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6 protocols using clara charge coupled device camera

1

Time-lapse Microscopy of Plasmid Dynamics

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Time lapses of strains containing the 10-kb lacO/LacI-GFP array or containing the dicentric plasmid were performed at room temperature (25°C) using an Eclipse Ti wide-field inverted microscope (Nikon) with a 100× Apo TIRF 1.49 NA objective (Nikon) and Clara charge-coupled device camera (Andor) using Nikon NIS Elements imaging software (Nikon). Time lapses of strains containing the 10-kb lacO/LacI-GFP array were 10 min in duration with 30 s intervals. At each interval a seven-step Z-stack of 300-nm step size was acquired in the GFP, RFP, and Trans channels. Time lapses of strains containing the dicentric plasmid were the same as above but with a duration of 20 min.
Population images of the dicentric plasmid strains and of strains containing the 1.2-kb lacO/LacI-GFP array were imaged at room temperature (25°C) using an Eclipse E600FN microscope (Nikon) with a 100× Plan Apo TIRF 1.45 NA objective (Nikon) and ImagEM EM-CCD digital camera (Hamamatsu) with a custom Lumencor LED illumination system (Lumencor) using MetaMorph 7.7 imaging software (Molecular Devices). Each acquisition was a seven-step Z-stack with a 300-nm step size in the GFP, RFP, and Trans channels.
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2

Chromosome Motion via Time-Lapse Imaging

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Population and time-lapse images were acquired at room temperature (24°C) using a Nikon Eclipse Ti wide-field inverted microscope with a 100× Apo total internal reflection fluorescence 1.49 numerical aperture objective (Nikon, Melville, NY) and Andor Clara charge-coupled device camera (Andor, South Windsor, CT). Time-lapse stacks, each of seven 200-nm z-planes, were acquired every 30 s over a 10-min period (147 total planes per time lapse) with Nikon NIS Elements imaging software. Images were taken in transilluminated light, GFP and RFP fluorescence illumination. We chose the 30-s intervals as the best compromise between rate of acquisition and duration of time lapse due to photobleaching. The 30-s intervals were used in Verdaasdonk et al. (2013 (link)), where we report the effect of tethering on chromosome motion. Of importance, the MSD slopes of a 10-kb lacO/LacI-GFP array, 6.8 from CEN XV (KBY8065), taken at 3- and 30-s intervals are overlapping (Supplemental Figure S4). The 3-s interval allows one to estimate the slope of the MSD on a log-log plot, and the 30-s interval over a longer time scale provides a better estimate of the plateau value, which provides a better measurement of Rc.
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3

Live-cell imaging of cell migration

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Twenty-four hours after transfection, cells were either plated on fibronectin (10 μg/ml)-coated, 35-mm glass-bottom imaging dishes (MatTek, Ashland, MA) or FluoroDish cell culture dishes (35 or 50 mm; World Precision Instruments, Sarasota, FL) or were embedded in collagen gels as described and imaged the next day. Before imaging, growth medium was replaced with CO2-independent imaging medium containing 134 mM NaCl, 5.4 mM KCl, 1.0 mM MgSO4, 1.8 mM CaCl2, 20 mM HEPES, and 5 mM d-glucose (pH 7.4). A stage warmer (NevTek Airstream, Williamsville, VA) was used to maintain cells at 37°C, and cells were imaged on an Eclipse TE-2000E inverted microscope (Nikon) equipped with a 40×/1.3 numerical aperture (NA) Plan Fluor or 60×/1.4 NA Plan Apo oil-immersion objective, the appropriate fluorophore-specific filters (Chroma Technology, Bellows Falls, VT), a Spectra X LED light engine (Lumencor, Beaverton, OR), and a Clara charge-coupled device camera (Andor, Concord, MA). Images were acquired every 5–60 s with 500- to 800-ms exposure times.
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4

Yeast Cell Imaging: Fluorescence Microscopy Protocol

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Fluorescent image stacks of unbudded yeast cells were acquired using a Eclipse Ti wide-field inverted microscope (Nikon) with a 100× Apo TIRF 1.49 NA objective (Nikon) and Clara charge-coupled device camera (Andor) using Nikon NIS Elements imaging software (Nikon). Each image stack contained 7 Z-planes with 200 nm step-size.
Image stacks of experimental images were cropped to 7 Z-plane image stacks of single cells using ImageJ and saved as TIFF files. The cropped Z-stacks were read into MATLAB 2018b (MathWorks), converted into maximum intensity projections, and the projections of hmo1Δ and fob1Δ were cropped to 55 × 55 pixels, to match the dimensions of WT projections, using MATLAB function padarray with replicate option specified to extend outer edge of pixel values to ensure the center of all cropped images was the brightest pixel. The intensity values of all projections were normalized by subtracting all intensity values by the minimum value and then dividing the resulting values by the maximum intensity value after subtraction. The normalized intensity values were stored with double point precision, preventing any loss in dynamic range.
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5

Imaging Yeast Spindle Dynamics

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Yeast cells containing the SPB protein Spc42-mCherry and the outer kinetochore protein Ndc80-GFP were imaged at 25°C on a Nikon Eclipse Ti wide-field inverted microscope with a 100×Apo total internal reflection fluorescence 1.49 numerical aperture objective (Nikon, Melville, NY) and Andor Clara charge-coupled device camera (Andor, South Windsor, CT). Images were acquired using Nikon Elements imaging software. Images were taken in transilluminated light and GFP and RFP fluorescence illumination. Metaphase spindles are in the length range of 1.4–1.7 µm.
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6

Yeast Imaging of Spindle Dynamics

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Immediately prior to imaging, yeast nitrogen base, casamino acids, uracil, tryptophan, and adenine (YPD) cultures were washed with YC complete + 2% filter sterile glucose and resuspended with YC complete + 2% filter sterile glucose. Yeast treated with benomyl were washed and resuspended with the YC complete + 2% filter sterile glucose with the same concentration of benomyl contained in the growth culture. Yeast were placed directly on glass coverslips and on glass slides. Coverslips were sealed with VALAP (equal parts Vaseline, lanolin, and paraffin). Imaging was performed at room temperature (25°C) using an Eclipse Ti wide-field inverted microscope (Nikon) with a 100 × Apo TIRF 1.49 NA objective (Nikon) and Clara charge-coupled device camera (Andor) using Nikon NIS Elements imaging software (Nikon). Images were acquired using the Scan Large Image program. Forty-nine z-stacks of seven z-steps with step size 300 nm were taken. At each interval a seven-step z-stack of 200-nm step size was acquired in the GFP (600 ms exposure), RFP (600 ms exposure), and Trans (25 ms exposure) channels. GFP, RFP, and Trans images were acquired before shifting Z position. All images were acquired from cells in the metaphase stage of the cell cycle, defined by the presence of a 1.2–1.7 µm spindle.
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