Model organism


Model organism
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 widely used to explore potential causes and treatments for human disease when human experimentation would be unfeasible or considered less ethical. 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.[2] Studying model organisms can be informative, but care must be taken when generalizing from one organism to another.

Contents

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 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.[3] Historically, model organisms include a handful of species with extensive genomic research data, such as the NIH model organisms.[4]

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

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

Viruses

Viruses include:

Prokaryotes

Sporulating Bacillus subtilis

Prokaryotes include:

Eukaryotes

Eukaryotes include:

Protists

Fungi

Budding yeast tomography

Plants

  • 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 is a model organism used in evolutionary and functional genomes studies. This specie pertain to Phrymaceae family, with ca. 120 species. Several genetic resources has been designed for the study of this genera, some are free access (http://www.mimulusevolution.org)
  • Tobacco BY-2 cells is suspension cell line from tobacco (Nicotiana tabaccum). Useful for general plant physiology studies on 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)

Animals

Invertebrates
Vertebrates
Laboratory mice
  • 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
  • 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 sylvestris catus) - used in neurophysiological research
  • Dog (Canis lupus familiaris) - an important respiratory and cardiovascular model, also contributed to the discovery of classical conditioning.
  • Hamster - first used to study kala-azar (leishmaniasis)
  • 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)
  • Lamprey - spinal cord research
  • Medaka (Oryzias latipes, the Japanese ricefish) - 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 (Macaca mulatta) - used for studies on infectious disease and cognition
  • Cotton rat (Sigmodon hispidus) - formerly used in polio research
  • Zebra finch (Taeniopygia guttata) - used in the study of the song system of songbirds and the study of non-mammalian auditory systems
  • Takifugu (Takifugu rubripes, a pufferfish) - has a small genome with little junk DNA
  • The African clawed frog (Xenopus laevis) - used in developmental biology because of its large embryos 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,[27] specific gene function and roles of signaling pathways.

Model organisms used for specific research objectives

Sexual selection and sexual conflict

Hybrid zones

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

Ecological genomics

Table of model genetic organisms

This table indicates the status of the genome sequencing project for each organism as well as whether the organism exhibits homologous recombination.

Organism Genome Sequenced Homologous Recombination
Prokaryote
Escherichia coli Yes Yes
Eukaryote, unicellular
Dictyostelium discoideum Yes Yes
Saccharomyces cerevisiae Yes Yes
Schizosaccharomyces pombe Yes Yes
Chlamydomonas reinhardtii Yes No
Tetrahymena thermophila Yes Yes
Eukaryote, multicellular
Caenorhabditis elegans Yes Difficult
Drosophila melanogaster Yes Difficult
Arabidopsis thaliana Yes No
Physcomitrella patens Yes Yes
Vertebrate
Danio rerio Yes Yes
Mus musculus Yes Yes
Xenopus laevis (Note: and X. tropicalis)[28] Yes No
Homo sapiens (Note:not a model organism) Yes Yes

See also

References

  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. http://www.sciencemag.org/cgi/content/summary/307/5717/1885. 
  2. ^ 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. 
  3. ^ What are model organisms?
  4. ^ NIH model organisms
  5. ^ Chlamydomonas reinhardtii resources at the Joint Genome Institute
  6. ^ Chlamydomonas genome sequenced published in Science, October 12, 2007
  7. ^ 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. http://mmbr.asm.org/cgi/pmidlookup?view=long&pmid=10839819. 
  8. ^ Davis, Rowland H. (2000). Neurospora: contributions of a model organism. Oxford [Oxfordshire]: Oxford University Press. ISBN 0-19-512236-4. 
  9. ^ 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.  edit
  10. ^ a b c d About Arabidopsis on The Arabidopsis Information Resource page (TAIR)
  11. ^ 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. doi:10.1126/science.1150646. PMID 18079367. http://www.sciencemag.org/cgi/content/abstract/319/5859/64. 
  12. ^ 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
  13. ^ 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): 720–6. Bibcode 2010Natur.466..720S. doi:10.1038/nature09201. PMC 3130542. PMID 20686567. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3130542.  edit
  14. ^ Holland, L. Z.; Albalat, R.; Azumi, K.; Benito-Gutierrez, 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. doi:10.1101/gr.073676.107. PMC 2493399. PMID 18562680. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2493399.  edit
  15. ^ Riddle, Donald L. (1997) (Full text). C. elegans II. Plainview, N.Y: Cold Spring Harbor Laboratory Press. ISBN 0-87969-532-3. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=ce2.TOC. 
  16. ^ 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. http://linkinghub.elsevier.com/retrieve/pii/S0165614702000044. 
  17. ^ 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): 592–6. Bibcode 2010Natur.464..592C. doi:10.1038/nature08830. PMID 20228792.  edit
  18. ^ 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. http://www3.interscience.wiley.com/journal/120712665/abstract. 
  19. ^ Pang, K.; Martindale, M. Q. (2008). "Ctenophores". Current Biology 18 (24): R1119. doi:10.1016/j.cub.2008.10.004. PMID 19108762.  edit
  20. ^ Ryan, J. F.; Pang, K.; Comparative Sequencing Program, N.; Mullikin, J. C.; Martindale, M. Q.; Baxevanis, A. D. (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. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2959044.  edit
  21. ^ 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. doi:10.1002/bies.20181. PMID 15666346.  edit
  22. ^ 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. Bibcode 2007Sci...317...86P. doi:10.1126/science.1139158. PMID 17615350.  edit
  23. ^ The Appendicularia Facility at the Sars International Centre for Marine Molecular Biology
  24. ^ 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
  25. ^ Tessmar-Raible, K.; Arendt, D. (2003). "Emerging systems: Between vertebrates and arthropods, the Lophotrochozoa". Current opinion in genetics & development 13 (4): 331–340. PMID 12888005.  edit
  26. ^ 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): 955–60. Bibcode 2008Natur.454..955S. doi:10.1038/nature07191. PMID 18719581.  edit
  27. ^ 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. http://tpx.sagepub.com/cgi/pmidlookup?view=long&pmid=12597434. 
  28. ^ "JGI-Led Team Sequences Frog Genome". GenomeWeb.com (Genome Web). 2010-04-29. http://www.genomeweb.com//node/939634?hq_e=el&hq_m=701632&hq_l=1&hq_v=2de76155bb. Retrieved 2010-04-30. 

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