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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A global synthesis reveals biodiversity-mediated benefits for crop production
Dainese, Matteo ; Martin, Emily A. ; Aizen, Marcelo A. ; Albrecht, Matthias ; Bartomeus, Ignasi ; Bommarco, Riccardo ; Carvalheiro, Luisa G. ; Chaplin-Kramer, Rebecca ; Gagic, Vesna ; Garibaldi, Lucas A. ; Ghazoul, Jaboury ; Grab, Heather ; Jonsson, Mattias ; Karp, Daniel S. ; Kennedy, Christina M. ; Kleijn, David ; Kremen, Claire ; Landis, Douglas A. ; Letourneau, Deborah K. ; Marini, Lorenzo ; Poveda, Katja ; Rader, Romina ; Smith, Henrik G. ; Tscharntke, Teja ; Andersson, Georg K.S. ; Badenhausser, Isabelle ; Baensch, Svenja ; Bezerra, Antonio D.M. ; Bianchi, Felix J.J.A. ; Boreux, Virginie ; Bretagnolle, Vincent ; Caballero-Lopez, Berta ; Cavigliasso, Pablo ; Ćetković, Aleksandar ; Chacoff, Natacha P. ; Classen, Alice ; Cusser, Sarah ; Silva E Silva, Felipe D. Da; Groot, A. de; Dudenhöffer, Jan H. ; Ekroos, Johan ; Fijen, Thijs ; Franck, Pierre ; Freitas, Breno M. ; Garratt, Michael P.D. ; Gratton, Claudio ; Hipólito, Juliana ; Holzschuh, Andrea ; Hunt, Lauren ; Iverson, Aaron L. ; Jha, Shalene ; Keasar, Tamar ; Kim, Tania N. ; Kishinevsky, Miriam ; Klatt, Björn K. ; Klein, Alexandra Maria ; Krewenka, Kristin M. ; Krishnan, Smitha ; Larsen, Ashley E. ; Lavigne, Claire ; Liere, Heidi ; Maas, Bea ; Mallinger, Rachel E. ; Pachon, Eliana Martinez ; Martínez-Salinas, Alejandra ; Meehan, Timothy D. ; Mitchell, Matthew G.E. ; Molina, Gonzalo A.R. ; Nesper, Maike ; Nilsson, Lovisa ; O'Rourke, Megan E. ; Peters, Marcell K. ; Plećaš, Milan ; Potts, Simon G. ; L. Ramos, Davi de; Rosenheim, Jay A. ; Rundlöf, Maj ; Rusch, Adrien ; Sáez, Agustín ; Scheper, Jeroen ; Schleuning, Matthias ; Schmack, Julia M. ; Sciligo, Amber R. ; Seymour, Colleen ; Stanley, Dara A. ; Stewart, Rebecca ; Stout, Jane C. ; Sutter, Louis ; Takada, Mayura B. ; Taki, Hisatomo ; Tamburini, Giovanni ; Tschumi, Matthias ; Viana, Blandina F. ; Westphal, Catrin ; Willcox, Bryony K. ; Wratten, Stephen D. ; Yoshioka, Akira ; Zaragoza-Trello, Carlos ; Zhang, Wei ; Zou, Yi ; Steffan-Dewenter, Ingolf - \ 2019
Science Advances 5 (2019)10. - ISSN 2375-2548

Human land use threatens global biodiversity and compromises multiple ecosystem functions critical to food production. Whether crop yield-related ecosystem services can be maintained by a few dominant species or rely on high richness remains unclear. Using a global database from 89 studies (with 1475 locations), we partition the relative importance of species richness, abundance, and dominance for pollination; biological pest control; and final yields in the context of ongoing land-use change. Pollinator and enemy richness directly supported ecosystem services in addition to and independent of abundance and dominance. Up to 50% of the negative effects of landscape simplification on ecosystem services was due to richness losses of service-providing organisms, with negative consequences for crop yields. Maintaining the biodiversity of ecosystem service providers is therefore vital to sustain the flow of key agroecosystem benefits to society.

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

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

Rapid plastic breeding response to rain matches peak prey abundance in a tropical savanna bird
Hidalgo Aranzamendi, Nataly ; Hall, Michelle L. ; Kingma, Sjouke A. ; Pol, Martijn van de; Peters, Anne - \ 2019
Journal of Animal Ecology (2019). - ISSN 0021-8790
annual cycle - avian life-history - phenology - phenotypic plasticity - timing of reproduction - trophic interactions - tropics - unpredictable environment

Changes in climate are shifting the timing of life cycle events in the natural world. Compared to northern temperate areas, these effects are relatively poorly understood in tropical and southern regions, where there is limited information on how timing of breeding and food availability are affected by climatic factors, and where patterns of breeding activity are more unpredictable within and between years. Combining a new statistical modelling approach with 5 years of continuous individual-based monitoring of a monsoonal tropical insectivorous bird, we quantified (a) the proximate climatic drivers at two trophic levels: timing of breeding and abundance of arthropod prey; (b) the effect of climate variation on reproductive output and (c) the role of individual plasticity. Rainfall was identified as the main determinant of phenology at both trophic levels. Throughout the year, likelihood of egg laying increased very rapidly in response to even small amounts of rain during the preceding 0–3 weeks. Adult body mass and male sperm storage also increased rapidly after rain, suggesting high breeding preparedness. Additionally, females were flexible, since they were more likely to nest whether their previous attempt was longer ago and unsuccessful. Arthropod abundance also increased after rainfall, but more slowly, with a peak around 10 weeks. Therefore, the peak food availability coincided with the presence of dependent fledglings. Fitness benefits of nesting after more rain appeared to be linked to offspring quantity rather than quality: nest attempts following higher rainfall produced larger clutches, but showed no improvement in nestling mass or relative fledging success. The response of clutch size to rainfall was plastic, since repeated sampling showed that individual females laid larger clutches after more rain, possibly mediated by improved body mass. Rapid, individually flexible breeding in response to rainfall and slower increase in arthropod abundance also as a response to rainfall, might buffer insectivorous species living in tropical seasonal environments from climate change-induced phenological trophic mismatches.

Voedselbewerking : De balans tussen veiligheid en gezondheid
Peters, S. ; Gerritsen, J. ; Huppertz, Thom - \ 2019
VoedingsMagazine 32 (2019)2. - ISSN 0922-8012 - p. 18 - 21.
Volgens een recent onderzoek hangt de consumptie van ultra-bewerkt voedsel samen met een toename van overgewicht en welvaartsziekten. Kan een classificatie van producten op hun bewerkingsgraad - zoals NOVA - consumenten helpen om gezondere keuzes te maken?
Determination of the triple oxygen and carbon isotopic composition of CO2 from atomic ion fragments formed in the ion source of the 253 Ultra high-resolution isotope ratio mass spectrometer
Adnew, Getachew A. ; Hofmann, Magdalena E.G. ; Paul, Dipayan ; Laskar, Amzad ; Surma, Jakub ; Albrecht, Nina ; Pack, Andreas ; Schwieters, Johannes ; Koren, Gerbrand ; Peters, Wouter ; Röckmann, Thomas - \ 2019
Rapid Communications in Mass Spectrometry 33 (2019)17. - ISSN 0951-4198 - p. 1363 - 1380.

Rationale: Determination of δ17O values directly from CO2 with traditional gas source isotope ratio mass spectrometry is not possible due to isobaric interference of 13C16O16O on 12C17O16O. The methods developed so far use either chemical conversion or isotope equilibration to determine the δ17O value of CO2. In addition, δ13C measurements require correction for the interference from 12C17O16O on 13C16O16O since it is not possible to resolve the two isotopologues. Methods: We present a technique to determine the δ17O, δ18O and δ13C values of CO2 from the fragment ions that are formed upon electron ionization in the ion source of the Thermo Scientific 253 Ultra high-resolution isotope ratio mass spectrometer (hereafter 253 Ultra). The new technique is compared with the CO2-O2 exchange method and the 17O-correction algorithm for δ17O and δ13C values, respectively. Results: The scale contractions for δ13C and δ18O values are slightly larger for fragment ion measurements than for molecular ion measurements. The δ17O and Δ17O values of CO2 can be measured on the 17O+ fragment with an internal error that is a factor 1–2 above the counting statistics limit. The ultimate precision depends on the signal intensity and on the total time that the 17O+ beam is monitored; a precision of 14 ppm (parts per million) (standard error of the mean) was achieved in 20 hours at the University of Göttingen. The Δ17O measurements with the O-fragment method agree with the CO2-O2 exchange method over a range of Δ17O values of −0.3 to +0.7‰. Conclusions: Isotope measurements on atom fragment ions of CO2 can be used as an alternative method to determine the carbon and oxygen isotopic composition of CO2 without chemical processing or corrections for mass interferences.

Global 3-D Simulations of the Triple Oxygen Isotope Signature Δ17O in Atmospheric CO2
Koren, Gerbrand ; Schneider, Linda ; Velde, Ivar R. van der; Schaik, Erik van; Gromov, Sergey S. ; Adnew, Getachew A. ; Mrozek Martino, Dorota J. ; Hofmann, Magdalena E.G. ; Liang, Mao Chang ; Mahata, Sasadhar ; Bergamaschi, Peter ; Laan-Luijkx, Ingrid T. van der; Krol, Maarten C. ; Röckmann, Thomas ; Peters, Wouter - \ 2019
Journal of Geophysical Research: Atmospheres (2019). - ISSN 2169-897X
O excess (ΔO) - carbon cycle - carbon dioxide (CO) - gross primary production (GPP) - mass-independent fractionation (MIF) - stable isotopes

The triple oxygen isotope signature Δ17O in atmospheric CO2, also known as its “17O excess,” has been proposed as a tracer for gross primary production (the gross uptake of CO2 by vegetation through photosynthesis). We present the first global 3-D model simulations for Δ17O in atmospheric CO2 together with a detailed model description and sensitivity analyses. In our 3-D model framework we include the stratospheric source of Δ17O in CO2 and the surface sinks from vegetation, soils, ocean, biomass burning, and fossil fuel combustion. The effect of oxidation of atmospheric CO on Δ17O in CO2 is also included in our model. We estimate that the global mean Δ17O (defined as Δ17O = ln(δ17O+1)−λRL·ln(δ18O+1) with λRL = 0.5229) of CO2 in the lowest 500 m of the atmosphere is 39.6 per meg, which is ∼20 per meg lower than estimates from existing box models. We compare our model results with a measured stratospheric Δ17O in CO2 profile from Sodankylä (Finland), which shows good agreement. In addition, we compare our model results with tropospheric measurements of Δ17O in CO2 from Göttingen (Germany) and Taipei (Taiwan), which shows some agreement but we also find substantial discrepancies that are subsequently discussed. Finally, we show model results for Zotino (Russia), Mauna Loa (United States), Manaus (Brazil), and South Pole, which we propose as possible locations for future measurements of Δ17O in tropospheric CO2 that can help to further increase our understanding of the global budget of Δ17O in atmospheric CO2.

Pathotyping the Zoonotic Pathogen Streptococcus suis: Novel genetic markers to differentiate invasive disease-associated isolates from non-disease-associated isolates from England and Wales
Wileman, Thomas M. ; Weinert, Lucy A. ; Howell, Kate J. ; Wang, Jinhong ; Peters, Sarah E. ; Williamson, Susanna M. ; Wells, Jerry M. ; Langford, Paul R. ; Rycroft, Andrew N. ; Wren, Brendan W. ; Maskell, Duncan J. ; Tucker, Alexander W. - \ 2019
Journal of Clinical Microbiology 57 (2019)7. - ISSN 0095-1137
Molecular diagnostics - Pathotyping - Streptococcus suis - Surveillance - Virulence markers

Streptococcus suis is one of the most important zoonotic bacterial pathogens of pigs, causing significant economic losses to the global swine industry. S. suis is also a very successful colonizer of mucosal surfaces, and commensal strains can be found in almost all pig populations worldwide, making detection of the S. suis species in asymptomatic carrier herds of little practical value in predicting the likelihood of future clinical relevance. The value of future molecular tools for surveillance and preventative health management lies in the detection of strains that genetically have increased potential to cause disease in presently healthy animals. Here we describe the use of genome-wide association studies to identify genetic markers associated with the observed clinical phenotypes (i) invasive disease and (ii) asymptomatic carriage on the palatine tonsils of pigs on UK farms. Subsequently, we designed a multiplex PCR to target three genetic markers that differentiated 115 S. suis isolates into disease-associated and non-disease-associated groups, that performed with a sensitivity of 0.91, a specificity of 0.79, a negative predictive value of 0.91, and a positive predictive value of 0.79 in comparison to observed clinical phenotypes. We describe evaluation of our pathotyping tool, using an out-of-sample collection of 50 previously uncharacterized S. suis isolates, in comparison to existing methods used to characterize and subtype S. suis isolates. In doing so, we show our pathotyping approach to be a competitive method to characterize S. suis isolates recovered from pigs on UK farms and one that can easily be updated to incorporate global strain collections.

Correction to: Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer
Bien, Stephanie A. ; Su, Yu Ru ; Conti, David V. ; Harrison, Tabitha A. ; Qu, Conghui ; Guo, Xingyi ; Lu, Yingchang ; Albanes, Demetrius ; Auer, Paul L. ; Banbury, Barbara L. ; Berndt, Sonja I. ; Bézieau, Stéphane ; Brenner, Hermann ; Buchanan, Daniel D. ; Caan, Bette J. ; Campbell, Peter T. ; Carlson, Christopher S. ; Chan, Andrew T. ; Chang-Claude, Jenny ; Chen, Sai ; Connolly, Charles M. ; Easton, Douglas F. ; Feskens, Edith J.M. ; Gallinger, Steven ; Giles, Graham G. ; Gunter, Marc J. ; Hampe, Jochen ; Huyghe, Jeroen R. ; Hoffmeister, Michael ; Hudson, Thomas J. ; Jacobs, Eric J. ; Jenkins, Mark A. ; Kampman, Ellen ; Kang, Hyun Min ; Kühn, Tilman ; Küry, Sébastien ; Lejbkowicz, Flavio ; Marchand, Loic Le; Milne, Roger L. ; Li, Li ; Li, Christopher I. ; Lindblom, Annika ; Lindor, Noralane M. ; Martín, Vicente ; McNeil, Caroline E. ; Melas, Marilena ; Moreno, Victor ; Newcomb, Polly A. ; Offit, Kenneth ; Pharaoh, Paul D.P. ; Potter, John D. ; Qu, Chenxu ; Riboli, Elio ; Rennert, Gad ; Sala, Núria ; Schafmayer, Clemens ; Scacheri, Peter C. ; Schmit, Stephanie L. ; Severi, Gianluca ; Slattery, Martha L. ; Smith, Joshua D. ; Trichopoulou, Antonia ; Tumino, Rosario ; Ulrich, Cornelia M. ; Duijnhoven, Fränzel J.B. van; Guelpen, Bethany Van; Weinstein, Stephanie J. ; White, Emily ; Wolk, Alicja ; Woods, Michael O. ; Wu, Anna H. ; Abeçasis, Goncalo R. ; Casey, Graham ; Nickerson, Deborah A. ; Gruber, Stephen B. ; Hsu, Li ; Zheng, Wei ; Peters, Ulrike - \ 2019
Human Genetics 138 (2019)7. - ISSN 0340-6717 - p. 789 - 791.

Every author has erroneously been assigned to the affiliation “62”. The affiliation 62 belongs to the author Graham Casey.

Data from: An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea)
Evangelista, Dominic A. ; Wipfler, Benjamin ; Béthoux, Olivier ; Donath, Alexander ; Fujita, Mari ; Kohli, Manpreet K. ; Legendre, Frédéric ; Liu, Shanlin ; Machida, Ryuichiro ; Misof, Bernhard ; Peters, Ralph S. ; Podsiadlowski, Lars ; Rust, Jes ; Schuette, Kai ; Tollenaar, Ward ; Ware, Jessica L. ; Wappler, Torsten ; Zhou, Xin ; Meusemann, Karen ; Simon, S. - \ 2019
gondwana - dating - phyloecology - transcriptomes - palaeontology - systematics - maternal care - sociality
Phylogenetic relationships among subgroups of cockroaches and termites are still matters of debate. Their divergence times and major phenotypic transitions during evolution are also not yet settled. We addressed these points by combining the first nuclear phylogenomic study of termites and cockroaches with a thorough approach to divergence time analysis, identification of endosymbionts, and reconstruction of ancestral morphological traits and behaviour. Analyses of the phylogenetic relationships within Blattodea robustly confirm previously uncertain hypotheses such as the sister-group relationship between Blaberoidea and remaining Blattodea, and Lamproblatta being the closest relative to the social and wood-feeding Cryptocercus and termites. Consequently, we propose new names for various clades in Blattodea: Cryptocercus þ termites ¼ Tutricablattae; Lamproblattidae þ Tutricablattae ¼ Kittrickea; and Blattoidea þ Corydioidea ¼ Solumblattodea. Our inferred divergence times contradict previous studies by showing that most subgroups of Blattodea evolved in the Cretaceous, reducing the gap between molecular estimates of divergence times and the fossil record. On a phenotypic level, the blatto-dean ground-plan is for egg packages to be laid directly in a hole while other forms of oviposition, including ovovivipary and vivipary, arose later. Finally, other changes in egg care strategy may have allowed for the adaptation of nest building and other novelties.
Determination of pentachlorophenol in feed materials and compound feed by LC-MS/MS
Peters, R.J.B. ; Gebbink, W. - \ 2019
Wageningen : Wageningen Food Safety Research (Wageningen Food Safety Research 2019.009) - 37
Brominated flame retardants in animal derived foods in the Netherlands between 2009 and 2014
Gebbink, Wouter A. ; Lee, Martijn K. van der; Peters, Ruud J.B. ; Traag, Wim A. ; Dam, Guillaume ten; Hoogenboom, Ron L.A.P. ; Leeuwen, Stefan P.J. van - \ 2019
Chemosphere 234 (2019). - ISSN 0045-6535 - p. 171 - 178.
Eggs - Fish - HBCDD - Meat - Milk - PBDE

Polybrominated diphenylethers (PBDEs), hexabromocyclododecanes (HBCDDs) and tetrabromobisphenol A (TBBPA) were monitored in various foods from terrestrial and aquatic animal origin (>850 samples), collected in the Netherlands between 2009 and 2014. The terrestrial samples included meat/fat from 7 animal species (including bovines, pigs, broilers and sheep), bovine milk and hen eggs. Dominant PBDE congeners in these samples were BDE-47, -99, -100, -153 and -183. The meat/fat generally contained the highest ∑PBDE concentrations compared to eggs and milk, with meat from deer, horse and sheep containing the highest concentrations. Generally declining ∑PBDE concentrations were observed between 2009 and 2014, however, this was only significant in pig meat and hen's eggs. The aquatic samples included fillets from 18 species (including herring, haddock and salmon), brown crab parts, shrimp and mussels, and the highest ∑PBDE concentrations were seen in body parts of brown crab, herring, mackerel, salmon and sea bass (on wet weight basis). Patterns generally contained more congeners (i.e., BDE-28, -49 and -66) additional to the aforementioned congeners found in terrestrial samples. Herring, sea bass and brown crab (body parts) contained among the highest PBDE concentrations. TBBPA was only detected in 3 individual samples (bovine and broiler meat and haddock), while α-HBCDD was the dominant diastereomer detected in several terrestrial and aquatic samples. When detected, TBBPA and HBCDD concentrations were generally in the same order as ∑PBDE concentrations in the same sample types.

Inferring causation from time series in Earth system sciences
Runge, Jakob ; Bathiany, Sebastian ; Bollt, Erik ; Camps-Valls, Gustau ; Coumou, Dim ; Deyle, Ethan ; Glymour, Clark ; Kretschmer, Marlene ; Mahecha, Miguel D. ; Muñoz-Marí, Jordi ; Nes, Egbert H. van; Peters, Jonas ; Quax, Rick ; Reichstein, Markus ; Scheffer, Marten ; Schölkopf, Bernhard ; Spirtes, Peter ; Sugihara, George ; Sun, Jie ; Zhang, Kun ; Zscheischler, Jakob - \ 2019
Nature Communications 10 (2019)1. - ISSN 2041-1723

The heart of the scientific enterprise is a rational effort to understand the causes behind the phenomena we observe. In large-scale complex dynamical systems such as the Earth system, real experiments are rarely feasible. However, a rapidly increasing amount of observational and simulated data opens up the use of novel data-driven causal methods beyond the commonly adopted correlation techniques. Here, we give an overview of causal inference frameworks and identify promising generic application cases common in Earth system sciences and beyond. We discuss challenges and initiate the benchmark platform causeme.net to close the gap between method users and developers.

Metabolomics of Thrips Resistance in Pepper (Capsicum spp.) Reveals Monomer and Dimer Acyclic Diterpene Glycosides as Potential Chemical Defenses
Macel, Mirka ; Visschers, I.S.G. ; Peters, Janny ; Kappers, I.F. ; Vos, C.H. de; Dam, Nicole M. van - \ 2019
Journal of Chemical Ecology 45 (2019)5-6. - ISSN 0098-0331 - p. 490 - 501.
Capsianosides . Frankliniella occidentalis . Liquid chromatography-mass spectrometry . Insects . Solanaceae . Thrips
The development of pesticide resistance in insects and recent bans on pesticides call for the identification of natural sources of
resistance in crops. Here, we used natural variation in pepper (Capsicum spp.) resistance combined with an untargeted metabolomics
approach to detect secondary metabolites related to thrips (Frankliniella occidentalis) resistance. Using leaf disc choice
assays, we tested 11 Capsicum accessions of C. annuum and C. chinense in both vegetative and flowering stages for thrips
resistance. Metabolites in the leaves of these 11 accessions were analyzed using LC-MS based untargeted metabolomics. The
choice assays showed significant differences among the accessions in thrips feeding damage. The level of resistance depended on
plant developmental stage. Metabolomics analyses showed differences in metabolomes among the Capsicum species and plant
developmental stages. Moreover, metabolomic profiles of resistant and susceptible accessions differed. Monomer and dimer
acyclic diterpene glycosides (capsianosides) were pinpointed as metabolites that were related to thrips resistance. Sucrose and
malonylated flavone glycosides were related to susceptibility. To our knowledge, this is the first time that dimer capsianosides of
pepper have been linked to insect resistance. Our results show the potential of untargeted metabolomics as a tool for discovering
metabolites that are important in plant – insect interactions.
Keywords Capsianosides . Frankliniella occidentalis . Liquid chromatography-mass spectrometry . Insects . Solanaceae . Thrips
Sticky Measurement Problem : Number Concentration of Agglomerated Nanoparticles
Minelli, Caterina ; Bartczak, Dorota ; Peters, Ruud ; Rissler, Jenny ; Undas, Anna ; Sikora, Aneta ; Sjöström, Eva ; Goenaga-Infante, Heidi ; Shard, Alexander G. - \ 2019
Langmuir 35 (2019)14. - ISSN 0743-7463 - p. 4927 - 4935.

Measuring the number concentration of colloidal nanoparticles (NPs) is critical for assessing reproducibility, enabling compliance with regulation, and performing risk assessments of NP-enabled products. For nanomedicines, their number concentration directly relates to their dose. However, the lack of relevant reference materials and established traceable measurement approaches make the validation of methods for NP number concentration difficult. Furthermore, commercial products often exhibit agglomeration, but guidelines for dealing with nonideal samples are scarce. We have compared the performance of five benchtop measurement methods for the measurement of colloidal number concentration in the presence of different levels of agglomeration. The methods are UV-visible spectroscopy, differential centrifugal sedimentation, dynamic light scattering, particle tracking analysis, and single-particle inductively coupled plasma mass spectrometry. We find that both ensemble and particle-by-particle methods are in close agreement for monodisperse NP samples and three methods are within 20% agreement for agglomerated samples. We discuss the sources of measurement uncertainties, including how particle agglomeration affects measurement results. This work is a first step toward validation and expansion of the toolbox of methods available for the measurement of real-world NP products.

Disentangling the genetics of lean mass
Karasik, David ; Zillikens, M.C. ; Hsu, Yi Hsiang ; Aghdassi, Ali ; Akesson, Kristina ; Amin, Najaf ; Barroso, Inês ; Bennett, David A. ; Bertram, Lars ; Bochud, Murielle ; Borecki, Ingrid B. ; Broer, Linda ; Buchman, Aron S. ; Byberg, Liisa ; Campbell, Harry ; Campos-Obando, Natalia ; Cauley, Jane A. ; Cawthon, Peggy M. ; Chambers, John C. ; Chen, Zhao ; Cho, Nam H. ; Choi, Hyung Jin ; Chou, Wen Chi ; Cummings, Steven R. ; Groot, Lisette C.P.G.M. De; Jager, Phillip L. De; Demuth, Ilja ; Diatchenko, Luda ; Econs, Michael J. ; Eiriksdottir, Gudny ; Enneman, Anke W. ; Eriksson, Joel ; Eriksson, Johan G. ; Estrada, Karol ; Evans, Daniel S. ; Feitosa, Mary F. ; Fu, Mao ; Gieger, Christian ; Grallert, Harald ; Gudnason, Vilmundur ; Lenore, Launer J. ; Hayward, Caroline ; Hofman, Albert ; Homuth, Georg ; Huffman, Kim M. ; Husted, Lise B. ; Illig, Thomas ; Ingelsson, Erik ; Ittermann, Till ; Jansson, John Olov ; Johnson, Toby ; Biffar, Reiner ; Jordan, Joanne M. ; Jula, Antti ; Karlsson, Magnus ; Khaw, Kay Tee ; Kilpeläinen, Tuomas O. ; Klopp, Norman ; Kloth, Jacqueline S.L. ; Koller, Daniel L. ; Kooner, Jaspal S. ; Kraus, William E. ; Kritchevsky, Stephen ; Kutalik, Zoltán ; Kuulasmaa, Teemu ; Kuusisto, Johanna ; Laakso, Markku ; Lahti, Jari ; Lang, Thomas ; Langdahl, Bente L. ; Lerch, Markus M. ; Lewis, Joshua R. ; Lill, Christina ; Lind, Lars ; Lindgren, Cecilia ; Liu, Yongmei ; Livshits, Gregory ; Ljunggren, Östen ; Loos, Ruth J.F. ; Lorentzon, Mattias ; Luan, Jian An ; Luben, Robert N. ; Malkin, Ida ; McGuigan, Fiona E. ; Medina-Gomez, Carolina ; Meitinger, Thomas ; Melhus, Håkan ; Mellström, Dan ; Michaëlsson, Karl ; Mitchell, Braxton D. ; Morris, Andrew P. ; Mosekilde, Leif ; Nethander, Maria ; Newman, Anne B. ; Oconnell, Jeffery R. ; Oostra, Ben A. ; Orwoll, Eric S. ; Palotie, Aarno ; Peacock, Munro ; Perola, Markus ; Peters, Annette ; Prince, Richard L. ; Psaty, Bruce M. ; Räikkönen, Katri ; Ralston, Stuart H. ; Ripatti, Samuli ; Rivadeneira, Fernando ; Robbins, John A. ; Rotter, Jerome I. ; Rudan, Igor ; Salomaa, Veikko ; Satterfield, Suzanne ; Schipf, Sabine ; Shin, Chan Soo ; Smith, Albert V. ; Smith, Shad B. ; Soranzo, Nicole ; Spector, Timothy D. ; StanÄ Áková, Alena ; Stefansson, Kari ; Steinhagen-Thiessen, Elisabeth ; Stolk, Lisette ; Streeten, Elizabeth A. ; Styrkarsdottir, Unnur ; Swart, Karin M.A. ; Thompson, Patricia ; Thomson, Cynthia A. ; Thorleifsson, Gudmar ; Thorsteinsdottir, Unnur ; Tikkanen, Emmi ; Tranah, Gregory J. ; Uitterlinden, André G. ; Duijn, Cornelia M. Van; Schoor, Natasja M. Van; Vandenput, Liesbeth ; Vollenweider, Peter ; Völzke, Henry ; Wactawski-Wende, Jean ; Walker, Mark ; J Wareham, Nicholas ; Waterworth, Dawn ; Weedon, Michael N. ; Wichmann, H.E. ; Widen, Elisabeth ; Williams, Frances M.K. ; Wilson, James F. ; Wright, Nicole C. ; Yerges-Armstrong, Laura M. ; Yu, Lei ; Zhang, Weihua ; Zhao, Jing Hua ; Zhou, Yanhua ; Nielson, Carrie M. ; Harris, Tamara B. ; Demissie, Serkalem ; Kiel, Douglas P. ; Ohlsson, Claes - \ 2019
American Journal of Clinical Nutrition 109 (2019)2. - ISSN 0002-9165 - p. 276 - 278.
body composition - body fat - meta-Analysis of genome-wide association studies - metabolic profile - skeletal muscle

Background Lean body mass (LM) plays an important role in mobility and metabolic function. We previously identified five loci associated with LM adjusted for fat mass in kilograms. Such an adjustment may reduce the power to identify genetic signals having an association with both lean mass and fat mass. Objectives To determine the impact of different fat mass adjustments on genetic architecture of LM and identify additional LM loci. Methods We performed genome-wide association analyses for whole-body LM (20 cohorts of European ancestry with n = 38,292) measured using dual-energy X-ray absorptiometry) or bioelectrical impedance analysis, adjusted for sex, age, age 2, and height with or without fat mass adjustments (Model 1 no fat adjustment; Model 2 adjustment for fat mass as a percentage of body mass; Model 3 adjustment for fat mass in kilograms). Results Seven single-nucleotide polymorphisms (SNPs) in separate loci, including one novel LM locus (TNRC6B), were successfully replicated in an additional 47,227 individuals from 29 cohorts. Based on the strengths of the associations in Model 1 vs Model 3, we divided the LM loci into those with an effect on both lean mass and fat mass in the same direction and refer to those as "sumo wrestler" loci (FTO and MC4R). In contrast, loci with an impact specifically on LM were termed "body builder" loci (VCAN and ADAMTSL3). Using existing available genome-wide association study databases, LM increasing alleles of SNPs in sumo wrestler loci were associated with an adverse metabolic profile, whereas LM increasing alleles of SNPs in "body builder" loci were associated with metabolic protection. Conclusions In conclusion, we identified one novel LM locus (TNRC6B). Our results suggest that a genetically determined increase in lean mass might exert either harmful or protective effects on metabolic traits, depending on its relation to fat mass.

Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer
Bien, Stephanie A. ; Su, Yu-Ru ; Conti, David V. ; Harrison, Tabitha A. ; Qu, Conghui ; Guo, Xingyi ; Lu, Yingchang ; Albanes, Demetrius ; Auer, Paul L. ; Banbury, Barbara L. ; Berndt, Sonja I. ; Bézieau, Stéphane ; Brenner, Hermann ; Buchanan, Daniel D. ; Caan, Bette J. ; Campbell, Peter T. ; Carlson, Christopher S. ; Chan, Andrew T. ; Chang-Claude, Jenny ; Chen, Sai ; Connolly, Charles M. ; Easton, Douglas F. ; Feskens, Edith J.M. ; Gallinger, Steven ; Giles, Graham G. ; Gunter, Marc J. ; Hampe, Jochen ; Huyghe, Jeroen R. ; Hoffmeister, Michael ; Hudson, Thomas J. ; Jacobs, Eric J. ; Jenkins, Mark A. ; Kampman, Ellen ; Kang, Hyun Min ; Kühn, Tilman ; Küry, Sébastien ; Lejbkowicz, Flavio ; Marchand, Loic Le; Milne, Roger L. ; Li, Christopher I. ; Lindblom, Annika ; Lindor, Noralane M. ; Martín, Vicente ; McNeil, Caroline E. ; Melas, Marilena ; Moreno, Victor ; Newcomb, Polly A. ; Offit, Kenneth ; Pharaoh, Paul D.P. ; Potter, John D. ; Qu, Chenxu ; Riboli, Elio ; Rennert, Gad ; Sala, Núria ; Schafmayer, Clemens ; Scacheri, Peter C. ; Schmit, Stephanie L. ; Severi, Gianluca ; Slattery, Martha L. ; Smith, Joshua D. ; Trichopoulou, Antonia ; Tumino, Rosario ; Ulrich, Cornelia M. ; Duijnhoven, Fränzel J.B. van; Guelpen, Bethany Van; Weinstein, Stephanie J. ; White, Emily ; Wolk, Alicja ; Woods, Michael O. ; Wu, Anna H. ; Abecasis, Goncalo R. ; Casey, Graham ; Nickerson, Deborah A. ; Gruber, Stephen B. ; Hsu, Li ; Zheng, Wei ; Peters, Ulrike - \ 2019
Human Genetics 138 (2019)4. - ISSN 0340-6717 - p. 307 - 326.
Genome-wide association studies have reported 56 independently associated colorectal cancer (CRC) risk variants, most of which are non-coding and believed to exert their effects by modulating gene expression. The computational method PrediXcan uses cis-regulatory variant predictors to impute expression and perform gene-level association tests in GWAS without directly measured transcriptomes. In this study, we used reference datasets from colon (n = 169) and whole blood (n = 922) transcriptomes to test CRC association with genetically determined expression levels in a genome-wide analysis of 12,186 cases and 14,718 controls. Three novel associations were discovered from colon transverse models at FDR ≤ 0.2 and further evaluated in an independent replication including 32,825 cases and 39,933 controls. After adjusting for multiple comparisons, we found statistically significant associations using colon transcriptome models with TRIM4 (discovery P = 2.2 × 10− 4, replication P = 0.01), and PYGL (discovery P = 2.3 × 10− 4, replication P = 6.7 × 10− 4). Interestingly, both genes encode proteins that influence redox homeostasis and are related to cellular metabolic reprogramming in tumors, implicating a novel CRC pathway linked to cell growth and proliferation. Defining CRC risk regions as one megabase up- and downstream of one of the 56 independent risk variants, we defined 44 non-overlapping CRC-risk regions. Among these risk regions, we identified genes associated with CRC (P < 0.05) in 34/44 CRC-risk regions. Importantly, CRC association was found for two genes in the previously reported 2q25 locus, CXCR1 and CXCR2, which are potential cancer therapeutic targets. These findings provide strong candidate genes to prioritize for subsequent laboratory follow-up of GWAS loci. This study is the first to implement PrediXcan in a large colorectal cancer study and findings highlight the utility of integrating transcriptome data in GWAS for discovery of, and biological insight into, risk loci.
Connecting the dots: Ethics, global citizenship and tourism
Hermann, Inge ; Weeden, Clare ; Peters, K.B.M. - \ 2019
Hospitality & Society 9 (2019)1. - ISSN 2042-7913 - p. 3 - 8.
Comparative analysis of repetitive sequences among species from the potato and the tomato clades
Gaiero Guadagna, P. ; Vaio, Magdalena ; Peters, S.A. ; Schranz, M.E. ; Jong, J.H.S.G.M. de; Speranza, P.R. - \ 2019
Annals of Botany 123 (2019)3. - ISSN 0305-7364 - p. 521 - 532.
Background and Aims
The genus Solanum includes important vegetable crops and their wild relatives. Introgression of their useful traits into elite cultivars requires effective recombination between hom(e)ologues, which is partially determined by genome sequence differentiation. In this study we compared the repetitive genome fractions of wild and cultivated species of the potato and tomato clades in a phylogenetic context.
Methods
Genome skimming followed by a clustering approach was used as implemented in the RepeatExplorer pipeline. Repeat classes were annotated and the sequences of their main domains were compared.
Key Results
Repeat abundance and genome size were correlated and the larger genomes of species in the tomato clade were found to contain a higher proportion of unclassified elements. Families and lineages of repetitive elements were largely conserved between the clades, but their relative proportions differed. The most abundant repeats were Ty3/Gypsy elements. Striking differences in abundance were found in the highly dynamic Ty3/Gypsy Chromoviruses and Ty1/Copia Tork elements. Within the potato clade, early branching Solanum cardiophyllum showed a divergent repeat profile. There were also contrasts between cultivated and wild potatoes, mostly due to satellite amplification in the cultivated species. Interspersed repeat profiles were very similar among potatoes. The repeat profile of Solanum etuberosum was more similar to that of the potato clade.
Conclusions
The repeat profiles in Solanum seem to be very similar despite genome differentiation at the level of collinearity. Removal of transposable elements by unequal recombination may have been responsible for structural rearrangements across the tomato clade. Sequence variability in the tomato clade is congruent with clade-specific amplification of repeats after its divergence from S. etuberosum and potatoes. The low differentiation among potato and its wild relatives at the level of interspersed repeats may explain the difficulty in discriminating their genomes by genomic in situ hybridization techniques.
An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea)
Evangelista, Dominic A. ; Wipfler, Benjamin ; Béthoux, Olivier ; Donath, Alexander ; Fujita, Mari ; Kohli, Manpreet K. ; Legendre, Frédéric ; Liu, Shanlin ; Machida, Ryuichiro ; Misof, Bernhard ; Peters, Ralph S. ; Podsiadlowski, Lars ; Rust, Jes ; Schuette, Kai ; Tollenaar, Ward ; Ware, Jessica L. ; Wappler, Torsten ; Zhou, Xin ; Meusemann, Karen ; Simon, Sabrina - \ 2019
Proceedings of the Royal Society. B: Biological Sciences 286 (2019)1895. - ISSN 0962-8452
Isoptera - Maternal care - Palaeontology - Sociality - Systematics - Transcriptomes

Phylogenetic relationships among subgroups of cockroaches and termites are still matters of debate. Their divergence times and major phenotypic transitions during evolution are also not yet settled. We addressed these points by combining the first nuclear phylogenomic study of termites and cockroaches with a thorough approach to divergence time analysis, identification of endosymbionts, and reconstruction of ancestral morphological traits and behaviour. Analyses of the phylogenetic relationships within Blattodea robustly confirm previously uncertain hypotheses such as the sister-group relationship between Blaberoidea and remaining Blattodea, and Lamproblatta being the closest relative to the social and wood-feeding Cryptocercus and termites. Consequently, we propose new names for various clades in Blattodea: Cryptocercus þ termites ¼ Tutricablattae; Lamproblattidae þ Tutricablattae ¼ Kittrickea; and Blattoidea þ Corydioidea ¼ Solumblattodea. Our inferred divergence times contradict previous studies by showing that most subgroups of Blattodea evolved in the Cretaceous, reducing the gap between molecular estimates of divergence times and the fossil record. On a phenotypic level, the blatto-dean ground-plan is for egg packages to be laid directly in a hole while other forms of oviposition, including ovovivipary and vivipary, arose later. Finally, other changes in egg care strategy may have allowed for the adaptation of nest building and other novelties.

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