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Results for “neural circuits”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 127 records · Page 7Linked to original sources

bioRxiv2019

Neural circuits mediating visual stabilization during active motion in zebrafish

Visual stabilization is an inevitable requirement for animals during active motion interaction with the environment. Visual motion cues of the surroundings or induced by self-generated behaviors are perceived then trigger proper motor responses mediated by neural representations conceptualized as the internal model: one part of it predicts the consequences of sensory dynamics as a forward model, another part generates proper motor control as a reverse model. However, the neural circuits between the two models remain mostly unknown. Here, we demonstrate that an internal component, the efference copy, coordinated the two models in a push-pull manner by generating extra reset saccades during active motion processing in larval zebrafish. Calcium imaging indicated that the saccade preparation circuit is enhanced while the velocity integration circuit is inhibited during the interaction, balancing the internal representations from both directions. This is the first model of efference copy on visual stabilization beyond the sensorimotor stage.

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bioRxiv2026

A neural circuit algorithm for action grammar

How does the brain generate sequences of discrete elements, such as actions or words, that follow an abstract rule (a grammar)? Motivated by an experiment in which monkeys learned to draw multi-object images according to grammatical rules, we trained a recurrent neural network to generate sequences Am Bn: producing shape A m times, then B n times, or vice versa. Our findings are threefold. First, the network plans the sequence by moving to an initial state encoding m and n along orthogonal directions for upcoming execution. Second, the network repeats each shape by progressing along a shape-specific manifold. Third, transitions from Am to Bn follow parallel trajectories between manifolds across values of n, thus preserving n. Each of these is an experimentally testable prediction. The network generalizes to longer novel sequences by starting further along the same orthogonal directions. These results reveal a neural circuit implementation of a symbolic algorithm for generating rule-based action sequences.

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bioRxiv2023

A Recurrent Neural Circuit Mechanism of Temporal-scaling Equivariant Representation

Time perception is fundamental in our daily life. An important feature of time perception is temporal scaling (TS): the ability to generate temporal sequences (e.g., movements) with different speeds. However, it is largely unknown about the mathematical principle underlying TS in the brain. The present theoretical study investigates temporal scaling from the Lie group point of view. We propose a canonical nonlinear recurrent circuit dynamics, modeled as a continuous attractor network, whose neuronal population responses embed a temporal sequence that is TS equivariant. We find the TS group operators can be explicitly represented by a time-invariant control input to the network, whereby the input gain determines the TS factor (group parameter), and the spatial offset between the control input and the network state on the continuous attractor manifold gives rise to the generator of the Lie group. The recurrent circuits neuronal responses are consistent with experimental data. The recurrent circuit can drive a feedforward circuit to generate complex sequences with different temporal scales, even in the case of negative temporal scaling ("time reversal"). Our work for the first time analytically links the abstract temporal scaling group and concrete neural circuit dynamics.

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bioRxiv2020

A neural circuit for competing approach andavoidance underlying prey capture

Predators must frequently balance competing approach and avoidance behaviors elicited by a moving and potentially dangerous prey. Several brain circuits supporting predation have recently been localized. However, the mechanisms by which these circuits balance the conflict between approach and avoidance responses remain unknown. Laboratory mice initially show alternating approach and avoidance responses toward cockroaches, a natural prey, but with repeated exposure become avid hunters. Here we used in vivo neural activity recording and cell-type specific manipulations in hunting mice to identify neurons in the lateral hypothalamus and periaqueductal grey that encode and control predatory approach and avoidance. We found a subset of GABAergic neurons in lateral hypothalamus that specifically encoded hunting behaviors and whose stimulation triggered predation, but not feeding. This population projects to the periaqueductal grey and stimulation of these projections promoted predation. Neurons in periaqueductal grey encoded both approach and avoidance behaviors, but only initially when the mouse showed high levels of fear of the prey. Our findings allow us to propose that GABAergic neurons in lateral hypothalamus facilitate predation in part by suppressing defensive responses to prey encoded in the periaqueductal grey. Our findings reveal a neural circuit mechanism for controlling the balance between conflicting approach and avoidance behaviors elicited by the same stimulus.

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bioRxiv2023

Development of neural circuits for social motion perception in schooling fish

Many animals move in groups, where collective behavior emerges from the interactions amongst individuals. These social interactions produce the coordinated movements of bird flocks and fish schools, but little is known about their developmental emergence and neurobiological foundations. By characterizing the visually-based schooling behavior of the micro glassfish Danionella cerebrum, here we found that social development progresses sequentially, with animals first acquiring the ability to aggregate, followed by postural alignment with social partners. This social maturation was accompanied by the development of neural populations in the midbrain and forebrain that were preferentially driven by visual stimuli that resemble the shape and movements of schooling fish. The development of these neural circuits enables the social coordination required for collective movement. One-Sentence SummaryThe collective behavior of schooling fish emerges with the development of neural populations selective to social motion.

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bioRxiv2020

Neural circuit analysis using a novel intersectional split intein-mediated split-Cre recombinase system.

The defining features of a neuron are its functional and anatomical connections with thousands of other neurons in the brain. Together, these neurons form functional networks that direct animal behaviour. Current approaches that allow the interrogation of specific populations of neurons and neural circuits rely heavily on targeting their gene expression profiles or connectivity. However, these approaches are often unable to delineate specific neuronal populations. Here, we developed a novel intersectional split intein-mediated split-Cre recombinase system that can selectively label specific types of neurons based on their gene expression profiles and structural connectivity. We developed this system by splitting Cre recombinase into two fragments with evolved split inteins and subsequently expressed one fragment under the influence of a cell type-specific promoter in a transgenic animal, and delivered the other fragment via retrograde viral gene transfer. This approach results in the reconstitution of Cre recombinase in only specific population of neurons projecting from a specific brain region or in those of a specific neuronal type. Taken together, our split intein-based split-Cre system will be useful for sophisticated characterization of mammalian brain circuits.

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bioRxiv2023

Transsynaptic labeling and transcriptional control of zebrafish neural circuits

Deciphering the connectome, the ensemble of synaptic connections that underlie brain function, is a central goal of neuroscience research. Here, we report mapping of connections between presynaptic and postsynaptic partners in a living vertebrate nervous system, that of the zebrafish, through the successful adaptation of the trans-Tango genetic approach, first developed for anterograde transsynaptic tracing in Drosophila. Neural connections were visualized between synaptic partners in the larval retina and brain and followed over development. Results were corroborated by functional experiments in which optogenetic activation of retinal ganglion cells elicited responses in neurons of the optic tectum, as measured by trans-Tango-dependent expression of a genetically encoded calcium indicator. Transsynaptic signaling through trans-Tango reveals predicted as well as previously undescribed synaptic connections in the zebrafish brain, providing a valuable in vivo tool to monitor and interrogate neural circuits over time.

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bioRxiv2019

A neural circuit basis for context-modulation of individual locomotor behavior

Defying the cliche that biological variation arises from differences in nature or nurture, genetically identical animals reared in the same environment exhibit striking differences in their behaviors. Innate behaviors can be surprisingly flexible, for example by exhibiting context-dependence. The intersection of behavioral individuality and context-dependence is largely unexplored, particularly at the neural circuit level. Here, we show that individual flies tendencies to turn left or right (locomotor handedness) changes when ambient illumination changes. This change is itself a stable individual behavioral characteristic. Silencing output neurons of the central complex (a premotor area that mediates goal-directed navigation) blocks this change. These neurons respond to light with idiosyncratic changes to their baseline calcium levels, and idiosyncratic morphological variation in their presynaptic arbors correlates with idiosyncratic sensory-context-specific turn biases. These findings provide a circuit mechanism by which individual locomotor biases arise and are modulated by sensory context.

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bioRxiv2023

Neural circuits for fast Poisson compressed sensing in the olfactory bulb

Within a single sniff, the mammalian olfactory system can decode the identity and concentration of odorants wafted on turbulent plumes of air. Yet, it must do so given access only to the noisy, dimensionally-reduced representation of the odor world provided by olfactory receptor neurons. As a result, the olfactory system must solve a compressed sensing problem, relying on the fact that only a handful of the millions of possible odorants are present in a given scene. Inspired by this principle, past works have proposed normative compressed sensing models for olfactory decoding. However, these models have not captured the unique anatomy and physiology of the olfactory bulb, nor have they shown that sensing can be achieved within the 100-millisecond timescale of a single sniff. Here, we propose a rate-based Poisson compressed sensing circuit model for the olfactory bulb. This model maps onto the neuron classes of the olfactory bulb, and recapitulates salient features of their connectivity and physiology. For circuit sizes comparable to the human olfactory bulb, we show that this model can accurately detect tens of odors within the timescale of a single sniff. We also show that this model can perform Bayesian posterior sampling for accurate uncertainty estimation. Fast inference is possible only if the geometry of the neural code is chosen to match receptor properties, yielding a distributed neural code that is not axis-aligned to individual odor identities. Our results illustrate how normative modeling can help us map function onto specific neural circuits to generate new hypotheses.

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bioRxiv2019

Distinct transcriptomic cell types and neural circuits of the subiculum and prosubiculum along the dorsal-ventral axis

Subicular region plays important roles in spatial processing and many cognitive functions and these were mainly attributed to subiculum (Sub) rather than prosubiculum (PS). Using single-cell RNA-sequencing (scRNA-seq) technique we have identified up to 27 distinct transcriptomic clusters/cell types, which were registered to anatomical sub-domains in Sub and PS. Based on reliable molecular markers derived from transcriptomic clustering and in situ hybridization data, the precise boundaries of Sub and PS have been consistently defined along the dorsoventral (DV) axis. Using these borders to evaluate Cre-line specificity and tracer injections, we have found bona fide Sub projections topographically to structures important for spatial processing and navigation. In contrast, PS along DV axis sends its outputs to widespread brain regions crucial for motivation, emotion, reward, stress, anxiety and fear. Brain-wide cell-type specific projections of Sub and PS have also been revealed using specific Cre-lines. These results reveal two molecularly and anatomically distinct circuits centered in Sub and PS, respectively, providing a consistent explanation to historical data and a clearer foundation for future functional studies. HighlightsO_LI27 transcriptomic cell types identified in and spatially registered to "subicular" regions. C_LIO_LIAnatomic borders of "subicular" regions reliably determined along dorsal-ventral axis. C_LIO_LIDistinct cell types and circuits of full-length subiculum (Sub) and prosubiculum (PS). C_LIO_LIBrain-wide cell-type specific projections of Sub and PS revealed with specific Cre-lines. C_LI In BriefDing et al. show that mouse subiculum and prosubiculum are two distinct regions with differential transcriptomic cell types, subtypes, neural circuits and functional correlation. The former has obvious topographic projections to its main targets while the latter exhibits widespread projections to many subcortical regions associated with reward, emotion, stress and motivation.

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bioRxiv2018

Neural circuit repair by low-intensity magnetic stimulation requires cryptochrome

Magnetic brain stimulation is a promising treatment in neurology and psychiatry, but clinical outcomes are variable. Unfortunately, mechanisms underlying magnetic stimulation effects are ill-defined, which impedes the development of stimulation protocols appropriate for different neurological conditions. Here we show, in vivo and ex vivo, that repetitive transcranial magnetic stimulation at low-intensity (LI-rTMS) induces axon outgrowth and synaptogenesis to repair a neural circuit. This repair depends on stimulation pattern, with complex patterns being particularly effective, and its mechanism requires the presence of cryptochrome (Cry), a putative magneto-receptor. Effective LI-rTMS patterns altered expression of Cry target genes known to promote neuronal repair. Because LI-rTMS generates electric fields too weak to depolarise neurons, these findings indicate that the magnetic field itself induces the repair. Our data open a new framework for magnetic stimulation - cryptochrome-mediated molecular and structural neuroplasticity. This information suggests new routes to treatments specific for each neurological disease.

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bioRxiv2018

Compensation Related Utilization of Neural Circuits Hypothesis Model in Response Inhibition in Premanifest Huntington’s Disease

During premanifest stages of Huntingtons disease (pre-HD), individuals typically show increased functional brain activity thought to compensate for widespread brain anomalies. What remains unknown, is to disentangle whether increased functional brain activity reflects compensation or whether it is more of a product of HD-related pathological processes. We used a quantitative model of compensation, known as the CRUNCH (Compensation-Related Utilization of Neural Circuits Hypothesis) to characterise compensatory function in pre-HD using functional magnetic resonance imaging (fMRI). To test CRUNCH predictions, pre-HD individuals (n = 15) and age- and gender-matched controls (n = 15) performed a modified stop-signal task that incremented in four levels of stop difficulty (low, intermediate-1, intermediate-2, and high). Our results did not support the critical assumption of the CRUNCH model - controls did not show increased fMRI activity with increased level of stop difficulty. By contrast, controls showed decreased fMRI activity with increased stop difficulty in right inferior frontal gyrus pars triangularis and right caudate nucleus. Relative to controls, pre-HD individuals showed increased fMRI activity in right inferior frontal gyrus pars triangularis at intermediate-2 and high level of stop difficulty, which is the opposite effect to that predicted by the CRUNCH model. Contrary to the CRUNCH prediction, the pre-HD group showed decreased fMRI activity in right caudate nucleus at low level of stop difficulty, compared with controls. Further to this, fMRI activity patterns in right inferior frontal gyrus pars triangularis and right caudate nucleus were not accompanied by a decline in the number of successful behavioural stops in pre-HD. We therefore suggest that the CRUNCH model does not apply to characterise compensatory processes associated with response inhibition in pre-HD.\n\nHighlightsO_LICRUNCH does not apply to characterise compensation during stop-signal in pre-HD\nC_LIO_LIDeficits in inhibitory control in pre-HD occur 25 years prior to clinical diagnosis\nC_LIO_LICRUNCH may show signs of selective reporting\nC_LI

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bioRxiv2021

Rapid reconstruction of neural circuits using tissue expansion and lattice light sheet microscopy

Electron microscopy (EM) allows for the reconstruction of dense neuronal connectomes but suffers from low throughput, limiting its application to small numbers of reference specimens. We developed a protocol and analysis pipeline using tissue expansion and lattice light-sheet microscopy (ExLLSM) to rapidly reconstruct selected circuits across many samples with single synapse resolution and molecular contrast. We validate this approach in Drosophila, demonstrating that it yields synaptic counts similar to those obtained by EM, can be used to compare counts across sex and experience, and to correlate structural connectivity with functional connectivity. This approach fills a critical methodological gap in studying variability in the structure and function of neural circuits across individuals within and between species.

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bioRxiv2022

Biomechanics and neural circuits for vestibular-induced fine postural control in larval zebrafish

Land-walking vertebrates maintain a desirable posture by finely controlling muscles. It is unclear whether fish also finely control posture in the water. Here, we showed that larval zebrafish have fine posture control. When roll-tilted, fish recovered their upright posture using a reflex behavior, which was a slight body bend near the swim bladder. The vestibular-induced body bend produces a misalignment between gravity and buoyancy, generating a moment of force that recovers the upright posture. We identified the neural circuits for the reflex, including the vestibular nucleus (tangential nucleus) through reticulospinal neurons (neurons in the nucleus of the medial longitudinal fasciculus) to the spinal cord, and finally to the posterior hypaxial muscles, a special class of muscles near the swim bladder. These results suggest that fish maintain a dorsal-up posture by frequently performing the body bend reflex and demonstrate that the reticulospinal pathway plays a critical role in fine postural control.

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bioRxiv2018

Cortical Column and Whole Brain Imaging of Neural Circuits with Molecular Contrast and Nanoscale Resolution

Optical and electron microscopy have made tremendous inroads in understanding the complexity of the brain, but the former offers insufficient resolution to reveal subcellular details and the latter lacks the throughput and molecular contrast to visualize specific molecular constituents over mm-scale or larger dimensions. We combined expansion microscopy and lattice light sheet microscopy to image the nanoscale spatial relationships between proteins across the thickness of the mouse cortex or the entire Drosophila brain, including synaptic proteins at dendritic spines, myelination along axons, and presynaptic densities at dopaminergic neurons in every fly neuropil domain. The technology should enable statistically rich, large scale studies of neural development, sexual dimorphism, degree of stereotypy, and structural correlations to behavior or neural activity, all with molecular contrast.\n\nOne Sentence SummaryCombined expansion and lattice light sheet microscopy enables high speed, nanoscale molecular imaging of neural circuits over large volumes.

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bioRxiv2018

A computational framework for converting high-throughput DNA sequencing data into neural circuit connectivity.

There is growing interest in determining the connectivity of neural circuits-the "connectome"-at single neuron resolution. Most approaches to circuit mapping rely on either microscopy or physiology, but these approaches have very limited throughput. We have recently proposed BOINC (Barcoding of Individual Neuronal Connectivity), a radically different approach to connectivity mapping based on high-throughput DNA sequencing. Here we describe the set of computational algorithms that serve to convert sequencing data into neural connectivity. We apply our computational pipeline to the results of proof-of-principle experiments illustrating an implementation of BOINC based on pseudorabies virus (PRV). PRV is capable of traversing individual synapses and carry DNA barcodes from one cell to another. Using this high-throughput sequencing data, we obtain 456-by-486 connectivity matrix between putative neurons. An inexpensive high-throughput technique for establishing circuit connectivity at single neuron resolution would represent a major advance in neuroscience.

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bioRxiv2020

Altered Expression of Cadherin-8 and Cadherin-11 in Neural Circuit Development: Implications for Autism

Autism spectrum disorder (ASD) is a neurological condition characterized by alterations in social interaction and communication, and restricted and/or repetitive behaviors. The classical type II cadherins cadherin-8 (Cdh8, CDH8) and cadherin-11 (Cdh11, CDH11) have been implicated as autism risk gene candidates. To explore the role of cadherins in the etiology of autism, we investigated their expression patterns during mouse brain development and in autism-specific human tissue. In mice, expression of cadherin-8 and cadherin-11 was developmentally regulated and enriched in the cortex, hippocampus, and thalamus/striatum during the peak of dendrite formation and synaptogenesis. Both cadherins were expressed in synaptic compartments but only cadherin-8 associated with the excitatory synaptic marker neuroligin-1. Induced pluripotent stem cell (iPSC)-derived cortical neural precursor cells (NPCs) and cortical organoids generated from individuals with autism showed upregulated CDH8 expression levels while CDH11 expression levels were downregulated. We used Cdh11 knockout mice of both sexes to analyze the function of cadherin-11, which could help explain phenotypes observed in autism. Cdh11-/- hippocampal neurons exhibited increased dendritic complexity along with altered neuronal and synaptic activity. Similar to the expression profiles in human tissue, levels of cadherin-8 were significantly elevated in Cdh11 knockout brains. Additionally, excitatory synaptic markers neuroligin-1 and PSD-95 were both increased. Together, these results strongly suggest that cadherin-11 is involved in regulating the development of neuronal circuitry and that alterations in the expression levels of cadherin-11 may contribute to the etiology of autism. Significance StatementAutism is a neurodevelopmental condition with high genetic and phenotypic heterogeneity. Multiple genes have been implicated in autism, including the cadherin superfamily of adhesion molecules, cadherin-8 and cadherin-11. This study first characterizes the expression profiles of cadherin-8 and cadherin-11 to understand the potential roles they play in the development of neurons. The study further describes novel contributions of cadherin-11 in neural circuit formation. Loss of cadherin-11 in mice results in altered levels of several synaptic proteins, including PSD-95, neuroligin-1, and cadherin-8, and changes the morphology and activity of excitatory neurons. The levels of cadherin-8 and cadherin-11 in human cells of autistic individuals are both altered, strengthening the hypothesis that these two cadherins may involve in aspects of autism etiology.

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bioRxiv2025

Neural circuits between nodose ganglion and pulmonary neuroendocrine cells regulate lung inflammatory responses

The lungs are organs exposed to the external environment, and the air we inhale contains various pathogens, such as endotoxins. The vagus nerve, which innervates the lungs, may play a role in detecting pathogens that invade the lungs. Through transcriptome analysis, tissue clearance imaging, electrical excitability recording, and gene- and cell-specific knockout experiments, we found that vagus nerve endings innervate pulmonary neuroendocrine cells (PNECs). These nerve endings sense bacterial endotoxins via pain receptors (TRPA1) rather than toll-like receptors (TLR4), eliciting electrical excitation and enhancing the production of neuropeptides (CGRP) in the nodose ganglia. In turn, CGRP released by sensory neurons from the nodose ganglia promotes both neuropeptide production and the proliferation of PNECs, thereby amplifying endotoxin-induced lung inflammatory responses. This reveals that the neural circuits between the nodose ganglion and PNECs play a critical role in regulating lung inflammatory responses.

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