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9 protocols using dylight 633

1

Purification and Labeling of BPIFA1 Proteins

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cDNA of full length and truncated BPIFA1 was transformed in BL21-Codon Plus competent cells (Agilent Technologies), and purified as previously described24 (link). S18 peptide was synthesized and purified by the UNC Microprotein Sequencing and Peptide Synthesis Facility, as described previously17 (link). Fluorescent labelling was done using DyLight 594 or DyLight 633 NHS ester (Thermo Fisher) by following the manufacturer's instructions.
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2

Immunofluorescence Assay for Aspergillus Infection

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For immunofluorescence assays, cells were allowed to adhere in a 24-well plate with poly-l-lysine-coated glass coverslips for 1 h (Merck). After infection with labeled A. fumigatus spores and incubation for the noted times, cells were fixed using 3.7% (vol/vol) formaldehyde in PBS for 10 min, rinsed three times with PBS, permeabilized for 15 min using 0.1% (vol/vol) Triton X-100 in PBS or 0.1% (wt/vol) saponin in PBS, and then blocked for 30 min with 2% (wt/vol) bovine serum albumin (BSA). After permeabilization, washed cells were incubated with primary rabbit anti-Lamp-1 antibody (Abcam ab24170; 1:100 dilution), anti-V-ATPase V1 subunit antibody (Abcam ab73404; 1:100 dilution), or anti-histone H3 (Cell Signaling DIH2; 1:200 dilution) antibody in 1% (wt/vol) BSA in PBS, followed by incubation with secondary goat anti-rabbit IgG antibody DyLight 633 (Thermo Fisher Scientific). The glass coverslips were mounted onto microscopy slides and visualized using a Zeiss LSM 780 confocal microscope (Carl Zeiss). LAMP-1 recruitment was quantified by comparing the positive signal from stained phagolysosomes to nonstained phagolysosomes.
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3

Dylight Labeling of Trichoderma Cellulase

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A cellulase cocktail from Trichoderma reesei ATCC 26921(C8546, lot # 031M1283V–Sigma-Aldrich Co. St. Louis MO63103, USA) was labelled with Dylight 633 (Thermo Fisher Scientific Ltd, Rockford, IL 61101, USA–Lot # NI 176327)28 (link)55 (link). 8.4 Milligrams of freeze dried cellulase powder was dissolved in 1 mL of 0.05 M borate-phosphate buffered saline at pH 7.5. This enzyme solution was mixed with Dylight reagent and vortexed gently to ensure complete mixing. The tube was covered with aluminium foil and incubated at 25 °C for 1 h with shaking at 50 rpm. The unlabelled dye in the reaction mixture was separated on 250 μl of supplied resin. The purified labelled protein was stored at 4 °C protected from light. Based on the reported average molecular weight (65 kDa) of cellulase (Cel7A and Cel7B) from T. reesei44 (link) the molar ratio of Dylight to protein was found to be 7.48 M label per mole of protein. We did not investigate the relative labelling of the component enzymes in the cocktail as it is beyond the current scope to investigate differences in behaviour between the various enzymes present44 (link).
The hydrodynamic radius of Dylight labelled cellulase was measured by dynamic light scattering.
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4

VLP Labeling with DyLight 633

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Purified VLP in PBS were coupled to 1∶1 molar equivalent of N-hydroxysuccinimide (NHS)-DyLight 633 (Thermo Scientific) to VP60 for 30 min at room temperature. Following removal of unconjugated DyLight 633 by dialysis, coupling was confirmed by SDS-PAGE (visualized under UV light), and quantified by determining the DyLight:VP60 molar ratio using a NanoDrop (DyLight 633 = λmax 627 nm, ε 170000 M−1 cm−1).
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5

Antibody Staining Protocol for Cell Analysis

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The following primary antibodies were used in this study: CC2C6 (Biolegend), B6H12 (BD Pharmingen) and BRIC126 (Santa Cruz Biotechnology) are α-CD47 monoclonals; Mcl-1, PARP-1 (Santa Cruz Biotechnology); NOXA (Cell Signaling); 9F10 (ITGA4), P84 (SIRPα), GAPDH, and Alexa Fluor 647-labelled F4/80 (Biolegend). Secondary antibodies used were Dylight488, Dylight633, Dylight680 and DyLight800 conjugates of goat-anti-mouse, and DyLight800 conjugated goat-anti-rabbit (all from Thermo Fisher).
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6

Characterizing FVIII and ADAMTS-13 interactions

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FVIII (50 nM, Helixate®), FVIIIHSQ (50 nM), FVIIIC1 (50 nM), ADAMTS-13 (50 nM) conjugated to Dylight 633 (Thermo Scientific, Courtaboeuf, France) or human Factor IX (50 nM, Benefix, Pfizer, France) were incubated with 20% normal serum (NS), heat-inactivated (56°C for 30 min) serum (HIS) or C3-depleted serum (ΔC3) in RPMI-1640 at 37°C for 1 hour (h). When indicated, FVIII or Dylight 633-labeled ADAMTS-13 were incubated with C3 (250 μg/mL), Factor B (50 μg/mL) and Factor D (1 μg/mL) or with C3b (250 μg/mL) in 20 mM HEPES 150 mM NaCl 10 mM MgCl2 for 1 h at 37°C. Samples were then incubated with 5-day-old immature MO-DCs (2.105 cells/100 μL) for 2 h at 4°C or 37°C. Cells were washed with ice-cold phosphate buffer saline, fixed with 4% paraformaldehyde (Sigma-Aldrich). In the case of FVIII, cells were permeabilized using 0.5% saponin (Sigma-Aldrich) and stained with an FITC-conjugated monoclonal mouse anti-human FVIII IgG (77IP52H7). Cells were analyzed by flow cytometry and data were computed using the BD FACS Diva software (v.6.1, BD Biosciences). The uptake was quantified as the difference in the median fluorescence intensities between 37°C and 4°C (ΔMFI37°C–4°C) to exclude the signal generated by the binding of FVIII to the cell surface.
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7

Immunofluorescence Analysis of DRG Neurons

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DRG neurons were cultured on glass Coverslips in a 6-well plate at 5000 cells/well seeding density and fixed with 4% paraformaldehyde solution and permeabilized with 0.5 percent Triton-X 100 for 15 min at room temperature, as described elsewhere. These cells were blocked for 2 h at room temperature with a 3 percent BSA solution in PBS. After blocking, the cells were incubated overnight at 4 °C with primary antibodies (p-AMPK, Complex I, and TFAM) at 1:200 dilutions in 3% BSA solution. The following day, cells were washed with PBST and incubated with secondary Goat anti-Mouse IgG (H + L) Secondary Antibody, DyLight 633 (Thermo Fischer scientific, Waltham, MA, USA, Cat# 35512) and Zenon Alexa Fluor 488 Rabbit IgG Labeling Kit (Thermo Fischer scientific, Waltham, MA, USA, Cat# Z25302) at room temperature for 2 h in 3% BSA solution at 1:100 dilution. Finally, the coverslips were adhered to the glass slide with DAPI mounting medium (Sigma Fluoroshield). A confocal microscope was used to capture the images (Leica TCS SP8 Laser Scanning Spectral Confocal microscope, Germany) [33 ].
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8

Immunofluorescence Staining of SPK2 and Bcl-2

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Cells were fixed with 4% paraformaldehyde for 15 min and incubated with PBS containing 0.1% Triton X-100 for 30 min. After blocking with 1% BSA for 1 h, cells were incubated with antibodies against SPK2 (1:100) and/or Bcl-2(1:20; Santa Cruz sc-7382) at 4 °C for 24 h, and with anti-rabbit IgG(H+L) secondary antibody, Dylight 633 (1:500; Invitrogen) and/or anti-mouse IgG (H+L) secondary antibody, DyLight 488 (1:500; Invitrogen) for 2 h. Then the cells were stained with DAPI (1:10000; sigma D9564) for 10 min. Images of fluorescence were acquired using a laser scanning confocal microscopy (ZEISS LSM710, Oberkochen, Germany).17 (link)
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9

Immunofluorescence Analysis of Neutrophil Binding

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The control samples from the inhibition assay were stained to confirm by immunofluorescence microscopy the binding of the CD18a antibody onto the surface of the neutrophils. The permeabilization and the blocking for the staining were performed as above. Myeloperoxidase was detected using a polyclonal rabbit anti-human myeloperoxidase (A039829-2, 3.3 mg, 1:309; Agilent, Santa Clara, CA, USA). For the isotype controls, a rabbit IgG (from rabbit serum, I5006, 1.16 mg, 1:108.75; Sigma-Aldrich GmbH,) and a IgG1 Isotype Control from murine myeloma (M5284, 0.2 mg, 1:200; Sigma-Aldrich GmbH) were used. The first antibodies were incubated for 1 h at room temperature. As secondary antibodies, a goat anti-mouse IgG (H + L) DyLight 633 (#35512, 1:500; Invitrogen) and a goat anti-rabbit IgG (H + L) cross-adsorbed Alexa Fluor 488 (A11008, 1:500; Invitrogen) were used. The secondary antibodies were incubated for 1 h in the dark and at room temperature. The processing of the samples was carried out as explained above. The images were taken using a Leica TCS SP5 AOBS confocal inverted-base fluorescence microscope with an HCX PL APO 40× 0.75–1.25 oil immersion objective (see Figure A5, Appendix A).
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