Staining in the context of Orthochromasia

In chemistry, orthochromasia is the property of a dye or stain to not change color on binding to a target, as opposed to metachromatic stains, which do change color. The word is derived from the Greek orthos (correct, upright), and chromatic (color). Toluidine blue is an example of a partially orthochromatic dye, as it stains nucleic acids by its orthochromatic color (blue), but stains mast cell granules in its metachromatic color (red).

In spectral terms, orthochromasia refers to maintaining the position of spectral peaks, while metachromasia refers to a shift in wavelength, becoming either shorter or longer.

Metachromasia (var. metachromasy) is a characteristic change in the color of staining carried out in biological tissues, exhibited by certain dyes when they bind to particular substances present in these tissues, called chromotropes. For example, toluidine blue becomes dark blue (with a colour range from blue-red dependent on glycosaminoglycan content) when bound to cartilage. Other widely used metachromatic stains include the family of Romanowsky stains that also contain thiazine dyes: the white cell nucleus stains purple, basophil granules intense magenta, whilst the cytoplasm (of mononuclear cells) stains blue, which is called the Romanowsky effect. The absence of color change in staining is named orthochromasia.

The underlying mechanism for metachromasia requires the presence of polyanions within the tissue. When these tissues are stained with a concentrated basic dye solution, such as toluidine blue, the bound dye molecules are close enough to form dimeric and polymeric aggregates. The light absorption spectra of these stacked dye aggregates differ from those of the individual monomeric dye molecules. Cell and tissue structures that have high concentrations of ionized sulfate and phosphate groups—such as the ground substance of cartilage, heparin-containing granules of mast cells, and rough endoplasmic reticulum of plasma cells—exhibit metachromasia. This depends on the charge density of the negative sulfate and carboxylate anions in the glycosaminoglycan (GAG). The GAG polyanion stabilizes the stacked, positively charged dye molecules, resulting in a spectral shift as the conjugated double bond π-orbitals of adjacent dye molecules overlap. The greater the degree of stacking, the greater the metachromatic shift. Thus, hyaluronic acid, lacking sulphate groups and with only moderate charge density, causes slight metachromasia; chondroitin sulfate, with an additional sulfate residue per GAG saccharide dimer, is an effective metachromatic substrate, whilst heparin, with further N-sulfation, is strongly metachromatic. Therefore, toluidine blue will appear purple to red when it stains these components.

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 diagnosis and is often the gold standard. For example, when a pathologist looks at a biopsy of a suspected cancer, the histological section is likely to be stained with H&E.

H&E is the combination of two histological stains: hematoxylin and eosin. The hematoxylin stains cell nuclei a purplish blue, and eosin stains the extracellular matrix and cytoplasm pink, with other structures taking on different shades, hues, and combinations of these colors. Hence a pathologist can easily differentiate between the nuclear and cytoplasmic parts of a cell, and additionally, the overall patterns of coloration from the stain show the general layout and distribution of cells and provides a general overview of a tissue sample's structure. Thus, pattern recognition, both by expert humans themselves and by software that aids those experts (in digital pathology), provides histologic information.

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 appear used, degraded or permanently unclean. Intentional staining is used in biochemical research, and for artistic effect, such as in wood staining, rust staining and stained glass.

Endospore staining is a technique used in bacteriology to identify the presence of endospores in a bacterial sample. Within bacteria, endospores are protective structures used to survive extreme conditions, including high temperatures making them highly resistant to chemicals. Endospores contain little or no ATP which indicates how dormant they can be. Endospores contain a tough outer coating made up of keratin which protects them from nucleic DNA as well as other adaptations. Endospores are able to regerminate into vegetative cells, which provides a protective nature that makes them difficult to stain using normal techniques such as simple staining and gram staining. Special techniques for endospore staining include the Schaeffer–Fulton stain and the Moeller stain.

Acid-fastness is a physical property of certain bacteria, protozoa, and eukaryotic cells, as well as some subcellular structures, referring to their resistance to decolorization by acids during laboratory staining procedures. Once stained as part of a sample, these organisms can resist the acid and/or ethanol-based decolorization procedures common in many staining protocols, hence the name acid-fast.

Historically, acid-fast stains were thought to stain lipids of the cells based on the observed charectistics of cell staining under a wide range of conditions, although the results were limited by the tools available, however as early as 1959 there were observations of how nucleic acids were acid fast. Dyes such as carbol fuchsin and auramine O penetrate the cell and bind to DNA and RNA, producing characteristic red or yellow-green fluorescence, respectively. The property of “acid-fastness” therefore reflects the organism’s ability to retain these dyes after acid–alcohol decolorization, a feature determined mainly by the integrity and composition of the outer cell wall rather than by any specific lipid chemistry.

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 from the Danish bacteriologist Hans Christian Gram, who developed the technique in 1884.

Gram staining differentiates bacteria by the chemical and physical properties of their cell walls. Gram-positive cells have a thick layer of peptidoglycan in the cell wall that retains the primary stain, crystal violet. Gram-negative cells have a thinner peptidoglycan layer that allows the crystal violet to wash out on addition of ethanol. They are stained pink or red by the counterstain, commonly safranin or fuchsine. Lugol's iodine solution is always added after addition of crystal violet to form a stable complex with crystal violet that strengthens the bonds of the stain with the cell wall.

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 staining method was initially introduced by Paul Ehrlich (1854–1915) and subsequently modified by the German bacteriologists Franz Ziehl (1859–1926) and Friedrich Neelsen (1854–1898) during the late 19th century.

The acid-fast staining method, in conjunction with auramine phenol staining, serves as the standard diagnostic tool and is widely accessible for rapidly diagnosing tuberculosis (caused by Mycobacterium tuberculosis) and other diseases caused by atypical mycobacteria, such as leprosy (caused by Mycobacterium leprae) and Mycobacterium avium-intracellulare infection (caused by Mycobacterium avium complex) in samples like sputum, gastric washing fluid, and bronchoalveolar lavage fluid. These acid-fast bacteria possess a waxy lipid-rich outer layer that contains high concentrations of mycolic acid, rendering them resistant to conventional staining techniques like the Gram stain.

Haematoxylin or hematoxylin (/ˌhiːməˈtɒksɪlɪn/), also called natural black 1 or C.I. 75290, is a compound extracted from heartwood of the logwood tree (Haematoxylum campechianum) with a chemical formula of C
₁₆H
₁₄O
₆. This naturally derived dye has been used as a histologic stain, as an ink and as a dye in the textile and leather industry. As a dye, haematoxylin has been called palo de Campeche, logwood extract, bluewood and blackwood. In histology, haematoxylin staining is commonly followed by counterstaining with eosin. When paired, this staining procedure is known as H&E staining and is one of the most commonly used combinations in histology. In addition to its use in the H&E stain, haematoxylin is also a component of the Papanicolaou stain (or Pap stain) which is widely used in the study of cytology specimens.

Eosinophils, sometimes called eosinophiles or, less commonly, acidophils, are a variety of white blood cells and one of the immune system components responsible for combating multicellular parasites and certain infections in vertebrates. Along with mast cells and basophils, they also control mechanisms associated with allergy and asthma. They are granulocytes that develop during hematopoiesis in the bone marrow before migrating into blood, after which they are terminally differentiated and do not multiply.

These cells are eosinophilic or "acid-loving" due to their large acidophilic cytoplasmic granules, which show their affinity for acids by their affinity to coal tar dyes: Normally transparent, it is this affinity that causes them to appear brick-red after staining with eosin, a red dye, using the Romanowsky method. The staining is concentrated in small granules within the cellular cytoplasm, which contain many chemical mediators, such as eosinophil peroxidase, ribonuclease (RNase), deoxyribonucleases (DNase), lipase, plasminogen, and major basic protein. These mediators are released by a process called degranulation following activation of the eosinophil, and are toxic to both parasite and host tissues.

Fine-needle aspiration (FNA) is a diagnostic procedure used to investigate lumps or masses. In this technique, a thin (23–25 gauge (0.52 to 0.64 mm outer diameter)), hollow needle is inserted into the mass for sampling of cells that, after being stained, are examined under a microscope (biopsy). The sampling and biopsy considered together are called fine-needle aspiration biopsy (FNAB) or fine-needle aspiration cytology (FNAC) (the latter to emphasize that any aspiration biopsy involves cytopathology, not histopathology). Fine-needle aspiration biopsies are very safe for minor surgical procedures. Often, a major surgical (excisional or open) biopsy can be avoided by performing a needle aspiration biopsy instead, eliminating the need for hospitalization. In 1981, the first fine-needle aspiration biopsy in the United States was done at Maimonides Medical Center. The modern procedure is widely used to diagnose cancer and inflammatory conditions. Fine needle aspiration is generally considered a safe procedure. Complications are infrequent.

Aspiration is safer and far less traumatic than an open biopsy; complications beyond bruising and soreness are rare. However, the few problematic cells can be too few (inconclusive) or missed entirely (a false negative).

Alizarin (also known as 1,2-dihydroxyanthraquinone, Mordant Red 11, C.I. 58000, and Turkey Red) is an organic compound with formula C₁₄H₈O₄ that has been used throughout history as a red dye, principally for dyeing textile fabrics. Historically it was derived from the roots of plants of the madder genus. In 1869, it became the first natural dye to be produced synthetically.

Alizarin is the main ingredient for the manufacture of the madder lake pigments known to painters as rose madder and alizarin crimson. Alizarin in the most common usage of the term has a deep red color, but the term is also part of the name for several related non-red dyes, such as Alizarine Cyanine Green and Alizarine Brilliant Blue. A use of alizarin in modern times is as a staining agent in biological research because it stains free calcium and certain calcium compounds a red or light purple color. Alizarin continues to be used commercially as a red textile dye, but to a lesser extent than in the past.

Amyloids are aggregates of proteins characterised by a fibrillar morphology of typically 7–13 nm in diameter, a β-sheet secondary structure (known as cross-β) and ability to be stained by particular dyes, such as Congo red. In the human body, amyloids have been linked to the development of various diseases. Pathogenic amyloids form when previously healthy proteins lose their normal structure and physiological functions (misfolding) and form fibrous deposits within and around cells. These protein misfolding and deposition processes disrupt the healthy function of tissues and organs.

Such amyloids have been associated with (but not necessarily as the cause of) more than 50 human diseases, including amyloidosis, and may play a role in some neurodegenerative diseases. Some of these diseases are mainly sporadic and only a few cases are familial. Others are only familial. Some result from medical treatment. Prions are an infectious form of amyloids that can act as a template to convert other non-infectious forms. Amyloids may also have normal biological functions; for example, in the formation of fimbriae in some genera of bacteria, transmission of epigenetic traits in fungi, as well as pigment deposition and hormone release in humans.

Fat body is a highly dynamic insect tissue composed primarily of storage cells. It is distributed throughout the insect's internal body cavity (the haemocoel), in close proximity to the hemolymph as well as organs such as the epidermis, digestive organs and ovaries. Its main functions are nutrient storage and metabolism, for which it is commonly compared to a combination of adipose tissue and liver in mammals. However, it may also serve a variety of other roles, such as: endocrine regulation, systemic immunity, vitellogenesis, and the main site of production of antimicrobial molecules called antimicrobial peptides (or AMPs).

Its presence, structure, cellular composition, location, and functions vary widely among insects, even between different species of the same genus or between developmental stages of the same individual, with other specialized organs taking over some or all of its functions.