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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.

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.

Failure of central nervous system (CNS) axons to regenerate after injury results in permanent disability. Several molecular neuro-protective and neuro-regenerative strategies have been proposed as potential treatments but do not provide the directional cues needed to direct target-specific axon regeneration. Here, we demonstrate that applying an external guidance cue in the form of electric field stimulation to adult rats after optic nerve crush injury was effective at directing long-distance, target-specific retinal ganglion cell (RGC) axon regeneration to native targets in the diencephalon. Stimulation was performed with asymmetric charged-balanced (ACB) waveforms that are safer than direct current and more effective than traditional, symmetric biphasic waveforms. In addition to partial anatomical restoration, ACB waveforms conferred partial restoration of visual function as measured by pattern electroretinogram recordings and local field potential recordings in the superior colliculus—and did so without the need for genetic manipulation. Our work suggests that exogenous electric field application can override cell-intrinsic and cell-extrinsic barriers to axon regeneration, and that electrical stimulation performed with specific ACB waveforms may be an effective strategy for directing anatomical and functional restoration after CNS injury. [ABSTRACT FROM AUTHOR]

Background: Mutations in the presenilin 1 (PSEN1) gene cause early onset autosomal dominant Alzheimer's Disease (AD), and the Jalisco mutation (A431E) is a subset found in people of Mexican descent (Yescas P, 2006). The Jalisco A431E mutation has been shown to produce distinct AD neuropathology such as cotton‐wool amyloid plaques as well as motor dysfunction like spastic paraparesis (Orozco‐Barajas, 2022). High levels of tau neuropathology have been observed with other PSEN1 mutations, but tau neuropathology in Jalisco patients has not been examined. Therefore, we sought to quantify the distribution of tau across a variety of brain regions in patients with A431E mutation and compare to patients with other PSEN1 mutations (A260V and T245P) or high stage sporadic AD. Method: Ten coronal brain sections from 9 PSEN1 (n = 5 A431E; n = 2 A260V, n = 2 T245P) and 9 high stage AD subjects immunohistochemically labelled with AT8 were obtained from the USC Alzheimer's Disease Research Center (ADRC). Regions analyzed included cerebral cortex (prefrontal, parietal, temporal, and occipital areas), hippocampus, striatum, midbrain, cerebellum, pons, and medulla. Ilastik, a machine‐learning based software, was trained on positive AT8 staining versus background pixels and applied this training to the whole slide image. This binary output was then overlaid with a manually drawn ROI atlas in the Quantitative Imaging Toolkit (QIT), and positive pixels per pixels of the region was used to calculate density of AT8 pathology. Result: AT8 density was significantly higher across the brain in patients with PSEN1 mutations compared to sporadic AD. Although small sample size is limited for these patient groups, we found that A431E patients had lower AT8 density in the hippocampus compared to other PSEN1 patients, most notably in dentate gyrus, as well as Brodmann Areas 35 and 36. Conclusion: These data show a high burden of tau fibrils as measured by AT8 across brain regions in people with PSEN1 mutations as compared to other high AD patients. Notably, A431E patients had different distributions than other PSEN1 patients. These findings help further characterize early onset autosomal dominant AD within patients of Mexican heritage and how tau neuropathology might contribute to its unique symptoms. [ABSTRACT FROM AUTHOR]

Background: Alzheimer's disease (AD) is a neurological disorder marked by progressive cognitive decline, memory deficits, and neuronal cell loss (Knopman, 2021). A brain region significantly impacted by the progression of AD is the subiculum, a structure responsible for spatial navigation, cognitive processes, and the modulation of emotional and affective behaviors within the hippocampus (Fanselow and Dong, 2010). Although subiculum cell loss has been well‐established as an early indicator of AD (Carlesimo et al., 2015), neurodegenerative changes to cell morphology can only be observed post‐mortem and are limited by tissue histology and staining approaches that cannot completely label neuronal morphology. Using AD mouse models, G‐deleted rabies viral tracers can fluorescently label full projection neuron cell type morphology for 3D reconstruction analysis and identify neurodegenerative changes to soma and dendrites across varying disease timepoints. Understanding morphological changes during disease progression can help identify neuronal cell type susceptibility, which precedes cell death. Methods: Using 5xFAD mice at 2 and 8 mo. timepoints, we injected G‐deleted rabies viral tracers into the medial mammillary (MM) and lateral hypothalamus (LHA) to retrogradely label MM‐ and LHA‐projecting subiculum neurons. After a 1‐week survival time, brains were extracted, sectioned into 500µm thick coronal sections, processed for SHIELD tissue clearing histology, and 3D imaged using a confocal microscope with 250nm isotropic resolution. Results: Our findings revealed that G‐deleted rabies vectors fluorescently labeled both 'healthy' and 'sick' pyramidal neurons within the subiculum, suggesting individual neurons at different stages of neurodegeneration. 'Sick' subiculum neurons displayed a variety of distinct alterations in their morphology, including shrunken cell bodies caused by decreased cytoplasm around the nucleus, the emergence of swellings and thinning of dendrites, and complete dendrite collapse. Our analysis of subiculum neurons suggests a progressive timeline of morphological degeneration that precedes cell death within the subiculum. Conclusion: Our findings have the potential to not only deepen our understanding of the degenerative morphological process in AD but also determine the cellular processes that precede neuronal death, which may in turn lead to developing targeted interventions that could prevent this fate. [ABSTRACT FROM AUTHOR]

Background: Microglia undergo varying regional dependent functional changes, which can exacerbate cognitive decline in Alzheimer's disease, but the full clinical relevance remains unclear. Ramified microglia survey the micro‐environment and inert/amoeboid microglia engulf debris. A third morphological type; rod microglia, have been observed in a number of pathological conditions, but are relatively understudied. It has been suggested that they form after acute neurological insult and understanding their anatomical distribution across brains with Alzheimer's disease may provide useful information regarding disease progression. Method: University of Southern California Alzheimer's Disease Research Center (USC ADRC) post‐mortem hippocampal and prefrontal cortical sections were immunostained with 4G8 for amyloid, AT8 for neurofibrillary tau tangles and Iba1 for microglia and imaged using an Olympus VS120 slide scanning microscope. 20 Alzheimer's disease cases and 10 control cases were selected to best represent population demographics (balanced for sex and ApoE genotype). We utilized Ilastik machine learning toolkit to classify amyloid pathology (dense, diffuse, and amyloid precursor protein), neurofibrillary tangles, neuritic plaques and microglia (rod, inert and ramified) within stained tissue section images. These classifications were then overlaid within manually segmented region maps (aligned with the Allen Human Brain Atlas) using the Quantitative Imaging Toolkit (QIT). Result: Our findings revealed elevated rod and inert microglial staining in Alzheimer's disease cases compared to controls alongside an increase in pathology burden across disease stage. Ramified microglia were reduced in Alzheimer's disease cases compared to controls. Iba1 was correlated with amyloid pathology, specifically in the dentate gyrus (DG) of the hippocampus. Rod microglia were significantly more elongated with more processes in Alzheimer's disease cases compared to controls. In general ramified had more processes, inert tended to be smaller with rod falling in between. Conclusion: Regional variations in microglia morphology and function in Alzheimer's disease could reflect differences in Alzheimer's disease cell type susceptibility and have implications for understanding the disease progression. [ABSTRACT FROM AUTHOR]

Background: Identification of cell‐type vulnerability in Alzheimer's Disease (AD) is critical to the clinical development of targeted treatments. Neurodegeneration of the subiculum (SUB) is an early biomarker of AD, but it is unknown if specific SUB cell‐types are susceptible to AD neurodegeneration. In the 5xFAD mouse model, significant cell loss occurs within the SUB by 8 months of age. Our previous work creating the mouse Hippocampus Gene Expression Atlas (HGEA) has defined cell‐type specific gene markers that can identify cell‐types within the SUB (Bienkowski et al, 2018). Within the ventral SUB (SUBv), three relatively discrete layers of gene expression define cell‐type organization. Quantification of SUBv cells identified by these gene markers can be utilized to determine SUB cell‐type susceptibility across disease timepoints. Method: To label SUBv gene expression patterns, we used RNAscope single molecule fluorescent in situ hybridization (smFISH) to label and quantify individual RNA transcript levels within SUB cell types. 5xFAD and wildtype (WT) mice (2, 6, 12, and 14 mo.) were perfused, dissected, and coronally sectioned into 20µm thick sections. SUBv tissue sections were hybridized with probes designed to target SUBv gene expression markers using RNAscope Multiplex Fluorescent V2 kit (Advanced Cell Diagnostics). Tissue sections were counterstained for DAPI cytoarchitecture, imaged at 40X with a spinning disk confocal microscope, and quantification was performed using QuPath (Quantitative Pathology and Bioimage Analysis) cell segmentation and SCAMPR analysis software (Ghoddousi et al, 2022). Result: RNAscope labeling produced robust datasets enabling quantification of single RNA transcript levels for each gene expression marker within 10,000+ SUBv cells. At late disease timepoints, we found that the number of SUBv layer 3 cells were significantly diminished compared to WT controls suggesting that SUBv layer 3 cells are primarily susceptible to AD neurodegeneration. No significant difference was found between 5xFAD and WT mice at 2 mo. of age. Conclusion: In the SUBv, layer 3 neurons are primarily susceptible to AD neurodegeneration in the 5xFAD mouse model. Future studies will investigate the transcriptomic changes that occur within SUBv layer 3 neurons that precede death. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]