A1r system

Manufactured by Nikon

Sourced in United States, Japan

The Nikon A1R system is a high-performance confocal microscope designed for advanced imaging applications. It provides users with a combination of speed, resolution, and sensitivity for a wide range of sample types and research needs. The core function of the A1R system is to enable high-quality, real-time confocal imaging with exceptional image quality.

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Lab products found in correlation

Alexa fluor 488 anti rabbit immunoglobulin g igg, by Thermo Fisher Scientific (1 mentions) Alexafluor 546 anti mouse igg, by Thermo Fisher Scientific (1 mentions) Fluorescent mounting media, by Agilent Technologies (1 mentions) 4 6 diamidino 2 phenylindole (dapi), by Vector Laboratories (1 mentions) Ptflc3, by Addgene (1 mentions) Ti e microscope, by Nikon (1 mentions) Atto 647n, by Active Motif (1 mentions) Oregon green 488, by Thermo Fisher Scientific (1 mentions) Propidium iodide, by Merck Group (1 mentions) Prolong gold antifade reagent with 4 6 diamidino 2 phenylindole, by Thermo Fisher Scientific (1 mentions) Lipofectamine 2000, by Thermo Fisher Scientific (1 mentions) Anti flag m2 antibody, by Merck Group (1 mentions) Cfi plan apo lambda 20, by Nikon (1 mentions) Cfi plan apo vc, by Nikon (1 mentions) Mas coated glass slide, by Matsunami (1 mentions) Nis elements c, by Nikon (1 mentions) Anti human gitrl antibody, by R&D Systems (1 mentions) Eight well culture slides, by Corning (1 mentions) 4 6 diamidino 2 phenylindole (dapi), by Cell Signaling Technology (1 mentions)

Close spelling variants of this product

A1RS confocal microscope system A1R-Ti2 confocal system A1R Eclipse confocal system Modular A1+/A1R+ confocal laser scanning microscope system A1R Si Confocal system A1R-TiE live-cell imaging confocal system A1R confocal microscope system Nikon A1R + HD confocal microscope system A1R-A1 Confocal Microscope System A1R confocal laser-scanning microscopy system

17 protocols using a1r system

Immunofluorescence Staining of Cultured Cells and Mouse Osteocytes

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For cultured cells, cells were washed with ice-cold PBS, fixed with 4% paraformaldehyde in PBS, permeabilized with 0.1% Triton X-100 in PBS, stained using anti-Cas and anti-RelA as primary antibodies as well as Alexa Fluor 488 anti-rabbit immunoglobulin G (IgG) and Alexa Fluor 546 anti-mouse IgG (Invitrogen, Carlsbad, CA, USA) as secondary antibodies, and then viewed with a confocal microscope (Nikon A1R system). 4′,6-Diamidino-2-phenylindole (DAPI; Vector Laboratories, Burlingame, CA, USA) was used to stain the nucleus.
For osteocytes in mouse midshaft tibiae, mice were transcardially perfused with 4% paraformaldehyde in phosphate buffer (pH 7.4). Tibiae were immersed in the same fixative at 4°C overnight and decalcified in 10% EDTA (pH 7.4) at 4°C for 14 days. The samples were embedded in paraffin, sectioned with 5-μm thickness, and incubated with primary antibodies (anti-Cas, anti-RelA, and anti–acetylated RelA) at 4°C overnight. Alexa Fluor 488–conjugated goat anti-mouse IgG, Alexa Fluor 488 anti-rabbit IgG, and Alexa Fluor 594 anti-mouse IgG were used as secondary antibodies. Nuclei were counterstained using DAPI. Sections were mounted with Fluorescent Mounting Media (Dako, CA, USA). Quantitative 3D analysis of nuclear/total Cas was conducted using Imaris software (Bitplane, Zurich, Switzerland).

Miyazaki T., Zhao Z., Ichihara Y., Yoshino D., Imamura T., Sawada K., Hayano S., Kamioka H., Mori S., Hirata H., Araki K., Kawauchi K., Shigemoto K., Tanaka S., Bonewald L.F., Honda H., Shinohara M., Nagao M., Ogata T., Harada I, & Sawada Y. (2019). Mechanical regulation of bone homeostasis through p130Cas-mediated alleviation of NF-κB activity. Science Advances, 5(9), eaau7802.

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Confocal FRET Microscopy Protocol

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All sections were assessed on a confocal Nikon A1 R+ System equipped with GaAsP detectors with 12-bit A/D conversion 12-bit detectors using a 60x plan apochromatic oil immersion objective (NA1.4). Alexa-488 labelled antibodies (FRET donors) were excited with a 488 nm Ar-laser with emission at 525 nm (band width 50 nm), Cy3-labels (FRET acceptors) were imaged with excitation at 562 nm and emission at 595 nm (band width 50 nm), and raw FRET signals were recorded with excitation at 488 nm and emission at 595 nm (band width 50 nm). Laser power was set to 2%.

Lutz M.I., Schwaiger C., Hochreiter B., Kovacs G.G, & Schmid J.A. (2017). Novel approach for accurate tissue-based protein colocalization and proximity microscopy. Scientific Reports, 7, 2668.

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Correlating ADN Activation with Autophagy

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Imaging was performed after 4 h of ADN exposure. Two sets of experiments were performed. To correlate the signal from activated ADN with a dual fluorescent LC3 plasmid, H9C2 cells were transfected with a dual fluorescent LC3 plasmid (pTF-LC3) from Addgene, with lipofectamine per the manufacturer’s instructions. After transfection, cells were cultured on glass chamber slides for imaging. ADN (10 μg Fe ml⁻¹) was added to the transfected cells for 4 h before imaging. Confocal fluorescent images were acquired on a Nikon A1R system attached to an inverted microscope, automated stage, and a stage-top incubator optimized for live cell imaging. ADN was imaged with the 640 nm laser for excitation, GFP was imaged with the 488 nm laser and 525/50 nm emission filter cube, and RFP was imaged with the 561 nm filter and 595/50 nm emission filter cube. The acquired images were processed in ImageJ. The second set of experiments were performed to correlate the signal from activated ADN with its detection using the DX1 antibody. Imaging was performed on a Leica SP8 microscopy system, as described above, using DAPI, Alexa 680 (for Cy5.5 signal) and Alexa 790 (for DX-1 signal) scan settings.

Chen H.H., Khatun Z., Wei L., Mekkaoui C., Patel D., Kim S.J., Boukhalfa A., Enoma E., Meng L., Chen Y.I., Kaikkonen L., Li G., Capen D.E., Sahu P., Kumar A.T., Blanton R.M., Yuan H., Das S., Josephson L, & Sosnovik D.E. (2022). A nanoparticle probe for the imaging of autophagic flux in live mice via magnetic resonance and near-infrared fluorescence. Nature biomedical engineering.

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High-Res Imaging of Muscle Fibers

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The fibers were imaged as previously described (Koenig et al., 2019 (link)), using a 20× water (Nikon, CFI APO 20× WI λS, long working distance, NA 0.95, or Plan Apo λ 20× NA 0.75) immersion objective on a Nikon laser scanning confocal microscope system (Nikon A1R+ system on an inverted Nikon Ti-E microscope) equipped with a 12 kHz resonant scanner and high-sensitivity GaAsP detectors. Rhod-5N and fluo-4 were excited at 488 and 561 nm at a laser power of 0.4–1% and 0.4–0.8%, and emitted light was collected at 525/50 nm and 595/50 nm, respectively. The pinhole was set to 4–7 Airy units. Acquired image series (xyt) had a physical dimension of x = 512 pixel and y = 32–128 pixel, resulting in a temporal resolution of Δt = 4–16 ms, or 250–62 frames s^–1. Fluorescence was averaged across a region of interest to improve the signal to noise ratio, in particular necessary to monitor rhod-5N fluorescence in the t-system.

Lilliu E., Hilber K., Launikonis B.S, & Koenig X. (2020). Phasic Store-Operated Ca2+ Entry During Excitation-Contraction Coupling in Skeletal Muscle Fibers From Exercised Mice. Frontiers in Physiology, 11, 597647.

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Imaging and Visualizing M. chelonae Biofilms

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eGFP-expressing M. chelonae biofilms t1 were formed as described for SEM, and stained with a single fluorophore targeting a specific component of the biofilm matrix. The conditions used for each fluorophore are summarized in Table 1. The stained pellicles then were fixed using paraformaldehyde 4% in PBS for 30 min, and mounted in microscope glass slides for further image acquisition. From three different experiments, five confocal z-stacks (covering approximately 4 μm) were acquired from each experimental sample. Images were acquired using a Nikon A1R system equipped with Ti microscope frame and a 100x/1.4 PlanApo objective.Table 1

Fluorophores and conditions used for staining M. chelonae biofilms for CLSM.

Fluorophore	Target	Concentration	Time
Nile Red	Lipids	1 μM	30 min
Propidium iodide	Nucleic acids	15 μM	15 min
Sypro Ruby	Proteins	As provided by the manufacturer.	30 min
Alexa Fluor	α-mannose and α-glucose in the pyranose configuration.	100 μg/mL	30 min

Vega-Dominguez P., Peterson E., Pan M., Di Maio A., Singh S., Umapathy S., Saini D.K., Baliga N, & Bhatt A. (2020). Biofilms of the non-tuberculous Mycobacterium chelonae form an extracellular matrix and display distinct expression patterns. The Cell Surface, 6, 100043.

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Confocal and STED Imaging Protocol

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Confocal imaging was carried out using a Nikon A1R system using 60x objective (100x was used for DNA FISH images). For DNA FISH imaging, nuclei from tissue were assessed by scanning through the z axis and 2D images were acquired selecting the plane giving the strongest FISH signal. For RNA polymerase II imaging, a 2-color in-house built stimulated emission depletion (STED) microscope was used. Samples were visualized with Atto647N (Active Motif) and Oregon Green 488 (Life Technologies) fluorophore-conjugated secondary antibodies and imaged using a 100x objective. We used 635nm excitation and 750nm depletion lasers for Atto647 visualization and 485nm excitation and 592nm depletion lasers for Oregon Green 488 labels.

Karbassi E., Rosa-Garrido M., Chapski D.J., Wu Y., Ren S., Wang Y., Stefani E, & Vondriska T.M. (2019). Direct visualization of cardiac transcription factories reveals regulatory principles of nuclear architecture during pathological remodeling. Journal of molecular and cellular cardiology, 128, 198-211.

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Quantitative Analysis of DRG Neuron Transduction

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For quantitative analysis of transduction in DRG neurons after intracolonic AAV delivery, native tdTomato and GFP fluorescence was imaged in whole-mounted L6 DRG (without clearing) on a two-photon Nikon A1R system as described above for Fig 4A1 and 4B1. tdTomato or GFP-expressing neurons in the z-stacks were manually counted by an observer blinded to the treatments.

Skorput A.G., Gore R., Schorn R., Riedl M.S., Marron Fernandez de Velasco E., Hadlich B., Kitto K.F., Fairbanks C.A, & Vulchanova L. (2022). Targeting the somatosensory system with AAV9 and AAV2retro viral vectors. PLoS ONE, 17(3), e0264938.

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Propidium Iodide Staining of Plant Tissues

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Tissue samples of rice or Arabidopsis were submerged for at least 3 h in a solution of 10 μg ml^–1 propidium iodide (PI; Sigma). The fluorescent signal of PI was visualized using a confocal laser-scanning microscope (Nikon A1R system), with 543 nm excitation and 615 nm emission signals.

Shi Y., Phan H., Liu Y., Cao S., Zhang Z., Chu C, & Schläppi M.R. (2020). Glycosyltransferase OsUGT90A1 helps protect the plasma membrane during chilling stress in rice. Journal of Experimental Botany, 71(9), 2723-2739.

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Confocal Imaging of ECFP and EYFP

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Confocal laser scanning microscopy was performed with an A1 R+ system from Nikon with a 12‐bit intensity range one or two days after cell transfection.
The Nikon system employed a Ti microscope with a 60× plan apochromatic oil immersion objective (NA1.4). Excitation was done with an Ar‐laser (457 nm for ECFP and 514 nm for EYFP in sequential mode) and detection with a pinhole value of 35.8. A 400–457/514 nm dichroic mirror was used; ECFP‐emission was recorded with a 482/33 nm filter and EYFP‐emission with a 540/30 nm filter with a line averaging of 4 or 8.
These imaging settings have been verified to discriminate clearly between ECFP and EYFP.

Moser B., Hochreiter B., Herbst R, & Schmid J.A. (2016). Fluorescence colocalization microscopy analysis can be improved by combining object‐recognition with pixel‐intensity‐correlation. Biotechnology Journal, 12(1), 1600332.

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Artificial Cell Membrane Synthesis

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The internal reaction mixture was prepared as described in Supplementary Table 2 (see For PA synthesis inside GUVs), then mixed with 12% (w/v) Ficoll PM70. This was encapsulated inside giant vesicles as described above with the outer solution. The collected 20 uL vesicle solution (i.e., artificial cells) was mixed with 6 µL of a feeding solution; containing 1×PUREfrex2.0 buffer, 13 mM ATP, 6 mM glycerol-3-phosphate, 4.8 mM CoA, 42 ng/µL RNaseA, and 300 mM glucose. Protein synthesis was performed at 37 ˚C for 3 h. After the protein synthesis within the artificial cells, the internal phospholipid synthesis was initiated by the addition of 5 µL of 48 mM NADPH dissolved in the outer solution. Phospholipid synthesis was carried out at 37 ˚C for 1–9 h. The resulting 30 µL artificial cell sample (1 µL was used for microscopy check) was mixed with 5 µL of 170 ng/µL GFP-Spo protein to stain the vesicle membrane and, then, incubated at 37 ˚C for 30 min followed by an additional 30 min incubation at room temperature (25 ˚C). The artificial cells were observed by confocal microscopy (Nikon A1R system).

Eto S., Matsumura R., Shimane Y., Fujimi M., Berhanu S., Kasama T, & Kuruma Y. (2022). Phospholipid synthesis inside phospholipid membrane vesicles. Communications Biology, 5, 1016.

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