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17 protocols using lsm 880 with airyscan

1

Visualizing Mono and Mixed Biofilms

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The biofilm formed by L. monocytogenes Scott A and S. aureus as mono species or mixed species was further observed by AFM. Biofilm samples were fixed by adding 1 mL of 2.5% glutaraldehyde and incubating at 4°C overnight. Then, the dehydrated samples were dried in a dry oven at 50°C for 10 min. Subsequently, all samples were scanned in the tapping mode, with the scan rate and step of 1.0 Hz and 2 μm, respectively. Rq (root mean square roughness) of the captured AFM images was analyzed by Nanoscope software (version 1.7).
The mixed-species biofilm was further observed by CLSM. After treatment, the dead and live bacterial cells were stained with propidium iodide (PI) and Syto-9 (SYT), respectively, for 30 min (LIVE/DEAD BacLight™ Bacterial Viability Kit, Molecular Probes, Invitrogen). All samples were observed by the CLSM equipment (SR-CLSM; LSM880 with Airyscan, ZEISS, Oberkochen, Germany) to capture microscopic images after treatment. The 60 × objective was used to observe nucleic acid dye fluorescence excited at 488–636 nm and emitted at 504–523 nm. The biofilm images were analyzed by the ZEN 3.1, and the structural parameters of intensity were calculated (Tan et al., 2022 (link)).
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2

Immunofluorescence Staining of Tissue and Cells

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Immunofluorescence staining was performed on tissue and cell samples. For tissue samples, slides were deparaffinized, rehydrated, and treated with sodium citrate buffer for antigen retrieval. Slides were incubated with 3% goat serum for 30 min followed by primary antibodies. Cell samples were fixed in poly‐l‐lysine polylysine (P2100, Solarbio, China), followed by permeabilization and non‐specific binding site blocking. Samples were treated at 4°C overnight with the following primary antibodies: rabbit anti‐MPO antibody, mouse anti‐NE antibody, goat anti‐shp2 antibody (ab9214, Abcam, USA), rabbit anti‐pad4 antibody (ab214810, Abcam, USA), and rabbit anti‐histone H3 (citrulline R2) antibody (ab174992, Abcam, USA). The next day, Samples were incubated with an Alexa fluorescein‐labeled secondary antibody for 2 h. DAPI (C1002, Beyotime, China) was used to stain cell nuclei. Then, samples were imaged by an inverted confocal microscope (LSM880 with airyscan, Carl Zeiss, Germany).
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3

Live-Cell Imaging in Controlled Environment

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Live-cell imaging was carried out in a temperature (37°C) and CO2-controlled environment using a Micro Confocal high-content imaging system (Molecular Devices, USA) or laser-scanning confocal LSM 880 with airy scan (Zeiss, Germany).
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4

Multimodal Imaging of Membrane Infoldings

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Wide-field fluorescence imaging was performed on inverted microscopes (IX83, Olympus) using an oil-immersion PlanApo 60× NA 1.42 objective lens. Digital still images were captured by ORCA-Flash4.0 LT+ digital CMOS camera (Hamamatsu) through the software MicroManager (Open Imaging) (62 (link)). For imaging of membrane infoldings, multiple z-stack images were captured on a confocal microscope (LSM 880 with Airyscan, Carl Zeiss) using an oil-immersion 63× NA 1.4 DIC objective lens. Images were captured with 32-channel GaAsp photomultiplier modules using ZEN 2.3 software (Carl Zeiss). All confocal z-stack images were subjected to Airyscan processing. For imaging and tracking of AChR vesicles, high-speed time-lapse images were captured at 200 ms per frame on live-SR super-resolution module on an iLas3 Ring-TIRF system (Gataca Systems). All acquisition settings (i.e., laser power and gain) were kept the same for different experimental groups in the same experiment. All acquired images were analyzed by ImageJ (NIH) or Imaris (Bitplane).
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5

FISH Assay for lncRNA HITT in LUAD

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Paraffin-embedded human tissue microarray containing 88 pairs of matched LUAD and corresponding normal control tissues (HLugA180Su03) were purchased from Shanghai Biochip (Shanghai, China). For the FISH assay, the tissue microarray was deparaffinized in xylene and rehydrated in serial dilutions of ethanol. After being washed in PBS for 5 min, the tissue microarray was treated with protein K at 37°C for 30 min. Next, the microarray was prehybridized in hybridization buffer (50% deionized formamide, 5× SSC, 5× Denhardt's, 250 μg/mL yeast tRNA, 500 μg/mL sperm DNA) at 37°C for 1 h. After that, the microarray was incubated with 200–300 ng/mL biotin-labeled anti-lncRNA HITT oligodeoxynucleotide probe at 37°C for 3 h. The microarray was then washed three times for 5 min each in 5× SSC, 2× SSC and 0.2× SSC at 37°C. After blocking in blocking buffer (10% milk dissolved in maleic acid buffer), the microarray was incubated in streptavidin Alexa Fluor 555 secondary antibody at room temperature for 1 h. DAPI was used as a nuclear counterstain. The fiuorescence was measured with a laser scanning confocal microscope (Zeiss LSM880 With Airyscan). The fluorescence signal was quantified by ImageJ software.
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6

Immunofluorescence Staining Protocol

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Cells grown on coverslips in a 24 well plate were fixed in 4% paraformaldehyde solution for 20 min after three washes in 1× PBS. After another round of washes in 1× PBS, cells were permeabilized with 0.1% Triton X-100 solution on ice for 4 min. The permeabilization solution was then removed by adding 1× PBS, following which cells were blocked in 3% BSA (Sigma-Aldrich) for 1 h. Incubation with the primary antibody was performed overnight at 4°C, followed by three washes in 1× PBS for 5 min each. Cells were then incubated with the fluorescently labeled secondary antibody for 1 h. After the cells had been washed three times with 1× PBS, DAPI was used for 5 min as a nuclei counterstain. The images were captured by a Zeiss LSM880 With Airyscan.
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7

Quantitative ROS Imaging in Diabetic Kidneys

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Kidney tissues from control or STZ-induced diabetic mice treated with or without APX-115 or losartan, were embedded as frozen block. DHE (5 µM, Molecular Probes) was applied to the freshly cut frozen kidney segments (10 µm) for 10 min at 37°C to reveal the presence of ROS with red fluorescence at 561 nm followed by DAPI staining and imaging by LSM880 with airy scan (Carl Zeiss Microscopy GmbH, 07745 Jena, Germany). Fluorescence intensities were then quantified using Image-Pro Plus 4.5 software (Media 149 Cybernetics, Silver Springs, MD, USA).
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8

Mesangial Cell Oxidative Stress Assay

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After serum starvation, mesangial cells were incubated either 5.5 mM glucose or 30 mM glucose for 24 h and then angII (1 µM, Sigma, St. Louis, MO, USA) for 30 min. To see the effect of APX-115, 1 µM APX-115 was treated for 30 min before treating high glucose. The cells were then washed with Hanks’ balanced salt solution (HBSS) and incubated for 10 min in the dark at 37°C HBSS containing 10 µM DCF-DA (Molecular probes). Fluorescence of oxidized DCF was detected using Zeiss LSM880 airy scan (Carl Zeiss Microscopy GmbH, 07745 Jena, Germany) at excitation wavelengths of 488 nm. Four fields of each cell were randomly selected and the fluorescence intensity was measured with a Zeiss vision system (LSM880 with airy scan) and the mean relative fluorescence intensity was measured by the average of random four values.
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9

Melanoma Cytoskeleton Visualization

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Melanoma cells were seeded in 35 mm dishes containing glass coverslips at a density of 5 × 105 for 8 h, then exposed to 0.5, 1 or 5 μM FBZ or media only as a control for 24 h. Cells were washed with PBS twice and fixed with 4% paraformaldehyde for 10 min at room temperature. 0.5% Triton X‐100 (Samchun chemicals, Seoul, Korea) was used for permeabilisation for 10 min and cells were blocked with 1% bovine serum albumin (MP biomedicals, Illkirch, France) for 30 min at room temperature. Cells were incubated in mouse monoclonal anti‐α‐tubulin antibody (1:500 dilution; ABclone) for 12 h at 4°C before incubating with goat anti‐mouse IgG labelled with FITC (1:500 dilution; ABclone) for 1 h at room temperature. Cells were washed with PBS and coverslips were mounted with mounting solution with DAPI (Invitrogen, California). Cells were examined by confocal microscopy using a fluorescein filter (LSM 880 with Airyscan, Carl zeiss, Germany).
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10

Immunofluorescence Staining of c-Fos in Mouse Brain

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Immunofluorescence staining was performed on different days with behavior tests. The procedures were described in previous work [24 (link)]. Briefly, 2 h after the acute drug injection, the mice were anesthetized with tribromoethanol (20 mg/kg), perfused with phosphate-buffered saline (PBS), and 4% paraformaldehyde (AR1068; Boster Biological Technology, Wuhan, China) for pre-fixation. The brain tissue was removed, placed in 4% paraformaldehyde, and stored at 4 °C for 24 h, then dehydrated with 20% and 30% sucrose solutions for 2 days. The OTC-embedded tissue was cut into 40-μm sections using a freezing microtome (CM1950; Leica, Wetzlar, Germany). After permeabilization and blocking, the sections were incubated with primary anti-c-fos antibody (1:500, rabbit, #2250; Cell Signaling Technology, Danvers, USA) at 4 °C for 20 h and then washed three times with PBS. Afterward, the sections were incubated with the secondary Alexa Fluor488-conjugated donkey anti-rabbit antibody (1:500, A21208; Invitrogen, Carlsbad, USA) at room temperature for about 2 h and washed with PBS. To stain the nuclei, 4′,6′-diamidino-2-phenylindole (DAPI, 0.1 μl/ml) was used for about 5 min. Sections were washed with PBS and covered on a glass slide. Brain slices were imaged using a confocal microscope (LSM 880 with Airyscan; Zeiss, Jena, Germany).
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