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82 protocols using axioscope 2 microscope

1

Oxidative Stress Induction and Antioxidant Evaluation

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For oxidative stress generation, 500 µM of TBH (tert-butyl hydroperoxide, Luperox® TBH70X, Merck Life Science S.r.l., Italy) was used for 2 h, alone and in combination with grapefruit-seed-extract treatment. The control (Ctrl) groups received an equal volume of the medium. For the DCFH-DA assay (Abcam, Milan, Italy) extracts were utilized at 100 µg/mL for 2 h. The treated and control cells were analyzed by using microscopy (Axio Scope 2 microscope, Zeiss, Germany). At the end of the treatments, each sample was added to DCFH-DA (100 µM) and placed in the dark for 10 min at room temperature. After washing with PBS, cells were analyzed using a Microplate Reader GloMax fluorimeter (Promega Corporation, Milan, Italy) at the excitation wavelength of 475 nm and emission wavelength 530 nm for fluorescence intensity detection, and results were expressed as a percentage of the control group. Cell fluorescence was also visualized using the fluorescence microscope Zeiss Axio Scope 2 microscope (Carl Zeiss, Oberkochen, Germany).
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2

Quantifying Vacuole Formation in Fly Brains

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Paraffin sections for light microscopy were prepared and analyzed for vacuole formation as described in (Botella et al., 2003 (link); Sunderhaus and Kretzschmar, 2016 ). Briefly, whole flies were fixed in Carney’s fixative and dehydrated in an ethanol series followed by incubation in methyl benzoate before embedding in paraffin. Sections were cut at 7 µm and analyzed with a Zeiss Axioscope 2 microscope using the auto-fluorescence caused by the dispersed eye pigment. To quantify the vacuolization, we photographed sections without knowing the genotype at the level of the great commissure and numbered the pictures for a double-blind analysis. The area of vacuoles in the deutocerebral neuropil was then calculated in ImageJ as total pixel number, converted into μm2, and the genotype/treatment determined. Statistical analyses were done using GraphPad Prism with an unpaired two tailed Student’s t-test or one-way ANOVA and a Sidak’s correction for multiple comparisons.
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3

Immunocytochemistry for ESRRB in mESCs

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mESCs grown on glass coverslips coated with gelatin were fixed with 4% PFA for 20 mins, blocked in 10% donkey serum (Sigma) in 0.1% Triton X-100 for 1 h and incubated o/n with primary antibody detecting ESRRB (Perseus Proteomics, PP-H6705-00) at a 1:500 dilution at 4°C. The following day, samples were incubated with Donkey anti mouse Alexafluor 555 (Cat: A-31570, Thermo Fisher) at room temperature for 1 h. Nuclei were counterstained with DAPI. Imaging was carried out using a Zeiss Axioscope 2 microscope.
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4

Age-Dependent Brain Vacuolization Analysis

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Flies of each genotype were aged to 20 days and heads were processed as previously described [19] (link), [20] (link). Briefly, heads were cut in 7 µm serial sections, the paraffin was removed in SafeClear (Fisher Scientific), sections were embedded in Permount, and analyzed with a Zeiss Axioscope 2 microscope using the auto-fluorescence caused by the eye pigment (no staining was used). Experimental and control flies were put next to each other in the same paraffin block, cut, and processed together. Microscopic pictures were taken at the same level of the brain, the vacuoles (identified by being unstained and exceeding 50 pixels in size) were counted and the vacuolized area was calculated using our established methods [19] (link), [20] (link).
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5

Fungal Culturing and Identification Protocol

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Agar plugs (6 mm diam) were taken from the edge of actively growing cultures on MEA and transferred onto the centre of 9 cm diam Petri dishes containing 2 % tap water agar supplemented with sterile pine needles (PNA; Smith et al. 1996 ), potato dextrose agar (PDA), oatmeal agar (OA) and MEA (Crous et al. 2009 ), and incubated at 20–21 °C under a 12 h near-ultraviolet light/12 h dark cycle to induce sporulation as described in recent studies (Gomes et al. 2013 (link), Lombard et al. 2014 ). Colony characters and pigment production on MEA, OA and PDA were noted after 10 d. Colony colours were rated according to Rayner (1970) . Cultures were examined periodically for the development of ascomata and conidiomata. Colony diameters were measured after 7 and 10 d. The morphological characteristics were examined by mounting fungal structures in clear lactic acid and 30 measurements at ×1000 magnification were determined for each isolate using a Zeiss Axioscope 2 microscope with interference contrast (DIC) optics. Descriptions, nomenclature and illustrations of taxonomic novelties are deposited in MycoBank (www.MycoBank.org;Crous et al. 2004b ).
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6

Fluorescence Analysis of Cultured Neurons

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For fluorescence and histochemistry of cultured primary neurons, isolated cells were seeded onto polylysine-treated 12 mm glass coverslips (placed in 12 well plates) and allowed to mature for 7 days in culture before glutamate treatment. Following treatment, cells were fixed in 4% paraformaldehyde for 20 min, permeabilized (10% goat serum in PBS containing 0.01% Triton-X) for 20 min, and then blocked (10% goat serum in PBS) for 60 min. Cells were incubated with anti-CRMP2 antibody (diluted 1:1000 in block buffer) overnight at 4 °C, then PBS washed, and incubated in an anti-rabbit-Alexa488 secondary antibody (1:500 in block buffer), anti-phalloidin-Tritc (1 μM, Sigma), and DAPI (1 μM, Sigma) for 60 min and a final PBS wash before being mounted onto glass slides using antifade mounting media (Prolong Gold, Invitrogen). A Zeiss axioscope2 microscope using a 40× objective lens equipped with Zeiss HRc camera with filter sets for FITC (green) and Rhodamine (red) was used to take images for histological analysis. Identical settings and exposure time were used to capture images for both peptides. Images were processed using Zen blue software (Zeiss) to generate tiff images before importing them into ImageJ software (NIH, version 1.5b), and the number of blebs were counted in fields.
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7

Fungal Morphological Characterization Protocol

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Axenic cultures were grown on synthetic nutrient-poor agar (SNA; Nirenburg 1981) amended with 1-cm2 sterile filter paper and carnation leaf pieces, and on PDA as described by Cabral et al. (2012a) . Gross morphological characteristics were studied by mounting the fungal structures in 85 % lactic acid and 30 measurements were made for all taxonomically informative characters at ×1000 magnification using a Plan-Apochromat × 100/1.4 oil immersion lens (Carl Zeiss, Germany) mounted on a Zeiss Axioscope 2 microscope, with differential interference contrast (DIC) illumination. The 95 % confidence levels were determined for the conidial measurements with extremes given in parentheses. For all other fungal structures measured, only the extremes are provided. Colony colour was assessed using 7-d-old cultures on PDA incubated at room temperature and the colour charts of Rayner (1970) . All descriptions, illustrations and nomenclatural data were deposited in MycoBank (Crous et al. 2004 ). Optimal and cardinal growth temperatures were determined by inoculating 90 mm diam PDA plates with a 4 mm diam plug cut from the edge of an actively growing colony. Each isolate was incubated at 4, 10, 15, 20, 25, 30, and 35 °C with three replicate plates per strain at each temperature. Colony diameter of each isolate was determined after 1 wk by measuring the orthogonal directions.
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8

Fluorescence Microscopy of Yeast Cultures

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Differential interference contrast (DIC) and fluorescence microscopy images were captured from living cells with Axioscope 2 microscope (Zeiss; Jena, Germany). Images were acquired with a Cool‐SNAP‐HQ 12‐bit monochrome digital camera (Roper Scientific; Trenton, NJ, USA). Yeast cultures were grown exponentially in liquid growth medium (YPD or YPG) supplemented with the indicated drugs. Cell samples were collected and concentrated 10‐fold by centrifugation (12 000 g, during 1 min at room temperature); then, cell suspensions were incubated with 1 μg ml−1 4′,6‐diamidino‐2‐phenylindole (DAPI) for 5 min to stain the DNA. More than 200 cells from at least three independent experiments were analysed in each measurement.
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9

Phagocytosis and Cell-Cell Interaction Assays

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Cells were grown in 1 cm2 wells with 500 µl culture medium for 24 h, washed once with medium and then incubated with 50 µl FITC-latex beads (0.1 µm particle size, Cayman Chemical Company, Ann Arbor USA) for 12 h. Alternatively, cells were incubated for 6 h with isolated PBLs (small cell suspension fraction of previously cryo-preserved peripheral blood mononuclear cells (PBMC) isolated from buffy-coats, according to standard Ficoll density gradient protocols). After incubation, cells were washed two times in PBS, detached with trypsin/EDTA, centrifuged at 600 rpm for 3 min and deposited onto glass slides using a cytocentrifuge (Shandon, Pittsburgh, PA, USA). Then the slides were fixed in 100% ethanol for 1 min and air-dried. PBL incubated cells were counterstained with Hematoxylin. Latex bead incubated cells were stained with anti-HLA-DR and the secondary antibody goat anti mouse-Cy3 (Jackson Immunoresearch, Newmarket, UK) according to standard immunocytochemical protocols, counterstained with DAPI (1 µg/ml) and mounted with Vectashield (Vector Laboratories, Burlingame, USA). The slides were analyzed using an Axioscope-2 microscope (Zeiss, Germany) equipped with appropriate filter sets (AHF, Tübingen, Germany), the CCD camera Jai-M 300 and the ISIS software from Metasystems (Altlussheim, Germany).
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10

Immunohistochemical Analysis of RAD6 and SOX2 in Ovarian Tumors

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Ovarian tumor tissues collected before and after chemotherapy were stained for the expression of RAD6 and SOX2 proteins by immunohistochemistry. Antigen retrieval was carried out by heating the tissue specimens in 10mM sodium citrate buffer, pH 6.0. Endogenous peroxidase activity was inhibited by incubating the sections in 3% hydrogen peroxidase for 10 min. Tissue sections were incubated with specific primary antibodies, followed by a specific biotinylated secondary antibody, and then conjugated HRP streptavidin and DAB (3,3′-Diaminobenzidine) chromogen (Vector Laboratories, Burlingame, CA) and tissues were counterstained with hematoxylin (Vector Laboratories). Stained sections were analyzed by Zeiss Axioscope 2 microscope and images captured by AxioCam camera. DAB intensity was analyzed by Fiji Image J software. This process was carried out without any knowledge of the identity of each tissue sample to prevent bias in scoring the samples.
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