The ones we left behind: Comparing plot sampling and floristic habitat sampling for estimating bryophyte diversity

An efficient method for estimating bryophyte diversity in forest stands must consider more than just the dominant forest mesohabitat. We compared two methodologies commonly used for estimating diversity in forest ecosystems. Floristic habitat sampling (FHS) utilizes stratification of all forest mesohabitats, which includes the natural diversity of microhabitats found within and stratifies a mosaic of mesohabitats (e.g. forest, streams, seeps, and cliffs) and microhabitats (e.g. rocks logs, etc.) that are often not considered in forest research projects that use plot sampling to estimate species diversity. In Canadian cedar hemlock forest, FHS methodology recorded more than twice as many bryophyte species as plot sampling (PS). A comparison of the dominant forest mesohabitat concluded that plot sampling was not as efficient as FHS in estimating bryophyte diversity and that plot sampling can result in different interpretations of species diversity. Rare species ordination of stands sampled using FHS showed strong clustering of sites with respect to biogeoclimatic zones and age since the last major disturbance (fire or logging) as compared with rare species ordinations from PS data, which showed no delineation of stands along temporal gradients. Plot sampling has many useful applications in ecology, but floristic habitat sampling is more efficient for quantifying overall bryophyte diversity. FHS provides an excellent way to record a comprehensive list of species.     

Woody plants diversity,floristic composition and land use history in the Amazonian rain forests of Madidi National Park,Bolivia

A floristic inventory of woody plants was carried out to analyse the relationships between floristic similarity and geographical distance, and to compare the effect of land use history on the floristic composition between sites. Three lowland and two submontane sites were studied in Madidi, Bolivia. In one site, there is evidence of an Inca ruin. A total of 877 species and 12,822 individuals of woody plants with a diameter at breast height ≥2.5 cm were recorded in 44 0.1–ha plots. Fisher’s Alpha index values were slightly higher for the lowlands than for the submontane. Floristic similarity was higher within sites than between sites as measured by both Sørensen and Steinhaus indexes. The fact that the 30 most important species per site (totalling 94 species) accounted for 61.7% of total individuals, support the hypothesis that Amazonian plant communities are dominated by a limited set of species, genera and families. On the other hand, 18 out of the 94 species were reported in a single site, suggesting that some species are patchy in distribution and may be environmentally determined. Both the oligarchy and environmental-determinism hypotheses can be complementary in order to understand floristic patterns of this region. The Ruins submontane site is floristically the most distinct, and past human disturbance is likely to be the main reason. Since species diversity (ranging from 53 to 122 species per plot) and density (ranging from 157 to 503 per plot) are highly variable in Madidi, to characterize the diversity of a site, it is necessary to quantify an average of 10 0.1-ha plots in a relatively small geographical area.     

The role of GA3 in the germination process of high-mountain endemic and threatened species: Leontopodium nivalePinguicula fiorii and Soldanella minima subsp. samnitica (central Apennines,Italy)

The ex situ conservation of biodiversity is an essential tool for environmental protection interventions. Germination studies of seeds that belong to endangered species are essential for ex situ conservation strategies. In this study, we investigate the germination responses of three high-altitude endemic and vulnerable species (Leontopodium nivale, Pinguicula fiorii and Soldanella minima subsp. samnitica). Specifically we identified potential dormancy mechanisms by investigating the responses of germination percentage and rate to different concentrations of gibberellic acid (GA₃), by performing a general linear model. L. nivale reached a germination percentage of 98.0 ± 2.0% (mean ± SE) under control conditions (20°C; 12/12 photoperiod; no GA₃ addition). P. fiorii showed the highest germination percentage (78.0 ± 2.0%) in the treatment with GA₃ 500 ppm. S. minima subsp. samnitica did not show sensitivity to GA₃ but responded positively to cold stratification (6 month at 5°C) with a germination percentage of 90 ± 6%. This study made it possible to acquire important information on the germination process of threatened and rare endemic taxa.     

Silver stains demonstrating neuroendocrine cells

During the preimmunohistochemical era, silver stains were an important part of the staining arsenal for identifying certain tissue structures and cell types in tissue sections. Some of them were useful for demonstrating endocrine cells, especially in the gastrointestinal tract. Until the late 1950s, silver stains, particularly those identifying endocrine cells, were accompanied by a number of technical difficulties resulting from uncontrolled staining factors. In the 1960s, new silver stains were developed for endocrine cell types and these stains gave reproducible results. One of the “older” silver stains and two of the “newer” ones are emphasized in this presentation, namely the Masson, the Grimelius and the Sevier-Munger techniques. The Masson stain demonstrates the enterochromaffin (EC, serotonin) cells, the Grimelius stain is a broad endocrine cell marker, and the Sevier-Munger technique demonstrates EC and EC-like cells and the C-cells of the thyroid. Especially in the preimmunohistochemical era, these staining methods often were used for histopathological diagnosis, particularly the Grimelius technique. The silver stains were developed empirically, and with few exceptions the chemical background is not known. Staining protocols are included.     

Enantioselective acetylation of racemic alcohols by Manihot esculenta and Passiflora edulis preparations

Immobilized Manihot esculenta and Passiflora edulis juice preparations have been employed as stereoselective biocatalysts in the enzymatic acetylation of a set of racemic alcohols. Depending on the reaction conditions and the substrate structure, good to excellent enantioselectivities can be achieved in the preparation of the (S)-alcohols and (R)-esters, compounds presenting high interest in organic synthesis.     

Comparison between procedures using SDS for shotgun proteomic analyses of complex samples

Filter-aided sample preparation (FASP) and a new sample preparation method using a modified commercial SDS removal spin column are quantitatively compared in terms of their performance for shotgun proteomic experiments in three complex proteomic samples: a Saccharomyces cerevisiae lysate (insoluble fraction), a Caenorhabditis elegans lysate (soluble fraction), and a human embryonic kidney cell line (HEK293T). The characteristics and total number of peptides and proteins identified are compared between the two procedures. The SDS spin column procedure affords a conservative fourfold improvement in throughput, is more reproducible, less expensive (i.e. requires less materials), and identifies between 30 and 107% more peptides at q≤0.01, than the FASP procedure. The peptides identified by SDS spin column are more hydrophobic than species identified by the FASP procedure as indicated by the distribution of GRAVY scores. Ultimately, these improvements correlate to as great as a 50% increase in protein identifications with two or more peptides.     

Monitoring exposure to avian influenza viruses in wild mammals

• 1 Avian influenza (AI) viruses primarily circulate in wild waterfowl populations and are occasionally transmitted to domestic poultry flocks. However, the possible roles of other wildlife species, such as wild mammals, in AI virus ecology have not been adequately addressed.
• 2 Due to their habitat and behaviour, many wild mammals may be capable of transmitting pathogens among wild and domestic populations. Exposure to AI viruses has been reported in an array of wild and domestic animals. The presence of wild mammals on farms has been identified as a risk factor for at least one poultry AI outbreak in North America. These reports suggest the need for seroprevalence studies examining the exposure of wild mammals to AI viruses.
• 3 Serological tests are routinely used to assess domestic poultry, domestic swine and human exposure to influenza A viruses, but these tests have not been validated for use in wild mammals. As such, some of these protocols may require adjustments or may be inappropriate for use in serology testing of wild mammals. Herein, we review these serological techniques and evaluate their potential usefulness in AI surveillance of wild mammals. We call for care to be taken when applying serological tests outside their original area of validation, and for continued assay verification for multiple species and virus strains.

     

Functional composition trajectory: a resolution to the debate between Suganuma,Durigan, and Reid

The selection of ecological indicators is an important step toward more effective restoration monitoring. The debate between Reid (2015) and Durigan and Suganuma (2015) regarding the usefulness of species composition for monitoring restoration trajectory is timely and salient, but it lacks a middle way proposal to balance ecological relevance and practical viability. We propose a way forward to resolving this debate, namely using easily measurable functional traits, a type of compositional measure, as an indicator. Assessing functional composition trajectory may help overcome some limitations with taxonomic identification and provide more meaningful outcomes to evaluate restoration success.     

Simplifying the Welfare Quality® assessment protocol for broiler chicken welfare

Welfare Quality® (WQ) assessment protocols place the emphasis on animal-based measures as an indicator for animal welfare. Stakeholders, however, emphasize that a reduction in the time taken to complete the protocol is essential to improve practical applicability. We studied the potential for reduction in time to complete the WQ broiler assessment protocol and present some modifications to the protocol correcting a few errors in the original calculations. Data was used from 180 flocks assessed on-farm and 150 flocks assessed at the slaughter plant. Correlations between variables were calculated, and where correlation was moderate, meaningful and promising (in terms of time reduction), simplification was considered using one variable predicted from another variable. Correlation analysis revealed a promising correlation between severe hock burn and gait scores on-farm. Therefore, prediction of gait scores using hock burn scores was studied further as a possible simplification strategy (strategy 1). Measurements of footpad dermatitis, hock burn, cleanliness and gait score on-farm correlated moderately to highly with slaughter plant measurements of footpad dermatitis and/or hock burn, supporting substitution of on-farm measurements with slaughter plant data. A simplification analysis was performed using footpad dermatitis, hock burn, cleanliness and gait scores measured on-farm predicted from slaughter plant measurements of footpad dermatitis and hock burn (strategy 2). Simplification strategies were compared with the full assessment protocol. Close agreement was found between the full protocol and both simplification strategies although large confidence intervals were found for specificity of the simplified models. It is concluded that the proposed simplification strategies are encouraging; strategy 1 can reduce the time to complete the on-farm assessment by ~1 h (25% to 33% reduction) and strategy 2 can reduce on-farm assessment time by ~2 h (50% to 67% reduction). Both simplification strategies should, however, be validated further, and tested on farms with a wide distribution across the different welfare categories of WQ.