Montell Jordan - This Is How We Do It (1995).zip: The Song that Changed the Sound of R&B

DROSOPHILA INFORMATION NEWSLETTERVolume 9, January 1993The Drosophila Information Newsletter has been establishedwith the hope of providing a timely forum for informalcommunication among Drosophila workers. The Newsletter will bepublished quarterly and distributed electronically, free ofcharge. We will try to strike a balance between maximizing theuseful information included and keeping the format short;priority will be given to genetic and technical information.Brevity is essential. If a more lengthy communication is felt tobe of value, the material should be summarized and an addressmade available for interested individuals to request moreinformation. Submitted material will be edited for brevity andarranged into each issue. Research reports, lengthy items thatcannot be effectively summarized, and material that requiresillustration for clarity should be sent directly to Jim Thompson(THOMPSON@AARDVARK.UCS.UOKNOR.EDU) for publication in DIS.Materials appearing in the Newsletter will be reprinted in DIS.Back issues of DIN are available from FlyBase in the directoryflybase/news/din. Material appearing in the Newsletter may becited unless specifically noted otherwise.Material for publication should be submitted by e-mail.Figures and photographs cannot be accepted at present. Sendtechnical notes to Carl Thummel and all other material to KathyMatthews. The e-mail format does not allow special characters tobe included in the text. Both superscripts and subscripts havebeen enclosed in square brackets; the difference should beobvious by context. Bold face, italics, underlining, etc. cannotbe retained. Please keep this in mind when preparing submissions.To maintain the original format when printing DIN, use Courier10cpi font on a standard 8.5" x 11" page with 1" margins.Drosophila Information Newsletter is a trial effort thatwill only succeed if a broad segment of the communityparticipates. If you have information that would be useful toyour colleagues, please take the time to pass it along.The editors:Carl Thummel Kathy MatthewsDept. of Human Genetics Dept. of BiologyEccles Institute - Bldg. 533 Indiana UniversityUniversity of Utah Bloomington, IN 47405Salt Lake City, UT 84112 812-855-5782; FAX/2577801-581-2937; FAX/5374 MATTHEWK@INDIANA.EDUCTHUMMEL@HMBGMAIL.MED.UTAH.EDU MATTHEWK@INDIANA.BITNET*** DIN 9To add your name to the Newsletter distribution list, send one ofthe following E-mail messages.Via Bitnet -- To: LISTSERV@IUBVMSubject:Message: SUB DIS-L Your real nameVia Internet -- To: LISTSERV@IUBVM.UCS.INDIANA.EDUSubject:Message: SUB DIS-L Your real nameLISTSERV will extract your user name and node from the E-mail header and add you to the list. Use your Internet address ifyou have one. You will receive confirmation by E-mail if you havesuccessfully signed on to the list. If you are on the list and donot wish to receive DIN, or you want to remove a defunct address,replace SUB in the above message with UNS. The SUB command canalso be used to correct spelling errors in your real name; thenew entry will simply replace the old as long as it was sent fromthe same USERID@NODE address.*** DIN 9DIN Vol. 9 TABLE OF CONTENTS>Introduction to Drosophila Information Newsletter>How to subscribe to the Newsletter>TABLE OF CONTENTS>ANNOUNCEMENTS>34th Drosophila Conference>REQUESTS FOR MATERIALS>Laboratory stock lists>MATERIALS AVAILABLE>Clones in 60C-D>Libraries>DATABASES/COMPUTING>FlyBase>GENETIC NOTES>New D. sechellia w mutant>New ri allele and its lethal interaction with H>Updates and corrections to the Redbook*** DIN 9ANNOUNCEMENTS34th ANNUAL DROSOPHILA RESEARCH CONFERENCEThe 1993 fly meetings will be held March 31-April 4, 1993,at the Town and Country Hotel in San Diego, California. TheProgram Chairman is Gerry Rubin, Life Sciences Annex Building, U.of California, Box 539, Berkeley, CA 94720-0001 (510-643-9945,FAX/9947). The 1993 meeting will have an experimental format thatdevotes more time to poster presentations and less to slide andplenary sessions. Registration materials can be obtained from theGSA Administrative Office, 9650 Rockville Pike, Bethesda, MD20814-3998 (301-571-1825, FAX/530-7079). Advance registrationdeadline is January 27, 1993 (deadline for abstacts has alreadypassed).*** DIN 9REQUESTS FOR MATERIALSLABORATORY STOCK LISTS WANTEDKathy Matthews, Dept. of Biology, Indiana U., Bloomington, IN47405-6801, USA. 812-855-5782; FAX/2577; MATTHEWK@INDIANA.EDU.One goal of the FlyBase project (see below) is to simplifythe process of identifying potentially useful mutations and thenlocating stocks that carry those mutations. To this end, we wouldlike to incorporate the stock collections of as many individuallaboratories into FlyBase as possible. If you are willing to makeyour laboratory stock list available, with the understanding thatonly stocks not available from any of the funded stock centersshould be requested from your lab, please contact me. I wouldlike to have computerized lists now for immediate incorporationinto FlyBase. Hardcopy lists, if typed, are also useful; I willconvert these to machine-readable format as time permits.*** DIN 9MATERIALS AVAILABLEMOLECULAR CLONING OF GENOMIC DNA FROM THE 60CD REGIONPhilip J. Gotwals and James W. Fristrom, Dept. of Molecular andCell Biology, U. of California, Berkeley, CA 94720.In two separate chromosomal walks, we have recovered 230kilobases of genomic DNA in the chromosomal region uncovered byDf(2R)Px2 (60C1/2-60D9/10). One walk was inititated by jumpingfrom the centromere-distal to the centromere-proximal breakpointof Df(2R)Px2 using a beta3-tubulin probe (Kimble et al, (1991)Genetics 126:991). We have recovered nearly 100 kilobases ofoverlapping genomic DNA, primarily carried in cosmids, around theproximal breakpoint.The other walk was initaited from within Df(2R)Px2 using afragment from the muscarinic acetylcholine receptor (MAR) gene(Shapiro et al., (1989) PNAS 86:9030). We have recovered nearly130 kilobases of overlapping DNA, housed in both phage andcosmids, surrounding the MAR gene.Anyone interested in obtaining clones from these walks orinformation regarding the region should contact: Philip J.Gotwals, HHMI, Bld. E17-225, 40 Ames St., MIT, Cambridge, MA02139, USA. (617) 253-6452; eMAIL: PJGOTWALS@wccf.mit.edu*** DIN 9COMPILATION OF DROSOPHILA CDNA AND GENOMIC LIBRARIESCarl Thummel, HHMI, 5200 Eccles Institute of Human Genetics,Bldg. 533, U. of Utah, Salt Lake City, UT 84112, USA.801-581-2937, FAX/5374, CTHUMMEL@HMBGMAIL.MED.UTAH.EDUThe following is a listing of Drosophila cDNA and genomiclibraries that are currently available and in common use. Pleasedo not request shipment of a library unless you have an immediateuse for it - many contributors are concerned about the time andmoney involved in mailing their libraries. Also, please inquirewith local colleagues before requesting a library since many ofthese libraries are already widely distributed.cDNA LIBRARIES--Nick Brown, Wellcome/CRC Institute, Tennis Court Rd, CambridgeCB2 1QR UK. Phone: 44-223-334128; FAX: 44-223-334089, Email:NB117@MB1.BIO.CAM.AC.UKVector/Insertion/Complexity/mRNA sourcepNB40/see ref./3x10[5]/0-4 hr embryopNB40/see ref./3x10[6]/4-8 hr embryopNB40/see ref./3x10[5]/8-12 hr embryopNB40/see ref./1x10[6]/12-24 hr embryopNB40/see ref./3x10[6]/imaginal discsThe Drosophila strain used is an isogenic second chromosomestock: dp cn bw, from the Gelbart lab. Ron Blackman has made agenomic library from this same strain (see below). The vector isa pUC based plasmid with a SP6 promoter at the 5' end of the cDNAand a T7 promoter at the 3' end of the cDNA. The cloning strategywas directional and designed to maximize the number of full-length cDNAs. A useful diagnostic of full-length cDNAs is a non-coding G nucleotide at the 5' end, after the polyC tract; theorigin of this nucleotide is, however, unknown.Reference: Brown, N.H., and F.C. Kafatos (1988) Functional cDNAlibraries from Drosophila embryos. J. Mol. Biol. 203: 425-437.--Steve Russell, Dept. of Genetics, Univ. of Cambridge, DowningSt., Cambridge, CB2 3EH UK. Phone: 44-223-337733, FAX:44-223-333992,Email: SR120@MOLECULAR-BIOLOGY-1.BIOLOGY.CAMBRIDGE.AC.UK.BITNETAll libraries were made with RNA isolated from Oregon R strainVector/Insertion/Complexity/mRNA sourceNM1149/RI/2x10[6]/Male 3rd instar larvaeNM1149/RI/6x10[5]/Female 3rd instar larvaeNM1149/Directional: RI-HIII/3x10[6]/Adult male headsNM1149/Directional: RI-HIII/1x10[6]/Adult female headslambda gt11/RI/3x10[5]/Testes--Charles P. Emerson, Jr. or Mary Beth Davis, Biology Dept.,Univ. of Virginia, Charlottesville, Virginia, 22901 USA.Phone: 215-728-5283 (Emerson); 215-728-5284 (Davis); FAX:215-728-2412, Email: emerson@castor.rm.fccc.edu ordavis@castor.rm.fccc.eduVector/Insertion/Complexity/mRNA source/Titerlambda gt10/RI/1x10[6]/late pupae/1x10[10]Blunt-ended cDNA was ligated to EcoRI adaptors, then ligated toEcoRI digested gt10 lambda arms. We have isolated cDNA clonescorresponding to MHC isoforms that were lengths of 5940 and 5500bases.Reference: George, E.L., M.B. Ober, and C.P. Emerson, Jr. (1989)Functional domains of the Drosophila melanogaster muscle myosinheavy-chain isoform are encoded by alternatively spliced exons.Mol. Cell Biol. 9: 2957-2974.--Bruce Hamilton, Division of Biology 216-76, CaliforniaInstitute of Technology, Pasadena, CA, 91125, USA. Phone:818-356-8353; FAX: 818-449-0756, Email: BAH@citromeo.bitnet orBRUCE@seqvax.caltech.eduLibrary name/Vector/Insertion/Complexity/mRNA sourceHead M/lambda EXLX/ApaI-SacI/1.1x10[7]/Oregon R adult headsHead P/lambda EXLX/ApaI-SacI/9x10[6]/Oregon R adult headsHead 1.2/lambda EXLX/ApaI-SacI/2.7x10[6]/Oregon R adult headsHead 2.0/lambda EXLX/ApaI-SacI/1.2x10[6]/Oregon R adult headsAdult/lambda EXLX/ApaI-SacI/>1x10[6]/Oregon R adults0-24 mojo/lambda EXLX/ApaI-SacI/3.4x10[6]/Can S, 0-24 hr embryosAll libraries were cloned directionally into the ApaI-SacI sitesof lambda EXLX, as described in ref. 1, with internal restrictionsites protected. Lambda EXLX allows in vivo excision of plasmidDNA using a CRE/loxP site-specific recombination system. Thisvector also allows regulated expression of the insert DNA as aphage T7 gene 10 N-terminal/cDNA fusion protein, under thecontrol of a T7 RNA polymerase promoter (1). The Head 1.2 librarywas prepared from cDNAs that were size-selected for molecules 1.2kb or larger by fractionation through an agarose gel. Head 2.0contains cDNAs that are 2 kb or larger. The cDNA for the Adultlibrary was not size-fractionated. The Adult and mojo librarieswere published in ref. 1. The Head M and Head P libraries areunpublished, but I have asked people who use them to refer toref. 1, since they were constructed in the same way and in thesame vector. The two size-selected libraries, Head 1.2 and Head2.0 were published in ref. 2, which also describes a rapidscreening procedure that is very straightforward.References:1. Palazzolo et al (1990) Gene 88, 25-36.2. Hamilton et al (1991) Nucl. Acids Res. 19, 1951-1952--Tom Kornberg, Department of Biochemistry, University ofCalifornia, San Francisco, CA 94143 USA. Phone: 415-476-8821,FAX: 415-476-3892, Email: tomk@ucsf.cgl.eduOur cDNA libraries were prepared from RNA isolated from Oregon Ranimals, with the cDNA sequences inserted into the EcoRI site oflambda gt10. Libraries will be shipped by Federal Express.Requests should be accompanied by an appropriate Federal ExpressAuthorization Number.Stage/Library designation/Complexity0-3 hr embryo/D/300,0003-12 hr embryo/E/500,00012-24 hr embryo/F/300,0001st and 2nd instar/G/200,000early 3rd instar/H/300,000late 3rd instar/I/300,000early pupal/P/300,000late pupal /Q/300,000adult male/R/300,000adult female/S/300,000Reference: Poole, S., Kauvar, L.M., Drees, B., and Kornberg, T.(1985) The engrailed locus of Drosophila: Structural analysis ofan embryonic transcript. Cell 40: 37-43.--Carl S. Thummel, Dept. of Human Genetics, 5200 EcclesInstitute, Bldg. 533, University of Utah, Salt Lake City, Utah,84112 USA. Phone: 801-581-2937, FAX: 801-581-5374, Email:cthummel@hmbgmail.med.utah.eduVector/Insertion/Complexity/mRNA sourcelambda gt10/RI/1x10[6]/larval tissues cultured in vitro withcycloheximide + ecdysonelambda ZAP/RI/3x10[5]/late 3rd instar larvaelambda ZAP/RI/4x10[5]/0-1 day prepupaeThe late third instar cDNA library is available in two size-fractionations that are enriched for either 1-3 kb or 3-6.5 kbcDNAs. Both libraries, however, do contain some smaller inserts.--Peter Tolias, Public Health Research Institute, 455 First Ave.,New York, New York, 10016 USA. Phone: 212-578-0815, FAX:212-578-0804, Email: tolias@wombat.phri.NYU.EDUVector/Insertion/Complexity/mRNA sourcelambda gt22A/SalI-NotI/5x10[5]/Canton S ovaries, stages 1-14This is a cDNA expression library in which the inserts aredirectionally cloned. A SalI site is present at the 5' end and aNotI site is at the 3' end.--Kai Zinn, Division of Biology, 216-76, Caltech, Pasadena, CA91125, USA. Phone: 818-356-8352, FAX: 818-449-0679,Email: kai@seqvax.caltech.eduVector/Insertion/Complexity/mRNA sourcelambda gt11/EcoRI/1.2x10[6]/Oregon R, 9-12 hr embryosThe complexity is an underestimate for larger cDNAs, since it was>5X size-selected for cDNAs larger than 1.8 kb. The complexitycould thus be as high as 6x10[6] for these larger inserts.GENOMIC LIBRARIES--Winifred W. Doane, Dept. of Zoology, Arizona State University,Tempe, Arizona 85287-1501 USA. Phone: 602-965-3571, FAX:602-965-2012, Email: icwwd@asuacadVector/Insertion/Complexity/DNA sourcepWE15/BamHI/4x10[4]-1x10[6]/Amy[1,6] mapP[12] strain of D.melanogasterThis cosmid vector contains a T3 and T7 promoter on either sideof the insertion site, to facilitate the preparation of end-specific probes for chromosomal walking.Reference: Thompson, D.B., and Doane, W.W. (1989) A compositerestriction map of the region surrounding the Amylase locus inDrosophila melanogaster. Isozyme Bull. 22: 61-62.--Ron Blackman, Dept. of Cell and Structural Biology, 505 S.Goodwin Ave., Univ. of Illinois, Urbana, Illinois 61801 USA.Phone: 217-333-4459, FAX: 217-244-1648, Email:Ron_Blackman@qms1.life.uiuc.eduVector/Insertion/Complexity/DNA sourcelambda EMBL3/BamHI/1x10[6]/Adult Drosophila virilislambda EMBL3/BamHI/1x10[6]/Embryonic D. melanogaster, see belowBoth libraries were prepared by MboI partial digestion of the DNAand insertion into the BamHI site of lambda EMBL3. The insertscan be excised by digestion with SalI. Titer is approximately5x10[9] pfu/ml. The D. melanogaster genomic library is made fromanimals that are isochromosomal for chromosome 2, dp cn bw. Thesame strain was used by Nick Brown for his cDNA libraries.--Howard Lipshitz, Division of Biology, 156-29, CaliforniaInstitute of Technology, Pasadena, CA 91125, USA. Phone:818-356-6446, FAX: 818-564-8709, Email: HDL@ROMEO.CALTECH.EDUVector/Insertion/Complexity/DNA sourceCharon 4/EcoRI/6x10[5]/Canton S embryosThis is the original Drosophila genomic library from the Maniatislab. It has been amplified several times but is still useful formost purposes.Reference: Maniatis et al., The isolation of structural genesfrom libraries of eucaryotic DNA. Cell 15: 687-701.*** DIN 9DATABASES/COMPUTINGFLYBASE - A DROSOPHILA GENETIC DATABASE, RELEASE 9301The FlyBase Consortium (see below for names and addresses)Editors' note: The following document has been edited forDIN; section 6 has been omitted, section 8 has been truncated toinclude only a list of subdirectories and not the files withinthem, and section 9 has been omitted. The complete document isavailable from FlyBase as described below.CONTENTS OF THIS DOCUMENT1. What is FlyBase2. The FlyBase Consortium3. How to contact FlyBase4. How to obtain FlyBase5. How to reference FlyBase6. Differences between printed and computer versions of FlyBaseomitted7. Allied databases8. The structure of FlyBase truncated9. Detailed description of FlyBase omitted10. Future plans for FlyBase11. Release notes12. Full addresses of members of the FlyBase Consortium13. The copyright of FlyBase13. Acknowledgements1. WHAT IS FLYBASEFlyBase is a comprehensive database for information on thegenetics and biology of Drosophila. It is, or will be (seebelow), available in several different formats. That released nowis a series of flat files in which different data are displayed.FlyBase includes (by permission of Academic Press) all of thematerial of the Redbook, i.e. The Genome of Drosophilamelanogaster by D.L. Lindsley and G. G. Zimm (Academic Press,1992). A short introduction to FlyBase is to be found in the fileflybase/about-flybase.txt.2. THE FLYBASE CONSORTIUMFlyBase is being built by a Consortium of researchers funded bythe National Institutes of Health. This Consortium includes bothDrosophila biologists and computer scientists. The Consortium issplit between four sites, at Harvard, Cambridge (England),Bloomington and Los Angeles. In addition the Consortium has veryclose links with the National Center for BiotechnologyInformation in Washington and with several other workers whoprovide us with data, either for FlyBase itself or for one of itsallied databases. The members of the Consortium are:o Biological Laboratories, Harvard University:William Gelbart (PI)Wayne RindoneJoe Chillemio Dept. of Genetics, University of Cambridge:Michael AshburnerRachel DrysdaleAubrey de Greyo Dept. of Biology, Indiana University, Bloomington:Thomas KaufmanKathy MatthewsDon Gilberto Dept. of Biology, University of California, Los Angeles:John MerriamBeverley MatthewsSoon-Young Huho National Center for Biotechnology Information, NIH,Washington:Carolyn Tolstoshev3. HOW TO CONTACT FLYBASEFlyBase has established a central e-mail address to which allcommunications and questions can be sent. This is:o FLYBASE@NUCLEUS.HARVARD.EDUCommunications or questions about the Indiana fileserver may beaddressed to:o FLYBASE@BIO.INDIANA.EDUWe very much welcome corrections and additions to the data inFlyBase, comments about the types of data the we now (or should)make available or about the structure of FlyBase. FlyBase ismeant to serve the Drosophila community. Only if we receive somefeedback from the community will we know how best to do this.Many of the working papers between members of the FlyBaseConsortium are publicly available (see below). The full mailaddresses, with telephone and fax numbers and e-mail addresses,of the members of the Consortium are given in the penultimatesection of this document.4. HOW TO OBTAIN FLYBASEFlyBase will be made available in several different ways andformats. These will include direct access to FlyBase servers,versions for stand alone access on different computer platforms,flat files and as printed text (as special issues of DrosophilaInformation Service, of which DIS 69 was a prototype) (see"Future plans for FlyBase"). In its present form FlyBase is onlyavailable as a series of flat files although these can be browsedand queried interactively using publicly available software (seebelow). The prime archive of FlyBase is maintained on a publiclyaccessible computer at the Department of Biology, IndianaUniversity (IUBio). The files can be obtained in two ways, eitherinteractively using a Gopher Client (see below) or by anonymousFTP (File Transfer Protocol). A subset of FlyBase files are alsokept on several other computers, from where they are availableeither interactively or by anonymous FTP. If all of this ismysterious to you, contact Don Gilbert, Wayne Rindone or Aubreyde Grey, by mail or phone, for help (see below for contactnumbers).WAIS/Gopher: By far the easiest way to access FlyBase iswith a Gopher Client. Gopher is a program that runs on a varietyof computer platforms (including Macs). To use Gopher you needthree things - a suitable computer, access to Internet and aGopher Client. We cannot help you for the first of these but inview of the plans to make FlyBase available using X-windowssoftware we recommend that, if purchasing, you buy a computerthat can support X-windows. For Internet access you must consultyour local computer advisors. For those without direct networkaccess there are commercial companies that provide Internetaccess across telephone lines using modems. The Gopher Clientsoftware is available by anonymous ftp fromboombox.micro.umn.edu, in the directory /pub/gopher/, or fromftp.bio.indiana.edu, in the directory /util/gopher/.Services on the IUBio Gopher host are also available usingWAIS client software. WAIS is the Wide Area Information System.Client software is available for a variety of computer platformsby FTP from IUBio (in the directory /util/wais) andftp.think.com. It may be convenient, if your main use of Gopheris to search FlyBase, to set up your Gopher client so that accessto Indiana is the default. Two of the great advantages of usingGopher are (a) that it allows you to search files interactivelyand (b) that you need not understand the structure of the FlyBasefiles. What Gopher provides is an interactive search of the flatfiles of FlyBase and the ability to transfer all or part of anyfile back to your home computer. FlyBase is accessible from theGopher hole at Indiana (IUBio) and most of the files (but notthose from the Redbook) are also accessible from the Gopher holeat the Biozentrum in Basel. The link to add to your Gopher serverto tunnel to Indiana is:Name=IUBio Biology Archive, Indiana University(experimental)Type=1Port=70Path=1/Host=ftp.bio.indiana.eduThe link for the Basel Biozentrum host is:Name=bioftp EMBnet Switzerland (experimental)Type=1Port=70Path=Host=bioftp.unibas.chThe WAIS source for the Indiana archive (IUBio) is:(:source:version 3:ip-address "129.79.224.25":ip-name "ftp.bio.indiana.edu":tcp-prot 210:database-name "INFO":cost 0.00:cost-unit none:maintainer "archive@bio.indiana.edu":description "This WAIS service includes several indexed BiologyInformation sources, including Genbank nucleic acid sequencedatabank, Drosophila genetics, Biosci/Bionet network news, andothers.File Transfer Protocol (FTP): FlyBase is available by FileTransfer Protocol (FTP) from several sources. However onlyIndiana has the complete set of files. The other sites have mostfiles except those that include the Redbook data. Note that sincemost of these machines run Unix, the commands and names ofdirectories and files are case sensitive. The FTP servers fromwhich FlyBase is now available are:FTP.BIO.INDIANA.EDU (129.79.224.25). Login with the usernameanonymous and use your e-mail address as password. FlyBaseis in the directory flybase/.NCBI.NLM.NIH.GOV (130.14.20.1). Login with the username anonymousand use your e-mail address as password. FlyBase is in thedirectory repository/FlyBase.FTP.EMBL-HEIDELBERG.DE (192.54.41.33). Login with the usernameanonymous and use your e-mail address as the password.FlyBase is in the directory /pub/databases/flybase.SUNBCD.WEIZMANN.AC.IL (132.76.64.79). Login with the usernameanonymous and your e-mail address as the password. FlyBaseis in the directory /pub/databases/flybase.FTP.NIG.AC.JP (133.39.16.66). Login with the username anonymousand your e-mail address as password. FlyBase is in thedirectory /pub/db/flybase. Once logged in to an FTP serverthe following commands can be used to obtain one or moreFlyBase files onto your own computer:ftp> cd directory name (i.e. cd flybase if using IUBio)ftp> get /documents/full.docftp> get/genes/loci.txt. et cetera. orftp> mget *.txt (to retrieve all text files)ftp> quitFor those without access to FTP there is a gateway betweenBITNET/EARN and the FTP part of IP at Princeton. This allows youto make an FTP request by BITNET/EARN mail, the file(s) requestedfrom the remote site being forwarded to you as mail fromPrinceton. This gateway is known as BITFTP. For information onhow you use it send the one-line message HELP toBITFTP@PUCC.BITNET. In brief, this service is used by sending aMAIL message (using BITNET) to BITFTP@PUCC as follows:FTP ftp.bio.indiana.edu NETDATAUSER anonymous guestQUITThe files will then be returned to you by e-mail.Netserver: These files are available from the Netserver at EMBL,and if you do not have the facility for FTP this is a way to getthem. For general help and a listing of files on the EMBLNetserver send an e-mail message to NETSERV@EMBL-HEIDELBERG.DEwith the text HELP FLYBASE. To obtain a particular file send ane-mail message with the text GET FLYBASE:FILENAME toNETSERV@EMBL-HEIDELBERG.DE, where FILENAME is one of thefilenames listed above.Direct logon access in the UK: In the UK FlyBase is available onboth the SEQNET and HGMP facilities. The SERC SEQNET computingfacility at the Daresbury Laboratory (UK.AC.DL.SEQNET) can bedirectly accessed via JANET. For an account write to Dr. AlanBleasby, SERC Daresbury Laboratory, Warrington WA4 4AD, Cheshireor send e-mail to AJB@UK.AC.DARESBURY. FlyBase is kept in adirectory called /data/flybase. The MRC Human Genome MappingProject is also accessed via JANET (MENU.CRC.AC.UK). Applicationsfor an account should be sent to The HGMP Resource Centre,Clinical Research Center, Watford Road, Harrow, Middx HA1 3UJ.Access to FlyBase is via the menu.CD ROM: Most of the files of FlyBase (except those of theRedbook) are included in the NCBI Data Repository and EMBL CD-ROMs. These are released periodically and are available from theNCBI Data Repository, National Library of Medicine, Bldg. 38A, Rm8N-803, NIH, Bethesda, MD 20894 ((1)-301-496-2475) or from theEMBL Data Library, Postfach 10.2209, 6900 Heidelberg, Germany(phone (49)-6221-387258; fax (49)-6221-387519). Dr. Amos Bairochhas made this database available as ascii files on CD ROM.Contact Dr. A. Bairoch, Department of Medical Biochemistry,University of Geneva, Geneva, Switzerland. e-mail:BAIROCH@CMU.UNIGE.CH.5. HOW TO REFERENCE FLYBASEWe suggest FlyBase be referenced in publications in the followingmanner: FlyBase (1993). A Drosophila Genetic Database. Availablefrom the FTP.BIO.INDIANA.EDU network server.6. DIFFERENCES BETWEEN PRINTED AND COMPUTER VERSIONS OF FLYBASE[omitted]7. ALLIED DATABASESIt is both undesirable and impossible for literally all data onDrosophila to be kept within FlyBase. However, FlyBase wishes toencourage collaboration between other workers who are buildingdifferent or more specialized Drosophila databases. For thisreason FlyBase has established the concept of allied databases.These databases are explicitly attributed to their authors, whoare responsible for the data they include. FlyBase encouragesother members of the community to make their databases availableassociated to FlyBase. In particular, FlyBase encourages otherdatabase curators to cross-reference FlyBase to ensureconsistency in, for example, gene names and symbols. FlyBaseoffers help to other curators in both ensuring nomenclaturalconsistency and in making their databases publicly availablethrough FlyBase. The allied databases now available are listed inthe detailed description of FlyBase, below.8. THE STRUCTURE OF FLYBASEThe presently available version of FlyBase is a series of filesarranged in a hierarchical structure of directories andsubdirectories. An inconvenience of this is that file names canbecome very long. However, on Unix operating systems, access to aparticular directory can be limited by using the cd (changedirectory) command. The command cd .. (i.e. cd followed by aspace and then two periods) will take you up one directory level.Against the disadvantage of cumbersome file names this structureis very logical and easy to maintain. Files are of differenttypes, indicated by the suffixes to their names:.doc an explanatory document, in plain text..txt a file in plain text, may be data, documentation orother information..rpt a formatted data file, suitable for viewing by people,in plain text..rtf a rich-text file, best read with common wordprocessors, but also readable by people, in plain text..gif an image file (graphic interchange format). Use a gifviewer to see..ps a postscript image file. Use a postscript viewer orprinter..tar.Z a Unix compressed archive file. Use uncompress and tarto extract..hqx a Macintosh binhex archive file. Use stuffit todecompress..zip an MSDos compressed archive file. Use unzip to extract.There now follows the complete structure of the FlyBase files askept on the IUBio server. The structure may differ when FlyBaseis mounted on other computers, but should reflect this structurein a logical way. A detailed description of the contents of eachfile is given in the next section of this document. Some fileshave yet to be implemented, but they have been listed here as itis expected that they will be available very soon. If you areusing FlyBase through a Gopher client the details of thisorganization are irrelevant, as you will be presented with theavailable files by the interactive Gopher menu.flybase/flybase/redbookflybase/redbook/genesflybase/redbook/lethalsflybase/redbook/aberrationsflybase/redbook/miscellanyflybase/genesflybase/aberrationsflybase/mapsflybase/functionflybase/clonesflybase/stocksflybase/stocks/stock-centersflybase/stocks/stock-centers/bloomingtonflybase/stocks/labsflybase/referencesflybase/miscellanyflybase/sequencesflybase/peopleflybase/newsflybase/news/newsflybase/news/oldnewsflybase/news/dinflybase/documentsflybase/documents/full.doc i.e. this documentflybase/working-papersflybase/allied-data9. DETAILED DESCRIPTION OF FLYBASE omitted10. FUTURE PLANS FOR FLYBASEIn this section of the documentation we indicate some of thefuture directions we are taking with the building of FlyBase.This text is supplemented by the papers in the files offlybase/working-papers. We encourage the fly community to respondto what we are doing - let us know (by e-mail toFLYBASE@NUCLEUS.HARVARD.EDU or by regular mail to any of us) ifyou think we are not doing something that should be done, or aredoing something that should not be done. Only by feedback fromthe community will we produce a product of the greatest utilityto all. As we have explained elsewhere in this document thepresent release of FlyBase is seen very much as a temporarymeasure, until the full relational schema has been implemented.The relational schema: FlyBase is being built and will bemaintained in a commercial relational database management systemcalled Sybase. The design of the relational schema can be foundin a series of files in flybase/working-papers/sybase-*. Thisschema was designed by Carolyn Tolstoshev. It is not yet stable -that is to say changes to the schema are still being made as aconsequence of experience and discussion. The Harvard group arenow implementing and testing this schema prior to the importationof data.The data: Any database is only as good as its data and theway these data are interrelated. At present, FlyBase data areavailable as a series of independent tables with fewrelationships between them. Not only does this mean that thereare major inconsistencies between tables (e.g. a gene may haveone symbol in one table but another in a second) but also itmeans that the user cannot automatically go from e.g. the locitable to a stock table. One of the major tasks that is now beingdone is to force consistency between tables.1. The bulk of the genetic data is now in two sets ofdirectories, flybase/redbook - the text material of Lindsley andZimm, and flybase/genes and flybase/aberrations (withflybase/maps, flybase/function, flybase/references). TheCambridge group is now integrating these two sets of tables intoa single structure. This will, in effect, be the replacement ofthe Redbook. Since science does not stop simply because we arebuilding this database the Cambridge group is also continuouslyupdating the data, by scanning the literature.2. There are now several different tables of clone data. Theseare being integrated and continuously updated by the Los Angelesgroup. This group is also developing software for the graphicaldisplay of molecular data.3. References can now be found in three different sets of tables,those in flybase/redbook, flybase/genes andflybase/clones/clonelist.txt. Not only is there redundancybetween these but each set differs in its reference format. TheCambridge group is dealing with this problem by building a singleDrosophila reference file. The objective is to have as complete abibliography on Drosophila biology as possible with all entriesin uniform format. The sources of this bibliography are several:the published bibliographies (Morgan et al. 1925, Muller,Herskowitz and some smaller more specialized ones) are being readby an optical character reader; we have concluded a licenseagreement with MEDLINE giving us a retrospective download from1966 (the year MEDLINE introduced computer files) with monthlyupdates from January 1993 (these entries will include abstracts)and Dr. G. Bachli's computer bibliography, which is especiallystrong on taxonomic and faunistic papers. When these have allbeen entered, duplicate entries removed and reformatted they willbe checked against the large Drosophila offprint collection inCambridge for errors and omissions. This reference table willserve all of the other tables of FlyBase. Users will be able torecover references from it in a variety of formats (e.g. thatused by ENDNOTE).4. The Bloomington group is working on the problem of stocklists, not only collecting stock lists from other laboratories(see flybase/stocks.doc) but also ensuring a consistency informat, so that all can be seen in a similar way. We hope topublish a recommendation for stock list format, with the hopethat others will use it and reduce the problems we have indisplaying stock list data. The second major problem with thestock lists is to ensure that they are consistent in the symbolsused for genes, alleles, aberrations and insertions.5. There are now several different files of addresses and/or e-mail addresses. These have been gathered from various sources.The aim is to have a single address file, in a consistent format.This work is being done in Bloomington.6. The formal description of chromosome aberrations, in a mannersuitable for manipulation by computer programs, is a difficultproblem. One approach is that discussed in flybase/working-papers/aberration-syntax.txt. We are writing software that willallow efficient searching of the aberration tables for, e.g.,breakpoints within a specific chromosome region, and allow thegraphical display of aberrant chromosomes.Output: Although FlyBase will be built and maintained inSybase we expect few to have the skills to use it as such or tohave the very considerable cash required for a Sybase operatinglicense. For this reason we are building a number of outputproducts that will make FlyBase available to as wide a communityas possible. (The Sybase implementation will be publiclyavailable should any users need it.)1. The simplest output will be printed text. We have, in pre-Consortium days, experimented with this with a special volume ofDIS (DIS 69) compiled by Michael Ashburner and edited (anddistributed) by William Gelbart. It is our intention to publishsuch special issues of DIS whenever the amount of new datawarrants. By doing this we will ensure that even those workerswho have no access to computers or networks will not bedisenfranchised. These issues of DIS will be produced as outputfrom the Sybase tables.2. The presentation of FlyBase as a series of ascii flat files oncomputer servers will be maintained. The prime server will bethat at IUBio and the Bloomington group will continue to makeimprovements in access and display of these tables. By far theeasiest way to access these files is by using a Gopher client(see "How to obtain FlyBase"). In addition these tables will bedistributed, as now, to a number of major servers used bybiologists and will be included on the CD-ROMs being distributedby NCBI, EMBL and others.3. There is now strong interest in the development of software todisplay databases such as FlyBase interactively using X-windowssystems. We are developing such tools for use with FlyBase. Weare concentrating our efforts in two ways. The first is toexploit the software tools written at the NCBI for use with theirEntrez system. The second is to develop the programs written byRichard Durbin and Jean Thierry-Meig for the C. elegansdatabase - acedb. acdeb is now being modified for Drosophila datain Berkeley and we are collaborating with Suzanna Lewis to makethese programs suitable for the display of FlyBase. Theseimplementations of FlyBase will be available from the IUBioserver (and probably from other servers), on CD-ROM and perhapson floppy discs. To make use of them you will need a computerthat can implement X-window software (or its equivalent). A colormonitor would be a great advantage.11. RELEASE NOTESSince FlyBase is still kept as a series of independent tables theconcept of a "release" or "version" of the database is difficultto apply. However, while this format continues we will signal newreleases (as yearmonth) whenever we consider that there has beena sufficient change in data or organization to warrant it. Newversions of particular tables may well be released withoutobvious notice. One way of finding out is to look at the datethat a particular file was last modified on IUBio. This can bedone by FTP using the dir command in the flybase directory. Thelast update of a file is automatically displayed by Gopher. Theindividual document files will be kept up to date and they willindicate any changes in organization or major changes in content.The last update of the .doc files is displayed on the top line ofeach.Release 9301 of FlyBase is the first by the Consortium. Itis released as a temporary measure to make the data that is inFlyBase already available to the community. In large part 9301 issimply a restructuring of data that had been previously availablefrom IUBio and other sources. It includes the tables from the9209 release of Michael Ashburner (seeflybase/news/oldnews/1992.txt). These tables include 5321 loci,4218 entries in the genetic map, 11940 aberrations and 3120references. Note that of the 5321 loci, about 800 are not inLindsley and Zimm (1992). The great majority of the referencesare also subsequent to Lindsley and Zimm. This release includestables from the 3/06/1992 release of John Merriam's clone lists.12. FULL ADDRESSES OF MEMBERS OF THE FLYBASE CONSORTIUMWilliam Gelbart, Biological Laboratories, Harvard University, 16Divinity Avenue, Cambridge, Massachusetts 02138, USA.Telephone: (1)-617-495-2906; fax: (1)-617-495-9300; e-mail:GELBART@MORGAN.HARVARD.EDU.Wayne Rindone, Biological Laboratories, Harvard University, 16Divinity Avenue, Cambridge, Massachusetts 02138, USA.Telephone: (1)-617-496-5668; fax: (1)-617-495-9300; e-mail:RINDONE@MORGAN.HARVARD.EDU.Joe Chillemi Biological Laboratories, Harvard University, 16Divinity Avenue, Cambridge, Massachusetts 02138, USA.Telephone: (1)-617-496-5667; fax: (1)-617-495-9300; e-mail:JOEC@MORGAN.HARVARD.EDU.Michael Ashburner, Department of Genetics, University ofCambridge, Downing Street, Cambridge, CB2 3EH, England.Telephone: (44)-223-333969; fax: (44)-223-333992; e-mail:MA11@GEN.CAM.AC.UK.Rachel Drysdale, Department of Genetics, University of Cambridge,Downing Street, Cambridge, CB2 3EH, England. Telephone:(44)-223-333963; fax: (44)-223-333992; e-mail:RD120@GEN.CAM.AC.UK.Aubrey de Grey, Department of Genetics, University of Cambridge,Downing Street, Cambridge, CB2 3EH, England. Telephone:(44)-223-333963; fax: (44)-223-333992; e-mail:AG24@GEN.CAM.AC.UK.Thomas Kaufman, Department of Biology, Indiana University,Bloomington, Indiana 47405, USA. Telephone (1)-812-855-3033;fax: (1)-812-855-2577; e-mail: KAUFMAN@BIO.INDIANA.EDU.Kathy Matthews, Department of Biology, Indiana University,Bloomington, Indiana 47405, USA. Telephone (1)-812-855-5782;fax: (1)-812-855-2577; e-mail: MATTHEWK@UCS.INDIANA.EDU.Don Gilbert, Department of Biology, Indiana University,Bloomington, Indiana 47405, USA. Telephone (1)-812-855-7807;e-mail: GILBERT@BIO.INDIANA.EDU.John Merriam, Department of Biology, University of California atLos Angeles, Los Angeles, California 90024-1606, USA.Telephone: (1)-310-825-2256; fax: (1)-213-206-3987; e-mail:IBENAPR@OAC.UCLA.EDU.Beverley Matthews, Department of Biology, University ofCalifornia at Los Angeles, Los Angeles, California90024-1606. Telephone: (1)-310-825-2256; fax: (1)-213-206-3987.Soon-Young Huh, Department of Biology, University of Californiaat Los Angeles, Los Angeles, California 90024-1606.Telephone: (1)-310-825-2256; fax: (1)-213-206-3987; e-mail:SHUH@AGSM.UCLA.EDU.Carolyn Tolstoshev, National Center for BiotechnologyInformation, National Institutes of Health, 8600 RockvillePike, Bethesda, Maryland 20894, USA. Telephone:(1)-301-496-2475; fax: (1)-301-480-9241; e-mail:CAROLYN@NCBI.NLM.NIH.GOV.13. THE COPYRIGHT OF FLYBASEThe files containing the text of Lindsley and Zimm (1992) Thegenome of Drosophila melanogaster are the copyright of AcademicPress and are redistributed in FlyBase by their agreement. Thesefiles cannot be redistributed by users without the explicitpermission of Academic Press. The copyright of FlyBase itself isheld by the Genetics Society of America.14. ACKNOWLEDGMENTSFlyBase is supported by a grant from The National Center forHuman Genome Research. In addition support has come from the HGMPProgramme of the MRC (London) in the form of both hardware andsoftware. Work in John Merriam's group has been supported by agrant from the National Library of Medicine. The Drosophila StockCenter at Bloomington is supported by NSF's Division ofInstrumentation and Resources. We acknowledge the help of Dr.Phyllis Moses (Academic Press) and Dr. D.L. Lindsley in makingthe Redbook data available to FlyBase. We thank Drs. D.J. Lipmanand J. Ostell and the staff at the NCBI in Washington for theirhelp in getting FlyBase launched. We are very grateful to RainerFuchs at EMBL, Amos Bairoch in Geneva, Alan Bleasby at Daresbury,Scott Federhen at the NCBI, Yoshihiro Ugawa and Takashi Gojoboriat the DDBJ, Martin Bishop at the HGMP and Reinhard Doelz at theBiozentrum for helping to make this database available. Thankstoo to John Garavelli (PIR), Rainer Fuchs (EMBL) and Amos Bairoch(Geneva) for help in cross-checking between FlyBase and theNucleic Acid/Protein databases. We also thank Dr. G. Bachli(Zurich) for a substantial contribution to the bibliographicfile.*** DIN 9GENETIC NOTESA NEW MUTANT OF D. SECHELLIAIsaya Higa and Yoshiaki Fuyama, Dept. of Biology, TokyoMetropolitan U., Hachioji-Shi, Tokyo 192-03, Japan.81-426-77-2575, FAX/2559; A910741@JPNTMU00.BITNET.A new white (w) mutant of D. sechellia spontaneouslyoccurred in an iso-female strain originally collected in PlaslinIsland, Seychelles in 1986. General features are the same asthose of white of D. simulans and white[1] of D. melanogaster.Homozygote fertile and viability normal. Sex-linked andrecessive. Does not complement white of D. simulans.*** DIN 9NEW RADIUS INCOMPLETUS ALLELE AND ITS LETHAL INTERACTION WITHHAIRLESSPetter Portin and Mirja Rantanen, Laboratory of Genetics, Dept.of Biology, U. of Turku, SF-20500 Turku, Finland.SEPNE@SARA.CC.UTU.FIIn June 1992 we began to suspect that a spontaneous radiusincompletus (ri) mutation had occurred in our Ax[ts1] stock. Wemapped this mutation with the aid of cu and es mutations, andfound that the new mutation really mapped to the position of ri(3-47.0). Our new mutation failed to complement ri, andconsequently it was named ri[92f].Even earlier we had found that in the cross ri[92f] cu es xH es cd/In(3R)P, spr only non-ebony progenies appeared. Thereforewe concluded that the interaction of ri and H is lethal eventhough both are in a heterozygous condition.*** DIN 9CORRECTIONS FOR REDBOOKDan Lindsley and Georgianna Zimm, Dept. of Biology, U. ofCalifornia, La Jolla, CA 92093. 619-534-3109, FAX/0053.p=page, L=left, R=rightp2L, line 12: choromosomes > chromosomesp8R, ABO table footnote: Sander> Sandlerp25L, Ama-1: alpha-amanatin> alpha-Amanatinp41R, zen: Location> locationp71R, bottom of page: Add entry "bcd:: see ANTC"p100: Add entry "Ubx[16K] X ray Ramey In(3R)79D;89B Ubx"p100: Add entry "Ubx[42T] X ray In(3R)70D;89E Ubx"p100: Add entry "homozygous lethal" to last column of Ubx[130].p101: Add entry "; T(2;3) " to cytology column and entry "Ubx" totype column of Ubx[A]p109: Add entry "extreme Ubx" to type column of Ubx[U]p109R: Add entry "cel: see l(3)84Ab"p128R: Add entry "cry: see Su(Ste)"p128R: Add entry "crystal: see Su(Ste)"p142L: Add entry "da[12] 7 recessive lethal"p142L: Add entry "da[13] 7 recessive lethal"p142L: Add entry "da[14] 7 recessive lethal"p142L: Add entry "da[15] 7 recessive lethal"p142L: Add entry "da[16] 7 recessive lethal"p142L: Add entry "da[17] 7 recessive lethal"p142L: Add entry "da[18] 7 recessive lethal"p142L: Add entry "da[19] 7 recessive lethal"p142L: Add entry "da[20] 7 recessive lethal"p142L, da table footnote: Add entry "7 = Grigliatti."p142L, da cytology: Change to "Placed in 32A by fine-structuredeficiency analysis of region 31A-32A by Grigliatti et al."p183R: E(Sd)> E(SD)p201R, err alleles: Add entry "err[2] - err[4] also isolated."p201R, err cytology: Change to "Placed in 31E by fine-structuredeficiency analysis of region 31A-32A."p249R, Gbeta13F location: 2-54> 2-51p255L: Add entry "Glucose-tasting-defective: see Gtd."p255L: Add entry "Glutamic acid decarboxylase: see Gad."p259R: Add entry "grh, grainy head: see Ntf."p259R: Add entry "groggy: see ggy."p268L, H references: Add entry "Plunkett, 1926, J. Exp. Zool. 46:181-244."p268L, H references: Add (after "Development") "111: 89-104."p268R, H[17] (in table): Add entry "gamma ray Posakony/Groger"p268R, H[18] (in table): Add entry "gamma ray Posakony/Groger"p268R, H[19] (in table): Add entry "gamma ray Posakony/Groger"p268R, H[20] (in table): Add entry "gamma ray Posakony/Groger"p268R, H[21] (in table): Add entry "gamma ray Posakony/Groger"p268R, H[21] (in table): H[C]> H[C23]p268R, H[22] (in table): Add entry "gamma ray"p268R, H[22] (in table): Bang> Posakonyp268R, H[22] (in table): H[C]> H[RP1]p268R, H[26] (in table): Add entry "X ray."p288L, inC alleles: InC[1] - InC[3]> inC[1] - inC[3]p309L (in l(1)2A table): l(1)2Af (bold face)> l(1)2Af (regular)p309L (in l(1)2A table): sta> sta (bold face)p509R, nod references: Genetics (submitted)> Genetics 125:115-27.p555L, pn: awk[K]> awd[K] (appears twice)p555R, pn: awk[K]> awd[K] (appears four times)p570R, qua: Nsslein-> Nusslein (diaeresis over the u)p570R, qua: f2qua[2] - qua[7]> qua[2] - qua[7] (in italics)p621L: Add entry "scabrous> sca"p621L: Add entry "shaven baby> sv"p740R: For the entry unk, see the CYTOGENETIC MAP, p1132.p1067: change figure explanation to "the third row shows the N-banding pattern (provided by Pimpinelli, Bonaccorsi,Dimitri, and Gatti.)."p1068L: Change reference for figure explanation to "(Pimpinelli,Bonaccorsi, Dimitri, and Gatti)."p1069L: Change reference for figure explanation to "(Pimpinelli,Bonaccorsi, Dimitri, and Gatti)."p1069R (upper): Change reference for figure explanation to"(Pimpinelli, Bonaccorsi, Dimitri, and Gatti)."p1069R (lower): Change reference for figure explanation to"(Pimpinelli, Bonaccorsi, Dimitri, and Gatti)."Notes appended to Redbook by attendees at the Philadelphia flymeeting:exo: exocephalon is allelic to phm: phantom (Eberl)mat(2)N mutations are hypomorphic alleles of l(2)31EiSryc likely to correspond to wdn (Lepesant)fs(1)A107 renamed brn: braniac (can't read signature)fs(1)1621 renamed snf: simply not fertile (Saltz)Kin: Kinesin should be Khc: Kinesin heavy chain (Saxton)l(1)3Ac renamed trol: troll by Datta and Kandel not l(1)trol asthey suggestl(3)73Ab will be named soon (Andrew)l(3)85Ee renamed hyd: hyperplastic discs (Shearn)l(3)SG29 renamed md: minidiscs (Shearn)l(3)SG56 renamed qrt: quartet (Shearn)New genes inserted into list by participants:Chc: Clathryn heavy chaindco: discs overgrown (see Developmental Biology 140: 413-429)Gprk1Gprk2Pra: ParamyosinrdgC: retinal degeneration Ctsh: teashirtA change that we suggest:ms(3)sa should be sa: spermatocyte arrestSymbols used by Ashburner that I prefer over ours:l(1)17Aa through l(1)17Ad instead of l(1)16Fa through l(1)16FdLanA, LanB, and LanC instead of Lam-A, Lam-B, and Lam-CPk17C instead of Pk?4Pk45C instead of Pk?3Pk53C instead of Pk?7Pk64F instead of Pk?6Pk91C instead of Pk?2Other new synonymy:Pkc2 is the same as inaCsbl mutations are allelic to para*** DIN 9

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