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40 protocols using mzfliii stereomicroscope

1

Embryonic Staging and Larval Measurement

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Embryos were staged at fixed time points according to Kimmel et al. (1995) [45 (link)] using a Leica MZ FLIII stereomicroscope (Leica microsystems, Wetzlar, Germany). Staging was based on clearly distinguishable features, i.e. 6 hours post fertilization (hpf, embryonic shield), 24 hpf (heart beat and early pigmentation), 30 hpf (weak circulation), 48 hpf (tapering yolk extension) and 72 hpf (protruding mouth). At each time point 5 embryos were staged from the diploid and cold shocked groups. At 5 dpf, length in mm (to the nearest 0.01 mm) was assessed from pictures of living larvae taken with a Leica MZ FLIII stereomicroscope and the segmented line tool in the ImageJ program (https://imagej.nih.gov/ij/).
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2

Embryonic Development Tracking Protocol

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Development of the embryos was followed up until 72 hours post-fertilization (hpf), by determining their developmental stage according to Kimmel et al. (1995) (link) at fixed time points using a Leica MZ FLIII stereomicroscope (Leica Microsystems, Wetzlar, Germany). For all temperature treatments, staging was performed at 6, 24, 30, 48, and 72 hpf in real-time, to be able to observe temperature effects on development. These time points were chosen because of the clearly distinguishable developmental features, namely: embryonic shield, heart beat and early pigmentation, weak circulation, tapering yolk extension and protruding mouth.
At each time point, five diploid and five cold shocked embryos were staged of all temperature treatments. In our final analysis, we only included development of embryos that morphologically appeared to have developed normally at 5 dpf (e.g., straight body axis, no pericardial edema and normally sized head and eyes). Length was measured at the developmental stage of 5 dpf (protruding mouth stage), using pictures of larvae taken with a Leica MZ FLIII stereomicroscope equipped with a Leica DFC450 C camera and the segmented line tool of the ImageJ program3.
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Imaging Embryos with Leica Stereomicroscope

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Images of the embryos were acquired with a Leica MZ FLIII stereomicroscope (Leica) equipped with a Leica DFC310FX digital camera (Leica).
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4

Multimodal Microscopy for Comprehensive Imaging

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Low magnification images were acquired with a Leica MZ FLIII stereomicroscope (Leica) equipped with a Leica DFC310FX digital camera (Leica). Whole-eye pictures were taken with a Leica upright wide-field epifluorescence microscope using a 20× oil immersion objective. A Zeiss LSM 780 confocal microscope (Zeiss) was used for confocal microscopy, employing a 40× water immersion or 10× objective. Z-volumes were acquired with a 1- to 2-μm resolution, and images were processed using ImageJ, Adobe Photoshop, and Adobe Illustrator software.
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5

Evaluating Cell Proliferation, Apoptosis, and Cell Cycle

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Cell proliferation/viability was evaluated by the tetrazolium dye (MTS) assay (Promega, Madison, WI). Each cell line was plated at a seeding density to give logarithmic growth over the course of the assay in a 96-well tissue culture plate. The concentration of final product is measured by absorbance at 490 nm and is proportional to the viable cell number in each well. For soft agar assays, 5 × 103 to 104 cells were suspended in 0.8% low melting point agarose (Difco Laboratories Inc., Detroit, MI) at room temperature, mixed with an equal volume of 2x concentrated culture media, and plated onto an agarose bed consisting of 2% low melting point agarose and the same medium. After 3–6 weeks, colonies were stained with neutral red and were enumerated using a Leica MZ FLIII Stereomicroscope (Leica, Germany).
Apoptosis was determined using the Annexin V assay (Biolegend, San Diego, CA) and cell cycle was analyzed using the Propidium Iodide assay (Invitrogen, MA). After treatment, cells were collected and stained with Annexin V-FITC and/or propidium iodide solution as per the manufacturer’s protocol and analyzed by flow cytometry. Cell death was recorded in a FACSCanto II (BD Biosciences, Mississauga, ON) in the total population (10,000 cells) and data were analyzed using FACSCanto II software and ModFit Software (Verity Software House, Topsham, ME).
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6

Imaging Melanoma Cell Migration in Zebrafish

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Starting from 30 hours post injection (hpi), embryos showing melanoma cells that had migrated were selected using a Leica MZ FLIII stereomicroscope (Leica) equipped with a Leica DFC310FX digital camera (Leica). Zeiss LSM 700 confocal microscope or Zeiss LSM 880 microscope (Zeiss) were used, employing a 25 × oil, a 40 × water immersion or a 63 × water immersion objective. For confocal microscopy, larvae were anesthetised in egg fish water containing 0.02% tricaine, immobilised in 1.2% low-melting agarose and then imaged up to 12 hours (one acquisition every 15–25 minutes), using 488 and 568 nm lasers. Z-volumes were acquired with a 1- to 2-μm resolution and images were processed using ImageJ, Imaris-Bitplane, Zen Blue and Adobe Illustrator software.
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7

Embryonic Lung Immunohistochemistry and Imaging

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Sample processing and whole-mount immunohistochemistry of dissected embryonic lungs at E11.5–E15.5 were performed as described previously (Alanentalo et al., 2007 (link)). Briefly, fixed lungs were dehydrated with methanol followed by rehydration and processing to immunohistochemical staining. Localization of anti-E-cadherin (Cell Signaling Technology) was detected either by fluorescently labeled secondary antibody conjugated to Alexa-Fluor-594-conjugated anti-rabbit IgG (Life Technologies/Thermo Fisher Scientific Inc.) or visualized by using the chromogenic DAB substrate (Immunologic, Duiven, The Netherlands) following the incubation with poly-HRP-conjugated anti-rabbit IgG antibody (Immunologic, Duiven, The Netherlands). Fluorescently labeled lungs were processed for OPT scanning as described previously (Alanentalo et al., 2007 (link)), using a Bioptonics OPT 3001M Scanner. Three-dimensional (3D) visualization and branch end-point analysis was performed with Imaris 3D and 4D data software, using the Filament analysis function (Bitplane AG, Switzerland). Chromogenically stained samples were imaged using a Leica MZFLIII stereomicroscope (Leica, Germany) and Colorview camera (Software imaging system, Olympus, Japan).
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8

Stereomicroscopy and Confocal Imaging

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For low magnification imaging, a Leica MZ FLIII stereomicroscope (Leica) equipped with a Leica DFC310FX digital camera (Leica) was used. Confocal microscopy was performed using a Zeiss LSM 710 confocal microscope (Zeiss) and a 40× or 25× water immersion or 10× objective. Z volumes were acquired with a 1- to 3-μm resolution and images processed using Adobe Photoshop and Adobe Illustrator software. Three-dimensional reconstructions of Z-volumes were done using Imaris.
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9

Multispectral Imaging of 5-ALA and Fluorophores

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Imaging for 5-ALA-treated tissues was performed using a custom Leica, MZFLIII stereo microscope (Leica). A liquid-crystal tunable wavelength filter in the Leica spectral camera was set for collection of emission images from 600 to 720 nm in 5-nm increments. Composite images (unmixed composites) were generated for each image cube by separating the spectral signature of the PPIX molecule from those of background autofluorescence using a spectral library that was compiled from numerous spectral profiles collected from control tissue under the same conditions. For PPIX imaging using the Odyssey CLx (LI-COR), an external ultraviolet source (405 nm) was used for excitation of PPIX and fluorescence emission was collected in the 700 nm channel. Imaging for tissues treated with panitumumab-IRDye800CW and IRDye800CW was performed using the Pearl Trilogy Imaging System (LI-COR). The Odyssey CLx (LI-COR) was used for high-resolution fluorescence scans.
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10

Histochemical GUS Assay for Plant Tissues

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Histochemical GUS assays were performed as described by Takata and Taniguchi [15] . Plant tissues such as leaves, stems and roots were harvested from transformants growing for 32 days in soil mix and fixed in cold 90% acetone for 30 min. Tissues were washed with 50 mM sodium phosphate (pH 7.0) and then incubated in GUS staining solution [50 mM sodium phosphate (pH 7.0), 0.5 mg ml -1 5-bromo-4-chloro-3-indolyl-b-D-glucuronic acid, 0.5 mM potassium ferrocyanide, 0.5 mM potassium ferricyanide, 0.1% Triton X-100] at 37 °C for 16 h. Samples postfixed in 2.5% (v/v) glutaraldehyde in 50 mM sodium phosphate (pH 7.0) were bleached in ethanol:acetic acid (6:1, v/v) for leaf blades and 70% ethanol for leaf veins, petioles, stems and roots. Leaf blades were cleared with chloral hydrate/ glycerol solution. Other tissues were infiltrated through a series of 25, 33, 50, 66, 75, and 100% 2.3 M sucrose in 100 mM sodium phosphate (pH 7.0). Leaves and stems were embedded in SCEM-L1 mounting medium (Leica, Solms, Germany) and frozen in liquid nitrogen-cooled hexane. Cryosections of 50 lm were cut using a Leica CM3050 S cryomicrotome (Leica). Roots were sectioned at a thickness of 80 lm using a vibratome (Dosaka EM, Kyoto, Japan). Samples were imaged by a Leica MZ FLIII stereomicroscope and a Leica DMR microscope (Leica).
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