Zebrafish Somitogenesis
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The zebrafish (''Danio rerio'') is a species of freshwater
ray-finned fish Actinopterygii (; ), members of which are known as ray-finned fish or actinopterygians, is a class of bony fish that comprise over 50% of living vertebrate species. They are so called because of their lightly built fins made of webbings of sk ...
belonging to the
family Family (from ) is a Social group, group of people related either by consanguinity (by recognized birth) or Affinity (law), affinity (by marriage or other relationship). It forms the basis for social order. Ideally, families offer predictabili ...
Danionidae The danionins are a group of small, minnow-type fish belonging to the family Danionidae. Species of this group are in the genera clades ''Danio'' and '' Devario'' (which also includes ''Chela'', ''Laubuka'', ''Microdevario'', and ''Microrasbora ...
of the
order Order, ORDER or Orders may refer to: * A socio-political or established or existing order, e.g. World order, Ancien Regime, Pax Britannica * Categorization, the process in which ideas and objects are recognized, differentiated, and understood ...
Cypriniformes Cypriniformes is an order of ray-finned fish, which includes many families and genera of cyprinid ( carps and their kin) fish, such as barbs, loaches, botias, and minnows (among others). Cypriniformes is an "order-within-an-order", placed ...
. Native to South Asia, it is a popular aquarium fish, frequently sold under the trade name zebra danio (and thus often called a "
tropical fish Tropical fish are fish found in aquatic tropical environments around the world. Fishkeepers often keep tropical fish in freshwater and saltwater aquariums. The term "tropical fish" is not a taxonomic group, but rather is a general term for f ...
" although it is both tropical and
subtropical The subtropical zones or subtropics are geographical zone, geographical and Köppen climate classification, climate zones immediately to the Northern Hemisphere, north and Southern Hemisphere, south of the tropics. Geographically part of the Ge ...
). The zebrafish is an important and widely used
vertebrate Vertebrates () are animals with a vertebral column (backbone or spine), and a cranium, or skull. The vertebral column surrounds and protects the spinal cord, while the cranium protects the brain. The vertebrates make up the subphylum Vertebra ...
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. Mo ...
in scientific research, particularly
developmental biology Developmental biology is the study of the process by which animals and plants grow and develop. Developmental biology also encompasses the biology of Regeneration (biology), regeneration, asexual reproduction, metamorphosis, and the growth and di ...
, but also gene function,
oncology Oncology is a branch of medicine that deals with the study, treatment, diagnosis, and prevention of cancer. A medical professional who practices oncology is an ''oncologist''. The name's Etymology, etymological origin is the Greek word ὄγ ...
,
teratology Teratology is the study of abnormalities of physiological development in organisms during their life span. It is a sub-discipline in medical genetics which focuses on the classification of congenital abnormalities in dysmorphology caused by ...
, and
drug development Drug development is the process of bringing a new pharmaceutical drug to the market once a lead compound has been identified through the process of drug discovery. It includes preclinical research on microorganisms and animals, filing for regu ...
, in particular pre-clinical development. It is also notable for its regenerative abilities, and has been modified by researchers to produce many
transgenic A transgene is a gene that has been transferred naturally, or by any of a number of genetic engineering techniques, from one organism to another. The introduction of a transgene, in a process known as transgenesis, has the potential to change the ...
strains.


Taxonomy

The zebrafish is a derived member of the genus ''
Brachydanio ''Danio'' is a genus of small freshwater fish in the family Cyprinidae found in South and Southeast Asia, commonly kept in aquaria. They are generally characterised by a pattern of horizontal stripes, rows of spots or vertical bars. Some species ...
'', of the family
Cyprinidae Cyprinidae is a family of freshwater fish commonly called the carp or minnow family, including the carps, the true minnows, and their relatives the barbs and barbels, among others. Cyprinidae is the largest and most diverse fish family, and t ...
. It has a sister-group relationship with '' Danio aesculapii''. Zebrafish are also closely related to the genus ''
Devario ''Devario'' is a genus of fish in the family (biology), family Danionidae, a family which also contains several other genera of popular freshwater aquarium fish such as ''Rasbora'' and ''Danio''. ''Devario'' are native to the rivers and streams ...
'', as demonstrated by a
phylogenetic tree A phylogenetic tree or phylogeny is a graphical representation which shows the evolutionary history between a set of species or taxa during a specific time.Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA. In ...
of close species.


Distribution


Range

The zebrafish is native to freshwater habitats in South Asia where it is found in India, Pakistan, Bangladesh, Nepal and Bhutan. The northern limit is in the South
Himalayas The Himalayas, or Himalaya ( ), is a mountain range in Asia, separating the plains of the Indian subcontinent from the Tibetan Plateau. The range has some of the Earth's highest peaks, including the highest, Mount Everest. More than list of h ...
, ranging from the
Sutlej The Sutlej River or the Satluj River is a major river in Asia, flowing through China, India and Pakistan, and is the longest of the five major rivers of the Punjab region. It is also known as ''Satadru''; and is the easternmost tributary of t ...
river basin in the Pakistan–India border region to the state of
Arunachal Pradesh Arunachal Pradesh (; ) is a States and union territories of India, state in northeast India. It was formed from the North-East Frontier Agency (NEFA) region, and India declared it as a state on 20 February 1987. Itanagar is its capital and la ...
in northeast India. Its range is concentrated in the
Ganges The Ganges ( ; in India: Ganga, ; in Bangladesh: Padma, ). "The Ganges Basin, known in India as the Ganga and in Bangladesh as the Padma, is an international which goes through India, Bangladesh, Nepal and China." is a trans-boundary rive ...
and
Brahmaputra River The Brahmaputra is a trans-boundary river which flows through Southwestern China, Northeastern India, and Bangladesh. It is known as Brahmaputra or Luit in Assamese language, Assamese, Yarlung Tsangpo in Lhasa Tibetan, Tibetan, the Siang/Dihan ...
basins, and the species was first described from Kosi River (lower Ganges basin) of India. Its range further south is more local, with scattered records from the
Western Western may refer to: Places *Western, Nebraska, a village in the US *Western, New York, a town in the US *Western Creek, Tasmania, a locality in Australia *Western Junction, Tasmania, a locality in Australia *Western world, countries that id ...
and
Eastern Ghats The Eastern Ghats is a mountain range that stretches along the East Coast of India, eastern coast of the Indian peninsula. Covering an area of , it traverses the states and union territories of India, states of Odisha, Telangana, Andhra Prade ...
regions. It has frequently been said to occur in Myanmar (Burma), but this is entirely based on pre-1930 records and likely refers to close relatives only described later, notably ''
Danio kyathit ''Danio kyathit'', also called ocelot danio, is a small, schooling species of fish in the family Danionidae. It is endemic to the upper reaches of Irrawaddy River near Myitkyina in northern Myanmar. species description, Described in 1998, it is c ...
''. Likewise, old records from Sri Lanka are highly questionable and remain unconfirmed. Zebrafish have been introduced to a variety of places outside their natural range, including California, Connecticut, Florida and New Mexico in the United States, presumably by deliberate release by aquarists or by escape from fish farms. The New Mexico population had been extirpated by 2003 and it is unclear if the others survive, as the last published records were decades ago. Elsewhere the species has been introduced to Colombia and Malaysia.


Habitats

Zebrafish typically inhabit moderately flowing to stagnant clear water of quite shallow depth in streams, canals, ditches,
oxbow lake An oxbow lake is a U-shaped lake or stream pool, pool that forms when a wide meander of a river is meander cutoff, cut off, creating a free-standing body of water. The word "oxbow" can also refer to a U-shaped bend in a river or stream, whether ...
s, ponds and rice paddies. There is usually some vegetation, either submerged or overhanging from the banks, and the bottom is sandy, muddy or silty, often mixed with pebbles or gravel. In surveys of zebrafish locations throughout much of its Bangladeshi and Indian distribution, the water had a near-neutral to somewhat basic pH and mostly ranged from in temperature. One unusually cold site was only and another unusually warm site was , but the zebrafish still appeared healthy. The unusually cold temperature was at one of the highest known zebrafish locations at above sea level, although the species has been recorded to .


Description

The zebrafish is named for the five uniform, pigmented, horizontal, blue stripes on the side of the body, which are reminiscent of a zebra's stripes, and which extend to the end of the
caudal fin Fins are moving appendages protruding from the body of fish that interact with water to generate thrust and help the fish swim. Apart from the tail or caudal fin, fish fins have no direct connection with the back bone and are supported only ...
. Its shape is
fusiform Fusiform (from Latin ''fusus'' ‘spindle’) means having a spindle (textiles), spindle-like shape that is wide in the middle and tapers at both ends. It is similar to the lemon (geometry), lemon-shape, but often implies a focal broadening of a ...
and laterally compressed, with its mouth directed upwards. The male is
torpedo A modern torpedo is an underwater ranged weapon launched above or below the water surface, self-propelled towards a target, with an explosive warhead designed to detonate either on contact with or in proximity to the target. Historically, such ...
-shaped, with gold stripes between the blue stripes; the female has a larger, whitish belly and silver stripes instead of gold. Adult females exhibit a small genital papilla in front of the
anal fin Fins are moving appendages protruding from the body of fish that interact with water to generate thrust and help the fish swim. Apart from the tail or caudal fin, fish fins have no direct connection with the back bone and are supported o ...
origin. The zebrafish can reach up to in length, although they typically are in the wild with some variations depending on location. Its lifespan in captivity is around two to three years, although in ideal conditions, this may be extended to over five years. In the wild it is typically an annual species.


Psychology

In 2015, a study was published about zebrafishes' capacity for
episodic memory Episodic memory is the memory of everyday events (such as times, location geography, associated emotions, and other contextual information) that can be explicitly stated or conjured. It is the collection of past personal experiences that occurred ...
. The individuals showed a capacity to remember context with respect to objects, locations and occasions (what, when, where). Episodic memory is a capacity of explicit memory systems, typically associated with conscious experience. The Mauthner cells integrate a wide array of sensory stimuli to produce the escape reflex. Those stimuli are found to include the
lateral line The lateral line, also called the lateral line organ (LLO), is a system of sensory organs found in fish, used to detect movement, vibration, and pressure gradients in the surrounding water. The sensory ability is achieved via modified epithelia ...
signals by McHenry et al. 2009 and visual signals consistent with looming objects by Temizer et al. 2015, Dunn et al. 2016, and Yao et al. 2016.


Reproduction

The approximate
generation time In population biology and demography Demography () is the statistical study of human populations: their size, composition (e.g., ethnic group, age), and how they change through the interplay of fertility (births), mortality (deaths), and mi ...
for ''Danio rerio'' is three months. A male must be present for
ovulation Ovulation is an important part of the menstrual cycle in female vertebrates where the egg cells are released from the ovaries as part of the ovarian cycle. In female humans ovulation typically occurs near the midpoint in the menstrual cycle and ...
and
spawning Spawn is the Egg cell, eggs and Spermatozoa, sperm released or deposited into water by aquatic animals. As a verb, ''to spawn'' refers to the process of freely releasing eggs and sperm into a body of water (fresh or marine); the physical act is ...
to occur. Zebrafish are asynchronous spawners and under optimal conditions (such as food availability and favorable water parameters) can spawn successfully frequently, even on a daily basis. Females are able to spawn at intervals of two to three days, laying hundreds of eggs in each
clutch A clutch is a mechanical device that allows an output shaft to be disconnected from a rotating input shaft. The clutch's input shaft is typically attached to a motor, while the clutch's output shaft is connected to the mechanism that does th ...
. Upon release, embryonic development begins; in absence of sperm, growth stops after the first few cell divisions. Fertilized eggs almost immediately become transparent, a characteristic that makes ''D. rerio'' a convenient research model species. Sex determination of common laboratory strains was shown to be a complex genetic trait, rather than to follow a simple ZW or XY system. The zebrafish embryo develops rapidly, with precursors to all major organs appearing within 36 hours of fertilization. The embryo begins as a yolk with a single enormous cell on top (see image, 0 h panel), which divides into two (0.75 h panel) and continues dividing until there are thousands of small cells (3.25 h panel). The cells then migrate down the sides of the yolk (8 h panel) and begin forming a head and tail (16 h panel). The tail then grows and separates from the body (24 h panel). The yolk shrinks over time because the fish uses it for food as it matures during the first few days (72 h panel). After a few months, the adult fish reaches reproductive maturity (bottom panel). To encourage the fish to spawn, some researchers use a fish tank with a sliding bottom insert, which reduces the depth of the pool to simulate the shore of a river. Zebrafish spawn best in the morning due to their Circadian rhythms. Researchers have been able to collect 10,000 embryos in 10 minutes using this method. In particular, one pair of adult fish is capable of laying 200–300 eggs in one morning in approximately 5 to 10 at time. Male zebrafish are furthermore known to respond to more pronounced markings on females, i.e., "good stripes", but in a group, males will mate with whichever females they can find. What attracts females is not currently understood. The presence of plants, even plastic plants, also apparently encourages spawning. Exposure to environmentally relevant concentrations of
diisononyl phthalate Diisononyl phthalate (DINP) is a phthalate used as a plasticizer. DINP is typically a mixture of chemical compounds consisting of various isononyl esters of phthalic acidÛ” Use It is commonly used in a large variety of plastic products includ ...
(DINP), commonly used in a large variety of plastic items, disrupt the
endocannabinoid system The endocannabinoid system (ECS) is a biological system composed of endocannabinoids, which are neurotransmitters that bind to cannabinoid receptors, and cannabinoid receptor proteins that are expressed throughout the central nervous system ( ...
and thereby affect reproduction in a sex-specific manner.


Feeding

Zebrafish feeding practices vary significantly across different developmental stages, reflecting their changing nutritional needs. For newly hatched larvae, which begin feeding at approximately 5 days post-fertilization (dpf), small live prey such as Paramecium or rotifers are commonly used until they reach 9–15 dpf. This early diet is crucial for their growth and survival, as these small organisms provide essential nutrients. As the larvae develop, from 15 dpf onwards, they are typically transitioned to a diet that includes brine shrimp nauplii and dry feeds, which are more nutritionally balanced and easier to manage in laboratory settings. For larvae aged 25 dpf, feeding rates can range from 50% to 300% of their body weight (BW) per day, depending on their size and growth requirements. As zebrafish grow into juveniles (30–90 dpf), the recommended feeding rate decreases to about 6–8% of their BW per day, with a focus on high-quality dry feeds that meet their protein and energy needs. Upon reaching adulthood (over 90 dpf), zebrafish typically require a feeding rate of around 5% of their BW per day. Throughout these stages, it is essential to adjust the particle size of the feed: less than 100 μm for newly hatched larvae, 100–200 μm for those between 16 and 30 dpf, and larger particles for juveniles and adults. This structured approach to feeding not only supports optimal growth and health but also enhances the reliability of experimental outcomes in research settings.


In the aquarium

Zebrafish are hardy fish and considered good for beginner aquarists. Their enduring popularity can be attributed to their playful disposition, as well as their rapid breeding, aesthetics, cheap price and broad availability. They also do well in schools or shoals of six or more, and interact well with other fish species in the aquarium. However, they are susceptible to '' Oodinium'' or velvet disease,
microsporidia Microsporidia are a group of spore-forming unicellular parasites. These spores contain an extrusion apparatus that has a coiled polar tube ending in an anchoring disc at the apical part of the spore.Franzen, C. (2005). How do Microsporidia inva ...
(''Pseudoloma neurophilia''), and ''
Mycobacterium ''Mycobacterium'' is a genus of over 190 species in the phylum Actinomycetota, assigned its own family, Mycobacteriaceae. This genus includes pathogens known to cause serious diseases in mammals, including tuberculosis (''Mycobacterium tuberculo ...
'' species. Given the opportunity, adults eat hatchlings, which may be protected by separating the two groups with a net, breeding box or separate tank. In captivity, zebrafish live approximately forty-two months. Some captive zebrafish can develop a curved spine. The zebra danio was also used to make genetically modified fish and were the first species to be sold as
GloFish The GloFish is a patented and trademarked brand of fluorescently colored genetically modified fish, genetically modified aquarium fish. They have been created from several different species of fish: zebrafish were the first GloFish available in ...
(fluorescent colored fish).


Strains

In late 2003,
transgenic A transgene is a gene that has been transferred naturally, or by any of a number of genetic engineering techniques, from one organism to another. The introduction of a transgene, in a process known as transgenesis, has the potential to change the ...
zebrafish that express
green Green is the color between cyan and yellow on the visible spectrum. It is evoked by light which has a dominant wavelength of roughly 495570 nm. In subtractive color systems, used in painting and color printing, it is created by a com ...
, red, and yellow fluorescent proteins became commercially available in the United States. The fluorescent strains are trade-named
GloFish The GloFish is a patented and trademarked brand of fluorescently colored genetically modified fish, genetically modified aquarium fish. They have been created from several different species of fish: zebrafish were the first GloFish available in ...
; other cultivated varieties include "golden", "sandy", "longfin" and "leopard". The leopard danio, previously known as ''Danio frankei'', is a spotted colour morph of the zebrafish which arose due to a pigment mutation. Xanthistic forms of both the zebra and leopard pattern, along with long-finned strains, have been obtained via selective breeding programs for the aquarium trade. Various transgenic and mutant strains of zebrafish were stored at the China Zebrafish Resource Center (CZRC), a non-profit organization, which was jointly supported by the
Ministry of Science and Technology of China Ministry may refer to: Government * Ministry (collective executive), the complete body of government ministers under the leadership of a prime minister * Ministry (government department), a department of a government Religion * Christian mi ...
and the
Chinese Academy of Sciences The Chinese Academy of Sciences (CAS; ) is the national academy for natural sciences and the highest consultancy for science and technology of the People's Republic of China. It is the world's largest research organization, with 106 research i ...
.


Wild-type strains

The Zebrafish Information Network ( ZFIN) provides up-to-date information about current known wild-type (WT) strains of ''D. rerio'', some of which are listed below. *''AB'' (AB) *''AB/C32'' (AB/C32) *''AB/TL'' (AB/TL) *''AB/Tuebingen'' (AB/TU) *''C32'' (C32) *''Cologne'' (KOLN) *''Darjeeling'' (DAR) *''Ekkwill'' (EKW) *''HK/AB'' (HK/AB) *''HK/Sing'' (HK/SING) *''Hong Kong'' (HK) *''India'' (IND) *''Indonesia'' (INDO) *''Nadia'' (NA) *''RIKEN WT'' (RW) *''Singapore'' (SING) *''SJA'' (SJA) *''SJD'' (SJD) *''SJD/C32'' (SJD/C32) *''Tuebingen'' (TU) *''Tupfel long fin'' (TL) *''Tupfel long fin nacre'' (TLN) *''WIK'' (WIK) *''WIK/AB'' (WIK/AB)


Hybrids

Hybrids between different ''Danio'' species may be fertile: for example, between ''D. rerio'' and '' D. nigrofasciatus''.


Scientific research

''D. rerio'' is a common and useful scientific
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. Mo ...
for studies of
vertebrate Vertebrates () are animals with a vertebral column (backbone or spine), and a cranium, or skull. The vertebral column surrounds and protects the spinal cord, while the cranium protects the brain. The vertebrates make up the subphylum Vertebra ...
development and
gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...
function. Its use as a laboratory animal was pioneered by the American
molecular biologist Molecular biology is a branch of biology that seeks to understand the molecule, molecular basis of biological activity in and between Cell (biology), cells, including biomolecule, biomolecular synthesis, modification, mechanisms, and interactio ...
George Streisinger and his colleagues at the
University of Oregon The University of Oregon (UO, U of O or Oregon) is a Public university, public research university in Eugene, Oregon, United States. Founded in 1876, the university is organized into nine colleges and schools and offers 420 undergraduate and gra ...
in the 1970s and 1980s; Streisinger's zebrafish clones were among the earliest successful vertebrate clones created. Its importance has been consolidated by successful large-scale forward genetic screens (commonly referred to as the Tübingen/Boston screens). The fish has a dedicated online database of genetic, genomic, and developmental information, the Zebrafish Information Network (ZFIN). The Zebrafish International Resource Center (ZIRC) is a genetic resource repository with 29,250
alleles An allele is a variant of the sequence of nucleotides at a particular location, or locus, on a DNA molecule. Alleles can differ at a single position through single nucleotide polymorphisms (SNP), but they can also have insertions and deletions ...
available for distribution to the research community. ''D. rerio'' is also one of the few fish species to have been sent into space. Research with ''D. rerio'' has yielded advances in the fields of
developmental biology Developmental biology is the study of the process by which animals and plants grow and develop. Developmental biology also encompasses the biology of Regeneration (biology), regeneration, asexual reproduction, metamorphosis, and the growth and di ...
,
oncology Oncology is a branch of medicine that deals with the study, treatment, diagnosis, and prevention of cancer. A medical professional who practices oncology is an ''oncologist''. The name's Etymology, etymological origin is the Greek word ὄγ ...
,
toxicology Toxicology is a scientific discipline, overlapping with biology, chemistry, pharmacology, and medicine, that involves the study of the adverse effects of chemical substances on living organisms and the practice of diagnosing and treating ex ...
, reproductive studies,
teratology Teratology is the study of abnormalities of physiological development in organisms during their life span. It is a sub-discipline in medical genetics which focuses on the classification of congenital abnormalities in dysmorphology caused by ...
,
genetics Genetics is the study of genes, genetic variation, and heredity in organisms.Hartl D, Jones E (2005) It is an important branch in biology because heredity is vital to organisms' evolution. Gregor Mendel, a Moravian Augustinians, Augustinian ...
,
neurobiology Neuroscience is the scientific study of the nervous system (the brain, spinal cord, and peripheral nervous system), its functions, and its disorders. It is a multidisciplinary science that combines physiology, anatomy, molecular biology, ...
, environmental sciences,
stem cell In multicellular organisms, stem cells are undifferentiated or partially differentiated cells that can change into various types of cells and proliferate indefinitely to produce more of the same stem cell. They are the earliest type of cell ...
research,
regenerative medicine Regenerative medicine deals with the "process of replacing, engineering or regenerating human or animal cells, tissues or organs to restore or establish normal function". This field holds the promise of engineering damaged tissues and organs by st ...
,
muscular dystrophies Muscular dystrophies (MD) are a genetically and clinically heterogeneous group of rare neuromuscular diseases that cause progressive weakness and breakdown of skeletal muscles over time. The disorders differ as to which muscles are primarily aff ...
and
evolutionary theory Evolution is the change in the heritable characteristics of biological populations over successive generations. It occurs when evolutionary processes such as natural selection and genetic drift act on genetic variation, resulting in certai ...
.


Model characteristics

As a model biological system, the zebrafish possesses numerous advantages for scientists. Its
genome A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...
has been fully sequenced, and it has well-understood, easily observable and testable developmental behaviors. Its
embryonic development In developmental biology, animal embryonic development, also known as animal embryogenesis, is the developmental stage of an animal embryo. Embryonic development starts with the fertilization of an egg cell (ovum) by a sperm, sperm cell (spermat ...
is very rapid, and its embryos are relatively large, robust, and transparent, and able to develop outside their mother. Furthermore, well-characterized mutant strains are readily available. Other advantages include the species' nearly constant size during early development, which enables simple
staining Staining is a technique used to enhance contrast in samples, generally at the Microscope, microscopic level. Stains and dyes are frequently used in histology (microscopic study of biological tissue (biology), tissues), in cytology (microscopic ...
techniques to be used, and the fact that its two-celled embryo can be fused into a single cell to create a
homozygous Zygosity (the noun, zygote, is from the Greek "yoked," from "yoke") () is the degree to which both copies of a chromosome or gene have the same genetic sequence. In other words, it is the degree of similarity of the alleles in an organism. Mos ...
embryo. The zebrafish embryos are transparent and they develop outside of the uterus, which allows scientists to study the details of development starting from fertilization and continuing throughout development. The zebrafish is also demonstrably similar to mammalian models and humans in toxicity testing, and exhibits a diurnal sleep cycle with similarities to mammalian sleep behavior. However, zebrafish are not a universally ideal research model; there are a number of disadvantages to their scientific use, such as the absence of a standard diet and the presence of small but important differences between zebrafish and mammals in the roles of some genes related to human disorders.


Regeneration

Zebrafish have the ability to regenerate their heart and
lateral line The lateral line, also called the lateral line organ (LLO), is a system of sensory organs found in fish, used to detect movement, vibration, and pressure gradients in the surrounding water. The sensory ability is achieved via modified epithelia ...
hair cell Hair cells are the sensory receptors of both the auditory system and the vestibular system in the ears of all vertebrates, and in the lateral line organ of fishes. Through mechanotransduction, hair cells detect movement in their environment. ...
s during their larval stages. The cardiac regenerative process likely involves signaling pathways such as Notch and Wnt; hemodynamic changes in the damaged heart are sensed by ventricular
endothelial cells The endothelium (: endothelia) is a single layer of squamous endothelial cells that line the interior surface of blood vessels and lymphatic vessels. The endothelium forms an interface between circulating blood or lymph in the lumen and the res ...
and their associated cardiac cilia by way of the mechanosensitive ion channel
TRPV4 Transient receptor potential cation channel subfamily V member 4 is an ion channel protein that in humans is encoded by the ''TRPV4'' gene. The ''TRPV4'' gene encodes TRPV4, initially named "vanilloid-receptor related osmotically activated chann ...
, subsequently facilitating the
Notch signaling pathway The Notch signaling pathway is a highly Conserved sequence, conserved cell signaling system present in most animal, animals. Mammals possess four different Notch proteins, notch receptors, referred to as NOTCH1, NOTCH2, Notch 3, NOTCH3, and NOTC ...
via KLF2 and activating various downstream effectors such as
BMP-2 The BMP-2 (''Boyevaya Mashina Pekhoty'', , literally "combat machine/vehicle f theinfantry") is an amphibious infantry fighting vehicle introduced in the 1980s in the Soviet Union, following on from the BMP-1 of the 1960s. Development his ...
and
HER2/neu Receptor tyrosine-protein kinase erbB-2 is a protein that normally resides in the membranes of cells and is encoded by the ''ERBB2'' gene. ERBB is abbreviated from erythroblastic oncogene B, a gene originally isolated from the avian genome. The ...
. In 2011, the British Heart Foundation ran an advertising campaign publicising its intention to study the applicability of this ability to humans, stating that it aimed to raise £50 million in research funding. Zebrafish have also been found to regenerate
photoreceptor cells A photoreceptor cell is a specialized type of neuroepithelial cell found in the retina that is capable of visual phototransduction. The great biological importance of photoreceptors is that they convert light (visible electromagnetic radiatio ...
and
retina The retina (; or retinas) is the innermost, photosensitivity, light-sensitive layer of tissue (biology), tissue of the eye of most vertebrates and some Mollusca, molluscs. The optics of the eye create a focus (optics), focused two-dimensional ...
l neurons following injury, which has been shown to be mediated by the dedifferentiation and proliferation of
Müller glia Müller glia, or Müller cells, are a type of retinal glial cells, first recognized and described by Heinrich Müller (physiologist), Heinrich Müller. They are found in the vertebrate retina, where they serve as support cells for the neurons, as ...
. Researchers frequently amputate the dorsal and ventral tail fins and analyze their regrowth to test for mutations. It has been found that histone demethylation occurs at the site of the amputation, switching the zebrafish's cells to an "active", regenerative, stem cell-like state. In 2012, Australian scientists published a study revealing that zebrafish use a specialised
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
, known as
fibroblast growth factor Fibroblast growth factors (FGF) are a family of cell signalling proteins produced by the macrophages. They are involved in a wide variety of processes, most notably as crucial elements for normal development in animal cells. Any irregularities in ...
, to ensure their
spinal cord The spinal cord is a long, thin, tubular structure made up of nervous tissue that extends from the medulla oblongata in the lower brainstem to the lumbar region of the vertebral column (backbone) of vertebrate animals. The center of the spinal c ...
s heal without
glial scar A glial scar formation (gliosis) is a reactive cellular process involving astrogliosis that occurs after injury to the central nervous system. As with scarring in other organs and tissues, the glial scar is the body's mechanism to protect and beg ...
ring after injury. In addition,
hair cell Hair cells are the sensory receptors of both the auditory system and the vestibular system in the ears of all vertebrates, and in the lateral line organ of fishes. Through mechanotransduction, hair cells detect movement in their environment. ...
s of the posterior
lateral line The lateral line, also called the lateral line organ (LLO), is a system of sensory organs found in fish, used to detect movement, vibration, and pressure gradients in the surrounding water. The sensory ability is achieved via modified epithelia ...
have also been found to regenerate following damage or developmental disruption. Study of gene expression during regeneration has allowed for the identification of several important signaling pathways involved in the process, such as Wnt signaling and
Fibroblast growth factor Fibroblast growth factors (FGF) are a family of cell signalling proteins produced by the macrophages. They are involved in a wide variety of processes, most notably as crucial elements for normal development in animal cells. Any irregularities in ...
. In probing disorders of the nervous system, including neurodegenerative diseases, movement disorders, psychiatric disorders and deafness, researchers are using the zebrafish to understand how the genetic defects underlying these conditions cause functional abnormalities in the human brain, spinal cord and sensory organs. Researchers have also studied the zebrafish to gain new insights into the complexities of human musculoskeletal diseases, such as
muscular dystrophy Muscular dystrophies (MD) are a genetically and clinically heterogeneous group of rare neuromuscular diseases that cause progressive weakness and breakdown of skeletal muscles over time. The disorders differ as to which muscles are primarily affe ...
. Another focus of zebrafish research is to understand how a gene called
Hedgehog A hedgehog is a spiny mammal of the subfamily Erinaceinae, in the eulipotyphlan family Erinaceidae. There are 17 species of hedgehog in five genera found throughout parts of Europe, Asia, and Africa, and in New Zealand by introduction. The ...
, a biological signal that underlies a number of human cancers, controls cell growth.


Genetics


Background genetics

Inbred strains and traditional outbred stocks have not been developed for laboratory zebrafish, and the genetic variability of wild-type lines among institutions may contribute to the
replication crisis The replication crisis, also known as the reproducibility or replicability crisis, refers to the growing number of published scientific results that other researchers have been unable to reproduce or verify. Because the reproducibility of empir ...
in biomedical research. Genetic differences in wild-type lines among populations maintained at different research institutions have been demonstrated using both
Single-nucleotide polymorphism In genetics and bioinformatics, a single-nucleotide polymorphism (SNP ; plural SNPs ) is a germline substitution of a single nucleotide at a specific position in the genome. Although certain definitions require the substitution to be present in a ...
s and
microsatellite A microsatellite is a tract of repetitive DNA in which certain Sequence motif, DNA motifs (ranging in length from one to six or more base pairs) are repeated, typically 5–50 times. Microsatellites occur at thousands of locations within an organ ...
analysis.


Gene expression

Due to their fast and short life cycles and relatively large clutch sizes, ''D. rerio'' or zebrafish are a useful model for genetic studies. A common
reverse genetics Reverse genetics is a method in molecular genetics that is used to help understand the function(s) of a gene by analysing the phenotypic effects caused by genetically engineering specific nucleic acid sequences within the gene. The process proce ...
technique is to reduce gene expression or modify splicing using
Morpholino A Morpholino, also known as a Morpholino oligomer and as a phosphorodiamidate Morpholino oligomer (PMO), is a type of oligomer molecule (colloquially, an oligo) used in molecular biology to modify gene expression. Its molecular structure contains ...
antisense In molecular biology and genetics, the sense of a nucleic acid molecule, particularly of a strand of DNA or RNA, refers to the nature of the roles of the strand and its complement in specifying a sequence of amino acids. Depending on the context, ...
technology. Morpholino
oligonucleotide Oligonucleotides are short DNA or RNA molecules, oligomers, that have a wide range of applications in genetic testing, Recombinant DNA, research, and Forensic DNA, forensics. Commonly made in the laboratory by Oligonucleotide synthesis, solid-phase ...
s (MO) are stable, synthetic
macromolecule A macromolecule is a "molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." Polymers are physi ...
s that contain the same bases as DNA or RNA; by binding to complementary RNA sequences, they can reduce the expression of specific genes or block other processes from occurring on RNA. MO can be injected into one cell of an embryo after the 32-cell stage, reducing gene expression in only cells descended from that cell. However, cells in the early embryo (less than 32 cells) are permeable to large molecules, allowing diffusion between cells. Guidelines for using Morpholinos in zebrafish describe appropriate control strategies. Morpholinos are commonly microinjected in 500pL directly into 1–2 cell stage zebrafish embryos. The morpholino is able to integrate into most cells of the embryo. A known problem with gene knockdowns is that, because the genome underwent a duplication after the divergence of
ray-finned fish Actinopterygii (; ), members of which are known as ray-finned fish or actinopterygians, is a class of bony fish that comprise over 50% of living vertebrate species. They are so called because of their lightly built fins made of webbings of sk ...
es and
lobe-finned fish Sarcopterygii (; )—sometimes considered synonymous with Crossopterygii ()—is a clade (traditionally a class or subclass) of vertebrate animals which includes a group of bony fish commonly referred to as lobe-finned fish. These vertebrates ar ...
es, it is not always easy to silence the activity of one of the two gene
paralog Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a sp ...
s reliably due to complementation by the other paralog. Despite the complications of the zebrafish
genome A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...
, a number of commercially available global platforms exist for analysis of both gene expression by
microarrays A microarray is a multiplex lab-on-a-chip. Its purpose is to simultaneously detect the expression of thousands of biological interactions. It is a two-dimensional array on a solid substrate—usually a glass slide or silicon thin-film cell†...
and promoter regulation using ChIP-on-chip.


Genome sequencing

The
Wellcome Trust Sanger Institute The Wellcome Sanger Institute, previously known as The Sanger Centre and Wellcome Trust Sanger Institute, is a non-profit organisation, non-profit British genomics and genetics research institute, primarily funded by the Wellcome Trust. It is l ...
started the zebrafish genome sequencing project in 2001, and the full genome sequence of the Tuebingen reference strain is publicly available at the
National Center for Biotechnology Information The National Center for Biotechnology Information (NCBI) is part of the National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The NCBI is lo ...
(NCBI)'
Zebrafish Genome Page
The zebrafish reference genome sequence is annotated as part of the
Ensembl Ensembl genome database project is a scientific project at the European Bioinformatics Institute, which provides a centralized resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other v ...
br>project
and is maintained by the Genome Reference Consortium. In 2009, researchers at the
Institute of Genomics and Integrative Biology CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB) is a scientific research institute devoted primarily to biological research. It is a part of Council of Scientific and Industrial Research (CSIR), India. The institute was founded ...
in Delhi, India, announced the sequencing of the genome of a wild zebrafish strain, containing an estimated 1.7 billion genetic letters. The genome of the wild zebrafish was sequenced at 39-fold coverage. Comparative analysis with the zebrafish reference genome revealed over 5 million single nucleotide variations and over 1.6 million insertion deletion variations. The zebrafish reference genome sequence of 1.4GB and over 26,000 protein coding genes was published by Kerstin Howe ''et al.'' in 2013.


Mitochondrial DNA

In October 2001, researchers from the
University of Oklahoma The University of Oklahoma (OU) is a Public university, public research university in Norman, Oklahoma, United States. Founded in 1890, it had existed in Oklahoma Territory near Indian Territory for 17 years before the two territories became the ...
published ''D. rerio's'' complete
mitochondrial DNA Mitochondrial DNA (mtDNA and mDNA) is the DNA located in the mitochondrion, mitochondria organelles in a eukaryotic cell that converts chemical energy from food into adenosine triphosphate (ATP). Mitochondrial DNA is a small portion of the D ...
sequence. Its length is 16,596 base pairs. This is within 100 base pairs of other related species of fish, and it is notably only 18 pairs longer than the goldfish (''Carassius auratus'') and 21 longer than the
carp The term carp (: carp) is a generic common name for numerous species of freshwater fish from the family (biology), family Cyprinidae, a very large clade of ray-finned fish mostly native to Eurasia. While carp are prized game fish, quarries and a ...
(''Cyprinus carpio''). Its gene order and content are identical to the common
vertebrate Vertebrates () are animals with a vertebral column (backbone or spine), and a cranium, or skull. The vertebral column surrounds and protects the spinal cord, while the cranium protects the brain. The vertebrates make up the subphylum Vertebra ...
form of mitochondrial DNA. It contains 13
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
-coding genes and a noncoding control region containing the
origin of replication The origin of replication (also called the replication origin) is a particular sequence in a genome at which replication is initiated. Propagation of the genetic material between generations requires timely and accurate duplication of DNA by semi ...
for the heavy strand. In between a grouping of five
tRNA Transfer ribonucleic acid (tRNA), formerly referred to as soluble ribonucleic acid (sRNA), is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes). In a cell, it provides the physical link between the gene ...
genes, a sequence resembling vertebrate origin of light strand replication is found. It is difficult to draw evolutionary conclusions because it is difficult to determine whether base pair changes have adaptive significance via comparisons with other vertebrates'
nucleotide Nucleotides are Organic compound, organic molecules composed of a nitrogenous base, a pentose sugar and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both o ...
sequences.


Developmental genetics

T-box T-box refers to a group of transcription factors involved in embryo, embryonic limb development, limb and heart development. Every T-box protein has a relatively large DNA-binding domain, generally comprising about a third of the entire protein ...
es and
homeobox A homeobox is a Nucleic acid sequence, DNA sequence, around 180 base pairs long, that regulates large-scale anatomical features in the early stages of embryonic development. Mutations in a homeobox may change large-scale anatomical features of ...
es are vital in ''Danio'' similarly to other vertebrates. The Bruce et al. team are known for this area, and in Bruce et al. 2003 & Bruce et al. 2005 uncover the role of two of these elements in
oocyte An oocyte (, oöcyte, or ovocyte) is a female gametocyte or germ cell involved in reproduction. In other words, it is an immature ovum, or egg cell. An oocyte is produced in a female fetus in the ovary during female gametogenesis. The female ger ...
s of this species. By interfering via a dominant nonfunctional
allele An allele is a variant of the sequence of nucleotides at a particular location, or Locus (genetics), locus, on a DNA molecule. Alleles can differ at a single position through Single-nucleotide polymorphism, single nucleotide polymorphisms (SNP), ...
and a
morpholino A Morpholino, also known as a Morpholino oligomer and as a phosphorodiamidate Morpholino oligomer (PMO), is a type of oligomer molecule (colloquially, an oligo) used in molecular biology to modify gene expression. Its molecular structure contains ...
they find the T-box transcription activator Eomesodermin and its target '' mtx2'' – a
transcription factor In molecular biology, a transcription factor (TF) (or sequence-specific DNA-binding factor) is a protein that controls the rate of transcription (genetics), transcription of genetics, genetic information from DNA to messenger RNA, by binding t ...
– are vital to epiboly. (In Bruce et al. 2003 they failed to support the possibility that Eomesodermin behaves like Vegt (development), Vegt. Neither they nor anyone else has been able to locate any mutation which – in the mother – will prevent initiation of the mesoderm or endoderm development processes in this species.)


Pigmentation genes

In 1999, the ''nacre'' mutation was identified in the zebrafish ortholog of the mammalian ''MITF'' transcription factor. Mutations in human ''MITF'' result in eye defects and loss of pigment, a type of Waardenburg Syndrome. In December 2005, a study of the ''golden'' strain identified the gene responsible for its unusual pigmentation as SLC24A5, a solute carrier that appeared to be required for melanin production, and confirmed its function with a Morpholino knockdown. The Orthologue, orthologous gene was then characterized in humans and a one base pair difference was found to strongly segregate fair-skinned Europeans and dark-skinned Africans. Zebrafish with the ''nacre'' mutation have since been bred with fish with a ''roy orbison (roy)'' mutation to make Casper strain fish that have no melanophores or iridophores, and are transparent into adulthood. These fish are characterized by uniformly pigmented eyes and translucent skin.


Transgenesis

Transgenesis is a popular approach to study the function of genes in zebrafish. Construction of transgenic zebrafish is rather easy by a method using the ''Tol2'' transposon system. ''Tol2'' element which encodes a gene for a fully functional transposase capable of catalyzing transposition in the zebrafish germ lineage. ''Tol2'' is the only natural DNA transposable element in vertebrates from which an autonomous member has been identified. Examples include the artificial interaction produced between Lymphoid enhancer-binding factor 1, LEF1 and Catenin beta-1/β-catenin/''CTNNB1''. Dorsky et al. 2002 investigated the developmental role of Wnt by transgenically expressing a Lef1/β-catenin reporter. The Tol2 transposon system was used to develop transgenic zebrafish as sensitive biosensors for heavy metal detection. This involved creating a transgenic zebrafish line expressing a fluorescent protein under the control of a heavy metal-responsive promoter, enabling the detection of low concentrations of cadmium (Cd2+) and zinc (Zn2+). There are well-established protocols for editing zebrafish genes using CRISPR gene editing, CRISPR-Cas9 and this tool has been used to generate genetically modified models.


Transparent adult bodies

In 2008, researchers at Boston Children's Hospital developed a new strain of zebrafish, named Casper, whose adult bodies had transparent skin. This allows for detailed visualization of cellular activity, circulation, metastasis and many other phenomena. In 2019 researchers published a crossing of a ''prkdc-/-'' and a ''IL2rga-/-'' strain that produced transparent, immunodeficient offspring, lacking natural killer cells as well as B cell, B- and T cell, T-cells. This strain can be adapted to warm water and the absence of an immune system makes the use of patient derived Xenotransplantation, xenografts possible. In January 2013, Japanese scientists genetically modified a transparent zebrafish specimen to produce a visible glow during periods of intense brain activity. In January 2007, Chinese researchers at Fudan University genetically modified zebrafish to detect oestrogen pollution in lakes and rivers, which is linked to male infertility. The researchers cloned oestrogen-sensitive genes and injected them into the fertile eggs of zebrafish. The modified fish turned green if placed into water that was polluted by oestrogen."Fudan scientists turn fish into estrogen alerts"
Xinhua. January 12, 2007. Retrieved November 15, 2012.


RNA splicing

In 2015, researchers at Brown University discovered that 10% of zebrafish genes do not need to rely on the U2AF2
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
to initiate RNA splicing. These genes have the DNA base pairs AC and TG as repeated sequences at the ends of each intron. On the 3'ss (3' splicing site), the base pairs adenine and cytosine alternate and repeat, and on the 5'ss (5' splicing site), their complements thymine and guanine alternate and repeat as well. They found that there was less reliance on U2AF2 protein than in humans, in which the protein is required for the splicing process to occur. The pattern of repeating base pairs around introns that alters RNA nucleic acid secondary structure, secondary structure was found in other teleosts, but not in tetrapods. This indicates that an evolutionary change in tetrapods may have led to humans relying on the U2AF2 protein for RNA splicing while these genes in zebrafish undergo splicing regardless of the presence of the protein.


Orthology

''D. rerio'' has three transferrins, all of which cluster closely with other
vertebrate Vertebrates () are animals with a vertebral column (backbone or spine), and a cranium, or skull. The vertebral column surrounds and protects the spinal cord, while the cranium protects the brain. The vertebrates make up the subphylum Vertebra ...
s.


Inbreeding depression

When close relatives mate, progeny may exhibit the detrimental effects of inbreeding depression. Inbreeding depression is predominantly caused by the Zygosity#homozygous, homozygous expression of recessive deleterious alleles. For zebrafish, inbreeding depression might be expected to be more severe in stressful environments, including those caused by Human impact on the environment, anthropogenic pollution. Exposure of zebrafish to environmental stress induced by the chemical clotrimazole, an imidazole fungicide used in agriculture and in veterinary and human medicine, amplified the effects of inbreeding on key reproductive traits. Embryo viability was significantly reduced in inbred exposed fish and there was a tendency for inbred males to sire fewer offspring.


Aquaculture research

Zebrafish are common models for research into fish farming, including fish pathogen, pathogens and fish parasite, parasites causing yield loss or spreading to adjacent wild populations. This usefulness is less than it might be due to ''Danio''s taxonomic distance from the most common aquaculture species. Because the most common are salmonids and cod in the Protacanthopterygii and sea bass, sea bream, tilapia, and flatfish, in the Percomorpha, zebrafish results may not be perfectly applicable. Various other model species, models Goldfish (''Carassius auratus''), Medaka (''Oryzias latipes''), Stickleback (''Gasterosteus aculeatus''), Roach (''Rutilus rutilus''), Pufferfish (''Takifugu rubripes''), Swordtail (''Xiphophorus hellerii'') are less used normally but would be closer to particular target species. The only exception are the Carp (including Grass Carp, ''Ctenopharyngodon idella'') and Milkfish (''Chanos chanos'') which are quite close, both being in the
Cyprinidae Cyprinidae is a family of freshwater fish commonly called the carp or minnow family, including the carps, the true minnows, and their relatives the barbs and barbels, among others. Cyprinidae is the largest and most diverse fish family, and t ...
. However it should also be noted that ''Danio'' consistently proves to be a useful model for mammals in many cases and there is dramatically more genetic distance between them than between ''Danio'' and any farmed fish.


Neurochemistry

In a glucocorticoid receptor-defective mutant with reduced exploration, exploratory behavior, fluoxetine rescued the normal exploratory behavior. This demonstrates relationships between glucocorticoids, fluoxetine, and exploration in this fish.


DNA repair

Zebrafish have been used as a model for studying DNA repair pathways. Embryos of externally fertilized fish species, such as zebrafish during their development, are directly exposed to environmental conditions such as pollutants and reactive oxygen species that may cause DNA damage (naturally occurring), damage to their DNA. To cope with such DNA damages, a variety of different DNA repair pathways are expressed during development. Zebrafish have, in recent years, proven to be a useful model for assessing environmental pollutants that might cause DNA damage.


Drug discovery and development

The zebrafish and zebrafish larva is a suitable model organism for drug discovery and development. As a vertebrate with 70% genetic homology with humans, it can be predictive of human health and disease, while its small size and fast development facilitates experiments on a larger and quicker scale than with more traditional Animal testing, in vivo studies, including the development of higher-throughput, automated investigative tools. As demonstrated through ongoing research programmes, the zebrafish model enables researchers not only to identify genes that might underlie human disease, but also to develop novel therapeutic agents in drug discovery programmes. Zebrafish embryos have proven to be a rapid, cost-efficient, and reliable Teratogen, teratology assay model.


Drug screens

Drug screens in zebrafish can be used to identify novel classes of compounds with biological effects, or to repurpose existing drugs for novel uses; an example of the latter would be a screen which found that a commonly used statin (rosuvastatin) can suppress the growth of prostate cancer. To date, 65 small-molecule screens have been carried out and at least one has led to clinical trials. Within these screens, many technical challenges remain to be resolved, including differing rates of drug absorption resulting in levels of internal exposure that cannot be extrapolated from the water concentration, and high levels of natural variation between individual animals.


Toxico- or pharmacokinetics

To understand drug effects, the internal drug exposure is essential, as this drives the pharmacological effect. Translating experimental results from zebrafish to higher vertebrates (like humans) requires concentration-effect relationships, which can be derived from pharmacokinetic and pharmacodynamic analysis. Because of its small size, however, it is very challenging to quantify the internal drug exposure. Traditionally multiple blood samples would be drawn to characterize the drug concentration profile over time, but this technique remains to be developed. To date, only a single pharmacokinetic model for paracetamol has been developed in zebrafish larvae.


Computational data analysis

Using smart data analysis methods, pathophysiological and pharmacological processes can be understood and subsequently translated to higher vertebrates, including humans. An example is the use of systems pharmacology, which is the integration of systems biology and pharmacometrics. Systems biology characterizes (part of) an organism by a mathematical description of all relevant processes. These can be for example different signal transduction pathways that upon a specific signal lead to a certain response. By quantifying these processes, their behaviour in healthy and diseased situation can be understood and predicted. Pharmacometrics uses data from preclinical experiments and clinical trials to characterize the pharmacological processes that are underlying the relation between the drug dose and its response or clinical outcome. These can be for example the drug absorption (pharmacology), absorption in or clearance (pharmacology), clearance from the body, or its interaction with the target to achieve a certain effect. By quantifying these processes, their behaviour after different doses or in different patients can be understood and predicted to new doses or patients. By integrating these two fields, systems pharmacology has the potential to improve the understanding of the interaction of the drug with the biological system by mathematical quantification and subsequent prediction to new situations, like new drugs or new organisms or patients. Using these computational methods, the previously mentioned analysis of paracetamol internal exposure in zebrafish larvae showed reasonable correlation between paracetamol clearance in zebrafish with that of higher vertebrates, including humans.


Medical research


Cancer

Zebrafish have been used to make several transgenic models of cancer, including melanoma, leukemia, pancreatic cancer and hepatocellular carcinoma. Zebrafish expressing mutated forms of either the BRAF or NRAS oncogenes develop melanoma when placed onto a p53 deficient background. Histology, Histologically, these tumors strongly resemble the human disease, are fully transplantable, and exhibit large-scale genomic alterations. The BRAF melanoma model was utilized as a platform for two screens published in March 2011 in the journal ''Nature''. In one study, the model was used as a tool to understand the functional importance of genes known to be amplified and overexpressed in human melanoma. One gene, SETDB1, markedly accelerated tumor formation in the zebrafish system, demonstrating its importance as a new melanoma oncogene. This was particularly significant because SETDB1 is known to be involved in the epigenetic regulation that is increasingly appreciated to be central to tumor cell biology. In another study, an effort was made to therapeutically target the genetic program present in the tumor's origin neural crest cell using a chemical screening approach. This revealed that an inhibition of the DHODH protein (by a small molecule called leflunomide) prevented development of the neural crest stem cells which ultimately give rise to melanoma via interference with the process of transcriptional elongation. Because this approach would aim to target the "identity" of the melanoma cell rather than a single genetic mutation, leflunomide may have utility in treating human melanoma.


Cardiovascular disease

In cardiovascular research, the zebrafish has been used to model human myocardial infarction model. The zebrafish heart completely regenerates after about 2 months of injury without any scar formation. The Alpha-1 adrenergic receptor, Alpha-1 adrenergic signalling mechanism involved in this process was identified in a 2023 study. Zebrafish is also used as a model for Coagulation, blood clotting, Angiogenesis, blood vessel development, and congenital heart defect, congenital heart and kidney disease.


Immune system

In programmes of research into acute inflammation, a major underpinning process in many diseases, researchers have established a zebrafish model of inflammation, and its resolution. This approach allows detailed study of the genetic controls of inflammation and the possibility of identifying potential new drugs. Zebrafish has been extensively used as a model organism to study vertebrate innate immunity. The innate immune system is capable of phagocytic activity by 28 to 30 h postfertilization (hpf) while adaptive immunity is not functionally mature until at least 4 weeks postfertilization.


Infectious diseases

As the immune system is relatively conserved between zebrafish and humans, many human infectious diseases can be modeled in zebrafish. The transparent early life stages are well suited for ''in vivo'' imaging and genetic dissection of host-pathogen interactions. Zebrafish models for a wide range of bacterial, viral and parasitic pathogens have already been established; for example, the zebrafish model for tuberculosis provides fundamental insights into the mechanisms of pathogenesis of mycobacteria. Other bacteria commonly studied using zebrafish models include ''Clostridioides difficile'', ''Staphylococcus aureus'', and ''Pseudomonas aeruginosa''. Furthermore, robotic technology has been developed for high-throughput antimicrobial drug screening using zebrafish infection models.


Repairing retinal damage

Another notable characteristic of the zebrafish is that it possesses four types of cone cell, with ultraviolet-sensitive cells supplementing the red, green and blue cone cell subtypes found in humans. Zebrafish can thus observe a very wide spectrum of colours. The species is also studied to better understand the development of the retina; in particular, how the cone cells of the retina become arranged into the so-called 'cone mosaic'. Zebrafish, in addition to certain other teleost fish, are particularly noted for having extreme precision of cone cell arrangement. This study of the zebrafish's retinal characteristics has also extrapolated into medical enquiry. In 2007, researchers at University College London grew a type of zebrafish adult
stem cell In multicellular organisms, stem cells are undifferentiated or partially differentiated cells that can change into various types of cells and proliferate indefinitely to produce more of the same stem cell. They are the earliest type of cell ...
found in the eyes of fish and mammals that develops into neurons in the retina. These could be injected into the eye to treat diseases that damage retinal neurons—nearly every disease of the eye, including macular degeneration, glaucoma, and diabetes-related blindness. The researchers studied Müller glial cells in the eyes of humans aged from 18 months to 91 years, and were able to develop them into all types of retinal neurons. They were also able to grow them easily in the lab. The stem cells successfully migrated into diseased rats' retinas, and took on the characteristics of the surrounding neurons. The team stated that they intended to develop the same approach in humans.


Muscular dystrophies

Muscular dystrophy, Muscular dystrophies (MD) are a heterogeneous group of genetic disorders that cause muscle weakness, abnormal contractions and muscle wasting, often leading to premature death. Zebrafish is widely used as model organism to study muscular dystrophies. For example, the ''sapje'' (''sap'') mutant is the zebrafish orthologue of human Duchenne muscular dystrophy (DMD). The Machuca-Tzili and co-workers applied zebrafish to determine the role of alternative splicing factor, MBNL, in Myotonic dystrophy, myotonic dystrophy type 1 (DM1) pathogenesis. More recently, Todd et al. described a new zebrafish model designed to explore the impact of CUG repeat expression during early development in DM1 disease. Zebrafish is also an excellent animal model to study congenital muscular dystrophies including CMD Type 1 A (CMD 1A) caused by mutation in the human laminin α2 (LAMA2) gene. The zebrafish, because of its advantages discussed above, and in particular the ability of zebrafish embryos to absorb chemicals, has become a model of choice in screening and testing new drugs against muscular dystrophies.


Bone physiology and pathology

Zebrafish have been used as model organisms for bone metabolism, tissue turnover, and resorbing activity. These processes are largely evolutionary conserved. They have been used to study osteogenesis (bone formation), evaluating differentiation, matrix deposition activity, and cross-talk of skeletal cells, to create and isolate mutants modeling human bone diseases, and test new chemical compounds for the ability to revert bone defects. The larvae can be used to follow new (''de novo'') osteoblast formation during bone development. They start mineralising bone elements as early as 4 days post fertilisation. Recently, adult zebrafish are being used to study complex age related bone diseases such as osteoporosis and osteogenesis imperfecta. The (elasmoid) Fish scale#Elasmoid scales, scales of zebrafish function as a protective external layer and are little bony plates made by osteoblasts. These exoskeletal structures are formed by bone matrix depositing osteoblasts and are remodeled by osteoclasts. The scales also act as the main calcium storage of the fish. They can be cultured ex-vivo (kept alive outside of the organism) in a multi-well plate, which allows manipulation with drugs and even screening for new drugs that could change bone metabolism (between osteoblasts and osteoclasts).


Diabetes

Zebrafish pancreas development is very homologous to mammals, such as mice. The signaling mechanisms and way the pancreas functions are very similar. The pancreas has an endocrine compartment, which contains a variety of cells. Pancreatic PP cells that produce polypeptides, and β-cells that produce insulin are two examples of those such cells. This structure of the pancreas, along with the glucose homeostasis system, are helpful in studying diseases, such as diabetes, that are related to the pancreas. Models for pancreas function, such as fluorescent staining of proteins, are useful in determining the processes of glucose homeostasis and the development of the pancreas. Glucose tolerance tests have been developed using zebrafish, and can now be used to test for glucose intolerance or diabetes in humans. The function of insulin are also being tested in zebrafish, which will further contribute to human medicine. The majority of work done surrounding knowledge on glucose homeostasis has come from work on zebrafish transferred to humans.


Obesity

Zebrafish have been used as a model system to study obesity, with research into both genetic obesity and over-nutrition induced obesity. Obese zebrafish, similar to obese mammals, show dysregulation of lipid controlling metabolic pathways, which leads to weight gain without normal lipid metabolism. Also like mammals, zebrafish store excess lipids in visceral, intramuscular, and subcutaneous adipose deposits. These reasons and others make zebrafish good models for studying obesity in humans and other species. Genetic obesity is usually studied in transgenic or mutated zebrafish with obesogenic genes. As an example, transgenic zebrafish with overexpressed AgRP, an endogenous melanocortin antagonist, showed increased body weight and adipose deposition during growth. Though zebrafish genes may not be the exact same as human genes, these tests could provide important insight into possible genetic causes and treatments for human genetic obesity. Diet-induced obesity zebrafish models are useful, as diet can be modified from a very early age. High fat diets and general overfeeding diets both show rapid increases in adipose deposition, increased BMI, hepatosteatosis, and hypertriglyceridemia. However, the normal fat, overfed specimens are still metabolically healthy, while high-fat diet specimens are not. Understanding differences between types of feeding-induced obesity could prove useful in human treatment of obesity and related health conditions.


Environmental toxicology

Zebrafish have been used as a model system in environmental toxicology studies.


Neurobiology

The combination of transparent zebrafish larva, light sheet fluorescence microscopy, and calcium imaging, optical calcium indicators such as GCaMP, allow the monitoring of all neurons in an awake, behaving animal.


Epilepsy

Zebrafish have been used as a model system to study epilepsy. Mammalian seizures can be recapitulated molecularly, behaviorally, and electrophysiologically, using a fraction of the resources required for experiments in mammals.


See also

* Japanese rice fish or medaka, another fish used for genetic, developmental, and biomedical research * List of freshwater aquarium fish species *Denison barb


References


Further reading

* * * * * * * *


External links


British Association of Zebrafish Husbandry

International Zebrafish Society
(IZFS)
European Society for Fish Models in Biology and Medicine
(EuFishBioMed)
The Zebrafish Information Network
(ZFIN)
The Zebrafish International Resource Center
(ZIRC)
The European Zebrafish Resource Center
(EZRC)
The China Zebrafish Resource Center
(CZRC)
The Zebrafish Genome Sequencing Project
at the Wellcome Trust Sanger Institute
FishMap: The Zebrafish Community Genomics Browser
at the
Institute of Genomics and Integrative Biology CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB) is a scientific research institute devoted primarily to biological research. It is a part of Council of Scientific and Industrial Research (CSIR), India. The institute was founded ...
(IGIB)
WebHome Zebrafish GenomeWiki Beta Preview
at the IGIB
Genome sequencing initiative
at the IGIB
''Danio rerio''
at Danios.info
Sanger Institute Zebrafish Mutation Resource

Zebrafish genome
via Ensembl
FishforScience.com
– using zebrafish for medical research
FishForPharma

Breeding Zebrafish
* {{Authority control Fish described in 1822 Danio Fish of Bangladesh Freshwater fish of India Freshwater fish of Pakistan Animal models Stem cell research Regenerative biomedicine Animal models in neuroscience Taxa named by Francis Buchanan-Hamilton Fish of Nepal Fish of Bhutan