Drivers of change in mountain farming in Slovakia: from socialist collectivisation to the Common Agricultural Policy

The transformations in Slovak agriculture from the 1950s to the present day, considering both the generic (National and EU) and site-specific (local) drivers of landscape change, were analysed in five mountain study areas in the country. An interdisciplinary approach included analysis of population trends, evaluation of land use and landscape change combined with exploration of the perceptions of local stakeholders and results of previous biodiversity studies. The generic processes active from the 1950s to 1970s were critical for all study areas with impacts lasting right up until the present day. Agricultural collectivisation, agricultural intensification and land abandonment had negative effects in all study areas. However, the precise impacts on the landscape were different in the different study areas due to site-specific attributes (e.g. population trends, geographic localisation and local attitudes and opportunities), and these played a decisive role in determining the trajectory of change. Regional contrasts in rural development between these territories have increased in the last two decades, also due to the imperfect preconditions of governmental support. The recent Common Agricultural Policy developments are focused on maintenance of intensive large-scale farming rather than direct enhancement of agro-biodiversity and rural development at the local scale. In this context, local, site-specific attributes can and must form an essential part of rural development plans, to meet the demands for management of the diversity of agricultural mountain landscapes and facilitate the multifunctional role of agriculture.

Assessment of plant uptake models used in exposure assessment tools for soils contaminated with organic pollutants

The aim of this study was to evaluate and improve the accuracy of plant uptake models for neutral hydrophobic organic pollutants (1 < logKOW < 9, −8 < logKAW < 0) used in regulatory exposure assessment tools, using uncertainty and sensitivity analyses. The models considered were RAIDAR, EUSES, CSOIL, CLEA, and CalTOX. In this research, CSOIL demonstrated the best performance of all five exposure assessment tools for root uptake from polluted soil in comparison with observed data, but no model predicted shoot uptake well. Recalibration of the transpiration and volatilisation parameters improved the performance of CSOIL and CLEA. The dominant pathway for shoot uptake simulated differed according to the properties of the chemical under consideration; those with a higher air–water partition coefficient were transported into shoots via the soil-air-plant pathway, while chemicals with a lower octanol–water partition coefficient and air–water partition coefficient were transported via the root. The soil organic carbon content was a particularly sensitive parameter in each model and using a site specific value improved model performance.

The economics of enhanced landfill mining: private and societal performance drivers

This paper addresses the economics of Enhanced Landfill Mining (ELFM) both from a private point of view as well as from a society perspective. The private potential is assessed using a case study for which an investment model is developed to identify the impact of a broad range of parameters on the profitability of ELFM. We found that especially variations in Waste-to-Energy (WtE efficiency, electricity price, CO2-price, WtE investment and operational costs) and ELFM support explain the variation in economic profitability measured by the Internal Rate of Return. To overcome site-specific parameters we also evaluated the regional ELFM potential for the densely populated and industrial region of Flanders (north of Belgium). The total number of potential ELFM sites was estimated using a 5-step procedure and a simulation tool was developed to trade-off private costs and benefits. The analysis shows that there is a substantial economic potential for ELFM projects on the wider regional level. Furthermore, this paper also reviews the costs and benefits from a broader perspective. The carbon footprint of the case study was mapped in order to assess the project’s net impact in terms of greenhouse gas emissions. Also the impacts of nature restoration, soil remediation, resource scarcity and reduced import dependence were valued so that they can be used in future social cost-benefit analysis. Given the complex trade-off between economic, social and environmental issues of ELFM projects, we conclude that further refinement of the methodological framework and the development of the integrated decision tools supporting private and public actors, are necessary.

Meteorological forcing data for urban outdoor thermal comfort models from a coupled convective boundary layer and surface energy balance scheme

Site-specific meteorological forcing appropriate for applications such as urban outdoor thermal comfort simulations can be obtained using a newly coupled scheme that combines a simple slab convective boundary layer (CBL) model and urban land surface model (ULSM) (here two ULSMs are considered). The former simulates daytime CBL height, air temperature and humidity, and the latter estimates urban surface energy and water balance fluxes accounting for changes in land surface cover. The coupled models are tested at a suburban site and two rural sites, one irrigated and one unirrigated grass, in Sacramento, U.S.A. All the variables modelled compare well to measurements (e.g. coefficient of determination = 0.97 and root mean square error = 1.5 °C for air temperature). The current version is applicable to daytime conditions and needs initial state conditions for the CBL model in the appropriate range to obtain the required performance. The coupled model allows routine observations from distant sites (e.g. rural, airport) to be used to predict air temperature and relative humidity in an urban area of interest. This simple model, which can be rapidly applied, could provide urban data for applications such as air quality forecasting and building energy modelling, in addition to outdoor thermal comfort.

Governing calculative practices: An investigation of development viability modelling in the English planning system

Over the last decade the English planning system has placed greater emphasis on the financial viability of development. ‘Calculative’ practices have been used to quantify and capture land value uplifts. Development viability appraisal (DVA) has become a key part of the evidence base used in planning decision-making and informs both ‘site-specific’ negotiations about the level of land value capture for individual schemes and ‘area-wide’ planning policy formation. This paper investigates how implementation of DVA is governed in planning policy formation. It is argued that the increased use of DVA raises important questions about how planning decisions are made and operationalised, not least because DVA is often poorly understood by some key stakeholders. The paper uses the concept of governance to thematically analyse semi-structured interviews conducted with the producers of DVAs and considers key procedural issues including (in)consistencies in appraisal practices, levels of stakeholder consultation and the potential for client and producer bias. Whilst stakeholder consultation is shown to be integral to the appraisal process in order to improve the quality of the appraisals and to legitimise the outputs, participation is restricted to industry experts and excludes some interest groups, including local communities. It is concluded that, largely because of its recent adoption and knowledge asymmetries between local planning authorities and appraisers, DVA is a weakly governed process characterised by emerging and contested guidance and is therefore ‘up for grabs’.

Understanding 2H/1H systematics of leaf wax n-alkanes in coastal plants at Stiffkey saltmarsh, Norfolk, UK

Interpretation of sedimentary n-alkyl lipid d2H data is complicated by a limited understanding of factors controlling interspecies variation in biomarker 2H/1H composition. To distinguish between the effects of interrelated environmental, physical and biochemical controls on the hydrogen isotope composition of n-alkyl lipids, we conducted linked d2H analyses of soil water, xylem water, leaf water and n-alkanes from a range of C3 and C4 plants growing at a UK saltmarsh (i) across multiple sampling sites, (ii) throughout the 2012 growing season, and (iii) at different times of the day. Soil waters varied isotopically by up to 35& depending on marsh sub-environment, and exhibited site-specific seasonal shifts in d2H up to a maximum of 31 per mil. Maximum interspecies variation in xylem water was 38 per mil, while leaf waters differed seasonally by a maximum of 29 per mil. Leaf wax n-alkane 2H/1H, however, consistently varied by over 100 per mil throughout the 2012 growing season, resulting in an interspecies range in the ewax/leaf water values of -79 per mil to –227 per mil. From the discrepancy in the magnitude of these isotopic differences, we conclude that mechanisms driving variation in the 2H/1H composition of leaf water, including (i) spatial changes in soil water 2H/1H, (ii) temporal changes in soil water 2H/1H, (iii) differences in xylem water 2H/1H, and (iv) differences in leaf water evaporative 2H-enrichment due to varied plant life forms, cannot explain the range of n-alkane d2H values we observed. Results from this study suggests that accurate reconstructions of palaeoclimate regimes from sedimentary n-alkane d2H require further research to constrain those biological mechanisms influencing species-specific differences in 2H/1H fractionation during lipid biosynthesis, in particular where plants have developed biochemical adaptations to water-stressed conditions. Understanding how these mechanisms interact with environmental conditions will be crucial to ensure accurate interpretation of hydrogen isotope signals from the geological record.

Collabowrighting the hyper(play)text: a postdramatic digital poetics

The aim of this research is to exhibit how literary playtexts can evoke multisensory trends prevalent in 21st century theatre. In order to do so, it explores a range of practical forms and theoretical contexts for creating participatory, site-specific and immersive theatre. With reference to literary theory, specifically to semiotics, reader-response theory, postmodernism and deconstruction, it attempts to revise dramatic theory established by Aristotle’s Poetics. Considering Gertrude Stein’s essay, Plays (1935), and relevant trends in theatre and performance, shaped by space, technology and the everchanging role of the audience member, a postdramatic poetics emerges from which to analyze the plays of Mac Wellman and Suzan-Lori Parks. Distinguishing the two textual lives of a play as the performance playtext and the literary playtext, it examines the conventions of the printed literary playtext, with reference to models of practice that radicalize the play form, including works by Mabou Mines, The Living Theatre and Fiona Templeton. The arguments of this practice-led Ph.D. developed out of direct engagement with the practice project, which explores the multisensory potential of written language when combined with hypermedia. The written thesis traces the development process of a new play, Rumi High, which is presented digitally as a ‘hyper(play)text,’ accessible through the Internet at www.RumiHigh.org. Here, ‘playwrighting’ practice is expanded spatially, collaboratively and textually. Plays are built, designed and crafted with many layers of meaning that explore both linguistic and graphic modes of poetic expression. The hyper(play)text of Rumi High establishes playwrighting practice as curatorial, where performance and literary playtexts are in a reciprocal relationship. This thesis argues that digital writing and reading spaces enable new approaches to expressing the many languages of performance, while expanding the collaborative network that produces the work. It questions how participatory forms of immersive and site-specific theatre can be presented as interactive literary playtexts, which enable the reader to have a multisensory experience. Through a reflection on process and an evaluation of the practice project, this thesis problematizes notions of authorship and text.

Decomposition in tropical forests: a pan-tropical study of the effects of litter type, litter placement and mesofaunal exclusion across a precipitation gradient

1. Litter decomposition recycles nutrients and causes large fluxes of carbon dioxide into the atmosphere. It is typically assumed that climate, litter quality and decomposer communities determine litter decay rates, yet few comparative studies have examined their relative contributions in tropical forests. 2. We used a short-term litterbag experiment to quantify the effects of litter quality, placement and mesofaunal exclusion on decomposition in 23 tropical forests in 14 countries. Annual precipitation varied among sites (760-5797 mm). At each site, two standard substrates (Raphia farinifera and Laurus nobilis) were decomposed in fine- and coarse-mesh litterbags both above and below ground for approximately 1 year. 3. Decomposition was rapid, with >95% mass loss within a year at most sites. Litter quality, placement and mesofaunal exclusion all independently affected decomposition, but the magnitude depended upon site. Both the average decomposition rate at each site and the ratio of above- to below-ground decay increased linearly with annual precipitation, explaining 60-65% of among-site variation. Excluding mesofauna had the largest impact on decomposition, reducing decomposition rates by half on average, but the magnitude of decrease was largely independent of climate. This suggests that the decomposer community might play an important role in explaining patterns of decomposition among sites. Which litter type decomposed fastest varied by site, but was not related to climate. 4. Synthesis. A key goal of ecology is to identify general patterns across ecological communities, as well as relevant site-specific details to understand local dynamics. Our pan-tropical study shows that certain aspects of decomposition, including average decomposition rates and the ratio of above- to below-ground decomposition are highly correlated with a simple climatic index: mean annual precipitation. However, we found no relationship between precipitation and effects of mesofaunal exclusion or litter type, suggesting that site-specific details may also be required to understand how these factors affect decomposition at local scales.

Structural and Biochemical Characterization of Peroxiredoxin Q beta from Xylella fastidiosa CATALYTIC MECHANISM AND HIGH REACTIVITY

The phytopathogenic bacterium Xylella fastidiosa is the etiological agent of various plant diseases. To survive under oxidative stress imposed by the host, microorganisms express antioxidant proteins, including cysteine-based peroxidases named peroxiredoxins. This work is a comprehensive analysis of the catalysis performed by PrxQ from X. fastidiosa (XfPrxQ) that belongs to a peroxiredoxin class still poorly characterized and previously considered as moderately reactive toward hydroperoxides. Contrary to these assumptions, our competitive kinetics studies have shown that the second-order rate constants of the peroxidase reactions of XfPrxQ with hydrogen peroxide and peroxynitrite are in the order of 107 and 106 M(-1) s(-1), respectively, which are as fast as the most efficient peroxidases. The XfPrxQ disulfides were only slightly reducible by dithiothreitol; therefore, the identification of a thioredoxin system as the probable biological reductant of XfPrxQ was a relevant finding. We also showed by site-specific mutagenesis and mass spectrometry that an intramolecular disulfide bond between Cys-47 and Cys-83 is generated during the catalytic cycle. Furthermore, we elucidated the crystal structure of XfPrxQ C47S in which Ser-47 and Cys-83 lie similar to 12.3 angstrom apart. Therefore, significant conformational changes are required for disulfide bond formation. In fact, circular dichroism data indicated that there was a significant redox-dependent unfolding of alpha-helices, which is probably triggered by the peroxidatic cysteine oxidation. Finally, we proposed a model that takes data from this work as well data as from the literature into account.

TAF15 and the leukemia-associated fusion protein TAF15-CIZ/NMP4 are cleaved by caspases-3 and-7

Caspases are central players in proteolytic pathways that regulate cellular processes Such as apoptosis and differentiation. To accelerate the discovery of novel caspase substrates we developed a method combining in silico screening and in vitro validation. With this approach, we identified TAH15 as a novel caspase Substrate in a trial Study. We find that TAF15 was specifically cleaved by caspases-3 and -7. Site-directed mutagenesis revealed the consensus sequence (106)DQPD/Y(110) as the only site recognized by these caspases. Surprisingly, TAF15 was cleaved at more than one site in staurosporine-treated Jurkat cells. In addition, we generated two oncogenic TAF15-CIZ/NMP4-fused proteins which have been found in acute myeloid leukemia and demonstrate that caspases-3 and -7 cleave the fusion proteins at one single site. Broad application of this combination approach should expedite identification of novel caspase-interacting proteins and provide new insights into the regulation of caspase pathways leading to cell death in normal and cancer cells. (C) 2009 Elsevier Inc. All rights reserved.

Template-based quadrilateral meshing

Generating quadrilateral meshes is a highly non-trivial task, as design decisions are frequently driven by specific application demands. Automatic techniques can optimize objective quality metrics, such as mesh regularity, orthogonality, alignment and adaptivity; however, they cannot make subjective design decisions. There are a few quad meshing approaches that offer some mechanisms to include the user in the mesh generation process; however, these techniques either require a large amount of user interaction or do not provide necessary or easy to use inputs. Here, we propose a template-based approach for generating quad-only meshes from triangle surfaces. Our approach offers a flexible mechanism to allow external input, through the definition of alignment features that are respected during the mesh generation process. While allowing user inputs to support subjective design decisions, our approach also takes into account objective quality metrics to produce semi-regular, quad-only meshes that align well to desired surface features. Published by Elsevier Ltd.

Direct Observation of Millisecond to Second Motions in Proteins by Dipolar CODEX NMR Spectroscopy

We present a site-resolved study of stow (ms to s) motions in a protein in the solid (microcrystalline) state performed with the use of a modified version of the centerband-only detection of exchange (CODEX) NMR experiment. CODEX was originally based on measuring changes in molecular orientation by means of the chemical shift anisotropy (CSA) tensor, and in our modification, angular reorientations of internuclear vectors are observed. The experiment was applied to the study of stow (15)N-(1)H motions of the SH3 domain of chicken a-spectrin. The protein was perdeuterated with partial back-exchange of protons at labile sites. This allowed indirect (proton) detection of (15)N nuclei and thus a significant enhancement of sensitivity. The diluted proton system also made negligible proton-driven spin diffusion between (15)N nuclei, which interferes with the molecular exchange (motion) and hampers the acquisition of dynamic parameters. The experiment has shown that approximately half of the peaks in the 2D (15)N-(1)H correlation spectrum exhibit exchange in a different extent. The correlation time of the slow motion for most peaks is 1 to 3 s. This is the first NMR study of the internal dynamics of proteins in the solid state on the millisecond to second time scale with site-specific spectral resolution that provides both time-scale and geometry information about molecular motions.

Semantic and Personalised Service Discovery

One of the most pervasive classes of services needed to support e-Science applications are those responsible for the discovery of resources. We have developed a solution to the problem of service discovery in a Semantic Web/Grid setting. We do this in the context of bioinformatics, which is the use of computational and mathematical techniques to store, manage, and analyse the data from molecular biology in order to answer questions about biological phenomena. Our specific application is myGrid (www.mygrid.org.uk) that is developing open source, service-based middleware upon which bioinformatics applications can be built. myGrid is specifically targeted at developing open source high-level service Grid middleware for bioinformatics.

Semantic and Personalised Service Discovery

One of the most pervasive classes of services needed to support e-Science applications are those responsible for the discovery of resources. We have developed a solution to the problem of service discovery in a Semantic Web/Grid setting. We do this in the context of bioinformatics, which is the use of computational and mathematical techniques to store, manage, and analyse the data from molecular biology in order to answer questions about biological phenomena. Our specific application is myGrid (http: //www.mygrid.org.uk) that is developing open source, service-based middleware upon which bioin- formatics applications can be built. myGrid is specif- ically targeted at developing open source high-level service Grid middleware for bioinformatics.

Structural and Biochemical Characterization of Peroxiredoxin Q beta from Xylella fastidiosa CATALYTIC MECHANISM and HIGH REACTIVITY

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)