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24 protocols using rm2016 microtome

1

Histological Analysis of Cyprinid Ovary Development

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At 2 years of age, 5 2nYC individuals were selected at random for histological observation of the gonadal structure via paraffin sectioning. The ovaries were fixed in Bouin’s solution, dehydrated in an increasing ethanol gradient, cleared in xylene, embedded in paraffin, sectioned using a Leica RM2016 microtome (Germany) and stained with haematoxylin and eosin. Ovary sections were examined and photographed using an Olympus microscope CX41 (Japan), and ovarian development in each sample was classified based on the previous standards for cyprinid fish [58 ].
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2

Histological Analysis of Plant Stem Nodes

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For histological analyses, the first basal stem nodes were collected from the main stem from the wild-type and transgenic plants to generate paraffin sections, according to the procedure described by Han et al. [31 (link)]. WT and transgenic plant samples were fixed in formaldehyde/acetic acid/alcohol fixation buffer (FAA; 70% ethanol: formaldehyde: acetic acid = 90:5:5) for 24 h at 4 °C and then stored in 70% ethanol. The stem nodes were gradually dehydrated with 70%, 80%, 95%, and 100% ethanol for 1h in each step. Then, 0.1% safranine O in ethanol was added to pre-stain the xylem, and embedded in paraffin (Sigma-Aldrich). The plant material was cut into 8 µm ultrathin sections on a Leica RM2016 microtome, dewaxed in dimethylbenzene, mounted in neutral balsam after drying, and observed under a Leica DCF500 microscope. Micrographs of sections from 3 specimens were examined. Statistical differences were determined. Xylem thickness and phloem thickness were measured using ImageJ software (https://imagej.nih.gov/ij, accessed on 12 March 2022). Statistical differences were determined using Student’s t-test.
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3

Histological Observation of Gonad Structure

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Ten RCC, 10 4nF1, and 40 G1 at age 9 months were randomly selected for histological observation of gonad structure. Gonads were fixed in Bouin’s solution, embedded in paraffin, sectioned with a Leica RM2016 microtome, and stained with hematoxylin and eosin. Tissue sections were observed and photographed with an Olympus CX41 microscope. Gonadal development was staged according to criteria established for cyprinid fish (Liu 1993 ). Observation of gonadal development was used to determine whether the gynogenetic progenies were fertile.
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4

Histological Analysis of Skeletal Muscles

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Skeletal muscles were dehydrated, clarified in xylene, and embedded in paraffin. Serial sections of paraffin were cut using an RM2016 microtome (Leica, Wetzlar, Germany) and mounted on glass slides (Servicebio, Wuhan, China). H&E staining images were acquired using a NIKON DS-U3 camera control unit (Nikon, Tokyo, Japan).
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5

Histological Analysis of Inflorescence Stem Development

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For histological analyses, we collected the first basal-end node of the main inflorescence stem, immediately above the uppermost rosette leaf, at different developmental stages from the wild-type, the cep1 T-DNA insertion mutant lines, and the CEP1-overexpressing transgenic lines. The basal nodes of inflorescence stems from early to late developmental stages were selected to produce paraffin sections. All samples were fixed in formaldehyde/acetic acid/alcohol fixation buffer (FAA; 70% ethanol:formaldehyde:acetic acid = 90:5:5) for 24 h at 4 °C and stored in 70% ethanol. The stem nodes were gradually dehydrated (70%, 80%, 95%, and 100% ethanol, 1 h each step) and 0.1% safranine O in ethanol was added to pre-stain the xylem. The stem nodes were then embedded in paraffin (Sigma-Aldrich) according to the manufacturer’s instructions. Transverse serial sections (8 μm thick) were prepared using a Leica RM2016 microtome, dewaxed in dimethylbenzene, mounted in neutral balsam after drying, placed on a cover glass, and observed under a Leica DCF500 microscope. Micrographs of sections from 9–12 specimens were examined. Statistical differences were determined using Student’s t-test.
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6

Quantifying Myocardial Infarct Size via TTC Assay

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Direct TTC assay according to our previous work (Li et al., 2012 (link)) was used to determine myocardial infarct size. In brief, the heart was transversely cut across both ventricles and sectioned into 2 mm thick. Sections were incubated at 37°C in 1% TTC-phosphate buffer (pH 7.4) for 30 min, following which they were fixed with 4% paraformaldehyde for 24 h. The non-ischemic myocardium and viable ischemic myocardium were stained red, while the infarcted myocardium appeared pale gray or white. The slices were photographed using a digital camera, and the % infarction was analyzed using the computerized Image-Pro Plus 6.0 software (Media Cybernetics, Inc., Silver Spring, MD, United States).
The tissues from ecardiac apex were fixed with 4% buffered paraformaldehyde for paraffin embedding. Sections were cut (by Leica RM2016 Microtome) into 5 μm and stained with hematoxylin and eosin (H&E). The sections were examined under light microscope (Nikon Eclipse E100) and micro graphed by Nikon DS-U3 digital camera controller at 200× magnification.
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7

Histological Analysis of Mouse Tissues

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Mouse muscle tissues were frozen in isopentane that had been cooled in liquid nitrogen. Wheat germ agglutinin (WGA) staining was performed using fluorescein isothiocyanate (FITC)–conjugated WGA (Sigma-Aldrich, #L4859). Quantification of cross-sectional area of the myofibers was performed with National Institutes of Health ImageJ software. Adipose tissues were fixed in 4% formaldehyde overnight at 4°C immediately after euthanasia, embedded in paraffin, and cut to 7-μm sections on slides using a Leica RM2016 microtome. H&E and Masson’s trichrome staining were conducted according to the standard protocol. For UCP1 IHC, brown adipose tissue sections were rehydrated and then boiled in 10 mM citric acid buffer, pH 6.0, at 95°C for antigen retrieval.  IHC was performed using the UltraSensitive SP (Rabbit) IHC Kit (Maxim) according to the manufacturer’s instructions using rabbit UCP1 antibodies (1:500; ab10983, Abcam). DAB Staining Kit (DAB-0031, Maxim) was used according to the manufacturer’s instructions. Livers of mice were embedded in Tissue-Tek OCT cryostat molds (Leica) and frozen at −80°C. Ten-micrometer-thick sections of livers were generated in a cryostat. Tissue sections were stained in 0.5% Oil Red O and counterstained with H&E.
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8

Quantifying Adipocyte Morphology and UCP1 Expression

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Livers of mice were embedded in Tissue-Tek OCT cryostat molds (Leica) and frozen at −80°C. 10-μm thick sections of livers were generated in a cryostat. Tissue sections were stained in 0.5% Oil-Red-O and H&E (Sigma-Aldrich) according to the standard protocol. Adipose tissues were fixed in 4% paraformaldehyde overnight at 4°C immediately after sacrifice, embedded in paraffin, and cut to 7-μm sections on slides using a Leica RM2016 microtome. The slides were stained with H&E. Quantification of cross-sectional area of the adipocyte was performed with NIH ImageJ software. At least 30 fields from random sections of each mouse sample were quantified. For UCP1 immunohistochemistry (IHC), adipose tissue sections were rehydrated and then boiled in 10 mM citric acid buffer, pH 6.0, at 95°C for antigen retrieval. Immunohistochemistry was performed using the UltraSensitiveTM SP (Rabbit) IHC Kit (Maxim) according to the manufacturer’s instructions using rabbit UCP1 antibodies (ab10983; 1:500; Abcam). DAB Staining Kit (DAB-0031, Maxim) was used according to the manufacturer’s instructions for development.
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9

Kitagawia Fruit Anatomy Analysis

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Mature fruits of five Kitagawia species (K. baicalensis, K. komarovii, K. praeruptora, K. stepposa, and K. terebinthacea) were collected from the wild and preserved in formaldehyde–acetic acid–alcohol (FAA) for morphological examination. Fruit anatomy was evaluated by paraffin section. For each of the five species, the fruits of at least three individuals from the same population were examined. All fruits were treated following the method of Feder and O’Brien [103 (link)] for embedding in glycol methacrylate (GMA). A Leica RM2016 microtome was used to prepare transverse sections through the center of the mericarp, about 3–5 mm in thickness, and they were stained with toluidine blue. Sections were observed and photographed under an Olympus BX43 microscope. Morphological terminology followed Kljuykov et al. [104 (link)].
Fruit micromorphology was examined by scanning electron microscope (SEM). After dehydration using graded ethanol, all mature fruits were directly mounted on clean aluminum stubs with conducting carbon adhesive tabs, coated, and then scanned with a JSM-7500F scanning electron microscope. The micromorphological characteristics studied and micromorphological terminology follow the contributions of Ostroumova [23 (link),24 (link)].
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10

Hamster Lung Tissue Preparation

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Hamster lung tissues were fixed in 4% paraformaldehyde for 10 days and, due to BSL-3 laboratory protocols, remained in the laboratory for that duration. After fixation, tissues were put into a dehydration container inside a fume hood. The tissues were then dehydrated using a gradient alcohol regimen in a DIPATH Donatello dehydration machine, progressing from 75% alcohol to paraffin III. These tissues, now soaked in paraffin, were embedded using a Wuhan Junjie Electronics JB-P5 machine: Melted paraffin was poured into molds, tissues from the dehydration container were added, labels were attached, and samples were cooled at −20°C. After solidification, paraffin blocks were trimmed and then sectioned to 4 μm in thickness using a Leica RM2016 microtome. These sections were floated on a 40°C water bath in a KD-P slide warmer to smooth out, then collected on glass slides, and oven-dried at 60°C. For deparaffinization, sections underwent treatment with eco-friendly solutions from Seville Biotechnology, followed by absolute ethanol washes and a final rinse in distilled water. After this process, sections were primed for H&E staining or immunohistochemistry.
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