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36 protocols using ti s inverted microscope

1

Fungal Isolate Characterization and Phylogeny

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The isolates were purified using single spore isolation and stored at 4°C on PDA slants for further use. They were stored on filter paper at -80°C for long-term preservation. Isolates were transferred from PDA slants to PDA plates and cultivated at 28°C under a 12-h photoperiod for 14 days. The following morphological characteristics were recorded: conidia, appressoria, conidiomata, and conidiophores. The mean lengths and widths of 100 randomly selected conidia from each isolate were measured using 100× magnification in a microscope (Nikon Ti-S inverted microscope, Japan). Among the 36 isolates thus obtained, 11 representative isolates were selected for further multi-locus phylogenetic analyses based on geographical location, morphology (e.g., colony shape and color and other physical characteristics of aerial mycelia and conidia), and ITS sequences.
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2

Wound Healing Assay for Cell Migration

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Wound healing assay was used to evaluate cell migration. HUVECs seeded in 6-well culture plate were incubated to full monolayer. Monolayer HUVECs were wounded by scratching with a pipette tip and washed twice with phosphate buffer solution (PBS). Fresh medium containing 1% FBS was then added together with caudatin or other reagents as designed. Cells were photographed under a Nikon Ti-S inverted microscope at the beginning and after incubation for 48 h (magnification, ×100; Nikon Corporation, Tokyo, Japan). Cell migration distance was measured by image plus software, and the migrated rate was expressed as percentage of control. Three independent experiments were performed.
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3

Measuring TCR-Induced Calcium Signaling

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Cells were loaded with Fura-2 AM as described previously [27 (link), 28 (link)] and placed in an imaging chamber with a glass bottom pre-coated with Poly-L-lysine. Images were taken on a Nikon TiS inverted microscope (Tokyo, Japan) with a 40× oil immersion objective, and images were taken every second with a Photometries Evolve electron-multiplying charged-coupled device camera (Tucson, AZ). Cells were pretreated with αCD3 antibody and secondary IgG antibody was added after baseline recording to initiate TCR signaling.
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4

Laser-Assisted Embryo Hatching and Biopsy

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On the third day of embryo development (D3), laser-assisted hatching (AH) was
performed on the zona pellucida to facilitate the hatching of the cells to be
biopsied. Only blastocysts categorized as grade 3 or better were biopsied.
During biopsy, six to ten trophectoderm cells were harvested.
All biopsies were performed using a Nikon Ti-S inverted microscope. An OCTAX
laser was used in the procedures. The blastocysts were biopsied on plates
containing three 10µL drops of Gmopsplus (Vitrolife, Sweden) covered with
mineral oil (Irvine Scientific).
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5

Microscopic Imaging of Tissue Samples

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Tissue sections were viewed using a Nikon Ti-S inverted microscope and digital images were captured with Nikon DS Ri2 cooled color camera, X-Cite 120LED BOOST System lamp from Excelitas, and Nikon Imaging Software, NIS Elements (Nikon, Tokyo, Japan). Bright field images of H&E, LDH, and Ki67 were taken at 40X magnification. IIF images were captured at 40X for K15 and using filters for Texas Red (K15) and DAPI (nuclear) and the images were then merged using NIS elements software.
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6

Immunohistochemical Analysis of 4-Hydroxynonenal

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After deparaffination and microwave antigen reparation, sections were pretreated with 3% H2O2 for 20 minutes to reduce the endogenous peroxidase activity. Then the sections were ordinally incubated with the blocking buffer (10% normal goat serum) at room temperature for 1 hour, then with primary antibodies of 4-hydroxynonenal (HNE) (1/100 dilution; Abcam, Cambridge, UK) at 4°C overnight, followed with biotinylated secondary antibody (1 : 200, Santa Cruz Biotechnology, Inc., Santa Cruz, CA, USA) and avidine-biotinylated peroxidase complex (Vectostain ABC-Kit, Vector Lab, Burlingame, CA, USA) at room temperature for 1 hour. Coloration of sections was processed with diaminobenzidine (DAB, Vector Laboratories, Burlingame, CA, USA) and finished with distilled water. After counterstaining with hematoxylin for 30 seconds, sections were dehydrated with graded ethanol, cleared with dimethylbenzene, and mounted with neutral gums. Figures were captured with a Ti-S inverted microscope (Nikon, Japan) and analyzed with Image-Pro Plus software (version 6.0, Media Cybernetics, USA).
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7

Fura-2-based Calcium Imaging of ASMCs

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Calcium imaging using fura-2 was adapted from a previously published protocol with minor modifications46 (link). Briefly, ASMCs were loaded with 2 μM fura-2-AM (Thermo Fisher) and 24 h old serosal media from HBECs or media containing recombinant BPIFA1 at 37 °C for 1 h. ASMCs were then washed with a standard Ringer's solution (101 mM NaCl, 12 mM NaHCO3, 1.2 mM MgCl2, 1.2 mM CaCl2, 0.2 mM KCl, 24 mM HEPES, 10 mM glucose, pH 7.4) or with Ca2+-free Ringer's solution as indicated. Cultures were then placed in the Ringer's solution, and images were collected with a 40 × 1.4 NA Plan Fluor oil objective on a Nikon Ti-S inverted microscope. Fura-2 fluorescence was acquired alternately at 340 and 380 nm (emission >450 nm) using LUDL filter wheels, obtained with an Orca FLASH 4.0 CMOS camera (Hammamatsu) and controlled with HCImageLive software (Hammamatsu). Cell bodies were identified as individual regions of interest (ROIs). Background subtraction was performed using a cell-free region as the background region. Signals were converted to relative changes (F/F0) where F0 was the ratio of the average fluorescent intensity (340/380) of ROIs at 0 time point. Typically, 20 cells per coverslip were recorded. ΔF/F0 represents average peak fluorescent intensity changes of three independent experiments.
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8

Imaging Single-Molecule Gyrase Activity

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The instrumentation used to collect data and correct for drift were the same as those used in previous work to image single-molecule gyrase activity (17 (link), 20 (link)). Magnetic tweezers were implemented on a modified Nikon Ti-S inverted microscope (20 (link)). The rotor beads were imaged via dark-field evanescent scattering using an 845-nm single-mode diode laser (Lumics, LU0845M200). A custom mount was used to hold diametrically opposed mirrors below the back pupil of the objective (0.13-0.21 WD, Nikon, TIRF, 60×/1.43) to provide separate paths for excitation path and the totally internally reflected return beam. The return beam was directed to a position-sensitive detector (Pacific Silicon) to provide a signal for focus stabilization feeding back to an xyz piezo stage (Mad City Labs). The light scattered by the rotor bead was imaged through an optical path splitter (Optosplit III, Cairn Research) onto a high-speed CMOS camera (Mikrotron, EoSens CL).
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9

Calcium Imaging of Staurosporine-Treated Cells

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Coverslips with GCaMP6s transfected HeLa cells or HEK293T cells were mounted in an imaging chamber and bathed in Leibovitz’s L-15 media at room temperature and allowed to rest for 30 min. Images were captured every 60 seconds on a Nikon TiS inverted microscope with a 40x oil objective. Baseline fluorescence (F0) was determined by using the average intensity of the first 20 images before treatment. Cells were imaged for up to 10 hrs after treatment with 10μM staurosporine (or DMSO for control). A calcium release event was defined as a 1.5-fold rise in fluorescence intensity over the baseline (ΔF/F0>1.5).
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10

Osteogenic Differentiation of hBMSCs by CQD

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To test the effect of CQD-1 on hBMSCs’ differentiation, hBMSCs were cultured in osteogenic medium (OM) containing 10 mM β-glycerophosphate, 100 μM l-ascorbic acid 2-phosphate, and 10 nM dexamethasone (Sigma). Cells were cultured in the presence of PBS (Control group), OM (OM group), 1 μg mL−1 CQD (OM + 1 μg mL−1 CQD group), 10 μg mL−1 CQD (OM + 10 μg mL−1 CQD group), and 100 μg mL−1 CQD (OM + 100 μg mL−1 CQD group) for 7 d and 14 d. To observe mineralized nodules, hBMSCs were stained with 1% Alizarin Red S (Sigma) for 15 min at RT to detect mineral nodules after being fixed with 4% PFA for 1 h at 4 °C, after 7 d and 14 d incubation with conditioned medium. The stained cells were observed under the TI-S inverted microscope (Nikon, Tokyo, Japan) at 10× magnification. Experiments were performed in triplicate and repeated at least 3 times.
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