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19 protocols using metamorph 4

1

Quantifying Goblet Cell Hyperplasia

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After BAL fluid collection, the left lung was inflated with 10% formalin at a standard pressure. Lung tissues were then embedded in paraffin, and 3-µm-thick sections were cut and stained with periodic acid-Schiff (PAS) to determine goblet cell hyperplasia. Stained tissue sections were examined with an Olympus BX40 microscope in conjunction with an Olympus U-TV0.63XC digital camera (Olympus Corp., NY, USA). Images were acquired using DP Controller and Manager software (Olympus Corp., NY, USA). The number of PAS-positive cells per millimeter of bronchial basement membrane (mmBM) was measured by MetaMorph 4.6 (Universal Imaging, PA, USA).
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2

Neuronal Actin Morphometry Analysis

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Neuronal actin-based structures were identified with fluorescein-phalloidin (Molecular Probes, Eugene OR) and nuclei were labeled with Hoechst 33258 (Sigma). Neuronal images were captured using a Zeiss Axiovert S100 (Carl Zeiss, Thornwood NY) microscope. Morphometric analyses were then performed using the MetaMorph™ 4.6 imaging software system (Universal Imaging Corp, West Chester, PA) as previously described (James et al., 2008 (link); Jones et al., 2004 (link)). Briefly, branch numbers were determined by applying the MEASURE COUNT OBJECT function. Branches were scored when they were longer than 10 μm. Processes shorter than 10 μm were designated as sprouts, and not counted as branches. The imaging system was calibrated so that dendrite length measurements were true values. Two-sided t-test analysis was performed using SigmaPlot 10.0 (Systat Software Inc., San Jose CA) to determine differences between drug treatment groups. n= 3 representative neurons/treatment group. Any null hypothesis with the probability level less than 95 % was rejected.
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3

Immunostaining and Fluorescence Microscopy Protocol

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Cultured cells were plated on the coverslips and fixed in warm 4% paraformaldehyde. Following permeabilization in 0.2% Triton X-100, the cells were stained using mouse monoclonal anti-p120ctn. The cells were then incubated with the goat anti-mouse Cy3 conjugated secondary antibodies. The nuclei of the cells were stained with Hoechst 33258. The cover slips were mounted on slides using Anti-Fade medium (Invitrogen) and photographed under the Zeiss Axiovert inverted fluorescent microscope.
To detect cell proliferation and apoptosis, frozen mouse prostate sections were immunostained using anti-Ki67, a marker of cell proliferation and TUNEL assay, which detects cells undergoing apoptosis. Hoechst, a marker for nuclei, was used to stain all cells. Immunofluorescent density analyses were performed using a MetaMorph 4.6 imaging software system (Universal Imaging Corp., West Chester, PA). All data was presented as Mean±SEM and statistically evaluated with a t-test. The confidence level was set at 0.05.
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4

Renal Scarring Quantification Protocol

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Renal scarring was studied using morphometry in previous studies [14 (link), 15 (link)]. Specifically, renal biopsy specimens that were 5 μm thick underwent Jones’ silver staining. Semi-quantitative computerized image analysis was then performed using the Leica Twin Pro image analysis system from Leica Microsystems in Wetzlar, Germany. The analysis utilized MetaMorph 4.0 image-analyzing software from Universal Imaging Corporation in Downingtown, PA, USA. Each patient’s sample included ten glomeruli and ten randomly selected areas, which were evaluated to determine the average percentage of scarred glomerular and tubulointerstitial areas.
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5

Quantitative Fluorescence Recovery After Photobleaching

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FRAP studies were performed as described elsewhere (Hamill et al., 2013 (link); Tsuruta et al., 2002 (link); Tsuruta et al., 2003 ). Time-lapse observations were made using a LSM 510 confocal microscope (Zeiss Inc.) under the following conditions: 100×, 1.4 numerical aperture oil immersion objective, maximum power 25 mW, tube current 5.1A (31% laser power), pinhole 1.33 airy units (optical slice 1.0 µm). GFP images were acquired by excitation at 488 nm and emission at 515–545 nm. Cell regions were bleached at the plane of the membrane at 488 nm, 100% laser power using the minimum number of iterations to cause complete bleaching (20–40). Recovery was monitored at 31% laser power at 1 minute intervals. For quantitative analyses, the fluorescence intensity of (1) the photobleached region, (2) the extracellular background intensity and (3) intracellular brightest intensity were determined using Metamorph 4.0 (Universal Imaging) software. All data were analyzed using Microsoft Excel. Data were adjusted for sample fading as detailed elsewhere (Hamill et al., 2013 (link); Tsuruta et al., 2002 (link); Tsuruta et al., 2003 ).
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6

Quantitative Fluorescence Recovery After Photobleaching

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FRAP studies were performed as described elsewhere (Hamill et al., 2013 (link); Tsuruta et al., 2002 (link); Tsuruta et al., 2003 ). Time-lapse observations were made using a LSM 510 confocal microscope (Zeiss Inc.) under the following conditions: 100×, 1.4 numerical aperture oil immersion objective, maximum power 25 mW, tube current 5.1A (31% laser power), pinhole 1.33 airy units (optical slice 1.0 µm). GFP images were acquired by excitation at 488 nm and emission at 515–545 nm. Cell regions were bleached at the plane of the membrane at 488 nm, 100% laser power using the minimum number of iterations to cause complete bleaching (20–40). Recovery was monitored at 31% laser power at 1 minute intervals. For quantitative analyses, the fluorescence intensity of (1) the photobleached region, (2) the extracellular background intensity and (3) intracellular brightest intensity were determined using Metamorph 4.0 (Universal Imaging) software. All data were analyzed using Microsoft Excel. Data were adjusted for sample fading as detailed elsewhere (Hamill et al., 2013 (link); Tsuruta et al., 2002 (link); Tsuruta et al., 2003 ).
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7

Quantifying Nephrosclerosis in Renal Biopsies

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Jones’ silver staining was performed on 5 µm thick sections of the renal biopsy specimens of each patient. As previously described by others [34 (link)], we used a computerized image analysis method to semi-quantify nephrosclerosis. Briefly, a Leica Twin Pro image analysis system (Leica Microsystems, Wetzlar, Germany) was connected to a Leica DC500 digital camera on a Leica DMRXA2 microscope working with a 40× objective (final calibration: 0.258 mm/pixel), which was connected to a microcomputer for storage of the morphometric measurements so that image analysis could be performed using image analysis software (MetaMorph 4.0; Universal Imaging Corporation TM, Downingtown, PA, USA). A total of 10 glomeruli and 10 randomly selected areas were assessed in each patient and the average percentage of scarred glomerular and tubulointerstitial areas, as represented by the percentage of the area with positive staining, was computed for each patient.
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8

Quantitative Histological Assessment of Renal Lesions

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Histological lesions were classified by the revised Oxford classification [19 (link)]. The severity of glomerulosclerosis and tubulointerstitial fibrosis were further assessed by morphometric study as described previously [20 (link), 21 (link)]. Briefly, Jones’ silver staining was performed on 4 μm thick sections of renal biopsy specimen. Computerized image analysis method was then performed by the MetaMorph 4.0 image-analyzing software (Universal Imaging Corporation™, Downingtown, PA). Ten glomeruli and 10 randomly selected tubulointerstitial areas were assessed for each patient.
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9

Hippocampal Trx2 and Prx3 in Aging Gerbils

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To compare the changes of Trx2 and Prx3 in the hippocampal CA1 region between adult and aged gerbils, immunohistochemistry for rabbit anti-Trx2 (1:500; cat. no. LF-PA0024, Ab Frontier, Seoul, Korea) and mouse anti-Prx3 (1:500; cat. no. LF-MA0045; Ab Frontier) was performed, according to the above-mentioned method. In order to establish the specificity of the immunostaining, a negative control was used, with only the secondary antibody and without primary antibody. This negative control resulted in the absence of immunoreactivity in any structures.
A total of six sections with a 120 μm interval per animal were selected to quantitatively analyze the Trx2 and Prx3 immunoreactivity. Digital images of the hippocampal CA1 region were captured using an AxioM1 light microscope (Carl ZeissAG), equipped with a digital camera (Axiocam; Carl Zeiss AG) connected to a PC monitor. According to the methods of our previous study (7 (link)), semi-quantification of the immunostaining intensities were evaluated using digital image analysis software (MetaMorph 4.01; Universal Imaging Corporation, Downingtown, PA, USA). The level of immunoreactivity was scaled as −, ±, +, ++ or +++ representing no staining (gray scale value ≥200), weakly positive (gray scale value=150–199), moderate (gray scale value=100–149), marked (gray scale value=50–99), or very marked (gray scale value ≤49), respectively.
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10

Immunohistochemical Analysis of Gliosis

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To examine the gliosis, the animals (n=7 at each time) were used at sham, 2, 4, and 7 days after ischemia-reperfusion, and immunohistochemistry for gliosis was performed according to our previous method [23 (link)]. In brief, immunohistochemical staining for rabbit antiglial fibrillary acidic protein (GFAP; 1:800, Chemicon) for astrocytes and rabbit anti-ionized calcium-binding adapter molecule 1 (Iba-1; 1:800, Chemicon) was performed according to the above-mentioned protocol. A negative control test was also carried out using preimmune serum instead of primary antibody in order to establish the specificity of the immunostaining. The negative control test resulted in the absence of immunoreactivity in all structures.
Digital images of the septal region were captured with an AxioM1 light microscope (Carl Zeiss) equipped with a digital camera (Axiocam, Carl Zeiss) connected to a PC monitor. Semiquantification of the immunostaining intensities was evaluated with digital image analysis software (MetaMorph 4.01, Universal Imaging Corp., Downingtown, PA, USA). The level of immunoreactivity was scaled as -, ±, +, or ++, representing no staining (gray scale value, ≥200), weakly positive (gray scale value, 150 to 199), moderate (gray scale value, 100 to 149), or strong (gray scale value, ≤99), respectively.
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