Awake Animals Research Articles

Hippocampal recording with a soft microelectrode array in a cranial window imaging scheme: a validation study

The hippocampus has a crucial role in the formation, consolidation and recall of memories as well as in navigation related processes. These functions are in the focus of neuroscience and different disciplines have contributed to this research field for decades. Two-photon imaging in awake animals is a valuable new aspect for these observations, especially when it is supported by electrophysiology. In this study, we applied high speed two-photon hippocampal imaging through a chronically implanted, soft, transparent microelectrode (STM) device incorporated into a cranial window chamber in awake mice. We monitored the impedance of the recording sites over the course of the experiments to observe long-term changes in recording quality. The large-scale ipsilateral local field potential (LFP) recordings from the dorsal hippocampus provided reliable sharp wave-ripples (SPW-Rs), multi-unit activity (MUA) and single-unit activity (SUA) for up to two months. Calcium imaging of GCaMP6f. labeled cells from the CA1 pyramidal layer under the transparent device was possible even after six months in thy1-GCaMP6f. transgenic mice. We investigated the immune response with GFAP staining after the end of the long-term experiments. Based on our results, this dedicated transparent electrode device proved to be suitable for simultaneous two-photon imaging and large-scale electrophysiological measurements in chronic experiments in mice.

Neuromodulator and neuropeptide sensors and probes for precise circuit interrogation in vivo.

To determine how neuronal circuits encode and drive behavior, it is often necessary to measure and manipulate different aspects of neurochemical signaling in awake animals. Optogenetics and calcium sensors have paved the way for these types of studies, allowing for the perturbation and readout of spiking activity within genetically defined cell types. However, these methods lack the ability to further disentangle the roles of individual neuromodulator and neuropeptides on circuits and behavior. We review recent advances in chemical biology tools that enable precise spatiotemporal monitoring and control over individual neuroeffectors and their receptors in vivo. We also highlight discoveries enabled by such tools, revealing how these molecules signal across different timescales to drive learning, orchestrate behavioral changes, and modulate circuit activity.

Glymphatic clearance is enhanced during sleep.

We here revisited the concept that glymphatic clearance is enhanced by sleep and anesthesia. Utilizing dynamic magnetic resonance imaging (MRI), single photon emission computed tomography (SPECT), and fluorescent fiber photometry, we report brain glymphatic clearance is enhanced by both sleep and anesthesia, and sharply suppressed by wakefulness. Another key finding was that less tracer enters the brains of awake animals and that brain clearance across different brain states can only be compared after adjusting for the injected tracer dose.

Receptive-field nonlinearities in primary auditory cortex: a comparative perspective.

Cortical processing of auditory information can be affected by interspecies differences as well as brain states. Here we compare multifeature spectro-temporal receptive fields (STRFs) and associated input/output functions or nonlinearities (NLs) of neurons in primary auditory cortex (AC) of four mammalian species. Single-unit recordings were performed in awake animals (female squirrel monkeys, female, and male mice) and anesthetized animals (female squirrel monkeys, rats, and cats). Neuronal responses were modeled as consisting of two STRFs and their associated NLs. The NLs for the STRF with the highest information content show a broad distribution between linear and quadratic forms. In awake animals, we find a higher percentage of quadratic-like NLs as opposed to more linear NLs in anesthetized animals. Moderate sex differences of the shape of NLs were observed between male and female unanesthetized mice. This indicates that the core AC possesses a rich variety of potential computations, particularly in awake animals, suggesting that multiple computational algorithms are at play to enable the auditory system's robust recognition of auditory events.

Identification of eupneic breathing using machine learning.

The diaphragm muscle (DIAm) is the primary inspiratory muscle in mammals. In awake animals, considerable heterogeneity in the electromyographic (EMG) activity of the DIAm reflects varied ventilatory and nonventilatory behaviors. Experiments in awake animals are an essential component to understanding the neuromotor control of breathing, which has especially begun to be appreciated within the last decade. However, insofar as the intent is to study the control of breathing, it is paramount to identify DIAm EMG activity that in fact reflects breathing. Current strategies for doing so in a reproducible, reliable, and efficient fashion are lacking. In the present article, we evaluated DIAm EMG from awake animals using hierarchical clustering across four-dimensional feature space to classify eupneic breathing. Our model, which can be implemented with automated threshold of the clustering dendrogram, successfully identified eupneic breathing with high F1 score (0.92), specificity (0.70), and accuracy (0.88), suggesting that it is a robust and reliable tool for investigating the neural control of breathing.NEW & NOTEWORTHY The heterogeneity of diaphragm muscle (DIAm) activity in awake animals reflects real motor behavior diversity but makes assessments of eupneic breathing challenging. The present article uses an unsupervised machine learning model to identify eupneic breathing amidst a deluge of different DIAm electromyography (EMG) burst patterns in awake rats. This technique offers a scalable and reliable tool that improves efficiency of DIAm EMG analysis and minimizes potential sources of bias.

Enhancing Flexible Neural Probe Performance via Platinum Deposition: Impedance Stability under Various Conditions and In Vivo Neural Signal Monitoring.

Monitoring neural activity in the central nervous system often utilizes silicon-based microelectromechanical system (MEMS) probes. Despite their effectiveness in monitoring, these probes have a fragility issue, limiting their application across various fields. This study introduces flexible printed circuit board (FPCB) neural probes characterized by robust mechanical and electrical properties. The probes demonstrate low impedance after platinum coating, making them suitable for multiunit recordings in awake animals. This capability allows for the simultaneous monitoring of a large population of neurons in the brain, including cluster data. Additionally, these probes exhibit no fractures, mechanical failures, or electrical issues during repeated-bending tests, both during handling and monitoring. Despite the possibility of using this neural probe for signal measurement in awake animals, simply applying a platinum coating may encounter difficulties in chronic tests and other applications. Furthermore, this suggests that FPCB probes can be advanced by any method and serve as an appropriate type of tailorable neural probes for monitoring neural systems in awake animals.

The brain simulates actions and their consequences during REM sleep.

Vivid dreams mostly occur during a phase of sleep called REM 1-5 . During REM sleep, the brain's internal representation of direction keeps shifting like that of an awake animal moving through its environment 6-8 . What causes these shifts, given the immobility of the sleeping animal? Here we show that the superior colliculus of the mouse, a motor command center involved in orienting movements 9-15 , issues motor commands during REM sleep, e.g. turn left, that are similar to those issued in the awake behaving animal. Strikingly, these motor commands, despite not being executed, shift the internal representation of direction as if the animal had turned. Thus, during REM sleep, the brain simulates actions by issuing motor commands that, while not executed, have consequences as if they had been. This study suggests that the sleeping brain, while disengaged from the external world, uses its internal model of the world to simulate interactions with it.

Hierarchical differences in the encoding of amplitude modulation in the subcortical auditory system of awake nonhuman primates.

Sinusoidal amplitude modulation (SAM) is a key feature of complex sounds. Although psychophysical studies have characterized SAM perception, and neurophysiological studies in anesthetized animals report a transformation from the cochlear nucleus' (CN; brainstem) temporal code to the inferior colliculus' (IC; midbrain's) rate code, none have used awake animals or nonhuman primates to compare CN and IC's coding strategies to modulation-frequency perception. To address this, we recorded single-unit responses and compared derived neurometric measures in the CN and IC to psychometric measures of modulation frequency (MF) discrimination in macaques. IC and CN neurons often exhibited tuned responses to SAM in rate and spike-timing measures of modulation coding. Neurometric thresholds spanned a large range (2-200 Hz ΔMF). The lowest 40% of IC thresholds were less than or equal to psychometric thresholds, regardless of which code was used, whereas CN thresholds were greater than psychometric thresholds. Discrimination at 10-20 Hz could be explained by indiscriminately pooling 30 units in either structure, whereas discrimination at higher MFs was best explained by more selective pooling. This suggests that pooled CN activity was sufficient for AM discrimination. Psychometric and neurometric thresholds decreased as stimulus duration increased, but IC and CN thresholds were higher and more variable than behavior at short durations. This slower subcortical temporal integration compared with behavior was consistent with a drift diffusion model that reproduced individual differences in performance and can constrain future neurophysiological studies of temporal integration. These measures provide an account of AM perception at the neurophysiological, computational, and behavioral levels.NEW & NOTEWORTHY In everyday environments, the brain is tasked with extracting information from sound envelopes, which involves both sensory encoding and perceptual decision-making. Different neural codes for envelope representation have been characterized in midbrain and cortex, but studies of brainstem nuclei such as the cochlear nucleus (CN) have usually been conducted under anesthesia in nonprimate species. Here, we found that subcortical activity in awake monkeys and a biologically plausible perceptual decision-making model accounted for sound envelope discrimination behavior.

In Vivo Calcium Imaging of Granule Cells in the Dentate Gyrus of Hippocampus in Mice.

Real-time approaches are typically needed in studies of learning and memory, and in vivo calcium imaging provides the possibility to investigate neuronal activity in awake animals during behavior tasks. Since the hippocampus is closely associated with episodic and spatial memory, it has become an essential brain region inthis field's research. In recent research, engram cells and place cells were studied by recording the neural activities in the hippocampal CA1 region using the miniature microscope in mice while performing behavioral tasks including open-field and linear track. Although the dentate gyrus is another important region in the hippocampus, it has rarely been studied with in vivo imaging due to its greater depth and difficulty for imaging. In this protocol, we present in detail a calcium imaging process, including how to inject the virus, implant a GRIN (Gradient-index) lens, and attach a base plate for imaging the dentate gyrus of the hippocampus. We further describe how to preprocess the calcium imaging data using MATLAB. Additionally, studies of other deep brain regions that require imaging may benefit from this method.

An Untethered Heart Rhythm Monitoring System with Automated AI‐Based Arrhythmia Detection for Closed‐Loop Experimental Application

AbstractThe heart produces bioelectrical signals, which can be measured as an electrocardiogram (ECG) for the detection of rhythm disturbances. Rapid and precise detection of these arrhythmias is crucial for their termination by closed‐looped therapeutic interventions to counteract detrimental effects. However, there is a current lack of such systems tailored for experimental cardiovascular applications. This hampers not only in‐depth mechanistic studies but also translational testing of new therapeutic strategies, especially in an untethered manner in awake animal models. To break new ground, recent advances to develop a non‐invasive AI‐supported heart rhythm monitoring system for untethered automated arrhythmia detection in a continuous manner is combined. This system is housed in a lightweight jacket for mobile use and includes an on‐skin ECG sensor, a low‐power microprocessor unit, a massive data storage unit, and a power‐management system. By implementing a novel hybrid algorithm based on so‐called heart rate (R‐R) variability and a case‐specific AI model, 100% sensitivity and 95% specificity is achieved in detecting atrial arrhythmias within 2 s upon initiation in adult rats. Thereby, the novel system sets the stage for advanced mechanistic studies and therapeutic testing, including closed‐loop applications aiming for the termination of a broad range of atrial arrhythmias.

Co-coding of head and whisker movements by both VPM and POm thalamic neurons

Rodents continuously move their heads and whiskers in a coordinated manner while perceiving objects through whisker-touch. Studies in head-fixed rodents showed that the ventroposterior medial (VPM) and posterior medial (POm) thalamic nuclei code for whisker kinematics, with POm involvement reduced in awake animals. To examine VPM and POm involvement in coding head and whisker kinematics in awake, head-free conditions, we recorded thalamic neuronal activity and tracked head and whisker movements in male mice exploring an open arena. Using optogenetic tagging, we found that in freely moving mice, both nuclei equally coded whisker kinematics and robustly coded head kinematics. The fraction of neurons coding head kinematics increased after whisker trimming, ruling out whisker-mediated coding. Optogenetic activation of thalamic neurons evoked overt kinematic changes and increased the fraction of neurons leading changes in head kinematics. Our data suggest that VPM and POm integrate head and whisker information and can influence head kinematics during tactile perception.

Concurrent optogenetic motor mapping of multiple limbs in awake mice reveals cortical organization of coordinated movements.

Motor mapping allows for determining the macroscopic organization of motor circuits and corresponding motor movement representations on the cortex. Techniques such as intracortical microstimulation (ICMS) are robust, but can be time consuming and invasive, making them non-ideal for cortex-wide mapping or longitudinal studies. In contrast, optogenetic motor mapping offers a rapid and minimally invasive technique, enabling mapping with high spatiotemporal resolution. However, motor mapping has seen limited use in tracking 3-dimensonal, multi-limb movements in awake animals. This gap has left open questions regarding the underlying organizational principles of motor control of coordinated, ethologically relevant movements involving multiple limbs. Our first objective was to develop Multi-limb Optogenetic Motor Mapping (MOMM) to concurrently map motor movement representations of multiple limbs with high fidelity in awake mice. Having established MOMM, our next objective was determine whether maps of coordinated and ethologically relevant motor output were topographically organized on the cortex. We combine optogenetic stimulation with a deep learning driven pose-estimation toolbox, DeepLabCut (DLC), and 3-dimentional triangulation to concurrently map motor movements of multiple limbs in awake mice. MOMM consistently revealed cortical topographies for all mapped features within and across mice. Many motor maps overlapped and were topographically similar. Several motor movement representations extended beyond cytoarchitecturally defined somatomotor cortex. Finer articulations of the forepaw resided within gross motor movement representations of the forelimb. Moreover, many cortical sites exhibited concurrent limb coactivation when photostimulated, prompting the identification of several cortical regions harboring coordinated and ethologically relevant movements. The cortex appears to be topographically organized by motor programs, which are responsible for coordinated, multi-limbed, and behavioral-like movements.

Effects of low-intensity extracorporeal shock wave on bladder and urethral dysfunction in spinal cord injured rats.

To investigate the effects of low-intensity extracorporeal shock wave therapy (LiESWT) on bladder and urethral dysfunction with detrusor overactivity and detrusor sphincter dyssynergia (DSD) resulting from spinal cord injury (SCI). At 3 weeks after Th9 spinal cord transection, LiESWT was performed on the bladder and urethra of adult female Sprague Dawley rats with 300 shots of 2Hz and an energy flux density of 0.12mJ/mm2, repeated four times every 3 days, totaling 1200 shots. Six weeks postoperatively, a single cystometrogram (CMG) and an external urethral sphincter electromyogram (EUS-EMG) were simultaneously recorded in awake animals, followed by histological evaluation. Voiding efficiency significantly improved in the LiESWT group (71.2%) compared to that in the control group (51.8%). The reduced EUS activity ratio during voiding (duration of reduced EUS activity during voiding/EUS contraction duration with voiding + duration of reduced EUS activity during voiding) was significantly higher in the LiESWT group (66.9%) compared to the control group (46.3%). Immunohistochemical examination revealed that fibrosis in the urethral muscle layer was reduced, and S-100 stained-positive area, a Schwann cell marker, was significantly increased in the urethra of the LiESWT group. LiESWT targeting the urethra after SCI can restore the EUS-EMG tonic activity during voiding, thereby partially ameliorating DSD. Therefore, LiESWT is a promising approach for treating bladder and urethral dysfunction following SCI.

Noradrenergic tuning of arousal is coupled to coordinated movements.

Matching arousal level to the motor activity of an animal is important for efficiently allocating cognitive resources and metabolic supply in response to behavioral demands, but how the brain coordinates changes in arousal and wakefulness in response to motor activity remains an unclear phenomenon. We hypothesized that the locus coeruleus (LC), as the primary source of cortical norepinephrine (NE) and promoter of cortical and sympathetic arousal, is well-positioned to mediate movement-arousal coupling. Here, using a combination of physiological recordings, fiber photometry, optogenetics, and behavioral tracking, we show that the LCNE activation is tightly coupled to the return of organized movements during waking from an anesthetized state. Moreover, in an awake animal, movement initiations are coupled to LCNE activation, while movement arrests, to LCNE deactivation. We also report that LCNE activity covaries with the depth of anesthesia and that LCNE photoactivation leads to sympathetic activation, consistent with its role in mediating increased arousal. Together, these studies reveal a more nuanced, modulatory role that LCNE plays in coordinating movement and arousal.

Sheep (Ovis aries) training protocol for voluntary awake and unrestrained structural brain MRI acquisitions

Magnetic resonance imaging (MRI) is a non-invasive technique that requires the participant to be completely motionless. To date, MRI in awake and unrestrained animals has only been achieved with humans and dogs. For other species, alternative techniques such as anesthesia, restraint and/or sedation have been necessary. Anatomical and functional MRI studies with sheep have only been conducted under general anesthesia. This ensures the absence of movement and allows relatively long MRI experiments but it removes the non-invasive nature of the MRI technique (i.e., IV injections, intubation). Anesthesia can also be detrimental to health, disrupt neurovascular coupling, and does not permit the study of higher-level cognition. Here, we present a proof-of-concept that sheep can be trained to perform a series of tasks, enabling them to voluntarily participate in MRI sessions without anesthesia or restraint. We describe a step-by-step training protocol based on positive reinforcement (food and praise) that could be used as a basis for future neuroimaging research in sheep. This protocol details the two successive phases required for sheep to successfully achieve MRI acquisitions of their brain. By providing structural brain MRI images from six out of ten sheep, we demonstrate the feasibility of our training protocol. This innovative training protocol paves the way for the possibility of conducting animal welfare-friendly functional MRI studies with sheep to investigate ovine cognition.

A minimally invasive thrombotic stroke model to study circadian rhythm in awake mice.

Experimental stroke models in rodents are essential for mechanistic studies and therapeutic development. However, these models have several limitations negatively impacting their translational relevance. Here we aimed to develop a minimally invasive thrombotic stroke model through magnetic particle delivery that does not require craniotomy, is amenable to reperfusion therapy, can be combined with in vivo imaging modalities, and can be performed in awake mice. We found that the model results in reproducible cortical infarcts within the middle cerebral artery (MCA) with cytologic and immune changes similar to that observed with more invasive distal MCA occlusion models. Importantly, the injury produced by the model was ameliorated by tissue plasminogen activator (tPA) administration. We also show that MCA occlusion in awake animals results in bigger ischemic lesions independent of day/night cycle. Magnetic particle delivery had no overt effects on physiologic parameters and systemic immune biomarkers. In conclusion, we developed a novel stroke model in mice that fulfills many requirements for modeling human stroke.

Simultaneous removal of noise and correction of motion warping in neuron calcium imaging using a pipeline structure of self-supervised deep learning models.

Calcium imaging is susceptible to motion distortions and background noises, particularly for monitoring active animals under low-dose laser irradiation, and hence unavoidably hinder the critical analysis of neural functions. Current research efforts tend to focus on either denoising or dewarping and do not provide effective methods for videos distorted by both noises and motion artifacts simultaneously. We found that when a self-supervised denoising model of DeepCAD [Nat. Methods18, 1359 (2021)10.1038/s41592-021-01225-0] is used on the calcium imaging contaminated by noise and motion warping, it can remove the motion artifacts effectively but with regenerated noises. To address this issue, we develop a two-level deep-learning (DL) pipeline to dewarp and denoise the calcium imaging video sequentially. The pipeline consists of two 3D self-supervised DL models that do not require warp-free and high signal-to-noise ratio (SNR) observations for network optimization. Specifically, a high-frequency enhancement block is presented in the denoising network to restore more structure information in the denoising process; a hierarchical perception module and a multi-scale attention module are designed in the dewarping network to tackle distortions of various sizes. Experiments conducted on seven videos from two-photon and confocal imaging systems demonstrate that our two-level DL pipeline can restore high-clarity neuron images distorted by both motion warping and background noises. Compared to typical DeepCAD, our denoising model achieves a significant improvement of approximately 30% in image resolution and up to 28% in signal-to-noise ratio; compared to traditional dewarping and denoising methods, our proposed pipeline network recovers more neurons, enhancing signal fidelity and improving data correlation among frames by 35% and 60% respectively. This work may provide an attractive method for long-term neural activity monitoring in awake animals and also facilitate functional analysis of neural circuits.

Anesthetized animal experiments for neuroscience research.

Brain research has progressed with anesthetized animal experiments for a long time. Recent progress in research techniques allows us to measure neuronal activity in awake animals combined with behavioral tasks. The trends became more prominent in the last decade. This new research style triggers the paradigm shift in the research of brain science, and new insights into brain function have been revealed. It is reasonable to consider that awake animal experiments are more ideal for understanding naturalistic brain function than anesthetized ones. However, the anesthetized animal experiment still has advantages in some experiments. To take advantage of the anesthetized animal experiments, it is important to understand the mechanism of anesthesia and carefully handle the obtained data. In this minireview, we will shortly summarize the molecular mechanism of anesthesia in animal experiments, a recent understanding of the neuronal activities in a sensory system in the anesthetized animal brain, and consider the advantages and disadvantages of the anesthetized and awake animal experiments. This discussion will help us to use both research conditions in the proper manner.

Virtual cylindrical PET for efficient DOI image reconstruction with sub-millimetre resolution

Objective. Image reconstruction in high resolution, narrow bore PET scanners with depth of interaction (DOI) capability presents a substantial computational challenge due to the very high sampling in detector and image space. The aim of this study is to evaluate the use of a virtual cylinder in reducing the number of lines of response (LOR) for DOI-based reconstruction in high resolution PET systems while maintaining uniform sub-millimetre spatial resolution. Approach. Virtual geometry was investigated using the awake animal mousePET as a high resolution test case. Using GEANT4 Application for Tomographic Emission (GATE), we simulated the physical scanner and three virtual cylinder implementations with detector size 0.74 mm, 0.47 mm and 0.36 mm (vPET1, vPET2 and vPET3, respectively). The virtual cylinder condenses physical LORs stemming from various crystal pairs and DOI combinations, and which intersect a single virtual detector pair, into a single virtual LOR. Quantitative comparisons of the point spread function (PSF) at various positions within the field of view (FOV) were compared for reconstructions based on the vPET implementations and the physical scanner. We also assessed the impact of the anisotropic PSFs by reconstructing images of a micro Derenzo phantom. Main results. All virtual cylinder implementations achieved LOR data compression of at least 50% for DOI PET reconstruction. PSF anisotropy in radial and tangential profiles was chiefly influenced by DOI resolution and only marginally by virtual detector size. Spatial degradation introduced by virtual cylinders was most prominent in the axial profile. All virtual cylinders achieved sub-millimetre volumetric resolution across the FOV when 6-bin DOI reconstructions (3.3 mm DOI resolution) were performed. Using vPET2 with 6 DOI bins yielded nearly identical reconstructions to the non-virtual case in the transaxial plane, with an LOR compression factor of 86%. Resolution modelling significantly reduced the effects of the asymmetric PSF arising from the non-cylindrical geometry of mousePET. Significance. Narrow bore and high resolution PET scanners require detectors with DOI capability, leading to computationally demanding reconstructions due to the large number of LORs. In this study, we show that DOI PET reconstruction with 50%–86% LOR compression is possible using virtual cylinders while maintaining sub-millimetre spatial resolution throughout the FOV. The methodology and analysis can be extended to other scanners with DOI capability intended for high resolution PET imaging.

Psilocybin decreases neural responsiveness and increases functional connectivity while preserving pure-tone frequency selectivity in mouse auditory cortex.

Psilocybin is a serotonergic psychedelic believed to have therapeutic potential for neuropsychiatric conditions. Despite well-documented prevalence of perceptual alterations, hallucinations, and synesthesia associated with psychedelic experiences, little is known about how psilocybin affects sensory cortex or alters the activity of neurons in awake animals. To investigate, we conducted two-photon imaging experiments in auditory cortex of awake mice and collected video of free-roaming mouse behavior, both at baseline and during psilocybin treatment. In comparison with pre-dose neural activity, a 2 mg/kg ip dose of psilocybin initially increased the amplitude of neural responses to sound. Thirty minutes post-dose, behavioral activity and neural response amplitudes decreased, yet functional connectivity increased. In contrast, control mice given intraperitoneal saline injections showed no significant changes in either neural or behavioral activity across conditions. Notably, neuronal stimulus selectivity remained stable during psilocybin treatment, for both tonotopic cortical maps and single-cell pure-tone frequency tuning curves. Our results mirror similar findings regarding the effects of serotonergic psychedelics in visual cortex and suggest that psilocybin modulates the balance of intrinsic versus stimulus-driven influences on neural activity in auditory cortex.NEW & NOTEWORTHY Recent studies have shown promising therapeutic potential for psychedelics in treating neuropsychiatric conditions. Musical experience during psilocybin-assisted therapy is predictive of treatment outcome, yet little is known about how psilocybin affects auditory processing. Here, we conducted two-photon imaging experiments in auditory cortex of awake mice that received a dose of psilocybin. Our results suggest that psilocybin modulates the roles of intrinsic neural activity versus stimulus-driven influences on auditory perception.