Model organism

From Wikipedia, the free encyclopedia
  (Redirected from Model organisms)
Jump to: navigation, search
Drosophila melanogaster, one of the most famous subjects for experiments

A model organism is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the organism model will provide insight into the workings of other organisms.[1] Model organisms are in vivo models and are widely used to research human disease when human experimentation would be unfeasible or unethical.[2] This strategy is made possible by the common descent of all living organisms, and the conservation of metabolic and developmental pathways and genetic material over the course of evolution.[3] Studying model organisms can be informative, but care must be taken when extrapolating from one organism to another.

Selecting a model organism[edit]

Models are those organisms with a wealth of biological data that make them attractive to study as examples for other species and/or natural phenomena that are more difficult to study directly. Continual research on these organisms focus on a wide variety of experimental techniques and goals from many different levels of biology—from ecology, behavior, and biomechanics, down to the tiny functional scale of individual tissues, organelles, and proteins. Inquiries about the DNA of organisms are classed as genetic models (with short generation times, such as the fruitfly and nematode worm), experimental models, and genomic parsimony models, investigating pivotal position in the evolutionary tree.[4] Historically, model organisms include a handful of species with extensive genomic research data, such as the NIH model organisms.[5]

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 (inbred strains, stem cell lines, and methods of transformation) 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 lineages on the tree of life.

Use of model organisms[edit]

There are many model organisms. One of the first model systems for molecular biology was the bacterium Escherichia coli, a common constituent of the human digestive system. Several of the bacterial viruses (bacteriophage) that infect E. coli also have been very useful for the study of gene structure and gene regulation (e.g. phages Lambda and T4). However, bacteriophages are not organisms because they lack metabolism and depend on functions of the host cells for propagation.

In eukaryotes, 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 humans and is regulated by 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.

Electron microphotograph of tobacco mosaic virus (TMV) particles

Important model organisms[edit]


Viruses include:


Sporulating Bacillus subtilis

Prokaryotes include:


Eukaryotes include:





Main article: Animal model
Laboratory mice
  • Cat (Felis sylvestris catus) - used in neurophysiological research.
  • 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.
  • Cotton rat (Sigmodon hispidus) - formerly used in polio research.
  • Dog (Canis lupus familiaris) - an important respiratory and cardiovascular model, also contributed to the discovery of classical conditioning.
  • Golden hamster (Mesocricetus auratus) - first used to study kala-azar (leishmaniasis).
  • Guinea pig (Cavia porcellus) - 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.
  • Little brown bat (Myotis lucifugus)- used to prove echolocation exists in bats in 1930s and also used in experiments predicting microbat behavior as it is a reliable species that has typical features of a temperate bat species.
  • Medaka (Oryzias latipes, or Japanese ricefish) - an important model in developmental biology, and has the advantage of being much sturdier than the traditional Zebrafish.
  • 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, voluntary wheel-running behavior.[39] (Quantitative genetics, Molecular evolution, Genomics)
  • 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 (or Rhesus monkey) (Macaca mulatta) - used for studies on infectious disease and cognition.
  • Sea lamprey (Petromyzon marinus) - spinal cord research
  • Takifugu (Takifugu rubripes, a pufferfish) - has a small genome with little junk DNA.
  • Xenopus tropicalis and Xenopus laevis (African clawed frog) - eggs and embryos from these frogs are used in developmental biology, cell biology, toxicology, and neuroscience[40][41]
  • Zebra finch (Taeniopygia guttata) - used in the study of the song system of songbirds and the study of non-mammalian auditory systems.
  • 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,[42] specific gene function and roles of signaling pathways.

Model organisms used for specific research objectives[edit]

Sexual selection and sexual conflict[edit]

Hybrid zones[edit]

  • Bombina bombina and variegata
  • Podisma spp. in the Alps
  • Caledia captiva (Orthoptera) in eastern Australia

Ecological genomics[edit]

Table of model genetic organisms[edit]

This table indicates the status of the genome sequencing project for each organism.

Organism Genome Sequenced
Escherichia coli Yes
Eukaryote, unicellular
Dictyostelium discoideum Yes
Saccharomyces cerevisiae Yes
Schizosaccharomyces pombe Yes
Chlamydomonas reinhardtii Yes
Tetrahymena thermophila Yes
Emiliania huxleyi Yes
Eukaryote, multicellular
Caenorhabditis elegans Yes
Drosophila melanogaster Yes
Arabidopsis thaliana Yes
Physcomitrella patens Yes
Danio rerio Yes
Mus musculus Yes
Xenopus laevis (Note: and X. tropicalis)[43] Yes
Homo sapiens (Note:not a model organism) Yes

See also[edit]


  1. ^ Fields S, Johnston M (Mar 2005). "Cell biology. Whither model organism research?". Science 307 (5717): 1885–6. doi:10.1126/science.1108872. PMID 15790833. 
  2. ^ Griffiths, E. C. (2010) What is a model?
  3. ^ Fox, Michael Allen (1986). The Case for Animal Experimention: An Evolutionary and Ethical Perspective. Berkeley and Los Angeles, California: University of California Press. ISBN 0-520-05501-2. 
  4. ^ What are model organisms?
  5. ^ NIH model organisms
  6. ^ Chlamydomonas reinhardtii resources at the Joint Genome Institute
  7. ^ Chlamydomonas genome sequenced published in Science, October 12, 2007
  8. ^ Kües U (June 2000). "Life history and developmental processes in the basidiomycete Coprinus cinereus". Microbiol. Mol. Biol. Rev. 64 (2): 316–53. doi:10.1128/MMBR.64.2.316-353.2000. PMC 98996. PMID 10839819. 
  9. ^ Bioanalytical Investigation of Asarone in Connection with Acorus calamus Oil Intoxications. Kristian Björnstad, Anders Helander, Peter Hultén and Olof Beck, Journal of Analytical Toxicology, Volume 33, Number 9, November/December 2009, pages 604-609 (abstrcat)
  10. ^ Moody, J. D.; Zhang, D.; Heinze, T. M.; Cerniglia, C. E. (2000). "Transformation of amoxapine by Cunninghamella elegans". Applied and environmental microbiology 66 (8): 3646–3649. doi:10.1128/AEM.66.8.3646-3649.2000. PMC 92200. PMID 10919836.  edit
  11. ^ Inducible nature of the steroid 11-hydroxylases in spores of Cunninghamella elegans (Lendner). A. Jaworski, Prof. Dr. L. Sedlaczek, J. Dlugoński and Ewa Zajaczkowska, Journal of Basic Microbiology, Volume 25, Issue 7, pages 423–427, 1985, doi:10.1002/jobm.3620250703
  12. ^ Davis, Rowland H. (2000). Neurospora: contributions of a model organism. Oxford [Oxfordshire]: Oxford University Press. ISBN 0-19-512236-4. 
  13. ^ Ohm, R.; De Jong, J.; Lugones, L.; Aerts, A.; Kothe, E.; Stajich, J.; De Vries, R.; Record, E.; Levasseur, A.; Baker, S. E.; Bartholomew, K. A.; Coutinho, P. M.; Erdmann, S.; Fowler, T. J.; Gathman, A. C.; Lombard, V.; Henrissat, B.; Knabe, N.; Kües, U.; Lilly, W. W.; Lindquist, E.; Lucas, S.; Magnuson, J. K.; Piumi, F. O.; Raudaskoski, M.; Salamov, A.; Schmutz, J.; Schwarze, F. W. M. R.; Vankuyk, P. A.; Horton, J. S. (2010). "Genome sequence of the model mushroom Schizophyllum commune". Nature Biotechnology 28 (9): 957–963. doi:10.1038/nbt.1643. PMID 20622885.  edit
  14. ^ a b c d About Arabidopsis on The Arabidopsis Information Resource page (TAIR)
  15. ^ Rushworth, C; et al. (2011). "Boechera, a model system for ecological genomics". Molecular Ecology 20: 4843–57. doi:10.1111/j.1365-294X.2011.05340.x. PMC 3222738. PMID 22059452. 
  16. ^ Brutnell, T; et al. (2010). "Setaria viridis: a model for C4 photosynthesis". Plant Cell 22: 2537–44. doi:10.1105/tpc.110.075309. PMC 2947182. PMID 20693355. 
  17. ^ Jiang, Hui; Barbier, Hugues; Brutnell, Thomas (2013). "Methods for Performing Crosses in Setaria viridis, a New Model System for the Grasses". Journal of Visualized Experiments (80). doi:10.3791/50527. ISSN 1940-087X. 
  18. ^ Goodin, Michael; David Zaitlin; Rayapati Naidu; Steven Lommel (August 2008). "Nicotiana benthamiana: its history and future as a model for plant-pathogen interactions". Molecular Plant-Microbe Interactions 21 (8): 1015–1026. doi:10.1094/MPMI-21-8-1015. PMID 18616398. 
  19. ^ Zhou, S.; Bechner, M. C.; Place, M.; Churas, C. P.; Pape, L.; Leong, S. A.; Runnheim, R.; Forrest, D. K.; Goldstein, S.; Livny, M.; Schwartz, D. C. (2007). "Validation of rice genome sequence by optical mapping". BMC Genomics 8: 278. doi:10.1186/1471-2164-8-278. PMC 2048515. PMID 17697381.  edit
  20. ^ a b Rensing SA, Lang D, Zimmer AD, et al. (Jan 2008). "The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants". Science 319 (5859): 64–9. Bibcode:2008Sci...319...64R. doi:10.1126/science.1150646. PMID 18079367. 
  21. ^ Ralf Reski (1998): Physcomitrella and Arabidopsis: the David and Goliath of reverse genetics. In: Trends in Plant Science. 3:209-210. doi:10.1016/S1360-1385(98)01257-6
  22. ^ "Populus trichocarpa (Western poplar)". Phytozome. Retrieved 22 July 2013. 
  23. ^ Srivastava, M.; Simakov, O.; Chapman, J.; Fahey, B.; Gauthier, M. E. A.; Mitros, T.; Richards, G. S.; Conaco, C.; Dacre, M.; Hellsten, U.; Larroux, C.; Putnam, N. H.; Stanke, M.; Adamska, M.; Darling, A.; Degnan, S. M.; Oakley, T. H.; Plachetzki, D. C.; Zhai, Y.; Adamski, M.; Calcino, A.; Cummins, S. F.; Goodstein, D. M.; Harris, C.; Jackson, D. J.; Leys, S. P.; Shu, S.; Woodcroft, B. J.; Vervoort, M.; Kosik, K. S. (2010). "The Amphimedon queenslandica genome and the evolution of animal complexity". Nature 466 (7307): 720–726. Bibcode:2010Natur.466..720S. doi:10.1038/nature09201. PMC 3130542. PMID 20686567.  edit
  24. ^ Holland, L. Z.; Albalat, R.; Azumi, K.; Benito-Gutiérrez, E.; Blow, M. J.; Bronner-Fraser, M.; Brunet, F.; Butts, T.; Candiani, S.; Dishaw, L. J.; Ferrier, D. E. K.; Garcia-Fernàndez, J.; Gibson-Brown, J. J.; Gissi, C.; Godzik, A.; Hallböök, F.; Hirose, D.; Hosomichi, K.; Ikuta, T.; Inoko, H.; Kasahara, M.; Kasamatsu, J.; Kawashima, T.; Kimura, A.; Kobayashi, M.; Kozmik, Z.; Kubokawa, K.; Laudet, V.; Litman, G. W.; McHardy, A. C. (2008). "The amphioxus genome illuminates vertebrate origins and cephalochordate biology". Genome Research 18 (7): 1100–1111. doi:10.1101/gr.073676.107. PMC 2493399. PMID 18562680.  edit
  25. ^ Riddle, Donald L. (1997). C. elegans II (Full text). Plainview, N.Y: Cold Spring Harbor Laboratory Press. ISBN 0-87969-532-3. 
  26. ^ Müller HG (1982). "Sensitivity of Daphnia magna straus against eight chemotherapeutic agents and two dyes". Bull. Environ. Contam. Toxicol. 28 (1): 1–2. doi:10.1007/BF01608403. PMID 7066538. 
  27. ^ Manev H, Dimitrijevic N, Dzitoyeva S. (2003). "Techniques: fruit flies as models for neuropharmacological research". Trends Pharmacol Sci. 24 (1): 41–3. doi:10.1016/S0165-6147(02)00004-4. PMID 12498730. 
  28. ^ Chapman, J. A.; Kirkness, E. F.; Simakov, O.; Hampson, S. E.; Mitros, T.; Weinmaier, T.; Rattei, T.; Balasubramanian, P. G.; Borman, J.; Busam, D.; Disbennett, K.; Pfannkoch, C.; Sumin, N.; Sutton, G. G.; Viswanathan, L. D.; Walenz, B.; Goodstein, D. M.; Hellsten, U.; Kawashima, T.; Prochnik, S. E.; Putnam, N. H.; Shu, S.; Blumberg, B.; Dana, C. E.; Gee, L.; Kibler, D. F.; Law, L.; Lindgens, D.; Martinez, D. E. et al. (2010). "The dynamic genome of Hydra". Nature 464 (7288): 592–596. Bibcode:2010Natur.464..592C. doi:10.1038/nature08830. PMID 20228792.  edit
  29. ^ Ladurner, P; Schärer, L; Salvenmoser, W; Rieger, R (2005). "A new model organism among the lower Bilateria and the use of digital microscopy in taxonomy of meiobenthic Platyhelminthes: Macrostomum lignano, n. sp. (Rhabditophora, Macrostomorpha)". Journal of Zoological Systematics and Evolutionary Research 43: 114–126. doi:10.1111/j.1439-0469.2005.00299.114-126. 
  30. ^ Pang, K.; Martindale, M. Q. (2008). "Ctenophores". Current Biology 18 (24): R1119–R1120. doi:10.1016/j.cub.2008.10.004. PMID 19108762.  edit
  31. ^ Ryan, J. F.; Pang, K.; Comparative Sequencing Program; Mullikin, J. C.; Martindale, M. Q.; Baxevanis, A. D.; NISC Comparative Sequencing Program (2010). "The homeodomain complement of the ctenophore Mnemiopsis leidyi suggests that Ctenophora and Porifera diverged prior to the ParaHoxozoa". EvoDevo 1 (1): 9. doi:10.1186/2041-9139-1-9. PMC 2959044. PMID 20920347.  edit
  32. ^ Darling, J. A.; Reitzel, A. R.; Burton, P. M.; Mazza, M. E.; Ryan, J. F.; Sullivan, J. C.; Finnerty, J. R. (2005). "Rising starlet: the starlet sea anemone,Nematostella vectensis". BioEssays 27 (2): 211–221. doi:10.1002/bies.20181. PMID 15666346.  edit
  33. ^ Putnam, N. H.; Srivastava, M.; Hellsten, U.; Dirks, B.; Chapman, J.; Salamov, A.; Terry, A.; Shapiro, H.; Lindquist, E.; Kapitonov, V. V.; Jurka, J.; Genikhovich, G.; Grigoriev, I. V.; Lucas, S. M.; Steele, R. E.; Finnerty, J. R.; Technau, U.; Martindale, M. Q.; Rokhsar, D. S. (2007). "Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization". Science 317 (5834): 86–94. Bibcode:2007Sci...317...86P. doi:10.1126/science.1139158. PMID 17615350.  edit
  34. ^ The Appendicularia Facility at the Sars International Centre for Marine Molecular Biology
  35. ^ Wang, X.; Lavrov, D. V. (2006). "Mitochondrial Genome of the Homoscleromorph Oscarella carmela (Porifera, Demospongiae) Reveals Unexpected Complexity in the Common Ancestor of Sponges and Other Animals". Molecular Biology and Evolution 24 (2): 363–373. doi:10.1093/molbev/msl167. PMID 17090697.  edit
  36. ^ Tessmar-Raible, K.; Arendt, D. (2003). "Emerging systems: Between vertebrates and arthropods, the Lophotrochozoa". Current opinion in genetics & development 13 (4): 331–340. doi:10.1016/s0959-437x(03)00086-8. PMID 12888005.  edit
  37. ^ Srivastava, M.; Begovic, E.; Chapman, J.; Putnam, N. H.; Hellsten, U.; Kawashima, T.; Kuo, A.; Mitros, T.; Salamov, A.; Carpenter, M. L.; Signorovitch, A. Y.; Moreno, M. A.; Kamm, K.; Grimwood, J.; Schmutz, J.; Shapiro, H.; Grigoriev, I. V.; Buss, L. W.; Schierwater, B.; Dellaporta, S. L.; Rokhsar, D. S. (2008). "The Trichoplax genome and the nature of placozoans". Nature 454 (7207): 955–960. Bibcode:2008Natur.454..955S. doi:10.1038/nature07191. PMID 18719581.  edit
  38. ^ Reynoldson TB, Thompson SP, Bamsey JL (1991). "A sediment bioassay using the tubificid oligochaete worm Tubifex tubifex". Environ. Toxicol. Chem. 10 (8): 1061–72. doi:10.1002/etc.5620100811. 
  39. ^ Kolb, E. M., E. L. Rezende, L. Holness, A. Radtke, S. K. Lee, A. Obenaus, and T. Garland, Jr. 2013. Mice selectively bred for high voluntary wheel running have larger midbrains: support for the mosaic model of brain evolution. Journal of Experimental Biology 216:515-523.
  40. ^ Wallingford, J., Liu, K., and Zheng, Y. 2010. Current Biology v. 20, p. R263-4
  41. ^ Harland, R.M. and Grainger, R.M. 2011. Trends in Genetics v. 27, p 507-15
  42. ^ Spitsbergen JM, Kent ML (2003). "The state of the art of the zebrafish model for toxicology and toxicologic pathology research—advantages and current limitations". Toxicol Pathol 31 (Suppl): 62–87. doi:10.1080/01926230390174959. PMC 1909756. PMID 12597434. 
  43. ^ "JGI-Led Team Sequences Frog Genome". (Genome Web). 2010-04-29. Retrieved 2010-04-30. 

External links[edit]