Network architecture of intrinsic connectivity in a mammalian spinal cord (the central nervous system's caudal sector).

The vertebrate spinal cord (SP) is the long, thin extension of the brain forming the central nervous system's caudal sector. Functionally, the SP directly mediates motor and somatic sensory interactions with most parts of the body except the face, and it is the preferred model for analyzing relatively simple reflex behaviors. Here, we analyze the organization of axonal connections between the 50 gray matter regions forming the bilaterally symmetric rat SP. The assembled dataset suggests that there are about 385 of a possible 2,450 connections between the 50 regions for a connection density of 15.7%. Multiresolution consensus cluster analysis reveals a hierarchy of structure-function subsystems in this neural network, with 4 subsystems at the top level and 12 at the bottom-level. The top-level subsystems include a) a bilateral subsystem related most clearly to somatic and autonomic motor functions and centered in the ventral horn and intermediate zone; b) a bilateral subsystem associated with general somatosensory functions and centered in the base, neck, and head of the dorsal horn; and c) a pair of unilateral, bilaterally symmetric subsystems associated with nociceptive information processing and occupying the apex of the dorsal horn. The intrinsic SP network displayed no hubs, rich club, or small-world attributes, which are common measures of global functionality. Advantages and limitations of our methodology are discussed in some detail. The present work is part of a comprehensive project to assemble and analyze the neurome of a mammalian nervous system and its interactions with the body.

Intrinsic circuitry of the rhombicbrain (central nervous system's intermediate sector) in a mammal.

The rhombicbrain (rhombencephalon or intermediate sector) is the vertebrate central nervous system part between the forebrain-midbrain (rostral sector) and spinal cord (caudal sector), and it has three main divisions: pons, cerebellum, and medulla. Using a data-driven approach, here we examine intrinsic rhombicbrain (intrarhombicbrain) network architecture that in rat consists of 52,670 possible axonal connections between 230 gray matter regions (115 bilaterally symmetrical pairs). Our analysis indicates that only 8,089 (15.4%) of these connections exist. Multiresolution consensus cluster analysis yields a nested hierarchy model of rhombicbrain subsystems that at the top level are associated with 1) the cerebellum and vestibular nuclei, 2) orofacial-pharyngeal-visceral integration, and 3) auditory connections; the bottom level has 68 clusters, ranging in size from 2 to 11 regions. The model provides a basis for functional hypothesis development and interrogation. More granular network analyses performed on the intrinsic connectivity of individual and combined main rhombicbrain divisions (pons, cerebellum, medulla, pons + cerebellum, and pons + medulla) demonstrate the mutability of network architecture in response to the addition or subtraction of connections. Clear differences between the structure-function network architecture of the rhombicbrain and forebrain-midbrain are discussed, with a stark comparison provided by the subsystem and small-world organization of the cerebellar cortex and cerebral cortex. Future analysis of the connections within and between the forebrain-midbrain and rhombicbrain will provide a model of brain neural network architecture in a mammal.

A brain flatmap data visualization tool for mouse, rat, and human.

Here we provide open-access brain data flatmap visualization and analysis tools for the mouse, rat, and human. The present work stems from a previous JCN Toolbox article that introduced a novel flatmap of the mouse brain and substantially enhanced flatmaps of the rat and human brain. These brain flatmap data visualization tools enable computer-generated graphical flatmap representation of tabulated user-entered data. For mouse and rat, they are designed to accommodate data resolved spatially up to the level of gray matter regions, supported by parcellation and nomenclature defined in current brain reference atlases. For human, Brodmann cerebral cortical parcellation is emphasized, and all other major brain divisions are represented. A comprehensive user guide is included along with several use examples. These brain data visualization tools enable the tabulation and automatic graphical flatmap representation of any type of mouse, rat, or human brain data that is spatially localized. The formalized presentation afforded by these graphical tools facilitates comparative analysis between data sets within or between the represented species.

Structure-function subsystem model and computational lesions of the central nervous system's rostral sector (forebrain and midbrain).

The craniote central nervous system has been divided into rostral, intermediate, and caudal sectors, with the rostral sector containing the vertebrate forebrain and midbrain. Here, network science tools were used to create and analyze a rat hierarchical structure-function subsystem model of intrarostral sector neural connectivity between gray matter regions. The hierarchy has 109 bottom-level subsystems and three upper-level subsystems corresponding to voluntary behavior control, cognition, and affect; instinctive survival behaviors and homeostasis; and oculomotor control. As in previous work, subsystems identified based on their coclassification as network communities are revealed as functionally related. We carried out focal perturbations of neural structural connectivity comprehensively by computationally lesioning each region of the network, and the resulting effects on the network's modular (subsystem) organization were systematically mapped and measured. The pattern of changes was found to be correlated with three structural attributes of the lesioned region: region centrality (degree, strength, and betweenness), region position in the hierarchy, and subsystem distribution of region neural outputs and inputs. As expected, greater region centrality results, on average, in stronger lesion impact and more distributed lesion effects. In addition, our analysis suggests that strongly functionally related regions, belonging to the same bottom-level subsystem, exhibit similar effects after lesioning. These similarities account for coherent patterns of disturbances that align with subsystem boundaries and propagate through the network. These systematic lesion effects and their similarity across functionally related regions are of potential interest for theoretical, experimental, and clinical studies.

Ventral hippocampus-lateral septum circuitry promotes foraging-related memory.

Remembering the location of a food or water source is essential for survival. Here, we reveal that spatial memory for food location is reflected in ventral hippocampus (HPCv) neuron activity and is impaired by HPCv lesion. HPCv mediation of foraging-related memory involves communication to the lateral septum (LS), as either reversible or chronic disconnection of HPCv-to-LS signaling impairs spatial memory retention for food or water location. This neural pathway selectively encodes appetitive spatial memory, as HPCv-LS disconnection does not affect spatial memory for escape location in a negative reinforcement procedure, food intake, or social and olfactory-based appetitive learning. Neural pathway tracing and functional mapping analyses reveal that LS neurons recruited during the appetitive spatial memory procedure are primarily GABAergic neurons that project to the lateral hypothalamus. Collective results emphasize that the neural substrates controlling spatial memory are outcome specific based on reinforcer modality.

Macroscale connections of the mouse lateral preoptic area and anterior lateral hypothalamic area.

The macroscale neuronal connections of the lateral preoptic area (LPO) and the caudally adjacent lateral hypothalamic area anterior region (LHAa) were investigated in mice by anterograde and retrograde axonal tracing. Both hypothalamic regions are highly and diversely connected, with connections to >200 gray matter regions spanning the forebrain, midbrain, and rhombicbrain. Intrahypothalamic connections predominate, followed by connections with the cerebral cortex and cerebral nuclei. A similar overall pattern of LPO and LHAa connections contrasts with substantial differences between their input and output connections. Strongest connections include outputs to the lateral habenula, medial septal and diagonal band nuclei, and inputs from rostral and caudal lateral septal nuclei; however, numerous additional robust connections were also observed. The results are discussed in relation to a current model for the mammalian forebrain network that associates LPO and LHAa with a range of functional roles, including reward prediction, innate survival behaviors (including integrated somatomotor and physiological control), and affect. The present data suggest a broad and intricate role for LPO and LHAa in behavioral control, similar in that regard to previously investigated LHA regions, contributing to the finely tuned sensory-motor integration that is necessary for behavioral guidance supporting survival and reproduction.

The mouse cortico-basal ganglia-thalamic network.

The cortico-basal ganglia-thalamo-cortical loop is one of the fundamental network motifs in the brain. Revealing its structural and functional organization is critical to understanding cognition, sensorimotor behaviour, and the natural history of many neurological and neuropsychiatric disorders. Classically, this network is conceptualized to contain three information channels: motor, limbic and associative1-4. Yet this three-channel view cannot explain the myriad functions of the basal ganglia. We previously subdivided the dorsal striatum into 29 functional domains on the basis of the topography of inputs from the entire cortex5. Here we map the multi-synaptic output pathways of these striatal domains through the globus pallidus external part (GPe), substantia nigra reticular part (SNr), thalamic nuclei and cortex. Accordingly, we identify 14 SNr and 36 GPe domains and a direct cortico-SNr projection. The striatonigral direct pathway displays a greater convergence of striatal inputs than the more parallel striatopallidal indirect pathway, although direct and indirect pathways originating from the same striatal domain ultimately converge onto the same postsynaptic SNr neurons. Following the SNr outputs, we delineate six domains in the parafascicular and ventromedial thalamic nuclei. Subsequently, we identify six parallel cortico-basal ganglia-thalamic subnetworks that sequentially transduce specific subsets of cortical information through every elemental node of the cortico-basal ganglia-thalamic loop. Thalamic domains relay this output back to the originating corticostriatal neurons of each subnetwork in a bona fide closed loop.

Cellular anatomy of the mouse primary motor cortex.

An essential step toward understanding brain function is to establish a structural framework with cellular resolution on which multi-scale datasets spanning molecules, cells, circuits and systems can be integrated and interpreted1. Here, as part of the collaborative Brain Initiative Cell Census Network (BICCN), we derive a comprehensive cell type-based anatomical description of one exemplar brain structure, the mouse primary motor cortex, upper limb area (MOp-ul). Using genetic and viral labelling, barcoded anatomy resolved by sequencing, single-neuron reconstruction, whole-brain imaging and cloud-based neuroinformatics tools, we delineated the MOp-ul in 3D and refined its sublaminar organization. We defined around two dozen projection neuron types in the MOp-ul and derived an input-output wiring diagram, which will facilitate future analyses of motor control circuitry across molecular, cellular and system levels. This work provides a roadmap towards a comprehensive cellular-resolution description of mammalian brain architecture.

Subsystem macroarchitecture of the intrinsic midbrain neural network and its tectal and tegmental subnetworks.

The midbrain is the smallest of three primary vertebrate brain divisions. Here we use network science tools to reveal the global organizing principles of intramidbrain axonal circuitry before adding extrinsic connections with the remaining nervous system. Curating the experimental neuroanatomical literature yielded 17,248 connection reports for 8,742 possible connections between the 94 gray matter regions forming the right and left midbrain. Evidence for the existence of 1,676 connections suggests a 19.2% connection density for this network, similar to that for the intraforebrain network [L. W. Swanson et al., Proc. Natl. Acad. Sci. U.S.A. 117, 31470-31481 (2020)]. Multiresolution consensus cluster analysis parceled this network into a hierarchy with 6 top-level and 30 bottom-level subsystems. A structure-function model of the hierarchy identifies midbrain subsystems that play specific functional roles in sensory-motor mechanisms, motivation and reward, regulating complex reproductive and agonistic behaviors, and behavioral state control. The intramidbrain network also contains four bilateral region pairs designated putative hubs. One pair contains the superior colliculi of the tectum, well known for participation in visual sensory-motor mechanisms, and the other three pairs form spatially compact right and left units (the ventral tegmental area, retrorubral area, and midbrain reticular nucleus) in the tegmentum that are implicated in motivation and reward mechanisms. Based on the core hypothesis that subsystems form functionally cohesive units, the results provide a theoretical framework for hypothesis-driven experimental analysis of neural circuit mechanisms underlying behavioral responses mediated in part by the midbrain.

Connectivity characterization of the mouse basolateral amygdalar complex.

The basolateral amygdalar complex (BLA) is implicated in behaviors ranging from fear acquisition to addiction. Optogenetic methods have enabled the association of circuit-specific functions to uniquely connected BLA cell types. Thus, a systematic and detailed connectivity profile of BLA projection neurons to inform granular, cell type-specific interrogations is warranted. Here, we apply machine-learning based computational and informatics analysis techniques to the results of circuit-tracing experiments to create a foundational, comprehensive BLA connectivity map. The analyses identify three distinct domains within the anterior BLA (BLAa) that house target-specific projection neurons with distinguishable morphological features. We identify brain-wide targets of projection neurons in the three BLAa domains, as well as in the posterior BLA, ventral BLA, posterior basomedial, and lateral amygdalar nuclei. Inputs to each nucleus also are identified via retrograde tracing. The data suggests that connectionally unique, domain-specific BLAa neurons are associated with distinct behavior networks.

An open access mouse brain flatmap and upgraded rat and human brain flatmaps based on current reference atlases.

Here we present a flatmap of the mouse central nervous system (CNS) (brain) and substantially enhanced flatmaps of the rat and human brain. Also included are enhanced representations of nervous system white matter tracts, ganglia, and nerves, and an enhanced series of 10 flatmaps showing different stages of rat brain development. The adult mouse and rat brain flatmaps provide layered diagrammatic representation of CNS divisions, according to their arrangement in corresponding reference atlases: Brain Maps 4.0 (BM4, rat) (Swanson, The Journal of Comparative Neurology, 2018, 526, 935-943), and the first version of the Allen Reference Atlas (mouse) (Dong, The Allen reference atlas, (book + CD-ROM): A digital color brain atlas of the C57BL/6J male mouse, 2007). To facilitate comparative analysis, both flatmaps are scaled equally, and the divisional hierarchy of gray matter follows a topographic arrangement used in BM4. Also included with the mouse and rat brain flatmaps are cerebral cortex atlas level contours based on the reference atlases, and direct graphical and tabular comparison of regional parcellation. To encourage use of the brain flatmaps, they were designed and organized, with supporting reference tables, for ease-of-use and to be amenable to computational applications. We demonstrate how they can be adapted to represent novel parcellations resulting from experimental data, and we provide a proof-of-concept for how they could form the basis of a web-based graphical data viewer and analysis platform. The mouse, rat, and human brain flatmap vector graphics files (Adobe Reader/Acrobat viewable and Adobe Illustrator editable) and supporting tables are provided open access; they constitute a broadly applicable neuroscience toolbox resource for researchers seeking to map and perform comparative analysis of brain data.

Structure-function subsystem models of female and male forebrain networks integrating cognition, affect, behavior, and bodily functions.

The forebrain is the first of three primary vertebrate brain subdivisions. Macrolevel network analysis in a mammal (rat) revealed that the 466 gray matter regions composing the right and left sides of the forebrain are interconnected by 35,738 axonal connections forming a large set of overlapping, hierarchically arranged subsystems. This hierarchy is bilaterally symmetrical and sexually dimorphic, and it was used to create a structure-function conceptual model of intraforebrain network organization. Two mirror image top-level subsystems are presumably the most fundamental ontogenetically and phylogenetically. They essentially form the right and left forebrain halves and are relatively weakly interconnected. Each top-level subsystem in turn has two second-level subsystems. A ventromedial subsystem includes the medial forebrain bundle, functionally coordinating instinctive survival behaviors with appropriate physiological responses and affect. This subsystem has 26/24 (female/male) lowest-level subsystems, all using a combination of glutamate and GABA as neurotransmitters. In contrast, a dorsolateral subsystem includes the lateral forebrain bundle, functionally mediating voluntary behavior and cognition. This subsystem has 20 lowest-level subsystems, and all but 4 use glutamate exclusively for their macroconnections; no forebrain subsystems are exclusively GABAergic. Bottom-up subsystem analysis is a powerful engine for generating testable hypotheses about mechanistic explanations of brain function, behavior, and mind based on underlying circuit organization. Targeted computational (virtual) lesioning of specific regions of interest associated with Alzheimer's disease, clinical depression, and other disorders may begin to clarify how the effects spread through the entire forebrain network model.

A qualitative solution with quantitative potential for the mouse hippocampal cortex flatmap problem.

The hippocampal formation (HPF) is a focus of intense experimental investigation, particularly because of its roles in conscious memory consolidation, spatial navigation, emotion, and motivated behaviors. However, the HPF has a complex three-dimensional geometry resulting from extreme curvature of its layers, and this presents a challenge for investigators seeking to decipher hippocampal structure and function at cellular and molecular scales (neuronal circuitry, gene expression, and other properties). Previously, this problem was solved qualitatively for the rat by constructing a physical surface model of the HPF based on histological sections, and then deriving from the model a flatmap. Its usefulness is exemplified by previous studies that used it to display topological relationships between different components of intrahippocampal circuitry derived from experimental pathway-tracing experiments. Here the rat HPF flatmap was used as a starting point to construct an analogous flatmap for the mouse, where the great majority of experimental hippocampal research is currently performed. A detailed account of underlying knowledge and principles is provided, including for hippocampal terminology, and development from an embryonic nonfolded sheet into differentiated multiple adjacent cortical areas, giving rise to the adult shape. To demonstrate its utility, the mouse flatmap was used to display the results of pathway-tracing experiments showing the dentate gyrus mossy fiber projection, and its relationship to the intrahippocampal Purkinje cell protein 4 gene-expression pattern. Finally, requirements for constructing a computer graphics quantitative intrahippocampal flatmap, with accompanying intrahippocampal coordinate system, are presented; they should be applicable to all mammals, including human.

The network architecture of rat intrinsic interbrain (diencephalic) macroconnections.

The endbrain and interbrain form 2 great vertebrate forebrain divisions, and the interbrain is subdivided into the hypothalamus ventrally and thalamus dorsally. General organizing principles of intrainterbrain axonal circuitry were examined here at the level of gray matter regions using network analysis tools in a mammal with the most complete available dataset-before examining interbrain input-output relationships with other nervous system parts. The dataset was curated expertly from the neuroanatomical literature using experimental axonal pathway-tracing methods, and evidence from 74,242 connection reports indicates the existence of 10,836 macroconnections of the possible 49,062 macroconnections between the 222 gray matter regions forming the right and left halves of the interbrain. Two identical sets of 6 putative hubs were identified in the intrainterbrain network and form a continuous tissue mass in a part of the right and left medial hypothalamus associated functionally with physiological mechanisms controlling bodily functions. The intrainterbrain network shows only weak evidence of small-world attributes, rich club organization is absent, and multiresolution consensus cluster analysis indicates a solution with only 3 top-level subsystems or modules. In contrast, a previous analysis employing the same methodology to the significantly denser 244-node intraendbrain network revealed 2 identical sets of 13 hubs, small-world and rich club attributes, and 4 top-level subsystems. These differences in intrinsic network architecture across subdivisions suggest that intrinsic connections shape regional functional specialization to a varying extent, in part driven by differences in density and centrality, with extrinsic input-output connectivity playing a greater role in subdivisions that are sparser and less centralized.

Hypothalamus-hippocampus circuitry regulates impulsivity via melanin-concentrating hormone.

Behavioral impulsivity is common in various psychiatric and metabolic disorders. Here we identify a hypothalamus to telencephalon neural pathway for regulating impulsivity involving communication from melanin-concentrating hormone (MCH)-expressing lateral hypothalamic neurons to the ventral hippocampus subregion (vHP). Results show that both site-specific upregulation (pharmacological or chemogenetic) and chronic downregulation (RNA interference) of MCH communication to the vHP increases impulsive responding in rats, indicating that perturbing this system in either direction elevates impulsivity. Furthermore, these effects are not secondary to either impaired timing accuracy, altered activity, or increased food motivation, consistent with a specific role for vHP MCH signaling in the regulation of impulse control. Results from additional functional connectivity and neural pathway tracing analyses implicate the nucleus accumbens as a putative downstream target of vHP MCH1 receptor-expressing neurons. Collectively, these data reveal a specific neural circuit that regulates impulsivity and provide evidence of a novel function for MCH on behavior.

The network organization of rat intrathalamic macroconnections and a comparison with other forebrain divisions.

The thalamus is 1 of 4 major divisions of the forebrain and is usually subdivided into epithalamus, dorsal thalamus, and ventral thalamus. The 39 gray matter regions comprising the large dorsal thalamus project topographically to the cerebral cortex, whereas the much smaller epithalamus (2 regions) and ventral thalamus (5 regions) characteristically project subcortically. Before analyzing extrinsic inputs and outputs of the thalamus, here, the intrinsic connections among all 46 gray matter regions of the rat thalamus on each side of the brain were expertly collated and subjected to network analysis. Experimental axonal pathway-tracing evidence was found in the neuroanatomical literature for the presence or absence of 99% of 2,070 possible ipsilateral connections and 97% of 2,116 possible contralateral connections; the connection density of ipsilateral connections was 17%, and that of contralateral connections 5%. One hub, the reticular thalamic nucleus (of the ventral thalamus), was found in this network, whereas no high-degree rich club or clear small-world features were detected. The reticular thalamic nucleus was found to be primarily responsible for conferring the property of complete connectedness to the intrathalamic network in the sense that there is, at least, one path of finite length between any 2 regions or nodes in the network. Direct comparison with previous investigations using the same methodology shows that each division of the forebrain (cerebral cortex, cerebral nuclei, thalamus, hypothalamus) has distinct intrinsic network topological organization. A future goal is to analyze the network organization of connections within and among these 4 divisions of the forebrain.

Macroscale intrinsic network architecture of the hypothalamus.

Control of multiple life-critical physiological and behavioral functions requires the hypothalamus. Here, we provide a comprehensive description and rigorous analysis of mammalian intrahypothalamic network architecture. To achieve this at the gray matter region (macroscale) level, macroscale connection (macroconnection) data for the rat hypothalamus were extracted from the primary literature. The dataset indicated the existence of 7,982 (of 16,770 possible) intrahypothalamic macroconnections. Network analysis revealed that the intrahypothalamic macroconnection network (its macroscale subconnectome) is divided into two identical top-level subsystems (or subnetworks), each composed of two nested second-level subsystems. At the top-level, this suggests a deeply integrated network; however, regional grouping of the two second-level subsystems suggested a partial separation between control of physiological functions and behavioral functions. Furthermore, inclusion of four candidate hubs (dominant network nodes) in the second-level subsystem that is associated prominently with physiological control suggests network primacy with respect to this function. In addition, comparison of network analysis with expression of gene markers associated with inhibitory (GAD65) and excitatory (VGLUT2) neurotransmission revealed a significant positive correlation between measures of network centrality (dominance) and the inhibitory marker. We discuss these results in relation to previous understandings of hypothalamic organization and provide, and selectively interrogate, an updated hypothalamus structure-function network model to encourage future hypothesis-driven investigations of identified hypothalamic subsystems.

Subsystem organization of axonal connections within and between the right and left cerebral cortex and cerebral nuclei (endbrain).

The endbrain (telencephalon) is at the rostral end of the central nervous system and is primarily responsible for supporting cognition and affect. Structurally, it consists of right and left cerebral hemispheres, each parceled into multiple cortical and nuclear gray matter regions. The global network organization of axonal macroconnections between the 244 regions forming the endbrain was analyzed with a multiresolution consensus clustering (MRCC) method that provides a hierarchical description of community clustering (modules or subsystems) within the network. Experimental evidence was collated from the neuroanatomical literature for the existence of 10,002 of a possible 59,292 connections within the network, and they cluster into four top-level subsystems and 60 bottom-level subsystems arranged in a 50-level hierarchy. Two top-level subsystems are bihemispheric: One deals with auditory and visual information, and the other corresponds broadly to the default mode network. The other two top-level subsystems are bilaterally symmetrical, and each deals broadly with somatic and visceral information. Because the entire endbrain connection matrix was assembled from multiple subconnectomes, it was easy to show that the status of a region as a connectivity hub is not absolute but, instead, depends on the size and coverage of its anatomical neighborhood. It was also shown numerically that creating an ultradense connection matrix by converting all "absent" connections to a "very weak" connection weight has virtually no effect on the clustering hierarchy. The next logical step in this project is to complete the forebrain connectome by adding the thalamus and hypothalamus (together, the interbrain) to the endbrain analysis.

Gut vagal sensory signaling regulates hippocampus function through multi-order pathways.

The vagus nerve is the primary means of neural communication between the gastrointestinal (GI) tract and the brain. Vagally mediated GI signals activate the hippocampus (HPC), a brain region classically linked with memory function. However, the endogenous relevance of GI-derived vagal HPC communication is unknown. Here we utilize a saporin (SAP)-based lesioning procedure to reveal that selective GI vagal sensory/afferent ablation in rats impairs HPC-dependent episodic and spatial memory, effects associated with reduced HPC neurotrophic and neurogenesis markers. To determine the neural pathways connecting the gut to the HPC, we utilize monosynaptic and multisynaptic virus-based tracing methods to identify the medial septum as a relay connecting the medial nucleus tractus solitarius (where GI vagal afferents synapse) to dorsal HPC glutamatergic neurons. We conclude that endogenous GI-derived vagal sensory signaling promotes HPC-dependent memory function via a multi-order brainstem-septal pathway, thereby identifying a previously unknown role for the gut-brain axis in memory control.