Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways

Cell Host & Microbe, Год журнала: 2020, Номер 29(2), С. 179 - 196.e9

Опубликована: Дек. 21, 2020

Язык: Английский

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The natverse, a versatile toolbox for combining and analysing neuroanatomical data

eLife, Год журнала: 2020, Номер 9

Опубликована: Апрель 14, 2020

To analyse neuron data at scale, neuroscientists expend substantial effort reading documentation, installing dependencies and moving between analysis visualisation environments. facilitate this, we have developed a suite of interoperable open-source R packages called the natverse. The natverse allows users to read local remote data, perform popular analyses including clustering graph-theoretic neuronal branching. Unlike most tools, enables comparison across many neurons morphology connectivity after imaging or co-registration within common template space. also transformations different spaces modalities. We demonstrate tools that integrate vast majority

Язык: Английский

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

Glia, Год журнала: 2020, Номер 68(12), С. 2451 - 2470

Опубликована: Май 31, 2020

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

Язык: Английский

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The tectum/superior colliculus as the vertebrate solution for spatial sensory integration and action

Current Biology, Год журнала: 2021, Номер 31(11), С. R741 - R762

Опубликована: Июнь 1, 2021

The superior colliculus, or tectum in the case of non-mammalian vertebrates, is a part brain that registers events surrounding space, often through vision and hearing, but also electrosensation, infrared detection, other sensory modalities diverse vertebrate lineages. This information used to form maps space positions different salient stimuli relation individual. are arranged layers with visual input uppermost layer, senses deeper positions, spatially aligned motor map deepest layer. Here, we will review organization intrinsic function tectum/superior colliculus processed within tectal circuits. We discuss tectal/superior outputs conveyed directly downstream circuits via thalamus cortical areas control various aspects behavior. evolutionarily conserved among all tailored specialties each lineage, its roles have shifted emergence cerebral cortex mammals. illustrate both divergent properties evolution by comparing processing lampreys belonging oldest group extant larval zebrafish, rodents, vertebrates including primates.

Язык: Английский

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Visualizing anatomically registered data with brainrender

eLife, Год журнала: 2021, Номер 10

Опубликована: Март 19, 2021

Three-dimensional (3D) digital brain atlases and high-throughput brain-wide imaging techniques generate large multidimensional datasets that can be registered to a common reference frame. Generating insights from such depends critically on visualization interactive data exploration, but this challenging task. Currently available software is dedicated single atlases, model species or types, generating 3D renderings merge anatomically diverse sources requires extensive development programming skills. Here, we present brainrender: an open-source Python package for of atlases. Brainrender facilitates the creation complex with different types in same enables seamless use atlas sources. High-quality visualizations used interactively exported as high-resolution figures animated videos. By facilitating data, brainrender should accelerate analysis, interpretation, dissemination data.

Язык: Английский

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The neuropeptidergic connectome of C. elegans

Neuron, Год журнала: 2023, Номер 111(22), С. 3570 - 3589.e5

Опубликована: Ноя. 1, 2023

Efforts are ongoing to map synaptic wiring diagrams, or connectomes, understand the neural basis of brain function. However, chemical synapses represent only one type functionally important neuronal connection; in particular, extrasynaptic, "wireless" signaling by neuropeptides is widespread and plays essential roles all nervous systems. By integrating single-cell anatomical gene-expression datasets with biochemical analysis receptor-ligand interactions, we have generated a draft connectome neuropeptide C. elegans system. This network characterized high connection density, extended cascades, autocrine foci, decentralized topology, large, highly interconnected core containing three constituent communities sharing similar patterns input connectivity. Intriguingly, several key hubs little-studied neurons that appear specialized for peptidergic neuromodulation. We anticipate neuropeptidergic will serve as prototype how networks neuromodulatory organized.

Язык: Английский

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Automated synapse-level reconstruction of neural circuits in the larval zebrafish brain

Nature Methods, Год журнала: 2022, Номер 19(11), С. 1357 - 1366

Опубликована: Окт. 24, 2022

Abstract Dense reconstruction of synaptic connectivity requires high-resolution electron microscopy images entire brains and tools to efficiently trace neuronal wires across the volume. To generate such a resource, we sectioned imaged larval zebrafish brain by serial block-face at voxel size 14 × 25 nm 3 . We segmented resulting dataset with flood-filling network algorithm, automated detection chemical synapses validated results comparisons transmission microscopic light-microscopic reconstructions. Neurons their connections are stored in form queryable expandable digital address book. reconstructed 208 neurons involved visual motion processing, most them located pretectum, which had been functionally characterized same specimen two-photon calcium imaging. Moreover, mapped all 407 presynaptic postsynaptic partners two superficial interneurons tectum. The resource developed here serves as foundation for synaptic-resolution circuit analyses nervous system.

Язык: Английский

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Neural dynamics and architecture of the heading direction circuit in zebrafish

Nature Neuroscience, Год журнала: 2023, Номер 26(5), С. 765 - 773

Опубликована: Апрель 24, 2023

Abstract Animals generate neural representations of their heading direction. Notably, in insects, direction is topographically represented by the activity neurons central complex. Although head cells have been found vertebrates, connectivity that endows them with properties unknown. Using volumetric lightsheet imaging, we find a topographical representation neuronal network zebrafish anterior hindbrain, where sinusoidal bump rotates following directional swims fish and otherwise stable over many seconds. Electron microscopy reconstructions show that, although cell bodies are located dorsal region, these arborize interpeduncular nucleus, reciprocal inhibitory stabilizes ring attractor encodes heading. These resemble those fly complex, showing similar circuit architecture principles may underlie across animal kingdom paving way to an unprecedented mechanistic understanding networks vertebrates.

Язык: Английский

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A single-cell resolution gene expression atlas of the larval zebrafish brain

Science Advances, Год журнала: 2023, Номер 9(8)

Опубликована: Фев. 22, 2023

The advent of multimodal brain atlases promises to accelerate progress in neuroscience by allowing silico queries neuron morphology, connectivity, and gene expression. We used multiplexed fluorescent situ RNA hybridization chain reaction (HCR) technology generate expression maps across the larval zebrafish for a growing set marker genes. data were registered Max Planck Zebrafish Brain (mapzebrain) atlas, thus covisualization expression, single-neuron tracings, expertly curated anatomical segmentations. Using post hoc HCR labeling immediate early cfos, we mapped responses prey stimuli food ingestion freely swimming larvae. This unbiased approach revealed, addition previously described visual motor areas, cluster neurons secondary gustatory nucleus, which express calb2a, as well specific neuropeptide Y receptor, project hypothalamus. discovery exemplifies power this new atlas resource neurobiology.

Язык: Английский

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Transcriptomic neuron types vary topographically in function and morphology

Nature, Год журнала: 2025, Номер unknown

Опубликована: Фев. 12, 2025

Abstract Neuronal phenotypic traits such as morphology, connectivity and function are dictated, to a large extent, by specific combination of differentially expressed genes. Clusters neurons in transcriptomic space correspond distinct cell types some cases—for example, Caenorhabditis elegans 1 retinal ganglion cells 2–4 —have been shown share morphology function. The zebrafish optic tectum is composed spatial array that transforms visual inputs into motor outputs. Although the visuotopic map continuous, subregions functionally specialized 5,6 . Here, uncover cell-type architecture tectum, we transcriptionally profiled its neurons, revealing more than 60 organized anatomical layers. We measured responses thousands tectal two-photon calcium imaging matched them with their transcriptional profiles. Furthermore, characterized morphologies identified using transgenic lines. Notably, found similar can diverge shape, responses. Incorporating coordinates within volume revealed morphologically defined subclusters individual clusters. Our findings demonstrate extrinsic, position-dependent factors expand repertoire genetically neurons.

Язык: Английский

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