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30 protocols using tcs sp2 spectral confocal microscope

1

Confocal Microscopy Imaging Protocol

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Fluorescent images were captured with the TCS SP2 Spectral Confocal Microscope (Leica Microsystems, Inc., Wetzlar, Germany). Scanware software (Leica Microsystems, Inc.) was used to acquire z-series stacks at a step size of 0.25–0.35 μm. Images were scanned using a 512 × 512-pixel format; scan lines were averaged twice, and frames were scanned three times. Digital images were cropped and arranged using Photoshop CS (Adobe Systems, Inc., San Jose, CA). Fluorescence images within a figure were adjusted for brightness and contrast for background standardization.
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2

Microscopy Imaging Workflow Optimization

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Bright-field images were generated using a Nikon DXM 1200C digital camera attached to a Nikon Eclipse 80i microscope and captured using Nikon NIS-Element F 3.00 software. Acquisition parameters were held constant for images with both antisense and sense probes. Fluorescent images were captured with the TCS SP2 Spectral Confocal Microscope (Leica Microsystems Wetzlar, Germany) using UV, Ar, GeNe, and HeNe lasers and appropriate excitation spectra. Scanware software (Leica Microsystems) was used to acquire z-series stacks captured at a step size of 2–3 μm. Acquisition parameters (i.e., gain, offset, PMT settings) were held constant for experiments with antibodies and for controls without antibodies. Digital images were cropped and arranged using Photoshop CS (Adobe Systems). Fluorescence images within a figure were adjusted for brightness and contrast for background standardization.
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3

Quantifying Centrosome Dynamics in Hepatocytes

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Liver cryosections (5μm) were fixed with 4% paraformaldehyde and blocked for 1 hour with mouse IgG blocking reagent (vector labs). After blocking with Donkey serum (5% in PBS-0.3%Tween), sections were incubated with 1/500 anti-pericentrin antibody (Abcam) overnight. Secondary 1/500 Anti-rabbit Cy3 (Jackson immunoresearch, stratech) and 1/500 Alexafluor 488 –phalloidin (invitrogen) was then applied on the sections for 1-2hours. Sections were mounted with vectashield plus DAPI medium. Sections were viewed and analysed using a Leica TCS SP2 spectral confocal microscope and Leica confocal software (Leica, Heidelberg, Germany). Centrosomes numbers were counted in at least 150 nuclei of hepatocytes from each mouse for each genotype (N=3-5) at D4 and D6.
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4

Quantifying Centrosome Dynamics in Hepatocytes

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Liver cryosections (5μm) were fixed with 4% paraformaldehyde and blocked for 1 hour with mouse IgG blocking reagent (vector labs). After blocking with Donkey serum (5% in PBS-0.3%Tween), sections were incubated with 1/500 anti-pericentrin antibody (Abcam) overnight. Secondary 1/500 Anti-rabbit Cy3 (Jackson immunoresearch, stratech) and 1/500 Alexafluor 488 –phalloidin (invitrogen) was then applied on the sections for 1-2hours. Sections were mounted with vectashield plus DAPI medium. Sections were viewed and analysed using a Leica TCS SP2 spectral confocal microscope and Leica confocal software (Leica, Heidelberg, Germany). Centrosomes numbers were counted in at least 150 nuclei of hepatocytes from each mouse for each genotype (N=3-5) at D4 and D6.
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5

Immunoprecipitation and Fractionation Protocol

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For immunoprecipitation, cells were lysed on ice in TNE buffer (50 mM Tris–HCl, pH 7.5, 150 mM NaCl, 0.5% Tergitol-type NP-40, 1 mM EDTA, and protease inhibitors). Anti-FLAG M2 magnetic beads (M8823, Sigma) were incubated overnight with cell lysate fractions. Samples were then washed 6 times with TBS. Western blotting was performed following standard principles and immunofluorescence was assessed using a Leica TCS SP2 spectral confocal microscope. Nuclear-cytoplasmic fractionation was performed following standard protocol. The following primary antibodies were used: anti-FLAG (F7425, Sigma), anti-NCoR (ABE251, Millipore), anti-HA (H6908, Sigma), anti-SMRT (ab24551, Abcam), anti-HDAC7 (ab12174, Abcam), anti-E-cadherin (BD Biosciences), anti-SSEA-1 (MC480, Cell Signaling), anti-SOX2 (MAB2018, R&D Systems), anti-OCT4 (sc-8628, Santa Cruz), anti-KLF4 (AF3158, R&D Systems), anti-MYC (AF3696, R&D Systems), anti-histone H3 (ab1791, Abcam), anti-ACTIN (A5316, Sigma), and anti-GAPDH (G8795, Sigma). DAPI was purchased from Sigma (D9542).
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6

Cellular Uptake of Nanoparticles by Fluorescence Microscopy

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For fluorescent microscopy, J774.E cells were seeded in 24-well plates while for confocal microscopy the cells were seeded in Laboratory-Tek II 4-chamber cover glasses slides. When the cells reached ~ 80% confluence they were incubated with 80 nM NCs in 20 mM HEPES-buffered Hanks’ balanced saline solution (HBSS) for 1 hour at 37°C. The incubation media included a general fluid endocytosis marker tetramethylrhodamine B dextran (10,000 MW) at 50 μM and the nuclear dye DAPI at 5 μg/ml. The cells were then washed with PBS five times. NC uptake into live J774.E cells was examined under an inverted Olympus fluorescence microscope (model IX71S1-F3) at the magnification of 40x objective. Confocal microscopy was performed on a Leica TCS SP2 Spectral confocal microscope using the XYZ mode. A sequential image acquisition mode was used to avoid possible partial light spillover from one color to another. The middle cell sections of selected Z-stacks are shown in Fig. 8. Quantification of green fluorescence within individual cells and in a middle section of an acquired Z-stack was performed using Leica’s software, LAS AF, version 2.4.1.
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7

HPLC Purification and Characterization of Biomolecules

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ALP was purchased from Biomatik, NBD-Cl from TCI and amino acids from GL
Biochem, PP1 from Sigma-Aldrich, PTP1B from Abcam. All the solvents and chemical reagents
were used directly as received from the commercial sources without further purification.
All the products were purified with Water Delta600 HPLC system, equipped with an XTerra
C18 RP column and an in-line diode array UV detector. Rheological data were obtained on TA
ARES G2 rheometer with 25 mm cone plate, confocal microscopy images on Leica TCS SP2
spectral confocal microscope. Electron microscopy imaging was performed on a FEI Morgagni
268 TEM with a 1k CCD camera (GATAN, Inc., Pleasanton, CA, USA) or a 300 keV Tecnai F30
intermediate voltage TEM (FEI, Inc., Hillsboro, OR, USA) with a 4k CCD camera (GATAN).
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8

Characterization of Iron Oxide Nanoparticles

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Iron oxide nanoparticles with amphiphilic polymer coating and a monolayer of oleic acid were purchased from the Ocean NanoTech company. Transmission electron microscope images were collected by using Morgagni 268 microscope. Confocal images were taken with the Leica TCS SP2 Spectral Confocal Microscope. The cells were counted by a hemacytometer.
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9

Immunofluorescence Staining of Autophagy and Aggresomes

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RPMI-8226 cells were incubated for 48 hours in the absence or presence of drugs and were plated on poly-l-lysine-coated coverslips for processing. The coverslips were then washed with PBS and cells were fixed with 4% formaldehyde, permeabilized in 0.1% Triton X-100 and blocked with 4% goat serum in PBS. For LC3 staining, cells were permeabilized with 0.1% saponin. The coverslips were incubated with primary antibodies for 1 hour, washed with PBS, and then incubated with secondary antibodies for 30 minutes. The coverslips were again washed with PBS and mounted in Vecta-Shield with DAPI. Supplementary Table 2 details the primary and secondary antibodies. Autophagosome and aggresome staining were performed using CYTO-ID® Autophagy (1:100) and PROTEOSTAT® Aggresome (1:2000) detection kits according to manufacturers' instructions (Enzo Life Sciences, Inc., Farmingdale, NY). [35 (link), 36 (link)] Microscopy was performed using a Leica TCS SP2 spectral confocal microscope with a 63× objective at the Flow and Image Cytometry Core facility at the Roswell Park Cancer Institute. Images were processed using ImageJ software
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10

Multimodal Characterization Techniques

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Example 1

Transmission electron microscope (TEM) images were taken on Morgagni 268 transmission electron microscope. Confocal images were obtained on a Leica TCS SP2 Spectral Confocal Microscope. Magnetic studies were carried out using a Lakeshore 7404 high sensitivity vibrating sample magnetometer (VSM). Samples were dried with Labconco Freezone 4.5 Plus vacuum lyophilizer. The cells were counted by Bio-Rad TC 20™ Automated cell counter.

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