Zebrafish

Danio rerio
Scientific classification
Kingdom: Animalia Phylum: Chordata Class: Actinopterygii Order: Cypriniformes Family: Cyprinidae Genus: Danio Species: D. rerio
Binomial name
Danio rerio (Hamilton-Buchanan, 1822)
Synonyms
Barilius rerio Brachydanio rerio Cyprinus chapalio Cyprinus rerio Danio frankei Danio lineatus Nuria rerio Perilampus striatus Zebra danio

The zebrafish, also known as Danio rerio, is a tropical freshwater fish belonging to the minnow family (Cyprinidae).^[1] It is a popular aquarium fish, frequently sold under the trade name zebra danio, and is an important vertebrate model organism in scientific research.

Taxonomy

The zebrafish is a derived member of the genus Danio. It has a sister group relationship with Danio kyathit.^[2]

Distribution

The zebrafish is native to the streams of the southeastern Himalayan region.^[2] It arose in the Ganges region in Eastern India and is also native to Pakistan, Bangladesh, Nepal, and Myanmar.^{[citation needed]} It commonly inhabits streams, canals, ditches, ponds, and slow-moving to stagnant water bodies, including rice fields.^{[citation needed]}

Zebrafish have been introduced in aquariums in Japan, Canada, the United States and Australia.^[3] They have also been sighted in Colombia, presumably having escaped from an aquarium.

Description

The fish is named for the five uniform, pigmented, horizontal blue stripes on the side of the body, all of which extend to the end of the caudal fin. Its shape can be described as fusiform and laterally compressed, with its mouth directed upwards. Males are torpedo shaped and have gold stripes between the blue stripes; females have a larger, whitish belly and have silver stripes instead of gold. Adult females will exhibit a small genital papilla in front of the anal fin origin. The zebrafish can grow to 6.4 centimetres (2.5 in), although it is uncommon for them to grow past 4 centimetres in captivity.

The approximate generation time for the Danio is 3–4 months. It has been observed that there must be a male present in order for ovulation and spawning of eggs to occur. Females are able to spawn as often as 2–3 days with hundreds of eggs being laid in each clutch. Upon release from the mother, developmental steps will be made, however without the presence of sperm growth will stop after the first few embryonic cleavages. Fertilized eggs will almost immediately become transparent, which is an important characteristic yielding D. rerio as a convenient research model^[4]. Developement rapidly progresses, with precursors to all major organs appearing within 36 hours of fertilization. Hatching will take place anywhere from 48–72 hours post-fertilization, depending on the internal conditions of the embryo itself and the external temperature (ideally 28.5 °C). Swimming and feeding behavior are observed to occur approximately 72 hours post-fertilization. The sex of juvenile zebrafish cannot be distinguished except by dissection, and the genetic sex determinants are not clearly understood. The range of life-span for a zebrafish in captivity is around 2–3 years, although in ideal conditions, they may live up to 5 years.^[4]

The zebrafish is omnivorous, and it primarily eats zooplankton, insects, and phytoplankton. It can eat a variety of foods if its main sources are not readily available.^[4]

Varieties

Recently, transgenic zebrafish have become commercially available that express green fluorescent protein, red fluorescent protein, and yellow fluorescent protein. They are tradenamed GloFish. Other varieties include golden, sandy, longfin and leopard.

The Leopard danio, previously known as Danio frankei, is a spotted colour morph of the zebrafish caused by a pigment mutation.^[5] Xanthistic forms of both the zebra and leopard pattern, along with long-finned varieties have been obtained via selective breeding programs for the aquarium trade.^[6]

Wild-Type Strains

The Zebra Fish Information Network [6] provides up-to-date information about current known Wild-Type strains of D. rerio. The most commonly found WT strains are: AB, TÜ, IN and WIK.

Hybrids

Hybrids between danios are common but they are sterile.

See link for photos of hybrids: http://www.nature.com/hdy/journal/v97/n3/fig_tab/6800867f1.html#figure-title

Brachydanio phylogenetic tree, see link: http://www.nature.com/hdy/journal/v97/n3/fig_tab/6800867f2.html#figure-title

Aquarium care

Zebrafish are hardy fish and considered good for beginner aquarists. Their ease of keeping and breeding, beauty, price, playful nature and broad availability all contribute to their popularity. They thrive best at temperatures above 22 °C (71.6 °F) and below 27 °C (80.6 °F). They feed on worms and small crustaceans and on insect larvae. They also thrive as shoals of six or more, although they do interact well with other fish types in the aquarium. However, they are susceptible to Oodinium, or Velvet disease, Microsporidia (Pseudoloma neurophilia), and mycobacterium species. Most Danios will accept common food flakes and tubifex worms. They are egglayers and as the female drops the eggs the male with fertilize them and within a few days the will hatch and some may be eaten by the parents unless the parents are in a separate tank or the eggs were scooped up into a breeder box or netted container.

Model organism for development and genetics

Zebrafish chromatophores, shown here mediating background adaptation, are studied by scientists

D. rerio are a common and useful model organism for studies of vertebrate development and gene function.^[2] They may supplement higher vertebrate models, such as rats and mice. Pioneering work of George Streisinger at the University of Oregon established the zebrafish as a model organism; its importance was consolidated by large scale forward genetic screens (commonly referred to as the Tübingen/Boston screens). The scholarly journal Development devoted an issue to research using the fish in celebration of this landmark. An online database of zebrafish genetic, genomic, and developmental information, the Zebrafish Information Network (ZFIN), has been established. D. rerio is one of the few species of fish to have been flown into space (see Animals in space).

A Zebrafish Pigment Mutant. The mutant called bleached blond was produced by insertional mutagenesis. The embryos in the picture are four days old. At the top is a wild-type embryo, below is the mutant. The mutant lacks black pigment in the melanocytes because it fails to synthesise melanin properly.

Research with D. rerio has allowed advances in the fields of developmental biology, oncology^[7], toxicology^[8], reproductive studies, teratology, genetics, neurobiology, environmental sciences, stem cell and regenerative medicine^[9], and evolutionary theory^[10]. Perhaps its greatest advantages for use in the laboratory as a model system come from its now sequenced genetic code, well understood, easily observable and testable developmental behaviors, and the availability of well-characterized mutants. Zebrafish embryonic development provides advantages over other vertebrate model organisms as well. Although the overall generation time of zebrafish is comparable to that of mice, zebrafish embryos develop rapidly, progressing from eggs to larvae in under three days. The embryos are large, robust, and transparent and develop externally to the mother, characteristics which all facilitate experimental manipulation and observation. ^[11] Their nearly constant size during early development facilitates simple staining techniques, and drugs may be administered by adding directly to the tank. Unfertilized eggs can be made to divide, and the two-celled embryo fused into a single cell, creating a fully homozygous embryo.

See link for pigmentation mutants of D rerio: http://www.nature.com/hdy/journal/v97/n3/fig_tab/6800867f5.html#figure-title

A common reverse genetics technique is to reduce gene expression or modify splicing in zebrafish using Morpholino antisense technology. Morpholino oligonucleotides are stable, synthetic macromolecules that contain the same bases as DNA or RNA; by binding to complementary RNA sequences, they reduce the expression of specific genes. The journal Genesis devoted an issue to research using Morpholino oligos, mostly in D. rerio. Morpholino oligonucleotides can be injected into one cell of a zebrafish embryo after the 32-cell stage, producing an organism in which gene expression is reduced in only the cells descended from the injected cell. However, cells in the early embryo (<32 cells) are interpermeable to large molecules,^[12][13] allowing diffusion of Morpholinos between cells. A known problem with gene knockdowns in zebrafish is that, because the genome underwent a duplication after the divergence of ray-finned fishes and lobe-finned fishes, it is not always easy to silence the activity one of the two gene paralogs reliably due to complementation by the other paralog.

Despite the complications of the zebrafish genome a number of commercially available global platforms for analysis of both gene expression by microarrays and promoter regulation using ChIP-on-chip exist.

Zebrafish have the ability to regenerate fins, skin, the heart, and the brain (in larval stages). Zebrafish have also been found to regenerate photoreceptors and retinal neurons following injury. The mechanisms of this regeneration are unknown, but are currently being studied. Researchers frequently cut the dorsal and ventral tail fins and analyze their regrowth to test for mutations. This research is leading the scientific community in the understanding of healing/repair mechanisms in vertebrates.

Recent developments

In October 2001, researchers from the University of Oklahoma published the complete mitochondrial DNA sequence of D. rerio^[14]. The length of the zebrafish mitochondrial genome is 16,596 base pairs. This is within 100 base pairs of other related species of fish, and it is notably only 18 bp longer than the goldfish (Carassius auratus) and 21 bp longer than the carp (Cyprinus carpio). The zebrafish gene order and content is identical to the common vertebrate form of mitochondrial DNA. It contains 13 protein-coding genes and a noncoding control region containing the origin of replication for the heavy strand. In between a grouping of five tRNA genes, a sequence resembling vertebrate origin of light strand replication is found. In comparing the nucleotide sequence to other vertebrates it is difficult to draw any evolutionary conclusions because it is difficult to determine as to whether base pair changes have adaptive significance.

In December 2005, a study of the golden strain identified the gene responsible for the unusual pigmentation of this strain as SLC24A5, a solute carrier that appeared to be required for melanin production, and confirmed its function with a Morpholino knockdown. The orthologous gene was then characterized in humans and a one base pair difference was found to segregate strongly between fair-skinned Europeans and dark-skinned Africans.^[15] This study featured on the cover of the academic journal Science and demonstrates the power of zebrafish as a model organism in the relatively new field of comparative genomics.

In January 2007, Chinese researchers at Fudan University raised genetically modified fish that can detect estrogen pollution in lakes and rivers, showing environmental officials what waterways need to be treated for the substance, which is linked to male infertility. Song Houyan and Zhong Tao, professors at Fudan's molecular medicine lab, spent three years cloning estrogen-sensitive genes and injecting them into the fertile eggs of zebrafish. The modified fish turn green if they are placed into water that is polluted by estrogen.^[16]

On August 1, 2007, researchers at University College London said they had grown in the laboratory a type of adult stem cell found in the eyes of fish and mammals that develops into neurons in the retina. These cells could be injected in the eye to treat all diseases where the retinal neurons are damaged — nearly every disease of the eye, including macular degeneration, glaucoma, and diabetes-related blindness. Damage to the retina — the part of the eye that sends messages to the brain — is responsible for most cases of sight loss. 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 neurons found in the retina. They were also able to grow them easily in the lab, they reported in the journal Stem Cells. The cells were tested in rats with diseased retinas, where they successfully migrated into the retina and took on the characteristics of the surrounding neurons. Now the team is working on the same approach in humans.^[17]

In February 2008, researchers at Children's Hospital Boston reported in the journal Cell Stem Cell the development of a new strain of zebrafish, named Casper, with see-through bodies.^[18] This allows for detailed visualization of individual blood stem cells and metastasizing (spreading) cancer cells within a living adult organism. Because the function of many genes are shared between fish and humans, this tool is expected to yield insight into human diseases such as leukemia and other cancers.^[19][18]

In April 2009, Researchers at the Institute of Genomics and Integrative Biology, Delhi announced the sequencing of the wild-type strain of Zebrafish, complete with with about 1.7 billion genetic alphabets^[20][21].

See also

• The subfamily Danionin
• Development of fish: post-fertilization development and axes formation Regional_specification#Fish
• GloFish
• List of freshwater aquarium fish species

References

Further reading

• Danio rerio (TSN 163699). Integrated Taxonomic Information System. Retrieved on 12 November 2004.
• "Danio rerio". FishBase. Ed. Ranier Froese and Daniel Pauly. October 2004 version. N.p.: FishBase, 2004.
• Lambert, Derek J (1997). Freshwater Aquarium Fish. Edison, New Jersey: Chartwell Books. pp. 19. ISBN 0-7858-0867-1. 
• Sharpe, Shirlie. "Zebra Danio". Your Guide to Freshwater Aquariums. http://freshaquarium.about.com/cs/cyprinids2/p/zebradanio.htm. Retrieved on December 15 2004. 
• Kocher TD, Jeffery WR, Parichy DM, Peichel CL, Streelman JT, Thorgaard GH (2005). "Special feature--roundtable discussion. Fish models for studying adaptive evolution and speciation". Zebrafish 2 (3): 147–56. doi:10.1089/zeb.2005.2.147. PMID 18248189. 
• The Zebrafish Information Network (ZFIN)
• Bradbury J (2004). "Small Fish, Big Science". PLoS Biology 2 (5): 568–72. doi:10.1371/journal.pbio.0020148. 

External links

Wikimedia Commons has media related to: Danio rerio

• The Zebrafish Information Network (ZFIN)
• The Zebrafish International Resource Center (ZIRC)
• The Zebrafish Genome Sequencing Project (Wellcome Trust Sanger Institute)
• FishMap : The Zebrafish Community Genomics Browser
• Zebrafish GenomeWiki Beta Preview maintained at the Institute of Genomics and Integrative Biology
• The Zebrafish wild-type strain Genome sequencing initiative at the Institute of Genomics and Integrative Biology
• Danio rerio
• Danio rerio embryonic development images
• Sanger Institute Zebrafish Mutation Resource