Staining is a technique used to enhance contrast in samples, generally at the
microscopic
The microscopic scale () is the scale of objects and events smaller than those that can easily be seen by the naked eye, requiring a lens or microscope to see them clearly. In physics, the microscopic scale is sometimes regarded as the scale betwe ...
level.
Stain
A stain is a discoloration that can be clearly distinguished from the surface, material, or medium it is found upon. They are caused by the chemical or physical interaction of two dissimilar materials. Accidental staining may make materials app ...
s and
dye
Juan de Guillebon, better known by his stage name DyE, is a French musician. He is known for the music video of the single "Fantasy
Fantasy is a genre of speculative fiction that involves supernatural or Magic (supernatural), magical ele ...
s are frequently used in
histology
Histology,
also known as microscopic anatomy or microanatomy, is the branch of biology that studies the microscopic anatomy of biological tissue (biology), tissues. Histology is the microscopic counterpart to gross anatomy, which looks at large ...
(microscopic study of biological
tissues), in
cytology
Cell biology (also cellular biology or cytology) is a branch of biology that studies the structure, function, and behavior of cells. All living organisms are made of cells. A cell is the basic unit of life that is responsible for the living an ...
(microscopic study of
cells), and in the
medical
Medicine is the science and Praxis (process), practice of caring for patients, managing the Medical diagnosis, diagnosis, prognosis, Preventive medicine, prevention, therapy, treatment, Palliative care, palliation of their injury or disease, ...
fields of
histopathology
Histopathology (compound of three Greek words: 'tissue', 'suffering', and '' -logia'' 'study of') is the microscopic examination of tissue in order to study the manifestations of disease. Specifically, in clinical medicine, histopatholog ...
,
hematology
Hematology (American and British English spelling differences#ae and oe, spelled haematology in British English) is the branch of medicine concerned with the study of the cause, prognosis, treatment, and prevention of diseases related to bloo ...
, and
cytopathology
Cytopathology (from Greek , ''kytos'', "a hollow"; , ''pathos'', "fate, harm"; and , ''-logia'') is a branch of pathology that studies and diagnoses diseases on the cellular level. The discipline was founded by George Nicolas Papanicolaou in ...
that focus on the study and
diagnoses of
disease
A disease is a particular abnormal condition that adversely affects the structure or function (biology), function of all or part of an organism and is not immediately due to any external injury. Diseases are often known to be medical condi ...
s at the microscopic level. Stains may be used to define
biological tissues (highlighting, for example,
muscle fiber
A muscle cell, also known as a myocyte, is a mature contractile cell in the muscle of an animal. In humans and other vertebrates there are three types: skeletal, smooth, and cardiac (cardiomyocytes). A skeletal muscle cell is long and threadl ...
s or
connective tissue
Connective tissue is one of the four primary types of animal tissue, a group of cells that are similar in structure, along with epithelial tissue, muscle tissue, and nervous tissue. It develops mostly from the mesenchyme, derived from the mesod ...
),
cell populations (classifying different
blood cell
A blood cell (also called a hematopoietic cell, hemocyte, or hematocyte) is a cell produced through hematopoiesis and found mainly in the blood. Major types of blood cells include red blood cells (erythrocytes), white blood cells (leukocytes), ...
s), or
organelle
In cell biology, an organelle is a specialized subunit, usually within a cell (biology), cell, that has a specific function. The name ''organelle'' comes from the idea that these structures are parts of cells, as Organ (anatomy), organs are to th ...
s within individual cells.
In
biochemistry
Biochemistry, or biological chemistry, is the study of chemical processes within and relating to living organisms. A sub-discipline of both chemistry and biology, biochemistry may be divided into three fields: structural biology, enzymology, a ...
, it involves adding a class-specific (
DNA
Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
,
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
s,
lipid
Lipids are a broad group of organic compounds which include fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The functions of lipids include storing ...
s,
carbohydrate
A carbohydrate () is a biomolecule composed of carbon (C), hydrogen (H), and oxygen (O) atoms. The typical hydrogen-to-oxygen atomic ratio is 2:1, analogous to that of water, and is represented by the empirical formula (where ''m'' and ''n'' ...
s) dye to a substrate to qualify or quantify the presence of a specific compound. Staining and
fluorescent tag
In molecular biology and biotechnology, a fluorescent tag, also known as a fluorescent label or fluorescent probe, is a molecule that is attached chemically to aid in the detection of a biomolecule such as a protein, antibody, or amino acid. Gener ...
ging can serve similar purposes. Biological staining is also used to mark cells in
flow cytometry
Flow cytometry (FC) is a technique used to detect and measure the physical and chemical characteristics of a population of cells or particles.
In this process, a sample containing cells or particles is suspended in a fluid and injected into the ...
, and to flag
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
s or
nucleic acid
Nucleic acids are large biomolecules that are crucial in all cells and viruses. They are composed of nucleotides, which are the monomer components: a pentose, 5-carbon sugar, a phosphate group and a nitrogenous base. The two main classes of nuclei ...
s in
gel electrophoresis
Gel electrophoresis is an electrophoresis method for separation and analysis of biomacromolecules (DNA, RNA, proteins, etc.) and their fragments, based on their size and charge through a gel. It is used in clinical chemistry to separate ...
. Light microscopes are used for viewing stained samples at high magnification, typically using bright-field or epi-fluorescence illumination.
Staining is not limited to only biological materials, since it can also be used to study the structure of other materials; for example, the
lamellar structures of
semi-crystalline polymers or the domain structures of
block copolymer
In polymer chemistry, a copolymer is a polymer derived from more than one species of monomer. The polymerization of monomers into copolymers is called copolymerization. Copolymers obtained from the copolymerization of two monomer species are som ...
s.
''In vivo'' vs ''In vitro''
''
In vivo
Studies that are ''in vivo'' (Latin for "within the living"; often not italicized in English) are those in which the effects of various biological entities are tested on whole, living organisms or cells, usually animals, including humans, an ...
staining'' (also called
vital staining
A vital stain in a casual usage may mean a stain that can be applied on living cells without killing them. Vital stains have been useful for diagnostic and surgical techniques in a variety of medical specialties. In supravital staining, living cell ...
or intravital staining) is the process of dyeing living tissues. By causing certain cells or structures to take on contrasting colours, their form (
morphology
Morphology, from the Greek and meaning "study of shape", may refer to:
Disciplines
*Morphology (archaeology), study of the shapes or forms of artifacts
*Morphology (astronomy), study of the shape of astronomical objects such as nebulae, galaxies, ...
) or position within a cell or tissue can be readily seen and studied. The usual purpose is to reveal cytological details that might otherwise not be apparent; however, staining can also reveal where certain chemicals or specific chemical reactions are taking place within cells or tissues.
''
In vitro
''In vitro'' (meaning ''in glass'', or ''in the glass'') Research, studies are performed with Cell (biology), cells or biological molecules outside their normal biological context. Colloquially called "test-tube experiments", these studies in ...
'' staining involves colouring cells or structures that have been removed from their biological context. Certain stains are often combined to reveal more details and features than a single stain alone. Combined with specific protocols for
fixation and sample preparation, scientists and physicians can use these standard techniques as consistent, repeatable diagnostic tools. A
counterstain is stain that makes cells or structures more visible, when not completely visible with the principal stain.
* Crystal violet stains both Gram positive and Gram negative organisms. Treatment with alcohol removes the crystal violet colour from gram negative organisms only.
Safranin
Safranin (Safranin O or basic red 2) is a biological stain used in histology and cytology. Safranin is used as a counterstain in some staining protocols, colouring cell nuclei red. This is the classic counterstain in both Gram stains and endo ...
as counterstain is used to colour the gram negative organisms that got decolorised by alcohol.
While ex vivo, many cells continue to live and metabolize until they are "fixed". Some staining methods are based on this property. Those stains excluded by the living cells but taken up by the already dead cells are called
vital stains (e.g.
trypan blue or
propidium iodide
Propidium iodide (or PI) is a Fluorescence#Biochemistry and medicine, fluorescent intercalating agent that can be used to Staining (biology), stain cell (biology), cells and nucleic acids. PI binds to DNA by intercalating between the bases with li ...
for eukaryotic cells). Those that enter and stain living cells are called
supravital stains (e.g.
New Methylene Blue and
brilliant cresyl blue for
reticulocyte staining). However, these stains are eventually toxic to the organism, some more so than others. Partly due to their toxic interaction inside a living cell, when supravital stains enter a living cell, they might produce a characteristic pattern of staining different from the staining of an already fixed cell (e.g. "reticulocyte" look versus diffuse "polychromasia"). To achieve desired effects, the stains are used in very dilute solutions ranging from to (Howey, 2000). Note that many stains may be used in both living and fixed cells.
Preparation
The preparatory steps involved depend on the type of analysis planned. Some or all of the following procedures may be required.
Wet mounts are used to view live organisms and can be made using water and certain stains. The liquid is added to the slide before the addition of the organism and a coverslip is placed over the specimen in the water and stain to help contain it within the
field of view
The field of view (FOV) is the angle, angular extent of the observable world that is visual perception, seen at any given moment. In the case of optical instruments or sensors, it is a solid angle through which a detector is sensitive to elec ...
.
Fixation, which may itself consist of several steps, aims to preserve the shape of the cells or tissue involved as much as possible. Sometimes
heat fixation is used to kill, adhere, and alter the specimen so it accepts stains. Most chemical fixatives (chemicals causing fixation) generate
chemical bond
A chemical bond is the association of atoms or ions to form molecules, crystals, and other structures. The bond may result from the electrostatic force between oppositely charged ions as in ionic bonds or through the sharing of electrons a ...
s between
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
s and other substances within the sample, increasing their rigidity. Common fixatives include
formaldehyde
Formaldehyde ( , ) (systematic name methanal) is an organic compound with the chemical formula and structure , more precisely . The compound is a pungent, colourless gas that polymerises spontaneously into paraformaldehyde. It is stored as ...
,
ethanol
Ethanol (also called ethyl alcohol, grain alcohol, drinking alcohol, or simply alcohol) is an organic compound with the chemical formula . It is an Alcohol (chemistry), alcohol, with its formula also written as , or EtOH, where Et is the ps ...
,
methanol
Methanol (also called methyl alcohol and wood spirit, amongst other names) is an organic chemical compound and the simplest aliphatic Alcohol (chemistry), alcohol, with the chemical formula (a methyl group linked to a hydroxyl group, often ab ...
, and/or
picric acid
Picric acid is an organic compound with the formula (O2N)3C6H2OH. Its IUPAC name is 2,4,6-trinitrophenol (TNP). The name "picric" comes from (''pikros''), meaning "bitter", due to its bitter taste. It is one of the most acidic phenols. Like ot ...
. Pieces of tissue may be embedded in
paraffin wax
Paraffin wax (or petroleum wax) is a soft colorless solid derived from petroleum, coal, or oil shale that consists of a mixture of hydrocarbon molecules containing between 20 and 40 carbon atoms. It is solid at room temperature and melting poi ...
to increase their mechanical strength and stability and to make them easier to cut into thin slices.
Mordant
A mordant or dye fixative is a substance used to set (i.e., bind) dyes on fabrics. It does this by forming a coordination complex with the dye, which then attaches to the fabric (or tissue). It may be used for dyeing fabrics or for intensifying ...
s are chemical agents which have power of making dyes to stain materials which otherwise are unstainable
Mordants are classified into two categories:
a) Basic mordant: React with acidic dyes e.g. alum, ferrous sulfate, cetylpyridinium chloride etc.
b) Acidic mordant : React with basic dyes e.g. picric acid, tannic acid etc.
Direct Staining: Carried out without mordant.
Indirect Staining: Staining with the aid of a mordant.
Permeabilization involves treatment of cells with (usually) a mild
surfactant
Surfactants are chemical compounds that decrease the surface tension or interfacial tension between two liquids, a liquid and a gas, or a liquid and a solid. The word ''surfactant'' is a Blend word, blend of "surface-active agent",
coined in ...
. This treatment dissolves
cell membrane
The cell membrane (also known as the plasma membrane or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane that separates and protects the interior of a cell from the outside environment (the extr ...
s, and allows larger dye molecules into the cell's interior.
Mounting usually involves attaching the samples to a glass microscope slide for observation and analysis. In some cases, cells may be grown directly on a slide. For samples of loose cells (as with a blood smear or a
pap smear
The Papanicolaou test (abbreviated as Pap test, also known as Pap smear (AE), cervical smear (BE), cervical screening (BE), or smear test (BE)) is a method of cervical screening used to detect potentially precancerous and cancerous processes in ...
) the sample can be directly applied to a slide. For larger pieces of tissue, thin sections (slices) are made using a
microtome
A microtome (from the Greek ''mikros'', meaning "small", and ''temnein'', meaning "to cut") is a cutting tool used to produce extremely thin slices of material known as ''sections'', with the process being termed microsectioning. Important in sc ...
; these slices can then be mounted and inspected.
Standardization
Most of the dyes commonly used in microscopy are available as BSC-certified stains. This means that samples of the manufacturer's batch have been tested by an independent body, the
Biological Stain Commission (BSC), and found to meet or exceed certain standards of purity, dye content and performance in staining techniques ensuring more accurately performed experiments and more reliable results. These standards are published in the commission's journal
Biotechnic & Histochemistry. Many dyes are inconsistent in composition from one supplier to another. The use of BSC-certified stains eliminates a source of unexpected results.
Some vendors sell stains "certified" by themselves rather than by the Biological Stain Commission. Such products may or may not be suitable for diagnostic and other applications.
Negative staining

A simple staining method for bacteria that is usually successful, even when the
positive staining methods fail, is to use a
negative stain In microscopy, negative staining is an established method, often used in diagnostic microscopy, for contrasting a thin specimen with an optically opaque fluid. In this technique, the background is stained, leaving the actual specimen untouched, ...
. This can be achieved by smearing the sample onto the slide and then applying
nigrosin (a black synthetic dye) or
India ink
India ink (British English: Indian ink; also Chinese ink) is a simple black or coloured ink once widely used for writing and printing and now more commonly used for drawing and outlining, especially when inking comic books and comic strips. In ...
(an aqueous suspension of carbon particles). After drying, the microorganisms may be viewed in bright field microscopy as lighter inclusions well-contrasted against the dark environment surrounding them. Negative staining is able to stain the background instead of the organisms because the cell wall of microorganisms typically has a negative charge which repels the negatively charged stain. The dyes used in negative staining are acidic.
Note: negative staining is a mild technique that may not destroy the microorganisms, and is therefore unsuitable for studying pathogens.
Positive staining
Unlike negative staining, positive staining uses basic dyes to color the specimen against a bright background. While
chromophore
A chromophore is the part of a molecule responsible for its color. The word is derived .
The color that is seen by our eyes is that of the light not Absorption (electromagnetic radiation), absorbed by the reflecting object within a certain wavele ...
is used for both negative and positive staining alike, the type of chromophore used in this technique is a positively charged ion instead of a negative one. The negatively charged cell wall of many microorganisms attracts the positively charged chromophore which causes the specimen to absorb the stain giving it the color of the stain being used. Positive staining is more commonly used than negative staining in microbiology. The different types of positive staining are listed below.
Simple versus differential
Simple Staining is a technique that only uses one type of stain on a slide at a time. Because only one stain is being used, the specimens (for positive stains) or background (for negative stains) will be one color. Therefore, simple stains are typically used for viewing only one organism per slide. Differential staining uses multiple stains per slide. Based on the stains being used, organisms with different properties will appear different colors allowing for categorization of multiple specimens. Differential staining can also be used to color different organelles within one organism which can be seen in
endospore staining.
Types
Techniques
Gram
Gram staining
Gram stain (Gram staining or Gram's method), is a method of staining used to classify bacterial species into two large groups: gram-positive bacteria and gram-negative bacteria. It may also be used to diagnose a fungal infection. The name comes ...
is used to determine gram status to classifying bacteria broadly based on the composition of their
cell wall
A cell wall is a structural layer that surrounds some Cell type, cell types, found immediately outside the cell membrane. It can be tough, flexible, and sometimes rigid. Primarily, it provides the cell with structural support, shape, protection, ...
. Gram staining uses
crystal violet
Crystal violet or gentian violet, also known as methyl violet 10B or hexamethyl pararosaniline chloride, is a triphenylmethane, triarylmethane dye used as a histological stain and in Gram staining, Gram's method of classifying bacteria. Crystal ...
to stain cell walls,
iodine
Iodine is a chemical element; it has symbol I and atomic number 53. The heaviest of the stable halogens, it exists at standard conditions as a semi-lustrous, non-metallic solid that melts to form a deep violet liquid at , and boils to a vi ...
(as a mordant), and a
fuchsin
Fuchsine (sometimes spelled fuchsin) or rosaniline hydrochloride is a magenta dye with chemical formula C20H19N3·HCl. or
safranin
Safranin (Safranin O or basic red 2) is a biological stain used in histology and cytology. Safranin is used as a counterstain in some staining protocols, colouring cell nuclei red. This is the classic counterstain in both Gram stains and endo ...
counterstain to (mark all bacteria). Gram status, helps divide specimens of bacteria into two groups, generally representative of their underlying phylogeny. This characteristic, in combination with other techniques makes it a useful tool in clinical microbiology laboratories, where it can be important in early selection of appropriate
antibiotic
An antibiotic is a type of antimicrobial substance active against bacteria. It is the most important type of antibacterial agent for fighting pathogenic bacteria, bacterial infections, and antibiotic medications are widely used in the therapy ...
s.
On most Gram-stained preparations,
Gram-negative
Gram-negative bacteria are bacteria that, unlike gram-positive bacteria, do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. Their defining characteristic is that their cell envelope consists ...
organisms appear red or pink due to their counterstain. Due to the presence of higher lipid content, after alcohol-treatment, the porosity of the cell wall increases, hence the CVI complex (crystal violet – iodine) can pass through. Thus, the primary stain is not retained. In addition, in contrast to most Gram-positive bacteria, Gram-negative bacteria have only a few layers of peptidoglycan and a secondary cell membrane made primarily of lipopolysaccharide.
Endospore
Endospore staining is used to identify the presence or absence of
endospore
An endospore is a dormant, tough, and non-reproductive structure produced by some bacteria in the phylum Bacillota. The name "endospore" is suggestive of a spore or seed-like form (''endo'' means 'within'), but it is not a true spore (i.e., not ...
s, which make bacteria very difficult to kill. Bacterial spores have proven to be difficult to stain as they are not permeable to aqueous dye reagents. Endospore staining is particularly useful for identifying endospore-forming bacterial
pathogen
In biology, a pathogen (, "suffering", "passion" and , "producer of"), in the oldest and broadest sense, is any organism or agent that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a Germ theory of d ...
s such as ''
Clostridioides difficile
''Clostridioides difficile'' ( syn. ''Clostridium difficile'') is a bacterium known for causing serious diarrheal infections, and may also cause colon cancer. It is known also as ''C. difficile'', or ''C. diff'' (), and is a Gram-positive spec ...
''. Prior to the development of more efficient methods, this stain was performed using the Wirtz method with heat fixation and counterstain. Through the use of malachite green and a diluted ratio of carbol fuchsin, fixing bacteria in osmic acid was a great way to ensure no blending of dyes. However, newly revised staining methods have significantly decreased the time it takes to create these stains. This revision included substitution of carbol fuchsin with aqueous Safranin paired with a newly diluted 5% formula of malachite green. This new and improved composition of stains was performed in the same way as before with the use of heat fixation, rinsing, and blotting dry for later examination. Upon examination, all endospore forming bacteria will be stained green accompanied by all other cells appearing red.
Ziehl-Neelsen
A
Ziehl–Neelsen stain
The Ziehl-Neelsen stain, also known as the acid-fast stain, is a bacteriological staining technique used in cytopathology and microbiology to identify acid-fast bacteria under microscopy, particularly members of the ''Mycobacterium'' genus. This ...
is an acid-fast stain used to stain species of ''
Mycobacterium tuberculosis
''Mycobacterium tuberculosis'' (M. tb), also known as Koch's bacillus, is a species of pathogenic bacteria in the family Mycobacteriaceae and the causative agent of tuberculosis.
First discovered in 1882 by Robert Koch, ''M. tuberculosis'' ha ...
'' that do not stain with the standard laboratory staining procedures such as Gram staining.
This stain is performed through the use of both red coloured
carbol fuchsin
Carbol fuchsin, carbol-fuchsin, carbolfuchsin, or Castellani's paint is a mixture of phenol and basic fuchsin that is used in bacterial staining procedures. It is commonly used in the staining of mycobacteria because it has an affinity for the my ...
that stains the bacteria and a counter stain such as
methylene blue
Methylthioninium chloride, commonly called methylene blue, is a salt used as a dye and as a medication. As a medication, it is mainly used to treat methemoglobinemia. It has previously been used for treating cyanide poisoning and urinary trac ...
.
Haematoxylin and eosin (H&E)
Haematoxylin and eosin staining is frequently used in
histology
Histology,
also known as microscopic anatomy or microanatomy, is the branch of biology that studies the microscopic anatomy of biological tissue (biology), tissues. Histology is the microscopic counterpart to gross anatomy, which looks at large ...
to examine thin tissue sections.
Haematoxylin
Haematoxylin American and British English spelling differences#ae and oe, or hematoxylin (), also called natural black 1 or Colour Index International, C.I. 75290, is a chemical compound, compound extracted from wood#Heartwood and sapwood, heart ...
stains cell nuclei blue, while
eosin
Eosin is the name of several fluorescent acidic compounds which bind to and from salts with basic, or eosinophilic, compounds like proteins containing basic amino acid residues such as histidine, arginine and lysine, and stains them dark red ...
stains cytoplasm, connective tissue and other extracellular substances pink or red.
Eosin is strongly absorbed by
red blood cell
Red blood cells (RBCs), referred to as erythrocytes (, with -''cyte'' translated as 'cell' in modern usage) in academia and medical publishing, also known as red cells, erythroid cells, and rarely haematids, are the most common type of blood cel ...
s, colouring them bright red. In a skillfully made H&E preparation the red blood cells are almost orange, and collagen and cytoplasm (especially muscle) acquire different shades of pink.
Papanicolaou
Papanicolaou staining, or PAP staining, was developed to replace fine needle aspiration cytology (FNAC) in hopes of decreasing staining times and cost without compromising quality. This stain is a frequently used method for examining cell samples from a variety of tissue types in various organs. PAP staining has endured several modifications in order to become a “suitable alternative” for FNAC. This transition stemmed from the appreciation of wet fixed smears by scientists preserving the structures of the nuclei opposed to the opaque appearance of air dried Romanowsky smears. This led to the creation of a hybrid stain of wet fixed and air dried known as the ultrafast papanicolaou stain. This modification includes the use of nasal saline to rehydrate cells to increase cell transparency and is paired with the use of alcoholic formalin to enhance colors of the nuclei. The papanicolaou stain is now used in place of cytological staining in all organ types due to its increase in morphological quality, decreased staining time, and decreased cost. It is frequently used to stain
Pap smear
The Papanicolaou test (abbreviated as Pap test, also known as Pap smear (AE), cervical smear (BE), cervical screening (BE), or smear test (BE)) is a method of cervical screening used to detect potentially precancerous and cancerous processes in ...
specimens.
It uses a combination of
haematoxylin
Haematoxylin American and British English spelling differences#ae and oe, or hematoxylin (), also called natural black 1 or Colour Index International, C.I. 75290, is a chemical compound, compound extracted from wood#Heartwood and sapwood, heart ...
,
Orange G,
eosin Y
Eosin Y, also called C.I. 45380 or C.I. Acid Red 87, is a member of the triarylmethane dyes. It is produced from fluorescein by bromination.
Use
Eosin Y is commonly used as the red dye in red inks.
It is commonly used in histology, most nota ...
,
Light Green SF yellowish, and sometimes
Bismarck Brown Y.
PAS
Periodic acid-Schiff is a histology special stain used to mark
carbohydrate
A carbohydrate () is a biomolecule composed of carbon (C), hydrogen (H), and oxygen (O) atoms. The typical hydrogen-to-oxygen atomic ratio is 2:1, analogous to that of water, and is represented by the empirical formula (where ''m'' and ''n'' ...
s (
glycogen
Glycogen is a multibranched polysaccharide of glucose that serves as a form of energy storage in animals, fungi, and bacteria. It is the main storage form of glucose in the human body.
Glycogen functions as one of three regularly used forms ...
,
glycoprotein
Glycoproteins are proteins which contain oligosaccharide (sugar) chains covalently attached to amino acid side-chains. The carbohydrate is attached to the protein in a cotranslational or posttranslational modification. This process is known a ...
,
proteoglycan
Proteoglycans are proteins that are heavily glycosylated. The basic proteoglycan unit consists of a "core protein" with one or more covalently attached glycosaminoglycan (GAG) chain(s). The point of attachment is a serine (Ser) residue to w ...
s). PAS is commonly used on liver tissue where glycogen deposits are made which is done in efforts to distinguish different types of glycogen storage diseases. PAS is important because it can detect glycogen granules found in tumors of the ovaries and pancreas of the endocrine system, as well as in the bladder and kidneys of the renal system. Basement membranes can also show up in a PAS stain and can be important when diagnosing renal disease. Due to the high volume of carbohydrates within the cell wall of hyphae and yeast forms of fungi, the Periodic acid -Schiff stain can help locate these species inside tissue samples of the human body.
Masson
Masson's trichrome is (as the name implies) a three-colour staining protocol. The recipe has evolved from Masson's original technique for different specific applications, but all are well-suited to distinguish cells from surrounding
connective tissue
Connective tissue is one of the four primary types of animal tissue, a group of cells that are similar in structure, along with epithelial tissue, muscle tissue, and nervous tissue. It develops mostly from the mesenchyme, derived from the mesod ...
. Most recipes produce red
keratin
Keratin () is one of a family of structural fibrous proteins also known as ''scleroproteins''. It is the key structural material making up Scale (anatomy), scales, hair, Nail (anatomy), nails, feathers, horn (anatomy), horns, claws, Hoof, hoove ...
and muscle fibers, blue or green staining of
collagen
Collagen () is the main structural protein in the extracellular matrix of the connective tissues of many animals. It is the most abundant protein in mammals, making up 25% to 35% of protein content. Amino acids are bound together to form a trip ...
and
bone
A bone is a rigid organ that constitutes part of the skeleton in most vertebrate animals. Bones protect the various other organs of the body, produce red and white blood cells, store minerals, provide structure and support for the body, ...
, light red or pink staining of
cytoplasm
The cytoplasm describes all the material within a eukaryotic or prokaryotic cell, enclosed by the cell membrane, including the organelles and excluding the nucleus in eukaryotic cells. The material inside the nucleus of a eukaryotic cell a ...
, and black
cell nuclei
The cell nucleus (; : nuclei) is a membrane-bound organelle found in eukaryotic cells. Eukaryotic cells usually have a single nucleus, but a few cell types, such as mammalian red blood cells, have no nuclei, and a few others including osteoc ...
.
Romanowsky
The
Romanowsky stains is considered a polychrome staining effect and is based on a combination of eosin plus (chemically
reduced eosin
Eosin is the name of several fluorescent acidic compounds which bind to and from salts with basic, or eosinophilic, compounds like proteins containing basic amino acid residues such as histidine, arginine and lysine, and stains them dark red ...
) and demethylated
methylene blue
Methylthioninium chloride, commonly called methylene blue, is a salt used as a dye and as a medication. As a medication, it is mainly used to treat methemoglobinemia. It has previously been used for treating cyanide poisoning and urinary trac ...
(containing its oxidation products
azure A
Azure A is an organic compound with the chemical formula
A chemical formula is a way of presenting information about the chemical proportions of atoms that constitute a particular chemical compound or molecule, using chemical element symbo ...
and
azure B). This stain develops varying colors for all cell structures (“Romanowsky-Giemsa effect) and thus was used in staining neutrophil polymorphs and cell nuclei. Common variants include
Wright's stain
Wright's stain is a hematologic stain that facilitates the differentiation of blood cell types. It is classically a mixture of eosin (red) and methylene blue dyes. It is used primarily to stain peripheral blood smears, urine samples, and bone marr ...
,
Jenner's stain, May-Grunwald stain,
Leishman stain and
Giemsa stain.
All are used to examine
blood
Blood is a body fluid in the circulatory system of humans and other vertebrates that delivers necessary substances such as nutrients and oxygen to the cells, and transports metabolic waste products away from those same cells.
Blood is com ...
or
bone marrow
Bone marrow is a semi-solid biological tissue, tissue found within the Spongy bone, spongy (also known as cancellous) portions of bones. In birds and mammals, bone marrow is the primary site of new blood cell production (or haematopoiesis). It i ...
samples. They are preferred over H&E for inspection of blood cells because different types of
leukocytes
White blood cells (scientific name leukocytes), also called immune cells or immunocytes, are cells of the immune system that are involved in protecting the body against both infectious disease and foreign entities. White blood cells are genera ...
(white blood cells) can be readily distinguished. All are also suited to examination of blood to detect blood-borne parasites such as
malaria
Malaria is a Mosquito-borne disease, mosquito-borne infectious disease that affects vertebrates and ''Anopheles'' mosquitoes. Human malaria causes Signs and symptoms, symptoms that typically include fever, Fatigue (medical), fatigue, vomitin ...
.
Silver
Silver staining is the use of
silver
Silver is a chemical element; it has Symbol (chemistry), symbol Ag () and atomic number 47. A soft, whitish-gray, lustrous transition metal, it exhibits the highest electrical conductivity, thermal conductivity, and reflectivity of any metal. ...
to stain
histologic section
Histology,
also known as microscopic anatomy or microanatomy, is the branch of biology that studies the microscopic anatomy of biological tissues. Histology is the microscopic counterpart to gross anatomy, which looks at larger structures visi ...
s. This kind of staining is important in the demonstration of
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
s (for example type III
collagen
Collagen () is the main structural protein in the extracellular matrix of the connective tissues of many animals. It is the most abundant protein in mammals, making up 25% to 35% of protein content. Amino acids are bound together to form a trip ...
) and
DNA
Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
. It is used to show both substances inside and outside
cells. Silver staining is also used in
temperature gradient gel electrophoresis
Temperature gradient gel electrophoresis (TGGE) and denaturing gradient gel electrophoresis (DGGE) are forms of electrophoresis which use either a temperature or chemical gradient to denature the sample as it moves across an acrylamide gel. TGGE ...
.
''Argentaffin cells''
reduce silver solution to metallic silver after
formalin
Formaldehyde ( , ) (systematic name methanal) is an organic compound with the chemical formula and structure , more precisely . The compound is a pungent, colourless gas that polymerises spontaneously into paraformaldehyde. It is stored as ...
fixation. This method was discovered by Italian
Camillo Golgi
Camillo Golgi (; 7 July 184321 January 1926) was an Italian biologist and pathologist known for his works on the central nervous system. He studied medicine at the University of Pavia (where he later spent most of his professional career) bet ...
, by using a reaction between
silver nitrate
Silver nitrate is an inorganic compound with chemical formula . It is a versatile precursor to many other silver compounds, such as those used in photography. It is far less sensitive to light than the halides. It was once called ''lunar causti ...
and
potassium dichromate, thus precipitating silver chromate in some cells (see
Golgi's method). A''rgyrophilic cells'' reduce silver solution to metallic silver after being exposed to the stain that contains a
reductant
In chemistry, a reducing agent (also known as a reductant, reducer, or electron donor) is a chemical species that "donates" an electron to an (called the , , , or ).
Examples of substances that are common reducing agents include hydrogen, carbon ...
. An example of this would be
hydroquinone
Hydroquinone, also known as benzene-1,4-diol or quinol, is an aromatic organic compound that is a type of phenol, a derivative of benzene, having the chemical formula C6H4(OH)2. It has two hydroxyl groups bonded to a benzene ring in a ''para' ...
or formalin.
Sudan
Sudan staining utilizes Sudan dyes to stain sudanophilic substances, often including
lipid
Lipids are a broad group of organic compounds which include fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The functions of lipids include storing ...
s.
Sudan III,
Sudan IV,
Oil Red O,
Osmium tetroxide
Osmium tetroxide (also osmium(VIII) oxide) is the chemical compound with the formula OsO4. The compound is noteworthy for its many uses, despite its toxicity and the rarity of osmium. It also has a number of unusual properties, one being that the ...
, and
Sudan Black B
Solvent Black 3 is an azo dye. It is a non-fluorescent, relatively thermostable lysochrome (fat-soluble dye) diazo dye used for Staining (biology), staining of neutral triglycerides and lipids on frozen sections and some lipoproteins on paraffin se ...
are often used. Sudan staining is often used to determine the level of
fecal fat in diagnosing
steatorrhea
Steatorrhea (or steatorrhoea) is the presence of excess fat in Human feces, feces. Stools may be bulky and difficult to flush, have a pale and oily appearance, and can be especially foul-smelling. An oily anal leakage or some level of fecal incon ...
.
Wirtz-Conklin
The Wirtz-Conklin stain is a special technique designed for staining true endospores with the use of malachite green dye as the primary stain and safranin as the counterstain. Once stained, they do not decolourize. The addition of heat during the staining process is a huge contributing factor. Heat helps open the spore's membrane so the dye can enter. The main purpose of this stain is to show germination of bacterial spores. If the process of germination is taking place, then the spore will turn green in color due to malachite green and the surrounding cell will be red from the safranin. This stain can also help determine the orientation of the spore within the bacterial cell; whether it being terminal (at the tip), subterminal (within the cell), or central (completely in the middle of the cell).
Collagen hybridizing peptide
Collagen hybridizing peptide (CHP) staining allows for an easy, direct way to stain denatured collagens of any type (Type I, II, IV, etc.) regardless if they were damaged or degraded via enzymatic, mechanical, chemical, or thermal means. They work by refolding into the collagen triple helix with the available single strands in the tissue. CHPs can be visualized by a simple
fluorescence microscope
A fluorescence microscope is an optical microscope that uses fluorescence instead of, or in addition to, scattering, reflection, and attenuation or absorption, to study the properties of organic or inorganic substances. A fluorescence micro ...
.
Common biological stains
Different stains react or concentrate in different parts of a cell or tissue, and these properties are used to advantage to reveal specific parts or areas. Some of the most common biological stains are listed below. Unless otherwise marked, all of these dyes may be used with fixed cells and tissues; vital dyes (suitable for use with living organisms) are noted.
Acridine orange
Acridine orange (AO) is a nucleic acid selective fluorescent cationic dye useful for cell cycle determination. It is cell-permeable, and interacts with DNA and RNA by intercalation or electrostatic attractions. When bound to DNA, it is very similar spectrally to fluorescein. Like fluorescein, it is also useful as a non-specific stain for backlighting conventionally stained cells on the surface of a solid sample of tissue (fluorescence backlighted staining).
Bismarck brown
Bismarck brown (also Bismarck brown Y or Manchester brown) imparts a yellow colour to acid
mucin
Mucins () are a family of high molecular weight, heavily glycosylated proteins ( glycoconjugates) produced by epithelial tissues in most animals. Mucins' key characteristic is their ability to form gels; therefore they are a key component in ...
s and an intense brown color to mast cells. One default of this stain is that it blots out any other structure surrounding it and makes the quality of the contrast low. It has to be paired with other stains in order to be useful. Some complementing stains used alongside Bismark brown are Hematoxylin and Toluidine blue which provide better contrast within the histology sample.
Carmine
Carmine
Carmine ()also called cochineal (when it is extracted from the Cochineal, cochineal insect), cochineal extract, crimson Lake pigment, lake, or carmine lake is a pigment of a bright-red color obtained from the aluminium coordination complex, compl ...
is an intensely red dye used to stain
glycogen
Glycogen is a multibranched polysaccharide of glucose that serves as a form of energy storage in animals, fungi, and bacteria. It is the main storage form of glucose in the human body.
Glycogen functions as one of three regularly used forms ...
, while Carmine alum is a nuclear stain. Carmine stains require the use of a mordant, usually
aluminum
Aluminium (or aluminum in North American English) is a chemical element; it has chemical symbol, symbol Al and atomic number 13. It has a density lower than that of other common metals, about one-third that of steel. Aluminium has ...
.
Coomassie blue
Coomassie brilliant blue
Coomassie brilliant blue is the name of two similar triphenylmethane dyes that were developed for use in the textile industry but are now commonly used for staining proteins in analytical biochemistry. Coomassie brilliant blue G-250 differs fr ...
nonspecifically stains proteins a strong blue colour. It is often used in gel electrophoresis.
Cresyl violet
Cresyl violet stains the acidic components of the neuronal cytoplasm a violet colour, specifically
nissl bodies. Often used in brain research.
Crystal violet
Crystal violet
Crystal violet or gentian violet, also known as methyl violet 10B or hexamethyl pararosaniline chloride, is a triphenylmethane, triarylmethane dye used as a histological stain and in Gram staining, Gram's method of classifying bacteria. Crystal ...
, when combined with a suitable mordant, stains
cell wall
A cell wall is a structural layer that surrounds some Cell type, cell types, found immediately outside the cell membrane. It can be tough, flexible, and sometimes rigid. Primarily, it provides the cell with structural support, shape, protection, ...
s purple. Crystal violet is the stain used in Gram staining.
DAPI
DAPI is a
fluorescent
Fluorescence is one of two kinds of photoluminescence, the emission of light by a substance that has absorbed light or other electromagnetic radiation. When exposed to ultraviolet radiation, many substances will glow (fluoresce) with color ...
nuclear stain, excited by
ultraviolet
Ultraviolet radiation, also known as simply UV, is electromagnetic radiation of wavelengths of 10–400 nanometers, shorter than that of visible light, but longer than X-rays. UV radiation is present in sunlight and constitutes about 10% of ...
light and showing strong blue fluorescence when bound to
DNA
Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
. DAPI binds with A=T rich repeats of chromosomes. DAPI is also not visible with regular transmission microscopy. It may be used in living or fixed cells. DAPI-stained cells are especially appropriate for cell counting.
Eosin
Eosin
Eosin is the name of several fluorescent acidic compounds which bind to and from salts with basic, or eosinophilic, compounds like proteins containing basic amino acid residues such as histidine, arginine and lysine, and stains them dark red ...
is most often used as a counterstain to haematoxylin, imparting a pink or red colour to
cytoplasm
The cytoplasm describes all the material within a eukaryotic or prokaryotic cell, enclosed by the cell membrane, including the organelles and excluding the nucleus in eukaryotic cells. The material inside the nucleus of a eukaryotic cell a ...
ic material,
cell membrane
The cell membrane (also known as the plasma membrane or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane that separates and protects the interior of a cell from the outside environment (the extr ...
s, and some extracellular structures. It also imparts a strong red colour to
red blood cell
Red blood cells (RBCs), referred to as erythrocytes (, with -''cyte'' translated as 'cell' in modern usage) in academia and medical publishing, also known as red cells, erythroid cells, and rarely haematids, are the most common type of blood cel ...
s. Eosin may also be used as a counterstain in some variants of Gram staining, and in many other protocols. There are actually two very closely related compounds commonly referred to as eosin. Most often used is
eosin Y
Eosin Y, also called C.I. 45380 or C.I. Acid Red 87, is a member of the triarylmethane dyes. It is produced from fluorescein by bromination.
Use
Eosin Y is commonly used as the red dye in red inks.
It is commonly used in histology, most nota ...
(also known as eosin Y ws or eosin yellowish); it has a very slightly yellowish cast. The other eosin compound is eosin B (eosin bluish or imperial red); it has a very faint bluish cast. The two dyes are interchangeable, and the use of one or the other is more a matter of preference and tradition.
Ethidium bromide
Ethidium bromide
Ethidium bromide (or homidium bromide, chloride salt homidium chloride) is an intercalating agent commonly used as a fluorescent tag (nucleic acid stain) in molecular biology laboratories for techniques such as agarose gel electrophoresis. It ...
intercalates and stains DNA, providing a fluorescent red-orange stain. Although it will not stain healthy cells, it can be used to identify cells that are in the final stages of
apoptosis
Apoptosis (from ) is a form of programmed cell death that occurs in multicellular organisms and in some eukaryotic, single-celled microorganisms such as yeast. Biochemistry, Biochemical events lead to characteristic cell changes (Morphology (biol ...
– such cells have much more permeable
membranes. Consequently, ethidium bromide is often used as a marker for apoptosis in cells populations and to locate bands of DNA in
gel electrophoresis
Gel electrophoresis is an electrophoresis method for separation and analysis of biomacromolecules (DNA, RNA, proteins, etc.) and their fragments, based on their size and charge through a gel. It is used in clinical chemistry to separate ...
. The stain may also be used in conjunction with
acridine orange (AO) in viable cell counting. This EB/AO combined stain causes live cells to fluoresce green whilst apoptotic cells retain the distinctive red-orange fluorescence.
Acid fuchsin
Acid fuchsine may be used to stain collagen, smooth muscle, or
mitochondria
A mitochondrion () is an organelle found in the cells of most eukaryotes, such as animals, plants and fungi. Mitochondria have a double membrane structure and use aerobic respiration to generate adenosine triphosphate (ATP), which is us ...
.
Acid fuchsin is used as the nuclear and cytoplasmic stain in Mallory's trichrome method. Acid fuchsin stains cytoplasm in some variants of Masson's trichrome. In Van Gieson's picro-fuchsine, acid fuchsin imparts its red colour to collagen fibres. Acid fuchsin is also a traditional stain for mitochondria (Altmann's method).
Haematoxylin
Haematoxylin
Haematoxylin American and British English spelling differences#ae and oe, or hematoxylin (), also called natural black 1 or Colour Index International, C.I. 75290, is a chemical compound, compound extracted from wood#Heartwood and sapwood, heart ...
(hematoxylin in North America) is a nuclear stain.
Used with a mordant, haematoxylin stains nuclei blue-violet or brown.
It is most often used with eosin in the
H&E stain
Hematoxylin and eosin stain ( or haematoxylin and eosin stain or hematoxylin–eosin stain; often abbreviated as H&E stain or HE stain) is one of the principal tissue stains used in histology. It is the most widely used stain in medical diag ...
(haematoxylin and eosin) staining, one of the most common procedures in
histology
Histology,
also known as microscopic anatomy or microanatomy, is the branch of biology that studies the microscopic anatomy of biological tissue (biology), tissues. Histology is the microscopic counterpart to gross anatomy, which looks at large ...
.
Hoechst stains
Hoechst is a ''bis''-benzimidazole derivative compound that binds to the ''minor groove'' of
DNA
Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
. Often used in fluorescence microscopy for DNA staining, Hoechst stains appear yellow when dissolved in aqueous solutions and emit blue light under UV excitation. There are two major types of
Hoechst: ''Hoechst 33258'' and ''Hoechst 33342''. The two compounds are functionally similar, but with a little difference in structure. Hoechst 33258 contains a terminal
hydroxyl
In chemistry, a hydroxy or hydroxyl group is a functional group with the chemical formula and composed of one oxygen atom covalently bonded to one hydrogen atom. In organic chemistry, alcohols and carboxylic acids contain one or more hydroxy ...
group and is thus more soluble in aqueous solution, however this characteristics reduces its ability to penetrate the
plasma membrane
The cell membrane (also known as the plasma membrane or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane that separates and protects the interior of a cell from the outside environment (the extr ...
. Hoechst 33342 contains an
ethyl substitution on the terminal hydroxyl group (i.e. an ethylether group) making it more hydrophobic for easier plasma membrane passage
Iodine
Iodine
Iodine is a chemical element; it has symbol I and atomic number 53. The heaviest of the stable halogens, it exists at standard conditions as a semi-lustrous, non-metallic solid that melts to form a deep violet liquid at , and boils to a vi ...
is used in
chemistry
Chemistry is the scientific study of the properties and behavior of matter. It is a physical science within the natural sciences that studies the chemical elements that make up matter and chemical compound, compounds made of atoms, molecules a ...
as an indicator for
starch
Starch or amylum is a polymeric carbohydrate consisting of numerous glucose units joined by glycosidic bonds. This polysaccharide is produced by most green plants for energy storage. Worldwide, it is the most common carbohydrate in human diet ...
. When starch is mixed with iodine in solution, an intensely dark blue colour develops, representing a starch/iodine complex. Starch is a substance common to most plant cells and so a weak iodine solution will stain starch present in the cells. Iodine is one component in the staining technique known as
Gram staining
Gram stain (Gram staining or Gram's method), is a method of staining used to classify bacterial species into two large groups: gram-positive bacteria and gram-negative bacteria. It may also be used to diagnose a fungal infection. The name comes ...
, used in
microbiology
Microbiology () is the branches of science, scientific study of microorganisms, those being of unicellular organism, unicellular (single-celled), multicellular organism, multicellular (consisting of complex cells), or non-cellular life, acellula ...
. Used as a
mordant
A mordant or dye fixative is a substance used to set (i.e., bind) dyes on fabrics. It does this by forming a coordination complex with the dye, which then attaches to the fabric (or tissue). It may be used for dyeing fabrics or for intensifying ...
in Gram's staining, iodine enhances the entrance of the dye through the pores present in the cell wall/membrane.
Lugol's solution or Lugol's iodine (IKI) is a brown solution that turns black in the presence of starches and can be used as a cell stain, making the cell
nuclei more visible.
Used with common vinegar (acetic acid), Lugol's solution is used to identify
pre-cancerous and cancerous changes in cervical and vaginal tissues during "Pap smear" follow up examinations in preparation for biopsy. The acetic acid causes the abnormal cells to blanch white, while the normal tissues stain a mahogany brown from the iodine.
Malachite green
Malachite green (also known as diamond green B or victoria green B) can be used as a blue-green counterstain to safranin in the
Gimenez staining technique for bacteria. It can also be used to directly stain
spores
In biology, a spore is a unit of sexual (in fungi) or asexual reproduction that may be adapted for dispersal and for survival, often for extended periods of time, in unfavourable conditions. Spores form part of the life cycles of many plant ...
.
Methyl green
Methyl green is used commonly with bright-field, as well as fluorescence microscopes to dye the chromatin of cells so that they are more easily viewed.
Methylene blue
Methylene blue
Methylthioninium chloride, commonly called methylene blue, is a salt used as a dye and as a medication. As a medication, it is mainly used to treat methemoglobinemia. It has previously been used for treating cyanide poisoning and urinary trac ...
is used to stain animal cells, such as human cheek cells, to make their nuclei more observable. Also used to stain blood films in cytology.
Neutral red
Neutral red
Neutral red (toluylene red, Basic Red 5, or C.I. 50040) is a eurhodin dye used for staining in histology. It stains lysosomes red. It is used as a general stain in histology, as a counterstain in combination with other dyes, and for many stain ...
(or toluylene red) stains
Nissl substance red. It is usually used as a counterstain in combination with other dyes.
Nile blue
Nile blue (or Nile blue A) stains nuclei blue. It may be used with living cells.
Nile red
Nile red (also known as Nile blue oxazone) is formed by boiling Nile blue with
sulfuric acid
Sulfuric acid (American spelling and the preferred IUPAC name) or sulphuric acid (English in the Commonwealth of Nations, Commonwealth spelling), known in antiquity as oil of vitriol, is a mineral acid composed of the elements sulfur, oxygen, ...
. This produces a mix of Nile red and Nile blue. Nile red is a
lipophilic
Lipophilicity (from Greek language, Greek λίπος "fat" and :wikt:φίλος, φίλος "friendly") is the ability of a chemical compound to dissolve in fats, oils, lipids, and non-polar solvents such as hexane or toluene. Such compounds are c ...
stain; it will accumulate in
lipid
Lipids are a broad group of organic compounds which include fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The functions of lipids include storing ...
globules inside cells, staining them red. Nile red can be used with living cells. It fluoresces strongly when partitioned into lipids, but practically not at all in aqueous solution.
Osmium tetroxide (formal name: osmium tetraoxide)
Osmium tetraoxide is used in optical microscopy to stain
lipid
Lipids are a broad group of organic compounds which include fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The functions of lipids include storing ...
s. It dissolves in fats, and is reduced by organic materials to elemental osmium, an easily visible black substance.
Propidium iodide
Propidium iodide
Propidium iodide (or PI) is a Fluorescence#Biochemistry and medicine, fluorescent intercalating agent that can be used to Staining (biology), stain cell (biology), cells and nucleic acids. PI binds to DNA by intercalating between the bases with li ...
is a fluorescent intercalating agent that can be used to stain cells. Propidium iodide is used as a DNA stain in flow cytometry to evaluate cell viability or DNA content in cell cycle analysis, or in microscopy to visualise the nucleus and other DNA-containing organelles. Propidium Iodide cannot cross the membrane of live cells, making it useful to differentiate necrotic, apoptotic and healthy cells. PI also binds to RNA, necessitating treatment with nucleases to distinguish between RNA and DNA staining
Rhodamine
Rhodamine
Rhodamine is a family of related dyes, a subset of the triarylmethane dyes. They are derivatives of xanthene. Important members of the rhodamine family are rhodamine 6G, Rhodamin WT, Texas Red (Sulforhodamin 101), rhodamine 123, and rhod ...
is a protein specific fluorescent stain commonly used in fluorescence microscopy.
Safranine
Safranine
Safranin (Safranin O or basic red 2) is a biological stain used in histology and cytology. Safranin is used as a counterstain in some staining protocols, colouring cell nuclei red. This is the classic counterstain in both Gram stains and endos ...
(or Safranine O) is a red cationic dye. It binds to nuclei (DNA) and other tissue
polyanions, including
glycosaminoglycan
Glycosaminoglycans (GAGs) or mucopolysaccharides are long, linear polysaccharides consisting of repeating disaccharide units (i.e. two-sugar units). The repeating two-sugar unit consists of a uronic sugar and an amino sugar, except in the case o ...
s in cartilage and mast cells, and components of lignin and plastids in plant tissues. Safranine should not be confused with saffron, an expensive natural dye that is used in some methods to impart a yellow colour to collagen, to contrast with blue and red colours imparted by other dyes to nuclei and cytoplasm in animal (including human) tissues.
The incorrect spelling "safranin" is in common use. The -ine ending is appropriate for safranine O because this dye is an amine.
Thiazole-Orange-Based DNA Dyes
Thiazole Orange derivatives, such as
SYBR Safe,
SYBR Green,
SYBR Gold, Pico Green, SYTO-16, SYTO-9 and TOPhBu are special cyanine dyes commonly used as fluorescent DNA sensors. The ability of the dyes to detect DNA at low concentrations was evaluated using two metrics: absolute fluorescence enhancement (AFE) and relative fluorescence enhancement (RFE).
Stainability of tissues
Tissues which take up stains are called chromatic.
Chromosomes
A chromosome is a package of DNA containing part or all of the genetic material of an organism. In most chromosomes, the very long thin DNA fibers are coated with nucleosome-forming packaging proteins; in eukaryotic cells, the most importa ...
were so named because of their ability to absorb a violet stain.
Positive affinity for a specific stain may be designated by the suffix ''-philic''. For example, tissues that stain with an
azure stain
Romanowsky staining is a prototypical staining (biology), staining technique that was the forerunner of several distinct but similar stains widely used in hematology (the study of blood) and cytopathology (the study of diseased cells). Romanowsky ...
may be referred to as
azurophilic. This may also be used for more generalized staining properties, such as
acidophilic
Acidophiles or acidophilic organisms are those that thrive under highly acidic conditions (usually at pH 5.0 or below). These organisms can be found in different branches of the tree of life, including Archaea, Bacteria,Becker, A.Types of Bacteri ...
for tissues that stain by
acidic
An acid is a molecule or ion capable of either donating a proton (i.e. hydrogen cation, H+), known as a Brønsted–Lowry acid, or forming a covalent bond with an electron pair, known as a Lewis acid.
The first category of acids are the ...
stains (most notably
eosin
Eosin is the name of several fluorescent acidic compounds which bind to and from salts with basic, or eosinophilic, compounds like proteins containing basic amino acid residues such as histidine, arginine and lysine, and stains them dark red ...
),
basophilic
Basophilic is a technical term used by pathologists. It describes the appearance of cells, tissues and cellular structures as seen through the microscope after a histological section has been stained with a basic dye. The most common such dye ...
when staining in
basic
Basic or BASIC may refer to:
Science and technology
* BASIC, a computer programming language
* Basic (chemistry), having the properties of a base
* Basic access authentication, in HTTP
Entertainment
* Basic (film), ''Basic'' (film), a 2003 film
...
dyes, and amphophilic when staining with either acid or basic dyes. In contrast,
chromophobic tissues do not take up coloured dye readily.
Electron microscopy
As in light microscopy, stains can be used to enhance contrast in
transmission electron microscopy
Transmission electron microscopy (TEM) is a microscopy technique in which a beam of electrons is transmitted through a specimen to form an image. The specimen is most often an ultrathin section less than 100 nm thick or a suspension on a g ...
. Electron-dense compounds of heavy metals are typically used.
Phosphotungstic acid
Phosphotungstic acid is a common
negative stain In microscopy, negative staining is an established method, often used in diagnostic microscopy, for contrasting a thin specimen with an optically opaque fluid. In this technique, the background is stained, leaving the actual specimen untouched, ...
for
virus
A virus is a submicroscopic infectious agent that replicates only inside the living Cell (biology), cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Viruses are ...
es,
nerve
A nerve is an enclosed, cable-like bundle of nerve fibers (called axons). Nerves have historically been considered the basic units of the peripheral nervous system. A nerve provides a common pathway for the Electrochemistry, electrochemical nerv ...
s,
polysaccharide
Polysaccharides (), or polycarbohydrates, are the most abundant carbohydrates found in food. They are long-chain polymeric carbohydrates composed of monosaccharide units bound together by glycosidic linkages. This carbohydrate can react with wat ...
s, and other biological tissue materials. It is mostly used in a .5-2% ph form making it neutral and is paired with water to make an aqueous solution. Phosphotungstic acid is filled with electron dense matter that stains the background surrounding the specimen dark and the specimen itself light. This process is not the normal positive technique for staining where the specimen is dark and the background remains light.
Osmium tetroxide
Osmium tetroxide
Osmium tetroxide (also osmium(VIII) oxide) is the chemical compound with the formula OsO4. The compound is noteworthy for its many uses, despite its toxicity and the rarity of osmium. It also has a number of unusual properties, one being that the ...
is used in optical microscopy to stain
lipid
Lipids are a broad group of organic compounds which include fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The functions of lipids include storing ...
s. It dissolves in fats, and is reduced by organic materials to elemental osmium, an easily visible black substance. Because it is a heavy metal that absorbs electrons, it is perhaps the most common stain used for morphology in biological electron microscopy. It is also used for the staining of various polymers for the study of their morphology by TEM. is very volatile and extremely toxic. It is a strong oxidizing agent as the osmium has an oxidation number of +8. It aggressively oxidizes many materials, leaving behind a deposit of non-volatile osmium in a lower oxidation state.
Ruthenium tetroxide
Ruthenium tetroxide is equally volatile and even more aggressive than osmium tetraoxide and able to stain even materials that resist the osmium stain, e.g. polyethylene.
Other chemicals used in electron microscopy staining include:
ammonium molybdate,
cadmium iodide,
carbohydrazide,
ferric chloride
Iron(III) chloride describes the inorganic compounds with the formula (H2O)x. Also called ferric chloride, these compounds are some of the most important and commonplace compounds of iron. They are available both in anhydrous and in hydrated f ...
,
hexamine,
indium trichloride,
lanthanum(III) nitrate,
lead acetate,
lead citrate,
lead(II) nitrate,
periodic acid
Periodic acid ( ) is an oxoacid of iodine. It can exist in two forms: orthoperiodic acid, with the chemical formula , and metaperiodic acid, which has the formula . Periodic acids are colourless crystals. Periodic acid features iodine in the hig ...
,
phosphomolybdic acid,
potassium ferricyanide
Potassium ferricyanide is the chemical compound with the formula K3 e(CN)6 This bright red salt contains the octahedral molecular geometry, octahedrally coordination compound, coordinated ferricyanide, e(CN)6− ion. It is soluble in wat ...
,
potassium ferrocyanide
Potassium hexacyanidoferrate(II) is the inorganic compound with formula K4 e(CN)6�3H2O. It is the potassium salt of the coordination complex e(CN)6sup>4−. This salt forms lemon-yellow monoclinic crystals.
Synthesis
In 1752, the French chemi ...
,
ruthenium red,
silver nitrate
Silver nitrate is an inorganic compound with chemical formula . It is a versatile precursor to many other silver compounds, such as those used in photography. It is far less sensitive to light than the halides. It was once called ''lunar causti ...
,
silver proteinate Silver proteinate (brand name: Protargol) is used in electron microscopy with periodic acid and thiocarbohydrazide or thiosemicarbohydrazide as a positive stain for carbohydrates such as glycogen. It can also be used for light microscopy to stain n ...
,
sodium chloroaurate,
thallium nitrate,
thiosemicarbazide
Thiosemicarbazide is the chemical compound with the formula H2NC(S)NHNH2. A white, odorless solid, it is related to thiourea (H2NC(S)NH2) by the insertion of an NH center. They are commonly used as ligands for transition metals. Many thiosemicar ...
,
uranyl acetate
Uranyl acetate is the acetate salt of uranium oxide, a toxic yellow-green powder useful in certain laboratory tests. Structurally, it is a coordination polymer with formula UO2(CH3CO2)2(H2O)·H2O.
Structure
left, 260px, Structure (from X-ray ...
,
uranyl nitrate
Uranyl nitrate is a water-soluble yellow uranium salt with the formula . The hexa-, tri-, and dihydrates are known. The compound is mainly of interest because it is an intermediate in the preparation of nuclear fuels. In the nuclear industry, it ...
, and
vanadyl sulfate.
See also
*
Biological Stain Commission: Third-party quality control and certification of stains
*
Cytology
Cell biology (also cellular biology or cytology) is a branch of biology that studies the structure, function, and behavior of cells. All living organisms are made of cells. A cell is the basic unit of life that is responsible for the living an ...
: the study of cells
*
Histology
Histology,
also known as microscopic anatomy or microanatomy, is the branch of biology that studies the microscopic anatomy of biological tissue (biology), tissues. Histology is the microscopic counterpart to gross anatomy, which looks at large ...
: the study of tissues
*
Immunohistochemistry
Immunohistochemistry is a form of immunostaining. It involves the process of selectively identifying antigens in cells and tissue, by exploiting the principle of Antibody, antibodies binding specifically to antigens in biological tissues. Alber ...
: the use of antisera to label specific antigens
*
Ruthenium(II) tris(bathophenanthroline disulfonate), a protein dye.
*
Vital stain: stains that do not kill cells
*
PAGE
Page most commonly refers to:
* Page (paper), one side of a leaf of paper, as in a book
Page, PAGE, pages, or paging may also refer to:
Roles
* Page (assistance occupation), a professional occupation
* Page (servant), traditionally a young m ...
: separation of protein molecules
*
Barium enema - a type of in vivo stain that creates contrast in the x-ray part of the light spectrum
*
Diaphonization
Diaphonization (or diaphonisation), also known as clearing and staining, is a staining technique used on animal specimens that first renders the body of the animal transparent by bathing it in trypsin, and then stains the bones and cartilage with ...
References
Further reading
*
*
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External links
The Biological Stain commissionis an independent non-profit company that has been testing dyes since the early 1920s and issuing Certificates of approval for batches of dyes that meet internationally recognized standards.
StainsFileReference for dyes and staining techniques.
~ Howey, 2000
and
ttp://www.microscopy-uk.org.uk/mag/indexmag.html?http://www.microscopy-uk.org.uk/mag/artdec00/fixation2.html Part 2– by M. Halit Umar
Photomicrographs of Histology Stainsat Sridhar Rao P.N's home page
{{Clinical microbiology techniques
dyes
Juan de Guillebon, better known by his stage name DyE, is a French musician. He is known for the music video of the single "Fantasy (DyE song), Fantasy" from his first album ''Taki 183 (album), Taki 183''. This video became popular, attracting ...
pigments
A pigment is a powder used to add or alter color or change visual appearance. Pigments are completely or nearly solubility, insoluble and reactivity (chemistry), chemically unreactive in water or another medium; in contrast, dyes are colored sub ...
Staining dyes
Scientific techniques
Biological techniques and tools