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17 protocols using eclipse ni upright microscope

1

Visualizing Bacteria-Infected Macrophages

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The mouse macrophage cell line RAW 264.7 was seeded at 6 × 104 cells per well in a 24-well plate containing a 10-mm microscope cover glass (Glaswarenfabrik Karl Hecht, Sondheim vor der Rhön, Germany). The cells were infected with bacteria carrying pBSK-Km:ZsGreen in DMEM-glucose medium containing IPTG (0.5 mM) and kanamycin (50 µg/mL) for 1 h. After washing twice with PBS, the cells were incubated in PBS containing 20 μg/mL gentamycin and 50 μg/mL streptomycin for 30 min to eliminate residual extracellular bacteria. Subsequently, cells were fixed in 3% paraformaldehyde at room temperature for 30 min and then permeabilized with 0.1% Triton X-100 in PBS. After washing with PBS, the cells were counterstained with CF®647 phalloidin (Biotium, Fremont, CA, USA) to stain F-actin and DAPI (Invitrogen, Thermo Fisher Scientific, Waltham, MA, USA) to identify the nuclei. A 10-mm microscope cover glass with cells was placed and mounted on a microscope glass slide for observation by a Nikon C2Si laser confocal microscope configured with a Nikon Eclipse Ni upright microscope (Nikon, Tokyo, Japan) at a magnification of 600×. Confocal images were analyzed using 64-bit NIS-Elements AR version 4.60.00 imaging software (Nikon, Tokyo, Japan).
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2

Visualizing Lysenin Distribution in Cells

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Cells plated on glass coverslips were permeabilized with 50 µg/ml digitonin in PBS for 10 min at RT. Cells were then washed three times with PBS and incubated in blocking solution (2% BSA in PBS) for 15 min at RT. After three washings with PBS, cells were incubated with 1 µg/ml lysenin in blocking for 2 h at RT. Cells were then washed three times with PBS and incubated with rabbit lysenin antiserum (1:500 in blocking solution, 1 h at RT). Cells were washed three times with PBS and incubated with anti-rabbit AlexaFluor488 antibody (1:600 in blocking solution, 45 min at RT). After PBS washes, coverslips were mounted on a glass slide with Dako fluorescent mounting medium. The fluorescence emitted by Lysenin was detected using a NikonEclipse Ni upright microscope (400 × magnification) and a Nikon DIGITAL SIGHT DS-U1 CCD camera. Images were analyzed and fluorescence intensity was quantified using the ImageJ software. At least 20 fields were examined for each sample.
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3

Histological Examination of Metastatic Tumor

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All mice, either upon sacrifice or upon reaching the end of the study, underwent necropsy. The primary tumor site, the left lung of each mouse, and any sites of obvious extrapulmonary metastatic disease were harvested and fixed in 10% neutral-buffered formalin, embedded in paraffin, sectioned at 4 µm, and stained with hematoxylin and eosin (HE). Bony tissues were decalcified in 10% formic acid. Stained sections were visually reviewed using a Nikon Eclipse Ni upright microscope (Nikon Instruments Inc., Melville, NY) by a board-certified veterinary pathologist.
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4

Histological Analysis of Pericardial Tissue

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For histological examinations, the post-Ozaki and pre-Ozaki samples (0.5 × 0.5 cm) were fixed in 4% paraformaldehyde, embedded in paraffin, then cut into 7 µm thick sections. For Hematoxylin/Eosin (H/E) staining, pericardium sections were stained with the nuclear dye hematoxylin (Kaltek S.r.l., Padova, Italy) for 10 min and the counterstain eosin (Kaltek S.r.l.) for 1 min. For the visualization of collagen and elastic fibers, pericardium sections were stained with Weigert’s solution (Sigma-Aldrich, St. Louis, MA, USA) for 10 min, differentiated in a solution of ferric chloride (Sigma-Aldrich), then stained in van Gieson’s solution (Sigma-Aldrich) for 1 min. Images were taken with a Nikon Eclipse Ni upright microscope (Nikon Corporation, Tokyo, Japan) equipped with a 20× objective, and analyzed with the Fiji software VS5 [14 (link)].
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5

Mitochondrial Dynamics in NPA Fibroblasts

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NPA Fibroblasts were plated at a density of 3000 cells/cm2 in 6-well plates on glass coverslips and were loaded or not with SM once a week. After 30 days, cells were incubated with 125 nM MitoTracker™ Deep Red FM in complete medium for 20 min. Cells were washed three times with cold PBS and fixed with 4% (v/v) paraformaldehyde in PBS (20 min, 23 °C). Cells were stained with 0.0002% (v/v) Hoechst in PBS (5 min, 23 °C), washed with PBS, and mounted with Dako fluorescent mounting medium. The fluorescence emitted by MitoTracker™ Deep Red FM was detected using a NikonEclipse Ni upright microscope (400 × magnification) and a Nikon DIGITAL SIGHT DS-U1 CCD camera. Images were analyzed and fluorescence intensity was quantified using the ImageJ software (at least 20 fields were examined for each sample).
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6

Comparative Analysis of Columellae Morphology

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Cell morphology in the fruit central columellae from the WT, OE2, and OE3 plants was analyzed using a NIKON Eclipse Ni upright microscope (Nikon Corporation, Tokyo, Japan) at 0, 10, and 40 DAA, respectively, according to the method of Zhang et al., with some modifications [13 (link)]. After being fixed, the middle parts of the central columellae were dissected from the fruit samples and embedded in paraffin. Then 4 μm-thick sections were generated in the transverse and longitudinal directions for staining and photographing. Cell size and number per unit area were determined using Image J software (v. 1.8.0, NIH, New York, NY, USA).
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7

Multimodal Fluorescence Imaging of Fixed Cells

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Fixed RPE-1 cells were imaged using appropriate optical filters on a multifluorescent bead calibrated AxioImager Z1 ApoTome microscope system (Carl Zeiss) equipped with a 100× or a 63× lens (both PlanApo N.A.1.4) and an AxioCam MRm camera. This setup gives confocal sections on an epifluorescence microscope. Images are presented as maximal projections of z-stacks using Axiovision 4.8.2 software (Carl Zeiss).
Fixed and stained COS-7 cells were imaged using widefield fluorescence illumination on a Nikon Eclipse Ni upright microscope equipped with a Nikon DS-Qi2 camera (Nikon), an Intensilight C-HGFI precentered fiber illuminator (Nikon), ET-DAPI, ET-EGFP, and ET-mCherry filters (Chroma), controlled by Nikon NIS Br software and using a Plan Apo Lambda 60× NA 1.4 oil objective (Nikon). For presentation, images were adjusted for brightness using ImageJ 1.50b.
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8

Mitochondrial Superoxide Production Assay

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The production of mitochondrial superoxide was performed with MitoSOX Red. NPA Fibroblasts were plated at a density of 3000 cells/cm2 in 6-well plates on glass coverslips and were loaded or not with SM once a week. After 30 days, cells were incubated with 2 μM MitoSOX (10 min, 37 °C). Cells were washed three times with cold PBS and fixed with 4% (v/v) paraformaldehyde in PBS (20 min, 23 °C). Cells were stained with 0.0002% (v/v) Hoechst in PBS (5 min, 23 °C) and mounted with Dako fluorescent mounting medium. The fluorescence emitted by MitoSOX Red was detected using a NikonEclipse Ni upright microscope (400 × magnification) and a Nikon DIGITAL SIGHT DS-U1 CCD camera. Images were analyzed and fluorescence intensity was quantified using ImageJ software. At least 20 fields were examined for each sample and images analyzed as specified above.
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9

Mitochondrial Superoxide Production Assay

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The production of mitochondrial superoxide was performed with MitoSOX Red as previously reported [31, 32] . Briefly, N2a cells, cultured in six well-plate on glass coverslips, were incubated or not with OligoGM1 for 24 h. Then, cells were treated with MPTP for 6, 10 or 24 h and, sequentially, incubated with 5 μM MitoSOX (10 min, 37°C). Cells were washed three times with cold PBS and were fixed with 4% (v/v) paraformaldehyde in PBS (20 min, 23°C). Cells were stained with 0.0002% (v/v) Hoechst in PBS (5 min, 23°C) and mounted with Dako fluorescent mounting medium [33] .
The fluorescence was detected using a NikonEclipse Ni upright microscope (400x magnification) and a Nikon DIGITAL SIGHT DS-U1 CCD camera. Images were analyzed and fluorescence intensity was quantified using ImageJ software (NIH, Bethesda, USA; http://rsbweb.nih.gov/ij/). At least 20 fields were examined for each sample.
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10

Stomatal Morphology in Sedum Album

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Epidermal peels from well-watered (C3) and drought stressed (CAM) S. album leaves were prepared according to Wu et al. [68 ]. Microscope slides were visualized using a Nikon Eclipse Ni-Upright microscope with 40X differential interference contrast objective lens and images were captured with Nikon DS-Fi3 camera. Stomatal width and length was measured using program NIS-Elements and recorded in an Excel file. A minimum of 10 individual stoma from 5 leaves were examined for each time point (ZT06 and ZT22) and condition (C3 and CAM-cycling). A Student’s t-test was performed to test for significant changes in stomatal aperture.
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