Neuronal ensembles: Building blocks of neural circuits

Neuronal ensembles, defined as groups of neurons displaying recurring patterns of coordinated activity, represent an intermediate functional level between individual neurons and brain areas. Novel methods to measure and optically manipulate the activity of neuronal populations have provided evidence of ensembles in the neocortex and hippocampus. Ensembles can be activated intrinsically or in response to sensory stimuli and play a causal role in perception and behavior. Here we review ensemble phenomenology, developmental origin, biophysical and synaptic mechanisms, and potential functional roles across different brain areas and species, including humans. As modular units of neural circuits, ensembles could provide a mechanistic underpinning of fundamental brain processes, including neural coding, motor planning, decision-making, learning, and adaptability.

The forkhead transcription factor Foxj1 controls vertebrate olfactory cilia biogenesis and sensory neuron differentiation

In vertebrates, olfactory receptors localize on multiple cilia elaborated on dendritic knobs of olfactory sensory neurons (OSNs). Although olfactory cilia dysfunction can cause anosmia, how their differentiation is programmed at the transcriptional level has remained largely unexplored. We discovered in zebrafish and mice that Foxj1, a forkhead domain-containing transcription factor traditionally linked with motile cilia biogenesis, is expressed in OSNs and required for olfactory epithelium (OE) formation. In keeping with the immotile nature of olfactory cilia, we observed that ciliary motility genes are repressed in zebrafish, mouse, and human OSNs. Strikingly, we also found that besides ciliogenesis, Foxj1 controls the differentiation of the OSNs themselves by regulating their cell type-specific gene expression, such as that of olfactory marker protein (omp) involved in odor-evoked signal transduction. In line with this, response to bile acids, odors detected by OMP-positive OSNs, was significantly diminished in foxj1 mutant zebrafish. Taken together, our findings establish how the canonical Foxj1-mediated motile ciliogenic transcriptional program has been repurposed for the biogenesis of immotile olfactory cilia, as well as for the development of the OSNs.

Elevated photic response is followed by a rapid decay and depressed state in ictogenic networks

OBJECTIVE

The switch between nonseizure and seizure states involves profound alterations in network excitability and synchrony. In this study, we aimed to identify and compare features of neural excitability and dynamics across multiple zebrafish seizure and epilepsy models.

METHODS

Inspired by video-electroencephalographic recordings in patients, we developed a framework to study spontaneous and photically evoked neural and locomotor activity in zebrafish larvae, by combining high-throughput behavioral tracking and whole-brain in vivo two-photon calcium imaging.

RESULTS

Our setup allowed us to dissect behavioral and physiological features that are divergent or convergent across multiple models. We observed that spontaneous locomotor and neural activity exhibit great diversity across models. Nonetheless, during photic stimulation, hyperexcitability and rapid response dynamics were well conserved across multiple models, highlighting the reliability of photically evoked activity for high-throughput assays. Intriguingly, in several models, we observed that the initial elevated photic response is often followed by rapid decay of neural activity and a prominent depressed state. Elevated photic response and following depressed state in seizure-prone networks are significantly reduced by the antiseizure medication valproic acid. Finally, rapid decay and depression of neural activity following photic stimulation temporally overlap with slow recruitment of astroglial calcium signals that are enhanced in seizure-prone networks.

SIGNIFICANCE

We argue that fast decay of neural activity and depressed states following photic response are likely due to homeostatic mechanisms triggered by excessive neural activity. An improved understanding of the interplay between elevated and depressed excitability states might suggest tailored epilepsy therapies.

Experience-dependent plasticity modulates ongoing activity in the antennal lobe and enhances odor representations

Ongoing neural activity has been observed across several brain regions and is thought to reflect the internal state of the brain. Yet, it is important to understand how ongoing neural activity interacts with sensory experience and shapes sensory representations. Here, we show that the projection neurons of the fruit fly antennal lobe exhibit spatiotemporally organized ongoing activity. After repeated exposure to odors, we observe a gradual and cumulative decrease in the amplitude and number of calcium events occurring in the absence of odor stimulation, as well as a reorganization of correlations between olfactory glomeruli. Accompanying these plastic changes, we find that repeated odor experience decreases trial-to-trial variability and enhances the specificity of odor representations. Our results reveal an odor-experience-dependent modulation of ongoing and sensory-evoked activity at peripheral levels of the fruit fly olfactory system.

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The fruit fly antennal lobe exhibits spatiotemporally organized ongoing activity

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Repeated odor experience decreases the amplitude and number of ongoing calcium events

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Odor experience enhances the robustness and the specificity of odor representations

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Representations of different odors become more dissimilar upon repeated exposure

Loss of glutamate transporter eaat2a leads to aberrant neuronal excitability, recurrent epileptic seizures, and basal hypoactivity

Astroglial excitatory amino acid transporter 2 (EAAT2, GLT‐1, and SLC1A2) regulates the duration and extent of neuronal excitation by removing glutamate from the synaptic cleft. Hence, an impairment in EAAT2 function could lead to an imbalanced brain network excitability. Here, we investigated the functional alterations of neuronal and astroglial networks associated with the loss of function in the astroglia predominant eaat2a gene in zebrafish. We observed that eaat2a^−/− mutant zebrafish larvae display recurrent spontaneous and light‐induced seizures in neurons and astroglia, which coincide with an abrupt increase in extracellular glutamate levels. In stark contrast to this hyperexcitability, basal neuronal and astroglial activity was surprisingly reduced in eaat2a^−/− mutant animals, which manifested in decreased overall locomotion. Our results reveal an essential and mechanistic contribution of EAAT2a in balancing brain excitability, and its direct link to epileptic seizures.

Ongoing habenular activity is driven by forebrain networks and modulated by olfactory stimuli

Ongoing neural activity, which represents internal brain states, is constantly modulated by the sensory information that is generated by the environment. In this study, we show that the habenular circuits act as a major brain hub integrating the structured ongoing activity of the limbic forebrain circuitry and the olfactory information. We demonstrate that ancestral homologs of amygdala and hippocampus in zebrafish forebrain are the major drivers of ongoing habenular activity. We also reveal that odor stimuli can modulate the activity of specific habenular neurons that are driven by this forebrain circuitry. Our results highlight a major role for the olfactory system in regulating the ongoing activity of the habenula and the forebrain, thereby altering brain's internal states.

Optimized protocol for conditioned place avoidance learning in juvenile zebrafish

Conditioned place avoidance assays are broadly used in mammals to study different cognitive aspects of operant learning. Here, we introduce a series of experimental designs for training juvenile zebrafish in short-term and long-term conditioned place avoidance assays. Our goal is to promote standardization of animal handling procedures and setup conditions to improve animal welfare and reproducibility while studying operant learning behaviors in juvenile zebrafish.

For complete details on the use and execution of this protocol, please refer to Palumbo et al. (2020).

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We describe juvenile zebrafish handling procedures for operant learning behavior

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We detail experimental designs for short- and long-term learning

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We introduce potential pitfalls for chemogenetic ablation of neurons

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We highlight the importance of animal welfare for successful learning performance

Past, present and future of zebrafish in epilepsy research

Animal models contribute greatly to our understanding of brain development and function as well as its dysfunction in neurological diseases. Epilepsy research is a very good example of how animal models can provide us with a mechanistic understanding of the genes, molecules, and pathophysiological processes involved in disease. Over the course of the last two decades, zebrafish came in as a new player in epilepsy research, with an expanding number of laboratories using this animal to understand epilepsy and to discover new strategies for preventing seizures. Yet, zebrafish as a model offers a lot more for epilepsy research. In this viewpoint, we aim to highlight some key contributions of zebrafish to epilepsy research, and we want to emphasize the great untapped potential of this animal model for expanding these contributions. We hope that our suggestions will trigger further discussions between clinicians and researchers with a common goal to understand and cure epilepsy.

Functional properties of habenular neurons are determined by developmental stage and sequential neurogenesis

The developing brain undergoes drastic alterations. Here, we investigated developmental changes in the habenula, a brain region that mediates behavioral flexibility during learning, social interactions, and aversive experiences. We showed that developing habenular circuits exhibit multiple alterations that lead to an increase in the structural and functional diversity of cell types, inputs, and functional modules. As the habenula develops, it sequentially transforms into a multisensory brain region that can process visual, olfactory, mechanosensory, and aversive stimuli. Moreover, we observed that the habenular neurons display spatiotemporally structured spontaneous activity that shows prominent alterations and refinement with age. These alterations in habenular activity are accompanied by sequential neurogenesis and the integration of distinct neural clusters across development. Last, we revealed that habenular neurons with distinct functional properties are born sequentially at distinct developmental time windows. Our results highlight a strong link between the functional properties of habenular neurons and their precise birthdate.

The Zebrafish Dorsolateral Habenula Is Required for Updating Learned Behaviors

Operant learning requires multiple cognitive processes, such as learning, prediction of potential outcomes, and decision-making. It is less clear how interactions of these processes lead to the behavioral adaptations that allow animals to cope with a changing environment. We show that juvenile zebrafish can perform conditioned place avoidance learning, with improving performance across development. Ablation of the dorsolateral habenula (dlHb), a brain region involved in associative learning and prediction of outcomes, leads to an unexpected improvement in performance and delayed memory extinction. Interestingly, the control animals exhibit rapid adaptation to a changing learning rule, whereas dlHb-ablated animals fail to adapt. Altogether, our results show that the dlHb plays a central role in switching animals' strategies while integrating new evidence with prior experience.

Stimulus-specific behavioral responses of zebrafish to a large range of odors exhibit individual variability

BACKGROUND

Odor-driven behaviors such as feeding, mating, and predator avoidance are crucial for animal survival. The neural pathways processing these behaviors have been well characterized in a number of species, and involve the activity of diverse brain regions following stimulation of the olfactory bulb by specific odors. However, while the zebrafish olfactory circuitry is well understood, a comprehensive characterization linking odor-driven behaviors to specific odors is needed to better relate olfactory computations to animal responses.

RESULTS

Here, we used a medium-throughput setup to measure the swimming trajectories of 10 zebrafish in response to 17 ecologically relevant odors. By selecting appropriate locomotor metrics, we constructed ethograms systematically describing odor-induced changes in the swimming trajectory. We found that adult zebrafish reacted to most odorants using different behavioral programs and that a combination of a few relevant behavioral metrics enabled us to capture most of the variance in these innate odor responses. We observed that individual components of natural food and alarm odors do not elicit the full behavioral response. Finally, we show that zebrafish blood elicits prominent defensive behaviors similar to those evoked by skin extract and activates spatially overlapping olfactory bulb domains.

CONCLUSION

Altogether, our results highlight a prominent intra- and inter-individual variability in zebrafish odor-driven behaviors and identify a small set of waterborne odors that elicit robust responses. Our behavioral setup and our results will be useful resources for future studies interested in characterizing innate olfactory behaviors in aquatic animals.

Radial glia in the zebrafish brain: Functional, structural, and physiological comparison with the mammalian glia

The neuroscience community has witnessed a tremendous expansion of glia research. Glial cells are now on center stage with leading roles in the development, maturation, and physiology of brain circuits. Over the course of evolution, glia have highly diversified and include the radial glia, astroglia or astrocytes, microglia, oligodendrocytes, and ependymal cells, each having dedicated functions in the brain. The zebrafish, a small teleost fish, is no exception to this and recent evidences point to evolutionarily conserved roles for glia in the development and physiology of its nervous system. Due to its small size, transparency, and genetic amenability, the zebrafish has become an increasingly prominent animal model for brain research. It has enabled the study of neural circuits from individual cells to entire brains, with a precision unmatched in other vertebrate models. Moreover, its high neurogenic and regenerative potential has attracted a lot of attention from the research community focusing on neural stem cells and neurodegenerative diseases. Hence, studies using zebrafish have the potential to provide fundamental insights about brain development and function, and also elucidate neural and molecular mechanisms of neurological diseases. We will discuss here recent discoveries on the diverse roles of radial glia and astroglia in neurogenesis, in modulating neuronal activity and in regulating brain homeostasis at the brain barriers. By comparing insights made in various animal models, particularly mammals and zebrafish, our goal is to highlight the similarities and differences in glia biology among species, which could set new paradigms relevant to humans.

Interhemispheric connections between olfactory bulbs improve odor detection

Interhemispheric connections enable interaction and integration of sensory information in bilaterian nervous systems and are thought to optimize sensory computations. However, the cellular and spatial organization of interhemispheric networks and the computational properties they mediate in vertebrates are still poorly understood. Thus, it remains unclear to what extent the connectivity between left and right brain hemispheres participates in sensory processing. Here, we show that the zebrafish olfactory bulbs (OBs) receive direct interhemispheric projections from their contralateral counterparts in addition to top-down inputs from the contralateral zebrafish homolog of olfactory cortex. The direct interhemispheric projections between the OBs reach peripheral layers of the contralateral OB and retain a precise topographic organization, which directly connects similarly tuned olfactory glomeruli across hemispheres. In contrast, interhemispheric top-down inputs consist of diffuse projections that broadly innervate the inhibitory granule cell layer. Jointly, these interhemispheric connections elicit a balance of topographically organized excitation and nontopographic inhibition on the contralateral OB and modulate odor responses. We show that the interhemispheric connections in the olfactory system enable the modulation of odor response and contribute to a small but significant improvement in the detection of a reproductive pheromone when presented together with complex olfactory cues by potentiating the response of the pheromone selective neurons. Taken together, our data show a previously unknown function for an interhemispheric connection between chemosensory maps of the olfactory system.

Interhemispheric connections enable interaction and integration of sensory information in bilaterian nervous systems and are thought to optimize sensory computations. This study shows that interhemispheric olfactory connections in the zebrafish brain improve the detection of a reproductive pheromone within a noisy odor background.

Habenula: A Role in Brain State Transitions during Coping Behavior

What is the link between behavioral states and neural dynamics in the brain? New research using zebrafish has revealed a unique activity pattern in the brain, sequentially recruiting multiple habenular neurons, during the transition from active to passive coping behavior.

Ciliary Beating Compartmentalizes Cerebrospinal Fluid Flow in the Brain and Regulates Ventricular Development

Motile cilia are miniature, propeller-like extensions, emanating from many cell types across the body. Their coordinated beating generates a directional fluid flow, which is essential for various biological processes, from respiration to reproduction. In the nervous system, ependymal cells extend their motile cilia into the brain ventricles and contribute to cerebrospinal fluid (CSF) flow. Although motile cilia are not the only contributors to CSF flow, their functioning is crucial, as patients with motile cilia defects develop clinical features, like hydrocephalus and scoliosis. CSF flow was suggested to primarily deliver nutrients and remove waste, but recent studies emphasized its role in brain development and function. Nevertheless, it remains poorly understood how ciliary beating generates and organizes CSF flow to fulfill these roles. Here, we study motile cilia and CSF flow in the brain ventricles of larval zebrafish. We identified that different populations of motile ciliated cells are spatially organized and generate a directional CSF flow powered by ciliary beating. Our investigations revealed that CSF flow is confined within individual ventricular cavities, with little exchange of fluid between ventricles, despite a pulsatile CSF displacement caused by the heartbeat. Interestingly, our results showed that the ventricular boundaries supporting this compartmentalized CSF flow are abolished during bodily movement, highlighting that multiple physiological processes regulate the hydrodynamics of CSF flow. Finally, we showed that perturbing cilia reduces hydrodynamic coupling between the brain ventricles and disrupts ventricular development. We propose that motile-cilia-generated flow is crucial in regulating the distribution of CSF within and across brain ventricles.

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Spatially organized motile cilia with rotational beats create directional CSF flow

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Ciliary beating, heartbeat, and locomotion generate distinct components of CSF flow

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Joint action of these components balances CSF compartmentalization and dispersion

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Disruption of ciliary beating leads to ventricular defects during brain development

Identification of a neuronal population in the telencephalon essential for fear conditioning in zebrafish

BACKGROUND

Fear conditioning is a form of learning essential for animal survival and used as a behavioral paradigm to study the mechanisms of learning and memory. In mammals, the amygdala plays a crucial role in fear conditioning. In teleost, the medial zone of the dorsal telencephalon (Dm) has been postulated to be a homolog of the mammalian amygdala by anatomical and ablation studies, showing a role in conditioned avoidance response. However, the neuronal populations required for a conditioned avoidance response via the Dm have not been functionally or genetically defined.

RESULTS

We aimed to identify the neuronal population essential for fear conditioning through a genetic approach in zebrafish. First, we performed large-scale gene trap and enhancer trap screens, and created transgenic fish lines that expressed Gal4FF, an engineered version of the Gal4 transcription activator, in specific regions in the brain. We then crossed these Gal4FF-expressing fish with the effector line carrying the botulinum neurotoxin gene downstream of the Gal4 binding sequence UAS, and analyzed the double transgenic fish for active avoidance fear conditioning. We identified 16 transgenic lines with Gal4FF expression in various brain areas showing reduced performance in avoidance responses. Two of them had Gal4 expression in populations of neurons located in subregions of the Dm, which we named 120A-Dm neurons. Inhibition of the 120A-Dm neurons also caused reduced performance in Pavlovian fear conditioning. The 120A-Dm neurons were mostly glutamatergic and had projections to other brain regions, including the hypothalamus and ventral telencephalon.

CONCLUSIONS

Herein, we identified a subpopulation of neurons in the zebrafish Dm essential for fear conditioning. We propose that these are functional equivalents of neurons in the mammalian pallial amygdala, mediating the conditioned stimulus-unconditioned stimulus association. Thus, the study establishes a basis for understanding the evolutionary conservation and diversification of functional neural circuits mediating fear conditioning in vertebrates.

Information processing in the vertebrate habenula

The habenula is a brain region that has gained increasing popularity over the recent years due to its role in processing value-related and experience-dependent information with a strong link to depression, addiction, sleep and social interactions. This small diencephalic nucleus is proposed to act as a multimodal hub or a switchboard, where inputs from different brain regions converge. These diverse inputs to the habenula carry information about the sensory world and the animal's internal state, such as reward expectation or mood. However, it is not clear how these diverse habenular inputs interact with each other and how such interactions contribute to the function of habenular circuits in regulating behavioral responses in various tasks and contexts. In this review, we aim to discuss how information processing in habenular circuits, can contribute to specific behavioral programs that are attributed to the habenula.

Reduced Lateral Inhibition Impairs Olfactory Computations and Behaviors in a Drosophila Model of Fragile X Syndrome

Fragile X syndrome (FXS) patients present neuronal alterations that lead to severe intellectual disability, but the underlying neuronal circuit mechanisms are poorly understood. An emerging hypothesis postulates that reduced GABAergic inhibition of excitatory neurons is a key component in the pathophysiology of FXS. Here, we directly test this idea in a FXS Drosophila model. We show that FXS flies exhibit strongly impaired olfactory behaviors. In line with this, olfactory representations are less odor specific due to broader response tuning of excitatory projection neurons. We find that impaired inhibitory interactions underlie reduced specificity in olfactory computations. Finally, we show that defective lateral inhibition across projection neurons is caused by weaker inhibition from GABAergic interneurons. We provide direct evidence that deficient inhibition impairs sensory computations and behavior in an in vivo model of FXS. Together with evidence of impaired inhibition in autism and Rett syndrome, these findings suggest a potentially general mechanism for intellectual disability.

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Lack of dFMRP leads to reduced olfactory attraction and aversion in fruit flies

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Odor selectivity of antennal lobe projection neurons is impaired in dfmr1⁻ flies

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GABAergic lateral inhibition within the antennal lobe is weaker in dfmr1⁻ flies

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Deficient lateral inhibition impairs sensory computations and animal behavior

Motile-Cilia-Mediated Flow Improves Sensitivity and Temporal Resolution of Olfactory Computations

Motile cilia are actively beating hair-like structures that cover the surface of multiple epithelia. The flow that ciliary beating generates is utilized for diverse functions and depends on the spatial location and biophysical properties of cilia. Here we show that the motile cilia in the nose of aquatic vertebrates are spatially organized and stably beat with an asymmetric pattern, resulting in a robust and stereotypical flow around the nose. Our results demonstrate that these flow fields attract odors to the nose pit and facilitate detection of odors by the olfactory system in stagnant environments. Moreover, we show that ciliary beating quickly exchanges the content of the nose, thereby improving the temporal resolution of the olfactory system for detecting dynamic changes of odor plumes in turbulent environments. Altogether, our work unravels a central function of ciliary beating for generating flow fields that increase the sensitivity and the temporal resolution of olfactory computations in the vertebrate brain.

Gustatory-mediated avoidance of bacterial lipopolysaccharides via TRPA1 activation in Drosophila

Detecting pathogens and mounting immune responses upon infection is crucial for animal health. However, these responses come at a high metabolic price (McKean and Lazzaro, 2011, Kominsky et al., 2010), and avoiding pathogens before infection may be advantageous. The bacterial endotoxins lipopolysaccharides (LPS) are important immune system infection cues (Abbas et al., 2014), but it remains unknown whether animals possess sensory mechanisms to detect them prior to infection. Here we show that Drosophila melanogaster display strong aversive responses to LPS and that gustatory neurons expressing Gr66a bitter receptors mediate avoidance of LPS in feeding and egg laying assays. We found the expression of the chemosensory cation channel dTRPA1 in these cells to be necessary and sufficient for LPS avoidance. Furthermore, LPS stimulates Drosophila neurons in a TRPA1-dependent manner and activates exogenous dTRPA1 channels in human cells. Our findings demonstrate that flies detect bacterial endotoxins via a gustatory pathway through TRPA1 activation as conserved molecular mechanism.

DOI:http://dx.doi.org/10.7554/eLife.13133.001

An immune system can fight bacterial infections, ensuring an animal’s health and survival. However, mounting an immune response to a bacterial infection requires a lot of energy. It also can be potentially dangerous if the immune system becomes too active. Therefore, avoiding bacteria and not getting infected to begin with may be a better strategy to stay healthy. Fruit flies, like humans, can detect dangerous substances in the environment via their sense of smell, but it is not known whether they also detect disease-causing organisms through their sense of taste.

Bacterial molecules called lipopolysaccharides (LPS) can alert the immune system to the presence of dangerous bacteria. Previous studies have found that when flies get in contact with LPS they begin cleaning themselves, which might help prevent infection. However it was not clear how the flies actually detected the LPS. Now, Soldano et al. show that fruit flies can taste LPS and avoid eating or laying eggs on food contaminated with LPS and bacteria. A series of experiments showed that when a fly tastes LPS it stimulates bitter-sensing neurons in the fly’s mouth and throat. The experiments also revealed that the protein that activates these neurons in response to LPS is the same protein that acts in humans as detector of pungent chemicals contained in ordinary food items like mustard, garlic and wasabi. This suggests this protein, called TRPA1, is part of a key survival mechanism that has been preserved in many species throughout evolution.

Soldano et al. showed that a fly’s senses and nervous system are actively involved in protecting it from bacterial infection. This is particularly important to flies, because unlike humans they don’t develop resistance to future infections with the same bacteria. Future studies are needed to determine if flies use their sense of taste to detect other chemicals that are signs of infections. Additionally, studies are needed to determine if the activated bitter-sensing nerves alert the fly’s immune system to a potential infection.

DOI:http://dx.doi.org/10.7554/eLife.13133.002

Evolutionary conserved brainstem circuits encode category, concentration and mixtures of taste

Evolutionary conserved brainstem circuits are the first relay for gustatory information in the vertebrate brain. While the brainstem circuits act as our life support system and they mediate vital taste related behaviors, the principles of gustatory computations in these circuits are poorly understood. By a combination of two-photon calcium imaging and quantitative animal behavior in juvenile zebrafish, we showed that taste categories are represented by dissimilar brainstem responses and generate different behaviors. We also showed that the concentration of sour and bitter tastes are encoded by different principles and with different levels of sensitivity. Moreover, we observed that the taste mixtures lead to synergistic and suppressive interactions. Our results suggest that these interactions in early brainstem circuits can result in non-linear computations, such as dynamic gain modulation and discrete representation of taste mixtures, which can be utilized for detecting food items at broad range of concentrations of tastes and rejecting inedible substances.

Methods for studying the zebrafish brain: past, present and future

The zebrafish (Danio rerio) is one of the most promising new model organisms. The increasing popularity of this amazing small vertebrate is evident from the exponentially growing numbers of research articles, funded projects and new discoveries associated with the use of zebrafish for studying development, brain function, human diseases and screening for new drugs. Thanks to the development of novel technologies, the range of zebrafish research is constantly expanding with new tools synergistically enhancing traditional techniques. In this review we will highlight the past and present techniques which have made, and continue to make, zebrafish an attractive model organism for various fields of biology, with a specific focus on neuroscience.

Tcf7l2 is required for left-right asymmetric differentiation of habenular neurons

BACKGROUND

Although left-right asymmetries are common features of nervous systems, their developmental bases are largely unknown. In the zebrafish epithalamus, dorsal habenular neurons adopt medial (dHbm) and lateral (dHbl) subnuclear character at very different frequencies on the left and right sides. The left-sided parapineal promotes the elaboration of dHbl character in the left habenula, albeit by an unknown mechanism. Likewise, the genetic pathways acting within habenular neurons to control their asymmetric differentiated character are unknown.

RESULTS

In a forward genetic screen for mutations that result in loss of habenular asymmetry, we identified two mutant alleles of tcf7l2, a gene that encodes a transcriptional regulator of Wnt signaling. In tcf7l2 mutants, most neurons on both sides differentiate with dHbl identity. Consequently, the habenulae develop symmetrically, with both sides adopting a pronounced leftward character. Tcf7l2 acts cell automously in nascent equipotential neurons, and on the right side, it promotes dHbm and suppresses dHbl differentiation. On the left, the parapineal prevents this Tcf7l2-dependent process, thereby promoting dHbl differentiation.

CONCLUSIONS

Tcf7l2 is essential for lateralized fate selection by habenular neurons that can differentiate along two alternative pathways, thereby leading to major neural circuit asymmetries.

Spontaneous activity governs olfactory representations in spatially organized habenular microcircuits

The medial habenula relays information from the sensory areas via the interpeduncular nucleus to the periaqueductal gray that regulates animal behavior under stress conditions. Ablation of the dorsal habenula (dHb) in zebrafish, which is equivalent to the mammalian medial habenula, was shown to perturb experience-dependent fear. Therefore, understanding dHb function is important for understanding the neural basis of fear. In zebrafish, the dHb receives inputs from the mitral cells (MCs) of the olfactory bulb (OB), and odors can trigger distinct behaviors (e.g., feeding, courtship, alarm). However, it is unclear how the dHb processes olfactory information and how these computations relate to behavior. In this study, we demonstrate that the odor responses in the dHb are asymmetric and spatially organized despite the unorganized OB inputs. Moreover, we show that the spontaneous dHb activity is not random but structured into functionally and spatially organized clusters of neurons, which reflects the favored states of the dHb network. These dHb clusters are also preserved during odor stimulation and govern olfactory responses. Finally, we show that functional dHb clusters overlap with genetically defined dHb neurons, which regulate experience-dependent fear. Thus, we propose that the dHb is composed of functionally, spatially, and genetically distinct microcircuits that regulate different behavioral programs.

Left-right asymmetry is required for the habenulae to respond to both visual and olfactory stimuli

Left-right asymmetries are most likely a universal feature of bilaterian nervous systems and may serve to increase neural capacity by specializing equivalent structures on left and right sides for distinct roles [1]. However, little is known about how asymmetries are encoded within vertebrate neural circuits and how lateralization influences processing of information in the brain. Consequently, it remains unclear the extent to which lateralization of the nervous system is important for normal cognitive and other brain functions and whether defects in lateralization contribute to neurological deficits [2]. Here we show that sensory responses to light and odor are lateralized in larval zebrafish habenulae and that loss of brain asymmetry leads to concomitant loss of responsiveness to either visual or olfactory stimuli. We find that in wild-type zebrafish, most habenular neurons responding to light are present on the left, whereas neurons responding to odor are more frequent on the right. Manipulations that reverse the direction of brain asymmetry reverse the functional properties of habenular neurons, whereas manipulations that generate either double-left- or double-right-sided brains lead to loss of habenular responsiveness to either odor or light, respectively. Our results indicate that loss of brain lateralization has significant consequences upon sensory processing and circuit function.

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Habenular neuron responses to light and odor stimuli are lateralized

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Lateralized habenular light responses depend upon the eyes

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Loss of brain asymmetry leads to a loss of either light or odor responses

Neural circuits mediating olfactory-driven behavior in fish

The fish olfactory system processes odor signals and mediates behaviors that are crucial for survival such as foraging, courtship, and alarm response. Although the upstream olfactory brain areas (olfactory epithelium and olfactory bulb) are well-studied, less is known about their target brain areas and the role they play in generating odor-driven behaviors. Here we review a broad range of literature on the anatomy, physiology, and behavioral output of the olfactory system and its target areas in a wide range of teleost fish. Additionally, we discuss how applying recent technological advancements to the zebrafish (Danio rerio) could help in understanding the function of these target areas. We hope to provide a framework for elucidating the neural circuit computations underlying the odor-driven behaviors in this small, transparent, and genetically amenable vertebrate.

Rer1p maintains ciliary length and signaling by regulating γ-secretase activity and Foxj1a levels

Rer1p is an ER/cis-Golgi membrane protein that maintains ciliary length and function by reducing γ-secretase complex assembly and activity (thereby balancing Notch signaling) and increasing Foxj1a expression.

Cilia project from the surface of most vertebrate cells and are important for several physiological and developmental processes. Ciliary defects are linked to a variety of human diseases, named ciliopathies, underscoring the importance of understanding signaling pathways involved in cilia formation and maintenance. In this paper, we identified Rer1p as the first endoplasmic reticulum/cis-Golgi–localized membrane protein involved in ciliogenesis. Rer1p, a protein quality control receptor, was highly expressed in zebrafish ciliated organs and regulated ciliary structure and function. Both in zebrafish and mammalian cells, loss of Rer1p resulted in the shortening of cilium and impairment of its motile or sensory function, which was reflected by hearing, vision, and left–right asymmetry defects as well as decreased Hedgehog signaling. We further demonstrate that Rer1p depletion reduced ciliary length and function by increasing γ-secretase complex assembly and activity and, consequently, enhancing Notch signaling as well as reducing Foxj1a expression.

Electrical coupling between olfactory glomeruli

In the Drosophila antennal lobe, excitation can spread between glomerular processing channels. In this study, we investigated the mechanism of lateral excitation. Dual recordings from excitatory local neurons (eLNs) and projection neurons (PNs) showed that eLN-to-PN synapses transmit both hyperpolarization and depolarization, are not diminished by blocking chemical neurotransmission, and are abolished by a gap-junction mutation. This mutation eliminates odor-evoked lateral excitation in PNs and diminishes some PN odor responses. This implies that lateral excitation is mediated by electrical synapses from eLNs onto PNs. In addition, eLNs form synapses onto inhibitory LNs. Eliminating these synapses boosts some PN odor responses and reduces the disinhibitory effect of GABA receptor antagonists on PNs. Thus, eLNs have two opposing effects on PNs, driving both direct excitation and indirect inhibition. We propose that when stimuli are weak, lateral excitation promotes sensitivity, whereas when stimuli are strong, lateral excitation helps recruit inhibitory gain control.

Diversity and wiring variability of olfactory local interneurons in the Drosophila antennal lobe

Local interneurons are essential in information processing by neural circuits. Here we present a comprehensive genetic, anatomical and electrophysiological analysis of local interneurons (LNs) in the Drosophila melanogaster antennal lobe, the first olfactory processing center in the brain. We found LNs to be diverse in their neurotransmitter profiles, connectivity and physiological properties. Analysis of >1,500 individual LNs revealed principal morphological classes characterized by coarsely stereotyped glomerular innervation patterns. Some of these morphological classes showed distinct physiological properties. However, the finer-scale connectivity of an individual LN varied considerably across brains, and there was notable physiological variability within each morphological or genetic class. Finally, LN innervation required interaction with olfactory receptor neurons during development, and some individual variability also likely reflected LN-LN interactions. Our results reveal an unexpected degree of complexity and individual variation in an invertebrate neural circuit, a result that creates challenges for solving the Drosophila connectome.

Processing of odor representations by neuronal circuits in the olfactory bulb

In order to analyze neuronal computations in the first olfactory processing center, the olfactory bulb, we measured odor-evoked activity patterns across large numbers of neurons within the intact olfactory bulb of zebrafish using optical and electrophysiological methods. We found that the olfactory bulb performs multiple computations including a decorrelation of overlapping inputs, a multiplexing of complementary information, and gain control. Patterns of olfactory bulb output activity are reorganized during the initial phase of an odor response, resulting in a partial loss of the topographic representation of molecular features and in the decorrelation of activity patterns evoked by similar stimuli. Physiological, pharmacological, and computational results provide initial insights into the mechanisms underlying these computations.

Multiple functions of GABA A and GABA B receptors during pattern processing in the zebrafish olfactory bulb

gamma-Aminobutyric acid (GABA)ergic synapses are thought to play pivotal roles in the processing of activity patterns in the olfactory bulb (OB), but their functions have been difficult to study during odor responses in the intact system. We pharmacologically manipulated GABA(A) and GABA(B) receptors in the OB of zebrafish and analysed the effects on odor responses of the output neurons, the mitral cells (MCs), by electrophysiological recordings and temporally deconvolved two-photon Ca2+ imaging. The blockade of GABA(B) receptors enhanced presynaptic Ca2+ influx into afferent axon terminals, and changed the amplitude and time course of a subset of MC responses, indicating that GABA(B) receptors have a modulatory influence on OB output activity. The blockade of GABA(A) receptors induced epileptiform firing, enhanced excitatory responses and abolished fast oscillations in the local field potential. Moreover, the topological reorganization and decorrelation of MC activity patterns during the initial phase of the response was perturbed. These results indicate that GABA(A) receptor-containing circuits participate in the balance of excitation and inhibition, the regulation of total OB output activity, the synchronization of odor-dependent neuronal ensembles, and the reorganization of odor-encoding activity patterns. GABA(A) and GABA(B) receptors are therefore differentially involved in multiple functions of neuronal circuits in the OB.

Topological reorganization of odor representations in the olfactory bulb

Odors are initially represented in the olfactory bulb (OB) by patterns of sensory input across the array of glomeruli. Although activated glomeruli are often widely distributed, glomeruli responding to stimuli sharing molecular features tend to be loosely clustered and thus establish a fractured chemotopic map. Neuronal circuits in the OB transform glomerular patterns of sensory input into spatiotemporal patterns of output activity and thereby extract information about a stimulus. It is, however, unknown whether the chemotopic spatial organization of glomerular inputs is maintained during these computations. To explore this issue, we measured spatiotemporal patterns of odor-evoked activity across thousands of individual neurons in the zebrafish OB by temporally deconvolved two-photon Ca²⁺ imaging. Mitral cells and interneurons were distinguished by transgenic markers and exhibited different response selectivities. Shortly after response onset, activity patterns exhibited foci of activity associated with certain chemical features throughout all layers. During the subsequent few hundred milliseconds, however, MC activity was locally sparsened within the initial foci in an odor-specific manner. As a consequence, chemotopic maps disappeared and activity patterns became more informative about precise odor identity. Hence, chemotopic maps of glomerular input activity are initially transmitted to OB outputs, but not maintained during pattern processing. Nevertheless, transient chemotopic maps may support neuronal computations by establishing important synaptic interactions within the circuit. These results provide insights into the functional topology of neural activity patterns and its potential role in circuit function.

Many sensory brain areas contain topographic maps where the physical location of neuronal activity contains information about a stimulus feature. In the first central processing center of the olfactory pathway, the olfactory bulb, chemically distinct odors often elicit spatially segregated input activity so that general chemical features are initially represented in a topographic fashion. It is, however, unclear whether this “chemotopic” organization of odor representations is maintained at subsequent stages of odor processing. To address this question, we visualized activity patterns across thousands of individual neurons in the intact olfactory bulb of zebrafish over time using two-photon calcium imaging. Our results demonstrate that odor-evoked activity across the output neurons of the olfactory bulb is chemotopically organized shortly after stimulus onset but becomes more widely distributed during the subsequent few hundred milliseconds of the response. This reorganization of olfactory bulb output activity is most likely mediated by inhibitory feedback and reduces the redundancy in activity patterns evoked by related stimuli. These results indicate that topographically organized activity maps in the olfactory bulb are not maintained during information processing, but contribute to the function of local circuits.

Two-photon calcium imaging in the zebrafish olfactory bulb reveals that mitral cells show more selective responses to odors than interneurons, and odor-evoked firing patterns of populations of mitral cells evolve over hundreds of milliseconds to become more distinct for different odors, thus providing more information about odor identity.

Reconstruction of firing rate changes across neuronal populations by temporally deconvolved Ca2+ imaging

Methods to record action potential (AP) firing in many individual neurons are essential to unravel the function of complex neuronal circuits in the brain. A promising approach is bolus loading of Ca(2+) indicators combined with multiphoton microscopy. Currently, however, this technique lacks cell-type specificity, has low temporal resolution and cannot resolve complex temporal firing patterns. Here we present simple solutions to these problems. We identified neuron types by colocalizing Ca(2+) signals of a red-fluorescing indicator with genetically encoded markers. We reconstructed firing rate changes from Ca(2+) signals by temporal deconvolution. This technique is efficient, dramatically enhances temporal resolution, facilitates data interpretation and permits analysis of odor-response patterns across thousands of neurons in the zebrafish olfactory bulb. Hence, temporally deconvolved Ca(2+) imaging (TDCa imaging) resolves limitations of current optical recording techniques and is likely to be widely applicable because of its simplicity, robustness and generic principle.

Early development of functional spatial maps in the zebrafish olfactory bulb

In the adult olfactory bulb (OB), particular chemical classes of odorants preferentially activate glomeruli within loosely defined regions, resulting in a coarse and fractured "chemotopic" map. In zebrafish, amino acids and bile acids predominantly stimulate glomeruli in the lateral and medial OB, respectively. We studied the development of these spatial response maps in zebrafish. At 3 d postfertilization (dpf), the OB contained protoglomerular structures that became refined and more numerous during subsequent days. In a transgenic zebrafish line expressing the Ca2+ indicator protein inverse pericam, mainly in mitral cells, odor responses in the OB were first detected at 2.5-3 dpf. Already at this stage, amino acids and bile acids evoked activity predominantly in the lateral and medial OB, respectively. Two-photon Ca2+ imaging using a synthetic indicator was used to reconstruct activity patterns at higher resolution in three dimensions. Responses to amino acids and bile acids were detected predominantly in the lateral and medial OB, respectively, with little overlap. Between 2.5 and 6 dpf, the number of odor-responsive units increased, but the overall spatial organization of activity persisted. Hence, a coarse spatial organization of functional activity maps is established very early during OB development when glomeruli are not yet differentiated. This spatial organization is maintained during development and growth of neuronal circuits and may have important functions for odor processing in larvae, for the differentiation of glomeruli, and for the refinement of activity maps at later developmental stages.

The recombination activation gene 1 (Rag1) is expressed in a subset of zebrafish olfactory neurons but is not essential for axon targeting or amino acid detection

Background

Rag1 (Recombination activation gene-1) mediates genomic rearrangement and is essential for adaptive immunity in vertebrates. This gene is also expressed in the olfactory epithelium, but its function there is unknown.

Results

Using a transgenic zebrafish line and immunofluorescence, we show that Rag1 is expressed and translated in a subset of olfactory sensory neurons (OSNs). Neurons expressing GFP under the Rag1 promoter project their axons to the lateral region of the olfactory bulb only, and axons with the highest levels of GFP terminate in a single glomerular structure. A subset of GFP-expressing neurons contain Gα_o, a marker for microvillous neurons. None of the GFP-positive neurons express Gα_olf, Gα_q or the olfactory marker protein OMP. Depletion of RAG1, by morpholino-mediated knockdown or mutation, did not affect axon targeting. Calcium imaging indicates that amino acids evoke chemotopically organized glomerular activity patterns in a Rag1 mutant.

Conclusion

Rag1 expression is restricted to a subpopulation of zebrafish olfactory neurons projecting to the lateral olfactory bulb. RAG1 catalytic activity is not essential for axon targeting, nor is it likely to be required for regulation of odorant receptor expression or the response of OSNs to amino acids.

Processing of odor mixtures in the zebrafish olfactory bulb

Components of odor mixtures often are not perceived individually, suggesting that neural representations of mixtures are not simple combinations of the representations of the components. We studied odor responses to binary mixtures of amino acids and food extracts at different processing stages in the olfactory bulb (OB) of zebrafish. Odor-evoked input to the OB was measured by imaging Ca2+ signals in afferents to olfactory glomeruli. Activity patterns evoked by mixtures were predictable within narrow limits from the component patterns, indicating that mixture interactions in the peripheral olfactory system are weak. OB output neurons, the mitral cells (MCs), were recorded extra- and intracellularly and responded to odors with stimulus-dependent temporal firing rate modulations. Responses to mixtures of amino acids often were dominated by one of the component responses. Responses to mixtures of food extracts, in contrast, were more distinct from both component responses. These results show that mixture interactions can result from processing in the OB. Moreover, our data indicate that mixture interactions in the OB become more pronounced with increasing overlap of input activity patterns evoked by the components. Emerging from these results are rules of mixture interactions that may explain behavioral data and provide a basis for understanding the processing of natural odor stimuli in the OB.