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27 protocols using clsm 780

1

Characterization of 3D Spheroid Cultures

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Indirect immunofluorescence was performed as described previously [32 (link)]. Spheroids in suspension were stained applying the same protocol but using centrifugation between every step. Primary antibodies: rabbit-anti-human EpCAM (EGP40/1556R; 1:100; Novus Biologicals, Centennial, CO, United States), rabbit-anti-human cytokeratin 14 (1:200, Thermo Fisher Scientific, Waltham, MA, United States), rabbit-anti-human cytokeratin 19 (1:75; Novus Biologicals), mouse-anti-human Vimentin (V9; 1:100; Santa Cruz Biotechnology Inc., Dallas, TX, United States), mouse-anti-human α-smooth muscle actin (1A4; 1:200; Sigma-Aldrich), mouse-anti-human Thy-1 (AS02; 1:100; Dianova, Hamburg, Germany), rabbit-anti-human ALDH1A1 (20H2L4, 1:100; Thermo Fisher Scientific), and rabbit-anti-human CDKN2A/p16INK4a (EPR1473; 1:200; Abcam, Cambridge, UK). Secondary antibodies were goat-anti-mouse-IgG-Alexa Fluor 555 and donkey-anti-rabbit-IgG-Alexa Fluor 488 (both Thermo Fisher Scientific). DNA was stained with Hoechst 33,342 and the actin cytoskeleton was visualized using phalliodin-PF647 (Promokine, Heidelberg, Germany). Imaging was conducted using a confocal laser scanning microscope CLSM 780 (Carl Zeiss, Oberkochen, Germany) and ZEN software (Carl Zeiss).
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2

Immunofluorescence Staining Protocol

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Fixed cells or tissue sections were permeablized in 0.2% Triton X-100/PBS for 10–30 minutes at room temperature. After blocking in 5% goat serum/0.2% Triton X-100/PBS for 30 minutes at room temperature, cells or tissue sections were incubated in primary antibodies overnight at 4°C. After three washes with PBS, cells or tissue sections were incubated with fluorescence-conjugated secondary antibodies for one hour at room temperature. After three washes with PBS, Cells or tissue sections were mounted with fluorescence mounting medium and examined under Olympus IX70 (Tokyo, Japan) fluorescent microscope or Zeiss CLSM 780 (Göttingen, Germany) confocal microscope.
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3

Confocal Microscopy of Organotypic Biofilm

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For confocal microscopy the biofilm on top of the organotypic slices was prepared as described in 2.7. After 6 h, the slices were fixed in 4% paraformaldehyde for 30 min and washed in PBS. The staining of DNA was accomplished by submerging the sample for 10 min in a solution of 1 μg/ml DAPI (Sigma-Aldrich, United States). To stain eukaryotic F-actins the slices were incubated for 20 min in PBS containing 4 units/ml Phalloidin coupled to Alexa Fluor 647 (Promocell, Germany). The slices were cut perpendicular to the epithelial layer in smaller pieces and prepared as hole mounts in mowiol between a microscopic slide and a cover slip separated by a 300 μm spacer. Imaging was performed with a confocal laser scanning microscope (CLSM; CLSM 780 Carl Zeiss, Germany).
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4

Multimodal Characterization of Nanomaterials

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1H NMR spectra were recorded on a Bruker AV-500NMR spectrometer in deuterated DMSO. Dynamic light scattering (DLS) was detected on a Wyatt QELS instrument with a vertically polarized He-Ne laser (DAWN EOS, Wyatt Technology Co., Santa Barbara, California, USA). The ultraviolet (UV) absorption spectrum was acquired on a UV-2401PC spectrophotometer (Shimadzu, Japan). Transmission electron microscopy (TEM) measurements were made on a JEOL JEM-1011 transmission electron microscope (Tokyo, Japan) with an accelerating voltage of 100 kV. Flow cytometry analysis (FCA) was conducted on a Guava EasyCyte™ 12 Flow Cytometer (Millipore, Billerica, MA, USA) and confocal laser scanning microscopy (CLSM) was performed on a CLSM 780 (Carl Zeiss). High-performance liquid chromatography (HPLC) was performed using a binary HPLC pump with a C18 column (250 mm × 4.6 mm; made in Ireland).
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5

Immunocytochemistry of hCSCs

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For immunocytochemistry, hCSCs were seeded in ibidi-μ-slides (ibidi GmbH, Gräfelfing, Germany) and treated as described above (Figure 1; Section 2.1). Biological replicates were performed of two individual serum donors. Cells were fixed in 4% paraformaldehyde (PFA), washed with phosphate-buffered saline (PBS) (Sigma Aldrich) and permeabilized in PBS with 0.02% Triton X-100 (Applichem, Darmstadt, Germany) supplemented with 5% goat serum for 30 min. The primary antibodies were diluted in PBS (mouse anti-Nestin 1:200 (Millipore, Burlington, MA, USA), rabbit anti-PhosphoHsp27 (Ser82) (Cell Signaling Technology, Danvers, MA, USA)) and applied for 1 h at room temperature (RT). After three washing steps, secondary fluorochrome-conjugated antibodies (Alexa 488 anti-mouse or Alexa 555 anti-rabbit, Invitrogen, Life Technologies GmbH, Carlsbad, CA, USA) were applied for 1 h at RT with a dilution ratio of 1:300. Nuclear staining was realized by incubation with 4,6-diamidin-2-phenylindol (DAPI) (1 μg/mL, Applichem) in PBS for 15 min at RT. Finally, the samples were mounted with Mowiol (self-made). Imaging was performed using a confocal laser scanning microscope (CLSM 780, Carl Zeiss, Oberkochen, Germany). Five images were taken of each treatment condition and serum-donor for following data analysis.
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6

DAPI Staining and Oil Emulsion Microscopy

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Cells were stained with blue fluorescent 4, 6-diamidino-2-phenyl-indole (DAPI, 10 μg/mL) in the absence of light at room temperature for 15 min. After that, cell pellets were collected, washed twice, and resuspended in PBS. Four milliliters of the DAPI-stained cells suspension were vigorously shaken with 1 mL of silicone oil, forming oil in water (o/w) emulsions. Spherical oil droplets from the o/w emulsion were transferred by using a micropipette to a slide glass and observed using confocal laser scanning microscopy (CLSM 780, Carl Zeiss, Oberlochen, Germany).
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7

Visualizing FITC-TP4 Peptide Morphology

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For observation of FITC-TP4 peptide in various sarkosyl buffers, 4 μg of TP4 peptides was dissolved in 20 μl sarkosyl buffer (0.25x, 0.5x and 1x Sar) and placed on glass slide for 30 min before examination. 1x Sar buffer contains 10 mM sodium phosphate, 100 mM NaCl, pH 7.4 and 2.6 mM sarkosyl (0.075% sarkosyl, w/v). Similarly, various concentrations of FITC-TP4 peptides (1, 4 and 16 μg/20 μl) or sarkosyl as indicated were also employed for the study. The morphologies and images of FITC-TP4 or Rhodamine-TP4 particles under various environments were observed and taken by CLSM 780 (ZEISS, Oberkochen, Germany).
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8

Quantifying Bacterial Biofilm Viability

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The green SYTO-9 (561 nm) probe marked live cells, and the red PI (488 nm) probe marked dead cells. Biofilms were stained with 30 μM propidium iodide (PI) and 6 μM SYTO-9 (LIVE/DEAD 7021 Bacterial Viability Kits; Thermo Fisher Scientific) for 15 minutes at 25°C. A confocal laser scanning microscope (CLSM 780, Zeiss, Oberkochen, Germany) was used to sequentially assess the specimens. The maximum projections of all image stacks were built using ZEN soft (Zeiss), and the green (live) and red areas (dead) in the biofilms were quantified. Additionally, the dead/live ratios and live cell percentages were analyzed.
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9

Mesenchymal Stem Cell Scaffold Characterization

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BM-MSCs were seeded onto experimental scaffolds in 12-well plates (5×104 cells/well) and incubated at 37°C in a humidified atmosphere with 5% CO2. After 1 or 5 days of culture, the samples were fixed in 2.5% glutaraldehyde and serially dehydrated in an increasing ethanol gradient, air-dried in a hood, and sputtered with gold prior to SEM imaging. Cell spreading area and cell elongation were measured using the ImageJ software, by using a random sampling method. For cytoskeleton observation, the attached cells after 5 days of culture were fixed with 4% paraformaldehyde, incubated with Alexa Fluor 546 phalloidin (50 μg/mL) for 1 h and stained with 4′, 6-diamidino-2-phenylindole (DAPI) for 10 min according to the manufacturer’s directions. The images were captured by a confocal laser scanning microscopy (CLSM; CLSM 780; Carl Zeiss Jena GmbH, Jena, Germany). Cell proliferation was assayed using a Cell Counting Kit-8 (CCK-8 kit, Dojindo Laboratory, Tokyo, Japan) at 1, 3, 5, and 7 days of culture, with absorbance being read at a wavelength of 450 nm, by using an enzyme linked immunosorbent assay reader (Bio-Rad, Hercules, CA, USA).
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10

Laminar Distribution Quantification

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For quantification of the laminar distribution of somata, low magnification fluorescent images were captured using an epifluorescent microscope equipped with a CCD camera [BX51 (OLYMPUS), 4x UPLSAPO, NA: 0.16 (OLYMPUS)]. Z-stack images were acquired using a confocal microscope [CLSM 780 (ZEISS), 20x Plan ApoChromat, NA: 0.8 (ZEISS)].
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