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210 protocols using eclipse te2000

1

Visualizing ROS and Apoptosis in Zebrafish Embryos

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Reactive oxygen species (ROS) in embryos were evaluated with dihydroethidium (DHE) fluorescent staining as in a previously described method [22 (link)]. In brief, zebrafish embryos (n = 20) at 5 h post-treatment were stained with DHE (30 μM). After 30 min incubation in the dark, embryos were rinsed twice with 1 × PBS and visualized under a fluorescent microscope (Nikon Eclipse TE2000, Tokyo, Japan) at the excitation and emission wavelengths of 588 nm and 605 nm, respectively. The apoptosis in the embryos was examined by acridine orange (AO) fluorescent staining [22 (link)]. At 5 h post-treatment, zebrafish embryos (n = 20) from different groups were suspended in 500 μL of AO (5 μg/mL). After 1 h staining, embryos were rinsed two times with 1 × PBS and visualized under a fluorescent microscope (Nikon Eclipse TE2000, Tokyo, Japan) at the excitation and emission wavelength of 502 nm and 525 nm, respectively. Image J software was employed for quantifying the fluorescently stained area.
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2

Assessing ROS and Apoptosis in Tissue

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The method described earlier [23 (link)] was employed to assess the production of reactive oxygen species (ROS) in the tissue section (n = 5 for each group) using dihydroethidium (DHE) fluorescent staining. Briefly, a 250 μL of DHE solution (final, 30 μM) was added to the tissue section. Following 30 min incubation in the dark at room temperature (RT), the stained area was rinsed with tap water and observed using a fluorescent microscope (Nikon Eclipse TE2000, Tokyo, Japan) with excitation at 588 nm and emission at 618 nm wavelength. The extent of apoptosis was examined using acridine orange (AO) fluorescent staining, following a method described previously [24 (link)] with slight modification. In summary, a tissue section (n = 5 for each group) was treated with 250 μL of AO (5 μg/mL). After 30 min incubation in the dark at RT, the stained section was washed two times with tap water and subsequently visualized under a fluorescent microscope (Nikon Eclipse TE2000, Tokyo, Japan) at an excitation wavelength of 505 nm and an emission wavelength of 535 nm.
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3

Genotoxicity Evaluation of Nanoparticles

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To estimate the genotoxic effect of the investigated nanoparticles, we used single-cell gel electrophoresis (SCGE) in the form of alkaline comet assay according to the procedure of [56 (link)]. In our experiments we applied the Comet Assay Kit (Trevigen, Minneapolis, MN, USA). The cells were plated onto a 24-well transparent plate. After 24 h the cells were treated with nanoparticles for a further 24 h. After this time, the cells were trypsinized and suspended in low melting point agarose in PBS, pH 7.4. 50 mL of cell suspension was spread on microscope slides supplied in Comet Assay Kit. After gelling, the slides were treated with lysis buffer containing 2.5 M NaCl, 100 mM EDTA, 1% Triton X-100, 10% DMSO and 10 mM Tris, pH 10 at 4 °C for 1 h. Slides were then placed in the electrophoresis solution (300 mM NaOH, 1 mM EDTA, pH > 13) for 40 min. Electrophoresis was carried out at 0.73 V/cm, 300 mA for 30 min. The slides were then neutralized, stained with 2 mg/mL DAPI and analyzed under fluorescent microscope (Nikon Eclipse TE2000, Nikon, Tokyo, Japan). All the steps of this procedure were performed in the dark. The level of DNA damage was determined on the basis of the comet tail moment using CaspLab software (1.2.3beta1 version, Comet Assay Software Project, Wrocław, Poland) [57 (link),58 (link)].
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4

Nuclear Morphology Imaging of Drug-Treated Cells

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Cells were seeded onto 24-well plates and cultured for 18–22 h to approximately 60% confluence. After 24 h of drug exposure, cells were stained with DAPI (0.5 μg/ml, a gift from Dr. Xiang-Xi Xu) and visualized immediately with the Nikon Eclipse TE2000 microscope (Nikon, Melville, NY) to analyze changes in nuclear condensation and fragmentation. Microphotographs of the center of each well were taken at 60X magnification with the aid of imaging-capture software (NIS-Elements from Nikon, Melville, NY). Cells shown were from one representative experiment out of at least three independent analyses.
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5

Tube Formation Assay for Angiogenesis

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Tube formation assay was performed in vitro using Matrigel (BD Biosciences, San Jose, CA) in 24-well plates (12 (link)). After thawing overnight at 4°C, 300 μl of Matrigel was added to designated wells and was incubated for 30 min at 37°C for solidification. PAEC (1.5 × 105) were added on top of the solidified Matrigel. Tube formation by PAEC was monitored over the next 4–6 h (12 (link)). One representative picture was taken per well using an inverted microscope at 20 × (objective) magnification (Nikon Eclipse TE2000, Nikon Instruments Inc., Melville, NY). Total tube length was measured in the presence/absence of PGI2 (100 pg/ml) at concentrations that simulate physiologic levels. Indomethacin (10−5 M) was then added to some wells, to inhibit PGI2 release. Data from control and PPHN PAEC were compared. Tube formation was also studied in control PAEC with/without PGIS knockdown and in PPHN cells with/without TXAS knockdown to determine their role in angiogenesis.
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Tube Formation Assay for Angiogenesis

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Tube formation assay was performed in vitro using Matrigel (BD Biosciences, San Jose, CA) in 24-well plates (12 (link)). After thawing overnight at 4°C, 300 μl of Matrigel was added to designated wells and was incubated for 30 min at 37°C for solidification. PAEC (1.5 × 105) were added on top of the solidified Matrigel. Tube formation by PAEC was monitored over the next 4–6 h (12 (link)). One representative picture was taken per well using an inverted microscope at 20 × (objective) magnification (Nikon Eclipse TE2000, Nikon Instruments Inc., Melville, NY). Total tube length was measured in the presence/absence of PGI2 (100 pg/ml) at concentrations that simulate physiologic levels. Indomethacin (10−5 M) was then added to some wells, to inhibit PGI2 release. Data from control and PPHN PAEC were compared. Tube formation was also studied in control PAEC with/without PGIS knockdown and in PPHN cells with/without TXAS knockdown to determine their role in angiogenesis.
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7

Kombucha Biofilm Formation at Oil-Water Interface

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90 mL of kombucha cell suspension (cells harvested from static culture and diluted to OD600 nm 0.05 in fresh HS medium) was added to 10 mL of n-decane (>99% pure, Sigma-Aldrich) or mineral oil (Sigma-Aldrich) in a 250 mL glass bottle and vigorously shaken for 2 min to investigate the adsorption and cellulosic biofilm formation at the interface by the presence of bacteria. The resulting emulsion was statically incubated at 28 °C for up to 30 days. A suspension without oil phase (kombucha suspension-air interface) was used as control. To determine the presence of bacteria in the droplets and at interfaces, small volumes of emulsions obtained through the mixing of kombucha suspension with n-decane or mineral oil were pipetted onto a clean glass slide and stained using 3.34 mM SYTO 9 green fluorescent nucleic acid stain (Thermo Fischer Scientific) in PBS. The emulsions were stained using 25 μM Calcofluor White (Sigma-Aldrich) in PBS for 15 min to confirm the presence of cellulose at the oil-kombucha suspension interface. The images were obtained using 40x objective lens, fluorescence microscopy (Nikon Eclipse TE2000, Nikon Europe B.V., Austria) equipped with Nikon DS-U1 camera. The experiments were performed in biological triplicates, each with three technical replicates.
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8

Immunofluorescence analysis of Nrf2 in CLL cells

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The CLL cells were cytospun at 20 × g for 5 min at room temperature, fixed with 3.7% (v/v) paraformaldehyde, permeabilized with 0.2% Triton X-100 and blocked with 5% (w/v) BSA. The fixed CLL cells were incubated with rabbit anti-human polyclonal Nrf2 antibody (1:50; cat no. sc-13032; Santa Cruz Biotechnology, Inc.), at 4°C overnight, followed by incubation with Alexa-Fluor-594 goat anti-rabbit polyclonal antibody (1:400; cat. no. A11594; Molecular Probes at room temperature for 1 h. Finally, the slides were washed with phosphate-buffered saline, mounted and counterstained with mounting medium supplemented with DAPI prior to examination with a Nikon Eclipse TE2000 confocal microscope and analysis with Nikon EZ-C1 3.80 software (Nikon Corporation, Tokyo, Japan).
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9

Detecting Protein Aggregation in PHT Cells

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PHT cells were plated on glass coverslips and grown in TM medium (ScienCell Research Laboratories, Carlsbad, CA, USA). After several washes, the cells were incubated in serum- and growth-factor-free TM medium and then treated with vehicle/chloroquine (50 μM, Sigma-Aldrich, St. Louis, MO, USA) or normoxia/hypoxia–reoxygenation. For detection of aggregated protein, fixed cells were stained with ProteoStat dye using ProteoStat Aggresome Detection Kit (ENZO, ENZ-51023-KP002, Farmingdale, NY, USA) according to the manufacturer’s instruction. Then, coverslips were mounted in VECTASHIELD anti-fade mounting medium containing DAPI (VECTOR LABORATORIE, H-1200, Burlingame, CA, USA). Fluorescence images were captured using a Nikon Eclipse TE2000 (Nikon, Tokyo, Japan) fluorescent microscope and analyzed using MetaVue Imaging software (Molecular Devices, San Jose, CA, USA).
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10

Microbead Rheology for Mucus Viscoelasticity

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Microbead rheology was performed by tracking the thermally driven motion of embedded 1 µm diameter carboxylated microspheres (FluoSpheres, Fischer Scientific)37 (link),48 (link),49 (link). Briefly, microspheres were added to mucus and allowed to mix while rotating overnight at 4 °C. After reduction, fifteen 30 s movies were collect at 60 frames per second on a Nikon Eclipse TE 2000 microscope at ×40 with a Flea 3 camera (FLIR Machine Vision, Richmond BC, Canada). Particle trajectories were subsequently tracked using TrackPy (v2.4, 10.5281/zenodo.12255). The track positions were corrected in Matlab (The MathWorks, Natick, MA) to account for linear drift and mean squared displacement (MSD) was calculated for each bead according to Equation 1 Δr2τ=1N-τi=1N-τxti+τ-xti2+yti+τ-yti2#, where N = 1800 total frames and τ is the time-lag.
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