A model organism is a non-human species that is extensively studied to understan d particular biological phenomena, with the expectation that

discoveries made in the organism model will provide insight into the workings of other organisms.[1 ] In particular, model organisms are widely used to explore potential causes and treatments for human disease when human experimentation would be unfeasible or unethical. This strategy is made possible by the common descent of all living or ganisms, and the conservation of metabolic and developmental pathways and geneti c material over the course of evolution.[2] Studying model organisms can be info rmative, but care must be taken when generalizing from one organism to another. Selecting a model organism Models are those organisms with a wealth of biological data that make them attra ctive to study as examples for other species including humans that are more diff icult to study directly. These can be classed as genetic models (with short gene ration times, such as the fruitfly and nematode worm), experimental models, and genomic models, with a pivotal position in the evolutionary tree [3]. Historical ly, 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 experim ental manipulation. This usually will include characteristics such as short life -cycle, techniques for genetic manipulation (inbred strains, stem cell lines, an d 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 sev eral traits. Among these are size, generation time, accessibility, manipulation, genetics, conservation of mechanisms, and potential economic benefit. As compar ative molecular biology has become more common, some researchers have sought mod el 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 bio logy was the bacterium Escherichia coli, a common constituent of the human diges tive system. Several of the bacterial viruses (bacteriophage) that infect E. col i 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 ve ry 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 g row for an animal, has various visible congenital traits and has a polytene (gia nt) chromosome in its salivary glands that can be examined under a light microsc ope. The roundworm Caenorhabditis elegans is studied because it has very defined development patterns involving fixed numbers of cells, and it can be rapidly as sayed for abnormalities. Important model organisms Viruses Viruses include: Phage Lambda Phi X 174 - its genome was the first ever to be sequenced. The genome is a circl e of 11 genes, 5386 base pairs in length. Tobacco mosaic virus Prokaryotes Sporulating Bacillus subtilis Prokaryotes include: Escherichia coli (E. coli) - This common, Gram-negative gut bacterium is the mos t widely-used organism in molecular genetics.

 Bacillus subtilis - an endospore forming Gram-positive bacterium Caulobacter crescentus - a bacterium that divides into two distinct cells used t o study cellular differentiation. Mycoplasma genitalium - a minimal organism Vibrio fischeri - quorum sensing, bioluminescence and animal-bacterial symbiosis with Hawaiian Bobtail Squid Synechocystis, a photosynthetic cyanobacterium widely used in photosynthesis res earch. Pseudomonas fluorescens, a soil bacterium that readily diversifies into differen t strains in the lab. Eukaryotes Eukaryotes include: Protists Protists: Chlamydomonas reinhardtii - a unicellular green alga used to study photosynthesi s, flagella and motility, regulation of metabolism, cell-cell recognition and ad hesion, response to nutrient deprivation and many other topics. Chlamydomonas re inhardtii has a well-studied genetics, with many known and mapped mutants and ex pressed sequence tags, and there are advanced methods for genetic transformation and selection of genes.[5] Sequencing of the Chlamydomonas reinhardtii genome w as reported in October 2007.[6] A Chlamydomonas genetic stock center exists at D uke University, and an international Chlamydomonas research interest group meets on a regular basis to discuss research results. Chlamydomonas is easy to grow o n an inexpensive defined medium. Dictyostelium discoideum is used in molecular biology and genetics (its genome h as been sequenced), and is studied as an example of cell communication, differen tiation, and programmed cell death. Tetrahymena thermophila - a free living freshwater ciliate protozoan. Emiliania huxleyi - a unicellular marine coccolithophore alga, extensively studi ed as a model phytoplankton species. Fungi Fungi: Budding yeast tomography Aspergillus nidulans, mold subject of genetics studies Coprinus cinereus, mushroom (genetic studies of mushroom development, genetic st udies of meiosis) [7] Neurospora crassa - orange bread mold (genetic studies of meiosis, metabolic reg ulation, and circadian rhythm)[8] Ashbya gossypii, cotton pathogen, subject of genetics studies (polarity, cell cy cle) Saccharomyces cerevisiae, baker's yeast or budding yeast (used in brewing and ba king) Schizosaccharomyces pombe, fission yeast, (cell cycle, cell polarity, RNAi, cent romere structure and function, transcription) Ustilago maydis, dimorphic yeast and plant pathogen of maize (dimorphism, plant pathogen, transcription) Plants Arabidopsis thaliana Plants: Arabidopsis thaliana, currently the most popular model plant. This herbaceous di cot is a crucifer, a member of the mustard family. Its small stature and short g eneration time facilitates genetic studies,[9] and many phenotypic and biochemic al mutants have been mapped.[9] Arabidopsis was the first plant to have its geno me sequenced.[9] Its genome sequence, along with a wide range of information con cerning Arabidopsis, is maintained by the TAIR database.[9] (Plant physiology, Developmental biology, Molecular genetics, Population genetic

s, Cytology, Molecular biology) Selaginella moellendorffii is a remnant of an ancient lineage of vascular plants and key to understanding the evolution of land plants. It has a small genome si ze (~110Mb) and its sequence will be released by the Joint Genome Institute in e arly 2008. (Evolutionary biology, Molecular biology) Brachypodium distachyon is an emerging experimental model grass that has many at tributes that make it an excellent model for temperate cereals. (Agronomy, Molec ular biology, Genetics) Lotus japonicus a model legume used to study the symbiosis responsible for nitro gen fixation. (Agronomy, Molecular biology) 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 pl ants 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 eco nomical production of complex biopharmaceuticals. It is also used in education t o demonstrate population growth curves. Zea mays Maize (Zea mays L.) is a cereal grain. It is a diploid monocot with 10 large chr omosome pairs, easily studied with the microscope. Its genetic features, includi ng many known and mapped phenotypic mutants and a large number of progeny per cr oss (typically 100-200) facilitated the discovery of transposons ("jumping genes "). Many DNA markers have been mapped and the genome has been sequenced. (Geneti cs, Molecular biology, Agronomy) Medicago truncatula is a model legume, closely related to the common alfalfa. It s rather small genome is currently being sequenced. It is used to study the symb iosis responsible for nitrogen fixation. (Agronomy, Molecular biology) Mimulus is a model organism used in evolutionary and functional genomes studies. This specie pertain to Scrophulariaceae family, with ca. 120 species. Several g enetic resources has been designed for the study of this genera, some are free a ccess (http://www.mimulusevolution.org) Tobacco BY-2 cells is suspension cell line from tobacco (Nicotiana tabaccum). Us eful for general plant physiology studies on cell level. Genome of this particul ar cultivar will be not sequenced (at least in near future), but sequencing of i ts wild species Nicotiana tabaccum is presently in progress. (Cytology, Plant ph ysiology, Biotechnology) Rice (Oryza sativa) is used as a model for cereal biology. It has one of the sma llest genomes of any cereal species, and sequencing of its genome is finished. ( Agronomy, Molecular biology) Physcomitrella patens Physcomitrella patens is a moss increasingly used for studies on development and molecular evolution of plants.[10] It is so far the only non-vascular plant (an d so the only "primitive" plant) with its genome completely sequenced.[10] (Plan t physiology, Evolutionary biology, Molecular genetics, Molecular biology) Populus is a genus used as a model in forest genetics and woody plant studies. I t has a small genome size, grows very rapidly, and is easily transformed. The ge nome sequence of Poplar (Populus trichocarpa) sequence is publicly available. See also Chlamydomonas reinhardtii, above under Protists. Animals Caenorhabditis elegans Arbacia punctulata, the purple-spined sea urchin, classical subject of embryolog ical studies

 Aplysia, a sea slug, whose ink release response serves as a model in neurobiolog y and whose growth cones serve as a model of cytoskeletal rearrangements. Caenorhabditis elegans, a nematode, usually called C. elegans[11] - an excellent model for understanding the genetic control of development and physiology. C. e legans was the first multicellular organism whose genome was completely sequence d Ciona intestinalis, a sea squirt Drosophila, usually the species Drosophila melanogaster - a kind of fruit fly, f amous as the subject of genetics experiments by Thomas Hunt Morgan and others. E asily raised in lab, rapid generations, mutations easily induced, many observabl e mutations. Recently, Drosophila has been used for neuropharmacological researc h[12]. (Molecular genetics, Population genetics, Developmental biology). Euprymna scolopes, the Hawaiian bobtail squid, model for animal-bacterial symbio sis, bioluminescent vibrios Hydra (genus), a Cnidarian, is the model organism to understand the processes of regeneration and morphogenesis, as well as the evolution of bilaterian body pla ns Loligo pealei, a squid, subject of studies of nerve function because of its gian t axon (nearly 1 mm diameter, roughly a thousand times larger than typical mamma lian axons) Macrostomum lignano, a free-living, marine flatworm, a model organism for the st udy of stem cells, regeneration, ageing, gene function, and the evolution of sex . Easily raised in the lab, short generation time, indetermined growth, complex behaviour[13] Oikopleura dioica[14], an appendicularia, a free-swimming tunicate (or urochorda te)) Pristionchus pacificus, a roundworm used in evolutionary developmental biology i n comparative analyses with C. elegans Schmidtea mediterranea a freshwater planarian; a model for regeneration and deve lopment of tissues such as the brain and germline Stomatogastric ganglion of various arthropod species; a model for motor pattern generation seen in all repetitive motions Strongylocentrotus purpuratus, the purple sea urchin, widely used in development al biology Symsagittifera roscoffensis, a flatworm, subject of studies of bilaterian body p lan development Tribolium castaneum, the flour beetle - a small, easily kept darkling beetle use d especially in behavioural ecology experiments Guinea pig (Cavia porcellus) - used by Robert Koch and other early bacteriologis ts as a host for bacterial infections, hence a byword for "laboratory animal" ev en 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-exp ression of gene products Cat (Felis cattus) - 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, G enomics) Lamprey - spinal cord research Medaka (Oryzias latipes, the Japanese ricefish) - an important model in developm ental biology, and has the advantage of being much sturdier than the traditional Zebrafish Rat (Rattus norvegicus) - particularly useful as a toxicology model; also partic ularly 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 cog nition Cotton rat (Sigmodon hispidus) - formerly used in polio research Zebra finch (Taeniopygia guttata) - used in the study of the song system of song birds 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 manipu lation Zebrafish (Danio rerio, a freshwater fish) - has a nearly transparent body durin g early development, which provides unique visual access to the animal's interna l anatomy. Zebrafish are used to study development, toxicology and toxicopatholo gy,[15] specific gene function and roles of signaling pathways. Model organisms used for specific research objectives Callosobruchus maculatus, the bruchid beetle Chorthippus parallelus, the meadow grasshopper Coelopidae - seaweed flies Diopsidae - stalk-eyed flies Drosophila spp. - fruit flies Macrostomum lignano, a sand flatworm Gryllus bimaculatus, the field cricket Scathophaga stercoraria, the yellow dung fly Hybrid zones Bombina bombina and variegata Podisma spp. in the Alps Caledia captiva (Orthoptera) in eastern Australia Ecological genomics Daphnia pulex, an environmental indicator model organism Table of model genetic organisms This table indicates the status of the genome sequencing project for each organi sm as well as whether the organism exhibits homologous recombination and the sta te of knowledge of the organism's biochemical pathways. Organism Genome Sequenced Homologous Recombination Biochemi stry Prokaryote Escherichia coli Yes Yes Excellent Eukaryote, unicellular Dictyostelium discoideum Yes Yes Excellent Saccharomyces cerevisiae Yes Yes Good Schizosaccharomyces pombe Yes Yes Good Chlamydomonas reinhardtii Yes No Good Tetrahymena thermophila Yes Yes Good Eukaryote, multicellular Caenorhabditis elegans Yes Difficult Not so good Drosophila melanogaster Yes Difficult Good Arabidopsis thaliana Yes No Poor Vertebrate Danio rerio

Yes Difficult? Good Mus musculus Yes Yes Good Xenopus laevis[16] Yes Homo sapiens (Note:not a model organism)

Yes

Yes

Good

Model organisms are those that useful data sets have been already gathered to de scribe basic biological processes. And they are more amenable to asking certain questions due to their simplicity of structure and features (Bolker, 1995). In o rder to explore the advantages of using model organisms in classrooms, I will ex amine their desirable attributes, why certain organisms have been chosen as mode l organisms for teaching, the advantages of using model organisms in teaching, a nd examples of model organisms popular in biology instruction. The Characteristics of Model Organisms for Research and Instruction C. elegans A model system is a simpler, idealized system that can be accessible and easily manipulated (Rosenblueth & Wiener, 1945). Therefore, when selecting living organ isms as models to work with, certain criteria are used depending upon the experi mental purposes. As a result, there is a wide range of characteristics common to model organisms, including: 1) rapid development with short life cycles, 2) sma ll adult size, 3) ready availability, and 4) tractability (Bolker, 1995). Being small, growing rapidly and being readily available are crucial in terms of housi ng them, given the budget and space limitations of research and teaching laborat ories. Tractability relates to the ease with which they can be manipulated. For example, C. elegans is a popular research organism as it possesses all the chara cteristics mentioned, yet shares many essential biological properties with human s. For instance, researchers who study apoptosis (programmed cell death) use C. elegans as an experimental organism in the hope of finding treatments for certai n types of human cancers, such as leukemia. By studying apoptosis in C. elegans, researchers hope to identify genes that switch-on cell death in cancer cells, t hus, using the cell's own genetic machinery to rid the body of malignant cells. Because leukemia is the unregulated growth of white blood cells, identifying gen es involved in apoptosis may provide researchers with a tool for treating the ra pid proliferation of cancer cells. Why Have Certain Living Organisms Been Chosen as Model Organisms in Teaching? In general, scientists have to work with organisms different from the ones they wish to apply their findings to for several reasons Model organisms act as surro gates that enable experiments to be carried out under a more favorable environme nt than would be available in the original system (Rosenblueth & Wiener, 1945). The biological insights gained from using model organisms have helped to cure hu man diseases and improve people's understanding of life. The characteristics of model organisms that have made them useful in research laboratories also make th em well-suited to classrooms (Manney & Manney, 1992). Compared to general living organisms, model organisms are well-established experimental systems and are of ten ready to be used in classrooms. The available resources, such as experimenta l protocols, for these model organisms make the transition of their use to curri cula relatively simple. Thus, many are amenable to be used as experimental organ isms in teaching. The Advantage of Using Model Organisms in Teaching Biology

E. coli Drosophila Model organisms have long been used in the classroom to help students learn impo rtant concepts in various disciplines. Each discipline has its own set of organi sms which have proven to be most suitable to use. For example, E. coli and Droso

phila have been widely used as model organisms in introductory biology courses t o teach microbiology and genetics. Examples of Model Organisms Popular in Classroom Use As discussed above, model organisms do play an important role in conveying biolo gical concepts. Many model organisms have been used in the classroom. The fruit fly, Drosophila melanogaster, is the most obvious organism used in teaching. It is often used for students to learn Mendelian genetics. E. coli, yeast, and Rana pipiens are also popular model organisms in biology education. Within the past two decades, due to its importance and popular use in research, C. elegans has b egun to take its place in the classroom as an important model organism. Below, I describe some of the model organisms, and the reasons that make them popular fo r classroom use. Escherichia coli Escherichia coli, a prokaryotic organism without a nuclear membrane, is a repres entative living material often used in laboratories and classrooms (Flannery, 19 97). E. coli reproduces rapidly (under optimal situation 0.5 hr/generation) such that results for a number of experiments can be quickly obtained. Certain mutan ts of E. coli have been defined that cannot express certain proteins at saturati on growth, and, therefore, die. E. coli was also the organism used to elucidate the regulation of the lac operon in genetics. E. coli's ability to take up exoge nous genetic material under the procedure known as DNA-mediated cell transformat ion has also made it a popular model for studies using recombinant DNA (Moss, 19 91). Using recombinant DNA techniques, E. coli can be manipulated in research la boratories and in the classroom to produce any DNA, RNA or protein of interest. Also, it is easy to manipulate both genetically and biochemically. Most importan tly, it shares fundamental characteristics, such as DNA and messenger RNA, with all other organisms (Botstein & Fink, 1988). The value of E. coli in recombinant DNA makes it a good model organism for students to study the genetic material. Drosophila The fruit fly, Drosophila melanogaster, has been the most popular eukaryotic org anism used in classrooms. It has been used in heredity and biomedical research w here the aims are to understand human genetics and developmental processes. It i s also a popular model for teaching Mendelian genetics. Drosophila is very popul ar and successful as a model organism because it has short life cycle of two wee ks, making it possible to study numerous generations in an academic year (Flanne ry, 1997; Kramer, 1986; Sofer & Tompkins, 1994). It is easy to culture and inexp ensive to house large numbers (Flannery, 1997; Jeszenszky, 1997; Kramer, 1986). Its size is amenable for cultivation in school laboratories. Also, it is large e nough that many attributes can be seen with the naked eye or under low-power mag nification (Sofer & Tompkins, 1994). Moreover, it has a very long history in bio logical research (since the early 1900s) and there are many useful tools to faci litate genetic study. For example, the use of antibodies makes the scoring of sp ecific cells or cell types possible in Drosophila (Rubin, 1988; Sofer & Tompkins , 1994). Because of the above properties, Drosophila has been used in research and teachi ng in a great variety of disciplines, such as classical and molecular genetics. Some researchers use Drosophila to study how its body plan is controlled by a se t of homeotic genes. The more research is done using Drosophila, the better we u nderstand it, thus making it an attractive model organism for class use (Flanner y, 1997; Rubin, 1988). Wisconsin Fast Plants Wisconsin Fast Plants (WFP), mainly rapid-cycling Brassica rapa (B.rapa), werede veloped by Dr. Paul Williams at the University of Wisconsin - Madison, using cla ssical selective breeding. The WFP, as well as Chinese cabbage and radish, belon g to the Brassica genus, which is part of the Crucifer as family. The selection of fast growing Creicifers was desirable to speed-up plant biological research a s traditional breeding of Brassica takes about six months. WFP has been used in the laboratory and classroom for studying basic and applied plant biology. For e xample, WFP can be used to study environmental science for students to see how p ollutants affect living organisms, plant responses such as phototropic and geotr

opic responses, cell biology and other biology issues. The advantages of using W FP is that under continuous fluorescent light, they have a short life cycle (35 - 40 days). Compared to normal B. rapa, which produces at most two generations p er year, one can harvest about ten generations per year from WFP. They are small (15 cm high, in a 2 cm2 pot) and can be housed in high densities and large numb ers which make them especially good for school use. They are low-cost and easy t o manage. They possess a wide variety of easily recognized traits that can be us ed in genetic studies. For instance, by crossing plants with light or dark plant colors, students can experiment on simple Mendelian genetics (WFP, 2003). Caenorhabditis elegans In the last two decades, a nematode, Caenorhabditis elegans, has captured the he arts of developmental biologists and geneticists hoping to solve the enigma of c ell development and related biological problems, such as aging. In addition, edu cators have begun to use it in classrooms to illustrate central biological conce pts, such as cell division (see "A Survey of Currently Used C. elegans Curricula "). Its popularity as a model organism is because it is transparent, thus cells of interest can be observed using a dissecting microscope. It is small (about 11.5 mm) and easy to cultivate, which makes it possible to house large numbers o f C. elegans. It has a short life cycle (3 days), which makes the production of numerous generations possible. It can be crossed at will. Male and hermaphrodite s are the two sexes. Hermaphrodites can self fertilize or mate with males to pro duce offspring. Thus, cross or self-fertilization can be manipulated as desired. There are numerous tools available to study C. elegans, including different typ es of antibodies and advanced microscopes. Its genome has been completely sequen ced. This is quite attractive and useful in genetic studies allowing researchers to pick a gene of interest to study (Donald, 1997; Wood, 1988). In sum, as discussed, some organisms are easy and amenable for use in the labora tory and the classroom to enhance our understanding of human biology. They are c alled "model organisms". A model organism is one that possesses the virtues of t ractability and accessibility that can be used in experimental manipulation both in school and research.