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292 protocols using ds fi1

1

Multizoom Makroscope Imaging and Confocal Scanning

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Imaging was done on a AZ100 multizoom makroscope (Nikon, Japan) with a AZ Plan Apo 1x objective (Nikon, Japan) with DS Fi1 (Nikon, Japan) for bright field images.
Confocal scan was done with the C2 + confocal scanner (Nikon, Japan). The confocal scanner settings were; first filter cube: 447/60, second filter cube: 525/50 561 LP, emission wavelength: 785 nm, laser power: 3.4 and pinhole size: 30 m 2 .
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2

Histological Analysis of Chicken Embryo Skeletal Muscle

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The muscle samples were carefully collected from E9–E20 chicken embryos and fixed in 4% neutral paraformaldehyde overnight. Tissues were rinsed in PBS for 3 h, and then dehydrated in a graded series of ethyl alcohol and embedded in paraffin wax. The transverse serial sections of 5 μm thickness were cut and stained with hematoxylin and eosin for morphological examination. Neutral gum was added and covers section with a cover slip. The morphology of skeletal muscles was observed and muscle fiber CSA (μm2) was determined under Eclipse 80i microscope (Nikon, Tokyo, Japan) and the pictures were captured with a digital camera (DS-Fi1, Nikon, Tokyo, Japan). Five fields in each section were randomly selected, and myofiber density was evaluated based on the number of myofiber per mm2. Three samples were taken from each group in each period, and five sections were selected for each sample to be photographed and counted to obtain data.
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3

Starch Deposition in Cotyledon Sections

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Sections approximately 6 µm thick were cut and collected on polylysine coated slides. Staining of section with 0.1% (w/v) toluidine blue in 1% (w/v) borax, pH 11 was done for general structure observations [35] (link).
To determine the location of starch deposits in cotyledons of ungerminated and germinated seeds, semithin sections of seeds were stained with I2-KI solution [25] (link). Slides were observed under light microscope (Nikon DS-Fi1).
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4

Hepatic Lipid Deposition Assessment

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Next, because hepatic lipid accumulation leads to insulin impairment and insulin insensitivity, we assessed how HFHC diet consumption and solTNF signaling impact ectopic lipid deposition in liver tissue [28 (link)] Liver tissue from the left lobe was fixed in 4% paraformaldehyde/PBS and cryoprotected in 30% sucrose solution. Tissue was frozen in OCT, sectioned (10 μm), and stained with Oil Red O (150678, Abcam) according to the manufacturer’s instructions. Images were obtained using a Nikon Eclipse 90i microscope with a DS-Fi1 (Nikon) camera and Nikon NIS-Elements AR 3.10 software, magnification × 40.
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5

Histopathological Analysis of Mouse Liver

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After the mice were euthanized, the livers were collected and stored in 10% formalin. The liver tissue was randomly chosen for sections processing. Microscopic slides were obtained after preparation of wax blocks and staining with hematoxylin and eosin (Leica, IL, United States). Tissue sections were observed under a microscope for differential cell counts. The histopathological sections from each mouse were analyzed quantitatively for the different cell populations percentage, including Kupffer cells, apoptotic cells, mononucleated hepatocytes, and binucleated hepatocytes. The sections were observed under a Nikon Eclipse 50i light microscope, and the image was captured with a Nikon DS-FI1 digital camera. Each slide contained three sections obtained at 15-μM intervals, and random six different areas were examined with 3 × 104 μm overlaid grid. The cells were scored with NIS elements D image analysis software (Nikon, New York, NY, United States). Each (mouse) slide was examined with six different areas of 18 × 104 μm2 and each group examined for 54 × 104 μm2. The hemorrhagic areas were observed in 20 magnifications (to include a wider area of 216 × 104 μm2 per group). All the mean values were analyzed using one-way ANOVA, IBM SPSS statistics version 23, and represented in bar chart.
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6

Kossel Diagram Characterization

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We used an inverted polarising microscope (Ti-U, Nikon) with ×100 oil immersion objective (NA = 1.4), Nikon DS-Fi1 digital camera (pixel size 3.4 × 3.4 μm). Kossel diagrams were recorded in conoscopic observation mode from a single domain with fully open illumination aperture diaphragm and fully closed eld diaphragm. Interference filters at 514.5 nm with 5 nm transmission bandwidth were used for wavelength selection. Due to low intensity of the reflected light and narrow filter bandwidth exposure times were from 4 to 30 seconds depending on wavelength and sample region.
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7

Monitoring 20E-Induced Pupal Development

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The aim of this experiment was to monitor pupal development after 20E-treatment. The pupae samples used for this experiment were collected from the wild at the end of November, 2014, thus, they had already entered into pupal diapause. 20E was applied as reported above to break the pupal diapause. Following this treatment, pupae from all groups were dissected to record their developmental process. This was done by taking photomicrographs (Nikon DS-Fi1) every 3 days under a dissecting microscope (JSZ5BS). The pupal development was continuously monitored through this process until the adult emerged.
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8

Immunohistochemistry Tissue Preparation Protocol

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The Tissue and Histology Core of the Comprehensive Cancer Center and the Pathology Core for Animal Research in the Unit for Laboratory Animal Medicine at the University of Michigan assisted in preparing specimens for immunohistochemistry. After the slides were deparaffinized in xylene and rehydrated using serial ethanol dilutions, antigen site unmasking was performed by immersing the slides in citrate buffer (pH 6.0) for 20 min at high pressure and temperature inside a microwave oven. Slides were then washed in PBS, blocked for 1 h, and incubated in the primary antibody at 4°C overnight. Slides were then again washed in PBS, incubated in secondary antibody for 1 h, rewashed, and probed using DAB detection kits with an extra washing step. Slides were counterstained with hematoxylin for 1 min, post-counterstained with bluing reagent for 1 min, washed with water, and then dehydrated in ethanol and xylene before coverslip application. Images were acquired using a DS-Fi1 (Nikon, Melville, NY) camera fitted on an Olympus IX-71 microscope.
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9

Immunohistochemistry and Lipid Staining

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For immunohistochemistry (IHC) staining, tumor samples were fixed in 4% formaldehyde for 2 to 4 hours on ice, moved in 70% ethanol for 12 hours, and then embedded in paraffin (Leica ASP300S). After cutting (Leica RM2235), baking and deparaffinization, slides were treated with Citra-Plus Solution (BioGenex) according to specifications. Endogenous peroxidases were inactivated by 3% hydrogen peroxide. Nonspecific signals were blocked using 3% BSA, 10% goat serum and 0.1% Triton. Tumor samples were stained with primary antibodies. ImmPress and ImmPress-AP (Vector Lab) were used as secondary antibodies;
Nova RED, Vector BLUE and DAB were used for detection (Vector Lab). Images were captured with a Nikon DS-Fi1 digital camera using a wide-field Nikon EclipseCi microscope. For Oil Red O Lipid staining, T98G were grown on coverslips and GSCs were attached to tissue slides by cytospin. Tumor tissues were 4% PFA fixed, cryoprotected with 30% sucrose, OCT embedded and sectioned (5 μm thick). Oil Red O Lipid staining was performed according to the manufacturer instructions (Abcam, ab150678).
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10

Microscopic Morphological Measurements

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Individuals used for measurements were stored in 70% ethanol at 4°C until photographed on millimetre paper using a Nikon SMZ800 stereo microscope with Nikon DS Fi1 camera attachment. Measurements on these photographed specimens were made with ImageJ (v. 1.53 k, see electronic supplementary material, figure S2 for definition of measurements). All statistical analysis was performed in R (v. 4.0.3). ANOVAs, t-tests, Pearson's χ2 and generalized linear models were performed within the R set of core functions (stats 4.0.3). All code and data are available in the electronic supplementary material. The estimation of pairwise sequence identity of the inr genes coding sequences was done with Muscle (v. 3.8.425 (alignment in Geneious (v. 2021.1.1) using standard parameters.
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