Model Organisms

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A model organism is a non-human species that is studied to understand biological processes, with the expectation that discoveries made in the organism model will provide insight into the workings of other organisms. Additionally they may occupy a pivotal position in the evolutionary tree, which gives scientists insight into evolutionary development. Model organisms became the irreplaceable tools of fundamental biological and clinical research, and helped scientists to amass an enormous amount of knowledge.

What is a Model Organism

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. Selected bacteria, fungi, plants or animals that can be bred and studied with simple methods and are therefore of great importance for biological and biomedical research. Model organisms are, as being used as a model, usually the first organisms of a kingdom whose entire genome was decoded. This further pushes their research capabilities.

History of Model Organisms

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Charles Darwin Tree of Life Sketch - 1837

The history of model organisms began with the idea that certain organisms can be studied and used to gain knowledge of other organisms or as a control (ideal) for other organisms of the same species. Model organisms offer standards that serve as the authorized basis for comparison of other organisms which crucial for the development of phylogenetic trees. Today, phylogenetic analyses have become central to understanding biodiversity, evolution, ecology, and genomes.

In the middle of the 19th century men like Charles Darwin and Gregor Mendel and their respective work on natural selection and the genetics of heredity were a corner stone for genetic research in general. Darwin's notebooks from 1837 shows one of the first evolutionary tree sketches. In the 20th century this elemental work on plants and free-living animals continued in laboratories where Drosophila, E.coli and lab mice where introduced as new model organism. These organisms have led to many advances in the past century.

Mammalian animal models of disease

In order to understand human processes and behavior mammalian models provide the biggest insights as they share a high degree of homology with humans. Due to their easy keeping, mouse and rat species are the most important representatives. But also huminidae, (guinea) pigs and dogs are closely being studied.

Animal models serving in research may have an existing, inbred or induced disease or injury that is similar to a human condition. The use of animal models allows researchers to investigate disease states with procedures that imply a level of harm that would not be considered ethical to inflict on a human. However complex human diseases can often be better understood in a simplified system in which individual parts of the disease process are isolated and examined.

The rat (Rattus norvegicus) is particularly useful as a toxicology model, and source of primary cell cultures.The aortic arches of the rat are among the most commonly studied in murine models due to marked anatomical homology to the human cardiovascular system. Additionally they are particular useful for psychological studies of learning and other mental processes as well as to understand group behavior and overcrowding. Still the rat has lost importance as role model in the last two to three decades simply because its genome cannot tolerate the insertion of foreign DNA to anywhere near the extent of the mouse genome.

Reasons to turn to nontraditional models

The group of organism used as model is not a fix term. New ones emerge; others have fallen from grace over time. Sometimes it makes sense to search for special organism in order to do research in a new field. The first studies on ends of chromosomes - the telomeres – were done in ciliated protozoan Tetrahymena. Each Tetrahymena cell has a huge number of tiny, linear chromosomes and so each cell is far more enriched with telomere sequences than is a typical eukaryotic cell.

Learn more about non mammalian model organism and their different advantages in the table down below!

Model Organism in different Kingdoms

Kingdom Model Organism Research Field
Prokaryote Bacillus subtilis In fundamental research B. subtilis ist the species of choice to study bacterial chromosome replication and cell differentiation. is considered the best studied. The bacterium is used in laboratory studies directed at discovering the fundamental properties and characteristics of Gram-positive spore-forming bacteria.
Escherichia coli E. coli can be grown and cultured easily and inexpensively. Cultivated strains (e.g. E. coli K12) are well-adapted to the laboratory environment where they have been intensively investigated for the past 60 years making it the most widely studied prokaryotic model organism. In 1946 the first bacterial conjugation was described using E. coli as a model bacterium, similar to the first experiments to understand phage genetics.
Fungi Aspergillus nidulans Aspergillus nidulans also known as Emericella nidulans when referring to its sexual form, is an important research organism for studying eukaryotic cell biology. Due to its parasexuality, transformation has quickly become an alternative to crossing in Aspergillus genetics. Thus, long before recombinant DNA became available, genetic markers were already recombined by exploiting parasexuality. A. nidulans quickly became the most important eukaryotic model organism. Since the 1950s it is being used to study a wide range of subjects including recombination, DNA repair, mutation, cell cycle control, tubulin, chromatin, nucleokinesis, pathogenesis, metabolism, and experimental evolution.
Neurospora crassa N. crassa is a type of red bread mold. Because of its haploid lifecycle which eases analysis of recessive traits and uncomplicated cultivation the fungi is frequently used for meiosis, metabolic regulation, and circadian rhythm research. X-rays experiments and analysis of malfunction in specific enzymes led to the "one gene, one enzyme" hypothesis. It is important in the elucidation of molecular events involved in circadian rhythms, epigenetics and gene silencing, cell polarity, cell fusion, development, as well as many aspects of cell biology and biochemistry. Knock out variants of wild type N. crassa are widely studied to determine the function of genes.
Schizosaccharomyces pombe The fission yeast S. pombe is an unicellar eukaryote. The cells grow exclusively through cell tips and produce two daugther cells of equal size, predestining for cell cycle research. S. pombe was the sixth model eukaryotic organism whose genome has been fully sequenced. Basic principles of a yeast cell can be used to understand more complex organisms like mammals and in particular humans. S. pombe has also become an important organism in studying the cellular responses to DNA damage and the process of DNA replication.
Saccharomyces cerevisiae A variety of human proteins like cell cycle and signaling proteins as well as enzymes were first discovered by studying their homologs in yeast, especially in S. cerevisiae. As a eukaryote, it shares the complex internal cell structure of plants and animals without the high percentage of non-coding DNA. The single-cell organism, has a short generation and can be easily cultured. It was the first eukaryotic genome to be fully sequenced and deletion mutants are covering more than 90 % of the genome. S. cerevisiae divides with meiosis, allowing it to be a candidate for sexual genetics research. td>
Algae Chlamydomonas reinhardtii C. reinhardtii is a single-cell green alga. Uncomplicated growth and the ability to manipulate its genetics encourage scientists to use C. reinhardtii as model organism for research on fundamental questions like cell movement and recognition, photosynthesis, flagella and motility, regulation of metabolism and response to starvation. As the alga is haploid, knock mutation experiments directly show in the phenotype. Half of the mitochondrial proteins are encoded in the nucleus, a unique feature making C. reinhardtii significant for mitochondrial studies.
Plants Arabidopsis thaliana A. thaliana is the most researched model organism in fundamental research in plant molecular genetics. Its small stature and genome and short generation time facilitates rapid genetic studies predestining the plant as a tool for understanding the molecular biology of many traits, including flower development and light sensing. Arabidopsis was the first plant to have its genome sequenced. A. thaliana can be genetically transformed using >A. tumefaciens via the 'floral dip' method. With the method plants and in specific A. thaliana are the most easily transformed multicellular organism, essential to many subsequent investigations. Many phenotypic and biochemical mutants have been mapped which helps to understand RNA-directed RNA methylation (transcriptional silencing).
Oryza sativa Rice (Oryza sativa) is one of the most important crops in the world. It has one of the smallest genomes of any cereal species, the International Rice Genome Sequencing Project (IRGSP) started in 1997 the decryption. Research into the genome is a step towards genetic modification, with the aim to increase resistance and production values. In order to combat vitamin A deficiency, Golden rice was created by transforming rice with two beta-carotene biosynthesis genes.
Zea mays Maize is a diploid monocot and one of the most used cereal grains. It has been a keystone model organism for basic research in genetics, molecular biology and agronomy for nearly a century. Some of the maize chromosomes show chromosomal knobs: highly repetitive heterochromatic domains. The knobs helped to discover transposons and validated the theory of jumping genes; about 85 % of the genome is composed of transposons. Many DNA markers have been mapped and the genome has been sequenced in 2008. Additionally Maize is used to study developmental physiology, epigenetics, pest resistance, heterosis, quantitative inheritance, and comparative genomics.
Animals Caenorhabditis elegans C. elegans is a free-living, transparent nematode. It is a multicellular eukaryotic organism, yet is simple enough to be studied in great detail - an excellent model for understanding the genetic control of development and physiology. C. elegans was the first multicellular organism whose genome was completely sequenced and a fixed number of 1031 cells. It is one of the simplest organisms with a nervous system and as of 2012, the only organism to have its connectome completed. The organism is used to study chemotaxis, thermotaxis, mechanotransduction, learning, memory, and mating behaviour.
Danio rerio D. rerio is a freshwater fish with nearly transparent body during early development, which provides unique visual access to the animal's internal anatomy. Zebrafish are used to study vertebrate development and specific gene function. Its regenerative abilities are in particular interesting for the roles of signaling pathways. Toxicology studies of D. rerio can be transferred to directly to mammalian models and humans.
Drosophila melanogaster The fruit fly D. melanogaster was one of the very first model organisms, jumping from nature to laboratory animal in the beginning of the 20th century. The fly is widely used for biological research in genetics, physiology, microbial pathogenesis, and life history evolution. Thomas Hunt Morgan was the first to realize the potential of mapping the chromosomes of D. melanogaster and all known mutants, today it is the genetically best-known eukaryotic organism. The principal of processes such as transcription and replication can be transferred to other eukaryotes, including humans - about 60% of genes are conserved between the two species. Recently, Drosophila has been used for neuropharmacological research.
Oryzias latipes O. latipes is a model organism extensively used in many areas of biological research, most notably in toxicology. With 7 weeks the generation cycle is faster than zebrafish, additionally the genome is with ~800 mega base pairs only half the size and O. latipes is much sturdier.
Platynereis dumerilii The Dumeril's Clam Worm, P. dumerilii,is a marine polychaetous annelid or ragworm. The worm lives in the same environment as its ancestors millions of years ago and still has many ancestral features therefore often called a living fossil. It conserved for example an eye like structure called eyespot, the simplest eyes that exist. Due to this evolutional conservations P. dumerilii is used in many phylogenetic studies as a model organism. The genome size is with 10 9 base pairs average for an animal and larger in comparison to other models however intron rich and therefore closer to vertebrates like humans.
Xenopus laevis The African clawed frog, X. laevis, is a species of aquatic frog found throughout much of Sub-Saharan Africa. It does have a large and easily manipulated embryo which allows molecular, developmental and cell biological studies. X. laevis benefits from the, in comparison to other model organisms, close evolutionary relationship to humans. It is the only vertebrate model system that allows for high-throughput in vivo analyses of gene function and high-throughput biochemistry. Additionally large oocytes of the frog are a keystone for studies of ion transport and channel physiology.