Open-source hardware designs for MRI of mice, rats, and marmosets: Integrated animal holders and radiofrequency coils

Investigating microstructural changes between in vivo and perfused ex vivo marmoset brains using oscillating gradient and b-tensor encoded diffusion MRI at 9.4 T

PURPOSE

To investigate microstructural alterations induced by perfusion fixation in brain tissues using advanced diffusion MRI techniques and estimate their potential impact on the application of ex vivo models to in vivo microstructure.

METHODS

We used oscillating gradient spin echo (OGSE) and b-tensor encoding diffusion MRI to examine in vivo and ex vivo microstructural differences in the marmoset brain. OGSE was used to shorten effective diffusion times, whereas b-tensor encoding allowed for the differentiation of isotropic and anisotropic kurtosis. Additionally, we performed Monte Carlo simulations to estimate the potential microstructural changes in the tissues.

RESULTS

We report large changes (˜50%-60%) in kurtosis frequency dispersion (OGSE) and in both anisotropic and isotropic kurtosis (b-tensor encoding) after perfusion fixation. Structural MRI showed an average volume reduction of about 10%. Monte Carlo simulations indicated that these alterations could likely be attributed to extracellular fluid loss possibly combined with axon beading and increased dot compartment signal fraction. Little evidence was observed for reductions in axonal caliber.

CONCLUSION

Our findings shed light on advanced MRI parameter changes that are induced by perfusion fixation and potential microstructural sources for these changes. This work also suggests that caution should be exercised when applying ex vivo models to infer in vivo tissue microstructure, as significant differences may arise.

Factors influencing JUUL e-cigarette nicotine vapour-induced reward, withdrawal, pharmacokinetics and brain connectivity in rats: sex matters

Though vaping likely represents a safer alternative to smoking, it is not without risks, many of which are not well understood, especially for vulnerable populations. Here we evaluate the sex- and age-dependent effects of JUUL nicotine vapour in rats. Following passive nicotine vapour exposures (from 59 mg/ml JUUL nicotine pods), rats were evaluated for reward-like behaviour, locomotion, and precipitated withdrawal. Pharmacokinetics of nicotine and its metabolites in brain and plasma and the long-term impact of nicotine vapour exposure on functional magnetic resonance imaging-based brain connectivity were assessed. Adult female rats acquired conditioned place preference (CPP) at a high dose (600 s of exposure) of nicotine vapour while female adolescents, as well as male adults and adolescents did not. Adult and adolescent male rats displayed nicotine vapour-induced precipitated withdrawal and hyperlocomotion, while both adult and adolescent female rats did not. Adult females showed higher venous and arterial plasma and brain nicotine and nicotine metabolite concentrations compared to adult males and adolescent females. Adolescent females showed higher brain nicotine concentration compared to adolescent males. Both network-based statistics and between-component group connectivity analyses uncovered reduced connectivity in nicotine-exposed rats, with a significant group by sex interaction observed in both analyses. The short- and long-term effects of nicotine vapour are affected by sex and age, with distinct behavioural, pharmacokinetic, and altered network connectivity outcomes dependent on these variables.

Open-source versatile 3D-print animal conditioning platform design for in vivo preclinical brain imaging in awake mice and anesthetized mice and rats

Proper animal conditioning is a key factor in the quality and success of preclinical neuroimaging applications. Here, we introduce an open-source easy-to-modify multimodal 3D printable design for rodent conditioning for magnetic resonance imaging (MRI) or other imaging modalities. Our design can be used for brain imaging in anesthetized or awake mice, and in anesthetized rats. We show ease of use and reproducibility of subject conditioning with anatomical T2-weighted imaging for both mice and rats. We also demonstrate the application of our design for awake functional MRI in mice using both visual evoked potential and olfactory stimulation paradigms. In addition, using a combined MRI, positron emission tomography and X-ray computed tomography experiment, we demonstrate that our proposed cradle design can be utilized for multiple imaging modalities.

Stretchable receive coil for 7T small animal MRI

Receive coils used in small animal MRI are rigid, inflexible surface loops that do not conform to the anatomy being imaged. The recent trend toward design of stretchable coils that are tailored to fit any anatomical curvature has been focused on human imaging. This work demonstrates the application of stretchable coils for small animal imaging at 7T. A stretchable coil measuring 3.5 × 3.5 cm was developed for acquisition of rat brain and spine images. The SNR maps of the stretchable coil were compared with those of a traditional flexible PCB coil and a commercial surface coil. Stretch and conformance testing of the coil was performed. Ex vivo images of rat brain and spine from the stretchable a coil was acquired using T1 FLASH and T2 Turbo RARE sequences. The axial phantom SNR maps showed that the stretchable coil provided 48.5% and 42.8% higher SNR than the commercial coil for T1-w and T2-w images within the defined ROI. A 33% increase in average penetration depth was observed within the ROI using the stretchable coil when compared to the commercial coil. The ex-vivo rat brain and spine images showed distinguishable anatomical details. Stretching the coil reduced the resonant frequency with reduction in SNR, while the conformance to varying sample volumes increased the resonant frequency with decreased SNR. This study also features an open-source plug-and-play system with preamplifiers that can be used to interface surface coils with the 7T Bruker scanner.

Intracellular Acidification in a Rat C6 Glioma Model following Cariporide Injection Investigated by CEST-MRI

Acidification of cancerous tissue induced pharmacologically may slow tumor growth and can be detected using magnetic resonance imaging. Numerous studies have shown that pharmacologically inhibiting specific transporters, such as the Na⁺/H⁺ exchanger 1 (NHE1), can alter glycolitic metabolism and affect tumor acidosis. The sodium proton exchanger inhibitor Cariporide can acidify U87MG gliomas in mice. This study aimed to determine whether Cariporide could acidify C6 glioma tumors in rats with an intact immune system. C6 glioma cells were implanted in the right brain hemisphere of ten rats. Chemical exchange saturation transfer (CEST) MRI (9.4T) was acquired on days 7-8 and 14-15 after implantation to measure in vivo tissue intracellular pH (pH_i) within the tumors and on the contralateral side. pH_i was basic relative to contralateral tissue at both time points assessed using the amine and amide concentration-independent detection (AACID) value. On day 14-15, measurements were made before and up to 160 min after Cariporide injection (N = 6). Twenty minutes after drug injection, the average AACID value in the tumor significantly increased by ∼6.4% compared to pre-injection, corresponding to 0.31 ± 0.20 lower pH_i, while in contralateral tissue, AACID value increased significantly by ∼4.3% compared to pre-injection, corresponding to 0.22 ± 0.19 lower pH_i. Control rats without tumors showed no changes following injection of Cariporide dissolved in 10% or 1% DMSO and diluted in PBS. This study demonstrates the sensitivity of CEST-based pH-weighted imaging for monitoring the response of tumors to pharmacologically induced acidification.

A radiofrequency coil to facilitate task-based fMRI of awake marmosets

BACKGROUND

The small common marmoset (Callithrix jacchus) is an ideal nonhuman primate for awake fMRI in ultra-high field small animal MRI scanners. However, it can often be challenging in task-based fMRI experiments to provide a robust stimulus within the MRI environment while using hardware (an RF coil and restraint system) that is compatible with awake imaging.

NEW METHOD

Here we present an RF coil and restraint system that permits unimpeded access to an awake marmoset's head subsequent to immobilization, thereby permitting the setup of peripheral devices and stimuli proximal to the head.

RESULTS

As an example application, an fMRI experiment probing whole-brain activation in response to marmoset vocalizations was conducted-this paradigm showed significant bilateral activation in the inferior colliculus, medial lateral geniculate nucleus, and auditory cortex.

COMPARISON WITH EXISTING METHOD(S)

The coil performance was evaluated and compared to a previously published restraint system with integrated RF coil. The image and temporal SNR were improved by up to 58 % and 27 %, respectively, in the peripheral cortex and by 30 % and 3 % in the centre of the brain. The restraint-system topology limited head motion to less than 100 µm of translation and 0.30° of rotation when measured over a 15-minute acquisition.

CONCLUSIONS

The proposed hardware solution provides a versatile approach to awake-marmoset imaging and, as demonstrated, can facilitate task-based fMRI.

Frontoparietal connectivity as a product of convergent evolution in rodents and primates: functional connectivity topologies in grey squirrels, rats, and marmosets

Robust frontoparietal connectivity is a defining feature of primate cortical organization. Whether mammals outside the primate order, such as rodents, possess similar frontoparietal functional connectivity organization is a controversial topic. Previous work has primarily focused on comparing mice and rats to primates. However, as these rodents are nocturnal and terrestrial, they rely much less on visual input than primates. Here, we investigated the functional cortical organization of grey squirrels which are diurnal and arboreal, thereby better resembling primate ecology. We used ultra-high field resting-state fMRI data to compute and compare the functional connectivity patterns of frontal regions in grey squirrels (Sciurus carolinensis), rats (Rattus norvegicus), and marmosets (Callithrix jacchus). We utilized a fingerprinting analysis to compare interareal patterns of functional connectivity from seeds across frontal cortex in all three species. The results show that grey squirrels, but not rats, possess a frontoparietal connectivity organization that resembles the connectivity pattern of marmoset lateral prefrontal cortical areas. Since grey squirrels and marmosets have acquired an arboreal way of life but show no common arboreal ancestor, the expansion of the visual system and the formation of a frontoparietal connectivity architecture might reflect convergent evolution driven by similar ecological niches in primates and tree squirrels.

Functional Connectivity of the Brain Across Rodents and Humans

Resting-state functional magnetic resonance imaging (rs-fMRI), which measures the spontaneous fluctuations in the blood oxygen level-dependent (BOLD) signal, is increasingly utilized for the investigation of the brain's physiological and pathological functional activity. Rodents, as a typical animal model in neuroscience, play an important role in the studies that examine the neuronal processes that underpin the spontaneous fluctuations in the BOLD signal and the functional connectivity that results. Translating this knowledge from rodents to humans requires a basic knowledge of the similarities and differences across species in terms of both the BOLD signal fluctuations and the resulting functional connectivity. This review begins by examining similarities and differences in anatomical features, acquisition parameters, and preprocessing techniques, as factors that contribute to functional connectivity. Homologous functional networks are compared across species, and aspects of the BOLD fluctuations such as the topography of the global signal and the relationship between structural and functional connectivity are examined. Time-varying features of functional connectivity, obtained by sliding windowed approaches, quasi-periodic patterns, and coactivation patterns, are compared across species. Applications demonstrating the use of rs-fMRI as a translational tool for cross-species analysis are discussed, with an emphasis on neurological and psychiatric disorders. Finally, open questions are presented to encapsulate the future direction of the field.

Analysis of Brain Structure and Neural Organization in Dystrophin-Deficient Model Mice with Magnetic Resonance Imaging at 7 T

Background:

Dystrophin strengthens muscle cells; however, in muscular dystrophy, dystrophin is deficient due to an abnormal sugar chain. This abnormality occurs in skeletal muscle and in brain tissue.

Objective:

This study aimed to non-invasively analyze the neural organization of the brain in muscular dystrophy. We used a mouse model of muscular dystrophy to study whether changes in brain structure and neurodegeneration following dystrophin deficiency can be assessed by 7T magnetic resonance imaging.

Methods:

C57BL/10-mdx (X chromosome-linked muscular dystrophy) mice were used as the dystrophic mouse model and healthy mice were used as controls. Ventricular enlargement is one of the most common brain malformations in dystrophin-deficient patients. Therefore, we examined whether ventricular enlargement was observed in C57BL/10-mdx using transverse-relaxation weighted images. Brain parenchyma analysis was performed using diffusion MRI with diffusion tensor images and neurite orientation dispersion and density imaging. Parenchymal degeneration was assessed in terms of directional diffusion, nerve fiber diffusion, and dendritic scattering density.

Results:

For the volume of brain ventricles analyzed by T2WI, the average size was 1.5 times larger in mdx mice compared to control mice. In the brain parenchyma, a significant difference (p < 0.05) was observed in parameters indicating disturbances in the direction of nerve fibers and dendritic scattering density in the white matter region.

Conclusion:

Our results show that changes in brain structure due to dystrophin deficiency can be assessed in detail without tissue destruction by combining diffusion tensor images and neurite orientation dispersion and density imaging analyses.

An open access resource for functional brain connectivity from fully awake marmosets

The common marmoset (Callithrix jacchus) is quickly gaining traction as a premier neuroscientific model. However, considerable progress is still needed in understanding the functional and structural organization of the marmoset brain to rival that documented in longstanding preclinical model species, like mice, rats, and Old World primates. To accelerate such progress, we present the Marmoset Functional Brain Connectivity Resource (marmosetbrainconnectome.org), currently consisting of over 70 h of resting-state fMRI (RS-fMRI) data acquired at 500 µm isotropic resolution from 31 fully awake marmosets in a common stereotactic space. Three-dimensional functional connectivity (FC) maps for every cortical and subcortical gray matter voxel are stored online. Users can instantaneously view, manipulate, and download any whole-brain functional connectivity (FC) topology (at the subject- or group-level) along with the raw datasets and preprocessing code. Importantly, researchers can use this resource to test hypotheses about FC directly - with no additional analyses required - yielding whole-brain correlations for any gray matter voxel on demand. We demonstrate the resource's utility for presurgical planning and comparison with tracer-based neuronal connectivity as proof of concept. Complementing existing structural connectivity resources for the marmoset brain, the Marmoset Functional Brain Connectivity Resource affords users the distinct advantage of exploring the connectivity of any voxel in the marmoset brain, not limited to injection sites nor constrained by regional atlases. With the entire raw database (RS-fMRI and structural images) and preprocessing code openly available for download and use, we expect this resource to be broadly valuable to test novel hypotheses about the functional organization of the marmoset brain.

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.

Magnetic Resonance Imaging of Marmoset Monkeys

The use of the common marmoset monkey (Callithrix jacchus) for neuroscientific research has grown markedly in the last decade. Magnetic resonance imaging (MRI) has played a significant role in establishing the extent of comparability of marmoset brain architecture with the human brain and brains of other preclinical species (eg, macaques and rodents). As a non-invasive technique, MRI allows for the flexible acquisition of the same sequences across different species in vivo, including imaging of whole-brain functional topologies not possible with more invasive techniques. Being one of the smallest New World primates, the marmoset may be an ideal nonhuman primate species to study with MRI. As primates, marmosets have an elaborated frontal cortex with features analogous to the human brain, while also having a small enough body size to fit into powerful small-bore MRI systems typically employed for rodent imaging; these systems offer superior signal strength and resolution. Further, marmosets have a rich behavioral repertoire uniquely paired with a lissencephalic cortex (like rodents). This smooth cortical surface lends itself well to MRI and also other invasive methodologies. With the advent of transgenic modification techniques, marmosets have gained significant traction as a powerful complement to canonical mammalian modelling species. Marmosets are poised to make major contributions to preclinical investigations of the pathophysiology of human brain disorders as well as more basic mechanistic explorations of the brain. The goal of this article is to provide an overview of the practical aspects of implementing MRI and fMRI in marmosets (both under anesthesia and fully awake) and discuss the development of resources recently made available for marmoset imaging.

A Magnetic Resonance-Guided Focused Ultrasound Neuromodulation System With a Whole Brain Coil Array for Nonhuman Primates at 3 T

The phased-array radio frequency (RF) coil plays a vital role in magnetic resonance-guided focused ultrasound (MRgFUS) neuromodulation studies, where accurate brain functional stimulations and neural circuit observations are required. Although various designs of phased-array coils have been reported, few are suitable for ultrasound stimulations. In this study, an MRgFUS neuromodulation system comprised of a whole brain coverage non-human primate (NHP) RF coil and an MRI-compatible ultrasound device was developed. When compared to a single loop coil, the NHP coil provided up to a 50% increase in the signal-to-noise ratio (SNR) in the brain and acquired better anatomical image-quality. The NHP coil also demonstrated the ability to achieve higher spatial resolution and reduce distortion in echo-planer imaging (EPI). Ultrasound beam characteristics and transcranial magnetic resonance acoustic radiation force (MR-ARF) were measured for simulated positions, and calculated B₀ maps were employed to establish MRI-compatibility. The differences between focused off and on ultrasound techniques were measured using SNR, g-factors, and temporal SNR (tSNR) analyses and all deviations were under 2.3%. The EPI images quality and stable tSNR demonstrated the suitability of the MRgFUS neuromodulation system to conduct functional MRI studies. Last, the time course of the blood oxygen level dependent (BOLD) signal of posterior cingulate cortex in a focused ultrasound neuromodulation study was detected and repeated with MR thermometry.

In vivo localization of chronically implanted electrodes and optic fibers in mice

Electrophysiology provides a direct readout of neuronal activity at a temporal precision only limited by the sampling rate. However, interrogating deep brain structures, implanting multiple targets or aiming at unusual angles still poses significant challenges for operators, and errors are only discovered by post-hoc histological reconstruction. Here, we propose a method combining the high-resolution information about bone landmarks provided by micro-CT scanning with the soft tissue contrast of the MRI, which allowed us to precisely localize electrodes and optic fibers in mice in vivo. This enables arbitrating the success of implantation directly after surgery with a precision comparable to gold standard histology. Adjustment of the recording depth with micro-drives or early termination of unsuccessful experiments saves many working hours, and fast 3-dimensional feedback helps surgeons avoid systematic errors. Increased aiming precision enables more precise targeting of small or deep brain nuclei and multiple targeting of specific cortical or hippocampal layers.

Divergence of rodent and primate medial frontal cortex functional connectivity

With the medial frontal cortex (MFC) centrally implicated in several major neuropsychiatric disorders, it is critical to understand the extent to which MFC organization is comparable between humans and animals commonly used in preclinical research (namely rodents and nonhuman primates). Although the cytoarchitectonic structure of the rodent MFC has mostly been conserved in humans, it is a long-standing question whether the structural analogies translate to functional analogies. Here, we probed this question using ultra high field fMRI data to compare rat, marmoset, and human MFC functional connectivity. First, we applied hierarchical clustering to intrinsically define the functional boundaries of the MFC in all three species, independent of cytoarchitectonic definitions. Then, we mapped the functional connectivity "fingerprints" of these regions with a number of different brain areas. Because rats do not share cytoarchitectonically defined regions of the lateral frontal cortex (LFC) with primates, the fingerprinting method also afforded the unique ability to compare the rat MFC and marmoset LFC, which have often been suggested to be functional analogs. The results demonstrated remarkably similar intrinsic functional organization of the MFC across the species, but clear differences between rodent and primate MFC whole-brain connectivity. Rat MFC patterns of connectivity showed greatest similarity with premotor regions in the marmoset, rather than dorsolateral prefrontal regions, which are often suggested to be functionally comparable. These results corroborate the viability of the marmoset as a preclinical model of human MFC dysfunction, and suggest divergence of functional connectivity between rats and primates in both the MFC and LFC.

Functional Localization of the Frontal Eye Fields in the Common Marmoset Using Microstimulation

The frontal eye field (FEF) is a critical region for the deployment of overt and covert spatial attention. Although investigations in the macaque continue to provide insight into the neural underpinnings of the FEF, due to its location within a sulcus, the macaque FEF is virtually inaccessible to electrophysiological techniques such as high-density and laminar recordings. With a largely lissencephalic cortex, the common marmoset (Callithrix jacchus) is a promising alternative primate model for studying FEF microcircuitry. Putative homologies have been established with the macaque FEF on the basis of cytoarchitecture and connectivity; however, physiological investigation in awake, behaving marmosets is necessary to physiologically locate this area. Here, we addressed this gap using intracortical microstimulation in a broad range of frontal cortical areas in three adult marmosets (two males, one female). We implanted marmosets with 96-channel Utah arrays and applied microstimulation trains while they freely viewed video clips. We evoked short-latency fixed vector saccades at low currents (<50 μA) in areas 45, 8aV, 8C, and 6DR. We observed a topography of saccade direction and amplitude consistent with findings in macaques and humans: small saccades in ventrolateral FEF and large saccades combined with contralateral neck and shoulder movements encoded in dorsomedial FEF. Our data provide compelling evidence supporting homology between marmoset and macaque FEF and suggest that the marmoset is a useful primate model for investigating FEF microcircuitry and its contributions to oculomotor and cognitive functions.SIGNIFICANCE STATEMENT The frontal eye field (FEF) is a critical cortical region for overt and covert spatial attention. The microcircuitry of this area remains poorly understood because in the macaque, the most commonly used model, it is embedded within a sulcus and is inaccessible to modern electrophysiological and imaging techniques. The common marmoset is a promising alternative primate model due to its lissencephalic cortex and potential for genetic manipulation. However, evidence for homologous cortical areas in this model remains limited and unclear. Here, we applied microstimulation in frontal cortical areas in marmosets to physiologically identify FEF. Our results provide compelling evidence for an FEF in the marmoset and suggest that the marmoset is a useful model for investigating FEF microcircuitry.

Integrated radiofrequency array and animal holder design for minimizing head motion during awake marmoset functional magnetic resonance imaging

Marmosets are small New World primates that are posited to become an important preclinical animal model for studying intractable human brain diseases. A critical step in the development of marmosets as a viable model for human brain dysfunction is to characterize brain networks that are homologous with human network topologies. In this regard, the use of functional magnetic resonance imaging (fMRI) holds tremendous potential for functional brain mapping in marmosets. Although possible, implementation of hardware for fMRI in awake marmosets (free of the confounding effects of anesthesia) is not trivial due to the technical challenges associated with developing specialized imaging hardware. Here, we describe the design and implementation of a marmoset holder and head-fixation system with an integrated receive coil for awake marmoset fMRI. This design minimized head motion, with less than 100  μm of translation and 0.5 degrees of rotation over 15 consecutive resting state fMRI runs (at 15 min each) across 3 different marmosets. The fMRI data was of sufficient quality to reliably extract 8 resting state networks from each animal with only 60-90 min of resting state fMRI acquisition per animal. The restraint system proved to be an efficient and practical solution for securing an awake marmoset and positioning a receive array within minutes, limiting stress to the animal. This design is also amenable for multimodal imaging, allowing for electrode or lens placement above the skull via the open chamber design. All computer-aided-design (CAD) files and engineering drawings are provided as an open resource, with the majority of the parts designed to be 3D printed.

Intrinsic Functional Boundaries of Lateral Frontal Cortex in the Common Marmoset Monkey

The common marmoset (Callithrix jacchus) is a small New World primate species that has been recently targeted as a potentially powerful preclinical model of human prefrontal cortex dysfunction. Although the structural boundaries of frontal cortex were described in marmosets at the start of the 20th century (Brodmann, 1909) and refined more recently (Paxinos et al., 2012), the broad functional boundaries of marmoset frontal cortex have yet to be established. In this study, we sought to functionally derive boundaries of the marmoset lateral frontal cortex (LFC) using ultra-high field (9.4 T) resting-state functional magnetic resonance imaging (RS-fMRI). We collected RS-fMRI data in seven (four females, three males) lightly anesthetized marmosets and used a data-driven hierarchical clustering approach to derive subdivisions of the LFC based on intrinsic functional connectivity. We then conducted seed-based analyses to assess the functional connectivity between these clusters and the rest of the brain. The results demonstrated seven distinct functional clusters within the LFC. The functional connectivity patterns of these clusters with the rest of the brain were also found to be distinct and organized along a rostrocaudal gradient, consonant with those found in humans and macaques. Overall, these results support the view that marmosets are a promising preclinical modeling species for studying LFC dysfunction related to neuropsychiatric or neurodegenerative human brain diseases.SIGNIFICANCE STATEMENT The common marmoset is a New World primate that has garnered recent attention as a powerful complement to canonical Old World primate (e.g., macaques) and rodent models (e.g., rats, mice) for preclinical modeling of the human brain in healthy and diseased states. A critical step in the development of marmosets for such models is to characterize functional network topologies of frontal cortex in healthy, normally functioning marmosets, that is, how these circuitries are functionally divided and how those topologies compare to human circuitry. To our knowledge, this is the first study to demonstrate functional boundaries of the lateral frontal cortex and the corresponding network topologies in marmoset monkeys.