MENDEL.LLNL.GOV!greg From: greg@MENDEL.LLNL.GOV Newsgroups: bionet.genome.chromosomes Subject: Is Taq to be discounted ? Message-ID: <9308032311.AA02790@mendel.llnl.gov.> Date: 3 Aug 93 23:11:20 GMT Sender: daemon@net.bio.net Reply-To: Greg Lennon Distribution: bionet Lines: 25 With the recent offer to Human Genome Centers of a half-price discount on large quantity purchases of AmpliTaq, it may be time to open up a brief discussion about the enzymes of choice for mapping and sequencing ... especially since other polymerase manufacturers are matching (or beating) the AmpliTaq pricing. So : to at least start on the topic of sequencing : How many folks out there have tried other enzymes for cycle sequencing using ABI 373's ? Which ones didn't work as well, which ones worked as well or better, and which one(s) are you actually using for "production" sequencing purposes ? [It may help to specify template type, and prep methods .... ] All responses appreciated ! Greg Lennon Human Genome Center, L-452 Lawrence Livermore National Lab Livermore, CA 94550 USA Email: greg@mendel.llnl.gov Phone: (510) 422-5711 Fax: (510) 423-3608 From owner-chromosomes@net.bio.net Mon Aug 02 23:00:00 1993 Path: biosci!fcircus.sat.tx.us!Jason_Burrell From: Jason_Burrell@fcircus.sat.tx.us (Jason Burrell) Newsgroups: bionet.genome.chromosomes Subject: HIV Virus Message-ID: <9308030229.AA01g9d@fcircus.sat.tx.us> Date: 3 Aug 93 02:29:59 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 12 Thank you to all that replied. I'm reposting this because I never saw the message, so am not sure if it was sent out. -- Jason_Burrell@fcircus.sat.tx.us Device Driver Stacker.sys not found. Hit (P) to panic! -- PGP public key available upon request. From owner-chromosomes@net.bio.net Thu Aug 05 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: datherto@uk.ac.crc (Mr. D.J. Atherton) Newsgroups: bionet.genome.chromosomes Subject: Comments on Happy mapping Message-ID: <1993Aug6.153843.18660@gserv1.dl.ac.uk> Date: 6 Aug 93 15:35:09 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 51 Precedence: first-class Original-To: biochrom@uk.ac.daresbury Dear Netters, The important bit:- Has anybody out there in Netland used or attempted Happy mapping? Any comments appreciated especially regarding efficacy, speed, accuracy, and problems. The story bit:- (For those who want to know.) One day, in a dark and dingy basement lab (OOH SCARY), Igor looked out from his hole in the corner and thought...Well it was more like he noticed some addled ramblings floating about in a phenol/chloroform fume steeped blob he lovingly refered to as his brain: It would have hurt such a simple creature, but years of slow, pains-taking and mind numbing mapping work had taken it's toll on the senses (AHH SHAME). Anyway, he thought "For the past two years, using standard mapping techniques, I've typed 500 backcross progeny for 6 loci (A-F) in and around a 4.2cM (8.4Mbp) region that contains X, the locus that Master is interested in. The data resulting so far indicates the gene locus order:- A - 3.5cM - (B/C/D/X) - 0.7cM - E/F Since X can only be typed by phenotypic tests, more backcross progeny will have to be typed until recombinants are found which resolve the order of B/C/D/X, but how many will this be? If happy mapping works, loci B,C,D,E and F may be ordered without further backcross typing, and the data generated should give an indication of the distances involved between these loci such that estimates can be made as to how many progeny would be necessary in order to find recombinants which seperate and order the loci. If C is an anchor marker, an initial strategy would probably be to show whether loci B and D are proximal or distal to C by happy mapping the 0.7cM region between C and E/F. According to the authors 7 loci over 1.24Mbp were mapped using 140 test aliquots, but they had foreknowledge of the real order. Assuming 0.7cM is equivalent to 1.4Mbp, is such a rapid mapping repeatable, or if not, what would be a real guesstimate of number of tests be? Mapping this region may also allow the ordering of E and F relative to C. If one or both of B and D prove to be proximal to C (in the 3.5cM region between A and C), could this be happy mapped with sufficient integrity of order and distance using A and C as boxing markers? Regards to all who got this far datherton@uk.ac.ox.path.vax David Atherton Univ. Oxford Oxford Oxon UK ! .. From owner-chromosomes@net.bio.net Sun Aug 08 23:00:00 1993 Path: biosci!MENDEL.LLNL.GOV!greg From: greg@MENDEL.LLNL.GOV Newsgroups: bionet.genome.chromosomes Subject: Forwarded Message re Sequitherm Message-ID: <9308092236.AA04753@mendel.llnl.gov.> Date: 9 Aug 93 22:36:35 GMT Sender: daemon@net.bio.net Reply-To: Greg Lennon Distribution: bionet Lines: 41 I have tried the enzyme that Epicentre Technologies calls Sequitherm. Although we do not use it regularly in production, I have done 600 or 700 reactions with it. The general conclusion is that it seems to be much like taq, with two exceptions: 1) It seems to give somewhat more even peak heights- some bands that are absent with taq are present with sequitherm 2) It seems to be somewhat more sensitive to contaminants in the template DNA than taq- a larger percentage of the reactions that we do with it fail to givwe good sequence I would be _very_ interested in hearing what experiences other people have had with other enzymes. I am particularly interested in trying to find a thermostable pyrophosphatase, so that we could do to taq what addition of PPase did for T7 Dna polymerase a la Tabor and Richardson. I don't know if it would work, but suspect that it could make a big difference... I have contacted 4 or 5 enzyme production companies, but no one has gotten back to me yet with an PPase sample yet. We are sequencing M13 ss templates purified in 96-well plates with an unpublished protocol based on ethanol lysis of the phage coat- basically Ethanol is used in place of phenol in the standard prep, and everything is carried out in 96-well plates, with an affinity resin as final cleanup. Samples are not as clean as phenol preps, but work well with standard taq dye primer cycle sequencing. Thanks for starting this discussion thread... John Mulligan Stanford Genomic Sequencing Center 415-725-7426 mulligan@genome.stanford.edu (Forwarded by:) Greg Lennon Human Genome Center, L-452 Lawrence Livermore National Lab Livermore, CA 94550 USA Email: greg@mendel.llnl.gov Phone: (510) 422-5711 Fax: (510) 423-3608 From owner-chromosomes@net.bio.net Mon Aug 09 23:00:00 1993 Path: biosci!NET.BIO.NET!kristoff From: kristoff@NET.BIO.NET (David Kristofferson) Newsgroups: bionet.genome.chromosomes Subject: IMPORTANT BIOSCI INFORMATION Message-ID: <9308100900.AA08692@net.bio.net> Date: 10 Aug 93 09:00:02 GMT Sender: kristoff@net.bio.net Distribution: bionet Lines: 243 Three important items follow: BIOSCI archive searching by e-mail, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our e-mail address directory, please take a few minutes to complete and return the form below. If your address information has changed since you listed yourself, please send us an updated form. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net **** SEARCHING BIOSCI ARCHIVES WITH WAISMAIL **** E-mail users can search the BIOSCI archives by using our waismail e-mail server. For instructions send the message help to waismail@net.bio.net. Leave the Subject: line blank. Other methods of searching the archives via WAIS and gopher are described in the BIOSCI FAQ. **** BIOSCI FREQUENTLY ASKED QUESTIONS (FAQ) SHEET **** New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and is available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/biosci.FAQ. It may also be requested by sending e-mail to biosci@net.bio.net (use plain English for your request). 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The raw unindexed data is available for FTP from net.bio.net and is atomized sufficiently to allow import into your local RDBMS should you so desire. Please carefully follow the instructions for completing the form below and return it to either of the following two addresses (whichever is more convenient for you). Thanks in advance for taking the time to complete and return the form. Addresses for returning forms Location Network ----------------------------- -------- ------- biovote@net.bio.net U.S.A. Internet/BITNET biovote@daresbury.ac.uk U.K. JANET MAKING SURE THAT YOUR INFORMATION IS CURRENT This notice will be mailed bimonthly to each newsgroup. You should check our WAIS source or waismail e-mail server from time-to-time to see if your address information is still up-to-date. Send the message help to waismail@net.bio.net for instructions on using waismail. Leave the Subject: line in your message blank. Using Gopher to complete the form --------------------------------- If you don't want to use a text editor, you can also use Dan Jacobson's gopher site to fill out the address database form as follows. Otherwise skip this section on gopher and proceed to the instructions for filling out the form below. > To add yourself to the database just point your > gopher client at merlot.welch.jhu.edu and select the following: > > --> 15. Searching For Biologists/ > > --> 9. E-mail Addresses of Biosci-Bionet Users/ > > --> 1. Add (or Correct) Your Address to the BIOSCI User Address > Data.. > > > And fill out the form. or Rob Harper's gopher site in Europe as follows: > Europeans can point their gopher client at gopher.csc.fi and add their > information to the database. All entries will be mailed directly to > Dave for incorporation in a wais source. > > The path to the questionare is as follows. > > ---> 10. Finnish EMBnet BioBox/ > > ---> 8. FAQ Files/ > > FAQ Files > > 1. EMBnet: Information. > 2. EMBnet: Internet resources guide. > 3. A Biologist's Guide to Internet Resources/ > 4. All FAQs (Frequently Asked Questions) Searches and Archives/ > --->5. Bionauts Address Database (questionaire) IMPORTANT INSTRUCTIONS - PLEASE READ CAREFULLY Please enter all responses after the : on each line, leaving one (1) blank space after the : (i.e., before the start of your text). Please do NOT extend your responses past the end of each line (80 characters) or alter any of the field identifiers such as "first name: ". Several lines are provided at the end of the form for comments, but, please adhere to the line length restriction. On the date: line, please enter the date in the DD-MM-YY format, e.g., 05-05-93 for 5 May 1993. This line will tell others when the information was last updated. Please be sure to include the 0's for single digit days or months, e.g., 05-05-93, not 5-5-93. 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This allows one to retrieve via WAIS or waismail the list of participants in a particular group. For example: comment: ARABIDOPSIS PLANT-BIOLOGY BIONEWS On the comment: lines use these names below ---- NOT the USENET names below MAILING LIST NAME USENET Newsgroup Name ----------------- --------------------- ACEDB-SOFT bionet.software.acedb AGEING bionet.molbio.ageing AGROFORESTRY bionet.agroforestry ARABIDOPSIS bionet.genome.arabidopsis BIOFORUM bionet.general BIO-INFORMATION-THEORY bionet.info-theory BIONAUTS bionet.users.addresses BIONEWS bionet.announce BIO-JOURNALS bionet.journals.contents BIO-MATRIX bionet.molbio.bio-matrix BIO-SOFTWARE bionet.software CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMPLOYMENT bionet.jobs GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage HIV-MOLECULAR-BIOLOGY bionet.molbio.hiv HUMAN-GENOME-PROGRAM bionet.molbio.genome-program IMMUNOLOGY bionet.immunology INFO-GCG bionet.software.gcg JOURNAL-NOTES bionet.journals.note METHODS-AND-REAGENTS bionet.molbio.methds-reagnts MOLECULAR-EVOLUTION bionet.molbio.evolution NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PHOTOSYNTHESIS bionet.photosy From owner-chromosomes@net.bio.net Mon Aug 16 23:00:00 1993 Path: biosci!MAILHOST.TCS.TULANE.EDU!dmsander From: dmsander@MAILHOST.TCS.TULANE.EDU (David M. Sander) Newsgroups: bionet.genome.chromosomes Subject: I need a map of Mouse Chromosome 11 Message-ID: <199308172248.RAA50839@mailhost.tcs.tulane.edu> Date: 17 Aug 93 22:48:20 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 3 I am interested in obtaining a map of mouse chromosome 11. Does anyone know where this could be obtained either in a database or other form? From owner-chromosomes@net.bio.net Tue Aug 17 23:00:00 1993 Path: biosci!WELCHDEV.WELCH.JHU.EDU!danj From: danj@WELCHDEV.WELCH.JHU.EDU (Dan Jacobson) Newsgroups: bionet.genome.chromosomes Subject: Re: I need a map of Mouse Chromosome 11 Message-ID: <9308181937.AA21503@welchdev.welch.jhu.edu> Date: 18 Aug 93 19:37:52 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 313 David M. Sander" writes: >I am interested in obtaining a map of mouse chromosome 11. Does anyone >know where this could be obtained either in a database or other form? There is a gopher version of the The Encyclopedia of the Mouse Genome. Here you can view the genetic maps of each mouse chromosome, search for specific loci on these maps as well as search for references and notes associated with each locus on the map. In addition you can search the Mouse Locus Catalog which contains detailed information on mouse loci. Now for a little tour: Point your gopher client at merlot.welch.jhu.edu and select the following: --> 13. Search Databases at Hopkins (Vectors, Promoters, NRL-3D, EST, OMIM../ --> 17. Mouse Databases (TBASE, Encyclopedia of the Mouse Genome)/ --> 1. Encyclopedia of the Mouse Genome/ And you'll see: --> 1. About the Encyclopedia of the Mouse Genome. 2. Browse through the Chromosomes/ 3. Search Maps for Loci 4. Notes 5. References 6. Mouse Locus Catalog (MLC) If you have a specific locus in mind that you would like to see it's map position select: --> 3. Search Maps for Loci If you want to see the map position of abl: +--------------------------Search Maps for Loci--------------------------+ | _____________________________ | | Words to search for | abl | | | ----------------------------- | | [Cancel ^G] [Accept - Enter] | | | +------------------------------------------------------------------------+ And you'll see: --> 1. Abl - Abelson murine leukemia oncogene (2) If you select this entry you will see the map for Chromosome 2 with the Expanded view which contains Abl. Note that above you are shown the Locus symbol, Abl, the locus name, Abelson murine leukemia oncogene, and the Chromosome on which it resides, (2). These are all searchable. For example your could search for: +--------------------------Search Maps for Loci--------------------------+ | _____________________________ | | Words to search for | leukemia and 2 | | | ----------------------------- | | [Cancel ^G] [Accept - Enter] | | | +------------------------------------------------------------------------+ And you'll see: --> 1. Abl - Abelson murine leukemia oncogene (2) 2. Glvr-1 - gibbon ape leukemia virus receptor-1 (2) 3. Mpmv-14 - modified polytropic murine leukemia virus-14 (2) 4. Mpmv-28 - modified polytropic murine leukemia virus-28 (2) 5. Mpmv-3 - modified polytropic murine leukemia virus-3 (2) 6. Mpmv-43 - modified polytropic murine leukemia virus-43 (2) 7. Pmv-33 - polytropic murine leukemia virus-33 (2) 8. Pmv-63 - polytropic murine leukemia virus-63 (2) 9. Pmv-7 - polytropic murine leukemia virus-7 (2) 10. Xmmv-71 - xenotropic-MCF leukemia virus-71 (2) 11. Xmv-10 - xenotropic murine leukemia virus-10 (2) 12. Xmv-48 - xenotropic murine leukemia virus-48 (2) You may use booleans (and, or, not) and wildcards (*) to broaden or narrow your searches. -------------------- If you would like the notes and references associated with each locus select: --> 4. Notes --> 5. References You can search for loci, authors or journals. You may use booleans (and, or, not), phrase searches ("...") and wildcards (*) to broaden or narrow your searches. -------------------- If you would like detailed information on a locus or to search for loci by topic select: --> 6. Mouse Locus Catalog (MLC) and for example search for: +--------------------------Mouse Locus Catalog (MLC)---------------------+ | _____________________________ | | Words to search for | leukemia and 2 | | | ----------------------------- | | [Cancel ^G] [Accept - Enter] | | | +------------------------------------------------------------------------+ And you will see: 1. LOCUS Igf1r locus, insulin-like growth factor 1 receptor. ... --> 2. LOCUS Insr locus, insulin receptor. CHROMOSOME 8 CLA... 3. LOCUS Igf2r locus, insulin-like growth factor II receptor. ... A sample entry is as follows: -------------------------------------------------------------------------- LOCUS Insr locus, insulin receptor. CHROMOSOME 8 CLASSES Receptors TEXT Insr locus, insulin receptor, Chr 8. The transmembrane allosteric enzyme which acts as an insulin receptor is composed of alpha and beta subunits. Both are thought to be derived through the cleavage of a common proreceptor precursor. When insulin interacts with its binding site on the extracellular alpha subunit, a cytoplasmic tyrosine kinase domain in the beta subunit is activated (3). The Insr gene in the mouse has been localized to the proximal end of Chr 8, using somatic cell hybrids (4) and two interspecific backcrosses (1, 2). See also the insulin-like growth factors (Igf-) and their receptors. REFERENCES 1. Ceci, J.D., M.L. Justice, L.F. Lock, N.A. Jenkins, and N.G. Copeland. 1990. An interspecific backcross linkage map of mouse Chromosome 8. Genomics 6:72-79. 2. Howard, T.A., J.M. Rochelle, A.M. Saunders, and M.F. Seldin. 1991. A linkage map of mouse Chromosome 8: further definition of the syntenic relationship between mouse Chromosome 8 and human Chromosomes 8, 16 and 19. Genomics 10:207-213. 3. Sibley, E., T. Kastelic, T.J. Kelly, and M.D. Lane. 1989. Characterization of the mouse insulin receptor gene promoter. Proc. Natl. Acad. Sci. USA 86:9732-9736. 4. Wang, L.-M., A.M. Killary, X.-E. Fang, S. K. Parriott, P.A.Lalley, G.I. Bell, and A.Y. Sakaguchi. 1988. Chromosome assignment of mouse insulin, colony stimulating factor 1, and low-density lipoprotein receptors. Genomics 3:172-175. UPDATED Wed May 13 14:59:40 EDT 1992 TAG Insr ---------------------------------------------------------------------- If you would simply like to browse through the Maps select: --> 2. Browse through the Chromosomes/ And you will see: --> 1. Chromosome 1/ 2. Chromosome 2/ 3. Chromosome 3/ 4. Chromosome 4/ 5. Chromosome 5/ 6. Chromosome 6/ 7. Chromosome 7/ 8. Chromosome 8/ 9. Chromosome 9/ 10. Chromosome 10/ 11. Chromosome 11/ 12. Chromosome 12/ 13. Chromosome 13/ 14. Chromosome 14/ 15. Chromosome 15/ 16. Chromosome 16/ 17. Chromosome 17/ 18. Chromosome 18/ 19. Chromosome 19/ 20. Chromosome X/ 21. Chromosome Y/ Now select the Chromosome that you are interested in browsing lets try Chromosome 1 - you will see: --> 1. Overview of Chromosome 1 2. Expanded View 1 (Region 5-7) 3. Expanded View 2 (Region 10-11) 4. Expanded View 3 (Region 15-21) 5. Expanded View 4 (Region 23-30) 6. Expanded View 5 (Region 31-40) 7. Expanded View 6 (Region 41-47) 8. Expanded View 7 (Region 48-54) 9. Expanded View 8 (Region 55-59) 10. Expanded View 9 (Region 60-68) 11. Expanded View 10 (Region 69-77) 12. Expanded View 11 (Region 79-81) 13. Expanded View 12 (Region 82-87) If you select "Overview of Chromosome 1" you will see a simple map containing some loci and with a number scale running down the left side of the map: | 10 | | 20 | | 30 | | 40 | | 50 | | 60 | | 70 | | 80 | | 90 | | 100| | | Use the numbers to define the Region where you would like to see an Expanded view of the map - which will show all the loci present in that section. ============================================================================== If you've never heard of gopher, don't worry - it's free and on the net. Write me a note if you'd like information on how to get started. To view the maps in the Encyclopedia you need to be able to display images. Many of the gopher clients will work just fine - a few hints: If you're using a Mac - go get the latest version of Turbogopher (earlier versions had trouble launching lin From owner-chromosomes@net.bio.net Wed Aug 18 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!noc.near.net!nic.umass.edu!usenet From: AMRUT@UCSVAX.UCS.UMASS.EDU (AMRUT S BHOGLE) Newsgroups: bionet.genome.chromosomes Subject: chromosome preps Message-ID: <24vtp7$4h3@nic.umass.edu> Date: 19 Aug 93 13:04:39 GMT Organization: UNIVERSITY OF MASSACHUSETTS - AMHERST Lines: 9 NNTP-Posting-Host: phobos.ucs.umass.edu X-News-Reader: VMS NEWS 1.24 Hi friends, A friend of mine wants to know of a protocol for preparing metaphase spread from avian species (not chicken). The protocol for chicken cells apparently doesn't seem to be working in my friends lab. Thanks AMRUT From owner-chromosomes@net.bio.net Thu Aug 19 23:00:00 1993 Path: biosci!ICBR.IFAS.UFL.EDU!SJJ From: SJJ@ICBR.IFAS.UFL.EDU ("JONG, SONG-MUH J") Newsgroups: bionet.genome.chromosomes Subject: Re. I need mouse chromosome 11 map Message-ID: <9308201634.AA20111@net.bio.net> Date: 20 Aug 93 17:27:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 20 "grave@cemetery.com" 20-AUG-1993 11:46:50.20 wrote: >Subj: Re: I need a map of Mouse Chromosome 11 > I was trying this, but Whenever my Gopher Client tried to connect >to said site (merlot.welch.jhu.edu) The connection was refused. >... >tell me much about this site. Is it perhaps closed? I just connected to that site successfully. Perhaps your gopher software is not working correctly. Are you able to connect to any site at all? I used the port 70 to merlot.welch.jhu.edu Another way to get all the chromosome map as idiograms is to contact David Adler at the Univ. of Washington. His E-Mail address is dadler@u.washington.edu Good luck! Song-Muh Jong sjj@icbr.ifas.ufl.edu From owner-chromosomes@net.bio.net Thu Aug 19 23:00:00 1993 Path: biosci!rutgers!cs.utexas.edu!wupost!howland.reston.ans.net!europa.eng.gtefsd.com!news.ans.net!cmcl2!panix!not-for-mail From: grave@cemetery.com Newsgroups: bionet.genome.chromosomes Subject: Re: I need a map of Mouse Chromosome 11 Message-ID: <252pjv$si0@panix.com> Date: 20 Aug 93 15:11:59 GMT References: <9308181937.AA21503@welchdev.welch.jhu.edu> Sender: tomb@panix.com Distribution: bionet Organization: The circle of the dead (my-coffin@basement.panix.com) Lines: 14 NNTP-Posting-Host: panix.com I was trying this, but Whenever my Gopher Client tried to connect to said site (merlot.welch.jhu.edu) The connection was refused. I grew curious so I tried various things, finger, nslookup. None could really tell me much about this site. Is it perhaps closed? Too bad, I was looking foward to browsing through the Mouse Genome. All flames come from the Devil! /-----\ / \ : grave : : : :/ \/ /: