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1.  Fiber-Optic Implantation for Chronic Optogenetic Stimulation of Brain Tissue 
Short Abstract
The development of optogenetics now provides the means to precisely stimulate genetically defined neurons and circuits, both in vitro and in vivo. Here we describe the assembly and implantation of a fiber optic for chronic photostimulation of brain tissue.
Long Abstract
Elucidating patterns of neuronal connectivity has been a challenge for both clinical and basic neuroscience. Electrophysiology has been the gold standard for analyzing patterns of synaptic connectivity, but paired electrophysiological recordings can be both cumbersome and experimentally limiting. The development of optogenetics has introduced an elegant method to stimulate neurons and circuits, both in vitro1 and in vivo2,3. By exploiting cell-type specific promoter activity to drive opsin expression in discrete neuronal populations, one can precisely stimulate genetically defined neuronal subtypes in distinct circuits4–6. Well described methods to stimulate neurons, including electrical stimulation and/or pharmacological manipulations, are often cell-type indiscriminate, invasive, and can damage surrounding tissues. These limitations could alter normal synaptic function and/or circuit behavior. In addition, due to the nature of the manipulation, the current methods are often acute and terminal. Optogenetics affords the ability to stimulate neurons in a relatively innocuous manner, and in genetically targeted neurons. The majority of studies involving in vivo optogenetics currently use a optical fiber guided through an implanted cannula6,7; however, limitations of this method include damaged brain tissue with repeated insertion of an optical fiber, and potential breakage of the fiber inside the cannula. Given the burgeoning field of optogenetics, a more reliable method of chronic stimulation is necessary to facilitate long-term studies with minimal collateral tissue damage. Here we provide our modified protocol as a video article to complement the method effectively and elegantly described in Sparta et al.8 for the fabrication of a fiber optic implant and its permanent fixation onto the cranium of anesthetized mice, as well as the assembly of the fiber optic coupler connecting the implant to a light source. The implant, connected with optical fibers to a solid-state laser, allows for an efficient method to chronically photostimulate functional neuronal circuitry with less tissue damage9 using small, detachable, tethers. Permanent fixation of the fiber optic implants provides consistent, long-term in vivo optogenetic studies of neuronal circuits in awake, behaving mice10 with minimal tissue damage.
PMCID: PMC3490315  PMID: 23128465
Neuroscience; optogenetics; fiber optics; implantation; neuronal circuitry; chronic stimulation
2.  Optogenetic dissection of neural circuits underlying emotional valence and motivated behaviors 
Brain research  2012;1511:73-92.
The neural circuits underlying emotional valence and motivated behaviors are several synapses away from both defined sensory inputs and quantifiable motor outputs. Electrophysiology has provided us with a suitable means for observing neural activity during behavior, but methods for controlling activity for the purpose of studying motivated behaviors have been inadequate: electrical stimulation lacks cellular specificity and pharmacological manipulation lacks temporal resolution. The recent emergence of optogenetic tools provides a new means for establishing causal relationships between neural activity and behavior. Optogenetics, the use of genetically-encodable light-activated proteins, permits the modulation of specific neural circuit elements with millisecond precision. The ability to control individual cell types, and even projections between distal regions, allows us to investigate functional connectivity in a causal manner. The greatest consequence of controlling neural activity with finer precision has been the characterization of individual neural circuits within anatomical brain regions as defined functional units. Within the mesolimbic dopamine system, optogenetics has helped separate subsets of dopamine neurons with distinct functions for reward, aversion and salience processing, elucidated GABA neuronal effects on behavior, and characterized connectivity with forebrain and cortical structures. Within the striatum, optogenetics has confirmed the opposing relationship between direct and indirect pathway medium spiny neurons (MSNs), in addition to characterizing the inhibition of MSNs by cholinergic interneurons. Within the hypothalamus, optogenetics has helped overcome the heterogeneity in neuronal cell-type and revealed distinct circuits mediating aggression and feeding. Within the amygdala, optogenetics has allowed the study of intra-amygdala microcircuitry as well as interconnections with distal regions involved in fear and anxiety. In this review, we will present the body of optogenetic studies that has significantly enhanced our understanding of emotional valence and motivated behaviors.
PMCID: PMC4099056  PMID: 23142759
Optogenetics; Systems; Circuit dissection; Behavior; Emotion; Motivation; Brain; Projections; ChR2; NpHR; Opsin; Valence
3.  Computational Optogenetics: Empirically-Derived Voltage- and Light-Sensitive Channelrhodopsin-2 Model 
PLoS Computational Biology  2013;9(9):e1003220.
Channelrhodospin-2 (ChR2), a light-sensitive ion channel, and its variants have emerged as new excitatory optogenetic tools not only in neuroscience, but also in other areas, including cardiac electrophysiology. An accurate quantitative model of ChR2 is necessary for in silico prediction of the response to optical stimulation in realistic tissue/organ settings. Such a model can guide the rational design of new ion channel functionality tailored to different cell types/tissues. Focusing on one of the most widely used ChR2 mutants (H134R) with enhanced current, we collected a comprehensive experimental data set of the response of this ion channel to different irradiances and voltages, and used these data to develop a model of ChR2 with empirically-derived voltage- and irradiance- dependence, where parameters were fine-tuned via simulated annealing optimization. This ChR2 model offers: 1) accurate inward rectification in the current-voltage response across irradiances; 2) empirically-derived voltage- and light-dependent kinetics (activation, deactivation and recovery from inactivation); and 3) accurate amplitude and morphology of the response across voltage and irradiance settings. Temperature-scaling factors (Q10) were derived and model kinetics was adjusted to physiological temperatures. Using optical action potential clamp, we experimentally validated model-predicted ChR2 behavior in guinea pig ventricular myocytes. The model was then incorporated in a variety of cardiac myocytes, including human ventricular, atrial and Purkinje cell models. We demonstrate the ability of ChR2 to trigger action potentials in human cardiomyocytes at relatively low light levels, as well as the differential response of these cells to light, with the Purkinje cells being most easily excitable and ventricular cells requiring the highest irradiance at all pulse durations. This new experimentally-validated ChR2 model will facilitate virtual experimentation in neural and cardiac optogenetics at the cell and organ level and provide guidance for the development of in vivo tools.
Author Summary
Optogenetics, the use of light-sensitive ion channels for stimulation of mammalian cells and tissues, offers specificity and superior precision of control compared to traditional chemical or electrical means of stimulation. In particular, Channelrhodospin-2 (ChR2), a light-sensitive ion channel, originally derived from algae, has found wide-spread application in neuroscience for controlled stimulation of different brain regions. More recently, this work was extended to other organs, including the heart, where it opens the possibility for a new generation of optical pacemakers. The development of new optogenetic tools that allow for more efficient optical stimulation can be guided by computational prediction of the response of different cells and tissues to light. In this report, we provide a new computational model of ChR2 that was empirically validated and can be inserted into different cell types – neurons or heart cells – for virtual optical stimulation and prediction of optimal light-delivery arrangements, minimum energy needs etc. Overall, virtual optogenetics can accelerate the development of new optical stimulation tools for better understanding and control of brain and heart function.
PMCID: PMC3772068  PMID: 24068903
4.  Silencer-delimited transgenesis: NRSE/RE1 sequences promote neural-specific transgene expression in a NRSF/REST-dependent manner 
BMC Biology  2012;10:93.
We have investigated a simple strategy for enhancing transgene expression specificity by leveraging genetic silencer elements. The approach serves to restrict transgene expression to a tissue of interest - the nervous system in the example provided here - thereby promoting specific/exclusive targeting of discrete cellular subtypes. Recent innovations are bringing us closer to understanding how the brain is organized, how neural circuits function, and how neurons can be regenerated. Fluorescent proteins enable mapping of the 'connectome', optogenetic tools allow excitable cells to be short-circuited or hyperactivated, and targeted ablation of neuronal subtypes facilitates investigations of circuit function and neuronal regeneration. Optimally, such toolsets need to be expressed solely within the cell types of interest as off-site expression makes establishing causal relationships difficult. To address this, we have exploited a gene 'silencing' system that promotes neuronal specificity by repressing expression in non-neural tissues. This methodology solves non-specific background issues that plague large-scale enhancer trap efforts and may provide a means of leveraging promoters/enhancers that otherwise express too broadly to be of value for in vivo manipulations.
We show that a conserved neuron-restrictive silencer element (NRSE) can function to restrict transgene expression to the nervous system. The neuron-restrictive silencing factor/repressor element 1 silencing transcription factor (NRSF/REST) transcriptional repressor binds NRSE/repressor element 1 (RE1) sites and silences gene expression in non-neuronal cells. Inserting NRSE sites into transgenes strongly biased expression to neural tissues. NRSE sequences were effective in restricting expression of bipartite Gal4-based 'driver' transgenes within the context of an enhancer trap and when associated with a defined promoter and enhancer. However, NRSE sequences did not serve to restrict expression of an upstream activating sequence (UAS)-based reporter/effector transgene when associated solely with the UAS element. Morpholino knockdown assays showed that NRSF/REST expression is required for NRSE-based transgene silencing.
Our findings demonstrate that the addition of NRSE sequences to transgenes can provide useful new tools for functional studies of the nervous system. However, the general approach may be more broadly applicable; tissue-specific silencer elements are operable in tissues other than the nervous system, suggesting this approach can be similarly applied to other paradigms. Thus, creating synthetic associations between endogenous regulatory elements and tissue-specific silencers may facilitate targeting of cellular subtypes for which defined promoters/enhancers are lacking.
PMCID: PMC3529185  PMID: 23198762
zebrafish; transgenesis; enhancer trap; NRSE/RE1; NRSF/REST; Gal4/UAS; neuron
5.  Using Optogenetics to Study Habits 
Brain research  2013;1511:102-114.
It is now well documented that optogenetics brings to neuroscience a long sought-after foothold to study the causal role of millisecond-scale activity of genetically or anatomically defined populations of neurons. Progress is rapid, and, as evidenced by the work collected in this Special Issue, the possibilities of what can now be done are almost dizzying. Even for those concerned with complex phenomena, such as behavioral habits and flexibility, signs are that we could be on the threshold of a leap in scientific understanding. In this article, we note this special time in neuroscience by the example of our use of optogenetics to study habitual behavior. We present a basic sketch of the neural circuitry of habitual behavior built mainly on findings from experiments in which lesion and drug microinjection techniques were employed in combination with sophisticated behavioral analysis. We then outline the types of questions that now can be approached through the use of optogenetic approaches, and, as an example, we summarize the results of a recent study of ours in which we took this approach to probe the neural basis of habit formation. With optogenetic methods, we were able to demonstrate that a small site in the medial prefrontal cortex can control habits on-line during their execution, and we were able to control new habits when they competed with prior ones. The nearly immediate effect of disabling this site optogenetically suggests the existence of a mechanism for moment-to-moment monitoring of behaviors that long have been thought to be almost automatic and reflexive. This example highlights the kind of new knowledge that can be gained by the carefully timed use of optogenetic tools.
PMCID: PMC3654045  PMID: 23313580
Basal ganglia; prefrontal cortex; reward; learning; plasticity; executive; time
6.  Optogenetic Strategies to Dissect the Neural Circuits that Underlie Reward and Addiction 
Optogenetic strategies for perturbation of neural circuit function have begun to revolutionize systems neuroscience. Whereas optogenetics has proven to be a powerful approach for studying neural systems, the tools to conduct these experiments are still continuously evolving. Here we briefly summarize available hardware and reagents that can be used for studying behaviors related to reward and addiction. In addition, we discuss recent studies in which these strategies have been applied to study neural circuit function in brain slices as well as awake and behaving animals. Collectively, this work serves as a brief introduction to optogenetic techniques and highlights how these tools can be applied to elucidate the neural circuits that underlie reward processing and addiction.
Optogenetics allows for pathway-specific manipulation of neural circuitry over a range of timescales. It can be effectively combined with slice electrophysiology and in vivo behavioral paradigms.
PMCID: PMC3543095  PMID: 23043156
7.  Dissecting local circuits in vivo: integrated optogenetic and electrophysiology approaches for exploring inhibitory regulation of cortical activity 
Journal of Physiology, Paris  2011;106(3-4):104-111.
Local cortical circuit activity in vivo comprises a complex and flexible series of interactions between excitatory and inhibitory neurons. Our understanding of the functional interactions between these different neural populations has been limited by the difficulty of identifying and selectively manipulating the diverse and sparsely represented inhibitory interneuron classes in the intact brain. The integration of recently developed optical tools with traditional electrophysiological techniques provides a powerful window into the role of inhibition in regulating the activity of excitatory neurons. In particular, optogenetic targeting of specific cell classes reveals the distinct impacts of local inhibitory populations on other neurons in the surrounding local network. In addition to providing the ability to activate or suppress spiking in target cells, optogenetic activation identifies extracellularly recorded neurons by class, even when naturally occurring spike rates are extremely low. However, there are several important limitations on the use of these tools and the interpretation of resulting data. The purpose of this article is to outline the uses and limitations of optogenetic tools, along with current methods for achieving cell type-specific expression, and to highlight the advantages of an experimental approach combining optogenetics and electrophysiology to explore the role of inhibition in active networks. To illustrate the efficacy of these combined approaches, I present data comparing targeted manipulations of cortical fast-spiking, parvalbumin-expressing and low threshold-spiking, somatostatin-expressing interneurons in vivo.
PMCID: PMC3277809  PMID: 21958624
interneuron; inhibition; fast-spiking; somatostatin; optogenetics; channelrhodopsin; halorhodopsin; archaerhodopsin; electrophysiology; tetrode; cortex
8.  Identification of Optogenetically Activated Striatal Medium Spiny Neurons by Npas4 Expression 
PLoS ONE  2012;7(12):e52783.
Optogenetics is a powerful neuromodulatory tool with many unique advantages to explore functions of neuronal circuits in physiology and diseases. Yet, interpretation of cellular and behavioral responses following in vivo optogenetic manipulation of brain activities in experimental animals often necessitates identification of photoactivated neurons with high spatial resolution. Although tracing expression of immediate early genes (IEGs) provides a convenient approach, neuronal activation is not always followed by specific induction of widely used neuronal activity markers like c-fos, Egr1 and Arc. In this study we performed unilateral optogenetic stimulation of the striatum in freely moving transgenic mice that expressed a channelrhodopsin-2 (ChR2) variant ChR2(C128S) in striatal medium spiny neurons (MSNs). We found that in vivo blue light stimulation significantly altered electrophysiological activity of striatal neurons and animal behaviors. To identify photoactivated neurons we then analyzed IEG expression patterns using in situ hybridization. Upon light illumination an induction of c-fos was not apparent whereas another neuronal IEG Npas4 was robustly induced in MSNs ipsilaterally. Our results demonstrate that tracing Npas4 mRNA expression following in vivo optogenetic modulation can be an effective tool for reliable and sensitive identification of activated MSNs in the mouse striatum.
PMCID: PMC3530472  PMID: 23300775
9.  Controlling fertilization and cAMP signaling in sperm by optogenetics 
eLife  null;4:e05161.
Optogenetics is a powerful technique to control cellular activity by light. The light-gated Channelrhodopsin has been widely used to study and manipulate neuronal activity in vivo, whereas optogenetic control of second messengers in vivo has not been examined in depth. In this study, we present a transgenic mouse model expressing a photoactivated adenylyl cyclase (bPAC) in sperm. In transgenic sperm, bPAC mimics the action of the endogenous soluble adenylyl cyclase (SACY) that is required for motility and fertilization: light-stimulation rapidly elevates cAMP, accelerates the flagellar beat, and, thereby, changes swimming behavior of sperm. Furthermore, bPAC replaces endogenous adenylyl cyclase activity. In mutant sperm lacking the bicarbonate-stimulated SACY activity, bPAC restored motility after light-stimulation and, thereby, enabled sperm to fertilize oocytes in vitro. We show that optogenetic control of cAMP in vivo allows to non-invasively study cAMP signaling, to control behaviors of single cells, and to restore a fundamental biological process such as fertilization.
eLife digest
Tiny hair-like structures called cilia on the outside of cells play many important roles, including detecting physical and chemical signals from the environment. Special cilia—called flagella—help cells to move around and perhaps the most well-known of these are sperm flagella, which propel sperm in their quest to fertilize the egg. A chemical messenger called cAMP is essential for the movement of sperm flagella.
When a sperm cell enters the female reproductive tract, an enzyme called SACY is activated. Within seconds, SACY produces cAMP and, thereby, causes the flagella to beat faster so that the sperm cell speeds toward the egg. cAMP also controls sperm maturation, which is needed to penetrate the egg. However, the precise details of the role of cAMP in sperm cells are not clear.
Here, Jansen et al. have investigated this role using a cutting-edge technique—called optogenetics—that was originally developed to study brain cells in living organisms. Jansen et al. genetically engineered a mouse so that exposing sperm to blue light activates a light-sensitive enzyme called bPAC that increases cAMP levels in sperm.
In these mice, the activation of bPAC by light accelerated the beating of the flagella so the sperm moved faster, in a way that was similar to the effects that are normally observed after the activation of the SACY enzyme. In mice lacking among other things the SACY enzyme—whose sperm cells are unable to move or fertilize an egg—activating the light-sensitive bPAC enzyme restored sperm motility and enabled the sperm to fertilize an egg.
These results show that optogenetics may be a useful tool for studying how flagella and other types of cilia work.
PMCID: PMC4298566  PMID: 25601414
cyclic nucleotide signaling; sperm; capacitation; cAMP; calcium; optogenetics; mouse
10.  A history of optogenetics: the development of tools for controlling brain circuits with light 
Understanding how different kinds of neuron in the brain work together to implement sensations, feelings, thoughts, and movements, and how deficits in specific kinds of neuron result in brain diseases, has long been a priority in basic and clinical neuroscience. “Optogenetic” tools are genetically encoded molecules that, when targeted to specific neurons in the brain, enable their activity to be driven or silenced by light. These molecules are microbial opsins, seven-transmembrane proteins adapted from organisms found throughout the world, which react to light by transporting ions across the lipid membranes of cells in which they are genetically expressed. These tools are enabling the causal assessment of the roles that different sets of neurons play within neural circuits, and are accordingly being used to reveal how different sets of neurons contribute to the emergent computational and behavioral functions of the brain. These tools are also being explored as components of prototype neural control prosthetics capable of correcting neural circuit computations that have gone awry in brain disorders. This review gives an account of the birth of optogenetics and discusses the technology and its applications.
PMCID: PMC3155186  PMID: 21876722
11.  Mushroom body output neurons encode valence and guide memory-based action selection in Drosophila 
eLife  null;3:e04580.
Animals discriminate stimuli, learn their predictive value and use this knowledge to modify their behavior. In Drosophila, the mushroom body (MB) plays a key role in these processes. Sensory stimuli are sparsely represented by ∼2000 Kenyon cells, which converge onto 34 output neurons (MBONs) of 21 types. We studied the role of MBONs in several associative learning tasks and in sleep regulation, revealing the extent to which information flow is segregated into distinct channels and suggesting possible roles for the multi-layered MBON network. We also show that optogenetic activation of MBONs can, depending on cell type, induce repulsion or attraction in flies. The behavioral effects of MBON perturbation are combinatorial, suggesting that the MBON ensemble collectively represents valence. We propose that local, stimulus-specific dopaminergic modulation selectively alters the balance within the MBON network for those stimuli. Our results suggest that valence encoded by the MBON ensemble biases memory-based action selection.
eLife digest
An animal's survival depends on its ability to respond appropriately to its environment, approaching stimuli that signal rewards and avoiding any that warn of potential threats. In fruit flies, this behavior requires activity in a region of the brain called the mushroom body, which processes sensory information and uses that information to influence responses to stimuli.
Aso et al. recently mapped the mushroom body of the fruit fly in its entirety. This work showed, among other things, that the mushroom body contained 21 different types of output neurons. Building on this work, Aso et al. have started to work out how this circuitry enables flies to learn to associate a stimulus, such as an odor, with an outcome, such as the presence of food.
Two complementary techniques—the use of molecular genetics to block neuronal activity, and the use of light to activate neurons (a technique called optogenetics)—were employed to study the roles performed by the output neurons in the mushroom body. Results revealed that distinct groups of output cells must be activated for flies to avoid—as opposed to approach—odors. Moreover, the same output neurons are used to avoid both odors and colors that have been associated with punishment. Together, these results indicate that the output cells do not encode the identity of stimuli: rather, they signal whether a stimulus should be approached or avoided. The output cells also regulate the amount of sleep taken by the fly, which is consistent with the mushroom body having a broader role in regulating the fly's internal state.
The results of these experiments—combined with new knowledge about the detailed structure of the mushroom body—lay the foundations for new studies that explore associative learning at the level of individual circuits and their component cells. Given that the organization of the mushroom body has much in common with that of the mammalian brain, these studies should provide insights into the fundamental principles that underpin learning and memory in other species, including humans.
PMCID: PMC4273436  PMID: 25535794
mushroom body; memory; behavioral valence; sleep; population code; action selection; D. melanogaster
12.  Genetically encoded molecular tools for light-driven silencing of targeted neurons 
Progress in brain research  2012;196:49-61.
The ability to silence, in a temporally precise fashion, the electrical activity of specific neurons embedded within intact brain tissue, is important for understanding the role that those neurons play in behaviors, brain disorders, and neural computations. “Optogenetic” silencers, genetically encoded molecules that, when expressed in targeted cells within neural networks, enable their electrical activity to be quieted in response to pulses of light, are enabling these kinds of causal circuit analyses studies. Two major classes of optogenetic silencer are in broad use in species ranging from worm to monkey: light-driven inward chloride pumps, or halorhodopsins, and light-driven outward proton pumps, such as archaerhodopsins and fungal light-driven proton pumps. Both classes of molecule, when expressed in neurons via viral or other transgenic means, enable the targeted neurons to be hyperpolarized by light. We here review the current status of these sets of molecules, and discuss how they are being discovered and engineered. We also discuss their expression properties, ionic properties, spectral characteristics, and kinetics. Such tools may not only find many uses in the quieting of electrical activity for basic science studies, but may also, in the future, find clinical uses for their ability to safely and transiently shut down cellular electrical activity in a precise fashion.
PMCID: PMC3553588  PMID: 22341320
optogenetics; opsins; neural silencing; halorhodopsin; archaerhodopsin; channelrhodopsin; control; cell types; neural circuits; causality
13.  Optogenetics and synaptic plasticity 
Acta Pharmacologica Sinica  2013;34(11):1381-1385.
The intricate and complex interaction between different populations of neurons in the brain has imposed limits on our ability to gain detailed understanding of synaptic transmission and its integration when employing classical electrophysiological approaches. Indeed, electrical field stimulation delivered via traditional microelectrodes does not permit the targeted, precise and selective control of neuronal activity amongst a varied population of neurons and their inputs (eg, cholinergic, dopaminergic or glutamatergic neurons). Recently established optogenetic techniques overcome these limitations allowing precise control of the target neuron populations, which is essential for the elucidation of the neural substrates underlying complex animal behaviors. Indeed, by introducing light-activated channels (ie, microbial opsin genes) into specific neuronal populations, optogenetics enables non-invasive optical control of specific neurons with milliseconds precision. These approaches can readily be applied to freely behaving live animals. Recently there is increased interests in utilizing optogenetics tools to understand synaptic plasticity and learning/memory. Here, we summarize recent progress in applying optogenetics in in the study of synaptic plasticity.
PMCID: PMC4006463  PMID: 24162508
synaptic plasticity; optogenetics; opsin; channelrhodopsin; halorhodopsin; LTP; LTD; learning and memory
14.  A High-Light Sensitivity Optical Neural Silencer: Development and Application to Optogenetic Control of Non-Human Primate Cortex 
Technologies for silencing the electrical activity of genetically targeted neurons in the brain are important for assessing the contribution of specific cell types and pathways toward behaviors and pathologies. Recently we found that archaerhodopsin-3 from Halorubrum sodomense (Arch), a light-driven outward proton pump, when genetically expressed in neurons, enables them to be powerfully, transiently, and repeatedly silenced in response to pulses of light. Because of the impressive characteristics of Arch, we explored the optogenetic utility of opsins with high sequence homology to Arch, from archaea of the Halorubrum genus. We found that the archaerhodopsin from Halorubrum strain TP009, which we named ArchT, could mediate photocurrents of similar maximum amplitude to those of Arch (∼900 pA in vitro), but with a >3-fold improvement in light sensitivity over Arch, most notably in the optogenetic range of 1–10 mW/mm2, equating to >2× increase in brain tissue volume addressed by a typical single optical fiber. Upon expression in mouse or rhesus macaque cortical neurons, ArchT expressed well on neuronal membranes, including excellent trafficking for long distances down neuronal axons. The high light sensitivity prompted us to explore ArchT use in the cortex of the rhesus macaque. Optical perturbation of ArchT-expressing neurons in the brain of an awake rhesus macaque resulted in a rapid and complete (∼100%) silencing of most recorded cells, with suppressed cells achieving a median firing rate of 0 spikes/s upon illumination. A small population of neurons showed increased firing rates at long latencies following the onset of light stimulation, suggesting the existence of a mechanism of network-level neural activity balancing. The powerful net suppression of activity suggests that ArchT silencing technology might be of great use not only in the causal analysis of neural circuits, but may have therapeutic applications.
PMCID: PMC3082132  PMID: 21811444
channelrhodopsin; halorhodopsin; archaerhodopsin; optogenetics; non-human primate; systems neuroscience; neurophysiology; neural silencing
15.  The optogenetic (r)evolution 
Molecular Genetics and Genomics  2011;287(2):95-109.
Optogenetics is a rapidly evolving field of technology that allows optical control of genetically targeted biological systems at high temporal and spatial resolution. By heterologous expression of light-sensitive microbial membrane proteins, opsins, cell type-specific depolarization or silencing can be optically induced on a millisecond time scale. What started in a petri dish is applicable today to more complex systems, ranging from the dissection of brain circuitries in vitro to behavioral analyses in freely moving animals. Persistent technical improvement has focused on the identification of new opsins, suitable for optogenetic purposes and genetic engineering of existing ones. Optical stimulation can be combined with various readouts defined by the desired resolution of the experimental setup. Although recent developments in optogenetics have largely focused on neuroscience it has lately been extended to other targets, including stem cell research and regenerative medicine. Further development of optogenetic approaches will not only highly increase our insight into health and disease states but might also pave the way for a future use in therapeutic applications.
PMCID: PMC3266495  PMID: 22183142
Optogenetics; Rhodopsin; Channelrhodopsin; Halorhodopsin; Optical tools; Arch; ChR2; NpHR
16.  A system for optically controlling neural circuits with very high spatial and temporal resolution 
Optogenetics offers a powerful new approach for controlling neural circuits. It has a vast array of applications in both basic and clinical science. For basic science, it opens the door to unraveling circuit operations, since one can perturb specific circuit components with high spatial (single cell) and high temporal (millisecond) resolution. For clinical applications, it allows new kinds of selective treatments, because it provides a method to inactivate or activate specific components in a malfunctioning circuit and bring it back into a normal operating range [1–3]. To harness the power of optogenetics, though, one needs stimulating tools that work with the same high spatial and temporal resolution as the molecules themselves, the channelrhodopsins. To date, most stimulating tools require a tradeoff between spatial and temporal precision and are prohibitively expensive to integrate into a stimulating/recording setup in a laboratory or a device in a clinical setting [4, 5]. Here we describe a Digital Light Processing (DLP)-based system capable of extremely high temporal resolution (sub-millisecond), without sacrificing spatial resolution. Furthermore, it is constructed using off-the-shelf components, making it feasible for a broad range of biology and bioengineering labs. Using transgenic mice that express channelrhodopsin-2 (ChR2), we demonstrate the system’s capability for stimulating channelrhodopsin-expressing neurons in tissue with single cell and sub-millisecond precision.
PMCID: PMC4331115
17.  Timing matters: using optogenetics to chronically manipulate neural circuitry and rhythms 
The ability to probe defined neural circuits with both the spatial and temporal resolution imparted by optogenetics has transformed the field of neuroscience. Although much attention has been paid to the advantages of manipulating neural activity at millisecond timescales in order to elicit time-locked neural responses, little consideration has been given to the manipulation of circuit activity at physiologically relevant times of day, across multiple days. Nearly all biological events are governed by the circadian clock and exhibit 24 h rhythms in activity. Indeed, neural circuit activity itself exhibits a daily rhythm with distinct temporal peaks in activity occurring at specific times of the day. Therefore, experimentally probing circuit function within and across physiologically relevant time windows (minutes to hours) in behaving animals is fundamental to understanding the function of any one particular circuit within the intact brain. Furthermore, understanding how circuit function changes with repeated manipulation is important for modeling the circuit-wide disruptions that occur with chronic disease states. Here, we review recent advances in optogenetic technology that allow for chronic, temporally specific, control of circuit activity and provide examples of chronic optogenetic paradigms that have been utilized in the search for the neural circuit basis of behaviors relevant to human neuropsychiatric disease.
PMCID: PMC3924037  PMID: 24592222
optogenetics; opsins; circadian rhythms; addiction; depression; bipolar disorder; obsessive-compulsive disorder; mouse models
18.  Laser-scanning photostimulation of optogenetically targeted forebrain circuits 
The sensory forebrain is composed of intricately connected cell types, of which functional properties have yet to be fully elucidated. Understanding the interactions of these forebrain circuits has been aided recently by the development of optogenetic methods for light-mediated modulation of neuronal activity. Here, we describe a protocol for examining the functional organization of forebrain circuits in vitro using laser-scanning photostimulation of channelrhodopsin, expressed optogenetically via viral-mediated transfection. This approach also exploits the utility of cre-lox recombination in transgenic mice to target expression in specific neuronal cell types. Following transfection, neurons are physiologically recorded in slice preparations using whole-cell patch clamp to measure their evoked responses to laser-scanning photostimulation of channelrhodopsin expressing fibers. This approach enables an assessment of functional topography and synaptic properties. Morphological correlates can be obtained by imaging the neuroanatomical expression of channelrhodopsin expressing fibers using confocal microscopy of the live slice or post-fixed tissue. These methods enable functional investigations of forebrain circuits that expand upon more conventional approaches.
PMCID: PMC3966657  PMID: 24430760
optogenetics; cortex; thalamus; channelrhodopsin; photostimulation; auditory; visual; somatosensory
19.  Optogenetically-induced behavioral and functional network changes in primates 
Current biology : CB  2012;22(18):1722-1726.
Optogenetics is currently the state-of-the-art method for causal-oriented brain research. Despite an increasingly large number of invertebrate and rodent studies showing profound electrophysiological and behavioral effects induced by optogenetics [1,2], only two primate studies have reported modulation of local single-cell activity, but with no behavioral effects [3,4]. Here, we show that optogenetic stimulation of cortical neurons within rhesus monkey arcuate sulcus, during the execution of a visually-guided saccade task, evoked significant and reproducible changes in saccade latencies as a function of target position. Moreover, using concurrent optogenetic stimulation and functional magnetic resonance imaging (aka opto-fMRI, [5,6]) we observed optogenetically-induced changes in fMRI activity in specific functional cortical networks throughout the monkey brain. This is critical information for the advancement of optogenetic primate research models and for initiating the development of optogenetically-based cell-specific therapies with which to treat neurological diseases in humans.
PMCID: PMC3461112  PMID: 22840516
20.  Virogenetic and Optogenetic Mechanisms to Define Potential Therapeutic Targets in Psychiatric Disorders 
Neuropharmacology  2011;62(1):89-100.
A continuously increasing body of knowledge shows that the brain is an extremely complex neural network and single neurons possess their own complicated interactive signaling pathways. Such complexity of the nervous system makes it increasingly difficult to investigate the functions of specific neural components such as genes, proteins, transcription factors, neurons and nuclei in the brain. Technically, it has been even more of a significant challenge to identify the molecular and cellular adaptations that are both sufficient and necessary to underlie behavioral functions in health and disease states. Defining such neural adaptations is a critical step to identify the potential therapeutic targets within the complex neural network that are beneficial to treat psychiatric disorders. Recently, the newly development and extensive application of in vivo viral-mediated gene transfer (virogenetics) and optical manipulation of specific neurons or selective neural circuits in freely-moving animals (optogenetics) make it feasible, through loss- and gain-of-function approaches, to reliably define sufficient and necessary neuroadaptations in the behavioral models of psychiatric disorders, including drug addiction, depression, anxiety and bipolar disorders. In this article, we focus on recent studies that successfully employ these advanced virogenetic and optogenetic techniques as a powerful tool to identify potential targets in the brain, and to provide highly useful information in the development of novel therapeutic strategies for psychiatric disorders.
PMCID: PMC3205991  PMID: 21945288
Neural target; Target defining; Viral-mediated gene transfer; Virogenetics; Optogenetics; Depression; Anxiety; Drug addiction; Bipolar disorder; Neurophysiology
21.  Achieving High-Frequency Optical Control of Synaptic Transmission 
The Journal of Neuroscience  2014;34(22):7704-7714.
The optogenetic tool channelrhodopsin-2 (ChR2) is widely used to excite neurons to study neural circuits. Previous optogenetic studies of synapses suggest that light-evoked synaptic responses often exhibit artificial synaptic depression, which has been attributed to either the inability of ChR2 to reliably fire presynaptic axons or to ChR2 elevating the probability of release by depolarizing presynaptic boutons. Here, we compare light-evoked and electrically evoked synaptic responses for high-frequency stimulation at three synapses in the mouse brain. At synapses from Purkinje cells to deep cerebellar nuclei neurons (PC→DCN), light- and electrically evoked synaptic currents were remarkably similar for ChR2 expressed transgenically or with adeno-associated virus (AAV) expression vectors. For hippocampal CA3→CA1 synapses, AAV expression vectors of serotype 1, 5, and 8 led to light-evoked synaptic currents that depressed much more than electrically evoked currents, even though ChR2 could fire axons reliably at up to 50 Hz. The disparity between optical and electrical stimulation was eliminated when ChR2 was expressed transgenically or with AAV9. For cerebellar granule cell to stellate cell (grc→SC) synapses, AAV1 also led to artificial synaptic depression and AAV9 provided superior performance. Artificial synaptic depression also occurred when stimulating over presynaptic boutons, rather than axons, at CA3→CA1 synapses, but not at PC→DCN synapses. These findings indicate that ChR2 expression methods and light stimulation techniques influence synaptic responses in a neuron-specific manner. They also identify pitfalls associated with using ChR2 to study synapses and suggest an approach that allows optogenetics to be applied in a manner that helps to avoid potential complications.
PMCID: PMC4035530  PMID: 24872574
AAV; channelrhodopsin; optogenetics; short-term plasticity; synapse
22.  Cell type-specific and time-dependent light exposure contribute to silencing in neurons expressing Channelrhodopsin-2 
eLife  2014;3:e01481.
Channelrhodopsin-2 (ChR2) has quickly gained popularity as a powerful tool for eliciting genetically targeted neuronal activation. However, little has been reported on the response kinetics of optogenetic stimulation across different neuronal subtypes. With excess stimulation, neurons can be driven into depolarization block, a state where they cease to fire action potentials. Herein, we demonstrate that light-induced depolarization block in neurons expressing ChR2 poses experimental challenges for stable activation of specific cell types and may confound interpretation of experiments when ‘activated’ neurons are in fact being functionally silenced. We show both ex vivo and in vivo that certain neuronal subtypes targeted for ChR2 expression become increasingly susceptible to depolarization block as the duration of light pulses are increased. We find that interneuron populations have a greater susceptibility to this effect than principal excitatory neurons, which are more resistant to light-induced depolarization block. Our results highlight the need to empirically determine the photo-response properties of targeted neurons when using ChR2, particularly in studies designed to elicit complex circuit responses in vivo where neuronal activity will not be recorded simultaneous to light stimulation.
eLife digest
The brain is a highly complex structure composed of trillions of interconnecting nerve cells. The pattern of connections between these cells gives rise to the various brain circuits that govern how the brain functions. Understanding how the brain is wired together is important for determining how ‘faulty circuits’ contribute to various neurological disorders.
New optogenetic technique tools allow neuroscientists to turn on specific neurons simply by shining light on them. These techniques involve genetically manipulating the organisms so that their neurons express proteins that are activated when they are exposed to light of a particular wavelength. However, it is important to understand the limitations of this approach—including the possibility that the light might actually turn off some neurons—when using it to study animal behavior.
Now, Herman, Huang et al. show that shining light pulses for long durations onto neurons expressing a light-activated protein called channelrhodopsin-2 causes the neurons to become silenced rather than activated. Moreover, certain types of neurons, called interneurons, are more susceptible to this effect—termed ‘depolarization block’—than the other types of neurons.
Researchers need to be mindful of this effect when channelrhodopsin-2 is used in optogenetic experiments to study the behavior of living animals. However, this silencing property could be useful in experiments that investigate situations in which depolarization block is thought to contribute to brain function and health: such as in the treatments of schizophrenia and Parkinson’s disease.
PMCID: PMC3904216  PMID: 24473077
optogenetics; action potential; in vivo; channelrhodopsin; silencing; mouse
23.  Recombineering strategies for developing next generation BAC transgenic tools for optogenetics and beyond 
The development and application of diverse BAC transgenic rodent lines has enabled rapid progress for precise molecular targeting of genetically-defined cell types in the mammalian central nervous system. These transgenic tools have played a central role in the optogenetic revolution in neuroscience. Indeed, an overwhelming proportion of studies in this field have made use of BAC transgenic Cre driver lines to achieve targeted expression of optogenetic probes in the brain. In addition, several BAC transgenic mouse lines have been established for direct cell-type specific expression of Channelrhodopsin-2 (ChR2). While the benefits of these new tools largely outweigh any accompanying challenges, many available BAC transgenic lines may suffer from confounds due in part to increased gene dosage of one or more “extra” genes contained within the large BAC DNA sequences. Here we discuss this under-appreciated issue and propose strategies for developing the next generation of BAC transgenic lines that are devoid of extra genes. Furthermore, we provide evidence that these strategies are simple, reproducible, and do not disrupt the intended cell-type specific transgene expression patterns for several distinct BAC clones. These strategies may be widely implemented for improved BAC transgenesis across diverse disciplines.
PMCID: PMC3982106  PMID: 24772073
bacterial artificial chromosome; transgenic mice; BAC recombineering; Drd1a; Drd2; Adora2a; Chat; DAT
24.  Stimulating Cardiac Muscle by Light: Cardiac Optogenetics by Cell Delivery 
After the recent cloning of light-sensitive ion channels and their expression in mammalian cells, a new field, optogenetics, emerged in neuroscience, allowing for precise perturbations of neural circuits by light. However, functionality of optogenetic tools has not been fully explored outside neuroscience; and a non-viral, non-embryogenesis based strategy for optogenetics has not been shown before.
Methods and Results
We demonstrate the utility of optogenetics to cardiac muscle by a tandem cell unit (TCU) strategy, where non-excitable cells carry exogenous light-sensitive ion channels, and when electrically coupled to cardiomyocytes, produce optically-excitable heart tissue. A stable channelrhodopsin2 (ChR2) expressing cell line was developed, characterized and used as a cell delivery system. The TCU strategy was validated in vitro in cell pairs with adult canine myocytes (for a wide range of coupling strengths) and in cardiac syncytium with neonatal rat cardiomyocytes. For the first time, we combined optical excitation and optical imaging to capture light-triggered muscle contractions and high-resolution propagation maps of light-triggered electrical waves, found to be quantitatively indistinguishable from electrically-triggered waves.
Our results demonstrate feasibility to control excitation and contraction in cardiac muscle by light using the TCU approach. Optical pacing in this case uses less energy, offers superior spatiotemporal control, remote access and can serve not only as an elegant tool in arrhythmia research, but may form the basis for a new generation of light-driven cardiac pacemakers and muscle actuators. The TCU strategy is extendable to (non-viral) stem cell therapy and is directly relevant to in vivo applications.
PMCID: PMC3209525  PMID: 21828312
optogenetics; channelrhodopsin2; light-sensitive ion channels; cardiac; optical mapping
25.  Optetrode: a multichannel readout for optogenetic control in freely moving mice 
Nature neuroscience  2011;15(1):163-170.
Recent advances in optogenetics have improved the precision with which defined circuit elements can be controlled optically in freely moving mammals; in particular, recombinase-dependent opsin viruses, used with a growing pool of transgenic mice expressing recombinases, allow manipulation of specific cell types. However, although optogenetic control has allowed neural circuits to be manipulated in increasingly powerful ways, combining optogenetic stimulation with simultaneous multichannel electrophysiological readout of isolated units in freely moving mice remains a challenge. We designed and validated the optetrode, a device that allows for colocalized multi-tetrode electrophysiological recording and optical stimulation in freely moving mice. Optetrode manufacture employs a unique optical fiber-centric coaxial design approach that yields a lightweight (2 g), compact and robust device that is suitable for behaving mice. This low-cost device is easy to construct (2.5 h to build without specialized equipment). We found that the drive design produced stable high-quality recordings and continued to do so for at least 6 weeks following implantation. We validated the optetrode by quantifying, for the first time, the response of cells in the medial prefrontal cortex to local optical excitation and inhibition, probing multiple different genetically defined classes of cells in the mouse during open field exploration.
PMCID: PMC4164695  PMID: 22138641

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