Classification and naming of dyes, stains and fluorochromes.

A classification of dyes and other colorants is proposed, based on the chemical features responsible for their visibility and generally consonant with the writings of modern color chemists. The scheme differs in several respects from that of the Colour Index (CI), but it retains some traditional small groups of dyes that include biological stains. Natural dyes, recognized as a group in the CI, are placed with or near synthetic dyes with identical or similar chromophores. The new scheme also provides categories for dyes and fluorochromes that do not have places in the CI classification. Some CI categories, including lactones, aminoketones and hydroxyketones, are not recognized in this new scheme, which is adopted in the forthcoming 10th edition of Conn's Biological Stains: a Handbook of Dyes and Fluorochromes for Use in Biology and Medicine. Some rules are also set out for the spelling of trivial names, which has long been inconsistent in scientific literature. The ending '-ine' is used for compounds derived from organic bases (e.g., fuchsine and thionine, not fuchsin or thionin), and names ending in '-in' are for compounds that are not bases or their derivatives (e.g., eosin and phloxin, not eosine or phloxine). Initial capital letters are used only for words that are names of people or places (e.g., Nile blue or Congo red) and for the 'generic' components of CI application names (as in Acid yellow 36). Other words, including trade names that have fallen into common usage are not capitalized (e.g., alcian blue, biebrich scarlet, coomassie blue). The recommended spellings of some dyes differ from those commonly seen in vendors' catalogs and in biological publications, but they are generally consistent with English and American dictionaries, with recent writings in English by color chemists, and with the trivial names of other organic compounds.     

Metallic Lakes of the oxazines (Gallamin Blue,Gallocyanin and Coelestin Blue) as Nuclear Stain Substitutes for Hematoxylin

Becher's investigations upon the soluble metallic lakes of the oxazines have been re-investigated, extended and results described. Gallamin blue, gallocyanin and coelestin blue in combination with ferric ammonium sulfate gave the best results. The dyes are dissolved in a five per cent aqueous solution of ferric ammonium sulfate. The solution is boiled for 2–3 minutes, cooled, filtered and ready for immediate use. The iron lakes of these dyes stain nuclei excellently giving a deep blue or blue black in 3–5 minutes. No differentiation with acid is required. Coelestin blue gives the most stable solution and is recommended as a routine nuclear stain. The protoplasm remains practically colorless and counter-staining with acid dyes such as ethyl-eosin, orange G, or fuchsin gives pictures which cannot be distinguished from a good hematoxylin stain.

Counter-staining with van Gieson solution is also possible. Benda's modification of the van Gieson solution is recommended. Staining of fat with Sudan, scarlet red, etc., does not interfere with nuclear staining by these dyes.

As applied to the central nervous system these dyes are far superior to hematoxylin. Ganglion and glia cells are as excellently stained as with thionin.

The most widely used fixatives, namely formaldehyde, Mueller-formaldehyde, Zenker's and alcohol, give equally as good results. The nature of the staining process is briefly discussed and a prospectus offered.     

Rank and sequence in Caspar Bauhin's Pinax

CAIN, A. J., 1994. Rank and sequence in Caspar Bauhin's Pinax. Bauhin's consistent use of genera, species and binominals, applauded by historians as anticipating Linnaeus's theory and practice, does not appear on closer examination to be intended as anything of the sort. His use of the terms genus and species is as in Aristotelian logic, with a shifting reference, at all taxonomic levels. His typographical layout, emphasizing (but far from invariably employing) single-word names for effectively generic entities, often qualified by ‘and its species’, gives the impression of Linnaean practice, and coincides with it not infrequently, but not with Linnaean theory. The main entities for which it can be said that Bauhin uses fairly consistently a biverbal binominal name-phrase, like Linnaeus' trivial names, were in fact in Linnaeus's eyes two levels of supraspecific groupings. The main entities in Bauhin which Linnaeus recognized as species, as is shown by his quotations in the Species plantarum, are subdivisions of his biverbally or nearly biverbally named groupings, but themselves have multiverbal names. These correspond closely to Linnaeus's diagnostic specific names, not at all to his biverbal trivial names. Bauhin probably had no conception of the species and genus as ranks in the modern sense, first adumbrated by Tournefort and utilized by Linnaeus. Bauhin certainly tried to group forms by natural affinity, as did Theophrastus before him and Linnaeus afterwards. Not being alerted to the importance of the details of the flower and fruit, he used what characters he could find, notably, but not by any means exclusively, leaf shape. He composed the Pinax as a nomenclatural concordance to earlier authors, notably Dioscorides, Theophrastus and Pliny. He retained the sequence of major groups of Theophrastus (as the greatest authority on plants) but reversed it to start with the best-known plants, grasses. Where Theophrastus gave no help, in the cryptogams, Bauhin inserted as a pendant his own series from ferns down to fungi, using the Aristotelian principles of the gradation of forms. His overall arrangement, therefore, is not a simple progression but a chain with pendants. Bauhin is far closer to earlier authors than to Linnaeus, but his typography, along with other authors, may well have helped to incite Linnaeus to a more rigorous and consistent use of ranked groups and biverbal names.     

Proposal for Naming Host Cell-Derived Inserts in Retrovirus Genomes

We propose a system for naming inserted sequences in transforming retroviruses (i.e., onc genes), based on using trivial names derived from a prototype strain of virus.     

Semisystematic nomenclature of brassinosteroids

The assignment of the trivial name to new isolated or detected brassinosteroid is based on the trivial names of seven different brassinosteroids, with names assigned according to the plant source from which they were first isolated. To avoid some observed mistakes in assigning trivial names to these compounds and the impractical constant usage of their systematic names, we propose a semisystematic nomenclature of brassinosteroids, in which (22R,23R)-2,3,22,23-tetrahydroxy-5-campestane, the trivial name of which is 6-deoxocastasterone, is considered the functional parent compound and is named brassinostane or brassinane. A set of rules for naming the remaining natural brassinosteroids is presented.     

Is Yuan in China’s Three Gorges a Gibbon or a Langur?

Clarifying the scientific identity of ancient biological names in historical archives is essential to understand traditional knowledge and literary metaphors of animals in human culture. Adopting a cross-disciplinary (Primatology, Linguistics, Historiography, Historical Sociology) analysis, we developed a theoretical framework for studies of the scientific identity of Chinese primate traditional names (e.g., Yuan _猿) throughout history, and interpret the historical evolution of the understanding of the Chinese word Yuan. Presently, the Chinese generally understand Yuan to be a gibbon (or “ape” in a broader sense), but this statement has many contradictions with the understanding of the word in relevant historical discourse. We review and comment on key evidence to support the traditional understanding of Yuan as a gibbon (Hylobatidae) and clarify the historical and current thought concerning Yuan. We find that the referent of the word Yuan has changed from “François’ langur (Trachypithecus francoisi) with long limbs” to the “long-armed ape or gibbon” known today through two major changes in the idea of Yuan. One transformation in the conceptualization of Yuan took place during the Tang-Song period, with the other beginning at the end of the nineteenth century and ending in the 1950s. An interaction between the conceptualization of animals and power (e.g., political opportunity; cultural movement toward learning western sciences in the semi-colonial era) played an important role in these two diachronic changes to the idea of Yuan. In contrast to the clear linear relation between a species and its Latin name, our study indicates that one traditional name can represent varying animal species in China. Our findings exemplify the implications of the sociocultural and linguistic basis for the species identification of primate names found in historical discourse for historical zoogeography, our understanding of the intricate cultural and religious connections between humans and primates, and efforts to decolonize primatology.

     

Staining Bacteria and Yeasts with Acid Dyes

Various acid dyes prove satisfactory for the routine staining of bacteria. Those used are acid fuchsin, anilin blue w. s., fast acid blue R, fast green FCF, light green, orseilline BB, erythrosin, phloxine and rose bengal. Acid fuchsin, fast green, anilin blue, and orseilline are especially recommended. Phenolic solutions of the dyes, acidified with acetic acid, with the addition of ferric chloride to those containing acid fuchsin, anilin blue, fast green or light green, are used. Procedures are given in detail for staining or demonstrating vegetative cells, resting and germinating spores, capsules, sheaths and glycogen in bacteria; germinating and conjugating spores of yeast; and for counterstaining after acid fast or Gram staining. The principal advantages of using acid dyes are better differentiation, and less tendency for slime amd debris to take the dye.     

Mechanisms of chromosome banding

A thorough understanding of the mechanisms of R-, C-and G-banding will come only from studies of the binding of Giemsa dyes to isolated and characterized preparations of heterochromatin and euchromatin. Since such studies require an exact knowledge of the optical characteristics of Giemsa, the spectral adsorption curves and extinction coefficients of Giemsa and its component dyes at various concentrations in the presence and absence of DNA were determined. — Although Giemsa is a complex mixture of thiazin dyes plus eosin; methylene blue, and azure A, B or C alone gave good banding. Thionin, with no methyl groups, gave poor or no banding. Eosin was not a necessary component for banding. — The most striking characteristic of the thiazin dyes is that they are strongly metachromatic, i.e., their adsorption spectra and extinction coefficients change as the concentration of the dye increases or as they bind to positively charged compounds (chromotropes). These changes, especially for methylene blue, are described in detail and allow a distinction between concentration dependent binding to DNA by intercalation and binding by side stacking.     

Raphael Meldola,his blue and his times

Raphael Meldola (1849–1915), English industrial and academic chemist, spectroscopist, naturalist, educator and lobbyist for science, is today almost a forgotten scientist whose life is celebrated only with a medal awarded by the Royal Society of Chemistry that honors achievement by younger chemists. In the 1870–80s, however, he invented a number of important synthetic dyestuffs including the cotton dyes isamine blue and Meldola's blue, and also naphthol green B, all of which have had application in biology and medicine. I describe here the early emergence of the synthetic dye industry, the first science-based industry, Meldola's role in its development, and his own inventions. Meldola's wide ranging achievements in science led to appointments as president of important professional scientific and manufacturers' societies. He was a fervent disciple of natural selection, a correspondent of Charles Darwin, and a prominent 19^th-century neo-Darwinian. In 1886, drawing on analogies with evolutionary theory, he warned the British that neglect of science, particularly chemistry, would lead to industrial decline and even extinction, though his message generally was ignored, at least until 1914.     

Confidence of paternity,divorce, and investment in children by Albuquerque men

Using a sample of men living in Albuquerque, NM, we examined the relationship between paternity confidence and men's investment in children. In humans, men may reduce their investment in a child in two ways: indirectly, by ending their relationship with the child's mother and ceasing to cohabit with the child (e.g., divorce), and directly, by allocating less time and fewer resources to the child. In this article, we tested two hypotheses regarding the effect of paternity confidence on investment in children: (1) men will be more likely to divorce women if they suspect or are sure that they are not the father of their wife's child, and (2) controlling for divorce, men will reduce direct investments in low paternity confidence children relative to high paternity confidence children. The first hypothesis was supported by the data. The second hypothesis was supported for two out of three measures of paternal investment we examined; low paternity confidence reduces the time men spend with a child in a group with other children or adults, and it reduces extensive involvement with the child's educational progress; there was no effect of paternity confidence on the amount of time men spend with children in one-on-one interactions. We also examined the effects of unstated paternity confidence (e.g., when men decline to answer the question) on divorce and paternal investment. Overall, the results suggested that paternity confidence plays an important role in shaping men's relationships with women and with their putative genetic children.     

Analysis of ultra acidic proteins by the use of anodic acidic gels

Ultra acidic proteins, generated by posttranslational modifications, are becoming increasingly important due to recent evidence showing their function as regulatory elements or as intermediates in degradation pathways in bacteria. Such proteins are important in neurodegenerative diseases and embryonic development, and they include the Alzheimer-related tau (τ) protein (resulting from posttranslational modifications) and the phosphor-storage embryonic proteins. The ultra acidic proteins are difficult to study because standard two-dimensional gel electrophoresis is inadequate for their analysis. Here we describe a novel electrophoresis system of anodic acidic gels that can replace isoelectric focusing as the first dimension of separation in two-dimensional electrophoresis. The system is based on a sodium acetate buffer (pH 4.6), is compatible with traditional stains (e.g., Coomassie blue) as well as novel fluorescent dyes (e.g., Pro-Q Diamond), and is quantitative for the analysis of ultra acidic proteins. The anodic acidic gels were used for the functional classification of the ultra acidic part of the Bacillus subtilis proteome, showing significant improvement over traditional two-dimensional electrophoresis.     

Fitness effects of two facultative endosymbiotic bacteria on the pea aphid,Acyrthosiphon pisum,and the blue alfalfa aphid,A. kondoi

The effects of two bacterial endosymbionts, designated PASS and PAR, were evaluated on the pea aphid, Acyrthosiphon pisum (Harris) (Hemiptera:Aphididae), in which they occur facultatively, and on the blue alfalfa aphid, A. kondoi Shinji, in which these bacteria have not been found in natural populations. Subclones of pea aphids and blue alfalfa aphids, derived from parent aphid clones that did not contain PASS or PAR, were infected with one or both bacteria, generating PASS- and/or PAR-positive subclones with minimal genetic differences from the parent clones. Under laboratory conditions at 20 °C, PAR consistently reduced the fecundity (by between 19 and 60%) of subclones derived from three different parent pea aphid clones on bur clover, Medicago hispida Gaertn. PAR had intermediate effects on pea aphids reared on sweet pea, Lathyrus odoratus L., and had no significant effect on pea aphids on alfalfa, Medicago sativa L. The effect of PASS was either neutral or negative, depending on parent clone as well as host plant. Also at 20 °C, PASS reduced fecundity (70–77%) and longevity (40–48%), and increased the age of first reproduction (by up to 1.5 days) of blue alfalfa aphid reared on alfalfa and clover. PAR had a less dramatic effect (e.g., 30–39% reduction in fecundity) on these traits of blue alfalfa aphid. In contrast, PAR and PASS increased the fitness of pea aphid subclones of one parent clone reared for three generations at 25 °C on each of the three test plants. Without facultative bacteria, fecundity of the parent clone was reduced to a mean total of < 6 offspring per adult at this elevated temperature, but with PASS or PAR, mean total fecundity of its subclones was > 35. However, this ameliorative effect of facultative bacteria at 25 °C was not found for two other sets of parent clones and their derived subclones. Alate production in pea aphids was significantly increased in large populations of two PASS- and PAR-positive subclones relative to their parent clones. Attempts to transmit PASS or PAR horizontally, i.e., from aphid to aphid via feeding on host plants (bur clover), were unsuccessful.     

Macrocarpones,novel metabolites from stromata of <Emphasis Type="Italic">Hypoxylon macrocarpum</Emphasis>, and new evidence on the chemotaxonomy of <Emphasis Type="Italic">Hypoxylon</Emphasis> species

Several species of the genus Hypoxylon (Xylariaceae) were studied for morphological characters and HPLC-based secondary metabolite profiles. It was confirmed that Hypoxylon is divided into two groups of species, containing either Mitorubrin type azaphilones or binaphthyls, respectively, as main metabolites. In Hypoxylon species of the latter group, some metabolites that are known from the allied genus Daldinia (i.e., Daldinal A in H. fuscum and Daldinin C in H. fuscopurpureum), were encountered for the first time. Moreover, three novel aromatic polyketides, for which the trivial names Macrocarpones A, B and C are proposed, were isolated from ascostromata of Hypoxylon macrocarpum and identified by high resolution mass spectrometry and 2D-NMR spectroscopy. Orsellinic Acid was also identified from ascostromata of H. howeianum and detected by HPLC-MS and HPLC-UV/Vis fingerprinting methodology in H. fragiforme and H. rubiginosum, but not in other examined Hypoxylon species. Due to these studies, H. fuscopurpureum sensu Y.-M. Ju & J.D. Rogers 1996 was identified as a new record for Germany.     

How Romanowsky stains work and why they remain valuable — including a proposed universal Romanowsky staining mechanism and a rational troubleshooting scheme

Abstract

An introduction to the nomenclature and concept of “Romanowsky stains” is followed by a brief account of the dyes involved and especially the crucial role of azure B and of the impurity of most commercial dye lots. Technical features of standardized and traditional Romanowsky stains are outlined, e.g., number and ratio of the acidic and basic dyes used, solvent effects, staining times, and fixation effects. The peculiar advantages of Romanowsky staining are noted, namely, the polychromasia achieved in a technically simple manner with the potential for stain intensification of “the color purple.” Accounts are provided of a variety of physicochemically relevant topics, namely, acidic and basic dyeing, peculiarities of acidic and basic dye mixtures, consequences of differential staining rates of different cell and tissue components and of different dyes, the chemical significance of “the color purple,” the substrate selectivity for purple color formation and its intensification in situ due to a template effect, effects of resin embedding and prior fixation. Based on these physicochemical phenomena, mechanisms for the various Romanowsky staining applications are outlined including for blood, marrow and cytological smears; G-bands of chromosomes; microorganisms and other single-cell entities; and paraffin and resin tissue sections. The common factors involved in these specific mechanisms are pulled together to generate a “universal” generic mechanism for these stains. Certain generic problems of Romanowsky stains are discussed including the instability of solutions of acidic dye–basic dye mixtures, the inherent heterogeneity of polychrome methylene blue, and the resulting problems of standardization. Finally, a rational trouble-shooting scheme is appended.     

A sensitive, viable-colony staining method using Nile red for direct screening of bacteria that accumulate polyhydroxyalkanoic acids and other lipid storage compounds

The oxazine dye Nile blue A and its fluorescent oxazone form, Nile red, were used to develop a simple and highly sensitive staining method to detect poly(3-hydroxybutyric acid) and other polyhydroxyalkanoic acids (PHAs) directly in growing bacterial colonies. In contrast to previously described methods, these dyes were directly included in the medium at concentrations of only 0.5 μg/ml, and growth of the cells occurred in the presence of the dyes. This allowed an estimation of the presence of PHAs in viable colonies at any time during the growth experiment and a powerful discrimination between PHA-negative and PHA-positive strains. The presence of Nile red or Nile blue A did not affect growth of the bacteria. This viable-colony staining method was in particular applicable to gram-negative bacteria such as Azotobacter vinelandii, Escherichia coli, Pseudomonas putida, and Ralstonia eutropha. It was less suitable for discriminating between PHA-negative and PHA-positive strains of gram-positive bacteria such as Bacillus megaterium or Rhodococcus ruber, but it could also be used to discriminate between wax-ester- and triacylglycerol-negative and -positive strains of Acinetobacter calcoaceticus or Rhodococcus opacus. The potential of this new method and its application to further investigations of PHA synthases and PHA biosynthesis pathways are discussed. Received: 12 August 1998 / Accepted: 11 November 1998     

Evaluating abundance estimates and evidence of breeding for Bobolinks from transect and point-count surveys

Estimating the abundance and breeding success of territorial songbirds is challenging. Various types of surveys and analyses are available, but all receive some criticism in the literature, and most methods are rarely compared with results obtained using intensive monitoring efforts. We assessed the efficacy of transect and point-count surveys to estimate the abundance of male Bobolinks (Dolichonyx oryzivorus) and detect evidence of nesting and fledging by comparing the results of those surveys to results from more intensive monitoring (i.e., spot mapping and nest monitoring). We monitored 36 fields (254 ha) of late-harvest hay, restored grassland, and fallow fields in the Luther Marsh Wildlife Management Area and on four farms in southern Ontario, Canada, in 2018. Compared to the number of territories identified based on spot mapping (197), distance sampling analysis of transect survey data provided a more accurate estimate of the abundance of male Bobolinks (230, 95% CI: 187, 282) than N-mixture models of transect (668, 95% CI: 332, 1342) and point-count (337, 95% CI: 203, 559) data. Three visits to survey transects and five to point counts did not effectively detect evidence of Bobolink breeding (i.e., nesting or fledging) in fields compared to spot mapping and nest monitoring. Distance sampling analysis of transect data appears promising for estimating the number of Bobolink territories in an area, e.g., those impacted by conservation programs. If estimates of the number of nesting Bobolinks and frequency of fledging are of interest, spot mapping and nest monitoring could be implemented at a subset of sampled fields. Our results suggest that additional studies to evaluate model-based estimates of abundance with the best available information (e.g., from spot mapping of marked or unmarked populations and nest monitoring) would be useful to ensure that robust estimates are provided to support population estimates and conservation actions.     

Current applications of orcein in histochemistry. A brief review with some new observations concerning influence of dye batch variation and aging of dye solutions on staining

Current uses of orcein to demonstrate elastic fibers and, following permanganate oxidation (Shikata's modification), hepatitis B surface antigen, copper associated protein, and sulfated mucins, are reviewed. Variations in staining performance with batch of dye and age of dye solution is also discussed. Additional experimental findings support the view that the orcein stain for elastic tissue and Shikata's modification produces consistent, high quality results as long as appropriate controls and suitable dye batches, e.g., Biological Stain Commission certified dyes, are used.     

Metallic Lakes of the oxazines (Gallamin Blue, Gallocyanin and Coelestin Blue) as Nuclear Stain Substitutes for Hematoxylin

Becher's investigations upon the soluble metallic lakes of the oxazines have been re-investigated, extended and results described. Gallamin blue, gallocyanin and coelestin blue in combination with ferric ammonium sulfate gave the best results. The dyes are dissolved in a five per cent aqueous solution of ferric ammonium sulfate. The solution is boiled for 2-3 minutes, cooled, filtered and ready for immediate use. The iron lakes of these dyes stain nuclei excellently giving a deep blue or blue black in 3-5 minutes. No differentiation with acid is required. Coelestin blue gives the most stable solution and is recommended as a routine nuclear stain. The protoplasm remains practically colorless and counter-staining with acid dyes such as ethyl-eosin, orange G, or fuchsin gives pictures which cannot be distinguished from a good hematoxylin stain.

Counter-staining with van Gieson solution is also possible. Benda's modification of the van Gieson solution is recommended. Staining of fat with Sudan, scarlet red, etc., does not interfere with nuclear staining by these dyes.

As applied to the central nervous system these dyes are far superior to hematoxylin. Ganglion and glia cells are as excellently stained as with thionin.

The most widely used fixatives, namely formaldehyde, Mueller-formaldehyde, Zenker's and alcohol, give equally as good results. The nature of the staining process is briefly discussed and a prospectus offered.     

George Gaylord Simpson as mentor and apologist for paleoanthropology

The influence of George Gaylord Simpson (1902–1984) on paleoanthropology provides a well-documented, historical example of how one scientific discipline can impact upon another, bringing the latter quickly “up to speed” without having to retrace ground covered by the former. Paleoanthropologists were bystanders during the formulation of the evolutionary synthesis (1936–1947). After World War II, the younger paleoanthropologists looked to George Gaylord Simpson as one of several mentors regarding the implications of the synthesis for their own discipline. But why Simpson? Having earlier defined the superfamily Hominoidea (1931) as holding the Pongidae and Hominidae and monographed lower primate fossils (e.g., “Studies on the earliest primates,” 1940), Simpson's “Principles of classification and a classification of mammals” (1945) further solidified his reputation as a mammalian systematist. Simpson's Meaning of Evolution (1949) was widely read as an introduction to the synthesis, and his Tempo and Mode in Evolution (1944) made accessible the more complex aspects. Consequently, in the 1950s and 1960s paleoanthropologists invited Simpson to participate in their symposia (e.g., “Some principles of historical biology bearing on human origins,” 1951; “The meaning of taxonomic statements,” 1964), used his books as classroom texts, and cited his publications to support claims for their own work. Later in the 1960s, Simpson moved from mentor to apologist, as the paleoanthropologists were by then familiar with the synthesis and incorporated its theoretical concepts in their interpretations of the many newly discovered hominoid fossils. Simpson now took special care to celebrate these results in his more general, less technical writings, acting as a forceful apologist for the materialistic view of human origins (e.g., “The biological nature of man,” 1966; “The evolutionary concept of man,” 1972). During the 1970s, Simpson's influence waned, and he became just another practitioner at the margin of the discipline. However, anthropologists acknowledged Simpson's earlier impact, for example, when he was invited, yet again, to address them at the 50th anniversary celebration of the American Association of Physical Anthropologists in 1981.