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62 protocols using mz16 stereomicroscope

1

Quantifying Drosophila Morphological Traits

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Fly heads were removed from newly eclosed flies. Heads were passed through a graded alcohol series for 24 hours each (25%–50%–75%-absolute), passed through Hexamethyldisalizane, and mounted on EM stubs using carbon tape (Ted Pella). Fly heads were dried for 24 hours, sputter coated with gold, and examined with a Hitachi scanning electron microscope at an accelerating voltage of 20 kV. Images were acquired as TIFF files that were collated using Adobe Illustrator. For quantitative analysis of eye size (facet number), crosses were established in duplicates, and ≥15 adult flies for each genotype were photographed using a Leica MZ16 stereomicroscope equipped with a Leica DFC-480 digital camera. Facet numbers were manually counted from TIFF images of the eyes and subjected to statistical analysis. For bristle phenotypes, newly eclosed adults were photographed using a Leica MZ16 stereomicroscope or by scanning EM. For quantitative analysis of the bristle phenotypes, multiple crosses were established (triplicates), and adults were scored for bristle defects. Wing margin phenotypes were documented using a Leica MZ16 stereomicroscope. Eye size (facet counts) and bristle and wing defects were statistically analyzed using the Student’s t-test, with the exception of Fig. 1F, which was determined using the chi-squared test.
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2

Quantification of Vascular Permeability in Mice

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Both flanks of adult anaesthetized mice were shaven. The next day, 100 µl of 1% Evans Blue (Sigma-Aldrich) in sterile saline (wt/vol) was injected intravenously through the lateral tail vein. In some experiments, mice received an intraperitoneal injection of pyrilamine maleate (4 mg/kg body weight in 0.9% saline; Sigma-Aldrich) before Evans Blue injection to inhibit release of endogenous histamine. 30 min after Evans Blue injection, 20 µl of PBS or PBS containing 50 ng VEGF164 (PeproTech), 300 ng SEMA3A (R&D Systems), or 50 ng histamine (Sigma-Aldrich) were injected intradermally each at three sites into the flank skin of anaesthetized mice. After 20 min, mice were culled, the skin was separated from the underlying muscle, and the tissue surrounding the injection sites excised (circled in Fig. 1 A) and dried overnight at 55°C. Evans Blue was extracted by incubation in formamide at 55°C overnight and quantified by spectrophotometry at 620 nm after subtraction of background absorbance at 740 nm. Data from the three sites injected with the same agent (ligand or PBS) were averaged and expressed as fold change relative to PBS control per each mouse. In some experiments, the inner side of the skin was imaged on an MZ16 stereomicroscope (Leica) equipped with a Micropublisher camera (Perkin-Elmer). In other experiments, a sample of liver or skin tissue was retained for immunoblotting.
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3

Morphometric Analysis of Insect Genitalia

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Measurements have been completed using a Leica graticule and × 10 eyepieces, through a Leica MZ16 stereomicroscope. Measurements are provided in Table 1 in millimetres. The scale bars are 1 mm for habitus images and 0.1 mm for genitalia.
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4

Ant Imaging and Mapping Protocol

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Photographs of the ants including dorsal, lateral and full-face views of workers and queens were taken at the MCZC with an imaging system that consisted of a Leica MZ16 stereo microscope, a Leica DCF 420 digital camera, and the Auto-Montage Professional software Leica Application Suite 3.7 and Helicon Focus 5.1; and at the USNM with an imaging system that consisted of a Leica Z16APO microscope and a JVC KY-F75U digital camera with a Leica Motor-focus System attached to an IBM IntelM Pro computer, on which composite images were assembled using Auto-Montage Pro Version 5.03.0018 BETA (Synoptics Ltd.). Scanning electron micrographs were taken with a LaB6 electron source. Images were processed with Adobe Photoshop CS. The distribution map was created using the software ArcGIS v10.1 (Esri, Redlands, CA).
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5

GFP Fluorescence Microscopy Protocol

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GFP fluorescence was monitored using a Leica MZ16 stereomicroscope equipped with a mercury lamp, a Leica GFP2 filter set, and a Leica DFC420 C digital camera.
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6

Analyzing Root Architecture and Nematode Development

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A solution of GA, MeJA or SA was added uniformly onto the surface of ICM plates using sterile glass beads. Two‐centimetre roots were then added and grown on each plate. After 1 day of growth on the plate, each root was treated with 400 juvenile HG 2.5.7‐type nematodes. For GA3 treatments, Peking unedited roots were treated with four different concentrations of GA3 (0, 0.1, 1 and 10 μm). One day later, 400 J2 HG 2.5.7‐type nematodes were added around the roots. An image of the whole root was captured 12 days after inoculation using a Leica MZ16 stereomicroscope with an attached camera. The length of first‐order fine roots and the diameters of the first‐order fine roots and main root were measured from at least 10 randomly selected roots. Measurements were performed using Adobe Illustrator. After imaging, the whole root was stained, and nematode development was quantified as described above. For MeJA treatment, DELLA‐edited roots and unedited roots both from Peking were placed on ICM plates with two MeJA concentration treatments (0, 150 μm) and inoculated with HG 2.5.7‐type SCN followed by a nematode demographics assay and the root architecture measurement as described above. For SA treatments, DELLA‐edited roots were placed on ICM plates with 1 mm SA and inoculated with HG 2.5.7‐type SCN followed by nematode demographics assays as described above.
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7

Histomorphometric Analysis of Bone-Implant Interface

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The fixed samples were dehydrated in a graded series of ethanol (60%, 80%, 96%, and absolute ethanol) using a dehydration system with agitation and vacuum. The blocks were infiltrated with Kulzer Technovit 7200 VLC-resin. Infiltrated specimens were placed into embedding molds, and polymerization was performed under blue- and white light. Polymerized blocks were sectioned in a mesio-distal direction and parallel to the long axis of each implant. The slices were reduced by microgrinding and polishing using an Exakt grinding unit to an even thickness of 60–70 µm. Sections were stained with RBS and counter-stained with acid fuchsin and examined using both a Leica MZ16 stereomicroscope and a Leica 6000DRB light microscope. Histomorphometric measurements were performed by using software (ImageAcess, Imagic, Switzerland) to calculate the percentage of osteoid, mineralized new bone, and remaining old bone along the bone–implant contact surface. BIC was calculated based on the sum of osteoid, mineralized new bone, and remaining old bone.
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8

Deep-sea Bryozoan Specimen Analysis

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Five specimens were examined from 46°59'45"S, 38°00'39"E, at depths of 360–376 m, between Marion and Prince Edward Island south of South Africa. The holotype was stained with methyl green for photography using a Canon EOS 7D camera with a Macro EF 100 mm lens and a Spot Flex CCD 15.2 fitted on a Leica MZ16 Stereo microscope at the Australian Museum, Sydney. The software Helicon Focus 5.3 was used for focus stacking. Another specimen from the same sample was dehydrated in ethanol, critical point dried, coated with 20 nm of gold and examined under a JEOL JSM-6480 Scanning Electron Microscope (SEM) at Macquarie University, Sydney. Terminology follows that of Hutchings et al. (2019). Data on the holotype are given, with the variations of the other material, all designated as paratypes, given in parentheses in the case of complete specimens. All material is deposited in Iziko Museums of South Africa (formerly South African Museum, Cape Town).
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9

Shape Recovery of Polymer Composites

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Specimens (25 × 3 × 1 mm) of SMP, CB5, CNT5, CB5/silicone-Al2O3, CNT5/silicone-Al2O3, CB5/silicone-silica and CNT5/silicone-silica were heated to 110 °C (T > Tg) and then immediately deformed into a temporary U-shape to approach an initial bending angle (θi) of 175~180°. The temporary shape was then fixed by equilibrating the specimens at RT (T < Tg). Next, the specimens were immersed in a 37 °C DI water bath for 0.5, 2, 6, 24, 48, 96, and 192 hr to measure the recovery of the original, permanent shape. The recovery angle (θr) images were recorded by a ProgRes digital camera (Jenoptik) attached to Leica MZ16 stereomicroscope. The shape recovery is expressed as: %Recovery=[θiθrθi]×100
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10

Timed Mating and Embryo Staging

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Mice were kept in a controlled 12-hour light/12-hour dark cycle, where the light cycle began at 7 am. Embryos were generated by timed mating between heterozygous animals, with noon on the day of finding a vaginal plug designated E0.5. To obtain E8.0 stage embryos, mice were housed using a reversed light/dark cycle, with the light cycle beginning at 10 pm. Embryos were dissected from the uterus in phosphate buffered saline (PBS) containing 10% newborn calf serum (Invitrogen), examined and photographed on a Leica MZ16 stereomicroscope. Embryos were scored as achieving Closure 1 when there was evidence of contact between the neural folds in the mid-region of the embryo, such that the neural folds could no longer be distinguished and a continuous surface ectoderm was observed.
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