Integration of optogenetics with complementary methodologies in systems neuroscience

Computing Potential of the Mean Force Profiles for Ion Permeation Through Channelrhodopsin Chimera, C1C2

Umbrella sampling, coupled with a weighted histogram analysis method (US-WHAM), can be used to construct potentials of mean force (PMFs) for studying the complex ion permeation pathways of membrane transport proteins. Despite the widespread use of US-WHAM, obtaining a physically meaningful PMF can be challenging. Here, we provide a protocol to resolve that issue. Then, we apply that protocol to compute a meaningful PMF for sodium ion permeation through channelrhodopsin chimera, C1C2, for illustration.

Animal Models for OCD Research

OCD has lagged behind other psychiatric illnesses in the identification of molecular treatment targets, due in part to a lack of significant findings in genome-wide association studies. However, while progress in this area is being made, OCD's symptoms of obsessions, compulsions, and anxiety can be deconstructed into distinct neural functions that can be dissected in animal models. Studies in rodents and non-human primates have highlighted the importance of cortico-basal ganglia-thalamic circuits in OCD pathophysiology, and emerging studies in human post-mortem brain tissue point to glutamatergic synapse abnormalities as a potential cellular substrate for observed dysfunctional behaviors. In addition, accumulated evidence points to a potential role for neuromodulators including serotonin and dopamine in both OCD pathology and treatment. Here, we review current efforts to use animal models for the identification of molecules, cell types, and circuits relevant to OCD pathophysiology. We start by describing features of OCD that can be modeled in animals, including circuit abnormalities and genetic findings. We then review different strategies that have been used to study OCD using animal model systems, including transgenic models, circuit manipulations, and dissection of OCD-relevant neural constructs. Finally, we discuss how these findings may ultimately help to develop new treatment strategies for OCD and other related disorders.

Temperature Dependence of the Krokinobacter rhodopsin 2 Kinetics

We investigated the temperature-dependent kinetics of the light-driven Na⁺ pump Krokinobacter rhodopsin 2 (KR2) at Na⁺-pumping conditions. The recorded microsecond flash photolysis data were subjected to detailed global target analysis, employing Eyring constraints and spectral decomposition. The analysis resulted in the kinetic rates, the composition of the different photocycle equilibria, and the spectra of the involved photointermediates. Our results show that with the temperature increase (from 10 to 40°C), the overall photocycle duration is accelerated by a factor of 6, with the L-to-M transition exhibiting an impressive 40-fold increase. It follows from the analysis that in KR2 the chromophore and the protein scaffold are more kinetically decoupled than in other microbial rhodopsins. We link this effect to the rigidity of the retinal protein environment. This kinetic decoupling should be considered in future studies and could potentially be exploited for fine-tuning biotechnological applications.

Emerging Frontier of Peripheral Nerve and Organ Interfaces

The development of new tools to interface with the nervous system, empowered by advances in electronics and materials science, has transformed neuroscience and is informing therapies for neurological and mental conditions. Although the vast majority of neural engineering research has focused on advancing tools to study the brain, understanding the peripheral nervous system and other organs can similarly benefit from these technologies. To realize this vision, the neural interface technologies need to address the biophysical, mechanical, and chemical challenges posed by the peripheral nerves and organs. In this Perspective, we discuss design considerations and recent technological advances to modulate electrical signaling outside the central nervous system. The innovations in bioelectronics borne out of interdisciplinary collaborations between biologists and physical scientists may not only advance fundamental study of peripheral (neuro)physiology but also empower clinical interventions for conditions including neurological, gastrointestinal, and immune dysfunction.

Real-time, low-latency closed-loop feedback using markerless posture tracking

The ability to control a behavioral task or stimulate neural activity based on animal behavior in real-time is an important tool for experimental neuroscientists. Ideally, such tools are noninvasive, low-latency, and provide interfaces to trigger external hardware based on posture. Recent advances in pose estimation with deep learning allows researchers to train deep neural networks to accurately quantify a wide variety of animal behaviors. Here, we provide a new DeepLabCut-Live! package that achieves low-latency real-time pose estimation (within 15 ms, >100 FPS), with an additional forward-prediction module that achieves zero-latency feedback, and a dynamic-cropping mode that allows for higher inference speeds. We also provide three options for using this tool with ease: (1) a stand-alone GUI (called DLC-Live! GUI), and integration into (2) Bonsai, and (3) AutoPilot. Lastly, we benchmarked performance on a wide range of systems so that experimentalists can easily decide what hardware is required for their needs.

Segment-specific optogenetic stimulation in Drosophila melanogaster with linear arrays of organic light-emitting diodes

Optogenetics allows light-driven, non-contact control of neural systems, but light delivery remains challenging, in particular when fine spatial control of light is required to achieve local specificity. Here, we employ organic light-emitting diodes (OLEDs) that are micropatterned into linear arrays to obtain precise optogenetic control in Drosophila melanogaster larvae expressing the light-gated activator CsChrimson and the inhibitor GtACR2 within their peripheral sensory system. Our method allows confinement of light stimuli to within individual abdominal segments, which facilitates the study of larval behaviour in response to local sensory input. We show controlled triggering of specific crawling modes and find that targeted neurostimulation in abdominal segments switches the direction of crawling. More broadly, our work demonstrates how OLEDs can provide tailored patterns of light for photo-stimulation of neuronal networks, with future implications ranging from mapping neuronal connectivity in cultures to targeted photo-stimulation with pixelated OLED implants in vivo.

The rise and shine of yeast optogenetics

Optogenetics refers to the control of biological processes with light. The activation of cellular phenomena by defined wavelengths has several advantages compared with traditional chemically inducible systems, such as spatiotemporal resolution, dose-response regulation, low cost, and moderate toxic effects. Optogenetics has been successfully implemented in yeast, a remarkable biological platform that is not only a model organism for cellular and molecular biology studies, but also a microorganism with diverse biotechnological applications. In this review, we summarize the main optogenetic systems implemented in the budding yeast Saccharomyces cerevisiae, which allow orthogonal control (by light) of gene expression, protein subcellular localization, reconstitution of protein activity, and protein sequestration by oligomerization. Furthermore, we review the application of optogenetic systems in the control of metabolic pathways, heterologous protein production and flocculation. We then revise an example of a previously described yeast optogenetic switch, named FUN-LOV, which allows precise and strong activation of the target gene. Finally, we describe optogenetic systems that have not yet been implemented in yeast, which could therefore be used to expand the panel of available tools in this biological chassis. In conclusion, a wide repertoire of optogenetic systems can be used to address fundamental biological questions and broaden the biotechnological toolkit in yeast.

How is flexible electronics advancing neuroscience research?

Innovative neurotechnology must be leveraged to experimentally answer the multitude of pressing questions in modern neuroscience. Driven by the desire to address the existing neuroscience problems with newly engineered tools, we discuss in this review the benefits of flexible electronics for neuroscience studies. We first introduce the concept and define the properties of flexible and stretchable electronics. We then categorize the four dimensions where flexible electronics meets the demands of modern neuroscience: chronic stability, interfacing multiple structures, multi-modal compatibility, and neuron-type-specific recording. Specifically, with the bending stiffness now approaching that of neural tissue, implanted flexible electronic devices produce little shear motion, minimizing chronic immune responses and enabling recording and stimulation for months, and even years. The unique mechanical properties of flexible electronics also allow for intimate conformation to the brain, the spinal cord, peripheral nerves, and the retina. Moreover, flexible electronics enables optogenetic stimulation, microfluidic drug delivery, and neural activity imaging during electrical stimulation and recording. Finally, flexible electronics can enable neuron-type identification through analysis of high-fidelity recorded action potentials facilitated by its seamless integration with the neural circuitry. We argue that flexible electronics will play an increasingly important role in neuroscience studies and neurological therapies via the fabrication of neuromorphic devices on flexible substrates and the development of enhanced methods of neuronal interpenetration.

Towards Cell and Subtype Resolved Functional Organization: Mouse as a Model for the Cortical Control of Movement

Despite a long history of interrogation, the functional organization of motor cortex remains obscure. A major barrier has been the inability to measure and perturb activity with sufficient resolution to reveal clear functional elements within motor cortex and its associated circuits. Increasingly, the mouse has been employed as a model to facilitate application of contemporary approaches with the potential to surmount this barrier. In this brief essay, we consider these approaches and their use in the context of studies aimed at resolving the logic of motor cortical operation.

Nitric oxide signalling in the brain and its control of bodily functions

Nitric oxide (NO) is a versatile molecule that plays key roles in the development and survival of mammalian species by endowing brain neuronal networks with the ability to make continual adjustments to function in response to moment-to-moment changes in physiological input. Here, we summarize the progress in the field and argue that NO-synthetizing neurons and NO signalling in the brain provide a core hub for integrating sensory- and homeostatic-related cues, control key bodily functions, and provide a potential target for new therapeutic opportunities against several neuroendocrine and behavioural abnormalities.

Novel Electrode Designs for Neurostimulation in Regenerative Medicine: Activation of Stem Cells

Neural stem and progenitor cells (i.e., neural precursors) are found within specific regions in the central nervous system and have great regenerative capacity. These cells are electrosensitive and their behavior can be regulated by the presence of electric fields (EFs). Electrical stimulation is currently used to treat neurological disorders in a clinical setting. Herein we propose that electrical stimulation can be used to enhance neural repair by regulating neural precursor cell (NPC) kinetics and promoting their migration to sites of injury or disease. We discuss how intrinsic and extrinsic factors can affect NPC migration in the presence of an EF and how this impacts electrode design with the goal of enhancing tissue regeneration. We conclude with an outlook on future clinical applications of electrical stimulation and highlight technological advances that would greatly support these applications.

Dynamic pulvino-cortical interactions in the primate attention network

While research in previous decades demonstrated a link between the pulvinar nucleus of the thalamus and visual selective attention, the pulvinar's specific functional role has remained elusive. However, methodological advances in electrophysiological recordings in non-human primates, including simultaneous recordings in multiple brain regions, have recently begun to reveal the pulvinar's functional contributions to selective attention. These new findings suggest that the pulvinar is critical for the efficient transmission of sensory information within and between cortical regions, both synchronizing cortical activity across brain regions and controlling cortical excitability. These new findings further suggest that the pulvinar's influence on cortical processing is embedded in a dynamic selection process that balances sensory and motor functions within the large-scale network that directs selective attention.

A Guide to Fluorescence Lifetime Microscopy and Förster's Resonance Energy Transfer in Neuroscience

Fluorescence lifetime microscopy (FLIM) and Förster's resonance energy transfer (FRET) are advanced optical tools that neuroscientists can employ to interrogate the structure and function of complex biological systems in vitro and in vivo using light. In neurobiology they are primarily used to study protein-protein interactions, to study conformational changes in protein complexes, and to monitor genetically encoded FRET-based biosensors. These methods are ideally suited to optically monitor changes in neurons that are triggered optogenetically. Utilization of this technique by neuroscientists has been limited, since a broad understanding of FLIM and FRET requires familiarity with the interactions of light and matter on a quantum mechanical level, and because the ultra-fast instrumentation used to measure fluorescent lifetimes and resonance energy transfer are more at home in a physics lab than in a biology lab. In this overview, we aim to help neuroscientists overcome these obstacles and thus feel more comfortable with the FLIM-FRET method. Our goal is to aid researchers in the neuroscience community to achieve a better understanding of the fundamentals of FLIM-FRET and encourage them to fully leverage its powerful ability as a research tool. Published 2020. U.S. Government.

Turning strains into strengths for understanding psychiatric disorders

There is a paucity in the development of new mechanistic insights and therapeutic approaches for treating psychiatric disease. One of the major challenges is reflected in the growing consensus that risk for these diseases is not determined by a single gene, but rather is polygenic, arising from the action and interaction of multiple genes. Canonically, experimental models in mice have been designed to ascertain the relative contribution of a single gene to a disease by systematic manipulation (e.g., mutation or deletion) of a known candidate gene. Because these studies have been largely carried out using inbred isogenic mouse strains, in which there is no (or very little) genetic diversity among subjects, it is difficult to identify unique allelic variants, gene modifiers, and epigenetic factors that strongly affect the nature and severity of these diseases. Here, we review various methods that take advantage of existing genetic diversity or that increase genetic variance in mouse models to (1) strengthen conclusions of single-gene function; (2) model diversity among human populations; and (3) dissect complex phenotypes that arise from the actions of multiple genes.

Translational opportunities for circuit-based social neuroscience: advancing 21st century psychiatry

The recent advancements of social behavioral neuroscience are unprecedented. Through manipulations targeting neural circuits, complex behaviors can be switched on and off, social bonds can be induced, and false memories can be 'incepted.' Psychiatry, however, remains tethered to concepts and techniques developed over half a century ago, including purely behavioral definitions of psychopathology and chronic, brain-wide pharmacological interventions. Drawing on recent animal and human research, we outline a circuit-level approach to the social brain and highlight studies demonstrating the translational potential of this approach. We conclude by suggesting ways both clinical practice and translational research can apply circuit-level neuroscientific knowledge to advance psychiatry, including adopting neuroscience-based nomenclature, stratifying patients into diagnostic subgroups based on neurobiological phenotypes, and pharmacologically enhancing psychotherapy.

The memory orchestra: the role of astrocytes and oligodendrocytes in parallel to neurons

For decades, the study of memory has been neuron-centric, yet neurons do not function in isolation. Today we know that neuronal activity is modulated by the environment within which it occurs, and is subject to modulation by different types of glial cells. In this review we summarize recent findings on the functional roles of astrocytes and oligodendrocytes, two major types of glia cells in the adult brain, in memory formation and its cellular underpinnings across multiple time points. We will discuss the different methods that are being used to investigate the astrocytic and oligodendroglial involvement in memory. We shall focus on chemogenetics and optogenetics, which support genetically specificity and high spatiotemporal resolution, attributes that are particularly well suited to the investigation of the contribution of unique cell types at the different stages of memory formation.

Tracing goes viral: Viruses that introduce expression of fluorescent proteins in chemically-specific neurons

Over the last century, there has been great progress in understanding how the brain works. In particular, the last two decades have been crucial in gaining more awareness over the complex functioning of neurotransmitter systems. The use of viral vectors in neuroscience has been pivotal for such development. Exploiting the properties of viral particles, modifying them according to the research needs, and making them target chemically-specific neurons, techniques such as optogenetics and chemogenetics have been developed, which could lead to a giant step toward gene therapy for brain disorders. In this review, we aim to provide an overview of some of the most widely used viral techniques in neuroscience. We will discuss advantages and disadvantages of these methods. In particular, attention is dedicated to the pivotal role played by the introduction of adeno-associated virus and the retrograde tracer canine-associated-2 Cre virus in order to achieve optimal visualization, and interrogation, of chemically-specific neuronal populations and their projections.

Neuropeptidomic Analysis of a Genetically Defined Cell Type in Mouse Brain and Pituitary

Neuropeptides and peptide hormones are important cell-cell signaling molecules that mediate many physiological processes. Unlike classic neurotransmitters, peptides undergo cell-type-specific post-translational modifications that affect their biological activity. To enable the identification of the peptide repertoire of a genetically defined cell type, we generated mice with a conditional disruption of the gene for carboxypeptidase E (Cpe), an essential neuropeptide-processing enzyme. The loss of Cpe leads to accumulation of neuropeptide precursors containing C-terminal basic residues, which serve as tags for affinity purification. The purified peptides are subsequently identified using quantitative peptidomics, thereby revealing the specific forms of neuropeptides in cells with the disrupted Cpe gene. To validate the method, we used mice expressing Cre recombinase under the proopiomelanocortin (Pomc) promoter and analyzed hypothalamic and pituitary extracts, detecting peptides derived from proopiomelanocortin (as expected) and also proSAAS in POMC neurons. This technique enables the analyses of specific forms of peptides in any Cre-expressing cell type.

Photocontrol of Endogenous Glycine Receptors In Vivo

Glycine receptors (GlyRs) are indispensable for maintaining excitatory/inhibitory balance in neuronal circuits that control reflexes and rhythmic motor behaviors. Here we have developed Glyght, a GlyR ligand controlled with light. It is selective over other Cys-loop receptors, is active in vivo, and displays an allosteric mechanism of action. The photomanipulation of glycinergic neurotransmission opens new avenues to understanding inhibitory circuits in intact animals and to developing drug-based phototherapies.

Multisite cell- and neural-dynamics-resolving deep brain imaging in freely moving mice with implanted reconnectable fiber bundles

We demonstrate a reconnectable implantable ultraslim fiber-optic microendoscope that integrates a branching fiber bundle (BFB) with gradient-index fiber lenses, enabling a simultaneous fluorescence imaging of individual cells in distinctly separate brain regions, including brain structures as distant as the neocortex and hippocampus. We show that fluorescence images of individual calcium-indicator-expressing neurons in the brain of freely moving transgenic mice can be recorded, via the implanted BFB probe, in parallel with time- and cell-resolved traces of calcium signaling, thus enabling correlated circuit-dynamics studies at -multiple sites within the brain of freely moving animals.

An optogenetic switch for the Set2 methyltransferase provides evidence for transcription-dependent and -independent dynamics of H3K36 methylation

Histone H3 lysine 36 methylation (H3K36me) is a conserved histone modification associated with transcription and DNA repair. Although the effects of H3K36 methylation have been studied, the genome-wide dynamics of H3K36me deposition and removal are not known. We established rapid and reversible optogenetic control for Set2, the sole H3K36 methyltransferase in yeast, by fusing the enzyme with the light-activated nuclear shuttle (LANS) domain. Light activation resulted in efficient Set2-LANS nuclear localization followed by H3K36me3 deposition in vivo, with total H3K36me3 levels correlating with RNA abundance. Although genes showed disparate levels of H3K36 methylation, relative rates of H3K36me3 accumulation were largely linear and consistent across genes, suggesting that H3K36me3 deposition occurs in a directed fashion on all transcribed genes regardless of their overall transcription frequency. Removal of H3K36me3 was highly dependent on the demethylase Rph1. However, the per-gene rate of H3K36me3 loss weakly correlated with RNA abundance and followed exponential decay, suggesting H3K36 demethylases act in a global, stochastic manner. Altogether, these data provide a detailed temporal view of H3K36 methylation and demethylation that suggests transcription-dependent and -independent mechanisms for H3K36me deposition and removal, respectively.

Brain Modeling ToolKit: An open source software suite for multiscale modeling of brain circuits

Experimental studies in neuroscience are producing data at a rapidly increasing rate, providing exciting opportunities and formidable challenges to existing theoretical and modeling approaches. To turn massive datasets into predictive quantitative frameworks, the field needs software solutions for systematic integration of data into realistic, multiscale models. Here we describe the Brain Modeling ToolKit (BMTK), a software suite for building models and performing simulations at multiple levels of resolution, from biophysically detailed multi-compartmental, to point-neuron, to population-statistical approaches. Leveraging the SONATA file format and existing software such as NEURON, NEST, and others, BMTK offers a consistent user experience across multiple levels of resolution. It permits highly sophisticated simulations to be set up with little coding required, thus lowering entry barriers to new users. We illustrate successful applications of BMTK to large-scale simulations of a cortical area. BMTK is an open-source package provided as a resource supporting modeling-based discovery in the community.

Viral tools for neuroscience

Recombinant viruses are the workhorse of modern neuroscience. Whether one would like to understand a neuron's morphology, natural activity patterns, molecular composition, connectivity or behavioural and physiologic function, most studies begin with the injection of an engineered virus, often an adeno-associated virus or herpes simplex virus, among many other types. Recombinant viruses currently enable some combination of cell type-specific, circuit-selective, activity-dependent and spatiotemporally resolved transgene expression. Viruses are now used routinely to study the molecular and cellular functions of a gene within an identified cell type in the brain, and enable the application of optogenetics, chemogenetics, calcium imaging and related approaches. These advantageous properties of engineered viruses thus enable characterization of neuronal function at unprecedented resolution. However, each virus has specific advantages and disadvantages, which makes viral tool selection paramount for properly designing and executing experiments within the central nervous system. In the current Review, we discuss the key principles and uses of engineered viruses and highlight innovations that are needed moving forward.

Dual Recombining-out System for Spatiotemporal Gene Expression in C. elegans

Specific recording, labeling, and spatiotemporal manipulating neurons are essential for neuroscience research. In this study, we developed a tripartite spatiotemporal gene induction system in C. elegans, which is based on the knockout of two transcriptional terminators (stops in short) by two different recombinases FLP and CRE. The recombinase sites (loxP and FRT) flanked stops after a ubiquitous promoter terminate transcription of target genes. FLP and CRE, induced by two promoters of overlapping expression, remove the stops (subsequent FLP/CRE-out). The system provides an "AND" gate strategy for specific gene expression in single types of cell(s). Combined with an inducible promoter or element, the system can control the spatiotemporal expression of genes in defined cell types, especially in cells or tissues lacking a specific promoter. This tripartite FLP/CRE-out gene expression system is a simple, labor- and cost-saving toolbox for cell type-specific and inducible gene expression in C. elegans.

Adaptation and survival: hypotheses about the neural mechanisms of unihemispheric sleep

Sleep and wakefulness are opposite brain and body conditions that accomplish different but complementary functions. However, these opposing conditions have been combined in some animals by the adoption of a sleep/wake strategy that allows them to survive, while maintaining both an interaction with the environment at the same time as enabling brain and body recovery. They sleep with half of the brain while keeping the other half awake: a state known as unihemispheric sleep (US). Sleep of cetaceans is exclusively in the form of US; therefore, they experience neither bihemispheric sleep (BS) nor REM sleep. US episodes have also been recorded in eared seals and some species of birds. In those animals, US episodes are intermingled with episodes of BS and REM sleep. Studies have reported both a lateralized release of some neurotransmitters and a drop of brain temperature during US. The aims of this article are to formulate hypotheses about the neural mechanisms of unihemispheric sleep(US) based on findings regarding the neural mechanisms of the sleep/wake cycle of mammals. The neural mechanisms of the sleep/wake cycle are largely preserved across species, allowing to hypothesize about those triggering and regulating US.

Synaptic inhibition in the neocortex: Orchestration and computation through canonical circuits and variations on the theme

The neocortex plays a crucial role in all basic and abstract cognitive functions. Conscious mental processes are achieved through a correct flow of information within and across neocortical networks, whose particular activity state results from a tight balance between excitation and inhibition. The proper equilibrium between these indissoluble forces is operated with multiscale organization: along the dendro-somatic axis of single neurons and at the network level. Fast synaptic inhibition is assured by a multitude of inhibitory interneurons. During cortical activities, these cells operate a finely tuned division of labor that is epitomized by their detailed connectivity scheme. Recent results combining the use of mouse genetics, cutting-edge optical and neurophysiological approaches have highlighted the role of fast synaptic inhibition in driving cognition-related activity through a canonical cortical circuit, involving several major interneuron subtypes and principal neurons. Here we detail the organization of this cortical blueprint and we highlight the crucial role played by different neuron types in fundamental cortical computations. In addition, we argue that this canonical circuit is prone to many variations on the theme, depending on the resolution of the classification of neuronal types, and the cortical area investigated. Finally, we discuss how specific alterations of distinct inhibitory circuits can underlie several devastating brain diseases.

Cell Calcium Imaging as a Reliable Method to Study Neuron-Glial Circuits

Complex dynamic cellular networks have been studied in physiological and pathological processes under the light of single-cell calcium imaging (SCCI), a method that correlates functional data based on calcium shifts operated by different intracellular and extracellular mechanisms integrated with their cell phenotypes. From the classic synaptic structure to tripartite astrocytic model or the recent quadripartite microglia added ensemble, as well as other physiological tissues, it is possible to follow how cells signal spatiotemporally to cellular patterns. This methodology has been used broadly due to the universal properties of calcium as a second messenger. In general, at least two types of receptor operate through calcium permeation: a fast-acting ionotropic receptor channel and a slow-activating metabotropic receptor, added to exchangers/transporters/pumps and intracellular Ca²⁺ release activated by messengers. These prototypes have gained an enormous amount of information in dynamic signaling circuits. SCCI has also been used as a method to associate phenotypic markers during development and stage transitions in progenitors, stem, vascular cells, neuro- and glioblasts, neurons, astrocytes, oligodendrocytes, and microglia that operate through ion channels, transporters, and receptors. Also, cancer cells or inducible cell lines from human organoids characterized by transition stages are currently being used to model diseases or reconfigure healthy cells in terms of the expression of calcium-binding/permeable molecules and shed light on therapy.

In vivo voltage-sensitive dye imaging of mouse cortical activity with mesoscopic optical tomography

Significance: Cellular layering is a hallmark of the mammalian neocortex with layer and cell type-specific connections within the cortical mantle and subcortical connections. A key challenge in studying circuit function within the neocortex is to understand the spatial and temporal patterns of information flow between different columns and layers. Aim: We aimed to investigate the three-dimensional (3D) layer- and area-specific interactions in mouse cortex in vivo. Approach: We applied a new promising neuroimaging method-fluorescence laminar optical tomography in combination with voltage-sensitive dye imaging (VSDi). VSDi is a powerful technique for interrogating membrane potential dynamics in assemblies of cortical neurons, but it is traditionally used for two-dimensional (2D) imaging. Our mesoscopic technique allows visualization of neuronal activity in a 3D manner with high temporal resolution. Results: We first demonstrated the depth-resolved capability of 3D mesoscopic imaging technology in Thy1-ChR2-YFP transgenic mice. Next, we recorded the long-range functional projections between sensory cortex (S1) and motor cortex (M1) in mice, in vivo, following single whisker deflection. Conclusions: The results show that mesoscopic imaging technique has the potential to investigate the layer-specific neural connectivity in the mouse cortex in vivo. Combination of mesoscopic imaging technique with optogenetic control strategy is a promising platform for determining depth-resolved interactions between cortical circuit elements.

Precision multidimensional neural population code recovered from single intracellular recordings

Neurons in sensory cortices are more naturally and deeply integrated than any current neural population recording tools (e.g. electrode arrays, fluorescence imaging). Two concepts facilitate efforts to observe population neural code with single-cell recordings. First, even the highest quality single-cell recording studies find a fraction of the stimulus information in high-dimensional population recordings. Finding any of this missing information provides proof of principle. Second, neurons and neural populations are understood as coupled nonlinear differential equations. Therefore, fitted ordinary differential equations provide a basis for single-trial single-cell stimulus decoding. We obtained intracellular recordings of fluctuating transmembrane current and potential in mouse visual cortex during stimulation with drifting gratings. We use mean deflection from baseline when comparing to prior single-cell studies because action potentials are too sparse and the deflection response to drifting grating stimuli (e.g. tuning curves) are well studied. Equation-based decoders allowed more precise single-trial stimulus discrimination than tuning-curve-base decoders. Performance varied across recorded signal types in a manner consistent with population recording studies and both classification bases evinced distinct stimulus-evoked phases of population dynamics, providing further corroboration. Naturally and deeply integrated observations of population dynamics would be invaluable. We offer proof of principle and a versatile framework.

The Spatial Extent of Optogenetic Silencing in Transgenic Mice Expressing Channelrhodopsin in Inhibitory Interneurons

Optogenetic stimulation of inhibitory interneurons has become a commonly used strategy for silencing neuronal activity. This is typically achieved using transgenic mice expressing excitatory opsins in inhibitory interneurons throughout the brain, raising the question of how spatially extensive the resulting inhibition is. Here, we characterize neuronal silencing in VGAT-ChR2 mice, which express channelrhodopsin-2 in inhibitory interneurons, as a function of light intensity and distance from the light source in several cortical and subcortical regions. We show that light stimulation, even at relatively low intensities, causes inhibition not only in brain regions targeted for silencing but also in their subjacent areas. In contrast, virus-mediated expression of an inhibitory opsin enables robust silencing that is restricted to the region of opsin expression. Our results reveal important constraints on using inhibitory interneuron activation to silence neuronal activity and emphasize the necessity of carefully controlling light stimulation parameters when using this silencing strategy.

Histaminergic neurons in the tuberomammillary nucleus as a control centre for wakefulness

Histamine plays pleiotropic roles as a neurotransmitter in the physiology of brain function, this includes the maintenance of wakefulness, appetite regulation and memory retrieval. Since numerous studies have revealed an association between histaminergic dysfunction and diverse neuropsychiatric disorders, such as Alzheimer's disease and schizophrenia, a large number of compounds acting on the brain histamine system have been developed to treat neurological disorders. In 2016, pitolisant, which was developed as a histamine H₃ receptor inverse agonist by Schwartz and colleagues, was launched for the treatment of narcolepsy, emphasising the prominent role of brain histamine on wakefulness. Recent advances in neuroscientific techniques such as chemogenetic and optogenetic approaches have led to remarkable progress in the understanding of histaminergic neural circuits essential for the control of wakefulness. In this review article, we summarise the basic knowledge about the histaminergic nervous system and the mechanisms underlying sleep/wake regulation that are controlled by the brain histamine system. LINKED ARTICLES: This article is part of a themed issue on Neurochemistry in Japan. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v178.4/issuetoc.

Monitoring of uncaging processes by designing photolytical reactions

The use of photolabile protecting groups (PPGs) has been growing in emphasis for decades, and nowadays they enable cutting-edge results in numerous fields ranging from organic synthesis to neurosciences. PPGs are chemical entities that can be conjugated to a biomolecule to hide its biological activity, forming a stable so called "caged compound". This conjugate can be simply cleaved by light and therefore, the functionality of the biomolecule is restored with the formation of a PPG by-product. However, there is a sizeable need for PPGs that are able to quantify the "uncaging" process. In this review, we will discuss several strategies leading to an acute quantification of the uncaging events by fluorescence. In particular, we will focus on how molecular engineering of PPG could open new opportunities by providing easy access to photoactivation protocols.

Engineering Photosensory Modules of Non-Opsin-Based Optogenetic Actuators

Optogenetic (photo-responsive) actuators engineered from photoreceptors are widely used in various applications to study cell biology and tissue physiology. In the toolkit of optogenetic actuators, the key building blocks are genetically encodable light-sensitive proteins. Currently, most optogenetic photosensory modules are engineered from naturally-occurring photoreceptor proteins from bacteria, fungi, and plants. There is a growing demand for novel photosensory domains with improved optical properties and light-induced responses to satisfy the needs of a wider variety of studies in biological sciences. In this review, we focus on progress towards engineering of non-opsin-based photosensory domains, and their representative applications in cell biology and physiology. We summarize current knowledge of engineering of light-sensitive proteins including light-oxygen-voltage-sensing domain (LOV), cryptochrome (CRY2), phytochrome (PhyB and BphP), and fluorescent protein (FP)-based photosensitive domains (Dronpa and PhoCl).

Enlightening the frontiers of neurogastroenterology through optogenetics

Neurogastroenterology refers to the study of the extrinsic and intrinsic nervous system circuits controlling the gastrointestinal (GI) tract. Over the past 5-10 yr there has been an explosion in novel methodologies, technologies and approaches that offer great promise to advance our understanding of the basic mechanisms underlying GI function in health and disease. This review focuses on the use of optogenetics combined with electrophysiology in the field of neurogastroenterology. We discuss how these technologies and tools are currently being used to explore the brain-gut axis and debate the future research potential and limitations of these techniques. Taken together, we consider that the use of these technologies will enable researchers to answer important questions in neurogastroenterology through fundamental research. The answers to those questions will shorten the path from basic discovery to new treatments for patient populations with disorders of the brain-gut axis affecting the GI tract such as irritable bowel syndrome (IBS), functional dyspepsia, achalasia, and delayed gastric emptying.

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.

Deciphering Brain Function by Miniaturized Fluorescence Microscopy in Freely Behaving Animals

Animal behavior is regulated by environmental stimuli and is shaped by the activity of neural networks, underscoring the importance of assessing the morpho-functional properties of different populations of cells in freely behaving animals. In recent years, a number of optical tools have been developed to monitor and modulate neuronal and glial activity at the protein, cellular, or network level and have opened up new avenues for studying brain function in freely behaving animals. Tools such as genetically encoded sensors and actuators are now commonly used for studying brain activity and function through their expression in different neuronal ensembles. In parallel, microscopy has also made major progress over the last decades. The advent of miniature microscopes (mini-microscopes also called mini-endoscopes) has become a method of choice for studying brain activity at the cellular and network levels in different brain regions of freely behaving mice. This technique also allows for longitudinal investigations while animals carrying the microscope on their head are performing behavioral tasks. In this review, we will discuss mini-endoscopic imaging and the advantages that these devices offer to research. We will also discuss current limitations of and potential future improvements in mini-endoscopic imaging.

Functional interrogation of neural circuits with virally transmitted optogenetic tools

The vertebrate brain comprises a plethora of cell types connected by intertwined pathways. Optogenetics enriches the neuroscientific tool set for disentangling these neuronal circuits in a manner which exceeds the spatio-temporal precision of previously existing techniques. Technically, optogenetics can be divided in three types of optical and genetic combinations: (1) it is primarily understood as the manipulation of the activity of genetically modified cells (typically neurons) with light, i.e. optical actuators. (2) A second combination refers to visualizing the activity of genetically modified cells (again typically neurons), i.e. optical sensors. (3) A completely different interpretation of optogenetics refers to the light activated expression of a genetically induced construct. Here, we focus on the first two types of optogenetics, i.e. the optical actuators and sensors in an attempt to give an overview into the topic. We first cover methods to express opsins into neurons and introduce strategies of targeting specific neuronal populations in different animal species. We then summarize combinations of optogenetics with behavioral read out and neuronal imaging. Finally, we give an overview of the current state-of-the-art and an outlook on future perspectives.

Optical interrogation of multi-scale neuronal plasticity underlying behavioral learning

Behavioral learning is driven by adaptive changes in the activation of behaviorally relevant neuronal ensembles. This learning-specific reorganization of neuronal circuits is correlated with activity-dependent modifications of synaptic dynamics. However, a definitive causal link remains to be established. How is synaptic plasticity distributed among circuits to eventually shape behavioral learning? A multi-scale understanding of the progressive plasticity is hindered by the lack of techniques for monitoring and manipulating these events. The current rise of synaptic optogenetics, especially combined with brain-wide circuit imaging, opens an entirely new avenue for studying causality at multiple scales. In this review, we summarize these technical achievements and discuss challenges in linking the plasticity across levels to elucidate the multi-scale mechanisms of learning.

Off-Peak 594-nm Light Surpasses On-Peak 532-nm Light in Silencing Distant ArchT-Expressing Neurons In Vivo

For large brain volume manipulations using optogenetics, both effective opsin excitation and efficient light delivery with minimal light absorption are required to minimize the illuminating light intensity and concomitant off-target effects. ArchT, a widely used potent inhibitory opsin, is commonly activated by 532-nm light, which lies on its in vitro excitation peak. However, 532-nm light also lies on a peak range of the hemoglobin absorption spectrum. Therefore, we predicted that 594-nm light is superior in suppressing distant ArchT-expressing neurons, which is slightly off the ArchT-excitation-plateau and largely off the peak of the hemoglobin absorption spectrum. We quantitatively tested this prediction by the electrophysiological recording of the rat cortex in vivo. At illumination distances greater than 500 μm, 594-nm light was more effective than 532-nm light. Its superiority increased with distance. These results validate our prediction and highlight the significance of excitation-absorption trade-off in selecting illumination wavelength for optogenetics in vivo.

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Wavelength-dependency of optogenetic neuronal control was directly measured in vivo

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Off-peak light silence 1-mm-distant ArchT-neuron twice more than on-peak light in vivo

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Superiority of off-peak light at distance arose from its less absorption of light

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Simulation of light propagation supported unexpectedly large effect of hemoglobin

Innovations in the Neurosurgical Management of Epilepsy

Technical limitations and clinical challenges have historically limited the diagnostic tools and treatment methods available for surgical approaches to the management of epilepsy. By contrast, recent technological innovations in several areas hold significant promise in improving outcomes and decreasing morbidity. We review innovations in the neurosurgical management of epilepsy in several areas, including wireless recording and stimulation systems (particularly responsive neurostimulation [NeuroPace]), conformal electrodes for high-resolution electrocorticography, robot-assisted stereotactic surgery, optogenetics and optical imaging methods, novel positron emission tomography ligands, and new applications of focused ultrasonography. Investigation into genetic causes of and susceptibilities to epilepsy has introduced a new era of precision medicine, enabling the understanding of cell signaling mechanisms underlying epileptic activity as well as patient-specific molecularly targeted treatment options. We discuss the emerging path to individualized treatment plans, predicted outcomes, and improved selection of effective interventions, on the basis of these developments.

The DMCdrive: practical 3D-printable micro-drive system for reliable chronic multi-tetrode recording and optogenetic application in freely behaving rodents

Electrophysiological recording and optogenetic control of neuronal activity in behaving animals have been integral to the elucidation of how neurons and circuits modulate network activity in the encoding and causation of behavior. However, most current electrophysiological methods require substantial economical investments and prior expertise. Further, the inclusion of optogenetics with electrophysiological recordings in freely moving animals adds complexity to the experimental design. Expansion of the technological repertoire across laboratories, research institutes, and countries, demands open access to high-quality devices that can be built with little prior expertise from easily accessible parts of low cost. We here present an affordable, truly easy-to-assemble micro-drive for electrophysiology in combination with optogenetics in freely moving rodents. The DMCdrive is particularly suited for reliable recordings of neurons and network activities over the course of weeks, and simplify optical tagging and manipulation of neurons in the recorded brain region. The highly functional and practical drive design has been optimized for accurate tetrode movement in brain tissue, and remarkably reduced build time. We provide a complete overview of the drive design, its assembly and use, and proof-of-principle demonstration of recordings paired with cell-type-specific optogenetic manipulations in the prefrontal cortex (PFC) of freely moving transgenic mice and rats.

Dopamine Suppresses Synaptic Responses of Fan Cells in the Lateral Entorhinal Cortex to Olfactory Bulb Input in Mice

The lateral entorhinal cortex (LEC) is involved in odor discrimination, odor-associative multimodal memory, and neurological or neuropsychiatric disorders. It receives direct axonal projections from both olfactory bulb (OB) output neurons and midbrain dopaminergic neurons. However, the cellular targets in LEC receiving direct synaptic input from OB output neuron, the functional characteristics of these synapses, and whether or how dopamine (DA) modulates the OB-LEC pathway remain undetermined. We addressed these questions in the present study by combing optogenetic and electrophysiological approaches with four major findings: (1) selective activation of OB input elicited glutamate-mediated monosynaptic responses in all fan cells, the major output neurons in layer II of the LEC; (2) this excitatory synaptic transmission exhibited robust paired-pulse facilitation (PPF), a presynaptically derived short-term synaptic plasticity; (3) DA dramatically attenuated the strength of the OB input-fan cell synaptic transmission via activation of D1 receptors; and (4) DA altered the PPF of this transmission but neither intrinsic properties of postsynaptic neurons nor the kinetic profile of postsynaptic responses, suggesting that presynaptic mechanisms underlie the DA inhibitory actions. This study for the first time demonstrates the FCs in the LEC layer II as the postsynaptic target of direct OB input and characterizes DA modulation of the OB input-fan cell pathway. These findings set the foundation for future studies to examine the synaptic transmission from the OB output neuron axon terminals to other potential cell types in the LEC and to pinpoint the pathophysiological mechanisms underlying olfactory deficits associated with DA-relevant neurological and neuropsychiatric disorders.

Histological assessment of optogenetic tools to study fronto-visual and fronto-parietal cortical networks in the rhesus macaque

Optogenetics offers unprecedented possibilities to investigate cortical networks. Yet, the number of successful optogenetic applications in non-human primates is still low, and the consequences of opsin expression in the primate brain are not well documented. We assessed histologically if we can target cerebrocortical networks with three common optogenetic constructs (AAV2/5-CaMKIIα-eNpHR3.0-mCherry, -ChR2-eYFP, -C1V1-mCherry). The frontal eye field or the dorsal premotor area of rhesus macaques were virally injected, and the resulting transduction spread, expression specificity, and opsin trafficking into axons projecting to parietal and visual areas were examined. After variable periods (2–24 months), expression was robust for all constructs at the injection sites. The CaMKIIα promoter driven-expression was predominant, but not exclusive, in excitatory neurons. In the case of eNpHR3.0-mCherry and ChR2-eYFP, opsins were present in axonal projections to target areas, in which sparse, retrogradely transduced neurons could also be found. Finally, the intracellular distribution of opsins differed: ChR2-eYFP had almost exclusive membrane localization, while eNpHR3.0-mCherry and C1V1-mCherry showed additional intracellular accumulations, which might affect neuronal survival in the long-term. Results indicate that all three constructs can be used for local neuronal modulation, but axonal stimulation and long-term use require additional considerations of construct selection and verification.

Spatio-molecular domains identified in the mouse subthalamic nucleus and neighboring glutamatergic and GABAergic brain structures

The subthalamic nucleus (STN) is crucial for normal motor, limbic and associative function. STN dysregulation is correlated with several brain disorders, including Parkinsonʼs disease and obsessive compulsive disorder (OCD), for which high-frequency stimulation of the STN is increasing as therapy. However, clinical progress is hampered by poor knowledge of the anatomical–functional organization of the STN. Today, experimental mouse genetics provides outstanding capacity for functional decoding, provided selective promoters are available. Here, we implemented single-nuclei RNA sequencing (snRNASeq) of the mouse STN followed through with histological analysis of 16 candidate genes of interest. Our results demonstrate that the mouse STN is composed of at least four spatio-molecularly defined domains, each distinguished by defined sets of promoter activities. Further, molecular profiles dissociate the STN from the adjoining para-STN (PSTN) and neighboring structures of the hypothalamus, mammillary nuclei and zona incerta. Enhanced knowledge of STN´s internal organization should prove useful towards genetics-based functional decoding of this clinically relevant brain structure.

Wallén-Mackenzie et al. investigate anatomical–functional organization of the subthalamic nucleus in mice, using single-nuclei RNA sequencing followed by histological analysis. They identify four domains distinguished by defined sets of promoter activities, providing a valuable resource for functional decoding of the subthalamic nucleus.

Neuropathic Pain: From Mechanisms to Treatment

Neuropathic pain caused by a lesion or disease of the somatosensory nervous system is a common chronic pain condition with major impact on quality of life. Examples include trigeminal neuralgia, painful polyneuropathy, postherpetic neuralgia, and central poststroke pain. Most patients complain of an ongoing or intermittent spontaneous pain of, for example, burning, pricking, squeezing quality, which may be accompanied by evoked pain, particular to light touch and cold. Ectopic activity in, for example, nerve-end neuroma, compressed nerves or nerve roots, dorsal root ganglia, and the thalamus may in different conditions underlie the spontaneous pain. Evoked pain may spread to neighboring areas, and the underlying pathophysiology involves peripheral and central sensitization. Maladaptive structural changes and a number of cell-cell interactions and molecular signaling underlie the sensitization of nociceptive pathways. These include alteration in ion channels, activation of immune cells, glial-derived mediators, and epigenetic regulation. The major classes of therapeutics include drugs acting on α₂δ subunits of calcium channels, sodium channels, and descending modulatory inhibitory pathways.

Optogenetics for neural transplant manipulation and functional analysis

Transplantation of neural stem cells (NSCs) or NSC-derived neurons into the brain is a promising therapeutic approach to restore neuronal function. Rapid progress in the NSCs research field, particularly due to the exploitation of induced pluripotent stem cells (iPSCs), offers great potential and an unlimited source of stem cell-derived neural grafts. Studying the functional integration of these grafts into host brain tissues and their effects on each other have been boosted by the implementation of optogenetic technologies. Optogenetics provides high spatiotemporal functional manipulations of grafted or host neurons in parallel. This review aims to highlight the impact of optogenetics in neural stem cell transplantations.