Abbreviations for dyes, stains and fluorescent probes used in biology and medicine in the 21st century. A bright future or the last gasp?

I summarize here the history of the use of abbreviations, mostly in subject areas related to dyes, stains and fluorescent probes used in biology and medicine. The dozen most popular abbreviations in these fields are identified and their salient characteristics noted. The pros and cons of each abbreviation are discussed with relevant citations. Certain abbreviations that are not in the list, e.g., AZAN and LN, are mentioned because they have an unusual origin; while others, i.e., INEPT and INADEQUATE are presented because they are bizarre. A related topic is abbreviations used for citations, which require further efforts to decipher. In the past, brevity helped conserve materials, such as ink and paper, and promoted more rapid publishing. I suggest that the use of many abbreviations in the current era of electronic publishing may not be necessary.

Quirks of dye nomenclature. 16. Dyes, and a pigment, named after places.

Many dyes produced during the 19th century were named after locations. Manufacturers proliferated the number of synonyms used and in time, the original names were forgotten. Therefore, in the headings below, the original names are followed by the current name(s) in parentheses. The stories of some of these dyes that survived into the 21st century are recounted here. Numerical identity data are provided. Chemical structures also are provided and for simplicity, ionic structures, which can be multiple and pH variable, are presented as their parents.

Hematoxylin in the 21st century.

Hematoxylin continues to be a popular substance in the 21st century. I present here some recent developments including the use and misuse of the terms, hematoxylin and hemalum, in biological staining. The medical use of hematoxylin and its application as a dye for hair or textiles continues to be of interest. Unusual applications including its use as a biosensor and for study of vibrational properties of wood are included.

Quirks of dye nomenclature. 15. Geranine - a simple name, with a less than straight forward identity.

Geranines were manufactured initially as textile dyes; they were made by coupling diazotized aromatic amines with sulfonated 1-naphthols. Most commonly encountered was geranine G, which for more than fifty years was thought to be derived from 1-naphthol monosulfonic acid, but later was considered to be derived from a 1-naphthol disulfonic acid. Currently, geranine G is thought to be a mixture of two isomers derived from 1-naphthol disulfonic acids. This species and others are described here by chemical structure and by other reference names and numbers where available. The occasional uses of geranines as biological stains are documented.

Quirks of dye nomenclature. 14. Madder: queen of red dyes.

The long history of madder as a source of red dyes and pigments is presented. The variety of plant sources and the range of anthraquinone components discovered over a long period are addressed. Topics such as analysis, industrial uses, biological staining, red bone staining in live animals and toxicity are outlined briefly. The contributions of many chemists are acknowledged.

Quirks of dye nomenclature. 13. Biebrich scarlet.

Biebrich scarlet was the first commercial bis-azo dye when it appeared on the market in 1879 in Biebrich on Rhine, Germany. The dye's early history is recounted here with details of the manufacturing process. The possibility that the dye exists in a keto form rather than an enol form is discussed. Application as a textile dye was soon followed by use as a biological stain and for medical applications. Efforts to decolorize the dye to reduce environmental impact are described.

Quirks of dye nomenclature. 12. Victoria's rainbow.

The identities of 18 dyes whose names begin with "Victoria" are described using their chemical structures, names and numerical identifiers. All are synthetic dyes originally synthesized in Germany during the late 19th century as colorants for textiles. Brief manufacturing details are included. All the colors of the rainbow are represented except indigo. Unusual properties including explosive tendency or toxicity are noted. Some of the applications as stains and for food coloring, anti-obesity medication and pigments for ball pen inks also are discussed.

Quirks of dye nomenclature. 11. Safranine and its relatives.

Safranine was one of the earliest coal tar dyes following mauveine. By the end of the 19th century, many alkylated derivatives of safranine had been made. The history, identity, names, manufacture, analysis, toxicity, textile dyeing, and biological staining applications, plus some nonstaining uses of safranine, phenosafranine, methylene violet, amethyst violet, azocarmine, and Magdala red are described here.

The red insect dyes: carminic, kermesic and laccaic acids and their derivatives.

Three groups of insect dyes are described: three cochineal dyes, the kermes dye and the lac dye. The major color components are carminic acid, kermesic acid and laccaic acids, respectively. These dyes are red anthraquinone derivatives. The chemical structures are described. All of these dyes have extensive histories that are related briefly; however, only American cochineal is of commercial importance today. Two manufactured derivatives of cochineal, carmine and acid-stable carmine (4-aminocarminic acid) are described in some detail including the chemical identity, toxicity, stability, and staining and non-staining applications.

Quirks of dye nomenclature. 10. Eosin Y and its close relatives.

The long history of eosin Y, eosin B and the methyl and ethyl eosins is recounted as well as their synthesis, the variety of their molecular species and some of the myriad applications of these dyes. Chromatographic techniques are described that reveal the purity or lack of it in commercial samples. Toxicological studies are discussed that suggest that the eosins are virtually non toxic, but efforts to remove them from the environment imply that there may be some risk.

Quirks of dye nomenclature. 9. Fluorescein.

Adolf Baeyer announced the discovery of fluorescein in 1871 and named it after its most striking property, i.e., fluorescence. I describe here the synthesis of fluorescein. There are seven molecular species in both the solid state or in solution. I also summarize some of the diverse applications of the dye, both medical and nonmedical, which depend mostly on the facile detection of fluorescein at low concentration. Both animal and human toxicity are examined.

Quirks of dye nomenclature. 8. Methylene blue, azure and violet.

Methylene blue was synthesized in 1877 and soon found application in medicine, staining for microscopy and as an industrial dye and pigment. An enormous literature has accumulated since its introduction. Early on, it was known that methylene blue could be degraded easily by demethylation; consequently, the purity of commercial samples often was low. Therefore, demethylation products, such as azures and methylene violet, also are considered here. The names and identity of the components, their varying modes of manufacture, analytical methods and their contribution to biological staining are discussed.

Turmeric: old spice, new spice.

The history of chemical investigations into the yellow components of turmeric can be traced from 1815. Although the major yellow component of turmeric, curcumin, often is represented as a 1,3-diketone in the solid state and in nonaqueous solution, it exists in the enol form. The struggle to identify the chemical structure of curcumin continued for nearly a century and was complicated by the difficult purification of curcumin and by the presence of two additional yellow components. Food remains the main use for turmeric (old spice); its use as a dye has diminished since the 19th century, but it may have pharmaceutical uses (new spice).

Quirks of dye nomenclature. 7. Gentian violet and other violets.

The name, gentian, appeared about 1880. Immediately following its discovery in 1861, this violet dye was known as Violet de Paris or as methyl violet. Initially used as a textile dye, it was soon used to color virtually anything. The names and identity of the components, the varying modes of manufacture, analytical methods and the dye's significant contribution to biological staining are discussed here. Finally, I discuss the dye's declining medical use following the revelation of its toxic nature.

Quirks of dye nomenclature. 6. Malachite green.

Malachite green was discovered independently by two researchers in Germany in the 19(th) century and found immediate employment as a dye and a pigment. Subsequently, other uses, such as staining biological specimens, emerged. A much later application was the control of fungal and protozoan infections in fish, for which the dye remains popular, although illegal in many countries owing to a variety of toxicity problems. In solution, malachite green can exist as five different species depending on the pH. The location of the positive charge of the colored cation on a carbon atom or a nitrogen atom is still debated. The original names of this dye, and their origins, are briefly surveyed.

Quirks of dye nomenclature. 5. Rhodamines.

Rhodamines were first produced in the late 19(th) century, when they constituted a new class of synthetic dyes. These compounds since have been used to color many things including cosmetics, inks, textiles, and in some countries, food products. Certain rhodamine dyes also have been used to stain biological specimens and currently are widely used as fluorescent probes for mitochondria in living cells. The early history and current biological applications are sketched briefly and an account of the ambiguities, complications and confusions concerning dye identification and nomenclature are discussed.

Broadband Radiometric LED Measurements.

At present, broadband radiometric measurements of LEDs with uniform and low-uncertainty results are not available. Currently, either complicated and expensive spectral radiometric measurements or broadband photometric LED measurements are used. The broadband photometric measurements are based on the CIE standardized V(λ) function, which cannot be used in the UV range and leads to large errors when blue or red LEDs are measured in its wings, where the realization is always poor. Reference irradiance meters with spectrally constant response and high-intensity LED irradiance sources were developed here to implement the previously suggested broadband radiometric LED measurement procedure [1, 2]. Using a detector with spectrally constant response, the broadband radiometric quantities of any LEDs or LED groups can be simply measured with low uncertainty without using any source standard. The spectral flatness of filtered-Si detectors and low-noise pyroelectric radiometers are compared. Examples are given for integrated irradiance measurement of UV and blue LED sources using the here introduced reference (standard) pyroelectric irradiance meters. For validation, the broadband measured integrated irradiance of several LED-365 sources were compared with the spectrally determined integrated irradiance derived from an FEL spectral irradiance lamp-standard. Integrated responsivity transfer from the reference irradiance meter to transfer standard and field UV irradiance meters is discussed.

Quirks of dye nomenclature. 4. Fuchsine: four shades of magenta.

Fuchsine, also called magenta, was the second coal tar dye to be produced after mauveine. Fuchsine is composed of a mixture of up to four triphenylmethane dyes that differ only in the number of substituent methyl groups. Unlike mauveine, fuchsine still is widely used today as a biological stain. We describe the progress of fuchsine from its birth as the second coal tar dye, through a variety of modes of manufacture and industrial application, to its current use. We discuss complexities of nomenclature and identification, and the hazards and risks of its various applications.

Distribution and sources of PCBs (Aroclor 1268) in the Sapelo Island National estuarine research reserve.

Aroclor 1268 is a highly chlorinated PCB mixture that was released into the aquatic environment near Brunswick, GA (BR), as a result of decades of local industrial activity. This extensive contamination has led to US EPA Superfund designation in estuarine areas in and around Purvis Creek, GA. Roughly 50 km to the northeast is the Sapelo Island National Estuarine Research Reserve (SI) where previous studies have documented unexpectedly high Aroclor 1268-like PCB levels in blubber and plasma samples of resident bottlenose dolphins. This result led to a collaborative effort to assess the PCB patterns and concentrations in SI sediment and fish (as potential vectors for PCB transfer to SI resident dolphins). Thirty SI randomly assigned stations were sampled for sediment PCB levels. Additionally, fish were collected and analyzed from SI (n = 31) and BR (n = 33). Results were pooled with regional assessments of PCB concentrations from South Carolina and North Carolina in an effort to determine the association of Aroclor 1268 levels in SI samples. Results indicated that PCB levels in sediment and fish are much lower in the SI estuary compared to BR sediment and fish concentrations. However, PCB congener profiles for both sediments and fish were similar between the two locations and consistent with the Aroclor 1268 signature, indicating possible transport from the Brunswick area. A likely source of Aroclor 1268 in dolphins from SI is contaminated fish prey.

Quirks of dye nomenclature. 3. Trypan blue.

Trypan blue is colorant from the 19(th) century that has an association with Africa as a chemotherapeutic agent against protozoan (Trypanosomal) infections, which cause sleeping sickness. The dye still is used for staining biopsies, living cells and organisms, and it also has been used as a colorant for textiles.