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    ABSTRACT: Changes in woodland management practices are implicated in observed population changes of many European woodland birds, yet the long-term effects of woodland management on bird demographics is poorly understood. Using detailed long-term (55 year) datasets of both woodland management to plot level, and breeding birds from nest box monitoring, from an upland oak woodland in southwest England, I investigated effects of conservation management aimed at restoring abandoned oak coppice to a more natural and varied vertical structure, and hence its suitability for hole nesting birds, through singling and thinning. Effects of management on nest site occupation and breeding parameters for four hole nesting birds; blue tit, great tit, pied flycatcher and common redstart were examined. Blue tit nest site occupation was higher in managed plots irrespective of time since management. Common redstart nest site occupation was lowest in plots managed >8 years previously. No convincing effects of management on nest site occupancy were found for great tit or pied flycatcher, with inter-specific competition most important. Management had no influence on clutch size or productivity of any of the four species; instead weather variables had some influence on clutch size and productivity. Blue tit clutch size was influenced by spring weather with smaller clutches associated with higher temperatures and increased rainfall. Productivity of blue tit, great tit, pied flycatcher and common redstart was influenced by weather, with lower productivity tending to be associated with rainfall in the months when they were provisioning young. Together this suggests management, at the intensity undertaken within the study site, has a very limited role in determining nest site occupation and demographic rates of hole nesting woodland birds and that other factors such as weather, particularly rainfall, is of greater importance.
    Forest Ecology and Management 10/2014; 330:205–217. DOI:10.1016/j.foreco.2014.07.019
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    ABSTRACT: We recently reported the genome sequence of a free-living strain of Vibrio furnissii (NCTC 11218) harvested from an estuarine environment. V. furnissii is a widespread, free-living proteobacterium and emerging pathogen that can cause acute gastroenteritis in humans and lethal zoonoses in aquatic invertebrates, including farmed crustaceans and molluscs. Here we present the analyses to assess the potential pathogenic impact of V. furnissii. We compared the complete genome of V. furnissii with 8 other emerging and pathogenic Vibrio species. We selected and analyzed more deeply 10 genomic regions based upon unique or common features, and used 3 of these regions to construct a phylogenetic tree. Thus, we positioned V. furnissii more accurately than before and revealed a closer relationship between V. furnissii and V. cholerae than previously thought. However, V. furnissii lacks several important features normally associated with virulence in the human pathogens V. cholera and V. vulnificus. A striking feature of the V. furnissii genome is the hugely increased Super Integron, compared to the other Vibrio. Analyses of predicted genomic islands resulted in the discovery of a protein sequence that is present only in Vibrio associated with diseases in aquatic animals. We also discovered evidence of high levels horizontal gene transfer in V. furnissii. V. furnissii seems therefore to have a dynamic and fluid genome that could quickly adapt to environmental perturbation or increase its pathogenicity. Taken together, these analyses confirm the potential of V. furnissii as an emerging marine and possible human pathogen, especially in the developing, tropical, coastal regions that are most at risk from climate change.
    Frontiers in Microbiology 08/2014; 5(435). DOI:10.3389/fmicb.2014.00435
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    ABSTRACT: Candida albicans demonstrates three main growth morphologies: yeast, pseudohyphal and true hyphal forms. Cell separation is distinct in these morphological forms and the process of separation is closely linked to the completion of mitosis and cytokinesis. In Saccharomyces cerevisiae the small GTPase Tem1 is known to initiate the mitotic exit network, a signalling pathway involved in signalling the end of mitosis and initiating cytokinesis and cell separation. Here we have characterised the role of Tem1 in C. albicans, and demonstrate that it is essential for mitotic exit and cytokinesis, and that this essential function is signalled through the kinase Cdc15. Cells depleted of Tem1 displayed highly polarised growth but ultimately failed to both complete cytokinesis and re-enter the cell cycle following nuclear division. Consistent with its role in activating the mitotic exit network Tem1 localises to spindle pole bodies in a cell cycle-dependent manner. Ultimately, the mitotic exit network in C. albicans appears to co-ordinate the sequential processes of mitotic exit, cytokinesis and cell separation.
    Fungal Genetics and Biology 08/2014; 69. DOI:10.1016/j.fgb.2014.06.007
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    ABSTRACT: In the world of high-throughput sequencing there are numerous challenges to effective data quality control. There are no single quality metrics which are appropriate in all conditions. Here we detail the different open source software used at the Exeter Sequencing Service to provide generic quality control information, as well as more specific metrics for genomic and transcriptomic libraries run on Illumina platforms.
    Frontiers in Genetics 05/2014; 5:157. DOI:10.3389/fgene.2014.00157
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    ABSTRACT: The vas::egfp transgenic zebrafish (Danio rerio) could significantly enhance studies on the mechanisms by which environmental estrogens disrupt sexual differentiation since the developing gonad can be visualized during early life via fluorescence detection. However, there are methodological challenges regarding dissecting out the gonads in early-life-stage fish and transgene responses to estrogen exposure have not been tested. We exposed vas::egfp transgenic zebrafish and their wild-type siblings to the model estrogen 17α-ethinylestradiol (EE2 ) (0.62 and 3.33 ng/L measured concentrations) during sexual development (20 to 60 days post hatch) and used the egfp fluorescence to identify and dissect single gonads (at 40 days post hatch) to provide sufficient RNA for individual gene expression analyses, retaining the remaining gonad in the body cavity for histological analyses of sex and stage of development. Genotyping confirmed that all transgenic control fish were phenotypically egfp-positive (showed green fluorescence). Interestingly, however, in a few transgenic fish exposed to EE2 there was no phenotypic egfp signal, most notably for the 3.33 ng/L EE2 exposure, and we subsequently found gonadal vasa expression was reduced by this concentration of EE2 . Hepatic vitellogenin expression demonstrated that the vas::egfp and wild-type lines responded to estrogen with an equivalent sensitivity. We conclude that the vas::egfp zebrafish provides an enhanced and practical system for mechanistic studies on the effects of environmentally relevant concentrations of estrogens on gonad development. Environ Toxicol Chem © 2013 SETAC.
    Environmental Toxicology and Chemistry 03/2014; 33(3). DOI:10.1002/etc.2467
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    ABSTRACT: This paper examines processes of chute channel formation in four tropical sand-bed meandering rivers; the Strickland and Ok Tedi in Papua New Guinea, the Beni in Bolivia, and the lower Paraguay on the Paraguay/Argentina border. Empirical planform analyses highlight an association between meander bend widening and chute initiation that is consistent with recent physics-based modelling work. GIS analyses indicate that bend widening may be driven by a variety of mechanisms, including scour and cutbank bench formation at sharply-curving bends, point bar erosion due to cutbank impingement against cohesive terrace material, rapid cutbank erosion at rapidly extending bends, and spontaneous mid-channel bar formation. Chute channel initiation is observed to be predominantly associated with two of these widening mechanisms; i) an imbalance between cutbank erosion and point bar deposition associated with rapid bend extension, and ii) bank erosion forced by spontaneous mid-channel bar development. The work extends previous empirical analyses, which highlighted the role of bend extension (elongation) in driving chute initiation, with the observation that the frequency of chute initiation increases once bend extension rates and/or widening ratios exceed a reach-scale threshold. A temporal pattern of increased chute initiation frequency on the Ok Tedi, in response to channel steepening and mid-channel bar development following the addition of mine tailings, mirrors the inter- and intra-reach spatial patterns of chute initiation frequency on the Paraguay, Strickland and Beni Rivers, where increased stream power and sediment load are associated with increased bend extension and chute initiation rates. The process of chute formation is shown to be rate-dependent, and the threshold values of bend extension and widening ratio for chute initiation are shown to scale with measures of river energy, reminiscent of slope–ratio thresholds in river avulsion. Furthermore, Delft3D simulations suggest that chute formation can exert negative feedback on shear stress and bank erosion in the adjacent mainstem bifurcate, such that the process of chute formation may also be rate-limiting. Chute formation is activated iteratively in space and time in response to changes in river energy (and sediment load), predominantly affecting sites of rapid channel elongation, and thereby mediating the river response.
    Sedimentary Geology 03/2014; 301:93–106. DOI:10.1016/j.sedgeo.2013.06.007
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    ABSTRACT: BACKGROUND: Bees in agricultural landscapes are exposed to dietary pesticides such as imidacloprid when they feed from treated mass-flowering crops. Concern about the consequent impact on bees makes it important to understand their resilience. In the laboratory, we therefore fed adult worker bees on dosed syrup (125 µg L(-1) imidacloprid, 98 µg kg(-1) ) either continuously or as a pulsed exposure and measured their behaviour (feeding and locomotory activity) and whole-body residues. RESULTS: On dosed syrup, honey bees maintained much lower bodily levels of imidacloprid than bumble bees (< 0.2 ng vs. 2.4 ng imidacloprid per bee). Dietary imidacloprid did not affect the behaviour of honey bees but it reduced feeding and locomotory activity in bumble bees. After the pulsed exposure, bumble bees cleared bodily imidacloprid after 48 hours and recovered behaviourally. CONCLUSION: We attribute the differential behavioural resilience of the two species to the observed differential in bodily residues. The ability of bumble bees to recover may be environmentally relevant in wild populations that face transitory exposures from the pulsed blooming of mass-flowering crops.
    Pest Management Science 02/2014; 70(2). DOI:10.1002/ps.3569
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    ABSTRACT: To date, limited research has explicitly examined the antecedents of challenge and threat states proposed by the biopsychosocial model. Thus, the aim of the present study was to examine the influence of perceived required effort and support availability on demand/resource evaluations, challenge and threat states, and motor performance. A 2 (required effort; high, low) x 2 (support availability; available, not available) between-subjects design was used with one hundred and twenty participants randomly assigned to one of four experimental conditions. Participants received instructions designed to manipulate perceptions of required effort and support availability before demand/resource evaluations and cardiovascular responses were assessed. Participants then performed the novel motor task (laparoscopic surgery) while performance was recorded. Participants in the low perceived required effort condition evaluated the task as more of a challenge (i.e., resources outweighed demands), exhibited a cardiovascular response more indicative of a challenge state (i.e., higher cardiac output and lower total peripheral resistance), and performed the task better (i.e., quicker completion time) than those in the high perceived required effort condition. However, perceptions of support availability had no significant impact on participants’ demand/resource evaluations, cardiovascular responses, or performance. Furthermore, there was no significant interaction effect between perceptions of required effort and support availability. The findings suggest that interventions aimed at promoting a challenge state should include instructions that help individuals perceive that the task is not difficult and requires little physical and mental effort to perform effectively.
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    ABSTRACT: Together with carbon monoxide (CO), nitric oxide (̇NO) and hydrogen sulfide (H2S) form a group of physiologically important gaseous transmitters, sometimes referred to as the “gaseous triumvirate”. The three molecules share a wide range of physical and physiological properties: they are small gaseous molecules, able to freely penetrate cellular membranes; they are all produced endogenously in the body and they seem to exert similar biological functions. In the cardiovascular system, for example, they are all vasodilators, promote angiogenesis and protect tissues against damage (e.g. ischemia-reperfusion injury). In addition, they have complex roles in inflammation, with both pro- and anti-inflammatory effects reported. Researchers have focused their efforts in understanding and describing the roles of each of these molecules in different physiological systems, and in the past years attention has also been given to the gases interaction or “cross-talk”. This review will focus on the role of ̇NO and H2S in inflammation and will give an overview of the evidence collected so far suggesting the importance of their cross-talk in inflammatory processes.
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    ABSTRACT: The ciliopathies are a group of related inherited diseases characterized by malformations in organ development. The diseases affect multiple organ systems, with kidney, skeleton, and brain malformations frequently observed. Research over the last decade has revealed that these diseases are due to defects in primary cilia, essential sensory organelles found on most cells in the human body. Here we discuss the genetic and cell biological basis of one of the most severe ciliopathies, Meckel-Gruber syndrome, and explain how primary cilia contribute to the development of the affected organ systems.
    Organogenesis 12/2013; 10(1). DOI:10.4161/org.27375
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