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10 protocols using axiovision z1

1

Immunostaining of Human and Mouse Corneas

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Three separate human corneas, ages 27, 42, and 62, were used with postmortem delay of no more than 72 hours (Eversight Eye Bank, Chicago, IL, USA). Frozen sections (5 μm) of optimal cutting temperature compound-embedded human and mouse corneas were fixed in 4% paraformaldehyde, blocked in 10% goat serum in PBS and incubated overnight with the following primary antibodies: rabbit polyclonal antibodies against Kl67 (SP6- 1:500 dil; Sigma-Aldrich Corp., St. Louis, MO, USA), PBK (16110–1-AP-1:100dil; Proteintech, Rosemont, IL, USA), TXNIP (40–3700- 1:100 dil; Thermo Scientific, Waltham, MA, USA), H2AX (10856–1-AP- 1:50 dil; Proteintech), ATF3 (HPA001562–1:50 dil; Sigma-Aldrich Corp.) or a mouse monoclonal antibody against K15 (MA5–11244–1:100 dil; Thermo Scientific). Appropriate secondary antibodies conjugated to Alexa-555 or Alexa-488 (Invitrogen, Carlsbad, CA, USA) at 1:300 dilution were used to detect primary antibodies. DAPI (4′,6-diamidino-2-phenylindole) was used to label nuclei, and mounted using Gelvatol. Images were acquired using a 20X 0.5 EC Plan-Neofluar objective on an epiflourescence microscope system (AxioVision Z1; Carl Zeiss, Thornwood, NY, USA) fitted with an Apotome slide module and a digital camera (AxioCam MRm).
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2

Multimodal Imaging of Cell Morphology

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Wide-field images were acquired on an Upright Leica Microscope (model DMR) fitted with an Orca-100 digital camera (model C4742-95; Hamamatsu Photonics) and a 40× 1.0 numerical aperture (NA) oil Plan Fluotar objective. Apotome images were acquired using an epifluorescence microscope system (AxioVision Z1; Carl Zeiss) fitted with an Apotome slide module, AxioCam MRm digital camera, and a 40× 0.5 EC Plan-Neofluar or 100× 1.4 NA oil Plan-Apochromat objective (Carl Zeiss). Confocal z-stacks (z-step size of 0.5 μm) of whole-mount samples were acquired using a Nikon A1R confocal laser microscope equipped with GaAsP detectors and a 60× Plan-Apochromat objective lambda with a NA of 1.4 and run by NIS-Elements software (Nikon). NIS-Elements (version 5.02) was used to generate 3D reconstructions of z-stacks using the Volume Viewer tool with z-depth coding blending (rainbow contrast look up table) and to determine the z position of the MC cell body centroid. For each experiment, images were acquired using the same imaging conditions.
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3

Epifluorescence and Confocal Imaging

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Epifluorescence imaging was performed in one or two of three channels (Cy3, GFP, and DAPI) on a Zeiss AxioVision Z1 using a 5× objective (NA 0.13) or a 10× objective (NA 0.45).
Confocal imaging was performed in two channels (AlexaFluor 488 and DAPI) or three (Brainbow) channels (AlexaFluor 488, AlexaFluor 594 or 546, and AlexaFluor 647) on a Leica SP8 resonant scanning confocal system. High-power images were obtained using a 63 × oil objective (NA 1.40) with the XY-resolution of 60–70 nm/pixel and the Z-resolution of 300 nm/optical section. Typical z-stacks consisted of around 100 optical sections. The figures show maximum-intensity projections.
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4

Lucifer Yellow Cell Labeling

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Following treatments, cells on coverslips were rinsed three times with calcium and magnesium free DPBS and covered with 1mg/ml Lucifer yellow CH solution in DPBS. Scrape were made with a metal blade and cells were kept at room temperature for 10 min. Coverslips were extensively rinsed several times with DPBS followed by fixation with 4% PFA for 10min and examined under an epifluorescence microscope system (AxioVision Z1; Carl Zeiss) fitted with a digital camera (AxioCam MRm; Carl Zeiss).
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5

Assessing Schwann Cell Adhesion to Matrilin-2

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Recombinant human matrilin-2 protein was purchased from R&D systems (Minneapolis, MN), coated onto 22 mm tissue glass coverslips at 20ug/ml as described previously (Malin et al., 2009 (link)) and incubated overnight. The agarose migration assay was performed as previously described (Chernousov et al., 2001 (link)). The agarose for the drop migration assay was diluted to a 0.03% concentration. After 24 h of incubation, the cells were visualized under phase-contrast microscopy.
For cellular adhesion, SCs were placed atop matrilin-2 coated plates and incubated for 24 h. Cells were then fixed at room temperature with 4% paraformaldehyde for 10 min. Subsequently, cells were washed with PBS, followed by permeabilization for 30 min using 0.1% Triton X-100. Cells were stained with rhodamine phalloidin (Cell Signaling Technology, Danvers, MA) for immunofluorescent imaging. After 30 min, the cells were washed three times with PBS and incubated in 4′,6′-diamidino-2-phenylindole dihydrochloride (1:1,000; Sigma-Aldrich, St. Louis, MO) for 5 min at room temperature to counterstain the cell nuclei. The specimens were washed three times with PBS, each for 5 min, and were then mounted with an antifade solution. Immunolabeled cells were examined via fluorescence microscopy (Zeiss Axiovision Z1, Oberkochen, Germany). All experiments were carried out in triplicate.
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6

Subcellular Localization of PKM2 by Immunofluorescence

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PKM2 subcellular localization was detected by immunofluorescence. After 24 h of attachment in cell chamber slides (Millipore), cells were treated with OXA and fixed to coverslips in cold acetone for 10 min at room temperature. Blocking and permeabilization was done with PBS-T/ FBS 10%. Cells were incubated at room temperature with a rabbit polyclonal anti-PKM2 primary antibody (Cell Signaling; 1:100) for 1.5 h and subsequently, with secondary antibody anti-rabbit Alexa-568 (Invitrogen; 1:200). Nuclei were stained with DAPI gold-antifade reagent (Invitrogen). Coverslips were observed with a fluorescence microscope Axiovision Z1 by using Apotome system at 40x immersion oil lens (Carl Zeiss, Heidelberg, Germany). Multiple images were taken at different focus distances by using z-stacking (thickness interval: 0.750–1 μm) to localize PKM2 at different focal depths.
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7

3D Raft Culture of miR-Transduced HEKs

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HEKs were transduced with either a GFP-tagged miR −103 or miR-107 construct or a GFP-tagged scrambled construct. Equal numbers of GFP-tagged and untagged HEKs were mixed and allowed to form 3-D raft cultures as described previously [39 (link)]. The raft cultures were embedded in OCT and frozen sections were fixed in 4% PFA and then washed with PBS. DAPI was used to counterstain nuclei. Images were acquired on an epifluorescence microscope system (AxioVision Z1; Carl Zeiss) fitted with a slide module (Apotome; Carl Zeiss) and a digital camera (AxioCam MRm;Carl Zeiss).
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8

Fluorescent Microscopy Analysis of Cell Morphology

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Pictures of DAPI-stained chromosomes or differentiated cells were photographed under a Zeiss Axiovision Z1 fluorescent microscope with 20× and 63× objectives, and analyzed with Axiovision 4.8 software. Morphology of vASC cultures and ASC.B6 cells was checked by Olympus CKX41 inverted light microscope with 4× objective and photomicrographs were taken with an Olympus Camedia C-5060 camera (Olympus Holding Europa GmbH).
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9

Autophagy Imaging and Corneal Epithelial Turnover

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Eyes of GFP-LC3 transgenic mice, which systemically express GFP fused to LC3 (Mizushima et al., 2004 (link)), were rapidly dissected out and embedded in optimal cutting temperature compound rapidly. 5-µm frozen sections were fixed in 4% PFA at RT for 10 min. After three washes with PBS, the sections were mounted using HardSet Antifade Mounting Medium with DAPI (VectaShield). Images were taken using a 100× objective in an epifluorescence microscope AxioVision Z1 (ZEISS). DAPI was used to counterstain nuclei, and GFP punctas were counted. The Beclin-1+/− mouse has been described (Qu et al., 2003 (link)). Central corneal epithelia of Beclin-1+/− and Beclin-1+/+ mice were removed by application of a rotating diamond burr to the surface of the central cornea. The limbal epithelium remained intact. Tissues were embedded in paraffin blocks for immunohistochemical analysis of BrdU. Animal procedures were approved by the Northwestern University Animal Care and Use Committee.
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10

Rhodamine 123 Uptake in 3D Cultures

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In total, 25 mmol of rhodamine 123 was added to the medium of cysts derived from cultured cells and incubated for 5 min. Some of them were incubated with 100 μM verapamil for 30 min before adding the dye. After washing with PBS 3 times, the 3D culture media were added and incubated for 40 min at 37 °C. Images were acquired with a FloidTM Cell Imaging Station (Life Technologies) and AxioVision Z1 microscopy (Carl Zeiss, Oberkochen, Germany).
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