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63 protocols using cx41 light microscope

1

Quantifying Brain Immunoreactivity

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Brain-region immunoreactivity was visualized with an Olympus CX41 light microscope (Olympus America, Center Valley, PA), images were captured with a digital camera (Regita model; QImaging, Burnaby, BC), and analyzed using Bioquant (Nashville, TN) image analysis to obtain linear integrated optical density for immunoreactivity assessment. The microscope, camera, and software were background corrected to eliminate nonspecific labeling and normalized to preset light levels to ensure fidelity of data acquisition. Positive pixel count of immunoreactivity was quantified from a circumscribed field, delineated as a brain region, divided by the area of the region in square millimeters, and expressed as pixels/ mm2. Data from 6 to 8 alternate sequential sections per animal per brain region from a single hemisphere were used to average 1 value per monkey. The experimenter was blind to the condition of each animal when analyses were conducted.
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2

Immunohistochemical Analysis of Tissue Markers

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Deparaffinized 4 μm sections were placed on coated slides and then treated for ten minutes at room temperature with hydrogen peroxide (0.3%/methanol) to stop the activity of endogenous peroxidase. Finally, sections were heated for ten minutes at 95 °C in 10 mM citrate buffer to induce antigen retrieval before being allowed to cool for 60 min.
Sections were incubated with the following primary antibodies for immunostaining: gamma H2Ax and Poly (ADP-ribose) polymerase 1 (PARP1), proliferating cell nuclear antigen (PCNA) [50 (link)], caspase-3, TGF-β1 [51 (link)], and alpha smooth muscle actin (α-SMA) [52 (link)] as presented in Table 2. Then, they were left in phosphate-buffered saline (PBS) at 4 °C overnight before adding the universal secondary anti-mouse IgGκ (sc-516102, Santa Cruz, CA, USA) or anti-rabbit IgG (sc-2357, Santa Cruz) for 30 min to localize the primary antibody binding followed by washing again with PBS. Finally, Diaminobenzidine (DAB) was added for four minutes to demonstrate peroxidase activity, followed by hematoxylin staining as counterstain [53 (link)]. Olympus® CX41 light microscope was used for examining the sections that have been photographed by its digital camera Olympus® SC100.
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3

Histological Muscle Fiber Analysis

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All samples blocked with FSC were cut into 8-μm-thick sections using the LEICA CM1950 (LEICA, Wetzlar, Germany). Three tissue cross-sections were taken and stained with hematoxylin-eosin (HE). Microscopic observation was carried out with an Olympus CX41 light microscope (Olympus Co., Tokyo, Japan). The muscle cross-sectional area was quantified using ImageJ software (http://rsb.info.nih.gov/ij/index.html, 21 April 2021). The sections were analyzed by three investigators who were blinded to the experimental group or condition. The value of the cross-sectional area was averaged from the results analyzed by the three investigators.
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4

Investigating Cell Scatter Regulation

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1 × 103 cells were seeded into 60-mm dishes for 96 hours until compact colonies of cells were formed and then incubated in serum free media for a further 48 hours. The cells were subsequently treated with mitomycin C (10 ug/ml) for 2 hours followed by the addition of S1P (1 μM or 5 μM) in the presence or absence of the Rac-1 inhibitor (NSC23766; 5 μM) or the MEK 1/2 inhibitor (UO126; 5 μM). After 72 hour incubation, the cells were fixed with formal saline and stained using haematoxylin and eosin (H&E). Stained cells were viewed using an Olympus CX-41 light microscope. Ten images were taken from each dish and the average area of scatter was calculated using Analysis software (Soft Imaging Systems) by drawing the smallest circle possible around the colonies of cells. The area of the circle was divided by the number of the cells within the circle to give the area relative to the number of cells. 5 μM epidermal growth factor (EGF) was used as a positive control of cell scatter.
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5

Syllinae Diversity in Bermuda

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A total of 803 specimens of Syllinae were collected during August of 2014 in Bermuda by snorkelling or SCUBA diving in different substrates and depths (electronic supplementary material, table S2). Specimens were sorted at the Bermuda Institute of Ocean Sciences (BIOS) using a Nikon SM7 stereoscope and preserved in 96% ethanol for the subsequent molecular and morphological analyses. Further examination and identification were completed at Universidad Autónoma de Madrid (UAM) using an Olympus SZ 40 stereoscope and an Olympus CX 43 light microscope. Drawings were made to scale with a camera lucida attached to a Nikon Optiphot light microscope and from pictures taken with an Olympus CX41 light microscope. The width of specimens was measured at the level of the proventricle, excluding the parapodia.
For scanning electron microscopy, selected specimens were prepared on an Emitech K850 Critical Point Dryer, gold-coated with a Q150T-S Turbo-Pumper Sputter Coater and examined with a Hitachi S 3000N scanning electron microscopy (SEM) at the Interdepartmental Research Service (SIDI) of the UAM.
Vouchers for all newly collected specimens were deposited at the Museo Nacional de Ciencias Naturales (MNCN) in Madrid (Spain). Catalogue numbers, collection dates, locality and additional relevant information are listed in electronic supplementary material, table S2.
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6

Comprehensive Analytical Characterization

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NMR measurements (1H, 13C)
were performed on a Varian INOVA 400 MHz spectrometer. MALDI-MS measurements
were performed using a Bruker Microflex MALDI-TOF. The samples were
prepared in a cyano-4-hydroxycinnamic acid matrix or a trans-2-[3-(4-tert-butylphenyl)-2-methyl-2-propenylidene]malononitrile
matrix. Attenuated total reflection–infrared (ATR–IR)
spectra were measured with a Perkin Elmer 100 Spectrum spectrometer
including an ATR unit. TGA was measured at Netzsch Jupiter STA 449
F3. Liquid chromatography was measured with Thermo Fisher Scientific
Dionex 3000. As the column, Agilent Poroshell 120 EC-C18 (2.1 ×
100 mm, 2.7 μm) was used. MeCN (5%) as eluent A and 95% water
as eluent B with 0.1% formic acid were used. A linear gradient of
5% A to 100% A was applied with a flow rate of 0.3 mL/min. The DLS
measurements were done by using a Malvern Zen5600. Liquid-crystal
pictures were taken with an Olympus CX41 light microscope. The high-resolution
TEM observations were carried out using JEOL JEM-2200FS, and the TEM
observations were carried out using Zeiss Libra120. The surface tension
measurements were performed using Krüss K100.
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7

Histological Analysis of Tracheal Tissues

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The tracheal tissues of the normal and model groups were fixed with 4% paraformaldehyde solution at 25°C for 24 h, then rinsed for 6–8 h and dehydrated with ethanol solutions of 70, 80 and 90% and a mixture of pure alcohol and xylene at 25°C for 15 min, xylene I for 15 min and xylene II for 15 min until tissues were transparent. Tissues were incubated in a mixture of xylene and paraffin at 25°C for 15 min and then placed in paraffin I followed by paraffin II at 25°C for 50–60 min each. Tissues were paraffin-embedded and sliced (5 µm thick). The paraffinized sections were baked at 45°C and Paraffin sections were dewaxed with xylene I followed by xylene II for 5 min each, then placed in 100, 95, 90, 80 and 70% alcohol solutions for 3 min each, and then placed in distilled water for 3 min. Once tissues were washed with distilled water, each section was placed in an 0.2% aqueous solution of hematoxylin at 25°C for 3 min and incubated in an 1% ethanol differentiation solution at 25°C for 15 sec, washed slightly with distilled water and returned to the blue hematoxylin solution at 25°C for 15 sec. Sections were then rinsed with water, stained with 0.5% eosin at 25°C for 3 min and rinsed with water again. Sections were placed in 95 and 100% alcohol for 3 min each for dehydration until transparent, sealed and examined by an Olympus CX41 light microscope at ×400 magnification.
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8

Muscle Morphometry Analysis Protocol

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All samples blocked with FSC were cut into 8 µm-thick sections using the LEICA CM1950 (LEICA, Wetzlar, Germany), and sections were stained with hematoxylin-eosin (HE) staining. Microscopic observation was carried out with an Olympus CX41 light microscope (Olympus Co., Tokyo, Japan). The muscle cross-sectional area (CSA) was quantified using ImageJ software (http://rsb.info.nih.gov/ij/index.html, 11 June 2019).
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9

Optical Analysis of Tomato Vinegar

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For optical microstructure, a small drop of vinegar (~40 µL) was placed onto a microscope slide and crosswise covered with a coverslip. A reflected fluorescence system in an Olympus CX41 light microscope (Olympus, Tokyo, Japan) was used to visually analyze the microstructure of the tomato vinegar. Tomato vinegars were dropped on slides and pictures were taken with a digital camera (Kameram 2.1, Argenit, Istanbul, Turkey) under a magnification of 200X.
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10

Histopathological Analysis of Liver Samples

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Liver samples, were fixed in formalin, treated with a standard alcohol and xylol blend, embedded in paraffin, and sectioned into 5 mm thick sections. Haematoxylin and eosin (H and E) staining were applied to the sections in order to examine the histopathological alteration. Images were taken at the National Research Center’s pathology lab using an Olympus CX41 light microscope and a SC100 digital camera connected to a computer system.
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