Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    How Do Configuration Shifts in Fragmented Energy Governance Affect Policy Output? A Case Study of Changing Biogas Regimes in Indonesia
    Budiman, Ibnu ; Smits, M. - \ 2020
    Sustainability 12 (2020)4. - ISSN 2071-1050 - 23 p.
    biogas - fragmentation - governance - Indonesia - regime complex - policy output
    Biogas technology to support rural livelihoods and low-carbon development has been developed in different projects and programs in the Global South over the last few decades. However, the existence of multiple projects, actors and designs involved may lead to so-called fragmentation in governance. This research addresses the fragmented governance amongst the biogas programmes in
    Indonesia to study their impact on the implementation; the numbers of biodigesters disseminated and knowledge transferred. Drawing on concepts of fragmentation, regime effectiveness, and policy output, the research uses data from interviews with relevant actors, supplemented with documents review. Findings show that the governance architecture of biogas regime in Indonesia consists of different types of biogas programmes championed by different types of actors pursuing different objectives. There had been patterns and periodical shifts of configuration within the Indonesian biogas regime, i.e., from administrative fragmentation (2007–2009), to conflictive fragmentation (2010–2012), to cooperative fragmentation (2013–2016), and reduced fragmentation (2017). Shifting
    from administrative to cooperative fragmentation resonates with the increase of the number of biodigesters dissemination more than fourfold in ten years, from 800 in 2007, to 37,999 in 2016. The distribution of power within the governance architecture among government bodies, NGOs, and the private sector influenced the speed of implementation and innovation of the biogas programs.
    This suggests that a higher degree of distribution of power and cooperation within a governance architecture contribute to increasing policy output of the regime complex of renewable energy.
    Gendered climate change adaptation practices in fragmented farm fields of Gamo Highlands, Ethiopia
    Cholo, Tesfaye C. ; Peerlings, Jack ; Fleskens, Luuk - \ 2020
    Climate and Development 12 (2020)4. - ISSN 1756-5529 - p. 323 - 331.
    fragmentation - gendered - Land management - sustainable - work division

    The objective of this study is to assess the existence of gendered climate change adaptation practices of smallholder farmers in the Gamo Highlands of Ethiopia. We hypothesized that smallholders’ adaptation practices are gendered because of land fragmentation and gendered division of labour. To explore this, we considered sustainable land management practices as a tool for sustainable adaptation and assessed the effect of land management practices deployed and land fragmentation on intra-household time allocation. The results indicate that although land fragmentation increased hours worked by men and women significantly, fragmentation increased the working hours of men more than women. Application of a larger number of sustainable land management practices increases the mean working hours of women, but leaves unaffected the working hours of men, implying that adaptation practices are gender-biased. Therefore, this study can guide land management decisions by pointing out that fragmentation results in long working hours and adaptation practices may disproportionately affect women.

    Behaviour of migrating toads under artificial lights differs from other phases of their life cycle
    Grunsven, Roy H.A. Van; Creemers, Raymond ; Joosten, Kris ; Donners, Maurice ; Veenendaal, Elmar M. - \ 2017
    Amphibia-Reptilia 38 (2017)1. - ISSN 0173-5373 - p. 49 - 55.
    Amphibian - Anura - fragmentation - light pollution - mitigation - phototaxis - spectra
    During annual spring migration in Western Europe many amphibians are killed by traffic when they cross roads moving to reproduction sites. Especially in urban settings these roads are often equipped with street lighting. The response of amphibians to this light during migration is however poorly known. Street lighting may attract migrating amphibians increasing the risk of being struck by traffic. Using experimental illumination we tested whether light affected the migration and if adjustment of the spectral composition could mitigate effects. Barriers used to catch toads and help them cross roads safely were divided in 25 meter long sections and these were illuminated with white, green or red light or kept dark. The number of toads caught in each section was counted. Common toads avoided sections of roads that were illuminated with white or green light but not red light. Street light thus affects migrating toads but not as expected and red light with low levels of short wavelength can be used to mitigate effects.
    Read all about it!? Public accountability, fragmented global climate governance and the media
    Karlsson-Vinkhuyzen, Sylvia I. ; Friberg, Lars ; Saccenti, Edoardo - \ 2017
    Climate Policy 17 (2017)8. - ISSN 1469-3062 - p. 982 - 997.
    Accountability - climate change - energy - fragmentation - global governance - media

    This study is instructive for the media and civil society, who should both act as accountholders of governments with regard to how they act in global climate governance and its implementation. Reporting and commentaries need to reflect the overarching process, not only sporadic coverage of high-level meetings, but also critical analysis of what is achieved. They should also take a broader scope in terms of the kinds of meetings and processes in global governance that they cover. Civil society should encourage the media to increase coverage along these lines, e.g. by adequate monitoring of government actions (or lack thereof) and share this with the media.

    Rapid assessment of historic, current and future habitat quality for biodiversity around UK Natura 2000 sites
    Vogiatzakis, I.N. ; Stirpe, M.T. ; Rickebusch, S. ; Metzger, M.J. ; Xu, G. ; Rounsevell, M.D.A. ; Bommarco, R. ; Potts, S.G. - \ 2015
    Environmental Conservation 42 (2015)1. - ISSN 0376-8929 - p. 31 - 40.
    use change scenarios - land-use - aerial-photography - conservation - fragmentation - landscapes - dynamics - cover - area - grasslands
    Changes in landscape composition and structure may impact the conservation and management of protected areas. Species that depend on specific habitats are at risk of extinction when these habitats are degraded or lost. Designing robust methods to evaluate landscape composition will assist decision- and policy-making in emerging landscapes. This paper describes a rapid assessment methodology aimed at evaluating land-cover quality for birds, plants, butterflies and bees around seven UK Natura 2000 sites. An expert panel assigned quality values to standard Coordination of Information on the Environment (CORINE) land-cover classes for each taxonomic group. Quality was assessed based on historical (1950, 1990), current (2000) and future (2030) land-cover data, the last projected using three alternative scenarios: a growth-applied strategy (GRAS), a business-as-might-be-usual (BAMBU) scenario, and sustainable European development goal (SEDG) scenario. A quantitative quality index weighted the area of each land-cover parcel with a taxa-specific quality measure. Land parcels with high quality for all taxonomic groups were evaluated for temporal changes in area, size and adjacency. For all sites and taxonomic groups, the rate of deterioration of land-cover quality was greater between 1950 and 1990 than current rates or as modelled using the alternative future scenarios (2000–2030). Model predictions indicated land-cover quality stabilized over time under the GRAS scenario, and was close to stable for the BAMBU scenario. The SEDG scenario suggested an ongoing loss of quality, though this was lower than the historical rate of c. 1% loss per decade. None of the future scenarios showed accelerated fragmentation, but rather increases in the area, adjacency and diversity of high quality land parcels in the landscape.
    The effectiveness of ditch banks as dispersal corridor for plants in agricultural landscapes depends on species' dispersal traits
    Dijk, W.F.A. van; Ruijven, J. van; Berendse, F. ; Snoo, G.R. de - \ 2014
    Biological Conservation 171 (2014). - ISSN 0006-3207 - p. 91 - 98.
    agri-environment schemes - european countries - biodiversity - grassland - farmland - habitat - colonization - fragmentation - connectivity - pollinators
    The effectiveness of agri-environment schemes (AES) in enhancing biodiversity in agricultural landscapes is still strongly debated. In the Netherlands, one of the most widely implemented AES is the management of ditch banks to enhance plant species diversity. Previous research has shown that this type of AES has not led to increases in plant diversity. However, this work also showed that the success of this type of AES may depend on the presence of source populations in the surrounding areas. In this study we investigated if species-rich nature reserves can act as seed sources for agricultural ditch banks under AES and whether this function of nature reserves differs among plant species with different dispersal capacities. We used data collected by farmers over a 10 year period to analyse trends in species richness of target plants and in different dispersal groups in ditch banks under AES at different distances from nature reserves. Our results demonstrate that nature reserves can act as species rich sources in agricultural landscapes and that adjacent AES ditch banks can facilitate the colonisation of the surrounding agricultural landscape. However, the suitability of ditch banks as corridors depends on the dispersal capacity of a species. Particularly water-dispersed species clearly spread from nature reserves into the surrounding agricultural landscape along ditches. In contrast, species without adaptations to disperse over long distances do not show these spatiotemporal patterns.
    Application of an integrated systemic framework for analysing agricultural innovation systems and informing innovation policies: Comparing the Dutch and Scottish agrifood sectors
    Lamprinopoulou, C. ; Renwick, A. ; Klerkx, L.W.A. ; Hermans, F. ; Roep, D. - \ 2014
    Agricultural Systems 129 (2014). - ISSN 0308-521X - p. 40 - 54.
    knowledge - management - networks - technology - sustainability - fragmentation - instruments - extension - services - ethiopia
    Innovation is receiving increased attention among policymakers as a means of addressing sustainable economic development challenges. However, a range of factors such as inappropriate physical and knowledge infrastructures, incoherence of institutional frameworks, or lack of specific capabilities may have a negative impact on the functioning of the agricultural innovation system. The purpose of this paper is to apply a comprehensive innovation systems analytical framework, reconciling analyses of systemic structures, functions, failures and merits of innovation systems to assess and compare the performance of the agricultural innovation systems of Scotland and the Netherlands. To achieve this an analytical framework was drawn up based on the available literature, and through a process that included document analysis and a series of semi-structured interviews and workshops with experts in the two countries the agrifood sectors were empirically assessed. In both countries, systemic failures in terms of actors’ interactions and competencies as well as market and incentive structures were revealed. However, differences emerge between the two countries that appear to relate more to social and cultural (soft institutions) differences rather than the formal legal and regulatory frameworks (hard institutions)
    Ambient Surface Analysis of Organic Monolayers using Direct Analysis in Real Time Orbitrap Mass Spectrometry
    Manova, R.K. ; Joshi, S. ; Debrassi, A. ; Bhairamadgi, N.S. ; Roeven, E. ; Gagnon, J. ; Tahir, M.N. ; Claassen, F.W. ; Scheres, L.M.W. ; Wennekes, T. ; Schroën, C.G.P.H. ; Beek, T.A. van; Zuilhof, H. ; Nielen, M.W.F. - \ 2014
    Analytical Chemistry 86 (2014)5. - ISSN 0003-2700 - p. 2403 - 2411.
    self-assembled monolayers - tof-sims - static sims - gold - silicon - biofunctionalization - functionalization - fragmentation - biosensors - layer
    A better characterization of nanometer-thick organic layers (monolayers) as used for engineering surface properties, biosensing, nanomedicine, and smart materials will widen their application. The aim of this study was to develop direct analysis in real time high-resolution mass spectrometry (DART-HRMS) into a new and complementary analytical tool for characterizing organic monolayers. To assess the scope and formulate general interpretation rules, DART-HRMS was used to analyze a diverse set of monolayers having different chemistries (amides, esters, amines, acids, alcohols, alkanes, ethers, thioethers, polymers, sugars) on five different substrates (Si, Si3N4, glass, Al2O3, Au). The substrate did not play a major role except in the case of gold, for which breaking of the weak Au–S bond that tethers the monolayer to the surface, was observed. For monolayers with stronger covalent interfacial bonds, fragmentation around terminal groups was found. For ester and amide-terminated monolayers, in situ hydrolysis during DART resulted in the detection of ions characteristic of the terminal groups (alcohol, amine, carboxylic acid). For ether and thioether-terminated layers, scission of C–O or C–S bonds also led to the release of the terminal part of the monolayer in a predictable manner. Only the spectra of alkane monolayers could not be interpreted. DART-HRMS allowed for the analysis of and distinction between monolayers containing biologically relevant mono or disaccharides. Overall, DART-HRMS is a promising surface analysis technique that combines detailed structural information on nanomaterials and ultrathin films with fast analyses under ambient conditions.
    Toward better application of minimum area requirements in conservation planning
    Pe’er, G. ; Tsianou, M.A. ; Franz, K.W. ; Matsinos, Y.G. ; Mazaris, A.D. ; Storch, D. ; Kopsova, L. ; Verboom, J. ; Baguette, M. ; Stevens, V.M. ; Henle, K. - \ 2014
    Biological Conservation 170 (2014). - ISSN 0006-3207 - p. 92 - 102.
    population viability analysis - home-range size - land-use change - body-size - extinction - mammals - birds - fragmentation - biodiversity - management
    The Minimum Area Requirements (MAR) of species is a concept that explicitly addresses area and therefore can be highly relevant for conservation planning and policy. This study compiled a comprehensive database of MAR estimates from the literature, covering 216 terrestrial animal species from 80 studies. We obtained estimates from (a) Population Viability Analyses (PVAs) which explored a range of area-related scenarios, (b) PVAs that provided a fixed value – either MAR or the minimum viable population size (MVP) alongside other area-relevant information, and (c) empirical studies of occupancy patterns in islands or isolated habitat patches across area. We assessed the explanatory power of life-history traits (body mass, feeding guild, generation length and offspring size), environmental variables (average precipitation and temperature), research approach and phylogenetic group on MAR estimates. PVAs exploring area showed strong correlation between MAR and body mass. One to two additional variables further improved the predictive power. PVA reporting fixed MAR, and occupancy-based studies, were better explained by the combination of feeding guild, climatic variables and additional life history traits. Phylogeny had a consistent but usually small contribution to the predictive power of models. Our work demonstrates that estimating the MAR across species and taxa is achievable but requires cautious interpretation. We further suggest that occupancy patterns are likely sensitive to transient dynamics and are therefore risky to use for estimating MAR. PVA-based evaluations enable considering time horizon and extinction probability, two aspects that are critical for future implementation of the MAR concept into policy and management.
    Can local landscape attributes explain species richness patterns at macroecological scales?
    Xu, C. ; Huang, Z. ; Chi, T. ; Chen, B.J.W. ; Zhang, M. ; Liu, M. - \ 2014
    Global Ecology and Biogeography 23 (2014)4. - ISSN 1466-822X - p. 436 - 445.
    habitat heterogeneity - plant diversity - nature-reserves - land-cover - biodiversity - climate - energy - china - models - fragmentation
    Although the influence on species richness of landscape attributes representing landscape composition and spatial configuration has been well documented at landscape scales, its effects remain little understood at macroecological scales. We aim to assess the role of landscape attributes, and their relative importance compared with climate, habitat heterogeneity and human influence (CHH) in particular, in shaping broad-scale richness patterns.
    Small island developing states and international climate change negotiations: the power of moral ‘‘leadership’’
    Águeda Corneloup, I. de; Mol, A.P.J. - \ 2014
    International Environmental Agreements: Politics, Law and Economics 14 (2014)3. - ISSN 1567-9764 - p. 281 - 297.
    regime formation - fragmentation - policy - aosis
    Being at the frontline of climate change, small island developing states (SIDS) hold a serious stake in climate negotiations. However, these countries usually are marginalized in the international political arena, due to their lack of structural power. This paper explores the strategic influence of SIDS and its representative organization, the Alliance of Small Island States, in the negotiations leading to the Copenhagen summit of December 2009. Using the concepts of leadership and discourses, the position, strategies, and impact of SIDS are analyzed on negotiation processes and their final outcome, focusing on three core demands of small island countries at Copenhagen: a temperature rise limit of 1.5 °C above preindustrial levels, funding for adaptation, and a legally binding outcome. Results reveal that SIDS practiced entrepreneurial, intellectual, and environmental leadership strategies and especially made use of moral claims in the debate. Given their near absence of structural power, they managed to secure a surprisingly large part of “their” agenda and interests in the final Copenhagen Accord, especially through (discourse) coalitions with various other state and non-state stakeholders.
    Chain length distribution and kinetic characteristics of an enzymatically produced polymer
    Mulders, K.J.M. ; Beeftink, H.H. - \ 2013
    e-Polymers 13 (2013)1. - ISSN 1618-7229 - p. 261 - 272.
    monte-carlo-simulation - multiple attack mechanism - sequential reactions - actin-filaments - enzyme - model - transglycosylation - fragmentation - competition - reactors
    Non-processive enzymatic polymerization leads to a distribution of polymer chain lengths. A polymerization model was developed to investigate the relation between the extent of this distribution on one hand, and the polymerization start conditions and reaction kinetics on the other hand. The model describes changes in concentration of chains of length n as the result of two elongation reactions: elongation by monomer addition to length n-1 and elongation by monomer addition to length n. Polymerization reactions were assumed to be zero order in monomer concentration and to obey Michaelis-Menten kinetics with respect to polymer concentrations. In addition, the amount of enzyme available for each individual reaction (n n+1) is assumed to be Non-processive enzymatic polymerization leads to a distribution of polymer chain lengths. A polymerization model was developed to investigate the relation between the extent of this distribution on one hand, and the polymerization start conditions and reaction kinetics on the other hand. The model describes changes in concentration of chains of length n as the result of two elongation reactions: elongation by monomer addition to length n-1 and elongation by monomer addition to length n. Polymerization reactions were assumed to be zero order in monomer concentration and to obey Michaelis-Menten kinetics with respect to polymer concentrations. In addition, the amount of enzyme available for each individual reaction (n n+1) is assumed to be proportional to the concentration of polymer substrate of length n. The development of the shape of the chain length distribution was found to be independent of the value of the overall reaction rate constant; only the rate at which these shapes developed was influenced by the 1st-order rate constant. The value of the Michaelis parameter did affect the form of the chain length distribution curve since it affects the reaction order. An increase in reaction order was found to promote widening of the chain length distribution. Differences in kinetic parameters between the subsequent polymerization reactions, if any, were also found to have a large effect on the development of the chain length distribution. An increase in rate constants with chain length entailed a wider distribution; a more narrow distribution would require a decrease in rate constants with chain length.proportional to the concentration of polymer substrate of length n. The development of the shape of the chain length distribution was found to be independent of the value of the overall reaction rate constant; only the rate at which these shapes developed was influenced by the 1st-order rate constant. The value of the Michaelis parameter did affect the form of the chain length distribution curve since it affects the reaction order. An increase in reaction order was found to promote widening of the chain length distribution. Differences in kinetic parameters between the subsequent polymerization reactions, if any, were also found to have a large effect on the development of the chain length distribution. An increase in rate constants with chain length entailed a wider distribution; a more narrow distribution would require a decrease in rate constants with chain length.
    Automatic Chemical Structure Annotation of an LC-MSn Based Metabolic Profile from Green Tea
    Ridder, L.O. ; Hooft, J.J.J. van der; Verhoeven, S. ; Vos, C.H. de; Bino, R.J. ; Vervoort, J. - \ 2013
    Analytical Chemistry 85 (2013)12. - ISSN 0003-2700 - p. 6033 - 6040.
    accurate mass-spectrometry - camelia-sinensis extracts - spectral trees - oolong tea - identification - fragmentation - elucidation - flavan-3-ols - polyphenols - software
    Liquid chromatography coupled with multistage accurate mass spectrometry (LC–MSn) can generate comprehensive spectral information of metabolites in crude extracts. To support structural characterization of the many metabolites present in such complex samples, we present a novel method (http://www.emetabolomics.org/magma) to automatically process and annotate the LC–MSn data sets on the basis of candidate molecules from chemical databases, such as PubChem or the Human Metabolite Database. Multistage MSn spectral data is automatically annotated with hierarchical trees of in silico generated substructures of candidate molecules to explain the observed fragment ions and alternative candidates are ranked on the basis of the calculated matching score. We tested this method on an untargeted LC–MSn (n = 3) data set of a green tea extract, generated on an LC-LTQ/Orbitrap hybrid MS system. For the 623 spectral trees obtained in a single LC–MSn run, a total of 116¿240 candidate molecules with monoisotopic masses matching within 5 ppm mass accuracy were retrieved from the PubChem database, ranging from 4 to 1327 candidates per molecular ion. The matching scores were used to rank the candidate molecules for each LC–MSn component. The median and third quartile fractional ranks for 85 previously identified tea compounds were 3.5 and 7.5, respectively. The substructure annotations and rankings provided detailed structural information of the detected components, beyond annotation with elemental formula only. Twenty-four additional components were putatively identified by expert interpretation of the automatically annotated data set, illustrating the potential to support systematic and untargeted metabolite identification.
    The (un)certainty of selectivity in liquid chromatography tandem mass spectrometry
    Berendsen, B.J.A. ; Stolker, A.A.M. ; Nielen, M.W.F. - \ 2013
    Journal of the American Society for Mass Spectrometry 24 (2013). - ISSN 1044-0305 - p. 154 - 163.
    drug residues - lc-ms - identification - confirmation - spectra - library - fragmentation - system - food
    We developed a procedure to determine the "identification power" of an LC-MS/MS method operated in the MRM acquisition mode, which is related to its selectivity. The probability of any compound showing the same precursor ion, product ions, and retention time as the compound of interest is used as a measure of selectivity. This is calculated based upon empirical models constructed from three very large compound databases. Based upon the final probability estimation, additional measures to assure unambiguous identification can be taken, like the selection of different or additional product ions. The reported procedure in combination with criteria for relative ion abundances results in a powerful technique to determine the (un)certainty of the selectivity of any LC-MS/MS analysis and thus the risk of false positive results. Furthermore, the procedure is very useful as a tool to validate method selectivity. Figure
    The impact of Soybean expansion on mammal and bird, in the Balsas rerion, north Brasilian Cerrado
    Barreto, L. ; Eupen, M. van; Kok, K. ; Jongman, R.H.G. ; Ribeiro, M.C. ; Veldkamp, A. ; Hass, A. ; Oliveira, T.G. - \ 2012
    Journal for Nature Conservation 20 (2012)6. - ISSN 1617-1381 - p. 374 - 383.
    land-cover change - atlantic forest - nature conservation - spatial scales - climate-change - landscape - biodiversity - model - fragmentation - populations
    In order to analyse the impact of land use change, it is particularly important to know how organisms use resources distributed across a heterogeneous landscape. The main objective of this study is to analyse the potential impact of land use change on bird and mammal fauna, by using a coupled model approach. The CLUE (Conversion of Land Use and its Effects) model has been applied to obtain the spatial pattern of land use change for a scenario with soybean expansion in the Cerrado of Maranhão State in Brazil. These land use change maps were used as the input for the LEDESS (Landscape Ecological Decision and Evaluation Support System) model to evaluate the impact of habitat fragmentation on mammal and bird species. The scenarios demonstrated that high quality habitat for all studied species will be lost in the future when current trends in agricultural expansion continue, but these changes will have species-specific impacts. The most relevant ecological impact under the explored scenarios was habitat fragmentation expressed by the increase the number of habitat clusters. The coupled model approach of LEDESS and CLUE made it possible to project the spatial impact of soybean expansion on habitat dynamics in the studied region. This model approach can help to design effective ecological infrastructure to facilitate species survival and to implement an effective habitat network in the Balsas region.
    Unbiased Selective Isolation of Protein N-Terminal Peptides from Complex Proteome Samples Using Phospho Tagging PTAG) and TiO2-based Depletion
    Mommen, G.P.M. ; Waterbeemd, B. van de; Meiring, H.D. ; Kersten, G. ; Heck, A.J.R. ; Jong, A.P.J.M. de - \ 2012
    Molecular and Cellular Proteomics 11 (2012)9. - ISSN 1535-9476 - p. 832 - 842.
    fractional diagonal chromatography - positional proteomics - in-vivo - proteolytic events - cleavage products - identification - phosphorylation - phosphoproteomics - fragmentation - acetylation
    A positional proteomics strategy for global N-proteome analysis is presented based on phospho tagging (PTAG) of internal peptides followed by depletion by titanium dioxide (TiO2) affinity chromatography. Therefore, N-terminal and lysine amino groups are initially completely dimethylated with formaldehyde at the protein level, after which the proteins are digested and the newly formed internal peptides modified with the PTAG reagent glyceraldhyde-3-phosphate in nearly perfect yields (> 99%). The resulting phosphopeptides are depleted through binding onto TiO2, keeping exclusively a set of N-acetylated and/or N-dimethylated terminal peptides for analysis by LC-MS/MS. Analysis of peptides derivatized with differentially labeled isotopic analogous of the PTAG reagent revealed a high depletion efficiency (> 95%). The method enabled identification of 753 unique N-terminal peptides (428 proteins) in N. meningitidis and 928 unique N-terminal peptides (572 proteins) in S cerevisiae. These included verified neo-N-termini from subcellular relocalized membrane and mitochondrial proteins. The presented PTAG approach is therefore a novel versatile and robust method for mass spectrometry-based N-proteome analysis and identification of protease-generated cleavage products
    Metabolite Identification Using Automated Comparison of High-Resolution Multistage Mass Spectral Trees
    Rojas-Cherto, M. ; Peironcely, J.E. ; Kasper, P.T. ; Hooft, J.J.J. van der; Vos, R.C.H. de; Vreeken, R. ; Hankemeier, T. ; Reijmers, T. - \ 2012
    Analytical Chemistry 84 (2012)13. - ISSN 0003-2700 - p. 5524 - 5534.
    development kit cdk - source java library - spectrometry data - chemical markup - fragmentation - web - optimization - instruments - algorithms - ms/ms
    Multistage mass spectrometry (MSn) generating so-called spectral trees is a powerful tool in the annotation and structural elucidation of metabolites and is increasingly used in the area of accurate mass LC/MS-based metabolomics to identify unknown, but biologically relevant, compounds. As a consequence, there is a growing need for computational tools specifically designed for the processing and interpretation of MSn data. Here, we present a novel approach to represent and calculate the similarity between high-resolution mass spectral fragmentation trees. This approach can be used to query multiple-stage mass spectra in MS spectral libraries. Additionally the method can be used to calculate structure-spectrum correlations and potentially deduce substructures from spectra of unknown compounds. The approach was tested using two different spectral libraries composed of either human or plant metabolites which currently contain 872 MSn spectra acquired from 549 metabolites using Orbitrap FTMSn. For validation purposes, for 282 of these 549 metabolites, 765 additional replicate MSn spectra acquired with the same instrument were used. Both the dereplication and de novo identification functionalities of the comparison approach are discussed. This novel MSn spectral processing and comparison approach increases the probability to assign the correct identity to an experimentally obtained fragmentation tree. Ultimately, this tool may pave the way for constructing and populating large MSn spectral libraries that can be used for searching and matching experimental MSn spectra for annotation and structural elucidation of unknown metabolites detected in untargeted metabolomics studies.
    Effects of Roads and Traffic on Wildlife Populations and Landscape Function Road Ecology is Moving toward Larger Scales
    Ree, R. van; Jaeger, J.A.G. ; Grift, E.A. van der; Clevenger, A.P. - \ 2011
    Ecology and Society 16 (2011)1. - ISSN 1708-3087 - 9 p.
    fragmentation - habitat - biodiversity - thresholds
    Road ecology has developed into a significant branch of ecology with steady growth in the number of refereed journal articles, books, conferences, symposia, and “best practice” guidelines being produced each year. The main objective of this special issue of Ecology and Society is to highlight the need for studies that document the population, community, and ecosystem-level effects of roads and traffic by publishing studies that document these effects. It became apparent when compiling this special issue that there is a paucity of studies that explicitly examined higher order effects of roads and traffic. No papers on landscape function or ecosystem-level effects were submitted, despite being highlighted as a priority for publication. The 17 papers in this issue, from Australia, Canada, the Netherlands, and USA, all deal to some extent with either population or community-level effects of roads and traffic. Nevertheless, many higher order effects remain unquantified, and must become the focus of future studies because the complexity and interactions among the effects of roads and traffic are large and potentially unexpected. An analysis of these complex interrelations requires systematic research, and it is necessary to further establish collaborative links between ecologists and transportation agencies. Many road agencies have “environmental sustainability” as one of their goals and the only way to achieve such goals is for them to support and foster long-term and credible scientific research. The current situation, with numerous small-scale projects being undertaken independently of each other, cannot provide the information required to quantify and mitigate the negative effects of roads and traffic on higher levels. The future of road ecology research will be best enhanced when multiple road projects in different states or countries are combined and studied as part of integrated, well-replicated research projects.
    Land rental market, off-farm employment and agricultural production in Southeast China
    Feng, S. ; Heerink, N. ; Ruben, R. ; Qu, F. - \ 2010
    China Economic Review 21 (2010)4. - ISSN 1043-951X - p. 598 - 606.
    rural china - labor-markets - migration - tenure - rights - fragmentation - investment - economics - costs
    This paper performs a plot-level analysis of the impact of land rentalmarket participation and offfarm employment on land investment, input use, and rice yields for 215 plots cultivated by 52 households in three villages inNortheast Jiangxi Province. Our findings showthat households that rent extra land are relativelymore productive, but contradict results of earlier studieswhich found that tenure status of plots affects the level of land investments. We further find that off-farm employment does not significantly affect rice yields. This result contradicts those of earlier studies which found that the negative lost-labor effect of off-farm employment dominates the positive income effect. Another novel finding is that people working locally off-farm tend to switch from green manure planting towards the use of organic manure on their rice plots. We conclude that policies that will further stimulate the development of land rental markets, which is still in its infancy, can contribute significantly to higher rice production in Southeast China. Another implication of our results is thatworries about the negative impact that the continuously growing off-farm employment may have on China's goal to remain self-sufficient in grain production are less relevant at the moment for the region examined in our study.
    Pervasive effects of dispersal limitation on within- and among-community species richness in agricultural landscapes
    Hendrickx, F. ; Maelfait, J.P. ; Desender, K. ; Aviron, S. ; Bailey, D. ; Diekotter, T. ; Lens, L. ; Liira, J. ; Schweiger, O. ; Speelmans, M. ; Vandomme, V. ; Bugter, R.J.F. - \ 2009
    Global Ecology and Biogeography 18 (2009)5. - ISSN 1466-822X - p. 607 - 616.
    source-sink metacommunities - habitat diversity affect - land-use intensity - beetle assemblages - spatial-pattern - ground beetles - patch size - biodiversity - fragmentation - traits
    Aim To determine whether the effect of habitat fragmentation and habitat heterogeneity on species richness at different spatial scales depends on the dispersal ability of the species assemblages and if this results in nested species assemblages. Location Agricultural landscapes distributed over seven temperate Europe countries covering a range from France to Estonia. Methods We sampled 16 local communities in each of 24 agricultural landscapes (16 km(2)) that differ in the amount and heterogeneity of semi-natural habitat patches. Carabid beetles were used as model organisms as dispersal ability can easily be assessed on morphological traits. The proximity and heterogeneity of semi-natural patches within the landscape were related to average local (alpha), between local (beta) and landscape (gamma) species richness and compared among four guilds that differ in dispersal ability. Results For species assemblages with low dispersal ability, local diversity increased as the proximity of semi-natural habitat increased, while mobile species showed an opposite trend. Beta diversity decreased equally for all dispersal classes in relation to proximity, suggesting a homogenizing effect of increased patch isolation. In contrast, habitat diversity of the semi-natural patches affected beta diversity positively only for less mobile species, probably due to the low dispersal ability of specialist species. Species with low mobility that persisted in highly fragmented landscapes were consistently present in less fragmented ones, resulting in nested assemblages for this mobility class only. Main conclusions The incorporation of dispersal ability reveals that only local species assemblages with low dispersal ability show a decrease of richness as a result of fragmentation. This local species loss is compensated at least in part by an increase in species with high dispersal ability, which obscures the effect of fragmentation when investigated across dispersal groups. Conversely, fragmentation homogenizes the landscape fauna for all dispersal groups, which indicates the invasion of non-crop habitats by similar good dispersers across the whole landscape. Given that recolonization of low dispersers is unlikely, depletion of these species in modern agricultural landscapes appears temporally pervasive.
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