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9 protocols using d eclipse c1si

1

Confocal Imaging of Cortical Layers

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All slices were imaged using a confocal microscope at 20x objective (Nikon D-eclipse C1si; Nikon Instruments, Melville, NY). Laser intensity and gain were held constant for each label across all slices. To obtain a broader field of view without losing resolution, each complete image contained 20 individual 20x images stitched together using Photoshop (Adobe Systems Inc., San Jose, CA). To control for naturally occurring variance in cell type density between cortical layers, complete images were cropped into individual layers according to Kandel et al. (2000 ). For some slices, the implanted devices extended past the cortex and into the white matter. These images were cropped at the end of layer six and the white matter was not analyzed.
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2

Immunofluorescence Staining Protocol for A549 Cells

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Immunofluorescence staining was performed as described previously.17 Briefly, A549 cells were seeded on glass slides in 12‐well plates and incubated as indicated for 24 hours. The slides were washed three times with PBS, fixed in 4% paraformaldehyde for 10 minutes and then permeabilized with 0.1% Triton X‐100 for 20 minutes. Whereafter, the cells were blocked with 3% BSA at room temperature for 1 hour and subsequently incubated with primary antibody (vimentin, 1:100; p‐Erk1/2, 1:100) at 4°C overnight. After incubation, slices were washed three times with PBS and incubated with corresponding secondary antibodies (1:200; Beyotime Institute of Biotechnology, Haimen, China). The nuclei were stained with DAPI (Beyotime Institute of Biotechnology) for 5 minutes. Samples were washed three times with PBS and mounted in antifade mounting medium, and fluorescence was detected using a confocal laser scanning microscope (Nikon D‐Eclipse C1si; Nikon Corporation, Tokyo, Japan) or a fluorescence microscope (EVOSTM Auto 2; Invitrogen, WA, USA).
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3

Immunofluorescence Staining of PCa Cells

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Immunofluorescence was carried out as previously described60 (link). PCa cells were cultured in chamber slides (Fisher Scientific, Hampton, NH), washed and fixed in 4% paraformaldehyde. After another series of washing, cells were permeabilized and blocked with 2% BSA in TBST buffer. Cells were incubated overnight at 4 °C with primary antibodies as indicated. Next, cells were incubated with Alexa Fluor® 488 secondary antibody, then stained with 4′ 6′-diamindino-2-phenylindole (DAPI) and mounting medium (Vector Laboratories, Burlingame, CA). Images were acquired under Nikon D-ECLIPSE C1si spectral laser-scanning confocal (Nikon Instruments, Melville, NY).
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4

Fluorescence Resonance Energy Transfer Analysis of Protein Interactions

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Agrobacterium harboring pBA-35S-SE-CFP and pBA-35S-PAG1-YFP were infiltrated separately or coinfiltrated into the leaves of 4-week-old tobacco plants (N. bentha). FRET assays were performed as previously described47 (link). YFP and CFP signals were captured with Olympus FV1000 confocal microscope with excitation wavelengths of 515 nm and 405 nm. ImageJ (v. 1.52a) was used for normalization and analysis. For the PAG1 and SE localization assay, stable transgenic plants were imaged on Nikon D-ECLIPSE C1si confocal laser scanning microscope.
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5

Quantitative Mast Cell Analysis

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The stained tissue sections were observed on a ZEISS Axio Imager.Z2 that was equipped with a Zeiss alpha Plan-Apochromat objective 100×/1.46 Oil DIC M27, a Zeiss Objective Plan-Apochromat 150×/1.35 Glyc DIC Corr M27, and a ZEISS Axiocam 712 color digital microscope camera. The captured images were processed with the software programs, “Zen 3.0 Light Microscopy Software Package”, “ZEN Module Bundle Intellesis & Analysis for Light Microscopy”, “ZEN Module Z Stack Hardware” (Carl Zeiss Vision, Aalen, Germany), and submitted with the final revision of the manuscript at 300 DPI. Photomicrographs were obtained in some cases with a confocal microscope, Nikon D-Eclipse C1 Si based on Nikon “Eclipse 90i”. The number of mast cells in the different areas of the ovary was determined per mm2 of tissue, using open-source software for the digital pathology image analysis, QuPath [90 (link)] (Bankhead P., et al., 2017) (Table 1).
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6

YFP Localization in dcl1-9 Mutants

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YFP signal was detected from the root tips of 7-day-old T1 dcl1–9/+; PPRP4KA-gPRP4KA-eYFP transgenic plants. PRP4KA localization was imaged on a Nikon D-ECLIPSE C1si confocal laser scanning microscope.
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7

Fluorescence Resonance Energy Transfer Analysis of Protein Interactions

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Agrobacterium harboring pBA-35S-SE-CFP and pBA-35S-PAG1-YFP were infiltrated separately or coinfiltrated into the leaves of 4-week-old tobacco plants (N. bentha). FRET assays were performed as previously described47 (link). YFP and CFP signals were captured with Olympus FV1000 confocal microscope with excitation wavelengths of 515 nm and 405 nm. ImageJ (v. 1.52a) was used for normalization and analysis. For the PAG1 and SE localization assay, stable transgenic plants were imaged on Nikon D-ECLIPSE C1si confocal laser scanning microscope.
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8

Imaging Tissue Sections with Advanced Microscopy

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Stained tissue sections were observed on a ZEISS Axio Imager.Z2 equipped with a Zeiss alpha Plan-Apochromat objective 100×/1.46 Oil DIC M27, a Zeiss Objective Plan-Apochromat 150×/1.35 Glyc DIC Corr M27, and a ZEISS Axiocam 712 color digital microscope camera. Captured images were processed with the software programs “Zen 3.0 Light Microscopy Software Package”, “ZEN Module Bundle Intellesis & Analysis for Light Microscopy”, and “ZEN Module Z Stack Hardware” (Carl Zeiss Vision, Jena, Germany) and submitted with the final revision of the manuscript at 300 DPI. Photomicrographs were obtained in some cases with a Nikon D-Eclipse C1 Si confocal microscope based on the Nikon Eclipse 90i.
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9

Tyrosine Hydroxylase Expression in Spleen

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Spleens were removed 17 days after infection, embedded in Tissue-Tek (Miles Inc., Elkhart, USA) and frozen in liquid nitrogen. Three serial 10 μm-sections from the proximal third of the spleen of 5 mice per group were cut using a freezing microtome, fixed in acetone, and washed three times with PBS. Tissue sections were incubated with sheep anti-tyrosine hydroxylase (Chemicon, USA) overnight at 18 °C, followed by 2 h incubation at 4 °C. After washing with PBS, sections were incubated with donkey anti-sheep-biotin and streptavidin FITC (Dianova, Hamburg, Germany) for 45 min at 25 °C. No binding was detected in the absence of the primary antibody. Following PBS washes, the sections were mounted in 25% glycerol/75% PBS. Ten fields per section were examined with a confocal microscope (Nikon eclipse TE2000-E inverted microscope, D-eclipse C1si, Melville, New York), and representative fields were photographed.
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