Optogenetics: 10 years of microbial opsins in neuroscience

Two-photon probes for in vivo multicolor microscopy of the structure and signals of brain cells

Imaging the brain of living laboratory animals at a microscopic scale can be achieved by two-photon microscopy thanks to the high penetrability and low phototoxicity of the excitation wavelengths used. However, knowledge of the two-photon spectral properties of the myriad fluorescent probes is generally scarce and, for many, non-existent. In addition, the use of different measurement units in published reports further hinders the design of a comprehensive imaging experiment. In this review, we compile and homogenize the two-photon spectral properties of 280 fluorescent probes. We provide practical data, including the wavelengths for optimal two-photon excitation, the peak values of two-photon action cross section or molecular brightness, and the emission ranges. Beyond the spectroscopic description of these fluorophores, we discuss their binding to biological targets. This specificity allows in vivo imaging of cells, their processes, and even organelles and other subcellular structures in the brain. In addition to probes that monitor endogenous cell metabolism, studies of healthy and diseased brain benefit from the specific binding of certain probes to pathology-specific features, ranging from amyloid-β plaques to the autofluorescence of certain antibiotics. A special focus is placed on functional in vivo imaging using two-photon probes that sense specific ions or membrane potential, and that may be combined with optogenetic actuators. Being closely linked to their use, we examine the different routes of intravital delivery of these fluorescent probes according to the target. Finally, we discuss different approaches, strategies, and prerequisites for two-photon multicolor experiments in the brains of living laboratory animals.

Acoustic mechanogenetics

From basic studies in understanding the role of signaling pathways to therapeutic applications in engineering new cellular functions, efficient and safe techniques to monitor and modulate molecular targets from cells to organs have been extensively developed. The developmental advancement of engineering devices such as microscope and ultrasonic transducers allows us to investigate biological processes at different scales. Synthetic biology has further emerged recently as a powerful platform for the development of new diagnostic and therapeutic molecular tools. The synergetic amalgamation between engineering tools and synthetic biology has rapidly become a new front in the field of bioengineering and biotechnology. In this review, ultrasound and its generated mechanical perturbation are introduced to serve as a non-invasive engineering approach and, integrated with synthetic biology, to remotely control signaling and genetic activities for the guidance of cellular functions deep inside tissue with high spatiotemporal resolutions. This ultrasound-based approach together with synthetic biology has been applied in immunotherapy, neuroscience, and gene delivery, paving the way for the development of next-generation therapeutic tools.

Crystal structure of the natural anion-conducting channelrhodopsin GtACR1

The naturally occurring channelrhodopsin variant anion channelrhodopsin-1 (ACR1), discovered in the cryptophyte algae Guillardia theta, exhibits large light-gated anion conductance and high anion selectivity when expressed in heterologous settings, properties that support its use as an optogenetic tool to inhibit neuronal firing with light. However, molecular insight into ACR1 is lacking owing to the absence of structural information underlying light-gated anion conductance. Here we present the crystal structure of G. theta ACR1 at 2.9 Å resolution. The structure reveals unusual architectural features that span the extracellular domain, retinal-binding pocket, Schiff-base region, and anion-conduction pathway. Together with electrophysiological and spectroscopic analyses, these findings reveal the fundamental molecular basis of naturally occurring light-gated anion conductance, and provide a framework for designing the next generation of optogenetic tools.

Structural mechanisms of selectivity and gating in anion channelrhodopsins

Both designed and natural anion-conducting channelrhodopsins (dACRs and nACRs, respectively) have been widely applied in optogenetics (enabling selective inhibition of target-cell activity during animal behaviour studies), but each class exhibits performance limitations, underscoring trade-offs in channel structure-function relationships. Therefore, molecular and structural insights into dACRs and nACRs will be critical not only for understanding the fundamental mechanisms of these light-gated anion channels, but also to create next-generation optogenetic tools. Here we report crystal structures of the dACR iC++, along with spectroscopic, electrophysiological and computational analyses that provide unexpected insights into pH dependence, substrate recognition, channel gating and ion selectivity of both dACRs and nACRs. These results enabled us to create an anion-conducting channelrhodopsin integrating the key features of large photocurrent and fast kinetics alongside exclusive anion selectivity.

Drosophila as a Model System for Neurotransmitter Measurements

Drosophila melanogaster, the fruit fly, is an important, simple model organism for studying the effects of genetic mutations on neuronal activity and behavior. Biologists use Drosophila for neuroscience studies because of its genetic tractability, complex behaviors, well-known and simple neuroanatomy, and many orthologues to human genes. Neurochemical measurements in Drosophila are challenging due to the small size of the central nervous system. Recently, methods have been developed to measure real-time neurotransmitter release and clearance in both larvae and adults using electrochemistry. These studies have characterized dopamine, serotonin, and octopamine release in both wild type and genetic mutant flies. Tissue content measurements are also important, and separations are predominantly used. Capillary electrophoresis, with either electrochemical, laser-induced fluorescence, or mass spectrometry detection, facilitates tissue content measurements from single, isolated Drosophila brains or small samples of hemolymph. Neurochemical studies in Drosophila have revealed that flies have functioning transporters and autoreceptors, that their metabolism is different than in mammals, and that flies have regional, life stage, and sex differences in neurotransmission. Future studies will develop smaller electrodes, expand optical imaging techniques, explore physiological stimulations, and use advanced genetics to target single neuron release or study neurochemical changes in models of human diseases.

Transient Magnetothermal Neuronal Silencing Using the Chloride Channel Anoctamin 1 (TMEM16A)

Determining the role and necessity of specific neurons in a network calls for precisely timed, reversible removal of these neurons from the circuit via remotely triggered transient silencing. Previously, we have shown that alternating magnetic field mediated heating of magnetic nanoparticles, bound to neurons, expressing temperature-sensitive cation channels TRPV1 remotely activates these neurons, evoking behavioral responses in mice. Here, we demonstrate how to apply magnetic nanoparticle heating to silence target neurons. Rat hippocampal neuronal cultures were transfected to express the temperature gated chloride channel, anoctamin 1 (TMEM16A). Spontaneous firing was suppressed within seconds of alternating magnetic field application to anoctamin 1 (TMEM16A) channel expressing, magnetic nanoparticle decorated neurons. Five seconds of magnetic field application leads to 12 s of silencing, with a latency of 2 s and an average suppression ratio of more than 80%. Immediately following the silencing period spontaneous activity resumed. The method provides a promising avenue for tether free, remote, transient neuronal silencing in vivo for both scientific and therapeutic applications.

State-of-the-Art Techniques in Treating Peripheral Nerve Injury

BACKGROUND

Peripheral nerve injuries remain a major clinical concern, as they often lead to chronic disability and significant health care expenditures. Despite advancements in microsurgical techniques to enhance nerve repair, biological approaches are needed to augment nerve regeneration and improve functional outcomes after injury.

METHODS

Presented herein is a review of the current literature on state-of-the-art techniques to enhance functional recovery for patients with nerve injury. Four categories are considered: (1) electroceuticals, (2) nerve guidance conduits, (3) fat grafting, and (4) optogenetics. Significant study results are highlighted, focusing on histologic and functional outcome measures.

RESULTS

This review documents the current state of the literature. Advancements in neuronal stimulation, tissue engineering, and cell-based therapies demonstrate promise with regard to augmenting nerve regeneration and appropriate rehabilitation.

CONCLUSIONS

The future of treating peripheral nerve injury will include multimodality use of electroconductive conduits, fat grafting, neuronal stimulation, and optogenetics. Further clinical investigation is needed to confirm the efficacy of these technologies on peripheral nerve recovery in humans, and how best to implement this treatment for a diverse population of nerve-injured patients.

Ancestral Adeno-Associated Virus Vector Delivery of Opsins to Spiral Ganglion Neurons: Implications for Optogenetic Cochlear Implants

Optogenetics is a transformative technology based on light-sensitive microbial proteins, known as opsins, that enable precise modulation of neuronal activity with pulsed radiant energy. Optogenetics has been proposed as a means to improve auditory implant outcomes by reducing channel interaction and increasing electrode density, but the introduction of opsins into cochlear spiral ganglion neurons (SGNs) in vivo has been challenging. Here we test opsin delivery using a synthetically developed ancestral adeno-associated virus (AAV) vector called Anc80L65. Wild-type C57BL/6 mouse pups were injected via the round window of cochlea with Anc80L65 carrying opsin Chronos under the control of a CAG promoter. Following an incubation of 6-22 weeks, pulsed blue light was delivered to cochlear SGNs via a cochleosotomy approach and flexible optical fiber. Optically evoked auditory brainstem responses (oABRs) and multiunit activity in inferior colliculus (IC) were observed. Post-experiment cochlear histology demonstrated opsin expression in SGNs (mean = 74%), with an even distribution of opsin along the cochlear basal/apical gradient. This study is the first to describe robust SGN transduction, opsin expression, and optically evoked auditory electrophysiology in neonatal mice. Ultimately, this work may provide the basis for a new generation of cochlear implant based on light.

Recent advances in the optical control of protein function through genetic code expansion

In nature, biological processes are regulated with precise spatial and temporal resolution at the molecular, cellular, and organismal levels. In order to perturb and manipulate these processes, optically controlled chemical tools have been developed and applied in living systems. The use of light as an external trigger provides spatial and temporal control with minimal adverse effects. Incorporation of light-responsive amino acids into proteins in cells and organisms with an expanded genetic code has enabled the precise activation/deactivation of numerous, diverse proteins, such as kinases, nucleases, proteases, and polymerases. Using unnatural amino acids to generate light-triggered proteins enables a rational engineering approach that is based on mechanistic and/or structural information. This review focuses on the most recent developments in the field, including technological advances and biological applications.

Biocompatible and Implantable Optical Fibers and Waveguides for Biomedicine

Optical fibers and waveguides in general effectively control and modulate light propagation, and these tools have been extensively used in communication, lighting and sensing. Recently, they have received increasing attention in biomedical applications. By delivering light into deep tissue via these devices, novel applications including biological sensing, stimulation and therapy can be realized. Therefore, implantable fibers and waveguides in biocompatible formats with versatile functionalities are highly desirable. In this review, we provide an overview of recent progress in the exploration of advanced optical fibers and waveguides for biomedical applications. Specifically, we highlight novel materials design and fabrication strategies to form implantable fibers and waveguides. Furthermore, their applications in various biomedical fields such as light therapy, optogenetics, fluorescence sensing and imaging are discussed. We believe that these newly developed fiber and waveguide based devices play a crucial role in advanced optical biointerfaces.

Simultaneous Optogenetics and Cellular Resolution Calcium Imaging During Active Behavior Using a Miniaturized Microscope

The ability to precisely monitor and manipulate neural circuits is essential to understand the brain. Advancements over the last decade in optical techniques such as calcium imaging and optogenetics have empowered researchers to gain insight into brain function by systematically manipulating or monitoring defined neural circuits. Combining these cutting-edge techniques enables a more direct mechanism for ascribing neural dynamics to behavior. Here, we developed a miniaturized integrated microscope that allows for simultaneous optogenetic manipulation and cellular-resolution calcium imaging within the same field of view in freely behaving mice. The integrated microscope has two LEDs, one filtered with a 435-460 nm excitation filter for imaging green calcium indicators, and a second LED filtered with a 590-650 nm excitation filter for optogenetic modulation of red-shifted opsins. We developed and tested this technology to minimize biological and optical crosstalk. We observed insignificant amounts of biological and optical crosstalk with regards to the optogenetic LED affecting calcium imaging. We observed some amounts of residual crosstalk of the imaging light on optogenetic manipulation. Despite residual crosstalk, we have demonstrated the utility of this technology by probing the causal relationship between basolateral amygdala (BLA) -to- nucleus accumbens (NAc) circuit function, behavior, and network dynamics. Using this integrated microscope we were able to observe both a significant behavioral and cellular calcium response of the optogenetic modulation on the BLA-to-NAc circuit. This integrated strategy will allow for routine investigation of the causality of circuit manipulation on cellular-resolution network dynamics and behavior.

Parvalbumin-containing GABA cells and schizophrenia: experimental model based on targeted gene delivery through adeno-associated viruses

Understanding the contribution of transmitter systems in behavioural pharmacology has a long tradition. Multiple techniques such as transmitter-specific lesions, and also localized administration of pharmacological toxins including agonists and antagonists of selected receptors have been applied. More recently, modern genetic tools have permitted cell-type selective interferences, for example by expression of light-sensitive channels followed by optogenetic stimulation in behaviourally meaningful settings or by engineered channels termed DREADDS that respond to peripherally administered drugs. We here took a similar approach and employed a Cre recombinase-dependent viral delivery system (adeno-associated virus) to express tetanus toxin light chain (TeLc) and thus, block neural transmission specifically in parvalbumin-positive (PV+) neurons of the limbic and infralimbic prefrontal circuitry. PV-TeLc cohorts presented with normal circadian activity as recorded in PhenoTyper home cages, but a reproducible increase in anxiety was extracted in both the open field and light-dark box. Interestingly, working memory assessed in a spontaneous alternation Y-maze task was impaired in PV-TeLc mice. We also recorded local field potentials from a separate cohort and found no global changes in brain activity, but found a behaviourally relevant lack of modulation in the gamma spectral band. These anomalies are reminiscent of endophenotypes of schizophrenia and appear to be critically dependent on GABAergic signalling through PV neurones. At the same time, these observations validate the use of viral vector delivery and its expression in Cre-lines as a useful tool for understanding the role of selective components of the brain in behaviour and the underpinning physiology.

Targeting AgRP neurons to maintain energy balance: Lessons from animal models

The current obesity epidemic is a major worldwide health and economic burden. In the modern environment, an increase in the intake of high-fat and high-sugar foods plays a crucial role in the development of obesity by disrupting the mechanisms governing food intake and energy balance. Food intake and whole-body energy balance are regulated by the central nervous system through a sophisticated neuronal network located mostly in the hypothalamus. In particular, the hypothalamic arcuate nucleus (ARC) is a fundamental center that senses hormonal and nutrient-related signals informing about the energy state of the organism. The ARC contains two small, defined populations of neurons with opposite functions: anorexigenic proopiomelanocortin (POMC)-expressing neurons and orexigenic Agouti-related protein (AgRP)-expressing neurons. AgRP neurons, which also co-produce neuropeptide Y (NPY) and γ-Aminobutyric acid (GABA), are involved in an increase in hunger and a decrease in energy expenditure. In this review, we summarize the key findings from the most common animal models targeting AgRP neurons and the tools used to discern the role of this specific neuronal population in the control of peripheral metabolism, appetite, feeding-related behavior, and other complex behaviors. We also discuss how knowledge gained from these studies has revealed new pathways and key proteins that could be potential therapeutic targets to reduce appetite and food addictions in obesity and other diseases.

The evolution of artificial light actuators in living systems: from planar to nanostructured interfaces

Artificially enhancing light sensitivity in living cells allows control of neuronal paths or vital functions avoiding the wiring associated with the use of stimulation electrodes. Many possible strategies can be adopted for reaching this goal, including the direct photoexcitation of biological matter, the genetic modification of cells or the use of opto-bio interfaces. In this review we describe different light actuators based on both inorganic and organic semiconductors, from planar abiotic/biotic interfaces to nanoparticles, that allow transduction of a light signal into a signal which in turn affects the biological activity of the hosting system. In particular, we will focus on the application of thiophene-based materials which, thanks to their unique chemical-physical properties, geometrical adaptability, great biocompatibility and stability, have allowed the development of a new generation of fully organic light actuators for in vivo applications.

Tissue-like Neural Probes for Understanding and Modulating the Brain

Electrophysiology tools have contributed substantially to understanding brain function, yet the capabilities of conventional electrophysiology probes have remained limited in key ways because of large structural and mechanical mismatches with respect to neural tissue. In this Perspective, we discuss how the general goal of probe design in biochemistry, that the probe or label have a minimal impact on the properties and function of the system being studied, can be realized by minimizing structural, mechanical, and topological differences between neural probes and brain tissue, thus leading to a new paradigm of tissue-like mesh electronics. The unique properties and capabilities of the tissue-like mesh electronics as well as future opportunities are summarized. First, we discuss the design of an ultraflexible and open mesh structure of electronics that is tissue-like and can be delivered in the brain via minimally invasive syringe injection like molecular and macromolecular pharmaceuticals. Second, we describe the unprecedented tissue healing without chronic immune response that leads to seamless three-dimensional integration with a natural distribution of neurons and other key cells through these tissue-like probes. These unique characteristics lead to unmatched stable long-term, multiplexed mapping and modulation of neural circuits at the single-neuron level on a year time scale. Last, we offer insights on several exciting future directions for the tissue-like electronics paradigm that capitalize on their unique properties to explore biochemical interactions and signaling in a "natural" brain environment.

Optogenetic Modulation of a Minor Fraction of Parvalbumin-Positive Interneurons Specifically Affects Spatiotemporal Dynamics of Spontaneous and Sensory-Evoked Activity in Mouse Somatosensory Cortex in Vivo

Parvalbumin (PV) positive interneurons exert strong effects on the neocortical excitatory network, but it remains unclear how they impact the spatiotemporal dynamics of sensory processing in the somatosensory cortex. Here, we characterized the effects of optogenetic inhibition and activation of PV interneurons on spontaneous and sensory-evoked activity in mouse barrel cortex in vivo. Inhibiting PV interneurons led to a broad-spectrum power increase both in spontaneous and sensory-evoked activity. Whisker-evoked responses were significantly increased within 20 ms after stimulus onset during inhibition of PV interneurons, demonstrating high temporal precision of PV-shaped inhibition. Multiunit activity was strongly enhanced in neighboring cortical columns, but not at the site of transduction, supporting a central and highly specific role of PV interneurons in lateral inhibition. Inversely, activating PV interneurons drastically decreased spontaneous and whisker-evoked activity in the principal column and exerted strong lateral inhibition. Histological assessment of transduced cells combined with quantitative modeling of light distribution and spike sorting revealed that only a minor fraction (~10%) of the local PV population comprising no more than a few hundred neurons is optogenetically modulated, mediating the observed prominent and widespread effects on neocortical processing.

Hyperpolarization by activation of halorhodopsin results in enhanced synaptic transmission: Neuromuscular junction and CNS circuit

Optogenetics offers a unique method to regulate the activity of select neural circuits. However, the electrophysiological consequences of targeted optogenetic manipulation upon the entire circuit remain poorly understood. Analysis of the sensory-CNS-motor circuit in Drosophila larvae expressing eHpHR and ChR2-XXL revealed unexpected patterns of excitability. Optical stimulation of motor neurons targeted to express eNpHR resulted in inhibition followed by excitation of body wall contraction with repetitive stimulation in intact larvae. In situ preparations with direct electrophysiological measures showed an increased responsiveness to excitatory synaptic activity induced by sensory stimulation within a functional neural circuit. To ensure proper function of eNpHR and ChR2-XXL they were expressed in body wall muscle and direct electrophysiological measurements were obtained. Under eNpHR induced hyperpolarization the muscle remained excitable with increased amplitude of excitatory postsynaptic synaptic potentials. Theoretical models to explain the observations are presented. This study aids in increasing the understanding of the varied possible influences with light activated proteins within intact neural circuits.

Design and manufacturing challenges of optogenetic neural interfaces: a review

Optogenetics is a relatively new technology to achieve cell-type specific neuromodulation with millisecond-scale temporal precision. Optogenetic tools are being developed to address neuroscience challenges, and to improve the knowledge about brain networks, with the ultimate aim of catalyzing new treatments for brain disorders and diseases. To reach this ambitious goal the implementation of mature and reliable engineered tools is required. The success of optogenetics relies on optical tools that can deliver light into the neural tissue. Objective/Approach: Here, the design and manufacturing approaches available to the scientific community are reviewed, and current challenges to accomplish appropriate scalable, multimodal and wireless optical devices are discussed.

SIGNIFICANCE

Overall, this review aims at presenting a helpful guidance to the engineering and design of optical microsystems for optogenetic applications.

Focal, remote-controlled, chronic chemical modulation of brain microstructures

Direct delivery of fluid to brain parenchyma is critical in both research and clinical settings. This is usually accomplished through acutely inserted cannulas. This technique, however, results in backflow and significant dispersion away from the infusion site, offering little spatial or temporal control in delivering fluid. We present an implantable, MRI-compatible, remotely controlled drug delivery system for minimally invasive interfacing with brain microstructures in freely moving animals. We show that infusions through acutely inserted needles target a region more than twofold larger than that of identical infusions through chronically implanted probes due to reflux and backflow. We characterize the dynamics of in vivo infusions using positron emission tomography techniques. Volumes as small as 167 nL of copper-64 and fludeoxyglucose labeled agents are quantified. We further demonstrate the importance of precise drug volume dosing to neural structures to elicit behavioral effects reliably. Selective modulation of the substantia nigra, a critical node in basal ganglia circuitry, via muscimol infusion induces behavioral changes in a volume-dependent manner, even when the total dose remains constant. Chronic device viability is confirmed up to 1-y implantation in rats. This technology could potentially enable precise investigation of neurological disease pathology in preclinical models, and more efficacious treatment in human patients.

Using Optogenetics to Understand Neuronal Mechanisms Underlying Behavior in C. elegans

Approaches for inhibiting and activating neurons are essential for understanding how neurons and neuronal circuits produce behavior. Optogenetics is a recently-developed technique which uses light to manipulate neuronal activity with temporal precision in behaving animals and is widely-used by neuroscience researchers. Optogenetics is also an excellent method to incorporate into an undergraduate neuroscience laboratory module because students can learn to conduct and analyze quantitative behavioral assays, reinforce their understanding of synaptic transmission, and investigate the genetic and neuronal basis of behavior. Here, we describe a module in which students use light to activate serotonergic neurons expressing the light-activated ion channel channelrhodopsin in wildtype and mutant Caenorhabditis elegans, and observe and analyze the effects on the movement behavior of the nematode. The methods described here provide a foundation which students can use to design and conduct additional experiments that may have never been done before. Thus, this laboratory module provides an opportunity for students to learn a state-of-the-art neuroscience technique, think about neuroscience on genetic, cellular and behavioral levels, and to develop an independent research project.

Specificity, Versatility, and Continual Development: The Power of Optogenetics for Epilepsy Research

Optogenetics is a powerful and rapidly expanding set of techniques that use genetically encoded light sensitive proteins such as opsins. Through the selective expression of these exogenous light-sensitive proteins, researchers gain the ability to modulate neuronal activity, intracellular signaling pathways, or gene expression with spatial, directional, temporal, and cell-type specificity. Optogenetics provides a versatile toolbox and has significantly advanced a variety of neuroscience fields. In this review, using recent epilepsy research as a focal point, we highlight how the specificity, versatility, and continual development of new optogenetic related tools advances our understanding of neuronal circuits and neurological disorders. We additionally provide a brief overview of some currently available optogenetic tools including for the selective expression of opsins.

Pharmaco-genetic therapeutics targeting parvalbumin neurons attenuate temporal lobe epilepsy

Temporal lobe epilepsy (TLE) is the most common type of epilepsy and is often medically refractory. Previous studies suggest that selective pharmaco-genetic inhibition of pyramidal neurons has therapeutic value for the treatment of epilepsy, however there is a risk of disrupting normal physical functions. Here, we test whether pharmaco-genetic activation of parvalbumin neurons, which are transgenetically transduced with the modified muscarinic receptor hM3Dq can attenuate TLE. We found that pharmaco-genetic activation of hippocampal parvalbumin neurons in epileptogenic zone not only significantly extends the latency to different seizure stages and attenuates seizure activities in acute seizure model, but also greatly alleviates the severity of seizure onsets in two chronic epilepsy models. This manipulation did not affect the normal physical function evaluated in various cognitive tasks. Further, the activation of parvalbumin neurons produced an inhibition on parts of surrounding pyramidal neurons, and the direct inactivation of pyramidal neurons via the viral expression of a modified muscarinic receptor hM4Di produced a similar anti-ictogenic effect. Interestingly, pharmaco-genetic inactivation of pyramidal neurons was more sensitive to impair cognitive function. Those data demonstrated that pharmaco-genetic seizure attenuation through targeting parvalbumin neurons rather than pyramidal neurons may be a novel and relatively safe approach for treating refractory TLE.

Optogenetic auditory fMRI reveals the effects of visual cortical inputs on auditory midbrain response

Sensory cortices contain extensive descending (corticofugal) pathways, yet their impact on brainstem processing - particularly across sensory systems - remains poorly understood. In the auditory system, the inferior colliculus (IC) in the midbrain receives cross-modal inputs from the visual cortex (VC). However, the influences from VC on auditory midbrain processing are unclear. To investigate whether and how visual cortical inputs affect IC auditory responses, the present study combines auditory blood-oxygenation-level-dependent (BOLD) functional MRI (fMRI) with cell-type specific optogenetic manipulation of visual cortex. The results show that predominant optogenetic excitation of the excitatory pyramidal neurons in the infragranular layers of the primary VC enhances the noise-evoked BOLD fMRI responses within the IC. This finding reveals that inputs from VC influence and facilitate basic sound processing in the auditory midbrain. Such combined optogenetic and auditory fMRI approach can shed light on the large-scale modulatory effects of corticofugal pathways and guide detailed electrophysiological studies in the future.

Fluorescent, Bioluminescent, and Optogenetic Approaches to Study Excitable Physiology in the Single Cardiomyocyte

This review briefly summarizes the single cell application of classical chemical dyes used to visualize cardiomyocyte physiology and their undesirable toxicities which have the potential to confound experimental observations. We will discuss, in detail, the more recent iterative development of fluorescent and bioluminescent protein-based indicators and their emerging application to cardiomyocytes. We will discuss the integration of optical control strategies (optogenetics) to augment the standard imaging approach. This will be done in the context of potential applications, and barriers, of these technologies to disease modelling, drug toxicity, and drug discovery efforts at the single-cell scale.

Oligomeric states of microbial rhodopsins determined by high-speed atomic force microscopy and circular dichroic spectroscopy

Oligomeric assembly is a common feature of membrane proteins and often relevant to their physiological functions. Determining the stoichiometry and the oligomeric state of membrane proteins in a lipid bilayer is generally challenging because of their large size, complexity, and structural alterations under experimental conditions. Here, we use high-speed atomic force microscopy (HS-AFM) to directly observe the oligomeric states in the lipid membrane of various microbial rhodopsins found within eubacteria to archaea. HS-AFM images show that eubacterial rhodopsins predominantly exist as pentamer forms, while archaeal rhodopsins are trimers in the lipid membrane. In addition, circular dichroism (CD) spectroscopy reveals that pentameric rhodopsins display inverted CD couplets compared to those of trimeric rhodopsins, indicating different types of exciton coupling of the retinal chromophore in each oligomer. The results clearly demonstrate that the stoichiometry of the fundamental oligomer of microbial rhodopsins strongly correlate with the phylogenetic tree, providing a new insight into the relationship between the oligomeric structure and function-structural evolution of microbial rhodopsins.

Graphene biointerfaces for optical stimulation of cells

Noninvasive stimulation of cells is crucial for the accurate examination and control of their function both at the cellular and the system levels. To address this need, we present a pioneering optical stimulation platform that does not require genetic modification of cells but instead capitalizes on unique optoelectronic properties of graphene, including its ability to efficiently convert light into electricity. We report the first studies of optical stimulation of cardiomyocytes via graphene-based biointerfaces (G-biointerfaces) in substrate-based and dispersible configurations. The efficiency of stimulation via G-biointerfaces is independent of light wavelength but can be tuned by changing the light intensity. We demonstrate that an all-optical evaluation of use-dependent drug effects in vitro can be enabled using substrate-based G-biointerfaces. Furthermore, using dispersible G-biointerfaces in vivo, we perform optical modulation of the heart activity in zebrafish embryos. Our discovery is expected to empower numerous fundamental and translational biomedical studies.

Extending the Time Domain of Neuronal Silencing with Cryptophyte Anion Channelrhodopsins

Optogenetic inhibition of specific neuronal types in the brain enables analysis of neural circuitry and is promising for the treatment of a number of neurological disorders. Anion channelrhodopsins (ACRs) from the cryptophyte alga Guillardia theta generate larger photocurrents than other available inhibitory optogenetic tools, but more rapid channels are needed for temporally precise inhibition, such as single-spike suppression, of high-frequency firing neurons. Faster ACRs have been reported, but their potential advantages for time-resolved inhibitory optogenetics have not so far been verified in neurons. We report RapACR, nicknamed so for "rapid," an ACR from Rhodomonas salina, that exhibits channel half-closing times below 10 ms and achieves equivalent inhibition at 50-fold lower light intensity in lentivirally transduced cultured mouse hippocampal neurons as the second-generation engineered Cl--conducting channelrhodopsin iC++. The upper limit of the time resolution of neuronal silencing with RapACR determined by measuring the dependence of spiking recovery after photoinhibition on the light intensity was calculated to be 100 Hz, whereas that with the faster of the two G. theta ACRs was 13 Hz. Further acceleration of RapACR channel kinetics was achieved by site-directed mutagenesis of a single residue in transmembrane helix 3 (Thr111 to Cys). We also show that mutation of another ACR (Cys to Ala at the same position) with a greatly extended lifetime of the channel open state acts as a bistable photochromic tool in mammalian neurons. These molecules extend the time domain of optogenetic neuronal silencing while retaining the high light sensitivity of Guillardia ACRs.

Genetic inhibition of neurotransmission reveals role of glutamatergic input to dopamine neurons in high-effort behavior

Midbrain dopamine neurons are crucial for many behavioral and cognitive functions. As the major excitatory input, glutamatergic afferents are important for control of the activity and plasticity of dopamine neurons. However, the role of glutamatergic input as a whole onto dopamine neurons remains unclear. Here we developed a mouse line in which glutamatergic inputs onto dopamine neurons are specifically impaired, and utilized this genetic model to directly test the role of glutamatergic inputs in dopamine-related functions. We found that while motor coordination and reward learning were largely unchanged, these animals showed prominent deficits in effort-related behavioral tasks. These results provide genetic evidence that glutamatergic transmission onto dopaminergic neurons underlies incentive motivation, a willingness to exert high levels of effort to obtain reinforcers, and have important implications for understanding the normal function of the midbrain dopamine system.

When the Ostrich-Algorithm Fails: Blanking Method Affects Spike Train Statistics

Modern electroceuticals are bound to employ the usage of electrical high frequency (130-180 Hz) stimulation carried out under closed loop control, most prominent in the case of movement disorders. However, particular challenges are faced when electrical recordings of neuronal tissue are carried out during high frequency electrical stimulation, both in-vivo and in-vitro. This stimulation produces undesired artifacts and can render the recorded signal only partially useful. The extent of these artifacts is often reduced by temporarily grounding the recording input during stimulation pulses. In the following study, we quantify the effects of this method, "blanking," on the spike count and spike train statistics. Starting from a theoretical standpoint, we calculate a loss in the absolute number of action potentials, depending on: width of the blanking window, frequency of stimulation, and intrinsic neuronal activity. These calculations were then corroborated by actual high signal to noise ratio (SNR) single cell recordings. We state that, for clinically relevant frequencies of 130 Hz (used for movement disorders) and realistic blanking windows of 2 ms, up to 27% of actual existing spikes are lost. We strongly advice cautioned use of the blanking method when spike rate quantification is attempted.

Impact statement

Blanking (artifact removal by temporarily grounding input), depending on recording parameters, can lead to significant spike loss. Very careful use of blanking circuits is advised.

Optogenetic Dissection of Sleep-Wake States In Vitro and In Vivo

Optogenetic tools have revolutionized insights into the fundamentals of brain function. This is particularly true for our current understanding of sleep-wake regulation and sleep rhythms. This is illustrated here through a comprehensive and step-by-step review over the major brain areas involved in transitions between sleep and wake states and in sleep rhythmogenesis.

Optogenetically controlled protein kinases for regulation of cellular signaling

Protein kinases are involved in the regulation of many cellular processes including cell differentiation, survival, migration, axon guidance and neuronal plasticity. A growing set of optogenetic tools, termed opto-kinases, allows activation and inhibition of different protein kinases with light. The optogenetic regulation enables fast, reversible and non-invasive manipulation of protein kinase activities, complementing traditional methods, such as treatment with growth factors, protein kinase inhibitors or chemical dimerizers. In this review, we summarize the properties of the existing optogenetic tools for controlling tyrosine kinases and serine-threonine kinases. We discuss how the opto-kinases can be applied for studies of spatial and temporal aspects of protein kinase signaling in cells and organisms. We compare approaches for chemical and optogenetic regulation of protein kinase activity and present guidelines for selection of opto-kinases and equipment to control them with light. We also describe strategies to engineer novel opto-kinases on the basis of various photoreceptors.

Theoretical analysis of low-power fast optogenetic control of firing of Chronos-expressing neurons

A detailed theoretical analysis of low-power, fast optogenetic control of firing of Chronos-expressing neurons has been presented. A three-state model for the Chronos photocycle has been formulated and incorporated in a fast-spiking interneuron circuit model. The effect of excitation wavelength, pulse irradiance, pulse width, and pulse frequency has been studied in detail and compared with ChR2. Theoretical simulations are in excellent agreement with recently reported experimental results and bring out additional interesting features. At very low irradiances ([Formula: see text]), the plateau current in Chronos exhibits a maximum. At [Formula: see text], the plateau current is 2 orders of magnitude smaller and saturates at longer pulse widths ([Formula: see text]) compared to ChR2 ([Formula: see text]). [Formula: see text] in Chronos saturates at much shorter pulse widths (1775 pA at 1.5 ms and [Formula: see text]) than in ChR2. Spiking fidelity is also higher at lower irradiances and longer pulse widths compared to ChR2. Chronos exhibits an average maximal driven rate of over [Formula: see text] in response to [Formula: see text] stimuli, each of 1-ms pulse-width, in the intensity range 0 to [Formula: see text]. The analysis is important to not only understand the photodynamics of Chronos and Chronos-expressing neurons but also to design opsins with optimized properties and perform precision experiments with required spatiotemporal resolution.

Three Research Strategies of Neuroscience and the Future of Legal Imaging Evidence

Neuroscientific imaging evidence (NIE) has become an integral part of the criminal justice system in the United States. However, in most legal cases, NIE is submitted and used only to mitigate penalties because the court does not recognize it as substantial evidence, considering its lack of reliability. Nevertheless, we here discuss how neuroscience is expected to improve the use of NIE in the legal system. For this purpose, we classified the efforts of neuroscientists into three research strategies: cognitive subtraction, the data-driven approach, and the brain-manipulation approach. Cognitive subtraction is outdated and problematic; consequently, the court deemed it to be an inadequate approach in terms of legal evidence in 2012. In contrast, the data-driven and brain manipulation approaches, which are state-of-the-art approaches, have overcome the limitations of cognitive subtraction. The data-driven approach brings data science into the field and is benefiting immensely from the development of research platforms that allow automatized collection, analysis, and sharing of data. This broadens the scale of imaging evidence. The brain-manipulation approach uses high-functioning tools that facilitate non-invasive and precise human brain manipulation. These two approaches are expected to have synergistic effects. Neuroscience has strived to improve the evidential reliability of NIE, with considerable success. With the support of cutting-edge technologies, and the progress of these approaches, the evidential status of NIE will be improved and NIE will become an increasingly important part of legal practice.

Imbalanced amplification: A mechanism of amplification and suppression from local imbalance of excitation and inhibition in cortical circuits

Understanding the relationship between external stimuli and the spiking activity of cortical populations is a central problem in neuroscience. Dense recurrent connectivity in local cortical circuits can lead to counterintuitive response properties, raising the question of whether there are simple arithmetical rules for relating circuits’ connectivity structure to their response properties. One such arithmetic is provided by the mean field theory of balanced networks, which is derived in a limit where excitatory and inhibitory synaptic currents precisely balance on average. However, balanced network theory is not applicable to some biologically relevant connectivity structures. We show that cortical circuits with such structure are susceptible to an amplification mechanism arising when excitatory-inhibitory balance is broken at the level of local subpopulations, but maintained at a global level. This amplification, which can be quantified by a linear correction to the classical mean field theory of balanced networks, explains several response properties observed in cortical recordings and provides fundamental insights into the relationship between connectivity structure and neural responses in cortical circuits.

Understanding how the brain represents and processes stimuli requires a quantitative understanding of how signals propagate through networks of neurons. Developing such an understanding is made difficult by the dense interconnectivity of neurons, especially in the cerebral cortex. One approach to quantifying neural processing in the cortex is derived from observations that excitatory (positive) and inhibitory (negative) interactions between neurons tend to balance each other in many brain areas. This balance is achieved under a class of computational models called “balanced networks.” However, previous approaches to the mathematical analysis of balanced network models is not possible under some biologically relevant connectivity structures. We show that, under these structures, balance between excitation and inhibition is necessarily broken and the resulting imbalance causes some stimulus features to be amplified. This “imbalanced amplification” of stimuli can explain several observations from recordings in mouse somatosensory and visual cortical circuits and provides fundamental insights into the relationship between connectivity structure and neural responses in cortical circuits.

Auditory perceptual learning and changes in the conceptualization of auditory cortex

Perceptual learning, improvement in discriminative ability as a consequence of training, is one of the forms of sensory system plasticity that has driven profound changes in our conceptualization of sensory cortical function. Psychophysical and neurophysiological studies of auditory perceptual learning have indicated that the characteristics of the learning, and by implication the nature of the underlying neural changes, are highly task specific. Some studies in animals have indicated that recruitment of neurons to the population responding to the training stimuli, and hence an increase in the so-called cortical "area of representation" of those stimuli, is the substrate of improved performance, but such changes have not been observed in other studies. A possible reconciliation of these conflicting results is provided by evidence that changes in area of representation constitute a transient stage in the processes underlying perceptual learning. This expansion - renormalization hypothesis is supported by evidence from studies of the learning of motor skills, another form of procedural learning, but leaves open the nature of the permanent neural substrate of improved performance. Other studies have suggested that the substrate might be reduced response variability - a decrease in internal noise. Neuroimaging studies in humans have also provided compelling evidence that training results in long-term changes in auditory cortical function and in the auditory brainstem frequency-following response. Musical training provides a valuable model, but the evidence it provides is qualified by the fact that most such training is multimodal and sensorimotor, and that few of the studies are experimental and allow control over confounding variables. More generally, the overwhelming majority of experimental studies of the various forms of auditory perceptual learning have established the co-occurrence of neural and perceptual changes, but have not established that the former are causally related to the latter. Important forms of perceptual learning in humans are those involved in language acquisition and in the improvement in speech perception performance of post-lingually deaf cochlear implantees over the months following implantation. The development of a range of auditory training programs has focused interest on the factors determining the extent to which perceptual learning is specific or generalises to tasks other than those used in training. The context specificity demonstrated in a number of studies of perceptual learning suggests a multiplexing model, in which learning relating to a particular stimulus attribute depends on a subset of the diverse inputs to a given cortical neuron being strengthened, and different subsets being gated by top-down influences. This hypothesis avoids the difficulty of balancing system stability with plasticity, which is a problem for recruitment hypotheses. The characteristics of auditory perceptual learning reflect the fact that auditory cortex forms part of distributed networks that integrate the representation of auditory stimuli with attention, decision, and reward processes.

Roadmap on semiconductor-cell biointerfaces

This roadmap outlines the role semiconductor-based materials play in understanding the complex biophysical dynamics at multiple length scales, as well as the design and implementation of next-generation electronic, optoelectronic, and mechanical devices for biointerfaces. The roadmap emphasizes the advantages of semiconductor building blocks in interfacing, monitoring, and manipulating the activity of biological components, and discusses the possibility of using active semiconductor-cell interfaces for discovering new signaling processes in the biological world.

Optochemical Control of Biological Processes in Cells and Animals

Biological processes are naturally regulated with high spatial and temporal control, as is perhaps most evident in metazoan embryogenesis. Chemical tools have been extensively utilized in cell and developmental biology to investigate cellular processes, and conditional control methods have expanded applications of these technologies toward resolving complex biological questions. Light represents an excellent external trigger since it can be controlled with very high spatial and temporal precision. To this end, several optically regulated tools have been developed and applied to living systems. In this review we discuss recent developments of optochemical tools, including small molecules, peptides, proteins, and nucleic acids that can be irreversibly or reversibly controlled through light irradiation, with a focus on applications in cells and animals.

A common neural circuit mechanism for internally guided and externally reinforced forms of motor learning

The complex skills underlying verbal and musical expression can be learned without external punishment or reward, indicating their learning is internally guided. The neural mechanisms that mediate internally guided learning are poorly understood, but a circuit comprising dopamine-releasing neurons in the midbrain ventral tegmental area (VTA) and their targets in the basal ganglia are important to externally reinforced learning. Juvenile zebra finches copy a tutor song in a process that is internally guided and, in adulthood, can learn to modify the fundamental frequency (pitch) of a target syllable in response to external reinforcement with white noise. Here we combined intersectional genetic ablation of VTA neurons, reversible blockade of dopamine receptors in the basal ganglia, and singing-triggered optogenetic stimulation of VTA terminals to establish that a common VTA-basal ganglia circuit enables internally guided song copying and externally reinforced syllable pitch learning.

A Comprehensive Atlas of E3 Ubiquitin Ligase Mutations in Neurological Disorders

Protein ubiquitination is a posttranslational modification that plays an integral part in mediating diverse cellular functions. The process of protein ubiquitination requires an enzymatic cascade that consists of a ubiquitin activating enzyme (E1), ubiquitin conjugating enzyme (E2) and an E3 ubiquitin ligase (E3). There are an estimated 600-700 E3 ligase genes representing ~5% of the human genome. Not surprisingly, mutations in E3 ligase genes have been observed in multiple neurological conditions. We constructed a comprehensive atlas of disrupted E3 ligase genes in common (CND) and rare neurological diseases (RND). Of the predicted and known human E3 ligase genes, we found ~13% were mutated in a neurological disorder with 83 total genes representing 70 different types of neurological diseases. Of the E3 ligase genes identified, 51 were associated with an RND. Here, we provide an updated list of neurological disorders associated with E3 ligase gene disruption. We further highlight research in these neurological disorders and discuss the advanced technologies used to support these findings.

Dopamine's Effects on Corticostriatal Synapses during Reward-Based Behaviors

Many learned responses depend on the coordinated activation and inhibition of synaptic pathways in the striatum. Local dopamine neurotransmission acts in concert with a variety of neurotransmitters to regulate cortical, thalamic, and limbic excitatory inputs to drive the direct and indirect striatal spiny projection neuron outputs that determine the activity, sequence, and timing of learned behaviors. We review recent advances in the characterization of stereotyped neuronal and operant responses that predict and then obtain rewards. These depend on the local release of dopamine at discrete times during behavioral sequences, which, acting with glutamate, provides a presynaptic filter to select which excitatory synapses are inhibited and which signals pass to indirect pathway circuits. This is followed by dopamine-dependent activation of specific direct pathway circuits to procure a reward. These steps may provide a means by which higher organisms learn behaviors in response to feedback from the environment.

The form and function of channelrhodopsin

Channelrhodopsins are light-gated ion channels that, via regulation of flagellar function, enable single-celled motile algae to seek ambient light conditions suitable for photosynthesis and survival. These plant behavioral responses were initially investigated more than 150 years ago. Recently, major principles of function for light-gated ion channels have been elucidated by creating channelrhodopsins with kinetics that are accelerated or slowed over orders of magnitude, by discovering and designing channelrhodopsins with altered spectral properties, by solving the high-resolution channelrhodopsin crystal structure, and by structural model-guided redesign of channelrhodopsins for altered ion selectivity. Each of these discoveries not only revealed basic principles governing the operation of light-gated ion channels, but also enabled the creation of new proteins for illuminating, via optogenetics, the fundamentals of brain function.

The promise and perils of causal circuit manipulations

The development of increasingly sophisticated methods for recording and manipulating neural activity is revolutionizing neuroscience. By probing how activity patterns in different types of neurons and circuits contribute to behavior, these tools can help inform mechanistic models of brain function and explain the roles of distinct circuit elements. However, in systems where functions are distributed over large networks, interpreting causality experiments can be challenging. Here we review common assumptions underlying circuit manipulations in behaving animals and discuss the strengths and limitations of different approaches.