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Stains

Stains are substances used to color or mark biological specimens to enhance their visibility and facilitate analysis.
They can be used to identify specific cellular or molecular components, reveal tissue structures, or highlight areas of interest.
Stains may be derived from natural sources, such as plants or animals, or synthetic compounds.
Their application is crucial in various fields, including histology, cytology, and pathology, enabling researchers and clinicians to gain valuable insights into the structure and function of biological systems.
Stains can be applied to a wide range of specimens, including cells, tissues, and microorganisms, and their selection and optimization are crucial for achieving reproducible and informative results.
Experence the future of stain optimization today with PubCompare.ai's AI-driven tools for seamless stain comparison and optimization.

Most cited protocols related to «Stains»

Standard IHC protocol was followed to stain the tumor tissue samples using the mouse monoclonal antibody against hNIS (human Sodium Iodide Symporter) (Abcam, ab17795), ER (Estrogen Receptor) (Abcam, ab16660, ab288). Briefly, 5 µm sized paraffin embedded tissue sections were de-paraffinized with xylene and endogenous peroxidase activity was quenched with 3% H2O2 in methanol for 30 minutes in the dark. Tissue sections were dehydrated through graded alcohols and subjected to antigen retrieval using 10mM sodium citrate. Sections were washed with TBST (Tris Borate Saline Tween-20) and then blocked with 5% BSA (Bovine Serum Albumin) for one hour. Slides were incubated with the respective mouse monoclonal primary antibody diluted with TBS. Slides were then washed for 5 minutes in TBST and incubated for 1 hour with the respective HRP (Horse Raddish Peroxidase) conjugated anti-mouse secondary antibody diluted with TBS in a ratio of 1∶200. After washing, slides were incubated with DAB (3,3′-diaminobenzidine tetrahydrochloride) (Sigma) and immediately washed under tap water after color development. Slides were then counter stained with hematoxylin. Slides were mounted with DPX (dibutyl phthalate xylene) and were then observed under a light microscope (Carl Zeiss).
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Publication 2014
Antibodies, Anti-Idiotypic Antigens Borates Equus caballus estrogen receptor alpha, human Ethanol Homo sapiens Light Microscopy Methanol Monoclonal Antibodies Mus Neoplasms Paraffin Peroxidase Peroxide, Hydrogen Phthalate, Dibutyl Saline Solution Serum Albumin, Bovine SLC5A5 protein, human Sodium Citrate Stains Tissues Tromethamine Tween 20 Xylene
Four 9 month old male mice (C57Bl/SJL) were used. Animals were anesthetized with choral hydrate (15% aqueous solution, i.p.) and were perfused transcardially with 4% paraformaldehyde and 0.125% glutaraldehyde in phosphate buffer saline (PBS; pH 7.4). The brains were then carefully removed from the skull and postfixed for 6 hours. All procedures were conducted in accordance with the National Institute of Health Guide for the Care and Use of Laboratory Animals and were approved by the Mount Sinai School of Medicine Institutional Animal Care and Uses Committee.
For intracellular injections, brains were coronally sectioned at 200 µm on a Vibratome (Leica, Nussloch, Germany). The sections were then incubated in 4,6-diamidino-2-phenylindole (DAPI; Sigma, St. Louis, MO, USA), a fluorescent nucleic acid stain, for 5 minutes, mounted on nitrocellulose filter paper and immersed in PBS. Using DAPI as a staining guide, individual layer II/III pyramidal neurons of the frontal cortex were loaded with 5% Lucifer Yellow (Molecular Probes, Eugene, OR, USA) in distilled water under a DC current of 3–8 nA for 10 minutes, or until the dye had filled distal processes and no further loading was observed [45] (link), [49] (link). Tissue slices were then mounted and coverslipped in Permafluor. Dendritic segment and spine imaging was performed using a Zeiss 410 confocal laser scanning microscope (Zeiss, Thornwood, NY, USA) using a 488 nm excitation wavelength, using a 1.4 N.A. Plan-Apochromat 100× objective with a working distance of 170 µm and a 5× digital zoom. After gain and offset settings were optimized, segments were digitally imaged at 0.1 µm increments, along the optical axis. The confocal stacks were then deconvolved with AutoDeblur (MediaCybernetics, Bethesda, MD, USA).
Supporting Information is available online (Box S1)
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Publication 2008
Animals Animals, Laboratory Brain Buffers Cranium DAPI Dendrites Epistropheus Fingers Glutaral Lobe, Frontal lucifer yellow Males Mice, House Microscopy, Confocal Molecular Probes Nitrocellulose Nucleic Acids paraform Phosphates Protoplasm Pyramidal Cells Saline Solution Stains Tissues Vertebral Column Vision
Separate projects were created within QuPath for each biomarker, and the slide images imported to the corresponding projects. QuPath’s automated TMA dearrayer was applied in batch over all slides within each project to identify tissue cores. The resulting TMA grid was manually verified and amended where necessary, e.g. to adjust the locations of cores that were outside their expected position, or to remove cores where prominent artefacts were visible. Patient identifiers were then imported into QuPath for each core to assist alignment with survival data later. Additionally, stain vector (i.e. color) and background estimates were applied for each IHC analysis project to improve stain separation within QuPath using color deconvolution17 (link). This was achieved by selecting a representative area containing an area of background along with examples of strong hematoxylin and DAB staining, and applying QuPath’s Estimate stain vectors command to identify stain vectors within this region. The resulting vectors were then used for all images in the project.
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Publication 2017
Biological Markers Cloning Vectors Hematoxylin Patients Stains Tissues

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Publication 2013
Buffers Cells Clustered Regularly Interspaced Short Palindromic Repeats Cytokinesis Genes Genome Gold INDEL Mutation Oligonucleotide Primers polyacrylamide gels Stains Taq Polymerase Transfection
2500 cells per well were plated in 12-well plates (Greiner Bio One Cellstar, Frickenhauser - Germany) and were allowed to grow for about 4 to 5 days until small colonies could be clearly seen. Cells were treated for 48 hrs with different concentrations (2–100 nM) of staurosporine or UCN-01 (7-hydroxystaurosporine) in growth media. For each concentration datapoint of the two drugs, cells were analyzed in quadruplicates. Staurosporine was purchased as 1 mM ready-made solution in DMSO (Sigma Cat # S6942) and UCN-01 as powder (Sigma Cat # U6508). UCN-01 was diluted in DMSO according to the manufacturer's instructions. Cell culture plates containing colonies were gently washed with PBS and fixed with 3.7% formaldehyde for 10 minutes. Wells were rinsed once again with PBS and colonies were stained with 0.2% crystal violet solution in 10% ethanol for 10 minutes. Excess stain was removed by washing repeatedly with PBS. All the procedures were done at room temperature. The plates can be stored at room temperature or at +4 °C for several months without any visible fading of the dye.
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Publication 2014
7-hydroxystaurosporine Cell Culture Techniques Cells Culture Media Ethanol Formaldehyde Pharmaceutical Preparations Powder Stains Staurosporine Sulfoxide, Dimethyl UCN 01 Violet, Gentian Vision

Most recents protocols related to «Stains»

Example 1

The ability of eyedrops to deliver Penl-XBIR3 in mice and rats was tested. Results are presented in FIG. 2 and FIG. 3.

In mice, Penl-XBIR3 (10 μg) eyedrops were applied, then the animals were sacrificed at the indicated times. In rabbits, 200 μg Penl-XBIR3 eyedrops or a saline vehicle were administered BID for 4.5 days. The final dose given 5 h prior to harvest of retinas. Plasma from rabbits obtained at baseline and harvest.

Retinal lysates were immunoprecipitated with XIAP, followed by western blotting for anti-His. XBIR3 contains a His tag, so uptake of XBIR3 is detectable using anti-His. Blots for the mouse and rabbit samples, along with graphs quantifying the results, are presented in FIG. 2. XBIT3 uptake was observed in both mouse and rabbit samples. Uptake in the mouse samples was detected by 1 h and maintained through 24 h. In rabbit there was significant XBIR3 in retina at 5d.

Baseline and post-treatment plasma from rabbits was analyzed by immunoprecipitation with XIAP followed by western blot with anti-His. A Ponceau protein stain was used to show input protein amounts. XBIR3 was not detected in rabbit plasma (FIG. 3), indicating that it remains localized in the eye.

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Patent 2024
Animals Eye Drops Immunoprecipitation Mice, House Oryctolagus cuniculus Plasma Proteins Rabbits Rattus Retina Saline Solution Stains Western Blotting

Example 2

Antimicrobial activity of the compositions according to the invention has been compared with compositions comprising either only the modified clay particle comprising an antimicrobial compound (‘CPC’, prepared as in Ex. 1), or only a nonionic triblock copolymer (‘pluronic’). Salivary flora and actives (according to Table 1 below) were co-incubated overnight and at the end of incubation biofilm was stained with crystal violet. Detailed protocol as mentioned below:

Treatment and Biofilm Formation

Early morning saliva samples before brushing was collected from 4-5 people, pooled together and washed twice in saline. Absorbance was set to 0.2 OD620 nm in ultra-filtered tryptone yeast extract broth (2% sucrose) and used for experiments as mentioned in further steps. 2 ml of set culture was added into 24/12 well plate to which test actives at varying concentrations were added into each of the wells. The plate was incubated anaerobically overnight at 37° C.

Staining Protocol

At the end overnight incubation, decant the plate out over a biohazard bag to remove all the planktonic bacteria. Rinse the plate in a tray of water and decant the water out over the tray. This step was done once to remove the loosely adhered biofilm. Place the plate on a blotting paper/paper towel over the bench top. Stain all the test wells with 1 ml of 1% Crystal violet stain (CV) for 10 min. This step was done using a pipette. Decant the plate out over the biohazard discard bag to remove all the stain. Rinse the plate in a tray of water and pour the water out over the tray. This step was done thrice consecutively, in three separate trays of water. (Each tray procedure was repeated thrice-total 9 rinse). Cover the bench top with more blotting paper/paper towel and hit the plate against the bench top until all the wells are free of any liquid. This step was done to ensure that only CV remaining is bound to a biofilm at the bottom of a well. Leave the plate face up on the bench top at room temperature (23+2° C.) until it dries completely. Add 1 ml of 33% glacial acetic acid to the test wells to solubilize the biofilm bound CV stain. Allow the acetic acid to sit for 10 mins. Pipette up and down the mix of acetic acid and CV in the wells.

Transfer 10 μl of above solution mix to 90 ul of 33% acetic acid in a well of flat bottom 96 well plate. Mix the solution well and absorbance is taken at 540 nm. All the test actives were done in duplicates.

TABLE 1
% Biofilm
Bacterial control100
0.01% CPC-Clay 83
0.001% Pluronic 76
0.001% Pluronic + 0.01% CPC-Clay 29
0.001% Pluronic + 0.005% CPC-Clay 52

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Patent 2024
Acetic Acid Bacteria Biofilms Biohazards Clay Desiccation Face Microbicides Plankton Pluronics Saline Solution Saliva Stains Strains Sucrose Violet, Gentian Yeast, Dried

Example 4

HEK293-hAQP4-GFP and LPS-stimulated RAW264.7 were co-cultured with CD4 antibody, commercial AQP4 antibody, A002 antibody (ten-fold serial dilution) or culture medium only at 37° C. and 5% CO 2 for 6 hours. Cells were stain with Fixable Far Red-labeled anti-amine, PE-labeled anti-mouse CD11 b then analyzed the % of amine in CD11b-/GFP+ cells. Cell death(%) increased in ADCC=(% cell death in presence of IgG-% cell death in absence of IgG)/(% Cell death in maximum lysis-% cell death in absence of IgG)×100. Antibody-dependent cell-mediated cytotoxicity Assay (ADCC) of A002 antibody by immunofluorescent stain. HEK293-hAQP4-GFP and LPS-stimulated RAW264.7 were co-cultured with CD4 antibody, commercial AQP4 antibody, A002 antibody (ten-fold serial dilution) or culture medium only at 37° C. and 5% CO2 for 6 hours. Then cells were stain with Propidium Iodide (PI). Histograms show quantification of Propidium Iodide (PI) of cells co-cultured with CD4 antibody, commercial AQP4 antibody or A002 antibody (ten-fold serial dilution) (FIG. 9). PI intensity was adjusted by Subtracting PI intensity of cells co-cultured with culture medium only.

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Patent 2024
Amines Biological Assay Cell Death Cells Cytotoxicities, Antibody-Dependent Cell Fluorescent Antibody Technique Immunoglobulins ITGAM protein, human Mus Propidium Iodide Stains Technique, Dilution
Not available on PMC !

Example 11

Serum stability of DsiRNA agents is assessed via incubation of DsiRNA agents in 50% fetal bovine serum for various periods of time (up to 24 h) at 37° C. Serum is extracted and the nucleic acids are separated on a 20% non-denaturing PAGE and can be visualized with Gelstar stain. Relative levels of protection from nuclease degradation are assessed for DsiRNAs (optionally with and without modifications).

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Patent 2024
Fetal Bovine Serum Native Polyacrylamide Gel Electrophoresis Nucleic Acids Serum Stains
Not available on PMC !

Example 5

Purified wild type and mutant polymerases in a heparin elution buffer was mixed with 1×SYPRO Orange Protein Gel Stain and run on a CFX384 thermocycler. The thermal melt data was analyzed using a CFX Maestro software (from Bio-Rad). Thermal melt data (™) for wild type and mutant polymerases having backbone sequences RLF 89458.1, NOZ 58130 or WP 175059460.1 were conducted.

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Patent 2024
Biological Assay Buffers Heparin Proteins Stains Vertebral Column

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DAPI is a fluorescent dye that binds strongly to adenine-thymine (A-T) rich regions in DNA. It is commonly used as a nuclear counterstain in fluorescence microscopy to visualize and locate cell nuclei.
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DAPI is a fluorescent dye used in microscopy and flow cytometry to stain cell nuclei. It binds strongly to the minor groove of double-stranded DNA, emitting blue fluorescence when excited by ultraviolet light.
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SYBR Safe DNA gel stain is a nucleic acid stain used for the detection and visualization of DNA in agarose gels. It is a sensitive and environmentally friendly alternative to traditional DNA stains.
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Hoechst 33342 is a fluorescent dye that binds to DNA. It is commonly used in various applications, such as cell staining and flow cytometry, to identify and analyze cell populations.
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Triton X-100 is a non-ionic surfactant commonly used in various laboratory applications. It functions as a detergent and solubilizing agent, facilitating the solubilization and extraction of proteins and other biomolecules from biological samples.
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The LIVE/DEAD Fixable Aqua Dead Cell Stain Kit is a fluorescent dye-based solution that allows for the identification of dead cells in a sample. The dye penetrates the compromised membranes of dead cells and binds to cellular proteins, providing a clear distinction between live and dead cells.
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Fetal Bovine Serum (FBS) is a cell culture supplement derived from the blood of bovine fetuses. FBS provides a source of proteins, growth factors, and other components that support the growth and maintenance of various cell types in in vitro cell culture applications.
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Bovine serum albumin (BSA) is a common laboratory reagent derived from bovine blood plasma. It is a protein that serves as a stabilizer and blocking agent in various biochemical and immunological applications. BSA is widely used to maintain the activity and solubility of enzymes, proteins, and other biomolecules in experimental settings.

More about "Stains"

Staining techniques are essential tools in various fields, including histology, cytology, and pathology, enabling researchers and clinicians to gain valuable insights into the structure and function of biological systems.
These techniques involve the use of specialized substances known as stains, which are used to color or mark biological specimens to enhance their visibility and facilitate analysis.
Stains can be derived from natural sources, such as plants or animals, or synthetic compounds, and their application is crucial for achieving reproducible and informative results.
Commonly used stains include DAPI, which is a fluorescent stain that binds to DNA and is often used to visualize cell nuclei, and SYBR Safe DNA gel stain, which is a sensitive and safe alternative to traditional DNA staining methods.
Another popular stain is Hoechst 33342, which is a cell-permeant nuclear counterstain that can be used to identify and quantify viable cells.
Flow cytometry instruments, such as the LSRFortessa and FACSCanto II, are often used in conjunction with these stains to analyze and sort cells based on their physical and fluorescent properties.
In addition to stains, other reagents and techniques are commonly used in biological research, including the detergent Triton X-100, which is used to permeabilize cell membranes, and the LIVE/DEAD Fixable Aqua Dead Cell Stain Kit, which is used to identify and exclude dead cells from analysis.
Serum supplements, such as fetal bovine serum (FBS) and bovine serum albumin (BSA), are also frequently used in cell culture and other biological applications to provide essential nutrients and support cell growth and viability.
Experence the future of stain optimization today with PubCompare.ai's AI-driven tools for seamless stain comparison and optimization.