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Hearing Research Dec 2015The basic architecture and functionality of ribbon synapses of mechanosensitive hair cells are well conserved among vertebrates. Forward and reverse genetic methods in... (Review)
Review
The basic architecture and functionality of ribbon synapses of mechanosensitive hair cells are well conserved among vertebrates. Forward and reverse genetic methods in zebrafish (Danio rerio) have identified components that are critical for the development and function of ribbon synapses. This review will focus on the findings of these genetic approaches, and discuss some emergent concepts on the role of the ribbon body and calcium in synapse development, and how perturbations in synaptic vesicles lead to a loss of temporal fidelity at ribbon synapses. This article is part of a Special Issue entitled
. Topics: Animals; Animals, Genetically Modified; Auditory Pathways; Calcium Signaling; Genotype; Hair Cells, Auditory; Hearing; Mechanotransduction, Cellular; Nerve Tissue Proteins; Phenotype; Synaptic Transmission; Zebrafish; Zebrafish Proteins
PubMed: 25916266
DOI: 10.1016/j.heares.2015.04.003 -
Progress in Neuro-psychopharmacology &... Dec 2014Due to the fish-specific genome duplication event (~320-350 mya), some genes which code for serotonin proteins were duplicated in teleosts; this duplication event was... (Review)
Review
Due to the fish-specific genome duplication event (~320-350 mya), some genes which code for serotonin proteins were duplicated in teleosts; this duplication event was preceded by a reorganization of the serotonergic system, with the appearance of the raphe nuclei (dependent on the isthmus organizer) and prosencephalic nuclei, including the paraventricular and pretectal complexes. With the appearance of amniotes, duplicated genes were lost, and the serotonergic system was reduced to a more complex raphe system. From a comparative point of view, then, the serotonergic system of zebrafish and that of mammals shows many important differences. However, many different behavioral functions of serotonin, as well as the effects of drugs which affect the serotonergic system, seem to be conserved among species. For example, in both zebrafish and rodents acute serotonin reuptake inhibitors (SSRIs) seem to increase anxiety-like behavior, while chronic SSRIs decrease it; drugs which act at the 5-HT1A receptor seem to decrease anxiety-like behavior in both zebrafish and rodents. In this article, we will expose this paradox, reviewing the chemical neuroanatomy of the zebrafish serotonergic system, followed by an analysis of the role of serotonin in zebrafish fear/anxiety, stress, aggression and the effects of psychedelic drugs.
Topics: Animals; Behavior, Animal; Brain; Humans; Serotonin; Serotonin Agents; Species Specificity; Zebrafish
PubMed: 24681196
DOI: 10.1016/j.pnpbp.2014.03.008 -
Nature Biotechnology Apr 2024Current N-methyladenosine (mA) mapping methods need large amounts of RNA or are limited to cultured cells. Through optimized sample recovery and signal-to-noise ratio,...
Current N-methyladenosine (mA) mapping methods need large amounts of RNA or are limited to cultured cells. Through optimized sample recovery and signal-to-noise ratio, we developed picogram-scale mA RNA immunoprecipitation and sequencing (picoMeRIP-seq) for studying mA in vivo in single cells and scarce cell types using standard laboratory equipment. We benchmark mA mapping on titrations of poly(A) RNA and embryonic stem cells and in single zebrafish zygotes, mouse oocytes and embryos.
Topics: Animals; Mice; Zebrafish; RNA; RNA, Messenger; Embryonic Stem Cells; Cells, Cultured
PubMed: 37349523
DOI: 10.1038/s41587-023-01831-7 -
Pharmacology & Therapeutics May 2016The zebrafish model is the only available high-throughput vertebrate assessment system, and it is uniquely suited for studies of in vivo cell biology. A sequenced and... (Review)
Review
The zebrafish model is the only available high-throughput vertebrate assessment system, and it is uniquely suited for studies of in vivo cell biology. A sequenced and annotated genome has revealed a large degree of evolutionary conservation in comparison to the human genome. Due to our shared evolutionary history, the anatomical and physiological features of fish are highly homologous to humans, which facilitates studies relevant to human health. In addition, zebrafish provide a very unique vertebrate data stream that allows researchers to anchor hypotheses at the biochemical, genetic, and cellular levels to observations at the structural, functional, and behavioral level in a high-throughput format. In this review, we will draw heavily from toxicological studies to highlight advances in zebrafish high-throughput systems. Breakthroughs in transgenic/reporter lines and methods for genetic manipulation, such as the CRISPR-Cas9 system, will be comprised of reports across diverse disciplines.
Topics: Animals; Animals, Genetically Modified; Gene Expression; High-Throughput Screening Assays; Humans; Models, Animal; Toxicology; Zebrafish
PubMed: 27016469
DOI: 10.1016/j.pharmthera.2016.03.009 -
Comparative Biochemistry and... 2022Activator of heat shock protein 90 (hsp90) ATPase (Aha1) is a Hsp90 co-chaperone required for Hsp90 ATPase activation. Aha1 is essential for yeast survival and muscle...
Activator of heat shock protein 90 (hsp90) ATPase (Aha1) is a Hsp90 co-chaperone required for Hsp90 ATPase activation. Aha1 is essential for yeast survival and muscle development in C. elegans under elevated temperature and hsp90-deficeiency induced stress conditions. The roles of Aha1 in vertebrates are poorly understood. Here, we characterized the expression and function of Aha1 in zebrafish. We showed that zebrafish genome contains two aha1 genes, aha1a and aha1b, that show distinct patterns of expression during development. Under the normal physiological conditions, aha1a is primarily expressed in skeletal muscle cells of zebrafish embryos, while aha1b is strongly expressed in the head region. aha1a and aha1b expression increased dramatically in response to heat shock induced stress. In addition, Aha1a-GFP fusion protein exhibited a dynamic translocation in muscle cells in response to heat shock. Moreover, upregulation of aha1 expression was also observed in hsp90a1 knockdown embryos that showed a muscle defect. Genetic studies demonstrated that knockout of aha1a, aha1b or both had no detectable effect on embryonic development, survival, and growth in zebrafish. The aha1a and aha1b mutant embryos showed normal muscle development and stress response in response to heat shock. Single or double aha1a and aha1b mutants could grow into normal reproductive adults with normal skeletal muscle structure and morphology compared with wild type control. Together, data from these studies indicate that Aha1a and Aha1b are involved in stress response. However, they are dispensable in zebrafish embryonic development, growth, and survival.
Topics: Adenosine Triphosphatases; Animals; Embryo, Nonmammalian; Gene Expression; HSP90 Heat-Shock Proteins; Heat-Shock Response; Molecular Chaperones; Zebrafish; Zebrafish Proteins
PubMed: 35830921
DOI: 10.1016/j.cbpb.2022.110777 -
Developmental Dynamics : An Official... Nov 2017The Zebrafish has emerged to become a powerful vertebrate animal model for cardiovascular research in recent years. Its advantages include easy genetic manipulation,... (Review)
Review
The Zebrafish has emerged to become a powerful vertebrate animal model for cardiovascular research in recent years. Its advantages include easy genetic manipulation, transparency, small size, low cost, and the ability to survive without active circulation at early stages of development. Sequencing the whole genome and identifying ortholog genes with human genome made it possible to induce clinically relevant cardiovascular defects via genetic approaches. Heart function and disturbed hemodynamics need to be assessed in a reliable manner for these disease models in order to reveal the mechanobiology of induced defects. This effort requires precise determination of blood flow patterns as well as hemodynamic stress (i.e., wall shear stress and pressure) levels within the developing heart. While traditional approach involves time-lapse brightfield microscopy to track cell and tissue movements, in more recent studies fast light-sheet fluorescent microscopes are utilized for that purpose. Integration of more complicated techniques like particle image velocimetry and computational fluid dynamics modeling for hemodynamic analysis holds a great promise to the advancement of the Zebrafish studies. Here, we discuss the latest developments in heart function and hemodynamic analysis for Zebrafish embryos and conclude with our future perspective on dynamic analysis of the Zebrafish cardiovascular system. Developmental Dynamics 246:868-880, 2017. © 2017 Wiley Periodicals, Inc.
Topics: Animals; Blood Flow Velocity; Embryo, Nonmammalian; Heart; Hemodynamics; Stress, Mechanical; Zebrafish
PubMed: 28249360
DOI: 10.1002/dvdy.24497 -
ELife Sep 2021The spatial organization of gut microbiota influences both microbial abundances and host-microbe interactions, but the underlying rules relating bacterial dynamics to...
The spatial organization of gut microbiota influences both microbial abundances and host-microbe interactions, but the underlying rules relating bacterial dynamics to large-scale structure remain unclear. To this end, we studied experimentally and theoretically the formation of three-dimensional bacterial clusters, a key parameter controlling susceptibility to intestinal transport and access to the epithelium. Inspired by models of structure formation in soft materials, we sought to understand how the distribution of gut bacterial cluster sizes emerges from bacterial-scale kinetics. Analyzing imaging-derived data on cluster sizes for eight different bacterial strains in the larval zebrafish gut, we find a common family of size distributions that decay approximately as power laws with exponents close to -2, becoming shallower for large clusters in a strain-dependent manner. We show that this type of distribution arises naturally from a Yule-Simons-type process in which bacteria grow within clusters and can escape from them, coupled to an aggregation process that tends to condense the system toward a single massive cluster, reminiscent of gel formation. Together, these results point to the existence of general, biophysical principles governing the spatial organization of the gut microbiome that may be useful for inferring fast-timescale dynamics that are experimentally inaccessible.
Topics: Animals; Bacteria; Bacterial Physiological Phenomena; Gastrointestinal Microbiome; Gastrointestinal Tract; Gels; Kinetics; Models, Theoretical; Population Density; Zebrafish
PubMed: 34490846
DOI: 10.7554/eLife.71105 -
Cells Apr 2022Zebrafish show an extraordinary potential for regeneration in several organs from fins to central nervous system. Most impressively, the outcome of an injury results in...
Zebrafish show an extraordinary potential for regeneration in several organs from fins to central nervous system. Most impressively, the outcome of an injury results in a near perfect regeneration and a full functional recovery. Indeed, among the various injury paradigms previously tested in the field of zebrafish retina regeneration, a perfect layered structure is observed after one month of recovery in most of the reported cases. In this study, we applied cryoinjury to the zebrafish eye. We show that retina exposed to this treatment for one second undergoes an acute damage affecting all retinal cell types, followed by a phase of limited tissue remodeling and regrowth. Surprisingly, zebrafish developed a persistent retinal dysplasia observable through 300 days post-injury. There is no indication of fibrosis during the regeneration period, contrary to the regeneration process after cryoinjury to the zebrafish cardiac ventricle. RNA sequencing analysis of injured retinas at different time points has uncovered enriched processes and a number of potential candidate genes. By means of this simple, time and cost-effective technique, we propose a zebrafish injury model that displays a unique inability to completely recover following focal retinal damage; an outcome that is unreported to our knowledge. Furthermore, RNA sequencing proved to be useful in identifying pathways, which may play a crucial role not only in the regeneration of the retina, but in the first initial step of regeneration, degeneration. We propose that this model may prove useful in comparative and translational studies to examine critical pathways for successful regeneration.
Topics: Animals; Heart Ventricles; Nerve Regeneration; Retina; Zebrafish
PubMed: 35456052
DOI: 10.3390/cells11081373 -
PloS One 2022The zebrafish is an excellent model system to study thrombocyte function and development. Due to the difficulties in separating young and mature thrombocytes,...
The zebrafish is an excellent model system to study thrombocyte function and development. Due to the difficulties in separating young and mature thrombocytes, comparative transcriptomics between these two cell types has not been performed. It is important to study these differences in order to understand the mechanism of thrombocyte maturation. Here, we performed single-cell RNA sequencing of the young and mature zebrafish thrombocytes and compared the two datasets for young and mature thrombocyte transcripts. We found a total of 9143 genes expressed cumulatively in both young and mature thrombocytes, and among these, 72% of zebrafish thrombocyte-expressed genes have human orthologs according to the Ensembl human genome annotation. We also found 397 uniquely expressed genes in young and 2153 uniquely expressed genes in mature thrombocytes. Of these 397 and 2153 genes, 272 and 1620 corresponded to human orthologous genes, respectively. Of all genes expressed in both young and mature thrombocytes, 4224 have been reported to be expressed in human megakaryocytes, and 1603 were found in platelets. Among these orthologs, 156 transcription factor transcripts in thrombocytes were found in megakaryocytes and 60 transcription factor transcripts were found in platelets including a few already known factors such as Nfe2 and Nfe212a (related to Nfe2) that are present in both megakaryocytes, and platelets. These results indicate that thrombocytes have more megakaryocyte features and since platelets are megakaryocyte fragments, platelets also appear to be thrombocyte equivalents. In conclusion, our study delineates the differential gene expression patterns of young and mature thrombocytes, highlighting the processes regulating thrombocyte maturation. Future knockdown studies of these young and mature thrombocyte-specific genes are feasible and will provide the basis for understanding megakaryocyte maturation.
Topics: Animals; Blood Platelets; Platelet Function Tests; Transcription Factors; Zebrafish; Zebrafish Proteins
PubMed: 35320267
DOI: 10.1371/journal.pone.0264776 -
Genetics Jul 2016In the last 30 years, the zebrafish has become a widely used model organism for research on vertebrate development and disease. Through a powerful combination of... (Review)
Review
In the last 30 years, the zebrafish has become a widely used model organism for research on vertebrate development and disease. Through a powerful combination of genetics and experimental embryology, significant inroads have been made into the regulation of embryonic axis formation, organogenesis, and the development of neural networks. Research with this model has also expanded into other areas, including the genetic regulation of aging, regeneration, and animal behavior. Zebrafish are a popular model because of the ease with which they can be maintained, their small size and low cost, the ability to obtain hundreds of embryos on a daily basis, and the accessibility, translucency, and rapidity of early developmental stages. This primer describes the swift progress of genetic approaches in zebrafish and highlights recent advances that have led to new insights into vertebrate biology.
Topics: Animals; Gene Expression Regulation; Models, Animal; Organogenesis; Regeneration; Zebrafish
PubMed: 27384027
DOI: 10.1534/genetics.116.190843