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8 protocols using plan apo lens

1

Visualization of GFP-tagged Proteins

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To visualize GFP-tagged proteins, cells from overnight cultures were back-diluted 50× into fresh SC medium and incubated at 30 °C and 200 r.p.m. for 4–6 h. Cells were washed with water and mounted unfixed on microscope slides. Images were captured using a Nikon Ti microscope with a 100× PlanAPO lens (NA 1.49). Cells were illuminated using high inclination laminated optical sheet TIRF illumination with 488 nm lasers, and its respective filter cube (Chroma). Images are of single planes. Image processing was done using Fiji (NIH).
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2

Evaluating Dendritic Cell Viability

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Ethidium homodimer (EthD-1; Thermo Fisher Scientific) was used to evaluate DC viability. After 24 h of incubation, DCs under gel confinement were stained with EthD-1 in complete medium (500 nM) in an incubator for 20 min. Fluorescent-stained dead cells were counted manually using epifluorescence microscopy with a 20× Plan Apo lens (Nikon TiE). Cell survival rate was calculated as the number of stained cells per the number of whole cells in the field of view. More than 50 cells were analyzed for each experiment, and three independent experiments were performed.
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3

Quantifying Somatic Nuclei Replication Patterns

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Somatic nuclei replication patterns were assessed as described [58 (link)]. Briefly, CHO nuclei replicating in egg extract were pulse-labelled with 25 μM Cy3-dUTP (GE Healthcare) for 2.5 min. Nuclei were isolated and fixed in 4% paraformaldehyde and spun down onto poly-l-lysine coverslips. Total DNA was stained with Hoechst 33258 and coverslips were mounted with Vectashield mounting medium and sealed. Images were acquired using a cooled camera (CoolSNAP HQ; Photometrics) on a restoration microscope (DeltaVision Spectris; Applied Precision) built around a stand (Eclipse TE200; Nikon) with a 100× 1.4 NA Plan Apo lens (Nikon). Images were taken every 0.25 μm, and 22 optical sections were recorded for every nucleus. Three-dimensional datasets were deconvoluted using the constrained iterative algorithm software (SoftWoRx; Applied Precision), and images were analysed in the Open Microscopy Environment (www.openmicroscopy.org). Timing patterns for 20 nuclei at each data point were classified as described [58 (link)] in three independent experiments.
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4

Confocal Microscopy Imaging Protocol

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Fluorescence images were acquired using Volocity software (PerkinElmer Life Sciences) with a Nikon Eclipse T.I confocal microscope equipped with a ×40 Plan Apo lens (Nikon). All images were captured with the same exposure and laser intensity at ×40 magnification. Images were processed using ImageJ (21 ) and JASC Paint Shop Pro V 9.0 (JASC Software Inc.). DAPI staining was used to identify the epidermal/dermal junction.
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5

Immunofluorescence Staining of Fixed Cells

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According to previously described protocol [18 (link)], cells were fixed in 4% paraformaldehyde (PFA) in phosphate-buffered saline (PBS) for 30 min and then permeabilized with methanol for 10 min at room temperature. After washing with PBS, the fixed cells were incubated with blocking buffer (1% bovine serum albumin (BSA) and 0.1% Triton X-100 in PBS) for 3 h at 4 °C followed by incubation with a primary antibody (1:300 dilution in blocking buffer) overnight at 4 °C. Methanol and Triton X-100 were not used for the ANXA2 externalization assay. The cells were then incubated with a fluorescein isothiocyanate (FITC)- or Cy3- conjugated secondary antibody (1:500 dilution in blocking buffer, Chemicon International Inc., Temecula, CA, USA). The nuclei were visualized with Hoechst 33342 (Molecular Probes, Eugene, OR, USA). Images were captured with a BZ-8000 microscope (Keyence, Osaka, Japan) with a 20× Plan APO lens (Nikon, Tokyo, Japan) or with a LSM 510 META confocal laser microscope with a 40× Plan-Neofluar lens or a 63× Plan-Apochromat lens (Carl Zeiss, Oberkochen, Germany).
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6

Quantifying Legionella Pneumophila Infection

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Kc167 cells were challenged with L. pneumophila GFP+ cells and treated with 10 µg/ml of erythromycin at 19 h after challenge. Infections were allowed to proceed for an additional 11 or 21 h, at which point, the cells were fixed in 3.7% paraformaldehyde in 1× PBS and stained with 1 µg/ml Hoechst stain. Images were taken using a Molecular Devices ImageXpress automated microscope with a Nikon 20× Plan Apo lens for 2 sites per well using the DAPI (4′,6-diamidino-2-phenylindole) and FITC (fluorescein isothiocyanate) optimized filter sets. Downloaded images were subjected to an automated MetaXpress script that counts for the total area of cell nuclei (based on Hoechst staining) and bacterial replication (based on total GFP signal).
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7

Rapid Microwave-Assisted Immunohistochemistry

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Mice peripheral tissues and specific brain regions were fixed by vascular perfusion with 30 mL of 4 % paraformaldehyde (PFA) after perfusion with PBS for about 20 min. Desired organs were isolated and washed with PBS then processed using a rapid microwave automatic histo-processor using a standard protocol and embedded into paraffin wax. Subsequent immunohistochemistry assays were then performed per standard protocols previously described [15 (link)]. Briefly, sectioned tissues were deparrafinized then permeabilized with methanol. The sections were then blocked with 3 % BSA for 1 h at room temperature and later incubated with primary antibody (1:300 mouse monoclonal IgG 2 F11; Enzo Life Sciences Int., PA, USA and AntiCT)) at 4 °C overnight, washed with PBST then with secondary antibody conjugated to AlexFluor (1:600) for 2 h at room temperature. Counterstaining with Hoechst 33342 (1:10,000) was effected. The slides were then mounted by pristine mount and left to dry overnight at 4 °C. Images were collected by BZ-8000 microscope (KEYENCE, Osaka, Japan) with a × 20 Plan APO lens (Nikon, Tokyo, Japan).
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8

Immunohistochemical Analysis of pH3

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Anesthetized animals were fixed in 4% paraformaldehyde (Electron Microscopy Sciences) in phosphate-buffered saline (pH 7.4). Dissected brains were incubated in blocking solution, followed by anti-pH3 antibody and Alexa488 donkey anti-mouse secondary antibody or Sytox Orange (SytoxO). Brains were mounted in 6 M urea in 50% glycerol for imaging (Nikon C2, 20× Plan Apo lens with 0.75 NA). ImageJ Cell Count plugin was used for analysis. See SI Appendix, Methods.
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