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68 protocols using nis elements d 3

1

Visualizing Lipid Stores in Insect Diapause

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Nile Red (Thermo Fisher Scientific) was used to visualize differences in lipid stores of adult females (6–9 days old) reared under diapause (19 °C, 9:15 L:D) and control conditions (25 °C, 16:8 L:D). Fat bodies were dissected in 4% paraformaldehyde and stained using a 1:100 PBS dilution of 500 μg/ml Nile Red powder in acetone stock as previously described18 (link),31 (link). After incubating tissues for 10 min, samples were imaged using a Nikon 50i fluorescent microscope and processed with Nikon imaging software (NIS Elements D 3.2).
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2

Histological Evaluation of Formalin-Fixed Tissues

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The formalin-fixed samples were processed in tissue processor (Leica TP 1020, Germany) and Tissue Embedding Console System (Leica EG1150) before they were embedded in paraffin wax and sectioned using the rotary microtome (Leica Jung Multicut 2045, Germany) at 4 μm thick. The mounted tissue sections were stained with Harris’ haematoxylin and eosin (HE). The slides were viewed under light microscope (Nikon Eclipse 50i, Japan) installed with Nikon imaging software (NIS-Elements D 3.2, Japan). The histological changes were noted and scored as 0: none, 1: 30% affected, 2: 30–60% affected and 3: > more than 60% affected [3 (link)]. All evaluations were duplicated and 5 microscopic fields of each slide were randomly selected for lesion scoring. The scores were reported as the average value of each lesion and average value for overall scoring.
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3

Genetic Modification of mES Cells

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MI-MAC mES cell line 4 was cultured to subconfluence. Before electroporation, MI-MAC mES cells were collected and plated on a gelatine-coated cell culture dish without feeder cells for 1 h, followed by recollection of cells in suspension. Plasmid vector carrying the gene of interest (8.5 µg) was co-transfected with the representative integrase/recombinase expression vector (3 µg) into 5.0 × 106 MI-MAC mES cells per sample with an Amaxa™ mouse ES Cell Nucleofector™ Kit (Lonza, Switzerland). Forty-eight hours after transfection, these mES cells were selected in 75–150 µg/mL G418 for 1 week, and G418-resistant colonies were counted and GFP expression was observed using an NIS-Elements D 3.2 (Nikon, Tokyo, Japan).
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4

Histological Analysis of Intestinal Structures

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Parts of the small intestine (duodenum, jejunum and ileum) and caecum fixed in 5% buffered formalin solution were embedded in paraffin using a standard procedure. Subsequently, an evenly spaced series of histologic section (50 μm intersection interval) were cut at 5 μm and stained with hematoxylin and eosin (H&E).
Histomorphometric analysis was performed on H&E-stained tissue sections using a Nikon Microphot FXA microscope equipped with a DS-Fi1 camera and the Imaging Software NIS Elements D.32 (Nikon instruments Europe B.V., Badhoevedorp, The Netherlands).
Villus height was measured from the tip to the crypt-villus junction and the crypt depth measured from the crypt-villus junction to the base as illustrated in Figure 1.
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5

Fluorescence Imaging of Cell Apoptosis

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The cells were fixed in 4% paraformaldehyde for 20 minutes. After washing with PBS three times, the cells were stained with Hoechst 33 258 (Beyotime, Beijing, China) for five minutes. The cells were then washed with PBS another three times and coverslips were sealed with a drop of Prolong Gold antifade reagent (Invitrogen, Carlsbad, CA, USA). Images were acquired by Eclipse Ti laser scanning microscopy and analyzed by NIS‐Elements D 3.2 (Nikon, Tokyo, Japan). Five random visual fields were counted to calculate the apoptosis rate.
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6

Histomorphometric Analysis of Myocardium and Adipose Tissue

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Myocardial tissue and epididymal fat pads were fixed in 4% paraformaldehyde for 24 h, routinely processed, and embedded in paraffin. Briefly, all tissue paraffin blocks were cut to a 5 µm thickness using a microtome. The paraffin sections (5 µm) were dewaxed and rehydrated using gradient alcohol and water. The sections were then washed with tap water and distilled water and then stained with hematoxylin and eosin (H&E) (Bio-Optica Milano SpA., Milano, Italy). For microscopic assessment, the images of heart sections were captured by a stereoscope (Nikon SMZ745T with NIS-elements D 3.2) with a 1× objective lens to observe the LV wall thickness, the cross-sectional area (CSA), the LV luminal area, and the wall-to-lumen ratio. These parameters were counted using Image J software (National Institutes of Health, Bethesda, MD, USA).
The measurement of the myocardium cell size and the area of cardiomyocytes was performed for 300 myocytes per group with a 40× objective lens using a Digital sight DS-2MV light microscope (Nikon, Tokyo, Japan). Mean values were obtained for 300 cells/group.
Epididymal fat sections were evaluated using a Digital sight DS-2MV light microscope (Nikon, Tokyo, Japan) with a 40× objective lens. Adipocytes were quantitated according to the cell size area (300 cells/group) using NIS-Elements software.
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7

Biometric and Cytometric Analyses of Coral Polyps

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Biometric analyses were performed by measuring length (L, maximum axis of the oral disc), width (W, minimum axis of the oral disc), and height (h, oral–aboral axis) of each sampled polyp. Polyp body volume (V), calculated using the formula V = (L/2) * (W/2) * h * π, was used to estimate reproductive parameters (oocyte and spermary abundance, and gonadal index) as described in the next section. Polyps have been processed following the histological protocols as described in Goffredo et al. [18 , 19 ].
Cytometric analyses were carried out with an optical microscope using the image analyzer NIKON NIS-Elements D 3.2. The maximum and minimum diameters of the oocytes in nucleated sections and spermaries were measured. Spermaries were classified into five developmental stages and oocytes were classified as immature or mature, according to earlier studies on gametogenesis of this species [18 ].
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8

Histopathological Evaluation of Organ Samples

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All organ samples for histopathological examination were embedded in paraffin wax, sectioned at 4 µm and stained with Harris’ Haematoxylin and Eosin (H&E). The slides were viewed under light microscope (Nikon Eclipse 50i, Tokyo, Japan) installed with Nikon imaging software (NIS-Elements D 3.2, Tokyo, Japan). The histological changes were noted and scored as 0: none, 1: mild, 2: moderate and 3: severe. Specific lesions like necrosis, atrophy, haemorrhage, congestion, infiltration of inflammatory cells and hyperplasia were graded based on these criteria; 0: none, 1: 30% affected, 2: 30–60% affected and 3: > more than 60% affected (Xavier et al. 2010 ). All samples were duplicated and 5 microscopic fields of each slide were randomly selected for lesion scoring. The scores were reported as the average value of each lesion and average value for overall scoring.
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9

Gametogenesis and Embryogenesis in Scleractinians

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Cytohistometric observations were performed with an optical microscope using the software NIKON NIS-Elements D 3.2. The maximum and minimum diameters of the oocytes in nucleated sections and spermaries were measured and classified into developmental stages according to earlier studies on gametogenesis in scleractinians [11 ,37 ,51 –54 ]. The presence of embryos in the gastrovascular cavity and mesenterial septa was recorded, and their stage of maturation identified [2 ,35 ]. The size of each reproductive element was determined as the mean of the two diameters [2 ,43 ].
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10

Contractility Evaluation of TGF-β1-Treated Cells

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Contractility of TGF-β1-treated and -non-treated cells was evaluated by a cell contraction assay in collagen I hydrogel. A 24-well plate was coated with 1 % BSA and incubated at 37 °C for at least 1 h. Cells from 3 donors were encapsulated in 1.81 mg/mL type I collagen with 4 technical replicates at a seeding density of 1.5 × 105 cells/mL. Cells were cultured at 37 °C 2 % O2 in αMEM with 10 % FBS. After 24 h, gels were photographed (Canon PowerShot SX50 HS) and well and gel diameters measured using NIS-Elements D 3.2 (NIKON Japan). Two gel diameters were averaged to calculate the gel area. The gel area after 24 h was divided by the well area, calculated from the well diameter.
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