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11 protocols using n sim e

1

Cellular Uptake of Rh B-labeled MPDA@Fe3O4-Era

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MPDA@Fe3O4-Era was modified by Rh B for cell imaging. 4T1 cells were seeded 12 well plate (1 ​× ​104 ​cell per well) and incubated for 24 ​h. Then, Rh B labeled MPDA@Fe3O4-Era (MPDA: 100 ​μg ​mL−1) were added to the incubation media (DMEM plus 10% FBS) at different times (0, 0.5, 1.0, 1.5, 2.0 ​h). The cells were washed with PBS for three times to remove the residual drug. The cellular internalization behavior of the MPDA@Fe3O4-Era was investigated by FCM (FACS Melody, Becton Dickinson).
To visualize the cellular uptake, 4T1 cells were co-incubated with Rh B labeled MPDA@Fe3O4-Era at a concentration of 100 ​μg ​mL−1 MPDA. After co-culture for different time (0.5, 1.0, 1.5 and 2.0 ​h), 4T1 cells were stained with DAPI for 10 ​min and washed with PBS for three times. After that, cells were imaged under a confocal laser scanning microscope (CLSM, N-SIM E, Nikon).
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2

3D Structured Illumination Microscopy of Yersinia T3SS

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We used 3D structured illumination microscopy to visualize the GFP-tagged basal body component YscD together with an antibody staining against the pore proteins YopB/D. Cells were imaged with a CFI Apochromat TIRF 100x Oil / NA 1.49 objective (Nikon, Tokio, Japan) on a Nikon N-SIM E equipped with a Ti eclipse inverted microscope (Nikon). Images were acquired using NIS Elements software steering a LU-N3-SIM 488/561/640 laser unit, an Orca flash 4.0 LT (Hamamatsu Photonics, Hamamatsu, Japan) sCMOS or Ultra EM-CCD DU-897 (Andor Technology, Belfast, Northern Ireland) camera, a Piezo z drive (Mad city labs, Wisconsin, USA), a N-SIM motorized quad band filter combined with N-SIM 488 and 561 bandpass emission filters using laser lines 488 and 561 at 100% output power and adjustable exposure times of 300–800 msec. Z-stacks were acquired at 200 nm step size, covering about 1.6–2.2 μm. Reconstruction was performed with the stack reconstruction tool (Nikon, NIS-Elements) using default parameters.
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3

Structured Illumination Microscopy for Live-Cell Imaging

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Data shown in Figs. 1 and 5 were acquired on a Zyla 4.2 sCMOS camera (Andor) with a CSU-W1 spinning disk (Yokogawa) mounted on a Ti2 eclipse microscope (Nikon). The Apo Plan 100 × oil/NA1.4 and 60 × oil/NA1.4 objectives and a 405/488/561/638 nm laser (Omicron) were used in combination with an Okolab stage top incubation chamber (Okolab) in case of live-cell experiments. For SIM (3D structured illumination microscopy) images shown in Figs. 3 and 4, an N-SIM E (Nikon) was used, built on a Ti-Eclipse microscope (Nikon). Data were acquired using a z Piezo drive (Mad city labs), an Apochromat TIRF 100 × Oil/NA 1.49 objective, an Orca flash 4.0 LT sCMOS camera (Hamamatsu), a LU-N3-SIM 488/561/640 laser unit (Nikon) and a motorized N-SIM quad band filter combined with a single 525/50 emission filter using the laser line 488 at maximum output power. Z-stacks were acquired with a step size of 200 nm. Both microscopes were controlled by NIS-Elements software (Nikon). Slice reconstruction (NIS-Elements, Nikon) was performed using reconstruction parameters IMC 0.7, HNS 0.7, OBS 0.2.
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4

Visualizing Resilin in Honeybee Arolium

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Honeybees were freshly frozen at 70°C , and then the legs with arolium were immersed in glycerine after thawing. The glycerine-coated arolium was transferred to a glass slide and covered externally with glycerine and a high-precision coverslip. Subsequently, the sample was examined with the confocal laser scanning microscopy system (N-SIM E, Nikon, Japan) equipped with four lasers (laser lines; 405 ​nm, blue; 488 ​nm, green; 561 ​nm, yellow and red; 640 ​nm, red). Finally, the resilin autofluorescence of honeybee arolium was observed using the 405 ​nm laser line, and then bright-field images and wide-field fluorescence images were captured and superimposed [25 (link)].
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5

Immunofluorescence Analysis of Autophagy Markers

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Cells were cultured on coverslips, fixed in 4% paraformaldehyde for 15 min, permeabilized with 0.1% Triton X‐100 (PBS) for 5 min, blocked with 1% (w/v) BSA (PBS) for 1 h, and then incubated with primary antibodies overnight. After washing, cells were incubated with fluorescence-labeled secondary antibody for 1 h at room temperature. The coverslips with cells were sealed with Fluor shield mounting medium with DAPI and imaged using a Super-Resolution Microscope (NIKON, N-SIM E). The number and size of p62 bodies were analyzed with the Image J software.
The primary antibodies were used: Smurf1 (Santa, sc100616; Abcam, ab57573), Keap1 (Proteintech, 10503-2-AP), Keap1 (Abcam, ab118285), p62 (Enzo, BML-PW9860), p62 (MBL, PM045), p62 (MBL, M162-3), LC3B (Sigma, L7543), LC3B (Novus, NB100-2220), NBR1 (Proteintech, 160004-1-AP), HA (MBL, M180-3), Nrf2 (Proteintech, 16396-1-AP), Flag (Sigma, F1804).
The secondary antibodies were used: Alexa Fluor® 555 goat anti-mouse IgG (Life Technologies, A21425). Alexa Fluor® 488 goat anti-rabbit IgG (Life technologies, A11008), Alexa Fluor® 555 goat anti-rabbit IgG (Life technologies, A21428), Alexa Fluor® 488 goat anti-mouse IgG (Life technologies, A11001), Alexa Fluor® 647 goat anti-mouse IgG (Abcam, ab150115), Alexa Fluor® 647 donkey anti-goat IgG (Abcam, ab150131), Alexa Fluor® 405 goat anti-rabbit IgG (Abcam, ab175652).
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6

Brain Tissue Preparation for Amyloid-Beta Imaging

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After the imaging of in vivo leakiness, the brains were fixed in 4% paraformaldehyde solution and removed after 48 h. Sucrose (30%) was added overnight for dehydration after brain fixation. They were then embedded with optimal cutting temperature (OCT) compound and sliced in 5 μm-thick transverse sections by a freezing microtome. Then, slices were incubated with 10% skimmed milk for 2 h, then incubated with anti-Aβ antibody (1:250 dilution) overnight. Alexa Fluor 488 or 647-conjugated secondary antibody (1:250 dilution) was used for fluorescence detection. DAPI was used for the visualization of nuclei and EBD was also observed at 555 nm with a super-resolution laser confocal microscope (Nikon, N-SIME).
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7

Visualizing PS Nanoplastic Effects on HUVECs

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HUVECs were seeded in confocal dishes at a density of 8 × 104 cells/well and cultivated for 24 h. Cells were treated with PS nanoplastic (0.05 or 0.5 mg/mL) for 6 h. Then, cells were stained with DAPI (200 μL) for 10 min. After washing with PBS three times, morphological features of the cells were captured using a confocal fluorescence microscope (Nikon, N-SIM E).
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8

Multimodal Imaging Techniques for Comprehensive Analysis

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To obtain confocal laser scanning micrographs, a Leica TCS‐SP5 system was used. Micrographs were acquired using a 40× 1.2 NA oil immersion objective with a voxel size of 189 × 189 × 500 nm (xyz). For whole‐slide near‐infrared imaging, an Olympus FV3000 system with a 20×, 0.8 NA air objective equipped with a 405, 488, 561 and 640 nm laser lines and an external NIR‐unit with a 730 nm laser line was used. The whole section was imaged as tiled stacks over 2 µm with a voxel size of 222 × 222 × 500 nm. Tile data were stitched within the Olympus FV3000 CellSense software. For super‐resolution 3D‐structured illumination microscopy, a Zeiss Elyra PS.1 system (Carl Zeiss Microsystems) or a Nikon N‐SIM‐E was used as described before.3 Whole‐slide images of PAS‐stained sections were acquired on a Leica SCN400 slidescanner. SCN files were imported and processed with QuPath (v0.3.0).
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9

Stx1B Labeling of Red Blood Cells

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RBCs were labeled with CellMask deep red stain (1:3000) for 15 min at rt and washed with PBS by centrifugation at 800× g for 10 min. Pelleted RBCs 4 × 105 cells/well were dissolved in FluoroBrite DMEM and added to a final volume of 300 µL/well in 8-well chamber slides. Stx1B:Alexa-488 (10 ng/mL, this concentration was optimized to achieve a low fluorescent background and a detectible Stx1B signal) was added to the cell medium during live cell imaging. Cells were imaged in a Nikon Ti-E microscope (×100 oil objective) equipped with N-SIM E (Nikon Instruments Inc., Tokyo, Japan) and a Hamamatsu Flash 4 camera (Hamamatsu photonics, Shizuoka, Japan) using NIS elements AR software V.5.11.01 (Nikon Instruments Inc.).
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10

High-Resolution 3D Imaging of Cellular Structures

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Cells were processed for IF as described above with the following changes: anti–protein A (1:3000), YL1/2 (1:3000), TAC102 (1:10,000) and Alexa Fluor 647 goat α-mouse 1:1000, Alexa Fluor 488 goat α-rabbit 1:250, and Alexa Fluor 546 goat α-rat 1:400 secondary. Three-dimensional SIM (3D-SIM) was performed using a Nikon N-SIM E superresolution microscope equipped with an ORCA-Flash 4.0 sCMOS camera (Hamamatsu Photonics K.K.) and a CFI SR Apochromat TIRF 100× oil-objective (NA 1.49) lens. Z-stacks (6 μm, 240 nm thickness each) were acquired using the NIS-Elements Ar software. Image slices were reconstructed default software parameters and deconvolved using the Automatic method in NSIM modality. The 3D SIM videos display a top-down x,y coordinate view, then rotate along the y-axis to show three-dimensionality on the x-axis and z-axis, and finally along various transverse rotations for a complete 360° view. Videos were created using the Movie Maker option in the NIS-Elements Ar software at 50% volume zoom, high-resolution setting and were projected using alpha blending mode.
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