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 FAIR Funder pilot programme to make it easy for funders to require and for grantees to produce FAIR Data
Wittenburg, Peter ; Sustkova, Hana Pergl ; Montesanti, Annalisa ; Bloemers, Margreet ; Waard, S.H. de; Musen, Mark A. ; Graybeal, John ; Hettne, Kristina M. ; Jacobsen, Annika ; Pergl, Robert ; Hooft, Rob W.W. ; Staiger, Christine ; Gelder, Celia W.G. van; Knijnenburg, Sebastiaan L. ; Arkel, A.C. van; Meerman, Bert ; Wilkinson, Mark D. ; Sansone, S.A. ; Rocca-Serra, Philippe ; McQuilton, Peter ; Gonzalez-Beltran, Alejandra N. ; Aben, G.J.C. ; Henning, P. ; Menezes Alencar, Maria Simone de; Ribeiro, C. ; Silva, C.R.L. ; Sayao, Luis ; Sales, Luana ; Veiga, Viviane ; Lima, Jefferson ; Dib, Simone ; Xavier dos Santos, Paula dos; Murtinho, R. ; Tendel, Jakob ; Schaap, B.F. ; Brouwer, P.M. ; Gavai, A.K. ; Bouzembrak, Yamine ; Marvin, Hans J.P. ; Mons, Albert ; Kuhn, Tobias ; Gambardella, A.A. ; Miranda Azevedo, Ricardo de; Muhonen, Vesa ; Naald, Mira van der; Smit, N.W. ; Buys, M.J. ; Bruin, Taco F. de; Schoots, Fieke ; Goodson, H.J.E. ; Rzepa, Henry S. ; Jeffery, Keith G. ; Shanahan, Hugh P. ; Axton, M. ; Tkachenko, Veniamin ; Deslattes Maya, Anne ; Meyers, Natalie ; Conlon, Michael ; Haak, Laurel L. ; Schultes, Erik - \ 2019
arXiv - 13 p.
There is a growing acknowledgement in the scientific community of the importance of making experimental data machine findable, accessible, interoperable, and reusable (FAIR). Recognizing that high quality metadata are essential to make datasets FAIR, members of the GO FAIR Initiative and the Research Data Alliance (RDA) have initiated a series of workshops to encourage the creation of Metadata for Machines (M4M), enabling any self-identified stakeholder to define and promote the reuse of standardized, comprehensive machine-actionable metadata. The funders of scientific research recognize that they have an important role to play in ensuring that experimental results are FAIR, and that high quality metadata and careful planning for FAIR data stewardship are central to these goals. We describe the outcome of a recent M4M workshop that has led to a pilot programme involving two national science funders, the Health Research Board of Ireland (HRB) and the Netherlands Organisation for Health Research and Development (ZonMW). These funding organizations will explore new technologies to define at the time that a request for proposals is issued the minimal set of machine-actionable metadata that they would like investigators to use to annotate their datasets, to enable investigators to create such metadata to help make their data FAIR, and to develop data-stewardship plans that ensure that experimental data will be managed appropriately abiding by the FAIR principles. The FAIR Funders design envisions a data-management workflow having seven essential stages, where solution providers are openly invited to participate. The initial pilot programme will launch using existing computer-based tools of those who attended the M4M Workshop.
Addendum: The FAIR Guiding Principles for scientific data management and stewardship
Wilkinson, Mark D. ; Dumontier, Michel ; Aalbersberg, Ijsbrand Jan ; Appleton, Gabrielle ; Axton, Myles ; Baak, Arie ; Blomberg, Niklas ; Boiten, Jan Willem ; Silva Santos, Luiz Bonino Da; Bourne, Philip E. ; Bouwman, Jildau ; Brookes, Anthony J. ; Clark, Tim ; Crosas, Mercè ; Dillo, Ingrid ; Dumon, Olivier ; Edmunds, Scott ; Evelo, Chris T. ; Finkers, Richard ; Gonzalez-Beltran, Alejandra ; Gray, Alasdair J.G. ; Groth, Paul ; Goble, Carole ; Grethe, Jeffrey S. ; Heringa, Jaap ; Hoen, Peter A.C. 't; Hooft, Rob ; Kuhn, Tobias ; Kok, Ruben ; Kok, Joost ; Lusher, Scott J. ; Martone, Maryann E. ; Mons, Albert ; Packer, Abel L. ; Persson, Bengt ; Rocca-Serra, Philippe ; Roos, Marco ; Schaik, Rene van; Sansone, Susanna Assunta ; Schultes, Erik ; Sengstag, Thierry ; Slater, Ted ; Strawn, George ; Swertz, Morris A. ; Thompson, Mark ; Lei, Johan van der; Mulligen, Erik van; Velterop, Jan ; Waagmeester, Andra ; Wittenburg, Peter ; Wolstencroft, Katherine ; Zhao, Jun ; Mons, Barend - \ 2019
Scientific Data 6 (2019). - ISSN 2052-4463

Benefits of Condensed Tannins in Forage Legumes Fed to Ruminants: Importance of Structure, Concentration, and Diet Composition
Mueller-Harvey, Irene ; Bee, Guiseppe ; Dohme-Meier, Frigga ; Hoste, Hervé ; Karonen, Maarit ; Kölliker, Roland ; Lüscher, Andreas ; Niderkorn, Vincent ; Pellikaan, W.F. ; Salminen, Juha-Pekka ; Skøt, L. ; Smith, Lydia M.J. ; Thamsborg, Stig M. ; Totterdell, Paul ; Wilkinson, Ian ; Williams, Andrew R. ; Azuhnwi, Blasius N. ; Baert, Nicolas ; Grosse Brinkhaus, Anja ; Copani, Giuseppe ; Desrues, Olivier ; Drake, Chris ; Engström, Marica ; Fryganas, Christos ; Girard, Marion ; Huyen, Nguyen Thi ; Kempf, Katharina ; Malisch, Carsten ; Ortiz, Marina Mora ; Quijada, Jessica N. ; Ramsay, Aina ; Ropiak, Honorate ; Waghorn, Garry C. - \ 2019
Crop Science 59 (2019)3. - ISSN 0011-183X - p. 861 - 885.
Condensed tannins (CTs) account for up to 20% of the dry matter in forage legumes used as ruminant feeds. Beneficial animal responses to CTs have included improved growth, milk and wool production, fertility, and reduced methane emissions and ammonia volatilization from dung or urine. Most important is the ability of such forages to combat the effects of gastrointestinal parasitic nematodes. Inconsistent animal responses to CTs were initially attributed to concentration in the diet, but recent research has highlighted the importance of their molecular structures, as well as concentration, and also the composition of the diet containing the CTs. The importance of CT structural traits cannot be underestimated. Interdisciplinary research is the key to unraveling the relationships between CT traits and bioactivities and will enable future on-farm exploitation of these natural plant compounds. Research is also needed to provide plant breeders with guidelines and screening tools to optimize CT traits, in both the forage and the whole diet. In addition, improvements are needed in the competitiveness and agronomic traits of CT-containing legumes and our understanding of options for their inclusion in ruminant diets. Farmers need varieties that are competitive in mixed swards and have predictable bioactivities. This review covers recent results from multidisciplinary research on sainfoin (Onobrychis Mill. spp.) and provides an overview of current developments with several other tanniniferous forages. Tannin chemistry is now being linked with agronomy, plant breeding, animal nutrition, and parasitology. The past decade has yielded considerable progress but also generated more questions—an enviable consequence of new knowledge!
CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software
Wilkinson, Toby J. ; Huws, Sharon A. ; Edwards, J.E. ; Kingston-Smith, Alison H. ; Siu-Ting, Karen ; Hughes, Martin ; Rubino, Francesco ; Friedersdorff, Maximillian ; Creevey, Christopher J. - \ 2018
rumen - microbiome - metataxonomics - metagenomics
Metataxonomic 16S rDNA based studies are a commonplace and useful tool in the research of the microbiome, but they do not provide the full investigative power of metagenomics and metatranscriptomics for revealing the functional potential of microbial communities. However, the use of metagenomic and metatranscriptomic technologies is hindered by high costs and skills barrier necessary to generate and interpret the data. To address this, a tool for Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was developed for inferring the functional potential of an observed microbiome profile, based on 16S data. This allows functional inferences to be made from metataxonomic 16S rDNA studies with little extra work or cost, but its accuracy relies on the availability of completely sequenced genomes of representative organisms from the community being investigated. The rumen microbiome is an example of a community traditionally underrepresented in genome and sequence databases, but recent efforts by projects such as the Global Rumen Census and Hungate 1000 have resulted in a wide sampling of 16S rDNA profiles and almost 500 fully sequenced microbial genomes from this environment. Using this information, we have developed “CowPI,” a focused version of the PICRUSt tool provided for use by the wider scientific community in the study of the rumen microbiome. We evaluated the accuracy of CowPI and PICRUSt using two 16S datasets from the rumen microbiome: one generated from rDNA and the other from rRNA where corresponding metagenomic and metatranscriptomic data was also available. We show that the functional profiles predicted by CowPI better match estimates for both the meta-genomic and transcriptomic datasets than PICRUSt, and capture the higher degree of genetic variation and larger pangenomes of rumen organisms. Nonetheless, whilst being closer in terms of predictive power for the rumen microbiome, there were differences when compared to both the metagenomic and metatranscriptome data and so we recommend, where possible, functional inferences from 16S data should not replace metagenomic and metatranscriptomic approaches. The tool can be accessed at http://www.cowpi.org and is provided to the wider scientific community for use in the study of the rumen microbiome
Using 'omic approaches to compare temporal bacterial colonization of lolium perenne, lotus corniculatus, and trifolium pratensein the Rumen
Elliott, Christopher L. ; Edwards, Joan E. ; Wilkinson, Toby J. ; Allison, Gordon G. ; McCaffrey, Kayleigh ; Scott, Mark B. ; Rees-Stevens, Pauline ; Kingston-Smith, Alison H. ; Huws, Sharon A. - \ 2018
Frontiers in Microbiology 9 (2018)SEP. - ISSN 1664-302X - 16 p.
16S rRNA gene - Birds foot trefoil - CowPI - FTIR - Microbiome - Perennial ryegrass - Red clover - Rumen

Understanding rumen plant-microbe interactions is central for development of novel methodologies allowing improvements in ruminant nutrient use efficiency. This study investigated rumen bacterial colonization of fresh plant material and changes in plant chemistry over a period of 24 h period using three different fresh forages: Lolium perenne (perennial ryegrass; PRG), Lotus corniculatus (bird's foot trefoil; BFT) and Trifolium pratense (red clover; RC). We show using 16S rRNA gene ion torrent sequencing that plant epiphytic populations present pre-incubation (0 h) were substantially different to those attached post incubations in the presence of rumen fluid on all forages. Thereafter primary and secondary colonization events were evident as defined by changes in relative abundances of attached bacteria and changes in plant chemistry, as assessed using Fourier transform infrared (FTIR) spectroscopy. For PRG colonization, primary colonization occurred for up to 4 h and secondary colonization from 4 h onward. The changes from primary to secondary colonization occurred significantly later with BFT and RC, with primary colonization being up to 6 h and secondary colonization post 6 h of incubation. Across all 3 forages the main colonizing bacteria present at all time points post-incubation were Prevotella, Pseudobutyrivibrio, Ruminococcus, Olsenella, Butyrivibrio, and Anaeroplasma (14.2, 5.4, 1.9, 2.7, 1.8, and 2.0% on average respectively), with Pseudobutyrivibrio and Anaeroplasma having a higher relative abundance during secondary colonization. Using CowPI, we predict differences between bacterial metabolic function during primary and secondary colonization. Specifically, our results infer an increase in carbohydrate metabolism in the bacteria attached during secondary colonization, irrespective of forage type. The CowPI data coupled with the FTIR plant chemistry data suggest that attached bacterial function is similar irrespective of forage type, with the main changes occurring between primary and secondary colonization. These data suggest that the sward composition of pasture may have major implications for the temporal availability of nutrients for animal.

CowPI: A rumen microbiome focussed version of the PICRUSt functional inference software
Wilkinson, Toby J. ; Huws, Sharon A. ; Edwards, Joan E. ; Kingston-Smith, Alison H. ; Siu-Ting, Karen ; Hughes, Martin ; Rubino, Francesco ; Friedersdorff, Maximillian ; Creevey, Christopher J. - \ 2018
Frontiers in Microbiology 9 (2018). - ISSN 1664-302X
16S amplicon - CowPI - Function - PICRUSt - Rumen

Metataxonomic 16S rDNA based studies are a commonplace and useful tool in the research of the microbiome, but they do not provide the full investigative power of metagenomics and metatranscriptomics for revealing the functional potential of microbial communities. However, the use of metagenomic and metatranscriptomic technologies is hindered by high costs and skills barrier necessary to generate and interpret the data. To address this, a tool for Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was developed for inferring the functional potential of an observed microbiome profile, based on 16S data. This allows functional inferences to be made from metataxonomic 16S rDNA studies with little extra work or cost, but its accuracy relies on the availability of completely sequenced genomes of representative organisms from the community being investigated. The rumen microbiome is an example of a community traditionally underrepresented in genome and sequence databases, but recent efforts by projects such as the Global Rumen Census and Hungate 1000 have resulted in a wide sampling of 16S rDNA profiles and almost 500 fully sequenced microbial genomes from this environment. Using this information, we have developed "CowPI," a focused version of the PICRUSt tool provided for use by the wider scientific community in the study of the rumen microbiome. We evaluated the accuracy of CowPI and PICRUSt using two 16S datasets from the rumen microbiome: one generated from rDNA and the other from rRNA where corresponding metagenomic and metatranscriptomic data was also available. We show that the functional profiles predicted by CowPI better match estimates for both the meta-genomic and transcriptomic datasets than PICRUSt, and capture the higher degree of genetic variation and larger pangenomes of rumen organisms. Nonetheless, whilst being closer in terms of predictive power for the rumen microbiome, there were differences when compared to both the metagenomic and metatranscriptome data and so we recommend, where possible, functional inferences from 16S data should not replace metagenomic and metatranscriptomic approaches. The tool can be accessed at http://www.cowpi.org and is provided to the wider scientific community for use in the study of the rumen microbiome.

Drought response in field grown potatoes and the interactions between canopy growth and yield
Aliche, Ernest B. ; Oortwijn, Marian ; Theeuwen, Tom P.J.M. ; Bachem, Christian W.B. ; Visser, Richard G.F. ; Linden, Gerard van der - \ 2018
Agricultural Water Management 206 (2018). - ISSN 0378-3774 - p. 20 - 30.
AUC - Irrigation - Maturity - Rainfall - Stress
Potato is an important food crop with high yields. However when exposed to drought it suffers major yield losses. Considering its global importance and the increasing incidence of drought due to climate change, research toward drought tolerance in potato remains imperative. We have studied a set of 103 commercial cultivars representing the genetic diversity in the European potato market. The cultivars were grown in different field locations in three subsequent years (2013–2015). Our aim was to understand how different field drought regimes affect canopy growth in potato, and how these effects translate to tuber yield. The field environmental conditions were monitored, and pictures of canopy ground cover during the growing season were taken. Canopy growth parameters were extracted by an iterative method using the beta sigmoid growth function to model canopy growth. At harvest, tuber yield was scored and tuber size was graded. The GGE (Genotype and Genotype-by-Environment) bi-plot and Finlay Wilkinson's Regression were used to investigate Genotype x Environment interactions. We observed that the timing of the drought occurrence differentially affected canopy growth and tuber yield. Under drought stress, fast attainment of exponential growth and maximum canopy cover had negative effects on tuber formation and tuber bulking. Growth rate, maximum canopy cover, and area under the canopy curve (photosynthetic capacity over the growth season) were more important for tuber bulking than they were for tuber formation under drought stress. Cultivars with high yield were identified as potential material for improvement to drought tolerance. These findings will contribute to the breeding for drought-tolerant potato amidst the threats of climate change.
The rumen microbiome : An underexplored resource for novel antimicrobial discovery
Oyama, Linda B. ; Girdwood, Susan E. ; Cookson, Alan R. ; Fernandez-Fuentes, Narcis ; Privé, Florence ; Vallin, Hannah E. ; Wilkinson, Toby J. ; Golyshin, Peter N. ; Golyshina, Olga V. ; Mikut, Ralf ; Hilpert, Kai ; Richards, Jennifer ; Wootton, Mandy ; Edwards, Joan E. ; Maresca, Marc ; Perrier, Josette ; Lundy, Fionnuala T. ; Luo, Yu ; Zhou, Mei ; Hess, Matthias ; Mantovani, Hilario C. ; Creevey, Christopher J. ; Huws, Sharon A. - \ 2017
npj Biofilms and Microbiomes 3 (2017)1. - ISSN 2055-5008
Antimicrobial peptides (AMPs) are promising drug candidates to target multi-drug resistant bacteria. The rumen microbiome presents an underexplored resource for the discovery of novel microbial enzymes and metabolites, including AMPs. Using functional screening and computational approaches, we identified 181 potentially novel AMPs from a rumen bacterial metagenome. Here, we show that three of the selected AMPs (Lynronne-1, Lynronne-2 and Lynronne-3) were effective against numerous bacterial pathogens, including methicillin-resistant Staphylococcus aureus (MRSA). No decrease in MRSA susceptibility was observed after 25 days of sub-lethal exposure to these AMPs. The AMPs bound preferentially to bacterial membrane lipids and induced membrane permeability leading to cytoplasmic leakage. Topical administration of Lynronne-1 (10% w/v) to a mouse model of MRSA wound infection elicited a significant reduction in bacterial counts, which was comparable to treatment with 2% mupirocin ointment. Our findings indicate that the rumen microbiome may provide viable alternative antimicrobials for future therapeutic application.
Cross continental increase in methane ebullition under climate change
Aben, Ralf C.H. ; Barros, Nathan ; Donk, Ellen Van; Frenken, Thijs ; Hilt, Sabine ; Kazanjian, Garabet ; Lamers, Leon P.M. ; Peeters, Edwin T.H.M. ; Roelofs, Jan G.M. ; Senerpont Domis, Lisette N. De; Stephan, Susanne ; Velthuis, Mandy ; De Waal, Dedmer B. Van; Wik, Martin ; Thornton, Brett F. ; Wilkinson, Jeremy ; Delsontro, Tonya ; Kosten, Sarian - \ 2017
Nature Communications 8 (2017)1. - ISSN 2041-1723
Methane (CH4) strongly contributes to observed global warming. As natural CH4 emissions mainly originate from wet ecosystems, it is important to unravel how climate change may affect these emissions. This is especially true for ebullition (bubble flux from sediments), a pathway that has long been underestimated but generally dominates emissions. Here we show a remarkably strong relationship between CH4 ebullition and temperature across a wide range of freshwater ecosystems on different continents using multi-seasonal CH4 ebullition data from the literature. As these temperature-ebullition relationships may have been affected by seasonal variation in organic matter availability, we also conducted a controlled year-round mesocosm experiment. Here 4 °C warming led to 51% higher total annual CH4 ebullition, while diffusion was not affected. Our combined findings suggest that global warming will strongly enhance freshwater CH4 emissions through a disproportional increase in ebullition (6-20% per 1 °C increase), contributing to global warming.
Soil protistology rebooted: 30 fundamental questions to start with
Geisen, Stefan ; Mitchell, Edward A.D. ; Wilkinson, David M. ; Adl, Sina ; Bonkowski, Michael ; Brown, Matthew W. ; Fiore-Donno, Anna Maria ; Heger, Thierry J. ; Jassey, Vincent E.J. ; Krashevska, Valentyna ; Lahr, Daniel J.G. ; Marcisz, Katarzyna ; Mulot, Matthieu ; Payne, Richard ; Singer, David ; Anderson, O.R. ; Charman, Dan J. ; Ekelund, Flemming ; Griffiths, Bryan S. ; Rønn, Regin ; Smirnov, Alexey ; Bass, David ; Belbahri, Lassaâd ; Berney, Cédric ; Blandenier, Quentin ; Chatzinotas, Antonis ; Clarholm, Marianne ; Dunthorn, Micah ; Feest, Alan ; Fernández, Leonardo D. ; Foissner, Wilhelm ; Fournier, Bertrand ; Gentekaki, Eleni ; Hájek, Michal ; Helder, Hans ; Jousset, Alexandre ; Koller, Robert ; Kumar, Santosh ; Terza, Antonietta La; Lamentowicz, Mariusz ; Mazei, Yuri ; Santos, Susana S. ; Seppey, Christophe V.W. ; Spiegel, Frederick W. ; Walochnik, Julia ; Winding, Anne ; Lara, Enrique - \ 2017
Soil Biology and Biochemistry 111 (2017). - ISSN 0038-0717 - p. 94 - 103.
Protists are the most diverse eukaryotes. These microbes are keystone organisms of soil ecosystems and
regulate essential processes of soil fertility such as nutrient cycling and plant growth. Despite this,
protists have received little scientific attention, especially compared to bacteria, fungi and nematodes in
soil studies. Recent methodological advances, particularly in molecular biology techniques, have made
the study of soil protists more accessible, and have created a resurgence of interest in soil protistology.
This ongoing revolution now enables comprehensive investigations of the structure and functioning of
soil protist communities, paving the way to a new era in soil biology. Instead of providing an exhaustive
review, we provide a synthesis of research gaps that should be prioritized in future studies of soil
protistology to guide this rapidly developing research area. Based on a synthesis of expert opinion we
propose 30 key questions covering a broad range of topics including evolution, phylogenetics, functional
ecology, macroecology, paleoecology, and methodologies. These questions highlight a diversity of topics
that will establish soil protistology as a hub discipline connecting different fundamental and applied
fields such as ecology, biogeography, evolution, plant-microbe interactions, agronomy, and conservation
biology. We are convinced that soil protistology has the potential to be one of the most exciting frontiers
in biology.
The science, policy and practice of nature-based solutions : An interdisciplinary perspective
Nesshöver, Carsten ; Assmuth, Timo ; Irvine, Katherine N. ; Rusch, Graciela M. ; Waylen, Kerry A. ; Delbaere, Ben ; Haase, Dagmar ; Jones-Walters, Lawrence ; Keune, Hans ; Kovacs, Eszter ; Krauze, Kinga ; Külvik, Mart ; Rey, Freddy ; Dijk, Jiska van; Vistad, Odd Inge ; Wilkinson, Mark E. ; Wittmer, Heidi - \ 2017
Science of the Total Environment 579 (2017). - ISSN 0048-9697 - p. 1215 - 1227.
Ecosystem management - Ecosystem services - Environmental governance - Sustainability
In this paper, we reflect on the implications for science, policy and practice of the recently introduced concept of Nature-Based Solutions (NBS), with a focus on the European context. First, we analyse NBS in relation to similar concepts, and reflect on its relationship to sustainability as an overarching framework. From this, we derive a set of questions to be addressed and propose a general framework for how these might be addressed in NBS projects by funders, researchers, policy-makers and practitioners. We conclude that: (1) NBS need to be developed and discussed in relation to existing concepts to clarify their added value;(2) When considering and implementing NBS, the ‘relabelling’ of related concepts and the misuse of the concept have to be prevented in order to avoid misunderstanding, duplication and unintended consequences;(3) NBS as currently framed by the European Commission provides an opportunity for: a) transdisciplinary research into the design and implementation of solutions based on nature; and b) overcoming a bias towards development alternatives with narrow perspectives that focus on short-term economic gains and effectiveness;(4) The strength of the NBS concept is its integrative, systemic approach which prevents it from becoming just another “green communication tool” that provides justification for a classical model of natural resource exploitation and management measures.To realise their full potential, NBS must be developed by including the experience of all relevant stakeholders such that ‘solutions’ contribute to achieving all dimensions of sustainability. As NBS are developed, we must also moderate the expectations placed on them since the precedent provided by other initiatives whose aim was to manage nature sustainably demonstrates that we should not expect NBS to be cheap and easy, at least not in the short-term.
Expansion of the molecular and morphological diversity of Acanthamoebidae (Centramoebida, Amoebozoa) and identification of a novel life cycle type within the group
Tice, A.K. ; Shadwick, Lora L. ; Fiore-Donno, Anna Maria ; Geisen, Stefan ; Kang, S. ; Schuler, Gabriel A. ; Spiegel, Frederick W. ; Wilkinson, Katherine A. ; Bonkowski, M. ; Dumack, K. ; Lahr, Daniel J.G. ; Voelcker, Eckhard ; Clauß, Steffen ; Zhang, Junling ; Brown, Matthew W. - \ 2016
Biology Direct 11 (2016). - ISSN 1745-6150
Acanthamoebidae is a “family” level amoebozoan group composed of the genera Acanthamoeba, Protacanthamoeba, and very recently Luapeleamoeba. This clade of amoebozoans has received considerable attention from the broader scientific community as Acanthamoeba spp. represent both model organisms and human pathogens. While the classical composition of the group (Acanthamoeba + Protacanthamoeba) has been well accepted due to the morphological and ultrastructural similarities of its members, the Acanthamoebidae has never been highly statistically supported in single gene phylogenetic reconstructions of Amoebozoa either by maximum likelihood (ML) or Bayesian analyses.
Potential and limitations of inferring ecosystem photosynthetic capacity from leaf functional traits
Musavi, Talie ; Migliavacca, Mirco ; Weg, Martine Janet van de; Kattge, Jens ; Wohlfahrt, Georg ; Bodegom, Peter M. van; Reichstein, Markus ; Bahn, Michael ; Carrara, Arnaud ; Domingues, Tomas F. ; Gavazzi, Michael ; Gianelle, Damiano ; Gimeno, Cristina ; Granier, André ; Gruening, Carsten ; Havránková, Kateřina ; Herbst, Mathias ; Hrynkiw, Charmaine ; Kalhori, Aram ; Kaminski, Thomas ; Klumpp, Katja ; Kolari, Pasi ; Longdoz, Bernard ; Minerbi, Stefano ; Montagnani, Leonardo ; Moors, Eddy ; Oechel, Walter C. ; Reich, Peter B. ; Rohatyn, Shani ; Rossi, Alessandra ; Rotenberg, Eyal ; Varlagin, Andrej ; Wilkinson, Matthew ; Wirth, Christian ; Mahecha, Miguel D. - \ 2016
Ecology and Evolution 6 (2016)20. - ISSN 2045-7758 - p. 7352 - 7366.
FLUXNET - Ecosystem functional property - Eddy covariance - Interannual variability - Photosynthetic capacity - Plant traits - Spatiotemporal variability - TRY database

The aim of this study was to systematically analyze the potential and limitations of using plant functional trait observations from global databases versus in situ data to improve our understanding of vegetation impacts on ecosystem functional properties (EFPs). Using ecosystem photosynthetic capacity as an example, we first provide an objective approach to derive robust EFP estimates from gross primary productivity (GPP) obtained from eddy covariance flux measurements. Second, we investigate the impact of synchronizing EFPs and plant functional traits in time and space to evaluate their relationships, and the extent to which we can benefit from global plant trait databases to explain the variability of ecosystem photosynthetic capacity. Finally, we identify a set of plant functional traits controlling ecosystem photosynthetic capacity at selected sites. Suitable estimates of the ecosystem photosynthetic capacity can be derived from light response curve of GPP responding to radiation (photosynthetically active radiation or absorbed photosynthetically active radiation). Although the effect of climate is minimized in these calculations, the estimates indicate substantial interannual variation of the photosynthetic capacity, even after removing site-years with confounding factors like disturbance such as fire events. The relationships between foliar nitrogen concentration and ecosystem photosynthetic capacity are tighter when both of the measurements are synchronized in space and time. When using multiple plant traits simultaneously as predictors for ecosystem photosynthetic capacity variation, the combination of leaf carbon to nitrogen ratio with leaf phosphorus content explains the variance of ecosystem photosynthetic capacity best (adjusted R2 = 0.55). Overall, this study provides an objective approach to identify links between leaf level traits and canopy level processes and highlights the relevance of the dynamic nature of ecosystems. Synchronizing measurements of eddy covariance fluxes and plant traits in time and space is shown to be highly relevant to better understand the importance of intra- and interspecific trait variation on ecosystem functioning.

Structural plasticity and in vivo activity of Cas1 from the type I-F CRISPR-Cas system
Wilkinson, Max E. ; Nakatani, Yoshio ; Staals, Raymond H.J. ; Kieper, Sebastian N. ; Opel-Reading, Helen K. ; McKenzie, Rebecca E. ; Fineran, Peter C. ; Krause, Kurt L. - \ 2016
Biochemical Journal 473 (2016)8. - ISSN 0264-6021 - p. 1063 - 1072.
Adaptation - Bacteriophages - Csy - Horizontal gene transfer - Plasmids - Protein structure

CRISPR-Cas systems are adaptive immune systems in prokaryotes that provide protection against viruses and other foreign DNA. In the adaptation stage, foreign DNA is integrated into CRISPR (clustered regularly interspaced short palindromic repeat) arrays as new spacers. These spacers are used in the interference stage to guide effector CRISPR associated (Cas) protein(s) to target complementary foreign invading DNA. Cas1 is the integrase enzyme that is central to the catalysis of spacer integration. There are many diverse types of CRISPR-Cas systems, including type I-F systems, which are typified by a unique Cas1-Cas2-3 adaptation complex. In the present study we characterize the Cas1 protein of the potato phytopathogen Pectobacterium atrosepticum, an important model organism for understanding spacer acquisition in type I-F CRISPR-Cas systems. We demonstrate by mutagenesis that Cas1 is essential for adaptation in vivo and requires a conserved aspartic acid residue. By X-ray crystallography, we show that although P. atrosepticum Cas1 adopts a fold conserved among other Cas1 proteins, it possesses remarkable asymmetry as a result of structural plasticity. In particular, we resolve for the first time a flexible, asymmetric loop that may be unique to type I-F Cas1 proteins, and we discuss the implications of these structural features for DNA binding and enzymatic activity.

The FAIR Guiding Principles for scientific data management and stewardship : Comment
Wilkinson, Mark D. ; Dumontier, Michel ; Aalbersberg, Ijsbrand Jan ; Appleton, Gabrielle ; Axton, Myles ; Baak, Arie ; Blomberg, Niklas ; Boiten, Jan Willem ; Silva Santos, Luiz Bonino Da; Bourne, Philip E. ; Bouwman, Jildau ; Brookes, Anthony J. ; Clark, Tim ; Crosas, Mercè ; Dillo, Ingrid ; Dumon, Olivier ; Edmunds, Scott ; Evelo, Chris T. ; Finkers, Richard ; Gonzalez-Beltran, Alejandra ; Gray, Alasdair J.G. ; Groth, Paul ; Goble, Carole ; Grethe, Jeffrey S. ; Heringa, Jaap ; Hoen, Peter A.C. 't; Hooft, Rob ; Kuhn, Tobias ; Kok, Ruben ; Kok, Joost ; Lusher, Scott J. ; Martone, Maryann E. ; Mons, Albert ; Packer, Abel L. ; Persson, Bengt ; Rocca-Serra, Philippe ; Roos, Marco ; Schaik, Rene van; Sansone, Susanna Assunta ; Schultes, Erik ; Sengstag, Thierry ; Slater, Ted ; Strawn, George ; Swertz, Morris A. ; Thompson, Mark ; Lei, Johan van der; Mulligen, Erik van; Velterop, Jan ; Waagmeester, Andra ; Wittenburg, Peter ; Wolstencroft, Katherine ; Zhao, Jun ; Mons, Barend - \ 2016
Scientific Data 3 (2016). - ISSN 2052-4463

There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders-representing academia, industry, funding agencies, and scholarly publishers-have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.

Minimum Information about a Biosynthetic Gene cluster
Medema, M.H. ; Kottmann, Renzo ; Yilmaz, Pelin ; Cummings, Matthew ; Biggins, J.B. ; Blin, Kai ; Bruijn, Irene De; Chooi, Yit Heng ; Claesen, Jan ; Coates, R.C. ; Cruz-Morales, Pablo ; Duddela, Srikanth ; Düsterhus, Stephanie ; Edwards, Daniel J. ; Fewer, David P. ; Garg, Neha ; Geiger, Christoph ; Gomez-Escribano, Juan Pablo ; Greule, Anja ; Hadjithomas, Michalis ; Haines, Anthony S. ; Helfrich, Eric J.N. ; Hillwig, Matthew L. ; Ishida, Keishi ; Jones, Adam C. ; Jones, Carla S. ; Jungmann, Katrin ; Kegler, Carsten ; Kim, Hyun Uk ; Kötter, Peter ; Krug, Daniel ; Masschelein, Joleen ; Melnik, Alexey V. ; Mantovani, Simone M. ; Monroe, Emily A. ; Moore, Marcus ; Moss, Nathan ; Nützmann, Hans Wilhelm ; Pan, Guohui ; Pati, Amrita ; Petras, Daniel ; Reen, F.J. ; Rosconi, Federico ; Rui, Zhe ; Tian, Zhenhua ; Tobias, Nicholas J. ; Tsunematsu, Yuta ; Wiemann, Philipp ; Wyckoff, Elizabeth ; Yan, Xiaohui ; Yim, Grace ; Yu, Fengan ; Xie, Yunchang ; Aigle, Bertrand ; Apel, Alexander K. ; Balibar, Carl J. ; Balskus, Emily P. ; Barona-Gómez, Francisco ; Bechthold, Andreas ; Bode, Helge B. ; Borriss, Rainer ; Brady, Sean F. ; Brakhage, Axel A. ; Caffrey, Patrick ; Cheng, Yi Qiang ; Clardy, Jon ; Cox, Russell J. ; Mot, René De; Donadio, Stefano ; Donia, Mohamed S. ; Donk, Wilfred A. Van Der; Dorrestein, Pieter C. ; Doyle, Sean ; Driessen, Arnold J.M. ; Ehling-Schulz, Monika ; Entian, Karl Dieter ; Fischbach, Michael A. ; Gerwick, Lena ; Gerwick, William H. ; Gross, Harald ; Gust, Bertolt ; Hertweck, Christian ; Höfte, Monica ; Jensen, Susan E. ; Ju, Jianhua ; Katz, Leonard ; Kaysser, Leonard ; Klassen, Jonathan L. ; Keller, Nancy P. ; Kormanec, Jan ; Kuipers, Oscar P. ; Kuzuyama, Tomohisa ; Kyrpides, Nikos C. ; Kwon, Hyung Jin ; Lautru, Sylvie ; Lavigne, Rob ; Lee, Chia Y. ; Linquan, Bai ; Liu, Xinyu ; Liu, Wen ; Luzhetskyy, Andriy ; Mahmud, Taifo ; Mast, Yvonne ; Méndez, Carmen ; Metsä-Ketelä, Mikko ; Micklefield, Jason ; Mitchell, Douglas A. ; Moore, Bradley S. ; Moreira, Leonilde M. ; Müller, Rolf ; Neilan, Brett A. ; Nett, Markus ; Nielsen, Jens ; O'Gara, Fergal ; Oikawa, Hideaki ; Osbourn, Anne ; Osburne, Marcia S. ; Ostash, Bohdan ; Payne, Shelley M. ; Pernodet, Jean Luc ; Petricek, Miroslav ; Piel, Jörn ; Ploux, Olivier ; Raaijmakers, Jos M. ; Salas, José A. ; Schmitt, Esther K. ; Scott, Barry ; Seipke, Ryan F. ; Shen, Ben ; Sherman, David H. ; Sivonen, Kaarina ; Smanski, Michael J. ; Sosio, Margherita ; Stegmann, Evi ; Süssmuth, Roderich D. ; Tahlan, Kapil ; Thomas, Christopher M. ; Tang, Yi ; Truman, Andrew W. ; Viaud, Muriel ; Walton, Jonathan D. ; Walsh, Christopher T. ; Weber, Tilmann ; Wezel, Gilles P. Van; Wilkinson, Barrie ; Willey, Joanne M. ; Wohlleben, Wolfgang ; Wright, Gerard D. ; Ziemert, Nadine ; Zhang, Changsheng ; Zotchev, Sergey B. ; Breitling, Rainer ; Takano, Eriko ; Glöckner, Frank Oliver - \ 2015
Nature Chemical Biology 11 (2015)9. - ISSN 1552-4450 - p. 625 - 631.

A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughout the literature, making it difficult to exploit. To facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters, we propose the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard.

Bioactive tannins in forage legumes: Myths, Ignorance and Aspirations
Mueller-Harvey, I. ; Ramsey, Aina ; Fryganas, Christos ; Ropiak, Honorate ; Drake, Chris ; Ortiz, Marina Mora ; Smith, Lydia M.J. ; Skot, L. ; Malisch, Carsten ; Luescher, Andreas ; Kempf, Katharina ; Kolliker, R. ; Desrues, Olivier ; Williams, Andrew R. ; Thamsborg, S.M. ; Azuhnwi, Blasius N. ; Quijada, J.N. ; Hoste, H. ; Girard, M. ; Grosse Brinkhaus, A. ; Dohme-Meier, F. ; Bee, G. ; Nguyen, T.H. ; Pellikaan, W.F. ; Copani, Giuseppe ; Niderkorn, Vincent ; Engstrom, Marica ; Salminen, J.P. ; Wilkinson, Ian ; Totterdell, Paul ; Waghorn, G.C. - \ 2015
Tannin-containing legumes have attracted much interest due to their animal health and nutritional benefits. Although several tannins are anti-nutritional, a few can generate valuable benefits for controlling parasitic nematodes that are resistant to anthelmintic drugs, for improving protein utilization by ruminants and fatty acid profiles in meat and milk products and for reducing greenhouse gases. A 5% dietary maximum limit of tannins has been suggested, but information on structure-activity relationships are essential in order to fully exploit the potential of these natural plant compounds. Breeders also require guidelines and screening tools for optimal tannin compositions, and farmers require tannin-containing forages that provide consistent results.

Plants vary in tannin contents and composition depending on species, variety and growing conditions. Recent research in Europe (‘LegumePlus' and other projects) has focused on new tools for analyzing soluble and insoluble tannins in plants, silages and digesta. This involved isolating different types of tannin standards from a wide range of different plants and thiolysis to assess their purity and composition. We also developed new UPLC-MS/MS, NIR- and NMR-analysis methods and tested tannin-protein interactions. Agronomists and plant breeders assembled germplasm collections, identified sainfoin-specific markers, and strategies for weed control. Ruminant nutritionists studied in vitro and in vivo fermentations, N-balances and the quality of meat and milk products. Parasitologists explored the anti-parasitic properties using a wide range of different tannin types.

The presentation will summarize current knowledge and conclude with a wishlist for ‘ideal' tannin-containing forages. It will emphasize that robust and stable tannin concentrations and compositions are required in addition to high yield, good weed suppression and resistance to climatic stress.
New ways of proving knowledge to tackle food and nutrition security: what should the EU do? : Expo 2015 EU Scientific Steering Committe: recommendations
Fischler, F. ; Wilkinson, D. ; Benton, T.G. ; Daniel, Hannelore ; Darcy-Vrillon, B. ; Hedlund, K. ; Heffernan, P. ; Kok, E.J. ; Jakubczyk, E. ; Sorlini, C. ; Swinnen, J. ; Braun, J. von; Ash, K. ; Guerreri, F. ; Buckwell, A. ; Frewen, M. ; Karlsson, M. - \ 2015
Milaan, Italy : EU - Scientific Steering Committee - ISBN 9789279534768 - 64 p.
The role of research in global food and nutrition security - Discussion paper
Fischler, F. ; Wilkinson, D. ; Benton, T. ; Daniel, H. ; Darcy-Vrillon, B. ; Hedlund, K. ; Heffernan, P. ; Kok, E.J. ; Saarela, M. ; Jakubczyk, E. ; Sorlini, C. ; Swinnen, J. ; Braun, J. von; Ash, K. ; Rojas Briales, E. ; Buckwell, A. ; Frewen, M. ; Karlsson, M. - \ 2015
Milaan, Italy : EU - Scientific Steering Committee (Discussion paper / Expo 2015 EU Scientific Steering Committee ) - ISBN 9789279458309 - 32
voedselzekerheid - voeding en gezondheid - europese unie - innovaties - duurzaamheid (sustainability) - food security - nutrition and health - european union - innovations - sustainability
The present discussion document gives an overview of where European research can add the most value in relation to tackling food and nutrition security challenges and points to areas where we can expand our research potential. Moreover, it highlights the need to develop a governance structure that will allow sharing of best practices and facilitate the transfer of knowledge and innovation to feed the planet sustainably. It should stimulate a global discussion with stakeholders and the general public, ultimately shaping a legacy for Expo 2015.
Challenges to scenario-guided adaptive action on food security under climate change
Vervoort, J.M. ; Thornton, P.K. ; Kristjansson, P. ; Foerch, W. ; Ericksen, P.J. ; Kok, K. ; Ingram, J.S. ; Herrero, M. ; Palazzo, A. ; Helfgott, A.E.S. ; Wilkinson, A. ; Havlik, P. ; Mason-D’Croz, D. ; Jost, C. - \ 2014
Global environmental change : human and policy dimensions 28 (2014). - ISSN 0959-3780 - p. 383 - 394.
sustainable development - uncertainty - agriculture - systems - adaptation - knowledge - science - scales
This paper examines the development and use of scenarios as an approach to guide action in multi-level, multi-actor adaptation contexts such as food security under climate change. Three challenges arehighlighted: (1) ensuring the appropriate scope for action; (2) moving beyond intervention-based decision guidance; and (3) developing long-term shared capacity for strategic planning. To overcome these challenges we have applied explorative scenarios and normative back-casting with stakeholders from different sectors at the regional level in East Africa. We then applied lessons about appropriate scope, enabling adaptation pathways, and developing strategic planning capacity to scenarios processes in multiple global regions. Scenarios were created to have a broad enough scope to be relevant to diverse actors, and then adapted by different actor groups to ensure their salience in specific decision contexts. The initial strategy for using the scenarios by bringing a range of actors together to explore new collaborative proposals had limitations as well as strengths versus the application of scenarios for specific actor groups and existing decision pathways. Scenarios development and use transitioned from an intervention-based process to an embedded process characterized by continuous engagement. Feasibility and long-term sustainability could be ensured by having decision makers own the process and focusing on developing strategic planning capacity within their home organizations.
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