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16 protocols using stereomicroscope m205fa

1

Larval Instar Identification through Morphometrics

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The adults of the above populations were placed in a nylon cage with potted tomato plants (1 × 1 m, 200 mesh) and raised at room temperature. After 24 hr of oviposition, the adults were removed, and the eggs were incubated. During the entire study period (from the newly hatched larvae to mature larva pupation), 20 larvae were randomly collected daily at 9:00 a.m. The end of larval instar was identified when the mature larvae dropped from infested leaves. Larvae were rinsed from the leaves and collected into a Petri dish using a paintbrush and a 2.5-ml liquid injector and then preserved in 70% alcohol (Jones et al. 2005 (link), Yang et al. 2018 (link), Zheng et al. 2019 ). The head capsule width and length and mandible width of the larvae were measured to the nearest 0.001 cm using a Leica stereomicroscope M205FA (Leica). These three characteristics were used together in the analysis to determine the instar stage.
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2

Evaluating Melanosome Aggregation in Teleost Scales

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Melanosome aggregation assays evaluated melanophores present on scales isolated from the dorsal flank, just anterior to the dorsal fin. Single scales were isolated from the dorsal flank of hypermelanic (“Asty66”; n = 10 individuals) and surface fish (“Asty 155 and 152”; n = 12 individuals) by gentle removal with the #5 fine forceps (World Precision Instruments, Sarasota, FL). Scales were immediately placed in 1 mL of sterile 1× Danieau’s solution (Cold Springs Harbor Protocols) in a 48-well plate. Each scale was imaged using montage imaging under identical bright field conditions using a Leica stereomicroscope (M205FA) at 80× magnification (brightness = 60 %, saturation = 1.25, automatic exposure; Leica Application Suite v3.8). Each scale was then immersed in 1 μM of melanin concentrating hormone (“MCH”; Sigma-Aldrich) and re-imaged following 5 min of treatment. Control scales were treated with 1× Danieau’s solution. Melanophore areas were measured from pre- and post-treatment images using the polygon selection and measurement tools in ImageJ. Three melanophores were measured on each scale for pre- and post-treatment with MCH. Additionally, we measured relative darkness (white = 0, black = 255) of each melanophore using the “mean” function in ImageJ, as previously described [12 (link)]. Surface and hypermelanic scales were compared using a Student’s T-test (StatPlus v5.8).
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3

Fluorescent Labeling of Bone and Neuromasts in Live Fish

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Live fish were stained with calcein (Sigma Aldrich C0875) to label bone and 2-(4-(dimethylamino)styryl)-N-ethylpyridinium iodide (DASPEI; Sigma Aldrich D3418) to label canal (CN) and superficial neuromasts (SN) as described in Powers et al. (2018b) (link). For imaging, fish were anesthetized by immersion in ice-cold system water for approximately 15 seconds. Fluorescent images were collected at 7.81x magnification under the GPF (calcein; 488nm) and TXR (DASPEI; 561nm) filters using a Leica stereomicroscope (M205FA) and Leica Application Suite software (LAS v3.8, Wetzlar, Germany). Images were overlaid to visualize bone and neuromasts (Figs. 1, 3 and 5).
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4

Alkaline Phosphatase Staining of Osteoblasts

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Alkaline Phosphatase (AP) staining was performed to detect osteoblast activity (Albertson & Yelick 2009 (link); Edsall & Odendaal 2010 (link)). Fish reared to approximately 12mm in SL were sacrificed by anesthetic overdose with 1% MS222 and preserved with 4% PFA in PBS for 2 hours (hrs) at room temperature (RT). Specimens were digested overnight in a solution of 3% trypsin and 50% sodium borate. Whole-mount AP staining was performed according to Edsall & Odendaal (2010) (link). Accordingly, specimens were incubated in 0.05M Tris-maleate buffer (pH 8.3) for 1 hr at RT. Next, specimens were incubated in AP substrate detection solution for 1 hr in the dark at RT. The staining reaction was terminated with 5% saturated sodium borate. Background staining was cleared using 1% KOH solution. Positive label was detected under bright field using a Leica stereomicroscope (M205FA) at 50x and 160x magnification (Fig. 1H–I).
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5

Micromorphological Characterization of Fungal Structures

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Morphological observations of the asexual/sexual morph in the natural environment were based on features of the conidiomata or ascomata on infected plant tissues and micromorphology, supplemented by cultural characteristics. Ascomata and conidiomata from tree barks were sectioned by hand, using a double-edged blade and structures were observed under a dissecting microscope. The gross morphology of conidiomata or ascomata was recorded using a Leica stereomicroscope (M205 FA). Fungal structures were mounted in clear lactic acid and micromorphological characteristics were examined using a Leica compound microscope (DM 2500) with differential interference contrast (DIC) optics. Thirty measurements of each structure were determined for each collection. Colony characters and pigment production on PDA were noted after 10 d. Colony colors were described according to Rayner (1970) .
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6

Morphological Characterization of Fungal Pathogens

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Samples were observed on infected plant tissues including the structure and size of fruiting bodies. The photographs of the macro-morphological characteristics were recorded using a Leica stereomicroscope (M205 FA) while the micro-morphological observations were determined under a Leica compound microscope (DM 2500) with differential interference contrast (DIC). Over 20 fruiting bodies were sectioned, both vertically and horizontally, and 50 conidia were selected randomly to get the measurement of their length and width. Cultural characteristics, including the colony characters and the production of pigment of isolates on PDA incubated at 25 °C in the dark were recorded, after 3, 7, and 30-days growth [19 ].
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7

Morphological Identification of Fungal Species

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Species identification was based on the morphological characters of apothecia and conidiomata produced on natural substrates. Cross-sections were prepared manually using a double-edged blade under a Leica stereomicroscope (M205 FA). Photomicrographs were captured with a Nikon Eclipse 80i microscope equipped with a Nikon digital sight DS-Ri2 high-definition colour camera, using differential interference contrast (DIC) illumination and the Nikon software, NIS-Elements D Package 3.00. Measurements of ascospores and conidia are reported as the maximum and minimum in parentheses and the range representing the mean ± standard deviation of the number of measurements is given in parentheses. Cultural characteristics of isolates incubated on MEA in the dark at 25 °C were recorded.
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8

Measuring Pharyngeal Pumping in C. elegans

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C. elegans CF4059 was exposed to the infection plates as described in the slow-killing assay. The pharyngeal pumping of three randomly picked worms was observed for 20 s at 12 h interval using Leica Stereomicroscope M205 FA. Pumping rate was measured by counting grinder movement and contraction/relaxation cycles of the bulb (Hobson et al., 2006 (link)).
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9

Quantifying Osteoblast Migration in Fish Fins

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To quantify osteoblast migration, fins of bglap:GFP transgenic fish were imaged with a GFP filter and in brightfield at 0 and 1 dpa with a Leica Stereomicroscope M205FA. Using Fiji (Schindelin et al., 2012 (link)), a threshold was set for the GFP signal to exclude background fluorescence and to select the bulk of GFP+ cells. The thresholded image was merged with the corresponding brightfield image and the distance between GFP+ cells and the joint at the ventral-distal centre of the segment was measured. For each fin, the second and third rays in the dorsal lobe of the fin were analysed. Statistical analysis was performed on the difference in distance between 0 and 1 dpa, while for illustration the change at 1 dpa is plotted, with migration across the whole distance to the joint counting as 100% migration.
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10

Quantifying Osteoblast Migration in Bglap:GFP Fish

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To quantify osteoblast migration, fins of bglap:GFP transgenic fish were imaged with a GFP filter and in brightfield at 0 and 1 dpa with a Leica Stereomicroscope M205FA. Using Fiji (Schindelin et al., 2012) (link), a threshold was set for the GFP signal to exclude background fluorescence and to select the bulk of GFP+ cells. The thresholded image was merged with the corresponding brightfield image and the distance between GFP+ cells and the joint at the ventral-distal centre of the segment was measured. For each fin, the 2 nd and 3 rd dorsal ray was analyzed. Statistical analysis was performed on the difference in distance between 0 and 1 dpa, while for illustration the change at 1 dpa is plotted, with migration across the whole distance to the joint counting as 100% migration.
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