Zebrafish | EPFL Graph Search

The zebrafish (Danio rerio) is a freshwater fish belonging to the minnow family (Cyprinidae) of the order Cypriniformes. Native to India and South Asia, it is a popular aquarium fish, frequently sold under the trade name zebra danio (and thus often called a "tropical fish" although both tropical and subtropical). It is also found in private ponds. The zebrafish is an important and widely used vertebrate model organism in scientific research, for example in drug development, in particular pre-clinical development. It is also notable for its regenerative abilities, and has been modified by researchers to produce many transgenic strains. Taxonomy The zebrafish is a derived member of the genus Brachydanio, of the family Cyprinidae. It has a sister-group relationship with Danio aesculapii. Zebrafish are also closely related to the genus Devario, as demonstrated by a phylogen

Role of glutathione S-transferases and the mercapturic acid pathway in the biotransformation potential of two zebrafish (Danio rerio) test systems: early life stages and PAC2 cells

Alena Tierbach

Zebrafish (Danio rerio) early life stages provide an important model for chemical risk assessment due to their genetic similarity to humans and the availability of well-established high-throughput techniques. Cells isolated from zebrafish conserve all these advantages and can, in addition, be multiplied in the laboratory to an unlimited extend. However, the biotransformation capacities of both systems have not been fully charac-terized. One biotransformation pathway, which is of utmost importance for the clearance of electrophilic compounds and phase I biotransformation products, is the mercapturic acid pathway. Its first step is the conjugation of the electrophile with glutathione, catalyzed by glutathione S-transferases (GSTs). The gluta-thione conjugates are usually further biotransformed within the mercapturic acid pathway by sequential re-moval of the glutamyl- and glycyl-moieties and an acetylation step followed by elimination of the mercap-turate. Considering the significance of this biotransformation route for the outcome of toxicological investi-gations, this thesis aims to close some major knowledge gaps regarding the protein expression of GSTs and the functionality of the mercapturic acid pathway in two test systems, zebrafish early life stages and the embryo-derived cell line PAC2. To investigate the repertoire of cytosolic GSTs and their expression dynamics, a targeted proteomics meth-od using electrospray ionization (ESI) was developed. Zebrafish embryos showed a basal expression of GST isoenzymes belonging to the classes alpha, mu, pi and rho as early as 4 hours post fertilization, indi-cating maternal transfer. After hatching, all cytosolic GST classes could be detected in the free-swimming larvae. The embryo-derived cell line PAC2 also expressed all cytosolic GST classes, except class alpha. Motivated by the abundant expression of GSTs in the zebrafish models, focus was set on the potential of GSTs to biotransform a model substrate (1-chloro-2,4-dinitrobenzene, CDNB) and to initiate its further bio-transformation within the mercapturic acid pathway. Since CDNB has no acid/base properties, an atmos-pheric pressure chemical ionization (APCI) method based on electron capture was developed for CDNB analysis at and below the nontoxic concentrations. For the determination of CDNB biotransformation prod-ucts of the mercapturic acid pathway, an ESI method was developed. In both test systems, the expression of cytosolic GSTs was not affected by non-toxic concentrations of the model substrate CDNB. Further-more, both test systems disclosed a fully functional mercapturic acid pathway with the first (glutathione conjugate) and last (mercapturate) biotransformation product being produced and excreted in zebrafish early life stages and PAC2 cells. To conclude, this thesis reveals the expression of a large GST repertoire and a functional mercapturic acid pathway in zebrafish early life stages and PAC2 cells. The presence of this important chemical activa-tion/deactivation and clearance route supports the application of these test systems as alternative models in toxicology and chemical hazard assessment.

EPFL2020

Modeling spinal locomotor circuits for movements in developing zebrafish

Yann Roussel

Many spinal circuits dedicated to locomotor control have been identified in the developing zebrafish. How these circuits operate together to generate the various swimming movements during development remains to be clarified. In this study, we iteratively built models of developing zebrafish spinal circuits coupled to simplified musculoskeletal models that reproduce coiling and swimming movements. The neurons of the models were based upon morphologically or genetically identified populations in the developing zebrafish spinal cord. We simulated intact spinal circuits as well as circuits with silenced neurons or altered synaptic transmission to better understand the role of specific spinal neurons. Analysis of firing patterns and phase relationships helped to identify possible mechanisms underlying the locomotor movements of developing zebrafish. Notably, our simulations demonstrated how the site and the operation of rhythm generation could transition between coiling and swimming. The simulations also underlined the importance of contralateral excitation to multiple tail beats. They allowed us to estimate the sensitivity of spinal locomotor networks to motor command amplitude, synaptic weights, length of ascending and descending axons, and firing behavior. These models will serve as valuable tools to test and further understand the operation of spinal circuits for locomotion. eLife digest The spinal cord is a column of nerve tissue that connects the brain to the rest of the body in vertebrate animals. Nerve cells in the spinal cord, called neurons, help to control and coordinate the body's movements. As the spinal cord develops, new neurons are born and new connections are made between neurons and muscles, resulting in more coordinated and skillful movements as time goes on. Zebrafish, for example, display body-bending maneuvers called coils within 24 hours of the egg being fertilized. Next, bursts of swimming movements emerge, which are driven by sporadic tail beats. These tail maneuvers become more consistent as the fish develops, and eventually result in smooth movements called beat-and-glide swimming. The groups of spinal cord neurons that appear at each stage of zebrafish development have been characterized, but it remains unclear how newly formed circuits (groups of neurons recently connected to each other) work together to produce swimming maneuvers. To answer this question, Roussel et al. simulated changes in the spinal cord that help zebrafish acquire new swimming movements as they grow. The computer models encoded neural circuits based on cell populations identified in experimental studies, and replicated swimming behaviors that emerge during the first few days of zebrafish development. Simulations tested how specific neural circuits generate the characteristic swimming movements that represent key developmental milestones in zebrafish. The results showed that adding new neurons and more cell-to-cell connections led to increasingly sophisticated swimming maneuvers. As the zebrafish spinal cord matured, the fish were better able to control the pace and duration of their swimming movements. Roussel et al. also identified specific patterns of neural activity linked to particular maneuvers. For example, tail beats switch direction when neurons on one side of the spinal cord excite neurons on the opposite side. This activity, which becomes more rhythmic, also needs to be exquisitely timed to produce and coordinate the right motion. Roussel et al.'s modelling of developmental milestones in growing zebrafish provides insights into how neural networks control movement. The computer models are among the first to accurately reproduce swimming behaviors in developing zebrafish. More experimental data could be added to the models to capture the full range of early zebrafish movements, and to further investigate how maturing spinal cord circuits control swimming. Since zebrafish and mammals have many spinal neurons in common, further research may aid our understanding of movement disorders in humans.

eLIFE SCIENCES PUBL LTD2021

Bigh3 Is Upregulated in Regenerating Zebrafish Fin

Zebrafish is a good model for studying regeneration because of the rapidity with which it occurs. Better understanding of this process may lead in the future to improvement of the regenerating capacity of humans. Signaling factors are the second largest category of genes, regulated during regeneration after the regulators of wound healing. Major developmental signaling pathways play a role in this multistep process, such as Bmp, Fgf, Notch, retinoic acid, Shh, and Wnt. In the present study, we focus on TGF-beta-induced genes, bigh3 and bambia. Bigh3 encodes keratoepithelin, a protein first identified as an extracellular matrix protein reported to play a role in cell adhesion, as well as in cornea formation and osteogenesis. The expression of bigh3 in zebrafish fins has previously been reported. Here we demonstrate that tgf-b1 and tgf-b3 mRNA reacted with delay, first showing no regulation at 3 dpa, followed by upregulation at 4 and 5 dpa. Tgf-b1, tgf-2, and tgf-brII mRNA were back to normal levels at 10 dpa. Only tgf-b3 mRNA was still upregulated at that time. Bigh3 mRNA followed the upregulation of tgf-b1, while bambia mRNA behaved similarly to tgf-b2 mRNA. We show that upregulation of bigh3 and bambia mRNA correlated with the process of fin regeneration and regulation of TGF-b signaling, suggesting a new role for these proteins.

Mary Ann Liebert Inc2013