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136 protocols using cpd300

1

Scanning Electron Microscopy of Cell Morphology

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The structure and morphology of cells on the surface of the models are important to define the health status of the models. Scanning electron microscopy (SEM) was used to visualise the morphology of cells on the apical side of membrane inserts. Briefly, the models were washed twice with PBS and fixed with 2.5% glutaraldehyde in PBS (cat: G5882, Sigma Aldrich) for 2 h. Models were washed with PBS for three times, each time for 5 min. Next, the membranes of the models were cut from the insert, dehydrated in graded ethanol solutions (from 30 to 100% ethanol) and dried using a critical point dryer (CPD300, Leica Microsystems). Models were then coated with gold at 10 nm coating thickness. Subsequently, the samples were kept in a desiccator filled up with silica gel prior to SEM imaging. SEM imaging was performed using Zeiss Sigma HD FEG SEM. Secondary electrons were acquired using the detectors of the SE2 mode for all models with an accelerating voltage of 5.0 kV and a working distance (W.D) = 8.0.
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2

Scanning Electron Microscopy of C. auris

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C. auris [DSM 21092] was incubated (37 °C, 24 h) with Rub C at the concentration of 250 and 15.6 μg/mL in 96-well non-tissue microtiter plates in RPMI 1640 medium supplemented with 0.165 mM MOPS. Cultures were fixed with 5% formaldehyde and 2% glutaraldehyde (final concentrations) and washed twice in TE buffer (20 mM TRIS with 1 mM EDTA, pH 6.9). A 50 µL aliquot was added to round poly-l-lysine pretreated coverslips and incubated (room temperature, 10 min). Further processing was carried out as previously described with slight modifications [45 (link)]. In brief, cells were fixed for 10 min on the coverslip with TE buffer including 1% glutaraldehyde (final concentration). The coverslips were washed twice in TE buffer and dehydrated in 10 min steps on ice with a graded series of acetone (10%, 30%, 50%, 70%, and 90%), followed by two steps in 100% acetone at room temperature. The coverslips were mounted onto aluminum stubs with carbon adhesive discs; they were critical-point-dried with the automated CPD300 (Leica Microsystems) and gold-palladium-sputter-coated (55 s at 45 mA) with a SCD500 (Bal-Tec, Balzers, Liechtenstein). Images were acquired with a field emission scanning electron microscope Zeiss Merlin (Zeiss, Oberkochen, Germany) using the Everhart Thornley HESE2 detector and the in lens SE detector in a 25:75 ratio with an acceleration voltage of 5 kV.
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Scanning Electron Microscopy of Leaf Stomatal Density

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Leaves of TH-0%, TH-75%, and CK groups were cut into pieces of about 3 mm × 3 mm size with a blade, quickly placed into 2.5% glutaraldehyde solution, fixed for 2 h at room temperature after pumping air to make the tissue sink, rinsed using the phosphoric acid buffer for three times, subjected to gradient dehydration with ethanol (50, 70, 80, 90, 95, and 100%), dehydrated with anhydrous ethanol, and dried using critical point dryer (CPD300, Leica Microsystems, Wetzlar, Germany). Then, the sample was pasted on the cover glass, put into the vacuum spray machine for spraying, and finally observed and photographed by scanning electron microscope (HITACHI SU3900, Shimadzu Corporation, Tokyo, Japan). The number of stomata was observed under the scanning electron microscope, and three replicate samples were used for each treatment group. The stomatal density (pieces/mm2 = number of stomata in the field of view/field area) was calculated by measuring the field of view using a micrometer scale and calculating the field of view.
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Scanning Electron Microscopy of Biological Samples

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Samples were fixed in 5% formaldehyde and 2% glutaraldehyde in 0.1 M HEPES buffer (HEPES 0.1 M, 0.09 M sucrose, 10 mM CaCl2, 10 mM MgCl2, pH 6.9) at 4°C and washed twice with TE buffer, pH 7.0 (20 mM Tris–HCl, 1.0 mM EDTA), before dehydrating in a graded series of ethanol for 15 min at each step. Samples were then subjected to critical-point drying with liquid CO2 (CPD 300, Leica Microsystems, Wetzlar, Germany) and sputter coated with a gold–palladium film (SCD 500, Bal-Tec, Liechtenstein) before examination in a field-emission scanning-electron microscope Zeiss Merlin (Oberkochen, Germany) using the Everhart–Thornley SE detector and the SE in-lens detector at a 75:25 ratio with an acceleration voltage of 5 kV.
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5

SEM Preparation of Biological Samples

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Samples for SEM were incubated in 2% glutaraldehyde for 10 min and then stored at −80°C until processing. The samples were then dehydrated with an ethanol dilution series of 30%, 50%, 70%, 80%, 90%, 95% each for 10 min and three times in 100% absolute ethanol for 10 min. The dehydrated samples were CO2 critical‐point dried with a CPD 300 auto critical‐point dryer (Leica Microsystems). The dried pieces were gold‐coated using a JFC‐2300HR sputter coater (JEOL) for 80 s. Pictures were taken using a secondary electron detector with a JEOL JSM‐IT300 scanning electron microscope with a 15 kV acceleration voltage in ultra‐high vacuum.
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6

SEM Analysis of Parasitophorous Vacuoles

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Parasites were inoculated on a confluent HFF monolayer 24 hr before fixation in EM fixative (2.5% gluteraldehyde, 4% formaldehyde in 0.1 M phosphate buffer) for 30 min. Cells were washed in 0.1 M phosphate buffer (PB) and stored in 1% formaldehyde in PB at 4°C. Cells were then washed in PB at room temperature, then washed in ddH2O at RT. The cells were dehydrated stepwise from 70% to 100% ethanol before critical point drying from acetone in a CPD300 (Leica Microsystems, Vienna, Austria). After drying, the coverslips were mounted on stubs, and the HFF cells were unroofed by placing Scotch tape on the coverslips and gently peeling it off, exposing the host cytoplasm and the parasitophorous vacuoles. The cells were coated with 7 nm platinum in a Q150R Sputter Coater (Quorum Tech, East Sussex, UK) before viewing in a Phenom ProX SEM (Thermo Scientific) at 10 kV, 1024 × 1024 pixel frame, on ‘high’ quality.
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7

Scanning Electron Microscopy of Mycobacterium tuberculosis

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For surface scanning electron microscopy, mihF-cKD mutant without ATc and H37Rv wild type strains were grown in 7H9 until mid-exponential phase, pelleted, washed in PBS and resuspended to OD600 = 0.5. The mihF-cKD mutant with ATc was diluted three times in fresh ATc-containing medium and then subjected to the same protocol. Samples were then fixed on a coverslip in a solution of 1.25% glutaraldehyde, 1% tannic acid in phosphate buffer (0.1 M, pH = 7.4) for 1 h, washed in PBS prior to fixing for 30 min in 1% osmium tetroxide. The samples were then dehydrated in a graded alcohol series and dried by passing through the supercritical point of carbon dioxide (Leica Microsystems CPD300) and coated with a 2 nm layer of osmium metal using an osmium plasma coater (Filgen OPC60). Scanning electron microscopy images were taken using a field emission scanning electron microscope (Merlin, Zeiss NTS) with an acceleration voltage of 2 kV and the in-lens secondary electron detector. Cell length of bacteria was measured in ImageJ (n = 110 for H37Rv wild type, n = 96 for mihF-cKD without ATc and n = 98 for mihF-cKD + ATc). Two-tailed, one-way analysis of variance (ANOVA) with Kruskal-Wallis post-test was performed with 303 degrees of freedom and F value = 184.2.
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8

Bacterial Fixation and SEM Imaging

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Bacteria were fixed by addition of glutaraldehyde (final concentration 2%) for 30 min, and addition of formaldehyde (final concentration 5%) into the culture medium. EM sample preparation was performed as previously described (44 (link)) with slight modifications. In brief, samples were washed twice with TE-buffer and fixed to poly-l-lysine coated round coverslips. After additional washing steps, the samples were dehydrated in a gradient series of acetone (10%, 30%, 50%, 70%, 90%) on ice and two steps with 100% acetone at room temperature (each step for 10 min). Afterwards, samples were critically point dried with the CPD300 (Leica Microsystems, Wetzlar, Germany), mounted to aluminum pads and sputter coated with gold-palladium. Images were acquired with a field emission scanning electron microscope Merlin (Zeiss, Jena, Germany) equipped with an Everhart Thornley and an inlens detector and operating at an acceleration voltage of 5 kV.
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9

Ultrastructural Analysis of Explant Grafts

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Explanted grafts were cut open longitudinally then fixed overnight in paraformaldehyde (4 %) at room temperature followed by glutaraldehyde (2.5 %) for one hour at room temperature, as previously described51 (link). Samples were then post-fixed with osmium tetroxide (1 %) in phosphate buffer (0.1 M) and dehydrated through an ethanol gradient before drying using a critical point dryer (Leica Microsystems CPD300). Samples were gold sputter coated and imaged with a Zeiss Sigma VP FEG.
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10

Scanning Electron Microscopy Sample Preparation

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Cells were fixed for 2 h with 1.25% glutaraldehyde in 0.1 M phosphate buffer, pH 7.4, and then washed in cacodylate buffer before a secondary fix for 30 min in 0.2% osmium tetroxide in the same buffer. The cells were then dehydrated in a graded alcohol series and dried by passing them through the supercritical point of carbon dioxide in a critical point dryer (Leica Microsystems CPD300). They were then coated with a 2 nm layer of osmium metal using an osmium plasma coater (Filgen OPC60). Images of the cells were taken with a field emission scanning electron microscope (Merlin, Zeiss NTS).
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