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68 protocols using tcs sp5x

1

Visualizing Cell Migration Dynamics

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Images were acquired with either a Leica TCS SP5X (20×/0.70 and 40×/0.85 objectives) or a PerkinElmer UltraViewVoX Spinning Disk microscope (20×/0.60, 40×/1.15 and 60×/1.20 objectives). To measure the transit times of click-iT EdU-labeled cells, images were acquired with a Leica TCS SP5X with the laser line 405, 488, and 568. Other specimens were excited by laser wavelengths of 405, 433, 488, 514 and 568nm for DAPI, CFP, Alexa Fluor 488, YFP, and RFP, respectively.
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2

Collagen Orientation Analysis in Valves

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Half leaflet sections of all (n = 5) valves were analyzed for the effect of the insert on the global collagen orientation. Samples were stained using a whole mount staining with the collagen specific dye CNA35-OG488,14 (link) for 1 h in PBS and visualized with a confocal microscope (TCS SP5X, Leica, Germany). The dye has an excitation and emission profile of 488 and 500–550 nm, respectively. Samples immerged in Mowiol (Sigma, USA) were mounted between two preparation glasses. The specimen was observed with a ×10 objective and Z-stacks were made throughout 200 μm of the entire arterial side of the sample using stitched adjacent tile scans. Afterwards, a maximum intensity projection was made in Z-direction.
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3

In Situ Hybridization and Live Imaging

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For in situ hybridization and phenotype analysis, embryos were imbedded in 70% Glycerol/PBS (v/v). Images were taken on an Olympus SZX16 microscope equipped with a DP71 digital camera by using Cell A imaging software. For confocal analysis, live embryos were embedded in 0.7% low melting Agarose (Sigma-Aldrich) dissolved in 1×Ringer's solution. Images were obtained by using a Leica TCS SP5 X confocal laser-scanning microscope with 40×or 63×dip-in objectives. Image processing was performed by using an Imaris 6.3.1 software (Bitplane AG).
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4

Immunofluorescence of Activated Hepatic Stellate Cells

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LX2 cells were grown on glass coverslips and treated as described in the Results and figure legends. Then, cells were washed twice with phosphate buffered saline (PBS), fixed in 4% paraformaldehyde for 10 min and processed for immunofluorescence with the indicated primary antibodies: anti-αSMA (A-2547) purchased from Sigma-Aldrich, anti-COL1A1 (sc-8784) and anti-MMP9 (sc-6840) from Santa Cruz Biotechnology (Santa Cruz, CA, USA) and the appropriate FITC-conjugated secondary antibodies [Alexa Fluor® 488 goat anti-rabbit IgG (A11034) or Alexa Fluor® 488 goat anti-mouse IgG (A11001), Life Technologies, Grand Island, NY, USA]. Mounting medium used was Fluoromont G® (BioNova cientifica, Madrid, Spain). Immunofluorescence was examined using a confocal microscope (Leica TCS SP5 X, Barcelona, Spain) and image analysis procedures were performed with Fiji software (NIH, Bethesda, MD).
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5

LysoTracker Quantification in Fly Fat Bodies

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For LysoTracker staining, fat bodies from female flies (10 days) were dissected in PBS and immediately stained with LysoTracker Red DND‐99 (Invitrogen) dye (1 μM in PBS) for 2 min. Tissues were then washed three times in PBS and mounted in mounting medium (VECTASHIELD H‐1200) containing DAPI. Images were taken using confocal microscope (Leica TCS SP5X) with 40x 1.25 oil objective. Laser power and optical settings were kept constant between images. Images were then analyzed using Imaris 8.0 software. The number of LysoTracker puncti and DAPI‐stained nuclei was quantified according to user manual guidelines and puncti/nucleus calculated. All image analysis and quantification were performed under blinded conditions.
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6

Fluorescence Microscopy of Glycosidase-reactive Probes

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For fluorescence microscopy, about 10 000 cells
in 200 μL of medium supplemented with 10% fetal bovine serum
and 1% penicillin/streptomycin were seeded in each well of an 8-well
chamber (μ-Slide 8 well; Ibidi) and cultured for 1–2
days. The medium was replaced with 200 μL of phenol red- and
serum-free RPMI-1640 or DMEM containing 10 μM glycosidase-reactive
fluorescent probe. The plate was incubated at 37 °C for 1 h in
a humidified incubator under 5% CO2 in air, and differential
interference contrast (DIC) and fluorescence images were obtained
using a Leica Application Suite Advanced Fluorescence with a TCS SP5
X. The light source was a white light laser. Excitation and emission
wavelengths were 498 nm/500–600 nm.
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7

Confocal Imaging and Analysis of Embryos

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For confocal analysis, live embryos were embedded in 0.7% low melting agarose (Sigma-Aldrich) dissolved in 1x Ringer’s solution. Images of cells and embryos were obtained with a Leica TCS SP5 X or SP8X confocal laser-scanning microscope using 20x or 63x dip-in objective or, for the kinase library screen, a Leica DMI600SD with 20x objective. Image processing was performed with Imaris 9.1 software (Bitplane AG, Switzerland). Filopodia and cytoneme measurements from confocal z-stacks of living embryos was performed via the semi-automated filopodia analysis software described before. Cell culture quantifications were carried out using Fiji software. Roundness of notochordal embryo cells was determined by calculating the width to length ratio of each cell in Fiji.
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8

Thrombus Formation and Lysis Protocols

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Thrombus models were established
by following the published protocols.63 (link) Fibrinogen from human plasma (1 mg/mL) as the
physiological source of thrombus was dissolved in a solution of 50
mM Tris-HCl (pH 7.4) and 140 mM NaCl. Thrombus formation was induced
by adding 1 U/mL thrombin and 2.5 mM CaCl2 to the fibrinogen
solution, which was then cultured at 37 °C for 1 h. A turbidity
assay was used to monitor the process of thrombus formation by measuring
the absorbance (340 nm) at 10 min intervals. Fluorescent-labeled thrombus
was formed by an additional supply of 10 μL of Alexa Fluor 488-conjugated
fibrinogen to the fibrinogen solution containing thrombin and CaCl2, followed by incubation at 50 °C for 2 h. The fluorescent
thrombus was characterized by CLSM (Leica, TCS SP5X). Thrombus models
and EM-JPMs (50 μL, ∼4.9 × 105 per μL)
in a μ-slide 8 well (ibidi, Germany) were irradiated with a
760 nm laser at a laser power of 2.43 J/cm2 (two-photon
laser, Chameleon Vision, Coherent, USA). Thrombus lysis was evaluated
by a fluorescence-based assay.
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9

Confocal Microscopy for 3D Imaging

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A confocal microscope (Leica TCS SP5 X) was used for imaging all samples. A diode 405 and an argon laser were used for violet and green excitation, respectively. The 3D images were reconstructed using ImageJ software.
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10

Embryo Imaging and Live Cell Analysis

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Prior to imaging, embryos were mounted in 70% glycerol. Images were taken with the help of an Olympus SZX16 microscope equipped with a DP71 digital camera using the imaging software Cell A. For confocal analysis, embryos were embedded for live imaging in 1.5% low melting point agarose (Sigma-Aldrich) dissolved in 1x E3 solution at 50% epiboly stage. Live embryos as well as cells were images using 20x and 63x water immersion objective. Confocal image stacks were then obtained using the Leica TCS SP5 X confocal laser-scanning microscope. Images were further processed using Imaris 6 (Bitplane AG).
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