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1.  Synaptic Encoding of Fear Extinction in mPFC-amygdala Circuits 
Neuron  2013;80(6):10.1016/j.neuron.2013.09.025.
Retrieval of fear extinction memory is associated with increased firing of neurons in the medial prefrontal cortex (mPFC). It is unknown, however, how extinction learning-induced changes in mPFC activity are relayed to target structures in the amygdala, resulting in diminished fear responses. Here, we show that fear extinction decreases the efficacy of excitatory synaptic transmission in projections from the mPFC to the basolateral nucleus of the amygdala (BLA), whereas inhibitory responses are not altered. In contrast,synaptic strength at direct mPFC inputs to intercalated neurons remains unchanged following extinction. Moreover, priming stimulation of mPFC projections induced heterosynaptic inhibition in auditory cortical inputs to the BLA. These synaptic mechanisms could contribute to the encoding of extinction memory by diminishing the ability of projections from the mPFC to drive BLA activity while retaining the ability of intercalated neurons to inhibit the output nuclei of the amygdala.
PMCID: PMC3872173  PMID: 24290204
2.  Cerebellar Purkinje cell activity drives motor learning 
Nature neuroscience  2013;16(12):1734-1736.
The climbing fiber input to the cerebellar cortex is thought to provide instructive signals that drive the induction of motor skill learning. We found that optogenetic activation of Purkinje cells, the sole output neurons of the cerebellar cortex, can also drive motor learning in mice. This dual control over the induction of learning by climbing fibers and Purkinje cells can expand the learning capacity of motor circuits.
PMCID: PMC3966616  PMID: 24162651
3.  Optogenetic Activation of an Inhibitory Network Enhances Feed-Forward Functional Connectivity in Auditory Cortex 
Neuron  2013;80(4):10.1016/j.neuron.2013.08.017.
The mammalian neocortex is a highly interconnected network of different types of neurons organized into both layers and columns. Overlaid on this structural organization is a pattern of functional connectivity that can be rapidly and flexibly altered during behavior. Parvalbumin-positive (PV) inhibitory neurons, which are implicated in cortical oscillations and can change neuronal selectivity, may play a pivotal role in these dynamic changes. We found that optogenetic activation of PV neurons in the auditory cortex enhanced feed-forward functional connectivity in the putative thalamorecipient circuit and in cortical columnar circuits. In contrast, PV stimulation induced no change in connectivity between sites in the same layers. The activity of PV neurons may thus serve as a gating mechanism to enhance feed-forward, but not lateral or feedback, information flow in cortical circuits. Functionally, it may preferentially enhance the contribution of bottom-up sensory inputs to perception.
PMCID: PMC3841078  PMID: 24267655
4.  A unique population of ventral tegmental area neurons inhibits the lateral habenula to promote reward 
Neuron  2013;80(4):10.1016/j.neuron.2013.08.023.
Lateral habenula (LHb) neurons convey aversive and negative reward conditions through potent indirect inhibition of ventral tegmental area (VTA) dopaminergic neurons. While VTA dopaminergic neurons reciprocally project to the LHb, the electrophysiological properties and the behavioral consequences associated with selective manipulations of this circuit are unknown. Here, we identify a novel inhibitory input to the LHb arising from a unique population of VTA neurons expressing dopaminergic markers. Optogenetic activation of this circuit resulted in no detectable dopamine release in LHb brain slices. Instead, stimulation produced GABA-mediated inhibitory synaptic transmission, which suppressed the firing of postsynaptic LHb neurons in brain slices and increased the spontaneous firing rate of VTA dopaminergic neurons in vivo. Furthermore, in vivo activation of this pathway produced reward-related phenotypes that were dependent on intra-LHb GABAA receptor signaling. These results suggest that non-canonical inhibitory signaling by these hybrid dopaminergic-GABAergic neurons act to suppress LHb output under rewarding conditions.
PMCID: PMC3873746  PMID: 24267654
5.  Leptin regulates the reward value of nutrient 
Nature neuroscience  2011;14(12):1562-1568.
We developed an assay for quantifying the reward value of nutrient and used it to analyze the effects of metabolic state and leptin. In this assay, mice chose between two sippers, one of which dispensed water and was coupled to optogenetic activation of dopaminergic (DA) neurons and the other of which dispensed natural or artificial sweeteners. This assay measured the reward value of sweeteners relative to lick-induced optogenetic activation of DA neurons. Mice preferred optogenetic stimulation of DA neurons to sucralose, but not to sucrose. However, the mice preferred sucralose plus optogenetic stimulation versus sucrose. We found that food restriction increased the value of sucrose relative to sucralose plus optogenetic stimulation, and that leptin decreased it. Our data suggest that leptin suppresses the ability of sucrose to drive taste-independent DA neuronal activation and provide new insights into the mechanism of leptin's effects on food intake.
PMCID: PMC4238286  PMID: 22081158
6.  Wave optics theory and 3-D deconvolution for the light field microscope 
Optics Express  2013;21(21):25418-25439.
Light field microscopy is a new technique for high-speed volumetric imaging of weakly scattering or fluorescent specimens. It employs an array of microlenses to trade off spatial resolution against angular resolution, thereby allowing a 4-D light field to be captured using a single photographic exposure without the need for scanning. The recorded light field can then be used to computationally reconstruct a full volume. In this paper, we present an optical model for light field microscopy based on wave optics, instead of previously reported ray optics models. We also present a 3-D deconvolution method for light field microscopy that is able to reconstruct volumes at higher spatial resolution, and with better optical sectioning, than previously reported. To accomplish this, we take advantage of the dense spatio-angular sampling provided by a microlens array at axial positions away from the native object plane. This dense sampling permits us to decode aliasing present in the light field to reconstruct high-frequency information. We formulate our method as an inverse problem for reconstructing the 3-D volume, which we solve using a GPU-accelerated iterative algorithm. Theoretical limits on the depth-dependent lateral resolution of the reconstructed volumes are derived. We show that these limits are in good agreement with experimental results on a standard USAF 1951 resolution target. Finally, we present 3-D reconstructions of pollen grains that demonstrate the improvements in fidelity made possible by our method.
PMCID: PMC3867103  PMID: 24150383
(180.6900) Three dimensional microscopy; (180.2520) Fluorescence microscopy; (100.1830) Deconvolution; (100.6950) Tomographic image processing; (100.3190) Inverse problems
7.  Tracking stem cell differentiation in the setting of automated optogenetic stimulation 
Stem cells (Dayton, Ohio)  2011;29(1):78-88.
Membrane depolarization has been shown to play an important role in the neural differentiation of stem cells as well as in the survival and function of mature neurons. Here we introduce a microbial opsin into embryonic stem cells and develop optogenetic technology for stem cell engineering applications, with an automated system for noninvasive modulation of embryonic stem cell differentiation employing fast optogenetic control of ion flux. Mouse embryonic stem cells (ESCs) were stably transduced with ChR2-YFP and purified by FACS. Illumination of resulting ChR2-ESCs with pulses of blue light triggered inward currents. These labeled ESCs retained the capability to differentiate into functional mature neurons, assessed by the presence of voltage-gated sodium currents, action potentials, fast excitatory synaptic transmission, and expression of mature neuronal proteins and neuronal morphology. We designed and tested an apparatus for optically stimulating ChR2-ESCs during chronic neuronal differentiation, with high-speed optical switching on a custom robotic stage with environmental chamber for automated stimulation and imaging over days, with tracking for increased expression of neural and neuronal markers. These data point to potential uses of ChR2 technology for chronic and temporally precise noninvasive optical control of embryonic stem cells both in vitro and in vivo, ranging from noninvasive control of stem cell differentiation to causal assessment of the specific contribution of transplanted cells to tissue and network function.
PMCID: PMC4182948  PMID: 21280159
embryonic stem cells; optogenetics; Channelrhodopsin-2; neuronal differentiation
8.  Designer Receptors Show Role for Ventral Pallidum Input to Ventral Tegmental Area in Cocaine Seeking 
Nature neuroscience  2014;17(4):577-585.
Ventral pallidum (VP) is centrally positioned within mesocorticolimbic reward circuits, and its dense projection to ventral tegmental area (VTA) regulates neuronal activity there. However, VP is a heterogeneous structure, and how this complexity affects its role within wider reward circuits is unclear. Here we demonstrate that projections to VTA from rostral (RVP), but not caudal VP (CVP) are robustly Fos-activated during cue-induced reinstatement of cocaine seeking—a rat model of relapse in addiction. Moreover, designer receptor-mediated transient inactivation of RVP neurons, their terminals in VTA, or functional connectivity between RVP and VTA dopamine neurons blocks the ability of drug-associated cues (but not a cocaine prime) to reinstate cocaine seeking. In contrast, CVP neuronal inhibition instead blocked cocaine-primed, but not cue-induced reinstatement. This novel double dissociation in VP sub-regional roles in drug seeking is likely important for understanding mesocorticolimbic circuits underlying reward seeking and addiction.
PMCID: PMC3973180  PMID: 24584054
9.  A Coaxial Optrode As Multifunction Write-Read Probe for Optogenetic Studies in Non-Human Primates 
Journal of neuroscience methods  2013;219(1):142-154.
Advances in optogenetics have led to first reports of expression of light-gated ion-channels in non-human primates (NHPs). However, a major obstacle preventing effective application of optogenetics in NHPs and translation to optogenetic therapeutics is the absence of compatible multifunction optoelectronic probes for (1) precision light delivery, (2) low-interference electrophysiology, (3) protein fluorescence detection, and (4) repeated insertion with minimal brain trauma.
New Method
Here we describe a novel brain probe device, a “coaxial optrode”, designed to minimize brain tissue damage while microfabricated to perform simultaneous electrophysiology, light delivery and fluorescence measurements in the NHP brain. The device consists of a tapered, gold-coated optical fiber inserted in a polyamide tube. A portion of the gold coating is exposed at the fiber tip to allow electrophysiological recordings in addition to light delivery/collection at the tip.
Coaxial optrode performance was demonstrated by experiments in rodents and NHPs, and characterized by computational models. The device mapped opsin expression in the brain and achieved precisely targeted optical stimulation and electrophysiology with minimal cortical damage.
Comparison with Existing Methods
Overall, combined electrical, optical and mechanical features of the coaxial optrode allowed a performance for NHP studies which was not possible with previously existing devices.
Coaxial optrode is currently being used in two NHP laboratories as a major tool to study brain function by inducing light modulated neural activity and behavior. By virtue of its design, the coaxial optrode can be extended for use as a chronic implant and multisite neural stimulation/recording.
PMCID: PMC3789534  PMID: 23867081
optogenetics; optoelectronic devices; non-human primates; fluorescence detection; tissue heating; light propagation in tissue
10.  A Major External Source of Cholinergic Innervation of the Striatum and Nucleus Accumbens Originates in the Brainstem 
The Journal of Neuroscience  2014;34(13):4509-4518.
Cholinergic transmission in the striatal complex is critical for the modulation of the activity of local microcircuits and dopamine release. Release of acetylcholine has been considered to originate exclusively from a subtype of striatal interneuron that provides widespread innervation of the striatum. Cholinergic neurons of the pedunculopontine (PPN) and laterodorsal tegmental (LDT) nuclei indirectly influence the activity of the dorsal striatum and nucleus accumbens through their innervation of dopamine and thalamic neurons, which in turn converge at the same striatal levels. Here we show that cholinergic neurons in the brainstem also provide a direct innervation of the striatal complex. By the expression of fluorescent proteins in choline acetyltransferase (ChAT)::Cre+ transgenic rats, we selectively labeled cholinergic neurons in the rostral PPN, caudal PPN, and LDT. We show that cholinergic neurons topographically innervate wide areas of the striatal complex: rostral PPN preferentially innervates the dorsolateral striatum, and LDT preferentially innervates the medial striatum and nucleus accumbens core in which they principally form asymmetric synapses. Retrograde labeling combined with immunohistochemistry in wild-type rats confirmed the topography and cholinergic nature of the projection. Furthermore, transynaptic gene activation and conventional double retrograde labeling suggest that LDT neurons that innervate the nucleus accumbens also send collaterals to the thalamus and the dopaminergic midbrain, thus providing both direct and indirect projections, to the striatal complex. The differential activity of cholinergic interneurons and cholinergic neurons of the brainstem during reward-related paradigms suggest that the two systems play different but complementary roles in the processing of information in the striatum.
PMCID: PMC3965779  PMID: 24671996
cholinergic; innervation; laterodorsal tegmental nucleus; pedunculopontine nucleus; striatum; topography
11.  Principles for applying optogenetic tools derived from direct comparative analysis of microbial opsins 
Nature methods  2011;9(2):159-172.
Diverse optogenetic tools have allowed versatile control over neural activity. Many depolarizing and hyperpolarizing tools have now been developed in multiple laboratories and tested across different preparations, presenting opportunities but also making it difficult to draw direct comparisons. This challenge has been compounded by the dependence of performance on parameters such as vector, promoter, expression time, illumination, cell type and many other variables. As a result, it has become increasingly complicated for end users to select the optimal reagents for their experimental needs. For a rapidly growing field, critical figures of merit should be formalized both to establish a framework for further development and so that end users can readily understand how these standardized parameters translate into performance. Here we systematically compared microbial opsins under matched experimental conditions to extract essential principles and identify key parameters for the conduct, design and interpretation of experiments involving optogenetic techniques.
PMCID: PMC4165888  PMID: 22179551
12.  The Microbial Opsin Family of Optogenetic Tools 
Cell  2011;147(7):1446-1457.
The capture and utilization of light is an exquisitely evolved process. The single-component microbial opsins, although more limited than multicomponent cascades in processing, display unparalleled compactness and speed. Recent advances in understanding microbial opsins have been driven by molecular engineering for optogenetics and by comparative genomics. Here we provide a Primer on these light-activated ion channels and pumps, describe a group of opsins bridging prior categories, and explore the convergence of molecular engineering and genomic discovery for the utilization and understanding of these remarkable molecular machines.
PMCID: PMC4166436  PMID: 22196724
13.  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
14.  Optical Neural Interfaces 
Genetically encoded optical actuators and indicators have changed the landscape of neuroscience, enabling targetable control and readout of specific components of intact neural circuits in behaving animals. Here, we review the development of optical neural interfaces, focusing on hardware designed for optical control of neural activity, integrated optical control and electrical readout, and optical readout of population and single-cell neural activity in freely moving mammals.
PMCID: PMC4163158  PMID: 25014785
optogenetics; neurophysiology; imaging; channelrhodopsin; halorhodopsin; GCaMP
15.  Crystal structure of the channelrhodopsin light-gated cation channel 
Nature  2012;482(7385):369-374.
Channelrhodopsins (ChRs) are light-gated cation channels derived from algae that have shown experimental utility in optogenetics; for example, neurons expressing ChRs can be optically controlled with high temporal precision within systems as complex as freely moving mammals. Although ChRs have been broadly applied to neuroscience research, little is known about the molecular mechanisms by which these unusual and powerful proteins operate. Here we present the crystal structure of a ChR (a C1C2 chimaera between ChR1 and ChR2 from Chlamydomonas reinhardtii) at 2.3 Å resolution. The structure reveals the essential molecular architecture of ChRs, including the retinal-binding pocket and cation conduction pathway. This integration of structural and electrophysiological analyses provides insight into the molecular basis for the remarkable function of ChRs, and paves the way for the precise and principled design of ChR variants with novel properties.
PMCID: PMC4160518  PMID: 22266941
16.  Dopamine neurons modulate neural encoding and expression of depression-related behaviour 
Nature  2012;493(7433):537-541.
Major depression is characterized by diverse debilitating symptoms that include hopelessness and anhedonia1. Dopamine neurons involved in reward and motivation2–9 are among many neural populations that have been hypothesized to be relevant10, and certain antidepressant treatments, including medications and brain stimulation therapies, can influence the complex dopamine system. Until now it has not been possible to test this hypothesis directly, even in animal models, as existing therapeutic interventions are unable to specifically target dopamine neurons. Here we investigated directly the causal contributions of defined dopamine neurons to multidimensional depression-like phenotypes induced by chronic mild stress, by integrating behavioural, pharmacological, optogenetic and electrophysiological methods in freely moving rodents. We found that bidirectional control (inhibition or excitation) of specified midbrain dopamine neurons immediately and bidirectionally modulates (induces or relieves) multiple independent depression symptoms caused by chronic stress. By probing the circuit implementation of these effects, we observed that optogenetic recruitment of these dopamine neurons potently alters the neural encoding of depression-related behaviours in the downstream nucleus accumbens of freely moving rodents, suggesting that processes affecting depression symptoms may involve alterations in the neural encoding of action in limbic circuitry.
PMCID: PMC4160519  PMID: 23235822
17.  Molecular and Cellular Approaches for Diversifying and Extending Optogenetics 
Cell  2010;141(1):154-165.
Optogenetic technologies employ light to control biological processes within targeted cells in vivo with high temporal precision. Here, we show that application of molecular trafficking principles can expand the optogenetic repertoire along several long-sought dimensions. Subcellular and transcellular trafficking strategies now permit (1) optical regulation at the far-red/infrared border and extension of optogenetic control across the entire visible spectrum, (2) increased potency of optical inhibition without increased light power requirement (nanoampere-scale chloride-mediated photocurrents that maintain the light sensitivity and reversible, step-like kinetic stability of earlier tools), and (3) generalizable strategies for targeting cells based not only on genetic identity, but also on morphology and tissue topology, to allow versatile targeting when promoters are not known or in genetically intractable organisms. Together, these results illustrate use of cell-biological principles to enable expansion of the versatile fast optogenetic technologies suitable for intact-systems biology and behavior.
PMCID: PMC4160532  PMID: 20303157
18.  Neocortical excitation/inhibition balance in information processing and social dysfunction 
Nature  2011;477(7363):171-178.
Severe behavioural deficits in psychiatric diseases such as autism and schizophrenia have been hypothesized to arise from elevations in the cellular balance of excitation and inhibition (E/I balance) within neural microcircuitry. This hypothesis could unify diverse streams of pathophysiological and genetic evidence, but has not been susceptible to direct testing. Here we design and use several novel optogenetic tools to causally investigate the cellular E/I balance hypothesis in freely moving mammals, and explore the associated circuit physiology. Elevation, but not reduction, of cellular E/I balance within the mouse medial prefrontal cortex was found to elicit a profound impairment in cellular information processing, associated with specific behavioural impairments and increased high-frequency power in the 30–80 Hz range, which have both been observed in clinical conditions in humans. Consistent with the E/I balance hypothesis, compensatory elevation of inhibitory cell excitability partially rescued social deficits caused by E/I balance elevation. These results provide support for the elevated cellular E/I balance hypothesis of severe neuropsychiatric disease-related symptoms.
PMCID: PMC4155501  PMID: 21796121
19.  GABAergic Projection Neurons Route Selective Olfactory Inputs to Specific Higher Order Neurons 
Neuron  2013;79(5):10.1016/j.neuron.2013.06.014.
We characterize an inhibitory circuit motif in the Drosophila olfactory system, parallel inhibition, which differs from feed-forward or feedback inhibition. Excitatory and GABAergic inhibitory projection neurons (ePNs and iPNs) each receive input from antennal lobe glomeruli and send parallel output to the lateral horn, a higher center implicated in regulating innate olfactory behavior. Ca2+ imaging of specific lateral horn neurons as an olfactory readout revealed that iPNs selectively suppress food-related odorant responses, but spared signal transmission from pheromone channels. Co-applying food odorant did not affect pheromone signal transmission, suggesting that the differential effects likely result from connection specificity of iPNs, rather than a generalized inhibitory tone. Ca2+ responses in the ePN axon terminals show no detectable suppression by iPNs, arguing against presynaptic inhibition as a primary mechanism. The parallel inhibition motif may provide specificity in inhibition to funnel specific olfactory information, such as food and pheromone, into distinct downstream circuits.
PMCID: PMC3838762  PMID: 24012005
20.  Virally mediated optogenetic excitation and inhibition of pain in freely moving non-transgenic mice 
Nature biotechnology  2014;32(3):274-278.
Primary nociceptors are the first neurons involved in the complex processing system that regulates normal and pathological pain1. Our ability to excite and inhibit these neurons has been limited by pharmacological and electrical stimulation constraints; non-invasive excitation and inhibition of these neurons in freely moving non-transgenic animals has not been possible. Here we use an optogenetic2 strategy to bidirectionally control nociceptors of non-transgenic mice. Intra-sciatic nerve injection of adeno-associated viruses encoding an excitatory opsin enabled light-inducible stimulation of acute pain, place aversion, and optogenetically mediated reductions in withdrawal thresholds to mechanical and thermal stimuli. In contrast, viral delivery of an inhibitory opsin enabled light-inducible inhibition of acute pain perception, and reversed mechanical allodynia and thermal hyperalgesia in a model of neuropathic pain. Light was delivered transdermally enabling these behaviors to be induced in freely moving animals. This approach may have utility in basic and translational pain research, and enable rapid drug screening and testing of newly engineered opsins.
PMCID: PMC3988230  PMID: 24531797
21.  Natural neural projection dynamics underlying social behavior 
Cell  2014;157(7):1535-1551.
Social interaction is a complex behavior essential for many species, and is impaired in major neuropsychiatric disorders. Pharmacological studies have implicated certain neurotransmitter systems in social behavior, but circuit-level understanding of endogenous neural activity during social interaction is lacking. We therefore developed and applied a new methodology, termed fiber photometry, to optically record natural neural activity in genetically- and connectivity-defined projections to elucidate the real-time role of specified pathways in mammalian behavior. Fiber photometry revealed that activity dynamics of a ventral tegmental area (VTA)-to-nucleus accumbens (NAc) projection could encode and predict key features of social but not novel-object interaction. Consistent with this observation, optogenetic control of cells specifically contributing to this projection was sufficient to modulate social behavior, which was mediated by type-1 dopamine receptor signaling downstream in the NAc. Direct observation of projection-specific activity in this way captures a fundamental and previously inaccessible dimension of circuit dynamics.
PMCID: PMC4123133  PMID: 24949967
22.  Medial prefrontal D1 dopamine neurons control food intake 
Nature neuroscience  2014;17(2):248-253.
Although the prefrontal cortex influences motivated behavior, its role in food intake remains unclear. Here, we demonstrate a role for D1-type dopamine receptor-expressing neurons in the medial prefrontal cortex (mPFC) in the regulation of feeding. Food intake increases activity in D1 neurons of the mPFC in mice, and optogenetic photostimulation of D1 neurons increases feeding. Conversely, inhibition of D1 neurons decreases intake. Stimulation-based mapping of prefrontal D1 neuron projections implicates the medial basolateral amygdala (mBLA) as a downstream target of these afferents. mBLA neurons activated by prefrontal D1 stimulation are CaMKII positive and closely juxtaposed to prefrontal D1 axon terminals. Finally, photostimulating these axons in the mBLA is sufficient to increase feeding, recapitulating the effects of mPFC D1 stimulation. These data describe a new circuit for top-down control of food intake.
PMCID: PMC3968853  PMID: 24441680
24.  Structure-Guided Transformation of Channelrhodopsin into a Light-Activated Chloride Channel 
Science (New York, N.Y.)  2014;344(6182):420-424.
Using light to silence electrical activity in targeted cells is a major goal of optogenetics. Available optogenetic proteins that directly move ions to achieve silencing are inefficient, pumping only a single ion per photon across the cell membrane rather than allowing many ions per photon to flow through a channel pore. Building on high-resolution crystal-structure analysis, pore vestibule modeling, and structure-guided protein engineering, we designed and characterized a class of channelrhodopsins (originally cation-conducting) converted into chloride-conducting anion channels. These tools enable fast optical inhibition of action potentials and can be engineered to display step-function kinetics for stable inhibition, outlasting light pulses and for orders-of-magnitude-greater light sensitivity of inhibited cells. The resulting family of proteins defines an approach to more physiological, efficient, and sensitive optogenetic inhibition.
PMCID: PMC4096039  PMID: 24763591
25.  Advanced CLARITY for rapid and high-resolution imaging of intact tissues 
Nature protocols  2014;9(7):1682-1697.
CLARITY is a method for chemical transformation of intact biological tissues into a hydrogel-tissue hybrid, which becomes amenable to interrogation with light and macromolecular labels while retaining fine structure and native biological molecules. This emerging accessibility of information from large intact samples has created both new opportunities and new challenges. Here we describe next-generation protocols spanning multiple dimensions of the CLARITY workflow, ranging from a novel approach to simple, reliable, and efficient lipid removal without electrophoretic instrumentation (passive CLARITY), to optimized objectives and integration with light-sheet optics (CLARITY-optimized light-sheet microscopy or COLM) for accelerating data collection from clarified samples by several orders of magnitude while maintaining or increasing quality and resolution. These methods may find application in the structural and molecular analysis of large assembled biological systems such as the intact mammalian brain.
PMCID: PMC4096681  PMID: 24945384

Results 1-25 (96)