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9 protocols using plan apo 63

1

Perfusion-Based Tissue Preservation and Imaging

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Images shown in all figures are representative of data acquired from at least N = 3 animals per experiment. Animals under deep isoflurane anesthesia were perfused transcardially with ice-cold PBS, followed by 4% paraformaldehyde (PFA) in 0.1 M PBS (pH 7.4). Before sectioning, tissues were cryoprotected by immersion overnight in 15% sucrose, followed by 24 h in 30% sucrose in PBS. Tissues were then frozen in OCT compound (Fisher) using a beaker of 2-methylbutane chilled in dry ice. Ten- or 50-µm-thick cryosections were stored at −80°C until use. Whole brains and hearts were imaged immediately after dissection using an Olympus SZX-12 with an SZX-RFL2 coaxial fluorescence attachment. Cryosections were imaged using a Leica TCS SP8X confocal microscope equipped with LAS X software and a 63× oil immersion objective (1.4 N/A). Some images were obtained using a Zeiss Axiovert 200 inverted microscope equipped with AxioVision software and a Plan-Neo 100 Å∼/1.30 and Plan-Apo 63 Å∼/1.40 oil-immersion objectives (Immersol 518F; Carl Zeiss, Inc.) or a Plan-Neofluor 20× dry objective.
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2

Quantifying Nuclear Microtubule Dynamics

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For nuclear microtubule analysis, an ROI was drawn in Fiji over the nucleus. Fiji was used to threshold α-tubulin signal, and the area of the signal was measured within the ROI. This was performed on 8 cells per field of view, with 3–6 fields per condition per experiment. For high-resolution microtubule analysis, high-resolution confocal images were acquired with a Zeiss 880 Confocal with AiryScan FAST microscope with GaAsP detector and camera (Zeiss) using a Plan-Apo 63× oil-immersion objective (NA 1.40) and 488 and 561 nm lasers. Imaging was performed at RT, and images were acquired with the Zeiss 880 software and with the AiryScan detector. Images were then processed with AiryScan. All image analysis, including Z-stack compression, was performed in Fiji. For microtubule density, an ROI was drawn at the MTOC and the cell periphery. Fiji was used to threshold α-tubulin signal, and the area of the signal was measured within the ROI. This was performed on at least 10 cells per condition per experiment. For junction analysis, the number of contacts between α-tubulin and VE-cadherin was counted and normalized to the junction length. At least 15 junctions were measured per condition per experiment.
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3

Immunofluorescence Microscopy of Cellular Lamin

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Cells were seeded on glass coverslips in 24 well plates. Cells were fixed in 4% PFA for 10 min and subsequently permeabilized for 5 min with 0.5% X-100 Triton. Cells were blocked in 0.5% skin fish gelatine for 1 h. Antibodies were diluted in the blocking solution. Primary antibodies were goat anti-lamin B1 (C-20, Santa Cruz Biotechnology, Santa Cruz, CA, USA), and mouse anti-lamin A/C (4C11) Active Motif (Carlsbad, CA, USA). Secondary antibodies used were donkey anti-mouse and donkey anti-goat conjugated to Alexa Fluor 488 and Alexa Fluor 647 (Invitrogen, Waltham, MA, USA). Cytoplasmic loading was conducted by permeabilising live cells with a 750 μg/mL solution of saponin containing a secondary goat anti rabbit IgG Alexa Fluor 546 (80 μL stock solution per 1mL of detergent solution) at 4 °C for 5 min then fixed immediately with cold 4% PFA. Samples were imaged immediately. Fixed cells were imaged on the LSM5 Zeiss Inverted 510 META laser scanning microscope (Zeiss, Oberkochen, Germany) using a Plan Apo 63 × 1.4 NA oil immersion lens. Images were acquired using Zen2009 operating software (Zeiss). Samples of cytoplasmic loading and the hormone removal experiment were imaged on a Zeiss LSM880 Airyscan using a Plan Apo 40 × 1.3 NA oil immersion lens. Images were acquired and pre-processed using ZenBlack (Zeiss). Collected images were analysed in FIJI [30 (link)].
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4

Stress Granule Imaging Protocols

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Stress granule (SG) imaging was performed using a Nikon Plan-Apo 40 × 0.95 NA air objective on a Nikon Eclipse TE2000 widefield microscope equipped with a Hamamatsu C9000-02 EM-CCD camera. All other samples, including tissue slides, were imaged using a Zeiss Plan-Apo 63 × 1.4 NA oil objective on an UltraVIEW Spinning Disk Confocal Microscope equipped with a Hamamatsu Flash 4.0v2 CMOS camera. The full dynamic range of the camera was necessary to capture intensities of large and small granules without undersampling or saturating images. All microscopes were controlled by the Volocity acquisition software (PerkinElmer).
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5

Fluorescence Recovery After Photobleaching Dynamics

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FRAP and fluorescence live cell imaging were carried out on a Zeiss (Jena) LSM780 confocal laser scanning microscope equipped with a Zeiss Plan-APO ×63–numerical aperture 1.46 oil immersion objective with environmental control (5% CO2 and humidification). Cells were cultured on 10 µg ml−1 FN-coated glass-bottom live cell imaging chambers (ibidi). For FRAP experiments, the ROI was bleached with full laser power at 488 nm for 30 iterations and fluorescence recovery was monitored for 5 min with 20 s intervals and 1% laser power for talin-GFP turnover, or was monitored for 5 min with 10 s intervals and 1% laser power for integrin α5-GFP turnover. No significant photobleaching was observed during the post-bleaching phase. FRAP data were extracted with ImageJ. Due to the rapid diffusion of cytosolic talin into the bleached area immediately after bleaching, the mean optical intensity outside adhesion was subtracted from the mean optical intensity in FAs to correct the background. FRAP curves were fitted to a one-phase association model to calculate the mobile fraction.
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6

Immunostaining of Cultured Cells

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For immunostaining, cells were cultured on glass coated with 10 µg ml−1 FN (Calbiochem) for 5 h, then fixed with cold methanol:acetone (1:1) for 5 min at −20 °C (for endogenous talin, vinculin and kindlin-2 staining) followed by 15 min rehydration in PBS at room temperature, or with 2% PFA–PBS for 15 min at room temperature (for other immunostaining). PFA-fixed cells were permeabilized when indicated with 0.1% Triton X-100–PBS for 30 min at room temperature. Fixed cells were blocked with 5% BSA in PBS for 1 h at room temperature followed by incubation with the primary antibodies in 5% BSA in PBS overnight at 4 °C and then with secondary antibodies for 1 h at room temperature. Images were collected at room temperature on a Zeiss (Jena) LSM780 confocal laser scanning microscope equipped with a Zeiss Plan-APO ×63–numerical aperture 1.46 oil immersion objective.
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7

Quantitative Analysis of Focal Contacts

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Images were taken on an inverted wide field Zeiss microscope equipped with a Plan-Apo 63× oil immersion objective with NA 1.4 using Axiovision 4.8.2 software (Carl Zeiss, Inc). For each field binning was set to 2×2 using a CoolSNAP HQ2 (Photometrics) camera and 60 z-stacks with a step size of 0.240 µm. Deconvolution was iterative with autolinear normalization for all images. Focal contacts were quantified using ImageJ. (Rasband, W.S)
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8

Quantifying Golgi Ribbon Disruption

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The cells were fixed with methanol at −30°C for 20 min or with 2% paraformaldehyde for 20 min, followed by permeabilization with 0.2% Triton X-100. After incubation with blocking buffer (0.2% Tween-20, 1 mg/ml bovine serum albumin, PBS) for 60 min at room temperature, the cells were incubated overnight at 4ºC with the indicated primary antibodies and for 1 h at room temperature with the indicated secondary antibodies. The cells were observed using a 1.4 numerical aperture CFI Plan-Apo VC 60× or Plan-Apo 63× oil immersion objective lens under a confocal laser microscope (LSM780; Carl Zeiss, Jena, Germany).
To quantify the disruption of the Golgi ribbon, the circularity index of the Golgi morphology was measured as described elsewhere (Miller et al., 2009 (link)). Briefly, a freehand selection option in ImageJ software (National Institutes of Health, Bethesda, MD) was used to outline the Golgi based on GM130 staining. Circularity index values were assigned to Golgi outlines by the ImageJ circularity plug-in (http://rsb.info.nih.gov/ij/plugins/circularity.html), where circularity = 4π(area/perimeter2). A circularity value of 1 corresponds to a perfect circle.
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9

Quantitative Analysis of Focal Contacts

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Images were taken on an inverted wide field Zeiss microscope equipped with a Plan-Apo 63× oil immersion objective with NA 1.4 using Axiovision 4.8.2 software (Carl Zeiss, Inc). For each field binning was set to 2×2 using a CoolSNAP HQ2 (Photometrics) camera and 60 z-stacks with a step size of 0.240 µm. Deconvolution was iterative with autolinear normalization for all images. Focal contacts were quantified using ImageJ. (Rasband, W.S)
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