Recreation shapes a “landscape of fear” for a threatened forest bird species in Central Europe

Predators can create a “landscape of fear” that influences the spatial distribution of their prey. Understanding whether human activity similarly affects the distribution of species beyond habitat suitability is crucial but difficult to assess for conservation managers. Here, we assessed the effect of recreation and forestry activity on a threatened forest-dwelling umbrella species, the Capercaillie (Tetrao urogallus). We followed the citizen science approach on the landscape scale in the Bohemian Forest. We analyzed species data non-invasively collected through intensive fieldwork by volunteers and assessed human activity in the entire study area by analyzing expert questionnaires. The study area extends over 119,000 ha and harbors one of the largest relict populations of this grouse species in Central European low mountain ranges. Our statistical models revealed a negative impact of recreational activities on the intensity of habitat use of the birds within suitable habitats, thereby pointing toward a landscape of fear. The influence of forestry activity, in contrast, was not clear. In comparison to existing regional tourism impact studies, we were able to elevate the examination to the landscape scale. Our results underlined the relevance of recreation in limiting the species’ habitat on an entire landscape and allow us to conclude that habitat managers should set aside well-defined zones without recreational activities to preserve the refuge of this umbrella species.     

Interaction of Grazing Muzzle Use and Grass Species on Forage Intake of Horses

The impact of horse preference and grass morphology on grazing muzzle effectiveness has not been investigated. The objective of this study was to determine the effectiveness of grazing muzzle use at reducing forage intake when horses grazed grasses with different morphology and preferences. The study was conducted in 2012 and 2013. Four horses were grazed in 2012, and three horses were grazed in 2013. Four species of perennial cool-season grasses were grazed in 2012 including Kentucky bluegrass (Poa pratensis L.), meadow fescue (Schedonorus pratensis Huds.), perennial ryegrass (Lolium perenne L.), and reed canarygrass (Phalaris arundinacea L.). In 2013, only Kentucky bluegrass and reed canarygrass were grazed because of winter kill of other species. Horses were allowed to graze a small pasture seeded with an individual species for 4 hours each day in June and August of 2012 and August and September of 2013. Horses grazed the same grass species for two consecutive days, one day with a muzzle and one day without. Before and after each grazing, a strip was mechanically harvested to determine initial and residual herbage mass. The difference was used to estimate forage intake. The effectiveness of a grazing muzzle was not affected by forage species (P ≥ .05). Use of a grazing muzzle decreased the amount of forage consumed by an average of 30% compared with not using a grazing muzzle (P < .0001). Results will aid horse owners and professionals in estimating forage intake of muzzled horses on pasture.     

Bioavailability as a Factor in Risk Assessment of Metal-Contaminated Soil

To accurately assess the risks of metal contaminants in soil, the bioavailability of the metals need to be considered. The bioavailable concentrations determined from homogenized, dried soils are not necessarily representative of in situ conditions of undisturbed field soils. In this study, we investigated the accumulation of metals in wheat (Triticum aestivum) grown in undisturbed contaminated (Pb, Zn, Cu, and Cd) soil cores, in relation to total soil, leachate, and diffusive gradients in thin films (DGT)-labile metal concentrations. Despite the fact that many of the samples contained metal concentrations above guideline values, no significant effects were observed on wheat growth. The bioavailability of metals in the most contaminated samples was estimated to be medium to low, possibly explaining why few effects were observed in the bioassay. For Cu, Zn, and especially for Pb, leachate and DGT-labile concentrations were better predictors of uptake by wheat than total concentrations based on correlations. It is suggested that DGT and leachate concentrations in combination with bioassays in undisturbed soil cores can be used to account for metal bioavailability in soil. These tests could be used during the ecological risk screening stage, in conjunction with total concentrations and guideline values to better estimate receptor exposure.     

Stable isotopes infer the value of Australia’s coastal vegetated ecosystems from fisheries

Wild capture fisheries provide substantial input to the global economy through employment and revenue. The coastal zone is especially productive, accounting for just 7% of the total area of the ocean, but supporting an estimated 50% of the world's fisheries. Vegetated coastal ecosystems—seagrass meadows, tidal marshes and mangrove forests—are widely cited as providing nutritional input that underpin coastal fisheries production; however, quantitative evidence of this relationship is scarce. Using Australia as a case study, we synthesized fisheries stable isotope data to estimate nutritional input derived from coastal vegetated ecosystems and combined these “proportional contribution” estimates with total annual catch data from commercial fisheries to determine species‐specific dollar values for coastal vegetated ecosystems. Based on the data from 96 commercially important fish species across Australian states (total landings 14 × 10⁶ tonnes pa), we provide a conservative estimate that Australia's coastal vegetated ecosystems contribute at least 78 million AUD per year to the fisheries economy. Two thirds of this contribution came from tidal marshes and seagrasses that were both equally valued at 31.5 million AUD per year (39.4%) followed by mangroves at 14.9 million AUD per year (18.6%). The highest dollar values of coastal ecosystems originated from eastern king prawn (Melicertus plebejus) and giant mud crab (Scylla serrata). This study demonstrates the substantial economic value supported by Australia's coastal vegetated ecosystems through commercial fisheries harvest. These estimates create further impetus to conserve and restore coastal wetlands and maintain their support of coastal fisheries into the future.     

History of fire and Douglas-fir establishment in a savanna and sagebrush–grassland mosaic, southwestern Montana, USA

Over the past century, trees have encroached into grass- and shrublands across western North America. These include Douglas-fir trees (Pseudotsuga menziesii (Mirb.) Franco var. glauca (Beissn.) Franco) encroaching into mountain big sagebrush (Artemisia tridentata Nutt. ssp. vaseyana (Rydb.) Beetle) from stable islands of savanna in southwestern Montana. Our objectives were to quantify the relative area occupied by mountain big sagebrush and grasslands versus Douglas-fir savanna in the Fleecer Mountains of southwestern Montana today and in the past, and to identify the historical role of fire and other factors in maintaining this distribution. To do this, we reconstructed a multicentury history of tree establishment and surface fires from 1120 trees sampled on a grid of 50 plots covering 1030 ha of a modern mosaic of sagebrush–grasslands and Douglas-fir trees. We compared these histories to time series of climate and land use, and to spatial variation in topography and soil moisture availability. Beginning in the mid-1800s, Douglas-fir trees established in areas in which trees did not persist historically. In 1855, less than half the plots (42%) had trees whereas today, most plots do (94%). This encroachment was synchronous with the cessation of frequent surface fires, likely caused by the advent of domestic livestock grazing, and perhaps by the start of several decades of relatively dry summers. Douglas-fir savannas historically occurred on fire-safe sites more often than did sagebrush–grass. Our inference that frequent fire excluded Douglas-fir in the past was supported by the results of a simulation model of fire and associated vegetation dynamics. In the continued absence of fire, mountain big sagebrush and grasslands in southwestern Montana are likely to become more homogeneous as Douglas-fir trees continue to encroach.     

A cross-sectional study of risk factors associated with pulmonary lesions in pigs at slaughter

A cross-sectional study was conducted to identify herd-level factors that may influence the prevalence and severity of macroscopically visible pulmonary lesions in pigs at slaughter. Data were collected following abattoir inspection of 50 randomly-selected batches of 6335 pigs and by interviewing the producers. Macroscopic lung lesions were identified and scored semi-quantitatively in ?80 pigs/herd and the prevalence of pleuritis and pneumonia was 20.76% and 23.85%, respectively. Following multivariable analysis, the seroprevalence of Actinobacillus pleuropneumoniae (P < 0.001) and Mycoplasma hyopneumoniae (P = 0.018) and the number of pigs/nursery pen (P = 0.023) were positively associated, whereas average weaning age was negatively associated (P = 0.001) with the pleuritis score. Risk factors associated with a higher prevalence of pneumonia were the presence of pleuritis (P = 0.001) and the frequent purchasing of pigs (P = 0.020). The findings of this study indicate that the prevalence of pleuritis and pneumonia remains high in Belgium and management factors are central to disease control.     

GOAnnotator: linking protein GO annotations to evidence text

Background

Annotation of proteins with gene ontology (GO) terms is ongoing work and a complex task. Manual GO annotation is precise and precious, but it is time-consuming. Therefore, instead of curated annotations most of the proteins come with uncurated annotations, which have been generated automatically. Text-mining systems that use literature for automatic annotation have been proposed but they do not satisfy the high quality expectations of curators.

Results

In this paper we describe an approach that links uncurated annotations to text extracted from literature. The selection of the text is based on the similarity of the text to the term from the uncurated annotation. Besides substantiating the uncurated annotations, the extracted texts also lead to novel annotations. In addition, the approach uses the GO hierarchy to achieve high precision. Our approach is integrated into GOAnnotator, a tool that assists the curation process for GO annotation of UniProt proteins.

Conclusion

The GO curators assessed GOAnnotator with a set of 66 distinct UniProt/SwissProt proteins with uncurated annotations. GOAnnotator provided correct evidence text at 93% precision. This high precision results from using the GO hierarchy to only select GO terms similar to GO terms from uncurated annotations in GOA. Our approach is the first one to achieve high precision, which is crucial for the efficient support of GO curators. GOAnnotator was implemented as a web tool that is freely available at http://xldb.di.fc.ul.pt/rebil/tools/goa/.

     

Bioavailability and efficacy of vitamin D2 from UV-irradiated yeast in growing, vitamin D-deficient rats

New food sources are needed to bridge the gap between vitamin D intake and recommended intake. We assessed the bioavailability and efficacy of vitamin D in an 8 week dose-response study of bread made with vitamin D2-rich yeast compared to vitamin D3 in growing, vitamin D-deficient rats. Plasma 25-hydroxyvitamin D (25OHD) levels increased in a curvilinear, dose-dependent manner with both forms of vitamin D, but rats fed vitamin D2-rich yeast achieved lower levels than rats fed vitamin D3. Rats fed the highest doses of vitamin D had significantly greater (p<0.05) trabecular BMC, BMD, bone volume, and connectivity density, and greater midshaft total cross-sectional area, compared to rats on the vitamin D-deficient diets, with no significant difference due to vitamin D source. Vitamin D2-rich yeast baked into bread is bioavailable and improves bone quality in vitamin D-deficient animals.