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Non-Classical Model Organisms

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Non-Classical Model Organisms nonnon--classicalclassical modelmodel organisms:organisms: What are they…. and should they be studied? Crown group radiation ~ 965 million years ago Classic eukaryote model organisms invertebrates & vertebrates invertebrates Arbacia punctulata, the purple-spined sea urchin, classical subject of embryological studies Aplysia, a sea slug, whose ink release response serves as a model in neurobiology and whose growth cones serve as a model of cytoskeletal rearrangements. Caenorhabditis elegans, a nematode, usually called C. elegans[2] - an excellent model for understanding the genetic control of development and physiology. C. elegans was the first multicellular organism whose genome was completely sequenced Ciona intestinalis, a sea squirt Drosophila, usually the species Drosophila melanogaster - a kind of fruit fly, famous as the subject of genetics experiments by Thomas Hunt Morgan and others. Easily raised in lab, rapid generations, mutations easily induced, many observable mutations. Recently, Drosophila has been used for neuropharmacological research[3]. (Molecular genetics, Population genetics, Developmental biology). Euprymna scolopes, the Hawaiian bobtail squid, model for animal-bacterial symbiosis, bioluminescent vibrios Hydra (genus), a Cnidarian, is the model organism to understand the evolution of bilaterian body plans Loligo pealei, a squid, subject of studies of nerve function because of its giant axon (nearly 1 mm diameter, roughly a thousand times larger than typical mammalian axons) Pristionchus pacificus, a roundworm used in evolutionary developmental biology in comparative analyses with C. elegans Stomatogastric ganglion, arthropods digestive systems are a model for motor pattern generation seen in all repetitive motions Symsagittifera roscoffensis, a flatworm, subject of studies of bilaterian body plan development Tribolium castaneum, the flour beetle - a small, easily kept darkling beetle used especially in behavioural ecology experiments vertebrates Cavius porcellus, the guinea pig, used by Robert Koch and other early bacteriologists as a host for bacterial infections, hence a byword for "laboratory animal" even though rarely used today Chick (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 Dog (Canis lupus familiaris) - an important respiratory and cardiovascular model 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) Human - used in various clinical studies Oryzias latipes, Medaka (the Japanese ricefish) is 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 - used for studies on infectious disease and cognition Sigmodon hispidus - Cotton rat formerly used in polio research Taeniopygia guttata or zebra finch - used in the study of the song system of songbirds and the study of non- mammalian auditory systems Takifugu rubipres, a pufferfish - has a small genome with little junk DNA Xenopus laevis, the African clawed frog - 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[4], specific gene function and roles of signaling pathways. Classic eukaryote model organisms fungi fungi Aspergillus nidulans, subject of genetics studies Neurospora crassa - orange bread mold (genetic studies of meiosis, metabolic regulation, and circadian rhythm)[1] Ashbya gossypii, cotton pathogen, subject of genetics studies (polarity, cell cycle) Saccharomyces cerevisiae, baker's yeast or budding yeast (used in brewing and baking) Schizosaccharomyces pombe, fission yeast, subject of genetic studies Classic eukaryote model organisms plants plants Arabidopsis thaliana, currently the most popular model plant. This herbaceous dicot is a crucifer, a member of the mustard family. Its small stature and short generation time facilitates genetic studies, and many phenotypic and biochemical mutants have been mapped. Arabidopsis was the first plant to have its genome sequenced. Its genome sequence, along with a wide range of information concerning Arabidopsis, is maintained by the TAIR database. (Plant physiology, Developmental biology, Molecular genetics, Population genetics, Cytology, Molecular biology) Brachypodium distachyon is an emerging experimental model grass that has many attributes that make it an excellent model for temperate cereals. (Agronomy, Molecular biology, Genetics) Lotus japonicus a model legume used to study the symbiosis responsible for nitrogen fixation. (Agronomy, Molecular biology) 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 plants 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 economical production of complex biopharmaceuticals. It is also used in education to demonstrate population growth curves. 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 is being 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) 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 in progress. (Agronomy, Molecular biology) Physcomitrella patens is a moss increasingly used for studies on development and molecular evolution of plants. It is so far the only non-vascular plant (and so the only "primitive" plant) with its genome completely sequenced . Populus is a genus used as a model in forest genetics and woody plant studies. It has a small genome size, grows very rapidly, and is easily transformed. “Classic” eukaryote model organisms the rest Chlamydomonas reinhardtii - a unicellular green alga used to study photosynthesis, flagella and motility, regulation of metabolism, cell-cell recognition and adhesion, response to nutrient deprivation and many other topics. Chlamy has a well-studied genetics, with many known and mapped mutants, and there are advanced methods for genetic transformation and selection of genes. A Chlamydomonas genetic stock center exists at Duke University, and an international Chlamydomonas research interest group meets on a regular basis to discuss research results. Chlamydomonas is easy to grow on an inexpensive defined medium. Silvetia compressa – polarity establishment and asymmetric cell division Dictyostelium discoideum is used in molecular biology and genetics (its genome has been sequenced), and is studied as an example of cell communication, differentiation, and programmed cell death. Tetrahymena thermophila - a free living freshwater ciliate protozoan. Publication levels (2006) ANIMALS Chick development: 11,911 C. elegans development: 2,502 Mouse development: 98,204 120,900 Xenopus development: 5,690 Zebra fish development: 2,593 FUNGI Ashbya development: 7,359 7,359 PLANTS Arabidopsis development: 5,999 5,999 THE REST Chlamydomonas development: 312 Dictyostelium development: 1,671 1,985 Silvetia compressa: 2 What about the rest of the Eukaryotic tree of life? What are these organisms and what do they do? Diplomonadida Hexamita inflata The diplomonads are a group of flagellates, most of which are parasitic. They include most notably Giardia lamblia, which causes giardiasis in humans. They are placed among the metamonads, and appear particularly close relatives of the retortamonads; these are very basal eukaryotes, classified as Protists (eukaryotes that are not animals or plants). Most diplomonads are double cells: they have two nuclei, each with four associated flagella, arranged symmetrically about the body's main axis. Like the retortamonads, they lack both mitochondria and a Golgi apparatus. However they are now known to possess mitochondrial relics, called mitosomes. These are
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