This web page was produced as an assignment for Genetics 564, an undergraduate capstone course at UW-Madison.
What are model organisms?
Model Organisms are organisms used in research due to easy maintenance and good breeding capabilities [1]. Additionally, these organisms often have short lifespans and rapid life cycles. Some model organisms’ biological processes are highly similar to humans, making them suitable to study diseases related to humans [2]. More importantly, these organisms allow rigorous experimental testing that cannot simply be done in other animals or humans such as control in diet, humidity and temperature of surroundings [2]. Model organisms serve as a tool for scientists to understand biological processes and different organisms have different advantages depending on a researcher’s topic of study. More commonly used model organisms also have online databases that host detailed information of an organisms's genes, proteins, interaction networks and functional information produced by organism-specific research projects. These databases provide query and visualization tools to access these data and are annotated in an organized manner [11]. These databases allow researchers to plan their studies effectively based on the wealth of information available online.
Choosing model organisms
Model organisms are essential for conducting experiments, so how do scientists choose model organisms? The list below shows some considerations to make when picking model organisms.
Mus Musculus (Mouse)
The mouse is very similar to humans in terms of physiology, genetics and anatomy [3]. They have short lifespans and reach maturity quickly, making them suitable in studying aging [4]. They also have short reproductive cycles as they can reproduce every 3 weeks, providing scientists with many samples to work with. Mice are useful in studying complex diseases such as immune, nervous and cardiovascular diseases because they often develop diseases similar to humans [3]. A useful database for mouse genetics is the Mouse Genome Informatics.
Danio rerio (Zebrafish)
Zebrafish are almost transparent, which makes them useful in studying neural diseases and development. Eggs are fertilised and develop outside the mother’s body, making it an ideal model organism for studying early development as well. Their genes are 70% identical to humans and 84% of genes related to human diseases are found in zebrafish. [5] They are also social animals, making them useful in studying behavioural diseases. [6] The database for zebrafish is the Zebrafish Information Network.
Drosophila melanogaster (Fruit fly)
Fruit flies are also very genetically similar to humans and about 75% of the genes that cause diseases in humans are also found in the fruit fly. It is relatively straightforward to genetically mutate fruit flies. It’s one of the most well known and used model organisms so there is a database of information ranging from genetics to behaviour, making them easy to work with. [7] The database for flies is Flybase.
Caenorhabditis elegans (Nematode worm)
C.elegans are fully transparent, making them useful in studying development and movement of cells in the organism. A major advantage of using this organism is that the development of cells are very stereotypical so all cell lineages can be traced back to its embryo. Because of their small size and rapid reproduction, they are suitable for conducting chemical or genetic screens. [8] The database for nematode worms is Wormbase.
Saccharomyces cerevisiae (Yeast)
Genetic manipulation is very easy and cheap in yeast compared to most model organisms. Although yeast share very little genes in common with humans, they are an emerging tool in the field of functional genomics and systems biology. These new fields look beyond the functions of individual genes and proteins, focusing on how they interact and work together to determine the properties of living cells and organisms [9].
Arabidopsis thaliana (Thale cress)
Arabidopsis is a popular organism for almost all aspects of plant biology, due to its short generation time, small genome size and the availability of its complete DNA sequence. In addition, Arabidopsis has proven to be an ideal organism for studying plant development at the molecular, cellular, organismal and ecological level. Arabidopsis is particularly useful in crop genetics and plant breeding [10]. The database for arabidopsis is The Arabidopsis Information Resource.
The mouse is very similar to humans in terms of physiology, genetics and anatomy [3]. They have short lifespans and reach maturity quickly, making them suitable in studying aging [4]. They also have short reproductive cycles as they can reproduce every 3 weeks, providing scientists with many samples to work with. Mice are useful in studying complex diseases such as immune, nervous and cardiovascular diseases because they often develop diseases similar to humans [3]. A useful database for mouse genetics is the Mouse Genome Informatics.
Danio rerio (Zebrafish)
Zebrafish are almost transparent, which makes them useful in studying neural diseases and development. Eggs are fertilised and develop outside the mother’s body, making it an ideal model organism for studying early development as well. Their genes are 70% identical to humans and 84% of genes related to human diseases are found in zebrafish. [5] They are also social animals, making them useful in studying behavioural diseases. [6] The database for zebrafish is the Zebrafish Information Network.
Drosophila melanogaster (Fruit fly)
Fruit flies are also very genetically similar to humans and about 75% of the genes that cause diseases in humans are also found in the fruit fly. It is relatively straightforward to genetically mutate fruit flies. It’s one of the most well known and used model organisms so there is a database of information ranging from genetics to behaviour, making them easy to work with. [7] The database for flies is Flybase.
Caenorhabditis elegans (Nematode worm)
C.elegans are fully transparent, making them useful in studying development and movement of cells in the organism. A major advantage of using this organism is that the development of cells are very stereotypical so all cell lineages can be traced back to its embryo. Because of their small size and rapid reproduction, they are suitable for conducting chemical or genetic screens. [8] The database for nematode worms is Wormbase.
Saccharomyces cerevisiae (Yeast)
Genetic manipulation is very easy and cheap in yeast compared to most model organisms. Although yeast share very little genes in common with humans, they are an emerging tool in the field of functional genomics and systems biology. These new fields look beyond the functions of individual genes and proteins, focusing on how they interact and work together to determine the properties of living cells and organisms [9].
Arabidopsis thaliana (Thale cress)
Arabidopsis is a popular organism for almost all aspects of plant biology, due to its short generation time, small genome size and the availability of its complete DNA sequence. In addition, Arabidopsis has proven to be an ideal organism for studying plant development at the molecular, cellular, organismal and ecological level. Arabidopsis is particularly useful in crop genetics and plant breeding [10]. The database for arabidopsis is The Arabidopsis Information Resource.
Discussion
After comparing the use of many model organisms using information from the different model organism databases, I have decided to use zebrafish as my model organism in studying MEF2C. This is because its gene is highly homologous to human MEF2C, at a percent identity of 74%. Additionally, Zebrafish possess all major neurotransmitters, hormones, and relevant receptors, and their neurotransmitter and neuroendocrine systems share structural properties with mammals. Zebrafish are also highly social animals, as they partake in hierarchical social interactions that have been shown to regulate brain neurotransmitter levels. Hence it is very easy to identify depressive phenotypes in zebrafish. Zebrafish with depressive phenotype show a global reduction of swimming, social withdrawal indicated by a lack of swimming in shoals and a droopy tail angle when at rest (Fig. 2). Last but not least, they are highly sensitive to a variety of prescribed psychotropic drugs such as antidepressants, mood stabilizers, and antipsychotics [6]. Hence, they are ideal to study the behavioral and physiological effects of depression for the MEF2C gene.
References:
[1] https://www.yourgenome.org/facts/what-are-model-organisms
[2] https://www.nigms.nih.gov/Education/Pages/modelorg_factsheet.aspx
[3] https://www.yourgenome.org/facts/why-use-the-mouse-in-research
[4] http://genomics.senescence.info/species/entry.php?species=Mus_musculus
[5] https://www.yourgenome.org/facts/why-use-the-zebrafish-in-research
[6] Fonseka, T. M., Wen, X. Y., Foster, J. A., & Kennedy, S. H. (2016). Zebrafish models of major depressive disorders. Journal of neuroscience research, 94(1), 3-14.
[7] https://www.yourgenome.org/facts/why-use-the-fly-in-research
[8] https://www.yourgenome.org/facts/why-use-the-worm-in-research
[9] Botstein, D., & Fink, G. R. (2011). Yeast: An Experimental Organism for 21st Century Biology. Genetics, 189(3), 695–704. http://doi.org/10.1534/genetics.111.130765
[10] https://www.nsf.gov/bio/pubs/reports/arabid/chap1.htm
[11] Oliver, S. G., Lock, A., Harris, M. A., Nurse, P., & Wood, V. (2016). Model organism databases: essential resources that need the support of both funders and users. BMC biology, 14(1), 49.
Images:
Header: https://www.nature.com/news/funding-for-model-organism-databases-in-trouble-1.20134
Figures are linked to source websites.
Fig. 2: Nguyen, M., Stewart, A. M., & Kalueff, A. V. (2014). Aquatic blues: modeling depression and antidepressant action in zebrafish. Progress in Neuro-Psychopharmacology and Biological Psychiatry, 55, 26-39.
[1] https://www.yourgenome.org/facts/what-are-model-organisms
[2] https://www.nigms.nih.gov/Education/Pages/modelorg_factsheet.aspx
[3] https://www.yourgenome.org/facts/why-use-the-mouse-in-research
[4] http://genomics.senescence.info/species/entry.php?species=Mus_musculus
[5] https://www.yourgenome.org/facts/why-use-the-zebrafish-in-research
[6] Fonseka, T. M., Wen, X. Y., Foster, J. A., & Kennedy, S. H. (2016). Zebrafish models of major depressive disorders. Journal of neuroscience research, 94(1), 3-14.
[7] https://www.yourgenome.org/facts/why-use-the-fly-in-research
[8] https://www.yourgenome.org/facts/why-use-the-worm-in-research
[9] Botstein, D., & Fink, G. R. (2011). Yeast: An Experimental Organism for 21st Century Biology. Genetics, 189(3), 695–704. http://doi.org/10.1534/genetics.111.130765
[10] https://www.nsf.gov/bio/pubs/reports/arabid/chap1.htm
[11] Oliver, S. G., Lock, A., Harris, M. A., Nurse, P., & Wood, V. (2016). Model organism databases: essential resources that need the support of both funders and users. BMC biology, 14(1), 49.
Images:
Header: https://www.nature.com/news/funding-for-model-organism-databases-in-trouble-1.20134
Figures are linked to source websites.
Fig. 2: Nguyen, M., Stewart, A. M., & Kalueff, A. V. (2014). Aquatic blues: modeling depression and antidepressant action in zebrafish. Progress in Neuro-Psychopharmacology and Biological Psychiatry, 55, 26-39.