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11 protocols using dm2000 optical microscope

1

Tumor Growth Evaluation in Mice

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For each mouse (n=6), tumor size was assessed thrice per week by caliper measurement. Tumor volume was calculated as follows:
Volume=D×d2×π/6 where D and d are the longer and the shorter diameters, respectively. After ex vivo OI acquisitions, explanted organs and sc tumor masses were fixed in 10% buffered-formalin solution and embedded in paraffin for histological analysis, or embedded in OCT (optimal cutting temperature) compound embedding medium (Miles, Inc., Diagnostics Division, Elkhart, IN, USA) and snap-frozen at −80°C for fluorescence microscopy. For confocal microscopy analysis, sections of 30 μm thickness were cut from frozen organs with a cryostat at −20°C and analyzed using confocal microscope Eclipse te300 (Nikon Corporation, Tokyo, Japan). Immunohistochemical analysis of the tumoral masses were performed with hematoxylin and eosin to evaluate the tissue morphology, and with the avidin–biotin–peroxidase complex to localize CD5, CD20, CD45, and CD79a antigens.25 (link) The slides were examined under a Leica DM2000 optical microscope (Leica Microsystems).
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2

Assessing Cancer Cell Migration

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Migration ability of cancer cells was assessed by wound-healing and Transwell assays. In the wound-healing assay, the cells were cultured into 6-well plates at a density of 2×105 cells/well. When the cells grew to 90% confluence, they were incubated with mitomycin-C (10 µg/ml) for 1 h to suppress proliferation and then starved in serum-free medium for 24 h. An artificial wound was created by scraping the cell confluent monolayer with a 10-µl pipette tip. The migration gap of the wound was assessed after 48 h. The migration and invasion potential was also evaluated by Transwell assay. The cells were treated with mitomycin-C (10 µg/ml) for 1 h at 37°C in serum-free medium and then plated into the upper chamber. For the migration assay the cells were seeded with a density of 2×104 cells/insert, and for the invasion assay cells are seeded into the top chamber coated with Matrigel (BD Biosciences, Franklin Lakes, NJ, USA) at a density of 4×104 cells/insert. Then DMEM with 10% fetal bovine serum (FBS) was added into the bottom chamber. After incubation for 24–48 h, the cells adhering to the lower membrane of the inserts were stained with 0.1% crystal violet and observed by a Leica DM2000 optical microscope (Leica Microsystems) then counted by ImageJ k1.45 software (National Institutes of Health). All the experiments were replicated in triplicate.
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3

Immunohistochemical Analysis of Prostate Samples

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Prostates were fixed in formalin and embedded in paraffin. 5 μM sections were stained with Mayer-Hematoxylin and Eosin (H&E). Alternatively, after re-hydratation and antigen retrieval, immunohistochemistry was performed using the streptavidin-biotin-peroxidase complex method, and 3,3′-Diaminobenzidine tetrahydrochloride as chromogenic substrate. Primary antibodies were: Ki67 (TEC-3, Dako, Glostrup Denmark), N-cadherin (Abcam, Cambridge, MA, USA), Laminin (Biodesign, Memphis, TN, USA), Androgen Receptor (Merck Millipore, Milano, Italy) Synaptophysin (Abcam,), SV40 Tag (clone pAb101, BD Biosciences, Buccinasco Italy), OPN (AbCam). Slides were analyzed under a Leica DM2000 optical microscope equipped with a Leica DFC320 digital camera (Leica Microsystems, Milan, Italy).
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4

Microscopic Imaging of Material Samples

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Samples were observed at room temperature using a Leica DM 2000 optical microscope (Leica Microsystems, Heerburg, Switzerland). The images were taken at 200Xmagnification using a Leica EC3 digital camera and elaborated with the Leica Suite Las EZ software (Leica Microsystems, Heerburg, Switzerland).
For scanning electron microscopy, samples were mounted on aluminium sample holders and sputter coated with 10 nm of gold using a Sputter Coater 108 auto (Cressington Scientific Instruments, Watford, United Kingdom). The aluminium holder was transferred to the SEM unit (EVO 40XVP, Carl Zeiss, Milan, Italy), which was at ambient temperature and under vacuum. Samples were imaged using an acceleration voltage of 20 kV and SmartSEM v. 5.09 (Carl Zeiss, Milan, Italy) application software was used to capture images of the samples. Images were taken at 1000X magnification and saved in tiff format resulting in 1696 x 2048 pixels.
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5

Microscopic Examination of Plant Cells

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Fresh cells from suspension and callus cultures were examined in filter-sterilized (0.2 μm) distilled water post-autoclaving (FDW) or autoclaved MS medium under 100× oil objective directly or after applying the bacterial stain, Gram’s crystal violet or safranin (0.1–0.5%). An Olympus BX50 photomicroscope equipped with QImaging Micropublisher RTV 5.0 megapixel digital camera (Olympus, Tokyo) and a Leica DM 2000 optical microscope with a DFC-295 digital live camera and Leica Application Suite (LAS) software version 3.8 (Leica Microsystems CMS GmbH, Wetzlar, Germany), were employed for bright-field and phase-contrast microscopy. Live movie files were recorded under bright-field for 20–30 s using the LAS software. The DM2000 microscope allowed generous horizontal scanning and 30–40 µm vertical scanning. Adobe Photoshop (7.0) was used for editing the images, and Microsoft Windows 10.0 Movie Maker for video editing.
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6

Evaluating Oxidant Toxicity on Oral Cells

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The toxicity of the oxidant solution was evaluated using the Trypan blue method on oral epithelial cells present in saliva after desquamation. Trypan blue that enters living cells is immediately expelled: the living cells do not have a colored appearance whereas the dead cells appear colored in blue. The saliva of 6 adults (5 women and 1 man aged 25–65 years) was collected in sterile containers (Deltalab™). A volume of 50 µL of saliva diluted twice (in 0.9% NaCl) was mixed with 50 µL of a Trypan blue solution (Merck™) at a concentration of 0.4 g/100 mL. The percentage of dead cells (on a total of at least 120 cells in each preparation) was observed between a slide (Thermo Scientific™, Braunschweig, Germany) and coverslip (Marienfeld, Lauda-Königshofen, Germany) on a Leica DM2000 optical microscope (Leica™, Wetzlar, Ger-many). A 30-minute incubation (room temperature) of 100 µL of saliva with 100 µL of iodine–thiocyanate complexes solution or 0.4% (w/v in phosphate buffer) chlorhexidine digluconate (Sigma-Aldrich™) preceded the microscopic examination to check the toxicity of these compounds.
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7

Immunohistochemical Analysis of AS Gut

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Gut specimens from patients with AS were divided according to the histological results as previously described 21 (link) into three groups: normal gut histology (n=10), acute (n=8) and chronic (n=12) inflammation. Immunohistochemistry was performed as previously described 3 on ileal samples obtained from patients with AS and controls and tonsils (considered as positive controls). A list of primary and secondary antibodies used is provided in online supplementary table S2. The number of positive cells was determined by counting positively stained cells on photomicrographs obtained from three random high-power microscopic fields (400× magnification) under a Leica DM2000 optical microscope, using a Leica DFC320 digital camera (Leica, Rijswijk, the Netherlands). To specifically address the presence of cryptopatches and ILCs, triple stainings were performed on paraffin-embedded sections of human ileum and the sections were treated with FITC-, Rhodamine Red or Cy-5-conjugated antimouse or antirabbit antibodies (Invitrogen), plus RNasi (200 ng/mL) and counterstained using Toto-3 iodide (642/660; Invitrogen) or 4 0 ,6-diamidino-2-phenylindole (DAPI) (Life Technologies). Confocal analysis was used to acquire fluorescence staining.
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8

Bright-field Microscopy of Intracellular Bacteria

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Bright-field microscopy was employed to assess the intracellular bacterial presence in field plant tissues of the major experimental species covered in this study. Tender shoots from pruned canes of grapevine “Flame Seedless” and “Thomson Seedless”, the hypocotyls part of 1-week-old seedlings of Arabidopsis and petiole sections from glasshouse grown periwinkle and tobacco, were employed for this. These tissue sections were prepared from surface-sterilized tissues, as per [25 (link)], and video-graphed under bright field microscopy using the Leica DM 2000 optical microscope, as described, for cell cultures.
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9

Immunohistochemical Analysis of Hippocampal Radiation Impact

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The hippocampus of the brain was collected for immunohistochemical analysis. Sections (3 µm in thickness) of formalin-fixed and paraffin-embedded samples were used to analyze the brain morphological changes induced by radiation and the expression of nuclear factor kappa-B (NF-κB) and vascular endothelial growth factor (VEGF). After deparaffinization, the antigen retrieval was performed in citric acid buffer (pH6.0) using an autoclave oven, then the naturally cooled sections were incubated in PBS containing 10% FBS overnight and incubated with NF-κB/VEGF polyclonal antibodies (ab16502 for NF-κB and ab1316 for VEGF, Abcam, Cambridge, MA, USA) at 4°C overnight. After thorough washing in PBS the sections were incubated with the HRP-conjugated secondary antibodies for 30 min. Then the antibody-antigen complex was visualized using DAB reaction and hematoxylin staining for cell nuclei. The stained sections were examined under a DM2000 optical microscope (Leica, Germany) and the images were captured at a magnification of 100×.
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10

Fluorescent Staining for Bacterial Viability

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Fluorescent dyes propidium iodide (PI) and 4′,6′-diamidino-2-phenylindole dihydrochloride (DAPI) can be used to distinguish the viable cell from the dead cells. After obtaining the mid-logarithmic phase bacteria solution as above, the bacteria solution was diluted 100 times and mixed with compound 2 at the concentration of 6 μg/mL. Then the mixture was incubated 2 h and centrifuged at 1,690 g (3,000 rpm) for 15 min at 4°C to harvest the cells. After washing with PBS for 3 times, PI (5 μg/mL) and DAPI (10 μg/mL) was used to dye cells 20 min respectively. Controls were carried out without compounds. The bacterial cells were then visualized and analyzed by employing the LEICA DM 2000 optical microscope with an oil-immersion objective (40 ×). The experiment was repeated three times with duplicates each time.
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