Zebrafish in the Net

Resource INTERNET Zebrafish in the Net Zebrafish in the Net In recent years we have witnessed an to map embryonic lethal or adult visible single uniform interface is needed. explosion in our understanding of how mutations by tetrad analysis2. The cur- Tools should be available for compar- genes regulate developmental and physio- rent map contains about 1800 markers. ing maps generated with various logical processes, largely based on work Because the linkage map is approxi- zebrafish mapping panels and for com- from a few model genetic organisms. mately 3000 cM long, and the genome paring zebrafish maps to maps from The zebrafish is the newest of these is about 1.7 3 109 base pairs, the aver- other species. Mapping data should be model organisms. Powerful techniques age inter-marker interval is about integrated with other information about allow efficient generation and recovery 1.7 cM or 0.9 kb. The National zebrafish genes and mutations. For of zebrafish mutations affecting genes Institutes of Health have recently example, a single click should take users that regulate developmental patterning, funded a zebrafish genome initiative to from a gene symbol on a graphical map organogenesis, physiology and behav- increase the resolution of the map to to comprehensive information about the ior, and the transparency of zebrafish 0.3 cM or better. gene sequence, the expression patterns embryos aids cellular analysis of gene of the gene, including images of repre- function. The need for an integrated sentative photomicrographs, PCR database primers for amplifying and mapping the The genetic map is a crucial The remarkable success of research gene, orthologs in other species, and tool for relating gene structure using zebrafish has generated a serious publications describing the gene. and function information access problem. Although Genetic screens in several laboratories the use of zebrafish in genetic research is The birth and design of ZFIN have identified over 7000 zebrafish relatively new, the number of labora- To meet these needs, the Zebrafish mutations and many more are being tories and the amount of data generated Information Network (ZFIN), a central- isolated in a growing number of new by these laboratories are increasing ized database for the zebrafish research screens in laboratories around the community was established8. It inte- world. For a thorough understanding of grates experimental data and infor- the processes disrupted by mutations, BOX 1. Online information about mation drawn from our earlier WWW we must study not only the mutant site (http://zfish.uoregon.edu) within an phenotype, but also learn the structure zebrafish bioinformatics object-relational database9. The data- of the protein product encoded by that base design team10 is composed of both mutated gene, its normal function dur- Zebrafish database project computer scientists and biologists, and ing development, and how the expres- http://zfish.uoregon.edu/zf_info/dbase/db.html a database administrator coordinates sion of the gene is regulated. To achieve communications among zebrafish lab- these goals, we must detemine the gene ZFIN oratories worldwide. ZFIN has been sequence by molecular cloning and http://zfish.uoregon.edu designed to provide a full range of develop molecular probes for the gene resources including the definitive collec- ZFIN data model and its transcripts. Zebrafish researchers http://zfish.uoregon.edu/ZDB/PAPERS/ZFIN_ tion of information about zebrafish use two main strategies for cloning DataModel/data_model.html genes, mutations, genetic maps, and the mutated genes, the candidate gene research community. These different approach and the positional cloning Zebrafish laboratory servers types of data are completely integrated approach. Both strategies require a http://zfish.uoregon.edu/zf_info/www_sites.html with each other and cross-referenced high-resolution genetic linkage map. with records in other databases. Data A genetic map has been established produced by individual laboratories, for zebrafish; each chromosome is rep- rapidly. The information already far particularly mapping laboratories, are resented by a single linkage group1–3. exceeds the ability of individual scien- usually collected and organized in local Among vertebrates, only human4, tists to track and organize it, thus databases and then are uploaded on a Monte Westerfield* mouse5, rat6,7 and zebrafish have closed requiring the use of computer data- regular basis to ZFIN to maintain a monte@uoneuro. linkage maps. The significance of this bases. For example, as more mutant comprehensive integrated dataset. uoregon.edu advance is that any newly discovered lines become available, information End-user usability has been a central mutation can be placed at a unique about these lines grows quickly; studies goal of ZFIN design. The ultimate use- Eckehard Doerry† location on the map. Genes that map of each mutant generate a description of fulness and usability of the ZFIN data- [email protected] nearby serve as candidates for the its phenotype, genetics, inheritance, base depend upon a careful assessment Sarah Douglas† mutated gene whereas nearby DNA map location, interactions with other of the requirements of the users, douglas@cs. polymorphisms can be used to generate genes, etc. Similarly, many markers detailed testing of prototypes by uoregon.edu DNA probes for positional cloning of have been added to the map recently biological researchers, and analysis of the gene responsible for the mutant and this number will increase dramati- users’ interactive behavior while using * Institute of phenotype. cally in the near future because of the the database. From the outset, both Neuroscience, Two methods have been developed zebrafish genome initiative. Because biologists and computer scientists par- † Department of to map zebrafish mutations quickly. map data are being generated in several ticipated as members of the design Computer and One of the methods utilizes DNA pool- different laboratories on different map- team. Database development followed Information ing protocols to identify DNA polymor- ping panels, the data are heterogeneous the basic steps of user-centered11 and Science, phisms closely linked to mutations in and distributed. participatory12 design, adapting these University of haploid embryos1. The other method To expedite research, a comprehen- methodologies to support input from Oregon, Eugene, exploits the high amount of chromo- sive database that seamlessly integrates collaborating designer-scientists in OR 97403, USA. somal interference in zebrafish meiosis these diverse mapping data within a zebrafish laboratories around the 248 TIG June 1999, volume 15, No. 6 0168-9525/99/$ – see front matter © 1999 Elsevier Science All rights reserved. PII: S0168-9525(99)01741-2 Zebrafish in the Net INTERNET Resource world10. The computer scientists inter- represented in the database are information in other species-specific viewed zebrafish researchers, partici- described in a data model document databases are still lacking. Ultimately, pated in experiments, and attended written to be intelligible to both com- ZFIN should allow researchers to access research talks at laboratory meetings puter scientists and biologists13. and integrate data from other species on and professional meetings, thus learning demand, displaying the data within the how biologists conduct research and the familiar ZFIN interface, rather than relationship of this research to the data- The future of ZFIN forcing scientists to link to an unfamil- base. The biologists used questionnaires A major challenge for zebrafish bio- iar database. The ZFIN design team is to poll the research community to learn informatics in the near future is better currently working with other database what kinds of information the database integration of zebrafish data with infor- developers to establish uniform formats should contain and together with the mation from other databases. ZFIN for data types common to studies of computer scientists, they formulated already extensively links descriptions of different species. This is a first step how the database should support the zebrafish genes, markers, and probes towards the exciting future goal of study of specific biological problems. with records in sequence databases like cross-species studies facilitated by inter- Specifications for how data are logically GenBank, SwissProt, etc., but links to linked (interoperable) databases. References and URLs 7 Jacob, H. et al. (1995) A genetic linkage map of the laboratory rat, Rattus novegicus. 1 Postlethwait, J. et al. (1994) A genetic map for the zebrafish. Science 264, 699–703 Nat. Genet. 9, 63–69 2 Johnson, S.L. et al. (1996) Centromere-linkage analysis and consolidation of the 8 Meeting reference, http://zfish.uoregon.edu/zf_info/dbase/mtgsum.html zebrafish genetic map. Genetics 142, 1277–1288 9 Westerfield, M. et al. (1997) An on-line database for zebrafish development and 3 Knapik, E.W. et al. (1996) A reference cross DNA panel for zebrafish (Danio rerio) genetics research. Semin. Cell Dev. Biol. 8, 477–488 anchored with simple sequence length polymorphisms. Development 123, 451–460 10 Doerry (1997) http://zfish.uoregon.edu/ZDB/PAPERS/WWW6/WWW6-97.html 4 Murray, J.C. et al. (1994) A comprehensive human linkage map with centimorgan 11 Newman, W.M. and Lamming, M.G. (1995) Interactive System Design, density. Science 265, 2049–2054 Addison–Wesley 5 Dietrich, W.F. et al. (1994) A genetic map of the mouse with 4,006 simple sequence 12 Schuler, D. and Namioka, A. (1993) Participatory Design: Principles and Practices, length polymorphisms. Nat. Genet. 7, 220–245 Lawrence Erlbaum Association 6 Yamada, J. et al. (1994) A rat genetic linkage map and comparative maps for mouse 13 Westerfield, M. et al. (1998) Zebrafish informatics and the ZFIN database. Method or human homologous rat genes. Mamm. Genome 5, 63–83 Cell Biol. 60, 339–355 http://tto.trends.com Editor: Adrian Bird, Institute for Cell and Molecular Biology at the University of Edinburgh New Technical Tip articles published recently in Technical Tips Online include: ■ First of an impressive core protocol trilogy: Parchaliuk, D. L., Kirkpatrick, R. D., Simon, S. L., Agatep, R. and Gietz, R. D. (1999) Yeast two-hybrid system – screen preparation (http://tto.trends.com) P01616 (coming soon by the same authors: Part (B): Screening procedure, and Part (C): Characterizing positives ■ Riva, P. et al. (1999) A rapid and simple method for the generation of locus-specific probes for fish analysis Technical Tips Online (http://tto.trends.com) T01618 ■ Möller, S. and Edvinsson, L. (1999) A strategy for the generation of RNA competitors in competitive RT-PCR Technical Tips Online (http://tto.trends.com) T01604 New products featured Technical Tips Online include: Technical Tips Online also features press releases on new products. Click on the ‘product news’ button and a simple reader- response facility allows you to e-mail the relevant company for more information. Recently featured new products include: Super Hyb Kit from Molecular Research Center The Super Hyb Kit is a complete hybridization system, including hybridization, pre-hybridization and wash solutions, for use in northern, southern and dot-blot hybridizations. The high sensitivity of the Super Hyb Kit allows detection of rare mRNA in total RNA and eliminates the need to isolate poly A1 RNA. The high-efficiency hybridization systems (HS-114 and HS114F with for- mamide) increase hybridization efficiency by blocking nonspecific binding of probes and enhancing signal intensity. There is no need for addition of salmon sperm DNA during hybridization, and pre- and post-hybridization washes can be performed at room or elevated temperatures. The kit works with radioactive or non-radioactive detection methods and is available in various sizes. Promega UK releases a unique antibody to detect the p85 fragment of PARP Poly(ADP-ribose) polymerase (PARP) has been identified as a substrate for the caspase group of enzymes, which are known to be integral components of programmed cell death (apoptosis). Caspases cleave PARP into 116-kDa and 85-kDa fragments, and the presence of these two products in the cell is a classical hallmark of apoptosis. The new Anti-PARP p85 Fragment pAb from Promega is the only commercially available antibody that can completely distinguish the cleaved fragments of PARP from the uncleaved holoenzyme. This specificity for the cleavage products of PARP makes the new Promega antibody a novel and ideal marker for apoptosis. TIG June 1999, volume 15, No. 6 249