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opencc-zeroJan 2022View details →

Severe hypoxia exposure inhibits larval brain development but does not affect the capacity to mount a cortisol stress response in zebrafish

Fish nursery habitats are increasingly hypoxic and the brain is recognized as highly hypoxia-sensitive, yet there is a lack of information on the effects of hypoxia on the development and function of the larval fish brain. Here, we tested the hypothesis that by inhibiting brain development, larval exposure to severe hypoxia has persistent functional effects on the cortisol stress response in zebrafish (Danio rerio). Exposing 5 days post-fertilization (dpf) larvae to 10% dissolved O2 (DO) for 16 h only marginally reduced survival, but it decreased forebrain neural proliferation by 55%, and reduced the expression of neurod1, gfap, and mbpa, markers of determined neurons, glia, and oligodendrocytes, respectively. The 5 dpf hypoxic exposure also elicited transient increases in whole body cortisol and in crf, uts1, and hsd20b2 expression, key regulators of the endocrine stress response. Hypoxia exposure at 5 dpf also inhibited the cortisol stress response to hypoxia in 10 dpf larvae and increased hypoxia tolerance. However, 10% DO exposure at 5 dpf for 16h did not affect the cortisol stress response to a novel stressor in 10 dpf larvae or the cortisol stress response to hypoxia in adult fish. Therefore, while larval exposure to severe hypoxia can inhibit brain development, it also increases hypoxia tolerance. These effects may transiently reduce the impact of hypoxia on the cortisol stress response but not its functional capacity to respond to novel stressors. We conclude that the larval cortisol stress response in zebrafish has a high capacity to cope with severe hypoxia-induced neurogenic impairment.

opencc-zeroFeb 2022View details →

Data for Rates of warming impact oxidative stress in zebrafish (Danio rerio)

Potentially negative effects of thermal variation on physiological functions may be modulated by compensatory responses, but their efficacy depends on the timescale of phenotypic adjustment relative to the rate of temperature change. Increasing temperatures in particular can affect mitochondrial bioenergetics and rates of reactive oxygen species (ROS) production. Our aim was to test whether different rates of temperature increase impact mitochondrial bioenergetics and modulate oxidative stress. We exposed zebrafish (Danio rerio) to warming from 20 to 28°C over 3, 6, 24, or 48 h, and compared these to a control group that was kept at constant 20°C. Fish exposed to the fastest (3 h) and slowest (48 h) rates of warming had significantly higher rates of H2O2 production relative to the control treatment, and the proportion of O2 converted to H2O2 (H2O2/O2 ratio) was significantly greater in these groups. However, ROS production was not paralleled by differences in mitochondrial substrate oxidation rates, leak respiration rates, or coupling (respiratory control ratios). Increased rates of ROS production did not lead to damage of proteins or membranes, which may be explained by a moderate increase in catalase activity at the fastest, but not the slowest rate of warming. The increase in ROS production at the slowest rate of heating indicates that even seemingly benign environments may be stressful. Understanding how animals respond to different rates of temperature change is important, because the rate determines the time period for phenotypic adjustments and it also alters the environmental thermal signal that triggers compensatory pathways.

opencc-by-4.0Feb 2022View details →

DeepCAD-RT datasets: zebrafish telencephalic neurons

DeepCAD-RT datasets: zebrafish telencephalic neurons

opencc-by-4.0Feb 2022View details →

DeepCAD-RT dataset: zebrafish multiple brain regions

DeepCAD-RT dataset: zebrafish multiple brain regions

opencc-by-4.0Mar 2022View details →

DeepCAD-RT dataset: zebrafish optic tectum neurons

DeepCAD-RT dataset: zebrafish optic tectum neurons

opencc-by-4.0May 2022View details →

Fluid Mechanics of the Zebrafish Embryonic Heart Trabeculation

Images, simulation files, and user-defined functions used for the data shown in the manuscript "Fluid Mechanics of the Zebrafish Embryonic Heart Trabeculation".

opencc-zeroJun 2022View details →

Diet and temperature modify the relationship between energy use and ATP production to influence behaviour in zebrafish (Danio rerio)

Food availability and temperature influence energetics of animals, and can alter behavioural responses such as foraging and spontaneous activity. Food availability, however, is not necessarily a good indictator of energy (ATP) available for cellular processes. The efficiency of energy transduction from food-derived substrate to ATP in mitochondria can change with environmental context. Our aim was to determine whether the interaction between food availability and temperature affects mitochondrial efficiency and behaviour in zebrafish (Danio rerio). We conducted a fully factorial experiment to test the effects of feeding frequency, acclimation temperature (three weeks to 18 or 28°C), and acute test temperature (18 and 28°C) on whole-animal oxygen consumption, mitochondrial bioenergetics and efficiency (ADP consumed per oxygen atom; P:O ratio), and behaviour (boldness and exploration). We show that infrequently fed (once per day on four days per week) zebrafish have greater mitochondrial efficiency than frequently fed (three times per day on five days er week) animals, particularly when warm-acclimated. The interaction between temperature and feeding frequency influenced exploration of a novel environment, but not boldness. Both resting rate of producing ATP and scope for increasing it were positively correlated with time spent exploring and distance moved in standardised trials. In contrast, behaviour was not associated with whole-animal aerobic (oxygen consumption) scope, but exploration was positively correlated with resting oxygen consumption rates. We highlight the importance of variation in both metabolic (oxygen consumption) rate and efficiency of producing ATP in determining animal performance and behaviour. Oxygen consumption represents energy use, and P:O ratio is a variable that determines how much of that energy is allocated to ATP production. Our results emphasise the need to integrate whole-animal responses with subcellular traits to evaluate the impact of environmental conditions on behaviour and movement. --

opencc-by-4.0Aug 2022View details →

Video Data: Optic flow in the natural habitats of zebrafish supports spatial biases in visual self-motion estimation

Video dataset accompanying "Spatial Biases in Optic-Flow Sampling for Self-Motion Estimation in Natural Environments." See accompanying <a href="https://github.com/eacooper/AlexanderOpticFlow">Github repository</a> for more documentation and analysis code.

opencc-zeroAug 2022View details →

The effects of exploratory behavior on physical activity in a common animal model of human disease, zebrafish (Danio rerio)

Zebrafish (Danio rerio) are widely accepted as a multidisciplinary vertebrate model for neurobehavioral and clinical studies, and more recently have become established as a model for exercise physiology and behavior. Individual differences in activity level (e.g., exploration) have been characterized in zebrafish, however, how different levels of exploration correspond to differences in motivation to engage in swimming behavior has not yet been explored. We screened individual zebrafish in two tests of exploration: the open field and novel tank diving tests. The fish were then exposed to a tank in which they could choose to enter a compartment with a flow of water (as a means of testing voluntary motivation to exercise). After a 2-day habituation period, behavioral observations were conducted. We used correlative analyses to investigate the robustness of the different exploration tests. Due to the complexity of dependent behavioral variables, we used machine learning to determine the personality variables that were best at predicting swimming behavior. Our results show that contrary to our predictions, the correlation between novel tank diving test variables and open field test variables was relatively weak. Novel tank diving variables were more correlated with themselves than open field variables were to each other. Males exhibited stronger relationships between behavioral variables than did females. In terms of swimming behavior, fish that spent more time in the swimming zone spent more time actively swimming, however, swimming behavior was inconsistent across the time of the study. All relationships between swimming variables and exploration tests were relatively weak, though novel tank diving test variables had stronger correlations. Machine learning showed that three novel tank diving variables (entries top/bottom, movement rate, average top entry duration) and one open field variable (proportion of time spent frozen) were the best predictors of swimming behavior, demonstrating that the novel tank diving test is a powerful tool to investigate exploration. Increased knowledge about how individual differences in exploration may play a role in swimming behavior in zebrafish is fundamental to their utility as a model of exercise physiology and behavior.

opencc-zeroSep 2022View details →

Single-molecule tracking of Nodal and Lefty in live zebrafish embryos supports hindered diffusion model

The hindered diffusion model postulates that the movement of a signaling molecule through an embryo is affected by tissue geometry and binding-mediated hindrance, but these effects have not been directly demonstrated in vivo. Here, we visualize extracellular movement and binding of individual molecules of the activator-inhibitor signaling pair Nodal and Lefty in live developing zebrafish embryos using reflected light-sheet microscopy. We observe that diffusion coefficients of molecules are high in extracellular cavities, whereas mobility is reduced and bound fractions are high within cell-cell interfaces. Counterintuitively, molecules nevertheless accumulate in cavities, which we attribute to the geometry of the extracellular space by agent-based simulations. We further find that Nodal has a larger bound fraction than Lefty and shows a binding time of tens of seconds. Together, our measurements and simulations provide direct support for the hindered diffusion model and yield insights into the nanometer-to-micrometer-scale mechanisms that lead to macroscopic signal dispersal.

opencc-by-4.0Sep 2022View details →

Dataset and code for "Tiltable objective microscope visualizes selectivity for head motion direction and dynamics in zebrafish vestibular system", Nat Commun 13, 7622 (2022). https://doi.org/10.1038/s41467-022-35190-9

Dataset and code for  "Tiltable objective microscope visualizes selectivity for head motion direction and dynamics in zebrafish vestibular system", Tanimoto, Watakabe, and Higashijima.   The spreadsheet files contain source data for the figures. The file named "register_rotated_images_demo.zip" contains the MATLAB code, example image data, and instruction text data. To use the code, unzip the file and follow the instructions in the "readme.txt" file. The file named "register_rotated_images_demo_output.zip" contains expected output image data.

opencc-zeroOct 2022View details →

Zbtb14 regulates monocyte and macrophage development through inhibiting pu.1 expression in zebrafish

To elucidate the mechanism underlying the aberrant monocyte/macrophage development of zbtb14-/- mutant, GFP-positive cells were isolated from either wild-type Tg(mpeg1.1:eGFP) or zbtb14 -/- //Tg(mpeg1.1:eGFP) larvae at 2dpf by FACS. mRNA was extracted from sorted cells using RNeasy Micro (Qiagen, Manchester, UK) and mRNA libraries were constructed using NEBNext Ultra RNA Library Prep Kit for52 Illumina and sequenced under Illumina HiSeq X Ten with pair end 150bp (PE150).

opencc-zeroOct 2022View details →

Wisenden zebrafish embryo early hatching

Plasticity in hatching time allows embryos to maximize fitness by balancing benefits and costs of remaining bound within the chorion against the benefits and costs of emerging as a free-swimming larva. In our first experiment, we exposed zebrafish (Danio rerio) embryos to either chemical cues from crushed embryos (simulating egg predation) or to blank water control. Embryos exposed to alarm cues hatched sooner with shorter body lengths and underdeveloped fins relative to larvae from the water treatment. Burst swimming speed was significantly slower for larvae that hatched from the alarm cue treatment. In a second 2 x 2 experiment, we exposed zebrafish embryos to either chemical alarm cues from conspecific embryos, mechanical disturbance (magnetic stir bar) to simulate a predator probing the substrate for developing embryos, both chemical and mechanical indicators of risk, or neither (control). We found similar effects in terms of earlier time to hatch at an earlier stage of development and poorer swimming performance of hatchling larvae. In the second experiment these effects occurred in response to mechanical disturbance with or without the presence of chemical alarm cues. Alarm cues alone produced no effects in the second experiment. Taken together, these data indicate that zebrafish embryos demonstrate a facultative tradeoff between risk of predation acting on two stages of their life history.

opencc-zeroMay 2024View details →

RNAseq of partially paralyzed zebrafish embryos at 5 days post-fertilization compared to normal siblings

Sofa potato (sop) is a mutant zebrafish line, whose synaptic transmission at the neuromuscular junction is absent due to a point mutation in the δ subunit gene of the acetylcholine receptor (AChR), leading to paralysis of its skeletal muscles. To explore genetic changes in embryos caused by the lack of synaptic transmission, we performed RNA-seq analysis of normal siblings (sop+/?) and sop homozygous embryos (sop-/-) at 5 days post-fertilization.

opengpl-3.0-or-laterJun 2024View details →

Kroll et al., 2024. Behavioural pharmacology predicts disrupted signalling pathways and candidate therapeutics from zebrafish mutants of Alzheimer's disease risk genes

Data repository for François Kroll, Joshua Donnelly, Joshua Donnelly, Güliz Gürel Özcan, Eirinn Mackay, Jason Rihel <div> <div>Behavioural pharmacology predicts disrupted signalling pathways and candidate therapeutics from zebrafish mutants of Alzheimer’s disease risk genes</div> <div>eLife, 2024.</div> <div><a href="https://doi.org/10.7554/eLife.96839.1">https://doi.org/10.7554/eLife.96839.1</a></div> <div> </div> <div>Code is found in the <a href="https://github.com/francoiskroll/ZFAD">GitHub repository</a>. Please see notes there.</div> </div> ___ Contact: Twitter: @francois_kroll Email: francois@kroll.be

Datasets for the manuscript: "Metabolic disruption of zebrafish (Danio rerio) embryos by bisphenol A. An integrated metabolomic and transcriptomic approach"

<h1>Metabolomics datasets for the manuscript: Metabolic disruption of zebrafish (Danio rerio) embryos by bisphenol A. An integrated metabolomic and transcriptomic approach</h1> <h2>Instrumental conditions</h2> LC-MS analyses were carried out using an Agilent Infinity 1200 series LC system coupled with an orthogonal G1385-44300 interface (Agilent Technologies, Waldbronn, Germany) to a 6220 oa-TOF LC/MS mass spectrometer (Agilent Technologies). LC control and separation data acquisition were performed using ChemStation software (Agilent Technologies) that was running in combination with the MassHunter workstation software (Agilent Technologies) for control and data acquisition of the TOF mass spectrometer. For the chromatographic separations, an HILIC TSK Gel Amide-80 column (250 mm length, 2.1 mm inner diameter and 5 μm particle size, Tosoh Bioscience, Tokyo, Japan) was used at 25 °C with gradient elution at a flow rate of 0.15 mL·min−1. Elution gradient was performed using solvent A (acetonitrile) and solvent B (5 mM of ammonium acetate adjusted to pH 5.5 with acetic acid) as follows: 0–8 min, linear gradient from 25 to 30% B; 8–12 min, from 30 to 60% B; 12–17 min, 60% B; 17–20 min, back linearly from 60% to 25% B; and from 20 to 27 min, 25% B. Solvents were degassed for 15 min by sonication before use. Sample injection was performed with an autosampler at 4 °C, and the injection volume was 5 μL. All samples (six replicates per treatment: control, 4.4 μM BPA, 8.8 μM BPA and 17.5 μM BPA) were randomly injected. Several blank samples and calibration standards were also randomly injected to further assess the stability of the instrument among runs. The TOF mass spectrometer operated both in positive and negative mode using the following parameters: capillary voltage 4000 V, drying gas temperature 350 °C, drying gas flow rate 8 L·min−1, nebulizer gas 32 psi, fragmentor voltage 150 V, skimmer voltage 65 V and OCT 1 RF Vpp voltage 300 V. Data were collected in profile mode at 1 spectrum/s (approximately 10 000 transients/spectrum) with an m/z range of 85–1000 working in the extended dynamic range mode (2 GHz) with the mass range set to standard. <h2>List of files</h2> <h3>Negative ionization</h3> <ul> <li>Control x 12 samples - 6 x 2 replicates</li> <li>BPA 1 ppm x 12 samples - 6 x 2 replicates</li> <li>BPA 2 ppm x 12 samples - 6 x 2 replicates</li> <li>BPA 4 ppm x 12 samples - 6 x 2 replicates</li> </ul> <h3>Positive ionization</h3> <ul> <li>Control x 12 samples - 6 x 2 replicates</li> <li>BPA 1 ppm x 12 samples - 6 x 2 replicates</li> <li>BPA 2 ppm x 12 samples - 6 x 2 replicates</li> <li>BPA 4 ppm x 12 samples - 6 x 2 replicates</li> </ul>

Removal of developmentally regulated microexons has a minimal impact on larval zebrafish brain morphology and function - behavior data input files

Unprocessed (tracking) larval zebrafish behavioral data from mutants with microexons removed. All genes are grouped by their beginning letter, and two runs are included for most mutants.

Removal of developmentally regulated microexons has a minimal impact on larval zebrafish brain morphology and function - imaging stacks

Results of brain activity mapping for zebrafish mutants with microexons removed. Both brain activity and structural data is included. These stacks are the significant signal that differs between the groups. They are compatable with the Z-Brain matlab viewer from Randlett, et al, 2015 Nature Methods.

Removal of developmentally regulated microexons has a minimal impact on larval zebrafish brain morphology and function - behavior data output

Graphs and quantification of larval zebrafish behavioral data from mutants with microexons removed. All genes are grouped by their beginning letter, and two runs are included for most mutants.