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Blagojević L, Pósfai M. Three-dimensional shape and connectivity of physical networks. Sci Rep 2024; 14:16874. [PMID: 39043747 PMCID: PMC11266587 DOI: 10.1038/s41598-024-67359-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 07/10/2024] [Indexed: 07/25/2024] Open
Abstract
Data describing the three-dimensional structure of physical networks is increasingly available, leading to a surge of interest in network science to explore the relationship between the shape and connectivity of physical networks. We contribute to this effort by standardizing and analyzing 15 data sets from different domains. Each network is made of tube-like objects bound together at junction points, which we treat as nodes, with the connections between them considered as links. We divide these networks into three categories: lattice-like networks, trees, and linked trees. The degree distribution of these physical networks is bounded, with most nodes having degrees one or three. Characterizing the physical properties of links, we show that links have an elongated shape and tend to follow a nearly straight trajectory, while a small fraction of links follow a winding path. These typical node and link properties must be reflected by physical network models. We also measure how confined a link is in space by comparing its trajectory to a randomized null model, showing that links that are central in the abstract network tend to be physically confined by their neighbors. The fact that the shape and connectivity of the physical networks are intertwined highlights that their three-dimensional layout must be taken into account to understand the evolution and function of physical networks.
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Affiliation(s)
- Luka Blagojević
- Department of Network and Data Science, Central European University, Vienna, Austria.
| | - Márton Pósfai
- Department of Network and Data Science, Central European University, Vienna, Austria
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2
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Baden T. Ancestral photoreceptor diversity as the basis of visual behaviour. Nat Ecol Evol 2024; 8:374-386. [PMID: 38253752 DOI: 10.1038/s41559-023-02291-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/10/2023] [Indexed: 01/24/2024]
Abstract
Animal colour vision is based on comparing signals from different photoreceptors. It is generally assumed that processing different spectral types of photoreceptor mainly serves colour vision. Here I propose instead that photoreceptors are parallel feature channels that differentially support visual-motor programmes like motion vision behaviours, prey capture and predator evasion. Colour vision may have emerged as a secondary benefit of these circuits, which originally helped aquatic vertebrates to visually navigate and segment their underwater world. Specifically, I suggest that ancestral vertebrate vision was built around three main systems, including a high-resolution general purpose greyscale system based on ancestral red cones and rods to mediate visual body stabilization and navigation, a high-sensitivity specialized foreground system based on ancestral ultraviolet cones to mediate threat detection and prey capture, and a net-suppressive system based on ancestral green and blue cones for regulating red/rod and ultraviolet circuits. This ancestral strategy probably still underpins vision today, and different vertebrate lineages have since adapted their original photoreceptor circuits to suit their diverse visual ecologies.
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Affiliation(s)
- Tom Baden
- University of Sussex, Sussex Neuroscience, Sussex Center for Sensory Neuroscience and Computation, Brighton, UK.
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3
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Cohen A, Popowitz J, Delbridge-Perry M, Rowe CJ, Connaughton VP. The Role of Estrogen and Thyroid Hormones in Zebrafish Visual System Function. Front Pharmacol 2022; 13:837687. [PMID: 35295340 PMCID: PMC8918846 DOI: 10.3389/fphar.2022.837687] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/28/2022] [Indexed: 12/23/2022] Open
Abstract
Visual system development is a highly complex process involving coordination of environmental cues, cell pathways, and integration of functional circuits. Consequently, a change to any step, due to a mutation or chemical exposure, can lead to deleterious consequences. One class of chemicals known to have both overt and subtle effects on the visual system is endocrine disrupting compounds (EDCs). EDCs are environmental contaminants which alter hormonal signaling by either preventing compound synthesis or binding to postsynaptic receptors. Interestingly, recent work has identified neuronal and sensory systems, particularly vision, as targets for EDCs. In particular, estrogenic and thyroidogenic signaling have been identified as critical modulators of proper visual system development and function. Here, we summarize and review this work, from our lab and others, focusing on behavioral, physiological, and molecular data collected in zebrafish. We also discuss different exposure regimes used, including long-lasting effects of developmental exposure. Overall, zebrafish are a model of choice to examine the impact of EDCs and other compounds targeting estrogen and thyroid signaling and the consequences of exposure in visual system development and function.
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Affiliation(s)
- Annastelle Cohen
- Department of Biology, American University, Washington, DC, WA, United States
| | - Jeremy Popowitz
- Department of Biology, American University, Washington, DC, WA, United States
| | | | - Cassie J. Rowe
- Department of Biology, American University, Washington, DC, WA, United States,Center for Neuroscience and Behavior, American University, Washington, DC, WA, United States
| | - Victoria P. Connaughton
- Department of Biology, American University, Washington, DC, WA, United States,Center for Neuroscience and Behavior, American University, Washington, DC, WA, United States,*Correspondence: Victoria P. Connaughton,
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Bartel P, Yoshimatsu T, Janiak FK, Baden T. Spectral inference reveals principal cone-integration rules of the zebrafish inner retina. Curr Biol 2021; 31:5214-5226.e4. [PMID: 34653362 PMCID: PMC8669161 DOI: 10.1016/j.cub.2021.09.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/09/2021] [Accepted: 09/17/2021] [Indexed: 01/05/2023]
Abstract
Retinal bipolar cells integrate cone signals at dendritic and axonal sites. The axonal route, involving amacrine cells, remains largely uncharted. However, because cone types differ in their spectral sensitivities, insights into bipolar cells' cone integration might be gained based on their spectral tunings. We therefore recorded in vivo responses of bipolar cell presynaptic terminals in larval zebrafish to widefield but spectrally resolved flashes of light and mapped the results onto spectral responses of the four cones. This "spectral circuit mapping" allowed explaining ∼95% of the spectral and temporal variance of bipolar cell responses in a simple linear model, thereby revealing several notable integration rules of the inner retina. Bipolar cells were dominated by red-cone inputs, often alongside equal sign inputs from blue and green cones. In contrast, UV-cone inputs were uncorrelated with those of the remaining cones. This led to a new axis of spectral opponency where red-, green-, and blue-cone "Off" circuits connect to "natively-On" UV-cone circuits in the outermost fraction of the inner plexiform layer-much as how key color opponent circuits are established in mammals. Beyond this, and despite substantial temporal diversity that was not present in the cones, bipolar cell spectral tunings were surprisingly simple. They either approximately resembled both opponent and non-opponent spectral motifs already present in the cones or exhibited a stereotyped non-opponent broadband response. In this way, bipolar cells not only preserved the efficient spectral representations in the cones but also diversified them to set up a total of six dominant spectral motifs, which included three axes of spectral opponency.
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Affiliation(s)
- Philipp Bartel
- School of Life Sciences, University of Sussex, Biology Road, BN1 9QG Brighton, UK
| | - Takeshi Yoshimatsu
- School of Life Sciences, University of Sussex, Biology Road, BN1 9QG Brighton, UK
| | - Filip K Janiak
- School of Life Sciences, University of Sussex, Biology Road, BN1 9QG Brighton, UK
| | - Tom Baden
- School of Life Sciences, University of Sussex, Biology Road, BN1 9QG Brighton, UK; Institute of Ophthalmic Research, University of Tübingen, Elfriede-Aulhorn-Strasse 7, 72076 Tübingen, Germany.
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Connaughton VP, Nelson R. Ganglion cells in larval zebrafish retina integrate inputs from multiple cone types. J Neurophysiol 2021; 126:1440-1454. [PMID: 34550015 DOI: 10.1152/jn.00082.2021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We recently showed the presence of seven physiological cone opsins-R1 (575 nm), R2 (556 nm), G1 (460 nm), G3 (480 nm), B1 (415 nm), B2 (440 nm), and UV (358 nm)-in electroretinogram (ERG) recordings of larval zebrafish (Danio rerio) retina. Larval ganglion cells (GCs) are generally thought to integrate only four cone opsin signals (red, green, blue, and UV). We address the question as to whether they may integrate seven cone spectral signals. Here we examined the 127 possible combinations of seven cone signals to find the optimal representation, as based on impulse discharge data sets from GC axons in the larval optic nerve. We recorded four varieties of light-response waveform, sustained-ON, transient-ON, ON-OFF, and OFF, based on the time course of mean discharge rates to all stimulus wavelengths combined. Modeling of GC responses revealed that each received 1-6 cone opsin signals, with a mean of 3.8 ± 1.3 cone signals/GC. Most onset or offset responses were opponent (ON, 80%; OFF, 100%). The most common cone signals were UV (93%), R2 (50%), G3 (55%), and G1 (60%). Seventy-three percent of cone opsin signals were excitatory, and 27% were inhibitory. UV signals favored excitation, whereas G3 and B2 signals favored inhibition. R1/R2, G1/G3, and B1/B2 opsin signals were selectively associated along a nonsynergistic/opponent axis. Overall, these results suggest that larval zebrafish GC spectral responses are complex and use inputs from the seven expressed opsins.NEW & NOTEWORTHY Ganglion cells in larval zebrafish retina have complex spectral responses driven by seven different cone opsin types. UV cone inputs are significant and excitatory to ganglion cells, whereas green and blue cone inputs favor inhibition. Most dramatic are the pentachromatic cells. These responses were identified at 5-6 days after fertilization, reflecting an impressive level of color processing not seen in older fish or mammals.
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Affiliation(s)
- V P Connaughton
- Department of Biology, American University, Washington, District of Columbia
| | - R Nelson
- Neural Circuits Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
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Abstract
The use of spectral information in natural light to inform behaviour is one of the oldest and most fundamental abilities of visual systems. It long-predates animals' venture onto the land, and even the appearance of image-forming eyes. Accordingly, circuits for colour vision evolved under the surface of ancient oceans for hundreds of millions of years. These aquatic beginnings fundamentally underpin, and likely constrain, the organisation of modern visual systems. In contrast to our detailed circuit level understanding from diverse terrestrial vertebrates, however, comparatively little is known about their aquatic counterparts. Here, I summarise some of what is known about neural circuits for colour vision in fish, the most species-diverse group of vertebrates. With a focus on zebrafish, I will explore how their computational strategies are linked to the statistics of natural light in the underwater world, and how their study might help us understand vision in general, including in our own eyes.
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Zhou M, Bear J, Roberts PA, Janiak FK, Semmelhack J, Yoshimatsu T, Baden T. Zebrafish Retinal Ganglion Cells Asymmetrically Encode Spectral and Temporal Information across Visual Space. Curr Biol 2020; 30:2927-2942.e7. [PMID: 32531283 PMCID: PMC7416113 DOI: 10.1016/j.cub.2020.05.055] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/31/2020] [Accepted: 05/18/2020] [Indexed: 12/23/2022]
Abstract
In vertebrate vision, the tetrachromatic larval zebrafish permits non-invasive monitoring and manipulating of neural activity across the nervous system in vivo during ongoing behavior. However, despite a perhaps unparalleled understanding of links between zebrafish brain circuits and visual behaviors, comparatively little is known about what their eyes send to the brain via retinal ganglion cells (RGCs). Major gaps in knowledge include any information on spectral coding and information on potentially critical variations in RGC properties across the retinal surface corresponding with asymmetries in the statistics of natural visual space and behavioral demands. Here, we use in vivo two-photon imaging during hyperspectral visual stimulation as well as photolabeling of RGCs to provide a functional and anatomical census of RGCs in larval zebrafish. We find that RGCs' functional and structural properties differ across the eye and include a notable population of UV-responsive On-sustained RGCs that are only found in the acute zone, likely to support visual prey capture of UV-bright zooplankton. Next, approximately half of RGCs display diverse forms of color opponency, including many that are driven by a pervasive and slow blue-Off system-far in excess of what would be required to satisfy traditional models of color vision. In addition, most information on spectral contrast was intermixed with temporal information. Taken together, our results suggest that zebrafish RGCs send a diverse and highly regionalized time-color code to the brain.
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Affiliation(s)
- Mingyi Zhou
- School of Life Sciences, University of Sussex, Brighton BN19QG, UK
| | - John Bear
- School of Life Sciences, University of Sussex, Brighton BN19QG, UK; Hong Kong University of Science and Technology, Hong Kong
| | - Paul A Roberts
- School of Life Sciences, University of Sussex, Brighton BN19QG, UK
| | - Filip K Janiak
- School of Life Sciences, University of Sussex, Brighton BN19QG, UK
| | | | | | - Tom Baden
- School of Life Sciences, University of Sussex, Brighton BN19QG, UK; Institute for Ophthalmic Research, University of Tübingen, Tübingen 72076, Germany.
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Abstract
The jawless fish that were ancestral to all living vertebrates had four spectral cone types that were probably served by chromatic-opponent retinal circuits. Subsequent evolution of photoreceptor spectral sensitivities is documented for many vertebrate lineages, giving insight into the ecological adaptation of color vision. Beyond the photoreceptors, retinal color processing is best understood in mammals, especially the blueON system, which opposes short- against long-wavelength receptor responses. For other vertebrates that often have three or four types of cone pigment, new findings from zebrafish are extending older work on teleost fish and reptiles to reveal rich color circuitry. Here, horizontal cells establish diverse and complex spectral responses even in photoreceptor outputs. Cone-selective connections to bipolar cells then set up color-opponent synaptic layers in the inner retina, which lead to a large variety of color-opponent channels for transmission to the brain via retinal ganglion cells.
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Affiliation(s)
- T Baden
- School of Life Sciences, University of Sussex, BN1 9QG Brighton, United Kingdom; ,
- Institute for Ophthalmic Research, University of Tübingen, 72076 Tübingen, Germany
| | - D Osorio
- School of Life Sciences, University of Sussex, BN1 9QG Brighton, United Kingdom; ,
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Abstract
Visual stimuli can evoke complex behavioral responses, but the underlying streams of neural activity in mammalian brains are difficult to follow because of their size. Here, I review the visual system of zebrafish larvae, highlighting where recent experimental evidence has localized the functional steps of visuomotor transformations to specific brain areas. The retina of a larva encodes behaviorally relevant visual information in neural activity distributed across feature-selective ganglion cells such that signals representing distinct stimulus properties arrive in different areas or layers of the brain. Motor centers in the hindbrain encode motor variables that are precisely tuned to behavioral needs within a given stimulus setting. Owing to rapid technological progress, larval zebrafish provide unique opportunities for obtaining a comprehensive understanding of the intermediate processing steps occurring between visual and motor centers, revealing how visuomotor transformations are implemented in a vertebrate brain.
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Affiliation(s)
- Johann H. Bollmann
- Developmental Biology, Institute of Biology I, Faculty of Biology, and Bernstein Center Freiburg, University of Freiburg, 79104 Freiburg, Germany
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10
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Tanvir Z, Nelson RF, DeCicco-Skinner K, Connaughton VP. One month of hyperglycemia alters spectral responses of the zebrafish photopic electroretinogram. Dis Model Mech 2018; 11:dmm.035220. [PMID: 30158110 PMCID: PMC6215424 DOI: 10.1242/dmm.035220] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 08/22/2018] [Indexed: 12/12/2022] Open
Abstract
Prolonged hyperglycemia can alter retinal function, ultimately resulting in blindness. Adult zebrafish adults exposed to alternating conditions of 2% glucose/0% glucose display a 3× increase in blood sugar levels. After 4 weeks of treatment, electroretinograms (ERGs) were recorded from isolated, perfused, in vitro eyecups. Control animals were exposed to alternating 2% mannitol/0% mannitol (osmotic control) or to alternating water (0% glucose/0% glucose; handling control). Two types of ERGs were recorded: (1) native ERGs measured using white-light stimuli and medium without synaptic blockers; and (2) spectral ERGs measured with an AMPA/kainate receptor antagonist, isolating photoreceptor-to-ON-bipolar-cell synapses, and a spectral protocol that separated red (R), green (G), blue (B) and UV cone signals. Retinas were evaluated for changes in layer thickness and for the inflammatory markers GFAP and Nf-κB (RelA or p65). In native ERGs, hyperglycemic b- and d-waves were lower in amplitude than the b- and d-waves of mannitol controls. Alteration of waveshape became severe, with b-waves becoming more transient and ERG responses showing more PIII-like (a-wave) characteristics. For spectral ERGs, waveshape appeared similar in all treatment groups. However, a1- and b2-wave implicit times were significantly longer, and amplitudes were significantly reduced, in response to hyperglycemic treatment, owing to the functional reduction in signals from R, G and B cones. Nf-κB increased significantly in hyperglycemic retinas, but the increase in GFAP was not significant and retinal layer thickness was unaffected. Thus, prolonged hyperglycemia triggers an inflammatory response and functional deficits localized to specific cone types, indicating the rapid onset of neural complications in the zebrafish model of diabetic retinopathy. Summary: Zebrafish can be used to examine diabetic complications, including vision loss. Here, in zebrafish, we show that prolonged (4 week) hyperglycemia causes an inflammatory response associated with functional deficits localized to specific cone types.
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Affiliation(s)
- Zaid Tanvir
- Department of Biology, American University, 4400 Massachusetts Ave NW, Washington, DC 20016, USA
| | - Ralph F Nelson
- Neural Circuitry Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 5625 Fisher's Lane, Rockville, MD 20852, USA
| | - Kathleen DeCicco-Skinner
- Department of Biology, American University, 4400 Massachusetts Ave NW, Washington, DC 20016, USA
| | - Victoria P Connaughton
- Department of Biology, American University, 4400 Massachusetts Ave NW, Washington, DC 20016, USA
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Meier A, Nelson R, Connaughton VP. Color Processing in Zebrafish Retina. Front Cell Neurosci 2018; 12:327. [PMID: 30337857 PMCID: PMC6178926 DOI: 10.3389/fncel.2018.00327] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/10/2018] [Indexed: 11/13/2022] Open
Abstract
Zebrafish (Danio rerio) is a model organism for vertebrate developmental processes and, through a variety of mutant and transgenic lines, various diseases and their complications. Some of these diseases relate to proper function of the visual system. In the US, the National Eye Institute indicates >140 million people over the age of 40 have some form of visual impairment. The causes of the impairments range from refractive error to cataract, diabetic retinopathy and glaucoma, plus heritable diseases such as retinitis pigmentosa and color vision deficits. Most impairments directly affect the retina, the nervous tissue at the back of the eye. Zebrafish with long or short-wavelength color blindness, altered retinal anatomy due to hyperglycemia, high intraocular pressure, and reduced pigment epithelium are all used, and directly applicable, to study how these symptoms affect visual function. However, many published reports describe only molecular/anatomical/structural changes or behavioral deficits. Recent work in zebrafish has documented physiological responses of the different cell types to colored (spectral) light stimuli, indicating a complex level of information processing and color vision in this species. The purpose of this review article is to consolidate published morphological and physiological data from different cells to describe how zebrafish retina is capable of complex visual processing. This information is compared to findings in other vertebrates and relevance to disorders affecting color processing is discussed.
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Affiliation(s)
- April Meier
- Zebrafish Ecotoxicology, Neuropharmacology, and Vision Lab, Department of Biology, and Center for Behavioral Neuroscience, American University, Washington, DC, United States
| | - Ralph Nelson
- Neural Circuits Unit, National Institute of Neurological Disorders and Stroke (NINDS), NIH, Bethesda, MD, United States
| | - Victoria P Connaughton
- Zebrafish Ecotoxicology, Neuropharmacology, and Vision Lab, Department of Biology, and Center for Behavioral Neuroscience, American University, Washington, DC, United States
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Tsang B, Zahid H, Ansari R, Lee RCY, Partap A, Gerlai R. Breeding Zebrafish: A Review of Different Methods and a Discussion on Standardization. Zebrafish 2017; 14:561-573. [PMID: 28873037 DOI: 10.1089/zeb.2017.1477] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In recent years, a rapidly increasing number of scientific papers have been published that utilize zebrafish (Danio rerio) as an alternative model organism in the study of a wide range of biological phenomena from cancer to behavior. This is, in large part, due to the prolific nature, relative ease of maintenance, and sufficiently high genetic homology of zebrafish to humans. With the surge of zebrafish use in animal research, the variations in methodologies of breeding and husbandry of this species have also increased. Investigators usually focus on the development and implementation of rigorous laboratory control that is specific to their studies. We suggest that the same scrutiny and attention may be required for the methods of breeding and housing of zebrafish. This article reviews a variety of zebrafish husbandry and breeding techniques and conditions employed around the world. It discusses factors ranging from numerous aspects of rearing/housing conditions through the sex ratio of the breeding group to the composition of the diet of zebrafish that may vary across laboratories. It provides some feedback on the potential pros and cons of the different methods. It argues that there is a substantial need for systematic analysis of these methods, that is, the effects of environmental factors on zebrafish health and breeding. It also discusses the question as to whether some degree of standardization of these methods is needed to enhance cross-laboratory comparability of results.
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Affiliation(s)
- Benjamin Tsang
- Department of Psychology, University of Toronto Mississauga , Mississauga, Canada
| | - Hifsa Zahid
- Department of Psychology, University of Toronto Mississauga , Mississauga, Canada
| | - Rida Ansari
- Department of Psychology, University of Toronto Mississauga , Mississauga, Canada
| | | | - Aman Partap
- Department of Psychology, University of Toronto Mississauga , Mississauga, Canada
| | - Robert Gerlai
- Department of Psychology, University of Toronto Mississauga , Mississauga, Canada
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