Advancing biology through a deeper understanding of zebrafish ecology and evolution

Parichy, David M.

doi:10.7554/elife.05635

Cited by 167 publications

(128 citation statements)

References 93 publications

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“…This assay has important implications across multiple fields of biology, considering the wide use of zebrafish from toxicology to biomedical sciences and extending to ecological studies (Engeszer et al, 2007; Lieschke and Currie, 2007; Parichy, 2015; Spence et al, 2008). It can be used to screen environmental chemicals and identify potential mitochondrial toxicants, explore the effects of environmental stressors on organismal fitness, and help understand the pathogenesis of mitochondrial diseases.…”

Section: Discussionmentioning

confidence: 99%

A bioenergetics assay for studying the effects of environmental stressors on mitochondrial function in vivo in zebrafish larvae

Raftery

Jayasundara

Giulio

2017

Comparative Biochemistry and Physiology Part C: Toxicology &

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Mitochondria, an integral component of cellular energy metabolism and other key functions, are extremely vulnerable to damage by environmental stressors. Although methods to measure mitochondrial function in vitro exist, sensitive, medium- to high-throughput assays that assess respiration within physiologically-relevant whole organisms are needed to identify drugs and/or chemicals that disrupt mitochondrial function, particularly at sensitive early developmental stages. Consequently, we have developed and optimized an assay to measure mitochondrial bioenergetics in zebrafish larvae using the XFe24 Extracellular Flux Analyzer. To prevent larval movement from confounding oxygen consumption measurements, we relied on MS-222-based anesthetization. We obtained stable measurement values in the absence of effects on average oxygen consumption rate and subsequently optimized the use of pharmacological agents for metabolic partitioning. To confirm assay reproducibility we demonstrated that triclosan, a positive control, significantly decreased spare respiratory capacity. We then exposed zebrafish from 5 hours post-fertilization (hpf) – 6 days post-fertilization (dpf) to three polycyclic aromatic hydrocarbons (PAHs) – benzo(a)pyrene (BaP), phenanthrene (Phe), and fluoranthene (FL) – and measured various fundamental parameters of mitochondrial respiratory chain function, including maximal respiration, spare respiratory capacity, mitochondrial and non-mitochondrial respiration. Exposure to all three PAHs decreased spare respiratory capacity and maximal respiration. Additionally, Phe exposure increased non-mitochondrial respiration and FL exposure decreased mitochondrial respiration and increased non-mitochondrial respiration. Overall, this whole organism-based assay provides a platform for examining mitochondrial dysfunction in vivo at critical developmental stages. It has important implications in biomedical sciences, toxicology and ecophysiology, particularly to examine the effects of environmental chemicals and/or drugs on mitochondrial bioenergetics.

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Section: Discussionmentioning

confidence: 99%

A bioenergetics assay for studying the effects of environmental stressors on mitochondrial function in vivo in zebrafish larvae

Raftery

Jayasundara

Giulio

2017

Comparative Biochemistry and Physiology Part C: Toxicology &

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“…Originating from India, the zebrafish is a diurnal species that prefers staying in groups both in nature and in the laboratory [9,27,28]. There is a wide variability in shoal sizes: zebrafish live in small groups in shallow freshwaters [29,30] and can aggregate into larger groups of 300 individuals [31]. Zebrafish living in a variety of habitats with varying structural complexities [31,32] (from river channels, irrigation canals to beels), we set our experimental method relying on the observations of fish freely swimming in an open environment along with heterogeneous landmarks rather than in a constraining set-up (i.e.…”

Section: Introductionmentioning

confidence: 99%

Strain differences in the collective behaviour of zebrafish (Danio rerio) in heterogeneous environment

Séguret¹,

Collignon²,

Halloy³

2016

R. Soc. open sci.

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Recent studies show differences in individual motion and shoaling tendency between strains of the same species. Here, we analyse collective motion and response to visual stimuli in two morphologically different strains (TL and AB) of zebrafish. For both strains, we observed 10 groups of 5 and 10 zebrafish swimming freely in a large experimental tank with two identical landmarks (cylinders or discs) for 1 h. We tracked the positions of the fish by an automated tracking method and compute several metrics at the group level. First, the probability of the presence shows that both strains avoid free space and are more likely to swim in the vicinity of the walls of the tank and the landmarks. Second, the analysis of landmarks occupancy shows that AB zebrafish are more present in their vicinity than TL ones and that both strains regularly transit from one to the other one with no preference on the long duration. Finally, TL zebrafish show a higher cohesion than AB zebrafish. Thus, environmental heterogeneity and duration of the trials allow to reveal individual and collective behavioural variabilities among different strains of zebrafish. These results provide a new insight into the need to take into account individual variability of zebrafish strains for studying collective behaviour.

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Section: Ethological Perspectivesmentioning

confidence: 99%

“…Zebrafish mainly reside in slow-moving shallow streams and still pools where water is clear (Parichy, 2015), and remain towards the surface of the water where their prey (larval and adult insects) is most visible (Colwill and Creton, 2011), but where risk from predators is high. Kingfisher and heron both prey upon zebrafish (Parichy, 2015). Therefore, in natural environments, a sudden shadow may predict a predation strike from overhead, and the responses that have been documented, including an initial turn away from the shadow (Temizer et al, 2015) and a spiral dive in which vertical and horizontal location are continually varying, are successful techniques for evasion (Domenici et al, 2011b).…”

Section: Ethological Perspectivesmentioning

confidence: 99%

Three-dimensional motion tracking reveals a diving component to visual and auditory escape swims in zebrafish larvae

Bishop

Spence-Chorman

Gahtan

2016

Journal of Experimental Biology

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Escape behaviors have been studied in zebrafish by neuroscientists seeking cellular-level descriptions of neural circuits but few studies have examined vertical swimming during escapes. We analyzed three-dimensional swimming paths of zebrafish larvae during visually-evoked and auditory-evoked escapes while the fish were in a cubical tank with equal vertical and lateral range. Visually evoked escapes, elicited by sudden dimming of ambient light, consistently elicited downward spiral swimming (dives) with faster vertical than lateral movement. Auditory taps also elicited rapid escape swimming with equivalent total distance traveled but with significantly less vertical and more lateral movement. Visually evoked dives usually ended with the zebrafish hitting the bottom of the 10 cm 3 tank. Therefore, visually evoked dives were also analyzed in a tubular tank with 50 cm of vertical range, and in most cases larvae reached the bottom of that tank during a 120 s dimming stimulus. Light-evoked spiral diving in zebrafish may be an innate defense reflex against specific predation threats. Since visual and auditory escapes are initially similar but dives persist only during visual escapes, our findings lay the groundwork for studying a type of decision-making within zebrafish sensorimotor circuits.

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Advancing biology through a deeper understanding of zebrafish ecology and evolution

Cited by 167 publications

References 93 publications

A bioenergetics assay for studying the effects of environmental stressors on mitochondrial function in vivo in zebrafish larvae

A bioenergetics assay for studying the effects of environmental stressors on mitochondrial function in vivo in zebrafish larvae

Strain differences in the collective behaviour of zebrafish (Danio rerio) in heterogeneous environment

Three-dimensional motion tracking reveals a diving component to visual and auditory escape swims in zebrafish larvae

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