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1

Meiotic Chromosome Immunostaining in Yeast

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Immunostaining of yeast meiotic nuclear spreads was performed as described [10 (link)]. Stained samples were observed using an epifluorescence microscope (Zeiss Axioskop 2) with LED fluorescence light sources (X-Cite; Excelitas Technologies) and a 100× objective (Zeiss AxioPlan, NA1.4). Images were captured with a CCD camera (Retiga; Qimaging) and processed using IP lab (Silicon) and Photoshop (Adobe). Antibodies used in these assays were anti-Hop1 (1:1000) and anti-Hop1-pT318 (1:500).
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2

Imaging and Analysis of Oocyte Morphology

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Prior to imaging, oocytes were washed in a petri dish containing ND96 solution for 1 minute. Once the wash step was completed, oocytes were then submerged in ND96 storage solution and placed in a glass dish on the microscope stage (BX51WI, Olympus, Tokyo, Japan). Fluorescent images were taken with a metal halide light source (X-Cite, Excelitas Technologies, Waltham, MA, USA), a FITC 5058A-OMF filtercube (Semrock, IDEX Corp., Lake Forest, IL, USA), NIKON LU Plan Fluor 5X/0.15 objective (Nikon, Tokyo, Japan), thermoelectrically cooled charge-coupled device (CCD) camera (ORCA-ER, Hamamatsu Photonics, Hamamatsu City, Japan) and recorded using HCImageLive software (Hamamatsu Photonics, Hamamatsu City, Japan). Fluorescence intensity was measured in the area corresponding to the oocyte’s vegetal pole region of interest (ROI). The ROI fluorescence corresponded to an average intensity of the similarly sized ROIs. Brightfield imaging was recorded using a halogen lamp attached to the microscope. Images were analyzed for circularity through ImageJ software. Circular shapes with measurement values closer to 1.0 indicate perfect circles while values closer to 0.0 indicate elongated polygons.
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3

Photolysis of Neurotransmitters in MGCs

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MNI-glutamate (2 mM, Tocris Biosciences) and RuBi-GABA (5–10 μM, R&D Systems) were puffed onto the tissue from a glass pipette. Photolysis of MNI-glutamate and RuBi-GABA was performed with light from a mercury arc lamp (X-cite, Excelitas Technologies). Light was delivered to the entire tissue in 50 ms pulses through the data-acquisition software (Symphony, Symphony-DAS, Seattle, USA). MGCs were identified based on their spike responses as shown in Figure 1 for fovea and periphery. Light-evoked responses were blocked by perfusing with a solution containing cadmium chloride (200 μM). Responses to uncaged GABA and glutamate were measured at the excitatory and inhibitory reversal potentials. A limitation in quantitative interpretation of these experiments is that previous studies have shown that MNI-glutamate can inhibit GABA receptors (Fino et al., 2009 (link); Maier et al., 2005 (link)). This could explain why the amplitude of GABA-mediated current is smaller than expected from the immunohistochemical analysis for both foveal and peripheral MGCs. Nonetheless, the relative amplitude of inhibitory to excitatory current is larger for peripheral MGCs compared to their foveal counterparts, consistent with the rest of our experiments.
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4

Quantifying Mitochondrial Light Exposure

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We employed an Olympus MVX stereomicroscope to expose worms to blue light using X-Cite® (Excelitas Technologies Corp., Waltham, MA) illumination filtered through a GFP filter set (470-nm excitation ± 20-nm; Chroma, Bellows Falls, VT). Worms were restricted by suspending them in a 10 μL drop of M9 buffer. Isolated mitochondria were also illuminated in 10 uL drop at a concentration of 25 mg/mL. Identical acquisition conditions, including optics (2x objective), magnification (4x) and illumination settings on the X-Cite were used to standardize light intensity for all of the strains and conditions tested in this work. This intensity was measured empirically at 10.2 mW/mm2 using a calibrated silicon photodetector connected to an optical power meter (model number 818 P-010-12, Newport Corporation, Irvine, CA).
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5

Evoking Locomotor-like Activity in Spinal Cords

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To activate Arch, we illuminated the cord ventrally with a continuous green light (540–600 nm) from a 3-mm-diameter light guide connected to a light-emitting diode (LED, X-cite, Excelitas, Waltham, MA, USA). As previously described [18 (link)], all the lumbar segments were illuminated. We illuminated the cords with the maximum light intensity because we showed in a previous study that the stronger intensity provides the more-stable results [18 (link)]. The same protocol was applied to mice devoid of the opsins (WT or En1-GFP) in control experiments to establish whether the light itself had any effects on the evoked locomotor-like activity. For all animals, when evoking locomotor-like activity with stimulation, 3–5 trials with and without the light were obtained. For drug-induced fictive locomotion, 3-min trials were used (3–7 trials) comprising 60 s prelight, 60 s with the light on, and 60 s postlight.
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6

Optogenetic Stimulation of Spinal Cords

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The protocol for activating the opsins was a control period of 60 s in the absence of light, 60 s with the light turned on and a recovery period of 60 s. Spinal cords expressing archaerhodopsin or halorhodopsin were stimulated with continuous green light (540–600 nm) applied from a 3 mm diameter light guide connected to a light emitting diode (X-Cite, Excelitas Technologies) positioned over the ventral surface of the cord to illuminate all the lumbar segments. In one set of experiments (Figure 4—figure supplement 3), we applied the green light to the rostral lumbar and caudal thoracic segments (leaving the L5 segment unilluminated). In another set of experiments (Figure 2—figure supplement 2), the light intensity was varied and the cord was illuminated from either the dorsal or the ventral side. Animals expressing channelrhodopsin were stimulated with a 60 s train (1 ms at 100 Hz) of blue light (415–475 nm) delivered using the same apparatus. We also used the same protocols on wild type and ChAT-EGFP cords to establish whether the light itself exerted any effects on the locomotor-like rhythm.
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7

Immunostaining Analysis of Yeast Meiotic Nuclei

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Cytological analysis by immunostaining of yeast meiotic nuclear spreads was performed as described (Shinohara et al. 2008 (link)). Stained samples were observed using an epifluorescence microscope (Axioskop2, Zeiss), with LED fluorescence light sources (X-Cite; Excelitas Technologies), and a 100 × objective (Axioplan, NA1.4, Zeiss). Images were captured with a CCD camera (Retiga, Qimaging), and processed using iVision (BioVision Technologies) and Photoshop (Adobe) software. More than 100 nuclei were counted for each sample, and more than five foci-positive nucleus in a cell indicated a focus-positive cell. Antibodies used for this study were anti-Zip1 [rat, 1:500 (Shinohara et al. 2008 (link))], anti-Rad51 [rabbit, 1:500 (Shinohara et al. 2015 ) or guinea pig, 1:500 (Shinohara et al. 2000 (link))], and anti-Dmc1 [rabbit, 1:500 (Hayase et al. 2004 (link))].
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8

NMJ Morphology and Myofiber Quantification

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An Olympus Fluoview FV 300 confocal system featuring three lasers and an Olympus BX60 fluorescent microscope (Olympus America, Melville, NY) was used to collect, and store, images of NMJs. Using a 100x oil immersion objective, it was initially established that the entire NMJ was within the longitudinal borders of the myofiber and that damage to the structure had not occurred during sectioning. A detailed image of the entire NMJ was constructed from a z-series of scans taken at 0.5 μm thick increments. Digitized, two-dimensional images of NMJs were stored on the system’s hard drive and later quantified with the Image-Pro Plus software (Media Cybernetics, Silver Spring, MD). In each muscle, 10–12 NMJs were quantified and measurements were averaged to represent NMJ morphology within that muscle.
In the quantification of myofiber profiles, an Olympus BX41 microscope equipped with fluorescence capacity (X-Cite, Excelitas Technologies, Ottawa, Canada) was used in conjunction with Infinity Analyze software (Lumenera Corporation, Ottawa, Canada). A random sample of 125–150 myofibers from each muscle was analyzed to determine average myofiber size (cross-sectional area), fiber type composition (% of each fiber type analyzed for that muscle), as well as percentage of total myofiber area measured that was occupied by each individual fiber type.
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9

Yeast Meiotic Nuclear Spread Immunostaining

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Immunostaining of yeast meiotic nuclear spreads was performed as previously described (SHINOHARA et al. 2015) . Stained samples were observed under epifluorescence using the Axioskop 2 microscope equipped with light-emitting diode fluorescence light sources (X-Cite; Excelitas Technologies) and a 100× objective (AxioPlan, NA1.4, Carl Zeiss). Images were captured with a CCD camera (Retiga; Qimaging) and processed using iVision (BioVision Technologies) and Photoshop (Adobe). The antibodies used in these assays were anti-Hop1 (IWASAKI et al. 2016) (guinea pig, 1:500) and anti-Hop1-pT318(IWASAKI et al. 2016) (rabbit, 1:500), anti-Red1 (chicken, 1:500) (SHINOHARA et al. 2008 ) and anti-Rec8 (rabbit, 1:1000) (ZHU et al. 2010) . Nuclei containing more than five foci were counted as focus-positive.
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10

Imaging of AWB neuron dynamics

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Imaging the AWB pair of neurons was performed using an Olympus IX-83 inverted microscope equipped with a Photometrics EMCCD camera and a × 40 magnification (0.95 NA) Olympus objective. A dual band filter (Chroma 59012) and a double-led illumination source (X-cite, Lumen Dynamics) were used to allow fast iterative imaging of the green and the red channels intermittently. Hardware was controlled using Micro-Manager73 (link). Red dye (Rhodamine) was used to quantify the temporal concentrations of TT or DA. Movies, imaged at a frame rate of 1.4 Hz, were analyzed using MATLAB scripts developed in-house to extract neural activity.
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