Using extract from alkanet (Alkanna tinctoria) as a source of both a red lipid stain and a blue counterstain for histology.

Alkanet (Alkanna tinctoria) is a plant native to and cultivated in parts of Europe, Asia and the Middle East. It has been used for thousands of years as a medicinal agent and as a colorant for textiles, food and cosmetics. An extract from the root of this plant has been used with a mordant to stain nuclei. We describe here the versatility of different extracts from this plant to stain lipids red and to counterstain certain other tissue elements blue. The color variation and selective differential staining is due to solvent polarity and pH. Extracts contain numerous chemical species, all of which are derivatives of the indicator dye, naphthazurin. Our red extract is nonionic below pH 7 and partitions from its somewhat polar solvent of 100% isopropanol to nonpolar lipids. The blue extract is dianionic at high pH in 70% isopropanol and binds ionically to cationic tissue structures such as collagen, muscle and cytoplasm of other cells.

Modeling the extent of conjugation in histochemical dyes and fluorescent probes: clarification in calculating conjugated bond number (CBN) and introduction of a new parameter, resonance energy.

Determining the extent of conjugation in dyes and fluorochromes is a helpful tool for understanding or predicting the behavior of these compounds when used as stains for microscopy. One measure that has been used repeatedly is conjugated bond number (CBN), which is the number of bonds in a conjugated system. CBN can be obtained by inspection of the structure of a compound, but the rules for how to determine what constitutes a conjugated system are not fully established. Using molecular modeling software, we have defined more clearly which groups contribute to conjugation and which do not. We accomplished this by using a new parameter, resonance energy (RE'), which is the energy differential between a conjugated compound and its unconjugated counterpart. Conjugated compounds possess less energy. If a compound contains a questionable atom or group, RE' can be calculated for the compound with and without that group. If RE' is the same for both, the group in question plays no role in the resonance and thus is not part of the conjugated system.

Betacyanins are plant-based dyes with potential as histological stains.

Interest is increasing in certain parts of the world in replacing synthetic dyes with dyes from natural sources, particularly from plants. Although textile dyers have used various groups of natural dyes, microscopists generally have restricted their use to anthocyanins. Recently, however, another class of plant-based dyes has found some favor, the betacyanins. Betacyanins are a group of red and violet betalain dyes found only in certain plants of the order Caryophyalles and in Basidiomycetes mushrooms. Although the chemical structures of betacyanins are known, little use has been made of that information to understand or predict their behavior with biomedical specimens. We investigated two common, widely distributed betacyanin-containing plants, edible beets (Beta vulgaris) and wild pokeweed (Phytolacca americana). Aqueous alcoholic extracts were made from beet root and pokeweed berries, adjusted to pH 4.1 or 5.3 and used together with Harris' hematoxylin to stain histological sections. We used a methanolic extract of pokeweed berries, pH 3.0, to stain cultured mycological specimens. Both extracts produced satisfactory staining that was equivalent to that of eosin Y, although the colors were more muted with the beet root extract. Epithelial cytoplasm, muscle, collagen and erythrocytes were well demonstrated. Betanin is the predominant component of beet root extract; it possesses one delocalized positive charge and three carboxylic acid substituents. The dyes are weak acids and the carboxylate anions are more diffuse than for eosin Y; this produces weaker bonding to tissue cations. The principal colored component of pokeweed berries, prebetanin, possesses a sulfonic acid group as well as carboxylic acids, which favors acid dyeing and more intense coloration. Both dyes show potential for hydrogen bonding and to a much lesser extent for some types of van der Waals forces. Complex formation with metals such as aluminum to create a nuclear stain is not likely with beet root dyes nor is it possible with pokeweed dyes. Betacyanins are suitable for staining microscopy preparations in place of other red acid dyes such as eosin. Of the two dyes tested here, prebetanin from pokeweed berries was superior to betanin from red beet roots. These berries are widely distributed and readily collected; the extraction procedure is simple and does not require expensive solvents.

Anthocyanins from a single botanical source can be used as a replacement for hemalum and eosin.

For various reasons, histologists in several parts of the world have tried to replace hematoxylin and eosin with locally available plant dyes of the anthocyanin family. Blue or violet nuclear stains have been created by combining an anthocyanin with iron or aluminum ions at low pH. Obtaining a pink or red cytoplasmic counterstain, however, has not been achieved previously, even with a red solution of anthocyanin, because the chemistry of the colorant does not allow bonding to cytoplasmic materials and collagen. We used two extracts from the petals of common mallow, Malva sylvestris, to create both a blue nuclear stain and a red counterstain. The two extracts contained two chemically distinct types of anthocyanins. The first extract contains vic-hydroxyls capable of complexing aluminum ions; its flavylium core is cationic. The second type lacks vic-hydroxyls on its core structure, but includes pendant glucosides that contain a malonic acid ester with a free carboxyl substituent. The precise identity of the first anthocyanin currently is unknown, but likely is one or more of the common anthocyanins such as cyanidin, delphinidin or petunidin, which complex readily with aluminum. The second anthocyanin is malonated malvidin, which does not complex with aluminum, but is anionic at the pH used here. The overall visual effect of applying the two anthocyanin extracts is remarkably similar to that of hemalum plus eosin.

Molecular stabilization and complexation: the secrets of making a nuclear-selective histological stain from naturally occurring anthocyanins without oxidation.

The natural colorant, roselle, found in Hibiscus sabdariffa, has been used as a histological dye since at least 1976. As a simple extract roselle acts as a general red counterstain, but when treated with an oxidant and metallic mordant it functions as a useful blue nuclear-selective stain. In the past 40 years it has been assumed that oxidation is necessary when preparing a stain from roselle, as of course it is for the related flavonoid dyes hematoxylin and brazilin. However, the chemistry of roselle argues against this. Roselle is a mixture of four closely related compounds: delphinidin 3-sambubioside and cyanidin 3-sambubioside, delphinidin 3-glucoside and cyanidin 3-glucoside. Each of these in turn can exist in 8 different configurations in a complex state of equilibrium largely dependent upon pH. Of these compounds, only three are colored. In plants, and in their complex extracts, formation of these colorless compounds is inhibited by the presence of other colorless aromatic molecules, a stabilizing process termed co-pigmentation. The color of such extracts may be red in the acid range and blue or violet above neutrality. Complexation (chelation) with metal cations occurs above pH 2.8 or 3.0, depending upon the concentration of the metal. Prior oxidation is not needed for such chelation to occur. With Al3+ the resulting metal complex, which we term rosalum, is violet or blue. Following spectrophotometric investigation of this complexation, we were able to formulate a nuclear-selective violet/blue stain without the use of an oxidant.

Use of roselle extracted from Hibiscus sabdariffa for histological staining: a critical review and rational stain formulation.

Roselle is the common name for a mixture of anthocyanin dyes derived from the plant, Hibiscus sabdariffa. During the past two decades, a sizable, but conflicting, body of literature has supported the use of roselle as a biological stain, and more specifically as a substitute for hematoxylin for staining nuclei selectively. We review the literature and suggest a rational explanation for divergent findings. When used without oxidation and mordanting, roselle is an indiscriminate oversight stain. With appropriate oxidation and mordanting, roselle can be an effective nuclear stain. We propose here use of a stain that is formulated rationally and followed by treatment in a differentiating solution that also acts as a counterstain. We also offer suggestions for improving roselle for the general scientific community.

Amyloid from a histochemical perspective. A review of the structure, properties and types of amyloid, and a proposed staining mechanism for Congo red staining.

Amyloid is a diverse group of unrelated peptides or proteins that have positive functionality or are associated with various pathologies. Despite vast differences, all amyloids share several features that together uniquely define the group. 1) All amyloids possess a characteristic cross-ß pattern with X-ray diffraction typical of ß-sheet secondary protein structures. 2) All amyloids are birefringent and dichroic under polarizing microscopy after staining with Congo red, which indicates a crystalline-like (ordered) structure. 3) All amyloids cause a spectral shift in the peak wavelength of Congo red with conventional light microscopy due to perturbation of π electrons of the dye. 4) All amyloids show heightened intensity of fluorescence with Congo red, which suggests an unusual degree of packing of the dye onto the substrate. The ß portion of amyloid molecules, the only logical substrate for specific Congo red staining under histochemical conditions, consists of a stack of ß-sheets laminated by hydrophilic and hydrophobic interactions between adjacent pairs. Only the first and last ß-sheets are accessible to dyes. Each sheet is composed of numerous identical peptides running across the width of the sheet and arranged in parallel with side chains in register over the length of the fibril. Two sets of grooves are bordered by side chains. X grooves run perpendicular to the long axis of the fibril; these grooves are short (the width of the sheet) and number in the hundreds or thousands. Y grooves are parallel with the long axis. Each groove runs the entire length of the fibril, but there are very few of them. While Congo red is capable of ionic bonding with proteins via two sulfonic acid groups, physical constraints on the staining solution preclude ionic interactions. Hydrogen bonding between dye amine groups and peptide carbonyls is the most likely primary bonding mechanism, because all ß-sheets possess backbone carbonyls. Various amino acid residues may form secondary bonds to the dye via any of three van der Waals forces. It is possible that Congo red binds within the Y grooves, but that would not produce the characteristic staining features that are the diagnostic hallmarks of amyloid. Binding in the X grooves would produce a tightly packed series of dye molecules over the entire length of the fibril. This would account for the signature staining of amyloid by Congo red: dichroic birefringence, enhanced intensity of fluorescence and a shift in visible absorption wavelength.

Alternative methods for estimating common descriptors for QSAR studies of dyes and fluorescent probes using molecular modeling software: 1. Concepts and procedures.

Quantitative structure activity relations (QSAR) models were developed to predict uptake and intracellular localization of probes or dyes in living cells. Many of the QSAR parameters used in such models are determined manually. Unfortunately, this requires a depth of chemical knowledge that biologists who wish to use these predictive tools do not necessarily possess. Moreover, some of the parameters are not easily obtained for all dyes and probes, which further restricts widespread use of QSAR methodology. Alternatives to some of these QSAR descriptors are defined and explained here. Estimation of these novel parameters using molecular modeling software, widely available and readily usable on personal computers in a variety of forms and brands, is described here. QSAR researchers need only draw the molecular structure and, with the proper commands, obtain either the parameters directly or the information to calculate them. I also demonstrate how the same software can generate some of the standard QSAR parameters, e.g., MW, Z, CBN, more reliably and conveniently than the manual procedures. A particularly problematic descriptor is log P, the logarithm of the octanol/water partition coefficient of a probe. This is discussed in detail and a novel alternative measure, the hydrophilic/lipophilic index (HLI), is introduced together with preliminary validation.

Alternative methods for estimating common descriptors for QSAR studies of dyes and fluorescent probes using molecular modeling software. 2. Correlations between log P and the hydrophilic/lipophilic index, and new methods for estimating degrees of amphiphilicity.

The log P descriptor, despite its usefulness, can be difficult to use, especially for researchers lacking skills in physical chemistry. Moreover this classic measure has been determined in numerous ways, which can result in inconsistant estimates of log P values, especially for relatively complex molecules such as fluorescent probes. Novel measures of hydrophilicity/lipophilicity (the Hydrophilic/Lipophilic Index, HLI) and amphiphilicity (hydrophilic/lipophilic indices for the head group and tail, HLIT and HLIHG, respectively) therefore have been devised. We compare these descriptors with measures based on log P, the standard method for quantitative structure activity relationships (QSAR) studies. HLI can be determined using widely available molecular modeling software, coupled with simple arithmetic calculations. It is based on partial atomic charges and is intended to be a stand-alone measure of hydrophilicity/lipophilicity. Given the wide application of log P, however, we investigated the correlation between HLI and log P using a test set of 56 fluorescent probes of widely different physicochemical character. Overall correlation was poor; however, correlation of HLI and log P for probes of narrowly specified charge types, i.e., non-ionic compounds, anions, conjugated cations, or zwitterions, was excellent. Values for probes with additional nonconjugated quaternary cations, however, were less well correlated. The newly devised HLI can be divided into domain-specific descriptors, HLIT and HLIHG in amphiphilic probes. Determinations of amphiphilicity, made independently by the authors using their respective methods, showed excellent agreement. Quantifying amphiphilicity from partial log P values of the head group (head group hydrophilicity; HGH) and tail (amphiphilicity index; AI) has proved useful for understanding fluorescent probe action. The same limitations of log P apply to HGH and AI, however. The novel descriptors, HLIT and HLIHG, offer analogous advantages to those seen with HLI over log P. The high correlation between log P and HLI, and the concordance between the two systems for assessing amphiphilicity, provide a powerful tool for QSAR studies. It is possible now to select a probe with missing fragments, and thus no log P, AI or HGH; and to estimate these important descriptors from parameters derived from HLI.