Standardization in Biological Staining. The Influence of Dye Manufacturing

The purpose of biological staining is to obtain specimens of biological material that can be assessed in the microscope. These specimens are influenced by all processes from removal from the intact organism to mounting on the microscopic slide. To achieve comparable results with various techniques for biological staining, standardization of all procedures and reagents is mandatory. In this paper, I focus particularly on dyes and consider the possibilities for obtaining standardized dyes. In general practice, most biological staining takes place with available commercial dyes. These dyes may or may not have been subjected to quality assessment either internally by the producer or vendor or externally by independent investigators or organizations such as the Biological Stain Commission. Concerted attempts at standardization in Europe are discussed. The latest results of this work, the European standard EN 12376, is presented. This standard is concerned with information supplied by the manufacturer with in vitro diagnostic reagents for biological staining. The standard has been prepared by a Working Group on Staining in Biology under Technical Committee 140, In Vitro Medical Devices, of the European committee for standardization, CEN.     

Molecular mechanisms of antigen retrieval: antigen retrieval reverses steric interference caused by formalin-induced cross-links

Abstract

The overwhelming majority of antibodies useful for formalin fixed, paraffin embedded (FFPE) tissues require antigen retrieval to reverse the effect of formalin fixation and re-establish immunoreactivity. How this reversal happens is poorly understood. We developed a new experimental model for studying the mechanism of formalin fixation and antigen retrieval. Epitope mapping studies on nine antibodies useful for FFPE tissues revealed that each consisted of a contiguous stretch of amino acids in the native protein (linear epitope). Small peptides representing the epitopes of antibodies to human epidermal growth factor receptor type (HER2), estrogen, and progesterone receptors were attached covalently to glass microscope slides in a peptide array. Most peptides retained immunoreactivity after formalin fixation. Immunoreactivity was completely abrogated for all peptides, however, if an irrelevant large protein was present during formalin-induced cross-linking. We hypothesize that cross-linking the irrelevant protein to the peptide epitopes sterically blocked antibodies from binding. Antigen retrieval dissociates irrelevant proteins and restores immunoreactivity. Because the epitopes for clinical antibodies require only primary protein structure, the fact that antigen retrieval probably denatures the secondary and tertiary structure of the protein is irrelevant. The same mechanism may occur in tissue samples subjected to formalin fixation and antigen retrieval.     

Controlled oxidation of calf thymus DNA to produce standard samples for 8-Oxodeoxyguanosine analysis; Effects of freeze-drying,storage and hydrolysis conditions

Calf thymus DNA containing defined levels of 8-hydroxy-2′-deoxyguanosine (8-oxodG) was prepared by treatment with visible light in the presence of photosensitiser Ro 19-8022. The DNA was checked for stability; after freeze-drying, the amount of 8-oxodG did not increase during 6 weeks' storage at room temperature. However, freeze-drying itself can introduce additional oxidative damage. Two enzymic hydrolysis regimes (DNase I, phosphodiesterases I and II, and alkaline phosphatase; or P1 nuclease and alkaline phosphatase) give similar values for 8-oxodG.     

Characterization of Indoor Environmental Quality in Primary Schools in Maia: A Portuguese Case Study

Scientific evidence associates indoor environment pollutants with respiratory effects (asthma and allergies), and children constitute one of most sensitive groups. Indoor air quality (IAQ) in schools may indeed be a significant health factor for children, with effects on school attendance and performance. Our aim was to characterize IAQ of classrooms in Maia County (north of Portugal) for which there was no information available. The study was conducted in 21 of the 40 primary schools, selected by stratified random sampling. Depending on the dimension, one or two classrooms were tested at each school. Walkthrough surveys of school grounds, buildings, and individual classrooms were done. Continuous measurements were taken of temperature, relative humidity, airborne respirable particles, total volatile organic compounds, and carbon dioxide, whereas bioaerosols were counted on Plate Count Agar during regular school activities. The indoor arithmetic mean for PM₁₀, CO₂, TCOV, and bioaerosol concentrations were 0.14 mg/m³, 999 ppm, 0.41 mg/m³, and 4140 UCF/m³, respectively. The values of PM₁₀ and CO₂ were close to their acceptable maximum values, but bioaerosols were much higher. This study supports previous studies conducted in school environments and emphasizes the need for proactive indoor air quality audits in school buildings.     

Invasion patterns in riparian habitats: The role of anthropogenic pressure in temperate streams

The riparian flora and the level of invasion in the rivers of the Cantabric watershed in Spain were studied in relation to the ecological status and the anthropogenic pressure. The level of invasion was also analyzed in different riparian habitats: forests, river bars and man-made slopes. For this purpose, 18 sites were sampled and a list of native and alien plant species was made along a 100-m strip at each site. The habitat/s where alien species were found and their abundance per habitat and in the total area were also indicated. Out of 112 alien taxa found, 51 were classified as invasive. Exotic plants native to America were the most common (35%). The level of invasion was significantly higher in the sampling sites subject to high levels of hydrological and morphological disturbances, proxies of the anthropogenic pressure. River bars and man-made slopes supported similar number of alien plant species, higher than forests. We suggest that disturbance in river banks should be minimized as much as possible in order to diminish the risk of invasion.     

Stand characteristics and biodiversity indicators along the productivity gradient in boreal forests: Defining a critical set of indicators for the monitoring of habitat nature quality

Abstract

We quantified the effects of anthropogenic disturbances on the structure and biodiversity of boreal forests on acidic soils and created a statistically supported rational set of indicators to monitor the stand “naturalness”. For that, we surveyed various traits of tree layer, understory, herb layer, forest floor and several widely accepted biodiversity epiphytic indicators in 252 old‐aged boreal stands in Estonia, mostly dominated by Scots pine or Norway spruce. Multifactorial general linear model analyses showed that many forest characteristics and potential indicators were confounded by the gradient of soil productivity (reflected by the forest site type), local biogeographic gradients and also by stand age. Considering confounding effects, boreal forests in a near‐natural state have more large‐diameter trees (diameter at breast height >40 cm) and larger variety of diameter classes, higher proportion of spruce or deciduous trees, a larger amount of coarse woody debris in various stages, a more closed tree canopy and denser understory than managed mature forests. By increasing light availability above the field layer, forest management indirectly increases the coverage of herbs and lichens on the forest floor but reduces the alpha‐ and beta‐diversity of herbs and the proportion of graminoids. Human disturbances reduce the relative incidence of many commonly accepted biodiversity indicators such as indicator lichens, woodpeckers, wood‐dwelling insects or fungi on trees. The test for the predictive power of characteristics reacting on disturbance revealed that only a fraction of them appeared to be included in a diagnostic easy‐to‐apply set of indicators to assess the nature quality of boreal forest: the amount of dead wood, the proportion of deciduous trees, the presence of specially shaped trees and woodpeckers and, as an indicator of disturbances, the forest herb Melampyrum pratensis. Many of these indicators have already been implemented in practice.     

Do species population parameters and landscape characteristics affect the relationship between local population abundance and surrounding habitat amount?

In landscape ecology, correlational approaches are typically used to analyse links between local population abundance, and the surrounding habitat amount to estimate biologically-relevant landscape size (extent) for managing endangered or pest populations. The direction, strength, and spatial extent of the correlations are then sometimes interpreted in terms of species population parameters. Here we simulated the population dynamics of generalized species across spatially explicit landscapes that included two distinct habitat types. We investigated how characteristics of a landscape (structure), including the variation in habitat quality and spatial aggregation of the habitat, and the precise population-dynamic properties of the simulated species (dispersal and growth rates) affect the correlation between population abundance and amount of surrounding favourable habitat in the landscape. To evaluate these spatial extents of correlation, proportions of favourable habitat were calculated within several circles of increasing diameter centred on sampling patches of favourable habitat where population abundance was recorded.We found that the value of the correlation coefficients between population abundance and amount of surrounding favourable habitat depended on both population dynamic parameters and landscape characteristics. Coefficients of correlation increased with the variation in habitat quality and the aggregation of favourable habitat in the landscape, but decreased with the dispersal distance. The distance at which the correlation was maximized was sensitive to an interaction between the level of aggregation of the habitat and the dispersal distance; whereas the greatest distance at which a significant correlation occurred was more sensitive to the variation in habitat quality. Our results corroborate the view that correlational analyses do provide information on the local population dynamics of a species in a given habitat type and on its dispersal rate parameters. However, even in simplified, model frameworks, direct relationships are often difficult to disentangle and global landscape characteristics should be reported in any studies intended to derive population-dynamic parameters from correlations. Where possible, replicated landscapes should be examined in order to control for the interaction between population dynamics and landscape structure. Finally, we recommend using species-specific, population-dynamic modelling in order to interpret correctly the observed patterns of correlation in the landscape.