Sample preparation methods for volume electron microscopy in mollusc Berghia stephanieae.

Creating a high-resolution brain atlas in diverse species offers crucial insights into general principles underlying brain function and development. A volume electron microscopy approach to generate such neural maps has been gaining importance due to advances in imaging, data storage capabilities, and data analysis protocols. Sample preparation remains challenging and is a crucial step to accelerate the imaging and data processing pipeline. Here, we introduce several replicable methods for processing the brains of the gastropod mollusc, Berghia stephanieae for volume electron microscopy. Although high-pressure freezing is the most reliable method, the depth of cryopreservation is a severe limitation for large tissue samples. We introduce a BROPA-based method using pyrogallol and methods to rapidly process samples that can save hours at the bench. This is the first report on sample preparation and imaging pipeline for volume electron microscopy in a gastropod mollusc, opening up the potential for connectomic analysis and comparisons with other phyla.

A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes.

BACKGROUND: How novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for many novel, or clade-restricted, phenotypes. This is especially true for understudied phyla such as mollusks, where limited genomic and functional biology resources for members of this phylum have long hindered assessments of genetic homology and function. To address this gap, we constructed a chromosome-level genome for the gastropod Berghia stephanieae (Valdés, 2005) to investigate the expression of clade-specific genes across both novel and conserved tissue types in this species. RESULTS: The final assembled and filtered Berghia genome is comparable to other high-quality mollusk genomes in terms of size (1.05 Gb) and number of predicted genes (24,960 genes) and is highly contiguous. The proportion of upregulated, clade-specific genes varied across tissues, but with no clear trend between the proportion of clade-specific genes and the novelty of the tissue. However, more complex tissue like the brain had the highest total number of upregulated, clade-specific genes, though the ratio of upregulated clade-specific genes to the total number of upregulated genes was low. CONCLUSIONS: Our results, when combined with previous research on the impact of novel genes on phenotypic evolution, highlight the fact that the complexity of the novel tissue or behavior, the type of novelty, and the developmental timing of evolutionary modifications will all influence how novel and conserved genes interact to generate diversity.

A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes.

How novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for many novel, or clade-restricted, phenotypes. This is especially true for understudied phyla such as mollusks, where limited genomic and functional biology resources for members of this phylum has long hindered assessments of genetic homology and function. To address this gap, we constructed a chromosome-level genome for the gastropod Berghia stephanieae (Valdés, 2005) to investigate the expression of clade-specific genes across both novel and conserved tissue types in this species. The final assembled and filtered Berghia genome is comparable to other high quality mollusk genomes in terms of size (1.05 Gb) and number of predicted genes (24,960 genes), and is highly contiguous. The proportion of upregulated, clade-specific genes varied across tissues, but with no clear trend between the proportion of clade-specific genes and the novelty of the tissue. However, more complex tissue like the brain had the highest total number of upregulated, clade-specific genes, though the ratio of upregulated clade-specific genes to the total number of upregulated genes was low. Our results, when combined with previous research on the impact of novel genes on phenotypic evolution, highlight the fact that the complexity of the novel tissue or behavior, the type of novelty, and the developmental timing of evolutionary modifications will all influence how novel and conserved genes interact to generate diversity.

Evolution of cephalopod nervous systems.

Giant brains have independently evolved twice on this planet, in vertebrates and in cephalopods (Figure 1A). Thus, the brains and nervous systems of cephalopods provide an important counterpoint to vertebrates in the search for generalities of brain organization and function. Their mere existence disproves various hypotheses proposed to explain the evolution of the mind and the human brain, such as cognition and large brains evolved only in long-lived animals with complex social systems and parental care, none of which is true of cephalopods. Therefore, it is worthwhile to review what is known about the evolution of cephalopod nervous systems to consider how it informs our understanding of general principles of brain evolution.

State-dependent, visually guided behaviors in the nudibranch Berghia stephanieae.

Nudibranch mollusks have structurally simple eyes whose behavioral roles have not been established. We tested the effects of visual stimuli on the behavior of the nudibranch Berghia stephanieae under different food and hunger conditions. In an arena that was half-shaded, animals spent most of their time in the dark, where they also decreased their speed and made more changes in heading. These behavioral differences between the light and dark were less evident in uniformly illuminated or darkened arenas, suggesting that they were not caused by the level of illumination. Berghia stephanieae responded to distant visual targets; animals approached a black stripe that was at least 15 deg wide on a white background. They did not approach a stripe that was lighter than the background but approached a stripe that was isoluminant with the background, suggesting the detection of spatial information. Animals traveled in convoluted paths in a featureless arena but straightened their paths when a visual target was present even if they did not approach it, suggesting that visual cues were used for navigation. Individuals were less responsive to visual stimuli when food deprived or in the presence of food odor. Thus, B. stephanieae exhibits visually guided behaviors that are influenced by odors and hunger state.

mEMbrain: an interactive deep learning MATLAB tool for connectomic segmentation on commodity desktops.

Connectomics is fundamental in propelling our understanding of the nervous system's organization, unearthing cells and wiring diagrams reconstructed from volume electron microscopy (EM) datasets. Such reconstructions, on the one hand, have benefited from ever more precise automatic segmentation methods, which leverage sophisticated deep learning architectures and advanced machine learning algorithms. On the other hand, the field of neuroscience at large, and of image processing in particular, has manifested a need for user-friendly and open source tools which enable the community to carry out advanced analyses. In line with this second vein, here we propose mEMbrain, an interactive MATLAB-based software which wraps algorithms and functions that enable labeling and segmentation of electron microscopy datasets in a user-friendly user interface compatible with Linux and Windows. Through its integration as an API to the volume annotation and segmentation tool VAST, mEMbrain encompasses functions for ground truth generation, image preprocessing, training of deep neural networks, and on-the-fly predictions for proofreading and evaluation. The final goals of our tool are to expedite manual labeling efforts and to harness MATLAB users with an array of semi-automatic approaches for instance segmentation. We tested our tool on a variety of datasets that span different species at various scales, regions of the nervous system and developmental stages. To further expedite research in connectomics, we provide an EM resource of ground truth annotation from four different animals and five datasets, amounting to around 180 h of expert annotations, yielding more than 1.2 GB of annotated EM images. In addition, we provide a set of four pre-trained networks for said datasets. All tools are available from https://lichtman.rc.fas.harvard.edu/mEMbrain/. With our software, our hope is to provide a solution for lab-based neural reconstructions which does not require coding by the user, thus paving the way to affordable connectomics.

mEMbrain: an interactive deep learning MATLAB tool for connectomic segmentation on commodity desktops.

Connectomics is fundamental in propelling our understanding of the nervous system’s organization, unearthing cells and wiring diagrams reconstructed from volume electron microscopy (EM) datasets. Such reconstructions, on the one hand, have benefited from ever more precise automatic segmentation methods, which leverage sophisticated deep learning architectures and advanced machine learning algorithms. On the other hand, the field of neuroscience at large, and of image processing in particular, has manifested a need for user-friendly and open source tools which enable the community to carry out advanced analyses. In line with this second vein, here we propose mEMbrain, an interactive MATLAB-based software which wraps algorithms and functions that enable labeling and segmentation of electron microscopy datasets in a user-friendly user interface compatible with Linux and Windows. Through its integration as an API to the volume annotation and segmentation tool VAST, mEMbrain encompasses functions for ground truth generation, image preprocessing, training of deep neural networks, and on-the-fly predictions for proofreading and evaluation. The final goals of our tool are to expedite manual labeling efforts and to harness MATLAB users with an array of semi-automatic approaches for instance segmentation. We tested our tool on a variety of datasets that span different species at various scales, regions of the nervous system and developmental stages. To further expedite research in connectomics, we provide an EM resource of ground truth annotation from 4 different animals and 5 datasets, amounting to around 180 hours of expert annotations, yielding more than 1.2 GB of annotated EM images. In addition, we provide a set of 4 pre-trained networks for said datasets. All tools are available from https://lichtman.rc.fas.harvard.edu/mEMbrain/ . With our software, our hope is to provide a solution for lab-based neural reconstructions which does not require coding by the user, thus paving the way to affordable connectomics.

Cephalopod vision: How to build a better eye.

Cephalopods' eyes superficially resemble our own, but because of their evolutionary and developmental history, the photoreceptors face forward, with the downstream neural circuitry in the brain, not the retina. Two new papers uncover molecular and developmental mechanisms underlying cephalopod visual development.

The Consistency of Gastropod Identified Neurons Distinguishes Intra-Individual Plasticity From Inter-Individual Variability in Neural Circuits.

Gastropod mollusks are known for their large, individually identifiable neurons, which are amenable to long-term intracellular recordings that can be repeated from animal to animal. The constancy of individual neurons can help distinguish state-dependent or temporal variation within an individual from actual variability between individual animals. Investigations into the circuitry underlying rhythmic swimming movements of the gastropod species, Tritonia exsulans and Pleurobranchaea californica have uncovered intra- and inter-individual variability in synaptic connectivity and serotonergic neuromodulation. Tritonia has a reliably evoked escape swim behavior that is produced by a central pattern generator (CPG) composed of a small number of identifiable neurons. There is apparent individual variability in some of the connections between neurons that is inconsequential for the production of the swim behavior under normal conditions, but determines whether that individual can swim following a neural lesion. Serotonergic neuromodulation of synaptic strength intrinsic to the CPG creates neural circuit plasticity within an individual and contributes to reorganization of the network during recovery from injury and during learning. In Pleurobranchaea, variability over time in the modulatory actions of serotonin and in expression of serotonin receptor genes in an identified neuron directly reflects variation in swimming behavior. Tracking behavior and electrophysiology over hours to days was necessary to identify the functional consequences of these intra-individual, time-dependent variations. This work demonstrates the importance of unambiguous neuron identification, properly assessing the animal and network states, and tracking behavior and physiology over time to distinguish plasticity within the same animal at different times from variability across individual animals.

Bursting emerges from the complementary roles of neurons in a four-cell network.

Reciprocally inhibitory modules that form half-center oscillators require mechanisms for escaping or being released from inhibition. The central pattern generator underlying swimming by the nudibranch mollusc, Dendronotus iris, is composed of only four neurons that are organized into two competing modules of a half-center oscillator. In this system, bursting activity in left-right alternation is an emergent property of the network as a whole; none of the neurons produces bursts on its own. We found that the unique synaptic actions and membrane properties of the two neurons in each module (Si2 and the contralateral Si3) play complementary roles in generating stable bursting in this network oscillator. Although Si2 and Si3 each inhibits its contralateral counterpart, Si2 plays a dominant role in evoking fast and strong inhibition of the other module, the termination of which initiates postinhibitory rebound in the Si3 of that module by activating a hyperpolarization-activated inward current. Within each module, the synaptic actions and membrane properties of the two neurons complement each other: Si3 excites Si2, which then feeds back slow inhibition to Si3, terminating the burst. Using dynamic clamp, we showed that the magnitude of the slow inhibition sets the period of the oscillator. Thus, the synaptic actions of Si2 provide the hyperpolarization needed for the other module to rebound stably, whereas the membrane properties of Si3 in each module cause it to rebound first and excite Si2 to maintain the burst until terminated by the slow inhibition from Si2, which releases the other module to become active.NEW & NOTEWORTHY Half-center oscillators composed of reciprocally inhibitory neurons have been posited for over a century to underlie the production of rhythmic movements. The Dendronotus swim central pattern generator may be the simplest such circuit with only two pairs of bilaterally represented neurons. This study completes the description of the mechanism by which this network oscillator functions, showing how stable rhythmic activity arises from the complementary membrane and synaptic properties of the two neurons in the competing modules.

Accelerated clearing and molecular labeling of biological tissues using magnetohydrodynamic force.

Techniques used to clear biological tissue for fluorescence microscopy are essential to connect anatomical principles at levels ranging from subcellular to the whole animal. Here we report a simple and straightforward approach to efficiently render opaque tissue samples transparent and show that this approach can be modified to rapidly label intact tissue samples with antibodies for large volume fluorescence microscopy. This strategy applies a magnetohydrodynamic (MHD) force to accelerate the removal of lipids from tissue samples at least as large as an intact adult mouse brain. We also show that MHD force can be used to accelerate antibody penetration into tissue samples. This strategy complements a growing array of tools that enable high-resolution 3-dimensional anatomical analyses in intact tissues using fluorescence microscopy. MHD-accelerated clearing is simple, fast, reliable, inexpensive, provides good thermal regulation, and is compatible with existing strategies for high-quality fluorescence microscopy of intact tissues.

Behavior-related gene regulatory networks: A new level of organization in the brain.

Neuronal networks are the standard heuristic model today for describing brain activity associated with animal behavior. Recent studies have revealed an extensive role for a completely distinct layer of networked activities in the brain-the gene regulatory network (GRN)-that orchestrates expression levels of hundreds to thousands of genes in a behavior-related manner. We examine emerging insights into the relationships between these two types of networks and discuss their interplay in spatial as well as temporal dimensions, across multiple scales of organization. We discuss properties expected of behavior-related GRNs by drawing inspiration from the rich literature on GRNs related to animal development, comparing and contrasting these two broad classes of GRNs as they relate to their respective phenotypic manifestations. Developmental GRNs also represent a third layer of network biology, playing out over a third timescale, which is believed to play a crucial mediatory role between neuronal networks and behavioral GRNs. We end with a special emphasis on social behavior, discuss whether unique GRN organization and cis-regulatory architecture underlies this special class of behavior, and review literature that suggests an affirmative answer.

The conservative bias of life scientists.

Life scientists may think of themselves as liberal, but they seem to have a strong conservative bias that negatively impacts diversity in research. The bias can be revealed with a Google Scholar search; the phrase "conserved from [species X] to humans" occurs over 90,000 times, yet the reverse, "conserved from humans to [species X]" is found fewer than 1000 times (Figure 1A). I will explore why this conservative bias in direction exists in the literature and the implications that it has on our thinking and choices for research.

Command or Obey? Homologous Neurons Differ in Hierarchical Position for the Generation of Homologous Behaviors.

In motor systems, higher-order neurons provide commands to lower-level central pattern generators (CPGs) that autonomously produce rhythmic motor patterns. Such hierarchical organization is often thought to be inherent in the anatomical position of the neurons. Here, however, we report that a neuron that is member of a CPG in one species acts as a higher-order neuron in another species. In the nudibranch mollusc, Melibe leonina, swim interneuron 1 (Si1) is in the CPG underlying swimming, firing rhythmic bursts of action potentials as part of the swim motor pattern. We found that its homolog in another nudibranch, Dendronotus iris, serves as a neuromodulatory command neuron for the CPG of a homologous swimming behavior. In Dendronotus, Si1 fired irregularly throughout the swim motor pattern. The burst and spike frequencies of Dendronotus swim CPG neurons correlated with Si1 firing frequency. Si1 activity was both necessary and sufficient for the initiation and maintenance of the swim motor pattern. Each Si1 was electrically coupled to all of the CPG neurons and made monosynaptic excitatory synapses with both Si3s. Si1 also bilaterally potentiated the excitatory synapse from Si3 to Si2. "Virtual neuromodulation" of both Si3-to-Si2 synapses using dynamic clamp combined with depolarization of both Si3s mimicked the effects of Si1 stimulation on the swim motor pattern. Thus, in Dendronotus, Si1 is a command neuron that turns on, maintains, and accelerates the motor pattern through synaptic and neuromodulatory actions, thereby differing from its homolog in Melibe in its functional position in the motor hierarchy.SIGNIFICANCE STATEMENT Cross-species comparisons of motor system organization can provide fundamental insights into their function and origin. Central pattern generators (CPGs) are lower in the functional hierarchy than the neurons that initiate and modulate their activity. This functional hierarchy is often reflected in neuroanatomical organization. This paper definitively shows that an identified cerebral ganglion neuron that is a member of a CPG underlying swimming in one nudibranch species serves as a command neuron for the same behavior in another species. We describe and test the synaptic and neuromodulatory mechanisms by which the command neuron initiates and accelerates rhythmic motor patterns. Thus, the functional position of neurons in a motor hierarchy can shift from one level to another over evolutionary time.

The importance of identified neurons in gastropod molluscs to neuroscience.

Gastropod molluscs have large neurons that are uniquely identifiable across individuals and across species based on neuroanatomical and neurochemical criteria, facilitating research into neural signaling and neural circuits. Novel neuropeptides have been identified through RNA sequencing and mass spectroscopic analysis of single neurons. The roles of peptides and other signaling molecules including second messengers have been placed in the context of small circuits that control simple behaviors. Despite the stereotypy, neurons vary over time in their activity in large ensembles. Furthermore, there is both intra-species and inter-species variation in synaptic properties and gene expression. Research on gastropod identified neurons highlights the features that might be expected to be stable in more complex systems when trying to identify cell types.

Sequences of Circadian Clock Proteins in the Nudibranch Molluscs Hermissenda crassicornis, Melibe leonina, and Tritonia diomedea.

While much is known about the genes and proteins that make up the circadian clocks in vertebrates and several arthropod species, much less is known about the clock genes in many other invertebrates, including nudibranchs. The goal of this project was to identify the RNA and protein products of putative clock genes in the central nervous system of three nudibranchs, Hermissenda crassicornis, Melibe leonina, and Tritonia diomedea. Using previously published transcriptomes (Hermissenda and Tritonia) and a new transcriptome (Melibe), we identified nudibranch orthologs for the products of five canonical clock genes: brain and muscle aryl hydrocarbon receptor nuclear translocator like protein 1, circadian locomotor output cycles kaput, non-photoreceptive cryptochrome, period, and timeless. Additionally, orthologous sequences for the products of five related genes-aryl hydrocarbon receptor nuclear translocator like, photoreceptive cryptochrome, cryptochrome DASH, 6-4 photolyase, and timeout-were determined. Phylogenetic analyses confirmed that the nudibranch proteins were most closely related to known orthologs in related invertebrates, such as oysters and annelids. In general, the nudibranch clock proteins shared greater sequence similarity with Mus musculus orthologs than Drosophila melanogaster orthologs, which is consistent with the closer phylogenetic relationships recovered between lophotrochozoan and vertebrate orthologs. The suite of clock-related genes in nudibranchs includes both photoreceptive and non-photoreceptive cryptochromes, as well as timeout and possibly timeless. Therefore, the nudibranch clock may resemble the one exhibited in mammals, or possibly even in non-drosopholid insects and oysters. The latter would be evidence supporting this as the ancestral clock for bilaterians.

Artificial Synaptic Rewiring Demonstrates that Distinct Neural Circuit Configurations Underlie Homologous Behaviors.

Behavioral homology is often assumed to involve similarity in underlying neuronal mechanisms. Here, we provide a counterexample where homologous behaviors are produced by neurons with different synaptic connectivity. The nudibranch molluscs Melibe leonina and Dendronotus iris exhibit homologous swimming behaviors, consisting of alternating left and right body flexions. The swim central pattern generators (CPGs) in both species are composed of bilaterally symmetric interneurons, which are individually identified and reciprocally inhibit their contralateral counterparts, contributing to left-right burst alternation in the swim motor patterns. In Melibe, the swim CPG contains two parts that interact to produce stable rhythmic bursting; one part is the primary half-center kernel, and the other part, which consists of a bilateral pair of neurons called Si3, regulates period length. The Dendronotus swim CPG is simpler, with Si3 being part of the primary half-center oscillator. Application of curare (d-tubocurarine) selectively blocked the Si3 synapses in both species. In Melibe, curare application caused the burst duration of the swim motor pattern to lengthen, whereas in Dendronotus, curare halted bursting altogether. In both species, replacing the curare-blocked Si3 synapses with artificial synapses using dynamic clamp restored the original rhythmic bursting, thereby affirming the roles of those synapses. The curare-impaired bursting in Dendronotus was also restored by rewiring the homologous neurons into a Melibe-like primary half-center oscillator configuration, indicating that the connectivity itself could account for species differences in circuit responses to curare. The results suggest that synaptic connectivity diverged during evolution while behavior was conserved.

Variations on a theme: species differences in synaptic connectivity do not predict central pattern generator activity.

A fundamental question in comparative neuroethology is the extent to which synaptic wiring determines behavior vs. the extent to which it is constrained by phylogeny. We investigated this by examining the connectivity and activity of homologous neurons in different species. Melibe leonina and Dendronotus iris (Mollusca, Gastropoda, Nudibranchia) have homologous neurons and exhibit homologous swimming behaviors consisting of alternating left-right (LR) whole body flexions. Yet, a homologous interneuron (Si1) differs between the two species in its participation in the swim motor pattern (SMP) and synaptic connectivity. In this study we examined Si1 homologs in two additional nudibranchs: Flabellina iodinea, which evolved LR swimming independently of Melibe and Dendronotus, and Tritonia diomedea, which swims with dorsal-ventral (DV) body flexions. In Flabellina, the contralateral Si1s exhibit alternating rhythmic bursting activity during the SMP and are members of the swim central pattern generator (CPG), as in Melibe The Si1 homologs in Tritonia do not burst rhythmically during the DV SMP but are inhibited and receive bilaterally synchronous synaptic input. In both Flabellina and Tritonia, the Si1 homologs exhibit reciprocal inhibition, as in Melibe However, in Flabellina the inhibition is polysynaptic, whereas in Tritonia it is monosynaptic, as in Melibe In all species, the contralateral Si1s are electrically coupled. These results suggest that Flabellina and Melibe convergently evolved a swim CPG that contains Si1; however, they differ in monosynaptic connections. Connectivity is more similar between Tritonia and Melibe, which exhibit different swimming behaviors. Thus connectivity between homologous neurons varies independently of both behavior and phylogeny.NEW & NOTEWORTHY This research shows that the synaptic connectivity between homologous neurons exhibits species-specific variations on a basic theme. The neurons vary in the extent of electrical coupling and reciprocal inhibition. They also exhibit different patterns of activity during rhythmic motor behaviors that are not predicted by their circuitry. The circuitry does not map onto the phylogeny in a predictable fashion either. Thus neither neuronal homology nor species behavior is predictive of neural circuit connectivity.

Recruitment of Polysynaptic Connections Underlies Functional Recovery of a Neural Circuit after Lesion.

The recruitment of additional neurons to neural circuits often occurs in accordance with changing functional demands. Here we found that synaptic recruitment plays a key role in functional recovery after neural injury. Disconnection of a brain commissure in the nudibranch mollusc, Tritonia diomedea, impairs swimming behavior by eliminating particular synapses in the central pattern generator (CPG) underlying the rhythmic swim motor pattern. However, the CPG functionally recovers within a day after the lesion. The strength of a spared inhibitory synapse within the CPG from Cerebral Neuron 2 (C2) to Ventral Swim Interneuron B (VSI) determines the level of impairment caused by the lesion, which varies among individuals. In addition to this direct synaptic connection, there are polysynaptic connections from C2 and Dorsal Swim Interneurons to VSI that provide indirect excitatory drive but play only minor roles under normal conditions. After disconnecting the pedal commissure (Pedal Nerve 6), the recruitment of polysynaptic excitation became a major source of the excitatory drive to VSI. Moreover, the amount of polysynaptic recruitment, which changed over time, differed among individuals and correlated with the degree of recovery of the swim motor pattern. Thus, functional recovery was mediated by an increase in the magnitude of polysynaptic excitatory drive, compensating for the loss of direct excitation. Since the degree of susceptibility to injury corresponds to existing individual variation in the C2 to VSI synapse, the recovery relied upon the extent to which the network reorganized to incorporate additional synapses.