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68 protocols using dissecting microscope

1

Subcellular Fractionation of Nucleus Accumbens

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Subjects were briefly exposed to CO2 and decapitated by guillotine. In Experiments 1 and 3, NAc was dissected from fresh brain on ice and 2-3 samples per treatment condition were pooled for fractionation. All subjects’ CPP expression in the final test was inspected and NAc samples from 2-3 rats with similar CPP expression were pooled per sample tube. The purpose of pooling was to ensure an adequate yield of synaptosomal fraction. The methods of subcellular fractionation were as described previously (e.g., Peng et al., 2014 (link)) and fractions were stored at −80°C until use.
In Experiment 2, brains were extracted and rapidly frozen in powdered dry ice. A series of 500-μm sections were cut using an IEC Minotome cryostat, and NAc core and shell were dissected using a combination of micropunch and microknife under an Olympus dissecting microscope. Tissue lysates were prepared as described previously (e.g., Zheng et al., 2013 (link)) and stored in sample buffer in aliquots at −80°C. The protein content was determined using the BCA reagent kit with bovine serum albumin as a standard (Pierce, Rockford, IL).
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2

Antifeedant Effect of Molluscicide on Predator

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The antifeedant effect of MB on the adults of N. tenuis (<3 days old) was assessed under laboratory conditions using the method developed by Roditakis et al. [2 (link)] and Fytrou et al. [33 ]. First, adults of B. tabaci (n = 30) were allowed to lay eggs on fresh tomato plants for 72 h. The number of eggs per leaf was counted under a dissecting microscope (Olympus, Tokyo, Japan). On average, the tomato leaves selected for use in this experiment carried 200 eggs. The test arena was prepared as described in the previous subsection. However, in this experiment, the adults of N. tenuis (n = 5) were sprayed directly with the MB solutions (0.25%, 0.5% and 1%), the negative control or the positive control. Each adult of N. tenuis was then placed individually on a tomato leaf with the eggs of B. tabaci. After adults of N. tenuis were placed in the test arena, sublethal antifeedant effects were assessed by counting the number of eggs of B. tabaci that each adult of N. tenuis consumed daily for 3 days. Three replicates were used for each treatment. These experiments were also carried out at 25 °C ± 1 °C, 60% ± 10% RH and with a 16:8 h L:D photoperiod.
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3

Tick Collection and Identification in Pakistan

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Single engorged adult female ticks (n = 235) were collected from clinically healthy farm dogs of both sexes (male, n = 70; female, n = 165) between June and October 2016 from three different districts in the province of Punjab, including Kasur (31°12'21"N, 74°45'81"E; n = 87), Muzaffargarh (30°07'36"N, 71°18'05"E; n = 75) and Rawalpindi (33°59'84"N, 73°04'41"E; n = 73) (Fig. 1). Following collection, each tick specimen was stored individually in 70% ethanol until used. For morphological identification, each tick was examined using a dissecting microscope (Olympus, Tokyo, Japan). Ticks were identified using the keys as described previously [40 ].

Map of Pakistan showing the sampling sites and the number of ticks tested per region

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4

Quantifying Lung Tumor Metastasis

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Lungs were harvested and fixed in Bouin’s solution (Bio-Optica) for examination with a dissecting microscope (Olympus). Macroscopic lung nodules were counted by an investigator blinded to the treatment group. The number of colonies per lung and the diameter were recorded. Metastasis volume was calculated as [(4/3 π radius3 (µm3)], and the lung tumor burden was derived from the sum of the volumes of all colonies counted. Histological validation of metastasis is detailed in Supplemental methods.
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5

Quantifying Hair Follicle Density

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To quantify the density of HFs, we obtained images of the skin tissue using a dissecting microscope (Olympus). The tissue area was first measured using ImageJ, after which the number of HFs found in the sample was quantified by counting the number of hair shafts. This frequency was then divided by the area to find the density.
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6

Arabidopsis-Meloidogyne Nematode Interaction

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A. thaliana seedlings (one month after transplant) were used for nematode inoculation. About 200 free-living J2s of M. incognita were inoculated per plant of different A. thaliana lines (WT, GFP-RNAi and Miatrr-RNAi lines). At 42 days post-inoculation (dpi), the roots were collected. Galls and egg masses were counted, and width of body size of worms in galls was measured under a dissecting microscope (Olympus, Tokyo, Japan). Each treatment had 20 plants, and the experiment was repeated three times. For observation of nematodes in plant roots, roots were stained with acid fuchsin [37 ] and observed under a microscope (OLYMPUS IX53). Live nematodes appeared bright pink.
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7

Brain region dissection protocol

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Immediately following the final expression test in each behavioral experiment,
subjects were briefly exposed to CO2 and decapitated by guillotine. Brains were
extracted and rapidly frozen in powdered dry ice. A series of 500-µm sections were
cut using an IEC Minotome cryostat, and NAc core and shell and caudate-putamen were
dissected using a combination of micropunch and microknife under an Olympus dissecting
microscope. Tissue lysates were prepared as described previously (e.g., Zheng et al. 2013 (link)) and stored in sample buffer in
aliquots at −80°C. The protein content was determined using the BCA
reagent kit with bovine serum albumin as a standard (Pierce, Rockford, IL).
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8

Epidermal Sheet Isolation from Mouse Ears

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Epidermal sheets were prepared as before4 (link) with slight modification. Briefly, ears were split into dorsal and ventral halves with forceps. Thioglycolic acid-containing Hair Removing Body Cream Epilat (Kracie) was used to remove hair in some experiments. Ear halves were incubated for 15 minutes at 37°C on 3.8% ammonium thiocyanate (Wako Pure Chemical Industries) in phosphate buffer (pH 7.0). Epidermal sheets were manually detached from the dermis under a dissecting microscope (Olympus).
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9

Epidermal Isolation from Mouse Ears

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Epidermal sheets were prepared as previously described (Nagao et al., 2009 (link)). Briefly, mouse ears were divided into dorsal and ventral halves with forceps and incubated for 15 min at 37 °C on 3.8% ammonium thiocyanate (Wako Pure Chemical Industries) in phosphate buffer (pH 7.0). The epidermal sheets were manually detached from the dermis under a dissecting microscope (Olympus). Tissue samples for cryosections were embedded in O.C.T. compound (Tissue Tek) and frozen at − 80 °C.
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10

Quantifying Shell Mineralization via Birefringence

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For each pCO2 treatment, 5 to 8 larvae were randomly chosen among the previous subsamples and observed under polarized light to determine birefringence patterns with an Olympus dissecting microscope equipped with polarizing filters. All polarized images were acquired with an Olympus camera at ×100 magnification with 40 ms light exposition. Birefringence under polarized light is due to the mineral phase composing the shell [40] , [68] (link), [70] (link), [71] . In the absence of mineralized structures, there is no birefringence and the picture looks totally black. Under identical light conditions, areas appearing more birefringent contain a much larger proportion of crystalline calcium carbonate [70] (link), [72] (link). The intensity of birefringence of each shell was used as a proxy for mineralization level for the three pCO2 treatments. It was quantified from pictures by using ImageJ software [69] . Pictures of polarized shells were first transformed into grayscale images. A mean gray value (in pixels) was determined for each birefringent zone. All birefringent zones of the shell were compiled to obtain a global mean gray value, giving the intensity of the birefringence of the whole shell.
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