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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The impact of networks on the innovative and financial performance of more entrepreneurial versus less entrepreneurial farmers in West Java, Indonesia
Etriya, Etriya ; Scholten, Victor E. ; Wubben, Emiel F.M. ; Omta, S.W.F. - \ 2019
NJAS Wageningen Journal of Life Sciences 89 (2019). - ISSN 1573-5214
Business ties - Entrepreneurship - Financial performance - Innovative performance - Network heterogeneity - Technology ties

Farmers may vary in their response to or anticipation of agrifood market changes, which probably depends on their entrepreneurial degree and networks. This paper aims to investigate the effects of farmers’ entrepreneurial degree and network content (i.e., business ties, technology ties, and network heterogeneity) on farm performance (i.e., innovative performance and financial performance). The data set was gathered through a survey of 262 vegetable farmers in West Java, Indonesia. Our findings reveal that more entrepreneurial farmers (106) have more business ties, technology ties, and heterogeneous networks compared to less entrepreneurial farmers (156). Further analyses using OLS regression confirm that farmers who are more entrepreneurial and have more business ties obtain both enhanced innovative and financial performance, while farmers who link to heterogeneous networks obtain only enhanced innovative performance. Overall, the findings of this study demonstrate that more entrepreneurial farmers with networks that are rich in business ties and diverse contacts have better farm performance.

Circulation of low pathogenic avian influenza (LPAI) viruses in wild birds and poultry in the Netherlands, 2006-2016
Bergervoet, Saskia A. ; Pritz-Verschuren, Sylvia B.E. ; Gonzales, Jose L. ; Bossers, Alex ; Poen, Marjolein J. ; Dutta, Jayeeta ; Khan, Zenab ; Kriti, Divya ; Bakel, Harm van; Bouwstra, Ruth ; Fouchier, Ron A.M. ; Beerens, Nancy - \ 2019
Scientific Reports 9 (2019)1. - ISSN 2045-2322 - 1 p.

In this study, we explore the circulation of low pathogenic avian influenza (LPAI) viruses in wild birds and poultry in the Netherlands. Surveillance data collected between 2006 and 2016 was used to evaluate subtype diversity, spatiotemporal distribution and genetic relationships between wild bird and poultry viruses. We observed close species-dependent associations among hemagglutinin and neuraminidase subtypes. Not all subtypes detected in wild birds were found in poultry, suggesting transmission to poultry is selective and likely depends on viral factors that determine host range restriction. Subtypes commonly detected in poultry were in wild birds most frequently detected in mallards and geese. Different temporal patterns in virus prevalence were observed between wild bird species. Virus detections in domestic ducks coincided with the prevalence peak in wild ducks, whereas virus detections in other poultry types were made throughout the year. Genetic analysis of the surface genes demonstrated that most poultry viruses were related to locally circulating wild bird viruses, but no direct spatiotemporal link was observed. Results indicate prolonged undetected virus circulation and frequent reassortment events with local and newly introduced viruses within the wild bird population. Increased knowledge on LPAI virus circulation can be used to improve surveillance strategies.

Nieuwe tekenziekte: 'Ik vind het heel link wat er gebeurt'
Meerburg, B.G. - \ 2019
An Average Consumer Concept of Bits and Pieces : Empirical Evidence on the Court of Justice of the European Union's Concept of the Average Consumer in the UCPD
Schebesta, H. ; Purnhagen, K. - \ 2019
In: The Transformation of Economic Law / de Almeida, Lucila, Cantero Gamito, Marta, Durovic, Mateja, Purnhagen, Kai, Hart Publishing - ISBN 9781509932580 - p. 13 - 27.
This article investigates the links of the average consumer concept in secondary legislation and the Court’s case law, using doctrinal and empirical methods. It addresses five research questions: How is the average consumer test conceptualised? How does the CJEU test the average consumer? How is the average consumer characterized? Who decides who the average consumer is (institutional dimension?) Is the ‘average consumer’ in the UCPD case law the same ‘average consumer’ as elsewhere? To answer these questions, we first illustrate the relationship of the average consumer benchmark in secondary legislation to the Court’s case law. We show that out of all secondary legislation which explicitly uses the “average consumer” in its wording, jurisprudence has only dealt with the UCPD. We acknowledge that a large bulk of jurisprudence concerns the average consumer test in primary law or has been applied to interpret secondary legislation which does not make explicit reference to the consumer benchmark. However, we limit our analysis to cases where this clear link between the wording of secondary law and the Court’s jurisprudence exists, leaving aside the cases where the CJEU interpreted secondary legislation in light of primary law or primary law directly. Consequently, we investigate only the cases where the Court has operationalised the “average consumer” benchmark of the UCPD. Lastly, we summarize and analyse our findings
Quantifying the dynamics of microtopography during a snowmelt event
Barneveld, Robert J. ; Zee, Sjoerd E.A.T.M. van der; Stolte, Jannes - \ 2019
Earth Surface Processes and Landforms (2019). - ISSN 0197-9337
frost heave - microtopography - snowmelt - soil roughness - terrestrial laser scanner

Knowledge of soil microtopography and its changes in space and over time is important to the understanding of how tillage influences infiltration, runoff generation and erosion. In this study, the use of a terrestrial laser scanner (TLS) is assessed for its ability to quantify small changes in the soil surface at high spatial resolutions for a relatively large surface area (100 m2). Changes in soil surface morphology during snow cover and melt are driven by frost heave, slaking, pressure exertion by the snowpack and overland flow (erosion and deposition). An attempt is undertaken to link these processes to observed changes at the soil surface. A new algorithm for soil surface roughness is introduced to make optimal use of the raw point cloud. This algorithm is less scale dependent than several commonly used roughness calculations. The results of this study show that TLSs can be used for multitemporal scanning of large surfaces and that small changes in surface elevation and roughness can be detected. Statistical analysis of the observed changes against terrain indices did not yield significant evidence for process differentiation.

Elucidating syntrophic butyrate-degrading populations in anaerobic digesters using stable-isotope-informed genome-resolved metagenomics
Ziels, Ryan M. ; Nobu, Masaru K. ; Sousa, Diana Z. - \ 2019
mSystems 4 (2019)4. - ISSN 2379-5077
Anaerobic catabolic pathways - Anaerobic digestion - Metagenomics - Methanogenesis - Stable-isotope probing - Syntrophy

Linking the genomic content of uncultivated microbes to their metabolic functions remains a critical challenge in microbial ecology. Resolving this challenge has implications for improving our management of key microbial interactions in biotechnologies such as anaerobic digestion, which relies on slow-growing syntrophic and methanogenic communities to produce renewable methane from organic waste. In this study, we combined DNA stable-isotope probing (SIP) with genome-centric metagenomics to recover the genomes of populations enriched in 13C after growing on [13C]butyrate. Differential abundance analysis of recovered genomic bins across the SIP metagenomes identified two metagenome-assembled genomes (MAGs) that were significantly enriched in heavy [13C]DNA. Phylogenomic analysis assigned one MAG to the genus Syntrophomonas and the other MAG to the genus Methanothrix. Metabolic reconstruction of the annotated genomes showed that the Syntrophomonas genome encoded all the enzymes for beta-oxidizing butyrate, as well as several mechanisms for interspecies electron transfer via electron transfer flavoproteins, hydrogenases, and formate dehydrogenases. The Syntrophomonas genome shared low average nucleotide identity (<95%) with any cultured representative species, indicating that it is a novel species that plays a significant role in syntrophic butyrate degradation within anaerobic digesters. The Methanothrix genome contained the complete pathway for acetoclastic methanogenesis, indicating that it was enriched in 13C from syntrophic acetate transfer. This study demonstrates the potential of stable-isotope-informed genome-resolved metagenomics to identify in situ interspecies metabolic cooperation within syntrophic consortia important to anaerobic waste treatment as well as global carbon cycling. IMPORTANCE Predicting the metabolic potential and ecophysiology of mixed microbial communities remains a major challenge, especially for slow-growing anaerobes that are difficult to isolate. Unraveling the in situ metabolic activities of uncultured species may enable a more descriptive framework to model substrate transformations by microbiomes, which has broad implications for advancing the fields of biotechnology, global biogeochemistry, and human health. Here, we investigated the in situ function of mixed microbiomes by combining stable-isotope probing with metagenomics to identify the genomes of active syntrophic populations converting butyrate, a C4 fatty acid, into methane within anaerobic digesters. This approach thus moves beyond the mere presence of metabolic genes to resolve "who is doing what" by obtaining confirmatory assimilation of the labeled substrate into the DNA signature. Our findings provide a framework to further link the genomic identities of uncultured microbes with their ecological function within microbiomes driving many important biotechnological and global processes.

Author Correction: Diversity-dependent temporal divergence of ecosystem functioning in experimental ecosystems
Guerrero-Ramírez, Nathaly R. ; Craven, Dylan ; Reich, Peter B. ; Ewel, John J. ; Isbell, Forest ; Koricheva, Julia ; Parrotta, John A. ; Auge, Harald ; Erickson, Heather E. ; Forrester, David I. ; Hector, Andy ; Joshi, Jasmin ; Montagnini, Florencia ; Palmborg, Cecilia ; Piotto, Daniel ; Potvin, Catherine ; Roscher, Christiane ; Ruijven, Jasper van; Tilman, David ; Wilsey, Brian ; Eisenhauer, Nico - \ 2019
Nature Ecology & Evolution 3 (2019). - ISSN 2397-334X - p. 1365 - 1365.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Clustering of oil droplets in o/w emulsions enhances perception of oil-related sensory attributes
Fuhrmann, P.L. ; Kalisvaart, Laura ; Sala, G. ; Scholten, E. ; Stieger, M.A. - \ 2019
Food Hydrocolloids 97 (2019). - ISSN 0268-005X
o/w emulsions - Sensory perception - Oil droplet clustering - creaminess - Saliva - Lubrication
The sensory perception of o/w emulsions is determined by their structure and physicochemical properties. The aims of this study were (a) to determine the influence of oil droplet clustering in o/w emulsions on sensory perception and (b) to link their sensory attributes to rheological, tribological and structural properties. Clustered emulsions were prepared by combining o/w emulsions stabilised by different sets of emulsifiers: (a) positively-charged gelatine and negatively-charged whey protein (WPI), and (b) positively-charged gelatine and negatively-charged diacetyl tartaric acid ester of mono- and diglycerides (DATEM). Oil droplet clusters ranging in diameter from 1 to 50 μm were obtained. The difference in charge density between gelatine- and DATEM-stabilised oil droplets was higher than that between gelatine- and WPI-stabilised droplets. This difference allowed to alter the interaction strength within oil droplet clusters. The sensory perception of clustered emulsions was quantified using the Rate-All-That-Apply (RATA) methodology with untrained subjects (n = 83). Participants assessed o/w emulsions varying in cluster size (1 μm–50 μm), cluster strength (tuned by changing the emulsifier-pairs), and single droplet emulsions with and without adjusted viscosity, as well as a reference emulsion with large single droplets (comparable in size to emulsions with large clusters). Creaminess and thickness intensities were significantly higher for clustered o/w emulsions compared to that of single droplet o/w emulsions with the same oil content and similar oil droplet/cluster size. With increasing cluster size, creaminess and thickness intensities increased significantly for hetero-aggregated clusters with weak interactions (gelatine-whey protein). When cluster interactions were stronger (gelatine-DATEM), creaminess intensity increased to a lesser extent and grittiness intensity increased considerably. Thickness and creaminess were strongly correlated to the rheological (e.g. consistency) and tribological properties (e.g. fiction coefficient at 10 mm/s) of o/w emulsions with clustered oil droplets. Grittiness and fattiness were strongly correlated to the tribological properties (slope of mixed regime) of o/w emulsions and their interactions with saliva. We conclude that clustering of oil droplets in o/w emulsions by hetero-aggregation allows to enhance the sensory perception of fat-related attributes by tuning rheological and tribological properties, and provides an effective method to structure liquid foods to obtain specific sensory properties.
Fishing activity near Wintershall offshore pipelines
Hintzen, Niels - \ 2019
IJmuiden : Wageningen Marine Research (Wageningen Marine Research report C073/19) - 22
On the North Sea bottom lie numerous pipelines to link oil- or gas offshore units, - platforms and processing stations on land. Although pipeline tubes are coated and covered with protective layers (Concrete Weight Coating), the pipelines risk being damaged through man-made threats like fishing activities with bottom trawls (trawling interference), anchoring and dropped objects. IRM Systems performs integrated risk assessments of pipelines for amongst others Wintershall. Spatial maps of fishing activity would contribute to this risk assessment. Therefore, WMR was tasked to quantify the amount of fishing activity in the vicinity of Wintershall pipelines. Fishing activity has been quantified at a spatial scale of approximate 2500 m2 blocks (50m by 50m) using fishing Vessel Monitoring System (VMS) data for 2016 and 2018. In total, for each year 69 shapefiles specifying the fishing intensity in a buffer area of 100m either side of the pipeline, were delivered. The overall total trawl fishing intensity in 2016 and 2018 along the pipeline trajectories ranges from 0 - 18.83 times per grid cell per year and is the result of combining all beam-trawl fleet activities, though split by large beam trawls and shrimp trawls. There is substantial difference in effort between 2016 and 2018 which varies up to 200% for some pipeline segments. Though, at the North Sea scale, fishing has been relatively stable over the past 10 years. Highest fishing intensities are recorded within the 12nm zone where the effort of the shrimp trawlers is most abundant and has increased almost 5-fold in some areas from 2010 and has not come to a halt yet. At the spatial scale relevant in this study, small spatial differences make for substantial differences though.
Validating the demethylating effects of 5-aza-20-deoxycytidine in insects requires a whole-genome approach (A reply to ellers et al.)
Cook, Nicola ; Parker, Darren J. ; Tauber, Eran ; Pannebakker, Bart A. ; Shuker, David M. - \ 2019
American Naturalist 194 (2019)3. - ISSN 0003-0147 - p. 432 - 438.
5-aza-2-deoxycytidine - DNA methylation - Nasonia vitripennis - Sex ratio

We previously demonstrated that treatment with the de-methylating agent 5-aza-20-deoxycytidine (5-aza-dC) alters the offspring sex ratios produced by females of the parasitoid wasp Nasonia vitripennis. Females allocate offspring sex ratio in line with local mate competition theory, producing more or less female-biased sex ratios as the number of other females laying eggs on a patch varies, thereby reducing competition among their sons for mates. Interestingly, treatment with 5-aza-dC did not ablate the facultative sex allocation re-sponse. Instead, sex ratios became less female biased, a shift in the direction of the optimum sex ratio for paternally inherited alleles ac-cording to genomic conflict theory. This was the first (albeit indirect) experimental evidence for genomic conflict over sex allocation. In their comment, Ellers and colleagues assayed the effects of 5-aza-dC on DNA methylation in 10 Nasonia genes, finding no evidence of demeth-ylation in these 10 genes, from which they conclude that 5-aza-dC has no demethylating capability in N. vitripennis. Quantifying the efficacy of 5-aza-dC in terms of demethylation is indeed crucial to in-depth interpretation of studies using 5-aza-dC to link phenotypes to epigenetic regulation. Here we outline the mode of action of 5-aza-dC and demonstrate that determining the efficacy of 5-aza-dC in insect systems requires a whole-genome approach.

Twenty-three unsolved problems in hydrology (UPH)–a community perspective
Blöschl, Günter ; Bierkens, Marc F.P. ; Chambel, Antonio ; Cudennec, Christophe ; Destouni, Georgia ; Fiori, Aldo ; Kirchner, James W. ; McDonnell, Jeffrey J. ; Savenije, Hubert H.G. ; Sivapalan, Murugesu ; Stumpp, Christine ; Toth, Elena ; Volpi, Elena ; Carr, Gemma ; Lupton, Claire ; Salinas, Josè ; Széles, Borbála ; Viglione, Alberto ; Aksoy, Hafzullah ; Allen, Scott T. ; Amin, Anam ; Andréassian, Vazken ; Arheimer, Berit ; Aryal, Santosh K. ; Baker, Victor ; Bardsley, Earl ; Barendrecht, Marlies H. ; Bartosova, Alena ; Batelaan, Okke ; Berghuijs, Wouter R. ; Beven, Keith ; Blume, Theresa ; Bogaard, Thom ; Borges de Amorim, Pablo ; Böttcher, Michael E. ; Boulet, Gilles ; Breinl, Korbinian ; Brilly, Mitja ; Brocca, Luca ; Buytaert, Wouter ; Castellarin, Attilio ; Castelletti, Andrea ; Chen, Xiaohong ; Chen, Yangbo ; Chen, Yuanfang ; Chifflard, Peter ; Claps, Pierluigi ; Clark, Martyn P. ; Collins, Adrian L. ; Croke, Barry ; Dathe, Annette ; David, Paula C. ; Barros, Felipe P.J. de; Rooij, Gerrit de; Baldassarre, Giuliano Di; Driscoll, Jessica M. ; Duethmann, Doris ; Dwivedi, Ravindra ; Eris, Ebru ; Farmer, William H. ; Feiccabrino, James ; Ferguson, Grant ; Ferrari, Ennio ; Ferraris, Stefano ; Fersch, Benjamin ; Finger, David ; Foglia, Laura ; Fowler, Keirnan ; Gartsman, Boris ; Gascoin, Simon ; Gaume, Eric ; Gelfan, Alexander ; Geris, Josie ; Gharari, Shervan ; Gleeson, Tom ; Glendell, Miriam ; Gonzalez Bevacqua, Alena ; González-Dugo, María P. ; Grimaldi, Salvatore ; Gupta, A.B. ; Guse, Björn ; Han, Dawei ; Hannah, David ; Harpold, Adrian ; Haun, Stefan ; Heal, Kate ; Helfricht, Kay ; Herrnegger, Mathew ; Hipsey, Matthew ; Hlaváčiková, Hana ; Hohmann, Clara ; Holko, Ladislav ; Hopkinson, Christopher ; Hrachowitz, Markus ; Illangasekare, Tissa H. ; Inam, Azhar ; Innocente, Camyla ; Istanbulluoglu, Erkan ; Jarihani, Ben ; Kalantari, Zahra ; Kalvans, Andis ; Khanal, Sonu ; Khatami, Sina ; Kiesel, Jens ; Kirkby, Mike ; Knoben, Wouter ; Kochanek, Krzysztof ; Kohnová, Silvia ; Kolechkina, Alla ; Krause, Stefan ; Kreamer, David ; Kreibich, Heidi ; Kunstmann, Harald ; Lange, Holger ; Liberato, Margarida L.R. ; Lindquist, Eric ; Link, Timothy ; Liu, Junguo ; Loucks, Daniel Peter ; Luce, Charles ; Mahé, Gil ; Makarieva, Olga ; Malard, Julien ; Mashtayeva, Shamshagul ; Maskey, Shreedhar ; Mas-Pla, Josep ; Mavrova-Guirguinova, Maria ; Mazzoleni, Maurizio ; Mernild, Sebastian ; Misstear, Bruce Dudley ; Montanari, Alberto ; Müller-Thomy, Hannes ; Nabizadeh, Alireza ; Nardi, Fernando ; Neale, Christopher ; Nesterova, Nataliia ; Nurtaev, Bakhram ; Odongo, Vincent O. ; Panda, Subhabrata ; Pande, Saket ; Pang, Zhonghe ; Papacharalampous, Georgia ; Perrin, Charles ; Pfister, Laurent ; Pimentel, Rafael ; Polo, María J. ; Post, David ; Prieto Sierra, Cristina ; Ramos, Maria Helena ; Renner, Maik ; Reynolds, José Eduardo ; Ridolfi, Elena ; Rigon, Riccardo ; Riva, Monica ; Robertson, David E. ; Rosso, Renzo ; Roy, Tirthankar ; Sá, João H.M. ; Salvadori, Gianfausto ; Sandells, Mel ; Schaefli, Bettina ; Schumann, Andreas ; Scolobig, Anna ; Seibert, Jan ; Servat, Eric ; Shafiei, Mojtaba ; Sharma, Ashish ; Sidibe, Moussa ; Sidle, Roy C. ; Skaugen, Thomas ; Smith, Hugh ; Spiessl, Sabine M. ; Stein, Lina ; Steinsland, Ingelin ; Strasser, Ulrich ; Su, Bob ; Szolgay, Jan ; Tarboton, David ; Tauro, Flavia ; Thirel, Guillaume ; Tian, Fuqiang ; Tong, Rui ; Tussupova, Kamshat ; Tyralis, Hristos ; Uijlenhoet, Remko ; Beek, Rens van; Ent, Ruud J. van der; Ploeg, Martine van der; Loon, Anne F. Van; Meerveld, Ilja van; Nooijen, Ronald van; Oel, Pieter R. van; Vidal, Jean Philippe ; Freyberg, Jana von; Vorogushyn, Sergiy ; Wachniew, Przemyslaw ; Wade, Andrew J. ; Ward, Philip ; Westerberg, Ida K. ; White, Christopher ; Wood, Eric F. ; Woods, Ross ; Xu, Zongxue ; Yilmaz, Koray K. ; Zhang, Yongqiang - \ 2019
Hydrological Sciences Journal 64 (2019)10. - ISSN 0262-6667 - p. 1141 - 1158.
hydrology - interdisciplinary - knowledge gaps - research agenda - science questions

This paper is the outcome of a community initiative to identify major unsolved scientific problems in hydrology motivated by a need for stronger harmonisation of research efforts. The procedure involved a public consultation through online media, followed by two workshops through which a large number of potential science questions were collated, prioritised, and synthesised. In spite of the diversity of the participants (230 scientists in total), the process revealed much about community priorities and the state of our science: a preference for continuity in research questions rather than radical departures or redirections from past and current work. Questions remain focused on the process-based understanding of hydrological variability and causality at all space and time scales. Increased attention to environmental change drives a new emphasis on understanding how change propagates across interfaces within the hydrological system and across disciplinary boundaries. In particular, the expansion of the human footprint raises a new set of questions related to human interactions with nature and water cycle feedbacks in the context of complex water management problems. We hope that this reflection and synthesis of the 23 unsolved problems in hydrology will help guide research efforts for some years to come.

Artisanal or industrial conflict minerals? Evidence from Eastern Congo
Stoop, Nik ; Verpoorten, Marijke ; Windt, Peter van der - \ 2019
World Development 122 (2019). - ISSN 0305-750X - p. 660 - 674.
Africa - Artisanal mining - Conflict - Democratic Republic of Congo - Industrial mining - Natural resources

Existing research suggests a strong link between mining and local conflict but makes no distinction between artisanal and industrial mining. We exploit variation in mineral prices and the granting of industrial mining concessions to investigate how the mode of extraction affects conflict in Eastern Congo. Rising mineral prices increase battles over artisanal mines, indicating competition between armed groups. This effect is much less pronounced for industrial mining. Moreover, the expansion of industrial mining decreases battles, suggesting that companies can secure their concessions. Such expansion does, however, trigger riots, and, when it crowds out artisanal mining, also increases violence against civilians and looting. In line with case-study evidence, these negative effects only materialize when industrial mining companies expand their activities from the research to the production phase.

Connecting business with the agricultural landscape: business strategies for sustainable rural development
Swaffield, Simon R. ; Corry, Robert C. ; Opdam, Paul ; McWilliam, Wendy ; Primdahl, Jørgen - \ 2019
Business Strategy and the Environment (2019). - ISSN 0964-4733
cogovernance - food supply systems - placemaking - provenance - socioecological networks

Agribusiness enterprises link rural landscapes to global and regional markets. The nature of these business–landscape relationships is vital to the sustainability transition. Decisions by farmers and agriculture policymakers aggregate to changes in the ecology of landscapes, but the influence of food supply system businesses on rural landscape sustainability also requires scrutiny. This article uses four international cases to present a conceptual framework for investigating how different business strategies can support agricultural landscape sustainability. Insights from North America, New Zealand, The Netherlands, and Denmark inform the framework dimensions of horizontal/territorial and vertical/systemic business–landscape relationships. Three types of business model that promote rural sustainability are highlighted: provenance, cogovernance, and placemaking. These models engage strategies such as environmental management systems, certification, ecosystem and landscape services, and spatial planning. Research directions that will improve understanding about how business can engage with rural stakeholders for more sustainable rural landscapes are identified, including the need for cross disciplinary perspectives incorporating social, ecological, and business knowledge.

Multi-objective optimization as a tool to identify possibilities for future agricultural landscapes
Todman, Lindsay C. ; Coleman, Kevin ; Milne, Alice E. ; Gil, Juliana D.B. ; Reidsma, Pytrik ; Schwoob, Marie Hélène ; Treyer, Sébastien ; Whitmore, Andrew P. - \ 2019
Science of the Total Environment 687 (2019). - ISSN 0048-9697 - p. 535 - 545.

Agricultural landscapes provide many functions simultaneously including food production, regulation of water and regulation of greenhouse gases. Thus, it is challenging to make land management decisions, particularly transformative changes, that improve on one function without unintended consequences for other functions. To make informed decisions the trade-offs between different landscape functions must be considered. Here, we use a multi-objective optimization algorithm with a model of crop production that also simulates environmental effects such as nitrous oxide emissions to identify trade-off frontiers and associated possibilities for agricultural management. Trade-offs are identified in three soil types, using wheat production in the UK as an example, then the trade-off for combined management of the three soils is considered. The optimization algorithm identifies trade-offs between different objectives and allows them to be visualised. For example, we observed a highly non-linear trade-off between wheat yield and nitrous oxide emissions, illustrating where small changes might have a large impact. We used a cluster analysis to identify distinct management strategies with similar management actions and use these clusters to link the trade-off curves to possibilities for management. There were more possible strategies for achieving desirable environmental outcomes and remaining profitable when the management of different soil types was considered together. Interestingly, it was on the soil capable of the highest potential profit that lower profit strategies were identified as useful for combined management. Meanwhile, to maintain average profitability across the soils, it was necessary to maximise the profit from the soil with the lowest potential profit. These results are somewhat counterintuitive and so the range of strategies supplied by the model could be used to stimulate discussion amongst stakeholders. In particular, as some key objectives can be met in different ways, stakeholders could discuss the impact of these management strategies on other objectives not quantified by the model.

Dynamics of faecal shedding of ESBL- or AmpC-producing Escherichia coli on dairy farms
Hordijk, Joost ; Fischer, Egil A.J. ; Werven, Tine van; Sietsma, Steven ; Gompel, Liese Van; Timmerman, Arjen J. ; Spaninks, Mirlin P. ; Heederik, Dick J.J. ; Nielen, Mirjam ; Wagenaar, Jaap A. ; Stegeman, Arjan - \ 2019
Journal of Antimicrobial Chemotherapy 74 (2019)6. - ISSN 0305-7453 - p. 1531 - 1538.

OBJECTIVES: To explore the dynamics of faecal ESBL/AmpC shedding in dairy cattle and farmers, a study was conducted to examine changes in shedding by individual animals, as well as environmental exposure, and to study the association between antimicrobial use (AMU) and ESBL/AmpC shedding. METHODS: The study comprised a cross-sectional survey of 20 farms and a 1 year follow-up of 10 farms. Faecal samples were cultured by both direct inoculation on MacConkey agar + 1 mg/L cefotaxime (MC+) and enrichment in LB-broth + 1 mg/L cefotaxime with subsequent inoculation on MC+. Dust samples were collected using electrostatic dustfall collectors (EDCs). Human faecal samples were collected by the farmers. Presence of ESBL/AmpC genes was screened for by PCR and sequencing. Using mixed effects logistic regression, ORs were determined and population-attributable fractions (PAFs) calculated subsequently. RESULTS: In Phase 1, 8/20 farms were positive for ESBL/AmpC and, with 2 negative farms, were selected for Phase 2. Transient shedding of dominant allele variants was observed in the animals. EDCs and human faecal samples did not reflect what was observed in the animals. AMU was related to shedding of ESBLs in the next sampling moment [OR 14.6 (95% CI 3.0-80.0)] and the PAF of AMU was 0.36 (95% CI 0.08-0.77). Calves fed with colostrum from cows on dry-off therapy was not a risk factor [OR 1.7 (95% CI 0.7-4.9, P = 0.28)]. CONCLUSIONS: The presence of ESBL/AmpC could only be partly explained by AMU. No link was shown between shedding in cattle and humans or the environment. Interventions should focus on prevention of introduction.

A genome-wide association study for susceptibility and infectivity of Holstein Friesian dairy cattle to digital dermatitis
Biemans, F. ; Jong, M.C.M. de; Bijma, P. - \ 2019
Journal of Dairy Science 102 (2019)7. - ISSN 0022-0302 - p. 6248 - 6262.
claw health - generalized linear mixed model - genetic parameter - heritability - transmission

Selection and breeding can be used to fight transmission of infectious diseases in livestock. The prevalence in a population depends on the susceptibility and infectivity of the animals. Knowledge on the genetic background of those traits would facilitate efficient selection for lower disease prevalence. We investigated the genetic background of host susceptibility and infectivity for digital dermatitis (DD), an endemic infectious claw disease in dairy cattle, with a genome-wide association study (GWAS), using either a simple linear mixed model or a generalized linear mixed model based on epidemiological theory. In total, 1,513 Holstein-Friesian cows of 12 Dutch dairy farms were scored for DD infection status and class (M0 to M4.1) every 2 wk for 11 times; 1,401 of these cows were genotyped with a 75k SNP chip. We performed a GWAS with a linear mixed model on 10 host disease status traits, and with a generalized linear mixed model with a complementary log-log link function (GLMM) on the probability that a cow would get infected between 2 scorings. With the GLMM, we fitted SNP effects for host susceptibility and host infectivity, while taking the variation in exposure of the susceptible cow to infectious herd mates into account. With the linear model we detected 4 suggestive SNP (false discovery rate < 0.20), 2 for the fraction of observations a cow had an active lesion on chromosomes 1 and 14, one for the fraction of observations a cow had an M2 lesion on at least one claw on chromosome 1 (the same SNP as for the fraction of observations with an active lesion), and one for the fraction of observations a cow had an M4.1 lesion on at least one claw on chromosome 10. Heritability estimates ranged from 0.09 to 0.37. With the GLMM we did not detect significant nor suggestive SNP. The SNP effects on disease status analyzed with the linear model had a correlation coefficient of only 0.70 with SNP effects on susceptibility of the GLMM, indicating that both models capture partly different effects. Because the GLMM better accounts for the epidemiological mechanisms determining individual disease status and for the distribution of the y-variable, results of the GLMM may be more reliable, despite the absence of suggestive associations. We expect that with an extended GLMM that better accounts for the full genetic variation in infectivity via the environment, the accuracy of SNP effects may increase.

Soil Salinity Limits Plant Shade Avoidance
Hayes, Scott ; Pantazopoulou, Chrysoula K. ; Gelderen, Kasper van; Reinen, Emilie ; Tween, Adrian Louis ; Sharma, Ashutosh ; Vries, Michel de; Prat, Salomé ; Schuurink, Robert C. ; Testerink, Christa ; Pierik, Ronald - \ 2019
Current Biology 29 (2019)10. - ISSN 0960-9822 - p. 1669 - 1676.e4.
abscisic acid - brassinosteroids - phytochrome - phytohormones - PIF - plant photobiology - salt response - salt stress

Global food production is set to keep increasing despite a predicted decrease in total arable land [1]. To achieve higher production, denser planting will be required on increasingly degraded soils. When grown in dense stands, crops elongate and raise their leaves in an effort to reach sunlight, a process termed shade avoidance [2]. Shade is perceived by a reduction in the ratio of red (R) to far-red (FR) light and results in the stabilization of a class of transcription factors known as PHYTOCHROME INTERACTING FACTORS (PIFs) [3, 4]. PIFs activate the expression of auxin biosynthesis genes [4, 5] and enhance auxin sensitivity [6], which promotes cell-wall loosening and drives elongation growth. Despite our molecular understanding of shade-induced growth, little is known about how this developmental program is integrated with other environmental factors. Here, we demonstrate that low levels of NaCl in soil strongly impair the ability of plants to respond to shade. This block is dependent upon abscisic acid (ABA) signaling and the canonical ABA signaling pathway. Low R:FR light enhances brassinosteroid (BR) signaling through BRASSINOSTEROID SIGNALING KINASE 5 (BSK5) and leads to the activation of BRI1 EMS SUPPRESSOR 1 (BES1). ABA inhibits BSK5 upregulation and interferes with GSK3-like kinase inactivation by the BR pathway, thus leading to a suppression of BES1:PIF function. By demonstrating a link between light, ABA-, and BR-signaling pathways, this study provides an important step forward in our understanding of how multiple environmental cues are integrated into plant development. Intensively farmed crops often experience multiple stresses simultaneously. Here, Hayes et al. show that low-level soil salinity suppresses shade avoidance in plants. Through investigation of the mechanisms underlying this trait, they uncover a regulatory pathway that converges at the level of brassinosteroid signaling.

Correlating Infant Fecal Microbiota Composition and Human Milk Oligosaccharide Consumption by Microbiota of 1-Month-Old Breastfed Infants
Borewicz, Klaudyna ; Gu, Fangjie ; Saccenti, Edoardo ; Arts, I.C.W. ; Penders, John ; Thijs, Carel ; Leeuwen, Sander S. van; Lindner, Cordula ; Nauta, Arjen ; Leusen, Ellen van; Schols, Henk A. ; Smidt, Hauke - \ 2019
Molecular Nutrition & Food Research (2019). - ISSN 1613-4125
breastfeeding - human milk oligosaccharide - microbial clusters - microbiome

Scope: Understanding the biological functions of human milk oligosaccharides (HMOs) in shaping gastrointestinal (GI) tract microbiota during infancy is of great interest. A link between HMOs in maternal milk and infant fecal microbiota composition is examined and the role of microbiota in degrading HMOs within the GI tract of healthy, breastfed, 1-month-old infants is investigated. Methods and results: Maternal breast milk and infant feces are from the KOALA Birth Cohort. HMOs are quantified in milk and infant fecal samples using liquid chromatography-mass spectrometry. Fecal microbiota composition is characterized using Illumina HiSeq 16S rRNA gene amplicon sequencing. The composition is associated with gender, delivery mode, and milk HMOs: Lacto-N-fucopentaose I and 2′-fucosyllactose. Overall, Bifidobacterium, Bacteroides, Escherichia–Shigella, and Parabacteroides are predominating genera. Three different patterns in infant fecal microbiota structure are detected. GI degradation of HMOs is strongly associated with fecal microbiota composition, and there is a link between utilization of specific HMOs and relative abundance of various phylotypes (operational taxonomic units). Conclusions: HMOs in maternal milk are among the important factors shaping GI tract microbiota in 1-month-old breastfed infants. An infant's ability to metabolize different HMOs strongly correlates with fecal microbiota composition and specifically with phylotypes within genera Bifidobacterium, Bacteroides, and Lactobacillus.

Knowledge, attitudes and practices of cervical cancer prevention among Zambian women and men
Nyambe, Anayawa ; Kampen, Jarl K. ; Baboo, Stridutt K. ; Hal, Guido Van - \ 2019
BMC Public Health 19 (2019)1. - ISSN 1471-2458
Attitude - Cervical cancer - Knowledge - Practices - Screening - Social ecological model - Theory of triadic influence - Vaccination - Zambia

Background: In Zambia, cervical cancer screening was started in 2006 and the human papillomavirus vaccine was piloted in 2013. Nevertheless, cervical cancer remains the leading cancer. It is assumed that knowledge, social interaction, health behaviors and religion are factors that can influence screening and vaccination practices. This study addresses the question, what is the relationship between knowledge about cervical cancer, attitudes, self-reported behavior, and immediate support system, towards screening and vaccination of cervical cancer of Zambian women and men. The results of this study serve as a basis for future research, an input for improvement and adjustment of the existing prevention program and build on documented health behavior frameworks. Methods: A cross-sectional mixed methods study was conducted from February to May 2016. Two separate questionnaires were used to collect data from women (N = 300) and men (N = 300) residing in Chilenje and Kanyama (two townships in the capital city Lusaka). Respondent's knowledge of cervical cancer was operationalized by grading their ability to correctly identify causes and protective factors if they were aware of cervical cancer. Besides providing descriptive statistics of all study variables, we tested four research hypotheses concerning the link between knowledge, attitudes and practices suggested by the literature, by applying appropriate statistical tests (chi square test, analysis of variance, logistic regression). Results: Less than half of the respondents (36.8%) had heard of cervical cancer, 20.7% of women had attended screening and 6.7% of the total sample had vaccinated their daughter. Knowledge of causes and prevention was very low. There was a strong association between having awareness of cervical cancer and practicing screening (odds ratio = 20.5, 95% confidence interval = [9.214, 45.516]) and vaccination (odds ratio = 5.1, 95% confidence interval = [2.473, 10.423]). Social interactions were also found to greatly influence screening and vaccination behaviors. Conclusions: The low level of knowledge of causes and prevention of cervical cancer suggests a need to increase knowledge and awareness among both women and men. Interpersonal interactions have great impact on practicing prevention behaviors, for instance, vaccination of daughters.

Differences in Fecal Gut Microbiota, Short-Chain Fatty Acids and Bile Acids Link Colorectal Cancer Risk to Dietary Changes Associated with Urbanization Among Zimbabweans
Katsidzira, L. ; Ocvirk, S. ; Wilson, A. ; Li, J. ; Mahachi, C.B. ; Soni, D. ; DeLany, J. ; Nicholson, J.K. ; Zoetendal, E.G. ; O’Keefe, S.J.D. - \ 2019
Nutrition and Cancer 71 (2019)8. - ISSN 0163-5581 - p. 1313 - 1324.

The incidence of colorectal cancer (CRC) is gradually rising in sub-Saharan Africa. This may be due to dietary changes associated with urbanization, which may induce tumor-promoting gut microbiota composition and function. We compared fecal microbiota composition and activity in 10 rural and 10 urban Zimbabweans for evidence of a differential CRC risk. Dietary intake was assessed by a food frequency questionnaire. Fecal microbiota composition, metabolomic profile, functional microbial genes were analyzed, and bile acids and short chain fatty acids quantified. Animal protein intake was higher among urban volunteers, but carbohydrate and fiber intake were similar. Bacteria related to Blautia obeum, Streptococcus bovis, and Subdoligranulum variabile were higher in urban residents, whereas bacteria related to Oscillospira guillermondii and Sporobacter termitidis were higher in rural volunteers. Fecal levels of primary bile acids, cholic acid, and chenodeoxycholic acid (P < 0.05), and secondary bile acids, deoxycholic acid (P < 0.05) and ursodeoxycholic acid (P < 0.001) were higher in urban residents. Fecal levels of acetate and propionate, but not butyrate, were higher in urban residents. The gut microbiota composition and activity among rural and urban Zimbabweans retain significant homogeneity (possibly due to retention of dietary fiber), but urban residents have subtle changes, which may indicate a higher CRC risk.

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