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22 protocols using nis elements f

1

Immunofluorescence Staining of Cells

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Following infection, cells seeded on glass coverslips were washed three times with PBS prior to be fixed in 4% paraformaldehyde for 20 min and permeabilized in 0.3% Triton X-100 for 10 min. After being blocked with 3% BSA, the coverslips were incubated with primary antibodies at 4°C overnight, developed with the appropriate Alexa Fluor® 555 secondary antibody (Thermo Fisher Scientific) for 1 h and then stained with Hoechst 33258 (Beyotime) for 10 min. All photomicrographs were taken with a Nikon Eclipse Ni-U fluorescence microscope (Nikon Corporation, Tokyo, Japan) with NIS-Elements F (Nikon Corporation).
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2

Quantifying Immunohistochemical Signals

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Photomicrographs of the slides were captured using a Nikon Eclipse 80i microscope equipped with a Nikon DS-U2 camera and by using Nis Elements-F acquisition software (Nikon Co, Tokyo, Japan, version 3.0). Images were digitized at 2560 × 1920 pixels. The images were acquired at 40× magnification and processed in TIF format.
The brown color corresponding to the immunostaining on the slides was quantified as the sum area or nuclei number and Integrative Optical Density (IOD) with Image-Pro Plus 7.0 software (Media Cybernetics, Rockville, MD, USA). First, a spatial calibration of 50 µm was done for each image and the ranges of area and OD were defined in Image-Pro Plus 7.0. Second, the color corresponding to the immunohistochemical signal was segmented according to the Hue, Saturation, Intensity (HSI) model. For a better representation of the assessment of expression levels, a total of 10 random images were acquired for each slide and analyzed using Image-Pro Plus 7.0 software as described in the technical manual with some modifications [26 ].
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3

Immunohistochemical Analysis of CCTα Expression

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Two pathologists, blinded to the study, carried out the evaluation independently at x1000 magnification, using Eclipse Ni-U (Nikon, Japan) upright microscope coupled with visual circuit and NIS Elements F (Nikon) software for computer image analysis. The evaluation of CCTα expression was determined with the use of five-point evaluation scale9 (link), taking into account the intensity of colour reaction (score 0–3) and percentage amount of positive cancer cells in a given specimen (score 0–4). The final result was the product of scores obtained for the evaluation of both parameters and values from 0 to 12 were considered9 (link).
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4

TUNEL Assay for Cardiac Cell Death Analysis

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Immunostaining of cardiac tissue was performed as previously described25 (link). To analyze the cell death in mouse heart samples, terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay was performed using Click-iT®TUNEL Alexa Fluor® kit according to manufacturer’s protocol (Invitrogen, C10246). Briefly, deparaffinized samples were incubated with TdT enzyme at 37 °C for 1 h and signals were developed with reaction buffer (Alexa Fluor 594) for 30 min in dark room. After wash the samples with 3% bovine serum albumin (BSA) solution, nucleus was stained with Hoechst 33342 and analyzed with confocal microscopy. For immunocytochemistry, cells were fixed with 4% PFA for 10 min and permeabilized with 0.1% Triton X-100 in phosphate-buffered saline (PBS) for 10 min. Cells were then blocked with blocking buffer (2% BSA in 0.1% PBST) for 30 min and incubated with primary antibodies diluted in blocking buffer for overnight at 4 °C. Images were analyzed with an LSM-710 confocal microscope system (Carl Zeiss), Tissue FAXS i8 plus (TissueGnostics) or Nikon ECLIPS TE-2000U and processed with ZEN software (Carl Zeiss), TissueQuest analyzer (TissueGnostics), NIS-Elements F (Nikon) or image J software.
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5

Fluorescent Staining of Cell Clusters

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The clusters of each cell line recovered from the chip were stained with AO. The AO fluorescent dye (60 µmol/l; AAT Bioquest, Inc., Sunnyvale, CA, USA) was mixed with the sample at a proportion of 1:5, with a final concentration of 10 µmol/l. Staining was performed for 10–15 min at 25°C. A total of 10 µl sample was placed onto a glass slide and images were captured under ×40 magnification with a fluorescence microscope (Eclipse Ni; Nikon Corporation, Tokyo, Japan) with a charge-coupled device camera (DS-Ril; Nikon Corporation) and saved using NIS-Elements F (ver 4.30.01, Nikon Corporation) software. The exposure time was 80–100 ms and the optical gain was ×4.0.
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6

Histological Lung Tissue Processing

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The lung tissues were immersed in 4% paraformaldehyde for 4 h, and transferred to 70% ethanol. Individual lobes of the lung tissue biopsy specimens were placed in processing cassettes, dehydrated through a serial alcohol gradient, and embedded in paraffin wax blocks. Prior to immunostaining, 4-µm-thick lung tissue sections were dewaxed in xylene, rehydrated through decreasing concentrations of ethanol and washed in PBS, followed by staining with H&E. Following staining, the sections were dehydrated through increasing concentrations of ethanol and xylene. A fluorescence microscope (Eclipse Ni; Nikon Corporation, Tokyo, Japan; magnification ×10 and ×40) was used to visualize staining, a charge-coupled device camera (DS-Ril; Nikon Corporation) was used to capture images and images were saved using NIS-Elements F (version 4.30.01, Nikon Corporation) software.
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7

Canine Blood Smear Microscopy

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Blood was collected by venipuncture of the jugular or cephalic veins of dogs into EDTA and clot tubes for hematology and serum biochemistry, respectively. Stained blood smears were examined by oil immersion light microscopy at 1000× magnification using the Nikon Eclipse N-U microscope, fitted with the Nikon DS-Ri1 camera (Nikon Corporation, Tokyo, Japan) operated by the NIS-Elements F software package (Nikon Corporation, Tokyo, Japan). Parasites were measured and photographed. All measurements are in micrometres and are given as the range followed by the mean ± standard deviation (SD) in parentheses.
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8

Microstructure Analysis of Phenolic Compounds

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The microstructure analysis was conducted following Hernández-Carrión et al. [37 (link)], with some modifications. A Nikon ECLIPSE 80i light microscope (Nikon Co., Ltd., Tokyo, Japan) was used working in the bright field and fluorescence modes. The autofluorescence of the phenolic compounds in the samples was observed using a mercury arc lamp with a tetramethyl rhodamine filter (λex = 543/22 nm, λem = 593/40 nm) as the excitation source. Samples were visualized using 10× and 20× objective lenses. The images were captured and stored at 1280 × 1024 pixels using the microscope software (NIS-Elements F, Version 4.0, Nikon, Tokyo, Japan).
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9

Visualizing Fungal Infection Stages with Fluorescence Microscopy

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A manual inverted microscope (Ti-S; Nikon, Tokyo, Japan) equipped with a Super Plan Fluor ELWD ADM 20/0.45 was used to observe the eGFP expression in mycelia, conidia, germ tube, appressorium and invasive hyphae. eGFP was exited using a HG fiber illuminator with filter cube (Excitation Filter EX450-490, Dichroic Mirror DM505, Barrier Filter BA520, Tokyo, Japan) and images were acquired using a high-resolution color camera head DS-Ri2 (Nikon, Tokyo, Japan). All parts of the system were under the control of the NIS-elements F (Nikon, Tokyo, Japan).
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10

Histological Analysis of Conjunctival Samples

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For histological analysis, samples of conjunctiva, both freshly explanted and after treatment at 37 °C for 5 h with the different blank vehicles reported in Table 2, were fixed in 10% formaldehyde. Subsequently, the samples were embedded in paraffin and sectioned using a microtome. Staining was carried out using Harris hematoxylin/eosin. Images were taken using an optical microscope Nikon Eclipse 80i, equipped with a camera Nikon Digital Sight DS-2Mv and connected to the control software, NIS Elements F (Nikon Instruments, Calenzano, Italy).
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