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The insular cortex (IC) plays key roles in emotional and regulatory brain functions and is affected across psychiatric diseases. However, the brain-wide connections of the mouse IC have not been comprehensively mapped. Here, we traced the whole-brain inputs and outputs of the mouse IC across its rostro-caudal extent. We employed cell-type-specific monosynaptic rabies virus tracings to characterize afferent connections onto either excitatory or inhibitory IC neurons, and adeno-associated viral tracings to label excitatory efferent axons. While the connectivity between the IC and other cortical regions was highly bidirectional, the IC connectivity with subcortical structures was often unidirectional, revealing prominent cortical-to-subcortical or subcortical-to-cortical pathways. The posterior and medial IC exhibited resembling connectivity patterns, while the anterior IC connectivity was distinct, suggesting two major functional compartments. Our results provide insights into the anatomical architecture of the mouse IC and thus a structural basis to guide investigations into its complex functions.

The basal ganglia and cerebellum are major subcortical structures that influence not only movement, but putatively also cognition and affect. Both structures receive input from and send output to the cerebral cortex. Thus, the basal ganglia and cerebellum form multisynaptic loops with the cerebral cortex. Basal ganglia and cerebellar loops have been assumed to be anatomically separate and to perform distinct functional operations. We investigated whether there is any direct route for basal ganglia output to influence cerebellar function that is independent of the cerebral cortex. We injected rabies virus (RV) into selected regions of the cerebellar cortex in cebus monkeys and used retrograde transneuronal transport of the virus to determine the origin of multisynaptic inputs to the injection sites. We found that the subthalamic nucleus of the basal ganglia has a substantial disynaptic projection to the cerebellar cortex. This pathway provides a means for both normal and abnormal signals from the basal ganglia to influence cerebellar function. We previously showed that the dentate nucleus of the cerebellum has a disynaptic projection to an input stage of basal ganglia processing, the striatum. Taken together these results provide the anatomical substrate for substantial two-way communication between the basal ganglia and cerebellum. Thus, the two subcortical structures may be linked together to form an integrated functional network.

The cerebellum has a medial, cortico-nuclear zone consisting of the cerebellar vermis and the fastigial nucleus. Functionally, this zone is concerned with whole-body posture and locomotion. The vermis classically is thought to be included within the \"spinocerebellum\" and to receive somatic sensory input from ascending spinal pathways. In contrast, the lateral zone of the cerebellum is included in the \"cerebro-cerebellum\" because it is densely interconnected with the cerebral cortex. Here we report the surprising result that a portion of the vermis receives dense input from the cerebral cortex. We injected rabies virus into lobules VB–VIIIB of the vermis and used retrograde transneuronal transport of the virus to define disynaptic inputs to it. We found that large numbers of neurons in the primary motor cortex and in several motor areas on the medial wall of the hemisphere project to the vermis. Thus, our results challenge the classical view of the vermis and indicate that it no longer should be considered as entirely isolated from the cerebral cortex. Instead, lobules VB–VIIIB represent a site where the cortical motor areas can influence descending control systems involved in the regulation of whole-body posture and locomotion. We argue that the projection from the cerebral cortex to the vermis is part of the neural substrate for anticipatory postural adjustments and speculate that dysfunction of this system may underlie some forms of dystonia.

The cerebellum and the basal ganglia are major subcortical nuclei that control multiple aspects of behavior largely through their interactions with the cerebral cortex. Discrete multisynaptic loops connect both the cerebellum and the basal ganglia with multiple areas of the cerebral cortex. Interactions between these loops have traditionally been thought to occur mainly at the level of the cerebral cortex. Here, we review a series of recent anatomical studies in nonhuman primates that challenge this perspective. We show that the anatomical substrate exists for substantial interactions between the cerebellum and the basal ganglia. Furthermore, we discuss how these pathways may provide a useful framework for understanding cerebellar contributions to the manifestation of two prototypical basal ganglia disorders, Parkinson’s disease and dystonia.

The CA1, an important subregion of the hippocampus, is anatomically and functionally heterogeneous in the dorsal and ventral hippocampus. Here, to dissect the distinctions between the dorsal (dCA1) and ventral CA1 (vCA1) in anatomical connections, we systematically analyzed the direct inputs to dCA1 and vCA1 projection neurons (PNs) with the rabies virus-mediated retrograde trans-monosynaptic tracing system in Thy1-Cre mice. Our mapping results revealed that the input proportions and distributions of dCA1 and vCA1 PNs varied significantly. Inside the hippocampal region, dCA1 and vCA1 PNs shared the same upstream brain regions, but with distinctive distribution patterns along the rostrocaudal axis. The intrahippocampal inputs to the dCA1 and vCA1 exhibited opposite trends, decreasing and increasing gradually along the dorsoventral axis, respectively. For extrahippocampal inputs, dCA1 and vCA1 shared some monosynaptic projections from certain regions such as pallidum, striatum, hypothalamus, and thalamus. However, vCA1, not dCA1, received innervations from the subregions of olfactory areas and amygdala nuclei. Characterization of the direct input networks of dCA1 and vCA1 PNs may provide a structural basis to understand the differential functions of dCA1 and vCA1.

Background Interhemispheric communication of olfactory information is crucial for accurate odor perception and odor source localization in animals. However, the underlying structural basis for this communication in mammals remains poorly understood. Using electrophysiological recordings and virus-mediated tracing, we systematically dissected the neural circuits involved in interhemispheric transmission between the bilateral olfactory bulbs (OBs). Results We identified the anterior olfactory nucleus (AON) as a central hub that facilitates direct communication between the OBs via three distinct pathways: the excitatory inter-bulbar pathway, the inhibitory inter-bulbar pathway, and the bi-bulbar co-innervation pathway. Notably, our results highlight the differential roles of AON subregions in these pathways: the pars externa (AONpE) primarily mediates the inhibitory pathway, while the pars principalis (AONpP) participates in all three pathways. These pathways recruit CaMKIIα-positive neurons in specific AON regions, which in turn project to distinct neuronal populations within the OBs.  Conclusions This study provides novel anatomical insights into the neural circuits underlying interhemispheric olfactory communication. The differential connectivity patterns of AON subregions contribute to a better understanding of how bilateral olfactory information is processed and transferred between the two OBs.

The orbitofrontal cortex (ORB) exhibits a complex structure and diverse functional roles, including emotion regulation, decision-making, and reward processing. Structurally, it comprises three distinct regions: the medial part (ORBm), the ventrolateral part (ORBvl), and the lateral part (ORBl), each with unique functional attributes, such as ORBm’s involvement in reward processing, ORBvl’s regulation of depression-like behavior, and ORBl’s response to aversive stimuli. Dysregulation of the ORB has been implicated in various psychiatric disorders. However, the neurocircuitry underlying the functions and dysfunctions of the ORB remains poorly understood. This study employed recombinant adeno-associated viruses (rAAV) and rabies viruses with glycoprotein deletion (RV-ΔG) to retrogradely trace monosynaptic inputs to three ORB subregions in male C57BL/6J mice. Inputs were quantified across the whole brain using fluorescence imaging and statistical analysis. Results revealed distinct input patterns for each ORB subregion, with significant contributions from the isocortex and thalamus. The ORBm received prominent inputs from the prelimbic area, agranular insular area, and hippocampal field CA1, while the ORBvl received substantial intra-ORB inputs. The ORBl exhibited strong inputs from the somatomotor and somatosensory areas. Thalamic inputs, particularly from the mediodorsal nucleus and submedial nucleus of the thalamus, were widespread across all ORB subregions. These findings provide novel insights into the functional connectivity of ORB subregions and their roles in neural circuit mechanisms underlying behavior and psychiatric disorders.

The medial part of the olfactory tubercle (OT) is a brain structure located at the interface of the reward and olfactory system. It is closely related to pheromone-rewards, natural reinforcement, addiction and many other behaviors. However, the structure of the anatomic circuitry of the medial part of the OT is still unclear. In the present study, the medial part of the OT was found to be highly connected with a wide range of brain areas with the help of the pseudorabies virus tracing tool. In order to further investigate the detailed connections for specific neurons, another tracing tool - rabies virus was utilized for D1R-cre and D2R-cre mice. The D1R and D2R neurons in the medial part of the OT were both preferentially innervated by the olfactory areas, especially the piriform cortex, and both had similar direct input patterns. With the help of the adeno-associated virus labeling, it was found that the two subpopulations of neurons primarily innervate with the reward related brain regions, with slightly less axons projecting to the olfactory areas. Thus, the whole-brain input and output circuitry structures for specific types of neurons in the medial part of the OT were systematically investigated, and the results revealed many unique connecting features. This work could provide new insights for further study into the physiological functions of the medial part of the OT.

For virus classification and tracing, one idea is to generate minimal models from the gene sequences of each virus group for comparative analysis within and between classes, as well as classification and tracing of new sequences. The starting point of defining a minimal model for a group of gene sequences is to find their longest common sequence (LCS), but this is a non-deterministic polynomial-time hard (NP-hard) problem. Therefore, we applied some heuristic approaches of finding LCS, as well as some of the newer methods of treating gene sequences, including multiple sequence alignment (MSA) and k-mer natural vector (NV) encoding. To evaluate our algorithms, a five-fold cross validation classification scheme on a dataset of H1N1 virus non-structural protein 1 (NS1) gene was analyzed. The results indicate that the MSA-based algorithm has the best performance measured by classification accuracy, while the NV-based algorithm exhibits advantages in the time complexity of generating minimal models.

The origin of COVID-19 remains unclear despite extensive research. Theoretical models can simplify complex epigenetic landscapes by reducing vast methylation sites into manageable sets, revealing fundamental pathogen interactions that leap medical advances for the first time in tracing virus origin in the literature and practices. In our study, a max-logistic intelligence classifier analyzed 865,859 Infinium MethylationEPIC sites (CpGs), identifying eight CpGs that achieved 100 % accuracy in distinguishing COVID-19 patients from other respiratory disease patients and healthy controls. One CpG, cg07126281, linked to the SAMM50 gene, shares genetic ties with rare infectious diseases like Sennetsu fever and glanders, suggesting a potential connection between COVID-19 and these diseases, possibly transmitted through contaminated seafood or glanders-infected individuals. Identifying such links among 865,859 CpG sites is challenging, with a random correlation probability of less than one in ten million. However, the likelihood of finding meaningful associations with rare diseases lowers this probability to one in one hundred million, reinforcing the credibility of our findings. These results highlight the importance of investigating seafood markets and global supply chains in tracing COVID-19's origins and emphasize the need for ongoing biosafety and biosecurity measures to prevent future outbreaks.