Biological staining: mechanisms and theory

New staining techniques continue to be introduced, and older ones continue to be used and improved. Several factors control specificity, selectivity and visibility of the end product in any procedure using dyes, fluorochromes, inorganic reagents or histochemical reactions applied to sections or similar preparations. Local concentration of the tissue target often determines the intensity of the observed color, as does the fine structure within the object being stained, which may facilitate or impede diffusion of dyes and other reagents. Several contributions to affinity control the specificity of staining. These include electrical forces, which result in accumulation of dye ions in regions of oppositely charged tissue polyions. Weaker short-range attractions (hydrogen bonding, van der Waals forces or hydrophobic bonding, depending on the solvent) hold dyes ions and histochemical end products in contact with their macromolecular substrates. Nonionic forces can also increase visibility of stained sites by causing aggregation of dye molecules. Covalent bonds between dye and tissue result in the strongest binding, such as in methods using Schiff's reagent and possibly also some mordant dyes. The rate at which a reagent gains access to or is removed from targets in a section or other specimen affect what is stained, especially when more then one dye is used, together or sequentially. Rate-controlled staining is greatly influenced by the presence and type of embedding medium, such as a resin, that infiltrates the tissue. The rates of chemical reactions are major determinants of outcome in many histochemical techniques. Selective staining of different organelles within living cells is accomplished mainly with fluorochromes and is controlled by mechanisms different from those that apply to fixed tissues. Quantitative structure-activity relations (QSAR) of such reagents can be derived from such molecular properties as hydrophilic-hydrophobic balance, extent of conjugated bond systems, acid-base properties and ionic charge. The QSAR correlates with staining of endoplasmic reticulum, lysosomes, mitochondria, DNA, or the plasma membranes of living cells.     

Benthic fauna in tropical tidal flats of Hinchinbrook Channel, NE Australia: diversity, abundance and their spatial and temporal variation

A survey of the benthic infauna (macro- and mesofauna) in tidalflats of Hinchinbrook Channel, north-east Australia, was carried out toassess the species diversity and individual abundances as well as theirtemporalvariations. Two sites were surveyed at five occassions from November 1988 toOctober 1991. In addition, spatial distributions over the intertidal gradientwere investigated once in May 1990. During the entire survey, over 200 specieswere recorded, with 53 species found on average at each sampling occassion.Species densities ranged from 4.0 to 8.2 species 177cm^–2 for macrofauna and from 4.1 to 11.8 species10 cm^–2 for mesofauna, but varied little betweensites. The average infaunal diversity (H') was 2.53. Individual abundancesreached median values of 14.0 individuals 177cm^–2for macrofauna and 14.5 individuals 10 cm^–2 formesofauna. Changes in total abundances were not related to season andinconsistent at the two study sites, with significantly higher abundancesoccurring either at site A or B on single sampling dates. Transects sampled inMay 1990 showed varying species compositions and abundances in the upper, midand lower intertidal, but no defined benthic communities were revealed bymultivariate analyses. Temporal variations in the benthic assemblages of thetwotidal flats in Hinchinbrook Channel were higher than variations between sites,with a separation of assemblages before and after 1989. Problems to assess andinterpret temporal changes in species rich tropical benthic communities arediscussed.     

MAGI: Methylation analysis using genome information

By incorporating annotation information into the analysis of next-generation sequencing DNA methylation data, we provide an improvement in performance over current testing procedures. Methylation analysis using genome information (MAGI) is applicable for both unreplicated and replicated data, and provides an effective analysis for studies with low sequencing depth. When compared with current tests, the annotation-informed tests provide an increase in statistical power and offer a significance-based interpretation of differential methylation.     

SALMFamide2 and serotonin immunoreactivity in the nervous system of some acoels (Xenacoelomorpha)

Acoel worms are simple, often microscopic animals with direct development, a multiciliated epidermis, a statocyst, and a digestive parenchyma instead of a gut epithelium. Morphological characters of acoels have been notoriously difficult to interpret due to their relative scarcity. The nervous system is one of the most accessible and widely used comparative features in acoels, which have a so‐called commissural brain without capsule and several major longitudinal neurite bundles. Here, we use the selective binding properties of a neuropeptide antibody raised in echinoderms (SALMFamide2, or S2), and a commercial antibody against serotonin (5‐HT) to provide additional characters of the acoel nervous system. We have prepared whole‐mount immunofluorescent stainings of three acoel species: Symsagittifera psammophila (Convolutidae), Aphanostoma pisae, and the model acoel Isodiametra pulchra (both Isodiametridae). The commissural brain of all three acoels is delimited anteriorly by the ventral anterior commissure, and posteriorly by the dorsal posterior commissure. The dorsal anterior commissure is situated between the ventral anterior commissure and the dorsal posterior commissure, while the statocyst lies between dorsal anterior and dorsal posterior commissure. S2 and serotonin do not co‐localise, and they follow similar patterns to each other within an animal. In particular, S2, but not 5‐HT, stains a prominent commissure posterior to the main (dorsal) posterior commissure. We have for the first time observed a closed posterior loop of the main neurite bundles in S. psammophila for both the amidergic and the serotonergic nervous system. In I. pulchra, the lateral neurite bundles also form a posterior loop in our serotonergic nervous system stainings.     

Role of Microcystins in Poisoning and Food Ingestion Inhibition of Daphnia galeata Caused by the Cyanobacterium Microcystis aeruginosa

The effects of microcystins on Daphnia galeata, a typical filter-feeding grazer in eutrophic lakes, were investigated. To do this, the microcystin-producing wild-type strain Microcystis aeruginosa PCC7806 was compared with a mcy⁻ PCC7806 mutant, which could not synthesize any variant of microcystin due to mutation of a microcystin synthetase gene. The wild-type strain was found to be poisonous to D. galeata, whereas the mcy⁻ mutant did not have any lethal effect on the animals. Both variants of PCC7806 were able to reduce the Daphnia ingestion rate. Our results suggest that microcystins are the most likely cause of the daphnid poisoning observed when wild-type strain PCC7806 is fed to the animals, but these toxins are not responsible for inhibition of the ingestion process.     

The abundance of an invasive freshwater snail Tarebia granifera (Lamarck, 1822) in the Nseleni River,South Africa

The invasive freshwater snail Tarebia granifera (Lamarck, 1822) was first reported in South Africa in 1999 and it has become widespread across the country, with some evidence to suggest that it reduces benthic macroinvertebrate biodiversity. The current study aimed to identify the primary abiotic drivers behind abundance patterns of T. granifera, by comparing the current abundance of the snail in three different regions, and at three depths, of the highly modified Nseleni River in KwaZulu-Natal, South Africa. Tarebia granifera was well established throughout the Nseleni River system, with an overall preference for shallow waters and seasonal temporal patterns of abundance. Although it is uncertain what the ecological impacts of the snail in this system are, its high abundances suggest that it should be controlled where possible and prevented from invading other systems in the region.     

Population dynamics of the invasive Pacific oyster Crassostrea gigas during the early stages of an outbreak in the Wadden Sea (Germany)

Since the late 1990s, the Pacific oyster (Crassostrea gigas) has spread into the East Frisian Wadden Sea (Germany). This invasion provided an opportunity to study the population dynamics and the patterns of spread during the initial bioinvasion process. With its source area in The Netherlands, the bioinvasion continues in an eastward direction, as documented by a gradient of high abundances in the west and low abundances in the east during the first study year. One year later, abundances of the Pacific oyster were more heterogenic and differed between adjacent tidal basins. The increase in population sizes at all study sites was very high, reaching levels similar to native occurrence populations. The growth constant (K) varied between 0.300 and 0.990 year⁻¹. The mussel bed with the highest densities had a mean abundance of >300 ind. m⁻², and a maximum of 1,460 ind. m⁻². Furthermore, the bioinvasion was facilitated by a low mortality (Z) found for populations between 0.5 and 1.5 years old (Z = 0.03–0.13 year⁻¹). At present, Pacific oysters are well established at several locations in the East Frisian Wadden Sea and may become with these reproductive potential self-sustaining populations.     

Synergistic effects of ovine-derived cathelicidins and other antimicrobials against Escherichia coli O157:H7 and Staphylococcus aureus 1056 MRSA

Synergistic effects of ovine-derived cathelicidins SMAP29 and OaBac5mini with the antimicrobials polymyxin B, lysozyme, nisin and lactoferrin were investigated against E. coli O157:H7 and S. aureus 1056 MRSA. Lysozyme showed synergy against E. coli O157:H7 with SMAP29, polymyxin B and lactoferrin. Synergy was also found between SMAP29 and lactoferrin against this host. Against S. aureus 1056 MRSA, lysozyme showed synergy with OaBac5mini, polymyxin B and nisin, while synergy was also found between nisin and OaBac5mini and polymyxin B. Other combinations of the antimicrobials were either additive or non-synergistic.     

Mytilid mussels: global habitat engineers in coastal sediments

Dense beds of mussels of the family Mytilidae occur worldwide on soft-bottoms in cold and warm temperate coastal waters and have usually been considered hot spots of biodiversity. We examined intertidal mussel beds at four distant locations around the globe with the same sampling method, to find out whether this “hot spot” designation holds universally. We studied species assemblages within the matrices of byssally interconnected mussels engineered by Mytilus edulis in the North Sea, by mixed Perumytilus purpuratus and Mytilus chilensis at the southern Chilean coast, by Musculista senhousia in the Yellow Sea and by Xenostrobus inconstans at the coast of southern Australia. In all cases, species assemblages inside mussel beds were significantly different from those outside with many species being restricted to one habitat type. However, species richness and diversity were not generally higher in mussel beds than in ambient sediments without mussels. In the North Sea (M. edulis) and at the Chilean coast (P. purpuratus, M. chilensis), mussel beds have markedly higher species numbers and diversities than surrounding sediments, but this was not the case for mussel beds in Australia (X. inconstans) and the Yellow Sea (M. senhousia) where numbers of associated species were only slightly higher and somewhat lower than in adjacent sediments, respectively. In conclusion, although soft bottom mytilid mussels generally enhance habitat heterogeneity and species diversity at the ecosystem level, mussel beds themselves are not universal centres of biodiversity, but the effects on associated species are site specific.     

Self-esteem in adolescent patients with attention-deficit/hyperactivity disorder during open-label atomoxetine treatment: psychometric evaluation of the Rosenberg Self-Esteem Scale and clinical findings

To report on (1) psychometric properties of the Rosenberg Self-Esteem Scale (SES) studied in adolescents with ADHD, (2) correlations of SES with ADHD scale scores, and (3) change in patient-reported self-esteem with atomoxetine treatment. ADHD patients (12–17 years), treated in an open-label study for 24 weeks. Secondary analyses on ADHD symptoms (assessed with ADHD-RS, CGI, GIPD scales) and self-esteem (SES) were performed. One hundred and fifty-nine patients were treated. A dichotomous structure of the SES could be confirmed. Reliability and internal consistency were moderate to excellent. Highest coefficients were found for the correlation between SES and GIPD scores. Self-esteem significantly increased over time, accompanied by an improvement of ADHD symptoms and related perceived difficulties. The Rosenberg SES was shown to be internally consistent, reliable, and sensitive to treatment-related changes of self-esteem. According to these findings, self-esteem may be an important individual patient outcome beyond the core symptoms of ADHD.