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98 protocols using nis elements br

1

Microscopic Analysis of Cell Dimensions

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For microscopic analysis, 5 μL of exponential growing cells at N = 70 were transferred onto a microscope slide and analyzed using an Eclipse E600 (Nikon, Tokyo, Japan) microscope equipped with a 100 × NA 1.4 oil immersion objective and a DXM1200C camera (Nikon, Tokyo, Japan). The image analysis and determination of the cell size were performed with the Nikon Nis-Elements BR (version 3.2) imaging software or/and ImageJ program (version 1.50). Fluorescence signals of GFP were visualized utilizing the Epi-FL filter block for fluorescence B-2E/C (EX: 465–495, DM: 505, BA: 515–555; Nikon, Tokyo, Japan), thereby using identical fluorescence intensity and exposure times between 1 and 2 s.
Cell length of parental strain R6, C405, and R62xC405 growing in C+Y medium at 30 °C were measured from phase-contrast images by using the Nikon Nis-Elements BR software (version 3.2), and the results were further analyzed in Microsoft Excel. More than 100 cells from at least two independent experiments were measured for each strain. Only cells showing a clear invagination at the division septum (late divisional cells) were measured.
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2

Quantifying Cardiac Fibrosis in Aging Mice

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Histological evaluation of fibrosis was performed on 20 male mice belonging to 4 groups (5 per group): (1) three-month-old untreated, (2) six-month-old untreated, (3) twelve-month-old untreated, and (4) twelve-month-old treated. At necropsy, heart ventriculi were collected and referred to the histology laboratory. Samples were paraffin embedded and sectioned to show both ventricular walls. After rehydration of sections, Mallory trichrome staining was performed by using a commercial kit (04-020802, Mallory trichrome, Bio Optica, Italy); slides were thus dehydrated, cleared, and mounted with permanent mounting medium. Five images at 20x magnification were collected focusing at connective tissue hot spots and semiautomatically analyzed with the image processing software Nis-Elements Br (Nis-Elements Br, Nikon Instruments, Italy). Fibrosis was expressed as percent of the images occupied by the connective tissue (stained in blue with Mallory trichrome).
Data analysis. Values were analyzed by Bonferroni's multiple comparison test as post hoc analysis after one-way analysis of variance; significance was set at p < 0.05.
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3

Histological Analysis of Mouse Kidneys

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For light microscopic analysis, mouse kidneys were fixed with 4% buffered paraformaldehyde (pH 7.4) at 4°C overnight, dehydrated in graded alcohols, and embedded in paraffin. The paraffin-embedded kidneys were cut into 4-μm sections and stained with periodic acid-Schiff (PAS) for the evaluation of pathologic changes. Twenty five glomeruli and approximately 80–100 proximal tubules in each mouse and six mice in each group were measured for mesangial matrix fraction and tubular area using Nikon NIS-Elements BR software version 4.10.00 (Nikon, Japan) by a pathologist in a blinded manner.
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4

Quantitative Immunohistochemical Analysis

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Immunolabelled sections were scanned at 40× using an Olympus BX51 microscope (Olympus, Tokyo, Japan) with an Olympus XC10 camera (Olympus, Tokyo, Japan). Scanned images were analyzed with digital image analysis software (Nikon NIS-Elements Br, Nikon, Japan). For each animal, five randomly selected areas were sourced as regions of interest (RI) and were analyzed using 200× magnification. The area with an immunohistochemical-positive reaction within RI was calculated by the Nikon NIS-Elements software after setting the thresholds. The results were expressed as the proportion of the positively immunolabelled area within the total area of the selected site.
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5

Histological and Immunohistochemical Analysis

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A 1 cm × 1 cm piece from each sample was taken and cut in half on the diagonal. Half of the sample was placed into 10% NBF for histologic processing and embedded into paraffin blocks; the other half was placed into 20% sucrose in preparation for cryoembedding in optimal cutting temperature media and subsequent immunohistochemical staining. Slides were stained either histologically with H&E or immunohistochemically using antibody probes to the inflammatory cell marker CD-68 to detect macrophages (Cat# MA5-13324, Thermo Fisher Scientific, Waltham, MA). A blinded histopathology reviewer evaluated slides under brightfield microscopy for evidence of cell infiltration, revascularization, and inflammation using a Nikon Eclipse microscope and Nikon NIS Elements BR imaging software (Nikon Instruments Inc, Melville, NY).
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6

Quantitative Microscopic Image Analysis

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The microscopic images were quantitatively analyzed using the Nikon NIS-elements BR software (V 2.03, Nikon Instruments, Melville, NY).
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7

Quantifying Renal Pathological Changes

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Renal pathological injury was evaluated using periodic acid-Schiff (PAS) and Masson’s trichrome stains. For quantitative analysis, 40–50 glomerular tuft area and 40–50 proximal tubular lumen cross-sectional area in each rat and five rats in each group were measured using Nikon NIS-Elements BR software version 4.10.00 (Nikon, Japan) to evaluate glomerular hypertrophy and tubular atrophy.
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8

Histological Assessment of Liver and Pancreas

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Paraformaldehyde-fixed liver and pancreas specimens were embedded in paraffin blocks and cut into 4 μm thick sections. The sections were then stained with Masson trichrome (MT) according to standard procedures. The islet surface distribution was determined in the pancreas. At least three sections were examined per animal. The islet surface area was measured using Nikon NIS Elements Br software (Nikon, Tokyo, Japan), and the distributions were reported using box and whiskers plots with median, first and third quartile and extreme values. In the liver, the degree of steatosis was defined on sections according to Kleiner et al.[32 (link)], with a maximum score of 3. No accumulation of lipids occurs in the pancreas.
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9

Histological Analysis of Synovial and Articular Tissue

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Synovial specimens from humans and the complete articular tissue of rats were fixed in 4% paraformaldehyde (PFA) solution for 48–72 h and embedded in paraffin for subsequent H&E staining. Specifically, the tissue was fixed on paraffin sections, dehydrated, and embedded in paraffin. Then, the paraffin-embedded samples were cut into 5 μm serial sections, stained with hematoxylin dye for 5 min and washed with water. Next, the sections were soaked with ammonia and then washed with water. The sections were stained with 1% eosin dye and then washed with water. Ten different fields of view were chosen for each sample, and all images were captured on a Nikon NIS Elements BR light microscope (Nikon, Tokyo, Japan).
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10

Histological Evaluation of Extracellular Matrix

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Mesh samples (1 cm × 1 cm) were fixed for 24 h in 10% neutral buffered formalin (NBF), sectioned to a thickness of 5 µm, placed on glass slides, and stained with hematoxylin and eosin (H&E) to observe collagen integrity and ECM microstructure. Stained slides were observed under brightfield microscopy using a Nikon Eclipse microscope and Nikon NIS Elements BR imaging software (Nikon Instruments Inc, Melville, NY). Images were captured at ×40 to ascertain matrix structure and ×100 to observe host response.
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