DROSOPHILA INFORMATION NEWSLETTER Volume 7, July 1992 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 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 should be submitted by e-mail. Figures and photographs cannot be accepted at present. Send technical notes to Carl Thummel and all other material 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. To maintain the original format when printing DIN, use Courier 10cpi font on a standard 8.5" x 11" page with 1" margins. 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 *** 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 DIN, 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 Vol. 7 TABLE OF CONTENTS >Introduction to Drosophila Information Newsletter >How to subscribe to the Newsletter >TABLE OF CONTENTS >ANNOUNCEMENTS >Educating non-population geneticists >Population biology meeting >Enhancer-trap stocks available >REQUESTS FOR MATERIALS >Old Redbook sought >Updates/corrections to new Redbook >Natural orcein >DATABASES/COMPUTING >Morphological mutants database *** AN OPEN LETTER FROM JAMES CROW: There is a growing concern among population geneticists regarding their communications with non-population geneticists, a problem which is perceived to affect the process of reviewing research grant applications. An ad hoc committee has been formed to prepare a series of mini- reviews that set forth the strengths and accomplishments of the various subjects and methods in population genetics. This is seen as a useful exercise for those in the field, as well as providing information for outsiders who must form judgements about research projects. The effort is being coordinated by Bruce Weir; other members of the committee are Francisco Ayala, Allan Campbell, Brian Charlesworth, Michael Clegg, Marcus Feldman, Daniel Hartl, Mary Claire King, Martin Krietman, Charles Langley, Richard Lewontin, Glenys Thomson, and Bruce Walsh. For information on submitting material for these reviews before the July 31, 1992 deadline, please contact: Dr. Bruce Weir, Dept. of Statistics, North Carolina State U., Raleigh, NC 27695-8203, (919)515-3574, FAX/7591. *** DROSOPHILA POPULATION BIOLOGY MEETING, to be held Monday 21 to Thursday 24 September 1992, Leeds University, Yorkshire, UK. This meeting, organized by the Drosophila Population Biology Unit (Professor Bryan Shorrocks) will cover wild Drosophila populations and their interactions with the environment. For further details contact the organizer Dr. Andrew Davis PAB6AWD@UK.AC.Leeds.CMS1 (or fax +44 532 332909). *** ENHANCER-TRAP STOCKS AVAILABLE Dan Lindsley has made a set of 232 enhancer-trap stocks carrying autosomal mini-w[+] inserts (Bier et al., Genes & Dev. 3:1273) available through the Bloomington stock center. The stocks were generated by undergraduate students and are a random set (i.e., nothing has been removed based on phenotype). 84 lines (42 on 2, 42 on 3) express lacz in the testis. Of the remaining 148 lines, 80 have inserts on 2 and 68 have inserts on 3. These stocks will be maintained by the stock center for a limited time. If you are interested in screening these lines you should plan to obtain them from the stock center within the next 18 months. *** REQUESTS FOR MATERIALS REDBOOK WANTED Roger J. Harris, Dept. Biology, U. of Oregon, Eugene, OR 97403, USA. 503-346-5090, FAX/2364, RJHARRIS@OREGON.UOREGON.EDU. I would like to purchase a used copy of "Genetic variations of Drosophila melanogaster" by Lindsley & Grell (1968), Carnegie Institute Publications No. 627. I will pay any reasonable price. If your lab has a spare copy please contact me. *** UPDATES AND CORRECTIONS TO THE REDBOOK Kathy Matthews, Dept. of Biology, Indiana U., Bloomington, IN 47405. 812-855-5782, FAX/2577, MATTHEWK@UCS.INDIANA.EDU. As you probably know, the new Redbook, "The Genome of Drosophila melanogaster" by Dan Lindsley and Georgianna Zimm, Academic Press, San Diego, is now available (call 1-800-321-5068 to order directly from the publisher). Dan and Georgianna have done an admirable job. The book is a pleasure to use, and all of our scientific lives are made easier by having access to the vast amount of information it contains. Producing this volume was a hugh task and future compilations will be increasingly difficult. Dan and Georgianna have passed the curatorial torch on to Michael Ashburner who, for reasons unknowable, is willing to perform this vital service to our community. Nevertheless, Michael cannot do it alone. We as individuals need to take an active role in updating information in our fields of expertise. With the hope of making that a bit easier, I am asking that you submit new/updated/corrected Redbook information to me by e-mail (only!). I will post your information on the stock center file server where it will be available to Michael and the rest of us as well. Corrections, new mutations, and other appropriate information that you provide will also be published in DIN. *** NATURAL ORCEIN Michael Ashburner, Dept. of Genetics, U. of Cambridge, Downing St., Cambridge CB2 3EJ, England. 44-223-333969, FAX/333992, MA11@PHX.CAM.AC.UK. Does anyone know a source for Natural Orcein? Gurr's (that is BDH) now only stock synthetic. If you let me know directly then I will broadcast the information in the next issue of the Newsletter. Thank you. *** DATABASES/COMPUTING MORPHOLOGICAL MUTANTS OF DROSOPHILA MELANOGASTER: A PRELIMINARY DATABASE FROM THE `RED BOOK' Roger J. Harris, Dept. of Biology, U. of Oregon, Eugene OR 97403-1210, USA. 503-346-5090, FAX/2364, RJHARRIS@OREGON.UOREGON.EDU. Lindsley and Grell's (1972) `Genetic variations of Drosophila melanogaster', also known as the `Red Book', is a unique tool for geneticists. Besides 3000 or so mutants there are lists for chromosome aberrations, special chromosomes and other genetic variants from a `wild-type' genotype. The mutation data is listed by code, name, location, origin, discoverer, references, phenotype and cytology. The salivary chromosome drawings and accompanying gene map enable the worker to quickly locate a mutant phenotype to a particular chromosomal region. Recently, the `Red Book' has been updated (by Lindsley and Zimm) so the information now includes data since 1972 (Brutlag, pers. comm.). This was recently published as `The Genome of Drosophila melanogaster' and is also available as a draft in recent special DIS issues. The new book is available from the publishers or as text files from GenBank, but as it is free text it is inaccessible for computer surveys. A detailed appendix does not exist (Ashburner, pers. comm.). To classify mutations by effects on particular traits, it is necessary to go through each description that lists phenotypic effects. To do this with the free text would be extremely tedious, so I coded the data to make computer searches more efficient. Towards this aim, I put all the data on 1016 mutations that affect morphology into a database much smaller than that of the free text. This article is to announce the completion of preliminary work on the database. Work remains but the database is available for use by others (details below). Compilation of data into the database: First, I got the updated `Red Book' by file transfer from GenBank via a VAX mainframe computer. Mutations that affect morphology were entered into the database. I used the MSExcel spreadsheet on a Macintosh microcomputer. The information in the database format is much easier to access and manipulate than the free text. The data for each mutation is entered in the same order as in the `Red Book': gene code, gene name, chromosome, position, origin, phenotype and cytology. I included only mutations that affect adult external morphology, so many details in the GenBank data are omitted. Mutations that affect internal adult structures are excluded, as are behavioral, biochemical and embryonic mutants and mutations which influence the expression of other mutations, such as those at suppressor loci. For brevity, alleles beside the first listed in the `Red Book' are also omitted from the database. This will be a problem for investigations of pleiotropic effects or if mutations for specific experimental purposes are needed. I should emphasize the database will be expanded. The effects for alleles other than the first listed, as well as other omitted data are in separate databases that are incomplete at the time of writing. Some mutations in the original `Red Book' are not listed in the new version because they were found to be part of a gene complex and so were subsumed under the name of the complex (e.g., scute is now listed under ASC, achaete-scute complex, rather than sc). In my database, I included the mutations from the first book and noted to which complex they belonged. The corresponding variant listed under the complex is cross-referenced. For example, the entry for the `allele' scute at the ASC complex is under scute and not ASC, but the scute entry notes it is a part of the ASC complex. The important difference between my database and the free text is that the phenotypic effects of the mutations are coded. This was to lessen the amount of memory occupied by the data. The total amount of memory occupied is 181K, whereas the original listing needs 4.2 MBytes (S. Maulik, pers. comm.). The coding speeds up data entry and forces the reduction of descriptions to a minimum. Thus there are no synonymous or redundant terms in the code. There are a total of 149 different effects listed. Single effect descriptors are reduced to three letters by use of the first three consonants (e.g., white is `wht'). This was to have a code which was shorter than the word itself, yet still intuitively meaningful. I did not use a numerical code because of the latter condition. The body parts affected by the mutations were coded with four letters and numbers. Table 1 lists the major body part groups. The list of all coded morphological structures is too large to include here but all those pictured in the fly drawings in Lindsley and Grell (1972: 472) are used in the database. The aim for coding the body parts was to have a hierarchical structure to the code. The body part affected is the first letter of the code which is always upper case. The second letter is the trait group which the mutation affects. The third and fourth letters (the fourth position may be a number) are unique identifiers for a particular body part. For example, "Wv15" is the fifth (5) longitudinal (1) wing (W) vein (v). Mutational effects on different body segments are separated by a solidus (/) and trait groups within a segment, by a comma. Multiple effects on the same trait are separated by a comma. Here is a typical example of an entry. The entry for the effects of the mutation bowed: "W bwd dwn, sml/B sml/E blg". Note that the part affected is listed first, the result of the mutation second. The wings (W) are bowed (bwd) down (dwn) and smaller (sml) than normal. The body (B) size is reduced (sml) and the eyes are bulging (blg). There is also a `Notes' column which is for data on viability, fertility and development time. This column may include information about other phenomena which may influence expression such as gene interaction and temperature effects. For bowed these are: "OL/V 75%", which means the mutant phenotype overlaps (OL) the wild-type and that viability (V) is 75% of the wild-type. Use of the database: While the code was established I compiled a dictionary. This allows mutations to be studied for particular phenotypic effects. For example, if I wanted to know which mutations caused pink eyes, I would look up `pink' in the dictionary and find the code "pnk", then do a computer search for the string, "pnk". With this, it is possible to quickly find mutants at different loci with similar phenotypic effects. The converse dictionary can be used to look up any code for the right description. With the dictionary the data can be quickly searched for information on specific effects, body parts affected or important effects on fitness. My immediate aim is to update Braver's (1956) list of mutations by body parts affected. With the database I can construct a list with a more detailed hierarchy of parts affected and greatly expand the original list. Limitations of the data set: There are some limitations that arise from the way the data is structured. The effects are not listed separately if there are multiple effects on the same trait. In the above example, if I wanted to search for mutations that cause smaller wings, the search string "W sml" would not have found bowed. Instead one would have to use the string ",sml" (comma included) and then omit entries which did not have W preceding sml. This flaw in the database can be amended by adding the trait code before the effect code. In the example, this would give "W bwd dwn, W sml/B sml/E blg". This would increase the amount of memory taken but simplify searches for entries with a particular code. I will incorporate this modification into a second version of the database. A more basic limitation is the loss of information necessary to streamline the database. As noted above, for brevity I omitted descriptions of alleles beside the one first listed in the `Red Book'. This is usually the first allele found at a locus. Certain non-morphological effects of listed alleles are not in the list. Variation in description is also lost. For example, quantitative differences of allelic effects are excluded, so a description of small wings will be "W sml" whether the effect is strong or weak. Improvements could be made to the biological basis of the database structure. For example, the hierarchical groups of traits are arbitrary and for convenience. Thus, mutations that affect eyes are in a separate group from those that affect other head structures, even though eyes are part of the head. So the hierarchical groups do not correspond to imaginal discs or homeotic segments, although it should be easy in principle to modify the database accordingly. These shortcomings may be important in some applications but I think the database will be useful for studies which need a general survey of morphological mutational effects. Availability: To obtain the database send a MacIntosh formatted 3 1/2-inch floppy disk (DD) to the author with return postage. The database will soon be available as a text file by anonymous FTP. The data will include the dictionaries as well as the listing of mutations. Acknowledgements: I thank Kathy Matthews and I. L. Heisler for helpful comments on the manuscript. Table 1. List of major body parts listed in the `Red Book' database. The list below does not include the specific structures within body parts, (e.g., orbital bristles on head) which are in the database. Body part: head, antenna, eyes, thorax, legs, wings, abdomen, cuticle, body, bristles, hairs. Non-morphological traits: lethality, viability, fertility, development, sterility. ***