Biology:List of model organisms

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Escherichia coli is a gram-negative prokaryotic model organism
Drosophila melanogaster, one of the most famous subjects for experiments

This is a list of model organisms used in scientific research.

Viruses

Prokaryotes

Sporulating Bacillus subtilis

Eukaryotes

Protists

  • Chlamydomonas reinhardtii - a unicellular green alga used to study photosynthesis, flagella and motility, regulation of metabolism, cell–cell recognition and adhesion, response to nutrient deprivation and many other topics. Chlamydomonas reinhardtii has 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.[2] Sequencing of the Chlamydomonas reinhardtii genome was reported in October 2007.[3] 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 defined medium.
  • Stentor coeruleus is used in molecular biology (its genome has been sequenced),[4] and is studied as a model of single-cell regeneration.
  • 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.
  • Thalassiosira pseudonana - a unicellular marine diatom alga, extensively studied as a model marine diatom since its genome was published in 2004
  • Naegleria gruberi is a freshwater non-pathogenic amoeboflagellate sometimes used in eukaryotic cell biology experiments

Fungi

Plants

Arabidopsis thaliana
Lemna gibba
  • 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 expression system for economical production of complex biopharmaceuticals. It is also used in education to demonstrate population growth curves.
  • 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 transposons ("jumping genes"). Many DNA markers have been mapped and the genome has been 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)
  • Mimulus guttatus is a model organism used in evolutionary and functional genomes studies. The genus Mimulus contains c. 120 species and is in the family Phrymaceae. Several genetic resources have been designed for the study of this genus and some are free access (http://www.mimulusevolution.org)
  • Nicotiana benthamiana is often considered a model organism for plant-pathogen studies.[12]
  • Tobacco BY-2 cells is a suspension cell line from tobacco (Nicotiana tabacum) that is useful for general plant physiology studies at the cell level. The genome of this particular cultivar will not be sequenced in the near future, but sequencing of its wild species Nicotiana tabacum 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.[13] (Agronomy, Molecular biology)
Physcomitrella patens

Animals

Invertebrates

Caenorhabditis elegans

Vertebrates

Laboratory mice
  • Axolotl (Ambystoma mexicanum), used to study regeneration and developmental processes
  • Bombina bombina and Bombina variegata, used to study sexual selection and sexual conflict
  • Carolina anole (Anolis carolinensis), used to study reptile genomics
  • 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 ethological or medical interest, e.g. body size, obesity, muscularity, voluntary wheel-running behavior.[34] (Quantitative genetics, Molecular evolution, Genomics)
  • Naked mole-rat, (Heterocephalus glaber), studied for their characteristic pain insensitivity, thermoregulation, cancer resistance, eusociality, and longevity.
  • Nothobranchius furzeri is studied because of their extreme short-lifespan in research on aging, disease and evolution.
  • Pigeon (Columba livia domestica), studied extensively for cognitive science and animal intelligence
  • Poecilia reticulata, the guppy, used to study sexual selection and sexual conflict
  • 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.
  • Three-spined stickleback (Gasterosteus aculeatus), a fish used to study ethology and behavioral ecology.
  • Xenopus tropicalis and Xenopus laevis (African clawed frog) - eggs and embryos from these frogs are used in developmental biology, cell biology, toxicology, and neuroscience[35][36]
  • 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,[37] specific gene function and roles of signaling pathways.

References

  1. "Streptomyces coelicolor". John Innes Center. http://www.jic.ac.uk/science/molmicro/Strept.html. Retrieved 13 April 2018. 
  2. "Chlamydomonas reinhardtii resources at the Joint Genome Institute". http://genome.jgi-psf.org/chlamy. 
  3. Chlamydomonas genome sequenced published in Science, October 12, 2007
  4. The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell
  5. 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. PMID 10839819. 
  6. Davis, Rowland H. (2000). Neurospora: contributions of a model organism. Oxford [Oxfordshire]: Oxford University Press. ISBN 978-0-19-512236-7. 
  7. Ohm, R.; De Jong, J.; Lugones, L.; Aerts, A.; Kothe, E.; Stajich, J.; De Vries, R.; Record, E. et al. (2010). "Genome sequence of the model mushroom Schizophyllum commune". Nature Biotechnology 28 (9): 957–963. doi:10.1038/nbt.1643. PMID 20622885. 
  8. 8.0 8.1 8.2 8.3 About Arabidopsis on The Arabidopsis Information Resource page (TAIR)
  9. Rushworth, C (2011). "Boechera, a model system for ecological genomics". Molecular Ecology 20 (23): 4843–57. doi:10.1111/j.1365-294X.2011.05340.x. PMID 22059452. 
  10. Brutnell, T (2010). "Setaria viridis: a model for C4 photosynthesis". Plant Cell 22 (8): 2537–44. doi:10.1105/tpc.110.075309. PMID 20693355. 
  11. 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): 50527. doi:10.3791/50527. ISSN 1940-087X. PMID 24121645. 
  12. 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. 
  13. Zhou, S.; Bechner, M. C.; Place, M.; Churas, C. P.; Pape, L.; Leong, S. A.; Runnheim, R.; Forrest, D. K. et al. (2007). "Validation of rice genome sequence by optical mapping". BMC Genomics 8: 278. doi:10.1186/1471-2164-8-278. PMID 17697381. 
  14. 14.0 14.1 "The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants". Science 319 (5859): 64–9. Jan 2008. doi:10.1126/science.1150646. PMID 18079367. Bibcode2008Sci...319...64R. http://www.sciencemag.org/cgi/content/abstract/319/5859/64. 
  15. Reski, Ralf (1998). "Physcomitrella and Arabidopsis: the David and Goliath of reverse genetics". Trends in Plant Science 3 (6): 209–210. doi:10.1016/S1360-1385(98)01257-6. 
  16. "Populus trichocarpa (Western poplar)". Phytozome. http://www.phytozome.net/poplar. Retrieved 22 July 2013. 
  17. Srivastava, M.; Simakov, O.; Chapman, J.; Fahey, B.; Gauthier, M. E. A.; Mitros, T.; Richards, G. S.; Conaco, C. et al. (2010). "The Amphimedon queenslandica genome and the evolution of animal complexity". Nature 466 (7307): 720–726. doi:10.1038/nature09201. PMID 20686567. Bibcode2010Natur.466..720S. 
  18. Holland, L. Z.; Albalat, R.; Azumi, K.; Benito-Gutiérrez, E.; Blow, M. J.; Bronner-Fraser, M.; Brunet, F.; Butts, T. et al. (2008). "The amphioxus genome illuminates vertebrate origins and cephalochordate biology". Genome Research 18 (7): 1100–1111. doi:10.1101/gr.073676.107. PMID 18562680. 
  19. Riddle, Donald L. (1997). C. elegans II. Plainview, N.Y: Cold Spring Harbor Laboratory Press. ISBN 978-0-87969-532-3. https://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=ce2.TOC. 
  20. 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. 
  21. "Techniques: fruit flies as models for neuropharmacological research". Trends Pharmacol. Sci. 24 (1): 41–3. 2003. doi:10.1016/S0165-6147(02)00004-4. PMID 12498730. 
  22. Chapman, J. A.; Kirkness, E. F.; Simakov, O.; Hampson, S. E.; Mitros, T.; Weinmaier, T.; Rattei, T.; Balasubramanian, P. G. et al. (2010). "The dynamic genome of Hydra". Nature 464 (7288): 592–596. doi:10.1038/nature08830. PMID 20228792. Bibcode2010Natur.464..592C. 
  23. 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.x. http://www3.interscience.wiley.com/journal/120712665/abstract. 
  24. Pang, K.; Martindale, M. Q. (2008). "Ctenophores". Current Biology 18 (24): R1119–R1120. doi:10.1016/j.cub.2008.10.004. PMID 19108762. 
  25. 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. PMID 20920347. 
  26. 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. 
  27. Putnam, N. H.; Srivastava, M.; Hellsten, U.; Dirks, B.; Chapman, J.; Salamov, A.; Terry, A.; Shapiro, H. et al. (2007). "Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization". Science 317 (5834): 86–94. doi:10.1126/science.1139158. PMID 17615350. Bibcode2007Sci...317...86P. https://digital.library.unt.edu/ark:/67531/metadc884638/. 
  28. The Appendicularia Facility at the Sars International Centre for Marine Molecular Biology
  29. Cade, W. (1975-12-26). "Acoustically Orienting Parasitoids: Fly Phonotaxis to Cricket Song". Science 190 (4221): 1312–1313. doi:10.1126/science.190.4221.1312. ISSN 0036-8075. Bibcode1975Sci...190.1312C. 
  30. 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. 
  31. 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. 
  32. Srivastava, M.; Begovic, E.; Chapman, J.; Putnam, N. H.; Hellsten, U.; Kawashima, T.; Kuo, A.; Mitros, T. et al. (2008). "The Trichoplax genome and the nature of placozoans". Nature 454 (7207): 955–960. doi:10.1038/nature07191. PMID 18719581. Bibcode2008Natur.454..955S. https://cloudfront.escholarship.org/dist/prd/content/qt57r2q3hw/qt57r2q3hw.pdf. 
  33. "A sediment bioassay using the tubificid oligochaete worm Tubifex tubifex". Environ. Toxicol. Chem. 10 (8): 1061–72. 1991. doi:10.1002/etc.5620100811. 
  34. Kolb, E. M.; Rezende, E. L.; Holness, L.; Radtke, A.; Lee, S. K.; Obenaus, A.; Garland Jr, T (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. doi:10.1242/jeb.076000. PMID 23325861. 
  35. Wallingford, J.; Liu, K.; Zheng, Y. (2010). "Xenopus". Current Biology 20: R263–4. doi:10.1016/j.cub.2010.01.012. PMID 20334828. 
  36. Harland, R.M.; Grainger, R.M. (2011). "Xenopus research: metamorphosed by genetics and genomics". Trends in Genetics 27: 507–15. doi:10.1016/j.tig.2011.08.003. PMID 21963197. 
  37. "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. 2003. doi:10.1080/01926230390174959. PMID 12597434.