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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Effects of political instability on the volatility of Palestinian food prices
Ihle, R. ; El-Jafari, Mahmoud Khader ; Cramon-Taubadel, Stephan von - \ 2019
New Medit 18 (2019)3. - ISSN 1594-5685 - p. 59 - 76.
Food prices - MENA - Middle East - Uncertainty - War
Political instabilities and violent political conflict have in recent years risen substantially throughout the world. Especially in the Middle East and North Africa they have grown to decisive factors permanently challenging the livelihoods of millions. We assess whether and to what extent varying intensities of conflict impact economic activity in Palestine which has been subject to substantial violent political conflict for decades. In particular, we analyse the relationship between various intensity levels of political instability measured by conflict-caused fatalities and uncertainty of weekly food prices in the West Bank between 2004 and 2011 using a GARCH model. We consider four food commodities covering vegetables, fruits and animal products. Banana and milk prices are found not to show clustered volatility while onion and pear prices do. The impact of varying conflict intensities on weekly average prices appears to be modest. This might suggest that effects happen on a temporally and geographically more disaggregated scale.
Urinary Taurine Excretion and Risk of Late Graft Failure in Renal Transplant Recipients
Post, Adrian ; Said, Yusof ; Gomes-Neto, Antonio W. ; Krogt, Jennifer van der; Blaauw, Pim de; Berger, Stefan P. ; Geleijnse, Johanna M. ; Borgonjen, Karin ; Berg, Else van den; Goor, Harry van; Rimbach, Gerald ; Kema, Ido P. ; Tsikas, Dimitrios ; Heiner-Fokkema, Rebecca ; Bakker, Stephan J.L. - \ 2019
Nutrients 11 (2019)9. - ISSN 2072-6643
graft survival - renal transplant recipients - taurine - taurine excretion

Taurine is a sulfur containing nutrient that has been shown to protect against oxidative stress, which has been implicated in the pathophysiology leading to late graft failure after renal transplantation. We prospectively investigated whether high urinary taurine excretion, reflecting high taurine intake, is associated with low risk for development of late graft failure in renal transplant recipients (RTR). Urinary taurine excretion was measured in a longitudinal cohort of 678 stable RTR. Prospective associations were assessed using Cox regression analyses. Graft failure was defined as the start of dialysis or re-transplantation. In RTR (58% male, 53 ± 13 years old, estimated glomerular filtration rate (eGFR) 45 ± 19 mL/min/1.73 m2), urinary taurine excretion (533 (210-946) µmol/24 h) was significantly associated with serum free sulfhydryl groups (β = 0.126; P = 0.001). During median follow-up for 5.3 (4.5-6.0) years, 83 (12%) patients developed graft failure. In Cox regression analyses, urinary taurine excretion was inversely associated with graft failure (hazard ratio: 0.74 (0.67-0.82); P < 0.001). This association remained significant independent of potential confounders. High urinary taurine excretion is associated with low risk of late graft failure in RTR. Therefore, increasing taurine intake may potentially support graft survival in RTR. Further studies are warranted to determine the underlying mechanisms and the potential of taurine supplementation.

Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe
Frantz, Laurent A.F. ; Haile, James ; Lin, Audrey T. ; Scheu, Amelie ; Geörg, Christina ; Benecke, Norbert ; Alexander, Michelle ; Linderholm, Anna ; Mullin, Victoria E. ; Daly, Kevin G. ; Battista, Vincent M. ; Price, Max ; Gron, Kurt J. ; Alexandri, Panoraia ; Arbogast, Rose Marie ; Arbuckle, Benjamin ; Bǎlǎşescu, Adrian ; Barnett, Ross ; Bartosiewicz, László ; Baryshnikov, Gennady ; Bonsall, Clive ; Borić, Dušan ; Boroneanţ, Adina ; Bulatović, Jelena ; Çakirlar, Canan ; Carretero, José Miguel ; Chapman, John ; Church, Mike ; Crooijmans, Richard ; Cupere, Bea De; Detry, Cleia ; Dimitrijevic, Vesna ; Dumitraşcu, Valentin ; Plessis, Louis Du; Edwards, Ceiridwen J. ; Erek, Cevdet Merih ; Erim-Özdoǧan, Asli ; Ervynck, Anton ; Fulgione, Domenico ; Gligor, Mihai ; Götherström, Anders ; Gourichon, Lionel ; Groenen, Martien A.M. ; Helmer, Daniel ; Hongo, Hitomi ; Horwitz, Liora K. ; Irving-Pease, Evan K. ; Lebrasseur, Ophélie ; Lesur, Joséphine ; Malone, Caroline ; Manaseryan, Ninna ; Marciniak, Arkadiusz ; Martlew, Holley ; Mashkour, Marjan ; Matthews, Roger ; Matuzeviciute, Giedre Motuzaite ; Maziar, Sepideh ; Meijaard, Erik ; McGovern, Tom ; Megens, Hendrik Jan ; Miller, Rebecca ; Mohaseb, Azadeh Fatemeh ; Orschiedt, Jörg ; Orton, David ; Papathanasiou, Anastasia ; Pearson, Mike Parker ; Pinhasi, Ron ; Radmanović, Darko ; Ricaut, François Xavier ; Richards, Mike ; Sabin, Richard ; Sarti, Lucia ; Schier, Wolfram ; Sheikhi, Shiva ; Stephan, Elisabeth ; Stewart, John R. ; Stoddart, Simon ; Tagliacozzo, Antonio ; Tasić, Nenad ; Trantalidou, Katerina ; Tresset, Anne ; Valdiosera, Cristina ; Hurk, Youri Van Den; Poucke, Sophie Van; Vigne, Jean Denis ; Yanevich, Alexander ; Zeeb-Lanz, Andrea ; Triantafyllidis, Alexandros ; Gilbert, M.T.P. ; Schibler, Jörg ; Rowley-Conwy, Peter ; Zeder, Melinda ; Peters, Joris ; Cucchi, Thomas ; Bradley, Daniel G. ; Dobney, Keith ; Burger, Joachim ; Evin, Allowen ; Girdland-Flink, Linus ; Larson, Greger - \ 2019
Proceedings of the National Academy of Sciences of the United States of America 116 (2019)35. - ISSN 0027-8424 - p. 17231 - 17238.
Domestication - Evolution - Gene flow - Neolithic

Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.

Fruit and vegetable intake and risk of post trans plantation diabetes in renal transplant recipients
Gomes-Neto, António W. ; Osté, Maryse C.J. ; Sotomayor, Camilo G. ; Berg, Else V.D. ; Geleijnse, Johanna M. ; Gans, Reinold O.B. ; Bakker, Stephan J.L. ; Navis, Gerjan J. - \ 2019
Diabetes Care 42 (2019)9. - ISSN 0149-5992 - p. 1645 - 1652.

OBJECTIVE Posttransplantation diabetes mellitus (PTDM) contributes to risk for cardiovascular morbidity and mortality in renal transplant recipients (RTRs). In the general population, consumption of a diet containing few fruits and vegetables predisposes to type 2 diabetes. The role of diet as a potential modifiable risk factor for PTDM has not been explored. Our focus was to investigate the prospective associations of fruit and vegetable intake with risk of PTDM in stable RTRs. RESEARCH DESIGN AND METHODS We included 472 adult RTRs who had a functioning graft ≥1 year. Fruit and vegetable intake was assessed by using a 177-item food frequency questionnaire. PTDM was defined according the American Diabetes Association's diagnostic criteria for diabetes. RESULTS During 5.2 years of follow-up, 52 RTRs (11%) developed PTDM. Fruit intake was not associated with PTDM (hazard ratio [HR] 0.90 [95% CI 0.79-1.03] per 2log g/day; P = 0.13), whereas vegetable intake was inversely associated with PTDM (HR 0.77 [95% CI 0.63-0.94] per 2log g/day; P = 0.009). Mediation analyses revealed that 650% of the association between vegetable intake and PTDM was mediated by variations in key components of the metabolic syndrome (i.e., HDL cholesterol, triglycerides, and waist circumference) as determined by the National Cholesterol Education Program's Adult Treatment Panel III Expert Panel. CONCLUSIONS In this study vegetable intake, but not fruit intake, was associated with lower risk of PTDM in RTRs, likely largely through beneficial effects on key components of the metabolic syndrome. These findings further support accumulating evidence that supports a recommendation of higher vegetable intake by RTRs.

In vier stappen experimenteren met Internet of Things
Robbemond, R.M. ; Voort, Manfred van der; Man, Ard-Pieter de; Strang, Stephan ; Beer, Colinda de; Verdouw, C.N. ; Savelkouls, Carlijn - \ 2019
Wageningen University & Research - 3 p.
Integrated modelling and management of water resources: the ecosystem perspective on the nexus approach
Hülsmann, Stephan ; Sušnik, Janez ; Rinke, Karsten ; Langan, Simon ; Wijk, Dianneke van; Janssen, Annette B.G. ; Mooij, Wolf M. - \ 2019
Current Opinion in Environmental Sustainability 40 (2019). - ISSN 1877-3435 - p. 14 - 20.

Addressing challenges of water, energy and food security, nexus approaches towards resources management are being developed and starting to be implemented. However, the ecosystem perspective, essential for sustainable resources management, has been identified as a missing element within earlier nexus assessments. With regard to water they have mainly focused on the allocation to different sectors and users, while ecosystem services were rarely explicitly addressed. Existing aquatic ecosystem models are capable of quantifying a wide range of ecosystem services, but have thus far not been comprehensively used in a nexus context. Recent developments in aquatic ecosystem modelling approaches provide opportunities to achieve the sought integration of ecosystem services in the nexus approach. Therefore, we argue for a stronger role of aquatic ecosystem models in nexus assessments.

HEVnet: A one health, collaborative, interdisciplinary network and sequence data repository for enhanced hepatitis e virus molecular typing, characterisation and epidemiological investigations
Mulder, Annemieke Christine ; Kroneman, Annelies ; Franz, Eelco ; Vennema, Harry ; Tulen, Anna D. ; Takkinen, Johanna ; Hofhuis, Agnetha ; Adlhoch, Cornelia ; Aberle, Stephan ; Subissi, Lorenzo ; Suin, Vanessa ; Midgley, Sofie ; Kuznetsova, Tatiana ; Izopet, Jacques ; Pavio, Nicole ; Baechlein, Christine ; Baylisa, Sally A. ; Corman, Victor M. ; Fabera, Mirko ; Johne, Reimar ; Kamp, Christel ; Wenzel, Juergen J. ; Coughlan, Suzie ; Bartolo, Ilaria Di; Bruni, Roberto ; Ciccaglionea, Anna Rita ; Garbuglia, Anna Rosa ; Suffredini, Elisabetta ; Boxman, Ingeborg ; Hogema, Boris ; Poel, Wim van der; Zaaijera, Hans ; Sousaa, Rita de; Velebit, Branko ; Avellóna, Ana ; Buti, Maria ; Girones, Rosina ; Quer, Josep ; Widén, Frederik ; Norder, Heléne ; Nyström, Kristina ; Bachofen, Claudia ; Sahli, Roland ; Ijaza, Samreen ; Treagus, Samantha ; Kulka, Michael ; Rizzi, Valentina - \ 2019
Eurosurveillance 24 (2019)10. - ISSN 1025-496X

Hepatitis E virus (HEV) is a common cause of acute hepatitis worldwide. In Europe, HEV is a zoonosis transmitted via contaminated pork meat or other pork food products. Genotype 3 is the most prevalent HEV type in the animal reservoir, as well as in humans. Despite an increased incidence of hepatitis E across Europe, much remains unknown about its spread, sources and transmission routes. A One Health approach is crucial to better understand the (molecular) epidemiology of HEV. HEVnet was established in April 2017 as a network and database for sharing sequences and accompanying metadata collected from human, animal, food and environmental sources. HEVnet members working in the public health, veterinary health, food, environmental and blood safety sectors have submitted 1,615 HEV sequences from nine countries as at January 2019. Most are from humans (89%), and sequences of animal (5%), food (6%) or environmental (0.3%) origin are rare. Metadata for human sequences capture mostly sex (93%), year of birth (92%) and sampling (100%); data on region of sampling (37%) and clinical information (hospitalisation 27%, symptoms 20% or mortality 8%) are limited. HEVnet aims to expand into a global network capable of performing cross-sectoral and supranational studies, with a joint repository of molecular and epidemiological data on HEV.

Combining market structure and econometric methods for pricetransmission analysis
Acosta, Alejandro ; Ihle, Rico ; Cramon-Taubadel, Stephan von - \ 2019
Food Security 11 (2019)4. - ISSN 1876-4517 - p. 941 - 951.
Food Policy Design - Food Price Formation - Market Structure - Price Transmission

Much attention has been devoted in the literature to the analysis of price transmission along food supply chains. Price transmission analysis has traditionally focused on applying econometric methods to assess price dynamics and interrelationships. However, the exclusive application of econometric methods without considering the market’s institutional context has limited potential to support evidence-based policy-making. In recent years, studies have thus attempted to combine the use of quantitative and qualitative methods to better understand the level of performance of food value chains. This study contributes to broadening these empirical toolkits by suggesting a structured analytical framework that benefits from the simultaneous application of econometric and market-structure methods in price transmission analysis. To illustrate the application of the framework, we analyzed the milk market of Panama.

Novel function of Bleutongue Virus NS3 Protein in Regulation of the MAPK/ERK Signaling Pathway
Kundlacz, Cindy ; Pourcelot, Marie ; Fablet, Aurore ; Amaral Da Silva Moraes, Rayane ; Leger, Thibaut ; Morlet, Bastien ; Viarouge, Cyril ; Sailleau, C. ; Turpaud, Mathilde ; Gorlier, Axel ; Breard, Emmanuel ; Lecollinet, S. ; Rijn, P.A. van; Zientara, Stephan ; Vitour, Damien ; Caignard, Gregory - \ 2019
Journal of Virology 93 (2019)16. - ISSN 0022-538X - 17 p.
Bluetongue virus (BTV) is an arbovirus transmitted by blood-feeding midges to a wide range of wild and domestic ruminants. In this report, we showed that BTV, through its nonstructural protein NS3 (BTV-NS3), is able to activate the mitogen-activated protein kinase/extracellular signal-regulated kinase (MAPK/ERK) pathway, as assessed by phosphorylation levels of ERK1/2 and the translation initiation factor eukaryotic translation initiation factor 4E (eIF4E). By combining immunoprecipitation of BTV-NS3 and mass spectrometry analysis from both BTV-infected and NS3-transfected cells, we identified the serine/threonine-protein kinase B-Raf (BRAF), a crucial player in the MAPK/ERK pathway, as a new cellular interactor of BTV-NS3. BRAF silencing led to a significant decrease in the MAPK/ERK activation by BTV, supporting a model wherein BTV-NS3 interacts with BRAF to activate this signaling cascade. This positive regulation acts independently of the role of BTV-NS3 in counteracting the induction of the alpha/beta interferon response. Furthermore, the intrinsic ability of BTV-NS3 to bind BRAF and activate the MAPK/ERK pathway is conserved throughout multiple serotypes/strains but appears to be specific to BTV compared to other members of Orbivirus genus. Inhibition of MAPK/ERK pathway with U0126 reduced viral titers, suggesting that BTV manipulates this pathway for its own replication. Altogether, our data provide molecular mechanisms that unravel a new essential function of NS3 during BTV infection.
Genetic and molecular analysis of trichome development in Arabis alpina
Chopra, Divykriti ; Mapar, Mona ; Stephan, Lisa ; Albani, Maria C. ; Deneer, Anna ; Coupland, George ; Willing, Eva Maria ; Schellmann, Swen ; Schneeberger, Korbinian ; Fleck, Christian ; Schrader, Andrea ; Hülskamp, Martin - \ 2019
Proceedings of the National Academy of Sciences of the United States of America 116 (2019)24. - ISSN 0027-8424 - p. 12078 - 12083.
Arabis alpina - Genetic analysis - Trichomes

The genetic and molecular analysis of trichome development in Arabidopsis thaliana has generated a detailed knowledge about the underlying regulatory genes and networks. However, how rapidly these mechanisms diverge during evolution is unknown. To address this problem, we used an unbiased forward genetic approach to identify most genes involved in trichome development in the related crucifer species Arabis alpina. In general, we found most trichome mutant classes known in A. thaliana. We identified orthologous genes of the relevant A. thaliana genes by sequence similarity and synteny and sequenced candidate genes in the A. alpina mutants. While in most cases we found a highly similar gene-phenotype relationship as known from Arabidopsis, there were also striking differences in the regulation of trichome patterning, differentiation, and morphogenesis. Our analysis of trichome patterning suggests that the formation of two classes of trichomes is regulated differentially by the homeodomain transcription factor AaGL2. Moreover, we show that overexpression of the GL3 basic helix–loop–helix transcription factor in A. alpina leads to the opposite phenotype as described in A. thaliana. Mathematical modeling helps to explain how this nonintuitive behavior can be explained by different ratios of GL3 and GL1 in the two species.

High Dietary Intake of Vegetable Protein Is Associated With Lower Prevalence of Renal Function Impairment: Results of the Dutch DIALECT-1 Cohort
Oosterwijk, Milou M. ; Soedamah-Muthu, Sabita S. ; Geleijnse, Johanna M. ; Bakker, Stephan J.L. ; Navis, Gerjan ; Binnenmars, S.H. ; Gant, Christina M. ; Laverman, Gozewijn D. - \ 2019
Kidney International Reports 4 (2019)5. - ISSN 2468-0249 - p. 710 - 719.
diabetes mellitus type 2 - diet - kidney function - lifestyle

Introduction: Dietary protein intake may influence development of renal function impairment in diabetes mellitus type 2 (T2DM). We assessed the association between sources of protein and prevalence of renal function impairment. Methods: Cross-sectional analyses were performed in baseline data of 420 patients of the DIAbetes and LifEstyle Cohort Twente-1 (DIALECT-1)study. Protein intake was assessed using a Food Frequency Questionnaire, modified for accurate assessment of protein intake, including types and sources of protein. Renal function impairment was defined as estimated glomerular filtration rate (eGFR)<60 ml/min per 1.73 m 2 (Chronic Kidney Disease Epidemiology Collaboration formula). Results: Among 420 patients with T2DM, 99 renal function impairment cases were identified. Multivariate Cox proportional hazard models were used and adjusted for the main lifestyle and dietary factors. The prevalence ratios in the fully adjusted model were 1 (reference), 0.74 (95% confidence interval [CI]: 0.44–1.27; P = 0.28)and 0.47 (95% CI: 0.23–0.98; P = 0.04)according to increasing tertiles of vegetable protein intake. For animal protein intake the prevalence ratios were 1 (reference), 1.10 (95% CI: 0.64–1.88; P = 0.74)and 1.06 (95% CI: 0.56–1.99; P = 0.87)according to increasing tertiles of intake. Theoretical replacement models showed that replacing 3 energy percent from animal protein by vegetable protein lowered the prevalence ratio for the association with renal function impairment to 0.20 (95% CI: 0.06–0.63; P = 0.01). Conclusion: In conclusion, we found that higher intake of vegetable protein was associated with a lower prevalence of renal function impairment, and theoretical replacement of animal protein with vegetable protein was inversely associated with renal function impairment among patients with T2DM.

Urban green infrastructure – connecting people and nature for sustainable cities
Pauleit, Stephan ; Andersson, Erik ; Anton, Barbara ; Buijs, Arjen ; Haase, Dagmar ; Hansen, Rieke ; Kowarik, Ingo ; Stahl Olafsson, Anton ; Jagt, Sander Van der - \ 2019
Urban Forestry and Urban Greening 40 (2019). - ISSN 1618-8667 - p. 1 - 3.
sPlot – A new tool for global vegetation analyses
Bruelheide, Helge ; Dengler, Jürgen ; Jiménez-Alfaro, Borja ; Purschke, Oliver ; Hennekens, Stephan M. ; Chytrý, Milan ; Pillar, Valério D. ; Jansen, Florian ; Kattge, Jens ; Sandel, Brody ; Aubin, Isabelle ; Biurrun, Idoia ; Field, Richard ; Haider, Sylvia ; Jandt, Ute ; Lenoir, Jonathan ; Peet, Robert K. ; Peyre, Gwendolyn ; Sabatini, Francesco Maria ; Schmidt, Marco ; Schrodt, Franziska ; Winter, Marten ; Aćić, Svetlana ; Agrillo, Emiliano ; Alvarez, Miguel ; Ambarlı, Didem ; Angelini, Pierangela ; Apostolova, Iva ; Arfin Khan, Mohammed A.S. ; Arnst, Elise ; Attorre, Fabio ; Baraloto, Christopher ; Beckmann, Michael ; Berg, Christian ; Bergeron, Yves ; Bergmeier, Erwin ; Bjorkman, Anne D. ; Bondareva, Viktoria ; Borchardt, Peter ; Botta-Dukát, Zoltán ; Boyle, Brad ; Breen, Amy ; Brisse, Henry ; Byun, Chaeho ; Cabido, Marcelo R. ; Casella, Laura ; Cayuela, Luis ; Černý, Tomáš ; Chepinoga, Victor ; Csiky, János ; Curran, Michael ; Ćušterevska, Renata ; Dajić Stevanović, Zora ; Bie, Els De; Ruffray, Patrice de; Sanctis, Michele De; Dimopoulos, Panayotis ; Dressler, Stefan ; Ejrnæs, Rasmus ; El-Sheikh, Mohamed A.E.R.M. ; Enquist, Brian ; Ewald, Jörg ; Fagúndez, Jaime ; Finckh, Manfred ; Font, Xavier ; Forey, Estelle ; Fotiadis, Georgios ; García-Mijangos, Itziar ; Gasper, André Luis de; Golub, Valentin ; Gutierrez, Alvaro G. ; Hatim, Mohamed Z. ; He, Tianhua ; Higuchi, Pedro ; Holubová, Dana ; Hölzel, Norbert ; Homeier, Jürgen ; Indreica, Adrian ; Işık Gürsoy, Deniz ; Jansen, Steven ; Janssen, John ; Jedrzejek, Birgit ; Jiroušek, Martin ; Jürgens, Norbert ; Kącki, Zygmunt ; Kavgacı, Ali ; Kearsley, Elizabeth ; Kessler, Michael ; Knollová, Ilona ; Kolomiychuk, Vitaliy ; Korolyuk, Andrey ; Kozhevnikova, Maria ; Kozub, Łukasz ; Krstonošić, Daniel ; Kühl, Hjalmar ; Kühn, Ingolf ; Kuzemko, Anna ; Küzmič, Filip ; Landucci, Flavia ; Lee, Michael T. ; Levesley, Aurora ; Li, Ching Feng ; Liu, Hongyan ; Lopez-Gonzalez, Gabriela ; Lysenko, Tatiana ; Macanović, Armin ; Mahdavi, Parastoo ; Manning, Peter ; Marcenò, Corrado ; Martynenko, Vassiliy ; Mencuccini, Maurizio ; Minden, Vanessa ; Moeslund, Jesper Erenskjold ; Moretti, Marco ; Müller, Jonas V. ; Munzinger, Jérôme ; Niinemets, Ülo ; Nobis, Marcin ; Noroozi, Jalil ; Nowak, Arkadiusz ; Onyshchenko, Viktor ; Overbeck, Gerhard E. ; Ozinga, Wim A. ; Pauchard, Anibal ; Pedashenko, Hristo ; Peñuelas, Josep ; Pérez-Haase, Aaron ; Peterka, Tomáš ; Petřík, Petr ; Phillips, Oliver L. ; Prokhorov, Vadim ; Rašomavičius, Valerijus ; Revermann, Rasmus ; Rodwell, John ; Ruprecht, Eszter ; Rūsiņa, Solvita ; Samimi, Cyrus ; Schaminée, Joop H.J. ; Schmiedel, Ute ; Šibík, Jozef ; Šilc, Urban ; Škvorc, Željko ; Smyth, Anita ; Sop, Tenekwetche ; Sopotlieva, Desislava ; Sparrow, Ben ; Stančić, Zvjezdana ; Svenning, Jens Christian ; Swacha, Grzegorz ; Tang, Zhiyao ; Tsiripidis, Ioannis ; Turtureanu, Pavel Dan ; Uğurlu, Emin ; Uogintas, Domas ; Valachovič, Milan ; Vanselow, Kim André ; Vashenyak, Yulia ; Vassilev, Kiril ; Vélez-Martin, Eduardo ; Venanzoni, Roberto ; Vibrans, Alexander Christian ; Violle, Cyrille ; Virtanen, Risto ; Wehrden, Henrik von; Wagner, Viktoria ; Walker, Donald A. ; Wana, Desalegn ; Weiher, Evan ; Wesche, Karsten ; Whitfeld, Timothy ; Willner, Wolfgang ; Wiser, Susan ; Wohlgemuth, Thomas ; Yamalov, Sergey ; Zizka, Georg ; Zverev, Andrei - \ 2019
Journal of Vegetation Science 30 (2019)2. - ISSN 1100-9233 - p. 161 - 186.
biodiversity - community ecology - ecoinformatics - functional diversity - global scale - macroecology - phylogenetic diversity - plot database - sPlot - taxonomic diversity - vascular plant - vegetation relevé

Aims: Vegetation-plot records provide information on the presence and cover or abundance of plants co-occurring in the same community. Vegetation-plot data are spread across research groups, environmental agencies and biodiversity research centers and, thus, are rarely accessible at continental or global scales. Here we present the sPlot database, which collates vegetation plots worldwide to allow for the exploration of global patterns in taxonomic, functional and phylogenetic diversity at the plant community level. Results: sPlot version 2.1 contains records from 1,121,244 vegetation plots, which comprise 23,586,216 records of plant species and their relative cover or abundance in plots collected worldwide between 1885 and 2015. We complemented the information for each plot by retrieving climate and soil conditions and the biogeographic context (e.g., biomes) from external sources, and by calculating community-weighted means and variances of traits using gap-filled data from the global plant trait database TRY. Moreover, we created a phylogenetic tree for 50,167 out of the 54,519 species identified in the plots. We present the first maps of global patterns of community richness and community-weighted means of key traits. Conclusions: The availability of vegetation plot data in sPlot offers new avenues for vegetation analysis at the global scale.

Biomarkers of food intake for nuts and vegetable oils : an extensive literature search
Garcia-Aloy, Mar ; Hulshof, Paul J.M. ; Estruel-Amades, Sheila ; Osté, Maryse C.J. ; Lankinen, Maria ; Geleijnse, Johanna M. ; Goede, Janette De; Ulaszewska, Marynka ; Mattivi, Fulvio ; Bakker, Stephan J.L. ; Schwab, Ursula ; Andres-Lacueva, Cristina - \ 2019
Genes & Nutrition 14 (2019)1. - ISSN 1555-8932
Biomarker - Intake - Metabolomics - Nuts - Oils

Nuts and vegetable oils are important sources of fat and of a wide variety of micronutrients and phytochemicals. Following their intake, several of their constituents, as well as their derived metabolites, are found in blood circulation and in urine. As a consequence, these could be used to assess the compliance to a dietary intervention or to determine habitual intake of nuts and vegetable oils. However, before these metabolites can be widely used as biomarkers of food intake (BFIs), several characteristics have to be considered, including specificity, dose response, time response, stability, and analytical performance. We have, therefore, conducted an extensive literature search to evaluate current knowledge about potential BFIs of nuts and vegetable oils. Once identified, the strengths and weaknesses of the most promising candidate BFIs have been summarized. Results from selected studies have provided a variety of compounds mainly derived from the fatty fraction of these foods, but also other components and derived metabolites related to their nutritional composition. In particular, α-linolenic acid, urolithins, and 5-hydroxyindole-3-acetic acid seem to be the most plausible candidate BFIs for walnuts, whereas for almonds they could be α-tocopherol and some catechin-derived metabolites. Similarly, several studies have reported a strong association between selenium levels and consumption of Brazil nuts. Intake of vegetable oils has been mainly assessed through the measurement of specific fatty acids in different blood fractions, such as oleic acid for olive oil, α-linolenic acid for flaxseed (linseed) and rapeseed (canola) oils, and linoleic acid for sunflower oil. Additionally, hydroxytyrosol and its metabolites were the most promising distinctive BFIs for (extra) virgin olive oil. However, most of these components lack sufficient specificity to serve as BFIs. Therefore, additional studies are necessary to discover new candidate BFIs, as well as to further evaluate the specificity, sensitivity, dose-response relationships, and reproducibility of these candidate biomarkers and to eventually validate them in other populations. For the discovery of new candidate BFIs, an untargeted metabolomics approach may be the most effective strategy, whereas for increasing the specificity of the evaluation of food consumption, this could be a combination of different metabolites.

How Can the Environmental Efficiency of Indonesian Cocoa Farms Be Increased?
Tothmihaly, A. ; Ingram, V.J. ; Cramon-Taubadel, Stephan von - \ 2019
Ecological Economics 158 (2019). - ISSN 0921-8009 - p. 134 - 145.
Increasing global cocoa demand in the new millennium has triggered farmers in developing countries to expand cocoa cultivation. A challenge is how to sustainably increase cocoa production without causing deforestation. We examine this trade-off around the Lore Lindu National Park in Indonesia and investigate the determinants of environmental efficiency by applying a distance output function that includes cocoa production and rainforest plant abundance. We analyze 208 cocoa producers' variables from 2015 using both measured and self-reported data. We find that cocoa intensification results in higher ecosystem degradation, and that producers in our sample display a 50% mean efficiency. This low value points to the increased infestation of cocoa pod borer and the failure of the Gernas government program. Increasing efficiency could lead to a win-win-win situation: higher cocoa production from fewer hectares, and with more native rainforest plants co-existing with cocoa on those hectares. On average, efficiency scores suggest that there is scope to expand production by 367 kg of cocoa per farm and year on the existing planted area, to increase rainforest plants per 5 ∗ 5 m area by 109 while maintaining existing areas and production levels, or to reduce acreage by 0.52 ha per farm without reducing production.
Taxonomy of the order Bunyavirales : second update 2018
Maes, Piet ; Adkins, Scott ; Alkhovsky, Sergey V. ; Avšič-Županc, Tatjana ; Ballinger, Matthew J. ; Bente, Dennis A. ; Beer, Martin ; Bergeron, Éric ; Blair, Carol D. ; Briese, Thomas ; Buchmeier, Michael J. ; Burt, Felicity J. ; Calisher, Charles H. ; Charrel, Rémi N. ; Choi, Il Ryong ; Clegg, J.C.S. ; Torre, Juan Carlos de la; Lamballerie, Xavier de; DeRisi, Joseph L. ; Digiaro, Michele ; Drebot, Mike ; Ebihara, Hideki ; Elbeaino, Toufic ; Ergünay, Koray ; Fulhorst, Charles F. ; Garrison, Aura R. ; Gāo, George Fú ; Gonzalez, Jean Paul J. ; Groschup, Martin H. ; Günther, Stephan ; Haenni, Anne Lise ; Hall, Roy A. ; Hewson, Roger ; Hughes, Holly R. ; Jain, Rakesh K. ; Jonson, Miranda Gilda ; Junglen, Sandra ; Klempa, Boris ; Klingström, Jonas ; Kormelink, Richard ; Lambert, Amy J. ; Langevin, Stanley A. ; Lukashevich, Igor S. ; Marklewitz, Marco ; Martelli, Giovanni P. ; Mielke-Ehret, Nicole ; Mirazimi, Ali ; Mühlbach, Hans Peter ; Naidu, Rayapati ; Zhang, Yong Zhen - \ 2019
Archives of Virology 164 (2019)3. - ISSN 0304-8608 - p. 927 - 941.

In October 2018, the order Bunyavirales was amended by inclusion of the family Arenaviridae, abolishment of three families, creation of three new families, 19 new genera, and 14 new species, and renaming of three genera and 22 species. This article presents the updated taxonomy of the order Bunyavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).

Advancing urban green infrastructure in Europe : Outcomes and reflections from the GREEN SURGE project
Pauleit, Stephan ; Ambrose-Oji, Bianca ; Andersson, Erik ; Anton, Barbara ; Buijs, Arjen ; Haase, Dagmar ; Elands, Birgit ; Hansen, Rieke ; Kowarik, Ingo ; Kronenberg, Jakub ; Mattijssen, Thomas ; Stahl Olafsson, Anton ; Rall, Emily ; Jagt, Alexander P.N. van der - \ 2019
Urban Forestry and Urban Greening 40 (2019). - ISSN 1618-8667 - p. 4 - 16.
Green governance and planning - Green infrastructure - GREEN SURGE - Sustainable urbanisation - Urban learning labs

Urban green infrastructure (UGI) is a promising concept when developing multifunctional green space systems to address major challenges of urbanization such as increasing social cohesion, promoting the transition to a green economy, adaptation to climate change and conservation of biodiversity. In response to the European Commission's Communication on Green Infrastructure from 2013, the GREEN SURGE project aimed to further advance the development of UGI in European cities by (i) strengthening the conceptual foundations of UGI, (ii) developing improved methods and tools for assessment of its state, benefits and governance and, (iii) applying these to build a stronger evidence base. This paper aims to provide an overall synthesis of the project's main achievements. GREEN SURGE adopted an inter- and transdisciplinary approach. Urban Learning Labs and focal Learning Alliances in five cities were instrumental for intensive collaboration between disciplines and across science and practice. Pan-European surveys, e.g. of planning and governance practice or human-nature interactions established the state-of-the-art across the continent and identified good practices. The project consolidated green infrastructure planning and governance conceptually, and it mapped opportunities for better linking government-led planning with bottom-up initiatives for creating and managing UGI. It also introduced a framework for knowledge integration to support UGI valuation. Importantly, development and application of the concept of biocultural diversity gave new insights into human–nature relationships in multicultural urban societies. The results strongly call for more context-sensitive development of UGI that addresses the different needs and diverse cultural practices of people engaging with nature. In a nutshell, GREEN SURGE showed that UGI indeed can make a major contribution to sustainable and resilient urbanisation. Transdisciplinary research in urban labs, if well-conceived, has shown to hold great potential to advance UGI concepts, methods, knowledge and practice.

Climate change opens new frontiers for marine species in the Arctic: Current trends and future invasion risks
Chan, Farrah T. ; Stanislawczyk, Keara ; Sneekes, A.C. ; Dvoretsky, Alexander ; Gollasch, Stephan ; Minchin, Dan ; David, Matej ; Jelmert, Anders ; Albretsen, Jon ; Bailey, Sarah A. - \ 2019
Global Change Biology 25 (2019)1. - ISSN 1354-1013 - p. 25 - 38.
alien species - aquaculture - climate warming - fisheries - invasion pathways - invasive species - knowledge gap - nonindigenous species - shipping - vessels
Climate change and increased anthropogenic activities are expected to elevate the potential of introducing nonindigenous species (NIS) into the Arctic. Yet, the knowledge base needed to identify gaps and priorities for NIS research and management is limited. Here, we reviewed primary introduction events to each ecoregion of the marine Arctic realm to identify temporal and spatial patterns, likely source regions of NIS, and the putative introduction pathways. We included 54 introduction events representing 34 unique NIS. The rate of NIS discovery ranged from zero to four species per year between 1960 and 2015. The Iceland Shelf had the greatest number of introduction events (n = 14), followed by the Barents Sea (n = 11), and the Norwegian Sea (n = 11). Sixteen of the 54 introduction records had no known origins. The majority of those with known source regions were attributed to the Northeast Atlantic and the Northwest
Pacific, 19 and 14 records, respectively. Some introduction events were attributed
to multiple possible pathways. For these introductions, vessels transferred the greatest number of aquatic NIS (39%) to the Arctic, followed by natural spread (30%) and aquaculture activities (25%). Similar trends were found for introductions attributed to a single pathway. The phyla Arthropoda and Ochrophyta had the highest number of recorded introduction events, with 19 and 12 records, respectively. Recommendations including vector management, horizon scanning, early detection, rapid response, and a pan‐Arctic biodiversity inventory are considered in this paper. Our study provides a comprehensive record of primary introductions of NIS for marine environments in the
circumpolar Arctic and identifies knowledge gaps and opportunities for NIS research and management. Ecosystems worldwide will face dramatic changes in the coming decades due to global change. Our findings contribute to the knowledge base needed to address two aspects of global change—invasive species and climate change.
Mosaic governance for urban green infrastructure: Upscaling active citizenship from a local government perspective
Buijs, Arjen ; Hansen, Rieke ; Jagt, Sander Van Der; Ambrose-Oji, Bianca ; Elands, Birgit ; Lorance Rall, Emily ; Mattijssen, Thomas ; Pauleit, Stephan ; Runhaar, Hens ; Stahl Olafsson, Anton ; Steen Møller, Maja - \ 2019
Urban Forestry and Urban Greening 40 (2019). - ISSN 1618-8667 - p. 53 - 62.
Compact urban development, social demands and austerity measures are increasing pressures on urban greenspace. Meanwhile, active citizens, defined as voluntary individuals or groups who self-organize to contribute to urban green space development, provide ecological and social benefits to urban societies. This has inspired local governments to seek collaborations with non-state actors, including active citizens. However, the diverging aims, place-specific focus, and varying expertise of active citizenship may inhibit its contribution to ecological connectivity and upscaling beyond the local scale.
In this paper, we investigate how “mosaic governance” has potential as a framework for understanding active citizenship, its potential for upscaling and its relationship to strategic UGI planning. Using the policy arrangements approach, we analyse the role of discourse, resources, actors and rules of the game in the upscaling of active citizenship. Based on eight empirical cases from seven European cities, we analyse the diversity of collaborations between local governments and active citizens in greenspace development.
The cases show how active citizens can significantly contribute to UGI planning and implementation, for example by developing large parks with volunteers or designing a network of green corridors. The cases reveal multiple ways citizens and local governments benefit from collaborations, as well as different pathways for upscaling innovative discourses and practices from local communities to formal policy or to other cities. To enable upscaling, UGI planning needs to combine long-term, more formalized and higher-scale strategic approaches with more incremental approaches that correspond with localized, fragmented and informal efforts of local communities. While collaborations between municipalities and active citizenship is not without its difficulties, the examples of upscaling in our cases demonstrate the transformative power active citizens may have towards a more green, just and democratic city.
Global trait–environment relationships of plant communities
Bruelheide, Helge ; Dengler, Jürgen ; Purschke, Oliver ; Lenoir, Jonathan ; Jiménez-Alfaro, Borja ; Hennekens, Stephan M. ; Botta-Dukát, Zoltán ; Chytrý, Milan ; Field, Richard ; Jansen, Florian ; Kattge, Jens ; Pillar, Valério D. ; Schrodt, Franziska ; Mahecha, Miguel D. ; Peet, Robert K. ; Sandel, Brody ; Bodegom, Peter van; Altman, Jan ; Alvarez-Dávila, Esteban ; Arfin Khan, Mohammed A.S. ; Attorre, Fabio ; Aubin, Isabelle ; Baraloto, Christopher ; Barroso, Jorcely G. ; Bauters, Marijn ; Bergmeier, Erwin ; Biurrun, Idoia ; Bjorkman, Anne D. ; Blonder, Benjamin ; Čarni, Andraž ; Cayuela, Luis ; Černý, Tomáš ; Cornelissen, J.H.C. ; Craven, Dylan ; Dainese, Matteo ; Derroire, Géraldine ; Sanctis, Michele De; Díaz, Sandra ; Doležal, Jiří ; Farfan-Rios, William ; Feldpausch, Ted R. ; Fenton, Nicole J. ; Garnier, Eric ; Guerin, Greg R. ; Gutiérrez, Alvaro G. ; Haider, Sylvia ; Hattab, Tarek ; Henry, Greg ; Hérault, Bruno ; Ozinga, Wim A. - \ 2018
Nature Ecology & Evolution 2 (2018)12. - ISSN 2397-334X - p. 1906 - 1917.

Plant functional traits directly affect ecosystem functions. At the species level, trait combinations depend on trade-offs representing different ecological strategies, but at the community level trait combinations are expected to be decoupled from these trade-offs because different strategies can facilitate co-existence within communities. A key question is to what extent community-level trait composition is globally filtered and how well it is related to global versus local environmental drivers. Here, we perform a global, plot-level analysis of trait–environment relationships, using a database with more than 1.1 million vegetation plots and 26,632 plant species with trait information. Although we found a strong filtering of 17 functional traits, similar climate and soil conditions support communities differing greatly in mean trait values. The two main community trait axes that capture half of the global trait variation (plant stature and resource acquisitiveness) reflect the trade-offs at the species level but are weakly associated with climate and soil conditions at the global scale. Similarly, within-plot trait variation does not vary systematically with macro-environment. Our results indicate that, at fine spatial grain, macro-environmental drivers are much less important for functional trait composition than has been assumed from floristic analyses restricted to co-occurrence in large grid cells. Instead, trait combinations seem to be predominantly filtered by local-scale factors such as disturbance, fine-scale soil conditions, niche partitioning and biotic interactions.

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