生命科学研究中的典型模式生物

    Model Organisms

Yeast

Budding yeast, Baker's yeast:  Saccharomyces cerevisiae

Saccharomyces cerevisiae  is a species of yeast. It has been instrumental towinemaking, baking, and brewing since ancient times. It is believed to have been originally isolated from the skin of grapes.

 It is one of the most intensively studied eukaryotic model organisms in molecular and cell biology,  much like Escherichia coli as the model bacterium. It is the microorganism behind the most common type offermentation. S. cerevisiae cells are round to ovoid, 5–10 μm in diameter. It reproduces by a division process known as budding.

Many proteins important in human biology were first discovered by studying their homologs in yeast; these proteins include cell cycle proteins, signaling proteins, and protein-processing enzymes

Life cycle   

Two forms of yeast cells can survive and grow: haploid and diploid.

Saccharomyces cerevisiae

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. The yeast species S. pombe and S. cerevisiae are both well studied; these two species diverged approximately 600 to 300 million years ago, and are significant tools in the study of DNA damage and repair mechanisms]

S. cerevisiae has developed as a model organism because it scores favorably on a number of these criteria.

As a single-cell organism, S. cerevisiae is small with a short generation time (doubling time 1.25–2 hours at 30 °C or 86 °F) and can be easily cultured. These are all positive characteristics in that they allow for the swift production and maintenance of multiple specimen lines at low cost.

S. cerevisiae divides with meiosis, allowing it to be a candidate for sexual genetics research.

S. cerevisiae can be transformed allowing for either the addition of new genes or deletion through homologous recombination. Furthermore, the ability to grow S. cerevisiae as a haploid simplifies the creation of gene knockouts strains.

As a eukaryote, S. cerevisiae shares the complex internal cell structure of plants and animals without the high percentage of non-coding DNA that can confound research in higher eukaryotes.

In the study of aging    

S. cerevisiae has been highly studied as a model organism to better understand aging for more than five decades and has contributed to the identification of more mammalian genes affecting aging than any other model organism. Some of the topics studied using yeast are calorie restriction, as well as in genes and cellular pathways involved in senescence

Meiosis, recombination and DNA repair

S. cerevisiae reproduces by mitosis as diploid cells when nutrients are abundant. However, when starved, these cells undergo meiosis to form haploid spores.

Evidence from studies of S. cerevisiae bear on the adaptive function of meiosis and recombination. Mutations defective in genes essential for meiotic and mitotic recombination in S. cerevisiae cause increased sensitivity to radiation or DNA damaging chemicals.

Genome sequencing   

S. cerevisiae was the first eukaryotic genome to be completely sequenced.[36] The genome sequence was released to the public domain on April 24, 1996. Since then, regular updates have been maintained at the Saccharomyces Genome Database. This database is a highly annotated and cross-referenced database for yeast researchers. Another important S. cerevisiae database is maintained by the Munich Information Center for Protein Sequences (MIPS). The S. cerevisiae genome is composed of about 12,156,677 base pairs and 6,275 genes, compactly organized on 16 chromosomes. Only about 5,800 of these genes are believed to be functional. It is estimated at least 31% of yeast genes have homologs in the human genome.

Gene function and interactions

The availability of the S. cerevisiae genome sequence and a set of deletion mutants covering 90% of the yeast genome has further enhanced the power of S. cerevisiae as a model for understanding the regulation of eukaryotic cells. A project underway to analyze the genetic interactions of all double-deletion mutants through synthetic genetic array analysis will take this research one step further. The goal is to form a functional map of the cell's processes.

Other tools in yeast research   

Approaches that can be applied in many different fields of biological and medicinal science have been developed by yeast scientists. These include yeast two-hybrid for studying protein interactions

Fission yeast:  S.pombe

黑腹果蝇 Drosophila melanogaster

中文学名 黑腹果蝇

拉丁学名 Drosophila melanogaster

别    称 黑尾果蝇

遗传研究

黑腹果蝇

腹果蝇在1830年首次被描述。而它第一次被用作试验研究对象则要到 1901年，由动物学家和遗传学家威廉·恩斯特·卡斯特 (William Ernest Castle) 通过对果蝇的种系研究，设法了解多代近亲繁殖的结果和取自其中某一代进行杂交所出现的现象。1910年，汤玛斯·亨特·摩尔根 (Thomas Hunt Morgan) 开始在实验室内培育果蝇并对它进行系统的研究。之后，很多遗传学家就开始用果蝇作研究材料，并且取得了很多遗传学方面的知识，包括这种蝇类基因组里的基因在染色体上的分布等。

黑腹果蝇只有四对染色体。它们包括一对性染色体, 通常被记作第一对染色体或者是X-和Y-染色体，和三对常染色体。 后者被记作第二，第三和第四对染色体。第四对染色体很小，所含的基因也很少。果蝇非常合适用于研究，在一个瓶子里就可以培育大量的果蝇，繁殖速度快。马田·布克斯在他2002年出版的书 <<果蝇 (Drosophila)>> 里这样写道: "用半瓶牛奶和一只开始腐烂的香蕉就够了，14天就可以得到200只果蝇”。科学家用果蝇进行了无数次杂交, 其中包括确定了基因里面的基因连锁群，它们位于同一基因上面, 科学家也因此发现了联会现象。科学家还对某些变异进行了描述和研究。 例如眼睛颜色有红变异为白色, 或者是微型翅膀, 这种果蝇丧失了飞行能力。赫尔曼·穆勒是第一位发现伦琴射线对遗传物质具有诱变作用的遗传学家。从此射线就被大量使用，以诱发果蝇发生变异。

黑腹果蝇

在2000年对其13600 基因测序完成。大部分基因与人类的基因有着惊人的相似。研究还在果蝇的遗传物质里找到了人类的致癌基因或者潜在的，在变异情况下参与癌症发生的致癌基因 (Oncogene，一译癌基因)。

在发育生物学研究方面, 人类也从果蝇身上获得了很多知识。早在1900年哈佛大学的教授威廉·卡斯特就首次将果蝇用作胚胎研究的对象。从此以后, 果蝇就在这一领域被广泛采用。20世纪70年代德国科学家克里斯蒂安娜·女斯莱.佛哈德 (Christiane Nüsslein-Volhard) 开始研究果蝇的发育基因。她从中得知，卵细胞中的四个基因决定了或是监控了受精卵的发育（参见Hox基因)。1980年她发表了论文“影响黑腹果蝇体节数目和极性的变异”，她也因此和美国的 Edward B. Lewis，Eric F. Wieschaus 共享了1995年的诺贝尔生理学或医学奖。

突变体编辑

在实验室里，科学家让果蝇产生了无数种变异体[2]  。通过系统筛选，科学家通常选择其基因组里面大概13400基因进行诱导，使果蝇变异。过程通常是用有明显表现型的纯合子杂交，已得到下一代F1和F2，就可对其进行研究了。常见的变异有眼睛颜色, 翅膀形态, 身体颜色，头部形态等等。

眼睛颜色突变体

白色眼睛 (white eye)：眼睛的颜色由红变成白色。是由于“白色”的基因产生

眼睛颜色突变体

眼睛颜色突变体(2张)

 缺陷, 不能产生红色颜料。这也是摩尔根科学研究的第一个变异体。通过该实验，他第一次在动物中验证了孟德尔遗传定律的正确性。

橙色眼睛 (orange eye): 这些果蝇的眼睛有橘黄色的。橙眼果蝇一样是由于它们的“白色”的基因有缺陷。但在这些果蝇中，它们的白色的基因只能产生较少的红色颜料。

翅膀形态突变体

 由于这些果蝇在第二染色体上有缺陷。这是一个隐性的突变，只有来自父母两者的基因都具有突变，才可也产生异常的翅膀形状。如果只有一个突变，健康的基因可以覆盖有缺陷的基因。

卷翅 (Curly wing): 这些果蝇有卷曲的翅膀。它们是由于第二个染色体上的卷曲基因有缺陷造成的。具有卷曲翅膀的是显性突变，只要有一个拷贝的基因被改变，就能产生缺陷。如果这两个副本都发生突变, 结果是是致死的，果蝇将不能存活。

身体颜色突变体

黄色(Yellow)果蝇: 这些果蝇的身体颜色比正常果蝇的黄。它们是由于在X

染色体上的“黄色基因”有一个缺陷造成的。由于需要黄色基因生产果蝇的正常的黑色色素，黄色突变的果蝇无法产生这种色素。

乌木色(Ebony)果蝇: 这些果蝇有一个黑暗的几乎是黑色的身体。它们是由于在第三号染色体上的“乌木基因”有缺陷而产生的。在通常情况下，乌木基因在正常果蝇是负责积累棕褐色色素。如果乌木基因有缺陷的，会导致黑色色素积累, 并遍布果蝇的全身。

头部形态突变体

无眼（Eyeless果蝇): 这些果蝇没有眼睛。这是由于它们的“眼睛缺席”基因有突

头部形态突变体

触角腿(Antenna-leg)果蝇: 这些果蝇的腿状触角长在它们的前额上。这是由于它们自己的“触角”基因，拉丁语为“触角腿” （"antenna-leg"）有缺陷造成的。在正常情况下, 这些基因指示一些人体细胞成为腿。在这些突变的果蝇中， 它们的触角基因错误地指示通常形成触角的细胞，形成腿。请和正常的果蝇（或“野生型”）做比较。正常的果蝇的触角在它们的红色的眼睛的前面伸出。

Drosophila melanogaster is a species of fly (the taxonomic order Diptera) in the family Drosophilidae. The species is known generally as the common fruit fly or vinegar fly. Starting with Charles W. Woodworth's proposal of the use of this species as a model organism, D. melanogaster continues to be widely used for biological research in studies of genetics, physiology, microbial pathogenesis, and life history evolution. It is typically used because it is an animal species that is easy to care for, has four pairs of chromosomes, breeds quickly, and lays many eggs.D. melanogaster is a common pest in homes, restaurants, and other occupied places where food is served.

History of use in genetic analysis

D. melanogaster was among the first organisms used for genetic analysis, and today it is one of the most widely used and genetically best-known of all eukaryotic organisms. All organisms use common genetic systems; therefore, comprehending processes such as transcription and replication in fruit flies helps in understanding these processes in other eukaryotes, including humans.[25]

Thomas Hunt Morgan began using fruit flies in experimental studies of heredity at Columbia University in 1910 in a laboratory known as the Fly Room. The Fly Room was cramped with eight desks, each occupied by students and their experiments. They started off experiments using milk bottles to rear the fruit flies and handheld lenses for observing their traits. The lenses were later replaced by microscopes, which enhanced their observations. Morgan and his students eventually elucidated many basic principles of heredity, including sex-linked inheritance, epistasis, multiple alleles, and gene mapping.[25]

Model organism in genetics

Thomas Hunt Morgan's Drosophila melanogaster genetic linkage map. This was the first successful gene mapping work and provides important evidence for the chromosome theory of inheritance. The map shows the relative positions of allelic characteristics on the second Drosophila chromosome. The distance between the genes (map units) are equal to the percentage of crossing-over events that occurs between different alleles.

D. melanogaster types (clockwise): brown eyes with black body, cinnabar eyes, sepia eyes with ebony body, vermilion eyes, white eyes, and wild-type eyes with yellow body

D. melanogaster is one of the most studied organisms in biological research, particularly in genetics and developmental biology. The several reasons include:

Its care and culture requires little equipment and uses little space even when using large cultures, and the overall cost is low.

It is small and easy to grow in the laboratory and its morphology is easy to identify once anesthetized (usually with ether, carbon dioxide gas, by cooling, or with products like FlyNap).

It has a short generation time (about 10 days at room temperature), so several generations can be studied within a few weeks.

It has a high fecundity (females lay up to 100 eggs per day, and perhaps 2000 in a lifetime).

Males and females are readily distinguished and virgin females are easily isolated, facilitating genetic crossing.

The mature larvae show giant chromosomes in the salivary glands called polytene chromosomes—"puffs" indicate regions of transcription and hence gene activity.

It has only four pairs of chromosomes: three autosomes, and one pair of sex chromosomes.

Males do not show meiotic recombination, facilitating genetic studies.

Recessive lethal "balancer chromosomes" carrying visible genetic markers can be used to keep stocks of lethal alleles in a heterozygous state without recombination due to multiple inversions in the balancer.

Genetic transformation techniques have been available since 1987.

Its complete genome was sequenced and first published in 2000.

Genome

D. melanogaster chromosomes to scale with megabase-pair references oriented as in the National Center for Biotechnology Information database, centimorgan distances are approximate and estimated from the locations of selected mapped loci.

The genome of D. melanogaster (sequenced in 2000, and curated at the FlyBase database) contains four pairs of chromosomes: an X/Y pair, and three autosomes labeled 2, 3, and 4. The fourth chromosome is so tiny, it is often ignored, aside from its important eyeless gene. The D. melanogaster sequenced genome of 139.5 million base pairs has been annotated and contains around 15,682 genes according to Ensemble release 73. More than 60% of the genome appears to be functional non-protein-coding DNA involved in gene expression control.

Similarity to humans

A March 2000 study by National Human Genome Research Institute comparing the fruit fly and human genome estimated that about 60% of genes are conserved between the two species. About 75% of known human disease genes have a recognizable match in the genome of fruit flies, and 50% of fly protein sequences have mammalian homologs. An online database called Homophila is available to search for human disease gene homologues in flies and vice versa. Drosophila is being used as a genetic model for several human diseases including the neurodegenerative disorders Parkinson's, Huntington's, spinocerebellar ataxia and Alzheimer's disease. The fly is also being used to study mechanisms underlying aging and oxidative stress, immunity, diabetes, and cancer, as well as drug abuse.

Development

Main article: Drosophila embryogenesis

Embryogenesis in Drosophila has been extensively studied, as its small size, short generation time, and large brood size makes it ideal for genetic studies. It is also unique among model organisms in that cleavage occurs in a syncytium.

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zebrafish

英[zi:b'rɑ:fi:ʃ]

美[zi:b'rɑ:fi:ʃ]

n.斑马鱼;

[例句]Haploid development in zebrafish has been applied for genetic screening.

对斑马鱼以开展了单倍体发育的遗传学筛选。

斑马鱼属卵生鱼类，4月龄进入性成熟期，一般用5月龄鱼繁殖较好。繁殖用水要求pH6.5～7.5,硬度6～8，水温25～26摄氏度。喜在水族箱底部产卵，斑马鱼最喜欢自食其卵，一般可选6月

水族箱中的斑马鱼

龄的亲鱼，在25厘米×25厘米×25厘米的方形缸底铺一层尼龙网板，或铺些鹅卵石，繁殖时产出后即落入网板下面或散落在小卵石的空隙中。选取2～3对亲鱼，同时放入繁殖缸中，一般在黎明到第二天上午10时左右产卵结束，将亲鱼捞出。其卵无粘性，直接落入缸底，到晚上10时左右，没有受精的鱼卵发白，可用吸管吸出。

发育阶段编辑

斑马鱼的发育分为6个阶段：卵裂期，囊胚期，原肠胚期、分裂期、成形期和孵化期。

。斑马鱼由于个体小，养殖花费少，能大规模繁育，且具许多优点，吸引了众多研究者的注意。经过30多年的研究应用和系统发展，已有约20个斑马鱼品系，斑马鱼基因数据库里有相关的资料可供查询和下载，方便了研究。斑马鱼的细胞标记技术、组织移植技术、突变技术、单倍体育种技术、转基因技术、基因活性抑制技术等已经成熟，且有数以千计的斑马鱼胚胎突变体，是研究胚胎发育分子机制的优良资源，有的还可做为人类疾病模型。斑马鱼已经成为最受重视的脊椎动物发育生物学模式之一，在其它学科上的利用也显示很大的潜力。由于斑马鱼基因与人类基因的相似度达到87%，这意味着在其身上做药物实验所得到的结果在多数情况下也适用于人体，因此它受到生物学家的重视。因为斑马鱼的胚胎是透明的，所以生物学家很容易观察到药物对其体内器官的影响。此外，雌性斑马鱼可产卵200枚，胚胎在24小时内就可发育成形，这使得生物学家可以在同一代鱼身上进行不同的实验，进而研究病理演化过程并找到病因。

斑马鱼由于养殖方便、繁殖周期短、产卵量大、胚胎体外受精、体外发育、胚体透明，已成为生命科学研究的新宠。全球范围内有超过1500个斑马鱼实验室。利用斑马鱼，可以研究生命科学的基础问题，揭示胚胎和组织器官发育的分子机理；可以构建人类的各种疾病和肿瘤模型，建立药物筛选和治疗的研究平台；可以建立毒理学和水产育种学模型，研究和解决环境科学和农业科学的重大问题。

科学研究

斑马鱼

在国际上，斑马鱼模式生物的使用正逐渐拓展和深入到生命体的多种系统（例如，神经系统、免疫系统、心血管系统、生殖系统等）的发育、功能和疾病（例如，神经退行性疾病、遗传性心血管疾病、糖尿病等）的研究中，并已应用于小分子化合物的大规模新药筛选。我国开展斑马鱼相关的研究无论在规模还是在重视程度上都远远落后于国际形势发展的需要。

Zebrafish

The zebrafish (Danio rerio) is a tropical freshwater fish belonging to the minnow family (Cyprinidae) of the order Cypriniformes.[1] Native to the Himalayan region, it is a popular aquarium fish, frequently sold under the trade name zebra danio.The zebrafish is also an important and widely used vertebrate model organism in scientific research, and was among the first vertebrates to be cloned (frogs were cloned decades earlier, in the 1950s by Briggs and King and by Gurdon).[3] It is particularly notable for its regenerative abilities, and has been modified by researchers to produce many transgenic strains

In scientific research

Zebrafish are widely studied by scientists.

D. rerio is a common and useful scientific model organism for studies of vertebrate development and gene function. Its use as a laboratory animal was pioneered by the American molecular biologist George Streisinger and his colleagues at the University of Oregon 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). 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, oncology, toxicology, reproductive studies, teratology, genetics, neurobiology, environmental sciences, stem cell research and regenerative medicine, and evolutionary theory.

Model characteristics

As a model biological system, the zebrafish possesses numerous advantages for scientists. Its genome has been fully sequenced, and it has well-understood, easily observable and testable developmental behaviors. Its embryonic development 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 techniques to be used, and the fact that its two-celled embryo can be fused into a single cell to create a homozygous embryo. 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 fins, skin, heart, lateral line hair cells, and brain during their larval stages.[30][31] 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 and retinal neurons following injury, which has been shown to be mediated by the dedifferentiation and proliferation of Müller glia. 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.[35] In 2012, Australian scientists published a study revealing that zebrafish use a specialised protein, known as fibroblast growth factor, to ensure their spinal cords heal without glial scarring after injury. In addition, hair cells of the posterior lateral line 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.

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.[38] Another focus of zebrafish research is to understand how a gene called Hedgehog, a biological signal that underlies a number of human cancers, controls cell growth.

Genetics

Gene expression

Due to their short lifecycles and relatively large clutch sizes, zebrafish are a useful model for genetic studies. A common reverse genetics technique is to reduce gene expression or modify splicing using Morpholino antisense technology. Morpholino oligonucleotides (MO) are stable, synthetic macromolecules 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 interpermeable to large molecules, allowing diffusion between cells.

A known problem with gene knockdowns 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.[41] Despite the complications of the zebrafish genome, a number of commercially available global platforms exist for analysis of both gene expression by microarrays and promoter regulation using ChIP-on-chip.

Genome sequencing

The Wellcome Trust Sanger Institute 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 (NCBI)'s Zebrafish Genome Page. The zebrafish reference genome sequence is annotated as part of the Ensembl project, and is maintained by the Genome Reference Consortium.[43]

In 2009, researchers at the Institute of Genomics and Integrative Biology 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 published D. rerio's complete mitochondrial DNA 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 (Cyprinus carpio). Its gene order and content are 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. 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 sequences.

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 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.

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.

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. Because many gene functions are shared between fish and humans, the Casper strain is expected to yield insights into human diseases such as leukemia and other cancers.[6] In January 2013, Japanese scientists genetically modified a transparent zebrafish specimen to produce a visible glow during periods of intense brain activity, allowing the fish's "thoughts" to be recorded as specific regions of its brain lit up in response to external stimuli.

if placed into water that was polluted by oestrogen.

 

RNA Splicing

In 2015, researchers at Brown University discovered that 10% of zebrafish genes do not need to rely on the U2AF2 protein 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 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.

 

In 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. 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, by Ceol, Houvras and Zon, the model was used as a tool to understand the functional importance of genes known to be amplified and overexpressed in human melanoma.[56] 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.

 

Cardiovascular disease

In cardiovascular research, the zebrafish has been used to model blood clotting, blood vessel development, heart failure, and congenital heart and kidney disease.

 

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)[61] while adaptive immunity is not functionally mature until at least 4 weeks postfertilization.

Repairing retinal damage

The development of a single zebrafish retina captured on a light sheet microscope approx. every 12 hours from 1.5 days to 3.5 days after birth of the embryo.

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 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.

Drug discovery

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 teratology assay model.[80] 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. However, many technical challenges remain to be resolved, including differing rates of drug absorption and high levels of natural variation between individual animals.