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9 protocols using plan apo 20x

1

Immunofluorescence Imaging of Mitotic Cells

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Cells were grown on plain glass or FBN-coated or gelatin-coated coverslips. For analysis, cells were either fixed in cold methanol followed by 4% paraformaldehyde, blocked with 10% FBS in PBS-T, or cold methanol containing 1% paraformaldehyde, blocked with 20% goat serum in antibody diluting buffer (Abdil; TBS, pH 7.4, 1% BSA, 0.1% Triton X-100, and 0.1% sodium azide) before incubating with the specified primary antibodies. Coverslips were mounted onto slides using Prolong Gold anti-fade mounting medium with DAPI (Molecular Probes). Images were acquired with a microscope (Axio Imager Z1; Carl Zeiss) equipped with CSU22 unit (Yokogawa Corporation of America) and CoolSnap HQ2 camera (Photometrics) controlled by SlideBook software or a Ti-E inverted microscope (Nikon Instruments) with a Clara cooled charge-coupled device (CCD) camera, Spectra-X light engine (Lumencore) (Andor) controlled by NIS Elements software (Nikon Instruments). Imaging of z stacks with 0.3 – 0.7 μm steps covering the entire volume of the mitotic apparatus were collected with a Plan-Apochromatic 1.40 NA 60× or 100x immersion oil objective lens. Live-cell imaging of cells in CO2-independent media (Gibco) utilized Nikon Plan Apo 20X or 40X DIC N2 0.75 NA objectives and an environmental chamber at 37°C.
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2

Immunofluorescence Imaging of Mitotic Apparatus

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Cells were grown on plain glass or FBNcoated or gelatin-coated coverslips. For analysis, cells were either fixed in cold methanol followed by 4% paraformaldehyde, blocked with 10% FBS in PBS-T, or cold methanol containing 1% paraformaldehyde, blocked with 20% goat serum in antibody diluting buffer (Abdil; TBS, pH 7.4, 1% BSA, 0.1% Triton X-100, and 0.1% sodium azide) before incubating with the specified primary antibodies. Coverslips were mounted onto slides using Prolong Gold anti-fade mounting medium with DAPI (Molecular Probes). Images were acquired with a microscope (Axio Imager Z1; Carl Zeiss) equipped with CSU22 unit (Yokogawa Corporation of America) and CoolSnap HQ2 camera (Photometrics) controlled by SlideBook software or a Ti-E inverted microscope (Nikon Instruments) with a Clara cooled charge-coupled device (CCD) camera, Spectra-X light engine (Lumencore) (Andor) controlled by NIS Elements software (Nikon Instruments). Imaging of z stacks with 0.3 -0.7 µm steps covering the entire volume of the mitotic apparatus were collected with a Plan-Apochromatic 1.40 NA 60× or 100x immersion oil objective lens. Live-cell imaging of cells in CO2independent media (Gibco) utilized Nikon Plan Apo 20X or 40X DIC N2 0.75 NA objectives and an environmental chamber at 37 o C.
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3

Fluorescence Imaging of C. elegans

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Fluorescence imaging was done by using a Nikon eclipse 90i microscope equipped with a Nikon Plan Apo 20x, 40x, 60x, and 100x oil objective (N.A. = 1.40), and a Photometrics Coolsnap ES2 camera or a Hamamatsu Orca Flash LT + CMOS camera. L4 animals were transferred to a fresh NGM plate seeded with OP50 bacterial lawn and were stored in a 20 °C incubator for 24 h prior to imaging. Adult animals were paralyzed with 30 mg/ml 2, 3- Butanedione monoxime (BDM, Sigma) in M9 buffer, and then mounted on 2% agarose imaging pad. Metamorph 7.0 software (Universal Imaging) was used to capture image stacks and to obtain maximum intensity projections. All images were captured from left or right laterally positioned animals facing up. Fluorescence imaging of AVL and hmc were captured from the neck region where the terminal bulb of the pharynx is located. To analyze the ablation of hmc in N2 and hlh-8, GFP was expressed in both AVL and hmc (Pnmur-3::GFP) and the neck region was imaged in adult animals.
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4

Quantitative Analysis of Autophagy and Mitophagy Proteins in Motor Neurons

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The signal intensities of autophagy- and mitophagy-related proteins in motor neurons were measured using the method described in our previous publication (Chen et al., 2011 (link)). In brief, confocal images were obtained using Nikon A1R confocal microscope using PlanApo 20x, NA = 0.75 or PlanFluor 40x, NA = 1.30 lenses. The circumference of the motor neuron cell bodies in the lumbar spinal cord transverse sections was defined by the anti-choline acetyltransferase staining patterns. The average signal intensity within motor neurons was measured using the Show Region Statistics function in MetaMorph software ver. 7.0 (Molecular Devices).
The signal intensities of ATP synthase β subunit in the presynaptic terminals of NMJs were measured using the method described above. The presynaptic terminals of NMJs in the muscle sections were defined by anti-neurofilament and anti-synaptophysin staining patterns. The average signal intensity within the presynaptic terminals of NMJs was measured using the Show Region Statistics function in MetaMorph software. The observer was blinded for the genotype.
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5

Immunofluorescence Staining of Cultured Cells

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Cells were seeded and cultured on Matrigel-coated glass-bottom culture dishes (MatTek, 12- or 24-well dishes) for differentiation. Cultured cells were then washed with PBS once then fixed with BD Cytofix at 4°C for 15 min. Cells were then permeabilized with 0.2% Triton X-100 (in PBS) at room temperature for 30 min. Cells were then blocked with blocking buffer (2%BSA and 1%FBS in PBS) for 1 h at room temperature followed by staining with primary antibody diluted in blocking buffer at 4°C overnight. The next day, the cells were washed three times with the blocking buffer before being incubated with AlexaFluor secondary antibodies (Thermo Fisher Scientific, 1:1000 dilutions in blocking buffer) and DAPI or Hoechst 33342 (Sigma, Cat. No. B2261) for 1 h at room temperature. Cells were then washed three times with the blocking buffer and ready for imaging. All the primary antibodies used in this study can be found in the Key Resources Table. Immunofluorescence images were collected using a Nikon A1R laser scanning confocal microscope with Plan Apo 10x, Plan Fluor 20x Ph1 DLL, or Plan Apo 20x DIC M objectives. Images were processed using NIS Elements or ImageJ. Z stacks are presented as maximum intensity projection images.
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6

Immunofluorescence Staining Protocol

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Samples were permeabilized and blocked in incubation buffer (0.25 % Triton X-100 and 1% bovine serum albumin in PBS) for 60 minutes. Samples were then treated with primary antibodies (see Table S1) in incubation buffer either at 4°C overnight or four hours at room temperature. Samples were rinsed with wash buffer (0.05% Triton X-100 in PBS; 2 x 60 minutes) and treated with incubation buffer at least 60 additional minutes at room temperature. Samples were treated with 1:200 secondary antibodies (Alexa-conjugated, Thermo Fisher Scientific, USA) and 5μg/mL DAPI (4′6-Diamidino-2-Phenylindole Dihydrochloride, MP Biomedicals, 157574) in incubation buffer overnight at 4°C or at least two hours at room temperature. Samples were mounted by adding a drop of Aqua Polymount solution (Polysciences, Inc.) to the well and placing a round glass coverslip over the top. The mounted samples were stored overnight at 4°C and then sealed around the edges with fingernail sealant until imaging.
Confocal immunofluorescence microscopy images were collected using a Nikon A1R laser scanning confocal microscope with Plan Apo 10x, Plan Fluor 20x Ph1 DLL, or Plan Apo 20x DIC M objectives. Images were processed using NIS Elements and ImageJ. Some z-stacks were aligned using the “Align Current ND Document” (NIS Elements) before creating maximum projection images.
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7

Confocal and TIRF Microscopy for Cochlear Imaging

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Images were captured on a Nikon C2+ or A1R confocal microscope with Plan Fluor 10X and Plan Apo 20X objectives (Nikon) controlled by NIS Element software. For TNM imaging, a Plan Apo 60X oil objective (Nikon) was used. Z-stack images were taken with 0.4 μm intervals and 3D images reconstructed using NIS Element software. Basilar membrane length was measured using ImageJ, and the numbers of remaining OHCs determined. A mouse cochlear place-frequency map68 (link) was used to determine the corresponding frequencies. An Andor XDI Revolution microscope with Apo TIRF 100X oil objective (Nikon) was used for TIRF imaging.
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8

Immunofluorescence Staining of Cultured Cells

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Cells were seeded and cultured on Matrigel-coated glass-bottom culture dishes (MatTek, 12- or 24-well dishes) for differentiation. Cultured cells were then washed with PBS once then fixed with BD Cytofix at 4°C for 15 min. Cells were then permeabilized with 0.2% Triton X-100 (in PBS) at room temperature for 30 min. Cells were then blocked with blocking buffer (2%BSA and 1%FBS in PBS) for 1 h at room temperature followed by staining with primary antibody diluted in blocking buffer at 4°C overnight. The next day, the cells were washed three times with the blocking buffer before being incubated with AlexaFluor secondary antibodies (Thermo Fisher Scientific, 1:1000 dilutions in blocking buffer) and DAPI or Hoechst 33342 (Sigma, Cat. No. B2261) for 1 h at room temperature. Cells were then washed three times with the blocking buffer and ready for imaging. All the primary antibodies used in this study can be found in the Key Resources Table. Immunofluorescence images were collected using a Nikon A1R laser scanning confocal microscope with Plan Apo 10x, Plan Fluor 20x Ph1 DLL, or Plan Apo 20x DIC M objectives. Images were processed using NIS Elements or ImageJ. Z stacks are presented as maximum intensity projection images.
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9

Immunohistochemical Analysis of Prestin Expression in Mouse Cochlea

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Mice were cardiac perfused with 4% paraformaldehyde and cochleae extracted. After post-fixation and decalcification, cochleae were dissected following the Eaton-Peabody Laboratory cochlear dissection protocol [28 (link)]. In order to detect prestin, N-terminal prestin rabbit antisera [58 (link)] was used at 1:1000 with goat anti-rabbit Alexa Fluor 488 (Thermo) as the secondary antibody at 1:500. Alexa 546-conjugated phalloidin and Hoechst 33342 (Thermo) were also used to stain actin and nuclei, respectively, as described before [45 (link)]. Stained cochlear sections were mounted onto slides using Dako fluorescent mounting medium (Agilent). Images were captured on a Nikon A1R confocal microscope with Plan Fluor 10X and Plan Apo 20X objectives (Nikon) controlled by NIS Element software. Basilar membrane length was measured using ImageJ, and the numbers of remaining OHCs determined. A mouse cochlear place-frequency map [32 (link)] was used to determine the corresponding frequencies.
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