Simultaneous Electrophysiology and Fiber Photometry in Freely Behaving Mice

Linking brain activity across scales with simultaneous opto- and electrophysiology

The brain enables adaptive behavior via the dynamic coordination of diverse neuronal signals across spatial and temporal scales: from fast action potential patterns in microcircuits to slower patterns of distributed activity in brain-wide networks. Understanding principles of multiscale dynamics requires simultaneous monitoring of signals in multiple, distributed network nodes. Combining optical and electrical recordings of brain activity is promising for collecting data across multiple scales and can reveal aspects of coordinated dynamics invisible to standard, single-modality approaches. We review recent progress in combining opto- and electrophysiology, focusing on mouse studies that shed new light on the function of single neurons by embedding their activity in the context of brain-wide activity patterns. Optical and electrical readouts can be tailored to desired scales to tackle specific questions. For example, fast dynamics in single cells or local populations recorded with multi-electrode arrays can be related to simultaneously acquired optical signals that report activity in specified subpopulations of neurons, in non-neuronal cells, or in neuromodulatory pathways. Conversely, two-photon imaging can be used to densely monitor activity in local circuits while sampling electrical activity in distant brain areas at the same time. The refinement of combined approaches will continue to reveal previously inaccessible and under-appreciated aspects of coordinated brain activity.

"There's plenty of room at the bottom": deep brain imaging with holographic endo-microscopy

Significance

Over more than 300 years, microscopic imaging keeps providing fundamental insights into the mechanisms of living organisms. Seeing microscopic structures beyond the reach of free-space light-based microscopy, however, requires dissection of the tissue-an intervention seriously disturbing its physiological functions. The hunt for low-invasiveness tools has led a growing community of physicists and engineers into the realm of complex media photonics. One of its activities represents exploiting multimode optical fibers (MMFs) as ultra-thin endoscopic probes. Employing wavefront shaping, these tools only recently facilitated the first peeks at cells and their sub-cellular compartments at the bottom of the mouse brain with the impact of micro-scale tissue damage.

Aim

Here, we aim to highlight advances in MMF-based holographic endo-microscopy facilitating microscopic imaging throughout the whole depth of the mouse brain.

Approach

We summarize the important technical and methodological prerequisites for stabile high-resolution imaging in vivo.

Results

We showcase images of the microscopic building blocks of brain tissue, including neurons, neuronal processes, vessels, intracellular calcium signaling, and red blood cell velocity in individual vessels.

Conclusions

This perspective article helps to understand the complexity behind the technology of holographic endo-microscopy, summarizes its recent advances and challenges, and stimulates the mind of the reader for further exploitation of this tool in the neuroscience research.

Demixing fluorescence time traces transmitted by multimode fibers

Optical methods based on thin multimode fibers (MMFs) are promising tools for measuring neuronal activity in deep brain regions of freely moving mice thanks to their small diameter. However, current methods are limited: while fiber photometry provides only ensemble activity, imaging techniques using of long multimode fibers are very sensitive to bending and have not been applied to unrestrained rodents yet. Here, we demonstrate the fundamentals of a new approach using a short MMF coupled to a miniscope. In proof-of-principle in vitro experiments, we disentangled spatio-temporal fluorescence signals from multiple fluorescent sources transmitted by a thin (200 µm) and short (8 mm) MMF, using a general unconstrained non-negative matrix factorization algorithm directly on the raw video data. Furthermore, we show that low-cost open-source miniscopes have sufficient sensitivity to image the same fluorescence patterns seen in our proof-of-principle experiment, suggesting a new avenue for novel minimally invasive deep brain studies using multimode fibers in freely behaving mice.

Acute and chronic alcohol modulation of extended amygdala calcium dynamics

The central amygdala (CeA) and bed nucleus of the stria terminalis (BNST) are reciprocally connected nodes of the extended amygdala thought to play an important role in alcohol consumption. Studies of immediate-early genes indicate that BNST and CeA are acutely activated following alcohol drinking and may signal alcohol reward in nondependent drinkers, while stress signaling in the extended amygdala following chronic alcohol exposure drives increased drinking via negative reinforcement. However, the temporal dynamics of neuronal activation in these regions during drinking behavior are poorly understood. In this study, we used fiber photometry and the genetically encoded calcium sensor GCaMP6s to assess acute changes in neuronal activity during alcohol consumption in BNST and CeA before and after a chronic drinking paradigm. Activity was examined in the pan-neuronal population and separately in dynorphinergic neurons. BNST and CeA showed increased pan-neuronal activity during acute consumption of alcohol and other fluid tastants of positive and negative valence, as well as highly palatable chow. Responses were greatest during initial consummatory bouts and decreased in amplitude with repeated consumption of the same tastant, suggesting modulation by stimulus novelty. Dynorphin neurons showed similar consumption-associated calcium increases in both regions. Following three weeks of continuous alcohol access (CA), calcium increases in dynorphin neurons during drinking were maintained, but pan-neuronal activity and BNST-CeA coherence were altered in a sex-specific manner. These results indicate that BNST and CeA, and dynorphin neurons specifically, are engaged during drinking behavior, and activity dynamics are influenced by stimulus novelty and chronic alcohol.

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.

The cognitive impact of light: illuminating ipRGC circuit mechanisms

Ever-present in our environments, light entrains circadian rhythms over long timescales, influencing daily activity patterns, health and performance. Increasing evidence indicates that light also acts independently of the circadian system to directly impact physiology and behaviour, including cognition. Exposure to light stimulates brain areas involved in cognition and appears to improve a broad range of cognitive functions. However, the extent of these effects and their mechanisms are unknown. Intrinsically photosensitive retinal ganglion cells (ipRGCs) have emerged as the primary conduit through which light impacts non-image-forming behaviours and are a prime candidate for mediating the direct effects of light on cognition. Here, we review the current state of understanding of these effects in humans and mice, and the tools available to uncover circuit-level and photoreceptor-specific mechanisms. We also address current barriers to progress in this area. Current and future efforts to unravel the circuits through which light influences cognitive functions may inform the tailoring of lighting landscapes to optimize health and cognitive function.

Identifying behavioral links to neural dynamics of multifiber photometry recordings in a mouse social behavior network

Distributed hypothalamic-midbrain neural circuits orchestrate complex behavioral responses during social interactions. How population-averaged neural activity measured by multi-fiber photometry (MFP) for calcium fluorescence signals correlates with social behaviors is a fundamental question. We propose a state-space analysis framework to characterize mouse MFP data based on dynamic latent variable models, which include continuous-state linear dynamical system (LDS) and discrete-state hidden semi-Markov model (HSMM). We validate these models on extensive MFP recordings during aggressive and mating behaviors in male-male and male-female interactions, respectively. Our results show that these models are capable of capturing both temporal behavioral structure and associated neural states. Overall, these analysis approaches provide an unbiased strategy to examine neural dynamics underlying social behaviors and reveals mechanistic insights into the relevant networks.

A cholinergic circuit that relieves pain despite opioid tolerance

Chronic pain is a tremendous burden for afflicted individuals and society. Although opioids effectively relieve pain, significant adverse outcomes limit their utility and efficacy. To investigate alternate pain control mechanisms, we explored cholinergic signaling in the ventrolateral periaqueductal gray (vlPAG), a critical nexus for descending pain modulation. Biosensor assays revealed that pain states decreased acetylcholine release in vlPAG. Activation of cholinergic projections from the pedunculopontine tegmentum to vlPAG relieved pain, even in opioid-tolerant conditions, through ⍺7 nicotinic acetylcholine receptors (nAChRs). Activating ⍺7 nAChRs with agonists or stimulating endogenous acetylcholine inhibited vlPAG neuronal activity through Ca2+ and peroxisome proliferator-activated receptor α (PPAR⍺)-dependent signaling. In vivo 2-photon imaging revealed that chronic pain induces aberrant excitability of vlPAG neuronal ensembles and that ⍺7 nAChR-mediated inhibition of these cells relieves pain, even after opioid tolerance. Finally, pain relief through these cholinergic mechanisms was not associated with tolerance, reward, or withdrawal symptoms, highlighting its potential clinical relevance.

Pathway specific interventions reveal the multiple roles of ventral hippocampus projections in cognitive functions

Since the 1950s study of Scoville and Milner on the case H.M., the hippocampus has attracted neuroscientists' attention. The hippocampus has been traditionally divided into dorsal and ventral parts, each of which projects to different brain structures and mediates various functions. Despite a predominant interest in its dorsal part in animal models, especially regarding episodic-like and spatial cognition, recent data highlight the role of the ventral hippocampus (vHPC), as the main hippocampal output, in cognitive processes. Here, we review recent studies conducted in rodents that have used advanced in vivo functional techniques to specifically monitor and manipulate vHPC efferent pathways and delineate the roles of these specific projections in learning and memory processes. Results highlight that vHPC projections to basal amygdala are implicated in emotional memory, to nucleus accumbens in social memory and instrumental actions and to prefrontal cortex in all the above as well as in object-based memory. Some of these hippocampal projections also modulate feeding and anxiety-like behaviours providing further evidence that the "one pathway-one function" view is outdated and future directions are proposed to better understand the role of hippocampal pathways and shed further light on its connectivity and function.

Acute and chronic alcohol modulation of extended amygdala calcium dynamics

The central amygdala (CeA) and bed nucleus of the stria terminalis (BNST) are reciprocally connected nodes of the extended amygdala thought to play an important role in alcohol consumption. Studies of immediate-early genes indicate that BNST and CeA are acutely activated following alcohol drinking and may signal alcohol reward in nondependent drinkers, while increased stress signaling in the extended amygdala following chronic alcohol exposure drives increased drinking via negative reinforcement. However, the temporal dynamics of neuronal activation in these regions during drinking behavior are poorly understood. In this study, we used fiber photometry and the genetically encoded calcium sensor GCaMP6s to assess acute changes in neuronal activity during alcohol consumption in BNST and CeA before and after a chronic drinking paradigm. Activity was examined in the pan-neuronal population and separately in dynorphinergic neurons. BNST and CeA showed increased pan-neuronal activity during acute consumption of alcohol and other fluid tastants of positive and negative valence, as well as highly palatable chow. Responses were greatest during initial consummatory bouts and decreased in amplitude with repeated consumption of the same tastant, suggesting modulation by stimulus novelty. Dynorphin neurons showed similar consumption-associated calcium increases in both regions. Following three weeks of continuous alcohol access (CA), calcium increases in dynorphin neurons during drinking were maintained, but pan-neuronal activity and BNST-CeA coherence were altered in a sex-specific manner. These results indicate that BNST and CeA, and dynorphin neurons specifically, are engaged during drinking behavior, and activity dynamics are influenced by stimulus novelty and chronic alcohol.

Light disrupts social memory via a retina-to-supraoptic nucleus circuit

The formation of social memory between individuals of the opposite sex is crucial for expanding mating options or establishing monogamous pair bonding. A specialized neuronal circuit that regulates social memory could enhance an individual's mating opportunities and provide a parallel pathway for computing social behaviors. While the influence of light exposure on various forms of memory, such as fear and object memory, has been studied, its modulation of social recognition memory remains unclear. Here, we demonstrate that acute exposure to light impairs social recognition memory (SRM) in mice. Unlike sound and touch stimuli, light inhibits oxytocin neurons in the supraoptic nucleus (SON) via M1 SON-projecting intrinsically photosensitive retinal ganglion cells (ipRGCs) and GABAergic neurons in the perinuclear zone of the SON (pSON). We further show that optogenetic activation of SON oxytocin neurons using channelrhodopsin is sufficient to enhance SRM performance, even under light conditions. Our findings unveil a dedicated neuronal circuit through which luminance affects SRM, utilizing a non-image-forming visual pathway, distinct from the canonical modulatory role of the oxytocin system.

Pontine Waves Accompanied by Short Hippocampal Sharp Wave-Ripples During Non-rapid Eye Movement Sleep

Ponto-geniculo-occipital or pontine (P) waves have long been recognized as an electrophysiological signature of rapid eye movement (REM) sleep. However, P-waves can be observed not just during REM sleep, but also during non-REM (NREM) sleep. Recent studies have uncovered that P-waves are functionally coupled with hippocampal sharp wave ripples (SWRs) during NREM sleep. However, it remains unclear to what extent P-waves during NREM sleep share their characteristics with P-waves during REM sleep and how the functional coupling to P-waves modulates SWRs. Here, we address these issues by performing multiple types of electrophysiological recordings and fiber photometry in both sexes of mice. P-waves during NREM sleep share their waveform shapes and local neural ensemble dynamics at a short (~100 milliseconds) timescale with their REM sleep counterparts. However, the dynamics of mesopontine cholinergic neurons are distinct at a longer (~10 seconds) timescale: although P-waves are accompanied by cholinergic transients, the cholinergic tone gradually reduces before P-wave genesis during NREM sleep. While P-waves are coupled to hippocampal theta rhythms during REM sleep, P-waves during NREM sleep are accompanied by a rapid reduction in hippocampal ripple power. SWRs coupled with P-waves are short-lived and hippocampal neural firing is also reduced after P-waves. These results demonstrate that P-waves are part of coordinated sleep-related activity by functionally coupling with hippocampal ensembles in a state-dependent manner.

A medullary hub for controlling REM sleep and pontine waves

Rapid-eye-movement (REM) sleep is a distinct behavioral state associated with vivid dreaming and memory processing. Phasic bursts of electrical activity, measurable as spike-like pontine (P)-waves, are a hallmark of REM sleep implicated in memory consolidation. However, the brainstem circuits regulating P-waves, and their interactions with circuits generating REM sleep, remain largely unknown. Here, we show that an excitatory population of dorsomedial medulla (dmM) neurons expressing corticotropin-releasing-hormone (CRH) regulates both REM sleep and P-waves in mice. Calcium imaging showed that dmM CRH neurons are selectively activated during REM sleep and recruited during P-waves, and opto- and chemogenetic experiments revealed that this population promotes REM sleep. Chemogenetic manipulation also induced prolonged changes in P-wave frequency, while brief optogenetic activation reliably triggered P-waves along with transiently accelerated theta oscillations in the electroencephalogram (EEG). Together, these findings anatomically and functionally delineate a common medullary hub for the regulation of both REM sleep and P-waves.

High resolution recording of local field currents simultaneously with sound-evoked calcium signals by a photometric patch electrode in the auditory cortex field L of the chick

BACKGROUND

Functioning of the brain is based on both electrical and metabolic activity of neural ensembles. Accordingly, it would be useful to measure intracellular metabolic signaling simultaneously with electrical activity in the brain in vivo.

NEW METHOD

We innovated a PhotoMetric-patch-Electrode (PME) recording system that has a high temporal resolution incorporating a photomultiplier tube as a light detector. The PME is fabricated from a quartz glass capillary to transmit light as a light guide, and it can detect electrical signals as a patch electrode simultaneously with a fluorescence signal.

RESULTS

We measured the sound-evoked Local Field Current (LFC) and fluorescence Ca²⁺ signal from neurons labeled with Ca²⁺-sensitive dye Oregon Green BAPTA1 in field L, the avian auditory cortex. Sound stimulation evoked multi-unit spike bursts and Ca²⁺ signals, and enhanced the fluctuation of LFC. After a brief sound stimulation, the cross-correlation between LFC and Ca²⁺ signal was prolonged. D-AP5 (antagonist for NMDA receptors) suppressed the sound-evoked Ca²⁺ signal when applied locally by pressure from the tip of PME.

COMPARISON WITH EXISTING METHODS

In contrast to existing multiphoton imaging or optical fiber recording methods, the PME is a patch electrode pulled simply from a quartz glass capillary and can measure fluorescence signals at the tip simultaneously with electrical signal at any depth of the brain structure.

CONCLUSION

The PME is devised to record electrical and optical signals simultaneously with high temporal resolution. Moreover, it can inject chemical agents dissolved in the tip-filling medium locally by pressure, allowing manipulation of neural activity pharmacologically.

A flexible and versatile system for multi-color fiber photometry and optogenetic manipulation

Here, we present simultaneous fiber photometry recordings and optogenetic stimulation based on a multimode fused fiber coupler for both light delivery and collection without the need for dichroic beam splitters. In combination with a multi-color light source and appropriate optical filters, our approach offers remarkable flexibility in experimental design and facilitates the exploration of new molecular tools in vivo at minimal cost. We demonstrate straightforward re-configuration of the setup to operate with green, red, and near-infrared calcium indicators with or without simultaneous optogenetic stimulation and further explore the multi-color photometry capabilities of the system. The ease of assembly, operation, characterization, and customization of this platform holds the potential to foster the development of experimental strategies for multi-color fused fiber photometry combined with optogenetics far beyond its current state.

Autonomic dysfunction in epilepsy mouse models with implications for SUDEP research

Epilepsy has a high prevalence and can severely impair quality of life and increase the risk of premature death. Sudden unexpected death in epilepsy (SUDEP) is the leading cause of death in drug-resistant epilepsy and most often results from respiratory and cardiac impairments due to brainstem dysfunction. Epileptic activity can spread widely, influencing neuronal activity in regions outside the epileptic network. The brainstem controls cardiorespiratory activity and arousal and reciprocally connects to cortical, diencephalic, and spinal cord areas. Epileptic activity can propagate trans-synaptically or via spreading depression (SD) to alter brainstem functions and cause cardiorespiratory dysfunction. The mechanisms by which seizures propagate to or otherwise impair brainstem function and trigger the cascading effects that cause SUDEP are poorly understood. We review insights from mouse models combined with new techniques to understand the pathophysiology of epilepsy and SUDEP. These techniques include in vivo, ex vivo, invasive and non-invasive methods in anesthetized and awake mice. Optogenetics combined with electrophysiological and optical manipulation and recording methods offer unique opportunities to study neuronal mechanisms under normal conditions, during and after non-fatal seizures, and in SUDEP. These combined approaches can advance our understanding of brainstem pathophysiology associated with seizures and SUDEP and may suggest strategies to prevent SUDEP.

Simultaneous dynamic glucose-enhanced (DGE) MRI and fiber photometry measurements of glucose in the healthy mouse brain

Glucose is the main energy source in the brain and its regulated uptake and utilization are important biomarkers of pathological brain function. Glucose Chemical Exchange Saturation Transfer (GlucoCEST) and its time-resolved version Dynamic Glucose-Enhanced MRI (DGE) are promising approaches to monitor glucose and detect tumors, since they are radioactivity-free, do not require ¹³C labeling and are is easily translatable to the clinics. The main principle of DGE is clear. However, what remains to be established is to which extent the signal reflects vascular, extracellular or intracellular glucose. To elucidate the compartmental contributions to the DGE signal, we coupled it with FRET-based fiber photometry of genetically encoded sensors, a technique that combines quantitative glucose readout with cellular specificity. The glucose sensor FLIIP was used with fiber photometry to measure astrocytic and neuronal glucose changes upon injection of D-glucose, 3OMG and L-glucose, in the anaesthetized murine brain. By correlating the kinetic profiles of the techniques, we demonstrate the presence of a vascular contribution to the signal, especially at early time points after injection. Furthermore, we show that, in the case of the commonly used contrast agent 3OMG, the DGE signal actually anticorrelates with the glucose concentration in neurons and astrocytes.

Calcium imaging: A versatile tool to examine Huntington's disease mechanisms and progression

Huntington's disease (HD) is a fatal, hereditary neurodegenerative disorder that causes chorea, cognitive deficits, and psychiatric symptoms. It is characterized by accumulation of mutant Htt protein, which primarily impacts striatal medium-sized spiny neurons (MSNs), as well as cortical pyramidal neurons (CPNs), causing synapse loss and eventually cell death. Perturbed Ca²⁺ homeostasis is believed to play a major role in HD, as altered Ca²⁺ homeostasis often precedes striatal dysfunction and manifestation of HD symptoms. In addition, dysregulation of Ca²⁺ can cause morphological and functional changes in MSNs and CPNs. Therefore, Ca²⁺ imaging techniques have the potential of visualizing changes in Ca²⁺ dynamics and neuronal activity in HD animal models. This minireview focuses on studies using diverse Ca²⁺ imaging techniques, including two-photon microscopy, fiber photometry, and miniscopes, in combination of Ca²⁺ indicators to monitor activity of neurons in HD models as the disease progresses. We then discuss the future applications of Ca²⁺ imaging to visualize disease mechanisms and alterations associated with HD, as well as studies showing how, as a proof-of-concept, Ca²⁺imaging using miniscopes in freely-behaving animals can help elucidate the differential role of direct and indirect pathway MSNs in HD symptoms.

Design of optoelectrodes for the remote imaging of cells and in situ electrochemical detection of neurosecretory events

Optical fibers have opened avenues for remote imaging, bioanalyses and recently optogenetics. Besides, miniaturized electrochemical sensors have offered new opportunities in sensing directly redox neurotransmitters. The combination of both optical and electrochemical approaches was usually performed on the platform of microscopes or within microsystems. In this work, we developed optoelectrodes which features merge the advantages of both optical fibers and microelectrodes. Optical fiber bundles were modified at one of their extremity by a transparent ITO deposit. The electrochemical responses of these ITO-modified bundles were characterized for the detection of dopamine, epinephrine and norepinephrine. The analytical performances of the optoelectrodes were equivalent to the ones reported for carbon microelectrodes. The remote imaging of model neurosecretory PC12 cells by optoelectrodes was performed upon cell-staining with common fluorescent dyes: acridine orange and calcein-AM. An optoelectrode placed by micromanipulation at a few micrometers-distance from the cells offered remote images with single cell resolution. Finally, in situ electrochemical sensing was demonstrated by additions of K⁺-secretagogue solutions near PC12 cells under observation, leading to exocytotic events detected as amperometric spikes at the ITO surface. Such dual sensors should pave the way for in vivo remote imaging, optogenetic stimulation, and simultaneous detection of neurosecretory activities.

Deep Brain Stimulation for Addictive Disorders-Where Are We Now?

In the face of a global epidemic of drug addiction, neglecting to develop new effective therapies will perpetuate the staggering human and economic costs of substance use. This review aims to summarize and evaluate the preclinical and clinical studies of deep brain stimulation (DBS) as a novel therapy for refractory addiction, in hopes to engage and inform future research in this promising novel treatment avenue. An electronic database search (MEDLINE, EMBASE, Cochrane library) was performed using keywords and predefined inclusion criteria between 1974 and 6/18/2021 (registered on Open Science Registry). Selected articles were reviewed in full text and key details were summarized and analyzed to understand DBS' therapeutic potential and possible mechanisms of action. The search yielded 25 animal and 22 human studies. Animal studies showed that DBS of targets such as nucleus accumbens (NAc), insula, and subthalamic nucleus reduces drug use and seeking. All human studies were case series/reports (level 4/5 evidence), mostly targeting the NAc with generally positive outcomes. From the limited evidence in the literature, DBS, particularly of the NAc, appears to be a reasonable last resort option for refractory addictive disorders. We propose that future research in objective electrophysiological (e.g., local field potentials) and neurochemical (e.g., extracellular dopamine levels) biomarkers would assist monitoring the progress of treatment and developing a closed-loop DBS system. Preclinical literature also highlighted the prefrontal cortex as a promising DBS target, which should be explored in human research.

Optogenetic Methods to Investigate Brain Alterations in Preclinical Models

Investigating the neuronal dynamics supporting brain functions and understanding how the alterations in these mechanisms result in pathological conditions represents a fundamental challenge. Preclinical research on model organisms allows for a multiscale and multiparametric analysis in vivo of the neuronal mechanisms and holds the potential for better linking the symptoms of a neurological disorder to the underlying cellular and circuit alterations, eventually leading to the identification of therapeutic/rescue strategies. In recent years, brain research in model organisms has taken advantage, along with other techniques, of the development and continuous refinement of methods that use light and optical approaches to reconstruct the activity of brain circuits at the cellular and system levels, and to probe the impact of the different neuronal components in the observed dynamics. These tools, combining low-invasiveness of optical approaches with the power of genetic engineering, are currently revolutionizing the way, the scale and the perspective of investigating brain diseases. The aim of this review is to describe how brain functions can be investigated with optical approaches currently available and to illustrate how these techniques have been adopted to study pathological alterations of brain physiology.

Neurogenesis mediated plasticity is associated with reduced neuronal activity in CA1 during context fear memory retrieval

Postnatal hippocampal neurogenesis has been demonstrated to affect learning and memory in numerous ways. Several studies have now demonstrated that increased neurogenesis can induce forgetting of memories acquired prior to the manipulation of neurogenesis and, as a result of this forgetting can also facilitate new learning. However, the mechanisms mediating neurogenesis-induced forgetting are not well understood. Here, we used a subregion-based analysis of the immediate early gene c-Fos as well as in vivo fiber photometry to determine changes in activity corresponding with neurogenesis induced forgetting. We found that increasing neurogenesis led to reduced CA1 activity during context memory retrieval. We also demonstrate here that perineuronal net expression in areas CA1 is bidirectionally altered by the levels or activity of postnatally generated neurons in the dentate gyrus. These results suggest that neurogenesis may induce forgetting by disrupting perineuronal nets in CA1 which may otherwise protect memories from degradation.

Red Light Optogenetics in Neuroscience

Optogenetics, a field concentrating on controlling cellular functions by means of light-activated proteins, has shown tremendous potential in neuroscience. It possesses superior spatiotemporal resolution compared to the surgical, electrical, and pharmacological methods traditionally used in studying brain function. A multitude of optogenetic tools for neuroscience have been created that, for example, enable the control of action potential generation via light-activated ion channels. Other optogenetic proteins have been used in the brain, for example, to control long-term potentiation or to ablate specific subtypes of neurons. In in vivo applications, however, the majority of optogenetic tools are operated with blue, green, or yellow light, which all have limited penetration in biological tissues compared to red light and especially infrared light. This difference is significant, especially considering the size of the rodent brain, a major research model in neuroscience. Our review will focus on the utilization of red light-operated optogenetic tools in neuroscience. We first outline the advantages of red light for in vivo studies. Then we provide a brief overview of the red light-activated optogenetic proteins and systems with a focus on new developments in the field. Finally, we will highlight different tools and applications, which further facilitate the use of red light optogenetics in neuroscience.

Light-guided sectioning for precise in situ localization and tissue interface analysis for brain-implanted optical fibers and GRIN lenses

Optical implants to control and monitor neuronal activity in vivo have become foundational tools of neuroscience. Standard two-dimensional histology of the implant location, however, often suffers from distortion and loss during tissue processing. To address that, we developed a three-dimensional post hoc histology method called “light-guided sectioning” (LiGS), which preserves the tissue with its optical implant in place and allows staining and clearing of a volume up to 500 μm in depth. We demonstrate the use of LiGS to determine the precise location of an optical fiber relative to a deep brain target and to investigate the implant-tissue interface. We show accurate cell registration of ex vivo histology with single-cell, two-photon calcium imaging, obtained through gradient refractive index (GRIN) lenses, and identify subpopulations based on immunohistochemistry. LiGS provides spatial information in experimental paradigms that use optical fibers and GRIN lenses and could help increase reproducibility through identification of fiber-to-target localization and molecular profiling.

Kahan et al. describe a 3D histology method (LiGS) to investigate with high fidelity the vicinity of an intact optical implant (e.g., GRIN lenses and optical fibers). LiGS is compatible with immunohistochemistry and single-molecule imaging. With the use of two-photon microscopy, LiGS can also link the functional properties of cells to their molecular identity.

Automated microscope-independent fluorescence-guided micropipette

Glass micropipette electrodes are commonly used to provide high resolution recordings of neurons. Although it is the gold standard for single cell recordings, it is highly dependent on the skill of the electrophysiologist. Here, we demonstrate a method of guiding micropipette electrodes to neurons by collecting fluorescence at the aperture, using an intra-electrode tapered optical fiber. The use of a tapered fiber for excitation and collection of fluorescence at the micropipette tip couples the feedback mechanism directly to the distance between the target and electrode. In this study, intra-electrode tapered optical fibers provide a targeted robotic approach to labeled neurons that is independent of microscopy.

Mutual Interactions between Brain States and Alzheimer's Disease Pathology: A Focus on Gamma and Slow Oscillations

Brain state varies from moment to moment. While brain state can be defined by ongoing neuronal population activity, such as neuronal oscillations, this is tightly coupled with certain behavioural or vigilant states. In recent decades, abnormalities in brain state have been recognised as biomarkers of various brain diseases and disorders. Intriguingly, accumulating evidence also demonstrates mutual interactions between brain states and disease pathologies: while abnormalities in brain state arise during disease progression, manipulations of brain state can modify disease pathology, suggesting a therapeutic potential. In this review, by focusing on Alzheimer's disease (AD), the most common form of dementia, we provide an overview of how brain states change in AD patients and mouse models, and how controlling brain states can modify AD pathology. Specifically, we summarise the relationship between AD and changes in gamma and slow oscillations. As pathological changes in these oscillations correlate with AD pathology, manipulations of either gamma or slow oscillations can modify AD pathology in mouse models. We argue that neuromodulation approaches to target brain states are a promising non-pharmacological intervention for neurodegenerative diseases.

Distinct Characteristics of Odor-evoked Calcium and Electrophysiological Signals in Mitral/Tufted Cells in the Mouse Olfactory Bulb

Fiber photometry is a recently-developed method that indirectly measures neural activity by monitoring Ca²⁺ signals in genetically-identified neuronal populations. Although fiber photometry is widely used in neuroscience research, the relationship between the recorded Ca²⁺ signals and direct electrophysiological measurements of neural activity remains elusive. Here, we simultaneously recorded odor-evoked Ca²⁺ and electrophysiological signals [single-unit spikes and local field potentials (LFPs)] from mitral/tufted cells in the olfactory bulb of awake, head-fixed mice. Odors evoked responses in all types of signal but the response characteristics (e.g., type of response and time course) differed. The Ca²⁺ signal was correlated most closely with power in the β-band of the LFP. The Ca²⁺ signal performed slightly better at odor classification than high-γ oscillations, worse than single-unit spikes, and similarly to β oscillations. These results provide new information to help researchers select an appropriate method for monitoring neural activity under specific conditions.

Hybrid Electrical and Optical Neural Interfaces

Neural interfaces bridge the nervous system and the outside world by recording and stimulating neurons. Combining electrical and optical modalities in a single, hybrid neural interface system could lead to complementary and powerful new ways to explore the brain. It has gained robust and exciting momentum recently in neuroscience and neural engineering research. Here, we review developments in the past several years aiming to achieve such hybrid electrical and optical microsystem platforms. Specifically, we cover three major categories of technological advances: transparent neuroelectrodes, optical neural fibers with electrodes, and neural probes/grids integrating electrodes and microscale light-emitting diodes. We discuss examples of these probes tailored to combine electrophysiological recording with optical imaging or optical neural stimulation of the brain and possible directions of future innovation.

Population imaging discrepancies between a genetically-encoded calcium indicator (GECI) versus a genetically-encoded voltage indicator (GEVI)

Genetically-encoded calcium indicators (GECIs) are essential for studying brain function, while voltage indicators (GEVIs) are slowly permeating neuroscience. Fundamentally, GECI and GEVI measure different things, but both are advertised as reporters of “neuronal activity”. We quantified the similarities and differences between calcium and voltage imaging modalities, in the context of population activity (without single-cell resolution) in brain slices. GECI optical signals showed 8–20 times better SNR than GEVI signals, but GECI signals attenuated more with distance from the stimulation site. We show the exact temporal discrepancy between calcium and voltage imaging modalities, and discuss the misleading aspects of GECI imaging. For example, population voltage signals already repolarized to the baseline (~ disappeared), while the GECI signals were still near maximum. The region-to-region propagation latencies, easily captured by GEVI imaging, are blurred in GECI imaging. Temporal summation of GECI signals is highly exaggerated, causing uniform voltage events produced by neuronal populations to appear with highly variable amplitudes in GECI population traces. Relative signal amplitudes in GECI recordings are thus misleading. In simultaneous recordings from multiple sites, the compound EPSP signals in cortical neuropil (population signals) are less distorted by GEVIs than by GECIs.

A selected review of recent advances in the study of neuronal circuits using fiber photometry

To understand the correlation between animal behaviors and the underlying neuronal circuits, it is important to monitor and record neurotransmission in the brain of freely moving animals. With the development of fiber photometry, based on genetically encoded biosensors, and novel electrochemical biosensors, it is possible to measure some key neuronal transmission events specific to cell types or neurotransmitters of interest with high temporospatial resolution. This review discusses the recent advances and achievements of these two techniques in the study of neurotransmission in animal models and how they can be used to complement other techniques in the neuroscientist's toolbox.

Effects of optogenetic stimulation of basal forebrain parvalbumin neurons on Alzheimer's disease pathology

Neuronal activity can modify Alzheimer's disease pathology. Overexcitation of neurons can facilitate disease progression whereas the induction of cortical gamma oscillations can reduce amyloid load and improve cognitive functions in mouse models. Although previous studies have induced cortical gamma oscillations by either optogenetic activation of cortical parvalbumin-positive (PV+) neurons or sensory stimuli, it is still unclear whether other approaches to induce gamma oscillations can also be beneficial. Here we show that optogenetic activation of PV+ neurons in the basal forebrain (BF) increases amyloid burden, rather than reducing it. We applied 40 Hz optical stimulation in the BF by expressing channelrhodopsin-2 (ChR2) in PV+ neurons of 5xFAD mice. After 1-h induction of cortical gamma oscillations over three days, we observed the increase in the concentration of amyloid-β42 in the frontal cortical region, but not amyloid-β40. Amyloid plaques were accumulated more in the medial prefrontal cortex and the septal nuclei, both of which are targets of BF PV+ neurons. These results suggest that beneficial effects of cortical gamma oscillations on Alzheimer's disease pathology can depend on the induction mechanisms of cortical gamma oscillations.

A wireless, implantable optoelectrochemical probe for optogenetic stimulation and dopamine detection

Physical and chemical technologies have been continuously progressing advances in neuroscience research. The development of research tools for closed-loop control and monitoring neural activities in behaving animals is highly desirable. In this paper, we introduce a wirelessly operated, miniaturized microprobe system for optical interrogation and neurochemical sensing in the deep brain. Via epitaxial liftoff and transfer printing, microscale light-emitting diodes (micro-LEDs) as light sources and poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS)-coated diamond films as electrochemical sensors are vertically assembled to form implantable optoelectrochemical probes for real-time optogenetic stimulation and dopamine detection capabilities. A customized, lightweight circuit module is employed for untethered, remote signal control, and data acquisition. After the probe is injected into the ventral tegmental area (VTA) of freely behaving mice, in vivo experiments clearly demonstrate the utilities of the multifunctional optoelectrochemical microprobe system for optogenetic interference of place preferences and detection of dopamine release. The presented options for material and device integrations provide a practical route to simultaneous optical control and electrochemical sensing of complex nervous systems.

Distributed mixed signal demultiplexer for electrocorticography electrodes

This work presents a novel architecture, exemplified for electrophysiological applications like ECoG that can be used to detect Epilepsy. The new ECoG is based on a mixed analog-digital architecture (Pulse Amplitude Modulation PAM), that allows the use of thousands of electrodes for recording. Whilst the increased number of electrodes helps to refine the spatial resolution of the medical application, the transmission of the signals from the electrodes to an external analysing device appears to be a bottleneck. To overcoming this, our work presents a hardware architecture and corresponding protocol for a mixed architecture that improves the information density between channels and their signal-to-noise ratio. This is shown by the correlation between the input and the transmitted signals in comparison to a classical digital transmission (Pulse Code Modulation PCM) system. We show in this work that it is possible to transmit the signals of 10 channels with a analog-digital architecture with the same quality of a full digital architecture.

Ray tracing models for estimating light collection properties of microstructured tapered optical fibers for optical neural interfaces

Tapered optical fibers (TFs) were recently employed for depth-resolved monitoring of functional fluorescence in subcortical brain structures, enabling light collection from groups of a few cells through small optical windows located on the taper edge [Pisano et al., Nat. Methods16, 1185 (2019)1548-709110.1038/s41592-019-0581-x]. Here we present a numerical model to estimate light collection properties of microstructured TFs implanted in scattering brain tissue. Ray tracing coupled with the Henyey-Greenstein scattering model enables the estimation of both light collection and fluorescence excitation fields in three dimensions, whose combination is employed to retrieve the volume of tissue probed by the device.