Imaging learned fear circuitry in awake mice using fMRI

Where do we stand on fMRI in awake mice?

Imaging awake animals is quickly gaining traction in neuroscience as it offers a means to eliminate the confounding effects of anesthesia, difficulties of inter-species translation (when humans are typically imaged while awake), and the inability to investigate the full range of brain and behavioral states in unconscious animals. In this systematic review, we focus on the development of awake mouse blood oxygen level dependent functional magnetic resonance imaging (fMRI). Mice are widely used in research due to their fast-breeding cycle, genetic malleability, and low cost. Functional MRI yields whole-brain coverage and can be performed on both humans and animal models making it an ideal modality for comparing study findings across species. We provide an analysis of 30 articles (years 2011-2022) identified through a systematic literature search. Our conclusions include that head-posts are favorable, acclimation training for 10-14 d is likely ample under certain conditions, stress has been poorly characterized, and more standardization is needed to accelerate progress. For context, an overview of awake rat fMRI studies is also included. We make recommendations that will benefit a wide range of neuroscience applications.

High-resolution awake mouse fMRI at 14 Tesla

High-resolution awake mouse fMRI remains challenging despite extensive efforts to address motion-induced artifacts and stress. This study introduces an implantable radiofrequency (RF) surface coil design that minimizes image distortion caused by the air/tissue interface of mouse brains while simultaneously serving as a headpost for fixation during scanning. Using a 14T scanner, high-resolution fMRI enabled brain-wide functional mapping of visual and vibrissa stimulation at 100×100×200μm resolution with a 2s per frame sampling rate. Besides activated ascending visual and vibrissa pathways, robust BOLD responses were detected in the anterior cingulate cortex upon visual stimulation and spread through the ventral retrosplenial area (VRA) with vibrissa air-puff stimulation, demonstrating higher-order sensory processing in association cortices of awake mice. In particular, the rapid hemodynamic responses in VRA upon vibrissa stimulation showed a strong correlation with the hippocampus, thalamus, and prefrontal cortical areas. Cross-correlation analysis with designated VRA responses revealed early positive BOLD signals at the contralateral barrel cortex (BC) occurring 2 seconds prior to the air-puff in awake mice with repetitive stimulation, which was not detectable with the randomized stimulation paradigm. This early BC activation indicated learned anticipation through the vibrissa system and association cortices in awake mice under continuous training of repetitive air-puff stimulation. This work establishes a high-resolution awake mouse fMRI platform, enabling brain-wide functional mapping of sensory signal processing in higher association cortical areas.

Odor-evoked layer-specific fMRI activities in the awake mouse olfactory bulb

Awake rodent fMRI is increasingly common over the use of anesthesia since it permits behavioral paradigms and does not confound normal brain function or neurovascular coupling. It is well established that adequate acclimation to the loud fMRI environment and head fixation reduces stress in the rodents and allows for whole brain imaging with little contamination from motion. However, it is unknown whether high-resolution fMRI with increased susceptibility to motion and lower sensitivity can measure small, but spatially discrete, activations in awake mice. To examine this, we used contrast-enhanced cerebral blood volume-weighted (CBVw) fMRI in the mouse olfactory bulb for its enhanced sensitivity and neural specificity. We determined that activation patterns in the glomerular layer to four different odors were spatially distinct and were consistent with previously established histological patterns. In addition, odor-evoked laminar activations were greatest in superficial layers that decreased with laminar depth, similar to previous observations. Interestingly, the fMRI response strengths in the granule cell layer were greater in awake mice than our previous anesthetized rat studies, suggesting that feedback neural activities were intact with wakefulness. We finally determined that fMRI signal changes to repeated odor exposure (i.e., olfactory adaptation) attenuated relatively more in the feedback granule cell layer compared to the input glomerular layer, which is consistent with prior observations. We, therefore, conclude that high-resolution CBVw fMRI can measure odor-specific activation patterns and distinguish changes in laminar activity of head and body restrained awake mice.

From safety to frustration: The neural substrates of inhibitory learning in aversive and appetitive conditioning procedures

Inhibitory associative learning counters the effects of excitatory learning, whether appetitively or aversively motivated. Moreover, the affective responses accompanying the inhibitory associations are of opponent valence to the excitatory conditioned responses. Inhibitors for negative aversive outcomes (e.g. shock) signal safety, while inhibitors for appetitive outcomes (e.g. food reward) elicit frustration and/or disappointment. This raises the question as to whether studies using appetitive and aversive conditioning procedures should demonstrate the same neural substrates for inhibitory learning. We review the neural substrates of appetitive and aversive inhibitory learning as measured in different procedural variants and in the context of the underpinning excitatory conditioning on which it depends. The mesocorticolimbic dopamine pathways, retrosplenial cortex and hippocampus are consistently implicated in inhibitory learning. Further neural substrates identified in some procedural variants may be related to the specific motivation of the learning task and modalities of the learning cues. Finally, we consider the translational implications of our understanding of the neural substrates of inhibitory learning, for obesity and addictions as well as for anxiety disorders.

The cerebellum and fear extinction: evidence from rodent and human studies

The role of the cerebellum in emotional control has gained increasing interest, with studies showing it is involved in fear learning and memory in both humans and rodents. This review will focus on the contributions of the cerebellum to the extinction of learned fear responses. Extinction of fearful memories is critical for adaptive behaviour, and is clinically relevant to anxiety disorders such as post-traumatic stress disorder, in which deficits in extinction processes are thought to occur. We present evidence that supports cerebellar involvement in fear extinction, from rodent studies that investigate molecular mechanisms and functional connectivity with other brain regions of the known fear extinction network, to fMRI studies in humans. This evidence is considered in relation to the theoretical framework that the cerebellum is involved in the formation and updating of internal models of the inner and outer world by detecting errors between predicted and actual outcomes. In the case of fear conditioning, these internal models are thought to predict the occurrence of an aversive unconditioned stimulus (US), and when the aversive US is unexpectedly omitted during extinction learning the cerebellum uses prediction errors to update the internal model. Differences between human and rodent studies are highlighted to help inform future work.

Functional network properties derived from wide-field calcium imaging differ with wakefulness and across cell type

To improve 'bench-to-bedside' translation, it is integral that knowledge flows bidirectionally-from animal models to humans, and vice versa. This requires common analytical frameworks, as well as open software and data sharing practices. We share a new pipeline (and test dataset) for the preprocessing of wide-field optical fluorescence imaging data-an emerging mode applicable in animal models-as well as results from a functional connectivity and graph theory analysis inspired by recent work in the human neuroimaging field. The approach is demonstrated using a dataset comprised of two test-cases: (1) data from animals imaged during awake and anesthetized conditions with excitatory neurons labeled, and (2) data from awake animals with different genetically encoded fluorescent labels that target either excitatory neurons or inhibitory interneuron subtypes. Both seed-based connectivity and graph theory measures (global efficiency, transitivity, modularity, and characteristic path-length) are shown to be useful in quantifying differences between wakefulness states and cell populations. Wakefulness state and cell type show widespread effects on canonical network connectivity with variable frequency band dependence. Differences between excitatory neurons and inhibitory interneurons are observed, with somatostatin expressing inhibitory interneurons emerging as notably dissimilar from parvalbumin and vasoactive polypeptide expressing cells. In sum, we demonstrate that our pipeline can be used to examine brain state and cell-type differences in mesoscale imaging data, aiding translational neuroscience efforts. In line with open science practices, we freely release the pipeline and data to encourage other efforts in the community.

Awake Mouse fMRI and Pupillary Recordings in the Ultra-High Magnetic Field

Awake rodent fMRI is becoming a promising non-invasive brain imaging module when investigating large-scale brain function given behavioral tasks. Previous studies have either applied sedatives during scanning or pre-treatment of anesthetics, e.g., isoflurane, to reduce the motion of animals, which could confound the brain function of "awake" states in rodents. Here, we have established a long training awake mouse fMRI-pupillometry paradigm/setup without the initial use of anesthesia. To validate the awake mouse fMRI platform, evoked BOLD-fMRI was performed to identify brain activation in the visual cortex, dorsal lateral geniculate nuclei, and superior colliculus. Furthermore, pupil signal fluctuation was investigated during scanning, showing a less dilated pupil after 5-8 weeks of intermittent training. Thus, using the awake mouse fMRI with real-time pupillometry provides a longitudinal functional mapping tool to study fully conscious mice.

Building bridges: simultaneous multimodal neuroimaging approaches for exploring the organization of brain networks

Brain organization is evident across spatiotemporal scales as well as from structural and functional data. Yet, translating from micro- to macroscale (vice versa) as well as between different measures is difficult. Reconciling disparate observations from different modes is challenging because each specializes within a restricted spatiotemporal milieu, usually has bounded organ coverage, and has access to different contrasts. True intersubject biological heterogeneity, variation in experiment implementation (e.g., use of anesthesia), and true moment-to-moment variations in brain activity (maybe attributable to different brain states) also contribute to variability between studies. Ultimately, for a deeper and more actionable understanding of brain organization, an ability to translate across scales, measures, and species is needed. Simultaneous multimodal methods can contribute to bettering this understanding. We consider four modes, three optically based: multiphoton imaging, single-photon (wide-field) imaging, and fiber photometry, as well as magnetic resonance imaging. We discuss each mode as well as their pairwise combinations with regard to the definition and study of brain networks.

Male and Female C57BL/6 Mice Respond Differently to Awake Magnetic Resonance Imaging Habituation

Traditionally, preclinical magnetic resonance imaging (MRI) has been performed in anesthetized animals. However, anesthesia has been shown to perturb normal brain function and physiology. Such effects limit our ability to detect subtle physiological alterations in disease models and treatment studies, thus hampering discovery and compromising generality of findings. Therefore, methods for awake animal MRI are needed to study the rodent brain in its natural physiological state, free of anesthetics. Current setups for awake animal MRI rely on restraining systems to avoid animal movement during scanning. To reduce restraint stress, animals are habituated to the scanner environment prior to MRI data collection. To date, however, most awake MRI studies employ male rodents only. This is a fundamental limitation as results obtained may be pertinent only to half of the population. We characterized training and habituation responses of male and female mice to provide improved, sex-dependent training procedures for awake mouse MRI. We recorded heart rate, monitored behavioral responses (body weight and fecal boli weight) and fecal corticosterone levels (FCM) as indicators of wellbeing and stress during a 14-day progressive habituation protocol. In addition, we also assessed discomfort levels and anxiety using the mouse grimace scale (MGS) and light/dark test (LDT), respectively. All scores were compared between both groups. We found that heart rate was significantly decreased after 10 and 11 days of training for both males and females, respectively. However, the specific time course for this decrease was significantly different between males and females, and females exhibited higher anxiety levels during habituation and 14 days after habituation than males. Lastly, we also found that mean FCM levels for both groups were decreased after 11 days of MRI habituation. The present work shows that mice can be successfully trained for extended MRI sessions which is necessary for many (particularly non-fMRI) studies. Importantly, we find that males and females differ in their response to awake MRI habituation, which should be considered in future awake MRI studies that aim to include male and female mice.

Striatal hub of dynamic and stabilized prediction coding in forebrain networks for olfactory reinforcement learning

Identifying the circuits responsible for cognition and understanding their embedded computations is a challenge for neuroscience. We establish here a hierarchical cross-scale approach, from behavioral modeling and fMRI in task-performing mice to cellular recordings, in order to disentangle local network contributions to olfactory reinforcement learning. At mesoscale, fMRI identifies a functional olfactory-striatal network interacting dynamically with higher-order cortices. While primary olfactory cortices respectively contribute only some value components, the downstream olfactory tubercle of the ventral striatum expresses comprehensively reward prediction, its dynamic updating, and prediction error components. In the tubercle, recordings reveal two underlying neuronal populations with non-redundant reward prediction coding schemes. One population collectively produces stabilized predictions as distributed activity across neurons; in the other, neurons encode value individually and dynamically integrate the recent history of uncertain outcomes. These findings validate a cross-scale approach to mechanistic investigations of higher cognitive functions in rodents.

Where and how the brain learns from experience is not fully understood. Here the authors use a hierarchical approach from behavioural modelling to systems fMRI to cellular coding reveals brain mechanisms for history informed updating of future predictions.

Light sedation with short habituation time for large-scale functional magnetic resonance imaging studies in rats

Traditionally, preclinical resting state functional magnetic resonance imaging (fMRI) studies have been performed in anesthetized animals. Nevertheless, as anesthesia affects the functional connectivity (FC) in the brain, there has been a growing interest in imaging in the awake state. Obviously, awake imaging requires resource- and time-consuming habituation prior to data acquisition to reduce the stress and motion of the animals. Light sedation has been a less widely exploited alternative for awake imaging, requiring shorter habituation times, while still reducing the effect of anesthesia. Here, we imaged 102 rats under light sedation and 10 awake animals to conduct an FC analysis. We established an automated data-processing pipeline suitable for both groups. Additionally, the same pipeline was used on data obtained from an openly available awake rat database (289 measurements in 90 rats). The FC pattern in the light sedation measurements closely resembled the corresponding patterns in both onsite and offsite awake datasets. However, fewer datasets had to be excluded due to movement in rats with light sedation. The temporal analysis of FC in the lightly sedated group indicated a lingering effect of anesthesia that stabilized after the first 5 min. In summary, our results indicate that the light sedation protocol is a valid alternative for large-scale studies where awake protocols may become prohibitively resource-demanding, as it provides similar results to awake imaging, preserves more scans, and requires shorter habituation times. The large amount of fMRI data obtained in this work are openly available for further analyses.

Applications in Awake Animal Magnetic Resonance Imaging

There are numerous publications on methods and applications for awake functional MRI across different species, e.g., voles, rabbits, cats, dogs, and rhesus macaques. Each of these species, most obviously rhesus monkey, have general or unique attributes that provide a better understanding of the human condition. However, much of the work today is done on rodents. The growing number of small bore (≤30 cm) high field systems 7T- 11.7T favor the use of small animals. To that point, this review is primarily focused on rodents and their many applications in awake function MRI. Applications include, pharmacological MRI, drugs of abuse, sensory evoked stimuli, brain disorders, pain, social behavior, and fear.

Cranioplastic Surgery and Acclimation Training for Awake Mouse fMRI

MRI is a promising tool for translational research to link brain function and structure in animal models of disease to patients with neuropsychiatric disorders. However, given that mouse functional MRI (fMRI) typically relies on anesthetics to suppress head motion and physiological noise, it has been difficult to directly compare brain fMRI in anesthetized mice with that in conscious patients. Here, we developed a new system to acquire fMRI in awake mice, which includes a head positioner and dedicated radio frequency coil. The system was used to investigate functional brain networks in conscious mice, with the goal of enabling future studies to bridge fMRI of disease model animals with human fMRI. Cranioplastic surgery was performed to affix the head mount and the cupped-hand handling method was performed to minimize stress during MRI scanning. Here we describe the new mouse fMRI system, cranioplastic surgery and acclimation protocol. Graphic abstract: Awake fMRI system to investigate the neuronal activity in awaked mice.

Characteristics of fMRI responses to visual stimulation in anesthetized vs. awake mice

The functional characteristics of the mouse visual system have not previously been well explored using fMRI. In this research, we examined 9.4 T BOLD fMRI responses to visual stimuli of varying pulse durations (1 - 50 ms) and temporal frequencies (1 - 10 Hz) under ketamine and xylazine anesthesia, and compared fMRI responses of anesthetized and awake mice. Under anesthesia, significant positive BOLD responses were detected bilaterally in the major structures of the visual pathways, including the dorsal lateral geniculate nuclei, superior colliculus, lateral posterior nucleus of thalamus, primary visual area, and higher-order visual area. BOLD responses increased slightly with pulse duration, were maximal at 3 - 5 Hz stimulation, and significantly decreased at 10 Hz, which were all consistent with previous neurophysiological findings. When the mice were awake, the BOLD fMRI response was faster in all active regions and stronger in the subcortical areas compared with the anesthesia condition. In the V1, the BOLD response was biphasic for 5 Hz stimulation and negative for 10 Hz stimulation under wakefulness, whereas prolonged positive BOLD responses were observed at both frequencies under anesthesia. Unexpected activation was detected in the extrastriate postrhinal area and non-visual subiculum complex under anesthesia, but not under wakefulness. Widespread positive BOLD activity under anesthesia likely results from the disinhibition and sensitization of excitatory neurons induced by ketamine. Overall, fMRI can be a viable tool for mapping brain-wide functional networks.

A Platform for Brain-wide Volumetric Functional Ultrasound Imaging and Analysis of Circuit Dynamics in Awake Mice

Imaging large-scale circuit dynamics is crucial to understanding brain function, but most techniques have a limited depth of field. Here, we describe volumetric functional ultrasound imaging (vfUSI), a platform for brain-wide vfUSI of hemodynamic activity in awake head-fixed mice. We combined a high-frequency 1,024-channel 2D-array transducer with advanced multiplexing and high-performance computing for real-time 3D power Doppler imaging at a high spatiotemporal resolution (220 × 280 × 175 μm³, up to 6 Hz). We developed a standardized software pipeline for registration, segmentation, and temporal analysis in 268 individual brain regions based on the Allen Mouse Common Coordinate Framework. We demonstrated the high sensitivity of vfUSI under multiple experimental conditions, and we successfully imaged stimulus-evoked activity when only a few trials were averaged. We also mapped neural circuits in vivo across the whole brain during optogenetic activation of specific cell types. Moreover, we identified the sequential activation of sensory-motor networks during a grasping water-droplet task.

Accelerating in vivo fast spin echo high angular resolution diffusion imaging with an isotropic resolution in mice through compressed sensing

PURPOSE

Echo planar imaging (EPI) is commonly used to acquire the many volumes needed for high angular resolution diffusion Imaging (HARDI), posing a higher risk for artifacts, such as distortion and deformation. An alternative to EPI is fast spin echo (FSE) imaging, which has fewer artifacts but is inherently slower. The aim is to accelerate FSE such that a HARDI data set can be acquired in a time comparable to EPI using compressed sensing.

METHODS

Compressed sensing was applied in either q-space or simultaneously in k-space and q-space, by undersampling the k-space in the phase-encoding direction or retrospectively eliminating diffusion directions for different degrees of undersampling. To test the replicability of the acquisition and reconstruction, brain data were acquired from six mice, and a numerical phantom experiment was performed. All HARDI data were analyzed individually using constrained spherical deconvolution, and the apparent fiber density and complexity metric were evaluated, together with whole-brain tractography.

RESULTS

The apparent fiber density and complexity metric showed relatively minor differences when only q-space undersampling was used, but deteriorate when k-space undersampling was applied. Likewise, the tract density weighted image showed good results when only q-space undersampling was applied using 15 directions or more, but information was lost when fewer volumes or k-space undersampling were used.

CONCLUSION

It was found that acquiring 15 to 20 diffusion directions with a full k-space and reconstructed using compressed sensing could suffice for a replicable measurement of quantitative measures in mice, where areas near the sinuses and ear cavities are untainted by signal loss.

Hyper BOLD Activation in Dorsal Raphe Nucleus of APP/PS1 Alzheimer's Disease Mouse during Reward-Oriented Drinking Test under Thirsty Conditions

Alzheimer's disease (AD), a neurodegenerative disease, causes behavioural abnormalities such as disinhibition, impulsivity, and hyperphagia. Preclinical studies using AD model mice have investigated these phenotypes by measuring brain activity in awake, behaving mice. In this study, we monitored the behavioural alterations of impulsivity and hyperphagia in middle-aged AD model mice. As a behavioural readout, we trained the mice to accept a water-reward under thirsty conditions. To analyse brain activity, we developed a measure for licking behaviour combined with visualisation of whole brain activity using awake fMRI. In a water-reward learning task, the AD model mice showed significant hyperactivity of the dorsal raphe nucleus in thirsty conditions. In summary, we successfully visualised altered brain activity in AD model mice during reward-oriented behaviour for the first time using awake fMRI. This may help in understanding the causes of behavioural alterations in AD patients.

Awake functional MRI detects neural circuit dysfunction in a mouse model of autism

MRI has potential as a translational approach from rodents to humans. However, given that mouse functional MRI (fMRI) uses anesthetics for suppression of motion, it has been difficult to directly compare the result of fMRI in "unconsciousness" disease model mice with that in "consciousness" patients. We develop awake fMRI to investigate brain function in 15q dup mice, a copy number variation model of autism. Compared to wild-type mice, we find that 15q dup is associated with whole-brain functional hypoconnectivity and diminished fMRI responses to odors of stranger mice. Ex vivo diffusion MRI reveals widespread anomalies in white matter ultrastructure in 15q dup mice, suggesting a putative anatomical substrate for these functional hypoconnectivity. We show that d-cycloserine (DCS) treatment partially normalizes these anormalies in the frontal cortex of 15q dup mice and rescues some social behaviors. Our results demonstrate the utility of awake rodent fMRI and provide a rationale for further investigation of DCS therapy.

Making translation work: Harmonizing cross-species methodology in the behavioural neuroscience of Pavlovian fear conditioning

Translational neuroscience bridges insights from specific mechanisms in rodents to complex functions in humans and is key to advance our general understanding of central nervous function. A prime example of translational research is the study of cross-species mechanisms that underlie responding to learned threats, by employing Pavlovian fear conditioning protocols in rodents and humans. Hitherto, evidence for (and critique of) these cross-species comparisons in fear conditioning research was based on theoretical viewpoints. Here, we provide a perspective to substantiate these theoretical concepts with empirical considerations of cross-species methodology. This meta-research perspective is expected to foster cross-species comparability and reproducibility to ultimately facilitate successful transfer of results from basic science into clinical applications.

Awake and behaving mouse fMRI during Go/No-Go task

Functional magnetic imaging (fMRI) has been widely used to examine the functional neural networks in both the evoked and resting states. However, most fMRI studies in rodents are performed under anesthesia, which greatly limits the scope of their application, and behavioral relevance. Efforts have been made to image rodents in the awake condition, either in the resting state or in response to sensory or optogenetic stimulation. However, fMRI in awake behaving rodents has not yet been achieved. In the current study, a novel fMRI paradigm for awake and behaving mice was developed, allowing functional imaging of the mouse brain in an olfaction-based go/no-go task. High resolution functional imaging with limited motion and image distortion were achieved at 9.4T with a cryogenic coil in awake and behaving mice. Distributed whole-brain spatiotemporal patterns were revealed, with drastically different activity profiles for go versus no-go trials. Therefore, we have demonstrated the feasibility of functional imaging of an olfactory behavior in awake mice. This fMRI paradigm in awake behaving mice could lead to novel insights into neural mechanisms underlying behaviors at a whole-brain level.

Awake Mouse Imaging: From Two-Photon Microscopy to Blood Oxygen Level-Dependent Functional Magnetic Resonance Imaging

BACKGROUND

Functional magnetic resonance imaging (fMRI) in awake behaving mice is well positioned to bridge the detailed cellular-level view of brain activity, which has become available owing to recent advances in microscopic optical imaging and genetics, to the macroscopic scale of human noninvasive observables. However, though microscopic (e.g., two-photon imaging) studies in behaving mice have become a reality in many laboratories, awake mouse fMRI remains a challenge. Owing to variability in behavior among animals, performing all types of measurements within the same subject is highly desirable and can lead to higher scientific rigor.

METHODS

We demonstrated blood oxygenation level-dependent fMRI in awake mice implanted with long-term cranial windows that allowed optical access for microscopic imaging modalities and optogenetic stimulation. We started with two-photon imaging of single-vessel diameter changes (n = 1). Next, we implemented intrinsic optical imaging of blood oxygenation and flow combined with laser speckle imaging of blood flow obtaining a mesoscopic picture of the hemodynamic response (n = 16). Then we obtained corresponding blood oxygenation level-dependent fMRI data (n = 5). All measurements could be performed in the same mice in response to identical sensory and optogenetic stimuli.

RESULTS

The cranial window did not deteriorate the quality of fMRI and allowed alternation between imaging modalities in each subject.

CONCLUSIONS

This report provides a proof of feasibility for multiscale imaging approaches in awake mice. In the future, this protocol could be extended to include complex cognitive behaviors translatable to humans, such as sensory discrimination or attention.

Mapping stress networks using functional magnetic resonance imaging in awake animals

The neurobiology of stress is studied through behavioral neuroscience, endocrinology, neuronal morphology and neurophysiology. There is a shift in focus toward progressive changes throughout stress paradigms and individual susceptibility to stress that requires methods that allow for longitudinal study design and study of individual differences in stress response. Functional magnetic resonance imaging (fMRI), with the advantages of noninvasiveness and a large field of view, can be used for functionally mapping brain-wide regions and circuits critical to the stress response, making it suitable for longitudinal studies and understanding individual variability of short-term and long-term consequences of stress exposure. In addition, fMRI can be applied to both animals and humans, which is highly valuable in translating findings across species and examining whether the physiology and neural circuits involved in the stress response are conserved in mammals. However, compared to human fMRI studies, there are a number of factors that are essential for the success of fMRI studies in animals. This review discussed the use of fMRI in animal studies of stress. It reviewed advantages, challenges and technical considerations of the animal fMRI methodology as well as recent literature of stress studies using fMRI in animals. It also highlighted the development of combining fMRI with other methods and the future potential of fMRI in animal studies of stress. We conclude that animal fMRI studies, with their flexibility, low cost and short time frame compared to human studies, are crucial to advancing our understanding of the neurobiology of stress.

A guide to using functional magnetic resonance imaging to study Alzheimer's disease in animal models

Alzheimer's disease is a leading healthcare challenge facing our society today. Functional magnetic resonance imaging (fMRI) of the brain has played an important role in our efforts to understand how Alzheimer's disease alters brain function. Using fMRI in animal models of Alzheimer's disease has the potential to provide us with a more comprehensive understanding of the observations made in human clinical fMRI studies. However, using fMRI in animal models of Alzheimer's disease presents some unique challenges. Here, we highlight some of these challenges and discuss potential solutions for researchers interested in performing fMRI in animal models. First, we briefly summarize our current understanding of Alzheimer's disease from a mechanistic standpoint. We then overview the wide array of animal models available for studying this disease and how to choose the most appropriate model to study, depending on which aspects of the condition researchers seek to investigate. Finally, we discuss the contributions of fMRI to our understanding of Alzheimer's disease and the issues to consider when designing fMRI studies for animal models, such as differences in brain activity based on anesthetic choice and ways to interrogate more specific questions in rodents beyond those that can be addressed in humans. The goal of this article is to provide information on the utility of fMRI, and approaches to consider when using fMRI, for studies of Alzheimer's disease in animal models.

Rodent models in neuroscience research: is it a rat race?

Rodents (especially Mus musculus and Rattus norvegicus) have been the most widely used models in biomedical research for many years. A notable shift has taken place over the last two decades, with mice taking a more and more prominent role in biomedical science compared to rats. This shift was primarily instigated by the availability of a much larger genetic toolbox for mice, particularly embryonic-stem-cell-based targeting technology for gene disruption. With the recent emergence of tools for altering the rat genome, notably genome-editing technologies, the technological gap between the two organisms is closing, and it is becoming more important to consider the physiological, anatomical, biochemical and pharmacological differences between rats and mice when choosing the right model system for a specific biological question. The aim of this short review and accompanying poster is to highlight some of the most important differences, and to discuss their impact on studies of human diseases, with a special focus on neuropsychiatric disorders.

Acute effects of vortioxetine and duloxetine on resting-state functional connectivity in the awake rat

The antidepressant vortioxetine exerts its effects via modulation of several serotonin (5-HT) receptors and inhibition of the 5-HT transporter (SERT). Additionally, vortioxetine has beneficial effects on aspects of cognitive dysfunction in depressed patients. However, a global examination of the drug effect on brain network connectivity is still missing. Here we compared the effects of vortioxetine and a serotonin norepinephrine reuptake inhibitor, duloxetine, on resting-state functional connectivity (RSFC) across the whole brain in awake rats using a combination of pharmacological and awake animal resting-state functional magnetic resonance imaging (rsfMRI) techniques. Our data showed that vortioxetine and duloxetine affected different inter-areal connections with limited overlap, indicating that in addition to different primary target profiles, these two antidepressants have distinct mechanisms of action at the systems level. Further, our data suggest that vortioxetine can affect specific brain areas with distinct 5-HT receptor expression profiles. Taken together, this study demonstrates that the awake animal fMRI approach provides a powerful tool to elucidate the effects of drugs on the brain with high spatial specificity and a global field of view. This capability is valuable to understand how different drugs affect the systems-level brain function, and provides important guidance to dissect specific brain regions and connections for further detailed mechanistic studies. This study also highlights the translational opportunity of the awake animal fMRI approach between preclinical results and human studies.

From engineering to editing the rat genome

Since its domestication over 100 years ago, the laboratory rat has been the preferred experimental animal in many areas of biomedical research (Lindsey and Baker The laboratory rat. Academic, New York, pp 1-52, 2006). Its physiology, size, genetics, reproductive cycle, cognitive and behavioural characteristics have made it a particularly useful animal model for studying many human disorders and diseases. Indeed, through selective breeding programmes numerous strains have been derived that are now the mainstay of research on hypertension, obesity and neurobiology (Okamoto and Aoki Jpn Circ J 27:282-293, 1963; Zucker and Zucker J Hered 52(6):275-278, 1961). Despite this wealth of genetic and phenotypic diversity, the ability to manipulate and interrogate the genetic basis of existing phenotypes in rat strains and the methodology to generate new rat models has lagged significantly behind the advances made with its close cousin, the laboratory mouse. However, recent technical developments in stem cell biology and genetic engineering have again brought the rat to the forefront of biomedical studies and enabled researchers to exploit the increasingly accessible wealth of genome sequence information. In this review, we will describe how a breakthrough in understanding the molecular basis of self-renewal of the pluripotent founder cells of the mammalian embryo, embryonic stem (ES) cells, enabled the derivation of rat ES cells and their application in transgenesis. We will also describe the remarkable progress that has been made in the development of gene editing enzymes that enable the generation of transgenic rats directly through targeted genetic modifications in the genomes of zygotes. The simplicity, efficiency and cost-effectiveness of the CRISPR/Cas gene editing system, in particular, mean that the ability to engineer the rat genome is no longer a limiting factor. The selection of suitable targets and gene modifications will now become a priority: a challenge where ES culture and gene editing technologies can play complementary roles in generating accurate bespoke rat models for studying biological processes and modelling human disease.

Altered Functional Connectivity Following an Inflammatory White Matter Injury in the Newborn Rat: A High Spatial and Temporal Resolution Intrinsic Optical Imaging Study

Very preterm newborns have an increased risk of developing an inflammatory cerebral white matter injury that may lead to severe neuro-cognitive impairment. In this study we performed functional connectivity (fc) analysis using resting-state optical imaging of intrinsic signals (rs-OIS) to assess the impact of inflammation on resting-state networks (RSN) in a pre-clinical model of perinatal inflammatory brain injury. Lipopolysaccharide (LPS) or saline injections were administered in postnatal day (P3) rat pups and optical imaging of intrinsic signals were obtained 3 weeks later. (rs-OIS) fc seed-based analysis including spatial extent were performed. A support vector machine (SVM) was then used to classify rat pups in two categories using fc measures and an artificial neural network (ANN) was implemented to predict lesion size from those same fc measures. A significant decrease in the spatial extent of fc statistical maps was observed in the injured group, across contrasts and seeds (^*p = 0.0452 for HbO₂ and ^**p = 0.0036 for HbR). Both machine learning techniques were applied successfully, yielding 92% accuracy in group classification and a significant correlation r = 0.9431 in fractional lesion volume prediction (^**p = 0.0020). Our results suggest that fc is altered in the injured newborn brain, showing the long-standing effect of inflammation.

Manganese-enhanced magnetic resonance imaging depicts brain activity in models of acute and chronic pain: A new window to study experimental spontaneous pain?

Application of functional imaging techniques to animal models is vital to understand pain mechanisms, but is often confounded by the need to limit movement artefacts with anaesthesia, and a focus on evoked responses rather than clinically relevant spontaneous pain and related hyperalgesia. The aim of the present study was to investigate the potential of manganese-enhanced magnetic resonance imaging (MEMRI) to measure neural responses during on-going pain that underpins hyperalgesia in pre-clinical models of nociception. As a proof of concept that MEMRI is sensitive to the neural activity of spontaneous, intermittent behaviour, we studied a separate positive control group undergoing a voluntary running wheel experiment. In the pain models, pain behaviour (weight bearing asymmetry and hindpaw withdrawal thresholds (PWTs)) was measured at baseline and following either intra-articular injection of nerve growth factor (NGF, 10µg/50µl; acute pain model, n=4 rats per group), or the chondrocyte toxin monosodium iodoacetate (MIA, 1mg/50µl; chronic model, n=8 rats per group), or control injection. Separate groups of rats underwent a voluntary wheel running protocol (n=8 rats per group). Rats were administered with paramagnetic ion Mn²⁺ as soluble MnCl₂ over seven days (subcutaneous osmotic pump) to allow cumulative activity-dependent neural accumulation in the models of pain, or over a period of running. T1-weighted MR imaging at 7T was performed under isoflurane anaesthesia using a receive-only rat head coil in combination with a 72mm volume coil for excitation. The pain models resulted in weight bearing asymmetry (NGF: 20.0 ± 5.2%, MIA: 15 ± 3%), and a reduction in PWT in the MIA model (8.3 ± 1.5g) on the final day of assessment before undergoing MR imaging. Voxel-wise and region-based analysis of MEMRI data did not identify group differences in T1 signal. However, MnCl₂ accumulation in the VTA, right Ce amygdala, and left cingulate was negatively correlated with pain responses (greater differences in weight bearing), similarly MnCl₂ accumulation was reduced in the VTA in line with hyperalgesia (lower PWTs), which suggests reduced regional activation as a result of the intensity and duration of pain experienced during the 7 days of MnCl₂ exposure. Motor cortex T1-weighted signal increase was associated with the distance ran in the wheel running study, while no between group difference was seen. Our data suggest that on-going pain related signal changes identified using MEMRI offers a new window to study the neural underpinnings of spontaneous pain in rats.

Time to wake up: Studying neurovascular coupling and brain-wide circuit function in the un-anesthetized animal

Functional magnetic resonance imaging (fMRI) has allowed the noninvasive study of task-based and resting-state brain dynamics in humans by inferring neural activity from blood-oxygenation-level dependent (BOLD) signal changes. An accurate interpretation of the hemodynamic changes that underlie fMRI signals depends on the understanding of the quantitative relationship between changes in neural activity and changes in cerebral blood flow, oxygenation and volume. While there has been extensive study of neurovascular coupling in anesthetized animal models, anesthesia causes large disruptions of brain metabolism, neural responsiveness and cardiovascular function. Here, we review work showing that neurovascular coupling and brain circuit function in the awake animal are profoundly different from those in the anesthetized state. We argue that the time is right to study neurovascular coupling and brain circuit function in the awake animal to bridge the physiological mechanisms that underlie animal and human neuroimaging signals, and to interpret them in light of underlying neural mechanisms. Lastly, we discuss recent experimental innovations that have enabled the study of neurovascular coupling and brain-wide circuit function in un-anesthetized and behaving animal models.

Physiological effects of a habituation procedure for functional MRI in awake mice using a cryogenic radiofrequency probe

BACKGROUND

Functional magnetic resonance imaging (fMRI) in mice is typically performed under anesthesia due to difficulties in holding the head of awake mice stably with a conventional three-point fixation method that uses a tooth-bar and earplugs. Although some studies have succeeded in fMRI in awake mice by attaching a head-post on the skull, this cannot be applied to fMRI using a high signal-to-noise ratio (SNR) cryogenic MRI-detector, CryoProbe, because it covers the head of a mouse closely.

NEW METHOD

We developed head-fixation implements for awake mice that are applicable to fMRI using CryoProbe.

RESULTS

A head-bar was surgically attached to the skull of a mouse that was then habituated to a mock fMRI-environment, two hours/day for eight days with physiological examinations of body-weight, fecal weight, electromyogram (EMG), and electrocardiogram. EMG power decreased with just one day of habituation, whereas heart rate decreased after at least seven days of habituation. Estimated head motions of awake mice during fMRI were significantly smaller than a voxel size. Unexpectedly, temporal SNR of fMRI signals for awake mice was higher than that for anesthetized mice held by a conventional method. Functional connectivity in the brain of both anesthetized and awake mice showed bilateral and unilateral networks. COMPARISON WITH EXISTING METHOD(S): fMRI using CryoProbe had been performed on anesthetized mice previously. Our method does not use anesthetics during habituation or fMRI.

CONCLUSION

Our method would be beneficial for translational research using fMRI in mice and humans because human fMRI is typically performed without anesthetics.

Restraint training for awake functional brain scanning of rodents can cause long-lasting changes in pain and stress responses

With the increased interest in longitudinal brain imaging of awake rodents, it is important to understand both the short-term and long-term effects of restraint on sensory and emotional processing in the brain. To understand the effects of repeated restraint on pain behaviors and stress responses, we modeled a restraint protocol similar to those used to habituate rodents for magnetic resonance imaging scanning, and studied sensory sensitivity and stress hormone responses over 5 days. To uncover lasting effects of training, we also looked at responses to the formalin pain test 2 weeks later. We found that while restraint causes acute increases in the stress hormone corticosterone, it can also cause lasting reductions in nociceptive behavior in the formalin test, coupled with heightened corticosterone levels and increased activation of the "nociceptive" central nucleus of the amygdala, as seen by Fos protein expression. These results suggest that short-term repeated restraint, similar to that used to habituate rats for awake functional brain scanning, could potentially cause long-lasting changes in physiological and brain responses to pain stimuli that are stress-related, and therefore could potentially confound the functional activation patterns seen in awake rodents in response to pain stimuli.

Novel method for functional brain imaging in awake minimally restrained rats

Functional magnetic resonance imaging (fMRI) in rodents holds great promise for advancing our knowledge about human brain function. However, the use of anesthetics to immobilize rodents during fMRI experiments has restricted the type of questions that can be addressed using this technique. Here we describe an innovative procedure to train rats to be constrained without the need of any anesthesia during the whole procedure. We show that with 8-10 days of acclimation rats can be conscious and remain still during fMRI experiments under minimal stress. In addition, we provide fMRI results of conscious rodents in a variety of commonly used fMRI experimental paradigms, and we demonstrate the improved quality of these scans by comparing results when the same rodents were scanned under anesthesia. We confirm that the awake scanning procedure permits an improved evaluation of brain networks and brain response to external stimuli with minimal movement artifact. The present study further advances the field of fMRI in awake rodents, which provide more direct, forward and reverse, translational opportunities regarding brain functional correspondences between human and rodent research.

The role of brain-derived neurotrophic factor in learned fear processing: an awake rat fMRI study

Brain‐derived neurotrophic factor (BDNF) signaling is implicated in the etiology of many psychiatric disorders associated with altered emotional processing. Altered peripheral (plasma) BDNF levels have been proposed as a biomarker for neuropsychiatric disease risk in humans. However, the relationship between peripheral and central BDNF levels and emotional brain activation is unknown. We used heterozygous BDNF knockdown rats (BDNF^+/−) to examine the effects of genetic variation in the BDNF gene on peripheral and central BDNF levels and emotional brain activation as assessed by awake functional magnetic resonance imaging (fMRI). BDNF^+/− and control rats were trained to associate a flashing light (conditioned stimulus; CS) with foot‐shock, and brain activation in response to the CS was measured 24 h later in awake rats using fMRI. Central and peripheral BDNF levels were decreased in BDNF^+/− rats compared with control rats. Activation of fear circuitry (amygdala, periaqueductal gray, granular insular) was seen in control animals; however, activation of this circuitry was absent in BDNF^+/− animals. Behavioral experiments confirmed impaired conditioned fear responses in BDNF^+/− rats, despite intact innate fear responses. These data confirm a positive correlation [r = 0.86, 95% confidence interval (0.55, 0.96); P = 0.0004] between peripheral and central BDNF levels and indicate a functional relationship between BDNF levels and emotional brain activation as assessed by fMRI. The results demonstrate the use of rodent fMRI as a sensitive tool for measuring brain function in preclinical translational studies using genetically modified rats and support the use of peripheral BDNF as a biomarker of central affective processing.