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10 protocols using csu x

1

Mitochondrial Visualization in Cells

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MitoTracker deep red FM (Invitrogen, M22426) was solubilized in DMSO to yield 100 μM frozen aliquots which were diluted into media to yield a 10 μM stock which was added directly to cell culture media already in the culture yielding a final concentration of 100 nM (to prevent media change derived fluid flow shear stress) 30 min before 4% PFA (MitoTracker red FM was used for PFA fixed samples). Samples were imaged with a Nikon Eclipse Ti spinning disc microscope, Yokogawa CSU-X, Andor Zyla sCMOS, Andor Multi-Port Laser unit, and analyzed with Molecular Devices MetaMorph imaging suite, ImageJ, and ilastik (Gaussian filter).
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2

Live-Cell Imaging with Confocal and TIRF Microscopy

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All live cells were maintained at 37°C, 5% CO2 with a stage top incubator (Okolab) during imaging. For confocal microscopy, cells were imaged with a spinning disk confocal microscope (Eclipse Ti, Nikon) with a spinning disk (Yokogawa CSU-X, Andor), CMOS camera (Zyla, Andor), and either a 20x objective (Plano Fluor, 0.45NA, Nikonor a 60x objective (Apo TIRF, 1.49NA, oil, Nikon). For total internal reflection fluorescence (TIRF) microscopy, cells were imaged with TIRF microscope (Eclipse Ti, Nikon), 60x objective (Apo TIRF, 1.49NA, oil, Nikon) and EMCCD camera (iXON Ultra, Andor). Both microscopes were controlled with Micro-Manager. Images were analyzed and prepared using FIJI (Schindelin et al., 2012 (link)).
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3

Live-cell Imaging with Confocal and TIRF Microscopes

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All live cells were maintained at 37°C, 5% CO2 with a stage top incubator (okolab) during imaging.
For confocal microscopy, cells were imaged with a spinning disk confocal microscope (Eclipse Ti, Nikon) with a spinning disk (Yokogawa CSU-X, Andor), CMOS camera (Zyla, Andor), and either a 4x objective (Plano Apo, 0.2NA, Nikon) or a 60x objective (Apo TIRF, 1.49NA, oil, Nikon). For total internal reflection fluorescence (TIRF) microscopy, cells were imaged with TIRF microscope (Eclipse Ti, Nikon), 60x objective (Apo TIRF, 1.49NA, oil, Nikon) and EMCCD camera (iXON Ultra, Andor). Both microscopes were controlled with Micro-Manager. Images were analyzed and prepared using ImageJ (National Institutes of Health).
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4

Live-Cell Imaging with Confocal and TIRF Microscopy

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All live cells were maintained at 37°C, 5% CO2 with a stage top incubator (Okolab) during imaging. For confocal microscopy, cells were imaged with a spinning disk confocal microscope (Eclipse Ti, Nikon) with a spinning disk (Yokogawa CSU-X, Andor), CMOS camera (Zyla, Andor), and either a 20x objective (Plano Fluor, 0.45NA, Nikonor a 60x objective (Apo TIRF, 1.49NA, oil, Nikon). For total internal reflection fluorescence (TIRF) microscopy, cells were imaged with TIRF microscope (Eclipse Ti, Nikon), 60x objective (Apo TIRF, 1.49NA, oil, Nikon) and EMCCD camera (iXON Ultra, Andor). Both microscopes were controlled with Micro-Manager. Images were analyzed and prepared using FIJI (Schindelin et al., 2012 (link)).
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5

Microscopy Methods for Cell Junction Dynamics

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The microscope used for each experiment is stated with the experimental genotypes:

Leica SPE2 scanning confocal with a 40x 1.3 NA oil objective.

For 30 s junction dynamics imaging. z-slices were 1μm, spanning 5μm and for long-term time-lapse at 5 min intervals (1μm x 20 z-slices).

Leica SP5 inverted confocal with a 40x 1.3 NA oil objective and 63x 1.3 NA oil objective.

For imaging of fixed samples.

Nikon Eclipse TI-E inverted system with a Yokogawa CSU-X confocal spinning disk unit fitted with an Andor EMCCD camera using a 100x 1.4 NA objective.

For two-color time-lapse (30 s interval) imaging.
Z-slices = 0.5 μm covering 4 μm. Maximum intensity projections were made of three slices in the focal plane for each time-point.
488 laser for GFP imaging at 5% power for 50 ms exposure. 561 laser for mCherry imaging at 20% power for 150 ms exposure.

Carl Zeiss LSM 200 M with a Yokogawa CSU-X confocal spinning disk unit and Andor Zyla cSMOS 5.5 camera with a 63x 1.3 NA water objective.

For two-color single time-point imaging at different stages of pupal development.
Z slices = 0.5μm covering 4μm. Maximum intensity projections were made of three slices in the focal plane.

Carl Zeiss LSM510 Meta upright confocal microscope with a Plan-Neofluor 40x/1.3 Oil DIC objective.

For laser ablation of adherens junctions.
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6

Apoptosis Signaling Pathway Immunostaining

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Cells or tissues were fixed in 4% paraformaldehyde (Electron Microscopy Services, 15710) in 1X PBS for 30 min at room temperature, washed and blocked with a blocking buffer (HBSS fortified with: 10% FBS (Hyclone), 0.1% BSA (Fischer, BP1600), 0.05% saponin (EMD Millipore, L3771), and 0.1% Tween 20 (Fischer, BP337500). Primary antibodies [1:100–1:200] for 2 h at RT or 24 h at 4 °C, Secondary antibodies [1:1000] for 2 h at 22 °C. Samples were imaged with a Nikon Eclipse Ti spinning disc microscope, Yokogawa CSU-X, Andor Zyla sCMOS, Andor Multi-Port Laser unit, and Molecular Devices MetaMorph imaging suite.
Antibodies used: Cleaved Caspase-3 (Asp175) (Cell Signaling, 9661, AB_2341188), HSF1 (Cell Signaling, 4356, AB_2120258), SLC9A1 (sc-136239, AB_2191254), and HSP60 (LK1, sc-59567, AB_783870).
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7

Confocal Imaging of Patched Cells

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After floating-slice HCR, slices were mounted between no.1 coverslips with antifade compound (ProLong Glass, Invitrogen) and images were collected on an Andor CSU-X spinning disk confocal system coupled to a Nikon Eclipse Ti microscope equipped with an Andor iKon-M camera. The images were acquired with an oil immersion objective at 60×. The Alexa 594 patched cell backfill channel (561 nm) plus associated HCR probe/hairpin channels (488 nm and 647 nm) were projected through a 10–20-μm thick z-series so that an unambiguous determination of the association between the patch-filled cell and its HCR gene expression could be made. Images were processed using Nikon NIS Elements 4.4 and Nikon NIS AR.
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8

Mitochondrial Labeling for Live Imaging

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MitoTracker deep red FM (Invitrogen, M22426) was solubilized in dimethyl sulfoxide to yield 100 μM frozen aliquots that were diluted into media to yield a 10 μM stock, which was added directly to cell culture media already in the culture yielding a final concertation of 100 nM (to prevent media change derived fluid flow shear stress) 30 min before 4% paraformaldehyde (PFA) fixation or live cell imaging (MitoTracker red FM was used for PFA-fixed samples). Samples were washed in 3× PBS and imaged with a Nikon Eclipse Ti spinning disc microscope, Yokogawa CSU-X, Andor Zyla sCMOS, Andor Multi-Port Laser unit, and Molecular Devices MetaMorph imaging suite.
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9

Dual-Color Lattice Light Sheet Imaging

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Images were taken using spinning disk microscope with a 100x Apo objective, NA 1.4 (Nikon Ti-E microscope equipped with Yokogawa spinning disk unit CSU-X and an Andor iXon 897 camera).
For lattice light sheet microscopy, 1 M cells were seeded in 6 well plates containing 5 mm cover glasses (#1.5 thickness) and transfected with either 0.1 μg pCDNA3.1-eGFP-SpRng2(1-189) or with 0.5 μg pEGFP-IQGAP1 (# 30112, Addgene) and 0.5 μg pTK93 Lifeact-mCherry. Cells were imaged 16-22 hours post transfection. Cover glasses were mounted on the imaging chamber and DMEM medium was replaced by pre-warmed L-15 imaging medium (cat. no. 11415049, Gibco, Fisher scientific). Imaging was done at 37°C on a 3i second generation lattice-light-sheet microscope with a 0.71 NA LWD WI objective for excitation and a 1.1 NA WI objective for imaging and equipped with 2 Hamamatsu ORCA-Flash 4.0v3 sCMOS cameras for simultaneous dual color imaging providing a 62.5x magnification with 230x230x370 nm (x-y-z) resolution using 488 nm and 561 nm lasers for excitation. 3D volumes were recorded with 0.57 μm step size for 150 planes with 100 ms exposure.
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10

Immunofluorescence Staining of Cells

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Cells or tissues were fixed in 4% paraformaldehyde (Electron Microscopy Services, 15710) in 1X PBS for 30 min at room temperature, washed and blocked with a blocking buffer (HBSS fortified with: 10% FBS (Hyclone), 0.1% BSA (Fischer, BP1600), 0.05% saponin (EMD, L3771), and 0.1% Tween 20 (Fischer, BP337500). Primary antibodies [1:100-1:200] for 2 h at RT or 24 h at 4 ºC, Secondary antibodies [1:1000] for 2 h at 22 ºC. Samples were imaged with a Nikon Eclipse Ti spinning disc microscope, Yokogawa CSU-X, Andor Zyla sCMOS, Andor Multi-Port Laser unit, and Molecular Devices MetaMorph imaging suite.
Antibodies used: Cleaved Caspase-3 (Asp175) (Cell Signaling, 9661, AB_2341188), HSF1 (Cell Signaling, 4356, AB_2120258), and HSP60 (LK1, sc-59567, AB_783870).
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