Model organism

A model organism is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the model organism will provide insight into the workings of other organisms.[1] Model organisms are widely used to research human disease when human experimentation would be unfeasible or unethical.[2] 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.[3]

Studying model organisms can be informative, but care must be taken when generalizing from one organism to another.[4]

In researching human disease, model organisms allow for better understanding the disease process without the added risk of harming an actual human. The species chosen will usually meet a determined taxonomic equivalency to humans, so as to react to disease or its treatment in a way that resembles human physiology as needed. Although biological activity in a model organism does not ensure an effect in humans, many drugs, treatments and cures for human diseases are developed in part with the guidance of animal models.[5][6] There are three main types of disease models: homologous, isomorphic and predictive. Homologous animals have the same causes, symptoms and treatment options as would humans who have the same disease. Isomorphic animals share the same symptoms and treatments. Predictive models are similar to a particular human disease in only a couple of aspects, but are useful in isolating and making predictions about mechanisms of a set of disease features.[7]

Drosophila melanogaster - side (aka)
Drosophila melanogaster, one of the most famous subjects for genetics experiments
S cerevisiae under DIC microscopy
Saccharomyces cerevisiae, one of the most intensively studied eukaryotic model organisms in molecular and cell biology

History

The use of animals in research dates back to ancient Greece, with Aristotle (384–322 BCE) and Erasistratus (304–258 BCE) among the first to perform experiments on living animals.[8] Discoveries in the 18th and 19th centuries included Antoine Lavoisier's use of a guinea pig in a calorimeter to prove that respiration was a form of combustion, and Louis Pasteur's demonstration of the germ theory of disease in the 1880s using anthrax in sheep.

Research using animal models has been central to many of the achievements of modern medicine.[9][10][11] It has contributed most of the basic knowledge in fields such as human physiology and biochemistry, and has played significant roles in fields such as neuroscience and infectious disease.[12][13] For example, the results have included the near-eradication of polio and the development of organ transplantation, and have benefited both humans and animals.[9][14] From 1910 to 1927, Thomas Hunt Morgan's work with the fruit fly Drosophila melanogaster identified chromosomes as the vector of inheritance for genes.[15][16] Drosophila became one of the first, and for some time the most widely used, model organisms,[17] and Eric Kandel wrote that Morgan's discoveries "helped transform biology into an experimental science."[18] D. melanogaster remains one of the most widely used eukaryotic model organisms. During the same time period, studies on mouse genetics in the laboratory of William Ernest Castle in collaboration with Abbie Lathrop led to generation of the DBA ("dilute, brown and non-agouti") inbred mouse strain and the systematic generation of other inbred strains.[19][20] The mouse has since been used extensively as a model organism and is associated with many important biological discoveries of the 20th and 21st centuries.[21]

In the late 19th century, Emil von Behring isolated the diphtheria toxin and demonstrated its effects in guinea pigs. He went on to develop an antitoxin against diphtheria in animals and then in humans, which resulted in the modern methods of immunization and largely ended diphtheria as a threatening disease.[22] The diphtheria antitoxin is famously commemorated in the Iditarod race, which is modeled after the delivery of antitoxin in the 1925 serum run to Nome. The success of animal studies in producing the diphtheria antitoxin has also been attributed as a cause for the decline of the early 20th-century opposition to animal research in the United States.[23]

Subsequent research in model organisms led to further medical advances, such as Frederick Banting's research in dogs, which determined that the isolates of pancreatic secretion could be used to treat dogs with diabetes. This led to the 1922 discovery of insulin (with John Macleod)[24] and its use in treating diabetes, which had previously meant death.[25] John Cade's research in guinea pigs discovered the anticonvulsant properties of lithium salts,[26] which revolutionized the treatment of bipolar disorder, replacing the previous treatments of lobotomy or electroconvulsive therapy. Modern general anaesthetics, such as halothane and related compounds, were also developed through studies on model organisms, and are necessary for modern, complex surgical operations.[27][28]

In the 1940s, Jonas Salk used rhesus monkey studies to isolate the most virulent forms of the polio virus,[29] which led to his creation of a polio vaccine. The vaccine, which was made publicly available in 1955, reduced the incidence of polio 15-fold in the United States over the following five years.[30] Albert Sabin improved the vaccine by passing the polio virus through animal hosts, including monkeys; the Sabin vaccine was produced for mass consumption in 1963, and had virtually eradicated polio in the United States by 1965.[31] It has been estimated that developing and producing the vaccines required the use of 100,000 rhesus monkeys, with 65 doses of vaccine produced from each monkey. Sabin wrote in 1992, "Without the use of animals and human beings, it would have been impossible to acquire the important knowledge needed to prevent much suffering and premature death not only among humans, but also among animals."[32]

Other 20th-century medical advances and treatments that relied on research performed in animals include organ transplant techniques,[33][34][35][36] the heart-lung machine,[37] antibiotics,[38][39][40] and the whooping cough vaccine.[41] Treatments for animal diseases have also been developed, including for rabies,[42] anthrax,[42] glanders,[42] feline immunodeficiency virus (FIV),[43] tuberculosis,[42] Texas cattle fever,[42] classical swine fever (hog cholera),[42] heartworm, and other parasitic infections.[44] Animal experimentation continues to be required for biomedical research,[45] and is used with the aim of solving medical problems such as Alzheimer's disease,[46] AIDS,[47][48][49] multiple sclerosis,[50] spinal cord injury, many headaches,[51] and other conditions in which there is no useful in vitro model system available.

Selection

Models are those organisms with a wealth of biological data that make them attractive to study as examples for other species and/or natural phenomena that are more difficult to study directly. Continual research on these organisms focus on a wide variety of experimental techniques and goals from many different levels of biology—from ecology, behavior and biomechanics, down to the tiny functional scale of individual tissues, organelles and proteins. Inquiries about the DNA of organisms are classed as genetic models (with short generation times, such as the fruitfly and nematode worm), experimental models, and genomic parsimony models, investigating pivotal position in the evolutionary tree.[52] Historically, model organisms include a handful of species with extensive genomic research data, such as the NIH model organisms.[53]

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 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 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.

Phylogeny and genetic relatedness

The primary reason for the use of model organisms in research is the evolutionary principle that all organisms share some degree of relatedness and genetic similarity due to common ancestry. The study of taxonomic human relatives, then, can provide a great deal of information about mechanism and disease within the human body that can be useful in medicine.

Various phylogenetic trees for vertebrates have been constructed using comparative proteomics, genetics, genomics as well as the geochemical and fossil record.[54] These estimations tell us that humans and chimpanzees last shared a common ancestor about 6 million years ago (mya). As our closest relatives, chimpanzees have a lot of potential to tell us about mechanisms of disease (and what genes may be responsible for human intelligence). However, chimpanzees are rarely used in research and are protected from highly invasive procedures. The most common animal model is the rodent. Phylogenetic trees estimate that humans and rodents last shared a common ancestor ~80-100mya.[55][56] Despite this distant split, humans and rodents have far more similarities than they do differences. This is due to the relative stability of large portions of the genome; making the use of vertebrate animals particularly productive.

Genomic data is used to make close comparisons between species and determine relatedness. As humans, we share about 99% of our genome with chimpanzees[57][58] (98.7% with bonobos)[59] and over 90% with the mouse.[56] With so much of the genome conserved across species, it is relatively impressive that the differences between humans and mice can be accounted for in approximately six thousand genes (of ~30,000 total). Scientists have been able to take advantage of these similarities in generating experimental and predictive models of human disease.

Use

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, it is debated whether bacteriophages should be classified as organisms, because they lack metabolism and depend on functions of the host cells for propagation.[60]

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.

Disease models

Animal models serving in research may have an existing, inbred or induced disease or injury that is similar to a human condition. These test conditions are often termed as animal models of disease. The use of animal models allows researchers to investigate disease states in ways which would be inaccessible in a human patient, performing procedures on the non-human animal that imply a level of harm that would not be considered ethical to inflict on a human.

The best models of disease are similar in etiology (mechanism of cause) and phenotype (signs and symptoms) to the human equivalent. 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. For instance, behavioral analogues of anxiety or pain in laboratory animals can be used to screen and test new drugs for the treatment of these conditions in humans. A 2000 study found that animal models concorded (coincided on true positives and false negatives) with human toxicity in 71% of cases, with 63% for nonrodents alone and 43% for rodents alone.[61]

In 1987, Davidson et al. suggested that selection of an animal model for research be based on nine considerations. These include "1) appropriateness as an analog, 2) transferability of information, 3) genetic uniformity of organisms, where applicable, 4) background knowledge of biological properties, 5) cost and availability, 6) generalizability of the results, 7) ease of and adaptability to experimental manipulation, 8) ecological consequences, and 9) ethical implications."[62]

Animal models can be classified as homologous, isomorphic or predictive. Animal models can also be more broadly classified into four categories: 1) experimental, 2) spontaneous, 3) negative, 4) orphan.[63]

Experimental models are most common. These refer to models of disease that resemble human conditions in phenotype or response to treatment but are induced artificially in the laboratory. Some examples include:

Spontaneous models refer to diseases that are analogous to human conditions that occur naturally in the animal being studied. These models are rare, but informative. Negative models essentially refer to control animals, which are useful for validating an experimental result. Orphan models refer to diseases for which there is no human analog and occur exclusively in the species studied.[63]

The increase in knowledge of the genomes of non-human primates and other mammals that are genetically close to humans is allowing the production of genetically engineered animal tissues, organs and even animal species which express human diseases, providing a more robust model of human diseases in an animal model.

Animal models observed in the sciences of psychology and sociology are often termed animal models of behavior. It is difficult to build an animal model that perfectly reproduces the symptoms of depression in patients. Depression, as other mental disorders, consists of endophenotypes[77] that can be reproduced independently and evaluated in animals. An ideal animal model offers an opportunity to understand molecular, genetic and epigenetic factors that may lead to depression. By using animal models, the underlying molecular alterations and the causal relationship between genetic or environmental alterations and depression can be examined, which would afford a better insight into pathology of depression. In addition, animal models of depression are indispensable for identifying novel therapies for depression.

Important model organisms

Model organisms are drawn from all three domains of life, as well as viruses. The most widely studied prokaryotic model organism is Escherichia coli (E. coli), which has been intensively investigated for over 60 years. It is a common, gram-negative gut bacterium which can be grown and cultured easily and inexpensively in a laboratory setting. It is the most widely used organism in molecular genetics, and is an important species in the fields of biotechnology and microbiology, where it has served as the host organism for the majority of work with recombinant DNA.[78]

Simple model eukaryotes include baker's yeast (Saccharomyces cerevisiae) and fission yeast (Schizosaccharomyces pombe), both of which share many characters with higher cells, including those of humans. For instance, many cell division genes that are critical for the development of cancer have been discovered in yeast. Chlamydomonas reinhardtii, a unicellular green alga with well-studied genetics, is used to study photosynthesis and motility. C. reinhardtii has many known and mapped mutants and expressed sequence tags, and there are advanced methods for genetic transformation and selection of genes.[79] Dictyostelium discoideum is used in molecular biology and genetics, and is studied as an example of cell communication, differentiation, and programmed cell death.

Lightmatter lab mice
Laboratory mice, widely used in medical research

Among invertebrates, the fruit fly Drosophila melanogaster is famous as the subject of genetics experiments by Thomas Hunt Morgan and others. They are easily raised in the lab, with rapid generations, high fecundity, few chromosomes, and easily induced observable mutations.[80] The nematode Caenorhabditis elegans is used for understanding the genetic control of development and physiology. It was first proposed as a model for neuronal development by Sydney Brenner in 1963, and has been extensively used in many different contexts since then.[81][82] C. elegans was the first multicellular organism whose genome was completely sequenced, and as of 2012, the only organism to have its connectome (neuronal "wiring diagram") completed.[83][84]

Arabidopsis thaliana is currently the most popular model plant. Its small stature and short generation time facilitates rapid genetic studies,[85] and many phenotypic and biochemical mutants have been mapped.[85] A. thaliana was the first plant to have its genome sequenced.[85]

Among vertebrates, guinea pigs (Cavia porcellus) were used by Robert Koch and other early bacteriologists as a host for bacterial infections, becoming a byword for "laboratory animal," but are less commonly used today. The classic model vertebrate is currently the mouse (Mus musculus). Many inbred strains exist, as well as lines selected for particular traits, often of medical interest, e.g. body size, obesity, muscularity, and voluntary wheel-running behavior.[86] The rat (Rattus norvegicus) is particularly useful as a toxicology model, and as a neurological model and source of primary cell cultures, owing to the larger size of organs and suborganellar structures relative to the mouse, while eggs and embryos from Xenopus tropicalis and Xenopus laevis (African clawed frog) are used in developmental biology, cell biology, toxicology, and neuroscience.[87][88] Likewise, the zebrafish (Danio rerio) has a nearly transparent body during early development, which provides unique visual access to the animal's internal anatomy during this time period. Zebrafish are used to study development, toxicology and toxicopathology,[89] specific gene function and roles of signaling pathways.

Other important model organisms and some of their uses include: T4 phage (viral infection), Tetrahymena thermophila (intracellular processes), maize (transposons), hydras (regeneration and morphogenesis),[90] cats (neurophysiology), chickens (development), dogs (respiratory and cardiovascular systems), Nothobranchius furzeri (aging),[91] and non-human primates such as the rhesus macaque and chimpanzee (hepatitis, HIV, Parkinson's disease, cognition, and vaccines).

Selected model organisms

The organisms below have become model organisms because they facilitate the study of certain characters or because of their genetic accessibility. For example, E. coli was one of the first organisms for which genetic techniques such as transformation or genetic manipulation has been developed.

The genomes of all model species have been sequenced, including their mitochondrial/chloroplast genomes. Model organism databases exist to provide researchers with a portal from which to download sequences (DNA, RNA, or protein) or to access functional information on specific genes, for example the sub-cellular localization of the gene product or its physiological role.

Model Organism Common name Informal classification Usage (examples)
Virus Phi X 174 Virus evolution[92]
Prokaryote Escherichia coli Bacteria bacterial genetics, metabolism
Eukaryote, unicellular Dictyostelium discoideum Amoeba
Saccharomyces cerevisiae Yeast cell division, organelles, etc.
Schizosaccharomyces pombe Yeast cell cycle, cytokinesis, chromosome biology, telomeres, DNA metabolism, cytoskeleton organization, industrial applications[93][94]
Chlamydomonas reinhardtii Algae
Tetrahymena thermophila Ciliate
Emiliania huxleyi Plankton
Eukaryote, multicellular Caenorhabditis elegans Worm differentiation, development
Drosophila melanogaster Fruit fly Insect developmental biology
Callosobruchus maculatus Cowpea Weevil Insect developmental biology
Arabidopsis thaliana Thale cress Flowering plant
Physcomitrella patens Spreading earthmoss Moss
Vertebrate Danio rerio Zebrafish Fish embryonic development
Fundulus heteroclitus Mummichog Fish
Nothobranchius furzeri Turquoise killifish Fish aging, disease, evolution
Oryzias latipes Japanese rice fish Fish
Anolis carolinensis Carolina anole Reptile reptile biology, evolution
Mus musculus House mouse Mammal disease model for humans
Gallus gallus Red junglefowl Bird embryological development and organogenesis
Xenopus laevis (Note: and X. tropicalis)[95] African clawed frog Amphibian embryonic development

Limitations

Many animal models serving as test subjects in biomedical research, such as rats and mice, may be selectively sedentary, obese and glucose intolerant. This may confound their use to model human metabolic processes and diseases as these can be affected by dietary energy intake and exercise.[96] Similarly, there are differences between the immune systems of model organisms and humans that lead to significantly altered responses to stimuli,[97][98][99][100] although the underlying principles of genome function may be the same.[100]

Unintended bias

Some studies suggests that inadequate published data in animal testing may result in irreproducible research, with missing details about how experiments are done omitted from published papers or differences in testing that may introduce bias. Examples of hidden bias include a 2014 study from McGill University in Montreal, Canada which suggests that mice handled by men rather than women showed higher stress levels.[101][102][103] Another study in 2016 suggested that gut microbiomes in mice may have an impact upon scientific research.[104]

Alternatives

Ethical concerns, as well as the cost, maintenance and relative inefficiency of animal research has encouraged development of alternative methods for the study of disease. Cell culture, or in vitro studies, provide an alternative that preserves the physiology of the living cell, but does not require the sacrifice of an animal for mechanistic studies. Human, inducible pluripotent stem cells can also elucidate new mechanisms for understanding cancer and cell regeneration. Imaging studies (such as MRI or PET scans) enable non-invasive study of human subjects. Recent advances in genetics and genomics can identify disease-associated genes, which can be targeted for therapies.

Ultimately, however, there is no substitute for a living organism when studying complex interactions in disease pathology or treatments.[105][106]

Ethics

Debate about the ethical use of animals in research dates at least as far back as 1822 when the British Parliament enacted the first law for animal protection preventing cruelty to cattle.[107] This was followed by the Cruelty to Animals Act of 1835 and 1849, which criminalized ill-treating, over-driving, and torturing animals. In 1876, under pressure from the National Anti-Vivisection Society, the Cruelty to Animals Act was amended to include regulations governing the use of animals in research. This new act stipulated that 1) experiments must be proven absolutely necessary for instruction, or to save or prolong human life; 2) animals must be properly anesthetized; and 3) animals must be killed as soon as the experiment is over. Today, these three principles are central to the laws and guidelines governing the use of animals and research. In the U.S., the Animal Welfare Act of 1970 (see also Laboratory Animal Welfare Act) set standards for animal use and care in research. This law is enforced by APHIS’s Animal Care program.[108]

In academic settings in which NIH funding is used for animal research, institutions are governed by the NIH Office of Laboratory Animal Welfare (OLAW). At each site, OLAW guidelines and standards are upheld by a local review board called the Institutional Animal Care and Use Committee (IACUC). All laboratory experiments involving living animals are reviewed and approved by this committee. In addition to proving the potential for benefit to human health, minimization of pain and distress, and timely and humane euthanasia, experimenters must justify their protocols based on the principles of Replacement, Reduction and Refinement.[109]

Replacement refers to efforts to engage alternatives to animal use. This includes the use of computer models, non-living tissues and cells, and replacement of “higher-order” animals (primates and mammals) with “lower” order animals (e.g. cold-blooded animals, invertebrates, bacteria) wherever possible.[110]

Reduction refers to efforts to minimize number of animals used during the course of an experiment, as well as prevention of unnecessary replication of previous experiments. To satisfy this requirement, mathematical calculations of statistical power are employed to determine the minimum number of animals that can be used to get a statistically significant experimental result.

Refinement refers to efforts to make experimental design as painless and efficient as possible in order to minimize the suffering of each animal subject.

See also

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Further reading

  • Marx, Vivien (29 May 2014). "Models: stretching the skills of cell lines and mice". Technology Feature. Nature Methods (Paper "Nature Reprint Collection, Technology Features" (Nov 2014)). 11 (6): 617–20. doi:10.1038/nmeth.2966. PMID 24874573.

External links

Amphidinium

Amphidinium is a genus of dinoflagellates. The type for the genus is Amphidinium operculatum Claparède & Lachmann. The genus includes the species Amphidinium carterae which is used as a model organism.

Biological database

Biological databases are libraries of life sciences information, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics. Information contained in biological databases includes gene function, structure, localization (both cellular and chromosomal), clinical effects of mutations as well as similarities of biological sequences and structures.

Biological databases can be broadly classified into sequence, structure and functional databases. Nucleic acid and protein sequences are stored in sequence databases and structure databases store solved structures of RNA and proteins. Functional databases provide information on the physiological role of gene products, for example enzyme activities, mutant phenotypes, or biological pathways. Model Organism Databases are functional databases that provide species-specific data. Databases are important tools in assisting scientists to analyze and explain a host of biological phenomena from the structure of biomolecules and their interaction, to the whole metabolism of organisms and to understanding the evolution of species. This knowledge helps facilitate the fight against diseases, assists in the development of medications, predicting certain genetic diseases and in discovering basic relationships among species in the history of life.

Biological knowledge is distributed among many different general and specialized databases. This sometimes makes it difficult to ensure the consistency of information. Integrative bioinformatics is one field attempting to tackle this problem by providing unified access. One solution is how biological databases cross-reference to other databases with accession numbers to link their related knowledge together.

Relational database concepts of computer science and Information retrieval concepts of digital libraries are important for understanding biological databases. Biological database design, development, and long-term management is a core area of the discipline of bioinformatics. Data contents include gene sequences, textual descriptions, attributes and ontology classifications, citations, and tabular data. These are often described as semi-structured data, and can be represented as tables, key delimited records, and XML structures.

Chlamydomonas reinhardtii

Chlamydomonas reinhardtii is a single-cell green alga about 10 micrometres in diameter that swims with two flagella. It has a cell wall made of hydroxyproline-rich glycoproteins, a large cup-shaped chloroplast, a large pyrenoid, and an "eyespot" that senses light.

Chlamydomonas species are widely distributed worldwide in soil and fresh water. Chlamydomonas reinhardtii is an especially well studied biological model organism, partly due to its ease of culturing and the ability to manipulate its genetics. When illuminated, C. reinhardtii can grow photoautotrophically, but it can also grow in the dark if supplied with organic carbon. Commercially, C. reinhardtii is of interest for producing biopharmaceuticals and biofuel, as well being a valuable research tool in making hydrogen.

Dictyostelid

The dictyostelids (Dictyostelia/Dictyostelea, ICZN, or Dictyosteliomycetes, ICBN) are a group of cellular slime molds, or social amoebae.

Euperipatoides kanangrensis

Euperipatoides kanangrensis is a species of velvet worm of the Peripatopsidae family, described in 1996 from specimens collected in Kanangra-Boyd National Park, New South Wales. It is endemic to Australia. The embryonic development of Euperipatoides kanangrensis has been described. This species is used as model organism for the last common ancestor of the Panarthropoda. It resembles fossil Cambrian lobopodians.

Euperipatoides rowelli

Euperipatoides rowelli is an ovoviviparous species of velvet worm of the Peripatopsidae family. It is found in New South Wales and the Australian Capital Territory.

FlyBase

FlyBase is an online bioinformatics database and the primary repository of genetic and molecular data for the insect family Drosophilidae. For the most extensively studied species and model organism, Drosophila melanogaster, a wide range of data are presented in different formats. Information in FlyBase originates from a variety of sources ranging from large-scale genome projects to the primary research literature. These data types include mutant phenotypes, molecular characterization of mutant alleles and other deviations, cytological maps, wild-type expression patterns, anatomical images, transgenic constructs and insertions, sequence-level gene models and molecular classification of gene product functions. Query tools allow navigation of FlyBase through DNA or protein sequence, by gene or mutant name, or through terms from the several ontologies used to capture functional, phenotypic, and anatomical data. The database offers several different query tools in order to provide efficient access to the data available and facilitate the discovery of significant relationships within the database. Links between FlyBase and external databases, such as BDGP or modENCODE, provide opportunity for further exploration into other model organism databases and other resources of biological and molecular information. The FlyBase project is carried out by a consortium of Drosophila researchers and computer scientists at Harvard University and Indiana University in the United States, and University of Cambridge in the United Kingdom.

FlyBase is one of the organizations contributing to the Generic Model Organism Database (GMOD).

Generic Model Organism Database

The Generic Model Organism Database (GMOD) project provides biological research communities with a toolkit of open-source software components for visualizing, annotating, managing, and storing biological data. The GMOD project is funded by the United States National Institutes of Health, National Science Foundation and the USDA Agricultural Research Service.

Holomycota

Holomycota or Nucletmycea are a basal Opisthokont clade as sister of the Holozoa. It consists of the Cristidiscoidea and the kingdom Fungi. The position of nucleariids, unicellular free-living phagotrophic amoebae, as the earliest lineage of Holomycota suggests that animals and fungi independently acquired complex multicellularity from a common unicellular ancestor and that the osmotrophic lifestyle (one of the fungal hallmarks) was originated later in the divergence of this eukaryotic lineage. Opisthosporidians is a recently proposed taxonomic group that includes aphelids, Microsporidia and Cryptomycota, three groups of endoparasites.Rozella (Cryptomycota) is the earliest fungal genus in which chitin has been observed at least in some stages of their life cycle, although the chitinus cell wall (another fungal hallmark) and osmotrophy originated in a common ancestor of Blastocladiomycota and Chytridiomycota, which still contain some ancestral characteristics such as the flagellum in zoosporic stage. The groups of fungi with the characteristic hyphal growth, Zoopagomycota, Mucuromycotina and Dikarya, originated from a common ancestor ~700 Mya. Zoopagomycota are mostly pathogens of animals or other fungi, Mucuromycotina is a more diverse group including parasites, saprotrophs or ectomycorrhizal. Dikarya is the group embracing Ascomycota and Basidiomycota, which comprise ~98% of the described fungal species. Because of this rich diversity, Dikarya includes highly morphologically distinct groups, from hyphae or unicellular yeasts (such as the model organism Saccharomyces cerevisiae) to the complex multicellular fungi popularly known as mushrooms. Contrary to animals and land plants with complex multicellularity, the inferred phylogenetic relationships indicate that fungi acquired and lost multicellularity multiple times along Ascomycota and Basidiomycota evolution.

List of biological databases

Biological databases are stores of biological information. The journal Nucleic Acids Research regularly publishes special issues on biological databases and has a list of such databases. The 2018 issue has a list of about 180 such databases and updates to previously described databases.

Membranome database

Membranome database provides structural and functional information about more than 6000 single-pass (bitopic) transmembrane proteins from Homo sapiens, Arabidopsis thaliana, Dictyostelium discoideum, Saccharomyces cerevisiae, Escherichia coli and Methanocaldococcus jannaschii. Bitopic membrane proteins consist of a single transmembrane alpha-helix connecting water-soluble domains of the protein situated at the opposite sides of a biological membrane. These proteins are frequently involved in the signal transduction and communication between cells in multicellular organisms.

The database provides information about the individual proteins including computationally generated three-dimensional models of their transmembrane alpha-helices spatially arranged in the membrane, topology, intracellular localizations, amino acid sequences, domain architecture, functional annotation and available experimental structures from the Protein Data Bank. It also provides a classification of bitopic proteins into 15 functional classes, more than 700 structural superfamilies and 1400 families, along with 3D structures of bitopic protein complexes which are also classified to different families.

The second Membranome version provides 3D models of more than 2000 parallel homodimers formed by TM α-helices of bitopic proteins from different organisms which were generated using TMDOCK program. The models of the homodimers were verified through comparison with available experimental data for nearly 600 proteins. The database includes downloadable coordinate files of transmembrane helices and their homodimers with calculated membrane boundaries.

The database website provides access to related webservers, FMAP and TMDOCK which have been developed for modeling individual alpha-helices and their dimeric complexes in membranes. The database and webservers were used in experimental and bioinformatics studies of bitopic membrane proteins

Model organism databases

Model organism databases (MODs) are biological databases, or knowledgebases, dedicated to the provision of in-depth biological data for intensively studied model organisms. MODs allow researchers to easily find background information on large sets of genes, plan experiments efficiently, combine their data with existing knowledge, and construct novel hypotheses. They allow users to analyse results and interpret datasets, and the data they generate are increasingly used to describe less well studied species. Where possible, MODs share common approaches to collect and represent biological information. For example, all MODs use the Gene Ontology to describe functions, processes and cellular locations of specific gene products. Projects also exist to enable software sharing for curation, visualization and querying between different MODs. Organismal diversity and varying user requirements however mean that MODs are often required to customize capture, display, and provision of data.

Mouse Genome Informatics

Mouse Genome Informatics (MGI) is a free, online database and bioinformatics resource hosted by The Jackson Laboratory, with funding by the National Human Genome Research Institute (NHGRI), the National Cancer Institute (NCI), and the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD). MGI provides access to data on the genetics, genomics and biology of the laboratory mouse to facilitate the study of human health and disease. The database integrates multiple projects, with the two largest contributions coming from the Mouse Genome Database and Gene Expression Database (GXD).The Mouse Genome Informatics resource is a collection of data, tools, and analyses created and tailored for use in the laboratory mouse, a widely used model organism. It is "the authoritative source of official names for mouse genes, alleles, and strains", which follow the guidelines established by the International Committee on Standardized Genetic Nomenclature for Mice. The history and focus of Jackson Laboratory research and production facilities generates tremendous knowledge and depth which researchers can mine to advance their research. A dedicated community of mouse researchers, worldwide enhances and contributes to the knowledge as well. This is an indispensable tool for any researcher using the mouse as a model organism for their research, and for researchers interested in genes that share homology with the mouse genes. Various mouse research support resources including animal collections and free colony management software are also available at the MGI site.

Oryza sativa

Oryza sativa, commonly known as Asian rice, is the plant species most commonly referred to in English as rice. Oryza sativa is a grass with a genome consisting of 430Mb across 12 chromosomes. It is renowned for being easy to genetically modify, and is a model organism for cereal biology.

Synechocystis

Synechocystis is a genus of unicellular, freshwater cyanobacteria in the family Merismopediaceae. It includes a strain, Synechocystis sp. PCC 6803, which is a well studied model organism.

The Arabidopsis Information Resource

The Arabidopsis Information Resource (TAIR) is a community resource and online model organism database of genetic and molecular biology data for the model plant Arabidopsis thaliana, commonly known as mouse-ear cress.TAIR integrates information about the Arabidopsis genome, genes, gene products, natural variants, mutant alleles and plant phenotypes and research literature. Data in TAIR can be retrieved using simple and advanced searches, bulk query and download tools, and in collections of prepared text files. The Arabidopsis genome and annotations can be visualized using the interactive SeqViewer and GBrowse tools. TAIR’s biocurators are responsible for acquiring and integrating data from the research literature (functional annotation) as well as for assisting the community in using Arabidopsis data and tools. TAIR collaborates with the Arabidopsis Biological Resource Consortium (ABRC) to allow researchers to search, browse and order seed and DNA stocks. The ABRC's mission is to acquire, preserve and distribute seed and DNA resources that are useful to the Arabidopsis research community. TAIR’s community includes over 28,000 registered users and the website draws about 60,000 unique visitors per month TAIR is located at Phoenix Bioinformatics, and funded by subscriptions.

Thermus thermophilus

Thermus thermophilus is a Gram negative bacterium used in a range of biotechnological applications, including as a model organism for genetic manipulation, structural genomics, and systems biology. The bacterium is extremely thermophilic, with an optimal growth temperature of about 65 °C (149 °F). Thermus thermophilus was originally isolated from a thermal vent within a hot spring in Izu, Japan by Tairo Oshima and Kazutomo Imahori. The organism has also been found to be important in the degradation of organic materials in the thermogenic phase of composting.T. thermophilus is classified into several strains, of which HB8 and HB27 are the most commonly used in laboratory environments. Genome analyses of these strains were independently completed in 2004.

WormBase

WormBase is an online biological database about the biology and genome of the nematode model organism Caenorhabditis elegans and contains information about other related nematodes. WormBase is used by the C. elegans research community both as an information resource and as a place to publish and distribute their results. The database is regularly updated with new versions being released every two months. WormBase is one of the organizations participating in the Generic Model Organism Database (GMOD) project.

Zebrafish Information Network

The Zebrafish Information Network (ZFIN) is an online biological database of information about the zebrafish (Danio rerio). The zebrafish is a widely used model organism for genetic, genomic, and developmental studies, and ZFIN provides an integrated interface for querying and displaying the large volume of data generated by this research. To facilitate use of the zebrafish as a model of human biology, ZFIN links these data to corresponding information about other model organisms (e.g., mouse) and to human disease databases. Abundant links to external sequence databases (e.g., GenBank) and to genome browsers are included. Gene product, gene expression, and phenotype data are annotated with terms from biomedical ontologies. ZFIN is based at the University of Oregon in the United States, with funding provided by the National Institutes of Health (NIH).

Major model organisms in genetics

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