DROSOPHILA INFORMATION NEWSLETTER Volume 4, October 1991 The Drosophila Information Newsletter has been established with the hope of providing a timely forum for informal communication among Drosophila workers. The Newsletter will be published quarterly and distributed electronically, free of charge. We will try to strike a balance between maximizing the useful 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 to be of value, the material should be summarized and an address made available for interested individuals to request more information. Submitted material will be edited for brevity and arranged into each issue. Research reports, lengthy items that cannot be effectively summarized, and material that requires illustration for clarity should be sent directly to Jim Thompson for publication in DIS. Materials appearing in the Newsletter will be reprinted, in unedited form, in the next issue of DIS. Back issues of DIN are posted on the Indiana fileserver in the directory fly/news. Material appearing in the Newsletter may be cited unless specifically noted otherwise. Material for publication may be submitted in any of the following formats - Macintosh Microsoft Word or MacWrite, MS-DOS WordPerfect, or text/ASCII file. Figures and photographs cannot be accepted at present. Send material, in order of preference, as E-mail (addresses below), on floppy disk, or as laserwriter or typed hard-copy (not bit-mapped). Technical notes should be sent to Carl Thummel, all other material should be sent to Kathy Matthews. The e-mail format does not allow special characters to be included in the text. Both superscripts and subscripts have been enclosed in square brackets; the difference should be obvious by context. Bold face, italics, underlining, etc. cannot be retained. Please keep this in mind when preparing submissions. Drosophila Information Newsletter is a trial effort that will only succeed if a broad segment of the community participates. If you have information that would be useful to your colleagues, please take the time to pass it along. The editors: Carl Thummel Kathy Matthews Dept. of Human Genetics Dept. of Biology Eccles Institute - Bldg. 533 Indiana University University of Utah Bloomington, IN 47405 Salt Lake City, UT 84112 812-855-5782; FAX/2577 801-581-2937; FAX/5374 MATTHEWK@IUBACS.BITNET THUMMEL@MEDSCHOOL.MED.UTAH.EDU MATTHEWK@UCS.INDIANA.EDU *** DIN 4 To add your name to the Newsletter distribution list, send one of the following E-mail messages. Via Bitnet -- To: LISTSERV@IUBVM Subject: Message: SUB DIS-L Your real name Via Internet -- To: LISTSERV@IUBVM.UCS.INDIANA.EDU Subject: Message: SUB DIS-L Your real name LISTSERV will extract your user name and node from the E-mail header and add you to the list. Use your Internet address if you have one. You will receive confirmation by E-mail. If you are on the list and do not wish to receive DIS, or you want to remove a defunct address, replace SUB in the above message with UNS. The SUB command can also be used to correct spelling errors in your real name; the new entry will simply replace the old as long as it was sent from the same USERID@NODE address. *** DIN 4 IF YOU AREN'T RECEIVING THE NEWSLETTER: With each mailing of the Newsletter, at least a dozen addresses are rejected by the mailer. For many subscribers, I have no way of contacting you except the e-mail address that isn't working. If you signed on to the DIN distribution list and are not receiving the Newsletter, please contact me so we can correct the problem. -- KM *** DIN 4 DIN Vol. 4 TABLE OF CONTENTS >Introduction to Drosophila Information Newsletter >How to subscribe to the Newsletter >Editor's note - rejected e-mail addresses >TABLE OF CONTENTS >ANNOUNCEMENTS >1992 Drosophila Conference >Funding opportunity >P-element insertion stocks >New phone numbers at ICRF >New phone numbers at UC Berkeley >REQUESTS FOR MATERIALS >Clones for Drosophila genome project >Information for libraries list >DATABASES/COMPUTING >FLY.BIO.INDIANA.EDU - A new server for the fly community >New release of Genetic Maps database >Cytological features database >TECHNICAL NOTES >P element vectors for analyzing enhancer elements >GENETIC NOTES >Stocks for P-element mutagenesis *** DIN 4 ANNOUNCEMENTS 1992 DROSOPHILA CONFERENCE. The 33rd Annual Drosophila Research Conference will be held March 11-15, 1991 at the Wyndham Hotel, Philadelphia, PA. The meeting organizer is Bill Gelbart, Biological Labs, Harvard U., 16 Divinity Ave., Cambridge, MA 02138; 617-495-2906. The 1993 meeting will be held April 1-4, 1993, in San Diego, CA. *** DIN 4 FUNDING OPPORTUNITY. The National Center for Human Genome Research, NIH, is preparing a Request for Applications to solicit applications to characterize the Drosophila melanogaster genome. Research projects should focus on (1) the development of high- resolution physical maps, (2) new technologies to detect all the coding regions or expressed genes in the Drosophila genome, and (3) feasibility studies for large-scale DNA sequencing using regions of biological interest for pilot studies. Applicants may request support for individual research projects, program projects, feasibility/pilot projects, developmental grants, and center grants. The Request for Applications is expected to be announced in late August in the NIH Guide to Grants and Contracts. The application receipt date will be November 15, 1991. Applications will be reviewed for scientific merit in February 1992 by the NCHGR's Genome Research Review Committee and for programmatic considerations by the National Advisory Committee on the Human Genome in May 1992. The earliest award date will be July 1, 1992. For further information contact Dr. Bettie J. Graham, Chief, Research Grants Branch, National Center for Human Genome Research, NIH, Bethesda, MD 20892, 301-496-7531, FAX/2770, B2G@CU.NIH.GOV or @NIHCU.bitnet. *** DIN 4 P-ELEMENT INSERTION STOCKS. The HHMI P-Element Stock Center ceased to exist on August 1, 1990. HHMI provided two years of funding for the creation of a collection of strains with single P-element insertions with the understanding that maintenance and distribution of the collection would be transferred to the NSF- funded "regular" stock center at Bloomington at the end of the HHMI funding period. The current collection of insertion stocks at Bloomington consists of 1,152 P and 111 TE insertions. A site of insertion has been reported for 685 of these stocks. P strains collection by the HHMI stock center are listed in the file PLIST.TXT on the Indiana file server; insertion stocks collected post-HHMI are listed in the file NEWP.TXT (eventually data in PLIST will be converted to the NEWP format). Stocks can be ordered by contacting Kathy Matthews (812-855-5783). *** DIN 4 NEW PHONE NUMBERS AT ICRF. On September 16th 1991, Phil Ingham's and David Ish-Horowicz's telephone numbers will change following the installation of Direct-Dialing at the ICRF Developmental Biology Unit, Oxford. The new numbers will be: ICRF DBU switchboard: (0)865 281300 FAX 281310 Phil Ingham 281323 (office)/ 281320 (lab) David Ish-Horowicz 281306 (o) / 281305 (l) *** DIN 4 NEW PHONE NUMBERS AT U.C. BERKELEY. The area code of all University of California at Berkeley phone numbers has been changed from 415 to 510. *** DIN 4 REQUESTS FOR MATERIALS REQUEST FOR CLONES Leonard Rabinow[1] and Robert Saunders[2]. [1]Waksman Institute, Rutgers Univ., Piscataway, NJ 08855-0759, USA. 908-932-0091/0092, FAX/5735, RABINOW@BIOVAX. [2]Dept. of Biochemistry, Univ. of Dundee, Dundee DD1 4HN, UK. (0382)23181 ext. 4790, FAX/201063, BI31@UK.AC.DUNDEE.PRIMEB (reverse node order from USA). Most readers of DIS are probably aware of a number of projects in progress with the aim of constructing a physical map of the Drosophila melanogaster genome. A collaboration among the laboratories of F.C. Kafatos, C. Louis, C. Savakis, D.M. Glover, and M. Ashburner is proceeding by fingerprinting cosmids selected with cytological division-specific probes produced by microdissection from polytene chromosomes (Nucl. Acids Res. (1990) 18, 6261-6270). J. Messing, L. Rabinow, W. Sofer and G. Hamm at the Waksman Institute, are initiating a project to produce a restriction map of the genome, using bacteriophage P1 and automated reading of partial restriction digests. Both projects will correlate their developing physical maps with the genetic and cytological maps of Drosophila. To achieve this, we would like to probe our libraries with loci cloned and mapped by members of the Drosophila community. We would greatly appreciate it if members of the fly community willing to contribute clones would send them to either of the above addresses. It would be most convenient if clones could be sent in plasmids (preferably bearing T7, SP6 or T3 RNA polymerase promoters), or M13, to avoid cross-hybridization problems. A few micrograms of a specific oligonucleotide, if available, could also be used. Submissions would be most useful if accompanied by information on the name, identity, and location of the clone, its vector, a restriction map or sequence, and a reference. To coordinate the overall efforts, clones and data will be exchanged among these groups. Submitted clones will be exchanged only between these two groups, unless specifically authorized by the sender. *** DIN 4 COMPILATION OF DROSOPHILA GENOMIC AND CDNA LIBRARIES Carl S. Thummel, HHMI, 5200 Eccles Institute, Bldg. 533, U. of Utah, Salt Lake City, Utah, 84112, USA. 801-581-2937, FAX/5374, THUMMEL@MEDSCHOOL.MED.UTAH.EDU. Although a number of Drosophila genomic and cDNA libraries have been constructed, one must depend on word-of-mouth and publications to learn which libraries are currently available and how useful they are for specific experimental purposes. I would like to create a listing of all available Drosophila genomic and cDNA libraries. This compilation should prevent the construction of duplicate libraries as well as facilitate the isolation of Drosophila genes. This listing will include the following categories: genomic (cosmid, phage) and cDNA (regular and expression). Please specify which libraries you have available and send the following additional information (preferably by Email or FAX). 1. Vector 2. Complexity (i.e. total number of clones that are present in the library) 3. Titer (if known) 4. Source of DNA (Drosophila strain; also stage and tissues for cDNA) 5. Your name, address, phone and FAX numbers 6. Any additional information that might be of use. 7. References (if any) Since amplified phage libraries can be safely shipped by regular mail, without wet or dry ice, the distribution of these libraries should entail little expense. Thank you for your help. This should be a valuable resource for the entire Drosophila community. *** DIN 4 DATABASES/COMPUTING FLY.BIO.INDIANA.EDU - A NEW SERVER FOR THE FLY COMMUNITY Kathy Matthews, Indiana Drosophila Stock Center, Dept. of Biology, Indiana U., Bloomington, IN 47405, USA. 812-855-5792, FAX/2577, MATTHEWK@UCS.INDIANA.EDU or @IUBACS. Through the Bloomington stock center, NSF's Division of Instrumentation and Resources has provided the funds for the purchase of a Sun Sparcstation 2 to function as the fly community's database server. Once Drosophila data have been transferred to this machine, you will automatically reach FLY.BIO.INDIANA.EDU (129.79.224.25) when you ftp to FTP.BIO.INDIANA.EDU. Don Gilbert will continue to maintain the public server on this new machine and will be helping us develop on line search capabilities for this system. With 1.2 GB of storage, the space crunch we were experiencing with IUBIO will not be a FLY problem for the foreseeable future. If you have a database in electronic format that would be of interest to the Drosophila community please consider posting it on FLY. *** DIN 4 NEW RELEASE OF GENETIC MAPS DATABASE Michael Ashburner, Dept. of Genetics, U. of Cambridge, Downing St., England CB2 3EH. 44-223-333969, FAX/333992, MA11@PHX.CAM.AC.UK. A new version of the Drosophila Genetic Maps (Version 9107, 27 July 1991) database has now been released. Information on obtaining it is given below. Note that this is the first version of the database to include genetic aberration data. Problems to Michael Ashburner. Obtaining the database: The database can be obtained electronically from three sources: the archive fileserver at the Dept. of Biology, Indiana U., Bloomington, IN and the Netserver at EMBL, Heidelberg. In addition these files are also available on the SEQNET facility to registered users within the United Kingdom. I am very grateful to Don Gilbert at Indiana, Rainer Fuchs at EMBL and Alan Bleasby at Daresbury for making this database available in these ways. The files are: GENES AND MAPS: o MAINDOC.TEXT - General documentation (this file) o FUNCTIONDOC.TEXT - Documentation of FUNCTION file o LOCIDOC.TEXT - Documentation of LOCI file o MAPDOC.TEXT - Documentation of MAPLOCI file o SYNONYMDOC.TEXT - Documentation of SYNONYM file o REFSDOC.TEXT - Documentation of REFS file o FUNCTION.TEXT - Genes sorted by function o LOCI.TEXT - Genes sorted by gene symbols o MAPLOCI.TEXT - Genes sorted by genetic map position o SYNONYMS.TEXT - Table of synonyms of gene symbols o REFS.TEXT - References ABERRATIONS: o ABDOC.TEXT - Documentation for the following tables o ABAS.TEXT - Table of autosynaptic elements o ABDF.TEXT - Table of deletions o ABDP.TEXT - Table of duplications o ABIN.TEXT - Table of inversions o ABI.TEXT - Table of insertions o ABT.TEXT - Table of translocations o ABTP.TEXT - Table of transpositions o ABREF.TEXT - References for these tables From Indiana: The files are kept on FTP.BIO.INDIANA.EDU and are accessible by FTP (File Transfer Protocol). The files are in the directory fly/loci. To obtain any of these files use the following commands: >ftp ftp.bio.indiana.edu ftp> user: anonymous ftp> password: guest ftp> cd fly/loci ftp> get DOC.TEXT ftp> get LOCI.TEXT ... et cetera ... or ftp> mget *.TEXT (to retrieve all TEXT files) ftp> bye The numeric address of FTP.BIO is 129.79.224.50 (this will change to 129.79.224.25 in the near future), in case your nameserver is as archaic as some. If you do not have the facility for FTP, it is possible to use an interface between BITNET and TCP/IP at Princeton University (see below). From EMBL: These files are available from the Netserver at EMBL, and if you do not have the facility for FTP this is the way to get them (but see below). For HELP send an e-mail message to NETSERV@EMBL.BITNET with the text HELP DROSOPHILA. For a listing of the files on the EMBL Netserver send the message DIR DROSOPHILA. To obtain a particular file send an e-mail message with the text GET FILENAME to NETSERV@EMBL.BITNET, where FILENAME is one of the filenames listed above. From SEQNET: The SERC SEQNET computing facility at the Daresbury Laboratory is available to researchers in the United Kingdom. This computer (UK.AC.DL.DLVH) can be directly accessed via JANET. For an account write to Dr. Alan Bleasby, SERC Daresbury Laboratory, Warrington WA4 4AD, Cheshire or send e-mail to AJB@UK.AC.DARESBURY.DLVH. These files are kept in a directory called DATA1:[DROSOPHILA]. Via BITFTP@PUCC: For those without access to FTP there is a gateway between BINET/EARN and the FTP part of TCP/IP at Princeton. This allows you to make an FTP request by BITNET/EARN mail, the file(s) requested from the remote site being forwarded to you as mail from Princeton. This gateway is known as BITFTP. For information on how you use it send the one-line message HELP to BITFTP@PUCC.BITNET. In brief, this service is used by sending a MAIL message (using BITNET) to BITFTP@PUCC as follows: FTP ftp.bio.indiana.edu NETDATA USER anonymous guest QUIT The files will then be returned to you by mail. *** DIN 4 CYTOLOGICAL FEATURES DATABASE Sally Amero, Dept. of Molecular and Cellular Biochemistry, Loyola University Medical Center, 2160 South First Ave., Maywood, IL 60153, USA. 708-216-3365, FAX/8523, and Michael Ashburner, Dept. of Genetics, U. of Cambridge, Downing St., England CB2 3EH. 44-223-333969, FAX/333992, MA11@PHX.CAM.AC.UK. The Cytological Features Database, Version 9108, is a database of polytene chromosome sites that have been found to bind antibodies to particular Drosophila proteins. The database is maintained by Sally Amero and has been formatted by Michael Ashburner. The formatted form of the database is available from the Indiana server in the directory fly (see previous article for server access). Direct comments, additions or corrections to Sally Amero. The format is as follows: line 1 - cytological position [field 1]/gene name [field 11]/ protein name [field 31]/antibody [field 51] line 2 - comments [if any] [field 11] lines 3 on - references [field 11] It should be quite easy for you to resort this database on another field, e.g. that of the gene. Should you want this and be unable to do it then send an e-mail message to M.A. If there is the demand then the database can be distributed in versions sorted on fields other than cytological location. Sally Amero's original database includes salivary gland puff sites. These have not been included here, but can be made available on demand to Michael Ashburner. *** DIN 4 TECHNICAL NOTES P ELEMENT VECTORS FOR ANALYZING ENHANCER ELEMENTS Keith Wharton, Molecular Biology Institute, Room 306, U. of California, Los Angeles, CA 90024-1570, USA. 213-206-3184, FAX/7286. Three P element vectors have been constructed that contain a weak promoter fused to coding sequences for a nuclear localization signal and a lacZ reporter gene. These constructs are all in the pCaSpeR vector, allowing the selection of transformants using the white minigene. A variety of unique restriction sites are available upstream from the lacZ gene, facilitating the insertion of enhancer sequences - CPLZ: SphI, BamHI, EcoRI; CPLZN: SphI, BamHI, NotI; C4PLZ: SphI, BamHI, SpeI, SfiI, NotI, SstII, KpnI, EcoRI. The effects of these sequences can then be monitored in the intact animal, by examining nuclear beta-galactosidase expression. DNA, restriction maps, and more information are available upon request. *** DIN 4 GENETIC NOTES USEFUL STOCKS FOR P-ELEMENT MUTAGENESIS Kathy Matthews, Indiana Drosophila Stock Center, Dept. of Biology, Indiana University, Bloomington, IN 47405, USA. 812-855- 5782/FAX 2577; MATTHEWK@UCS.INDIANA.EDU or @IUBACS. A variety of stocks useful for P-element mutagenesis are available from the Bloomington stock center. New and/or most widely useful lines are listed below, beginning with the stock number. Ammunition chromosomes #2538 Birm2; ry[506] (Birm2 carries 17 unmarked P elements) #2539 Birm2; TM6/Sb #P20 y w P{w[+]-lacW}3-76a #3697 C(1)RM, y P{w[+]-lacW}5-45fD w P{w[+]-lacW}4-5fP P{w[+]-lacW}3-52d P{w[+]-lacW}3-76a/+/Y #3709 y P{w[+]-lacW}5-45fD w P{w[+]-lacW}4-5fP P{w[+]-lacW}3-52d P{w[+]-lacW}3-76a #3710 O/C(1;Y), y P{w[+]-lacW}5-45fD w P{w[+]-lacW}4-5fP P{w[+]-lacW}3-52d P{w[+]-lacW}3-76a y[+]/C(1)RM, y pn #3711 C(1)RM, y P{w[+]-lacW}5-45fD w P{w[+]-lacW}4-5fP P{w[+]-lacW}3-52d P{w[+]-lacW}3-76a/w[1118]/Y Sources of transposase #406 Dr/TMS, Sb P{ry[+]-delta2-3}99B (TMS = MKRS + In(3R)87A-B;97F-98A) #1610 w; Dr/TMS, Sb P{ry[+]-delta2-3}99B #1798 w; ry[506] Sb P{ry[+]-delta2-3}99B/TM6B #2383 TM2, ry P{ry[+]-delta2-3}/TMS, Sb P{ry[+]-delta2-3} #2534 ry[506] P{ry[+]-delta2-3}99B #2535 CyO/Sp; ry[506] Sb P{ry[+]-delta2-3}99B/TM6, Ubx #2536 w; ry[506] P{ry[+]-delta2-3}99B #2540 C(1)DX, y f; ry[506] P{ry[+]-delta2-3}99B #3612 w; Sp/CyO; ry[506] P{ry[+]-delta2-3} Dr/TM6 #3629 w; Sp/CyO; ry[506] Sb P{ry[+]-delta2-3}99B/TM6B #3664 y w; ry[506] Sb P{ry[+]-delta2-3}/TM6 #3712 T(Y;3)TMS, Sb P{ry[+]-delta2-3}99B/+ References: #2534-2536, #2538-2540, Robertson et al., 1988, Genetics 118:461; #P20, #3709, Bier et al., 1989, Genes & Devel. 3:1273. *** DIN 4