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75 protocols using imager a2

1

Visualizing H2O2 Accumulation in Rice Plants

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To observe the H2O2 accumulation in rice plants, the leaves or the 5-cm-long leaf sheaths of the three- to five-leaf-stage seedlings were inoculated with M. oryzae strain Guy11 at the concentration of 5 × 105 conidia ml–1 as described previously (Kankanala et al., 2007 (link)). Then, the inoculated leaves or the excised epidermal layer of the leaf sheaths were incubated in 1 mg/ml 3,3′-diaminobenzidine (DAB; Sigma–Aldrich, Germany) at 22°C for 8 h. The DAB-stained leaves and leaf sheaths were cleaned in 95% ethanol and then observed under a microscope (Zeiss Imager A2, Carl Zeiss, Germany).
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2

Histological Evaluation of Tight Junction Proteins

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The brain tissue was post-fixed (4% paraformaldehyde for 72 h), dehydrated, embedded in paraffin, and sectioned at 4-μm thickness. The sections were dried at 40°C, followed by deparaffinization and rehydration using a series of ethanol solutions. The hematoxylin and eosin (H&E) staining was performed according to the manufacture’s protocol.
For in vivo protein evaluation, paraffin-embedded sections were deparaffinized and rehydrated as described above. Immunofluorescence staining was performed as previously described [13 (link),23 (link)]. The primary antibodies used in the present study were against claudin-5 (1: 200; Genetex, Irvine, CA, USA), ZO-1 (1: 100; Novus Biological, Centennial, CO, USA), occludin (1: 200; Abcam, Cambridge, MA, USA), or β-catenin (1: 100, CST, Danvers, MA, USA), followed by incubation with goat anti-rabbit or goat anti-mouse secondary fluorescein isothiocyanate-labeled antibody (1: 500; ZhongShan Golden Bridge Bio-technology, Beijing, China). Cellular nuclei were counterstained with Hoechst 33258 (Beyotime-Bio, Shanghai, China). The samples were imaged under ×200 magnification with a Zeiss Imager A2 (Zeiss, Jena, Germany).
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3

Fungal Resistance and Defense Response Assays

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We used the three‐ to five‐leaf‐stage seedlings for resistance and defence response assay. We inoculated the transgenic lines and the controls with or without the spores (1 × 105 spores/ mL) of indicated isolates by punch or spray inoculation. For resistance assays, we observed the symptom on the inoculated leaves at 5‐7 days post‐inoculation (dpi) and examined the fungal biomass as previously reported (Park et al., 2012 (link)). In brief, we extracted the DNA from the inoculated leaves and determined the relative fungal biomass by qRT‐PCR using the DNA levels of the M. oryzae MoPot2 gene against that of the rice Ubiquitin gene. For detection of H2O2 amounts, we collected the spray‐inoculated leaves at 36 hpi and placed the leaves in 3, 3’‐diaminobenzidine (DAB) (1 mg /ml, Sigma, Alorich, USA) for staining at room temperature without light treatment for 12 hours. Subsequently, we decoloured the stained leaves in 90% ethyl alcohol at 65°C several times (Xiao et al., 2003 (link)). The H2O2 accumulation was captured with a stereomicroscope (Zeiss imager A2).
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4

Differentiated P19 Cell Staining Protocol

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For differentiated P19 cells, spheres were fixed in 4% PFA in PBS for 5 minutes, washed 3 times in PBS, then stored in 20% sucrose (Sigma) in PBS overnight. Cells were stained with methylene-blue then mounted in OCT, cryosectioned at 12μm thickness, and melted directly onto glass slides. Slides were allowed to dry, washed with PBS, then cold absolute methanol for 10 minutes, followed by a PBS wash. Slides were blocked for 1 hour at room temperature in PBST (2% w/v BSA, .5% Triton X 100, PBS). Primary and secondary antibody stains were carried out in PBST. Coverslips were prepared with Vectashield (Vector Laboratories) containing DAPI. Images were taken on a Zeiss Imager.A2 with Nikon Elements Software package. Images were formatted and compiled with Adobe Photoshop.
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5

Aspergillus fumigatus Morphology and Cell Wall Analysis

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Growth of the A. fumigatus strains was carried out onto solid CM or MM at 37 °C. For morphological observation, 2 × 108 spores were inoculated into 200 ml liquid CM and incubated at 37 °C at 200 rpm, then stained with 10 μg/ml Calcofluor white (Sigma) and 1 mg/ml 4′-6-diamidino-2-phenylindole (DAPI; Sigma) as previously described36 (link), prior to fluorescence microscopy using a Zeiss Imager A2 (Zeiss, Japan). For propidium iodide (PI) staining, 2 × 108 conidia were inoculated in 200 ml of CM and incubated at 37 °C with 200 rpm. The mycelia were collected, stained with PI, and then examined under the fluorescence microscope.
For scanning electron microscopy (SEM) or transmission electron microscopy (TEM), the mycelia cultivated in liquid CM at 37 °C were collected and fixed as previously described11 (link),36 (link) prior to examining the sections with a Tecnai Spirit (120 kV) transmission electron microscope (FEI, USA). For chemical analysis of the cell wall, cell wall components were isolated and determined as previously described11 (link).
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6

Visualizing H2O2 Accumulation in Rice

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To observe the H2O2 accumulation in rice plants, three-leaf-stage seedlings were inoculated with M. oryzae strain Guy11 at the concentration of 5 × 105 conidia mL−1. At 40 hpi, leaves were collected and incubated in 1 mg/mL DAB (Sigma, Merck Life Science Co., Ltd. Shanghai, China) at 22 °C for 8 h at illumination. The DAB-stained leaves were cleaned in 95% ethanol and then observed under a microscope (Zeiss imager A2, Carl Zeiss (Chengdu) Co. Ltd, China).
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7

Transient Expression of Proteins in N. benthamiana

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The Agrobacterium strain GV3101 carrying the individual construct in the binary vector pCAMBIA1300 was incubated in LB media containing specific antibiotics (rifampin, 50 μg/mL; kanamycin, 50 μg/mL) at 28°C incubation. The bacteria were collected at 5,000 rpm for 5 min and resuspended in MMA buffer (10 mM MES, 10 mM MgCl2, and 100 μM AS). The Agrobacteria containing the expression constructs were infiltrated into leaves of N. benthamiana for transient expression assay. Leaves were examined for image acquisition by using the Zeiss fluorescence microscope (Zeiss imager A2) between 36 and 72 hpi. Western blot analyses were performed following a previous protocol (Li et al., 2017 (link)). Total proteins were extracted from equal amounts of leaves with the protein extraction buffer with 1 × loading buffer (0.05 mg/mL Bromophneil blue; 0.065 M Tris-HCl, pH 6.8; 0.02 g/mL SDS; 0.05 mL/mL 2-mercaptoethanol; 0.1 mL/mL glycerol; 1 × protease inhibitor cocktail EDTA-free, Bimake, b14002). Total proteins were separated by 10% SDS-PAGE and transferred to PVDF membrane (Millipore) by using Trans-Blot Turbo (BIO-RAD). Protein blot was hybridized with the rabbit anti-GFP to determine YFP accumulation, and membranes were stained with Ponceau S as the loading control.
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8

Immunohistochemical Analysis of Growth Factors

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Formaldehyde-fixed tissue was embedded in paraffin wax for further immunohistochemical examination. Sections were deparaffinized in xylene and passed through descending alcohol series. The antigen retrieval process was performed in citrate buffer solution (pH 6.0) for 15 min in a microwave oven at 700 W. Sections were allowed to cool at room temperature for 30 min and washed twice in phosphate buffered saline (PBS) for 5 min. Endogenous peroxidase blockage was performed in a 3% hydrogen peroxide solution for 7 min. The washed samples were incubated in Ultra V block for 8 min. Blocking solution was removed from the sections and allowed to incubate overnight at +4 °C with primary antibodies epidermal growth factor, (catalog no: ab9695, Abcam, Cambridge, UK) and fibroblast growth factor (catalog no: ab92337, Abcam, Cambridge, UK). After washing the sections in PBS, secondary antibody was applied for 20 min. The sections were washed in PBS for 2×5 min and then exposed to streptavidin-peroxidase for 20 min. Sections washed with PBS were allowed to react with 3,3′-diaminobenzidine chromogen. Counterstaining with hematoxylin was applied and after washing, the preparations were mounted. Sections were examined under a light microscope (Zeiss Imager A2, Jena, Germany)18
-20 .
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9

Histological Evaluation of Lung Tissues

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The lung tissues were fixed with 10% formalin and embedded in paraffin. The tissue sections (thickness, 4 µm) were stained with Mayer's hematoxylin (H) for 30 sec and eosin (E) for 20 sec at room temperature and Masson's trichrome (ponceau red acid magenta dye for 10 min and aniline blue for 5–10 min) at room temperature. Images of the slides were obtained using a digital camera mounted on a light microscope (Imager A2; Zeiss AG). Each H&E tissue section was given a score between 0–4 based on the area affected by interstitial inflammation, alveolar wall thickening, peribronchial inflammation and interstitial edema as follows: Score 0, ≤10%; 1, ≤30%; 2 ≤50%; 3, ≤70% and 4, ≥70%. A mean inflammation score was determined for each group of mice (19 (link)). The grade of fibrosis of each section stained with Masson's trichrome was evaluated with a modified scale of 0–8, as previously reported (20 (link)). Briefly, on a scale of 0–8, grade 0 represents normal lung and grade 8 represents total fibrous obliteration of the field. This evaluation was performed by two blind independent observers (Department of Thoracic Oncology, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China).
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10

Histological Analysis of Renal Injury

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The renal cross sections were subjected to haematoxylin and eosin (H&E) and periodic acid‐Schiff (PAS) staining. The tissue damage was examined and scored based on the percentage of damaged tubules as follows: 0, no damage; 1, <25%; 2, 25%‐50%; 3, 50%‐75%; 4, >75%. The samples were blinded to the assessor. The mean tubular injury scores for each mouse represented the average score of the 20 fields examined.28, 29, 30 The expression levels of CD3, Ki67 and CDK (Santa Cruz Biotechnology) in the kidney tissues were evaluated by immunohistochemical (IHC) staining. The digital images of stained sections were captured under a light microscope (Zeiss Imager A2).
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