Model organizma

Model canlı veya model organizma, belirli biyolojik olayların anlaşılması için yapılan deneylerde yaygın olarak kullanılan canlılara verilen genel isimdir. Bu canlılarda çalışılarak bulunması ümit edilen keşiflerle, canlılardaki diğer süreçlerin de açıklanacakları düşünülmektedir.

Model organizma

thumb|right|Elektron mikroskobunda birkaç coli hücresi] thumb| melanogaster|Drosophila, deneylerde kullanılan ünlü canlılardan biridir.] Model organizma veya model canlı, belirli biyolojik olayların anlaşılması için yapılan deneylerde yaygın olarak kullanılan canlılara verilen genel isimdir. Bu canlılarda çalışılarak bulunması ümit edilen keşiflerle, diğer canlılardaki süreçlerin de açıklanmaları düşünülmektedir.

Model organizmalar özellikle, insan hastalıklarının muhtemel sebepleri ve bunların tedavileri için, bu deneylerin insan üzerinde gerçekleştirilmemediği ve etik olmadığında yaygın olarak kullanılırlar. çeviri This strategy is made possible by the common descent of all living organisms, and the conservation of metabolic and developmental pathways and genetic material over the course of evolution.<ref> kitap belirt|son=Fox |ilk=Michael Allen |başlık=The Case for Animal Experimention: An Evolutionary and Ethical Perspective |yıl=1986 |yayımcı=University of California Press |yer=Berkeley and Los Angeles, California |isbn=0-520-05501-2 </ref>

Model organizmanın seçilmesi

Often, model organisms are chosen on the basis that they are amenable to experimental manipulation. This usually will include characteristics such as short life-cycle, techniques for genetic manipulation (inbred strains, stem cell lines, and transfection systems) 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 several traits. Among these are size, generation time, accessibility, manipulation, genetics, conservation of mechanisms, and potential economic benefit. As comparative molecular biology has become more common, some researchers have sought model organisms from a wider assortment of lineages on the tree of life.

Model organizmaların kullanımı

There are many model organisms. One of the first model systems for molecular biology was the bacterium ``Escherichia coli``, a common constituent of the human digestive system. Several of the bacterial viruses (bacteriophage) that infect ``E. coli`` 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 very 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 grow for an animal, has various visible congenital traits and has a polytene (giant) chromosome in its salivary glands that can be examined under a light microscope. The roundworm ``Caenorhabditis elegans`` is studied because it has very defined development patterns involving fixed numbers of cells, and it can be rapidly assayed for abnormalities.

thumb|right|Electron microphotograph of mosaic virus (TMV) particles]

Önemli model organizmalar

Virüsler

Viruses include:

Prokaryotlar

thumb|right|Sporulating `` subtilis``] Prokaryotes include:



Ökaryotlar

Ökaryotlar şöyledir:

Protistler

* ``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. ``Chlamydomonas reinhardtii`` has a well-studied genetics, with many known and mapped mutants and expressed sequence tags, and there are advanced methods for genetic transformation and selection of genes.<ref> Chlamydomonas reinhardtii resources at the Joint Genome Institute</ref> Sequencing of the ``Chlamydomonas reinhardtii`` genome was reported in October 2007.<ref> Chlamydomonas genome sequenced published in Science, October 12, 2007</ref> 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.
* ``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.
* ``Emiliania huxleyi`` - a unicellular marine coccolithophore alga, extensively studied as a model phytoplankton species.


Mantarlar

thumb|Budding tomography]
* ``Aspergillus nidulans``, subject of genetics studies
* ``Neurospora crassa`` - orange bread mold (genetic studies of meiosis, metabolic regulation, and circadian rhythm)<ref>Rowland H. Davis: Neurospora. Contributions of a Model Organism. Oxford University Press, Oxford, 2000. ISBN 0-19-512236-4.</ref>
* ``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


Bitkiler

thumb|`` thaliana``]
* ``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, <ref name="TAIR"> About Arabidopsis on the The Arabidopsis Information Resource page (TAIR)</ref> and many phenotypic and biochemical mutants have been mapped.<ref name="TAIR"> About Arabidopsis on the The Arabidopsis Information Resource page (TAIR)</ref> Arabidopsis was the first plant to have its genome sequenced.<ref name="TAIR"> About Arabidopsis on the The Arabidopsis Information Resource page (TAIR)</ref> Its genome sequence, along with a wide range of information concerning ``Arabidopsis``, is maintained by the TAIR database.<ref name="TAIR"> About Arabidopsis on the The Arabidopsis Information Resource page (TAIR)</ref> <br />``(Plant physiology, Developmental biology, Molecular genetics, Population genetics, 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 the smallest genome size of any plant reported (~110Mb) and its sequence will be released by the Joint Genome Institute in early 2008. ``(Evolutionary biology, 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)``thumb|left|`` 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 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.
thumb|right|`` mays``]
*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 finished. ``(Agronomy, Molecular biology)``
*``Physcomitrella patens`` is a moss increasingly used for studies on development and molecular evolution of plants.<ref name="Rensing">Rensing, S. A., Lang, D., Zimmer, A. D., Terry, A., Salamov, A., Shapiro, H. et al. (2008). The physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science, 319(5859), 64-69.</ref> It is so far the only non-vascular plant (and so the only "primitive" plant) with its genome completely sequenced .<ref name="Rensing">Rensing, S. A., Lang, D., Zimmer, A. D., Terry, A., Salamov, A., Shapiro, H. et al. (2008). The physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science, 319(5859), 64-69.</ref> ``(Plant physiology, Evolutionary biology, Molecular genetics, Molecular biology)``
*``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. The genome sequence of Poplar (Populus trichocarpa) sequence is publicly available.
*See also ``Chlamydomonas reinhardtii``, above under Protists.


Hayvanlar

Omurgasızlar
]
* ``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``<ref> Riddle, Donald L.; Blumenthal, Thomas; Meyer, Barbara J.; and Priess, James R. (Eds.). (1997). ``C. ELEGANS II``. Woodbury, NY: Cold Spring Harbor Press. ISBN 0-87969-532-3. Full text available on-line.</ref> - 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<ref>cite journal | author=Manev H, Dimitrijevic N, Dzitoyeva S. | journal=Trends Pharmacol. Sci. | title=Techniques: fruit flies as models for neuropharmacological research. | volume=24 | issue=1 | pages=41-43 | year=2003 | url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12498730&query_hl=1 </ref>. ``(Molecular genetics, Population genetics, Developmental biology)``.
* ``Euprymna scolopes``, the Hawaiian bobtail squid, model for animal-bacterial symbiosis, bioluminescent vibrios
*``Hydra ``, 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
* ``Strongylocentrotus purpuratus``, the purple sea urchin, widely used in developmental biology
* ``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


Omurgalılar
thumb|Laboratuvar faresi
* ``Cavia porcellus``, Gine domuzu, Robert Koch ve diğer erken dönem bakteriyolojistler tarafından, bakteriyal enfeksiyonlarda konak olarak kullanılmış, bu nedenle deyim yerindeyse, günümüzde de, az da olsa "laboratuvar hayvanı" olarak adlandırılmaktadır.
* Tavuk (``Gallus gallus domesticus``) - bir amniyota olarak gelişim çalışmalarında kullanılır ve mikromanüplasyon için kusursuzdur (örneğin doku aşılama) ve gen ürünlerinin üst ifadesinde.
* Kedi (``Felis cattus``) - nörofizyolojik araştırmalarda kullanılır
* Köpek (``Canis lupus familiaris``) - solunumla ilgili ve kardiyovaskülerde önemli bir modeldir
* Hamster - kala-azarda (leishmania) ilk çalışılan canlı
* Fare (``Mus musculus``) - omurgalıların klasik canlısıdır. <!--Soyundan olan bazı döllerin var oluşunda, any 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)``-->
* ``Homo sapiens`` (insanlar) - çeşitli klinik çalışmalarda kullanılır.
*``Oryzias latipes``, Medaka (Japon pirinç balığı) gelişim biyolojisinde kullanılan önemli bir canlıdır, sıradan Zebra balığından daha dayanıklı olması gibi avantajları vardır.
* Sıçan (``Rattus norvegicus``) - özellikle toksikoloji modeli olarak kullanışlıdır; ayrıca nörolojik model ve akrabası fareden daha büyük organlara ve alt organeler yapılara sahip olmasıyla ilkel hücre kültürleri kaynaklarında, ``(moleküler evrim, genomik)`` çalışmalarında kullanılır.
* ``Rhesus macaque`` - makak maymunu enfeksiyon hastalıkları ve akıl-kavrama çalışmalarında
*``Sigmodon hispidus`` - pamuk sıçanı polio araştırmalarında ilk kullanılan canlı
* ``Taeniopygia guttata`` - zebra ispinozu - ötücü kuşların ötme sistemleri ve memeli olmayanlarda işitme sistemleri
* ``Takifugu rubripres``, bir şişen balık türü - bir miktar junk DNA`ya sahip genom
* ``Xenopus laevis``, Afrika pençeli kurbağası - büyük embriyosu nedeniyle gelişim çalışmalarında, fiziksel ve farmakolojik işleyişlerde yüksek dayanıklılığı nedeniyle.
* Zebra balığı (``Danio rerio``), gelişmesinin erken dönemlerinde hayvanın iç vücut anatomisinin görülmesine benzersiz olarak imkan veren, neredeyse şeffaf vücuda sahip bir tatlı su balığı. Zebra balıkları gelişim çalışmalarında, toksikoloji ve toksikopatolojide <ref>Spitsbergen J.M. and Kent M.L. (2003). The state of the art of the zebrafish model for toxicology and toxicologic pathology research--advantages and current limitations. ``Toxicol Pathol.`` 31 (Supplement), 62-87. PubMed Abstract Link => PMID 12597434.</ref>, özgül gen fonksiyonları ve sinyalleme yollarının araştırılmasında kullanılır.


Özel araştırmalar için kullanılan model organizmalar

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|url=http://en.wikipedia.org/wiki/Model_organisms
|tarih= 09 Mart 2008
|dil= İngilizce
|madde=Model organisms




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