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7 protocols using image software

1

Quantifying Splenic Bcl2 Expression

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Five non-overlapping random fields (magnification: 400×; area: 0.071 mm2) of splenic tissue sections were chosen, photographed, and submitted for morphometric study. Quantification of optical color density and the mean area percentage of bcl2 immunohistochemical positive cells in DAB-stained sections was performed using Image software (Media Cybernetics).
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2

Western Blot Analysis of Colorectal Cancer Markers

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CRC tissue samples and cells were washed with ice-cold phosphate-buffered saline (PBS) 3 times and lysed in RIPA buffer supplemented with protease inhibitor. The protein concentration was determined using the bicinchoninic acid method. Equal amounts of proteins (30 µg) were separated by 15% SDS-PAGE and transferred to a PVDF membrane (Immobilon; Millipore Corp., Bedford, MA, USA). After blocking with 5% non-fat milk (diluted with phosphate-buffered saline/Tween-20, TBST) at 37°C for 1 h, the membranes were incubated with primary antibodies: anti-LRH-1 (1:1000, ab41901), anti-matrix metalloproteinase (MMP)2 (1:1,000, ab80737), anti-MMP9 (1:1,000, ab119906), anti-β-catenin (1:500, ab92514), cyclin D1 (1:1,000, ab134175), c-Myc (1:500, ab51156) and GAPDH (1:1,000, ab8245; Abcam, Cambridge, UK) at 4°C overnight. After rinsing with TBST, they were incubated with horseradish peroxidase-conjugated goat anti-mouse or rabbit immunoglobulin G antibodies (1:200; Santa Cruz Biotechnology, Inc., Santa Cruz, CA). Protein bands were detected using an enhanced chemiluminescence reagent (Pierce Biotechnology, Inc., Rockford, IL, USA). Band intensity was quantified using Image software (Media Cybernetics, Inc., Rockville, MD, USA).
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3

Cerebellar Astrocyte Quantification

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Five non-overlapping random fields (magnification: X400; area: 0.071 mm2) of each cerebellar hemisphere of each animal were chosen, photographed, and submitted for morphometric study. Quantification of optical color density and the mean area percentage of GFAP immunohistochemical positive astrocytes in DAB-stained sections was performed using Image software (Media Cybernetics). The sections for S100 were analyzed using ImageJ Software to count the immunoreactive cells in each cutting.
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4

Scratch Wound Healing Assay

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A linear scratch was made using a sterile pipet tip after growing to 90%–100% confluence. Pictures were taken of the same area of the scratch after 0 and 24 h of incubation at 37℃. The remaining area of the wound was judged by Image software (Media Cybernetics, Silver Spring, MD, USA).
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5

Cytoplasmic p65 Translocation Assay

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Primary bone marrow cells were isolated form MKR mice and seeded on glass coverslips. The cells were incubated in the absence or presence of TNFα (10 ng/mL) in combination with or without PGRN (200 ng/mL) at 4 °C overnight. Following treatment, the medium was removed and cells were fixed using cold acetone/methanol (1:1). Cells were air-dried and rehydrated following fixation. The samples were blocked with 50% goat serum for 30 min at room temperature, and incubated with primary antibody against p65 (1:50 dilution) for 1 h at room temperature. After washing, a secondary goat anti-rabbit IgG antibody conjugated with fluorescein isothiocyanate (Santa Cruz Biotechnology #SC-2012) diluted 1:100 was added for 1 hour at room temperature, and 4,6-diamidino-2-phenylindole (DAPI) was used for staining nuclei. Image software (Media Cybernetics, Rockville, MD, USA) was used to the capture images under Zeiss Axioscope A1 microscope.
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6

Gas Exchange Measurement of Seedlings

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The gas exchanges were measured from 9:00 to 11:00, using an LI-6800 portable photosynthetic system (LI-COR, Lincoln, NE, USA) equipped with a CO2 control module and a red–blue LED-light source. The photosynthetic-photon-flux density of the leaf chamber was set to 700 μmol m–2 s–1. The airflow rate in the leaf chamber was set as 700 μmol s–1. The concentration of CO2 in the reference chamber was set at 400 μmol mol–1 for the measurements. The net photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (E), intercellular CO2 concentration (Ci), and CO2 concentration in the leaf chamber (Ca) were simultaneously recorded from seven seedlings per treatment.
The leaf used to measure the gas-exchange parameters were collected, promptly immersed in N2, and stored at −80 °C. The leaves were positioned with the main veins cut out on A4 paper, and a 4 × 4 cm piece of green cardboard was added as a control. Leaf images were obtained with a digital camera (7D, Canon, Inc., Tokyo, Japan), and image software (Media Cybernetics, Silver Spring, MD, USA) was utilized to measure the leaf area.
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7

Western Blot Analysis of Stress Proteins

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Total protein extracted by RIPA lysis buffer (Thermo Scientific) was determined with an enhanced bicinchoninic acid assay kit (CWBio). The protein from each sample was separated by sodium dodecyl sulfate‐polyacrylamide gel electrophoresis and transferred to polyvinylidene difluoride membranes (CWBio). The membranes blocked with 5% non‐fat milk for 1 h at room temperature (RT) later were incubated the whole night with primary antibodies targeting HSPA6 (1:2000, ab212044, Abcam), Cyclin B1 (1:3000, ab32053, Abcam), YAP1 (1:5000, ab56701, Abcam), p‐S127‐YAP1 (1:3000, ab226760, Abcam) and β‐actin (1:5000, ab8226, Abcam) at 4°C. The membranes were washed three times with tris‐buffered saline with Tween 60 (TBST) and probed with horseradish peroxidase‐conjugated secondary antibody (1:5000) for 1.5 h at RT. Protein bands were exposed by a chemiluminescence system, and the membranes were visualized by X‐ray films (Bio‐Rad). Densitometric analysis was performed by image software (Media Cybernetics). The relative protein expression levels of proteins measured in this study were normalized to β‐actin.
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