Spectral fiber photometry derives hemoglobin concentration changes for accurate measurement of fluorescent sensor activity

Distinct spatially organized striatum-wide acetylcholine dynamics for the learning and extinction of Pavlovian associations

Striatal acetylcholine (ACh) signaling is thought to counteract reinforcement signals, promoting extinction and behavioral flexibility. Changes in striatal ACh signals have been reported during learning, but how ACh signals for learning and extinction are spatially organized to enable region-specific plasticity is unclear. We used array photometry in mice to reveal a topography of opposing changes in ACh release across distinct striatal regions. Reward prediction error encoding was localized to specific phases of ACh dynamics in anterior dorsal striatum (aDS): positive and negative prediction errors were expressed in dips and elevations respectively. Silencing ACh release in aDS impaired extinction, suggesting a role for ACh elevations in down-regulating cue-reward associations. Dopamine release in aDS dipped for cues during extinction, inverse to ACh, while glutamate input onto cholinergic interneurons was unchanged. These findings pinpoint where and suggest an intrastriatal mechanism for how ACh dynamics shape region-specific plasticity to gate learning and promote extinction.

Quantification of the effect of hemodynamic occlusion in two-photon imaging of mouse cortex

The last few years have seen an explosion in the number of tools available to measure neuronal activity using fluorescence imaging (Chen et al., 2013; Feng et al., 2019; Jing et al., 2019; Sun et al., 2018; Wan et al., 2021). When performed in vivo, these measurements are invariably contaminated by hemodynamic occlusion artifacts. In widefield calcium imaging, this problem is well recognized. For two-photon imaging, however, the effects of hemodynamic occlusion have only been sparsely characterized. Here, we perform a quantification of hemodynamic occlusion effects using measurements of fluorescence changes observed with GFP expression using both widefield and two-photon imaging in mouse cortex. We find that in many instances the magnitude of signal changes attributable to hemodynamic occlusion is comparable to that observed with activity sensors. Moreover, we find that hemodynamic occlusion effects were spatially heterogeneous, both over cortical regions and across cortical depth, and exhibited a complex relationship with behavior. Thus, hemodynamic occlusion is an important caveat to consider when analyzing and interpreting not just widefield but also two-photon imaging data.

Next-Generation Wearable/Implanted Sensors Based on Fiber Optic and Its Application: From in Vitro to in Vivo

Wearable sensors are significant for health status, diagnosing diseases, and adjusting postoperative interventions to monitor the physiological information on humans continuously. The first generation of wearable sensors has gained rapid growth in medical health for monitoring physical parameters. Recently, emerging fiber optics (FOs) with small diameters have been attached to desired locations of the human epidermis or fabrics for monitoring physiological change activity. Because of its strong soft tissue affinity and excellent biocompatibility, FO has been injected into human skin, blood vessels, and the brain for sensing of biological parameters. The detection of FO has been extended, ranging from physical parameters to chemical and biological parameters. Also, the application of FO has shifted from wearable sensors in vitro to implanted sensors in vivo. Thus, FO is expected to launch a milestone contribution to next-generation wearable/implanted sensors. Based on the success, this review focuses on wearable and implantable FO-based sensors. The three main design strategies of single point, distributed, and FO array were profiled. The significant application of the detection of the physical, chemical, and biological parameters was discussed. The opportunities and challenges of wearable/implantable FO-based sensors were highlighted to promote their development for commercial applications.

Obtaining artifact-corrected signals in fiber photometry via isosbestic signals, robust regression, and dF/F calculations

Significance

Fiber photometry is a powerful tool for neuroscience. However, measured biosensor signals are contaminated by various artifacts (photobleaching and movement-related noise) that undermine analysis and interpretation. Currently, no universal pipeline exists to deal with these artifacts.

Aim

We aim to evaluate approaches for obtaining artifact-corrected neural dynamic signals from fiber photometry data and provide recommendations for photometry analysis pipelines.

Approach

Using simulated and real photometry data, we tested the effects of three key analytical decisions: choice of regression for fitting isosbestic control signals onto experimental signals [ordinary least squares (OLS) versus iteratively reweighted least squares (IRLS)], low-pass filtering, and dF/F versus dF calculations.

Results

IRLS surpassed OLS regression for fitting isosbestic control signals to experimental signals. We also demonstrate the efficacy of low-pass filtering signals and baseline normalization via dF/F calculations.

Conclusions

We conclude that artifact-correcting experimental signals via low-pass filter, IRLS regression, and dF/F calculations is a superior approach to commonly used alternatives. We suggest these as a new standard for preprocessing signals across photometry analysis pipelines.

SORDINO for Silent, Sensitive, Specific, and Artifact-Resisting fMRI in awake behaving mice

Blood-oxygenation-level-dependent (BOLD) functional magnetic resonance imaging (fMRI) has revolutionized our understanding of the brain activity landscape, bridging circuit neuroscience in animal models with noninvasive brain mapping in humans. This immensely utilized technique, however, faces challenges such as acoustic noise, electromagnetic interference, motion artifacts, magnetic-field inhomogeneity, and limitations in sensitivity and specificity. Here, we introduce Steady-state On-the-Ramp Detection of INduction-decay with Oversampling (SORDINO), a transformative fMRI technique that addresses these challenges by maintaining a constant total gradient amplitude while acquiring data during continuously changing gradient direction. When benchmarked against conventional fMRI on a 9.4T system, SORDINO is silent, sensitive, specific, and resistant to motion and susceptibility artifacts. SORDINO offers superior compatibility with multimodal experiments and carries novel contrast mechanisms distinct from BOLD. It also enables brain-wide activity and connectivity mapping in awake, behaving mice, overcoming stress- and motion-related confounds that are among the most challenging barriers in current animal fMRI studies.

Distinct spatially organized striatum-wide acetylcholine dynamics for the learning and extinction of Pavlovian associations

Striatal acetylcholine (ACh) signaling has been proposed to counteract reinforcement signals to promote extinction and behavioral flexibility. ACh dips to cues and rewards may open a temporal window for associative plasticity to occur, while elevations may promote extinction. Changes in multi-phasic striatal ACh signals have been widely reported during learning, but how and where signals are distributed to enable region-specific plasticity for the learning and degradation of cue-reward associations is poorly understood. We used array fiber photometry in mice to investigate how ACh release across the striatum evolves during learning and extinction of Pavlovian associations. We report a topographic organization of opposing changes in ACh release to cues, rewards, and consummatory actions across distinct striatum regions. We localized reward prediction error encoding in particular phases of the ACh dynamics to a specific region of the anterior dorsal striatum (aDS). Positive prediction errors in the aDS were expressed in ACh dips, and negative prediction errors in long latency ACh elevations. Silencing aDS ACh release impaired behavioral extinction, suggesting a role for ACh elevations in down-regulating cue-reward associations. Dopamine release in aDS dipped for cues during extinction, but glutamate input onto cholinergic interneurons did not change, suggesting an intrastriatal mechanism for the emergence of ACh elevations. Our large scale measurements indicate how and where ACh dynamics can shape region-specific plasticity to gate learning and promote extinction of Pavlovian associations.

Revealing excitation-inhibition imbalance in Alzheimer's disease using multiscale neural model inversion of resting-state functional MRI

BACKGROUND

Alzheimer's disease (AD) is a serious neurodegenerative disorder without a clear understanding of pathophysiology. Recent experimental data have suggested neuronal excitation-inhibition (E-I) imbalance as an essential element of AD pathology, but E-I imbalance has not been systematically mapped out for either local or large-scale neuronal circuits in AD, precluding precise targeting of E-I imbalance in AD treatment.

METHOD

In this work, we apply a Multiscale Neural Model Inversion (MNMI) framework to the resting-state functional MRI data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) to identify brain regions with disrupted E-I balance in a large network during AD progression.

RESULTS

We observe that both intra-regional and inter-regional E-I balance is progressively disrupted from cognitively normal individuals, to mild cognitive impairment (MCI) and to AD. Also, we find that local inhibitory connections are more significantly impaired than excitatory ones and the strengths of most connections are reduced in MCI and AD, leading to gradual decoupling of neural populations. Moreover, we reveal a core AD network comprised mainly of limbic and cingulate regions. These brain regions exhibit consistent E-I alterations across MCI and AD, and thus may represent important AD biomarkers and therapeutic targets. Lastly, the E-I balance of multiple brain regions in the core AD network is found to be significantly correlated with the cognitive test score.

CONCLUSIONS

Our study constitutes an important attempt to delineate E-I imbalance in large-scale neuronal circuits during AD progression, which may facilitate the development of new treatment paradigms to restore physiological E-I balance in AD.

Absolute measurement of fast and slow neuronal signals with fluorescence lifetime photometry at high temporal resolution

The concentrations of extracellular and intracellular signaling molecules, such as dopamine and cAMP, change over both fast and slow timescales and impact downstream pathways in a cell-type specific manner. Fluorescence sensors currently used to monitor such signals in vivo are typically optimized to detect fast, relative changes in concentration of the target molecule. They are less well suited to detect slowly-changing signals and rarely provide absolute measurements of either fast and slow signaling components. Here, we developed a system for fluorescence lifetime photometry at high temporal resolution (FLIPR) that utilizes frequency-domain analog processing to measure the absolute fluorescence lifetime of genetically-encoded sensors at high speed but with long-term stability and picosecond precision in freely moving mice. We applied FLIPR to investigate dopamine signaling in two functionally distinct regions in the striatum, the nucleus accumbens core (NAC) and the tail of striatum (TOS). We observed higher tonic dopamine levels at baseline in the TOS compared to the NAC and detected differential and dynamic responses in phasic and tonic dopamine to appetitive and aversive stimuli. Thus, FLIPR enables simple monitoring of fast and slow time-scale neuronal signaling in absolute units, revealing previously unappreciated spatial and temporal variation even in well-studied signaling systems.

Interactions between Arousal State and CO2 Determine the Activity of Central Chemoreceptor Neurons That Drive Breathing

The homeostatic regulation of pulmonary ventilation, and ultimately arterial PCO2, depends on interactions between respiratory chemoreflexes and arousal state. The ventilatory response to CO2 is triggered by neurons in the retrotrapezoid nucleus (RTN) that function as sensors of central pH, which can be identified in adulthood by the expression of Phox2b and neuromedin B. Here, we examine the dynamic response of genetically defined RTN neurons to hypercapnia and arousal state in freely behaving adult male and female mice using the calcium indicator jGCaMP7 and fiber photometry. We found that hypercapnia vigorously activates RTN neurons with a low CO2 recruitment threshold and with response kinetics that match respiratory activity whereas hypoxia had little effect. RTN activity increased transiently during wakefulness and respiratory-related arousals and rose persistently during rapid eye movement sleep, and their CO2 response persisted under anesthesia. Complementary studies using inhibitory optogenetics show that RTN activity supports eupneic breathing under anesthesia as well as during states of high arousal, but their activity is redundant for voluntary breathing patterns. Collectively, this study demonstrates that CO2-activated RTN neurons are exquisitely sensitive to the arousal state, which determines their contribution to alveolar ventilation in relation to arterial PCO2.

Fiber photometry in neuroscience research: principles, applications, and future directions

In recent years, fluorescent sensors are enjoying a surge of popularity in the field of neuroscience. Through the development of novel genetically encoded sensors as well as improved methods of detection and analysis, fluorescent sensing has risen as a new major technique in neuroscience alongside molecular, electrophysiological, and imaging methods, opening up new avenues for research. Combined with multiphoton microscopy and fiber photometry, these sensors offer unique advantages in terms of cellular specificity, access to multiple targets - from calcium dynamics to neurotransmitter release to intracellular processes - as well as high capability for in vivo interrogation of neurobiological mechanisms underpinning behavior. Here, we provide a brief overview of the method, present examples of its integration with other tools in recent studies ranging from cellular to systems neuroscience, and discuss some of its principles and limitations, with the aim of introducing new potential users to this rapidly developing and potent technique.

Preexisting risk-avoidance and enhanced alcohol relief are driven by imbalance of the striatal dopamine receptors in mice

Alcohol use disorder (AUD) is frequently comorbid with anxiety disorders, yet whether alcohol abuse precedes or follows the expression of anxiety remains unclear. Rodents offer control over the first drink, an advantage when testing the causal link between anxiety and AUD. Here, we utilized a risk-avoidance task to determine anxiety-like behaviors before and after alcohol exposure. We found that alcohol's anxiolytic efficacy varied among inbred mice and mice with high risk-avoidance showed heightened alcohol relief. While dopamine D1 receptors in the striatum are required for alcohol's relief, their levels alone were not correlated with relief. Rather, the ratio between striatal D1 and D2 receptors was a determinant factor for risk-avoidance and alcohol relief. We show that increasing striatal D1 to D2 receptor ratio was sufficient to promote risk-avoidance and enhance alcohol relief, even at initial exposure. Mice with high D1 to D2 receptor ratio were more prone to continue drinking despite adverse effects, a hallmark of AUD. These findings suggest that an anxiety phenotype may be a predisposing factor for AUD.

Distinguishing motion artifacts during optical fiber-based in-vivo hemodynamics recordings from brain regions of freely moving rodents

Significance

Motion artifacts in the signals recorded during optical fiber-based measurements can lead to misinterpretation of data. In this work, we address this problem during in-vivo rodent experiments and develop a motion artifacts correction (MAC) algorithm for single-fiber system (SFS) hemodynamics measurements from the brains of rodents.

Aim

(i) To distinguish the effect of motion artifacts in the SFS signals. (ii) Develop a MAC algorithm by combining information from the experiments and simulations and validate it.

Approach

Monte-Carlo (MC) simulations were performed across 450 to 790 nm to identify wavelengths where the reflectance is least sensitive to blood absorption-based changes. This wavelength region is then used to develop a quantitative metric to measure motion artifacts, termed the dissimilarity metric (DM). We used MC simulations to mimic artifacts seen during experiments. Further, we developed a mathematical model describing light intensity at various optical interfaces. Finally, an MAC algorithm was formulated and validated using simulation and experimental data.

Results

We found that the 670 to 680 nm wavelength region is relatively less sensitive to blood absorption. The standard deviation of DM (σ D M ) can measure the relative magnitude of motion artifacts in the SFS signals. The artifacts cause rapid shifts in the reflectance data that can be modeled as transmission changes in the optical lightpath. The changes observed during the experiment were found to be in agreement to those obtained from MC simulations. The mathematical model developed to model transmission changes to represent motion artifacts was extended to an MAC algorithm. The MAC algorithm was validated using simulations and experimental data.

Conclusions

We distinguished motion artifacts from SFS signals during in vivo hemodynamic monitoring experiments. From simulation and experimental data, we showed that motion artifacts can be modeled as transmission changes. The developed MAC algorithm was shown to minimize artifactual variations in both simulation and experimental data.

Viscerosensory signalling to the nucleus accumbens via the solitary tract nucleus

The nucleus of the solitary tract (NTS) receives direct viscerosensory vagal afferent input that drives autonomic reflexes, neuroendocrine function and modulates behaviour. A subpopulation of NTS neurons project to the nucleus accumbens (NAc); however, the function of this NTS-NAc pathway remains unknown. A combination of neuroanatomical tracing, slice electrophysiology and fibre photometry was used in mice and/or rats to determine how NTS-NAc neurons fit within the viscerosensory network. NTS-NAc projection neurons are predominantly located in the medial and caudal portions of the NTS with 54 ± 7% (mice) and 65 ± 3% (rat) being TH-positive, representing the A2 NTS cell group. In horizontal brainstem slices, solitary tract (ST) stimulation evoked excitatory post-synaptic currents (EPSCs) in NTS-NAc projection neurons. The majority (75%) received low-jitter, zero-failure EPSCs characteristic of monosynaptic ST afferent input that identifies them as second order to primary sensory neurons. We then examined whether NTS-NAc neurons respond to cholecystokinin (CCK, 20 μg/kg ip) in vivo in both mice and rats. Surprisingly, there was no difference in the number of activated NTS-NAc cells between CCK and saline-treated mice. In rats, just 6% of NTS-NAc cells were recruited by CCK. As NTS TH neurons are the primary source for NAc noradrenaline, we measured noradrenaline release in the NAc and showed that NAc noradrenaline levels declined in response to cue-induced reward retrieval but not foot shock. Combined, these findings suggest that high-fidelity afferent information from viscerosensory afferents reaches the NAc. These signals are likely unrelated to CCK-sensitive vagal afferents but could interact with other sensory and higher order inputs to modulate learned appetitive behaviours.

Space wandering in the rodent default mode network

The default mode network (DMN) is a large-scale brain network known to be suppressed during a wide range of cognitive tasks. However, our comprehension of its role in naturalistic and unconstrained behaviors has remained elusive because most research on the DMN has been conducted within the restrictive confines of MRI scanners. Here, we use multisite GCaMP (a genetically encoded calcium indicator) fiber photometry with simultaneous videography to probe DMN function in awake, freely exploring rats. We examined neural dynamics in three core DMN nodes-the retrosplenial cortex, cingulate cortex, and prelimbic cortex-as well as the anterior insula node of the salience network, and their association with the rats' spatial exploration behaviors. We found that DMN nodes displayed a hierarchical functional organization during spatial exploration, characterized by stronger coupling with each other than with the anterior insula. Crucially, these DMN nodes encoded the kinematics of spatial exploration, including linear and angular velocity. Additionally, we identified latent brain states that encoded distinct patterns of time-varying exploration behaviors and found that higher linear velocity was associated with enhanced DMN activity, heightened synchronization among DMN nodes, and increased anticorrelation between the DMN and anterior insula. Our findings highlight the involvement of the DMN in collectively and dynamically encoding spatial exploration in a real-world setting. Our findings challenge the notion that the DMN is primarily a "task-negative" network disengaged from the external world. By illuminating the DMN's role in naturalistic behaviors, our study underscores the importance of investigating brain network function in ecologically valid contexts.

Lights, fiber, action! A primer on in vivo fiber photometry

Fiber photometry is a key technique for characterizing brain-behavior relationships in vivo. Initially, it was primarily used to report calcium dynamics as a proxy for neural activity via genetically encoded indicators. This generated new insights into brain functions including movement, memory, and motivation at the level of defined circuits and cell types. Recently, the opportunity for discovery with fiber photometry has exploded with the development of an extensive range of fluorescent sensors for biomolecules including neuromodulators and peptides that were previously inaccessible in vivo. This critical advance, combined with the new availability of affordable "plug-and-play" recording systems, has made monitoring molecules with high spatiotemporal precision during behavior highly accessible. However, while opening exciting new avenues for research, the rapid expansion in fiber photometry applications has occurred without coordination or consensus on best practices. Here, we provide a comprehensive guide to help end-users execute, analyze, and suitably interpret fiber photometry studies.

Distinct neurochemical influences on fMRI response polarity in the striatum

The striatum, known as the input nucleus of the basal ganglia, is extensively studied for its diverse behavioral roles. However, the relationship between its neuronal and vascular activity, vital for interpreting functional magnetic resonance imaging (fMRI) signals, has not received comprehensive examination within the striatum. Here, we demonstrate that optogenetic stimulation of dorsal striatal neurons or their afferents from various cortical and subcortical regions induces negative striatal fMRI responses in rats, manifesting as vasoconstriction. These responses occur even with heightened striatal neuronal activity, confirmed by electrophysiology and fiber-photometry. In parallel, midbrain dopaminergic neuron optogenetic modulation, coupled with electrochemical measurements, establishes a link between striatal vasodilation and dopamine release. Intriguingly, in vivo intra-striatal pharmacological manipulations during optogenetic stimulation highlight a critical role of opioidergic signaling in generating striatal vasoconstriction. This observation is substantiated by detecting striatal vasoconstriction in brain slices after synthetic opioid application. In humans, manipulations aimed at increasing striatal neuronal activity likewise elicit negative striatal fMRI responses. Our results emphasize the necessity of considering vasoactive neurotransmission alongside neuronal activity when interpreting fMRI signal.

In Vivo Two-Photon Microscopy Reveals Sensory-Evoked Serotonin (5-HT) Release in Adult Mammalian Neocortex

The recent development of genetically encoded fluorescent neurotransmitter biosensors has opened the door to recording serotonin (5-hydroxytryptamine, 5-HT) signaling dynamics with high temporal and spatial resolution in vivo. While this represents a significant step forward for serotonin research, the utility of available 5-HT biosensors remains to be fully established under diverse in vivo conditions. Here, we used two-photon microscopy in awake mice to examine the effectiveness of specific 5-HT biosensors for monitoring 5-HT dynamics in somatosensory cortex. Initial experiments found that whisker stimulation evoked a striking change in 5-HT biosensor signal. However, similar changes were observed in controls expressing green fluorescent protein, suggesting a potential hemodynamic artifact. Subsequent use of a second control fluorophore with emission peaks separated from the 5-HT biosensor revealed a reproducible, stimulus-locked increase in 5-HT signal. Our data highlight the promise of 5-HT biosensors for in vivo application, provided measurements are carried out with appropriate optical controls.

How can I measure brain acetylcholine levels in vivo? Advantages and caveats of commonly used approaches

The neurotransmitter acetylcholine (ACh) plays a central role in the regulation of multiple cognitive and behavioral processes, including attention, learning, memory, motivation, anxiety, mood, appetite, and reward. As a result, understanding ACh dynamics in the brain is essential for elucidating the neural mechanisms underlying these processes. In vivo measurements of ACh in the brain have been challenging because of the low concentrations and rapid turnover of this neurotransmitter. Here, we review a number of techniques that have been developed to measure ACh levels in the brain in vivo. We follow this with a deeper focus on use of genetically encoded fluorescent sensors coupled with fiber photometry, an accessible technique that can be used to monitor neurotransmitter release with high temporal resolution and specificity. We conclude with a discussion of methods for analyzing fiber photometry data and their respective advantages and disadvantages. The development of genetically encoded fluorescent ACh sensors is revolutionizing the field of cholinergic signaling, allowing temporally precise measurement of ACh release in awake, behaving animals. Use of these sensors has already begun to contribute to a mechanistic understanding of cholinergic modulation of complex behaviors.

Dopamine release in the nucleus accumbens promotes REM sleep and cataplexy

Patients with the sleep disorder narcolepsy suffer from excessive daytime sleepiness, disrupted nighttime sleep, and cataplexy-the abrupt loss of postural muscle tone during wakefulness, often triggered by strong emotion. The dopamine (DA) system is implicated in both sleep-wake states and cataplexy, but little is known about the function of DA release in the striatum and sleep disorders. Recording DA release in the ventral striatum revealed orexin-independent changes across sleep-wake states as well as striking increases in DA release in the ventral, but not dorsal, striatum prior to cataplexy onset. Tonic low-frequency stimulation of ventral tegmental efferents in the ventral striatum suppressed both cataplexy and rapid eye movement (REM) sleep, while phasic high-frequency stimulation increased cataplexy propensity and decreased the latency to REM sleep. Together, our findings demonstrate a functional role of DA release in the striatum in regulating cataplexy and REM sleep.

Space wandering in the rodent default mode network

The default mode network (DMN) is a large-scale brain network known to be suppressed during a wide range of cognitive tasks. However, our comprehension of its role in naturalistic and unconstrained behaviors has remained elusive because most research on the DMN has been conducted within the restrictive confines of MRI scanners. Here we use multisite GCaMP fiber photometry with simultaneous videography to probe DMN function in awake, freely exploring rats. We examined neural dynamics in three core DMN nodes- the retrosplenial cortex, cingulate cortex, and prelimbic cortex- as well as the anterior insula node of the salience network, and their association with the rats' spatial exploration behaviors. We found that DMN nodes displayed a hierarchical functional organization during spatial exploration, characterized by stronger coupling with each other than with the anterior insula. Crucially, these DMN nodes encoded the kinematics of spatial exploration, including linear and angular velocity. Additionally, we identified latent brain states that encoded distinct patterns of time-varying exploration behaviors and discovered that higher linear velocity was associated with enhanced DMN activity, heightened synchronization among DMN nodes, and increased anticorrelation between the DMN and anterior insula. Our findings highlight the involvement of the DMN in collectively and dynamically encoding spatial exploration in a real-world setting. Our findings challenge the notion that the DMN is primarily a "task-negative" network disengaged from the external world. By illuminating the DMN's role in naturalistic behaviors, our study underscores the importance of investigating brain network function in ecologically valid contexts.

Sensitive multicolor indicators for monitoring norepinephrine in vivo

Genetically encoded indicators engineered from G-protein-coupled receptors are important tools that enable high-resolution in vivo neuromodulator imaging. Here, we introduce a family of sensitive multicolor norepinephrine (NE) indicators, which includes nLightG (green) and nLightR (red). These tools report endogenous NE release in vitro, ex vivo and in vivo with improved sensitivity, ligand selectivity and kinetics, as well as a distinct pharmacological profile compared with previous state-of-the-art GRABNE indicators. Using in vivo multisite fiber photometry recordings of nLightG, we could simultaneously monitor optogenetically evoked NE release in the mouse locus coeruleus and hippocampus. Two-photon imaging of nLightG revealed locomotion and reward-related NE transients in the dorsal CA1 area of the hippocampus. Thus, the sensitive NE indicators introduced here represent an important addition to the current repertoire of indicators and provide the means for a thorough investigation of the NE system.

Using Fiber Photometry in Mice to Estimate Fluorescent Biosensor Levels During Sleep

Sleep is not homogenous but contains a highly diverse microstructural composition influenced by neuromodulators. Prior methods used to measure neuromodulator levels in vivo have been limited by low time resolution or technical difficulties in achieving recordings in a freely moving setting, which is essential for natural sleep. In this protocol, we demonstrate the combination of electroencephalographic (EEG)/electromyographic (EMG) recordings with fiber photometric measurements of fluorescent biosensors for neuromodulators in freely moving mice. This allows for real-time assessment of extracellular neuromodulator levels during distinct phases of sleep with a high temporal resolution.

Striatal dopamine regulates sleep states and narcolepsy-cataplexy

Disruptions to sleep can be debilitating and have a severe effect on daily life. Patients with the sleep disorder narcolepsy suffer from excessive daytime sleepiness, disrupted nighttime sleep, and cataplexy - the abrupt loss of postural muscle tone (atonia) during wakefulness, often triggered by strong emotion. The dopamine (DA) system is implicated in both sleep-wake states and cataplexy, but little is known about the function of DA release in the striatum - a major output region of midbrain DA neurons - and sleep disorders. To better characterize the function and pattern of DA release in sleepiness and cataplexy, we combined optogenetics, fiber photometry, and sleep recordings in a murine model of narcolepsy (orexin-/-; OX KO) and in wildtype mice. Recording DA release in the ventral striatum revealed OX-independent changes across sleep-wake states as well as striking increases in DA release in the ventral, but not dorsal, striatum prior to cataplexy onset. Tonic low frequency stimulation of ventral tegmental efferents in the ventral striatum suppressed both cataplexy and REM sleep, while phasic high frequency stimulation increased cataplexy propensity and decreased the latency to rapid eye movement (REM) sleep. Together, our findings demonstrate a functional role of DA release in the striatum in regulating cataplexy and REM sleep.

Putative neurochemical and cell type contributions to hemodynamic activity in the rodent caudate putamen

Functional magnetic resonance imaging (fMRI) is widely used by researchers to noninvasively monitor brain-wide activity. The traditional assumption of a uniform relationship between neuronal and hemodynamic activity throughout the brain has been increasingly challenged. This relationship is now believed to be impacted by heterogeneously distributed cell types and neurochemical signaling. To date, most cell-type- and neurotransmitter-specific influences on hemodynamics have been examined within the cortex and hippocampus of rodent models, where glutamatergic signaling is prominent. However, neurochemical influences on hemodynamics are relatively unknown in largely GABAergic brain regions such as the rodent caudate putamen (CPu). Given the extensive contribution of CPu function and dysfunction to behavior, and the increasing focus on this region in fMRI studies, improved understanding of CPu hemodynamics could have broad impacts. Here we discuss existing findings on neurochemical contributions to hemodynamics as they may relate to the CPu with special consideration for how these contributions could originate from various cell types and circuits. We hope this review can help inform the direction of future studies as well as interpretation of fMRI findings in the CPu.

Neuronal dynamics of the default mode network and anterior insular cortex: Intrinsic properties and modulation by salient stimuli

The default mode network (DMN) is critical for self-referential mental processes, and its dysfunction is implicated in many neuropsychiatric disorders. However, the neurophysiological properties and task-based functional organization of the rodent DMN are poorly understood, limiting its translational utility. Here, we combine fiber photometry with functional magnetic resonance imaging (fMRI) and computational modeling to characterize dynamics of putative rat DMN nodes and their interactions with the anterior insular cortex (AI) of the salience network. Our analysis revealed neuronal activity changes in AI and DMN nodes preceding fMRI-derived DMN activations and cyclical transitions between brain network states. Furthermore, we demonstrate that salient oddball stimuli suppress the DMN and enhance AI neuronal activity and that the AI causally inhibits the retrosplenial cortex, a prominent DMN node. These findings elucidate the neurophysiological foundations of the rodent DMN, its spatiotemporal dynamical properties, and modulation by salient stimuli, paving the way for future translational studies.

The impact of vasomotion on analysis of rodent fMRI data

Introduction

Small animal fMRI is an essential part of translational research in the cognitive neurosciences. Due to small dimensions and animal physiology preclinical fMRI is prone to artifacts that may lead to misinterpretation of the data. To reach unbiased translational conclusions, it is, therefore, crucial to identify potential sources of experimental noise and to develop correction methods for contributions that cannot be avoided such as physiological noise. Aim of this study was to assess origin and prevalence of hemodynamic oscillations (HDO) in preclinical fMRI in rat, as well as their impact on data analysis.

Methods

Following the development of algorithms for HDO detection and suppression, HDO prevalence in fMRI measurements was investigated for different anesthetic regimens, comprising isoflurane and medetomidine, and for both gradient echo and spin echo fMRI sequences. In addition to assessing the effect of vasodilation on HDO, it was studied if HDO have a direct neuronal correlate using local field potential (LFP) recordings. Finally, the impact of HDO on analysis of fMRI data was assessed, studying both the impact on calculation of activation maps as well as the impact on brain network analysis. Overall, 303 fMRI measurements and 32 LFP recordings were performed in 71 rats.

Results

In total, 62% of the fMRI measurements showed HDO with a frequency of (0.20 ± 0.02) Hz. This frequent occurrence indicated that HDO cannot be generally neglected in fMRI experiments. Using the developed algorithms, HDO were detected with a specificity of 95%, and removed efficiently from the signal time courses. HDO occurred brain-wide under vasoconstrictive conditions in both small and large blood vessels. Vasodilation immediately interrupted HDO, which, however, returned within 1 h under vasoconstrictive conditions. No direct neuronal correlate of HDO was observed in LFP recordings. HDO significantly impacted analysis of fMRI data, leading to altered cluster sizes and F-values for activated voxels, as well as altered brain networks, when comparing data with and without HDO.

Discussion

We therefore conclude that HDO are caused by vasomotion under certain anesthetic conditions and should be corrected during fMRI data analysis to avoid bias.

Simultaneous recording of neuronal and vascular activity in the rodent brain using fiber-photometry

Coupling of hemodynamic responses to neuronal activity is the foundation of several functional neuroimaging techniques. Here, we provide three fiber-photometry approaches to simultaneously measure neuronal and vascular signals in the rodent brain using a spectrometer-based system. Two out of these three approaches allow the removal of hemoglobin (Hb)-absorption artifacts and restore the underlying neuronal activity. This technique is applicable to different fluorescent sensors and provides a more accurate measurement of hemodynamic response function in any location of the rodent brain. For complete details on the use and execution of this protocol, please refer to Zhang et al. (2022).

Correcting for the hemoglobin absorption artifact in fiber photometry data

Fiber photometry is a widely used fluorescence approach for measuring neuronal activity in freely behaving animals; however, these signals can be contaminated by hemoglobin absorption artifacts. Zhang et al. propose a computational method to quantify and correct hemoglobin photon absorption effects using spectral fiber photometry, resulting in more accurate neuronal activity measurements.

Fiber-based lactate recordings with fluorescence resonance energy transfer sensors by applying an magnetic resonance-informed correction of hemodynamic artifacts

Significance: Fluorescence resonance energy transfer (FRET) sensors offer enormous benefits when studying neurophysiology through confocal microscopy. Yet, their use for fiber-based in vivo recordings is hampered by massive confounding effects and has therefore been scarcely reported. Aim: We aim to investigate whether in vivo fiber-based lactate recordings in the rodent brain are feasible with FRET sensors and implement a correction algorithm for the predominant hemodynamic artifact. Approach: We performed fiber-based FRET recordings of lactate (Laconic) and calcium (Twitch-2B) simultaneously with functional MRI and pharmacological MRI. MR-derived parameters were applied to correct hemodynamic artifacts. Results of FRET measurements were validated by local field potential, magnetic resonance spectroscopy, and blood analysis. Results: Hemodynamic artifacts dominated fiber-based in vivo FRET measurements with both Laconic and Twitch-2B. Our MR-based correction algorithm enabled to remove the artifacts and detect lactate and calcium changes during sensory stimulation or intravenous lactate injections. Conclusions: In vivo fiber-based lactate recordings are feasible using FRET-based sensors. However, signal corrections are required. MR-derived hemodynamic parameters can successfully be applied for artifact correction.

Computing hemodynamic response functions from concurrent spectral fiber-photometry and fMRI data

Significance: Although emerging evidence suggests that the hemodynamic response function (HRF) can vary by brain region and species, a single, canonical, human-based HRF is widely used in animal studies. Therefore, the development of flexible, accessible, brain-region specific HRF calculation approaches is paramount as hemodynamic animal studies become increasingly popular. Aim: To establish an fMRI-compatible, spectral, fiber-photometry platform for HRF calculation and validation in any rat brain region. Approach: We used our platform to simultaneously measure (a) neuronal activity via genetically encoded calcium indicators (GCaMP6f), (b) local cerebral blood volume (CBV) from intravenous Rhodamine B dye, and (c) whole brain CBV via fMRI with the Feraheme contrast agent. Empirical HRFs were calculated with GCaMP6f and Rhodamine B recordings from rat brain regions during resting-state and task-based paradigms. Results: We calculated empirical HRFs for the rat primary somatosensory, anterior cingulate, prelimbic, retrosplenial, and anterior insular cortical areas. Each HRF was faster and narrower than the canonical HRF and no significant difference was observed between these cortical regions. When used in general linear model analyses of corresponding fMRI data, the empirical HRFs showed better detection performance than the canonical HRF. Conclusions: Our findings demonstrate the viability and utility of fiber-photometry-based HRF calculations. This platform is readily scalable to multiple simultaneous recording sites, and adaptable to study transfer functions between stimulation events, neuronal activity, neurotransmitter release, and hemodynamic responses.