Model organism 19374 219237404 2008-06-14T06:44:49Z DOI bot 6652755 Citation maintenance. Initiated by [[User:Fconaway|Fconaway]]. You can [[WP:DOI|use this bot]] yourself! Please [[User:DOI_bot/bugs|report any bugs]]. [[Image:E coli at 10000x, original.jpg|thumb|right|Electron micrograph of several [[E. coli]] cells]] [[Image:Drosophila melanogaster - side (aka).jpg|thumb|[[Drosophila melanogaster|Drosophila]], one of the most famous subjects for experiments]] A '''model organism''' is a [[species]] that is extensively studied to understand particular [[biology|biological]] [[phenomena]], with the expectation that discoveries made in the organism model will provide insight into the workings of other organisms. In particular, model organisms are widely used to explore potential causes and treatments for human [[disease]] when [[human experimentation]] would be unfeasible or [[bioethics|unethical]]. This strategy is made possible by the [[common descent]] of all living organisms, and the conservation of [[Metabolic pathway|metabolic]] and [[developmental biology|developmental]] pathways and [[genetic material]] over the course of [[evolution]].<ref> {{cite book |last=Fox |first=Michael Allen |title=The Case for Animal Experimention: An Evolutionary and Ethical Perspective |year=1986 |publisher=University of California Press |location=Berkeley and Los Angeles, California |isbn=0-520-05501-2 }}</ref> Studying model organisms can be informative, but we must be careful when generalizing from one organism to another. ==Selecting a model organism== Models are those organisms with a wealth of biological data that make them attractive to study as examples for other species – including humans – that are more difficult to study directly. These can be classed as [[genetic]] models (with short generation times, such as the [[fruitfly]] and [[nematode]] worm), [[experimental]] models, and [[genomic]] models, with a pivotal position in the evolutionary tree <ref>[http://genome.wellcome.ac.uk/doc_WTD020803.html What are model organisms?<!-- Bot generated title -->]</ref>. Historically, model organisms include a handful of species with extensive genomic research data, such as the NIH model organisms.<ref>http://www.nih.gov/science/models/ NIH model organisms</ref> Often, model organisms are chosen on the basis that they are amenable to experimental manipulation. This usually will include characteristics such as short life-cycle, techniques for genetic manipulation ([[inbreeding|inbred]] strains, [[stem cell]] lines, and [[transfection]] systems) and non-specialist living requirements. Sometimes, the genome arrangement facilitates the sequencing of the model organism's genome, for example, by being very compact or having a low proportion of [[junk DNA]] (e.g. [[yeast]], ''[[Arabidopsis]]'', or [[pufferfish]]). When researchers look for an organism to use in their studies, they look for several traits. Among these are size, generation time, accessibility, manipulation, genetics, conservation of mechanisms, and potential economic benefit. As comparative [[molecular biology]] has become more common, some researchers have sought model organisms from a wider assortment of [[Kinship and descent|lineages]] on the [[Tree of life (science)|tree of life]]. ==Use of model organisms== There are many model organisms. One of the first model systems for [[molecular biology]] was the bacterium ''[[E. coli|Escherichia coli]]'', a common constituent of the human digestive system. Several of the bacterial viruses ([[bacteriophage]]) that infect ''[[Escherichia coli|E. coli]]'' also have been very useful for the study of gene structure and [[gene regulation]] (e.g. phages [[Lambda phage|Lambda]] and [[Enterobacteria phage T4|T4]]). However, bacteriophages are not organisms because they lack metabolism and depend on functions of the host cells for propagation. In [[eukaryote]]s, several yeasts, particularly ''[[Saccharomyces cerevisiae]]'' ("baker's" or "budding" yeast), have been widely used in [[genetics]] and [[cell biology]], largely because they are quick and easy to grow. The [[cell cycle]] in a simple [[yeast]] is very similar to the cell cycle in [[human]]s and is regulated by [[homology (biology)|homologous]] proteins. The fruit fly ''[[Drosophila melanogaster]]'' is studied, again, because it is easy to grow for an animal, has various visible congenital traits and has a polytene (giant) chromosome in its salivary glands that can be examined under a light microscope. The [[roundworm]] ''[[Caenorhabditis elegans]]'' is studied because it has very defined development patterns involving fixed numbers of cells, and it can be rapidly assayed for abnormalities. [[Image:TMV.jpg|thumb|right|Electron microphotograph of [[tobacco mosaic virus]] (TMV) particles]] ==Important model organisms== ===Viruses=== [[Virus]]es include: * [[lambda phage|Phage Lambda]] * [[Phi X 174]] - its [[genome]] was the first ever to be sequenced. The genome is a circle of 11 [[gene]]s, 5386 [[base pair]]s in length. *[[Tobacco mosaic virus]] ===Prokaryotes=== [[Image:Bacillus subtilis Spore.jpg|thumb|right|Sporulating ''[[Bacillus subtilis]]'']] [[Prokaryote]]s include: * ''[[Escherichia coli]]'' (''E. coli'') - This common gut bacterium is the most widely-used organism in [[molecular genetics]]. * ''[[Bacillus subtilis]]'' * ''[[Caulobacter crescentus]]'' - a bacterium that divides into two distinct cells used to study [[cellular differentiation]]. * ''[[Mycoplasma genitalium]]'' - a minimal organism * ''[[Vibrio fischeri]]'' - [[quorum sensing]], [[bioluminescence]] and animal-bacterial [[symbiosis]] with [[Hawaiian Bobtail Squid]] *''[[Synechocystis]]'', a photosynthetic [[cyanobacteria]] widely used in [[photosynthesis]] research. *''[[Pseudomonas fluorescens]]'', a soil bacterium that readily diversifies into different strains in the lab. ===Eukaryotes=== [[Eukaryote]]s include: ====Protists==== *[[Protist]]s: :* ''[[Chlamydomonas reinhardtii]]'' - a unicellular [[green alga]] used to study [[photosynthesis]], [[flagella]] and [[motility]], regulation of [[metabolism]], cell-cell recognition and [[Cell adhesion|adhesion]], response to [[starvation|nutrient deprivation]] and many other topics. ''Chlamydomonas reinhardtii'' has a well-studied genetics, with many known and mapped mutants and expressed sequence tags, and there are advanced methods for genetic transformation and selection of genes.<ref>[http://genome.jgi-psf.org/chlamy Chlamydomonas reinhardtii resources at the Joint Genome Institute]</ref> Sequencing of the ''Chlamydomonas reinhardtii'' genome was reported in October 2007.<ref>[http://www.jgi.doe.gov/News/news_10_11_07.html Chlamydomonas genome sequenced] published in Science, [[October 12]], [[2007]]</ref> A ''Chlamydomonas'' genetic stock center exists at [[Duke University]], and an international ''Chlamydomonas'' research interest group meets on a regular basis to discuss research results. ''Chlamydomonas'' is easy to grow on an inexpensive [[Growth medium|defined medium]]. :* ''[[Dictyosteliida|Dictyostelium discoideum]]'' is used in [[molecular biology]] and [[genetics]] (its [[genome]] has been sequenced), and is studied as an example of [[cell communication]], [[differentiation]], and [[programmed cell death]]. :* ''[[Tetrahymena thermophila]]'' - a free living freshwater [[ciliate]] [[protozoan]]. :* ''[[Emiliania huxleyi]]'' - a unicellular marine [[coccolithophore]] alga, extensively studied as a model [[phytoplankton]] species. ====Fungi==== *[[Fungus|Fungi]]: [[Image:Budding yeast tomography.jpg|thumb|Budding [[yeast]] tomography]] :* ''[[Aspergillus nidulans]]'', subject of genetics studies :* ''[[Neurospora crassa]]'' - orange bread [[mold]] (genetic studies of meiosis, metabolic regulation, and circadian rhythm)<ref>Rowland H. Davis: Neurospora. Contributions of a Model Organism. Oxford University Press, Oxford, 2000. ISBN 0-19-512236-4.</ref> :* ''[[Ashbya gossypii]]'', cotton pathogen, subject of genetics studies (polarity, cell cycle) :* ''[[Saccharomyces cerevisiae]]'', baker's [[yeast]] or budding yeast (used in brewing and baking) :* ''[[Schizosaccharomyces pombe]]'', fission yeast, subject of genetic studies ====Plants==== [[Image:Arabidopsis thaliana.jpg|thumb|''[[Arabidopsis thaliana]]'']] *[[Plant]]s: :* ''[[Arabidopsis thaliana]]'', currently the most popular model plant. This herbaceous [[dicot]] is a [[crucifer]], a member of the [[mustard plant|mustard]] family. Its small stature and short generation time facilitates genetic studies, <ref name="TAIR">[http://www.arabidopsis.org/portals/education/aboutarabidopsis.jsp#hist About Arabidopsis on The Arabidopsis Information Resource page ([[TAIR]])]</ref> and many phenotypic and biochemical mutants have been mapped.<ref name="TAIR">[http://www.arabidopsis.org/portals/education/aboutarabidopsis.jsp#hist About Arabidopsis on The Arabidopsis Information Resource page ([[TAIR]])]</ref> Arabidopsis was the first plant to have its [[genome]] [[DNA sequencing|sequenced]].<ref name="TAIR">[http://www.arabidopsis.org/portals/education/aboutarabidopsis.jsp#hist About Arabidopsis on The Arabidopsis Information Resource page ([[TAIR]])]</ref> Its genome sequence, along with a wide range of information concerning ''Arabidopsis'', is maintained by the [[TAIR]] database.<ref name="TAIR">[http://www.arabidopsis.org/portals/education/aboutarabidopsis.jsp#hist About Arabidopsis on The Arabidopsis Information Resource page ([[TAIR]])]</ref> <br />''([[Plant physiology]], [[Developmental biology]], [[Molecular genetics]], [[Population genetics]], [[Cytology]], [[Molecular biology]])'' :*''[[Selaginella moellendorffii]]'' is a remnant of an ancient lineage of vascular plants and key to understanding the evolution of land plants. It has the smallest genome size of any plant reported (~110Mb) and its sequence will be released by the Joint Genome Institute in early 2008. ''([[Evolutionary biology]], [[Molecular biology]])'' :*''[[Brachypodium distachyon]]'' is an emerging experimental model grass that has many attributes that make it an excellent model for temperate cereals. ''([[Agronomy]], [[Molecular biology]], [[Genetics]])'' :*''[[Lotus (genus)|Lotus japonicus]]'' a model [[legume]] used to study the symbiosis responsible for [[nitrogen fixation]]. ''([[Agronomy]], [[Molecular biology]])''[[Image:L gibba2.jpg|thumb|left|''[[Lemna|Lemna gibba]]'']] :*''[[Lemna|Lemna gibba]]'' is a rapidly-growing aquatic [[monocot]], one of the smallest flowering plants. Lemna growth assays are used to evaluate the toxicity of chemicals to plants in [[ecotoxicology]]. Because it can be grown in [[pure culture]], microbial action can be excluded. Lemna is being used as a recombinant [[gene expression|expression system]] for economical production of complex [[biopharmaceutical]]s. It is also used in education to demonstrate [[Exponential growth|population growth curves]]. [[Image:Maize ear.jpg|thumb|right|''[[maize|Zea mays]]'']] :*[[Maize]] (''Zea mays'' L.) is a cereal grain. It is a diploid monocot with 10 large chromosome pairs, easily studied with the microscope. Its genetic features, including many known and mapped phenotypic mutants and a large number of progeny per cross (typically 100-200) facilitated the discovery of [[transposon]]s ("jumping genes"). Many DNA markers have been mapped and the genome is being sequenced. ''([[Genetics]], [[Molecular biology]], [[Agronomy]])'' :*''[[Medicago truncatula]]'' is a model legume, closely related to the common [[alfalfa]]. Its rather small genome is currently being sequenced. It is used to study the symbiosis responsible for nitrogen fixation. ''([[Agronomy]], [[Molecular biology]])'' :*''[[Nicotiana tabaccum cv. BY-2|Tobacco BY-2 cells]]'' is suspension [[cell culture|cell line]] from [[tobacco]] ''(Nicotiana tabaccum)''. Useful for general plant physiology studies on [[cell (biology)|cell]] level. Genome of this particular [[cultivar]] will be not sequenced (at least in near future), but sequencing of its wild [[species]] ''Nicotiana tabaccum'' is presently in progress. ''([[Cytology]], [[Plant physiology]], [[Biotechnology]])'' :*[[Rice]] ''(Oryza sativa)'' is used as a model for [[cereal]] biology. It has one of the smallest genomes of any cereal species, and sequencing of its genome is finished. ''([[Agronomy]], [[Molecular biology]])'' :*''[[Physcomitrella patens]]'' is a [[moss]] increasingly used for studies on development and [[molecular evolution]] of plants.<ref name="Rensing">Rensing, S. A., Lang, D., Zimmer, A. D., Terry, A., Salamov, A., Shapiro, H. et al. (2008). [http://www.sciencemag.org/cgi/content/abstract/319/5859/64 The physcomitrella genome reveals evolutionary insights into the conquest of land by plants.] Science, 319(5859), 64-69.</ref> It is so far the only [[non-vascular plants|non-vascular plant]] (and so the only "[[cladistics#Definitions|primitive]]" plant) with its genome completely sequenced.<ref name="Rensing">Rensing, S. A., Lang, D., Zimmer, A. D., Terry, A., Salamov, A., Shapiro, H. et al. (2008). [http://www.sciencemag.org/cgi/content/abstract/319/5859/64 The physcomitrella genome reveals evolutionary insights into the conquest of land by plants.] Science, 319(5859), 64-69.</ref> ''([[Plant physiology]], [[Evolutionary biology]], [[Molecular genetics]], [[Molecular biology]])'' :*''[[Populus]]'' is a genus used as a model in forest genetics and woody plant studies. It has a small genome size, grows very rapidly, and is easily transformed. The genome sequence of [[Poplar]] ([[Populus trichocarpa]]) sequence is publicly available. :*See also ''[[Model organism#Protists|Chlamydomonas reinhardtii]]'', above under Protists. ====[[Animal]]s==== =====[[Invertebrates]]===== [[Image:Caenorhabditis elegans.jpg|thumb|[[Caenorhabditis elegans]]]] :* ''[[Arbacia punctulata]]'', the purple-spined [[sea urchin]], classical subject of embryological studies :* ''[[Aplysia]]'', a sea slug, whose ink release response serves as a model in [[neurobiology]] and whose [[growth cones]] serve as a model of [[cytoskeletal]] rearrangements. :* ''[[Caenorhabditis elegans]]'', a [[nematode]], usually called ''C. elegans''<ref> Riddle, Donald L.; Blumenthal, Thomas; Meyer, Barbara J.; and Priess, James R. (Eds.). (1997). ''C. ELEGANS II''. Woodbury, NY: Cold Spring Harbor Press. ISBN 0-87969-532-3. [http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=ce2.TOC Full text available on-line].</ref> - an excellent model for understanding the genetic control of development and physiology. ''C. elegans'' was the first multicellular organism whose genome was completely sequenced :* ''[[Ciona intestinalis]]'', a sea squirt :* ''[[Drosophila]]'', usually the species ''[[Drosophila melanogaster]]'' - a kind of [[Drosophilidae|fruit fly]], famous as the subject of genetics experiments by [[Thomas Hunt Morgan]] and others. Easily raised in lab, rapid generations, mutations easily induced, many observable mutations. Recently, Drosophila has been used for neuropharmacological research<ref>{{cite journal | author=Manev H, Dimitrijevic N, Dzitoyeva S. | journal=Trends Pharmacol. Sci. | title=Techniques: fruit flies as models for neuropharmacological research. | volume=24 | issue=1 | pages=41–43 | year=2003 | url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12498730&query_hl=1 | doi = 10.1016/S0165-6147(02)00004-4 <!--Retrieved from CrossRef by DOI bot-->}}</ref>. ''([[Molecular genetics]], [[Population genetics]], [[Developmental biology]])''. :* ''[[Euprymna scolopes]]'', the Hawaiian bobtail squid, model for animal-bacterial [[symbiosis]], [[bioluminescence|bioluminescent]] [[vibrio]]s :*''[[Hydra (genus)]]'', a [[Cnidarian]], is the model organism to understand the evolution of bilaterian body plans :* ''[[Loligo pealei]]'', a squid, subject of studies of nerve function because of its giant axon (nearly 1 mm diameter, roughly a thousand times larger than typical mammalian axons) :*''[[Pristionchus pacificus]]'', a roundworm used in evolutionary developmental biology in comparative analyses with ''C. elegans'' :* [[Stomatogastric nervous system|Stomatogastric ganglion]] of various [[arthropod]] species; a model for [[motor pattern generation]] seen in all repetitive motions :* ''[[Strongylocentrotus purpuratus]]'', the purple [[sea urchin]], widely used in developmental biology :* ''[[Symsagittifera roscoffensis]]'', a [[flatworm]], subject of studies of bilaterian body plan development :* ''[[Tribolium castaneum]]'', the flour beetle - a small, easily kept [[darkling beetle]] used especially in [[behavioural ecology]] experiments =====[[Vertebrates]]===== [[Image:Lightmatter lab mice.jpg|thumb|Laboratory [[House mouse|mice]]]] :* ''[[Cavia porcellus]]'', the [[guinea pig]], used by [[Robert Koch]] and other early bacteriologists as a host for bacterial infections, hence a byword for "laboratory animal" even though less commonly used today :* [[Chicken]] (''Gallus gallus domesticus'') - used for developmental studies, as it is an [[amniote]] and excellent for micromanipulation (e.g. tissue grafting) and over-expression of gene products :* [[Cat]] (''Felis cattus'') - used in neurophysiological research :* [[Dog]] (''Canis lupus familiaris'') - an important respiratory and cardiovascular model :* [[Hamster]] - first used to study kala-azar ([[leishmaniasis]]) :* Mouse (''[[House Mouse|Mus musculus]]'') - the classic model vertebrate. Many inbred strains exist, as well as lines selected for particular traits, often of medical interest, e.g. body size, obesity, muscularity. ''([[Quantitative genetics]], [[Molecular evolution]], [[Genomics]])'' :* ''[[Homo sapiens]]'' (humans) - used in various clinical studies :* ''[[Lamprey]]'' - spinal cord research :*''[[Oryzias latipes]]'', Medaka (the Japanese ricefish) is an important model in developmental biology, and has the advantage of being much sturdier than the traditional Zebrafish :* Rat (''[[Rattus norvegicus]]'') - particularly useful as a toxicology model; also particularly useful as a neurological model and source of primary cell cultures, owing to the larger size of organs and suborganellar structures relative to the mouse. ''([[Molecular evolution]], [[Genomics]])'' :* [[Rhesus macaque]] - used for studies on [[infectious disease]] and [[cognition]] :*''Sigmodon hispidus'' - [[Cotton rat]] formerly used in polio research :* ''[[Taeniopygia guttata]]'' or zebra finch - used in the study of the [[song system]] of [[songbird]]s and the study of non-mammalian [[auditory system]]s :* ''[[Fugu|Takifugu rubripres]]'', a [[pufferfish]] - has a small genome with little [[junk DNA]] :* ''[[Xenopus laevis]]'', the African clawed [[frog]] - used in developmental biology because of its large [[embryo]]s and high tolerance for physical and pharmacological manipulation :* [[Zebrafish]] (''Danio rerio''), a freshwater fish, has a nearly transparent body during early development, which provides unique visual access to the animal's internal anatomy. Zebrafish are used to study development, toxicology and toxicopathology,<ref>Spitsbergen J.M. and Kent M.L. (2003). The state of the art of the zebrafish model for toxicology and toxicologic pathology research&mdash;advantages and current limitations. ''Toxicol Pathol.'' '''31''' (Supplement), 62-87. PubMed Abstract Link => PMID 12597434.</ref> specific gene function and roles of signaling pathways. ==Model organisms used for specific research objectives== ===Sexual selection and sexual conflict=== *''[[Callosobruchus maculatus]]'', the bruchid beetle *''[[Chorthippus parallelus]]'', the meadow grasshopper *[[Coelopidae]] - seaweed flies *[[Diopsidae]] - stalk-eyed flies *''[[Drosophila]]'' spp. - fruit flies *''[[Gryllus bimaculatus]]'', the field cricket *''[[Scathophaga stercoraria]]'', the yellow dung fly ===Hybrid zones=== *''[[Bombina]] bombina'' and ''variegata'' *''[[Podisma]]'' spp. in the Alps ===Ecological genomics=== *''[[Daphnia]] pulex'', an environmental indicator model organism ==References== <references /> ==See also== * [[Animal model]] * [[Ensembl]] genome database of model organisms * [[History of model organisms]] * [[Animals in space]] * [[Animal testing]] * [[Animal testing on invertebrates]] * [[Animal testing on rodents]] * [[Generic Model Organism Database]] * [[History of animal testing]] * [[RefSeq]] - the Reference Sequence database == External links == * [http://genome.wellcome.ac.uk/doc_WTD020803.html Wellcome Trust description of model organisms] * [http://ceolas.org/VL/mo/ WWW Virtual Library guide to several model organism resource lists] * [http://www.gmod.org/ The Generic Model Organism Database project] * [http://www.nih.gov/science/models/ The US National Institutes of Health page] * [http://developmentalbiology.de/en/modelorganisms.php Model organisms in developmental biology] * [http://www.biologie.uni-muenchen.de/ou/cellbio/forschung.php Ludwig-Maximillians-Universität Department Biologie II] * Mandoli DF, Olmstead R (2000): ''[http://www.springerlink.com/content/hx8h7hdhmjppbd63/fulltext.pdf The importance of emerging model systems in plant biology].'' Journal of plant growth regulation 19 (3): 249-252 * [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16973872&ordinalpos=18&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Link to the publication of the Populus trichocarpa genome sequence] * [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16100779&ordinalpos=20&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Link to the publication of the Oryza sativa genome sequence] * [http://miracle.igib.res.in/cgi-bin/fishmap/gbrowse/ FishMap: The Zebrafish Community Genomics Browser] maintained at the Institute of Genomics and Integrative Biology {{Model Organisms}} [[Category:Model organisms| ]] [[Category:Animal testing]] [[ca:Organisme model]] [[cs:Modelový organismus]] [[de:Modellorganismus]] [[es:Organismo modelo]] [[fr:Organisme modèle]] [[id:Organisme model]] [[it:Organismo modello]] [[he:אורגניזם מודל]] [[la:Instar animans]] [[nl:Modelorganisme]] [[ja:モデル生物]] [[nn:Modellorganisme]] [[pl:Organizmy modelowe]] [[tr:Model organizma]] [[uk:Модельний організм]] [[zh:模式生物]]