What are model organisms?
Model organisms, by definition, are the non-human species which allow us to answer question about biology in ways that are accessible for experimental investigation (Rine 2014). These organisms were originally selected based on their simplicity which made them easy targets to examine. As knowledge has evolved however, the definition has expanded to more complex species as long as they are relatively easy to breed and maintain in a laboratory (Hunter 2008). Studies done on these model organisms can provide insight into the complicated biological processes of the human body. Found below is a compilation of a fraction of the commonly used model organisms.
How to select a model organism
When selecting a model organism for use in a lab there are a variety of factors that a scientist should consider. They should start by asking themselves a series of questions, depicted by the National Research Council Committee on Dogs in 1994.
To aid in answering some of these questions, some background information on a few model organisms may be found useful.
Escherichia coli (E. coli)
Ideal for examination of basic molecular genetic processes
Baker's yeast (S. cerevisiae)
Great for studying recessive mutations due to their ability to grow as haploids or diploids
Nematodes (C. elegans)
Often used to study development or programmed cell death (Hong 2016)
Aradibopsis thaliana (A. thaliana)
Small plant which is easy to genetically transform using bacterial plasmids
Fruit fly (D. melanogaster)
Good for studying developmental genetic systems due to its similarity to the human system
House mouse (M. musculus)
Excellent for studying human diseases due to a highly conserved gene order between mice and humans
Zebrafish (D. rerio)
Used to study pharmacogenetics and neuropharmacology (Kalueff 2014)
Website Used to Determine SHANK3 Model Organism
WormBase
WormBase identified the C. elegan ortholog of the vertebrate SHANK3 gene to be shn-1. This gene is required for the regulation of calcium-related behaviors like defecation, pharyngeal pumping and male fertility. It is expressed in neurons, the pharynx, and the intestine (Bono 2005).
FlyBase
FlyBase identified the D. melanogaster ortholog of the vertebrate SHANK3 gene to be prosap. This gene is involved in the regulation of signaling pathways and synaptic growth at the neuromuscular junction. When mutated, most flies were viable but had neuroanatomy defects.
MGI
MGI identified the M. musculus ortholog of the vertebrate SHANK3 gene which is also named SHANK3. This gene is involved in the nervous system, more specifically, in cell differentiation, cellular component organization, response to stimulus, and signaling.
ZFIN
ZFIN identified the the D. rerio ortholog of the vertebrate SHANK3 gene to be shank3a. This gene is involved in brain morphogenesis and swimming behaviors in the zebrafish.
Discussion
As shown above, a large amount of model organisms are readily available for scientists' use. However, not all model organisms are made alike. A careful selection of the most relevant model organism can make an experimenter's research much more efficient and telling. Because of SHANK3's involvement in neurological development and support of synapses, I was able to limit my choices to the C. elegan, D. melanogaster, M. musculus and D. rerio. Each of these model organisms processes their own set of advantages and disadvantages. After weighing the potential costs and benefits of each, I decided upon using the D. rerio, more commonly known as the zebrafish. Within the past few years, advancements in imaging tools have allowed researchers to study neural networks in the zebrafish with much more ease (Leung 2013). This will allow me to closely examine synaptic connectivity in the zebrafish model. I chose this model specifically over the other three listed options because its protein domains were much more highly conserved in comparison with the human SHANK3 domains (see domains). Please refer to specific aims to learn more about how the D. rerio model organism can be used to study SHANK3 expression.
References:
Bono, M., & Maricq, A. V. (2005). Neuronal substrates of complex behaviors in C. elegans.., 451-501. doi:10.1146/annurev.neuro.27.070203.144259
Hunter, P. (2008). The paradox of model organisms. The use of model organisms in research will continue despite their shortcomings. EMBO Reports, 9(8), 717–720. http://doi.org/10.1038/embor.2008.142
Hong, J.-H., & Park, M. (2016). Understanding Synaptogenesis and Functional Connectome in C. elegans by Imaging Technology. Frontiers in Synaptic Neuroscience, 8, 18. http://doi.org/10.3389/fnsyn.2016.00018
Kalueff, A. V., Stewart, A. M., & Gerlai, R. (2014). Zebrafish as an emerging model for studying complex brain disorders. Trends in Pharmacological Sciences, 35(2), 63–75. http://doi.org/10.1016/j.tips.2013.12.002
Leung, L. C., Wang, G. X., & Mourrain, P. (2013). Imaging zebrafish neural circuitry from whole brain to synapse. Frontiers in Neural Circuits, 7, 76. http://doi.org/10.3389/fncir.2013.00076
National Research Council (US) Committee on Dogs. Laboratory Animal Management: Dogs. Washington (DC): National Academies Press (US); 1994. 2, Criteria for Selecting Experimental Animals. Available from: https://www.ncbi.nlm.nih.gov/books/NBK236591/
Rine, J. (2014). A future of the model organism model. Molecular Biology of the Cell, 25(5), 549–553. http://doi.org/10.1091/mbc.E12-10-0768
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https://www.yourgenome.org/facts/what-are-model-organisms
Bono, M., & Maricq, A. V. (2005). Neuronal substrates of complex behaviors in C. elegans.., 451-501. doi:10.1146/annurev.neuro.27.070203.144259
Hunter, P. (2008). The paradox of model organisms. The use of model organisms in research will continue despite their shortcomings. EMBO Reports, 9(8), 717–720. http://doi.org/10.1038/embor.2008.142
Hong, J.-H., & Park, M. (2016). Understanding Synaptogenesis and Functional Connectome in C. elegans by Imaging Technology. Frontiers in Synaptic Neuroscience, 8, 18. http://doi.org/10.3389/fnsyn.2016.00018
Kalueff, A. V., Stewart, A. M., & Gerlai, R. (2014). Zebrafish as an emerging model for studying complex brain disorders. Trends in Pharmacological Sciences, 35(2), 63–75. http://doi.org/10.1016/j.tips.2013.12.002
Leung, L. C., Wang, G. X., & Mourrain, P. (2013). Imaging zebrafish neural circuitry from whole brain to synapse. Frontiers in Neural Circuits, 7, 76. http://doi.org/10.3389/fncir.2013.00076
National Research Council (US) Committee on Dogs. Laboratory Animal Management: Dogs. Washington (DC): National Academies Press (US); 1994. 2, Criteria for Selecting Experimental Animals. Available from: https://www.ncbi.nlm.nih.gov/books/NBK236591/
Rine, J. (2014). A future of the model organism model. Molecular Biology of the Cell, 25(5), 549–553. http://doi.org/10.1091/mbc.E12-10-0768
Header:
https://www.yourgenome.org/facts/what-are-model-organisms
This web page was produced as an assignment for Genetics 564, an undergraduate capstone course at UW-Madison.