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The scientific literature contains many accounts of application of polymethine dyes, including cyanine dyes, as imaging agents, i.e., "biological stains," for microscopic investigation of biological materials. Currently, many such dyes are used as probes for living cells, i.e., "fluorescent probes." Polymethine dyes are defined here by two criteria. First, they possess a conjugated chain of (2n + 1) sp2-hybridized carbon atoms that connect a terminal π-electron-accepting (π-electron withdrawing) group with a terminal π-electron-donating group. Second, they have an odd number (2n + 3) of π-centers and an even number (2n + 4) of π-electrons in this chain, where n equals the number of –CR2=CR3– groups, usually vinylene groups –CH=CH–. Commercialization of diverse chemical types of many polymethine dyes has been attempted. The dyes that have achieved wide application, however, are limited in number and it is these dyes that are emphasized here. Because these polymethine dyes sometimes have been described by confusing, and sometimes confused, names, we clarify here the chemical categories and names of such dyes for the nonchemist, biomedical end user of such imaging agents. Nevertheless, the nomenclature presented here is not intended to replace the traditional "chromophore" categories of dyestuff chemistry, because the latter are held in place both by wide usage and by venerable authorities, such as the Colour Index. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 undertanding 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. [ABSTRACT FROM AUTHOR]

Many drug molecules exert their biological action on intracellular molecular targets present on or inside various cellular organelles. Consequently, it has become more evident that the efficiency and efficacy of drug action is dependent largely on how well an unaided drug molecule is able to reach its intracellular target. We hypothesized that the biological action of such drug molecules might be improved by specific delivery to the appropriate sub-cellular site by a pharmaceutical carrier designed for the purpose. To test our hypothesis, we used paclitaxel, a molecule that has recently been shown to have pro-apoptotic biological targets on the mitochondria but has a quantitative structure-activity relationship-predicted cytosolic accumulation and no affinity for mitochondria. Using a mitochondria-specific nanocarrier system (DQAsomes) prepared from the amphiphilic quinolinium derivative dequalinium chloride to deliver paclitaxel to mitochondria in cells, we report that it is possible to improve the pro-apoptotic action of paclitaxel. [ABSTRACT FROM AUTHOR]

The article discusses informations from the meeting of the 2007 International Standards Organization (ISO) in China. Agenda of the meeting focuses on the specific necessities for quality and competence in the medical laboratory particularly accounted in the revision of ISO 15189. It also centers ISO 15190 that demands for a safety medical laboratories, thus requires more skills pertaining to safety from other medical laboratory experts. Practical implications on the discussion are also stated.

Trustees of the Biological Stain Commission have produced an online I Stain Glossary i of staining methods, stains and other reagents, plus some information on relevant historical figures and organizations in this field. Glossary items address dye-based ("tinctorial") routines and special stains, histochemistry and enzyme histochemistry, and immunostaining. These investigations have been undertaken because an understanding of staining mechanisms can lead to increased ability to troubleshoot existing staining methods and to design new staining procedures. [Extracted from the article]

This article presents an introduction to the 2007 issue of "Biotechnic and Histochemistry."

This article presents a study analysing the failure to specify sources of dyes, chromogens and fluorescent probes with illustrating certain suggestive proposals for action. Recently, Hans Lyon, a Trustee of the Biological Stain Commission, has reviewed and documents how reagent content, the amounts of colored and colorless impurities, and indeed the very identity of the reagent in the bottle can vary among batches, even when purchased from the same vendor. It is suggested that the impurity and heterogeneity of dyes, chromogens and fluorescent probes can give rise to experimental errors, inconsistent results, and perhaps even to diagnostic errors.

An introduction to the journal is presented in which the guest editors present papers, from the Symposium on Fluorochromes of Biological Stain Commission held in Rochester, New York in June 2012, that details different methods of imaging live cell utilizing fluorescence.

The sources cited within this issue are presented including "FDA regulation of immunochemicals used in immunohistochemistry: our view," by WE Grizzle and RW Mowry, "The success of a clinical librarian program in an academic autopsy pathology service," by M Royal, WE Grizzle, V Algermissen, and RW Mowry, and "Unusual object in the infratemporal fossa," by RS Mowry.

The article focuses on the applications and understanding of new dyes and fluorochromes. A dye or fluorochrome will be regarded as new if its structure was reported after 1999 or if while the compound may have been synthesized or offered for sale some years. They have also compared the effectiveness of new and old reagents.