Utilizing Zebrafish Visual Behaviors in Drug Screening for Retinal Degeneration

Zebrafish are a popular vertebrate model in drug discovery. They produce a large number of small and rapidly-developing embryos. These embryos display rich visual-behaviors that can be used to screen drugs for treating retinal degeneration (RD). RD comprises blinding diseases such as Retinitis Pigmentosa, which affects 1 in 4000 people. This disease has no definitive cure, emphasizing an urgency to identify new drugs. In this review, we will discuss advantages, challenges, and research developments in using zebrafish behaviors to screen drugs in vivo. We will specifically discuss a visual-motor response that can potentially expedite discovery of new RD drugs

Adaptive Locomotor Behavior in Larval Zebrafish

In this study we report that larval zebrafish display adaptive locomotor output that can be driven by unexpected visual feedback. We develop a new assay that addresses visuomotor integration in restrained larval zebrafish. The assay involves a closed-loop environment in which the visual feedback a larva receives depends on its own motor output in a way that resembles freely swimming conditions. The experimenter can control the gain of this closed feedback loop, so that following a given motor output the larva experiences more or less visual feedback depending on whether the gain is high or low. We show that increases and decreases in this gain setting result in adaptive changes in behavior that lead to a generalized decrease or increase of motor output, respectively. Our behavioral analysis shows that both the duration and tail beat frequency of individual swim bouts can be modified, as well as the frequency with which bouts are elicited. These changes can be implemented rapidly, following an exposure to a new gain of just 175 ms. In addition, modifications in some behavioral parameters accumulate over tens of seconds and effects last for at least 30 s from trial to trial. These results suggest that larvae establish an internal representation of the visual feedback expected from a given motor output and that the behavioral modifications are driven by an error signal that arises from the discrepancy between this expectation and the actual visual feedback. The assay we develop presents a unique possibility for studying visuomotor integration using imaging techniques available in the larval zebrafish

Exploring behavioral circuits with holographic optogenetics and network imaging

Included works This thesis contains three previously published works: Semmelhack, Donovan, et al.; eLife 2014 Temizer, Donovan, et al.; Current Biology 2015 Thiele, Donovan, Baier; Neuron 2014 And one full manuscript, soon to be in the second round of review: Dal Maschio*, Donovan*, et al. *(Equal contributions) The work presented in these manuscripts is equivalent to a standard thesis

An alternative approach for assessing drug induced seizures, using non-protected larval zebrafish

As many as 9% of epileptic seizures occur as a result of drug toxicity. Identifying compounds with seizurogenic side effects is imperative for assessing compound safety during drug development, however, multiple marketed drugs still have clinical associations with seizures. Moreover, current approaches for assessing seizurogenicity, namely rodent EEG and behavioural studies, are highly resource intensive. This being the case, alternative approaches have been postulated for assessing compound seizurogenicity, including in vitro, in vivo, and in silico methods. In this thesis, experimental work is presented supporting the use of larval zebrafish as a candidate model organism for developing new seizure liability screening approaches. Larval zebrafish are translucent, meaning they are highly amenable to imaging approaches while offering a more ethical alternative to mammalian research. Zebrafish are furthermore highly fecund facilitating capacity for both high replication and high throughput. The primary goal of this thesis was to identify biomarkers in larval zebrafish, both behavioural and physiological, of compounds that increase seizure liability. The efficacy of this model organism for seizure liability testing was assessed through exposure of larval zebrafish to a mechanistically diverse array of compounds, selected for their varying degrees of seizurogenicity. Their central nervous systems were monitored using a variety of different techniques including light sheet microscopy, local field potential recordings, and behavioural monitoring. Data acquired from these measurements were then analysed using a variety of techniques including frequency domain analysis, clustering, functional connectivity, regression, and graph theory. Much of this analysis was exploratory in nature and is reflective of the infancy of the field. Experimental findings suggest that larval zebrafish are indeed sensitive to a wide range of pharmacological mechanisms of action and that drug actions are reflected by behavioural and direct measurements of brain activity. For example, local field potential recordings revealed electrographic responses akin to pre-ictal, inter-ictal and ictal events identified in humans. Ca2+ imaging using light sheet microscopy found global increases in fluorescent intensity and functional connectivity due to seizurogenic drug administration. In addition, [2] further functional connectivity and graph analysis revealed macroscale network changes correlated with drug seizurogenicity and mechanism of action. Finally, analysis of swimming behaviour revealed a strong correlation between high speed swimming behaviours and administration of convulsant compounds. In conclusion, presented herein are data demonstrating the power of functional brain imaging, LFP recordings, and behavioral monitoring in larval zebrafish for assessing the action of neuroactive drugs in a highly relevant vertebrate model. These data help us to understand the relevance of the 4 dpf larval zebrafish for neuropharmacological studies and reveal that even at this early developmental stage, these animals are highly responsive to a wide range of neuroactive compounds across multiple primary mechanisms of action. This represents compelling evidence of the potential utility of larval zebrafish as a model organism for seizure liability testing

Neurobehavioral and Gene Expression Effects of Early Embryonic Methylmercury Exposure in Yellow Perch (Perca flavescens) and Zebrafish (Danio rerio) Larvae

Methylmercury (MeHg) is a pervasive and persistent neurotoxic environmental pollutant known to affect the behavior of fish, birds and mammals. The present study addresses the neurobehavioral and gene expression effects of MeHg in yellow perch (Perca flavescens) and zebrafish (Danio rerio) embryos. The rationale for this study originated from an interest to understand the behavioral and molecular phenotypes of environmental MeHg exposure in the yellow perch, an ecologically and economically relevant species of the North American Great Lakes region. Both MeHg and the yellow perch coexist in a common ecosystem: the North American Great Lakes. However, the effects of this organism-contaminant interaction are poorly understood. The zebrafish was utilized here as a surrogate model for yellow perch, due to its ease of rearing, whole sequenced genome and its status as an NIH endorsed model organism. The objectives of this study were to understand the effects of MeHg on behaviors that are critical for survival both in yellow perch and zebrafish. Among the behavioral paradigms tested, this study addressed fundamental behaviors for the survival of young larval fish, namely swimming and prey capture. Furthermore, this study screened for gene expression alterations in the same cohorts of fish for which behavioral analysis was performed; this was done to gain insight into the gene pathways involved in MeHg-induced neurotoxicity, as well as to expand the knowledge about biomarkers of MeHg exposure in the yellow perch. Here, we have uncovered important differences and similarities between the effects of MeHg exposure in yellow perch and zebrafish larvae, both in terms of behavioral and molecular responses to MeHg. The findings of this study suggest that environmentally relevant MeHg exposure can adversely affect the behavior of yellow perch larvae and impair fundamental survival skills. Furthermore, this study determined that although it would be challenging to relate behavioral endpoints between yellow perch and zebrafish, molecular responses between these two species could be more conserved

Spinal V2b neurons reveal a role for ipsilateral inhibition in speed control

The spinal cord contains a diverse array of interneurons that govern motor output. Traditionally, models of spinal circuits have emphasized the role of inhibition in enforcing reciprocal alternation between left and right sides or flexors and extensors. However, recent work has shown that inhibition also increases coincident with excitation during contraction. Here, using larval zebrafish, we investigate the V2b (Gata3+) class of neurons, which contribute to flexor-extensor alternation but are otherwise poorly understood. Using newly generated transgenic lines we define two stable subclasses with distinct neurotransmitter and morphological properties. These V2b subclasses synapse directly onto motor neurons with differential targeting to speed-specific circuits. In vivo, optogenetic manipulation of V2b activity modulates locomotor frequency: suppressing V2b neurons elicits faster locomotion, whereas activating V2b neurons slows locomotion. We conclude that V2b neurons serve as a brake on axial motor circuits. Together, these results indicate a role for ipsilateral inhibition in speed control

Intégration sensorimotrice dans la moelle épinière en mouvement

There is converging evidence that mechanosensory feedback modulates the activity of spinal central pattern generators underlying vertebrate locomotion. However, probing the underlying circuits in behaving animals is not possible in “fictive” locomotion electrophysiological recordings. Here, we achieve selective and non-invasive monitoring of spinal motor and sensory neurons during active locomotion by genetically targeting the bioluminescent sensor GFP-Aequorin in larval zebrafish. Using GCaMP imaging of individual neurons, we confirm that bioluminescence signals reflect the differential recruitment of motor pools during motion. Their significant reduction in paralyzed animals and immotile mutants demonstrates that mechanosensory feedback enhances the recruitment of spinal motor neurons during active locomotion. Accordingly, we show that spinal mechanosensory neurons are recruited in moving animals and that their silencing impairs escapes in freely behaving larvae. Altogether, these results shed light on the contribution of mechanosensory feedback to motor output and the resulting differences between active and fictive locomotion.Certaines observations suggèrent que les afférences méchano-sensorielles peuvent moduler l’activité des générateurs centraux du rythme locomoteur (ou Central Pattern Generators, CPGs). Cependant, il est impossible d’explorer les circuits neuronaux sous-jacents chez l’animal en mouvement à l’aide d’enregistrements électrophysiologiques lors d’expériences de locomotion dite « fictive ». Dans cette étude, nous avons enregistré de façon sélective et non-invasive les neurones moteurs et sensoriels dans la moelle épinière pendant la locomotion active en ciblant génétiquement le senseur bioluminescent GFP-Aequorin chez la larve de poisson zèbre. En utilisant l’imagerie calcique à l’échelle des neurones individuels, nous confirmons que les signaux de bioluminescence reflètent bien le recrutement différentiel des groupes de motoneurones spinaux durant la locomotion active. La diminution importante de ces signaux chez des animaux paralysés ou des mutants immobiles démontre que le retour méchano-sensoriel augmente le recrutement des motoneurones spinaux pendant la locomotion active. En accord avec cette observation, nous montrons que les neurones méchano-sensoriels spinaux sont en effet recrutés chez les animaux en mouvement, et que leur inhibition affecte les réflexes d’échappement chez des larves nageant librement. L’ensemble de ces résultats met en lumière la contribution du retour méchano-sensoriel sur la production locomotrice et les différences qui en résultent entre les locomotions active et fictive

Automated processing of zebrafish imaging data: a survey

Due to the relative transparency of its embryos and larvae, the zebrafish is an ideal model organism for bioimaging approaches in vertebrates. Novel microscope technologies allow the imaging of developmental processes in unprecedented detail, and they enable the use of complex image-based read-outs for high-throughput/high-content screening. Such applications can easily generate Terabytes of image data, the handling and analysis of which becomes a major bottleneck in extracting the targeted information. Here, we describe the current state of the art in computational image analysis in the zebrafish system. We discuss the challenges encountered when handling high-content image data, especially with regard to data quality, annotation, and storage. We survey methods for preprocessing image data for further analysis, and describe selected examples of automated image analysis, including the tracking of cells during embryogenesis, heartbeat detection, identification of dead embryos, recognition of tissues and anatomical landmarks, and quantification of behavioral patterns of adult fish. We review recent examples for applications using such methods, such as the comprehensive analysis of cell lineages during early development, the generation of a three-dimensional brain atlas of zebrafish larvae, and high-throughput drug screens based on movement patterns. Finally, we identify future challenges for the zebrafish image analysis community, notably those concerning the compatibility of algorithms and data formats for the assembly of modular analysis pipelines

From disease genes to behavioural screen in zebrafish: early onset Alzheimer’s as case study

To design prevention strategies and disease-modifying therapies in Alzheimer’s disease, we must discover biological processes which contribute to disease. Genomic studies can point to such causal processes, but their findings are rarely exploited in a systematic, hypothesis-free manner. In this thesis, we present a strategy in zebrafish to link disease-associated genes to likely causal processes. The first step is to inactivate each gene in zebrafish larvae. For this purpose, we developed a rapid CRISPR-Cas9 method capable of converting wild-type eggs directly into knockout larvae for any gene of interest. The method effectively cuts the experimental time from gene to knockout zebrafish from months to one day. The second step is to monitor the behaviour of the mutated larvae. As a case study, we targeted the three genes associated with early-onset Alzheimer’s disease. We found, for example, that larvae with loss-of-function mutations in presenilin 2 are less active during the day. The third step will be to use predictive pharmacology to identify drugs which cause the same phenotype in wild- type animals, thereby pointing to the defective process. This strategy is both scalable thanks to the knockout method and generalisable beyond Alzheimer’s disease. It can now be employed to screen tens or hundreds of genes associated with other conditions, such as schizophrenia or epilepsy

Microfluidics for Investigation of Electric-Induced Behaviors of Zebrafish Larvae

Zebrafish has emerged as a model organism for studying the genetic, neuronal and behavioral bases of diseases and for drug screening. Being a vertebrate, they are phylogenetically closer to humans than invertebrates, possess complex organs and the overall organization of their brain shows structural similarities with human. They are small at larval stages, optically transparent and easy to culture. In addition, zebrafish models of human diseases and genetic mutants are widely available. These characteristics make this vertebrate model an ideal organism for neurodegeneration study and drug screening from the molecule to whole organism level. Despite these attractive features, the conventional zebrafish screening methods used for movement-based behavioral tests are mostly time-consuming, uncontrollable, qualitative, low-throughput and inaccurate. Zebrafish larvae behavioral response to various stimulations including optical and chemical stimuli, have been already investigated. However, zebrafish sensory-motor responses to electrical signals, a controllable stimulus which its potential in inducing locomotion response was proven in research done before, have not been broadly studied. Examples of research questions remaining to be answered are if zebrafish electric induced response is sensitive to different electric current intensities, voltage drops, multiple electrical stimulation, and the electric field direction. The involvement of different pathways and genes in this response and its potential for utilization in disease studies and chemical screening, and drug discovery can also be investigated. This research aims to enhance our understanding of zebrafish electric-induced response via presenting novel microfluidic devices that address the challenges associated with monitoring the behavioral activities of zebrafish larvae in response to various electrical signals. In Objective 1 of the thesis, we designed a microfluidic device to deliver electrical stimuli to the awake and partially immobilized zebrafish larvae, screen and study their phenotypic behavioral responses and analyze the outputs. Behavioral response was characterized in terms of response duration and tail beat frequency. A multi-phenotypic microfluidic device was also developed to study the effect of electric stimulation on the heartrate. In Objective 2, attention was given to investigate the effect of electric current, voltage, and field direction on the zebrafish larvae’s response to find an optimized setting which can induce a traceable response in zebrafish. Using different habituation-dishabituation strategies, we also investigated if the zebrafish larvae show adaptation towards repeated exposures to electric stimuli. In Objective 3, we developed a quadruple-fish device to enhance the behavioral throughput of our microfluidic platform and showed the technique's effectiveness for larger sample size and faster behavioral assay. In Objective 4, our quadruple-fish device was employed to investigate the involvement of dopaminergic neurons in electric-induced movement response of zebrafish larvae. Lastly, since we could monitor the electric-induced behavioral responses of zebrafish larvae, in Objective 5, the applicability of our proposed technique in chemical toxicity and gene screening assays was investigated. This study is expected to introduce a microfluidic platform for on-demand and phenotypic behavioral screening of zebrafish larvae with applications in chemical screening and drug discovery