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18 protocols using axioscope 40

1

Histological Analysis of Zebrafish Hearts

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Hearts dissected from 9 months old wild type (bh+/+) and mutant (bh−/−) were fixed in 4% paraformaldehyde, embedded in paraffin, and cross sections were obtained. The sections were stained with hematoxylin and eosin (H&E) (Fisher Scientific) using a standard protocol. Heart tissue sections were observed under an inverted light microscope (Zeiss Axioscope 40) at a magnification of ×5, and details were documented using ×40 magnification. The cytoskeletal structure of heart tissue was observed using Invitrogen™ Texas Red™-X Phalloidin (Thermofisher Scientific), a stain that specifically stains F-actin filaments. Hearts were dissected from nine-month-old adult wild type and bh−/− mutant zebrafish as described previously (Singh et al., 2016 (link)) and fixed in 4% paraformaldehyde for overnight at 4°C. The heart tissue was processed as per the following protocol: 1X PBS wash for 1 min × 3 times; 0.1% TBST for 5 min × 3 times; 1X PBS wash for 5 min × 2 times. The tissues were incubated with PBS with 1% BSA for 5 min -pre-staining. A total of 5 µL of 6.6 µM of phalloidin conjugated with texas red in methanol was added to 200 µL of detection solution. Tissues were incubated in the dark for 20 min and were washed with 1X PBS × 3 times for 5 min each. Stained tissues were observed using an inverted light microscope (Zeiss Axioscope 40).
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2

Histological Assessment of Liver Fibrosis

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Liver specimens were collected from the tissue and kept in 10% formalin solution. After fixation the tissues were processed by serial dehydration, clearing in xylene and then embedded in paraffin wax. 5 µm slices were sectioned and stained by routine Hematoxylin and eosin (H&E) and Masson’s trichrome (M&T). Picro-sirius red was used to stain the liver tissue sections to visualize the collagen content under fluorescence at 475–500 nm61 (link)–63 (link). Photomicrographs were taken on Zeiss Axioscope A1 with Jenoptik Prog Res C5 camera model and Zeiss Axioscope 40.
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3

Fluorescent Imaging of Zebrafish Embryos

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To inhibit pigment formation, embryos were treated with phenyl thiourea (PTU) (0.003%). Embryos were anesthetized using 4 mg/mL Tricaine methanesulfonate (Sigma, A5040) and mounted in 0.8%–1% low melting agarose gel (Biorad, 161-3111) in embryo water for imaging. GFP expression was observed, and fish were imaged using an upright Zeiss Axioscope 40 fluorescent microscope (Carl Zeiss, Germany). Image processing was done using Zeiss AxioVision 4.6 and Adobe Photoshop CS software.
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4

Live/Dead Bacterial Viability Assay

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The live/dead assay was performed according to LIVE/DEAD™ BacLight™ Bacterial Viability Kit (Invitrogen, Thermo Fisher Scientific, Waltham, MA, USA) protocol. Briefly, cells at mid-log growth phase (0.3 OD600) and at stationary growth phase (overnight cultures) were collected and washed once and resuspended in 0.85% NaCl. Five microliters of cells and 5 µL of 2× stain were thoroughly mixed by pipetting and incubated at room temperature for 15 min while protected from light. Stained cells (7 µL) were pipetted onto a glass slide with a coverslip and observed via fluorescent microscopy using Zeiss Axioscope 40 (Carl Zeiss Microscopy, White Plains, NY, USA) and a FITC filter at 1000× magnification and imaged with Axiovision 4.7 imaging software. Images were quantified by recording chain lengths for each strain using 10 fields of view per sample.
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5

Pyrite Crystal Morphology Analysis

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The mineralogical analyses were carried out at the Mineralogy Laboratory
of China University of Geoscience (Beijing) using a ZEISS Axioscope
40 petrological microscope. The scanning electron microscope (SEM)
analyses were carried out at the Microstructure Laboratory for Energy
Materials of China University of Petroleum (Beijing) using a HITACHI
SU8010 SEM at a working distance of 15 mm, voltage of 20 kV, current
of 10 nA, and signal intensity of 5000 cps. Before the sample was
observed and imaged, a Buehler Automet 250 polishing machine in the
DGS sample preparation laboratory was used for cleaning and polishing
preparation.36 (link) Due to the unique crystal
morphology and high atomic number of pyrite crystals, they show bright
colors in the backscattered electron mode of SEM. Next, NIH software
Fiji was used to process and analyze SEM images. Finally, the size
of the framboid pyrite is measured. Because it is difficult to ensure
that the size of each framboid is measured through the axis, the measured
diameter of framboid pyrite is generally smaller than the actual diameter.
Wilkin et al.14 (link) studied and found that
the deviation of this method is small (usually less than 10%), so
it can ensure the practicability of this method.
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6

Collagen Structural Evaluation via Picrosirius Red

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Structural and conformational modifications to type I collagen were histologically evaluated using picrosirius red staining by enhancing their natural birefringence under polarized light [25 (link),26 (link),27 (link)]. Briefly, crown dentin specimens were treated in the same manner described above up to 21 days incubation (n = 5). Specimens were then cryo-sectioned (CM 3050 S, Leica Biosystems, Nussloch, Germany) into 8 μm-thick slices. Sections were stained with 0.1% picrosirius red (Electron Microscopy Sciences) in saturated picric acid for 90 min followed by a 0.01 N HCl rinse (1 min twice). Sections were dehydrated, sealed in xylene and mounted for observation under polarized light microscope (Axioscope 40, Carl Zeiss, Goettingen, Germany). Images were captured at 40x magnification using a digital camera (AxioCam HRc, Zeiss). Quantitative assessment was done by converting the images to grayscale and inverting bright and dark regions (ImageJ software, NIH, USA). Threshold tool settings were determined to quantify the counts of staining and expressed in area percentage [25 (link)]. Data were analyzed using two-way ANOVA and Tukey post hoc test for comparisons among groups (α = 0.05).
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7

Histomorphometry of Bone Microarchitecture

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ABH/OG stained slides were visualized using an Axioscope 40 (Zeiss) microscope equipped with an Olympus DP72 camera (Olympus) and evaluated with Osteomeasure software (OsteoMetrics). Slides were analyzed to measure trabecular bone area to total area in proximal tibia, distal femur, and L3. Three different slides were counted per mouse and averaged. There were at least five mice per age group.
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8

Immunohistochemistry of Paraffin-Embedded Bone Marrow

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In Paraffin-embedded EDTA-decalcified bone marrow biopsies, the immunohistochemistry was performed in a dilution of 1:500 using an automated immunostainer (Ventana BenchMark ULTRA IHC/ISH staining module, Ventana Medical Systems, Tuscon, USA) with the U OptiView DAB IHC v5 procedure according to the manufacturer's protocols. Slides were evaluated on a Zeiss Axioscope 40.
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9

Quantifying Chain Length of Cocci

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Overnight cultures were pipetted onto a microscope slide with a coverslip and observed using a Zeiss Axioscope 40 bright field microscopy at 1000× magnification and imaged with Axiovision 4.7. Chain lengths were quantified using 10 fields of view per sample. A minimum of 2500 cocci per strain were quantified.
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10

Identification of CCND1 Translocations by FISH

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Fluorescent in-situ Hybridization (FISH) was performed with IGH/CCND1 XT, IGH break apart (Abbott Molecular, Downers Grove, IL) and MTCP1 (Empire Genomics, Williamsville, NY) probes. FISH was done according to the manufacturer’s recommendations, except prior to hybridization slides were pretreated with pepsin and postfix solution. Co-denaturation of probe and sample was done on HyBrite (Abbott Molecular, Downers Grove, IL) for 5 min at 73 C. Hybridization was carried out overnight at 37 C, and slides were washed in 0.4 x SSC/0.3%NP-40 for 2 min at 73 C. The signals were viewed using a fluorescent microscope (Zeiss Axioscope 40) equipped with appropriate filters and analyzed with Applied Imaging System.
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