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20 protocols using metamorph 6

1

Tissue Fixation and Immunohistochemical Analysis

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Tissues were fixed in 10% (v/v) phosphate-buffered formalin according to standard procedures,16 (link) paraffin-embedded and cut into consecutive 2.5–3 μm sections that were then stained either with either hematoxylin–eosin and Gomori silver (MicroStain MicroKit, Bologna, Italy), or immunostained with anti-transforming growth factor (TGF)-β1 (sc-146, Santa Cruz Biotechnology) antibodies. Immunoreactions were detected with STAT-Q Peroxidase–AEC Staining System Kit (Innovex Biosciences, Richmond, CA, USA). Images acquired with the Light microscope (ZEISS, Axioskop, Germany) equipped with a Coolsnap Videocamera were quantified with the MetaMorph 6.1 Software (Universal Imaging Corp., Downingtown, PA, USA). Electron microscopyand immuno-electron microscopy observations were performed as described previously.16 (link), 17 (link)
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2

Immunofluorescence analysis of VEGF and VEGF-R1

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To evaluate the expression of vascular endothelial growth factor (VEGF) and its receptor (VEGF-R1) adherent cells were fixed, permeabilized, and blocked as mentioned above. Samples were then incubated with anti-human VEGF and VEGF-R1 (Becton Dickinson Biosciences, San Jose, California, USA) (working dilution, 1 : 500) followed by FITC-conjugated IgG and TRITC-conjugated IgG (working dilution, 1 : 100) (Jackson ImmunoResearch, West Grove, PA, USA), respectively, as secondary antibodies. Cell nuclei were counterstained with DAPI (Vector Laboratories, Inc., Burlingame, CA). All observations were performed under a ZEISS Axioskop 40 light microscope equipped with a CoolSNAP video camera (Photometrics) to acquire images to analyse with MetaMorph® 6.1 software (Universal Imaging Corp, Downingtown, PA, USA).
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3

Quantifying Myelin Loss in Brain Regions

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Six sections were prepared from specific regions within the middle corpus callosum that showed severe myelin loss in LFB stain (region from bregma 0.14 mm to −0.82 mm, 0.16-mm intervals). Brain sections were dehydrated with ethanol grades, incubated in 0.1% luxol fast blue stain solution (solvent blue 38 0.1 g, ethyl alcohol 95% 100 ml, glacial acetic acid 0.5 ml) at 56 °C overnight, and washed with distilled water. Sections were dipped in 0.05% lithium carbonate 30 sec and 70% regent alcohol for gray and white matter differentiation. The slices were incubated in cresyl violet stain for 1 min, dipped in 70% regent alcohol, dehydrated through 2 changes of absolute alcohol, and mounted with Permount (Fisher Scientific). The myelin loss area and integrated optical density (IOD) were analyzed with MetaMorph 6.1 software (Universal Imaging Corp.; Downingtown, PA).
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4

Imaging Lipid Peroxidation in Cells

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For imaging the above described microscopy system was used. Cellular and mitochondria-specific lipid peroxidation were assessed using the C11-BODIPY581/591 (Invitrogen) and a mitochondria-targeted variant of this molecule (MitoPerOx; [55] (link)) biosensor, respectively. Cells were washed with PBS, covered with HT buffer (see above) and mounted onto an inverted microscope equipped with a ×40 1.3 NA Fluar oil-immersion objective. C11-BODIPY581/591 and MitoPerOx display similar spectral properties and were excited at 488 nm for 200 ms using a 505DRLPXR dichroic mirror (Omega Optical Inc.). Emission signals were detected using 510BW40 (oxidized form) and 565ALP (non-oxidized form) emission filters (Omega Optical Inc). 10–15 Random fields of view were routinely analyzed per coverslip using MetaMorph 6.1 software (Universal Imaging Corporation).
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5

Ratiometric Imaging of pH Changes

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For imaging the above described microscopy system was used. Five to 10 min prior to imaging, cells were covered by HT buffer. HyPer and SypHer were alternatingly excited at 420 nm and 470 nm for 200 ms using a 505DRLPXR and 505DRLPXR dichroic mirror (Omega Optical Inc.). Emission signals were directed through a 535AF45 (Omega Optical Inc.) emission filter onto the CCD camera. 10–15 Random fields of view were routinely analyzed per coverslip using MetaMorph 6.1 software (Universal Imaging Corporation).
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6

Time-lapse Microscopy of Cytokinetic Abscission

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Two-dimensional cultures (Supplementary Movie 4 and Supplementary Fig. 4a): For time-lapse phase-contrast microscopy, transient or stably transfected MDCK cells were plated on 35-mm glass dishes (MatTek) and put in an open chamber (Life Imaging) equilibrated in 5% CO2 and maintained at 37 °C. Time-lapse sequences were recorded every 5 min for 48 h (Supplementary Fig. 2a) or every second (Supplementary Movie 4) using a Nikon Eclipse Ti inverted microscope with a × 20 0.45 NA Plan FluorELWD objective (Supplementary Fig. 4a) or a × 100 1.4 NA PL-APO objective (Supplementary Movie 4) controlled by Metamorph 6.1 software (Universal Imaging). This microscope was equipped with a cooled CCD camera (HQ2; Roper Scientific). In Supplementary Fig. 4a, cytokinetic abscission time was quantified in mCherry-tubulin-transfected cells by time-lapse microscopy starting from furrow ingression until the cut of the intracellular bridge. In all, 100 cells per condition were analysed. Supplementary Movie 4 was deconvolved using Huygens Professional software SVI (2 iterations, signal/noise 10).
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7

Rat Colon Tissue Immunostaining and Mucin Analysis

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The 5 μm-thick rat colon tissue slices (paraffin embedded) were deparaffinized with xylene and rehydrated with graded ethanol. The slices were then immunostained with the primary antibody anti-AQP3 (1:30, ab153694; Abcam) and biotinylated secondary antibody (goat antirabbit IgG H&L, ab207995; Abcam). Mucin staining was performed using the Alcian blue stain kit (Abcam) according to the manufacturer's protocol. The 5 μm-thick rat colon tissue slices were stained with an Alcian blue solution (pH 2.5). Digital images were acquired by an optical microscope (Olympus, Tokyo, Japan) and software (MetaMorph 6.1 software; Universal Imaging Corp., Dowingtown, PA, USA).
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8

Cardiomyocyte Mitochondrial Membrane Potential

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ΔΨm was assessed in intact cardiomyocytes using the laser-scanning confocal microscope (Eclipse TE2000-U; Nikon, Tokyo, Japan) and the fluorescence indicator tetramethylrhodamine ethyl ester (TMRE, 100 nM, Molecular Probes, USA), as we previously described (Sedlic et al., 2010b (link)). Excitation/emission wavelengths, λex/λem, for TMRE were 543/560–610 nm, respectively. TMRE was loaded for 20 min, followed by dye washout and dana acquisition. Data were analyzed with MetaMorph 6.1 software (Universal Imaging, USA). High glucose, DNP or mannitol were present during the dye loading and throughout recording. In groups with APC, TMRE was loaded into cells after the application of isoflurane for 20 min and its washout for 10 min.
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9

TIRF Imaging of US28-pHluorin in HeLa Cells

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For US28-pHluorin TIRF imaging, HeLa cells on poly-l-lysine-coated round 18 mm coverslips in a 12 wells plate were transfected with 500 ng HA-US28-pHluorin plasmid using Lipofectamine 2000 (Invitrogen). 24 hours after transfection, coverslips were placed in an imaging chamber, perfused with Tyrode’s solution and imaged on a microscope (Zeiss, Axiovert 200M) equipped with an EMCCD camera (Cascade, Roper Scientific). For TIRF imaging, a laser beam from an air-cooled argon ion laser was coupled into a 100 × 1.45 N.A. TIRF objective via a TIRF condenser (TILL Photonics). Images were acquired at 2 Hz with MetaMorph 6.2 software (Universal Imaging). Imaging experiments were performed at room temperature (21°C–24°C).
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10

Confocal Microscopy of Cardiomyocytes

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Isolated cardiomyocytes were placed in a polycarbonate recording chamber (Warner Instruments, Hamden, CT) on a confocal microscope stage, and cells were allowed to settle and spontaneously attach to the bottom of the recording chamber for 10 min. Cells were imaged using an inverted laser-scanning confocal microscope (Nikon Eclipse TE2000-U, Tokyo, Japan) with a 60x/1.4 oil-immersion objective (Nikon). Settings of the confocal microscope were consistent in all experimental groups. Fluorescent images were acquired using the EZ-C1 2.10 software (Nikon) and data were analyzed off-line with the MetaMorph 6.2 software (Universal Imaging, West Chester, PA). Results were expressed as percent change in fluorescence intensity relative to baseline (F0; where baseline = 100%).
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