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12 protocols using uplanapo objective

1

Immunofluorescence Microscopy of Microtubules and Centromeres

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For immunofluorescence, cells were fixed with 3.7% formaldehyde in PHEM buffer. Microtubules were visualized using 1:3,000 DM1A (Sigma Aldrich) and centromeres were visualized using 1:300 anti-centromere antibody (ACA). DNA was visualized with 100 ng/ml Hoechst-33342 (Sigma Aldrich). Images were acquired on a DeltaVision Core deconvolution microscope (Applied Precision/GE Healthsciences) equipped with a CoolSnap HQ2 CCD camera with a 100× 1.40 NA Olympus U-PlanApo objective. Images were deconvolved and maximally projected. For time-lapse microscopy, the media was changed to CO2-independent media prior to imaging and imaging was performed at 37°C. 3 Z-sections were acquired with 5 μm spacing using fluorescent light at the lowest level usable for data collection. Images were collected at 5-min intervals for 12 hrs using a using a 40×, 1.35-NA U-PlanApo objective (Olympus).
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2

Chromosome Imaging and Pole Tracking Analysis

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For imaging of chromosomes and pole tracking analysis, images were acquired on a deconvolution microscope (DeltaVision; Applied Precision/GE Healthcare) equipped with a charge-coupled device camera (CoolSnap; Roper Scientific, Sarasota, FL) with 5 × 2–μm z-stacks, 2 × 2 binning, and a 60×/1.3 numerical aperture (NA) U-planApo objective (Olympus, Tokyo, Japan) at 10-s intervals and 100-ms exposure at 18°C. Spindle pole separation was quantified as described (Desai et al., 2003 (link)).
For KNL-1 localization, embryos expressing GFP::H2b/GFP::γ-tubulin/KNL-1::mCherry were filmed every 20 s with 5 × 2–μm z-stacks on an Andor Revolution XD Confocal System (Andor Technology, Belfast, UK) and a confocal scanner unit (CSU-10; Yokogawa) mounted on an inverted microscope (TE2000-E; Nikon, Tokyo, Japan) equipped with 100×/1.4 NA Plan Apochromat lens and outfitted with an electron multiplying, back-thinned charge-coupled device camera (binning 1 × 1; iXon; Andor Technology) at 20°C. Exposure was 100 ms for GFP and 300 ms for mCherry.
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3

Fluorescence Microscopy for Protein Localization

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For analysis of localisation of tagged proteins or soluble fluorescent protein by native fluorescence, cells were harvested from mid-log phase cultures, washed twice in phosphate-buffered saline (PBS; 137 mM NaCl, 3 mM KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4) and allowed to settle for 5 min onto glass slides at ~2x107 cell ml-1 density. Cells were fixed for 5 min in 2% (w/v) formaldehyde, permeabilised in -20°C methanol for 10 min, re-hydrated in PBS and incubated with 15 ng ml-1 4′,6-diamidino-2-phenylindole for 5 min, before mounting in 1% (w/v) 1,4-diazabicyclo[2.2.2]octane, 90% (v/v) glycerol, 50 mM sodium phosphate, pH 8.0. Counter-staining of cells expressing ESP14-sfGFP was by incubation with 25 μg ml-1 tomato lectin conjugated to AlexaFluor 594 (Invitrogen) for 20 min. Images were captured on an Olympus BX51 microscope equipped with a 100x UPlanApo objective (1.35 NA; Olympus) and Retiga R1 CCD camera (Qimaging) without binning. All images of fluorescent proteins were captured at equal exposure settings without prior illumination. Images for level comparison were also processed in parallel with the same alterations to minimum and maximum display levels, except where stated. Image acquisition was controlled by μManager open source software [58 (link)]. Processing and analysis were performed in ImageJ [59 (link)].
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4

Single-molecule Fluorescence Microscopy Setup

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A diode-pumped solid-state green laser (532 nm; CrystaLaser GCL-100-M) and a red laser (637 nm; Coherent, maximum power 50 mW) were directed through a prism at an angle that allows TIR at the surface of the sample channel, which was constructed from a glass cover slip adhered to a quartz slide with double-sided tape. The surfaces of both the cover slip and slide were passivated with a mixture of mPEG and biotin-PEG, allowing for ribozyme immobilization while preventing protein adsorption to the slide surface (see Text S2 for description of slide preparation). Images were collected using a 60× water-immersion Olympus UPlanApo objective (numerical aperture, 1.2), filtered through a 550-nm long-pass filter (Chroma Technology) to remove scattered excitation light, separated into “green” and “red” images using dichroic mirrors, and focused onto the two halves of a microchannel plate intensified charge-multiplying charge-coupled device (CCD) (I-PentaMAX, Princeton Instruments, Roper Scientific, Inc.).
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5

Quantification of Dynein Spindle Pole Localization

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Images were acquired on a DeltaVision Core microscope (Applied Precision) equipped with a CoolSnap HQ2 CCD camera (Photometrics). A 100×, 1.4 NA U-PlanApo objective (Olympus) was used to image fixed cells, and a 60×, 1.42 NA Plan Apo N objective (Olympus) was used for live-cell imaging. Images were deconvolved and maximally projected. The fluorescence is not scaled equivalently in each panel to clearly demonstrate the qualitative localization of each protein.
To quantify the spindle pole accumulation frequency of dynein heavy chain, each replicate included 100 cells for each condition. The percentage of mitotic cells with clear, strong foci of the dynein-GFP signal on the spindle poles was denoted. 3-4 biological replicates were analysed for each condition and the mean percentage of cells (±s.d.) with strong dynein signal for those replicates was plotted. For ZW10 and MAD1, 2 biological replicates were analysed for each condition and the mean percentage of cells (±s.d.) with spindle pole-localized signal for those replicates was plotted.
Line scans were generated through the ‘Plot profile’ function in ImageJ, using maximally projected, but not deconvolved, images.
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6

Quantifying Nascent mRNA Transcription

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Images were acquired using an Olympus BX61 widefield epi-fluorescence microscope outfitted with a 100X/1.35 NA UPlanApo objective. Samples were visualized using the Chroma 41007 filter (Cy3), Chroma 31000 filter (DAPI), and DIC. Metamorph (Molecular Devices) was used as the acquisition software in combination with a CoolSNAP HQ CCD camera (Photometrics). Z-sections were acquired at 200 nm intervals over an optical range of 4.0 um. Exposure times for each z-section include 1200 ms (Cy3), 200 ms (Cy5) and 25 ms (DAPI). Cell volumes are then assembled by maximum intensity projections of z-sections using Metamorph. Localize, developed by Dr. Daniel Larson, was used to detect, locate and quantify intensities for fluorescent spots based on a two-dimensional Gaussian mask algorithm detailed previously5 (link)26 (link). Cell-segmentation software was used to identify cell and nuclear boundaries, and nascent mRNA counts were determined by dividing the transcription site intensity by the mean single transcript intensities, and rounding up or down to the nearest whole number5 (link). The mean initiation interval = ((lenth of the gene in Kb/mean # of nascent mRNA)/1.5 Kb per minute)). The maximum initiation interval = ((lenth of the gene in Kb/maximun # of nascent mRNA)/1.5 Kb per minute)).
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7

Oocyte Fixation and Immunostaining Protocol

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Oocytes were fixed for 3 hours to overnight in a buffer modified
from (von Dassow et al., 2009 (link))
containing 2% paraformaldehyde, 0.1% Triton X-100, 100 mM Hepes, pH 7.0, 50
mM EGTA, 10 mM MgSO4, and 400 mM dextrose. Oocytes were blocked for 15
minutes in AbDil (3% BSA, 1 × TBS, 0.1% triton X-100, 0.1% Na Azide)
and then stained with primary antibodies overnight at 4° C.
Anti-CENP-C antibodies were used at 1 μg/ml. Pol II pSer5 antibody
(ab5408, Abcam) was used at 1:1000. Microtubules were stained with 1:1000
DM1α (Sigma). GFP booster (Chromotek) was used at 1:500 to amplify
the signal from GFP expression. DNA was visualized using Hoechst. Nascent
RNA (EU) was detected as described by the manufacturer’s instructions
(Click-iT RNA imaging kit, Invitrogen). Oocytes were imaged using a
DeltaVision Core microscope (Applied Precision/GE Healthsciences) with a
CoolSnap HQ2 CCD camera and a 100× 1.40 NA Olympus U- PlanApo
objective. Confocal images (Fig. 3A)
were collected on a Zeiss 710 confocal microscope.
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8

Optical Stretching of Cells in Flow

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We employ a linear diode-bar based optical stretcher to generate the asymmetric intensity profile necessary to apply antipodal deformation forces (Figure 1b) required to stretch cells in flow and generate small non-destructive perturbations (~ 1%) in their size (Figure 1c)4 (link),23 . Figure 1 illustrates the direction of forces on a cell, where cells are pulled into the linear optical trap and exposed to oscillating stress generated by the modulated optical intensity as they translate down the trap length. We generate the optical trap using a linear diode bar laser (2495-Y-5.0 W, 810 nm, JDSU, Milpitas, CA) with an emitter of size 1 µm×100 µm. The laser light is collimated using a 20× objective (Aplan 20×/0.45, Zeiss, Jena, Germany) and focused within the sample plane using a 40×/.85 Olympus UplanApo objective. A frequency generator (DS 360 Stanford Research Systems) is used to modulate the laser intensity and generate sinusoidal stretching forces of ~20 pN4.
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9

3D Fluorescence Imaging of Cellular Structures

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Images of fixed cells were acquired on an Olympus BX41 wide field microscope equipped with a mercury lamp for epi-fluorescence, a Photometrics DV2 dual view apparatus for signal separation of red and green channels, and a Hamamatsu ORCA-R2 CCD camera for signal detection. 16 to 20 Z-sections were acquired at 0.2 µm steps using a 100X 1.4 NA Olympus U-PlanApo objective with 1×1 binning. Cells with buds, with multiple fluorescent spots of the same color and with deformed cell membrane were excluded from imaging to protect sample uniformity.
Cells were imaged using a GFP-DsRed dichromatic excitation/emission filter cube set with exposure time of 0.3 s. Images were recorded with Metamorph software (Molecular Devices) and analyzed with the ImageJ plugin, SpotDistance (EPFL Biomedical Imaging Group) [82] (link), with pixel sizes 64.5 nm, 64.5 nm and 200 nm for x, y and z axes respectively to calculate the three-dimensional distances between the fluorescent spots. Corresponding distance measurements are given in Data S1.
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10

Multimodal Histological Imaging Approach

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The same slides were used both for digital autoradiography and
fluorescence microscopy. Histology images of 10 μm fresh-frozen
sliced sections were analyzed using an Olympus BX-60 microscope equipped
with a CoolSNAP EZ camera (Photometrics, Tucson, AZ) for fluorescent
pictures, a CC12 Soft Imaging Systems camera (Olympus, Hauppauge,
NY) for RGB pictures, a Olympus UPlanFl objective with 10× magnification,
and a Olympus UPlanApo objective with 20× magnification. Fluorescence
images were obtained using appropriate filter cubes for each wavelength
(Hoechst, GFP, and NIR fluorescence). A computer controlled motorized
stage allowed images of whole sections to be generated as a mosaic
with a 10× magnification with identical exposure time per frame.
MicroSuite FIVE software was used to fuse images and Adobe Photoshop
and Fiji software was used to manually adjust and analyze images.
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