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325 protocols using eclipse te2000 s

1

Automated Microscopy for Parasite Analysis

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To measure parasite size and number, images for each condition were acquired in a Nikon Eclipse TE2000-S automated widefield screening microscope using a 40× air lens (CFI PLAN APO, NA: 0.95) or in a Leica TCS SP5 microscope (©Leica Microsystems), using a 63× immersion oil lens (HCX PL APO CS, NA: 1.40-0.60). Parasite area (in μm2) was measured by drawing manually the circumference around the parasite and automatically calculated using ImageJ software (NIH). The number of parasites was counted and corrected for the number of images acquired for each condition (200-400 images) and is presented as total number of parasites per microscope field. The Nikon Eclipse TE2000-S automated widefield screening microscope was controlled by μManager software [46 ].
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2

Cell Adhesion on Polymer Films

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First, 3 × 103 cells were seeded on PBCE and BDG50 films and on CTR (glass coverslip (GC)). The time-course adhesion of both cell types on the polymer films and CTR was evaluated at the time of seeding (t = 0 min), as well as after t = 45 min and t = 2.5 h of cell seeding. Images were captured with a Canon digital camera (PowerShot G10, Canon, Tokyo, Japan) and a brightfield microscope (Eclipse-TE2000-S, Nikon, Tokyo, Japan). The cell adhesion on PBCE and BDG50 was tested also at day 3 by staining with Phalloidin and Vinculin. Fluorescence images were captured with a fluorescence microscope (Eclipse-TE2000-S, Nikon, Tokyo, Japan) equipped with an F-ViewII FireWire camera (Soft Imaging System, Olympus, Münster, Germany).
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3

Examining Spreading and Motility of Cytophaga hutchinsonii

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To examine C. hutchinsonii spreading, an aliquot of cells were transferred to an autoclaved glass slide that was covered with a thin layer of PY10 medium containing 0.6% agar, and incubated at 28°C for 2 days. The morphology of bacterial colony edges was observed by using phase contrast microscopy (Nikon Eclipse TE2000-S, Tokyo, Japan). Individual cell movement was examined essentially as described previously (Zhou et al., 2016 (link)). Briefly, the harvested cells were diluted in MMC buffer (10 mM MOPS, 4 mM MgSO4, 2 mM CaCl2, pH 7.6) to ~106 cell/ml. Five microliters of the suspension was transferred onto glass slides, and then were overlaid with about 200 μl of 1% methylcellulose in MMC buffer and placed at room temperature for 1 h. The motility of C. hutchinsonii cells was monitored with inverted phase contrast microscope (Nikon Eclipse TE2000-S), and continuous images were recorded at 1 s intervals. The images were analyzed using the ImageJ software, and Microsoft videos (7 frames/s, wmv file) were exported resulting in a 7 × faster speed than real-time replay.
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4

Monocyte Adhesion Assay on Vascular Sheet

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VS was made using RFP-hAoSMCs, GFP-hAECs and hAAFs using the procedure described in the earlier section 2.5. Then, the VS was treated with TNF-α (40 ng/mL) (Sino Biological) and Ox-LDL (50 μg/mL) (Athens Research & Technology) to initiate endothelial dysfunction. To study the monocyte adhesion on the sheet, firstly, U937 cells were cultured with Calcein Blue, AM (Invitrogen) in the dark for 30 min and then washed with PBS to remove the excess Calcein Blue, AM. Then the stained U937 cells were added to the VS with dysfunctional endothelial layer, incubated for 30 min, washed to remove the unattached U937 cells, immediately imaged using the microscope with blue fluorescence channel for the top view image (Nikon, eclipse TE2000-s). The cross-sectional image of monocytes recruited on VS with dysfunctional endothelial layer was obtained (Fig. 4E) by firstly embedding the sheet in the agarose gel and then cut agarose-embedded sheet into slices and then imaging the sliced sheet using a microscope with red fluorescence channel, green fluorescence channel, and blue fluorescence channel (Nikon, eclipse TE2000-s).
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5

Standardized immunostaining protocol

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Conventional immunostaining techniques were performed following standard protocols. Specifically, samples were fixed with 4 % formaldehyde for 10 min, then treated with PBS containing 0.25 % Triton X-100 for 10 min followed by PBS with 0.1 % Tween 20, 1 % BSA, and 22.52 mg/mL glycine for 30 min. Primary antibodies (Abcam), diluted 100 times in PBS with 0.1 % Tween 20 and 1 % BSA, were added to the samples (VSs or VSAs) and incubated overnight at 4 °C. After the removal of primary antibody, secondary antibodies (Abcam), diluted 100 times in 1 % BSA, were added and incubated for 1 h in the dark before they were imaged immediately using a fluorescent microscope. For each step, samples were washed 3 times with PBS. The immunostaining images were captured by using microscope with green fluorescence channel, red fluorescence channel or blue fluorescence channel, dependent on the fluorescent tag for the secondary antibodies (Nikon, eclipse TE2000-s). DAPI staining was imaged using microscope with blue fluorescence channel (Nikon, eclipse TE2000-s).
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6

Fluorescence Microscopy of Cell Area

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Fluorescence microscopy studies on the cell area were performed using a Nikon Eclipse TE2000-S (Nikon Instruments, Japan) inverse fluorescence microscope with a LH-M100C mercury lamp and GFP (G) bandpass filter (exc. 480, em. 535 nm). A 20x air objective and a 10x were used. Staining of the cell body was done with Calcein AM (1:100) (Sigma Aldrich, USA). Staining of the nucleus was performed using Hoechst dye (Sigma Aldrich, USA). Micrographs were processed with the Fiji distribution of ImageJ and the ZEN Imaging Software (Zeiss). The cell area of at least three independent samples was measured for all cells in the area of the micrograph at 20 °C.
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7

Mitochondrial Membrane Potential Analysis

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In our experiment, the changes of MMP were analyzed by 5,5′,6,6′-tetrachloro-1,1′,3,3′ tetraethylbenzimidazolylcarbocyanine iodide (JC-1; Calbiochem, USA) staining. Cells were seeded into 6-well plates at 1 × 105 cells/well and incubated with 2.5 and 5 mg/kg of TM for 6 h, following with another 15 min exposure to 2 μM of JC-1 at 37°C in darkness. After three washes, fluorescent color changes were analyzed using fluorescent microscopy under Nikon Eclipse TE 2000-S fluorescence microscope (20x; CCD camera; Nikon Instruments Inc., Japan).
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8

Quantifying Epithelial and Fibroblast Cells

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Adherent epithelial cells and adherent residual cells were analyzed by immunofluorescence with anti-Mucin8-FITC or fibroblast marker-FITC (Santa Cruz Biotechnology, TX, USA) and anti-HLA-G 87G-PE (Exbio). All samples were observed under a UV light microscope (Nikon Eclipse TE2000S, Nikon, Italy).
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9

Microscopic Analysis of HPH-Treated Plant Cells

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The effectiveness of the HPH treatment in disrupting plant cells was examined by conducting microscopic analysis on both the untreated and HPH-treated suspensions. Microscopic examination was performed using an optical inverted microscope (Nikon Eclipse TE 2000S, Nikon Instruments Europe B.V., Amsterdam, The Netherlands). The microscope was equipped with a polarization filter and utilized a 10× objective lens, coupled to a DS Camera Control Unit (DS–5M–L1, Nikon Instruments Europe B.V.), for image acquisition.
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10

Assessing Oxidative Stress and Apoptosis

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MG63 cells were seeded into 6-well plates at a density of 2 × 105 cells / well. The cells were then treated with 1, 2.5, or 5 μM AU for 2 h followed by 4 μM Dex or 200 μM of H2O2 for 24 h. Following the incubation, the cells were harvested, resuspended in solution at a concentration of 1×106 cells / mL, and stained with propidium iodide and/or Annexin V for 20 min at room temperature. The rate of apoptosis was measured using a Muse Cell Analyzer (Millipore, USA).
The MMP was evaluated by staining the cells with 2 μmoL / L 5,5’,6,6’-Tetrachloro-1,1’,3,3’-tetraethylbenzimidazolylcarbocyanine iodide (JC-1; Sigma-Aldrich, USA) at 37°C for 15 min in the dark. The cells were then washed three times with phosphate buffered saline (PBS) and red and green fluorescence recorded using a fluorescence microscope (20×; CCD camera, TE2000, Nikon, Japan).
Intracellular ROS was quantified by staining the cells with 10 μM 2’-7’-dichlorodihydrofluorescein diacetate (DCFH-DA, Sigma-Aldrich) for 15 min at 37°C in the dark. The cells were then washed three times with PBS and green fluorescence, which reflects the intracellular ROS level, recorded using a Nikon Eclipse TE 2000-S fluorescence microscope (Nikon, Japan).
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