Caveats of fungal barcoding: a case study in Trametes s.lat. (Basidiomycota: Polyporales) in Vietnam reveals multiple issues with mislabelled reference sequences and calls for third-party annotations

DNA barcoding using the nuclear internal transcribed spacer (ITS) has become prevalent in surveys of fungal diversity. This approach is, however, associated with numerous caveats, including the desire for speed, rather than accuracy, through the use of automated analytical pipelines, and the shortcomings of reference sequence repositories. Here we use the case of a specimen of the bracket fungus Trametes s.lat. (which includes the common and widespread turkey tail, T. versicolor) to illustrate these problems. The material was collected in Vietnam as part of a biodiversity inventory including DNA barcoding approaches for arthropods, plants and fungi. The ITS barcoding sequence of the query taxon was compared against reference sequences in GenBank and the curated fungal ITS database UNITE, using BLASTn and MegaBLAST, and was subsequently analysed in a multiple alignment-based phylogenetic context through a maximum likelihood tree including related sequences. Our results initially indicated issues with BLAST searches, including the use of Frairwise local alignments and sorting through Total score and E value, rather than Percentage identity, as major shortcomings of the DNA barcoding approach. However, after thorough analysis of the results, we concluded that the single most important problem of this approach was incorrect sequence labelling, calling for the implementation of third-party annotations or analogous approaches in primary sequence repositories. In addition, this particular example revealed problems of improper fungal nomenclature, which required reinstatement of the genus name Cubamyces (= Leioirametes), with three new combinations: C. flavidus, C lactineus and C. menziesii. The latter was revealed as the correct identification of the query taxon, although the name did not appear among the best BLAST hits. While the best BLAST hits did correspond to the target taxon in terms of sequence data, their label names were misleading or unresolved, including [Fungal endophyte], [Uncultured fungus], Basidiomycota, Trametes cf. cubensis, Lenzites elegans and Geotrichum candidum (an unrelated ascomycetous contaminant). Our study demonstrates that accurate identification of fungi through molecular barcoding is currently not a fast-track approach that can be achieved through automated pipelines

Comparative prebiotic activity of mixtures of cereal grain polysaccharides

The main components of the non-starch polysaccharide (NSP) fraction of wheat flour are arabinoxylan (AX) and β-glucan. These are also present in other cereal grains, but their proportions vary with AX being the major component in wheat and rye and β-glucan in barley and oats. Therefore, it was hypothesised that these NSPs could act synergistically when fermented in vitro at the ratios present in the major foods consumed, resulting in increased prebiotic activity. AX and β-glucan were therefore tested in in vitro fermentation studies to assess their prebiotic activity when used individually and/or in different ratios. Short-chain fatty-acids (SCFAs) produced from in vitro fermentation were measured using HPLC and bacterial populations were measured using flow cytometry with fluorescence in situ hybridisation (Flow-FISH). Fermentation of AX alone resulted in a significant bifidogenic activity and increased concentrations of SCFAs, mainly acetate, after 8-24 h of fermentation, however β-glucan alone did not show prebiotic activity. The greatest prebiotic activity, based on concentration of total SCFAs and increases in total bacteria as well as beneficial Bifidobacterium and Clostridium coccoides/Eubacterium groups, was observed when AX and β-glucan were combined at a 3:1 ratio, which corresponds to their ratios in wheat flour which is major source of cereal fibre in the diet. This indicates that the population of bacteria in the human GI tract may be modulated by the composition of the fibre in the diet, to maximise the prebiotic potential

Optimizing the use of InSAR observations in data assimilation problems to estimate reservoir compaction

Hydrocarbon production may cause subsidence as a result of the pressure reduction in the gas-producing layer and reservoir compaction. To analyze the process of subsidence and estimate reservoir parameters, we use a particle method to assimilate Interferometric synthetic-aperture radar (InSAR) observations of surface deformation with a conceptual model of reservoir. As example, we use an analytical model of the Groningen gas reservoir based on a geometry representing the compartmentalized structure of the subsurface at the reservoir depth. The efficacy of the particle method becomes less when the degree of freedom is large compared to the ensemble size. This degree of freedom, in turn, varies because of spatial correlation in the observed field. The resolution of the InSAR data and the number of observations affect the performance of the particle method. In this study, we quantify the information in a Sentinel-1 SAR dataset using the concept of Shannon entropy from information theory. We investigate how to best capture the level of detail in model resolved by the InSAR data while maximizing their information content for a data assimilation use. We show that incorrect representation of the existing correlations leads to weight collapse when the number of observation increases, unless the ensemble size growths. However, simulations of mutual information show that we could optimize data reduction by choosing an adequate mesh given the spatial correlation in the observed subsidence. Our approach provides a means to achieve a better information use from available InSAR data reducing weight collapse without additional computational cost

The nation branding opportunities provided by a sport mega-event: South Africa and the 2010 FIFA World Cup

Over the past decade there has been a growing awareness of the significant impact that hosting sport mega-events can have on a nation[U+05F3]s brand. This paper discusses the context of nation branding and the role of sport mega-events in generating a nation branding legacy. A nation brand is not owned or controlled by a single organisation, but rather jointly developed and delivered by a network of public and private sector organisations. The examination of both event and brand stakeholder perceptions and experiences post the event was therefore identified as an important research area. The case of South Africa and the 2010 FIFA World Cup was selected as improving the brand image was clearly stated as an aim for the host nation. The paper is based on a qualitative study that featured in-depth interviews conducted with definitive stakeholders from the public and private sectors (. n=8), within two of the major host cities of Johannesburg and Cape Town that took place two years post the event. The paper details the perceptions, experiences and reflections of these stakeholders relating to the branding opportunities and the legacy from the event and the degree to which these were leveraged. The paper contends that there are significant branding opportunities for nations beyond merely publicity, brand awareness and short-term perception changes. Greater knowledge and understanding of a brand can be developed through the experiences and engagement of visitors, citizens and members of the international business community, leading to the establishment of a more authentic brand image. Furthermore, there is also the opportunity to use these new image perceptions to position the nation brand for competitive advantage in tourism as well as business and investment sectors. Two key influencing factors of the nation branding legacy were identified, namely the media (including traditional and new media) and the role of local citizens. The discourse surrounding leveraging of legacies is furthered and supported, as it is clear that the success and legacy of the mega-event are a result of strategic activities of stakeholders. A nation branding legacy is therefore a combination of the opportunities provided by the sport mega-event and the strategic intention and activities of stakeholders

Kinetics of GLUT4 Trafficking in Rat and Human Skeletal Muscle

OBJECTIVE—In skeletal muscle, insulin stimulates glucose transport activity three- to fourfold, and a large part of this stimulation is associated with a net translocation of GLUT4 from an intracellular compartment to the cell surface. We examined the extent to which insulin or the AMP-activated protein kinase activator AICAR can lead to a stimulation of the exocytosis limb of the GLUT4 translocation pathway and thereby account for the net increase in glucose transport activity. RESEARCH DESIGN AND METHODS—Using a biotinylated photoaffinity label, we tagged endogenous GLUT4 and studied the kinetics of exocytosis of the tagged protein in rat and human skeletal muscle in response to insulin or AICAR. Isolated ep-itrochlearis muscles were obtained from male Wistar rats. Vastus lateralis skeletal muscle strips were prepared from open muscle biopsies obtained from six healthy men (age 39 11 years an

Opportunities and challenges in value chain analysis for sustainable management of sharks and rays

Studies on elasmobranch trade have often focused on a single commodity, shark fins. Such a narrow focus can result in an incomplete understanding of the socio-cultural importance of sharks, limiting discussion on the range and efficacy of potential management interventions. Assessments must be performed across the value chain from fisher to retail vendor to better conserve vulnerable elasmobranch species, offering a broader view of capture, use, and trade. Here, we collate insights from shark value chain assessments conducted in eight countries (Mexico, Peru, Guinea-Bissau, India, Bangladesh, Sri Lanka, Indonesia and Fiji) spanning five continents. Approaches and processes implemented in a shark value chain analysis (VCA) were reviewed to: (1) understand better approaches and tools and (2) collate shared experiences. Our results demonstrate that VCAs broaden the outlook of fishery and trade assessments when capturing a more comprehensive range of economic and socio-cultural aspects (e.g., livelihoods, cultural use of commodities) of trade in all shark commodities. Time invested in various components of assessments produced different outcomes, with considerable returns from stakeholder selection, survey design, and assessor/stakeholder relationship building. Contrastingly, results demonstrated that efforts in communication with stakeholder groups and policymakers could be further streamlined to focus on key results using a variety of communication formats. Outcomes from this study offer guidance to those embarking on shark VCAs, facilitating improving the assessment process and outcomes

PROMISING THE DREAM: changing destination image of London through the effect of website place

Drawing on theories of place identity and social identity, this study aims to fill a gap in place identity studies regarding the effect of a place website on the destination image of customers/visitors/tourists. The research addresses three questions: (1) what are the main impacts of tourists’ attitude on place identity and the place website, (2) what are the factors that influence destination image, and (3) what are the main impacts of a favorable destination image? The favorability of a destination image is reflected by the extent to which visitors positively regard that place website. Results reveal the importance of the destination image in enhancing the intention to revisit and recommend. Also, visitors’ satisfaction impacts on their intention to revisit and recommend the place. Significant implications for place managers and researchers are highlighted

Evidence for 'critical slowing down' in seagrass:a stress gradient experiment at the southern limit of its range

The theory of critical slowing down, i.e. the increasing recovery times of complex systems close to tipping points, has been proposed as an early warning signal for collapse. Empirical evidence for the reality of such warning signals is still rare in ecology. We studied this on Zostera noltii intertidal seagrass meadows at their southern range limit, the Banc d'Arguin, Mauritania. We analyse the environmental covariates of recovery rates using structural equation modelling (SEM), based on an experiment in which we assessed whether recovery after disturbances (i.e. seagrass & infauna removal) depends on stress intensity (increasing with elevation) and disturbance patch size (1 m(2) vs. 9 m(2)). The SEM analyses revealed that higher biofilm density and sediment accretion best explained seagrass recovery rates. Experimental disturbances were followed by slow rates of recovery, regrowth occurring mainly in the coolest months of the year. Macrofauna recolonisation lagged behind seagrass recovery. Overall, the recovery rate was six times slower in the high intertidal zone than in the low zone. The large disturbances in the low zone recovered faster than the small ones in the high zone. This provides empirical evidence for critical slowing down with increasing desiccation stress in an intertidal seagrass system

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data