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8 protocols using oil immersion lens

1

Immunofluorescence and Immunohistochemistry Protocols

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In brief, cells were fixed in 4% paraformaldehyde in PBS (pH 7.4) for 10 min at RT and permeabilized with 0.25% Triton X-100 in PBS for 10 min. Blocking was done by using 10% goat serum containing 0.25% Triton X-100 in PBS and incubated overnight at 4°C in primary antibody. The cells were subsequently incubated in secondary antibody for 3 hours and mounted with ProLong Gold Antifade Mountant with DAPI (Thermo Fisher). The images were captured by an inverted laser-scanning confocal microscope, equipped with an oil immersion lens (Carl Zeiss). The fluorescence signals were quantified using Image J software (NIH).
For immunohistochemistry, briefly, tumor sections were rehydrated and antigen retrieved in sodium citrate buffer (10 mM sodium citrate, 0.05% Tween 20, pH 6.0) in Decloaking Chamber (Biocare Medical). The tissue were peroxide quenched, and non-specific staining was blocked by bovine serum albumin along with goat serum. The tissue sections were incubated overnight at 4°C with primary antibodies, subsequently incubated with secondary antibodies for 1 hour at RT and developed by DAB. The images were captured by Nikon Eclipse Ti microscope (Nikon).
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2

Immunolabeling and Confocal Imaging of Cytoskeleton

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Cytoskeleton arrangement (α-tubulin) was studied using immunolabeling followed by confocal microscopy as described previously (Gogada et al., 2011 (link)). Briefly, control or treated cells (6000 cells/coverslip) were stained live with MitoTracker Orange (100 nM) and DAPI (1 μg/ml) for 15 min at 37°C in CO2 incubator. Cells were fixed with 4% formaldehyde containing 5% sucrose for 10 min at RT followed by permeabilization with 1% Triton X-100 in PBS for 10 min. Following washing and blocking with 10% goat serum containing 1% Triton X-100 in 1X PBS, primary antibody was applied for overnight at 4°C. Cells were incubated with AlexaFluor-488-conjugated secondary antibody for 2 h. Prolong gold antifade reagent (Molecular Probes and ThermoFisher Scientific, Grand Island, NY, USA) was used as mounting medium. Fluorescence images were acquired using a laser-scanning confocal system on an inverted microscope equipped with an oil-immersion lens (Carl Zeiss, Thornwood, NY).
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3

Immunofluorescence Analysis of LC3 Puncta

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Cells were grown to 50% confluence on glass coverslips in a 12-well tissue culture plate and then treated with the appropriate drug at the indicated concentrations for the stated duration. Next, cells were washed thrice with sterile PBS (8.4 mM Na 2 HPO 4 , 1.5 mM KH 2 PO 4 , 136.9 mM NaCl and 2.7 mM KCl, pH 7.2), fixed and permeabilized in acetone for 10 min and blocked with 3% bovine serum albumin (ST023; Beyotime Biotechnology) for 2 h. Primary immunostaining with the LC3 antibody (L7543; Sigma-Aldrich) was performed at room temperature overnight, followed by immunostaining with Alexa Fluor 488-conjugated secondary antibody (A-11008; Invitrogen). Subsequently, the nucleus was counterstained with 4′,6-diamidino-2-phenylindole (28718-90-3; Sigma-Aldrich) for 15 min at room temperature. Staining was visualized and photographed using an LSM710 laser scanning confocal microscope with an oil immersion lens (Carl Zeiss). Cell images were independently validated by performing cell counting on five different magnification fields per image: LC3 puncta per cell = number of LC3 puncta/total number of cells.
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4

Fluorescence Microscopy of Yeast Transformants

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Yeast transformants were grown in minimal selective repressing liquid media overnight, washed three times in TE and incubated in minimal selective liquid media containing 2% (w/v) raffinose for 4 h, then washed once in TE and incubated in minimal-selective inducing liquid media for 24 h. Cells were washed once in phosphate-buffered saline (PBS) and then fixed in 4% formaldehyde for 20 min and incubated in PBS containing DAPI (0.5 μg/mL) for 30 min in the dark. Cells were then washed and resuspended in PBS, mounted on coverslips 1:1 with 1% low-melting agarose and then imaged using a Zeiss 780 confocal microscope with a 63× oil immersion lens (Zeiss, Oberkochen, Germany). Scoring was performed visually in a blinded manner.
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5

Adenoviral Transfection of FRET Sensors

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For adenoviral transfection, the media was replaced with 500 μL of serum-free medium containing adenoviral vectors carrying different versions of the FRET-based CUTie sensor (75 (link)). Accordingly, we employed the cytosolic CUTie, the membrane-targeted AKAP79-CUTie, and SR-targeted AKAP18δ-CUTie. Cells infected with the desired adenoviral vectors were incubated at 37°C with 5% CO2 for 36–40 hours. Adenoviral vectors were produced using the AdEasy system (Qbiogene Inc.) (76 (link)). A Zeiss LSM 700 laser scanning confocal microscope paired with a Zeiss 63× oil immersion lens (numerical aperture = 1.4) was used to collect images at different optical planes (z axis steps: 0.4 μm) of the yellow fluorescent protein (YFP) fluorescence associated with each FRET construct to confirm expression and expected localization.
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6

NGF-Induced Differentiation of PC12 Cells

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Undifferentiated PC12 cells
were grown in DMEM (Invitrogen) supplemented with 5% fetal bovine
serum (FBS, Invitrogen) and 10% horse serum (HS, Invitrogen) and subcultured
every 3 days. For nerve growth factor (NGF)-induced differentiation,
PC12 cells were grown on 100 μg/mL poly-d-lysine-coated
eight-well plates or 35 mm culture dishes (ibidi LLC) in DMEM supplemented
with 0.5% FBS, 1% HS, and 100 ng/mL NGF (Invitrogen). PC12 cells were
transfected with GFP-Tmod1, GFP-Tmod1[1–159], GFP-Tmod1[DDD],
mChFP-Tmod2, mChFP-Tmod2[1–162], or GFP and mChFP constructs
using lipofectamine 2000 (Invitrogen) according to the manufacturer’s
instructions. GFP-Tmod1/Tmod2 and mChFP-Tmod2/Tmod1 chimeras were
transfected separately in PC12 cells before being plated and cocultured
together before NGF induction. Twenty-four hours after transfection,
NGF was used to induce differentiation outgrowth of neurite-like processes
(neurites) monitored on days 3 and 6 on a laser scanning confocal
microscope (LSM710, Zeiss) with a 63× oil immersion lens (Zeiss).
Images were acquired with Zen software (Zeiss), and the number and
length of neurites were analyzed with Imaris (Bitplane). Statistical
analysis was performed by one-way analysis of variance (ANOVA).
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7

Platelet Activation and Signaling

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Platelets were seeded onto fibrinogen-coated slides for 45 min and then fixed with 4% PFA. Cells were then permeabilized with a blocking solution containing 0.1% SDS in PBS and stained with primary antibodies for STAT5a and STAT5b (15 μg/ml) overnight at 4°C. Alexa Fluor secondary antibodies (1:500) were added in blocking buffer for 2h at rt. After washing with PBS, platelet samples were mounted and imaged with a Zeiss 63× oil immersion lens.
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8

Immunofluorescent Staining of MPO

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Cells were fixed with 4% paraformaldehyde at room temperature (RT) for 30 min and then, permeabilized with 0.3% Triton X-100 (Sigma-Aldrich, St. Louis, MO, USA) for 30 min at RT and 0.1% SDS for 10 min at RT. Then, slides were washed three times with PBS 10 mM for 5 min and blocked with 10% goat serum (G9023; Sigma-Aldrich) for 1 h at RT. Slides were rinsed with PBS to wash cells. Then, cells were incubated overnight at 4 °C with 1:100 anti-MPO primary antibody (ab9535; Abcam). After three washes with PBS of 5 min each, cells were incubated with a fluorescently labeled Alexa Fluor 635 goat anti-rabbit IgG secondary antibody (A31576; Invitrogen) for 1.5 h at RT in darkness. Then, slides were washed four times with PBS for 5 min each. Cells were counterstained with ProLong Antifade containing 4′,6-diamidino-2-phenylindole (DAPI) (Molecular Probes, Eugene, OR, USA; blue-stained) and imaged with a Zeiss LSM800 confocal microscope using 63× oil immersion lens (Carl Zeiss, Oberkochen, Germany).
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