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297 protocols using ds ri1

1

Multimodal analysis of nanoparticles

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FTIR measurements were carried out with ALPHA-T (BRUKER Inc. Billerica, MA, USA). TEM images were observed using a JEM-2100F, 200 kV (JEOL LTD., Tokyo, Japan). Dynamic light scattering (DLS) and zeta-potential were conducted on an ELS-Z (Otsuka Electronic CO., LTD., Tokyo, Japan). Fluorescence spectra and intensity values were recorded on the FS-2 (SINCO CO., LTD., Daejeon, Korea) and spectraMax M2e. (Molecular Devices, LLC., San Jose, CA, USA). An upright fluorescence microscope (Nikon, Eclipse Ni, Tokyo, Japan) and digital camera system DS-Ri1 (Nikon, DS-Ri1, Tokyo, Japan) were used for the visualization of the bacteria for FISH. Fluorescence filters are longpass: green (excitation filter 460–500, dichroic mirror 505, and barrier filters 510–560), red (excitation filter 540/25, dichroic mirror 565, and barrier filters 605/55).
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2

Generation and Localization of FgFAD12-GFP Fusion

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FgFAD12-GFP fusion construct was generated using the ClonExpress® II One Step Cloning Kit (Vazyme, Nanjing, China). To generate the FAD12-GFP fusion construct, the FAD12 gene with its native promoter was amplified with primer pair Fad12/HF-HR (Table S1). Subsequently, the FAD12 gene fragments were cloned into the pKNT-GFP vector by Hind III/Kpn I double-digested to obtain FAD12-GFP fusion construct [36 (link)]. The resulting FgFAD12-GFP fusion construct was transformed into ∆Fgfad12 mutants. Transformants containing hygromycin and genecin resistance were verified by PCR, and GFP signals were observed with epifluorescence microscope (Nikon, DS-Ri1, Tokyo, Japan).
For co-localization transformants, FgKar2-mCherry-T-vector was obtained from Shuli Cao of Jiangsu Academy of Agricultural Sciences. FgKar2-mCherry and Fad12-GFP were co-transformed into the wild-type PH-1. Transformants were examined GFP and mCherry signals with epifluorescence microscope (Nikon, DS-Ri1, Tokyo, Japan).
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3

Quantitative Analysis of Immunoreactive Cells

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All images were acquired using a Nikon ECLIPSE 90i microscope and a Nikon DS-Ri 1 digital camera (Nikon Inc., Japan) and LSM700 (+ Zeiss slide scanner). Digital images were processed adjusting only brightness, contrast, and color balance. The numbers of immunoreactive cells were counted manually by two independent investigators blinded to the experimental conditions. Three slides were analyzed for each animal and observed under a microscope (× 100–400). To quantify the reciprocal intensity, the intensity per unit area was measured using Image J and the color deconvolution plug-in (http://wiki.imagej.net/Colour_Deconvolution). The target unit area of images was processed using the color deconvolution tool in Image J to separate brown from other colors. The area of brown staining was then quantified and divided by the total area to yield a percentage of staining area. Stereological analyses were conducted using Prism software (GraphPad software, USA).
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4

Lung Tissue Histological Analysis

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The lungs were fixed in 4% paraformaldehyde and were processed for paraffin embedding. Next, 4-µm sections of paraffin blocks were stained with H&E. Images were captured with a digital camera (Nikon DS-Ri1; Nikon, Japan) coupled to a Nikon Eclipse Ni microscope (Nikon) under 20× magnification.
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5

Quantification of Dopaminergic Neurons in Substantia Nigra

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Free floating sections were pretreated with peroxidase block and incubated for 1 h in goat serum using the ImmunoCruz staining system. Sections were then incubated overnight at 4 °C with rabbit anti-TH (1:1000). The following day sections were treated with the biotinylated secondary, the HRP-streptavidin complex and visualized with diaminobenzidine. Cells were counted as described previously [30 (link),65 (link)] using stereotaxic coordinates defined by Franklin and Paxinos [63 ]. Stained sections were visualized by light microscopy (Nikon Eclipse TE300, Nikon USA, Melville, NY). Images were taken with the Nikon DS-Ri1 and processed with the NIS-Elements 3.2 (Nikon). The substantia nigra boundaries were established as previously described [30 (link)]. Microphotographs for TH neurons were taken at a 40× magnification. Neurons were counted under a light microscope at a magnification of ×400. A neuron was counted if nucleus was visible and one or more clearly defined processes tapered gradually from the cell body. This number was considered to be representative of the number of dopaminergic nigral cells in each animal. The counts were taken of three individual sections from each mouse.
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6

Fluorescent and Histochemical Imaging Protocol

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Histological examination of the slide-mounted tissue was examined using a Nikon epifluorescent microscope 80i (Nikon Instruments Inc., Melville, NY) and an X-Cite 120 LED light source (Excelitas Technologies®, Waltham, MA). The following sets of filters were used for visualization fluorescent labeling in conjunction with the histochemical or immunohistological labeling: TRITC excitation of 533–553 nm and an emission of 573–613 nm and FITC excitation of 464.5–499.5 and an emission of 516–556 nm. Combinations of these filters resulted in negligible cross-talk between the signals from individual fluorochromes, such that there was minimal to no observable bleed-through between any of the three signals. Visualization of DAB-labeled sections was done with incandescent illumination. All photomicrographs of the images were taken using a Nikon DS-Ri1 using the NIS software from Nikon.
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7

Comprehensive Tissue Fixation and X-gal Staining

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Mice were deeply anesthetized via Ketamine/Xylazine (120/5 mg/kg) intraperitoneal (IP) injection and fixed by cardiac perfusion using a 0.2% glutaraldehyde, 4% paraformaldehyde (PFA) solution. Brain, ribcage, lymph nodes, salivary glands, thymus, heart, lung, liver, spleen, stomach, kidney, intestine, urogenital, muscle, and hind limb tissues were dissected, rinsed in phosphate buffered saline (PBS) and post-fixed for 30 minutes in a 0.2% glutaraldehyde, 4% PFA solution. Tissues were washed and incubated in X-gal (1 mg/mL) staining solution for roughly 12 hours at 37 °C. After staining, tissues were washed, post-fixed in 4% PFA and cleared in a series of 50%, 70% and 100% glycerol. Photographs were taken with a Nikon SMZ1500 stereomicroscope and Nikon DS-Ri1 digital camera using NIS-Elements D Imaging Software (Nikon).
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8

Invasion Assay with Chemotherapeutics

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Fifty thousand 24-hour sera deprived cells/well were plated on type IV collagen-coated microporous polyester membrane (InnoCyte cell invasion kit, Calbiochem, San Diego, CA) with the following treatments: (5 μM 4-HPR (2095sc log and SEL cells), 10 μM 4-HPR (JSCC2 log and SEL cells), 2) 1 μg/ml tocilizumab, 3) 10 μM reparixin, 4) fenretinide+ tocilizumab, 5) fenretinide+ reparixin, 6) tocilzumab + reparixin, 7) fenretinide+tocilizumab+ reparixin, 8) DMSO control. Preliminary studies confirmed all cell line viabilities remained ≥96% and cell numbers remained comparable during all treatments. JSCC3 conditioned medium was used as the chemoattractant [15 ]. After 16 hours of invasion (37°C, 5% CO2), cells were formalin fixed and stained with 0.1% v/v crystal violet solution. Images were captured by Nikon DS-Ri1 using NIS Elements (Nikon, Melville, NY), followed by target pixelation analyses by image segmentation [ImagePro software (Media Cybernetics, Inc., Rockville, MD)].
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9

Localization of Proliferating Cells

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For each animal treated with [3H]-thymidine, a minimum of 45 semithin section were examined for the presence of [3H]-thymidine labeled cells and photographed under a Nikon microscope (Eclipse E800, Nikon with digital camera Nikon DS-Ri1). A cell was considered labeled if it had eight or more silver grains over the nucleus. The semithin sections containing the selected cells were re-embedded, and ultrathin sections were cut and examined under a FEI Tecnai G2 Spirit transmission electron microscope (FEI Company, Tokyo, Japan). Images were acquired using Radius software (Version 2.1) with a XAROSA digital camera (EMSIS GmbH, Münster, Germany).
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10

Microscopic Imaging Techniques

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Chartings and high magnification drawings were made using an Olympus BH-2 microscope (Olympus, Center Valley, PA) equipped with a drawing tube. Low magnification section drawings were made with a Wild M8 stereoscope (Leica Microsystems, Buffalo Grove, IL) with attached drawing tube. Photomicrographs were made with a Nikon Eclipse E600 microscope using a Nikon DS-Ri1 digital camera controlled by Nikon Elements software (Nikon Instruments, Inc., Melville, NY). Multiple Z-axis focal planes were combined digitally. The brightness and contrast of the images were adjusted to match the view seen by the eye through the use of Adobe Photoshop (Adobe, San Jose, CA).
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