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Model &
other Organisms Glossary Evolving terminology for emerging
technologies Suggestions? Comments? Questions? mchitty@healthtech.com Last revised December 26, 2001
The preeminent French scientist and 1965 Nobel laureate Jacques Monod famously remarked, "What's true for E. coli is true for an elephant." http://www.cshl.org/public/releases/press121801.html amoeba: See Dictyostelium discoideum animal model: A laboratory animal useful for medical research because it has specific characteristics that resemble a human disease or disorder. Scientists can create animal models, usually laboratory mice, by transferring new genes into them. [NHGRI] With the ongoing sequencing of the genomes of several animal species ranging from Drosophila and zebra fish to rats and mice, their simpler genomes have given researchers a tool for exploring gene function as applied to the more extensive and complex human genome. The use of genetically engineered rats and mice to explore the function of genes and for the selection of appropriate drug targets holds great promise in speeding the development of valuable therapies. These models provide effective ways to test new drug compounds, as well as aid in our understanding of specific disease processes. Application of Genomics to Animal Models for Pharmaceutical Studies Oct. 11-12, 2001, Cambridge, MA Contrast with model organisms. Arabidopsis thaliana: The first plant genome to be completely sequenced. Not of agricultural significance, but a model system for plant development, genetics and physiology. Nature 408 (6814): 816-826, 14 Dec. 2000 Arabidopsis links Caenorhabditis elegans (C. elegans) : Nematode worm, a model organism, the first multicellular organism to have a completely sequenced genome (97 megabases of DNA with 19,099 predicted protein-coding genes) as of December 11 1998. [ C. elegans Sequencing Consortium "Genome Sequence of the Nematode C. Elegans" Science 282:2012 Dec 11, 1998] C. elegans Links C. elegans Gene Knockout Consortium, University of British Columbia, Canada http://elegans.bcgsc.bc.ca/knockout.shtml Trans NIH C. elegans Initiative http://www.nih.gov/science/models/c_elegans/ WormBase http://www.wormbase.org/ or http://wormbase.sanger.ac.uk Worm Chip Directory, Stanford University, US http://cmgm.stanford.edu/~kimlab/wmdirectorybig.html Worm PD, http://www.proteome.com/DB-demo/intro-to-WormPD.html Dictyostelium discoideum (amoeba): A soil- living amoeba, many of the known genes show a high degree of sequence similarity to genes in vertebrate species. Dictybase, Northwestern Univ. US http://dictybase.org/ Part of the Virtual Library Trans NIH Dictyostelium discoideum http://www.nih.gov/science/models/d_discoideum/ Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes. [MeSH] Despite the fact that Drosophila is a much studied organism, Celera (working with BDGP Berkeley Drosophila Genome Project annotators) identified thousands of new genes in commercially important protein families such as kinases, ion channels, secreted proteins, and G-protein coupled receptors during the sequencing phase. [CHI Functional Genomics] Drosophila Genome special section in Science 287: 2181-2225, 2272-2274, March 24, 2000. Drosophila melanogaster Links FlyView, Universitat Muenster, Germany http://pbio07.uni-muenster.de/ Image database for Drosophila gene expression. Interactive Fly, Society of Developmental Biology http://sdb.bio.purdue.edu/fly/aimain/1aahome.htm Trans NIH Fly Initiative, NIH, US http://www.nih.gov/science/models/fly/ WWW Virtual Library: Drosophila http://ceolas.org/fly/ E. coli Escherichia coli: Common bacterium that has been studied intensively by geneticists because of its small genome size, normal lack of pathogenicity, and ease of growth in the laboratory. [DOE] The archetypal model organism...has revealed many fundamental principles of cell metabolism, macromolecular synthesis, and gene regulation. It is better characterized than any other cell. But there remains so much more to learn. [Kenneth Rudd 'New tools for an old workhorse" Nature Biotechnology 18: 1241-1242 Dec. 2000] E. coli links E. coli genome Nature 409 (6819), 529-533 Jan. 25, 2001. Profiling of Escherichia coli chromosome (PEC), SHared Information of GENetic Resource, National Institute of Genetics, Japan http://www.shigen.nig.ac.jp/ecoli/pec/index.html Database has been constructed to compile any relevant information that could help to characterize the E. coli genome, especially with respect to discovering the function of each gene. fly: See Drosophila. frog: See Xenopus. GMO Genetically Modified Organism: Related term transgenic. Gene OntologyTM Consortium: Functional
genomics glossary model organisms: Model organisms are of key importance in both creating databases of gene sequences for homology searching, and as platforms for investigating the biology of genes of interest. Over the last few years, the use - and sophistication - of such models has increased substantially. Findings from the recent publications by the Human Genome Project and Celera Genomics support that homology between human and animal- model genes and proteins is significant, particularly among vertebrate species. Still, the conservation of genes and genetic pathways between humans and invertebrate organisms is great enough that some of these organisms have become critical model systems. [CHI Target Validation] Because they are amenable to linking genes with cellular and physiological responses, simple model organisms are expected to be highly useful in understanding evolution and development with a biomedical perspective. [CHI Breaking Bottlenecks] Related terms knockdown, knockin, knockout Functional genomics glossary Model organisms links Trans-NIH Model Organisms Initiative, NIH, US http://www.nih.gov/science/models/ WWW Resources for Model Organisms, Pam M. Gannon HMS Beagle July 24, 1998 http://news.bmn.com/hmsbeagle/35/webres/insitu.htm Reviews of websites for E. coli, yeast, C. elegans, Drosophila, and mouse. WWW Virtual Library Model Organisms http://ceolas.org/VL/mo/ WWW Virtual Library
Genetics http://www.ornl.gov/TechResources/Human_Genome/vl.html mouse Mus musculus: Having long been used as a model for genetic studies, offers a highly characterized genetic system with many established inbred strains available for study. Within the best mapped homologous mouse and human regions, the presence and location of specific genes and gene families can be predicted in one species based on mapping results obtained in the other. [Human Genome News, Oak Ridge National Lab "Leaping across genomes" April - June 1996] http://www.ornl.gov/hgmis/publicat/hgn/v7n6/08mice.html Mouse Links Mouse Genome Informatics, Jackson Lab, US http://www.informatics.jax.org/ Mouse Genome Informatics Glossary, Jackson Lab, US http://www.informatics.jax.org/userdocs/glossary.shtml#transversion Mouse Phenome Project, Jackson Lab, US http://aretha.jax.org/pub-cgi/phenome/mpdcgi?rtn=docs/home Trans NIH Mouse Initiative, NIH, US http://www.nih.gov/science/models/mouse/ A central information resource for mouse genomics. Other mouse databases are listed in Databases & software directory. murine: mouse rat Rattus Norvegicus: Used extensively as a model organism for studying normal and disease processes in the human, primarily because of an extensive body of knowledge of rat physiological mechanisms, a significant number of rat models that mimic human diseases, the ease of breeding the rat, and the ability to generate inbred congenic and consomic rat strains. Once genes are identified in rats, pathophysiological mechanisms can be elucidated lending clues to the identification of human genetic counter- parts. [Rat Genome Database Request For Applications, NIH April 1999] http://grants.nih.gov/grants/guide/rfa-files/RFA-HL-99-013.html A rat genome project is underway, with a public- private coalition composed of NHGRI, NHLBI, people at Baylor College of Medicine, Celera Genomics, Genome Therapeutics Corp, with other organizations also participating. [Eliot Marshall "Rat Genome spurs an unusual partnership" Science 291: 1872 Mar. 9, 2001] Rat Links Rat Genome Resources, NCBI, US http://www.ncbi.nlm.nih.gov/genome/guide/R_norvegicus.html Rat Genome Data, Jackson Lab, US http://www.informatics.jax.org/rat/index.shtml Other rat databases are listed in Databases & software directory. Saccharomyces cerevisae (S. cerevisae): Yeast, perhaps the best understood eukaryotic organism at the molecular and cellular levels. However [forward genetics] had, prior to the systematic sequencing of the yeast genome (completed in 1996) resulted in the discovery of less than half of yeast genes. Now the yeast genomics community has turned to a large- scale, high- throughput approach to determining gene function, largely based on reverse genetics. Since yeast is the first eukaryotic model organism whose genome has been completely sequenced, many of the issues currently being faced by the yeast genomics community will eventually be of concern to people working with other organisms, including humans … There are also parallel efforts to produce an annotated yeast genome database, and a pilot proposal to construct a human annotated database. [CHI Functional genomics] Yeast can in certain cases serve as a model of human disease ... The general rationale for this strategy is that many core cellular processes (as opposed to processes involved in differentiation and development, integration of tissues and organ systems, and activities of specialized cells and tissues) are conserved between yeast and mammals. In fact, many molecules and pathways that are known to be involved in processes that go awry in cancer (e.g., the cell cycle and its control, DNA repair, telomere maintenance) were either first discovered by yeast researchers, or research in yeast made major contributions to their understanding. [CHI Target Validation] Saccharomyces cerevisae Links SGD Saccharomyces Genome Database, Stanford Univ., US http://genome-www.stanford.edu/Saccharomyces/ SGD Glossary Terms, Stanford Univ., US http://genome-www.stanford.edu/Saccharomyces/help/glossary.html Saccharomyces Genome Deletion
Project WWW Virtual Library: Saccharomyces http://genome-www.stanford.edu/Saccharomyces/VL-yeast.html Other yeast databases are listed in Databases & software directory. slime mold: See Dictyostelium discoideum species: Functional genomics glossary transgenic: An experimentally produced organism in which DNA has been artificially introduced and incorporated into the organism’s germ line, usually by injecting the foreign DNA into the nucleus of a fertilized embryo. [NHGRI] Plants can be transgenic as well as animal, though the field is not as highly developed. Transgenics can be a means of production as well as a way of systematic experimenting with knockouts. Related terms knockdown, knockin, knockout; crop genomics Genomics glossary virtual organism: If the genome sequence of an organism has been established, theoretically an in silico model may be reconstructed to assemble the components of the metabolic and genetic networks into a functional, virtual organism. Escherichia coli is a suitable first organism with which to attempt the creation of a virtual organism. Igor Goryanin "In Silico E. Coli: Development, Validation, and Analysis of the Whole Cell Model" Metabolic Profiling Dec. 3-4, 2001 Chapel Hill, NC worm: See Caenorhabditis elegans (C. elegans) Xenopus frog: The Xenopus embryo has long served as a major model for the study of embryonic development because of its numerous advantages, including external development, large size, identifiable blastomeres, and its ability to withstand extensive surgical intervention and culture in vitro. These advantages enable extensive investigation of the earliest embryonic patterning events. [Xenopus Initiative, NIH "Advantages of xenopus research"] http://www.nih.gov/science/models/xenopus/advantages.html Xenopus Links Xenbase A Xenopus Resource http://xenbase.org/ Xenopus group, Univ. of Dundee, Scotland http://www.dundee.ac.uk/xenopus/ yeast: If not otherwise specified generally refers to Saccharomyces cerevisae. Other species of yeast, including Schizosaccharomyces pombe are also studied. zebrafish Danio rerio: A species of North American fishes of the family Cyprinidae. They are used in embryological studies and to study the effects of certain chemicals on development. [MeSH] The zebrafish is a powerful model system for the genetic analysis of vertebrate embryogenesis, organ development, and disease. Its unique power is its tractable, phenotype driven mutation screens and readily accessible transparent embryos. Because of its facile forward genetics, zebrafish accelerates gene discovery; because of its accessible embryos, it promotes deep understanding of gene function; because of its phylogenetic position, it informs mechanisms of genome conservation. [Zebrafish Breakout Group, Non- Mammalian Models Workshop, NIH Feb. 1999] http://www.nih.gov/science/models/nmm/appb4.html Zebrafish breed quickly and remain transparent. Zebrafish Links Zebrafish Information Network, University of Oregon, US http://zfin.org/ Zebrafish Anatomical dictionary, Zebrafish Information Network http://zfin.org/zf_info/anatomy/dict/sum.html Zebrafish Nomenclature http://zfin.org/zf_info/nomen_comm.html BIOSIS Controlled Vocabulary Lists http://www.biosis.org/training_support/reference_shelf/list_toc.html Mouse Genome Informatics Glossary, Jackson Lab, US http://www.informatics.jax.org/userdocs/glossary.shtml#transversion SGD Glossary Terms, Stanford Univ., US http://genome-www.stanford.edu/Saccharomyces/help/glossary.html Zebrafish Anatomical dictionary, Zebrafish Information Network http://zfin.org/zf_info/anatomy/dict/sum.html Zoological Record Thesaurus, BIOSIS, 1999 http://www.biosis.org/free_resources/zr_taxhier.html |
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