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223 results for “Danio rerio”
Data from: Feeding in murky waters: acclimatization and landmarks improve foraging efficiency of zebrafish (Danio rerio) in turbid waters
Fish inhabiting human-dominated ecosystems are prone to altered sensory environments in which they must live and function. Increased turbidity is one such change that they must deal with. We tested whether an increase in water turbidity and presence of visual landmarks (coloured stones) affect the foraging efficiency of wild zebrafish. We also tested the influence of extended exposure to differing turbidity levels on the subsequent foraging efficiency of acclimatized individuals. Feeding latency (time taken to find food) increased significantly with increase in turbidity levels from a minimum of 4 s to ca. 300 s. However, extended exposure of fish to varying levels of turbidity decreased feeding latencies in acclimatized conditions, indicating that acclimatization to the immediate visual environment plays an important role in determining foraging success. Most significantly, we found that feeding latencies in turbid conditions decreased significantly if visual landmarks were present. This demonstrates that zebrafish utilize visual landmark cues to navigate to foraging sites when visibility is impaired. This study has important implications on the role of behavioural plasticity and spatial learning in animals that allow them to cope with altered sensory environments such as episodes of enhanced turbidity that could be natural or anthropogenic.
Data from: Mate competition and evolutionary outcomes in genetically modified Zebrafish (Danio rerio)
Demonstrating relationships between sexual selection mechanisms and trait evolution is central to testing evolutionary theory. Using zebrafish, we found that wild-type males possessed a significant advantage in mate competition over transgenic RFP Glofish™ males. In mating trials, wild-type males were aggressively superior to transgenic males in male-male chases and male-female chases; as a result, wild-type males sired 2.5x as many young as did transgenic males. In contrast, an earlier study demonstrated that female zebrafish preferred transgenic males as mates when mate competition was excluded experimentally. We tested the evolutionary consequence of this conflict between sexual selection mechanisms in a long-term study. The predicted loss of the transgenic phenotype was confirmed. More than 18,500 adults collected from 18 populations across 15 generations revealed that the frequency of the transgenic phenotype declined rapidly and was eliminated entirely in all but one population. Fitness component data for both sexes indicated that only male mating success differed between wild-type and transgenic individuals. Our predictive demographic model based on fitness components closely matched the rate of transgenic phenotype loss observed in the long-term study, thereby supporting its utility for studies assessing evolutionary outcomes of escaped or released genetically modified animals.
Curated RNA Sequencing Data for Zebrafish (Danio rerio) snoRNA Expression Analysis
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The influence of an enriched environment in enhancing recognition memory in zebrafish (Danio rerio)
<p>Environmental enrichment is used to increase social and physical stimulation for animals in captivity which can lead to enhanced cognition. Fundamental to the positive effect enrichment has on the brain is that it provides opportunities for captive animals to recognize and discriminate between different stimuli in the environment. In the wild, being able to discriminate between novel or familiar stimuli has implications for survival, for example finding food, hiding from predators, or even choosing a mate. The novel object recognition (NOR) test is a cognitive task that is used extensively in the rodent literature to assess object recognition and memory, where the amount of time an animal spends exploring a novel vs. familiar object is quantified. Enrichment has been shown to enhance object recognition in rodents. More recently, the use of the NOR test has been applied to another animal model, zebrafish (<em>Danio rerio</em>), however, the effects of enrichment have not yet been explored. In the current study we looked at the effects of enrichment on object recognition in zebrafish using the NOR test. Adult zebrafish were housed in either enriched conditions (gravel substrate, plastic plants, shelter, heater and a filter) or plain conditions (heater and filter only) for 6months before behavioral NOR tests were conducted. Enriched fish showed a preference for a novel object over a familiar one at a distance but did not show a preference during close inspection. Control fish did not show a preference at either distance. Our results suggest that enrichment can enhance zebrafish ability to discriminate between novel and familiar objects, but distance from the object may be an important factor. Future research is needed to determine whether any enhancements in object recognition are a result of an increase in sensory stimulation from being reared with enrichment, or whether it is due to a reduction in stress reactivity. </p>
Data from: Extraocular motoneuron pools develop along a dorsoventral axis in zebrafish, Danio rerio
Both spatial and temporal cues determine the fate of immature neurons. A major challenge at the interface of developmental and systems neuroscience is to relate this spatiotemporal trajectory of maturation to circuit‐level functional organization. This study examined the development of two extraocular motor nuclei (nIII and nIV), structures in which a motoneuron's identity, or choice of muscle partner, defines its behavioral role. We used retro‐orbital dye fills, in combination with fluorescent markers for motoneuron location and birthdate, to probe spatial and temporal organization of the oculomotor (nIII) and trochlear (nIV) nuclei in the larval zebrafish. We describe a dorsoventral organization of the four nIII motoneuron pools, in which inferior and medial rectus motoneurons occupy dorsal nIII, while inferior oblique and superior rectus motoneurons occupy distinct divisions of ventral nIII. Dorsal nIII motoneurons are, moreover, born before motoneurons of ventral nIII and nIV. The order of neurogenesis can therefore account for the dorsoventral organization of nIII and may play a primary role in determining motoneuron identity. We propose that the temporal development of extraocular motoneurons plays a key role in assembling a functional oculomotor circuit.
Figure 2 in The ontogeny and homology of the Weberian apparatus in the zebrafish Danio rerio (Ostariophysi: Cypriniformes)
Figure 2. Development of the Weberian apparatus in Danio rerio. (A) LU F.082411, 4.4 mm SL. (B) LU F.082311, 5.0 mm SL. (C) LU F.082312, 5.5 mm SL. (D) LU F.082313, 10.5 mm SL. Os suspensorium is positioned medial to the tripus and not shown in this illustration. (E) LU F.082314, 30.0 mm SL. Anterior to the left. Stippling indicates bone, black shading indicates cartilage.
Data set for: Long-term Perfluorooctanesulfonic acid (PFOS) exposure alters anxiety-like behaviour but not boldness in zebrafish (Danio rerio)
<p>Perfluorooctanesulfonic acid (PFOS) is an organic pollutant that is commonly detected in wildlife, humans, and the environment. PFOS can cause a variety of toxic effects in zebrafish, however, the impact on complex behaviours like boldness and anxiety-like behaviour is unknown. To investigate the behavioural effects of PFOS in zebrafish, we exposed adult zebrafish to either 0, 0.1, or 1.0 mg/L PFOS for 40 days. After 20- and 40-days anxiety-like behaviour and boldness were assessed using the novel approach test and novel tank dive test, respectively. After 40- day exposure at a concentration of 1.0 mg/L, PFOS caused a significant increase in time spent in the upper zone and a significant decrease in time spent in the bottom zone of the novel tank dive test, suggesting decreased anxiety-like behaviour compared to controls. Neither 0.1 or 1.0 mg/L had an impact on zebrafish boldness at any time point. Exposure to 1.0 mg/L PFOS significantly decreased locomotion in the novel tank dive test after 20 days, whereas after 40 days there was no impact of PFOS on locomotion at any concentration, indicating potential short-term influences on locomotion. These results suggest chronic PFOS exposure can modulate anxiety-like behaviour, while exploratory activity and locomotion are not altered.</p>
Data files and R scripts for manuscript: Acute warming tolerance (CTmax) in zebrafish (Danio rerio) appears unaffected by changes in water salinity
<p>See README and R-scripts for more info.</p> <p>Update for v2: model is now fit using <em>lmerTest</em> package. Previous version erroneously used <em>lme4</em>, which does not work for using type 3 sums of squares in anova.</p> <p>Update for v3: 1) An additional term has been added to the model, including the number of minutes passed from the start of the salinity treatment until the CTmax test for each fish (for the 2 hr treatment). 2) A table including the daily salinity measurements has been added.</p> <p>Update for v4: Minor error fix in "script-preload-resources.R" using wrong filename for table-salinities.txt</p> <p>Preprint: https://www.biorxiv.org/content/10.1101/2022.08.02.502531v1</p>
Data from: Strain differences in the collective behaviour of zebrafish (Danio rerio) in heterogeneous environment
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Data from: Extraocular motoneuron pools develop along a dorsoventral axis in zebrafish, Danio rerio
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Data from: The telomere bouquet is a hub where meiotic double-strand breaks, synapsis, and stable homolog juxtaposition are coordinated in the zebrafish, Danio rerio
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Data from: Hypoxia-inducible factor-1 mediates adaptive developmental plasticity of hypoxia tolerance in zebrafish, Danio rerio
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Data from: Glutathione S-transferase protein expression in different life stages of zebrafish (Danio rerio)
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Data from: Feeding in murky waters: acclimatization and landmarks improve foraging efficiency of zebrafish (Danio rerio) in turbid waters
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The influence of an enriched environment in enhancing recognition memory in zebrafish (Danio rerio)
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Data from: Mate competition and evolutionary outcomes in genetically modified Zebrafish (Danio rerio)
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Data set for: Long-term Perfluorooctanesulfonic acid (PFOS) exposure alters anxiety-like behaviour but not boldness in zebrafish (Danio rerio)
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Zebrafish (Danio rerio) neural crest cell RNA-sequencing
GEO Series GSE135237. Danio rerio. 6 samples. Type: Expression profiling by high throughput sequencing.
Chronic dietary exposure to the food preservative tert-Butylhydroquinone (tBHQ) impairs zebrafish (Danio rerio) survival, growth, organ development, and gene expression in Nrf2a-dependent and independ
GEO Series GSE220834. Danio rerio. 12 samples. Type: Expression profiling by high throughput sequencing.
Gene expression changes in the female zebrafish (Danio rerio) brain in response to acute exposure to methylmercury
GEO Series GSE22662. Danio rerio. 9 samples. Type: Expression profiling by array.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
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.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.