Recent Advances in Danio rerio Biology Review Paper PDF

Developmental Biology Review Paper Recent Advances in DevelopmentalBiology of Danio rerio (Zebrafish) Submitted by: Aleria, Angela Evianne C. Cuizion, Ronnah Jane B. Roble, Krissy Moehl...

Developmental Biology Review Paper Recent Advances in DevelopmentalBiology of Danio rerio (Zebrafish) Submitted by: Aleria, Angela Evianne C. Cuizion, Ronnah Jane B. Roble, Krissy Moehl Tori B. 1. INTRODUCTION various biological processes. These processes include developmental biology, neurobiology, genetics, drug discovery, and regenerative medicine. Zebrafish share significant genetic and physiological similarities with humans, making them an ideal model for FIGURE 1.–- Adult female Danio rerio understanding human diseases and The zebrafish, Danio rerio, is a developing potential treatments. small freshwater fish native to the Indian subcontinent that has become a TAXONOMY AND SYSTEMATICS valuable model organism in biomedical research. They are small, freshwater The zebrafish is a derived member of fish characterized by their distinctive the genus Brachydanio, Cyprinidae blue-purple stripes, and are relatively family. It has a sister-group relationship small, typically reaching 3-4 cm in with Danio aesculapii. Zebrafish are also length. As social animals, they exhibit closely related to the genus Devario, as complex behaviors like schooling and demonstrated by a phylogenetic tree of territoriality. One of their most notable close species. features is their high fecundity, with females capable of producing hundreds This taxonomic classification of eggs per spawning event. This, highlights the zebrafish's position within combined with their rapid development the evolutionary tree of life and its and external fertilization, makes them relationship to other organisms. Its ideal for genetic studies and large-scale unique combination of characteristics, screens. including rapid development, external fertilization, optical clarity, and genetic Zebrafish's transparent embryos, tractability, has made it an invaluable rapid development, genetic tractability, model organism for biomedical and physiological relevance to humans research, particularly in developmental make them powerful tools for studying biology, genetics, and neuroscience. 2. DEVELOPMENT Adult zebrafish are sexually Life cycle mature and capable of spawning The zebrafish life cycle begins multiple times per week. During with external fertilization. Female spawning, females release hundreds of zebrafish release hundreds of eggs, eggs, which are fertilized by males. This which are fertilized by male sperm. The high fecundity, coupled with the rapid fertilized eggs undergo rapid cell development of zebrafish embryos, division and differentiation, forming a allows for large-scale genetic screens blastula, gastrula, and eventually a and studies of developmental biology. neurula. Within 24 hours post-fertilization, the embryo hatches into a larval stage. The larval stage is characterized by rapid organogenesis. During this period, the heart, brain, and sensory organs develop. The larvae feed on yolk reserves and, as they grow, transition to an external feeding stage. By 3-4 days post-fertilization, the larvae exhibit FIGURE 2.--- The life cycle of zebrafish (Ramcharran, 2016). pigmentation and fin development. Embryonic development The juvenile stage marks the Danio rerio, commonly known as transition from larval to adult zebrafish, typically reaches reproductive morphology. Juvenile zebrafish maturity in three months. For successful proliferate, and their fins and spawning, the presence of a male is pigmentation become more pronounced. crucial to induce ovulation and egg They develop the ability to swim and release. These fish are asynchronous feed independently. Within 3-4 months, spawners, meaning they can spawn juvenile zebrafish reach sexual maturity. frequently under optimal conditions like ample food and suitable water parameters. Females can spawn every two to three days, producing hundreds of eggs per clutch. Fertilization is necessary for embryonic development to proceed; unfertilized eggs cease development after a few cell divisions. The transparent nature of zebrafish embryos makes them a valuable model organism for research. Unlike simple genetic systems like ZW or XY, sex determination in common laboratory zebrafish strains involves complex genetic factors. Zebrafish embryos exhibit rapid development, with the formation of FIGURE 3.--- Stages of zebrafish development. Photos to scale except adult, which is about 2.5 cm (1 major organ precursors within 36 hours in) long of fertilization. The initial single-cell embryo undergoes rapid cell division, To stimulate spawning, followed by cell migration and researchers often employ a tank with a differentiation into distinct body parts. sliding bottom insert that mimics a The yolk sac, serving as a nutrient shallow riverbed. Zebrafish exhibit a source, gradually shrinks as the embryo preference for morning spawning, matures. After several months, the aligned with their circadian rhythms. By zebrafish reaches adulthood and using this method, researchers can becomes capable of reproduction. collect thousands of embryos within a short period. A single pair of adult zebrafish can produce 200-300 eggs in a morning, laying them in small batches. Male zebrafish are attracted to females with distinct markings, but they will mate with available females in a group changes, allowing the fish to sense its setting. The factors that attract females surroundings and avoid predators. to males remain unclear. The presence Zebrafish possess large lateral eyes that of plants, even artificial ones, can provide a broad field of vision, although encourage spawning behavior. they lack eyelids. It also has paired nostrils that lead to olfactory organs Exposure to diisononyl phthalate used to detect chemical signals in the (DINP), a common plasticizer, can water, and the anteriorly positioned disrupt the endocannabinoid system in mouth facilitates feeding and water zebrafish, leading to sex-specific intake. reproductive impairments. Anatomy and Physiology Skeletal System External Anatomy The zebrafish exhibits a streamlined, fusiform body shape designed for efficient swimming, reducing water resistance and allowing swift movement. Its fins are specialized for various Figure 4 - Olfactory organ (a) olfactory organ; (b) olfactory bulb; (c) telencephalon functions; the dorsal and anal fins stabilize the body and prevent rolling, Its skeletal system provides while the caudal fin provides thrust for structural support and protection for vital propulsion. The pectoral and pelvic fins organs. The cranial skeleton encases enable precise steering and balance, the brain and supports sensory organs and the anal fin assists in maintaining like the eyes and olfactory bulbs. The stability. The zebrafish is covered with vertebral column consists of a series of thin, overlapping scales that serve as a vertebrae, offering exile support while protective barrier and enhance shielding the spinal cord. Fin hydrodynamics. Its lateral line system, a movements are controlled by fin rays sensory organ running along the body, (lepidotrichia), flexible bony structures detects water vibrations and pressure that provide support for fins and enable complex swimming behaviors. The jaw mesencephalon, responsible for bones including the maxilla, mandible, processing vital and auditory signals; and premaxilla, play critical roles in the metencephalon, which houses the feeding by facilitating biting and cerebellum for motor coordination and capturing prey. balance; and the myelencephalon, which controls vital reflexes such as Muscular System respiration and circulation. The spinal The muscular system of the cord connects the brain to the body and zebrafish consists of myomers, and transmits motor and sensory signals, zigzag-shaped muscle segments that while peripheral nerves extend to contract in a wave-like pattern to muscles, fins, and sensory organs, generate propulsion. These muscles, enabling precise control and absolute running along the body, provide the responsiveness. primary force for forward movement and enable rapid escape responses. Circulatory System Additionally, small fin muscles control the precise movement of individual fins, allowing for fine adjustments during swimming, hovering, or turning. Nervous System The nervous system of zebrafish is highly specialized and includes the FIGURE 5.—Heart and thyroid. (a) Sinus venosus; (b) brain, spinal cord, and peripheral atrium; (c) ventricle; (d) bulbus arteriosus; (e) ventral aorta; (f) thyroid follicles. nerves. The brain is divided into five The circulatory system of the regions; the telencephalon, which zebrafish is composed of two chambers, governs memory, sensory processing, the atrium and the ventricle. The atrium and locomotion; the diencephalon, collects deoxygenated blood from the which regulates homeostasis and body, and the ventricle pumps it to the endocrine functions, including circadian gills for oxygenation. The sinus venosus rhythms via the pineal gland; the serves as a blood reservoir before blood enters the heart, while the bulbus further. The liver produces bile, essential arteriosus, an elastic structure, for fat digestion, while also storing smoothens the pressure pulses from the glycogen and detoxifying harmful ventricle before the blood flows into the substances. The pancreas secretes gills. Blood vessels distribute oxygen, digestive enzymes to aid nutrient nutrients, and waste products breakdown and regulates blood glucose throughout the body via a network of levels through insulin secretion. arteries, veins, and capillaries. Excretory System Respiratory System The zebrafish rely on gills for respiration, extracting oxygen from water and expelling carbon dioxide. Gill FIGURE 6 — Kidney. (a) Glomerulus; (b) proximal or distal tubulus; (c) collecting duct; (d) hematopoietic tissue arches are equipped with filaments and lamellae that maximize surface area, The kidney of the zebrafish plays employing a counter-current flow a dual role in filtering nitrogenous waste, mechanism for efficient gas exchange. such as ammonia, from the blood and The swim bladder, a gas-filled organ, maintaining water and ionic balance– a plays a crucial role in buoyancy process critical for osmoregulation in regulation, enabling the fish to maintain freshwater environments. The filtered its position in the water column without waste exits the body through the expending energy. urogenital pore, which serves as the common exit for both excretory and Digestive System reproductive systems. The digestive tract of zebrafish begins at the mouth, where food is Reproductive System ingested and partially broken down. The esophagus transports food to the stomach, where enzymatic digestion occurs. Nutrient absorption is completed in the intestine, which processes food FIGURE 7.— Testis.  growth through hormone production, and the pineal gland, which influences circadian rhythms and seasonal behaviors. The pituitary gland coordinates hormonal signals for FIGURE 8.— Ovary. growth, reproduction, and stress responses, controlling other endocrine Zebrafish are oviparous, with organs and ensuring physiological females producing eggs and males homeostasis. producing sperm for external fertilization. The gonads include ovaries Immune System in females, which release eggs, and testes in males, which release sperm into the water. Fertilization occurs externally, and zebrafish embryos develop rapidly, hatching within 2-3 days. This reproductive strategy ensures a high reproductive output. FIGURE 10-– Thymus. (a) cortex; (b) medulla. The zebrafish immune system Endocrine System includes both innate and adaptive components. The thymus, located near the gills, is responsible for the development of T cells, which are crucial for adaptive immunity. It consists of two regions; the cortex, which contains a higher density of developing FIGURE 9.--- (a) Olfactory bulb; (b) telencephalon; (c) cerebellum; (d) optic nerve; (e) pituitary gland; (f) pineal T cells (thymocytes), and the medulla, gland; (g) saccus dorsalis; which has more epithelial cells and The endocrine system of the fewer thymocytes (Baubak Bajoghli et zebrafish includes glands like the al., 2019). thyroid, which regulates metabolism and  chemical cues in the water, which are essential for feeding, reproduction, and predator detection. The lateral line system detects water vibrations and FIGURE 11.— Spleen. a) red pulp pressure changes, aiding in navigation and social behavior. Additionally, the The spleen, located in the auditory systems, using otoliths in the peritoneal cavity, filters blood, removes inner ear, detect sound vibrations and damaged red blood cells, and supports help maintain balance (Menke et al., immune cell production. The red pulp is 2011). involved in filtering blood and removing old or damaged red blood cells, while Morphology the white pulp contains lymphoid tissue Zebrafish is recognized for its that plays a critical role in immune distinct morphology and coloration. It responses (Radhakrishnan et al., 2021). has key morphological features including, body size and shape, Sensory Systems coloration, eyes, mouth, fins, and axial skeleton. The adult size of zebrafish typically ranges from 4 to 5 cm, and some individuals grow up to 6.5 cm. In wild populations, they generally FIGURE 12.--- Olfactory organ (a) olfactory organ; (b) measure between 3 to 4 cm (Piferrer olfactory bulb; (c) telencephalon and Ribas 2020). Adult zebrafish are The zebrafish have sexually dimorphic, exhibiting physical well-developed sensory systems to and behavioral differences, adult interact with their environment. Their females are generally larger and have large lateral eyes provide excellent fuller bodies compared to the smaller vision and are adapted for aquatic and more slender males. They exhibit a conditions. Olfactory organs detect torpedo-like or fusiform body shape that is laterally compressed and anteriorly (Sire and Akimenko 2004). well-adapted for swift swimming (Esmail They possess an upward-pointed and others 2015). Zebrafish are mouth, located ventrally and are characterized by five horizontal stripes terminal in position, featuring that are either black or dark blue which well-defined lips and two sets of jaws extend from behind the head to the tail. lined with small, pointed teeth. This Males display alternating golden and structure aids in their feeding habits. blue stripes, with a more intense yellow The eyes of zebrafish share similarities coloration on the ventral side, their with human eyes, it is large, and intense coloration is often exhibited positioned laterally on the head, which during mating displays. Females have provides a wide field of vision. The silver stripes and a larger, rounder body retina consists of three nuclear layers with a silvery-blue streak along their and two plexiform layers, akin to the sides (Avdesh and others 2012). human retinal structure. Zebrafish have four types of cone photoreceptors, such as blue, green, red, and ultraviolet, mainly mediating their vision through cone cells (Richardson and others 2017). Zebrafish possess several types of fins, including caudal fin, pectoral fins, and anal fin, for stabilization and propulsion. The caudal fin, composed of 16 to 18 bony rays, serves as a model FIGURE 13.--- (Our Marine Species 2019) for studying bone development due to its regenerative capabilities. Pectoral The scales of zebrafish are fins develop through two phases; initially classified as cycloid or elasmoid scales, vertical in larvae and later rotate to a which are smooth and overlapping for horizontal position in adults. Anal fin, protection, forming an integumentary distinctively striped with 10 to 12 skeleton. They begin developing in the branched rays, differing in coloration posterior region of the body and spread between sexes. Anal fins in males are longer and pointed, whereas in females, homology with humans, with about 70% it is shorter and more rounded (Siomava of human genes having analogs in and Diogo 2018). zebrafish. Notably, 84% of human disease genes have counterparts in zebrafish, making them an effective model for studying various conditions such as cancer, heart disease, and neurodegenerative disorders. Their FIGURE 14.---(Bird and Mabee 2003) rapid external development allows for The diagram depicts the efficient drug screening and toxicity zebrafish axial skeleton, centra (black), assessment. Additionally, manipulating Weberian apparatus (green), caudal fin gene expression in zebrafish provides skeleton (purple), and dorsal and anal insights into the human developmental fin endoskeletons (blue). process. The axial skeleton of Danio rerio zebrafish has two centers of development: the caudal fin and the Weberian apparatus. Key features include sequential formation of centra, development of neural arches from cartilage or membrane bone precursors, and ossification occurring without cartilage involvement (Bird and Mabee 2003; Mariotti and others 2015). Genetics Danio rerio or commonly known as Zebrafish are increasingly recognized as valuable models for studying human diseases due to their high genetic Table 1. Summarizing the key genes and proteins in D. rerio development and their human homologs Gene/ Protein Function in Human Relevance to Zebrafish Homolog Human Biology Body Axis wnt8a, wnt11 Establishes body axis WNT family Regulates embryonic Formation and promotes cell devt., stem cell proliferation during renewal, and cancer embryogenesis progression. Anterior-Post hoxa1a, hoxb1b Guides segmentation HOX genes Critical in body erior Axis and hindbrain patterning and linked development. to developmental disorders. Neural shh,gli2a Regulates neural tube SHH, GLI Implicated in Development formation, fin family holoprosencephaly development, and and basal cell left-right asymmetry. carcinoma Mesodermal fgf8a, fgf3 Promotes heart and FGF family Essential for limb Patterning mesodermal tissue development, development angiogenesis, and tissue repair Dorsoventral bmp2b, bmp7 Governs BMP family Associated with Patterning dorsal-ventral axis skeletal formation patterning and organogenesis Cell Fate notch1a, deltaD Determines cell NOTCH family Key in neurogenesis, Determination differentiation and immune system fate development, and cancer Cartilage sox9a Drives cartilage and SOX9 Linked to campomelic Development skeletal development. dysplasia and sex s determination. Cardiac tbx5, gata4 Essentialfor heart and TBX5, GATA4 Mutations linked to development pectoral fin formation congenital heart defects and Holt-Oram syndrome. Blood gata1 Regulates GATA1 Associated with blood formation erythropoiesis (red disorders such as  blood cell formation) anemia and leukemia. Apoptosis tp53, bcl2, bax Controls cell death TP53, BCL2, Implicated in cancer Regulation and survival BAX biology and therapy mechanisms. resistance. Signal kras, braf Involved in the KRAS, BRAF Mutations contribute Transduction RAS-MAPK signaling to cancers like pathway for cell melanoma and growth and colorectal cancer. differentiation Neurodevelop sox10, pax6 Guides neural crest SOX10, PAX6 Implicated in ment and eye Waardenburg development. syndrome and aniridia, respectively. Metabolism igf1, igf1r Regulates growth, IGF1, IGF1R Implicated in aging, and Aging metabolism, and diabetes, and growth aging processes. disorders. Regenerative cxcl12a, mmp9 Involved in tissue CXCL12, Relevant to wound Processes repair and MMP family healing and cardiac regeneration, repair after injury especially in fins and heart 3. SYNTHESIS (Ochenkowska and others 2022). Over the next five years, research on Researchers can examine the the Danio rerio will focus on underlying genetic and molecular neurodegenerative diseases, pathways of some human regenerative medicine, and cancer neurodegenerative disorders by creating research (Alla and others 2024). zebrafish models that mimic such Zebrafish embryos are used to study diseases (Wang and others 2021b). neurodegenerative disorders, tumor initiation, progression, and metastasis, 2. Cancer Research and to identify therapeutic targets for Using zebrafish as a model organism to tissue repair and organ regeneration. investigate the development, spread, and metastasis of tumors and to find 1. Neurodegenerative diseases possible anticancer medications (Dash Utilizing the quick development and and Patnaik 2023). The initiation and transparent embryos of zebrafish to progression of cancer, including investigate the cellular and molecular leukemia, melanoma, and breast processes that underlie neurological cancer, can be studied in this model diseases such as Parkinson's and organism (Zampedri and others 2021). Alzheimer's (Wang and others 2021a). Drug screenings based on zebrafish can Zebrafish presents a unique opportunity find new anticancer drugs that target to investigate the real-time course of particular disease pathways (Dang and neurodegenerative diseases. The others 2016). Moreover, by identifying transparent embryos and larvae of genes implicated in tumorigenesis and zebrafish allow researchers to see how metastasis, genetic screens in zebrafish neurons develop and degenerate, as can shed light on the genetic foundation well as how harmful substances tau and of cancer (Raby and others 2020). amyloid-beta build-up. Zebrafish can be used for high-throughput drug screening 3. Regenerative medicine to find possible therapeutic compounds Examining zebrafish's extraordinary that can halt or reverse capacity for regeneration to find new neurodegenerative processes therapeutic targets for human tissue repair and organ regeneration (Angom and Nakka 2024). Zebrafish are remarkably regenerative, with the capacity to regenerate sections of their brains, hearts, and fins. Researchers can determine the main signaling channels and biological mechanisms that propel regeneration by examining these activities (Marques and Mercader 2019). The development of cell-based treatments for tissue regeneration and repair can be tested in zebrafish. In this case, to encourage tissue regeneration, for instance, damaged zebrafish can get stem cell transplants (Zeng and Tsai 2023). Furthermore, drug screens can also be used to identify compounds that will improve regeneration processes (Karathanasis 2014). References peripheral nerve sheath tumors. Alla, R. 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