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9 protocols using imageem

1

Single-Molecule Imaging of EGFR-GFP in MEFs

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An expression vector for green fluorescent protein-tagged epidermal growth factor receptor (EGFR-GFP), pEGFR-GFP, was constructed as described previously49 (link). In this vector, a monomeric mutation was introduced into the GFP-coding region (A206K) to prevent self-association50 (link). pEGFR-GFP was transiently transfected into MEFs grown on glass coverslips using Lipofectamine 2000 Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. After incubation overnight, the MEFs were treated with MMC or fixed with 2.5, 5, 10, or 14% FA as described above. Immediately before experimental observations, the solution was replaced with minimum essential medium (Nissui, Tokyo, Japan) containing 1% bovine serum albumin and 5 mM Pipes (pH 7.2).
Single molecules of EGFR-GFP were observed by TIRF microscopy using a Nikon TE2000 inverted fluorescence microscope equipped with a 60 × NA 1.49 objective lens (Plan Apo, Nikon, Tokyo, Japan). The specimens were exposed to a 488-nm wavelength laser, and fluorescence images were acquired using an EM-CCD camera (Image EM; Hamamatsu Photonics, Hamamatsu, Japan) at a temporal resolution of 30.5 ms. All the single-molecule experiments were performed at 25 °C.
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2

Live-Cell Imaging of Cells

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Cells were imaged at room temperature exposed to ambient atmosphere on either a Nikon Diaphot 300, a Nikon Eclipse TiE, or a Zeiss TIRF Axiovert. Fluorescence images were acquired with high numerical aperture oil immersion objectives, using either wide field illumination or total internal reflection excitation. Transmitted light images were obtained using phase-contrast optics with both oil and air immersion objectives. Images were collected on 1k back-thinned cooled EM-CCD cameras, Andor DU888 (Andor) or Hamamatsu ImageEM (Hamamatsu). Long tracks of cells were obtained from cells replated into an Ibidi μ-Dish 35 mm I high (Ibidi) sealed with Parafilm and imaged across a 4×4 grid of images with each position sampled every minute. A red filter was applied to the transmitted light illuminating cells to be imaged over a long period of time in blebbistatin.
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3

Live-cell Imaging of Mitotic Fidelity

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Cell lines and PDO were plated in LabTek chamber slides and incubated with SiR-DNA stain (Cytoskeleton; 333 nM for cell lines and 1 μM for PDO) for 2 hours before imaging. For live-cell experiments with CFI-402257 treatment, 150 nM CFI-402257 or dimethyl sulfoxide (DMSO) was coadded to the medium with SiR-DNA. Cells were held in a humidified Chamlide stage incubator kept at 37°C and 5% CO2 (Live Cell Instrument). Time-lapse images were captured using Volocity 6.3 software (Quorum Technologies) on a Quorum WaveFX spinning disk confocal microscope (Quorum Technologies) equipped with a Hamamatsu ImageEM electron-multiplying charge-coupled device camera at ×20 magnification every 4 min for 20 to 24 hours. The time from nuclear envelope breakdown to mitotic exit (i.e., anaphase or chromatin decondensation) was recorded for each dividing cell. For all dividing cells, mitoses were scored as normal, mild segregation errors (i.e., micronuclei, anaphase bridges, and lagging chromosomes), severe segregation errors (i.e., several micronuclei, thick anaphase bridges, asymmetric segregation, multipolar spindles, and multinucleated cells), and mitotic exit without segregation.
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4

Live Cell Imaging of Spindle Dynamics

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Live imaging at 37°C was performed with a confocal microscope (DM4000; Leica), equipped with a 100× 1.4 NA oil immersion objective (Leica), an XY Piezo-Z stage (Applied Scientific Instrumentation), a CSU10 spinning disk (Yokogawa), an electron multiplier charge-coupled device camera (ImageEM; Hamamatsu Photonics), and a laser merge module (LMM5; Spectral Applied Research) equipped with 488- and 593-nm lasers, as previously described (Zhang et al., 2017 (link)). To minimize photobleaching in monopolar spindle assays, images were acquired with a 1-min time interval, with 1-µm spacing for GFP and mCherry z-stacks covering 15 µm total. To improve precision for the bipolar spindle assays, the time interval was 30 s with 0.5-µm z-spacing covering 3 µm total, so not all kinetochore pairs are visualized. For fixed cell imaging, the same microscope was used with a four-line laser module (405 nm, 488 nm, 561 nm, and 639 nm; Vortran Stradus VersaLase 4).
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5

Photoreceptor Dye Uptake Dynamics

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After letting cells settle onto coverslips, isolated photoreceptors were incubated with SR101, 3-, 10-, 70-kDa dextran-conjugated Texas Red, or 10-kDa dextran-conjugated pHrodo (Molecular Probes, Invitrogen, 7 μM) in amphibian saline for 3 or 10 min. Basal release was measured by incubating photoreceptors for 10 min with dye in Ca2+-free, high-Mg2+ solution containing 0.1 mM Cd2+. Cells were superfused with oxygenated amphibian saline for at least 10 min before measurements.
In experiments with dynasore (Abcam) and pitstop-2, retinal pieces were pre-treated with drug in Ca2+-free high-Mg2+ saline for 20 min and then transferred to a solution containing dye (67 μM 3-kDa Texas Red or 50 μM 10-kDa Texas Red) and drug for 10 min. Photoreceptors were isolated and plated after dye loading.
Whole-terminal fluorescence was measured on an inverted microscope (Olympus IX71) through a 1.45 NA/60×, oil-immersion objective. Fluorescence emission was collected with 40-ms exposure times by an EMCCD camera (Hamamatsu ImageEM) through a 609 nm (54 nm wide) bandpass filter (Semrock). Background fluorescence was measured in adjacent regions outside the cell and subtracted from measurements of terminal fluorescence. Data were acquired and analyzed using MetaMorph software (Molecular Devices).
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6

Live Imaging of Light-Induced Microtubule Reorientation

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All live imaging experiments were conducted using variable-angle epifluorescence microscopy. Unless otherwise stated, images were collected from epidermal cells in the apical hypocotyl region of four-day-old, light-grown seedlings. Seedlings were gently mounted in water between two layers of double-sided adhesive tape on a slide and covered with No. 1.5 glass coverslip. GFP was excited using 2-mW, 488-nm diode-pumped solid-state laser (Melles Griot). mCherry and mRuby were excited using 2-mW and 5mW 561-nm diode-pumped solid-state laser (Melles Griot), respectively. Images were collected by a 100X (NA 1.45) objective and a back-illuminated electron-multiplying CCD camera (ImageEM; Hamamatsu) at 2-s intervals.
For light-induced microtubule reorientation experiments, seedlings were germinated in the dark for two days at 23°C. The etiolated seedlings were then mounted in half-strength liquid MS media under green safelight and microtubules images were collected at 1-min intervals using GFP imaging settings described above.
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7

Probing Chromatin Structure in hMSCs

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Bone Marrow-Derived Mesenchymal Stromal Cells (hMSCs) were cultured in 35 mm glass-bottom Petri dishes (Cellvis, Mountain View, CA) with a micropatterned or flat mPOC surface in growth medium or osteogenic differentiation medium at 37°C and 5% CO2. The PWS microscopy images were acquired on a commercial inverted microscope (Leica, Buffalo Grove, IL, DMIRB) with a Hamamatsu Image EM charge-coupled device camera (C9100-13) coupled to a liquid crystal tunable filter (CRi, Woburn, MA) to collect spectrally resolved images between 500 to 700 nm with 1 nm step size. Further, broadband illumination is provided by an Xcite-120 LED lamp (Excelitas, Waltham, MA). PWS microscopy was used to capture spatial variations of the refractive index distribution or chromatin packing density heterogeneity ( ) within the nucleus. Further, the statistical parameter of chromatin structure, packing scaling ( D ) was calculated from .31 (link) At least 10 independent fields of view were utilized for each experiment and four biological replicates were used for the analysis. D was calculated for 111 hMSCs from the flat surface, and 110 hMSCs on micropillar surfaces.
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8

Visualizing SPR2 Binding Dynamics on MTs

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The GMPCPP-stabilized MTs were assembled using 50 µM unlabeled porcine tubulin containing 1:12 biotin-labeled porcine tubulin (Cytoskeleton Inc.) and polymerized in the presence of 1 mM GMPCPP (Jena Bioscience) at 37 °C for 30 min. Approximately 300 nM GMPCPP-stabilized MTs were introduced into a flow chamber and allowed to bind to a 20% antibiotin antibody (clone BN-34, MilliporeSigma) for 10 min. Then, 100 nM of the specified SPR2-GFP proteins along with 2.5 µM 1:9 rhodamine-labeled porcine tubulin were introduced into the flow chamber in BRB80 buffer containing 1% methyl cellulose (4,000 cP, MilliporeSigma), 50 mM DTT, and an oxygen-scavenging system (Fan et al. 2018 (link)). GFP and rhodamine were excited using 5 mW 488 and 561 nm diode-pumped solid-state lasers, and the images were collected by a 100× (NA 1.45) objective and a back-illuminated electron-multiplying CCD camera (Image EM; Hamamatsu) at 2 s intervals. The extent of colocalization between SPR2-GFP and soluble rhodamine-tubulin was analyzed using the JACoP plugin (Bolte and Cordelieres 2006 (link)).
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9

Dynamic Microtubule Polymerization Assay

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In vitro assays with dynamic MTs were conducted as described in Fan et al. (2018) (link). Briefly, 300 nM GMPCPP-stabilized MT seeds containing 1:12 biotin-labeled and 1:10 rhodamine-labeled porcine tubulins (Cytoskeleton Inc.) bound to coverslips were used to initiate MT polymerization by flowing into 20 mM 1:25 rhodamine-labeled porcine tubulin in BRB80 buffer containing 1% methyl cellulose (4,000 cP, MilliporeSigma), 50 mM DTT, 2 mM GTP, an oxygen-scavenging system, and 500 nM of either full-length or truncated SPR2-GFP proteins. Images were collected by a 100× (NA 1.45) objective and a back-illuminated electron-multiplying CCD camera (ImageEM; Hamamatsu) at 2 s intervals.
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