From basic brain research to treating human brain disorders

Implication of regional selectivity of dopamine deficits in impaired suppressing of involuntary movements in Parkinson's disease

To improve the initiation and speed of intended action, one of the crucial mechanisms is suppressing unwanted movements that interfere with goal-directed behavior, which is observed relatively aberrant in Parkinson's disease patients. Recent research has highlighted that dopamine deficits in Parkinson's disease predominantly occur in the caudal lateral part of the substantia nigra pars compacta (SNc) in human patients. We previously found two parallel circuits within the basal ganglia, primarily divided into circuits mediated by the rostral medial part and caudal lateral part of the SNc dopamine neurons. We have further discovered that the indirect pathway in caudal basal ganglia circuits, facilitated by the caudal lateral part of the SNc dopamine neurons, plays a critical role in suppressing unnecessary involuntary movements when animals perform voluntary goal-directed actions. We thus explored recent research in humans and non-human primates focusing on the distinct functions and networks of the caudal lateral part of the SNc dopamine neurons to elucidate the mechanisms involved in the impairment of suppressing involuntary movements in Parkinson's disease patients.

Using camera-guided electrode microdrive navigation for precise 3D targeting of macaque brain sites

Spatial accuracy in electrophysiological investigations is paramount, as precise localization and reliable access to specific brain regions help the advancement of our understanding of the brain's complex neural activity. Here, we introduce a novel, multi camera-based, frameless neuronavigation technique for precise, 3-dimensional electrode positioning in awake monkeys. The investigation of neural functions in awake primates often requires stable access to the brain with thin and delicate recording electrodes. This is usually realized by implanting a chronic recording chamber onto the skull of the animal that allows direct access to the dura. Most recording and positioning techniques utilize this implanted recording chamber as a holder of the microdrive or to hold a grid. This in turn reduces the degrees of freedom in positioning. To solve this problem, we require innovative, flexible, but precise tools for neuronal recordings. We instead mount the electrode microdrive above the animal on an arch, equipped with a series of translational and rotational micromanipulators, allowing movements in all axes. Here, the positioning is controlled by infrared cameras tracking the location of the microdrive and the monkey, allowing precise and flexible trajectories. To verify the accuracy of this technique, we created iron deposits in the tissue that could be detected by MRI. Our results demonstrate a remarkable precision with the confirmed physical location of these deposits averaging less than 0.5 mm from their planned position. Pilot electrophysiological recordings additionally demonstrate the accuracy and flexibility of this method. Our innovative approach could significantly enhance the accuracy and flexibility of neural recordings, potentially catalyzing further advancements in neuroscientific research.

Deep Learning-Based Ensembling Technique to Classify Alzheimer's Disease Stages Using Functional MRI

The major issue faced by elderly people in society is the loss of memory, difficulty learning new things, and poor judgment. This is due to damage to brain tissues, which may lead to cognitive impairment and eventually Alzheimer's. Therefore, the detection of such mild cognitive impairment (MCI) becomes important. Usually, this is detected when it is converted into Alzheimer's disease (AD). AD is irreversible and cannot be cured whereas mild cognitive impairment (MCI) can be cured. The goal of this research is to diagnose Alzheimer's patients for timely treatment. For this purpose, functional MRI images from the publicly available dataset are used. Various deep-learning models have been used by the scientific community for the automatic detection of Alzheimer's subjects. These include the binary classification of scans of patients into MCI and AD stages, and limited work is carried out for multiclass classification of Alzheimer's disease up to six different stages. This study is divided into two steps. In the first step, a binary classification of the subject's scan is performed using Custom CNN. The second step involves the use of different deep learning models along with Custom CNN for multiclass classification of a subject's scan into one of the six stages of Alzheimer's disease. The models are evaluated based on different evaluation metrics, and the overall result of the models is improved using the max-voting ensembling technique. The experimental results show that an overall average accuracy of 98.8% is achieved for Alzheimer's stages classification.

Hierarchical action encoding in prefrontal cortex of freely moving macaques

Our natural behavioral repertoires include coordinated actions of characteristic types. To better understand how neural activity relates to the expression of actions and action switches, we studied macaques performing a freely moving foraging task in an open environment. We developed a novel analysis pipeline that can identify meaningful units of behavior, corresponding to recognizable actions such as sitting, walking, jumping, and climbing. On the basis of transition probabilities between these actions, we found that behavior is organized in a modular and hierarchical fashion. We found that, after regressing out many potential confounders, actions are associated with specific patterns of firing in each of six prefrontal brain regions and that, overall, encoding of action category is progressively stronger in more dorsal and more caudal prefrontal regions. Together, these results establish a link between selection of units of primate behavior on one hand and neuronal activity in prefrontal regions on the other.

Animal models to study the neurological manifestations of the post-COVID-19 condition

More than 40% of individuals infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have experienced persistent or relapsing multi-systemic symptoms months after the onset of coronavirus disease 2019 (COVID-19). This post-COVID-19 condition (PCC) has debilitating effects on the daily life of patients and encompasses a broad spectrum of neurological and neuropsychiatric symptoms including olfactory and gustative impairment, difficulty with concentration and short-term memory, sleep disorders and depression. Animal models have been instrumental to understand acute COVID-19 and validate prophylactic and therapeutic interventions. Similarly, studies post-viral clearance in hamsters, mice and nonhuman primates inoculated with SARS-CoV-2 have been useful to unveil some of the aspects of PCC. Transcriptomic alterations in the central nervous system, persistent activation of immune cells and impaired hippocampal neurogenesis seem to have a critical role in the neurological manifestations observed in animal models infected with SARS-CoV-2. Interestingly, the proinflammatory transcriptomic profile observed in the central nervous system of SARS-CoV-2-inoculated mice partially overlaps with the pathological changes that affect microglia in humans during Alzheimer's disease and aging, suggesting shared mechanisms between these conditions. None of the currently available animal models fully replicates PCC in humans; therefore, multiple models, together with the fine-tuning of experimental conditions, will probably be needed to understand the mechanisms of PCC neurological symptoms. Moreover, given that the intrinsic characteristics of the new variants of concern and the immunological status of individuals might influence PCC manifestations, more studies are needed to explore the role of these factors and their combinations in PCC, adding further complexity to the design of experimental models.

Hierarchical organization of rhesus macaque behavior

Primatologists, psychologists and neuroscientists have long hypothesized that primate behavior is highly structured. However, delineating that structure has been impossible due to the difficulties of precision behavioral tracking. Here we analyzed a dataset consisting of continuous measures of the 3D position of two male rhesus macaques (Macaca mulatta) performing three different tasks in a large unrestrained environment over several hours. Using an unsupervised embedding approach on the tracked joints, we identified commonly repeated pose patterns, which we call postures. We found that macaques' behavior is characterized by 49 distinct postures, lasting an average of 0.6 seconds. We found evidence that behavior is hierarchically organized, in that transitions between poses tend to occur within larger modules, which correspond to identifiable actions; these actions are further organized hierarchically. Our behavioral decomposition allows us to identify universal (cross-individual and cross-task) and unique (specific to each individual and task) principles of behavior. These results demonstrate the hierarchical nature of primate behavior, provide a method for the automated ethogramming of primate behavior, and provide important constraints on neural models of pose generation.

Trends and Treatment Approaches for Complications in Neuroscience Experiments with Monkey Species

Our goal in this manuscript is to advance the assessment and treatment of monkey species in neuroscience research. We hope to begin a discussion and establish baseline data on how complications are identified and treated. We surveyed the neuroscience research community working with monkeys and compiled responses to questions about investigator demographics, assessment of animal wellbeing, treatment choices, and approaches to mitigate risks associated with CNS procedures and promote monkey health and wellbeing. The majority of the respondents had worked with nonhuman primates (NHP) for over 15 y. Identification of procedure-related complications and efficacy of treatment generally rely on common behavioral indices. Treatments for localized inflammatory responses are generally successful, whereas the treatment success for meningitis or meningoencephalitis, abscesses, and hemorrhagic stroke are less successful. Behavioral signs of pain are treated successfully with NSAIDs and opioids. Our future plans are to collate treatment protocols and develop best practices that can be shared across the neuroscience community to improve treatment success rates and animal welfare and therefore science. Human protocols can be used to develop best practices, assess outcomes, and promote further refinements in treatment practices for monkeys to enhance research outcomes.

Comparative connectomics reveals noncanonical wiring for color vision in human foveal retina

The Old World macaque monkey and New World common marmoset provide fundamental models for human visual processing, yet the human ancestral lineage diverged from these monkey lineages over 25 Mya. We therefore asked whether fine-scale synaptic wiring in the nervous system is preserved across these three primate families, despite long periods of independent evolution. We applied connectomic electron microscopy to the specialized foveal retina where circuits for highest acuity and color vision reside. Synaptic motifs arising from the cone photoreceptor type sensitive to short (S) wavelengths and associated with "blue-yellow" (S-ON and S-OFF) color-coding circuitry were reconstructed. We found that distinctive circuitry arises from S cones for each of the three species. The S cones contacted neighboring L and M (long- and middle-wavelength sensitive) cones in humans, but such contacts were rare or absent in macaques and marmosets. We discovered a major S-OFF pathway in the human retina and established its absence in marmosets. Further, the S-ON and S-OFF chromatic pathways make excitatory-type synaptic contacts with L and M cone types in humans, but not in macaques or marmosets. Our results predict that early-stage chromatic signals are distinct in the human retina and imply that solving the human connectome at the nanoscale level of synaptic wiring will be critical for fully understanding the neural basis of human color vision.

BBB opening with focused ultrasound in nonhuman primates and Parkinson's disease patients: Targeted AAV vector delivery and PET imaging

Intracerebral vector delivery in nonhuman primates has been a major challenge. We report successful blood-brain barrier opening and focal delivery of adeno-associated virus serotype 9 vectors into brain regions involved in Parkinson's disease using low-intensity focus ultrasound in adult macaque monkeys. Openings were well tolerated with generally no associated abnormal magnetic resonance imaging signals. Neuronal green fluorescent protein expression was observed specifically in regions with confirmed blood-brain barrier opening. Similar blood-brain barrier openings were safely demonstrated in three patients with Parkinson's disease. In these patients and in one monkey, blood-brain barrier opening was followed by ¹⁸F-Choline uptake in the putamen and midbrain regions based on positron emission tomography. This indicates focal and cellular binding of molecules that otherwise would not enter the brain parenchyma. The less-invasive nature of this methodology could facilitate focal viral vector delivery for gene therapy and might allow early and repeated interventions to treat neurodegenerative disorders.

Recent Development of Brain Organoids for Biomedical Application

Over the years, scientists have studied the behavior and anatomy of many animals to understand the own species. However, despite the continuous efforts, it is often difficult to know for certain how the brain works due to the differences between the brains of animals and the human brain. While the use of animal models for research continues, the origin of human cognition and neurological disorders needs further elucidation. To that end, in vitro organoids that exhibit in vivo characteristics of the human brain have been recently developed. These brain-like organoids enable researchers to dive deeper into understanding the human brain, its neurological structures, and the causes of neurological pathologies. This paper reviews the recent developments in the regeneration of brain-like organoids using Matrigel and other alternatives. Further, gel-free methods that may enhance the regeneration process of organoids are discussed. Finally, the vascularized brain organoid growth and development in both in vitro and in vivo conditions are detailed.

Visualizing advances in the future of primate neuroscience research

Future neuroscience and biomedical projects involving non-human primates (NHPs) remain essential in our endeavors to understand the complexities and functioning of the mammalian central nervous system. In so doing, the NHP neuroscience researcher must be allowed to incorporate state-of-the-art technologies, including the use of novel viral vectors, gene therapy and transgenic approaches to answer continuing and emerging research questions that can only be addressed in NHP research models. This perspective piece captures these emerging technologies and some specific research questions they can address. At the same time, we highlight some current caveats to global NHP research and collaborations including the lack of common ethical and regulatory frameworks for NHP research, the limitations involving animal transportation and exports, and the ongoing influence of activist groups opposed to NHP research.

An integrated resource for functional and structural connectivity of the marmoset brain

Comprehensive integration of structural and functional connectivity data is required to model brain functions accurately. While resources for studying the structural connectivity of non-human primate brains already exist, their integration with functional connectivity data has remained unavailable. Here we present a comprehensive resource that integrates the most extensive awake marmoset resting-state fMRI data available to date (39 marmoset monkeys, 710 runs, 12117 mins) with previously published cellular-level neuronal tracing data (52 marmoset monkeys, 143 injections) and multi-resolution diffusion MRI datasets. The combination of these data allowed us to (1) map the fine-detailed functional brain networks and cortical parcellations, (2) develop a deep-learning-based parcellation generator that preserves the topographical organization of functional connectivity and reflects individual variabilities, and (3) investigate the structural basis underlying functional connectivity by computational modeling. This resource will enable modeling structure-function relationships and facilitate future comparative and translational studies of primate brains.

Data-driven learning to identify biomarkers in bipolar disorder

BACKGROUND AND OBJECTIVE

Bipolar disorder (BD) is one of the primary causes of disability globally and can be easily misdiagnosed as schizophrenia or major depression due to their similar symptoms. Hence, it is of great significance to explore the pathogenesis of BD. Statistical analysis is currently the most common method for exploring the neuropathological mechanisms of psychiatric disorders. However, this method only considers the relationship between groups and does not reflect the individual-level diagnosis. Therefore, we developed machine learning algorithms to measure pathological brain changes in psychiatric disorders.

METHODS

An autoencoder and a feature selection method are proposed to identify the abnormal structural patterns of BD in this study. The autoencoder was constructed using structural imaging data from 1113 healthy controls, which aims to define the normal range of anatomical deviations to distinguish healthy individuals from BD patients. The biomarkers of BD were identified by the reconstruction errors in each brain region. The proposed feature selection (FS)-select framework aimed to determine the optimal FS method and identify the most reproducible feature associated with BD.

RESULTS

We found that the left orbital region of the middle frontal gyrus had the greatest difference between healthy controls and BD patients using a trained autoencoder. The most reproducible feature was the left orbital region of the middle frontal gyrus by FS-select framework when using the different cross-validation strategies.

CONCLUSIONS

A consistent result was obtained from the above two proposed methods wherein a significant difference between healthy controls and BD patients was identified in the left orbital region of the middle frontal gyrus.

Automated pose estimation in primates

Understanding the behavior of primates is important for primatology, for psychology, and for biology more broadly. It is also important for biomedicine, where primates are an important model organism, and whose behavior is often an important variable of interest. Our ability to rigorously quantify behavior has, however, long been limited. On one hand, we can rigorously quantify low-information measures like preference, looking time, and reaction time; on the other, we can use more gestalt measures like behavioral categories tracked via ethogram, but at high cost and with high variability. Recent technological advances have led to a major revolution in behavioral measurement that offers affordable and scalable rigor. Specifically, digital video cameras and automated pose tracking software can provide measures of full-body position (i.e., pose) of primates over time (i.e., behavior) with high spatial and temporal resolution. Pose-tracking technology in turn can be used to infer behavioral states, such as eating, sleeping, and mating. We call this technological approach behavioral imaging. In this review, we situate the behavioral imaging revolution in the history of the study of behavior, argue for investment in and development of analytical and research techniques that can profit from the advent of the era of big behavior, and propose that primate centers and zoos will take on a more central role in relevant fields of research than they have in the past.

An ecological animal model of subthreshold depression in adolescence: behavioral and resting state 18F-FDG PET imaging characterization

The different depressive disorders that exist can take root at adolescence. For instance, some functional and structural changes in several brain regions have been observed from adolescence in subjects that display either high vulnerability to depressive symptoms or subthreshold depression. For instance, adolescents with depressive disorder have been shown to exhibit hyperactivity in hippocampus, amygdala and prefrontal cortex as well as volume reductions in hippocampus and amygdala (prefrontal cortex showing more variable results). However, no animal model of adolescent subthreshold depression has been developed so far. Our objective was to design an animal model of adolescent subthreshold depression and to characterize the neural changes associated to this phenotype. For this purpose, we used adolescent Swiss mice that were evaluated on 4 tests assessing cognitive abilities (Morris water maze), anhedonia (sucrose preference), anxiety (open-field) and stress-coping strategies (forced swim test) at postnatal day (PND) 28-35. In order to identify neural alterations associated to behavioral profiles, we assessed brain resting state metabolic activity in vivo using ¹⁸F-FDG PET imaging at PND 37. We selected three profiles of mice distinguished in a composite Z-score computed from performances in the behavioral tests: High, Intermediate and Low Depressive Risk (HDR, IDR and LDR). Compared to both IDR and LDR, HDR mice were characterized by passive stress-coping behaviors, low cognition and high anhedonia and anxiety and were associated with significant changes of ¹⁸F-FDG uptakes in several cortical and subcortical areas including prelimbic cortex, infralimbic cortex, nucleus accumbens, amygdala, periaqueductal gray and superior colliculus, all displaying higher metabolic activity, while only the thalamus was associated with lower metabolic activity (compared to IDR). LDR displayed an opposing behavioral phenotype and were associated with significant changes of ¹⁸F-FDG uptakes in the dorsal striatum and thalamus that both exhibited markedly lower metabolic activity in LDR. In conclusion, our study revealed changes in metabolic activities that can represent neural signatures for behavioral profiles predicting subthreshold depression at adolescence in a mouse model.

The Promise of Behavioral Tracking Systems for Advancing Primate Animal Welfare

Simple Summary

Computerized tracking systems for primates and other animals are one of the great inventions of the 21st century. These systems have already revolutionized the study of primatology, psychology, neuroscience, and biomedicine. Less discussed is that they also promise to greatly enhance animal welfare. Their potential benefits include identifying and reducing pain, suffering, and distress in captive populations, improving laboratory animal welfare, and applying our understanding of animal behavior to increase the “natural” behaviors in captive and wild populations, especially those under threat. We are optimistic that these changes will greatly increase the welfare of primates, including those in laboratories, zoos, primate centers, and in the wild.

Abstract

Recent years have witnessed major advances in the ability of computerized systems to track the positions of animals as they move through large and unconstrained environments. These systems have so far been a great boon in the fields of primatology, psychology, neuroscience, and biomedicine. Here, we discuss the promise of these technologies for animal welfare. Their potential benefits include identifying and reducing pain, suffering, and distress in captive populations, improving laboratory animal welfare within the context of the three Rs of animal research (reduction, refinement, and replacement), and applying our understanding of animal behavior to increase the “natural” behaviors in captive and wild populations facing human impact challenges. We note that these benefits are often incidental to the designed purpose of these tracking systems, a reflection of the fact that animal welfare is not inimical to research progress, but instead, that the aligned interests between basic research and welfare hold great promise for improvements to animal well-being.

How Can Animal Models Inform the Understanding of Cognitive Inflexibility in Patients with Anorexia Nervosa?

Deficits in cognitive flexibility are consistently seen in patients with anorexia nervosa (AN). This type of cognitive impairment is thought to be associated with the persistence of AN because it leads to deeply ingrained patterns of thought and behaviour that are highly resistant to change. Neurobiological drivers of cognitive inflexibility have some commonalities with the abnormal brain functional outcomes described in patients with AN, including disrupted prefrontal cortical function, and dysregulated dopamine and serotonin neurotransmitter systems. The activity-based anorexia (ABA) model recapitulates the key features of AN in human patients, including rapid weight loss caused by self-starvation and hyperactivity, supporting its application in investigating the cognitive and neurobiological causes of pathological weight loss. The aim of this review is to describe the relationship between AN, neural function and cognitive flexibility in human patients, and to highlight how new techniques in behavioural neuroscience can improve the utility of animal models of AN to inform the development of novel therapeutics.

Genetically modified mice for research on human diseases: A triumph for Biotechnology or a work in progress?

Genetically modified mice are engineered as models for human diseases. These mouse models include inbred strains, mutants, gene knockouts, gene knockins, and ‘humanized’ mice. Each mouse model is engineered to mimic a specific disease based on a theory of the genetic basis of that disease. For example, to test the amyloid theory of Alzheimer’s disease, mice with amyloid precursor protein genes are engineered, and to test the tau theory, mice with tau genes are engineered. This paper discusses the importance of mouse models in basic research, drug discovery, and translational research, and examines the question of how to define the “best” mouse model of a disease. The critiques of animal models and the caveats in translating the results from animal models to the treatment of human disease are discussed. Since many diseases are heritable, multigenic, age-related and experience-dependent, resulting from multiple gene-gene and gene-environment interactions, it will be essential to develop mouse models that reflect these genetic, epigenetic and environmental factors from a developmental perspective. Such models would provide further insight into disease emergence, progression and the ability to model two-hit and multi-hit theories of disease. The summary examines the biotechnology for creating genetically modified mice which reflect these factors and how they might be used to discover new treatments for complex human diseases such as cancers, neurodevelopmental and neurodegenerative diseases.

Electrophysiological dataset from macaque visual cortical area MST in response to a novel motion stimulus

Establishing the cortical neural representation of visual stimuli is a central challenge of systems neuroscience. Publicly available data would allow a broad range of scientific analyses and hypothesis testing, but are rare and largely focused on the early visual system. To address the shortage of open data from higher visual areas, we provide a comprehensive dataset from a neurophysiology study in macaque monkey visual cortex that includes a complete record of extracellular action potential recordings from the extrastriate medial superior temporal (MST) area, behavioral data, and detailed stimulus records. It includes spiking activity of 172 single neurons recorded in 139 sessions from 4 hemispheres of 3 rhesus macaque monkeys. The data was collected across 3 experiments, designed to characterize the response properties of MST neurons to complex motion stimuli. This data can be used to elucidate visual information processing at the level of single neurons in a high-level area of primate visual cortex. Providing open access to this dataset also promotes the 3R-principle of responsible animal research.

Measurement(s)	spike train • eye movement measurement
Technology Type(s)	single-unit recording • eye tracking device
Factor Type(s)	direction, location, and speed of moving random dot patterns
Sample Characteristic - Organism	Macaca mulatta
Sample Characteristic - Environment	laboratory environment
Sample Characteristic - Location	Germany

A naturalistic environment to study visual cognition in unrestrained monkeys

Macaque monkeys are widely used to study vision. In the traditional approach, monkeys are brought into a lab to perform visual tasks while they are restrained to obtain stable eye tracking and neural recordings. Here, we describe a novel environment to study visual cognition in a more natural setting as well as other natural and social behaviors. We designed a naturalistic environment with an integrated touchscreen workstation that enables high-quality eye tracking in unrestrained monkeys. We used this environment to train monkeys on a challenging same-different task. We also show that this environment can reveal interesting novel social behaviors. As proof of concept, we show that two naive monkeys were able to learn this complex task through a combination of socially observing trained monkeys and solo trial-and-error. We propose that such naturalistic environments can be used to rigorously study visual cognition as well as other natural and social behaviors in freely moving monkeys.

The connectome from the cerebral cortex to the viscera using viral transneuronal tracers

As an emerging framework in neuroscience, brain connectomics is well suited for investigating key questions on brain complexity by combining viral transneuronal tracing and whole brain graphic methodologies using analytical tools of network science. Transsynaptic viral tract-tracing in the toolbox of neural labeling methods has been a significant development in the connectomics field to decipher the circuit-level architecture of the cerebral cortex. In the present work, we reviewed the current methods enabling structural connectivity from the viscera to the cerebral cortex mapping with viral transneuronal tracers and showed how such neuroanatomic connectomic data could be used to infer new structural and functional information in viscera-cerebral cortex circuits.

Multi-Omics for the Understanding of Brain Diseases

Brain diseases, including both neurodegenerative diseases and mental disorders, represent the third largest healthcare problem in developed countries, after cardiovascular disorders and cancer [...].

Human iPSC-Derived Neurons as A Platform for Deciphering the Mechanisms behind Brain Aging

With an increased life expectancy among humans, aging has recently emerged as a major focus in biomedical research. The lack of in vitro aging models-especially for neurological disorders, where access to human brain tissues is limited-has hampered the progress in studies on human brain aging and various age-associated neurodegenerative diseases at the cellular and molecular level. In this review, we provide an overview of age-related changes in the transcriptome, in signaling pathways, and in relation to epigenetic factors that occur in senescent neurons. Moreover, we explore the current cell models used to study neuronal aging in vitro, including immortalized cell lines, primary neuronal culture, neurons directly converted from fibroblasts (Fib-iNs), and iPSC-derived neurons (iPSC-iNs); we also discuss the advantages and limitations of these models. In addition, the key phenotypes associated with cellular senescence that have been observed by these models are compared. Finally, we focus on the potential of combining human iPSC-iNs with genome editing technology in order to further our understanding of brain aging and neurodegenerative diseases, and discuss the future directions and challenges in the field.

Improving rigor and reproducibility in nonhuman primate research

Nonhuman primates (NHPs) are a critical component of translational/preclinical biomedical research due to the strong similarities between NHP and human physiology and disease pathology. In some cases, NHPs represent the most appropriate, or even the only, animal model for complex metabolic, neurological, and infectious diseases. The increased demand for and limited availability of these valuable research subjects requires that rigor and reproducibility be a prime consideration to ensure the maximal utility of this scarce resource. Here, we discuss a number of approaches that collectively can contribute to enhanced rigor and reproducibility in NHP research.

Nonhuman primates (NHP) are a crucial component of biomedical research due to their similarities with human physiology and pathobiology.

Increased rigor and reproducibility in NHP research are critical to maximizing the information obtained from this scarce and valuable resource.

More widespread adoption of approaches such as normative protocols, preregistration, and data sharing, as well as more extensive training in biostatistics, can enhance rigor and reproducibility in NHP studies.

Co-editing PINK1 and DJ-1 Genes Via Adeno-Associated Virus-Delivered CRISPR/Cas9 System in Adult Monkey Brain Elicits Classical Parkinsonian Phenotype

Whether direct manipulation of Parkinson's disease (PD) risk genes in the adult monkey brain can elicit a Parkinsonian phenotype remains an unsolved issue. Here, we used an adeno-associated virus serotype 9 (AAV9)-delivered CRISPR/Cas9 system to directly co-edit PINK1 and DJ-1 genes in the substantia nigras (SNs) of two monkey groups: an old group and a middle-aged group. After the operation, the old group exhibited all the classic PD symptoms, including bradykinesia, tremor, and postural instability, accompanied by key pathological hallmarks of PD, such as severe nigral dopaminergic neuron loss (>64%) and evident α-synuclein pathology in the gene-edited SN. In contrast, the phenotype of their middle-aged counterparts, which also showed clear PD symptoms and pathological hallmarks, were less severe. In addition to the higher final total PD scores and more severe pathological changes, the old group were also more susceptible to gene editing by showing a faster process of PD progression. These results suggested that both genetic and aging factors played important roles in the development of PD in the monkeys. Taken together, this system can effectively develop a large number of genetically-edited PD monkeys in a short time (6-10 months), and thus provides a practical transgenic monkey model for future PD studies.

Strengths and challenges of longitudinal non-human primate neuroimaging

Longitudinal non-human primate neuroimaging has the potential to greatly enhance our understanding of primate brain structure and function. Here we describe its specific strengths, compared to both cross-sectional non-human primate neuroimaging and longitudinal human neuroimaging, but also its associated challenges. We elaborate on factors guiding the use of different analytical tools, subject-specific versus age-specific templates for analyses, and issues related to statistical power.

Disentangling the influences of multiple thalamic nuclei on prefrontal cortex and cognitive control

The prefrontal cortex (PFC) has a complex relationship with the thalamus, involving many nuclei which occupy predominantly medial zones along its anterior-to-posterior extent. Thalamocortical neurons in most of these nuclei are modulated by the affective and cognitive signals which funnel through the basal ganglia. We review how PFC-connected thalamic nuclei likely contribute to all aspects of cognitive control: from the processing of information on internal states and goals, facilitating its interactions with mnemonic information and learned values of stimuli and actions, to their influence on high-level cognitive processes, attentional allocation and goal-directed behavior. This includes contributions to transformations such as rule-to-choice (parvocellular mediodorsal nucleus), value-to-choice (magnocellular mediodorsal nucleus), mnemonic-to-choice (anteromedial nucleus) and sensory-to-choice (medial pulvinar). Common mechanisms appear to be thalamic modulation of cortical gain and cortico-cortical functional connectivity. The anatomy also implies a unique role for medial PFC in modulating processing in thalamocortical circuits involving other orbital and lateral PFC regions. We further discuss how cortico-basal ganglia circuits may provide a mechanism through which PFC controls cortico-cortical functional connectivity.

The Role of Neurod Genes in Brain Development, Function, and Disease

Transcriptional regulation is essential for the correct functioning of cells during development and in postnatal life. The basic Helix-loop-Helix (bHLH) superfamily of transcription factors is well conserved throughout evolution and plays critical roles in tissue development and tissue maintenance. A subgroup of this family, called neural lineage bHLH factors, is critical in the development and function of the central nervous system. In this review, we will focus on the function of one subgroup of neural lineage bHLH factors, the Neurod family. The Neurod family has four members: Neurod1, Neurod2, Neurod4, and Neurod6. Available evidence shows that these four factors are key during the development of the cerebral cortex but also in other regions of the central nervous system, such as the cerebellum, the brainstem, and the spinal cord. We will also discuss recent reports that link the dysfunction of these transcription factors to neurological disorders in humans.

CRISPR/Cas9 Technology as a Modern Genetic Manipulation Tool for Recapitulating of Neurodegenerative Disorders in Large Animal Models

BACKGROUND

Neurodegenerative diseases are often the consequence of alterations in structures and functions of the Central Nervous System (CNS) in patients. Despite obtaining massive genomic information concerning the molecular basis of these diseases and since the neurological disorders are multifactorial, causal connections between pathological pathways at the molecular level and CNS disorders development have remained obscure and need to be elucidated to a great extent.

OBJECTIVE

Animal models serve as accessible and valuable tools for understanding and discovering the roles of causative factors in the development of neurodegenerative disorders and finding appropriate treatments. Contrary to rodents and other small animals, large animals, especially non-human primates (NHPs), are remarkably similar to humans; hence, they establish suitable models for recapitulating the main human's neuropathological manifestations that may not be seen in rodent models. In addition, they serve as useful models to discover effective therapeutic targets for neurodegenerative disorders due to their similarity to humans in terms of physiology, evolutionary distance, anatomy, and behavior.

METHODS

In this review, we recommend different strategies based on the CRISPR-Cas9 system for generating animal models of human neurodegenerative disorders and explaining in vivo CRISPR-Cas9 delivery procedures that are applied to disease models for therapeutic purposes.

RESULTS

With the emergence of CRISPR/Cas9 as a modern specific gene-editing technology in the field of genetic engineering, genetic modification procedures such as gene knock-in and knock-out have become increasingly easier compared to traditional gene targeting techniques. Unlike the old techniques, this versatile technology can efficiently generate transgenic large animal models without the need to complicate lab instruments. Hence, these animals can accurately replicate the signs of neurodegenerative disorders.

CONCLUSION

Preclinical applications of CRISPR/Cas9 gene-editing technology supply a unique opportunity to establish animal models of neurodegenerative disorders with high accuracy and facilitate perspectives for breakthroughs in the research on the nervous system disease therapy and drug discovery. Furthermore, the useful outcomes of CRISPR applications in various clinical phases are hopeful for their translation to the clinic in a short time.

The nonhuman primate neuroimaging and neuroanatomy project

Multi-modal neuroimaging projects such as the Human Connectome Project (HCP) and UK Biobank are advancing our understanding of human brain architecture, function, connectivity, and their variability across individuals using high-quality non-invasive data from many subjects. Such efforts depend upon the accuracy of non-invasive brain imaging measures. However, 'ground truth' validation of connectivity using invasive tracers is not feasible in humans. Studies using nonhuman primates (NHPs) enable comparisons between invasive and non-invasive measures, including exploration of how "functional connectivity" from fMRI and "tractographic connectivity" from diffusion MRI compare with long-distance connections measured using tract tracing. Our NonHuman Primate Neuroimaging & Neuroanatomy Project (NHP_NNP) is an international effort (6 laboratories in 5 countries) to: (i) acquire and analyze high-quality multi-modal brain imaging data of macaque and marmoset monkeys using protocols and methods adapted from the HCP; (ii) acquire quantitative invasive tract-tracing data for cortical and subcortical projections to cortical areas; and (iii) map the distributions of different brain cell types with immunocytochemical stains to better define brain areal boundaries. We are acquiring high-resolution structural, functional, and diffusion MRI data together with behavioral measures from over 100 individual macaques and marmosets in order to generate non-invasive measures of brain architecture such as myelin and cortical thickness maps, as well as functional and diffusion tractography-based connectomes. We are using classical and next-generation anatomical tracers to generate quantitative connectivity maps based on brain-wide counting of labeled cortical and subcortical neurons, providing ground truth measures of connectivity. Advanced statistical modeling techniques address the consistency of both kinds of data across individuals, allowing comparison of tracer-based and non-invasive MRI-based connectivity measures. We aim to develop improved cortical and subcortical areal atlases by combining histological and imaging methods. Finally, we are collecting genetic and sociality-associated behavioral data in all animals in an effort to understand how genetic variation shapes the connectome and behavior.

International primate neuroscience research regulation, public engagement and transparency opportunities

Scientific excellence is a necessity for progress in biomedical research. As research becomes ever more international, establishing international collaborations will be key to advancing our scientific knowledge. Understanding the similarities in standards applied by different nations to animal research, and where the differences might lie, is crucial. Cultural differences and societal values will also contribute to these similarities and differences between countries and continents. Our overview is not comprehensive for all species, but rather focuses on non-human primate (NHP) research, involving New World marmosets and Old World macaques, conducted in countries where NHPs are involved in neuroimaging research. Here, an overview of the ethics and regulations is provided to help assess welfare standards amongst primate research institutions. A comparative examination of these standards was conducted to provide a basis for establishing a common set of standards for animal welfare. These criteria may serve to develop international guidelines, which can be managed by an International Animal Welfare and Use Committee (IAWUC). Internationally, scientists have a moral responsibility to ensure excellent care and welfare of their animals, which in turn, influences the quality of their research. When working with animal models, maintaining a high quality of care ("culture of care") and welfare is essential. The transparent promotion of this level of care and welfare, along with the results of the research and its impact, may reduce public concerns associated with animal experiments in neuroscience research.

Biological implications and limitations of a cynomolgus monkey with naturally occurring Parkinson's disease

We recently identified a cynomolgus monkey with naturally occurring Parkinson's disease (PD), indicating that PD may not be a uniquely human disease (Li et al, 2020). In our previous study, four lines of evidence, including typical PD clinical symptoms, pharmacological responses, pathological hallmarks, and genetic mutations, strongly supported the identification of a monkey with spontaneous PD (Figure 1). To the best of our knowledge, this is the first reported case of naturally developed PD in animals. This suggests that PD is not a disease restricted to humans, with its existence in a non-human primate providing a novel evolutionary angle for understanding PD. As a close relative to humans (Buffalo et al, 2019; Phillips et al, 2014; Yan et al, 2011), this rare case of PD in another primate species provides solid evidence that monkeys are ideal candidates for the development of a genuine "animal version of PD", with conserved etiology and pathogenesis (Li et al, 2020). Furthermore, it allows us to compare similarities and differences in PD development between species and to understand PD pathogenesis from an evolutionary point of view.

Primate extrastriate cortical area MST: a gateway between sensation and cognition

Primate visual cortex consists of dozens of distinct brain areas, each providing a highly specialized component to the sophisticated task of encoding the incoming sensory information and creating a representation of our visual environment that underlies our perception and action. One such area is the medial superior temporal cortex (MST), a motion-sensitive, direction-selective part of the primate visual cortex. It receives most of its input from the middle temporal (MT) area, but MST cells have larger receptive fields and respond to more complex motion patterns. The finding that MST cells are tuned for optic flow patterns has led to the suggestion that the area plays an important role in the perception of self-motion. This hypothesis has received further support from studies showing that some MST cells also respond selectively to vestibular cues. Furthermore, the area is part of a network that controls the planning and execution of smooth pursuit eye movements and its activity is modulated by cognitive factors, such as attention and working memory. This review of more than 90 studies focuses on providing clarity of the heterogeneous findings on MST in the macaque cortex and its putative homolog in the human cortex. From this analysis of the unique anatomical and functional position in the hierarchy of areas and processing steps in primate visual cortex, MST emerges as a gateway between perception, cognition, and action planning. Given this pivotal role, this area represents an ideal model system for the transition from sensation to cognition.

Using non-invasive neuroimaging to enhance the care, well-being and experimental outcomes of laboratory non-human primates (monkeys)

Over the past 10-20 years, neuroscience witnessed an explosion in the use of non-invasive imaging methods, particularly magnetic resonance imaging (MRI), to study brain structure and function. Simultaneously, with access to MRI in many research institutions, MRI has become an indispensable tool for researchers and veterinarians to guide improvements in surgical procedures and implants and thus, experimental as well as clinical outcomes, given that access to MRI also allows for improved diagnosis and monitoring for brain disease. As part of the PRIMEatE Data Exchange, we gathered expert scientists, veterinarians, and clinicians who treat humans, to provide an overview of the use of non-invasive imaging tools, primarily MRI, to enhance experimental and welfare outcomes for laboratory non-human primates engaged in neuroscientific experiments. We aimed to provide guidance for other researchers, scientists and veterinarians in the use of this powerful imaging technology as well as to foster a larger conversation and community of scientists and veterinarians with a shared goal of improving the well-being and experimental outcomes for laboratory animals.

PREEMACS: Pipeline for preprocessing and extraction of the macaque brain surface

Accurate extraction of the cortical brain surface is critical for cortical thickness estimation and a key element to perform multimodal imaging analysis, where different metrics are integrated and compared in a common space. While brain surface extraction has become widespread practice in human studies, several challenges unique to neuroimaging of non-human primates (NHP) have hindered its adoption for the study of macaques. Although, some of these difficulties can be addressed at the acquisition stage, several common artifacts can be minimized through image preprocessing. Likewise, there are several image analysis pipelines for human MRIs, but very few automated methods for extraction of cortical surfaces have been reported for NHPs and none have been tested on data from diverse sources. We present PREEMACS, a pipeline that standardizes the preprocessing of structural MRI images (T1- and T2-weighted) and carries out an automatic surface extraction of the macaque brain. Building upon and extending pre-existing tools, the first module performs volume orientation, image cropping, intensity non-uniformity correction, and volume averaging, before skull-stripping through a convolutional neural network. The second module performs quality control using an adaptation of MRIqc method to extract objective quality metrics that are then used to determine the likelihood of accurate brain surface estimation. The third and final module estimates the white matter (wm) and pial surfaces from the T1-weighted volume (T1w) using an NHP customized version of FreeSurfer aided by the T2-weighted volumes (T2w). To evaluate the generalizability of PREEMACS, we tested the pipeline using 57 T1w/T2w NHP volumes acquired at 11 different sites from the PRIME-DE public dataset. Results showed an accurate and robust automatic brain surface extraction from images that passed the quality control segment of our pipeline. This work offers a robust, efficient and generalizable pipeline for the automatic standardization of MRI surface analysis on NHP.

Age-related decline in executive function as a hallmark of cognitive ageing in primates: an overview of cognitive and neurobiological studies

Executive function (EF) is a complex construct that reflects multiple higher-order cognitive processes such as planning, updating, inhibiting and set-shifting. Decline in these functions is a hallmark of cognitive ageing in humans, and age differences and changes in EF correlate with age-related differences and changes in association cortices, particularly the prefrontal areas. Here, we review evidence for age-related decline in EF and associated neurobiological changes in prosimians, New World and Old World monkeys, apes and humans. While EF declines with age in all primate species studied, the relationship of this decline with age-related alterations in the prefrontal cortex remains unclear, owing to the scarcity of neurobiological studies focusing on the ageing brain in most primate species. In addition, the influence of sex, vascular and metabolic risk, and hormonal status has rarely been considered. We outline several methodological limitations and challenges with the goal of producing a comprehensive integration of cognitive and neurobiological data across species and elucidating how ageing shapes neurocognitive trajectories in primates with different life histories, lifespans and brain architectures. Such comparative investigations are critical for fostering translational research and understanding healthy and pathological ageing in our own species. This article is part of the theme issue 'Evolution of the primate ageing process'.

Long-term labeling of microelectrode tracks with fluorescent latex microspheres

BACKGROUND

After physiological recordings are performed in behaving animals, it is valuable to identify microelectrode tracks in histological sections so that neuronal responses can be correlated with brain anatomy. However, no good method currently exists for long-term labeling, so that microelectrode tracks can be recovered months or even years after recording sessions.

NEW METHOD

Penetrations were made into the brains of mice with microelectrodes coated with fluorescent dyes packaged into 0.2 μm polystyrene microspheres, followed by survival periods of 3 days, 2, 4, or 6 months. Sections were examined by fluorescence microscopy before and after cytochrome oxidase histochemistry to identify microelectrode tracks.

RESULTS

After all 4 survival periods, 0.2 μm fluorescent microspheres clearly marked the tracks of microelectrode penetrations.

COMPARISON WITH EXISTING METHODS

Fluorescent microspheres label microelectrode penetrations for longer than do fluorescent lipophilic dyes, such as FM 1-43FX. The label appears punctate, and resistant to degradation, because it is protected by the barrier of the polystyrene micro-container.

CONCLUSIONS

Coating of microelectrodes with fluorescent microspheres allows one to identify the penetration track in histological sections half a year later. This technique may be useful when electrophysiological recording sessions are being carried out in behaving animals, with plans to identify electrode tracks in histological sections many months later.