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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Mapping topsoil organic carbon concentrations and stocks for Tanzania
Kempen, Bas ; Dalsgaard, Soren ; Kaaya, Abel K. ; Chamuya, Nurdin ; Ruiperez Gonzalez, Maria ; Pekkarinen, Anssi ; Walsh, Markus G. - \ 2019
Geoderma 337 (2019). - ISSN 0016-7061 - p. 164 - 180.
Tanzania is one of the countries that has embarked on a national programme under the United Nations collaborative initiative on Reducing Emissions from Deforestation and forest Degradation (REDD). Tanzania is currently developing the capacity to enter into a carbon monitoring REDD+ regime. In this context spatially representative soil carbon datasets and accurate predictive maps are important for determining the soil organic carbon pool. The main objective of this study was to model and map the SOC stock for the 0–30-cm soil layer to provide baseline information for REDD+ purposes. Topsoil data of over 1400 locations spread throughout Tanzania from the National Forest Monitoring and Assessment (NAFORMA), were used, supplemented by two legacy datasets, to calibrate simple kriging with varying local means models. Maps of SOC concentrations (g kg−1) were generated for the 0–10-cm, 10–20-cm, 20–30-cm, 0–30-cm layers, and maps of bulk density and SOC stock (kg m−2) for the 0–30-cm layer. Two approaches for modelling SOC stocks were considered here: the calculate-then-model (CTM) approach and the model-then-calculate approach (MTC). The spatial predictions were validated by means of 10-fold cross-validation. Uncertainty associated to the estimated SOC stocks was quantified through conditional Gaussian simulation. Estimates of SOC stocks for the main land cover classes are provided. Environmental covariates related to soil and terrain proved to be the strongest predictors for all properties modelled. The mean predicted SOC stock for the 0–30-cm layer was 4.1 kg m−2 (CTM approach) translating to a total national stock of 3.6 Pg. The MTC approach gave similar results. The largest stocks are found in forest and grassland ecosystems, while woodlands and bushlands contain two thirds of the total SOC stock. The root mean squared error for the 0–30-cm layer was 1.8 kg m−2, and the R2-value was 0.51. The R2-value of SOC concentration for the 0–30-cm layer was 0.60 and that of bulk density 0.56. The R2-values of the predicted SOC concentrations for the 10-cm layers vary between 0.46 and 0.54. The 95% confidence interval of the predicted average SOC stock is 4.01–4.15 kg m−2, and that of the national total SOC stock 3.54–3.65 Pg. Uncertainty associated with SOC concentration had the largest contribution to SOC stock uncertainty. These findings have relevance for the ongoing REDD+ readiness process in Tanzania by supplementing the previous knowledge of significant carbon pools. The soil organic carbon pool makes up a relatively large proportion of carbon in Tanzania and is therefore an important carbon pool to consider alongside the ones related to the woody biomass. Going forward, the soil organic carbon data can potentially be used in the determination of reference emission levels and the future monitoring, reporting and verification of organic carbon pools.
Catalysing food safety in the domestic horticulture sector in Kenya : The potential link between export production and evolving domestic supply chains
Gema, Joyce ; Keige, John ; Ngetich, Titus ; Moreno Echeverri, Indira ; Saavedra Gonzalez, Y.R. ; Koomen, I. - \ 2018
Wageningen : Wageningen Centre for Development Innovation (Report WCDI 18-051) - 101 p.
Quality of dietary fat intake and body weight and obesity in a mediterranean population : Secondary analyses within the PREDIMED trial
Beulen, Yvette ; Martínez-González, Miguel A. ; Rest, Ondine van de; Salas-Salvadó, Jordi ; Sorlí, José V. ; Gómez-Gracia, Enrique ; Fiol, Miquel ; Estruch, Ramón ; Santos-Lozano, José M. ; Schröder, Helmut ; Alonso-Gómez, Angel ; Serra-Majem, Luis ; Pintó, Xavier ; Ros, Emilio ; Becerra-Tomas, Nerea ; González, José I. ; Fitó, Montserrat ; Martínez, J.A. ; Gea, Alfredo - \ 2018
Nutrients 10 (2018)12. - ISSN 2072-6643
Body weight - Cohort study - Fat - Obesity - Substitution models

A moderately high-fat Mediterranean diet does not promote weight gain. This study aimed to investigate the association between dietary intake of specific types of fat and obesity and body weight. A prospective cohort study was performed using data of 6942 participants in the PREDIMED trial, with yearly repeated validated food-frequency questionnaires, and anthropometric outcomes (median follow-up: 4.8 years). The effects of replacing dietary fat subtypes for one another, proteins or carbohydrates were estimated using generalized estimating equations substitution models. Replacement of 5% energy from saturated fatty acids (SFA) with monounsaturated fatty acids (MUFA) or polyunsaturated fatty acids (PUFA) resulted in weight changes of −0.38 kg (95% Confidece Iinterval (CI): −0.69, −0.07), and −0.51 kg (95% CI: −0.81, −0.20), respectively. Replacing proteins with MUFA or PUFA decreased the odds of becoming obese. Estimates for the daily substitution of one portion of red meat with white meat, oily fish or white fish showed weight changes up to −0.87 kg. Increasing the intake of unsaturated fatty acids at the expense of SFA, proteins, and carbohydrates showed beneficial effects on body weight and obesity. It may therefore be desirable to encourage high-quality fat diets like the Mediterranean diet instead of restricting total fat intake.

Best practices to train deep models on imbalanced datasets - a case study on animal detection in aerial imagery
Kellenberger, B.A. ; Marcos Gonzalez, D. ; Tuia, D. - \ 2018
- 4 p.
We introduce recommendations to train a Convolutional Neural Network for grid-based detection on a dataset that has a substantial class imbalance. These include curriculum learning, hard negative mining, a special border class, and more. We evaluate the recommendations on the problem of animal detection in aerial images, where we obtain an increase in precision from 9% to 40% at high recalls, compared to state-of-the-art.
Scale equivariance in CNNs with vector fields
Marcos Gonzalez, D. ; Kellenberger, B.A. ; Lobry, Sylvain ; Tuia, D. - \ 2018
- 5 p.
We study the effect of injecting local scale equivariance into Convolutional Neural Networks. This is done by applying each convolutional filter at multiple scales. The output is a vector field encoding for the maximally activating scale and the scale itself, which is further processed by the following convolutional layers. This allows all the intermediate representations to be locally scale equivariant. We show that this improves the performance of the model by over 20% in the scale equivariant task of regressing the scaling factor applied to randomly scaled MNIST digits. Furthermore, we find it also useful for scale invariant tasks, such as the actual classification of randomly scaled digits. This highlights the usefulness of allowing for a compact representation that can also learn relationships between different local scales by keeping internal scale equivariance.
Learning deep structure active contours end-to-end
Marcos Gonzalez, D. ; Tuia, D. ; Kellenberger, B.A. ; Zhang, L. ; Bai, M. ; Liao, R. ; Urtasun, R. - \ 2018
- 9 p.
Deep learning based methods for building segmentation from remote sensing data
Lobry, Sylvain ; Marcos Gonzalez, D. ; Vargas Munoz, John ; Kellenberger, B.A. ; Srivastava, S. ; Tuia, D. - \ 2018
- 4 p.
A protocol for an intercomparison of biodiversity and ecosystem services models using harmonized land-use and climate scenarios
Kim, Hyejin ; Rosa, Isabel M.D. ; Alkemade, Rob ; Leadley, Paul ; Hurtt, George ; Popp, Alexander ; Vuuren, Detlef P. van; Anthoni, Peter ; Arneth, Almut ; Baisero, Daniele ; Caton, Emma ; Chaplin-Kramer, Rebecca ; Chini, Louise ; Palma, Adriana De; Fulvio, Fulvio Di; Marco, Moreno Di; Espinoza, Felipe ; Ferrier, Simon ; Fujimori, Shinichiro ; Gonzalez, Ricardo E. ; Gueguen, Maya ; Guerra, Carlos ; Harfoot, Mike ; Harwood, Thomas D. ; Hasegawa, Tomoko ; Haverd, Vanessa ; Havlík, Petr ; Hellweg, Stefanie ; Hill, Samantha L.L. ; Hirata, Akiko ; Hoskins, Andrew J. ; Janse, Jan H. ; Jetz, Walter ; Johnson, Justin A. ; Krause, Andreas ; Leclère, David ; Martins, Ines S. ; Matsui, Tetsuya ; Merow, Cory ; Obersteiner, Michael ; Ohashi, Haruka ; Poulter, Benjamin ; Purvis, Andy ; Quesada, Benjamin ; Rondinini, Carlo ; Schipper, Aafke M. ; Sharp, Richard ; Takahashi, Kiyoshi ; Thuiller, Wilfried ; Titeux, Nicolas - \ 2018
Geoscientific Model Development 11 (2018)11. - ISSN 1991-959X - p. 4537 - 4562.

To support the assessments of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES), the IPBES Expert Group on Scenarios and Models is carrying out an intercomparison of biodiversity and ecosystem services models using harmonized scenarios (BES-SIM). The goals of BES-SIM are (1) to project the global impacts of land-use and climate change on biodiversity and ecosystem services (i.e., nature's contributions to people) over the coming decades, compared to the 20th century, using a set of common metrics at multiple scales, and (2) to identify model uncertainties and research gaps through the comparisons of projected biodiversity and ecosystem services across models. BES-SIM uses three scenarios combining specific Shared Socio-economic Pathways (SSPs) and Representative Concentration Pathways (RCPs)-SSP1xRCP2.6, SSP3xRCP6.0, SSP5xRCP8.6-to explore a wide range of land-use change and climate change futures. This paper describes the rationale for scenario selection, the process of harmonizing input data for land use, based on the second phase of the Land Use Harmonization Project (LUH2), and climate, the biodiversity and ecosystem services models used, the core simulations carried out, the harmonization of the model output metrics, and the treatment of uncertainty. The results of this collaborative modeling project will support the ongoing global assessment of IPBES, strengthen ties between IPBES and the Intergovernmental Panel on Climate Change (IPCC) scenarios and modeling processes, advise the Convention on Biological Diversity (CBD) on its development of a post-2020 strategic plans and conservation goals, and inform the development of a new generation of nature-centred scenarios.

Combining heterogeneous across-country data for prediction of enteric methane from proxies in dairy cattle
Negussie, E. ; Gonzalez Recio, O. ; Haas, Y. de; Gengler, N. ; Soyeurt, H. ; Peiren, N. ; Pszczola, M. ; Garnsworthy, P.C. ; Battagin, M. ; Bayat, A.R. ; Lassen, Jan ; Yan, T. ; Boland, T. ; Kuhla, B. ; Strabel, T. ; Schwarm, A. ; Vanlierde, A. ; Biscarini, F. - \ 2018
In: Proceedings of the World Congress on Genetics Applied to Livestock Production. - - 8 p.
Large-scale measurement of enteric methane (CH4) from individual animals is a requisite for estimation of genetic parameters and prediction of breeding values. Direct measurement of individual CH4 emissions is logistically demanding and expensive, and correlated traits (proxies) or models can be used instead as a means to predict emissions. However, most predictive models tend to be specific and are valid mainly within the circumstances under which they were developed. Robust prediction models that work across countries and production environments may be built by combining heterogeneous data from several sources. However, combining heterogeneous individual animal observations on CH4 proxies from several sources is challenging and reports are scant in literature. The main objective of this study was to combine heterogeneous individual animal observations on CH4 proxies to develop robust enteric CH4 prediction models. Data on dairy cattle CH4 emissions and related proxies from 16 herds were made available by 13 research centers across 9 European countries within the Methagene EU COST Action FA1302 consortium on “Large-scale methane measurements on individual ruminants for genetic evaluations”. After a through edition and harmonization, the final dataset comprised 48,804 observations from 2,391 cows. Random Forest (RF) models were used to predict CH4 emissions and to estimate the relative importance of proxies for across-country predictions. Principal component analysis (PCA) was used to detect potential data stratifications. Milk yield, milk fat, DIM, BW, herd and country of origin appeared to be the most relevant proxies in the prediction model. An overall prediction accuracy of 0.81 was estimated from the combined heterogeneous data. This study is a first attempt to develop methods and approaches to combine heterogeneous individual animal data on proxies for CH4 to build robust models for prediction of CH4 emissions across diverse production systems and environments. The methodology outlined here can be extended to combining heterogeneous data, pedigree information and genome-wide dense marker information for estimation of genetic parameters and prediction of breeding values for traits related to dairy system CH4 emissions. Keywords: enteric methane, heterogeneous data, prediction accuracy, methane proxies, random forest, dairy cattle.
Biological control of an invasive pest eases pressures on global commodity markets
Wyckhuys, K.A.G. ; Zhang, W. ; Prager, S.D. ; Kramer, D.B. ; Delaquis, E. ; Gonzalez, C.E. ; Werf, W. van der - \ 2018
Environmental Research Letters 13 (2018)9. - ISSN 1748-9318
biological control - ecosystem services - invasion biology - social-ecological systems - sustainable intensification - tele-coupling

In an increasingly globalized world, invasive species cause major human, financial, and environmental costs. A cosmopolitan pest of great concern is the cassava mealybug Phenacoccus manihoti (Hemiptera: Pseudococcidae), which invaded Asia in 2008. Following its arrival, P. manihoti inflicted measurable yield losses and a 27% drop in aggregate cassava production in Thailand. As Thailand is a vital exporter of cassava-derived commodities to China and supplies 36% of the world's internationally-traded starch, yield shocks triggered price surges and structural changes in global starch trade. In 2009 a biological control agent was introduced in Asia-the host-specific parasitoid, Anagyrus lopezi (Hymenoptera: Encyrtidae). This parasitoid had previously controlled the cassava mealybug in Africa, and its introduction in Asia restored yield levels at a continent-wide scale. Trade network and price time-series analyses reveal how both mealybug-induced production loss and subsequent parasitoid-mediated yield recovery coincided with price fluctuations in futures and spot markets, with important cascading effects on globe-spanning trade networks of (cassava) starch and commodity substitutes. While our analyses may not imply causality, especially given the concurrent 2007-2011 food crises, our results do illuminate the important interconnections among subcomponents of the global commodity system. Our work underlines how ecologically-based tactics support resilience and safeguard primary productivity in (tropical) agro-ecosystems, which in turn help stabilize commodity markets in a similar way as pesticide-centered approaches. Yet, more importantly, (judiciously-implemented) biological control can deliver ample 'hidden' environmental and human-health benefits that are not captured by the prices of globally-traded commodities.

Sourcing overseas biomass for EU ambitions: assessing net sustainable export potential from various sourcing countries
Mai-Moulin, Thuy ; Visser, Lotte ; Fingerman, Kevin R. ; Elbersen, Wolter ; Elbersen, Berien ; Nabuurs, Gert-Jan ; Fritsche, Uwe R. ; Campo Colmenar, Inés Del; Rutz, Dominik ; Diaz-Chavez, Rocio A. ; Roozen, Axel ; Weck, Mathijs ; Iriarte, Leire ; Pelkmans, Luc ; Sanchez Gonzalez, David ; Janssen, Rainer ; Junginger, Martin - \ 2018
Biofuels Bioproducts and Biorefining (2018). - ISSN 1932-104X - 32 p.
Low‐cost sustainable biomass availability in the European Union may not be able to meet increasing demand; exploring the option of importing biomass is therefore imperative for the years to come. This article assesses sustainable biomass export potential from Brazil, Colombia, Indonesia, Kenya, Ukraine, and the United States by applying a number of sustainability criteria. Only biomass types with the highest potential are selected, to take advantage of economies of scale, e.g. pulpwood, wood waste, and residues in the United States, and agricultural residues in Ukraine. This study found that, except for the United States, pellet markets in the sourcing regions are largely undeveloped. The export potential depends strongly on pellet mill capacity and assumed growth rates in the pellet industry. Results show that the United States, Ukraine, Indonesia, and Brazil offer the highest biomass export potential. In the Business As Usual 2030 scenario, up to 204 PJ could potentially be mobilized; in the High Export scenario this could increase to 1423 PJ, with 89% of the potential being available for costs ranging from 6.4 to 15 €/GJ. These potentials meet the European Commission requirements for a 70% reduction in greenhouse gas emissions set in the Renewable Energy Directive. The total export potentials do not reflect the net possible import potentials to the European Union, as biomass could be imported to other countries where there is a demand for it, where less strict sustainability requirements are applied, and which are proximate to the sourcing regions, notably South Korea, Japan, and China.
Nutrimetabolomics: An Integrative Action for Metabolomic Analyses in Human Nutritional Studies
Ulaszewska, Marynka M. ; Weinert, Christoph H. ; Trimigno, Alessia ; Portmann, Reto ; Andres Lacueva, Cristina ; Badertscher, René ; Brennan, Lorraine ; Brunius, Carl ; Bub, Achim ; Capozzi, Francesco ; Cialiè Rosso, Marta ; Cordero, Chiara E. ; Daniel, Hannelore ; Durand, Stéphanie ; Egert, Bjoern ; Ferrario, Paola G. ; Feskens, Edith J.M. ; Franceschi, Pietro ; Garcia-Aloy, Mar ; Giacomoni, Franck ; Giesbertz, Pieter ; González-Domínguez, Raúl ; Hanhineva, Kati ; Hemeryck, Lieselot Y. ; Kopka, Joachim ; Kulling, Sabine E. ; Llorach, Rafael ; Manach, Claudine ; Mattivi, Fulvio ; Migné, Carole ; Münger, Linda H. ; Ott, Beate ; Picone, Gianfranco ; Pimentel, Grégory ; Pujos-Guillot, Estelle ; Riccadonna, Samantha ; Rist, Manuela J. ; Rombouts, Caroline ; Rubert, Josep ; Skurk, Thomas ; Sri Harsha, Pedapati S.C. ; Meulebroek, Lieven Van; Vanhaecke, Lynn ; Vázquez-Fresno, Rosa ; Wishart, David ; Vergères, Guy - \ 2018
Molecular Nutrition & Food Research (2018). - ISSN 1613-4125
GC–MS - LC–MS - metabolomics - NMR - nutrition
The life sciences are currently being transformed by an unprecedented wave of developments in molecular analysis, which include important advances in instrumental analysis as well as biocomputing. In light of the central role played by metabolism in nutrition, metabolomics is rapidly being established as a key analytical tool in human nutritional studies. Consequently, an increasing number of nutritionists integrate metabolomics into their study designs. Within this dynamic landscape, the potential of nutritional metabolomics (nutrimetabolomics) to be translated into a science, which can impact on health policies, still needs to be realized. A key element to reach this goal is the ability of the research community to join, to collectively make the best use of the potential offered by nutritional metabolomics. This article, therefore, provides a methodological description of nutritional metabolomics that reflects on the state-of-the-art techniques used in the laboratories of the Food Biomarker Alliance (funded by the European Joint Programming Initiative “A Healthy Diet for a Healthy Life” (JPI HDHL)) as well as points of reflections to harmonize this field. It is not intended to be exhaustive but rather to present a pragmatic guidance on metabolomic methodologies, providing readers with useful “tips and tricks” along the analytical workflow.
Bottom trawl fishing footprints on the world’s continental shelves
Amoroso, Ricardo O. ; Pitcher, C.R. ; Rijnsdorp, Adriaan D. ; Mcconnaughey, Robert A. ; Parma, Ana M. ; Suuronen, Petri ; Eigaard, Ole R. ; Bastardie, Francois ; Hintzen, Niels T. ; Althaus, Franziska ; Baird, Susan Jane ; Black, Jenny ; Buhl-Mortensen, Lene ; Campbell, Alexander B. ; Catarino, Rui ; Collie, Jeremy ; Cowan, James H. ; Durholtz, Deon ; Engstrom, Nadia ; Fairweather, Tracey P. ; Fock, Heino O. ; Ford, Richard ; Gálvez, Patricio A. ; Gerritsen, Hans ; Góngora, María Eva ; González, Jessica A. ; Hiddink, Jan G. ; Hughes, Kathryn M. ; Intelmann, Steven S. ; Jenkins, Chris ; Jonsson, Patrik ; Kainge, Paulus ; Kangas, Mervi ; Kathena, Johannes N. ; Kavadas, Stefanos ; Leslie, Rob W. ; Lewis, Steve G. ; Lundy, Mathieu ; Makin, David ; Martin, Julie ; Mazor, Tessa ; Gonzalez-Mirelis, Genoveva ; Newman, Stephen J. ; Papadopoulou, Nadia ; Posen, Paulette E. ; Rochester, Wayne ; Russo, Tommaso ; Sala, Antonello ; Semmens, Jayson M. ; Silva, Cristina - \ 2018
Proceedings of the National Academy of Sciences of the United States of America 115 (2018)43. - ISSN 0027-8424 - p. E10275 - E10282.
Bottom trawlers land around 19 million tons of fish and invertebrates annually, almost one-quarter of wild marine landings. The extent of bottom trawling footprint (seabed area trawled at least once in a specified region and time period) is often contested but poorly described. We quantify footprints using high-resolution satellite vessel monitoring system (VMS) and logbook data on 24 continental shelves and slopes to 1,000-m depth over at least 2 years. Trawling footprint varied markedly among regions: from <10% of seabed area in Australian and New Zealand waters, the Aleutian Islands, East Bering Sea, South Overall, 14% of the 7.8 million-km2 study area was trawled, and 86% was not trawled. Trawling activity was aggregated; the most intensively trawled areas accounting for 90% of activity comprised 77% of footprint on average. Regional swept area ratio (SAR; ratio of total swept area trawled annually to total area of region, a metric of trawling intensity) and footprint area were related, providing an approach to estimate regional trawling footprints when highresolution spatial data are unavailable. If SAR was ≤0.1, as in 8 of 24 regions, therewas >95% probability that >90%of seabed was not trawled. If SAR was 7.9, equal to the highest SAR recorded, there was >95% probability that >70% of seabed was trawled. Footprints were smaller and SAR was ≤0.25 in regions where fishing rates consistently met international sustainability benchmarks for fish stocks, implying collateral environmental benefits from sustainable fishing.
Climate-Smart Forestry: mitigation implact in three European regions
Nabuurs, G.J. ; Verkerk, P.J. ; Schelhaas, M. ; González-Olabarria, J.R. ; Trasobares, A. ; Cienciala, E. - \ 2018
European Forest Institute (From Science to Policy ) - ISBN 9789525980530 - 32 p.
Guide to evaluation of quality of surface water in coffee river basins of Colombia
Rodríguez Valencia, Nelson ; Quintero Yepes, Laura Vanessa ; Gómez Zuluaga, Gustavo Adolfo ; Bohórquez Zapata, Viviana Lorena ; González Durán, Cristy Mayerly ; Osorio Ocampo, Andrés Felipe ; Miguel García, Ángel de; Harmsen, Joop ; Wolters, W. ; Miguel Ayala, L. - \ 2018
Bogota : APC Columbia - 206
Guía para la evaluación de la calidad del agua superficial en microcuencas cafeteras de Colombia
Rodríguez Valencia, Nelson ; Quintero Yepes, Laura Vanessa ; Gómez Zuluaga, Gustavo Adolfo ; Bohórquez Zapata, Viviana Lorena ; González Durán, Cristy Mayerly ; Osorio Ocampo, Andrés Felipe ; Miguel García, Ángel de; Harmsen, Joop ; Wolters, W. ; Miguel Ayala, L. - \ 2018
Bogota : APC Columbia - ISBN 9789588490304 - 206
Análisis del retorno social de la inversión del proyecto Manos al Agua : Estudio de caso en la microcuenca Edén-Bareño, Aguadas-Caldas
Serna Giraldo, César Alberto ; González González, Marisol ; Wolters, W. ; Miguel Ayala, L. - \ 2018
Bogota : APC Columbia - ISBN 9789588490267 - 88
Author Correction: Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries
Munk, Patrick ; Knudsen, Berith Elkær ; Lukjancenko, Oksana ; Duarte, Ana Sofia Ribeiro ; Gompel, Liese Van; Luiken, Roosmarijn E.C. ; Smit, Lidwien A.M. ; Schmitt, Heike ; Garcia, Alejandro Dorado ; Hansen, Rasmus Borup ; Petersen, Thomas Nordahl ; Bossers, Alex ; Ruppé, Etienne ; Lund, Ole ; Hald, Tine ; Pamp, Sünje Johanna ; Vigre, Håkan ; Heederik, Dick ; Wagenaar, Jaap A. ; Mevius, Dik ; Aarestrup, Frank M. ; Graveland, Haitske ; Essen, Alieda van; Gonzalez-Zorn, Bruno ; Moyano, Gabriel ; Sanders, Pascal ; Chauvin, Claire ; David, Julie ; Battisti, Antonio ; Caprioli, Andrea ; Dewulf, Jeroen ; Blaha, Thomas ; Wadepohl, Katharina ; Brandt, Maximiliane ; Wasyl, Dariusz ; Skarzyńska, Magdalena ; Zajac, Magdalena ; Daskalov, Hristo ; Saatkamp, Helmut W. ; Stärk, Katharina D.C. - \ 2018
Nature Microbiology 3 (2018). - ISSN 2058-5276

In the version of this Article originally published, the surname of author Oksana Lukjancenko was spelt incorrectly as ‘Lukjacenko’. This has now been corrected.

Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries
Munk, Patrick ; Knudsen, Berith Elkær ; Lukjacenko, Oksana ; Duarte, Ana Sofia Ribeiro ; Gompel, Liese Van; Luiken, Roosmarijn E.C. ; Smit, Lidwien A.M. ; Schmitt, Heike ; Garcia, Alejandro Dorado ; Hansen, Rasmus Borup ; Petersen, Thomas Nordahl ; Bossers, Alex ; Ruppé, Etienne ; Graveland, Haitske ; Essen, Alieda van; Gonzalez-Zorn, Bruno ; Moyano, Gabriel ; Sanders, Pascal ; Chauvin, Claire ; David, Julie ; Battisti, Antonio ; Caprioli, Andrea ; Dewulf, Jeroen ; Blaha, Thomas ; Wadepohl, Katharina ; Brandt, Maximiliane ; Wasyl, Dariusz ; Skarzyńska, Magdalena ; Zajac, Magdalena ; Daskalov, Hristo ; Saatkamp, Helmut W. ; Stärk, Katharina D.C. ; Lund, Ole ; Hald, Tine ; Pamp, Sünje Johanna ; Vigre, Håkan ; Heederik, Dick ; Wagenaar, Jaap A. ; Mevius, Dik ; Aarestrup, Frank M. - \ 2018
Nature Microbiology 3 (2018)8. - ISSN 2058-5276 - p. 898 - 908.

Antimicrobial resistance (AMR) in bacteria and associated human morbidity and mortality is increasing. The use of antimicrobials in livestock selects for AMR that can subsequently be transferred to humans. This flow of AMR between reservoirs demands surveillance in livestock and in humans. We quantified and characterized the acquired resistance gene pools (resistomes) of 181 pig and 178 poultry farms from nine European countries, sequencing more than 5,000 Gb of DNA using shotgun metagenomics. We quantified acquired AMR using the ResFinder database and a second database constructed for this study, consisting of AMR genes identified through screening environmental DNA. The pig and poultry resistomes were very different in abundance and composition. There was a significant country effect on the resistomes, more so in pigs than in poultry. We found higher AMR loads in pigs, whereas poultry resistomes were more diverse. We detected several recently described, critical AMR genes, including mcr-1 and optrA, the abundance of which differed both between host species and between countries. We found that the total acquired AMR level was associated with the overall country-specific antimicrobial usage in livestock and that countries with comparable usage patterns had similar resistomes. However, functionally determined AMR genes were not associated with total drug use.

Stability estimation of autoregulated genes under Michaelis-Menten-type kinetics
Arani, Babak M.S. ; Mahmoudi, Mahdi ; Lahti, Leo ; González, Javier ; Wit, Ernst C. - \ 2018
Physical Review. E, Statistical nonlinear, and soft matter physics 97 (2018)6. - ISSN 2470-0045

Feedback loops are typical motifs appearing in gene regulatory networks. In some well-studied model organisms, including Escherichia coli, autoregulated genes, i.e., genes that activate or repress themselves through their protein products, are the only feedback interactions. For these types of interactions, the Michaelis-Menten (MM) formulation is a suitable and widely used approach, which always leads to stable steady-state solutions representative of homeostatic regulation. However, in many other biological phenomena, such as cell differentiation, cancer progression, and catastrophes in ecosystems, one might expect to observe bistable switchlike dynamics in the case of strong positive autoregulation. To capture this complex behavior we use the generalized family of MM kinetic models. We give a full analysis regarding the stability of autoregulated genes. We show that the autoregulation mechanism has the capability to exhibit diverse cellular dynamics including hysteresis, a typical characteristic of bistable systems, as well as irreversible transitions between bistable states. We also introduce a statistical framework to estimate the kinetics parameters and probability of different stability regimes given observational data. Empirical data for the autoregulated gene SCO3217 in the SOS system in Streptomyces coelicolor are analyzed. The coupling of a statistical framework and the mathematical model can give further insight into understanding the evolutionary mechanisms toward different cell fates in various systems.

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