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71 protocols using dmc2900

1

Maintaining Ae. aegypti Mosquito Colonies

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Mosquitoes used in all experiments were derived from the Ae. aegypti Liverpool strain (designated as wild-type [wt], Supplementary file 8a). Of note, the Ae. aegypti reference genome sequences were generated using this strain (Matthews et al., 2018 (link); Nene et al., 2007 (link)). Mosquitoes were raised in incubators at 28.0°C with 70–80% humidity and a 12 hr light/dark cycle. Larvae were fed ground fish food (TetraMin Tropical Flakes, Tetra Werke, Melle, Germany) and adults were provided 0.3 M aqueous sucrose ad libitum. Adult females were blood fed three to five days after eclosion using anesthetized mice. Mosquitoes were examined, scored, and imaged using the Leica M165FC fluorescent stereo microscope equipped with the Leica DMC2900 camera. All animals were handled in accordance with the Guide for the Care and Use of Laboratory Animals as recommended by the National Institutes of Health and supervised by the local Institutional Animal Care and Use Committee (S17187).
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2

Histochemical Analysis of Rhaponticum carthamoides

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For the histochemical analysis, thin transverse sections (4–5 μm) of roots and rhizomes of both wild and cultivated R. carthamoides samples were obtained using a rotary microtome (Leica RM 2155) after the plant material had been fixed in a solution of 60% ethanol and glycerol in a ratio of 9:1, as a softening procedure of tissue prior to sectioning [17 ]. For the localization of lipophilic substances, the sections were treated with Sudan staining solution (Sudan III in 70% ethanol) for 20 min, rinsed in 50% ethanol to remove excess stain, and mounted in 50% glycerol [18 ]. Observations and photomicrographs were performed using a light microscope (Leica DM 2000 LED, Leica Microsystems, Wetzlar, Germany), equipped with a digital camera (Leica DMC 2900) and software for processing images (Leica Application Suite, LAS).
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3

Drosophila Eye Imaging Protocol

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Drosophila eye pictures were taken using a Leica Z16 APO with the DMC2900 camera and a ring light.
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4

Fluorescent Imaging of Fly Specimens

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Flies were scored and imaged on the Leica M165FC fluorescent stereomicroscope equipped with the Leica DMC2900 camera. A GFP long pass filter, ET GFP (Leica Microsystems Inc., Buffalo Grove, Illinois, Article No. 10447408), set was used to assess GFP fluorescence and for imaging. To assess both GFP and RFP, we used a double filter GFP3/mCH (Leica Microsystems Inc., Buffalo Grove, Illinois, Article No. 10450203 ). Images were done under constant conditions.
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5

Quantifying Quartz Lamellae in Garnet

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Vertically integrated images of thin- and thick-section core zones were taken with the Leica DMC2900 camera attachment and LASv.4.10 software. These images have a scale calibrated to the microscope objective used while acquiring the image. Thin sections cut perpendicular to garnet <111> were selected. Using measuring tools in the Leica Application Suite software, quartz needles were measured for diameter and length, which were used to calculate the volume of each quartz needle assuming a cylindrical shape. Because the sections are viewed along <111>, lamellae are foreshortened because of their dip angles of 35.26°. To correct for this, we multiplied measured lamellae length by 1/cos(35.26°). The vertically integrated images do not show the length of lamellae parallel to the <111> coming out of the image, and consequently, SiO2 estimates are minima because this direction should account for ~25% of all lamellae. The measured quartz mode for sample 58A-8 (30,000 μm2) is 0.46 vol%, and the corrected is 0.77 vol%. The measured quartz mode for sample 374B-1 (71,780 μm2) is 0.25 vol%, and the corrected is 0.31 vol%. These increase to 1.03 and 0.41 vol% if the additional inferred ~25% of the lamellae parallel to <111> are included.
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6

Skeletal Staining and Imaging

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Fixed animals were stained with Alcian blue and Alizarin red as described previously (Brooks and Nichols, 2017 (link); Walker and Kimmel, 2007 (link)). Alcian blue- and Alizarin red-stained 6 days post fertilization (dpf) skeletons were dissected and flat mounted for Nomarski imaging on a Leica DMi8 inverted microscope equipped with a Leica DMC2900 as previously described (Nichols et al., 2013 (link)).
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7

Histological Observations and Staining of Plant Tissues

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For general histological observations, the plant material was fixed in a solution of 60% ethanol and glycerol in a ratio of 9:1 as a softening procedure of the tissues prior to sectioning [98 ]. Temporary preparations of hand-cut transverse sections were made from the middle part of the leaf and stem of the plant. For the presence of lipids in tissues, the sections were treated with a Sudan staining solution (Sudan III in 70% ethanol) for 20 min, rinsed in 50% ethanol, and mounted in 50% glycerol [99 ]. To reveal the presence of terpenes in the tissues, the sections were treated with a NADI staining solution (0.5 mL of 0.1% α-naphthol, 0.5 mL of 1% N,N-dimethyl-p-phenylenediamine, and 49 mL of 0.1 M sodium phosphate buffer, pH 7.2) for 1 h, rinsed in 0.1 M sodium phosphate buffer, pH 7.2 for 2 min, and immediately analyzed under a microscope [100 ]. The image analysis was performed using a light microscope (Leica DM 2000 LED, Leica Microsystems, Wetzlar, Germany) equipped with a digital camera (Leica DMC 2900) and software for processing images (Leica Application Suite, LAS).
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8

Karyological analysis of sporangia and zoospores

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The karyological status of sporangia and zoospores was investigated with fluorescence microscopy (Zeiss Axioplan, filter combination UV 395–440 excitation/FT 460/ LP 470 barrier; documentation system Leica DMC2900 with software LAS V4.6) using 4′,6-diamidin-2-phenylindol (DAPI) or Hoechst 33342 as DNA staining dyes.
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9

Microscopy Imaging Techniques for Spinal Cord

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Light and fluorescent images were obtained using the Olympus, BX51 with the following objectives: X20 and X40 and equipped with the following cameras: Leica CCD Microscope DFC3000 G and DMC2900. Sixteen-bit images (1296 × 966 pixels) were acquired for each channel and merges were done using Photoshop (Adobe) CS4. Confocal images were obtained using Leica SP8 with X40 objective equipped with super-sensitive HyD detectors. Fluorescence was recorded as square 8-bit images (1024 × 1024 pixels) and stored as separate image stacks for each channel. Alignment of images to obtain largest field of view of spinal cord sections was done applying the automatic stitching of stack images using the Leica dedicated application (Las-X, Leica). Images in figures show the maximal projections of Z-stacks acquired with a 0.7 µm step and pseudo-colored using Las-X software.
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10

Immunohistochemical Analysis of Cellular Markers

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Formalin-fixed paraffin-embedded tissue sections were de-paraffinized and then incubated with rabbit anti-APE2 polyclonal antibody (Bioss, bs-6587R), rabbit anti-cleaved caspase-3monoclonal antibody (Cell Signaling Technology, #9664S), rabbit anti-MYH9 antibody (GeneTex GTX113236), or rabbit anti-phosphor-histone H2A.X(Ser139) polyclonal antibody (Cell Signaling, #2577) at 4°C overnight. After incubation with HRP-conjugated goat anti-rabbit secondary antibody, signal was detected using a DAB Substrate kit (Abcam, ab64238) according the manufacturer’s instructions. Images were obtained by means of a phase-contrast microscope (Leica DM2000 LED) and a digital camera (Leica DMC 2900).
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