Optical inhibition of larval zebrafish behaviour with anion channelrhodopsins
© Jesuthasan et al. 2017
Received: 17 July 2017
Accepted: 25 September 2017
Published: 3 November 2017
Optical silencing of activity provides a way to test the necessity of neurons in behaviour. Two light-gated anion channels, GtACR1 and GtACR2, have recently been shown to potently inhibit activity in cultured mammalian neurons and in Drosophila. Here, we test the usefulness of these channels in larval zebrafish, using spontaneous coiling behaviour as the assay.
When the GtACRs were expressed in spinal neurons of embryonic zebrafish and actuated with blue or green light, spontaneous movement was inhibited. In GtACR1-expressing fish, only 3 μW/mm2 of light was sufficient to have an effect; GtACR2, which is poorly trafficked, required slightly stronger illumination. No inhibition was seen in non-expressing siblings. After light offset, the movement of GtACR-expressing fish increased, which suggested that termination of light-induced neural inhibition may lead to activation. Consistent with this, two-photon imaging of spinal neurons showed that blue light inhibited spontaneous activity in spinal neurons of GtACR1-expressing fish, and that the level of intracellular calcium increased following light offset.
These results show that GtACR1 and GtACR2 can be used to optically inhibit neurons in larval zebrafish with high efficiency. The activity elicited at light offset needs to be taken into consideration in experimental design, although this property can provide insight into the effects of transiently stimulating a circuit.
One approach to understanding the role of specific neurons in a given behaviour is to experimentally alter their activity. A precise means of doing this is by using light-gated channels [1–4]. Optogenetic activators such as channelrhodopsin-2 , ChIEF  and CsChrimson  can reversibly depolarize membrane potential with millisecond resolution and have been widely used in a range of organisms [8–11]. For numerous different behavioural functions, these tools have enabled the determination of neuronal sufficiency. However, establishing whether neurons are normally involved requires additional experiments. Optical or electrical recording can determine which activity patterns are correlated with behaviour. However, for the crucially important loss-of-function experiment, effective tools for neuronal inhibition are required.
A number of different optogenetic inhibitors have been developed. The first generation of these tools include light-actuated channels like halorhodopsin [12, 13], which facilitates light-dependent chloride entry, and archaerhodopsin [14, 15], a proton pump that is also hyperpolarizing. A limitation of these molecules is their low conductance and the high levels of expression and illumination that are required for effective silencing. For example, the archaerhodopsin derivative Archer1 requires 3 mW/mm2 of light to inhibit action potentials in cultured mammalian neurons , while halorhodopsin requires ~20 mW/mm2 to inhibit activity in zebrafish neurons . A second generation of optogenetic inhibitors includes genetically modified channelrhodopsins such as ChloC  and iC1C2 , which hyperpolarize neurons by light-gated conductance of chloride. Both require similar levels of illumination, although an improved version of ChloC, iChloC, requires 10 times less light . More recently, naturally evolved anion-conducting channels from the alga Guillardia theta were shown to silence neurons at very low light levels, i.e. in the range of microwatts per square millimetre . Drosophila experiments have confirmed that these optogenetic tools are potent inhibitors in vivo . Here, we ask whether Guillardia theta anion channelrhodopsins (GtACR1 and GtACR2) are effective inhibitors of neural activity in the larval zebrafish, a genetically tractable vertebrate.
The experiments here were carried out in accordance with guidelines approved by the Institutional Animal Care and Use Committee of Biopolis, Singapore.
Generation of GtACR1 and GtACR2 transgenic zebrafish lines
Sequences encoding GtACR1 and GtACR2 fused to eYFP  were placed downstream of the upstream activating sequence (UAS) using Gateway cloning (Thermo Fisher Scientific). The resulting construct was cloned into a plasmid containing Tol2 sequences to facilitate integration into the zebrafish genome [23, 24]. The constructs (33 ng/μl) were then injected into nacre -/- eggs at the one-cell stage, along with elavl3:Gal4 DNA (15 ng/μl, lacking Tol2 sequences) to induce GtACR expression, and Tol2 mRNA (33 ng/μl) to facilitate genomic integration. Embryos were screened after 24–36 hs for eYFP expression. Healthy embryos with eYFP expression were grown to adulthood. At 2 months, fish were fin-clipped and PCR-screened with GtACR-specific primers (GtACR1 forward 5’-CACCGTGTTCGGCATCAC-3’, GtACR1 reverse 5’-GCCACCACCATCTCGAAG-3’; GtACR2 forward 5’-ATTACCGCTACCATCTCCCC-3’, GtACR2 reverse 5’-TGGTGAACACCACGCTGTAT-3’) to test for the presence of transgene. This led to the generation of two transgenic lines, Tg(UAS:GtACR1-eYFP)sq211 and Tg(UAS:GtACR2:eYFP)sq212.
Transgenic lines used in this study are elavl3:GCaMP6f , TgBAC(gng8:GAL4) c416 , Et(-0.6hsp70l:Gal4-VP16)s1020t , Et(-0.6hsp70l:Gal4-VP16)s1011t  and UAS:NpHR-mCherry . For brevity, the enhancer trap lines are referred to as GAL4s1020t and GAL4s1011t in the text and figures.
Twenty-four-hour-old F1 embryos were dechorionated, anaesthetized with 160 mg/L tricaine, and mounted in 1% low melting agarose in E3. Imaging was carried out using a Zeiss LSM800 confocal microscope with a 10× and a 40× water immersion objective.
Spontaneous movement and light stimulation
GAL4s1020t, UAS:ACR1-eYFP and GAL4s1020t, UAS:ACR2-eYFP embryos were screened with a fluorescence stereomicroscope at 23–24 h post-fertilization to identify ACR-expressing fish. Embryos, still within their chorions, were then placed in a glass dish with 24 concave wells on a stereomicroscope (Zeiss Stemi 2000) with a transmitted light base. Behaviour was recorded on the microscope using a Point Gray Flea2 camera controlled by MicroManager. Stimulating light was delivered by LED backlights (TMS Lite), with peak intensity at 470 nm (blue), 525 nm (green) or 630 nm (red), placed adjacent to the glass dish. The power used for high intensity illumination was the maximum that could be delivered by these LEDs. The same voltage settings were used with the three light boxes to give high, medium and low intensities, but the irradiance produced differed. We provided 595-nm (amber) illumination using LEDs from CREE (XR7090-AM-L1-0001), which were mounted onto thermal LED holders (803122; Bergquist Company). The intensity of light was measured using an S120VC power sensor and a PM100A console (Thorlabs, Newton, NJ, USA). LEDs were switched on and off using an Arduino board controlled by MicroManager to regulate the power supply unit. Embryos were recorded for a total of 45 s, with the LED being turned on 15 s after the start of recording and turned off 15 s later. Each embryo was tested once for each condition and tested with different intensities and wavelengths.
Analysis of behaviour recordings
Image analysis was carried out using Fiji (RRID:SCR_002285)  as well as scripts written in Python. From the raw recordings, one frame was extracted per second to obtain a total of 46 frames (including the first and last frames). Circular regions of interest (ROIs) were manually drawn around each chorion to isolate each fish. Each frame was then subtracted from the next frame to identify the differences between frames. The number of different pixels in each ROI was taken as a measure of movement of each embryo . Any embryo that did not move during the entire recording was discarded from analysis. Estimation statistical methods were employed to analyse mean differences between control and experimental groups [29–31]. The 95% confidence intervals (CIs) for the mean difference were calculated using bootstrap methods . All CIs were bias-corrected and accelerated , with resampling performed 5000 times. All reported P values are the results of Wilcoxon t tests.
Two-photon calcium imaging
Triple transgenic zebrafish embryos (Et(-0.6hsp70l:Gal4-VP16)s1020t, UAS:ACR1-eYFP, elavl3:GCaMP6f) were mounted in agarose (2% low melting temperature, in E3). To enable individual cells to be followed without motion artefacts, fish were anesthetized with mivacurium chloride (Mivacron; GSK, Auckland, New Zealand). All imaging was performed using an upright Nikon A1RMP two-photon microscope equipped with a 25× 1.1 NA water immersion objective. Images were captured at a rate of 1 Hz, with the laser tuned to 920 nm. Blue light was delivered with the same light box used for behaviour experiments, at the maximum intensity. Green light was not used, as this overlaps with the emission spectrum of GCaMP6f and would saturate the detector.
Analysis of calcium imaging data
Analysis was carried out using Fiji , unless otherwise stated. Background correction was first performed by subtracting the average value of a region outside the embryo for each frame. This was done to eliminate the bleed-through from the illuminating LED. A median filter with a radius of 1 pixel was then applied. Images were registered using TurboReg in Fiji . ROIs were drawn manually around cells. The average fluorescence intensity of cells within an ROI was obtained by measuring only pixels above a threshold, so that pixels without a signal, but that were located within the ROI, did not reduce the value.
Acridine orange label
Embryos were incubated in acridine orange (Sigma A6014) at a concentration of 0.01 mg/ml for 30 min, then rinsed three times in E3. They were then anesthetized in buffered MS222, mounted in 2% agarose in E3 and imaged with a 10× water immersion objective on an LSM 800 laser scanning confocal microscope (Zeiss) at 1024 × 1024 resolution. The number of labelled nuclei in the nervous system was counted manually with the aid of the multipoint tool in Fiji.
Transgenic zebrafish express GtACR1 and GtACR2 in neurons
Light-actuated GtACR1 and GtACR2 inhibit spontaneous movement
High and medium intensities of green and blue light had a similar effect on GtACR1-expressing fish, namely inhibition of coiling (Figs. 2a, b, 3a–d; Movie 1, see Additional file 1). Siblings that did not express the channel continued to coil in the presence of high intensity light (fourth column of Fig. 2a, b; Movie 2, see Additional file 2). Low intensities (3 μW/mm2 for blue and 2 μW/mm2 for green light) were able to cause freezing, but at reduced efficiency compared to the higher intensities (compare the third column in Fig. 2a, b with the first two columns). For GtACR2-expressing fish, high and medium intensities of blue light were able to induce similar levels of freezing, while a low level of blue had a small effect (Figs. 2c, 4a, b); green light inhibited embryo movement only when used at high intensity (Figs. 2d, 4c, d). Red light did not inhibit coiling of either GtACR1 or GtACR2 fish at the intensity tested (Figs. 2e, f, 3e, f, 4e, f), consistent with the reported action spectrum of both GtACR1 and GtACR2 . Together, these data suggest that GtACR1 is more effective than GtACR2.
Additional file 1: Movie 1. The effect of 10 μW/mm2 green light on spontaneous movement of GAL4s1020t, UAS:GtACR1 embryos. Twenty-four-hour-old embryos exhibit spontaneous coiling, except during the period of green light delivery, which is indicated by the green dot on the bottom left. (MP4 975kb)
Additional file 2: Movie 2. The effect of 10 μW/mm2 green light on spontaneous movement of embryos without GtACR1 expression. Spontaneous coiling persists during delivery of green light. (MP4 921kb)
GtACRs increase behavioural activity at light offset
This effect was observed in larvae expressing GtACR1 in both green and blue light, at all three light intensities tested (Fig. 3a–d). However, for larvae expressing GtACR2, this effect was only observed upon exposure to blue light (Fig. 4a, b). This suggests that the movement to light offset is not due purely to change in illumination (i.e. a startle response), but is caused by the light-gated anion channel.
Comparison of GtACRs with halorhodopsin
Calcium imaging of spinal neurons
Additional file 3: Movie 3. The effects of blue light on the trunk of GAL4s1020t, UAS:GtACR1, elavl3:GCaMP6f fish. Twitches of the body are accompanied by increase in GCaMP6f fluorescence. In the presence of blue light (from 60 to 120 s), which can be seen by an overall increase in brightness, the embryo no longer twitches and there is no fluctuation in GCaMP6f fluorescence. After the blue light is switched off, movement and change in GCaMP6f fluorescence resume. This is a dorsal view, with anterior to the left. (AVI 2660kb)
To test whether offset of the actuating light can drive neural firing in fish expressing GtACR1, as suggested by behavioural data, we used fish at a later stage where spontaneous activity was not as prominent, so that signals evoked by loss of light can be clearly distinguished from spontaneous activity. As seen in Fig. 6 g, h, spinal neurons that had no activity before light showed an increase in fluorescence after the offset of blue light. This observation suggests that the termination of light-gated silencing mediated by GtACR1 can lead to depolarization of neurons within the spinal network.
We have investigated the usefulness of anion channelrhodopsins from Guillardia theta as a tool for optical control of larval zebrafish behaviour. By expressing these channels in spinal neurons of larval zebrafish and exposing the animals to light, spontaneous coiling movements could be completely and reversibly inhibited. GtACR1 appears to be a more effective tool, as ACR1-expressing fish were affected by both green and blue light at the lowest intensity tested, which is ~3 μW/mm2. GtACR2 was able to inhibit movement, but it was effective mainly with blue light at medium or high intensity; green light could inhibit movement only at high intensity. This is similar to findings in Drosophila, where 1.3 μW/mm2 of green light was sufficient to actuate GtACR1, whereas a higher intensity of blue or green light was required for GtACR2 . Halorhodopsin, which has been shown to be effective in GAL4s1020t zebrafish when actuated with amber light at ~20 mW/mm2 , appeared to be unaffected by the low intensity that could be used with GtACR-expressing embryos. This suggests that, as in Drosophila , the anion channelrhodopsins are potent tools for light-mediated reversible inhibition of neural activity in zebrafish.
The assay adopted here to establish parameters for use of GtACR1 and GtACR2 in zebrafish larvae is spontaneous coiling. Friedman et al. have found that dark-adapted AB wild-type larvae, which coil in the dark, stop coiling when exposed to light due to the presence of extraretinal opsins . We find no light-evoked inhibition of coiling in control fish that lacked GtACRs in our experiments. The reason for this difference is unclear. Regardless of the cause, this observation reflects an important factor that should be taken into consideration when designing optogenetic experiments with larval zebrafish, namely the presence of extraretinal opsins. The zebrafish has at least 42 opsins , many of which are expressed outside the retina [42, 43] and can affect behaviour independently of the visual system [44, 45]. Innate behaviours can be triggered by low levels of light  — within the range that actuates GtACRs. Thus, when performing optogenetic manipulations, an essential control is the use of siblings that do not express the channel that is being used to manipulate the cells of interest.
Although the GtACRs are potent tools, there may be some limitations that should be borne in mind. Anion channelrhodopsins may not be able to silence neural activity in all cells. As noted by Wiegert et al. , actuating these channels in cells with high levels of intracellular chloride may lead to depolarization. Thus, characterization of cellular response should be undertaken to confirm that there is loss of activity. Additionally, these channels may be useful only for short-term inhibition, in the range of seconds and possibly up to 1 min (see the companion manuscript  and Fig. 6c, d) [47, 48]. It is unclear whether they can be chronically actuated. Although the channels are sensitive, it does not seem that expression during larval development and growth has strong adverse effects. We do not find evidence that expression of the channels causes cell death, and larvae expressing GtACR1 or GtACR2 can grow to adulthood and give rise to viable offspring. Nevertheless, to control for potential developmental effects, the behaviour of siblings that do not express the transgene can be compared to that of expressing siblings, in the absence of the actuating light. The use of GtACR2, which is less sensitive than GtACR1, may also minimize potential adverse effects from ambient light. Finally, it should be noted that the termination of light-evoked silencing can lead to depolarization of neurons. This could be seen in larval zebrafish where GtACRs were expressed in spinal motor neurons, as judged by increased coiling behaviour as well as a rise in intracellular calcium of spinal neurons at the offset of light. This property of GtACRs has been observed in other light-gated chloride channels, including halorhodopsin , and it is linked to an increase in excitability due to accumulation of chloride ions inside the cell, which elevates mean spike probability and mean stimulus-evoked spike rate by changing the reversal potential of the GABAA receptor . Thus, in designing experiments where the goal is to test the effects of silencing a particular set of neurons, it would be advisable to restrict observations to the period during which light is delivered. The burst of activity that occurs after the offset of light may be problematic in a study of long-term processes, such as memory  or emotion . For acute processes, however, this property may be beneficial, as it provides a way to test the effects of activating the same set of neurons. An example of this is shown in the companion manuscript , where the direction of swimming is reversed in light versus darkness when GtACRs are expressed in the anterior thalamus.
The anion channelrhodopsins GtACR1 and GtACR2 enable optical inhibition of neural circuits in zebrafish. They are effective at illumination levels that fail to actuate NpHR, and may thus enable efficient testing of the necessity of neurons in a given behaviour.
We thank John Spudich (The University of Texas Medical School at Houston) for sharing the GtACR sequences and Claire Wyart (Institut Du Cerveau et de La Moelle Epiniere, Paris) for sharing the GAL4s1020t, UAS:NpHR-mCherry line.
Major support for GAM, RKC and SJ was from a Lee Kong Chian School of Medicine, Nanyang Technological University Start-Up Grant to SJ. ACC and SJ were supported by A*STAR Joint Council Office grant 1431AFG120. JH was supported by the A*STAR Scientific Scholars Fund. FM and ACC received support from Duke-NUS Medical School and Ministry of Education grant MOE-2013-T2-2-054. SK was supported by an NUS Graduate School for Integrative Sciences and Engineering (NGS) Scholarship. The authors were supported by a Biomedical Research Council block grant to the Institute of Molecular and Cell Biology.
Availability of materials
The transgenic lines UAS:GtACR1-eYFP and UAS:GtACR2-eYFP can be obtained from the Jesuthasan laboratory and will be deposited at the European zebrafish stock center.
SJ and ACC conceived the study; GAM, SK and SJ provided the methodology. JH and SK were responsible for the software(Python); GAM for investigation (behaviour, transgenic design, genetics), SJ for investigation (confocal microscopy) and RKC for investigation (calcium imaging). FM was responsible for resources (synthetic GtACR genes), GAM, FM and JH for data analysis (behaviour), and SJ for data analysis (calcium imaging). SJ and GAM wrote the original draft with contributions from all authors; SJ and ACC were responsible for writing and revision. JH, FM and SJ were responsible for visualization, SJ and ACC for supervision and SJ and ACC for project administration and funding acquisition. All authors read and approved the final manuscript.
Ethics approval and consent to participate
The experiments here were carried out in accordance with guidelines approved by the Institutional Animal Care and Use Committee of Biopolis, Singapore.
The authors declare that they have no competing interests.
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- Guru A, Post RJ, Ho Y-Y, Warden MR. Making sense of optogenetics. Int J Neuropsychopharmacol. 2015;18:yv079.View ArticleGoogle Scholar
- Häusser M. Optogenetics: the age of light. Nat Methods. 2014;11:1012–4.View ArticlePubMedGoogle Scholar
- Deisseroth K. Optogenetics: 10 years of microbial opsins in neuroscience. Nat Neurosci. 2015;18:1213–25.View ArticlePubMedPubMed CentralGoogle Scholar
- Sjulson L, Cassataro D, DasGupta S, Miesenböck G. Cell-specific targeting of genetically encoded tools for neuroscience. Annu Rev Genet. 2016;50:571–94.View ArticlePubMedPubMed CentralGoogle Scholar
- Boyden ES, Zhang F, Bamberg E, Nagel G, Deisseroth K. Millisecond-timescale, genetically targeted optical control of neural activity. Nat Neurosci. 2005;8:1263–8.View ArticlePubMedGoogle Scholar
- Lin JY, Lin MZ, Steinbach P, Tsien RY. Characterization of engineered channelrhodopsin variants with improved properties and kinetics. Biophys J. 2009;96:1803–14.View ArticlePubMedPubMed CentralGoogle Scholar
- Klapoetke NC, Murata Y, Kim SS, Pulver SR, Birdsey-Benson A, Cho YK, et al. Independent optical excitation of distinct neural populations. Nat Methods. 2014;11:338–46.View ArticlePubMedPubMed CentralGoogle Scholar
- Douglass AD, Kraves S, Deisseroth K, Schier AF, Engert F. Escape behavior elicited by single, channelrhodopsin-2-evoked spikes in zebrafish somatosensory neurons. Curr Biol. 2008;18:1133–7.View ArticlePubMedPubMed CentralGoogle Scholar
- Schroll C, Riemensperger T, Bucher D, Ehmer J, Völler T, Erbguth K, et al. Light-induced activation of distinct modulatory neurons triggers appetitive or aversive learning in Drosophila larvae. Curr Biol. 2006;16:1741–7.View ArticlePubMedGoogle Scholar
- Nagel G, Brauner M, Liewald JF, Adeishvili N, Bamberg E, Gottschalk A. Light activation of channelrhodopsin-2 in excitable cells of Caenorhabditis elegans triggers rapid behavioral responses. Curr Biol. 2005;15:2279–84.View ArticlePubMedGoogle Scholar
- Arenkiel BR, Peca J, Davison IG, Feliciano C, Deisseroth K, Augustine GJ, et al. In vivo light-induced activation of neural circuitry in transgenic mice expressing channelrhodopsin-2. Neuron. 2007;54:205–18.View ArticlePubMedPubMed CentralGoogle Scholar
- Zhang F, Wang L-P, Brauner M, Liewald JF, Kay K, Watzke N, et al. Multimodal fast optical interrogation of neural circuitry. Nature. 2007;446:633–9.View ArticlePubMedGoogle Scholar
- Han X, Boyden ES. Multiple-color optical activation, silencing, and desynchronization of neural activity, with single-spike temporal resolution. PLoS One. 2007;2:e299.View ArticlePubMedPubMed CentralGoogle Scholar
- El-Gaby M, Zhang Y, Wolf K, Schwiening CJ, Paulsen O, Shipton OA. Archaerhodopsin selectively and reversibly silences synaptic transmission through altered pH. Cell Rep. 2016;16:2259–68.View ArticlePubMedPubMed CentralGoogle Scholar
- Chow BY, Han X, Dobry AS, Qian X, Chuong AS, Li M, et al. High-performance genetically targetable optical neural silencing by light-driven proton pumps. Nature. 2010;463:98–102.View ArticlePubMedPubMed CentralGoogle Scholar
- Flytzanis NC, Bedbrook CN, Chiu H, Engqvist MKM, Xiao C, Chan KY, et al. Archaerhodopsin variants with enhanced voltage-sensitive fluorescence in mammalian and Caenorhabditis elegans neurons. Nat Commun. 2014;5:4894.View ArticlePubMedPubMed CentralGoogle Scholar
- Arrenberg AB, Del Bene F, Baier H. Optical control of zebrafish behavior with halorhodopsin. Proc Natl Acad Sci U S A. 2009;106:17968–73.View ArticlePubMedPubMed CentralGoogle Scholar
- Wietek J, Wiegert JS, Adeishvili N, Schneider F, Watanabe H, Tsunoda SP, et al. Conversion of channelrhodopsin into a light-gated chloride channel. Science. 2014;344:409–12.View ArticlePubMedGoogle Scholar
- Berndt A, Lee SY, Ramakrishnan C, Deisseroth K. Structure-guided transformation of channelrhodopsin into a light-activated chloride channel. Science. 2014;344:420–4.View ArticlePubMedPubMed CentralGoogle Scholar
- Wietek J, Beltramo R, Scanziani M, Hegemann P, Oertner TG, Wiegert JS. An improved chloride-conducting channelrhodopsin for light-induced inhibition of neuronal activity in vivo. Sci Rep. 2015;5:14807.View ArticlePubMedPubMed CentralGoogle Scholar
- Govorunova EG, Sineshchekov OA, Janz R, Liu X, Spudich JL. Natural light-gated anion channels: a family of microbial rhodopsins for advanced optogenetics. Science. 2015;349:647–50.View ArticlePubMedPubMed CentralGoogle Scholar
- Mohammad F, Stewart JC, Ott S, Chlebikova K, Chua JY, Koh T-W, et al. Optogenetic inhibition of behavior with anion channelrhodopsins. Nat Methods. 2017;14:271–4.View ArticlePubMedGoogle Scholar
- Kwan KM, Fujimoto E, Grabher C, Mangum BD, Hardy ME, Campbell DS, et al. The Tol2kit: a multisite gateway-based construction kit for Tol2 transposon transgenesis constructs. Dev Dyn. 2007;236:3088–99.View ArticlePubMedGoogle Scholar
- Kawakami K, Shima A, Kawakami N. Identification of a functional transposase of the Tol2 element, an Ac-like element from the Japanese medaka fish, and its transposition in the zebrafish germ lineage. Proc Natl Acad Sci U S A. 2000;97:11403–8.View ArticlePubMedPubMed CentralGoogle Scholar
- Wolf S DA, Bertoni T, Böhm UL, Bormuth V, Candelier R, Karpenko S, et al. Sensorimotor computation underlying phototaxis in zebrafish. Nat Commun. 2017;8:651.Google Scholar
- Hong E, Santhakumar K, Akitake CA, Ahn SJ, Thisse C, Thisse B, et al. Cholinergic left-right asymmetry in the habenulo-interpeduncular pathway. Proc Natl Acad Sci U S A. 2013;110:21171–6.View ArticlePubMedPubMed CentralGoogle Scholar
- Scott EK, Baier H. The cellular architecture of the larval zebrafish tectum, as revealed by gal4 enhancer trap lines. Front Neural Circuits. 2009;3:13.View ArticlePubMedPubMed CentralGoogle Scholar
- Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, et al. Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012;9:676–82.View ArticlePubMedGoogle Scholar
- Altman D, Machin D, Bryant T, Gardner S. Statistics with confidence: confidence interval and statistical guidelines. Bristol: BMJ Books; 2000.Google Scholar
- Claridge-Chang A, Assam PN. Estimation statistics should replace significance testing. Nat Methods. 2016;13:108–9.View ArticlePubMedGoogle Scholar
- Cumming G. Understanding the new statistics effect sizes, confidence intervals, and meta-analysis. New York: Routledge; 2012.Google Scholar
- Efron B. Bootstrap methods: another look at the jackknife. Ann Stat. 1979;7:1–26.View ArticleGoogle Scholar
- DiCiccio TJ, Efron B. Bootstrap confidence intervals. Stat Sci Institute of Mathematical Statistics. 1996;11:189–212.Google Scholar
- Thevenaz P, Ruttimann UE, Unser M. A pyramid approach to subpixel registration based on intensity. IEEE Trans Image Process. 1998;7:27–41.View ArticlePubMedGoogle Scholar
- Cheng RK, Krishnan S, Lin Q, Kibat C, Jesuthasan S. Characterization of a thalamic nucleus mediating habenula responses to changes in ambient illumination. BMC Biol. 2017;15:104.Google Scholar
- Abrams JM, White K, Fessler LI, Steller H. Programmed cell death during Drosophila embryogenesis. Development. 1993;117:29–43.PubMedGoogle Scholar
- Saint-Amant L, Drapeau P. Time course of the development of motor behaviors in the zebrafish embryo. J Neurobiol. 1998;37:622–32.View ArticlePubMedGoogle Scholar
- Downes GB, Granato M. Supraspinal input is dispensable to generate glycine-mediated locomotive behaviors in the zebrafish embryo. J Neurobiol. 2006;66:437–51.View ArticlePubMedGoogle Scholar
- Warp E, Agarwal G, Wyart C, Friedmann D, Oldfield CS, Conner A, et al. Emergence of patterned activity in the developing zebrafish spinal cord. Curr Biol. 2012;22:93–102.View ArticlePubMedGoogle Scholar
- Friedmann D, Hoagland A, Berlin S, Isacoff EY. A spinal opsin controls early neural activity and drives a behavioral light response. Curr Biol. 2015;25:69–74.View ArticlePubMedGoogle Scholar
- Davies WIL, Tamai TK, Zheng L, Fu JK, Rihel J, Foster RG, et al. An extended family of novel vertebrate photopigments is widely expressed and displays a diversity of function. Genome Res. 2015;25:1666–79.View ArticlePubMedPubMed CentralGoogle Scholar
- Fernandes AM, Fero K, Driever W, Burgess HA. Enlightening the brain: linking deep brain photoreception with behavior and physiology. Bioessays. 2013;35:775–9.View ArticlePubMedPubMed CentralGoogle Scholar
- Fischer RM, Fontinha BM, Kirchmaier S, Steger J, Bloch S, Inoue D, et al. Co-expression of VAL- and TMT-opsins uncovers ancient photosensory interneurons and motorneurons in the vertebrate brain. PLoS Biol. 2013;11:e1001585.View ArticlePubMedPubMed CentralGoogle Scholar
- Kokel D, Dunn TW, Ahrens MB, Alshut R, Cheung CYJ, Saint-Amant L, et al. Identification of nonvisual photomotor response cells in the vertebrate hindbrain. J Neurosci. 2013;33:3834–43.View ArticlePubMedPubMed CentralGoogle Scholar
- Fernandes AM, Fero K, Arrenberg AB, Bergeron SA, Driever W, Burgess HA. Deep brain photoreceptors control light-seeking behavior in zebrafish larvae. Curr Biol. 2012;22:2042–7.View ArticlePubMedPubMed CentralGoogle Scholar
- Lin Q, Jesuthasan S. Masking of a circadian behavior in larval zebrafish involves the thalamo-habenula pathway. Sci Rep. 2017;7:4104.View ArticlePubMedPubMed CentralGoogle Scholar
- Wiegert JS, Mahn M, Prigge M, Printz Y, Yizhar O. Silencing neurons: tools, applications, and experimental constraints. Neuron. 2017;95:504–29.View ArticlePubMedGoogle Scholar
- Mattis J, Tye KM, Ferenczi EA, Ramakrishnan C, O’Shea DJ, Prakash R, et al. Principles for applying optogenetic tools derived from direct comparative analysis of microbial opsins. Nat Methods. 2011;9:159–72.View ArticlePubMedPubMed CentralGoogle Scholar
- Raimondo JV, Kay L, Ellender TJ, Akerman CJ. Optogenetic silencing strategies differ in their effects on inhibitory synaptic transmission. Nat Neurosci. 2012;15:1102–4.View ArticlePubMedPubMed CentralGoogle Scholar
- Takeuchi T, Duszkiewicz AJ, Sonneborn A, Spooner PA, Yamasaki M, Watanabe M, et al. Locus coeruleus and dopaminergic consolidation of everyday memory. Nature. 2016;537:357–62.View ArticlePubMedPubMed CentralGoogle Scholar
- Kravitz AV, Bonci A. Optogenetics, physiology, and emotions. Front Behav Neurosci. [Internet]. 2013;7:169.Google Scholar