Using DNA Barcoding to Investigate Patterns of Species Utilisation in UK Shark Products Reveals Threatened Species on Sale

This is the final version. Available on open access from Nature Research via the DOI in this recordMany shark populations are in decline, primarily due to overexploitation. In response, conservation measures have been applied at differing scales, often severely restricting sales of declining species. Therefore, DNA barcoding was used to investigate sales of shark products in fishmongers and fish and chip takeaways in England. The majority of samples were identified as Spiny Dogfish (Squalus acanthias), which is critically endangered in the Northeast Atlantic and landings have been prohibited (although there is evidence of importation of this species). Significant differences in the species sold between retailer types were also identified, suggesting differing supply chains. The results underline issues surrounding the use of ‘umbrella’ sales terms where many species are labelled with the same designation. This denies consumer choice as purchasers cannot easily avoid declining species or those associated with high levels of toxicants. For the first time in Europe, minibarcodes are also used to identify species from dried shark fins. Despite a small sample size, analysis of UK wholesaler fins identified threatened sharks, including the endangered and CITES listed Scalloped Hammerhead (Sphyrna lewini). This highlights the global nature of the damaging trade in endangered shark species, in which Europe and the UK have a continuing role.Fisheries Society of the British IslesHampshire & Isle of Wight Wildlife TrustUniversity of Exete

Circulating granulocyte lifespan in compensated alcohol-related cirrhosis: a pilot study.

Although granulocyte dysfunction is known to occur in cirrhosis, in vivo studies of granulocyte lifespan have not previously been performed. The normal circulating granulocyte survival half-time (G - t½), determined using indium-111 ((111)In)-radiolabeled granulocytes, is ~7 h. In this pilot study, we aimed to measure the in vivo G - t½ in compensated alcohol-related cirrhosis. Sequential venous blood samples were obtained in abstinent subjects with alcohol-related cirrhosis over 24 h post injection (PI) of minimally manipulated (111)In-radiolabeled autologous mixed leukocytes. Purified granulocytes were isolated from each sample using a magnetic microbead-antibody technique positively selecting for the marker CD15. Granulocyte-associated radioactivity was expressed relative to peak activity, plotted over time, and G - t½ estimated from data up to 12 h PI This was compared with normal neutrophil half-time (N - t½), determined using a similar method specifically selecting neutrophils in healthy controls at a collaborating center. Seven patients with cirrhosis (six male, aged 57.8 ± 9.4 years, all Child-Pugh class A) and seven normal controls (three male, 64.4 ± 5.6 years) were studied. Peripheral blood neutrophil counts were similar in both groups (4.6 (3.5 - 5.5) × 10(9)/L vs. 2.8 (2.7 - 4.4) × 10(9)/L, respectively, P = 0.277). G - t½ in cirrhosis was significantly lower than N - t½ in controls (2.7 ± 0.5 h vs. 4.4 ± 1.0 h, P = 0.007). Transient rises in granulocyte and neutrophil-associated activities occurred in four patients from each group, typically earlier in cirrhosis (4-6 h PI) than in controls (8-10 h), suggesting recirculation of radiolabeled cells released from an unidentified focus. Reduced in vivo granulocyte survival in compensated alcohol-related cirrhosis is a novel finding and potentially another mechanism for immune dysfunction in chronic liver disease. Larger studies are needed to corroborate these pilot data and assess intravascular neutrophil residency in other disease etiologies.Asthma UK (08/2011) MRC (MR/J00345X/1)This is the final version of the article. It first appeared from the American Physiological Society via http://dx.doi.org/10.14814/phy2.1283

A Traditional Diet Is Associated with a Reduced Risk of Eczema and Wheeze in Colombian Children

Background: Diet might influence the risk of allergic diseases. Evidence from developing countries with high prevalence of childhood asthma is scant. Methods: Information on wheeze, rhinitis, and eczema was collected from 3209 children aged 6–7 years in 2005, who were taking part in the International Study on Asthma and Allergy in Children (ISAAC) in Colombia. Intake frequency of twelve food groups was assessed. Associations between each food group and current wheeze, rhino-conjunctivitis, and eczema were investigated with multiple logistic regressions, adjusting for potential confounders. Simes’ procedure was used to test for multiple comparisons. Results: 14.9% of children reported wheeze in the last 12 months, 16% rhino-conjunctivitis, and 22% eczema. Eczema was negatively associated with consumption of fresh fruits and pulses three or more times per week (adjusted Odds ratio (aOR): 0.64; 95% Confidence Interval (CI): 0.49 to 0.83; p value = 0.004; and aOR: 0.62, 95% CI: 0.47 to 0.80; p value < 0.001, respectively). Current wheeze was negatively associated with intake of potatoes (aOR: 0.44, 95% CI: 0.31 to 0.62, p value = 0.005), whilst this outcome was positively associated with consumption of fast food (aOR: 1.76, 95% CI: 1.32 to 2.35, p value = 0.001). These associations remained statistically significant after controlling for multiple comparisons. Conclusions: A traditional diet might have a protective effect against eczema and wheeze in Colombian children, whilst intake of fast foods increases this risk

Chemical variation in a dominant tree species: population divergence, selection and genetic stability across environments

Understanding among and within population genetic variation of ecologically important plant traits provides insight into the potential evolutionary processes affecting those traits. The strength and consistency of selection driving variability in traits would be affected by plasticity in differences among genotypes across environments (G×E). We investigated population divergence, selection and environmental plasticity of foliar plant secondary metabolites (PSMs) in a dominant tree species, Eucalyptus globulus. Using two common garden trials we examined variation in PSMs at multiple genetic scales; among 12 populations covering the full geographic range of the species and among up to 60 families within populations. Significant genetic variation in the expression of many PSMs resides both among and within populations of E. globulus with moderate (e.g., sideroxylonal A h2op = 0.24) to high (e.g., macrocarpal G h2op = 0.48) narrow sense heritabilities and high coefficients of additive genetic variation estimated for some compounds. A comparison of Qst and Fst estimates suggest that variability in some of these traits may be due to selection. Importantly, there was no genetic by environment interaction in the expression of any of the quantitative chemical traits despite often significant site effects. These results provide evidence that natural selection has contributed to population divergence in PSMs in E. globulus, and identifies the formylated phloroglucinol compounds (particularly sideroxylonal) and a dominant oil, 1,8-cineole, as candidates for traits whose genetic architecture has been shaped by divergent selection. Additionally, as the genetic differences in these PSMs that influence community phenotypes is stable across environments, the role of plant genotype in structuring communities is strengthened and these genotypic differences may be relatively stable under global environmental changes

Staphylococcal Periscope proteins Aap, SasG, and Pls project noncanonical legume-like lectin adhesin domains from the bacterial surface

Staphylococcus aureus and Staphylococcus epidermidis are frequently associated with medical device infections that involve establishment of a bacterial biofilm on the device surface. Staphylococcal surface proteins Aap, SasG, and Pls are members of the Periscope Protein class and have been implicated in biofilm formation and host colonization; they comprise a repetitive region ("B region") and an N-terminal host colonization domain within the "A region," predicted to be a lectin domain. Repetitive E-G5 domains (as found in Aap, SasG, and Pls) form elongated "stalks" that would vary in length with repeat number, resulting in projection of the N-terminal A domain variable distances from the bacterial cell surface. Here, we present the structures of the lectin domains within A regions of SasG, Aap, and Pls and a structure of the Aap lectin domain attached to contiguous E-G5 repeats, suggesting the lectin domains will sit at the tip of the variable length rod. We demonstrate that these isolated domains (Aap, SasG) are sufficient to bind to human host desquamated nasal epithelial cells. Previously, proteolytic cleavage or a deletion within the A domain had been reported to induce biofilm formation; the structures suggest a potential link between these observations. Intriguingly, while the Aap, SasG, and Pls lectin domains bind a metal ion, they lack the nonproline cis peptide bond thought to be key for carbohydrate binding by the lectin fold. This suggestion of noncanonical ligand binding should be a key consideration when investigating the host cell interactions of these bacterial surface proteins

Better off dead: assessment of aquatic disinfectants and thermal shock treatments to prevent the spread of invasive freshwater bivalves

Biosecurity protocols designed to prevent further spread of invasive alien species have become a key component of invader management strategies. Yet, the species-specific efficacy of many biosecurity treatments are frequently unclear or unknown. Invasive quagga, Dreissena bugensis, and zebra mussels, D. polymorpha, are a serious threat to freshwater ecosystems worldwide. Here, we examine the effectiveness of immersion (≤ 90 min) within 2% or 4% solutions for two commonly used disinfectants (Virasure® Aquatic and Virkon® Aquatic) to cause mortality of adult Dreissena bivalves. Further, we assessed the effectiveness of thermal treatments: steam spray (≥ 100 °C; ≤ 120 s); hot air (− 500 °C; ≤ 60 s); and dry ice exposure (− 78 °C; ≤ 300 g; 15 min). Complete mortality of D. polymorpha was observed following exposure to both disinfectants for 90 min, at both concentrations. However, high but incomplete mortality (40–90%) was recorded for D. bugensis across disinfectant treatments. For both species, complete mortality was achieved following 30 s of steam. In addition, 10 s of hot air and 15 min exposure to 300 g of dry ice can both completely killed groups of D. polymorpha. Overall, although the disinfectants did not cause complete mortality, it appears that relatively brief exposure to thermal treatments could be used to curtail the further spread of Dreissena species

Costing conservation: an expert appraisal of the pollinator habitat benefits of England’s entry level stewardship

Pollination services provided by insects play a key role in English crop production and wider ecology. Despite growing evidence of the negative effects of habitat loss on pollinator populations, limited policy support is available to reverse this pressure. One measure that may provide beneficial habitat to pollinators is England’s entry level stewardship agri-environment scheme. This study uses a novel expert survey to develop weights for a range of models which adjust the balance of Entry Level Stewardship options within the current area of spending. The annual costs of establishing and maintaining these option compositions were estimated at £59.3–£12.4 M above current expenditure. Although this produced substantial reduction in private cost:benefit ratios, the benefits of the scheme to pollinator habitat rose by 7–140 %; significantly increasing the public cost:benefit ratio. This study demonstrates that the scheme has significant untapped potential to provide good quality habitat for pollinators across England, even within existing expenditure. The findings should open debate on the costs and benefits of specific entry level stewardship management options and how these can be enhanced to benefit both participants and biodiversity more equitably

XIAP impairs Smac release from the mitochondria during apoptosis

X-linked inhibitor of apoptosis protein (XIAP) is a potent inhibitor of caspases 3, 7 and 9, and mitochondrial Smac (second mitochondria-derived activator of caspase) release during apoptosis inhibits the activity of XIAP. In this study we show that cytosolic XIAP also feeds back to mitochondria to impair Smac release. We constructed a fluorescent XIAP-fusion protein by labelling NH2- and COOH-termini with Cerulean fluorescent protein (C-XIAP-C). Immunoprecipitation confirmed that C-XIAP-C retained the ability to interact with Smac and impaired extrinsically and intrinsically activated apoptosis in response to tumour necrosis factor-related apoptosis-inducing ligand/cycloheximide and staurosporine. In C-XIAP-C-expressing cells, cytochrome c release from mitochondria proceeded normally, whereas Smac release was significantly prolonged and incomplete. In addition, physiological expression of native XIAP prolonged or limited Smac release in HCT-116 colon cancer cells and primary mouse cortical neurons. The Smac-binding capacity of XIAP, but not caspase inhibition, was central for mitochondrial Smac retention, as evidenced in experiments using XIAP mutants that cannot bind to Smac or effector caspases. Similarly, the release of a Smac mutant that cannot bind to XIAP was not impaired by C-XIAP-C expression. Full Smac release could however be provoked by rapid cytosolic C-XIAP-C depletion upon digitonin-induced plasma membrane permeabilization. Our findings suggest that although mitochondria may already contain pores sufficient for cytochrome c release, elevated amounts of XIAP can selectively impair and limit the release of Smac

Impacts of selected Ecological Focus Area options in European farmed landscapes on climate regulation and pollination services: a systematic map protocol

Background: This systematic map protocol responds to an urgent policy need to evaluate key environmental benefits of new compulsory greening measures in the European Union’s Common Agricultural Policy (CAP), with the aim of building a policy better linked to environmental performance. The systematic map will focus on Ecological Focus Areas (EFAs), in which larger arable farmers must dedicate 5% of their arable land to ecologically beneficial habitats, landscape features and land uses. The European Commission’s Joint Research Centre has used a software tool called the ‘EFA calculator’ to inform the European Commission about environmental benefits of EFA implementation. However, there are gaps in the EFA calculator’s coverage of ecosystem services, especially ‘global climate regulation’, and an opportunity to use systematic mapping methods to enhance its capture of evidence, in advance of forthcoming CAP reforms. We describe a method for assembling a database of relevant, peer-reviewed research conducted in all agricultural landscapes in Europe and neighbouring countries with similar biogeography, addressing the primary question: what are the impacts of selected EFA features in agricultural land on two policy-relevant ecosystem service outcomes—global climate regulation and pollination? The method is streamlined to allow results in good time for the current, time-limited opportunity to influence reforms of the CAP greening measures at European and Member State level. Methods: We will search four bibliographic databases in English, using a predefined and tested search string that focuses on a subset of EFA options and ecosystem service outcomes. The options and outcomes are selected as those with particular policy relevance and traction. Only articles in English will be included. We will screen search results at title, abstract and full text levels, recording the number of studies deemed non-relevant (with reasons at full text). A systematic map database that displays the meta-data (i.e. descriptive summary information about settings and methods) of relevant studies will be produced following full text assessment. The systematic map database will be published as a MS-Excel database. The nature and extent of the evidence base will be discussed, and the applicability of methods to convert the available evidence into EFA calculator scores will be assessed

Interactive Effects of Large- and Small-Scale Sources of Feral Honey-Bees for Sunflower in the Argentine Pampas

Pollinators for animal pollinated crops can be provided by natural and semi-natural habitats, ranging from large vegetation remnants to small areas of non-crop land in an otherwise highly modified landscape. It is unknown, however, how different small- and large-scale habitat patches interact as pollinator sources. In the intensively managed Argentine Pampas, we studied the additive and interactive effects of large expanses (up to 2200 ha) of natural habitat, represented by untilled isolated “sierras”, and narrow (3–7 m wide) strips of semi-natural habitat, represented by field margins, as pollinator sources for sunflower (Helianthus annus). We estimated visitation rates by feral honey-bees, Apis mellifera, and native flower visitors (as a group) at 1, 5, 25, 50 and 100 m from a field margin in 17 sunflower fields 0–10 km distant from the nearest sierra. Honey-bees dominated the pollinator assemblage accounting for >90% of all visits to sunflower inflorescences. Honey-bee visitation was strongly affected by proximity to the sierras decreasing by about 70% in the most isolated fields. There was also a decline in honey-bee visitation with distance from the field margin, which was apparent with increasing field isolation, but undetected in fields nearby large expanses of natural habitat. The probability of observing a native visitor decreased with isolation from the sierras, but in other respects visitation by flower visitors other than honey-bees was mostly unaffected by the habitat factors assessed in this study. Overall, we found strong hierarchical and interactive effects between the study large and small-scale pollinator sources. These results emphasize the importance of preserving natural habitats and managing actively field verges in the absence of large remnants of natural habitat for improving pollinator services