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Topic: Model organism

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Animal model

Mathematical model

Model

Fruit fly

Developmental genetics

Xenopus laevis

Caenorhabditis elegans

Arabidopsis

Saccharomyces cerevisiae

Brachydanio rerio

Xenopus

Zebrafish

Simulation

Arabidopsis thaliana

Drosophila melanogaster

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	Model organisms
		Model organisms are less costly, fewer ethical constraints are encountered using them, and, historically, more research data have been generated in the past (e.g.
		Model organisms are those that useful data sets have been already gathered to describe basic biological processes.
		A model organism is one that possesses the virtues of tractability and accessibility that can be used in experimental manipulation both in school and research.
	www.loci.wisc.edu /outreach/text/model.html (1861 words)

	Model organism - Wikipedia, the free encyclopedia
		A model organism is a species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the organism model will provide insight into the workings of other organisms.
		Lotus japonicus a model legume used to study the symbiosis responsible for nitrogen fixation.
		Rice (Oryza sativa) is used as a model for cereal biology.
	en.wikipedia.org /wiki/Model_organism (1341 words)

	Model organism: Facts and details from Encyclopedia Topic (Site not responding. Last check: 2007-10-21)
		Arabidopsis thaliana, thale cress, or mouse-ear cress, a small flowering plant related to cabbage and mustard, is one of the model organisms...
		Medicago truncatula is a small forage legume that has been chosen as a model organism for legume biology....
		An animal model usually refers to a non-human animal with a disease or altered health state that is similar to a human condition, these test subjects are often...
	www.absoluteastronomy.com /encyclopedia/m/mo/model_organism.htm (2363 words)

	Neurospora Section A
		Hence, once a model organism is developed by a few people with specific interests, it then acts as a nucleus for the development of a research community, a group of researchers with an interest in various features of one particular model organism.
		The feeling for the organism is a difficult idea to convey, but it centers on the fact that within an organism no biological system works in isolation: to study meiosis (for example) requires knowledge of other aspects of the ways of that species, such as its subcellular structure, its biochemistry and its life cycle.
		Hence, as opposed to the earlier approaches of geneticists working on model organisms, which were essentially reductionist, focusing on small parts of the organism, the more recent view is holistic, encompassing the integrated workings of all the parts of the organism's makeup.
	www.fgsc.net /Neurospora/sectionA.htm (951 words)

	Model organism - Biocrawler (Site not responding. Last check: 2007-10-21)
		The fruit fly Drosophila melanogaster was studied, again because it was easy to grow for a multicellular organism.
		Rice is used as a model for cereal biology.
		Spitsbergen J.M. and Kent M.L. The state of the art of the zebrafish model for toxicology and toxicologic pathology research--advantages and current limitations.
	www.biocrawler.com /encyclopedia/Model_organism (707 words)

	Table of Contents (Site not responding. Last check: 2007-10-21)
		It is important that a model organism be relatively inexpensive to maintain because millions of the given organism are needed to develop a sophisticated understanding of it.
		It is preferable for an experimental model organism to have a small genome size because it makes sequencing, isolating, and understanding the function of its genes much simpler and easier (12).
		In experimental model organism research, it is ideal to have a plant that reproduces readily and frequently such that it is easy to obtain rapidly many copies of the desired model organism.
	dragon.zoo.utoronto.ca /~B03T0601D/realcomparison.htm (2315 words)

	Brunswik Essay #6
		Brunswik's structure model (which must not be confused with the lens model) was first presented in 1939 and was modified 13 years later.
		The recognition of this structure-model is a prerequisite for the understanding of his whole theory, especially with regard to many process-characteristics of Brunswik's theory (for example for the understanding of the lens model process).
		On the left side of the organism you will find in spatial respect four regions which are characterized by the act of receiving or input.
	www.albany.edu /cpr/brunswik/notes/essay6.html (948 words)

	Tree of Life Glossary
		Organisms living on or in trees, fequenting trees, or a part of an organism resembling a tree in form and branching structure.
		Organisms which trap energy from physical or chemical sources and use the energy to assemble the macromolecules of which they are made.
		A region of the ingestion apparatus lying internal to the mouth (of a metazoan organism) or internal to the cytostome of a protist.
	tolweb.org /tree/home.pages/glossary.html (6229 words)

	Institute for Systems Biology: Using Model Organisms
		The simplicity of a model organism allows a scientist to more easily zero in on the properties and functions of interest, without having to sort out the complexity arising from additional systems embodied in more complex organisms.
		Model organisms are carefully selected to provide simple cases for our initial studies of biological systems.
		But studies on model organisms are crucial to eventually answering the central biological questions regarding human life.
	www.systemsbiology.org /Intro_to_ISB_and_Systems_Biology/Using_Model_Organisms (697 words)

	Mammalian Models
		The most popular model organisms have strong advantages for experimental research, such as rapid development with short life cycles, small adult size, ready availability, and tractability, and become even more useful when many other scientists work on them.
		The mouse is the closest mammalian model organism to humans.
		The rat is also a model of choice for many physiological studies related to cardiac and vascular function, pulmonary circulation, metabolism, neurological control, age- and gender-related differences, and studies related to hypertension and signal transduction.
	www.ncbi.nlm.nih.gov /About/model/mammal.html (360 words)

	NIH Model Organism Information - Main Page
		A simple plan (MS Word - 25 KB) that may be appropriate for a project, which has the goal of producing a model organism but has not produced one (Organism Sharing Simple).
		NIH Policy on the Sharing of Model Organisms for Biomedical Research (PDF - 443 KB) 09/09/2004 – Printable brochure that summarizes main elements of the NIH Model Organism Sharing Policy.
		NIH Model Organisms for Biomedical Research - web site providing information about national and international activities and major resources that are being developed to facilitate biomedical research using the animal models.
	grants.nih.gov /grants/policy/model_organism/index.htm (415 words)

	[No title]
		We are considering the combinatorial model of organism, where the main variables are the main systems of organism, and its application in telemedicine by means of computer network, special data bases and special decision making support system.
		In general we have the representative point of organism in parameters space, each organism has the zone of health,where the parameters correspond the health of concrete man. During illness the representative point of organism is found in another zone of parameters - in illnes zone.
		Models of concrete patients are imbedded in general model of organism.
	www.ehto.org /hps/Med7.doc (2408 words)

	Model Organism Database Workshop Report
		These model organism databases have allowed researchers to sift through masses of data, to gain access to information or materials they might have missed, and to go in new research directions.
		Model organism community: This community provides the data to a MOD, adds value by contributing to the curation of the data, and comprises a major set of users who need access to a great deal of specialized information, such as strain collections.
		Unlike the model organism community, the general community does not usually understand the specialized jargon and nomenclature for a model organism.
	www.nhlbi.nih.gov /meetings/modeldb/report.htm (2557 words)

	Model & other Organisms for pharmaceutical rsearch Glossary
		Nematode worm, a model organism, the first multicellular organism to have a completely sequenced genome (97 megabases of DNA with 19,099 predicted protein-coding genes) as of December 11 1998.
		Knockout mice are used as animal models for various diseases, such as cystic fibrosis, and are helping to clarify the functions of the genes studied within the fields of immunology, cancer genetics, and developmental biology.
		Model organisms are of key importance in both creating databases of gene sequences for homology searching, and as platforms for investigating the biology of genes of interest.
	www.genomicglossaries.com /content/model_organisms_glossary.asp (2539 words)

	Learn more about Model organism in the online encyclopedia. (Site not responding. Last check: 2007-10-21)
		A model organism is one that is used for close study because it is particularly easy to study a particular biological phenomenon using it, rather than because it has economic or other importance.
		Using model organisms works because evolution reuses fundamental biological principles and conserves metabolic and developmental pathways.
		In eukaryotes, several yeasts, particularly Saccharomyces cerevisiae ("baker's" or "budding" yeast), have been widely studied, largely because they are quick and easy to grow.
	www.onlineencyclopedia.org /m/mo/model_organism.html (342 words)

	genome.gov \| Background on Mouse as a Model Organism
		Although yeasts, worms and flies are excellent models for studying the cell cycle and many developmental processes, mice are far better tools for probing the immune, endocrine, nervous, cardiovascular, skeletal and other complex physiological systems that mammals share.
		Adding to the mouse's appeal as a model for biomedical research is the animal's relatively low cost of maintenance and its ability to quickly multiply, reproducing as often as every nine weeks.
		In recent decades, researchers have utilized an array of innovative genetic technologies to produce custom-made mouse models for a wide array of specific diseases, as well as to study the function of targeted genes.
	www.genome.gov /10005834 (1182 words)

	Learning and Model-Building
		This may still appear simple in our model with 27 possible architectures, but it suffices to observe that for more complex organisms there are typically millions of possible perceptions and thousands of possible actions to conclude that the space of possible models or control architectures is absolutely astronomical.
		Therefore, the burden of developing an adequate model is largely on the system itself, which will need to rely on various internal heuristics, combinations of pre-existing components, and subjective selection criteria to efficiently construct models that are likely to work.
		Natural selection of organisms is obviously a quite wasteful method to develop knowledge, although it is responsible for most knowledge that living systems have evolved in their genes.
	pespmc1.vub.ac.be /LEARNMOD.html (736 words)

	Model organism - for printer (Site not responding. Last check: 2007-10-21)
		The model required 136 equations and more than 50 'free parameters' expressing such things as the half-lives of the RNA and protein products of genes, the rates at which these diffuse between cells, and the strengths with which they bind to their gene and protein targets.
		Plus, the fact that von Dassow's team had to introduce 'fudges' to their model to make it work hints at the predictive power of such a process.
		By analysing their initial failure, the researchers isolated the discrepancies between experiment and theoretical prediction: a capability that will undoubtedly be useful for directing future experiments.
	www.nature.com /nsu_new/nsu_pf/000713/000713-9.html (596 words)

	Scientists elucidate the kinome of key model organism
		Dictyostelium is a widely used model organism for scientific study, as it is remarkably similar to mammalian cells, and it is amenable to a range of laboratory techniques.
		According to Dr. Smith, Dictyostelium provides a simple model in which to study conserved cellular processes, and illuminates a period in the evolutionary history of the metazoa after the divergence of the plants but before that of the fungi.
		By comparing the Dictyostelium kinome with those of other organisms, the authors find 46 types of kinases that appear to be conserved in all organisms, and are likely to be involved in fundamental cellular processes.
	www.eurekalert.org /pub_releases/2006-03/plos-set032706.php (316 words)

	Arabidopsis as a Model Organism (21 Aug 1996) (Site not responding. Last check: 2007-10-21)
		The procedures of seed mutagenesis are described in some detail, the importance of "knowing the organism" in order to detect mutant phenotypes is emphasised and the different phenotypes of the different classes of floral mutants are nicely illustrated.
		Then a model of floral development is proposed in which three classes of homeotic genes interact in the organ whorls.
		The hypothesis or the ABC model is then tested and confirmed by the construction of double mutants with predicted phenotypes.
	weedsworld.arabidopsis.org.uk /Vol3ii/mulligan.html (385 words)

	Tardigrades: A new model organism (Site not responding. Last check: 2007-10-21)
		We here propose to ustilise tardigrades as a new model for examining the evolution of core developmental processes such as axis formation and appendage evolution using a combination of genomic, molecular genetic and developmental biology approaches.
		The Ecdysozoa brings together the two foremost invertebrate model organisms, Drosophila melanogaster and Caenorhabditis elegans, suggesting that the evolutionary history of these two diverse animals might include the acquisition of extremely divergent modes of development.
		A clarification of the differences and similarities between nematodes and arthropods would be of utility in both universalising the lessons learned (and to be learnt) from the fly and worm projects and in itemising the peculiarities of both systems.
	nema.cap.ed.ac.uk /tardigrades/Tardigrades.html (4143 words)

	BioMed Central \| Full text \| Selecting representative model micro-organisms
		In microbiology the initial choice of model strain is frequently a well-characterized laboratory strain, often selected at a time when the ability to determine population structure and to measure genetic distances was limited (see for example [1,2]).
		Likewise if we were to investigate another, less conserved ORF across the group, the model organism may fail to show significant homology to a large number of members of the group even at the amino acid sequence level.
		Choosing a model organism in the example in Figure 1A is trivial because the members of the group are distributed in a highly symmetrical fashion.
	www.biomedcentral.com /1471-2180/5/26 (4238 words)

	Electronically inferred events in Reactome
		Reactions that were themselves inferred based on data from the model organism, and reactions involving species in addition to human (e.g., HIV infection of human cells) are excluded from electronic inference.
		For human proteins that lack a model organism OP but that are included in complexes inferred due to the 75% threshold rule, placeholder model organism entities (called 'Ghost homologue of...') are created.
		On the other hand we may miss a truly orthologous reaction in the model organism because it is mediated by structurally divergent proteins and the OrthoMCL strategy failed to identify them.
	www.reactome.org /electronic_inference.html (565 words)

	Functional Genomics (Site not responding. Last check: 2007-10-21)
		Comparative Genomics includes DNA sequence comparisons between humans and model organisms, and tests performed in model organisms that can be used to study and predict gene function in genomes such as humans.
		Zebrafish (Danio rerio) A relatively new model organism.ideally suited for functional genomics as its transparent larvae, which develop outside the mother's body, allow easy visual inspection of many traits such as heart function and angiogenesis.
		Mouse (Mus musculus)The closest model organism to humans is especially used in development, genetic and immunology studies.
	www.biology.iupui.edu /biocourses/Biol540/19functional.html (1157 words)

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