Model Organism In Neuroscience Research Articles

Sedative effect of U-49900 (3,4-dichloro-N- (2-(diethylamino)cyclohexyl)-N-methyl-benzamide) in adult Zebrafish

BACKGROUND:U-49900 is a chemical analog of U-47700. Despite the growing abuse of synthetic opioids, including U-49900, its psychopharmacological and toxicological profiles remain poorly understood. The zebrafish (Danio rerio) is a promising model organism in neuroscience often used for the psychopharmacological evaluation of neurotropic drugs. OBJECTIVE:To evaluate the effects of U-49900 on the behavior of adult zebrafish in a new tank. MATERIALS AND METHODS:The effect of the test compound U-49900 at 1, 5, 10, and 25 mg/L concentrations (incubation for 20 minutes) on the behavior of adult zebrafish was assessed using the “new aquarium” test. U-49900 is 3.4-dichloro-N-(2-(diethylamino)cyclohexyl)-N-methylbenzamide and is considered an analog of the synthetic opioid U-47700, causing withdrawal in humans. RESULTS:The psychopharmacological profile of U-49900 at 1, 5, 10, and 25 mg/l concentrations (water immersion) in adult zebrafish was evaluated with the novel tank test. U-49900 at 25 mg/l for 20 min reduced the distance traveled and number of top entries in the novel tank test (p 0.001 vs. control group), but unaltered other parameters.CONCLUSIONS:Overall, the sensitivity of zebrafish to synthetic non-fentanyl opioids such as U-49900 indicates the possibility of developing high-throughput screening platforms for finding effective therapies for pathological conditions caused by synthetic opioids.

An atlas and database of neuropeptide gene expression in the adult zebrafish forebrain.

Zebrafish is a useful model organism in neuroscience; however, its gene expression atlas in the adult brain is not well developed. In the present study, we examined the expression of 38 neuropeptides, comparing with GABAergic and glutamatergic neuron marker genes in the adult zebrafish brain by comprehensive in situ hybridization. The results are summarized as an expression atlas in 19 coronal planes of the forebrain. Furthermore, the scanned data of all brain sections were made publicly available in the Adult Zebrafish Brain Gene Expression Database (https://ssbd.riken.jp/azebex/). Based on these data, we performed detailed comparative neuroanatomical analyses of the hypothalamus and found that several regions previously described as one nucleus in the reference zebrafish brain atlas contain two or more subregions with significantly different neuropeptide/neurotransmitter expression profiles. Subsequently, we compared the expression data in zebrafish telencephalon and hypothalamus obtained in this study with those in mice, by performing a cluster analysis. As a result, several nuclei in zebrafish and mice were clustered in close vicinity. The present expression atlas, database, and anatomical findings will contribute to future neuroscience research using zebrafish.

Biophysical modeling of the whole-cell dynamics of C. elegans motor and interneurons families.

The nematode Caenorhabditis elegans is a widely used model organism for neuroscience. Although its nervous system has been fully reconstructed, the physiological bases of single-neuron functioning are still poorly explored. Recently, many efforts have been dedicated to measuring signals from C. elegans neurons, revealing a rich repertoire of dynamics, including bistable responses, graded responses, and action potentials. Still, biophysical models able to reproduce such a broad range of electrical responses lack. Realistic electrophysiological descriptions started to be developed only recently, merging gene expression data with electrophysiological recordings, but with a large variety of cells yet to be modeled. In this work, we contribute to filling this gap by providing biophysically accurate models of six classes of C. elegans neurons, the AIY, RIM, and AVA interneurons, and the VA, VB, and VD motor neurons. We test our models by comparing computational and experimental time series and simulate knockout neurons, to identify the biophysical mechanisms at the basis of inter and motor neuron functioning. Our models represent a step forward toward the modeling of C. elegans neuronal networks and virtual experiments on the nematode nervous system.

A complete reconstruction of the early visual system of an adult insect

For most model organisms in neuroscience, research into visual processing in the brain is difficult because of a lack of high-resolution maps that capture complex neuronal circuitry. The microinsect Megaphragma viggianii, because of its small size and non-trivial behavior, provides a unique opportunity for tractable whole-organism connectomics. We image its whole head using serial electron microscopy. We reconstruct its compound eye and analyze the optical properties of the ommatidia as well as the connectome of the first visual neuropil-the lamina. Compared with the fruit fly and the honeybee, Megaphragma visual system is highly simplified: it has 29 ommatidia per eye and 6 lamina neuron types. We report features that are both stereotypical among most ommatidia and specialized to some. By identifying the "barebones" circuits critical for flying insects, our results will facilitate constructing computational models of visual processing in insects.

Systematic generation of biophysically detailed models with generalization capability for non-spiking neurons.

Unlike spiking neurons which compress continuous inputs into digital signals for transmitting information via action potentials, non-spiking neurons modulate analog signals through graded potential responses. Such neurons have been found in a large variety of nervous tissues in both vertebrate and invertebrate species, and have been proven to play a central role in neuronal information processing. If general and vast efforts have been made for many years to model spiking neurons using conductance-based models (CBMs), very few methods have been developed for non-spiking neurons. When a CBM is built to characterize the neuron behavior, it should be endowed with generalization capabilities (i.e. the ability to predict acceptable neuronal responses to different novel stimuli not used during the model’s building). Yet, since CBMs contain a large number of parameters, they may typically suffer from a lack of such a capability. In this paper, we propose a new systematic approach based on multi-objective optimization which builds general non-spiking models with generalization capabilities. The proposed approach only requires macroscopic experimental data from which all the model parameters are simultaneously determined without compromise. Such an approach is applied on three non-spiking neurons of the nematode Caenorhabditis elegans (C. elegans), a well-known model organism in neuroscience that predominantly transmits information through non-spiking signals. These three neurons, arbitrarily labeled by convention as RIM, AIY and AFD, represent, to date, the three possible forms of non-spiking neuronal responses of C. elegans.

Objective unsupervised learning of behavioral dynamics at the frontier of information bottleneck principles, physics informed priors, and maximum mean discrepancy statistical testing

When studying model organisms in neuroscience, it is customary to observe their response to various sensory stimuli. A common way to characterize this response is to classify it into a set of discrete behaviors. Those behaviors are defined by specialists after careful observation. Recently, a growing body of literature aims to discover relevant segmentations of the output using unsupervised machine-learning techniques, allowing for objective definitions of a behavior (Berman et al., 2014; Luxem et al., 2020).

A 3D adult zebrafish brain atlas (AZBA) for the digital age.

Zebrafish have made significant contributions to our understanding of the vertebrate brain and the neural basis of behavior, earning a place as one of the most widely used model organisms in neuroscience. Their appeal arises from the marriage of low cost, early life transparency, and ease of genetic manipulation with a behavioral repertoire that becomes more sophisticated as animals transition from larvae to adults. To further enhance the use of adult zebrafish, we created the first fully segmented three-dimensional digital adult zebrafish brain atlas (AZBA). AZBA was built by combining tissue clearing, light-sheet fluorescence microscopy, and three-dimensional image registration of nuclear and antibody stains. These images were used to guide segmentation of the atlas into over 200 neuroanatomical regions comprising the entirety of the adult zebrafish brain. As an open source, online (azba.wayne.edu), updatable digital resource, AZBA will significantly enhance the use of adult zebrafish in furthering our understanding of vertebrate brain function in both health and disease.

Embryonic development of the camouflaging dwarf cuttlefish, Sepia bandensis.

The dwarf cuttlefish Sepia bandensis, a camouflaging cephalopod from the Indo-Pacific, is a promising new model organism for neuroscience, developmental biology, and evolutionary studies. Cuttlefish dynamically camouflage to their surroundings by altering the color, pattern, and texture of their skin. The skin's "pixels" (chromatophores) are controlled by motor neurons projecting from the brain. Thus, camouflage is a visible representation of neural activity. In addition to camouflage, the dwarf cuttlefish uses dynamic skin patterns for social communication. Despite more than 500 million years of evolutionary separation, cuttlefish and vertebrates converged to form limbs, camera-type eyes and a closed circulatory system. Moreover, cuttlefish have a striking ability to regenerate their limbs. Interrogation of these unique biological features will benefit from the development of a new set of tools. Dwarf cuttlefish reach sexual maturity in 4months, they lay dozens of eggs over their 9-month lifespan, and the embryos develop to hatching in 1month. Here, we describe methods to culture dwarf cuttlefish embryos in vitro and define 25 stages of cuttlefish development. This staging series serves as a foundation for future technologies that can be used to address a myriad of developmental, neurobiological, and evolutionary questions.

On the Modeling of the Three Types of Non-spiking Neurons of the Caenorhabditis elegans.

The nematode Caenorhabditis elegans (C. elegans) is a well-known model organism in neuroscience. The relative simplicity of its nervous system, made up of few hundred neurons, shares some essential features with more sophisticated nervous systems, including the human one. If we are able to fully characterize the nervous system of this organism, we will be one step closer to understanding the mechanisms underlying the behavior of living things. Following a recently conducted electrophysiological survey on different C. elegans neurons, this paper aims at modeling the three non-spiking RIM, AIY and AFD neurons (arbitrarily named with three upper case letters by convention). To date, they represent the three possible forms of non-spiking neuronal responses of the C. elegans. To achieve this objective, we propose a conductance-based neuron model adapted to the electrophysiological features of each neuron. These features are based on current biological research and a series of in-silico experiments which use differential evolution to fit the model to experimental data. From the obtained results, we formulate a series of biological hypotheses regarding currents involved in the neuron dynamics. These models reproduce experimental data with a high degree of accuracy while being biologically consistent with state-of-the-art research.

An acetylcholinesterase inhibitor, donepezil, increases anxiety and cortisol levels in adult zebrafish.

A potent acetylcholinesterase inhibitor, donepezil is a cognitive enhancer clinically used to treat neurodegenerative diseases. However, its complete pharmacological profile beyond cognition remains unclear. The zebrafish (Danio rerio) is rapidly becoming a powerful novel model organism in neuroscience and central nervous system drug screening. Here, we characterize the effects of 24-h donepezil administration on anxiety-like behavioral and endocrine responses in adult zebrafish. We evaluated zebrafish anxiety-like behaviors in the novel tank, the light-dark and the shoaling tests, paralleled by assessing brain acetylcholinesterase activity and whole-body cortisol levels. Overall, donepezil dose-dependently decreased zebrafish locomotor activity in the novel tank test and reduced time in light in the light-dark test, likely representing hypolocomotion and anxiety-like behaviors. Donepezil predictably decreased brain acetylcholinesterase activity, also increasing whole-body cortisol levels, thus further linking acetylcholinesterase inhibition to anxiety-like behavioral and endocrine responses. Collectively, these findings suggest negative modulation of zebrafish affective behavior by donepezil, support the key role of cholinergic mechanisms in behavioral regulation in zebrafish, and reinforce the growing utility of zebrafish models for studying complex behavioral processess and their neuroendocrine and neurochemical regulation.

A 3D MRI‐based atlas of a lizard brain

Magnetic resonance imaging (MRI) is an established technique for neuroanatomical analysis, being particularly useful in the medical sciences. However, the application of MRI to evolutionary neuroscience is still in its infancy. Few magnetic resonance brain atlases exist outside the standard model organisms in neuroscience and no magnetic resonance atlas has been produced for any reptile brain. A detailed understanding of reptilian brain anatomy is necessary to elucidate the evolutionary origin of enigmatic brain structures such as the cerebral cortex. Here, we present a magnetic resonance atlas for the brain of a representative squamate reptile, the Australian tawny dragon (Agamidae: Ctenophorus decresii), which has been the subject of numerous ecological and behavioral studies. We used a high-field 11.74T magnet, a paramagnetic contrasting-enhancing agent and minimum-deformation modeling of the brains of thirteen adult male individuals. From this, we created a high-resolution three-dimensional model of a lizard brain. The 3D-MRI model can be freely downloaded and allows a better comprehension of brain areas, nuclei, and fiber tracts, facilitating comparison with other species and setting the basis for future comparative evolution imaging studies. The MRI model and atlas of a tawny dragon brain (Ctenophorus decresii) can be viewed online and downloaded using the Wiley Biolucida Server at wiley.biolucida.net.

HOPE: Hybrid-Drive Combining Optogenetics, Pharmacology and Electrophysiology.

Understanding the neural mechanisms underlying human cognition and determining the causal factors for the development of brain pathologies are among the greatest challenges for society. Electrophysiological recordings offer remarkable observations of brain activity as they provide highly precise representations of information coding in both temporal and spatial domains. With the development of genetic tools over the last decades, mice have been a key model organism in neuroscience. However, conducting chronic in vivo electrophysiology in awake, behaving mice remains technically challenging, and this difficulty prevents many research teams from acquiring critical recordings in their mouse models. Behavioral training, implant fabrication, brain surgery, data acquisition and data analysis are all required steps that must be mastered in order to perform cutting-edge experiments in systems neuroscience. Here, we present a new method that simplifies the construction of a drivable and multi-task electrophysiological recording implant without loss of flexibility and recording power. The hybrid-drive combining optogenetics, pharmacology and electrophysiology (HOPE) can support up to 16 tetrodes, attached to a single drive mechanism, organized in two bundles of eight tetrodes, allowing recordings in two different mouse brain regions simultaneously with two optical fibers for optogenetic manipulation or two injection cannulas for drug-delivery experiments. Because it can be printed with a latest-generation desktop 3D printer, the production cost is low compared to classical electrophysiology implants, and it can be built within a few hours. The HOPE implant is also reconfigurable to specific needs as it has been created in a computer-aided design (CAD) software and all the files used for its construction are open-source1.

A programmable platform for sub-second multichemical dynamic stimulation and neuronal functional imaging in C. elegans.

Caenorhabditis elegans (C. elegans) is a prominent model organism in neuroscience, as its small stereotyped nervous system offers unique advantages for studying neuronal circuits at the cellular level. Characterizing temporal dynamics of neuronal circuits is essential to fully understand neuronal processing. Characterization of the temporal dynamics of chemosensory circuits requires a precise and fast method to deliver multiple stimuli and monitor the animal's neuronal activity. Microfluidic platforms have been developed that offer an improved control of chemical delivery compared to manual methods. However, stimulating an animal with multiple chemicals at high speed is still difficult. In this work, we have developed a platform that can deliver any sequence of multiple chemical reagents, at sub-second resolution and without cross-contamination. We designed a network of chemical selectors wherein the chemical selected for stimulation is determined by the set of pressures applied to the chemical reservoirs. Modulation of inlet pressures has been automated to create robust, programmable sequences of subsecond chemical pulses. We showed that stimulation with sequences of different chemicals at the second to sub-second range can generate different neuronal activity patterns in chemosensory neurons; we observed previously unseen neuronal responses to a controlled chemical stimulation. Because of the speed and versatility of stimulus generated, this platform opens new possibilities to investigate neuronal circuits.

Sex steroid profiles in zebra finches: Effects of reproductive state and domestication

The zebra finch is a common model organism in neuroscience, endocrinology, and ethology. Zebra finches are generally considered opportunistic breeders, but the extent of their opportunism depends on the predictability of their habitat. This plasticity in the timing of breeding raises the question of how domestication, a process that increases environmental predictability, has affected their reproductive physiology. Here, we compared circulating steroid levels in various “strains” of zebra finches. In Study 1, using radioimmunoassay, we examined circulating testosterone levels in several strains of zebra finches (males and females). Subjects were wild or captive (Captive Wild-Caught, Wild-Derived, or Domesticated). In Study 2, using liquid chromatography–tandem mass spectrometry (LC–MS/MS), we examined circulating sex steroid profiles in wild and domesticated zebra finches (males and females). In Study 1, circulating testosterone levels in males differed across strains. In Study 2, six steroids were detectable in plasma from wild zebra finches (pregnenolone, progesterone, dehydroepiandrosterone (DHEA), testosterone, androsterone, and 5α-dihydrotestosterone (5α-DHT)). Only pregnenolone and progesterone levels changed across reproductive states in wild finches. Compared to wild zebra finches, domesticated zebra finches had elevated levels of circulating pregnenolone, progesterone, DHEA, testosterone, androstenedione, and androsterone. These data suggest that domestication has profoundly altered the endocrinology of this common model organism. These results have implications for interpreting studies of domesticated zebra finches, as well as studies of other domesticated species.

A genome-wide search for epigenetically [corrected] regulated genes in zebra finch using MethylCap-seq and RNA-seq.

Learning and memory formation are known to require dynamic CpG (de)methylation and gene expression changes. Here, we aimed at establishing a genome-wide DNA methylation map of the zebra finch genome, a model organism in neuroscience, as well as identifying putatively epigenetically regulated genes. RNA- and MethylCap-seq experiments were performed on two zebra finch cell lines in presence or absence of 5-aza-2′-deoxycytidine induced demethylation. First, the MethylCap-seq methodology was validated in zebra finch by comparison with RRBS-generated data. To assess the influence of (variable) methylation on gene expression, RNA-seq experiments were performed as well. Comparison of RNA-seq and MethylCap-seq results showed that at least 357 of the 3,457 AZA-upregulated genes are putatively regulated by methylation in the promoter region, for which a pathway analysis showed remarkable enrichment for neurological networks. A subset of genes was validated using Exon Arrays, quantitative RT-PCR and CpG pyrosequencing on bisulfite-treated samples. To our knowledge, this study provides the first genome-wide DNA methylation map of the zebra finch genome as well as a comprehensive set of genes of which transcription is under putative methylation control.

Elemental bioimaging of manganese uptake in C. elegans

A new method for elemental bioimaging with laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) was developed and applied to study the uptake of manganese (Mn) in Caenorhabditis elegans (C. elegans). C. elegans is a well-established model organism in neuroscience, genetics and genomics, which has been extensively studied to decipher mechanisms of heavy metal induced toxicity. Knowledge about the distribution of manganese (Mn) and other metals in this organism will be helpful in elucidating pathways and mechanisms of transport, distribution and excretion. The LA-ICP-MS method requires limited sample preparation and can be used rapidly and easily to visualize the Mn distribution in C. elegans. Due to thorough optimization of the analytical parameters, intense Mn signals in C. elegans wild-type (WT) and mutants were obtained at a spatial resolution as small as 4 μm, thus proving the suitability of LA-ICP-MS to study the uptake of metals in C. elegans.

Developing zebrafish models of autism spectrum disorder (ASD)

Autism spectrum disorder (ASD) is a serious neurodevelopmental disorder with complex symptoms and unclear, multi-factorial pathogenesis. Animal (rodent) models of ASD-like behavior are extensively used to study genetics, circuitry and molecular mechanisms of ASD. The evolutionarily conserved nature of social behavior and its molecular pathways suggests that alternative experimental models can be developed to complement and enhance the existing rodent ASD paradigms. The zebrafish (Danio rerio) is rapidly becoming a popular model organism in neuroscience and biological psychiatry to study brain function, model human brain disorders and explore their genetic or pharmacological modulation. Representing highly social animals, zebrafish emerge as a strong potential model organism to study normal and pathological social phenotypes, as well as several other ASD-like symptoms. Here, we discuss the developing utility of zebrafish in modeling ASD as a new emerging field in translational neuroscience and drug discovery.

Behavioral Phenotyping ofCasperMutant and 1-Pheny-2-Thiourea Treated Adult Zebrafish

The ability to visualise neural circuits in zebrafish in vivo is one of the most useful aspects of this model organism in neuroscience. To maintain the transparency of embryos, however, drugs, such as 1-pheyl-2-thiourea (PTU) must be added, or researchers can use mutants that do not develop pigment (e.g., the casper). The behavioural characteristics of such strains, however, have not been documented. Here, we tested adult zebrafish from the casper line, as well as wild-type (Tübingen, TU) and wild-types treated as embryos with PTU on three commonly used behavioural endpoints in neuroscience: novel tank test (similar to open-field in rodents), conditioned place preference for nicotine, and social cohesion (using a new method of cluster analysis). We found no differences between the casper and the TU, but the adult TU treated with PTU as embryos showed a marked increase in anxiety during the novel tank test. These data suggest that where possible, labs interested in analysis of developmental processes involved in adult phenotypes should avoid the use of PTU in favour of transparent mutants, such as casper.

Time for Zebrafish

Time for Zebrafish

Simple cDNA normalization using kamchatka crab duplex-specific nuclease.

We developed a novel simple cDNA normalization method [termed duplex-specific nuclease (DSN) normalization] that may be effectively used for samples enriched with full-length cDNA sequences. DSN normalization involves the denaturation-reassociation of cDNA, degradation of the double-stranded (ds) fraction formed by abundant transcripts and PCR amplification of the equalized single-stranded (ss) DNA fraction. The key element of this method is the degradation of the ds fraction formed during reassociation of cDNA using the kamchatka crab DSN, as described recently. This thermostable enzyme displays a strong preference for cleaving ds DNA and DNA in DNA-RNA hybrid duplexes compared with ss DNA and RNA, irrespective of sequence length. We developed normalization protocols for both first-strand cDNA [when poly(A)+ RNA is available] and amplified cDNA (when only total RNA can be obtained). Both protocols were evaluated in model experiments using human skeletal muscle cDNA. We also employed DSN normalization to normalize cDNA from nervous tissues of the marine mollusc Aplysia californica (a popular model organism in neuroscience) to illustrate further the efficiency of the normalization technique.