Microbial opsins: a family of single-component tools for optical control of neural activity

Optogenetics for controlling seizure circuits for translational approaches

The advent of optogenetic tools has had a profound impact on modern neuroscience research, revolutionizing our understanding of the brain. These tools offer a remarkable ability to precisely manipulate specific groups of neurons with an unprecedented level of temporal precision, on the order of milliseconds. This breakthrough has significantly advanced our knowledge of various physiological and pathophysiological processes in the brain. Within the realm of epilepsy research, optogenetic tools have played a crucial role in investigating the contributions of different neuronal populations to the generation of seizures and hyperexcitability. By selectively activating or inhibiting specific neurons using optogenetics, researchers have been able to elucidate the underlying mechanisms and identify key players involved in epileptic activity. Moreover, optogenetic techniques have also been explored as innovative therapeutic strategies for treating epilepsy. These strategies aim to halt seizure progression and alleviate symptoms by utilizing the precise control offered by optogenetics. The application of optogenetic tools has provided valuable insights into the intricate workings of the brain during epileptic episodes. For instance, researchers have discovered how distinct interneuron populations contribute to the initiation of seizures (ictogenesis). They have also revealed how remote circuits in regions such as the cerebellum, septum, or raphe nuclei can interact with hyperexcitable networks in the hippocampus. Additionally, studies have demonstrated the potential of closed-loop systems, where optogenetics is combined with real-time monitoring, to enable precise, on-demand control of seizure activity. Despite the immense promise demonstrated by optogenetic approaches, it is important to acknowledge that many of these techniques are still in the early stages of development and have yet to reach potential clinical applications. The transition from experimental research to practical clinical use poses numerous challenges. In this review, we aim to introduce optogenetic tools, provide a comprehensive survey of their application in epilepsy research, and critically discuss their current potential and limitations in achieving successful clinical implementation for the treatment of human epilepsy. By addressing these crucial aspects, we hope to foster a deeper understanding of the current state and future prospects of optogenetics in epilepsy treatment.

Bioelectricity in Developmental Patterning and Size Control: Evidence and Genetically Encoded Tools in the Zebrafish Model

Developmental patterning is essential for regulating cellular events such as axial patterning, segmentation, tissue formation, and organ size determination during embryogenesis. Understanding the patterning mechanisms remains a central challenge and fundamental interest in developmental biology. Ion-channel-regulated bioelectric signals have emerged as a player of the patterning mechanism, which may interact with morphogens. Evidence from multiple model organisms reveals the roles of bioelectricity in embryonic development, regeneration, and cancers. The Zebrafish model is the second most used vertebrate model, next to the mouse model. The zebrafish model has great potential for elucidating the functions of bioelectricity due to many advantages such as external development, transparent early embryogenesis, and tractable genetics. Here, we review genetic evidence from zebrafish mutants with fin-size and pigment changes related to ion channels and bioelectricity. In addition, we review the cell membrane voltage reporting and chemogenetic tools that have already been used or have great potential to be implemented in zebrafish models. Finally, new perspectives and opportunities for bioelectricity research with zebrafish are discussed.

A Fast and Robust Strategy to Remove Variant-Level Artifacts in Alzheimer Disease Sequencing Project Data

Background and Objectives

Exome sequencing (ES) and genome sequencing (GS) are expected to be critical to further elucidate the missing genetic heritability of Alzheimer disease (AD) risk by identifying rare coding and/or noncoding variants that contribute to AD pathogenesis. In the United States, the Alzheimer Disease Sequencing Project (ADSP) has taken a leading role in sequencing AD-related samples at scale, with the resultant data being made publicly available to researchers to generate new insights into the genetic etiology of AD. To achieve sufficient power, the ADSP has adapted a study design where subsets of larger AD cohorts are collected and sequenced across multiple centers, using a variety of sequencing platforms. This approach may lead to variable variant quality across sequencing centers and/or platforms. In this study, we sought to implement and evaluate filters that can be applied fast to robustly remove variant-level artifacts in the ADSP data.

Methods

We implemented a robust quality control procedure to handle ADSP data. We evaluated this procedure while performing exome-wide and genome-wide association analyses on AD risk using the latest ADSP whole ES (WES) and whole GS (WGS) data releases (NG00067.v5).

Results

We observed that many variants displayed large variation in allele frequencies across sequencing centers/platforms and contributed to spurious association signals with AD risk. We also observed that sequencing platform/center adjustment in association models could not fully account for these spurious signals. To address this issue, we designed and implemented variant filters that could capture and remove these center-specific/platform-specific artifactual variants.

Discussion

We derived a fast and robust approach to filter variants that represent sequencing center-related or platform-related artifacts underlying spurious associations with AD risk in ADSP WES and WGS data. This approach will be important to support future robust genetic association studies on ADSP data, as well as other studies with similar designs.

Rhodopsin-bestrophin fusion proteins from unicellular algae form gigantic pentameric ion channels

Many organisms sense light using rhodopsins, photoreceptive proteins containing a retinal chromophore. Here we report the discovery, structure and biophysical characterization of bestrhodopsins, a microbial rhodopsin subfamily from marine unicellular algae, in which one rhodopsin domain of eight transmembrane helices or, more often, two such domains in tandem, are C-terminally fused to a bestrophin channel. Cryo-EM analysis of a rhodopsin-rhodopsin-bestrophin fusion revealed that it forms a pentameric megacomplex (~700 kDa) with five rhodopsin pseudodimers surrounding the channel in the center. Bestrhodopsins are metastable and undergo photoconversion between red- and green-absorbing or green- and UVA-absorbing forms in the different variants. The retinal chromophore, in a unique binding pocket, photoisomerizes from all-trans to 11-cis form. Heterologously expressed bestrhodopsin behaves as a light-modulated anion channel.

Stimuli-Responsive Natural Proteins and Their Applications

Natural proteins are essential biomacromolecules that fulfill versatile functions in the living organism, such as their usage as cytoskeleton, nutriment transporter, homeostasis controller, catalyzer, or immune guarder. Due to the excellent mechanical properties and good biocompatibility/biodegradability, natural protein-based biomaterials are well equipped for prospective applications in various fields. Among these natural proteins, stimuli-responsive proteins can be reversibly and precisely manipulated on demand, rendering the protein-based biomaterials promising candidates for numerous applications, including disease detection, drug delivery, bio-sensing, and regenerative medicine. Therefore, we present some typical natural proteins with diverse physical stimuli-responsive properties, including temperature, light, force, electrical, and magnetic sensing in this review. The structure-function mechanism of these proteins is discussed in detail. Finally, we give a summary and perspective for the development of stimuli-responsive proteins.

Liposome-based measurement of light-driven chloride transport kinetics of halorhodopsin

We report a simple and direct fluorimetric vesicle-based method for measuring the transport rate of the light-driven ions pumps as specifically applied to the chloride pump, halorhodopsin, from Natronomonas pharaonis (pHR). Previous measurements were cell-based and methods to determine average single channel permeability challenging. We used a water-in-oil emulsion method for directional pHR reconstitution into two different types of vesicles: lipid vesicles and asymmetric lipid-block copolymer vesicles. We then used stopped-flow experiments combined with fluorescence correlation spectroscopy to determine per protein Cl- transport rates. We obtained a Cl^- transport rate of 442 (±17.7) Cl^-/protein/s in egg phosphatidyl choline (PC) lipid vesicles and 413 (±26) Cl^-/protein/s in hybrid block copolymer/lipid (BCP/PC) vesicles with polybutadine-polyethylene oxide (PB₁₂PEO₈) on the outer leaflet and PC in the inner leaflet at a photon flux of 1450 photons/protein/s. Normalizing to a per photon basis, this corresponds to 0.30 (±0.07) Cl^-/photon and 0.28 (±0.04) Cl^-/photon for pure PC and BCP/PC hybrid vesicles respectively, both of which are in agreement with recently reported turnover of ~500 Cl^-/protein/s from flash photolysis experiments and with voltage-clamp measurements of 0.35 (±0.16) Cl^-/photon in pHR-expressing oocytes as well as with a pHR quantum efficiency of ~30%.

Ecological and Biotechnological Aspects of Pigmented Microbes: A Way Forward in Development of Food and Pharmaceutical Grade Pigments

Microbial pigments play multiple roles in the ecosystem construction, survival, and fitness of all kinds of organisms. Considerably, microbial (bacteria, fungi, yeast, and microalgae) pigments offer a wide array of food, drug, colorants, dyes, and imaging applications. In contrast to the natural pigments from microbes, synthetic colorants are widely used due to high production, high intensity, and low cost. Nevertheless, natural pigments are gaining more demand over synthetic pigments as synthetic pigments have demonstrated side effects on human health. Therefore, research on microbial pigments needs to be extended, explored, and exploited to find potential industrial applications. In this review, the evolutionary aspects, the spatial significance of important pigments, biomedical applications, research gaps, and future perspectives are detailed briefly. The pathogenic nature of some pigmented bacteria is also detailed for awareness and safe handling. In addition, pigments from macro-organisms are also discussed in some sections for comparison with microbes.

Electrophysiology Read-Out Tools for Brain-on-Chip Biotechnology

Brain-on-Chip (BoC) biotechnology is emerging as a promising tool for biomedical and pharmaceutical research applied to the neurosciences. At the convergence between lab-on-chip and cell biology, BoC couples in vitro three-dimensional brain-like systems to an engineered microfluidics platform designed to provide an in vivo-like extrinsic microenvironment with the aim of replicating tissue- or organ-level physiological functions. BoC therefore offers the advantage of an in vitro reproduction of brain structures that is more faithful to the native correlate than what is obtained with conventional cell culture techniques. As brain function ultimately results in the generation of electrical signals, electrophysiology techniques are paramount for studying brain activity in health and disease. However, as BoC is still in its infancy, the availability of combined BoC-electrophysiology platforms is still limited. Here, we summarize the available biological substrates for BoC, starting with a historical perspective. We then describe the available tools enabling BoC electrophysiology studies, detailing their fabrication process and technical features, along with their advantages and limitations. We discuss the current and future applications of BoC electrophysiology, also expanding to complementary approaches. We conclude with an evaluation of the potential translational applications and prospective technology developments.

Cardiac optogenetics: a decade of enlightenment

The electromechanical function of the heart involves complex, coordinated activity over time and space. Life-threatening cardiac arrhythmias arise from asynchrony in these space-time events; therefore, therapies for prevention and treatment require fundamental understanding and the ability to visualize, perturb and control cardiac activity. Optogenetics combines optical and molecular biology (genetic) approaches for light-enabled sensing and actuation of electrical activity with unprecedented spatiotemporal resolution and parallelism. The year 2020 marks a decade of developments in cardiac optogenetics since this technology was adopted from neuroscience and applied to the heart. In this Review, we appraise a decade of advances that define near-term (immediate) translation based on all-optical electrophysiology, including high-throughput screening, cardiotoxicity testing and personalized medicine assays, and long-term (aspirational) prospects for clinical translation of cardiac optogenetics, including new optical therapies for rhythm control. The main translational opportunities and challenges for optogenetics to be fully embraced in cardiology are also discussed.

Light-Driven Chloride Transport Kinetics of Halorhodopsin

Despite growing interest in light-driven ion pumps for use in optogenetics, current estimates of their transport rates span two orders of magnitude due to challenges in measuring slow transport processes and determining protein concentration and/or orientation in membranes in vitro. In this study, we report, to our knowledge, the first direct quantitative measurement of light-driven Cl^- transport rates of the anion pump halorohodopsin from Natronomonas pharaonis (NpHR). We used light-interfaced voltage clamp measurements on NpHR-expressing oocytes to obtain a transport rate of 219 (± 98) Cl^-/protein/s for a photon flux of 630 photons/protein/s. The measurement is consistent with the literature-reported quantum efficiency of ∼30% for NpHR, i.e., 0.3 isomerizations per photon absorbed. To reconcile our measurements with an earlier-reported 20 ms rate-limiting step, or 35 turnovers/protein/s, we conducted, to our knowledge, novel consecutive single-turnover flash experiments that demonstrate that under continuous illumination, NpHR bypasses this step in the photocycle.

Advances in Engineering and Application of Optogenetic Indicators for Neuroscience

Our ability to investigate the brain is limited by available technologies that can record biological processes in vivo with suitable spatiotemporal resolution. Advances in optogenetics now enable optical recording and perturbation of central physiological processes within the intact brains of model organisms. By monitoring key signaling molecules noninvasively, we can better appreciate how information is processed and integrated within intact circuits. In this review, we describe recent efforts engineering genetically-encoded fluorescence indicators to monitor neuronal activity. We summarize recent advances of sensors for calcium, potassium, voltage, and select neurotransmitters, focusing on their molecular design, properties, and current limitations. We also highlight impressive applications of these sensors in neuroscience research. We adopt the view that advances in sensor engineering will yield enduring insights on systems neuroscience. Neuroscientists are eager to adopt suitable tools for imaging neural activity in vivo, making this a golden age for engineering optogenetic indicators.

State-of-the-Art Techniques to Causally Link Neural Plasticity to Functional Recovery in Experimental Stroke Research

Current experimental stroke research faces the same challenge as neuroscience: to transform correlative findings in causative ones. Research of recent years has shown the tremendous potential of the central nervous system to react to noxious stimuli such as a stroke: Increased plastic changes leading to reorganization in form of neuronal rewiring, neurogenesis, and synaptogenesis, accompanied by transcriptional and translational turnover in the affected cells, have been described both clinically and in experimental stroke research. However, only minor attempts have been made to connect distinct plastic remodeling processes as causative features for specific behavioral phenotypes. Here, we review current state-of the art techniques for the examination of cortical reorganization and for the manipulation of neuronal circuits as well as techniques which combine anatomical changes with molecular profiling. We provide the principles of the techniques together with studies in experimental stroke research which have already applied the described methodology. The tools discussed are useful to close the loop from our understanding of stroke pathology to the behavioral outcome and may allow discovering new targets for therapeutic approaches. The here presented methods open up new possibilities to assess the efficiency of rehabilitative strategies by understanding their external influence for intrinsic repair mechanisms on a neurobiological basis.

Current Genetic Techniques in Neural Circuit Control of Feeding and Energy Metabolism

The current epidemic of obesity and its associated metabolic syndromes imposes unprecedented challenges to our society. Despite intensive research focus on obesity pathogenesis, an effective therapeutic strategy to treat and cure obesity is still lacking. The obesity development is due to a disturbed homeostatic control of feeding and energy expenditure, both of which are controlled by an intricate neural network in the brain. Given the inherent complexity of brain networks in controlling feeding and energy expenditure, the understanding of brain-based pathophysiology for obesity development is limited. One key limiting factor in dissecting neural pathways for feeding and energy expenditure is unavailability of techniques that can be used to effectively reduce the complexity of the brain network to a tractable paradigm, based on which a strong hypothesis can be tested. Excitingly, emerging techniques have been involved to be able to link specific groups of neurons and neural pathways to behaviors (i.e., feeding and energy expenditure). In this chapter, novel techniques especially those based on animal models and viral vector approaches will be discussed. We hope that this chapter will provide readers with a basis that can help to understand the literatures using these techniques and with a guide to apply these exciting techniques to investigate brain mechanisms underlying feeding and energy expenditure.

Illuminating Brain Activities with Fluorescent Protein-Based Biosensors

Fluorescent protein-based biosensors are indispensable molecular tools for life science research. The invention and development of high-fidelity biosensors for a particular molecule or molecular event often catalyze important scientific breakthroughs. Understanding the structural and functional organization of brain activities remain a subject for which optical sensors are in desperate need and of growing interest. Here, we review genetically encoded fluorescent sensors for imaging neuronal activities with a focus on the design principles and optimizations of various sensors. New bioluminescent sensors useful for deep-tissue imaging are also discussed. By highlighting the protein engineering efforts and experimental applications of these sensors, we can consequently analyze factors influencing their performance. Finally, we remark on how future developments can fill technological gaps and lead to new discoveries.

Behavioral Manipulation by Optogenetics in the Nonhuman Primate

Given their neuroanatomical similarities to humans and their ability to perform complex behaviors, the nonhuman primate has been an important model for understanding complex systems such as sensory processing, motor control, social interaction, and nervous system disorders. Optogenetics offers cell-type specific neural control with millisecond precision, making it a powerful neural modulation technique. Combining optogenetics with the nonhuman primate model promises to lead to significant advances in both basic and applied research. In the past few years, optogenetics has made considerable progress in the nonhuman primate. Here, we systematically review the current state-of-art of optogenetics in the nonhuman primate with an emphasis on behavioral manipulation. Given its recent successes, we believe that the progress in the nonhuman primate will boost the translation of optogenetics to clinical applications in the near future.

Methods to investigate the structure and connectivity of the nervous system

Understanding the computations that take place in neural circuits requires identifying how neurons in those circuits are connected to one another. In addition, recent research indicates that aberrant neuronal wiring may be the cause of several neurodevelopmental disorders, further emphasizing the importance of identifying the wiring diagrams of brain circuits. To address this issue, several new approaches have been recently developed. In this review, we describe several methods that are currently available to investigate the structure and connectivity of the brain, and discuss their strengths and limitations.

Microbial Proteins as Novel Industrial Biotechnology Hosts to Treat Epilepsy

Epilepsy is characterized by the hyperexcitability of various neuronal circuits that results due to the imbalance between glutamate-mediated excitation of voltage-gated cation channels and γ-amino butyric acid (GABA)-mediated inhibition of anion channels leading to aberrant, sporadic oscillations or fluctuations in neuronal electrical activity. Epilepsy with a risk of mortality and around 65 million sufferers of all ages all over the world is limited therapeutically with high rates of adverse reactions, lack of complete seizure control, and over 30% patients with refractory epilepsy. The only alternative to medicines is to identify and surgically remove the seizure foci in the brain or to abort the seizures just as they begin using an implanted cerebral electrode. However, these alternatives are unable to precisely aim aberrant neuronal circuits while leaving others unaltered. Epilepsy animal models also constitute the identical constraint. Thus, a better target-specific approach is needed to study and treat epilepsy. Unicellular green algae Chlamydomonas reinhardtii expresses a channelrhodopsin-2 (ChR2) sodium ion channel protein that controls the phototaxis movement of algae in response to blue light. Similarly, archaeon Natronomonas pharaonis (NpHR) expresses a monovalent Cl^- channel protein halorhodopsin that responds to yellow light. These features of ChR2 and NpHR proteins can be used in optogenetic techniques to manipulate the bi-directional firing pattern of neuronal circuits in an attempt to better understand the pathophysiology of epileptic seizures as well as to discover novel potential drugs to treat epilepsy.

Optogenetic silencing of locus coeruleus activity in mice impairs cognitive flexibility in an attentional set-shifting task

The locus coeruleus (LC) is the sole source of noradrenergic projections to the cortex and essential for attention-dependent cognitive processes. In this study we used unilateral optogenetic silencing of the LC in an attentional set-shifting task (ASST) to evaluate the influence of the LC on prefrontal cortex-dependent functions in mice. We expressed the halorhodopsin eNpHR 3.0 to reversibly silence LC activity during task performance, and found that silencing selectively impaired learning of those parts of the ASST that most strongly rely on cognitive flexibility. In particular, extra-dimensional set-shifting (EDS) and reversal learning was impaired, suggesting an involvement of the medial prefrontal cortex (mPFC) and the orbitofrontal cortex. In contrast, those parts of the task that are less dependent on cognitive flexibility, i.e., compound discrimination (CD) and the intra-dimensional shifts (IDS) were not affected. Furthermore, attentional set formation was unaffected by LC silencing. Our results therefore suggest a modulatory influence of the LC on cognitive flexibility, mediated by different frontal networks.

Optogenetics in Freely Moving Mammals: Dopamine and Reward

Brain reward systems play a central role in the cognitive and hedonic behaviors of mammals. Multiple neuron types and brain regions are involved in reward processing, posing fascinating scientific questions, and major experimental challenges. Using diverse approaches including genetics, electrophysiology, imaging, and behavioral analysis, a large body of research has focused on both normal functioning of the reward circuitry and on its potential significance in neuropsychiatric diseases. In this introduction, we illustrate a real-world application of optogenetics to mammalian behavior and physiology, delineating procedures and technologies for optogenetic control of individual components of the reward circuitry. We describe the experimental setup and protocol for integrating optogenetic modulation of dopamine neurons with fast-scan cyclic voltammetry, conditioned place preference, and operant conditioning to assess the causal role of well-defined electrical and biochemical signals in reward-related behavior.

Optogenetics: opsins and optical interfaces in neuroscience

Optogenetics is defined as the integration of optics and genetics to control well-defined events within specified cells of living tissue. In this introduction, we focus on the basic techniques necessary for employing microbial opsins as optogenetic tools in mammalian brains. We provide a guide for the fundamentals of optogenetic application-selecting an opsin, implementing expression of opsins based on the neuroscientific experimental requirements, and adapting the corresponding optical hardware for delivery of light into mammalian brains.

Identifying and quantifying multisensory integration: a tutorial review

We process information from the world through multiple senses, and the brain must decide what information belongs together and what information should be segregated. One challenge in studying such multisensory integration is how to quantify the multisensory interactions, a challenge that is amplified by the host of methods that are now used to measure neural, behavioral, and perceptual responses. Many of the measures that have been developed to quantify multisensory integration (and which have been derived from single unit analyses), have been applied to these different measures without much consideration for the nature of the process being studied. Here, we provide a review focused on the means with which experimenters quantify multisensory processes and integration across a range of commonly used experimental methodologies. We emphasize the most commonly employed measures, including single- and multiunit responses, local field potentials, functional magnetic resonance imaging, and electroencephalography, along with behavioral measures of detection, accuracy, and response times. In each section, we will discuss the different metrics commonly used to quantify multisensory interactions, including the rationale for their use, their advantages, and the drawbacks and caveats associated with them. Also discussed are possible alternatives to the most commonly used metrics.

Intramolecular proton transfer in channelrhodopsins

Channelrhodopsins serve as photoreceptors that control the motility behavior of green flagellate algae and act as light-gated ion channels when heterologously expressed in animal cells. Here, we report direct measurements of proton transfer from the retinylidene Schiff base in several channelrhodopsin variants expressed in HEK293 cells. A fast outward-directed current precedes the passive channel current that has the opposite direction at physiological holding potentials. This rapid charge movement occurs on the timescale of the M intermediate formation in microbial rhodopsins, including that for channelrhodopsin from Chlamydomonas augustae and its mutants, reported in this study. Mutant analysis showed that the glutamate residue corresponding to Asp(85) in bacteriorhodopsin acts as the primary acceptor of the Schiff-base proton in low-efficiency channelrhodopsins. Another photoactive-site residue corresponding to Asp(212) in bacteriorhodopsin serves as an alternative proton acceptor and plays a more important role in channel opening than the primary acceptor. In more efficient channelrhodopsins from Chlamydomonas reinhardtii, Mesostigma viride, and Platymonas (Tetraselmis) subcordiformis, the fast current was apparently absent. The inverse correlation of the outward proton transfer and channel activity is consistent with channel function evolving in channelrhodopsins at the expense of their capacity for active proton transport.

Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics

Genetically encoded calcium indicators (GECIs) are powerful tools for systems neuroscience. Here we describe red, single-wavelength GECIs, “RCaMPs,” engineered from circular permutation of the thermostable red fluorescent protein mRuby. High-resolution crystal structures of mRuby, the red sensor RCaMP, and the recently published red GECI R-GECO1 give insight into the chromophore environments of the Ca²⁺-bound state of the sensors and the engineered protein domain interfaces of the different indicators. We characterized the biophysical properties and performance of RCaMP sensors in vitro and in vivo in Caenorhabditis elegans, Drosophila larvae, and larval zebrafish. Further, we demonstrate 2-color calcium imaging both within the same cell (registering mitochondrial and somatic [Ca²⁺]) and between two populations of cells: neurons and astrocytes. Finally, we perform integrated optogenetics experiments, wherein neural activation via channelrhodopsin-2 (ChR2) or a red-shifted variant, and activity imaging via RCaMP or GCaMP, are conducted simultaneously, with the ChR2/RCaMP pair providing independently addressable spectral channels. Using this paradigm, we measure calcium responses of naturalistic and ChR2-evoked muscle contractions in vivo in crawling C. elegans. We systematically compare the RCaMP sensors to R-GECO1, in terms of action potential-evoked fluorescence increases in neurons, photobleaching, and photoswitching. R-GECO1 displays higher Ca²⁺ affinity and larger dynamic range than RCaMP, but exhibits significant photoactivation with blue and green light, suggesting that integrated channelrhodopsin-based optogenetics using R-GECO1 may be subject to artifact. Finally, we create and test blue, cyan, and yellow variants engineered from GCaMP by rational design. This engineered set of chromatic variants facilitates new experiments in functional imaging and optogenetics.

Cardiac optogenetics

Optogenetics is an emerging technology for optical interrogation and control of biological function with high specificity and high spatiotemporal resolution. Mammalian cells and tissues can be sensitized to respond to light by a relatively simple and well-tolerated genetic modification using microbial opsins (light-gated ion channels and pumps). These can achieve fast and specific excitatory or inhibitory response, offering distinct advantages over traditional pharmacological or electrical means of perturbation. Since the first demonstrations of utility in mammalian cells (neurons) in 2005, optogenetics has spurred immense research activity and has inspired numerous applications for dissection of neural circuitry and understanding of brain function in health and disease, applications ranging from in vitro to work in behaving animals. Only recently (since 2010), the field has extended to cardiac applications with less than a dozen publications to date. In consideration of the early phase of work on cardiac optogenetics and the impact of the technique in understanding another excitable tissue, the brain, this review is largely a perspective of possibilities in the heart. It covers the basic principles of operation of light-sensitive ion channels and pumps, the available tools and ongoing efforts in optimizing them, overview of neuroscience use, as well as cardiac-specific questions of implementation and ideas for best use of this emerging technology in the heart.

Recent developments in optical neuromodulation technologies

The emergence of optogenetics technology facilitated widespread applications for interrogation of complex neural networks, such as activation of specific axonal pathways, previously found impossible with electrical stimulation. Consequently, within the short period of its application in neuroscience research, optogenetics has led to findings of significant importance both during normal brain function as well as in disease. Moreover, the optimization of optogenetics for in vivo studies has allowed the control of certain behavioral responses such as motility, reflex, and sensory responses, as well as more complex emotional and cognitive behaviors such as decision-making, reward seeking, and social behavior in freely moving animals. These studies have produced a wide variety of animal models that have resulted in fundamental findings and enhanced our understanding of the neural networks associated with behavior. The increasing number of opsins available for this technique enabled even broader regulation of neuronal activity. These advancements highlight the potential of this technique for future treatment of human diseases. Here, we provide an overview of the recent developments in the field of optogenetics technology that are relevant for a better understanding of several neuropsychiatric and neurodegenerative disorders and may pave the way for future therapeutic interventions.

Enhancement of the long-wavelength sensitivity of optogenetic microbial rhodopsins by 3,4-dehydroretinal

Electrogenic microbial rhodopsins (ion pumps and channelrhodopsins) are widely used to control the activity of neurons and other cells by light (optogenetics). Long-wavelength absorption by optogenetic tools is desirable for increasing the penetration depth of the stimulus light by minimizing tissue scattering and absorption by hemoglobin. A2 retinal (3,4-dehydroretinal) is a natural retinoid that serves as the chromophore in red-shifted visual pigments of several lower aquatic animals. Here we show that A2 retinal reconstitutes a fully functional archaerhodopsin-3 (AR-3) proton pump and four channelrhodopsin variants (CrChR1, CrChR2, CaChR1, and MvChR1). Substitution of A1 with A2 retinal significantly shifted the spectral sensitivity of all tested rhodopsins to longer wavelengths without altering other aspects of their function. The spectral shift upon substitution of A1 with A2 in AR-3 was close to that measured in other archaeal rhodopsins. Notably, the shifts in channelrhodopsins were larger than those measured in archaeal rhodopsins and close to those in animal visual pigments with similar absorption maxima of their A1-bound forms. Our results show that chromophore substitution provides a complementary strategy for improving the efficiency of optogenetic tools.

A comprehensive concept of optogenetics

Fundamental questions that neuroscientists have previously approached with classical biochemical and electrophysiological techniques can now be addressed using optogenetics. The term optogenetics reflects the key program of this emerging field, namely, combining optical and genetic techniques. With the already impressively successful application of light-driven actuator proteins such as microbial opsins to interact with intact neural circuits, optogenetics rose to a key technology over the past few years. While spearheaded by tools to control membrane voltage, the more general concept of optogenetics includes the use of a variety of genetically encoded probes for physiological parameters ranging from membrane voltage and calcium concentration to metabolism. Here, we provide a comprehensive overview of the state of the art in this rapidly growing discipline and attempt to sketch some of its future prospects and challenges.

Optogenetics in neural systems

Both observational and perturbational technologies are essential for advancing the understanding of brain function and dysfunction. But while observational techniques have greatly advanced in the last century, techniques for perturbation that are matched to the speed and heterogeneity of neural systems have lagged behind. The technology of optogenetics represents a step toward addressing this disparity. Reliable and targetable single-component tools (which encompass both light sensation and effector function within a single protein) have enabled versatile new classes of investigation in the study of neural systems. Here we provide a primer on the application of optogenetics in neuroscience, focusing on the single-component tools and highlighting important problems, challenges, and technical considerations.