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A1r laser confocal microscope

Manufactured by Nikon
Sourced in Japan

The Nikon A1R laser confocal microscope is a high-performance imaging system designed for advanced biological and materials research. It utilizes a laser-scanning technology to capture high-resolution, optical sections of samples with excellent signal-to-noise ratio and contrast. The system is capable of acquiring images with minimal photobleaching and phototoxicity, making it suitable for live-cell imaging and time-lapse experiments.

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60 protocols using a1r laser confocal microscope

1

Confocal Microscopy and FRAP Analysis

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Confocal microscopy was performed using the A1R laser confocal microscope (Nikon) with 60 × 1.27 Plan-Apochromat water immersion lens. Images were analyzed with FIJI (NIH). FRAP were performed on an A1R laser confocal microscope (Nikon), and FRAP analysis of EGFR-GFP was performed as described previously (Kay et al, 2012 (link)).
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2

Visualization of Internalized Siglec-8 in Eosinophils

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The cells were incubated in the presence or absence of DQ Green BSA, a self-quenched dye conjugate of BSA that fluoresces when the BSA is cleaved by proteases and the quenching is relieved (10 μg/mL; Thermo Fisher Scientific, Carlsbad, Calif) for 120 minutes at 37°C to mark lysosomes either before labeling of Siglec-8 on the cell surface or following Siglec-8 labeling that would lead to the visualization of internalized Siglec-8. Eosinophils were incubated with Alexa Fluor 647–conjugated anti–Siglec-8 mAb (2C4) or Alexa Fluor 647– conjugated isotype-matched control mAb (MOPC-21; both at 2.5 μg/mL) during a 20-minute incubation at 4°C. The eosinophils were cytospun onto glass slides and fixed with 4% paraformaldehyde (Affymetrix, Santa Clara, Calif) for 15 minutes at room temperature. Slides were mounted using Fluoromount-G mounting medium (Electron Microscopy Services, Hatfield, Pa) and imaged using a Nikon A1R+ confocal laser microscope (Tokyo, Japan) using a 100×/1.45 NA oil-immersion objective lens and 488-and 640-nm lasers with a 1.5-AU pinhole. Images were acquired and analyzed using Nikon Elements software.
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3

Immunofluorescence Imaging of Cellular Proteins

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Cells were treated as described in the text, harvested on slides and fixed. After permeabilization with 0.1% (v/v) Triton X-100 in PBS and blocking with 2% (w/v) BSA in PBS, cells were incubated overnight with the indicated antibodies followed by secondary antibodies conjugated either with Alexa Fluor 555 dye (Invitrogen) or Alexa Fluor 488 dye for 1 h. Cellular DNA was counterstained with 4, 6-diamidino-2-phenylindole (DAPI; Molecular Probes). Fluorescence signals were detected on a Nikon A1R confocal laser microscope.
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4

Visualizing Cell Proliferation in Transgenic Zebrafish

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Tg(5×UAS:EGFP-P2A-krasG12D)+/Tg; Tg(pInt-Gal4)+/Tg and Tg(pInt-Gal4)+/Tg; Tg(UAS:EGFP)+/Tg larvae from the same clutch were used. BrdU incorporation experiments were performed essentially as described previously (Takada et al., 2010 (link)). At 4 dpf, 20 larvae were transferred into egg water containing 0.5 mM bromodeoxyuridine (BrdU; Nacalai Tesque) and incubated for 24 h. At 5 dpf, larvae were rinsed with egg water and then fixed with 4% PFA in PBS. Agarose embedding and cryosectioning were performed as described above. After rehydration of cryosections by PBS, sections were treated with 2N hydrochloric acid to denature DNA at room temperature for 1 h and then washed with PBS. Blocking and antibody treatment were performed as described above. Primary antibodies, mouse anti-BrdU antibody (Developmental Studies Hybridoma Bank, G3G4; 1:500 dilution) and rabbit anti-GFP antibody (MBL, 598; 1:500 dilution), and secondary antibodies, Alexa-Fluor-568-conjugated anti-mouse IgG (Life Technologies; 1:500 dilution) and Alexa-Fluor-488-conjugated anti-rabbit IgG (Life Technologies; 1:500 dilution), were used. Sections were counterstained with Hoechst 33342 (Life Technologies; 1:2000 dilution) and mounted with 80% glycerol in PBS. Fluorescent images were taken with a Nikon A1R confocal laser microscope (Nikon).
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5

Quantifying Nuclear Protein Localization

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Cells were imaged with the Nikon A1R confocal laser microscope (Nikon Corporation) with the 100X Plan-Apo/1.4 NA oil lens. N-TASQ was imaged with the 488-nm laser, and the DAPI dye was imaged with the 405-nm laser. N-TASQ and γH2A.X fluorescence was analyzed by the puncta index, which is the standard deviation of the intensities measured among pixels within the neuronal nuclei. Low puncta index represents diffuse localization, whereas a high puncta index represents punctate localization.
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6

Videomicroscopy Tracking of Cell Migration

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Cells were plated on 24-well plates (25–35,000 cells /well) coated with laminin (5 µg/mL; Sigma). Videomicroscopy was carried out at least 8 h after plating using an inverted microscope (Olympus IX81) coupled with a Coolsnap HQ camera (Princeton Instruments) controlled with Metamorph software (Universal Imaging) as previously described57 (link) or using a NIKON A1R confocal laser microscope (Nikon Corp. Tokyo). Imaging conditions were maintained at 37 °C (The Box & The Cube, LIS), 5% CO2 and 18% O2 with a relative humidity of 95% controlled by an active gas supply system (the Brick, LIS). Images were taken of 6–20 fields per condition using a 10X objective (Olympus IX81) or in mosaic acquisition with a 20X objective (Nikon A1R) every 10 min. Tracking and overlay of individual cell tracks over a period of 4 h were carried out using the track object function in Metamorph software (Molecular Devices) or using the MTrackJ plugin in ImageJ software. Dynamic parameters as migration velocity, mean square displacement (MSD) and directional persistence were calculated with an Excel macro developed by F. Cordelières (Bordeaux imaging center, UMS 3420 CNRS, France) and/or with the custom-made open-source computer program DiPer58 (link).
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7

Hepatic Lipid and Enzyme Analysis

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Liver tissues were collected and fixed in 10% formalin on a shaking device for 24–48 hours, paraffin-embedded, and sliced into 5 μm sections for the following H&E staining according to the standard protocol. For IHC, Abs against CYP4A (sc-271983) and CYP2E1 (AB1252, Millipore) were used to stain the paraffin sections and visualized with DAB Peroxidase Substrate Kit (Vector Laboratories). For the Oil Red O staining, 5 μm frozen sections were prepared by cryosection from snap-frozen liver tissues. The primary hepatocytes or human hepatocyte cell line HC04 was treated and fixed with 4% paraformaldehyde. The sections or cells were stained in 0.5% Oil Red O in 60% isopropanol for 30 minutes. The images were taken by Olympus BX41 microscope. Cultured cells or frozen sections were fixed with 4% paraformaldehyde and stained with 250 μg/mL Nile Red solution for 15 minutes. The images were obtained by Nikon A1R confocal laser microscope (Nikon).
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8

Confocal Imaging of TRPV4 in CD

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Freshly-isolated split-open CD were fixed with 4% paraformaldehyde in PBS (pH = 7.4) for 15 min at RT. After fixation the samples were permeabilized by addition of 0.1% Triton X-100 in PBS for 10 min and washed in PBS 3 times for 5 min. Nonspecific staining was blocked with 10% normal goat serum (NGS, Jackson Immunoresearch, USA) in PBS for 30 min at RT. After washing with PBS (3 times for 5 min) the samples were incubated for 3 hr at room temperature in dark with anti-TRPV4 tagged with ATTO 550 (1:50, Alomone Labs, Israel; Cat. # ACC-034-AO) in 2% serum in PBS. After washing with PBS (3 times for 5 min) the samples were stained with DAPI (1.5 μM concentration, Calbiochem, San Diego, CA, USA) to visualize nuclei. Subsequently the samples were dehydrated, and mounted with permanent mounting medium (SouthernBiotech, Birmingham, AL, USA). Labeled tissue samples were examined with an inverted Nikon A1R confocal laser microscope using a 60X Plan-Fluor oil-immersion (1.3 NA) objective. Samples were excited with 405 and 561.7 nm laser diodes and emission captured with a 16-bit Cool SNAP HQ2 camera (Photometrics, Tucson, AZ, USA) interfaced to a computer running Nikon NIS Elements 4.3 elements software. 3-D stacks of split-open CD were generated from series of confocal plane images with 0.25 μm step.
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9

Wholemount Immunohistochemistry Protocol

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Standard wholemount immunohistochemical protocols were followed (see Vaasjo et al., 2018 (link); Beach et al., 2019 (link)). Tissues were dissected in normal saline (in mmol l−1: NaCl 51.3, KCl 1.7, MgCl2 1.5, CaCl2 4.1, HEPES 5, pH 7.8.), and pinned in a Sylgard plate. Tissues were incubated in protease (0.5%; Type VI, Sigma; 10–15 min), washed thoroughly with normal saline, and then fixed in Zamboni’s fixative overnight (Mercedes Scientific, EKI 15395). Fixed tissues were washed 5 x 20 min in PTA (0.1 M phosphate buffer containing 2% Triton X-100 and 0.1% sodium azide) at room temperature. Following pre-incubation with normal goat or donkey serum (0.8%, 3–12 h, room temperature), tissues were transferred to the primary antibody (1:200 dilution in PTA, 3–5 days). Samples were washed (5 x 20 min in PTA) and incubated in secondary antibodies conjugated to a fluorescent marker (Alexa 488 goat anti-rabbit IgG (H+L) conjugate; Molecular Probes, Eugene OR) at dilutions ranging from 1:500 to 1: 1,000). Quality of the staining was assessed using a Nikon Eclipse fluorescence microscope prior to imaging. Confocal imaging was performed on a Nikon A1R Confocal Laser Microscope using the NIS Elements AR (Version. 4.5, Nikon Instruments). Stacks, z-series, overlays, and calibrations were obtained using the Fiji software (v. 2.00, NIH public domain).
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10

Probing SHP-REV-ERBα Interaction

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The cells were fixed with 4% paraformaldehyde in 1× PBS for 15 minutes. followed by blocking with 5% normal goat serum with 0.3% Triton X-100 in PBS. mouse anti-FLAG (F1804, MilliporeSigma) and rabbit anti-GFP (SAB4701015, MilliporeSigma) were used to incubate the slices overnight for detecting the interaction between SHP and REV-ERBα. In situ PLA was carried out using Duolink In Situ Red Starter Kit mouse/rabbit (MilliporeSigma) according to the manufacturer’s protocol. The images were taken by Nikon A1R confocal laser microscope (Nikon). For the IP, HEK 293 cells were transfected with indicated plasmids for 24 hours before the treatment. Then, cells were lysed with Pierce IP lysis buffer (Thermo) and the complex was pulled down with the anti-flag M2 magnetic beads (MilliporeSigma). The interacted protein was detected with mouse anti-FLAG (MilliporeSigma) and rabbit anti-GFP Abs (MilliporeSigma).
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