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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Rootstocks: an extra instrument to achieve production goals : renewed interest by researchers
Heuvelink, E. ; Schwarz, Dietmar ; Kierkels, Tijs - \ 2018
In Greenhouses : the international magazine for greenhouse growers 7 (2018)3. - ISSN 2215-0633 - p. 44 - 45.
Agent-based modeling of environment-migration linkages: a review
Thober, Jule ; Schwarz, Nina ; Hermans, Kathleen - \ 2018
Ecology and Society 23 (2018)2. - ISSN 1708-3087
Environmental change can lead to human migration and vice versa. Agent-based models (ABMs) are valuable tools to study these linkages because they can represent individual migration decisions of human actors. Indeed, there is an increasing, yet small, number of ABMs that consider the natural environment in rural migration processes. Therefore, we reviewed 15 ABMs of environment-migration linkages in rural contexts to synthesize the current state of the art. The reviewed ABMs are mostly applied in tropical contexts, serve a wide range of purposes, and cover diverse scales and types of environmental factors, migration processes, and social-ecological feedbacks. We identified potential for future model development with respect to the (1) complexity of environmental influence factors, (2) representation of relevant migration flows, and (3) type of social-ecological couplings. We found that existing models tend to not include fully integrated feedbacks and provide recommendations for the further development of ABMs to contribute to an understanding of the environment-migration-nexus in the future.
Carbapenem-resistant Enterobacteriaceae in wildlife, food-producing, and companion animals : a systematic review
Köck, R. ; Daniels-Haardt, I. ; Becker, K. ; Mellmann, A. ; Friedrich, A.W. ; Mevius, D. ; Schwarz, S. ; Jurke, A. - \ 2018
Clinical Microbiology and Infection 24 (2018)12. - ISSN 1198-743X - p. 1241 - 1250.
Antibiotic resistance - Carbapenemase - Enterobacteriales - Epidemiology - Livestock - Zoonosis
Objectives: The spread of carbapenem-resistant Enterobacteriaceae (CRE) in healthcare settings challenges clinicians worldwide. However, little is known about dissemination of CRE in livestock, food, and companion animals and potential transmission to humans. Methods: We performed a systematic review of all studies published in the PubMed database between 1980 and 2017 and included those reporting the occurrence of CRE in samples from food-producing and companion animals, wildlife, and exposed humans. The primary outcome was the occurrence of CRE in samples from these animals; secondary outcomes included the prevalence of CRE, carbapenemase types, CRE genotypes, and antimicrobial susceptibilities. Results: We identified 68 articles describing CRE among pigs, poultry, cattle, seafood, dogs, cats, horses, pet birds, swallows, wild boars, wild stork, gulls, and black kites in Africa, America, Asia, Australia, and Europe. The following carbapenemases have been detected (predominantly affecting the genera Escherichia and Klebsiella): VIM, KPC, NDM, OXA, and IMP. Two studies found that 33–67% of exposed humans on poultry farms carried carbapenemase-producing CRE closely related to isolates from the farm environment. Twenty-seven studies selectively screened samples for CRE and found a prevalence of <1% among livestock and companion animals in Europe, 2–26% in Africa, and 1–15% in Asia. Wildlife (gulls) in Australia and Europe carried CRE in 16–19%. Conclusions: The occurrence of CRE in livestock, seafood, wildlife, pets, and directly exposed humans poses a risk for public health. Prospective prevalence studies using molecular and cultural microbiological methods are needed to better define the scope and transmission of CRE.
Metatranscriptome analysis of the microbial fermentation of dietary milk proteins in the murine gut
Hugenholtz, Floor ; Davids, Mark ; Schwarz, Jessica ; Müller, Michael ; Tomé, Daniel ; Schaap, Peter ; Hooiveld, Guido J.E.J. ; Smidt, Hauke ; Kleerebezem, Michiel - \ 2018
PLoS One 13 (2018)4. - ISSN 1932-6203
Undigestible food ingredients are converted by the microbiota into a large range of metabolites, predominated by short chain fatty acids (SCFA). These microbial metabolites are subsequently available for absorption by the host mucosa and can serve as an energy source. Amino acids fermentation by the microbiota expands the spectrum of fermentation end-products beyond acetate, propionate and butyrate, to include in particular branched-SCFA. Here the long-term effects of high protein-diets on microbial community composition and functionality in mice were analyzed. Determinations of the microbiota composition using phylogenetic microarray (MITChip) technology were complemented with metatranscriptome and SCFA analyses to obtain insight in in situ expression of protein fermentation pathways and the phylogenetic groups involved. High protein diets led to increased luminal concentrations of branched-SCFA, in accordance with protein fermentation in the gut. Bacteria dominantly participating in protein catabolism belonged to the Lachnospiraceae, Erysipelotrichaceae and Clostridiaceae families in both normal- and high- protein diet regimes. This study identifies the microbial groups involved in protein catabolism in the intestine and underpins the value of in situ metatranscriptome analyses as an approach to decipher locally active metabolic networks and pathways as a function of the dietary regime, as well as the phylogeny of the microorganisms executing them.
Functionality of whey proteins covalently modified by allyl isothiocyanate. Part 2 : Influence of the protein modification on the surface activity in an O/W system
Keppler, Julia K. ; Steffen-Heins, Anja ; Berton-Carabin, Claire C. ; Ropers, Marie Hélène ; Schwarz, Karin - \ 2018
Food Hydrocolloids 81 (2018). - ISSN 0268-005X - p. 286 - 299.
142-148) - 5971) - Allyl isothiocyanate (PubChem CID - Beta-Lactoglobulin (PubChem CID
Allyl isothiocyanate (AITC) is a small electrophilic molecule which can be found in cabbage after degradation of glucosinolates. The covalent attachment of AITC to whey protein isolate (WPI) was previously reported to increase their hydrophobicity and structural flexibility at acidic pH values. It is thus hypothesized, that the o/w interface adsorption behaviour and interfacial structure will be altered. To further understand the effect of the AITC-modification on the emulsifying capacity, adsorption kinetic and interfacial properties of unmodified and modified WPI were investigated at the o/w interface. The WPI-modification resulted in a significantly increased surface adsorption kinetic and a lower equilibrium interfacial tension at acidic pH values. The ratio of α-lactalbumin (ALA) and β-lactoglobulin (BLG) at the oil droplet surface differed between unmodified and modified WPI (modBLG > ALA+modALA). Several layers of loosely attached proteins were evident on the oil droplet surface in all modified WPI emulsions. The hyperfine coupling (aN) of the EPR spin probe TB residing at the oil droplet surface reflected an increased hydrophobicity of the modified proteins. A lower order parameter (S) in the lipid phase of the modified WPI emulsions gave evidence of an altered alignment of the modified proteins at the interface, probably sticking into the oil phase. In conclusion, the present results indicate that the increased flexibility and hydrophobicity of the modified whey proteins, especially of modified BLG, surpass the surface activity of unmodified ALA in acidic pH values.
Pollutants in Plastics within the North Pacific Subtropical Gyre
Chen, Qiqing ; Reisser, Julia ; Cunsolo, Serena ; Kwadijk, Christiaan ; Kotterman, M.J.J. ; Proietti, Maira ; Slat, Boyan ; Ferrari, Francesco ; Schwarz, Anna ; Levivier, Aurore ; Yin, Daqiang ; Hollert, Henner ; Koelmans, A.A. - \ 2018
Environmental Science and Technology 52 (2018)2. - ISSN 0013-936X - p. 446 - 456.
Here we report concentrations of pollutants in floating plastics from the North Pacific accumulation zone (NPAC). We compared chemical concentrations in plastics of different types and sizes, assessed ocean plastic potential risks using sediment quality criteria, and discussed the implications of our findings for bioaccumulation. Our results suggest that at least a fraction of the NPAC plastics is not in equilibrium with the surrounding seawater. For instance, ‘hard plastic’ samples had significantly higher PBDE concentrations than ‘nets and ropes’ samples, and 29% of them had PBDE composition similar to a widely used flame-retardant mixture. Our findings indicate that NPAC plastics may pose a chemical risk to organisms as 84% of the samples had at least one chemical exceeding sediment threshold effect levels. Furthermore, our surface trawls collected more plastic than biomass (180 times on average), indicating that some NPAC organisms feeding upon floating particles may have plastic as a major component of their diets. If gradients for pollutant transfer from NPAC plastic to predators exist (as indicated by our fugacity ratio calculations), plastics may play a role in transferring chemicals to certain marine organisms.
Data from 'Pollutants in Plastics within the North Pacific Subtropical Gyre'
Chen, Qiqing ; Reisser, Julia ; Cunsolo, Serena ; Kwadijk, C.J.A.F. ; Kotterman, M.J.J. ; Proietti, Maira ; Slat, Boyan ; Ferrari, Francesco ; Schwarz, Anna ; Levivier, Aurore ; Yin, Daqiang ; Hollert, Henner ; Koelmans, A.A. - \ 2017
plastic pollution - Great Pacific garbage pack - North Pacific subtropical gyre - persistant organic pollutants - marine debris - microplastics
Recommendations for the use of grafted plants in greenhouses. The case of the Netherlands
Dieleman, J.A. ; Janse, J. - \ 2017
In: Vegetable Grafting / Colla, G., Pérez-Alfocea, F., Schwarz, D., Wallingford : CABI Publishing Wallingford - ISBN 9781780648972 - p. 245 - 269.
Towards systematic analyses of ecosystem service trade-offs and synergies : Main concepts, methods and the road ahead
Cord, Anna F. ; Bartkowski, Bartosz ; Beckmann, Michael ; Dittrich, Andreas ; Hermans, Kathleen ; Kaim, Andrea ; Lienhoop, Nele ; Locher-Krause, Karla ; Priess, Jörg ; Schröter-Schlaack, Christoph ; Schwarz, Nina ; Seppelt, Ralf ; Strauch, Michael ; Václavík, Tomáš ; Volk, Martin - \ 2017
Ecosystem Services 28 (2017)part C. - ISSN 2212-0416 - p. 264 - 272.
Ecosystem service bundles - Ecosystem service demand - Ecosystem service supply - Optimization - Spatio-temporal scales - Stakeholders

Ecosystem services (ES), the benefits that humans obtain from nature, are of great importance for human well-being. The challenge of meeting the growing human demands for natural resources while sustaining essential ecosystem functions and resilience requires an in-depth understanding of the complex relationships between ES. These conflicting ('trade-offs') or synergistic ('synergies') relationships mean that changes in one ES can cause changes in other ES. By synthesizing the growing body of literature on ES relationships, we identified the following four main study objectives: (i) the identification and characterization of co-occurrences of ES, (ii) the identification of drivers that shape ES relationships, (iii) the exploration of biophysical constraints of landscapes and limitations to their multifunctionality, and (iv) the support of environmental planning, management and policy decisions. For each of these objectives we here describe the key concepts, including viewpoints of different disciplines, and highlight the major challenges that need to be addressed. We identified three cross-cutting themes being relevant to all four main types of studies. To help guiding researchers towards more systematic analyses of ES trade-offs and synergies, we conclude with an outlook on suggested future research priorities.

Environmental influences on the growing season duration and ripening of diverse Miscanthus germplasm grown in six countries
Nunn, Christopher ; Hastings, Astley Francis St John ; Kalinina, Olena ; Özgüven, Mensure ; Schüle, Heinrich ; Tarakanov, Ivan G. ; Weijde, Tim van der; Anisimov, Aleksander A. ; Iqbal, Yasir ; Kiesel, Andreas ; Khokhlov, Nikolay F. ; McCalmont, Jon P. ; Meyer, Heike ; Mos, Michal ; Schwarz, Kai Uwe ; Trindade, Luisa M. ; Lewandowski, Iris ; Clifton-Brown, John - \ 2017
Frontiers in Plant Science 8 (2017). - ISSN 1664-462X - 14 p.
Miscanthus - Modeling - Multi-location - Ripening - Senescence

The development of models to predict yield potential and quality of a Miscanthus crop must consider climatic limitations andthe duration of growing season. As a biomass crop, yield and quality are impacted by the timing of plant developmental transitions such as flowering andsenescence. Growth models are available for the commercially grown clone Miscanthus x giganteus (Mxg), but breeding programs have been working to expand the germplasmavailable, including development of interspecies hybrids. The aimof this study was to assess the performance of diverse germplasmbeyond the range of environments considered suitable for a Miscanthus crop to be grown. To achieve this, six field sites were planted as part of the EU OPTIMISC project in 2012 in a longitudinal gradient from West to East: Wales—Aberystwyth, Netherlands—Wageningen, Stuttgart—Germany, Ukraine—Potash, Turkey—Adana, and Russia—Moscow. Each field trial contained three replicated plots of the same 15 Miscanthus germplasmtypes. Through the 2014 growing season, phenotypic traits were measured to determine the timing of developmental stages key to ripening; the tradeoff between growth (yield) and quality (biomass ash and moisture content). The hottest site (Adana) showed an accelerated growing season, with emergence, flowering and senescence occurring before the other sites. However, the highest yields were produced at Potash, where emergence was delayed by frost and the growing season was shortest. Flowering triggers varied with species and only in Mxg was strongly linked to accumulated thermal time. Our results show that a prolonged growing season is not essential to achieve high yields if climatic conditions are favorable and in regions where the growing season is bordered by frost, delaying harvest can improve quality of the harvested biomass.

Extending miscanthus cultivation with novel germplasm at six contrasting sites
Kalinina, Olena ; Nunn, Christopher ; Sanderson, Ruth ; Hastings, Astley F.S. ; Weijde, Tim van der; Özgüven, Mensure ; Tarakanov, Ivan ; Schüle, Heinrich ; Trindade, Luisa M. ; Dolstra, Oene ; Schwarz, Kai Uwe ; Iqbal, Yasir ; Kiesel, Andreas ; Mos, Michal ; Lewandowski, Iris ; Clifton-Brown, John C. - \ 2017
Frontiers in Plant Science 8 (2017). - ISSN 1664-462X
Establishment - Marginal land - Miscanthus - Multi-location field trials - Novel hybrids - Productivity

Miscanthus is a genus of perennial rhizomatous grasses with C4 photosynthesis which is indigenous in a wide geographic range of Asian climates. The sterile clone, Miscanthus × giganteus (M. × giganteus), is a naturally occurring interspecific hybrid that has been used commercially in Europe for biomass production for over a decade. Although, M. × giganteus has many outstanding performance characteristics including high yields and low nutrient offtakes, commercial expansion is limited by cloning rates, slow establishment to a mature yield, frost, and drought resistance. In this paper, we evaluate the performance of 13 novel germplasm types alongside M. × giganteus and horticultural “Goliath” in trials in six sites (in Germany, Russia, The Netherlands, Turkey, UK, and Ukraine). Mean annual yields across all the sites and genotypes increased from 2.3 ± 0.2 t dry matter ha−1 following the first year of growth, to 7.3 ± 0.3, 9.5 ± 0.3, and 10.5 ± 0.2 t dry matter ha−1 following the second, third, and fourth years, respectively. The highest average annual yields across locations and four growth seasons were observed for M. × giganteus (9.9 ± 0.7 t dry matter ha−1) and interspecies hybrid OPM-6 (9.4 ± 0.6 t dry matter ha−1). The best of the new hybrid genotypes yielded similarly to M. × giganteus at most of the locations. Significant effects of the year of growth, location, species, genotype, and interplay between these factors have been observed demonstrating strong genotype × environment interactions. The highest yields were recorded in Ukraine. Time needed for the crop establishment varied depending on climate: in colder climates such as Russia the crop has not achieved its peak yield by the fourth year, whereas in the hot climate of Turkey and under irrigation the yields were already high in the first growing season. We have identified several alternatives to M. × giganteus which have provided stable yields across wide climatic ranges, mostly interspecies hybrids, and also Miscanthus genotypes providing high biomass yields at specific geographic locations. Seed-propagated interspecific and intraspecific hybrids, with high stable yields and cheaper reliable scalable establishment remain a key strategic objective for breeders.

Genetic diversity of salt tolerance in Miscanthus
Chen, Charlie ; Schoot, Hanneke van der; Dehghan, Shiva ; Alvim Kamei, Claire L. ; Schwarz, Kai Uwe ; Meyer, Heike ; Visser, Richard G.F. ; Linden, Gerard van der - \ 2017
Frontiers in Plant Science 8 (2017). - ISSN 1664-462X
Ion homeostasis - Ionic stress - Miscanthus - Osmotic stress - Salt tolerance
Miscanthus is a woody rhizomatous C4 grass that can be used as a CO2 neutral biofuel resource. It has potential to grow in marginal areas such as saline soils, avoiding competition for arable lands with food crops. This study explored genetic diversity for salt tolerance in Miscanthus and discovered mechanisms and traits that can be used to improve the yield under salt stress. Seventy genotypes of Miscanthus (including 57 M. sinensis, 5 M. sacchariflorus, and 8 hybrids) were evaluated for salt tolerance under saline (150 mM NaCl) and normal growing conditions using a hydroponic system. Analyses of shoot growth traits and ion concentrations revealed the existence of large variation for salt tolerance in the genotypes. We identified genotypes with potential for high biomass production both under control and saline conditions that may be utilized for growth under marginal, saline conditions. Several relatively salt tolerant genotypes had clearly lower Na+ concentrations and showed relatively high K+/Na+ ratios in the shoots under salt stress, indicating that a Na+ exclusion mechanismwas utilized to prevent Na+ accumulation in the leaves. Other genotypes showed limited reduction in leaf expansion and growth rate under saline conditions, which may be indicative of osmotic stress tolerance. The genotypes demonstrating potentially different salt tolerance mechanisms can serve as starting material for breeding programs aimed at improving salinity tolerance of Miscanthus.
Functionality of whey proteins covalently modified by allyl isothiocyanate. Part 1 physicochemical and antibacterial properties of native and modified whey proteins at pH 2 to 7
Keppler, Julia Katharina ; Martin, Dierk ; Garamus, Vasil M. ; Berton-Carabin, Claire ; Nipoti, Elia ; Coenye, Tom ; Schwarz, Karin - \ 2017
Food Hydrocolloids 65 (2017). - ISSN 0268-005X - p. 130 - 143.
Allyl isothiocyanate - Antimicrobial effect - Covalent modification - Hydrophobicity - SAXS - Whey protein isolate

Whey protein isolate (WPI) (∼75% β-lactoglobulin (β-LG)) is frequently used in foods as a natural emulsifying agent. However, at an acidic pH value, its emulsification capacity is greatly reduced. The covalent attachment of natural electrophilic hydrophobic molecules to WPI proteins is a promising method for changing the physicochemical properties of WPI in favor of a higher functionality at acidic pH values. In the present study, different concentrations of allyl isothiocyanate (AITC) were covalently bound to WPI and the related changes in physicochemical properties (charge, aggregation, surface hydrophobicity and secondary structure) were monitored over a wide pH range (pH 2 to 7). In addition, the antibacterial activity against different strains of S. aureus and E. coli before and after AITC modification was assessed. The results showed that both whey proteins β-LG and α-lactalbumin (ALA) were modified by AITC. This modification remained stable during pH adjustment. Unbound AITC was successfully removed by the lyophilization process, which reduced the strong odor of the volatile AITC. A shift of the isoelectric point towards acidic conditions was observed. The hydrophobicity of the modified WPI increased significantly and the protein's secondary and tertiary structure was altered. In addition, a more loose protein folding was observed. These effects were less pronounced at pH 6 and 7. The relatively mild antibacterial effect of native WPI was not significantly influenced by the addition of AITC.

Progress on optimizing miscanthus biomass production for the european bioeconomy : Results of the EU FP7 project OPTIMISC
Lewandowski, Iris ; Clifton-Brown, John ; Trindade, Luisa M. ; Linden, Gerard C. van der; Schwarz, Kai Uwe ; Müller-Sämann, Karl ; Anisimov, Alexander ; Chen, C.L. ; Dolstra, Oene ; Donnison, Iain S. ; Farrar, Kerrie ; Fonteyne, Simon ; Harding, Graham ; Hastings, Astley ; Huxley, Laurie M. ; Iqbal, Yasir ; Khokhlov, Nikolay ; Kiesel, Andreas ; Lootens, Peter ; Meyer, Heike ; Mos, Michal ; Muylle, Hilde ; Nunn, Chris ; Özgüven, Mensure ; Roldán-Ruiz, Isabel ; Schüle, Heinrich ; Tarakanov, Ivan ; Weijde, Tim van der; Wagner, Moritz ; Xi, Qingguo ; Kalinina, Olena - \ 2016
Frontiers in Plant Science 7 (2016). - ISSN 1664-462X - 23 p.
Bioeconomy - Costs - Genotypes - LCA - Marginal land - Miscanthus - Stress tolerance - Value chains

This paper describes the complete findings of the EU-fundedresearch project OPTIMISC,which investigated methods to optimize the production and use of miscanthus biomass. Miscanthus bioenergy and bioproduct chains were investigated by trialing 15 diverse germplasm types in a range of climatic and soil environments across central Europe,Ukraine,Russia,and China. The abiotic stress tolerances of a wider panel of 100 germplasm types to drought,salinity,and low temperatures were measured in the laboratory and a field trial in Belgium. Asmall selection of germplasmtypes was evaluated for performance in grasslands on marginal sites in Germany and the UK. The growth traits underlying biomass yield and quality were measured to improve regional estimates of feedstock availability. Several potential high-value bioproducts were identified. The combined results provide recommendations to policymakers,growers and industry. The major technical advances in miscanthus production achieved by OPTIMISC include: (1) demonstration that novel hybrids can out-yield the standard commercially grown genotype Miscanthus x giganteus; (2) characterization of the interactions of physiological growth responses with environmental variation within andbetween sites; (3) quantification of biomass-quality-relevant traits; (4) abiotic stress tolerances of miscanthus genotypes; (5) selections suitable for production on marginal land; (6) field establishment methods for seeds using plugs; (7) evaluation of harvesting methods; and (8) quantification of energy used in densification (pellet) technologies with a range of hybrids with differences in stem wall properties. End-user needs were addressed by demonstrating the potential of optimizing miscanthus biomass composition for the production of ethanol and biogas as well as for combustion. The costs and life-cycle assessment of seven miscanthus-based value chains,including small- and large-scale heat and power,ethanol,biogas,and insulation material production,revealed GHG-emission- and fossil-energy-saving potentials of up to 30.6 t CO2eq C ha−1 y−1 and 429 GJ ha−1 y−1 ,respectively. Transport distance was identified as an important cost factor. Negative carbon mitigation costs of –78€−1 CO2eq C were recorded for local biomass use. The OPTIMISC results demonstrate the potential of miscanthus as a crop for marginal sites and provide information and technologies for the commercial implementation of miscanthus-based value chains.

Standardising the assessment of environmental enrichment and tail-docking legal requirements for finishing pigs in Europe
Hothersall, B. ; Whistance, L.K. ; Zedlacher, H. ; Algers, B. ; Andersson, E. ; Bracke, M.B.M. ; Courboulay, V. ; Ferrari, P. ; Leeb, C. ; Mullan, S. ; Nowicki, J. ; Meunier-Salaün, M.C. ; Schwarz, T. ; Stadig, L. ; Main, D. - \ 2016
Animal Welfare 25 (2016)4. - ISSN 0962-7286 - p. 499 - 515.
animal welfare - enrichment - inspector - legislation - pig - tail-docking - legisation
An online training package providing a concise synthesis of the scientific data underpinning EU legislation on enrichment and tail-docking of pigs was produced in seven languages, with the aim of improving consistency of professional judgements regarding legislation compliance on farms. In total, 158 participants who were official inspectors, certification scheme assessors and advisors from 16 EU countries completed an initial test and an online training package. Control group participants completed a second identical test before, and Training group participants after, viewing the training. In Section 1 of the test participants rated the importance of modifying environmental enrichment defined in nine scenarios from 1 (not important) to 10 (very important). Training significantly increased participants' overall perception of the need for change. Participants then rated nine risk factors for tail-biting from 1 (no risk) to 10 (high risk). After training scores were better correlated with risk rankings already described by scientists. Scenarios relating to tail-docking and management were then described. Training significantly increased the proportion of respondents correctly identifying that a farm without tail lesions should stop tail-docking. Finally, participants rated the importance of modifying enrichment in three further scenarios. Training increased ratings in all three. The pattern of results indicated that participants' roles influenced scores but overall the training improved: i) recognition of enrichments that, by virtue of their type or use by pigs, may be insufficient to achieve legislation compliance; ii) knowledge on risk factors for tail-biting; and iii) recognition of when routine tail-docking was occurring.
On the potential of plant species invasion influencing bio-geomorphologic landscape formation in salt marshes
Schwarz, Christian ; Ysebaert, Tom ; Vandenbruwaene, Wouter ; Temmerman, Stijn ; Zhang, Li Quan ; Herman, Peter M.J. - \ 2016
Earth Surface Processes and Landforms 41 (2016)14. - ISSN 0197-9337 - p. 2047 - 2057.
invasive (exotic, non-native) species - salt marsh, sediment - Spartina - tidal channel

Species invasions are known to change biotic and abiotic ecosystem characteristics such as community structure, cycling of materials and dynamics of rivers. However, their ability to alter interactions between biotic and abiotic ecosystem components, in particular bio-geomorphic feedbacks and the resulting landscape configuration in tidal wetlands, such as tidal channels have not yet been demonstrated. We studied the impact of altered bio-geomorphic feedbacks on geomorphologic features (i.e. tidal wetland channels), by comparing proxies for channel network geometry (unchanneled flow lengths, fractal dimension) over time between non-invaded and invaded salt marsh habitats. The non-invaded habitats (the south of eastern Chongming Island, Yangtze estuary, China) show little change in network geometry over time with a tendency for an increased drainage density. The invaded site (salt marshes in the north of eastern Chongming Island invaded by the exotic plant species Spartina alterniflora) showed a decreasing tendency in channel drainage density throughout and after the species invasion. This suggests that species invasions might not only affect biotic ecosystem characteristics, but also their ability to change bio-geomorphic feedback loops, potentially leading to changes in existing geomorphologic features and therefore landscape configuration. Our results further suggest that the species invasion also altered sediment composition. Based on observations we propose a mechanism explaining the change in channel drainage density by an alteration in plant properties. The physical and physiological characteristics of the invading species Spartina alterniflora clearly differ from the native species Scirpus mariqueter, inducing different bio-geomorphic feedback loops leading to the observed change in salt marsh channel configuration.

Diversity of STs, plasmids and ESBL genes among Escherichia coli from humans, animals and food in Germany, the Netherlands and the UK
Day, Michaela J. ; Rodríguez, Irene ; Essen-Zandbergen, Alieda van; Dierikx, Cindy ; Kadlec, Kristina ; Schink, Anne Kathrin ; Wu, Guanghui ; Chattaway, Marie A. ; DoNascimento, Vivienne ; Wain, John ; Helmuth, Reiner ; Guerra, Beatriz ; Schwarz, Stefan ; Threlfall, John ; Woodward, Martin J. ; Coldham, Nick ; Mevius, Dik ; Woodford, Neil - \ 2016
Journal of Antimicrobial Chemotherapy 71 (2016)5. - ISSN 0305-7453 - p. 1178 - 1182.

Objectives: This study aimed to compare ESBL-producing Escherichia coli causing infections in humans with infecting or commensal isolates from animals and isolates from food of animal origin in terms of the strain types, the ESBL gene present and the plasmids that carry the respective ESBL genes. Methods: A collection of 353 ESBL-positive E. coli isolates from the UK, the Netherlands and Germany were studied by MLST and ESBL genes were identified. Characterization of ESBL gene-carrying plasmids was performed using PCR-based replicon typing. Moreover, IncI1-Iγ and IncN plasmids were characterized by plasmid MLST. Results: The ESBL-producing E. coli represented 158 different STs with ST131, ST10 and ST88 being the most common. Overall, blaCTX-M-1 was the most frequently detected ESBL gene, followed by blaCTX-M-15, which was the most common ESBL gene in the human isolates. The most common plasmid replicon type overall was IncI1-Ig followed by multiple IncF replicons. Conclusions: ESBL genes were present in a wide variety of E. coli STs. IncI1-Iγ plasmids that carried the blaCTX-M-1 gene were widely disseminated amongst STs in isolates from animals and humans, whereas other plasmids and STs appeared to be more restricted to isolates from specific hosts.

High dietary protein decreases fat deposition induced by high-fat and high-sucrose diet in rats
Chaumontet, C. ; Even, P.C. ; Schwarz, Jessica ; Simonin-Foucault, A. ; Piedcoq, J. ; Fromentin, G. ; Tomé, D. ; Azzout-Marniche, D. - \ 2015
GSE47570 - Rattus norvegicus - PRJNA206079
High-protein diets are known to reduce adiposity in the context of high carbohydrate and Western diets. However, few studies have investigated the specific high-protein effect on lipogenesis induced by a high-sucrose (HS) diet or fat deposition induced by high-fat feeding. We aimed to determine the effects of high protein intake on the development of fat deposition and partitioning in response to high-fat and/or HS feeding. A total of thirty adult male Wistar rats were assigned to one of the six dietary regimens with low and high protein, sucrose and fat contents for 5 weeks. Body weight (BW) and food intake were measured weekly. Oral glucose tolerance tests and meal tolerance tests were performed after 4th and 5th weeks of the regimen, respectively. At the end of the study, the rats were killed 2 h after ingestion of a calibrated meal. Blood, tissues and organs were collected for analysis of circulating metabolites and hormones, body composition and mRNA expression in the liver and adipose tissues. No changes were observed in cumulative energy intake and BW gain after 5 weeks of dietary treatment. However, high-protein diets reduced by 20 % the adiposity gain induced by HS and high-sucrose high-fat (HS-HF) diets. Gene expression and transcriptomic analysis suggested that high protein intake reduced liver capacity for lipogenesis by reducing mRNA expressions of fatty acid synthase (fasn), acetyl-CoA carboxylase a and b (Acaca and Acacb) and sterol regulatory element binding transcription factor 1c (Srebf-1c). Moreover, ketogenesis, as indicated by plasma β-hydroxybutyrate levels, was higher in HS-HF-fed mice that were also fed high protein levels. Taken together, these results suggest that high-protein diets may reduce adiposity by inhibiting lipogenesis and stimulating ketogenesis in the liver.
The influence of C3 and C4 vegetation on soil organic matter dynamics in contrasting semi-natural tropical ecosystems
Saiz, G. ; Bird, M. ; Wurster, C. ; Quesada, C.A. ; Ascough, P. ; Domingues, T. ; Schrodt, F. ; Schwarz, M. ; Feldpausch, T.R. ; Veenendaal, E. ; Djagbletey, G. ; Jacobsen, G. ; Hien, F. ; Compaore, H. ; Diallo, A. ; Lloyd, J. - \ 2015
Biogeosciences 12 (2015)16. - ISSN 1726-4170 - p. 5041 - 5059.

Variations in the carbon isotopic composition of soil organic matter (SOM) in bulk and fractionated samples were used to assess the influence of C3 and C4 vegetation on SOM dynamics in semi-natural tropical ecosystems sampled along a precipitation gradient in West Africa. Differential patterns in SOM dynamics in C3/C4 mixed ecosystems occurred at various spatial scales. Relative changes in C / N ratios between two contrasting SOM fractions were used to evaluate potential site-scale differences in SOM dynamics between C3- and C4-dominated locations. These differences were strongly controlled by soil texture across the precipitation gradient, with a function driven by bulk δ13C and sand content explaining 0.63 of the observed variability. The variation of δ13C with soil depth indicated a greater accumulation of C3-derived carbon with increasing precipitation, with this trend also being strongly dependant on soil characteristics. The influence of vegetation thickening on SOM dynamics was also assessed in two adjacent, but structurally contrasting, transitional ecosystems occurring on comparable soils to minimise the confounding effects posed by climatic and edaphic factors. Radiocarbon analyses of sand-size aggregates yielded relatively short mean residence times (τ) even in deep soil layers, while the most stable SOM fraction associated with silt and clay exhibited shorter τ in the savanna woodland than in the neighbouring forest stand. These results, together with the vertical variation observed in δ13C values, strongly suggest that both ecosystems are undergoing a rapid transition towards denser closed canopy formations. However, vegetation thickening varied in intensity at each site and exerted contrasting effects on SOM dynamics. This study shows that the interdependence between biotic and abiotic factors ultimately determine whether SOM dynamics of C3- and C4-derived vegetation are at variance in ecosystems where both vegetation types coexist. The results highlight the far-reaching implications that vegetation thickening may have for the stability of deep SOM. Â

Mimosoid legume plastome evolution : IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP
Dugas, D.V. ; Hernandez, David ; Koenen, Erik J.M. ; Schwarz, Erika ; Straub, Shannon ; Hughes, C.E. ; Jansen, R.K. ; Nageswara-Rao, Madhugiri ; Staats, Martijn ; Trujillo, J.T. ; Hajrah, N.H. ; Alharbi, N.S. ; Al-Malki, A.L. ; Sabir, J.S.M. ; Bailey, C.D. - \ 2015
Scientific Reports 5 (2015). - ISSN 2045-2322 - 13 p.

The Leguminosae has emerged as a model for studying angiosperm plastome evolution because of its striking diversity of structural rearrangements and sequence variation. However, most of what is known about legume plastomes comes from few genera representing a subset of lineages in subfamily Papilionoideae. We investigate plastome evolution in subfamily Mimosoideae based on two newly sequenced plastomes (Inga and Leucaena) and two recently published plastomes (Acacia and Prosopis), and discuss the results in the context of other legume and rosid plastid genomes. Mimosoid plastomes have a typical angiosperm gene content and general organization as well as a generally slow rate of protein coding gene evolution, but they are the largest known among legumes. The increased length results from tandem repeat expansions and an unusual 13 kb IR-SSC boundary shift in Acacia and Inga. Mimosoid plastomes harbor additional interesting features, including loss of clpP intron1 in Inga, accelerated rates of evolution in clpP for Acacia and Inga, and dN/dS ratios consistent with neutral and positive selection for several genes. These new plastomes and results provide important resources for legume comparative genomics, plant breeding, and plastid genetic engineering, while shedding further light on the complexity of plastome evolution in legumes and angiosperms.

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