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20 protocols using plan apochromat 63 1.40 oil dic m27

1

Confocal Microscopy Imaging Protocol

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Stained coverslips were examined with a Zeiss LSM 710, or 780 confocal microscope (Carl Zeiss) equipped with an Ar laser multiline (458/488/514 nm), a DPSS-561 10 (561 nm), a laser diode 405-30 CW (405 nm), and a HeNe laser (633 nm). The objective used was a Zeiss Plan-Apochromat 63 ×/1.40 Oil DIC M27 (Carl Zeiss). Image processing was performed with ImageJ software (version 1.52p). Intensity settings for the relevant channels were kept constant during imaging. Images shown in figures are representative of at least three independent experiments
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Confocal Microscopy of Stained Samples

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Stained coverslips were examined with a Zeiss LSM 780 confocal microscope (Carl Zeiss) equipped with an Ar laser multiline (458/488/514 nm), a DPSS‐561 10 (561 nm), a laser diode 405‐30 CW (405 nm), and a HeNe laser (633 nm). The objective used was a Zeiss Plan‐Apochromat 63×/1.40 Oil DIC M27 (Carl Zeiss). Intensity settings for the relevant channels were kept constant during imaging. Image processing was performed with ImageJ software (National Institutes of Health).
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Intracellular ROS and NO Quantification

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Intracellular ROS and NO production ([ROS]i, [NO]i) in atrial CM were measured using the superoxide indicator dihydroethidium (DHE) and diaminofluorescein-FM diacetate (DAF-FM), respectively. CM were stained with 5 µM DHE at room temperature or with 5 µM DAF-FM at 37°C for 30 min in darkness and then washed with a low-Ca2+ modified Tyrode solution. [ROS]i and [NO]i were recorded in resting (non-stimulated) CM within 20 min after staining using a confocal laser scanning microscopy system (LSM 710, Carl Zeiss, Jena, Germany) with a 63× oil-immersion objective (Plan-Apochromat 63×/1.40 Oil DIC M27) and Zen 2010 software. The DHE was excited optically using Ar-laser at 405 nm, and emission was collected at 410–480 nm. The DAF-FM was excited using Ar-laser at 488 nm. The intensity of emitted fluorescence was collected at 495–565 nm. The analysis of confocal 2D images of stained CM was performed using FIJI ImageJ software (National Institutes of Health, Bethesda, MD, USA). To validate DHE signal stability, we also recorded the fluorescence intensity in electrically stimulated CM over a period of 20 min (25 (link)). In the end of these experiments, H2O2 (1 mM) was applied to increase ROS production (Supplementary Material Figure S1).
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4

Confocal Imaging of Multicellular Tumor Spheroids

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Laser scanning confocal imaging (Zeiss LSM 880) was performed with the microwell chip mounted in a custom holder using a 63 × oil-immersion objective (Plan-Apochromat 63 × /1.40 Oil DIC M27, Zeiss) and a pixel resolution of 512 × 512, with the pixel dimension 0.4393 × 0.4393 µm2, in combination with a pinhole size corresponding to 0.9 µm thick optical sections to allow interpolation along the z-axis and isotropic voxel size in the nuclear segmentation stage. Laser intensity and image acquisition parameters were adjusted to avoid overexposed pixels throughout the MCTS volume. Optical sections were acquired with 0.9 µm section steps and the z-stacks covered the full MCTS volume.
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5

Confocal 3D Imaging of Retinal Samples

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Confocal three-dimensional scans were taken with a Zeiss LSM 700 Axio Imager Z2 laser-scanning confocal microscope using Plan-Apochromat 63×/1.40 Oil DIC M27 or EC Plan-Neofluar 40×/1.30 Oil M27 oil-immersion objective lenses at four excitation laser lines (405 nm for Hochst, 488 nm for GFP, and 555 nm or 639 nm for opsin). All images were taken within retina’s central disk of 3 mm in diameter (the center being the optic nerve). Optical sections of 1 μm were acquired.
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6

Immunofluorescence Staining of Cells

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Cells were grown on glass cover slips in 12-well plates before fixed with 4% paraformaldehyde. Permeabilized with 0.1% Triton X-100 for 15 min, and blocked with 10% normal goat serum for 1 hour. The coverslips incubation with the primary antibody at a 1:100 dilution overnight at 4°C. FITC-or Alexa fluor-labeled anti-rabbit or anti-mouse antibody was added to the incubation. The nuclei were stained with DAPI (Beyotime). The samples were observed under ZEISS LSM 510 META confocal microscope (Carl Zeiss, Jena, Germany) and all images were captured using a 63×oil immersion objective (Plan-Apochromat 63×/1.40 Oil DIC M27).
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7

HER2 Expression Profiling using Nanobodies

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Two hundred thousand HER2 high or HER2 low expressing cells were grown on coverslips for 2 days. On the day of the assay, cells were washed with CO2-independent medium and incubated for 1.5 h at 4 °C with a 50 nM solution of a nanobody (namely 1D5, 18A12, 1D5-18A12). Unbound nanobodies were removed and cells were fixed with 4% paraformaldehyde (PFA). Bound nanobody was detected with rabbit anti-VHH K1219 (1:1000 for 1 h at RT) (QVQ, Utrecht, The Netherlands), followed by goat anti-rabbit Alexa 488 (1:1000 for 1 h at RT) (Invitrogen, Breda, The Netherlands). Cell nuclei were stained with DAPI (Roche, Almere, The Netherlands). Images were acquired using a confocal laser scanning microscope LSM700 (Carl Zeiss Microscopy GmbH) with a x63 oil objective (Plan-Apochromat 63×/1.40 Oil DIC M27). Of note, difficulties in observing the individual cellular memembranes were occasionally noticed, in particular for HCC1914, which was attributed to more pronounced rounded morphology of cells that coincided with rapid detachment of these cells.
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8

Quantitative Localization Analysis of ESCRT Proteins

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For localization studies, cells were seeded on coverslips, fixed with 3% PFA (Sigma-Aldrich) or methanol, permeabilized with 0.05% saponin in PBS and stained with antibodies. In CHMP6 overexpression experiments, cells were permeabilized with PEM buffer (80 mM K-Pipes, pH 6.8, 5 mM EGTA, and 1 mM MgCl2) before fixation.
Stained coverslips were viewed with an LSM 710 or 780 confocal microscope (Carl Zeiss) equipped with an Ar-laser multiline (458/488/514 nm), a DPSS-561 10 (561 nm), a laser diode 405–30 CW (405 nm), and an HeNe laser (633 nm). The objective used was a Plan-Apochromat 63×/1.40 oil DIC M27 (Carl Zeiss). Image processing was performed with basic software ZEN 2009 (Carl Zeiss) and ImageJ software (National Institutes of Health). CHMP4B and CHMP4C intensities at the intercellular bridge were scored manually using constant settings for the relevant channels. For CHMP6, EAP20 and α-tubulin intensity assessments values of gray intensities from 16-bit images were measured in a line along the intercellular bridge and plotted relative to the distance from the midbody identified by lack of tubulin staining. The mean intensity along the line (control set to 1) was compared between different treatments. The SEM is calculated between individual experiments.
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9

Confocal Microscopy for Imaging Fluorescent Samples

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Samples were imaged using a LSM 510 META (Carl Zeiss Jena) system equipped with a C-Apochromat 40×/1.20 W Corr M27 (WD=0.17 mm) or a Plan-Apochromat 63×/1.40 Oil DIC M27 (WD=0.19 mm) objective (Carl Zeiss Jena). The Ti:Sapphire 720-930 (Coherent Chameleon Ultra), 458, 488, 514 Ar-Ion 30 mW (Lasos LGK 7812 ML4, 577009-2125-000) and 561 DPSS 15 mW (Melles Griot, 85-YCA-010) lasers were used to excite the fluorescent dyes. DAPI was visualized by two-photon excitation at 750 nm to avoid out-of-focus bleaching, and fluorescence emission was collected between 390 and 465 nm. For IF and FISH, excitation at 488 or 561 was used depending on the conjugated dye and emission was collected between 505 and 550 nm, LP 575 nm and 710 nm, respectively. Images were processed in Imaris (Bitplane) or Image J (NIH). Maximum projections of a subset of the raw data stacks are shown. A Gaussian blur with a radius of 0.8 pixels (ImageJ) or a 3×3×3 Median filter (Imaris) were applied in some cases.
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10

Microscopic Examination of Cowpea Seed Autofluorescence

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Untreated cowpea seeds were used for microscopic examination. Five randomly selected seeds of each accession were used for research. The transverse dissection of seeds was performed with an MS-2 sledge microtome (Tochmedpribor, Kharkiv, Ukraine). Autofluorescence of anthocyanins was observed using a confocal laser scanning microscope (LSM 800, Carl Zeiss Microscopy GmbH AG, Berlin, Germany). According to the published data, anthocyanins should be registered in the red region of the spectrum [58 (link),59 (link),60 (link)]. The samples were excited at 488 nm with the emission in 620–700 nm. The objective lens Plan-Apochromat 63×/1.40 Oil DIC M27 with 63× magnification and the ZEN 2.1 software (Carl Zeiss Microscopy GmbH, Berlin, Germany) were used for image acquisition and processing.
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