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2,481 results for “zebrafish”
Loss of the glucocorticoid receptor causes accelerated reproductive aging in female zebrafish
<p>Reproductive decline in mid-adult females isstablished phenotype of the aging process. Stress and the rise in glucocorticoids (GCs) accelerate reproductive aging, but little is known about the mechanisms involved. During stress, GCs activate the glucocorticoid receptor (GR), a ubiquitously expressed, ligand-bound transcription factor, to elicit physiological changes for restoring homeostasis. Here we tested the hypothesis that GC-GR signalling is essential for accelerating reproductive aging. To test this, we used a ubiquitous GR knockout (GRKO) zebrafish, which is inherently hypercortisolemic, to delineate the role of high cortisol and GR signalling on reproductive aging. The loss of GR led to premature reproductive aging, including high frequency of typical and atypical follicular atresia in vitellogenic oocytes, including yolk liquefaction and large inflammatory infiltrates. The reduction in oocyte quality was also associated with a decline in ovarian <i>tert</i> expression in the adult GRKO fish compared to the early-adult GRKO and adult wildtype zebrafish. Accelerated reproductive aging also impacted the progeny, including lower breeding success, fecundity, egg fertilization rate, and delayed somitogenesis and embryo survival in the adult GRKO fish. We adduce that GR signalling is essential for prolonging the reproductive life span and improving the egg quality and embryo viability in zebrafish.</p>
Hydrogen sulfide exposure reduces thermal set point in zebrafish
<p>Behavioural flexibility allows ectotherms to exploit the environment to govern their metabolic physiology, including in response to environmental stress. Hydrogen sulfide (H<sub>2</sub>S) is a widespread environmental toxin that can lethally inhibit metabolism. However, H<sub>2</sub>S can also alter behaviour and physiology, including a hypothesised induction of hibernation-like states characterised by downward shifts of the innate thermal setpoint (anapyrexia). Support for this hypothesis has proved controversial because it is difficult to isolate active and passive components of thermoregulation, especially in animals with high resting metabolic heat production. Here, we directly test this hypothesis by leveraging the natural behavioural thermoregulatory drive of fish to move between environments of different temperatures in accordance with their current physiological state and thermal preference. We observed a decrease in adult zebrafish (<i>Danio rerio</i>) preferred body temperature with exposure to 0.02% H<sub>2</sub>S, which we interpret as a shift in thermal setpoint. Individuals exhibited consistent differences in shuttling behaviour and preferred temperatures, which were reduced by a constant temperature magnitude during H<sub>2</sub>S exposure. Seeking lower temperatures alleviated H<sub>2</sub>S-induced metabolic stress, as measured by reduced rates of aquatic surface respiration. Our findings highlight the interactions between individual variation and sublethal impacts of environmental toxins on behaviour.</p>
Data from: Tek/Tie2 is not required for cardiovascular development in zebrafish
<p>Angiopoietin/TIE signalling plays a major role in blood and lymphatic vessel development. In mouse, <i>Tek/Tie2</i> mutants die prenatally due to a severely underdeveloped cardiovascular system. In contrast, in zebrafish, previous studies have reported that while embryos injected with <i>tek</i> morpholinos (MOs) exhibit severe vascular defects, <i>tek</i> mutants display no obvious vascular malformations. To further investigate the function of zebrafish Tek, we generated a panel of loss-of-function <i>tek</i> mutants, including RNA-less alleles, an allele lacking the MO-binding site, an in-frame deletion allele, and a premature termination codon-containing allele. Our data show that all these mutants survive to adulthood with no obvious cardiovascular defects. MO injections into <i>tek</i> mutants lacking the MO-binding site or the entire <i>tek</i> locus cause similar vascular defects as those observed in MO-injected <i>+/+</i> siblings, indicating off-target effects of the MOs. Surprisingly, comprehensive phylogenetic profiling and synteny analyses reveal that <i>Tek</i> was lost in the largest teleost clade, suggesting a lineage-specific shift in the function of TEK during vertebrate evolution. Altogether, these data show that Tek is dispensable for zebrafish development, and probably dispensable in most teleost species.</p>
Example Data for 3D quantification of zebrafish cerebrovascular architecture
<p>Example data for:</p> <p>E. C. Kugler, J. Frost, V. Silva, K. Plant, K. Chhabria, T. J.A. Chico, P. A. Armitage</p> <p>3D quantification of zebrafish cerebrovascular architecture by automated image analysis of light sheet fluorescence microscopy datasets</p> <p>bioRxiv 2020.08.06.239905; doi: https://doi.org/10.1101/2020.08.06.239905</p> <p>Link: https://www.biorxiv.org/content/10.1101/2020.08.06.239905v2</p> <p><br> Code: https://github.com/ElisabethKugler/ZFVascularQuantification (doi:https://doi.org/10.5281/zenodo.3978278)</p> <p>Transgenic zebrafish 3dpf: Tg(kdrl:HRAS-mCherry)s916<br> Acquisition: Zeiss Z.1 light sheet microscope with a Plan-Apochromat 20x/1.0 Corr nd=1.38 objective, sCMOS detection unit. <br> Activated pivot scan, dual-sided illumination and online fusion; <br> properties of acquired data are as follows: 0.7x zoom, 16bit image depth, 1920 x 1920px (approximately 0.33 x 0.33 µm) image size and minimum z-stack interval (approximately 0.5µm), <br> 561nm laser, LP560, and LP585.</p> <p>Data: <br> - tiff and MIPs<br> - TF: pre-processed with Sato enhancement<br> - TH: segmented with Otsu thresholding<br> - 512x512: downsampled<br> - Reg: intersample registration<br> - analysis: folder for quantification</p>
Liquiritigenin reduces osteoclast activity in zebrafish model of glucocorticoid-induced osteoporosis
<p>Drug and therapies currently used to treat human bone diseases have a lot of severe side effects. Liquiritigenin is a flavonoid extracted from Glycyrrhiza glabra roots which has been reported to have positive effects in vitro on osteoblasts activity and bone mineralization as well as inhibitory effect on osteoclasts differentiation and activity in vitro. The present study was aimed to evaluate the in vivo effects of liquiritigenin on bone structure and metabolism in physiological and pathological conditions using Danio rerio as experimental animal model. Treatments with liquiritigenin were performed on embryos to evaluate the osteogenesis during skeletal development. Other treatments were performed on adult fish affected by glucocorticoid-induced osteoporosis to assay the therapeutic potential of liquiritigenin in the reversion of bone-loss phenotype in scale model. Liquiritigenin treatment of zebrafish embryo significantly enhances the osteogenesis during development in a dose-dependent manner. In addition, liquiritigenin inhibits the formation of the osteoporotic phenotype in adult zebrafish model of glucocorticoid-induced osteoporosis preventing osteoclast activation in scales. Interestingly, liquiritigenin does not counteract the loss of osteoblastic activity in scales. The liquiritigenin exhibits in vivo anti-osteoporotic activity on adult fish scale model. It can be considered a good candidate to develop new drugs against osteoporosis.</p>
Age-dependent modulation of bone metabolism in zebrafish scales as new model of male osteoporosis in lower vertebrates
<p>After middle age, in human bone, the resorption usually exceeds formation resulting in bone loss and increased risk of fractures in the aged population. Only few in vivo models in higher vertebrates are available for pathogenic and therapeutic studies about bone aging. Among these, male Danio rerio (zebrafish) can be successfully used as low vertebrate model to study degenerative alterations that affect the skeleton during aging, reducing the role of sex hormones.In this paper, we investigated the early bone aging mechanisms in male zebrafish (3, 6, 9 months old) scales evaluating the physiological changes and the effects of prednisolone, a pro-osteoporotic drug.The results evidentiated an age-dependent reduction of the mineralization rate in the fish scales, as highlighted by growing circle measurements. Indeed, the osteoblastic ALP activity at the matrix deposition site was found progressively downregulated.The higher TRAP activity was found in 63% of 9-month-old fish scales associated with resorption lacunae along the scale border. Gene expression analysis evidentiated that an increase of the tnfrsf1b (homolog of human rank) in aging scales may be responsible for resorption stimulation.Interestingly, prednisolone inhibited the physiological growth of the scale and induced in aged scales a more significant bone resorption compared with untreated fish (3.8% vs 1.02%). Bone markers analysis shown a significant reduction of ALP/TRAP ratio due to a prednisolone-dependent stimulation of tnfsf11 (homolog of human rankl) in scales of older fish.The results evidentiated for the first time the presence of a senile male osteoporosis in lower vertebrate. This new model could be helpful to identify the early mechanisms of bone aging and new therapeutic strategies to prevent age-related bone alterations in humans.</p>
Map-projected time-lapse of zebrafish left-right somite formation
<p>Zebrafish embryos in their chorions were imaged from 6 angles in a multiview light sheet microscope. The imaging was started 10 hours post fertilization and was performed for about 4 to 5 hours at a frame interval of 5 min. The resulting images were fused using FIJI, followed by nuclei detection in the fused images and map projection. This data set contains map projected time-lapses of 6 utr::mcherry transgenic embryos. Utrophin binds to actin filaments and was used as a somite boundary marker. The pixel size varies spatially in a map as well as across different projection layers in a single time-lapse. The corresponding Map_pixel_size mat file for each time-lapse contains respective pixel sizes.</p>
Microscopy of RNA Polymerase II clusters in live zebrafish embryos
<p>This data set contains raw image data and derived images illustrating clusters of RNA polymerase II as observed in zebrafish embryos. The clusters are labelled by fluorescently marked antibody fragments (Fab) that detect phosphorylation of the C-terminal roman of RNA polymerase II. Antibody fragments were provided by the laboratory of Hiroshi Kimura.</p>
Observation of RNA polymerase clusters in a live zebrafish embryo
<p>Data showing the distribution of RNA polymerase II with serine 5 phosphorylation in the C-terminal domain (CTD) of the subunit 1 (Pol II Ser5P) in a live zebrafish embryo. Images were acquired by instant-SIM microscopy, Pol II Ser5P was marked by fluorescently labeled antibody fragments (Fab) provided by the laboratory of Hiroshi Kimura, Tokyo Institute of Technology. Data were processed using FIJI.</p>
Time-lapse recordings of RNA polymerase in a live zebrafish embryo
<p>Raw data and derived data showing the distribution of RNA polymerase II with serine 5 phosphorylation in the C-terminal domain (CTD) of the subunit 1 (Pol II Ser5P) in a live zebrafish embryo. Images were acquired by instant-SIM microscopy, with a time step of 40 second between consecutive time points. Pol II Ser5P was marked by fluorescently labeled antibody fragments (Fab) provided by the laboratory of Hiroshi Kimura, Tokyo Institute of Technology. Data were processed using FIJI.</p>
Effect of hexanediol treatment on clusters of RNA polymerase II in zebrafish embryo primary cell culture
<p>This data set assesses changes in RNA polymerase II clusters upon treatment with 3% 1,6-hexanediol in zebrafish embryos. RNA polymerase was labeled by immunofluorescence, microscopy images were acquired by instant-SIM microscopy and analyzed using MatLab scripts and the bioformats importer. This data set contains the raw image data as well as all further analysis scripts.</p>
Scripts and raw data for comparing 2D vs 3D image analysis of zebrafish embryo microscopic data
<p>Raw data and MatLab scripts used for image analysis of RNA polymerase II with serine 5 phosphorylation in the C-terminal domain (CTD) of the subunit 1 (Pol II Ser5P) in a fixed zebrafish embryo, comparing a 2D vs 3D approach to segment out the Pol II Ser5P clusters. Pol II Ser5P was labeled by immunofluorescence, microscopy images were acquired by instant-SIM microscopy and analyzed using MatLab scripts and the bioformats importer.</p>
Data from: Zebrafish differentially process colour across visual space to match natural scenes
Animal eyes have evolved to process behaviorally important visual information, but how retinas deal with statistical asymmetries in visual space remains poorly understood. Using hyperspectral imaging in the field, in vivo 2-photon imaging of retinal neurons, and anatomy, here we show that larval zebrafish use a highly anisotropic retina to asymmetrically survey their natural visual world. First, different neurons dominate different parts of the eye and are linked to a systematic shift in inner retinal function: above the animal, there is little color in nature, and retinal circuits are largely achromatic. Conversely, the lower visual field and horizon are color rich and are predominately surveyed by chromatic and color-opponent circuits that are spectrally matched to the dominant chromatic axes in nature. Second, in the horizontal and lower visual field, bipolar cell terminals encoding achromatic and color-opponent visual features are systematically arranged into distinct layers of the inner retina. Third, above the frontal horizon, a high-gain UV system piggybacks onto retinal circuits, likely to support prey capture.
Data from: Density and group size influence shoal cohesion, but not coordination in zebrafish (Danio rerio)
The formations made by gregarious animals can range from loose aggregates to highly synchronized and ordered structures. For very large, coordinated groups, both physical and social environments are important for determining the physical arrangement of individuals in the group. Here we tested whether physical and social factors are also important in determining the structure of small, loosely coordinated groups of zebrafish. We found that even though our fish were not crowded and did not use most of the available space, the distance between individual fish was explained primarily by the amount of available space (i.e., density). Zebrafish in a larger space spread out more and the total dimensions of the shoal were an additive function also of group size. We, however, did not find any impact of social or physical environment on the orientation of individual fish or shoal. Thus, both physical and social factors were important for shoal spatial arrangements, but not individual orientation and shoal alignment.
Data from: Ultraviolet B radiation alters movement and thermal selection of zebrafish (Danio rerio)
Temperature and ultraviolet B (UV-B) interact in causing cellular damage and impairing locomotor performance. Here, we test the hypothesis that movement and thermal selection of zebrafish (Danio rerio) change in the presence of UV-B, and in particular, that fish which were chronically exposed to UV-B avoid high and low temperature extremes to maximize activities of antioxidant enzymes. Fish chronically (two to three weeks) exposed to UV-B had increased reactive oxygen species (ROS)-induced damage to proteins and membranes, and reduced swimming performance at high (more than 26°C) temperatures. In an open field arena with a thermal gradient, chronically exposed fish avoided high and low temperature extremes compared with control fish. Additionally, both control and chronically exposed fish showed slower voluntary swimming speeds in the presence of UV-B. We suggest that in the presence of UV-B fish may reduce muscular activity to minimize intrinsic ROS production. Our data show that the interaction between UV-B and temperature determines movement and microhabitat selection of fish, which is therefore of ecological importance particularly in anthropogenically modified environments.
In-plate toxicometabolomics of single zebrafish embryos
<p>Toxicometabolomic studies involving zebrafish embryos have become increasingly popular for linking apical endpoints to biochemical perturbations as part of adverse outcome pathway determination. These experiments involve pooling embryos to generate sufficient biomass for metabolomic measurement, which adds both time and cost. To address this limitation, we developed a high-throughput toxicometabolomic assay involving single zebrafish embryos. Incubation, microscopy, embryo extraction, and instrumental metabolomic analysis were all performed in the same 96-well plate, following acquisition of conventional toxicological endpoints. The total time for the assay (including testing of 6 doses/<em>n</em> = 12 embryos per dose plus positive and negative controls, assessing conventional endpoints, instrumental analysis, data processing and multivariate statistics) is <14 days. Metabolomic perturbations at low dose were linked statistically to those observed at high dose and in the presence of an adverse effect, thereby contextualizing omic data amongst apical endpoints. Overall, this assay enables collection of high resolution metabolomic data in a high throughput manner, suitable for mode of action hypothesis generation in the context of pharmaceutical or toxicological screening.</p>
Data from: Lateralisation correlates with individual differences in inhibitory control in zebrafish
<p class="MsoNoSpacing"><span><span><span><span><span><span><span><span><span><span><span>The study investigated the relationship between cerebral lateralisation and inhibitory control in zebrafish. Lateralisation was assessed using a mirror test. Fish were observed in an apparatus with mirror walls and eye preference for observing the mirror image was recorded. This preference was used to calculate the relative and the absolute lateralisation index. Inhibitory control was assessed using a foraging task. Fish were exposed to live prey enclosed inside a transparent tube. The number of attacks and its reduction over time were used as measures of inhibition.</span></span></span></span></span></span></span></span></span></span></span></p>
Data accompanying The preoptic area and dorsal habenula jointly support homeostatic navigation in larval zebrafish
<p>"<strong>The preoptic area and dorsal habenula jointly support homeostatic navigation in larval zebrafish"</strong></p><p>This repository contains the data presented in Palieri et al, 2023 (preprint <a href="https://www.biorxiv.org/content/10.1101/2023.05.18.541289v1">https://www.biorxiv.org/content/10.1101/2023.05.18.541289v1</a> ).</p><p>The data is organized into the following subfolders:</p><ul><li><strong>Behavior</strong>: This folder contains all the data related to freely swimming experiments, including both spatial (spatial_gradient subfolder) and temporal (temporal_gradient subfolder) temperature gradients. The former also includes data from chemogenetic and 2-photon mediated ablations.</li><li><strong>Imaging</strong>: Within this folder, you will find data obtained through confocal microscopy (in the confocal subfolder) and lightsheet microscopy (in the lightsheet subfolder). Confocal imaging was used to verify proper habenula ablation (dHb_preablation and dHb_postablation). Lightsheet imaging was performed for functional calcium imaging experiments during temperature and salinity gradients. The lightsheet subfolder is further subdivided into long and short experiments, with each fish having its own dedicated folder. Inside each fish's folder, you can access imaging data (traces, local coordinates, coordinates in reference space, along with relevant indexes such as the reliability index) and behavioral data (acquired using the Stytra software).</li></ul><p>Please contact Ruben Portugues for further information.</p>
Loss of atm in zebrafish as a model of ataxia-telangiectasia syndrome
<p>Supplementary figures of "<em>Loss of atm in zebrafish as a model of ataxia-telangiectasia syndrome</em>" in <em>Biomedicines</em></p>
A quantitative approach to study the adaptation of rhythmic eye movements in larval zebrafish
<p>Optokinetic nystagmus; quick phases; spontaneous saccades; saccadic adaptation; congenital ocular motor apraxia</p>
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Allen Brain Atlas
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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