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33 protocols using q color 3

1

Fungal Micromorphological Characterization

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Dried specimens of the fungi treated in this paper were obtained from the following fungaria: BPI, CBS, DAOM, ILL, ILLS, IMUR, K (incl. IMI), L, NY, NYS, and W. Microscopic specimens were rehydrated in distilled water and mounted on microscopic slides with a No. 1 cover slip. Permanent mounts were made in lactophenol and stained with acid fuchsin. Measurements were made from water or lactophenol mounts. All observations and measurements were made with a Zeiss Universal compound microscope equipped with brightfield, phase, and Nomarski optics. The line drawing was prepared using a Camera Lucida on a Wild compound microscope and illustrated using India ink.
Images of micromorphological structures were captured with a QImaging QColor 3 digital camera mounted on an Olympus BX51 compound microscope using differential interference microscopy. Images were processed using Adobe Photoshop CS6 (Adobe Systems, Mountain View, CA). A minimum of 30 measurements was taken for all morphological structures whenever possible.
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2

Visualizing Mycobacterium leprae Internalization in Amoebae

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Both fluorescence and confocal microscopes were used to visualize extracted and internalized M. leprae by all amoebae spp. studied. Fluorescence microscopy was performed with an Olympus IX71 microscope (Center Valley, PA) using Retiga 2000R (Qimaging, Surrey, BC, Canada) and Qcolor3 (Olympus) cameras. Qimaging and Slidebook software (Intelligent Imaging Innovations, Inc., Denver, CO) were used for image acquisition and analysis on a Macintosh G5 dual processor computer (Apple Computer, Cupertino, CA). Confocal microscopy was performed on a Zeiss LSM 510 confocal microscope. To determine the spatial occupancy of M. leprae within amoebae, serial optical sections were imaged of infected amoebae and were taken at 0.2 nm intervals using a 514 nm excitation laser and 560±20 nm emission filters.
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3

Polarized Light Microscopy Analysis

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All formulations were applied (10 μL) on a glass slide and covered with a coverslip. Samples were observed by PLM (Olympus BX41, Tokyo, Japan) with a plug (QColor3 Olympus America, Inc.) at 20 × magnification and 25 °C. The samples were then analyzed for the presence of anisotropy or isotropy within the dispersion29 .
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4

Intracellular Adriamycin Delivery via A-NOA Particles

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For the intracellular adriamycin delivery, A-NOA particles (1 mg/1 mL) were internalized into MCF-7 cells which are placed in a petri dish. The cells are removed from the petri dish after 30 min, and are washed three times with 1X PBS. Afterward, the cell is mounted on a microscope slide and a PDMS micro chamber was placed on the microscope slide. The microscopy system consisted of an inverted microscope (Olympus IX73) equipped with a dark-field condenser (1.2–1.4 numerical aperture) and a white light source (Xenon Arc Lamp) to acquire images. Then, using a digital camera, the dark images of the treated cell and A-NOA were acquired (Q-color3, Olympus). A monochromator (Acton Research) with a cooled spectrograph coupled charge device (CCD) camera was used to gather scattering spectra from the samples at different locations (Roper Scientific). In front of the monochromator, we set up a 2 μm-wide aperture to hold only a single probe in the region of interest.
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5

Intestinal Tissue Absorptive Capacity Evaluation

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After euthanasia, jejunum samples were removed and fixed in 10% buffered formalin for 24 h and then stored in 70% alcohol. Soon after, samples were dehydrated in alcohol and fixed in paraffin. The sections were stained with hematoxylin-eosin (H&E) for villus height measurement, which is a marker of intestinal tissue absorptive surface. Villus height was measured from the baseline to the top in clear transversal sections. Ten villi per animal were analyzed using an optical microscope (Olympus CX3, Japan) and an image acquisition system (Q-Color 3, Olympus). Measurements were taken from captured digitalized images using ImageJ 1.4® software (NIH, USA) after proper calibration. All analyses were done blindly by an experienced histologist.
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6

Stereological Analysis of Testis Microstructure

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After albuginea removal, fixed testis samples were dehydrated in ethanol and embedded in glycol methacrylate (Leica Microsystems, Wetzlar, Germany). Three-micrometer-thick semiserial sections were obtained in a rotary microtome. To avoid analyzing the same histologic area, one out of every 20 sections was collected and used. Testis slices were stained with 1% toluidine blue/sodium borate [6 (link)]. Stereological estimations were obtained from digital images captured at different magnifications using a light microscope (Olympus BX-60, Tokyo, Japan) equipped with a digital camera (Olympus QColor-3; Tokyo, Japan) [29 (link)]. Stereological principles [30 (link)] were applied to investigate the general testis microstructure. The volume densities (Vv) (%) of seminiferous tubules, intertubules, blood vessels, lymphatic vessels, and connective tissue were estimated in 10 histological fields per animal (200x magnification) using a point counting method and the equation Vv = Pp/Pt, where Pp is the number of test points hitting the structure of interest and Pt is the total points in the test system (Pt = 266).
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7

Histological Assessment of Cardiac and Vascular Pathology

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Ventricles were harvested following sacrifice and processed as previously described [9 (link)]. Ventricular transverse sections (8 μm) were stained with Masson’s trichrome to assess LV fibrosis. Macrophage content was detected by RAM-11 staining as previously described [10 (link)]. Aortic valves were opened longitudinally, and the three valvular cusps were separated. Left coronary cusps were immediately frozen in an embedding medium and stored at -80°C. The region of analysis (ROA) was composed of 1000 μm of the Valsalva sinus from the leaflet base and 500 μm of the leaflet from the leaflet base as previously described [12 (link)]. Haematoxylin-phloxin-safran (HPS) and von Kossa stained sections were prepared for plaque examination and tissue calcification, respectively and as previously described [10 (link),12 (link)]. Pictures were taken at 4X (HPS and Von Kossa staining on left coronary cusp), 10X (for RAM-11 and Sirius Red staining on LV sections) or 20X magnification (for Masson’s trichrome staining on LV sections) using a computer-based digitizing image system using a light microscope (Olympus BX41, Richmond Hill, ON, Canada) connected to a digital video camera Q-Color3 (Olympus, Richmond Hill, ON, Canada) using Image Pro Plus version 9.2 (Media Cybernetics, Bethesda, MD, USA) for picture acquisition and analysis (5 pictures/ LV section).
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8

Histological Analyses and LV Morphometry

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Histological analyses and LV morphometry were performed as previously described [37 (link)]. Briefly, LV sample fragments were collected, fixed in 10% formalin, dehydrated in ethanol, clarified in xylol, and embedded in paraffin. Blocks were cross-sectioned into 5 μm-thick histological sections and subsequently stained with hematoxylin–eosin (H&E) and mounted on histology slides. To avoid repeated analyses of the same histological area, sections were evaluated in a semi-series using one of every 10 sections. Slides were visualized, and images were captured using a light microscope (Olympus BX-50, Tokyo, Japan) connected to a digital camera (Olympus Q Color-3, Tokyo, Japan). Subsequently, analyses of the myocyte cross-sectional area (CSA), total collagen, percentage of cardiomyocytes, and extracellular matrix were performed.
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9

Immunohistochemical Evaluation of ER Stress in FFPE Tissues

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All tissue samples (mouse and human) were processed as 5-mm-thick FFPE tissue sections and stained by the pathology core laboratory. Antibodies included: acetylated α-tubulin (Sigma 17451) 1:1000 for 90 min at RT, GRP78 (Santa Cruz sc-1050) 1:250 overnight at 4 °C, XBP-1 (Santa Cruz) 1:150 overnight at 4 °C, HDAC6 (Cell Signaling) 1:100 90 min at RT, CHOP (Cell Signaling 1:300 90 min RT). After washing biotinylated secondary antibody (Vector Laboratories) and diaminobenzidine (DAKO) were applied then counterstained with Harris hematoxylin. The TUNEL assay was performed by the pathology core facility in accordance with the manufacturer’s instructions (Roche 11068408170910).
All samples were evaluated and marker analysis results were recorded in a double blind fashion by two independent investigators at two different time points. A positive result was defined as >20% tumor cells demonstrating protein expression (29 (link), 30 (link)). Samples were scored in a semi-quantitative manner into high intensity staining (+2) or low intensity staining (+1). Staining results were correlated with clinical data. Images were obtained with an Olympus BX41 microscope and captured with Camera Olympus q capture, q color-3 at 20× and 40× magnification.
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10

Lung Tissue Histological Analysis

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After BAL fluid was collected, lungs were inflated with 1 ml 10% formalin through the trachea and fixed in formalin by immersion. Blocks of lung tissue were cut from around the main bronchus and embedded in paraffin; 2–3 tissue sections (4 μm) per mouse were then affixed to microscope slides and deparaffinized. The slides were then stained with hematoxylin and eosin (H/E) or periodic acid-Schiff (PAS). The pictures of slides were taken with a microscope (BX40; Olympus America Inc., Melville, NY) equipped with a digital camera (Q-color 3; Olympus America Inc.). Goblet cell metaplasia was quantified from PAS+ areas along the airway epithelium using NIH ImageJ software (version 1.38), available on the Internet at http://rsb.info.nih.gov/ij/download.html. Four different fields per slide in 5 samples from each group of mice were examined in a blinded manner.
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