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59 protocols using tcs sp5 2 microscope

1

Ddx4 N1 Organelle Partitioning Imaging

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Ddx4 N1 organelle partitioning of fluorescent nucleic acids and proteins was imaged using a Leica TCS SP5II microscope equipped with a motorised stage and HCX PL APO CS 40x NA 1.3 oil immersion objective. Illumination was provided by Argon (458, 488 and 514 nm) and Helium-Neon (543 and 633 nm) lasers. Imaging scan speed was 400 Hz with a format of 512 x 512 pixels at 8 bit depth. Z-stacks were taken +/-10 µm from the brightest plane of the sample in 1 µm increments. Experimental parameters (laser intensity, detector sensitivity etc.) remained constant for each set of experiments and associated controls. Typical excitation and emission schemes for the fluorophores used in partitioning experiments are summarised in table S4. FRET measurements made between Cy3 and Cy5-labelled oligonucleotides were made using the same Leica TCS SP5II microscope setup. Detailed description of the analysis of FRET data can be found in the supplementary material.
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2

Retinal Vasculature Immunostaining Protocol

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Dissection and labelling of retinas was performed as previously described27 (link). Briefly, retinas were fixed for 2 h on ice in 4% paraformaldehyde, incubated in 1% BSA and 0.3% Triton X-100, washed two times in Pblec (1% Triton X-100, 1 mM CaCl2, 1 mM MgCl2, and 1 mM MnCl2 PBS (pH 6.8)), and incubated overnight with isolectin-B4 (1:50) and antibodies diluted in Pblec. Images were acquired and processed using a Leica TCS SP5 II microscope, LAS Montage Imaging software (Leica) and the IMARIS Digital Imaging software (Biplane). Biotinylated Griffonia simplicifolia lectin I (IB4), (B-1205) was purchased from Vector Laboratories.
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3

Immunohistochemical analysis of brain tissue

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Using previously established methods8 (link), brains were post-fixed in 4% paraformaldehyde in PBS at 4° C for ten 99mTc-albumin half-lives (~60 h). Hemisections were equilibrated in 30% sucrose in PBS for 24 h at 4 °C and embedded in OCT (Tissue-Tek, Torrance, CA). Antigen retrieval was performed with 50 mM sodium citrate (pH 9.0) and then heating at 80 °C for 30 min. Immunostaining was performed as previously described14 (link). Floating tissue sections were cover slipped with a drop of Prolong Gold Antifade Reagent. The following antibodies were used: rabbit polyclonal anti-EAAT4 (Abcam, Cambridge, MA; 1:1,000), mouse monoclonal calbindin (Abcam; 1:1,000), rabbit polyclonal anti-GLUT1 (Millipore, Billerica, MA; 1:500), and goat polyclonal anti-ICAM-1 (Novus Biologics, Centennial, CO; 1:1,000). Corresponding secondary antibodies labeled with Alexa 488, and Cy3 were applied for 2 h (Jackson Immunoresearch, West Grove, PA; 1:1,000). Confocal microscopy was performed with a Leica TCS SP5 II microscope. Microscopic images were acquired with the Leica Application Suite and processed using image adjustments limited only to linear contrast and brightness adjustments applied identically to data from blast- and sham-treated animals in each experiment.
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4

Live-cell confocal imaging of cells

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Live-cell confocal imaging was performed on a TCS SP5 II microscope (Leica, Wetzlar, Germany) equipped with a temperature-controlled chamber. The videos were routinely recorded with a 63× objective. Live cell imaging was conducted in 35 mm Mattek No. 1.5 dishes in a medium supplemented with 20 mM HEPES buffer pH 7.5.
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5

Lignin Visualization in N. benthamiana

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After 5 days of ectopic expression, N. benthamiana leaves were embedded in 6% agarose and hand-sectioned with a razor blade. For Basic Fuchsin staining, cross-sections were cleared and fixed for 15 min in methanol, before they were incubated in 10% (w/v) NaOH at 65 °C for 1 h. Lignin was stained with 0.01% (w/v) Basic Fuchsin (Sigma-Aldrich, Taufkirchen, Germany) in water for five minutes and washed briefly with 70% (v/v) ethanol. Cross-sections were mounted in 50% (v/v) glycerol and imaged on a confocal TCS SP5II microscope (Leica, Mannheim, Germany) equipped with a 40.0 × 1.25 NA objective under 561 nm excitation and 593/40 nm emission. ImageJ v1.52 software (https://imagej.nih.gov/ij/, accessed on 12 November 2021) was used to produce orthogonal sections and scale bars.
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6

Neuromast Ablation in Tg(Eya1:EGFP) Embryos

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We used a multi-photon laser coupled to a Leica TCS SP5 II microscope to perform specific ablations of the neuromastP0 on Tg(Eya1:EGFP) embryos. We chose the option ‘Area ablations’ and used the 880 nm wavelength with a laser power ranging from 25% to 30%. The absence of the neuromastP0 was checked immediately after the ablation and confirmed 24 hr later.
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7

Cuticular Cap Morphology Analysis

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For study by confocal microscopy, cuticle of the proximal tibia was isolated and placed in Conray (a radiopaque dye that can be used as a clearing agent for insect cuticle) (22 (link), 29 (link), 30 (link)). Specimens were imaged using a Leica TCS SP5 II microscope at the Marshall University Microscopy facility. Measurements of cuticular caps were made on projection images and optical sections using ImageJ (v.1.43 u, NIH; RRID:SCR_003070).
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8

Quantifying ROS in Cells Treated with PP-PP+ Derivative

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Cells grown in 12-well plates were incubated with 10 μM DCFH-DA in KRB-HEPES for 1 h. DCFH-DA-loaded cells were washed with ice-cold KRB-HEPES and treated with the desired concentration of PP-PP+ derivative in the same buffer for 1 h at 37 °C. After the incubations, cells were washed, harvested, solubilized with 0.1 M Tris buffer (pH 7.5) containing 1% Triton X-100, and cell debris were removed by centrifugation at 13,200 g for 8 min at 4 °C. The content of ROS-oxidized DCFH product, 2′,7′-dichlorofluorescein (DCF) in the supernatants was quantified by fluorescence (Ex/Em 488/524 nm) (40 (link)). The data were normalized to the protein contents of individual samples. ROS production in DCFH-DA (50 μM) loaded PP-PP+ treated MN9D and HepG2 cells was visualized by confocal fluorescence microscopy at Ex/Em 488/524 nm using a Leica TCS SP5II microscope.
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9

Immunofluorescent Staining of BCR-ABL1- Pre-B-ALL

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BCR-ABL1 pre-B-ALL cells were fixed and permeated. Staining was performed according to conventional immunohistochemistry using anti-HDAC7 and anti-MEF2C monoclonal antibodies, fluorescein isothiocyanate-conjugated immunoglobulin G (IgG), and rhodamine-conjugated IgG antibodies. DAPI (4′,6-diamidino-2-phenylindole) staining was also included in the experiment. After staining, cells were spread and enriched on glass slides by a cytospin device (StatSpin, Westwood, MA). Fluorescence signals were detected and photographed using a Leica TCS SP5 II microscope.
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10

Confocal Imaging of Fluorescent Proteins in Plants

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Confocal images were acquired by a Leica TCS SP5 II microscope. The excitation/emission spectra for various fluorescent proteins are: CFP, 458 nm/480–500 nm; GFP, 488 nm/501–528 nm; YFP, 514 nm/520–540 nm; mRFP, 594 nm/600–620 nm, and propidium iodide (PI), 594 nm/591–636 nm. Images were taken from similar central areas in the adaxial side of developing cotyledons of Arabidopsis seedlings or N. benthamiana leaves. Cells outlines in Arabidopsis were visualized by propidium iodide (PI, Invitrogen) staining. All imaging processing was performed with Fiji (Image J) software (http://fiji.sc/Fiji). Whenever possible, z-stacked images were obtained. Quantifications and statistical analyses were performed using Fiji and GraphPad Prism 5.1, respectively.
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