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410 protocols using axioskop 2

1

Quantifying Doxorubicin Accumulation in Cells

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Doxorubicin has an intrinsic fluorescence detectable in the visible spectral region and it can be efficiently excited with a blue light source [49 (link)]. For a quantitative estimation of doxorubicin accumulation, cells were seeded on laminin-coated 12-well plates at the density of 2 × 105 cells/well. The next day, cells were treated with doxorubicin (100 μM). After 1 h, cells were observed under a fluorescence microscope (Axioskop2, Zeiss, Oberkochen, Germany), using a 40× objective through the Axion Vision program (Zeiss, Oberkochen, Germany).
The culture media were then supplied with verapamil (100 μM) or N-8-Iper (1.5 μM for GB7 cells and 12.5 μM for G166 cells) where required. After 3 h, the treated cells were observed again, and representative fields were photographed by fluorescence microscope (Axioskop2, Zeiss, Oberkochen, Germany). The culture media were collected from each well and the fluorescence intensity was measured. At the same time, to assess the amount of doxorubicin accumulated into the cells, they were collected, and fluorescence was measured in the cell lysates. The fluorescence intensity for both media and lysates were measured by the GloMax Multi Detection System (Promega, Madison, WI, USA) (λex, 470 nm; λem, 590 nm). The lysates and the protein content were obtained as indicated below in the Western blot section.
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Investigating Cell Adhesion Mechanisms

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To investigate adhesion to matrix, A431 cells were plated on fibronectin-coated coverslips for 1 h and treated with recombinant FIX for 5 min. To investigate intercellular adhesion, A431 cells or HUVECs were cultured for 48 h on fibronectin-coated coverslips and treated with recombinant FIX for 1 h. Cells were fixed in PBS with 4% paraformaldehyde and then permeabilized in PBS with 0.1% Triton X-100. Cells were then incubated with primary antibodies, and staining was detected with Alexa Fluor 488 anti-rat IgG (Invitrogen), Alexa Fluor 568 anti-mouse IgG (Invitrogen), or Alexa Fluor 488 anti-mouse IgG (Invitrogen). When necessary, cells were then stained with Alexa Fluor 568-phalloidin to detect actin or stained with Hoechst 33342 to detect nuclei. Cells were examined using a fluorescent microscope (Axioskop 2; Carl Zeiss, Oberkochen, Germany). Images acquired using the Axioskop 2 at 100Â final magnification were analyzed using Axiovision software (Carl Zeiss). For quantitative evaluation of intercellular adhesion, the intensity of yellow fluorescence in immunohistochemistry was measured using Popimaging software (Digital Being Kid, Kanagawa, Japan).
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Quantifying Intestinal Nuclei with elt-2::GFP

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To examine the number of intestinal nuclei marked by GFP using an elt-2::GFP transgene, worms were transferred to 0.2 mM tetramisole in M9 buffer on a poly-L-lysine-coated slide glass, covered with a coverslip and observed using a fluorescence microscope (Zeiss Axioskop 2, Carl Zeiss, Germany). Otherwise, DNA of some strains, whose intestine is not marked with intestinal GFP, was stained with Hoechst 33342 solution (40 mM NaCl, 10 mM Tris-HCl (pH7.5), 1 mM EDTA, 20% Glycerol, 20 μg/ml Hoechst 33342). The worms were placed on a water drop on a poly-L-lysine-coated slide glass and fixed by quickly dehydrating on an alcohol lamp. The fixed worms were covered with a coverslip containing Hoechst 33342 solution and gelutol. The samples prepared on a slide glass were observed using a fluorescence microscope (Zeiss Axioskop 2, Carl Zeiss, Germany). Images were taken using an Orca-ERG digital camera (Hamamatsu, Japan) and NIS-elements software (Nikon, Japan).
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Histological and Hematological Analysis

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Tissues were fixed in 10% neutral-buffered formalin (NBF) for about 24 h, followed by dehydration, embedded in paraffin blocks, and then cut into 5 μm sections, which were stained with hematoxylin-eosin (H&E). Images were obtained using the ZEISS Axioskop2 plus advanced positive microscope.
Mice blood was collected in EDTA-coated tubes and analyzed on an automatic blood analyzer (SYSMEX, Tokyo, Japan, XT-1800i) according to manufacturer’s instructions. Serum was collected and tested by automatic biochemical analyzer according to manufacturer’s instructions.
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Dendritic Spine Density Analysis

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Randomly selected dendritic segments (~60 μm length) in the distal half of the molecular layer of the dentate gyrus or within either stratum lacunosum moleculare or stratum oriens of the CA1 region were analyzed. Spines were observed and identified with a Zeiss Axioskop 2 equipped and with a Neurolucida System and a 100X/NA1.4 lens. Spine density was obtained by dividing their number of by the dendritic length.
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Fluorescence Imaging of NMJs and Cells

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Fluorescence images of NMJs and cells were acquired with Zeiss microscope (AxioImager.M2) supplied with the Apotome.2 system to mimic a confocal microscope. Images were acquired as Z-stacks with 20×, 40× and 63× objectives. The quantitative analysis was performed with ZEN (RRID:SCR_013672) (Zeiss) and Fiji software. Bright field images for muscle fiber analysis were acquired with Zeiss microscope (Axioskop.2) equipped with AxioCamICc1 and 20× objective.
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7

Immunofluorescence Staining of Goblet Cells

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The goblets cells were cultivated on slides and treated with RPMI media or diluted eye drops 1:7 (v/v) for 30 min at 37 °C 5% CO. With the use of paraformaldehyde 4% (v/v), the slides were fixated and stored at 4 °C. The cell membranes of the goblet cells were permeated using 0.1% v/v Triton X-100 in PBS, and by using 3% (w/v) bovine serum albumin in PBS, unspecific binding was blocked. The cells were treated with the primary antibodies Cytokeratin-7 (anti-cytokeratin7, 1:500 v/v) and monoclonal anti-human gastric mucin (anti-mucin, 1:200 v/v), diluted in 0.25% bovine serum albumin/0.1% saponin in PBS and washed with PBS thereafter. The fluorescent secondary antibodies, Alexa488 (anti-rabbit, 1:500 v/v) and Texas red (anti-mouse, 1:200 v/v), both diluted in 0.25% bovine serum albumin/0.1% saponin in PBS, were added. Then, 0.3 µM of DAPI in PBS stained the nuclei of the goblet cells. Imaging was performed using an Axioskop 2 (Zeiss; Göttingen, Germany) with an Axio Cam MRm camera (Zeiss; Göttingen, Germany) and an HXP 120 lighting unit (Zeiss; Göttingen, Germany). Image scaling and the merging of pictures were conducted using ImageJ 1.52q (Wayne Rasband, National Institute of Health, Bethesda, MD, USA).
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8

Chromosome Spread Immunofluorescence Analysis

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Chromosome spreads were performed as described previously (Crotti and Basrai 2004 (link); Collins et al. 2004 (link)) with some modifications. Cells were grown in YPD logarithmically. 16B12 Mouse anti-HA antibody (Covance, Babco; MMS-101P) was used as primary antibody at 1:2500 dilution. Cy3 conjugated Goat anti mouse (Jackson ImmunoResearch Laboratories, Inc., 115165003) was used as secondary antibody at 1:5000 dilution. DNA was visualized by DAPI (4’,6-diamidino-2-phenylindole) staining (1 μg/ml in phosphate-buffered saline) mounted in antifade mountant (Molecular Probes, P36935). Cells were examined under an Axioskop 2 (Zeiss) fluorescence microscope equipped with a Plan-APOCHROMAT 100X (Zeiss) oil immersion lens. Image acquisition and processing were performed with the IP Lab version 3.9.9 r3 software (Scanalytics, Inc.).
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9

Chromatin Enrichment Assay for Cse4

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Subcellular fractionation to assay chromatin enrichment of Cse4 was performed as described previously (Au et al., 2008 (link)). Cells were grown to logarithmic phase of growth in 1% yeast extract, 2% bactopeptone, and 2% glucose (YPD) at 25°C. Chromosome spreads were performed as described previously (Collins et al., 2004 (link); Crotti and Basrai, 2004 (link)) with some modifications. 16B12 mouse anti-HA antibody (MMS-101P; Covance, Emeryville, CA) was used as primary antibody at 1:2500 dilution. Cy3-conjugated goat anti-mouse (115165003; Jackson ImmunoResearch Laboratories, West Grove, PA) was used as secondary antibody at 1:5000 dilution. Cells were visualized by DAPI staining (1 μg/ml in phosphate-buffered saline) mounted in antifade mountant (P36935; Molecular Probes, Eugene, OR). Cells were observed under an Axioskop 2 (Zeiss) fluorescence microscope equipped with a Plan-Apochromat 100× (Zeiss, Thornwood, NY) oil immersion lens. Image acquisition and processing were performed with the IP Lab version 3.9.9 r3 software (Scanalytics, Fairfax, VA).
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10

FFPE Tissue HER2 Gene Quantification

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Formalin-fixed Paraffin-embedded (FFPE) cancer tissue was delivered from clinical institutions from all over Germany. FFPE tissue was cut into small pieces (2 µm) on a slide and dehydrated using first a xylene washing step subsequent flowed by a series of ethanol steps (100%, 96%, 70%). After drying the slide at room temperature slides were incubated with sodium thiocyanate followed by a wash step using distilled water. Subsequently, slides were incubated with pepsin and hydrochloric acid, washed using distilled water and dried at room temperature. Probes (PathVysion HER-2 DNA Probe Kit II, Abbott Inc.) were hybridized at 37 °C in a wet chamber overnight. Washing of slides was performed in 2x saline-sodium citrate (SSC) buffer and DAPI counterstaining was conducted. Images were taken using fluorescence microscope (Axioskop 2, Zeiss Inc.) using a graded filter (Filter Set 23 (488023-0000-000), emission: 515–530 nm + 580–630 nm, Zeiss Inc.), recording HER2 gene signals, CEN17 signals and a small subset of DAPI signals at once. Images were captured at a magnification of 40x and processed using the Image-Pro 6.0 software (Media Cybernetics) and saved in JPEG file format with a size of 1200 × 1600 pixel.
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