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31 protocols using ds u3 camera

1

Fluorescence and Light Microscopy Imaging

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A fluorescence microscope (Nikon Eclipse C1,NikonGmbH, Vienna, Austria) and a Nikon DS-U3 camera (Nikon Corporation, Shinagawa, Tokyo, Japan) were used to obtain the fluorescent images. A light microscope was applied to acquire images of the samples without immunofluorescence, and representative photomicrographs were taken for analysis using Leica QWin (Wetzlar, Germany).
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2

FcγR-mediated Phagocytosis Assay

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FITC-conjugated polystyrene latex beads covalently were opsonized with mouse IgG1 (Sigma-Aldrich) to study the FcγR-mediated phagocytosis. In brief, latex beads (diameter, 1.0 μm) were washed three times and then incubated in HBSS containing 3 mg/ml of mouse IgG1 at 4 °C on a rotator for 8 h to allow sufficient binding. After incubation, the beads were resuspended and washed three times with cold HBSS to remove any unbound IgG1. Macrophages (106/well, seeded in 6-well plates) were incubated with IgG1-opsonized beads at a ratio of 10 beads per cell at 37°C for 20 min, washed with ice-cold HBSS, fixed in 4% paraformaldehyde. Phagocytosis was visualized by a DS-Fi2 fluorescence microscope (Nikon) and images were captured using a Nikon DS-U3 camera. The phagocytic index was calculated using the following formula: phagocytic index = number of latex beads internalized by 100 macrophages counted in 10 random fields (21 (link)).
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3

Localization of YbaBC Protein in C. crescentus

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Expression from Pxyl promoter was obtained by addition of xylose to the growth media at an optical density OD600 0.2. For studying localization of YbaBCc, expression of CFP-fused YbaBCc was obtained from pXCFPN-5 vector in PBP3 temperature-sensitive mutant C. crescentus by addition of xylose (0.2%) at an optical density OD600 0.1 in PYE broth. Cultures were incubated at 30°C for 1 h and then shifted to 37°C and grown for 4.5 h. After this, cells were harvested and washed with M2 medium and processed for 4′, 6′-diamidino-2-phenylindole (DAPI) staining. Cell samples (5 μl) were imaged as described before (Dubey and Priyadarshini, 2018 (link)) using Nikon Eclipse Ti microscope (United States) equipped with Nikon DS-U3 camera. Images were processed with Adobe Photoshop CS6. Cell length, nucleoid length, and cell width were analyzed with Fiji (ImageJ) software (Schindelin et al., 2012 (link)) and Oufti software (Paintdakhi et al., 2015 (link)).
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4

Histological Characterization of Liver Steatosis

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The tissues of the liver samples were fixed in 10% neutral-buffered formalin for at least 24 h. Then, the tissues were embedded in paraffin and stained with hematoxylin and eosin (H&E) to assess the histologic features of steatosis and inflammation. Frozen liver tissues embedded in an optimal cutting temperature compound (Sakura, Torrance, CA, USA) were cut and stained with Oil Red O. Based on the observation using a laser-scanning confocal microscopy, the images were captured using a Nikon DSU3 camera (Nikon Corporation, Chiyoda Ward, Tokyo, Japan). For the immunofluorescence investigation of intestinal tight junction proteins, frozen intestinal sections were treated with anti-occludin and anti-claudin-2 antibodies (Thermo Fisher Scientific, Waltham, MA, USA), followed by labeling with a FITC-conjugated secondary antibody (Servicebio, Wuhan, China).
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5

Immunohistochemical Analysis of Autophagy Markers

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Following isolation and plating, cells were subjected to immunohistochemical staining and microscopic imaging to assess the presence and activation state of TFEB (Bethyl Laboratories, Montgomery, TX) LAMP1 (ThermoFisher Scientific, Waltham, MA ), and LC3 (Sigma-Aldrich, St. Louis, MO) at dilutions of 1:5000, 1:500, and 1:200, respectively, following the manufacturers immunofluorescence histochemistry protocols. Immunohistochemical staining of the macrophage antigen F4/80 (Abcam, Cambridge, UK) was performed at a 1:500 dilution. The secondary antibody was Alexa-Fluor 488 (1:500 dilution) (Abcam, Cambridge, UK). Immunohistochemistry of TUNEL (R&D Systems, Minneapolis, MN) was performed using manufacturer’s protocol for tissue cryosections. After staining, cells or tissues were imaged using a Nikon Eclipse Ti inverted microscope (Nikon Instruments, Melville, NY) and Nikon DS-U3 camera (Nikon Instruments) and Photometrics CoolSnap MYO camera system (Photometrics, Tucscon, AZ), under control of Nikon NIS-Elements AR Software (Nikon Instruments). Illumination for fluorescence imaging is generated using the X-Cite 120Q Widefield Fluorescence Microscope Excitation Light Source (Excelitas Technology, Waltham, MA).
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6

Apoptosis Visualization in Zebrafish

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Zebrafish were incubated in a culture medium containing 2 µg/mL acridine orange (AO) (Sigma-Aldrich, St. Louis, MO, USA) for 30 min. Before observation, embryos were washed in fresh ERS three times and anesthetized by 0.08% MS-222. Images were captured using a microscope equipped with a Nikon DS-U3 camera (Nikon Inc., Melville, NY, USA). NIS-Elements software (Nikon Inc., Melville, NY, USA) was used.
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7

Time-Lapse Imaging of Live Cells

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Cells were collected at different time points and immobilized on 1% 1 X PBS agarose padded slides and were subjected to phase contrast microscopy using a Nikon Eclipse Ts2R microscope (Nikon, Japan) attached with a Nikon DS-Fi3 camera equipped with Nikon Plan Fluor 100X oil Ph3 objective. Time-lapse imaging of live cells harvested at mid-exponential phase (OD600 ∼ 0.4) was performed on LB 0.7% agarose padded slides supplemented with or without 0.4% L-arabinose using a Nikon Eclipse Ti microscope (Nikon, Japan) with Nikon DS-U3 camera and Plan Apo 100 X oil objective. Image processing was performed with ImageJ [37 (link)] and Adobe Photoshop CS6 (Adobe Inc. U.S.A).
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8

Immunohistochemical Analysis of NODAL and α-SMA

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Light microscopy and semi-quantitative scoring were performed by 2 pathologists. The entirety of each slide was assessed. Scores for NODAL were 0, absent; 1, weak or very focal staining; 2, strong but focal or moderate intensity; and 3, strong and extensive staining. The score reflects the intensity of staining observed in the majority of cells. When scored 1 to 3, NODAL distribution was further identified as focal, diffuse or scattered, and an estimated proportion of tumor cells staining with NODAL was calculated (NODAL percentage in Table 1). α-SMA was scored in the same manner on serial sections from the same cases. Intensity association was measured based on the extent to which α-SMA staining was increased in areas with NODAL-positive cells. Representative images were taken from a Nikon DS U3 camera on Nikon eclipse 80i microscrope (Nikon, Tokyo, Japan) at 400 x (500 px bar = 40 μm).

NODAL and α-SMA evaluation by immunohistochemistry.

Table 1
n (%)
NODAL score – median (range)2 (0–3)
03 (7.3)
110 (24.4)
219 (46.3)
39 (22.0)
NODAL percentage (%) – median (range)50 (5–100)
NA3 (7.3)
5–2012 (29.3)
30–407 (17.1)
60–8014 (34.1)
90–1005 (12.2)
NODAL distribution
NA3 (7.3)
Diffuse17 (41.5)
Scattered20 (48.8)
Focal1 (2.4)
α-SMA score – median (range)2 (1–3)
13 (7.3)
229 (70.7)
39 (22.0)
Intensity Association
NA3 (NA)
Yes36 (94.7)
No2 (5.3)
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9

Dendritic Spine Analysis of Layer 5 Pyramidal Neurons

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Pyramidal cells from L5 PL were identified using The Mouse Brain in Stereotaxic Coordinates (4th Edition, Paxinos, and Franklin, 2012) and the Allen Brain Institute’s Mouse Brain Atlas (http://mouse.brain-map.org). The L5 PL neurons were approximately 1.7 mm ventral from the dorsal surface and the cell bodies were 500–700 μm from the medial surface. Individual neurons in these regions were viewed using a 100× oil objective on a Nikon Eclipse Ci-L microscope. Images of the basilar dendrites were acquired using Z-stack projection photomicrographs (0.1–0.9 μm steps) taken using a Nikon DS-U3 camera mounted on the microscope and were analyzed using NIS-Elements D 4.40.00 software. Three to four neurons (middle 80%) were sampled per mouse, and six segments in the same field of view were assessed per neuron (20–50 μm). Each dendrite segment was ~ 1 μm thick and was taken from a 2° or 3° order dendrite. Spine density was expressed as the number of spines/10 μm. To determine the type of dendritic spine, we used parameters described by Risher et al.86 (link): filopodia, length > 2 µM; long thin, length < 2 µM; thin, length < 1 µM, stubby, width ratio < 1 µM, mushroom, width > 0.06 µM; bifurcated, two or more heads.
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10

Golgi Staining of CA3 Pyramidal Cells

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Whole brains were prepared using the Golgi stain (FD Rapid Golgi Stain kit, FD Neurotechnologies, Columbia, MD). Following staining, brains were sectioned at 200 µm using a vibratome (Leica VT 100M). Images of CA3 pyramidal cells were taken with a Nikon DS-U3 camera mounted on a Nikon Eclipse Ci-L microscope at 100X oil. Z-stack projection photomicrographs (0.1 μm steps) were captured with NIS-Elements AR 4.40.00 software for spine count analysis.
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