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Thionin

Manufactured by Merck Group
Sourced in United States, Australia

Thionin is a staining dye commonly used in biological and medical applications. It is a metachromatic dye that can bind to nucleic acids, allowing for the visualization of cellular structures under a microscope. Thionin is a simple, cost-effective staining solution that can be used in a variety of laboratory settings.

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33 protocols using thionin

1

Hippocampal Morphometric Analysis Protocol

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Brain sections were mounted on slides and dried overnight under vacuum. Slides were washed (2×10 min) in KPBS, and then fixed for 20 min in 4% (w/v) PFA. They were then dehydrated according to the following sequence: H2O, 50% (v/v) EtOH, 70% (v/v) EtOH, twice in 95% (v/v) EtOH, and thrice in 100% (v/v) EtOH; each dip carried out for 3 min), transferred next into xylene for 5, 30 and 2 min, and finally rehydrated using the reverse-order sequence (thrice in 100% (v/v) EtOH, twice in 95% (v/v) EtOH, and then 70% (v/v) EtOH, 50% (v/v) EtOH and H2O; 2 min for each dip). Slides were next dipped 20 times in 0.25% thionin (Sigma-Aldrich). Mounted brain slides were dehydrated again (20 dips in each of H2O, 50% (v/v) EtOH, and 70% (v/v) EtOH, and then 2 and 3 cycles of 3-min dips in 95% (v/v) and 100% (v/v) EtOH, respectively, and finally, 2 cycles of 3-min dips in xylene) before overlaying with coverslips in DPX mounting medium (Electron Microscopy Sciences).
For stereological analysis, 3 sections (−1.46, −2.06, and −2.46 mm from the bregma) were analyzed using the Stereo Investigator software. For each section, the cornu ammonis 1 through 3 (CA1/CA2, CA3) areas and the dentate gyrus area were defined and expressed as ratio of total hippocampus area for both hemispheres. Photographs were obtained with a Nikon C80i microscope equipped with a QImaging® color camera.
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2

Immunohistochemical Analysis of Neural Markers

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Animals were perfused within 2 weeks of recording with 10% buffered formalin (Fisher Scientific, Pittsburgh PA) and brains were transferred to a solution of 20% sucrose and PBS containing 0.02% sodium azide overnight, then sliced into four series of 40 μm sections using a freezing microtome. For characterizing lesions, sections were stained with 0.1% Thionin (Sigma, St Louis MO). We stained for YFP or mCherry by incubating tissue in primary polyclonal anti-GFP 1:20,000 (Invitrogen) or rabbit anti-mCherry (1:10,000; Clontech) for 24 h, followed by 1 h incubation in biotinylated secondary antiserum in PBST (Vector Laboratories). We stained for c-Fos by incubating tissue in primary cFos (1:20,000 Ab-5, PC38, rabbit polyclonal, Calbiochem, Billerica, MA) for 48 h, followed by 1 h incubation in biotinylated secondary antiserum in PBST (Vector Laboratories).
After washing with PBS, tissue was incubated with an avidin-biotin-horseradish peroxidase conjugate (Vector laboratories) and stained brown (YFP) with 0.05% 3,3-diaminobenzidine tetrahydrochloride (Sigma, St. Louis MO) and 0.02% H2O2, or black (c-Fos) with the addition of 0.05% cobalt chloride and 0.01% nickel ammonium sulfate for double-stained sections showing the presence of both YFP and c-Fos.
Sections were then mounted onto slides, dehydrated, and coverslipped.
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3

Nissl Staining for Anatomical Overview

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For anatomical overview, one series per brain was Nissl stained. After cryo-sectioning, the sections were mounted directly on SuperFrost Plus glass adhesion slides (Epredia), dried for 30 min, and kept at −20°C until staining. Sections were stained with 0.125% Thionin (Sigma-Aldrich, cat. no. 861340, USA) for 60 s, dehydrated in a graded series of ethanol solutions (1 min in 70%; 2 min in 96%; 2 × 5 min in 99%), and cleared for 5 + 10 min in xylene. Coverslips (24 × 50 mm, #0, Menzel-Gläser, Hounisen) were mounted with Eukitt® Quick-hardening mounting medium (CAS. 25608-33-7, Sigma-Aldrich, Steinheim, DE).
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4

Perfusion and Tissue Processing for Brain Analysis

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After all recordings were completed, animals were anesthetized with 7% chloral hydrate (i.p. 500 mg/kg; Sigma, St. Louis, MO) and perfused with 10% buffered formalin (Fisher Scientific, Pittsburgh, PA) intracardially. Brains were removed and moved to 20% sucrose and phosphate-buffered saline (PBS) with 0.02% sodium azide overnight. Brains were sliced into 4 series of 40-μm sections using a freezing microtome, and these sections were stored in PBS–0.02% sodium azide at 20 °C. Tissue was washed with PBS, mounted onto slides, and stained with 0.1% thionin (Sigma). Slides were dehydrated, placed in xylene, cover-slipped, and imaged. All images were processed using the programs GIMP and Inkscape.
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5

Visualizing Neuroanatomical Infusion Sites

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At the end of each experiment, rats were deeply anesthetized (90 mg/kg sodium pentobarbital, i.p.) and infused with thionin (1%; Sigma-Aldrich) into the BLA at the same volume and rate used for experimental drug infusion to subsequently visualize the location of the injector tip. The injectors remained in place for 2 min following the infusion. Animals were euthanized and brains were stored in 4% paraformaldehyde overnight and then transferred to 30% sucrose. The brains were sliced in 50 µm coronal sections using a cryostat at approximately −16°C. Every fourth slice was mounted on a microscope slide. Verification of infusion site was based on Paxinos and Watson [30] , and the location was plotted on the coronal plate that most closely corresponded to its anterior–posterior position.
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6

Quantifying Brain Infarct Volume

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thionin staining was used to measure infarct volume. thionin stains Nissl substances in soma and dendrites, where neuronal bodies stain dark blue, neuropil stains purple, whilst the infarcted tissue does not retain stain and appears white22 (link). Brain tissue sections (30 µm thick) were stained with 0.1% thionin (Sigma, Australia, diluted in acetic acid, Ajax Chemicals, Australia), for 2 min, rinsed in dH2O water for 5 s, placed in 70% and 100% ethanol for 2 min each, and then coverslipped with xylene (Merck, Australia) and distyrene plasticiser (DPX; Merck, Australia).
The sections were then photographed using a charge coupled device (CCD) camera (Cohu Inc., San Diego, CA, USA) mounted above a lightbox (Biotec-Fischer Colour Control 5000, Reishkirchin, Germany) using IS capture imaging software. Infarct volume was analysed using image analysis software (Image J, version 1.52a, NIH, Bethesda, MD, USA, available at https://imagej.nih.gov/ij/download.html). The area of infarct for each section was measured and the sum of the total infarct area for all the stained sections was multiplied by the distance between the sections to give an approximation of the total infarct volume. Edema was corrected for using the following formula: Corrected infarct area = [left hemisphere area – (right hemisphere area – right hemisphere infarct area)]23 (link).
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7

Visualization and Quantification of ARC Neurons

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The ARC lesion was confirmed by ARC cell nuclei counting after thionin staining and by estimations of the number of specific neuronal populations known to be located within this nucleus including NPY, dopamine or POMC-producing neurons that were identified after immunostaining against NPY, tyrosine hydroxylase (TH) or adrenocorticotropic hormone (ACTH), respectively. In order to visualize cell nuclei, brain sections were stained with thionin (Sigma, cat# T7029), dehydrated in an ascending alcohol series, cleared in xylene and coverslipped. In order to perform IHC, brain sections were pretreated with 0.5% H2O2, treated with blocking solution and incubated with the primary antibody (anti-NPY Abcam, cat# ab30914, 1:10,000; anti-TH, Santa Cruz (H-196), cat# sc-14007, 1:20,000; and, anti-ACTH, generated in rabbit by our laboratory, 1:3,000) overnight at room temperature. Then, sections were treated with biotinylated anti-rabbit antibody, with Vectastain Elite ABC kit and DAB/Nickel solution, as described above. Sections were sequentially mounted and cover slipped with mounting media.
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8

Visualizing ARC Lesions via Thionin and NPY Staining

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The ARC lesion was confirmed by ARC cell nuclei counting after thionin staining and NPY immunostaining, as described elsewhere (Cabral et al., 2014 (link)). In order to visualize cell nuclei, brain sections were stained with thionin (Sigma, cat. T7029). In order to perform NPY immunostaining, brain sections were incubated with anti-NPY antibody (Abcam, cat. ab30914, 1:10,000). Then, immunoreactive signal was visualized using the chromogenic staining described above.
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9

Hippocampal Subfield Volume and Astrocyte Analysis

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One hour after the S-ketamine injection, the animals were deeply anesthetized with an intraperitoneal injection of pentobarbital sodium/lidocaine (Unikem A/S, Copenhagen, Denmark) and perfused transcardially with heparinized (10 U/ml) 0.9% saline (pH=7.3) for 4 min, followed by ice cold 4% paraformaldehyde (pH=7.2–7.4) for 6 min. Following a random selection of the right or left hemisphere of the brains, the brains were embedded in 5% agar and were cut in 60-μm thick coronal sections on a vibratome 1200 S (Leica VT 1200 S vibrating blade microtome). The first section of each series was randomly chosen by using a random table.
Two sets of sections were selected based on a systematic sampling principle, and a section sampling fraction of 1/10. One set of sections was Nissl stained with a 0.25% thionin solution (thionin, Sigma T3387) and used for quantifying the hippocampal subfields volume. The second set of sections was stained for glial fibrillary acidic protein (GFAP), quantifying the size of GFAP positive astrocytes in the hippocampal subfields.
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10

Nissl Staining and Cell Quantification

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Nissl staining was performed according to our previously described method [21 (link)]. Briefly, brain tissue sections were stained with thionin (Sigma-Aldrich), dehydrated in alcohol, cleared in xylene, and then sealed with coverslips to allow the perihematomal brain tissues to be observed. For the quantification of the Nissl staining results, the number of cells in each standardized microscope field was analyzed independently by three researchers using ImageJ (version 1.46J). The average value of three regions of interest was used as the final value.
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