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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Top-down NOx emissions of european cities based on the downwind plume of modelled and space-borne tropospheric NO2 columns
Verstraeten, Willem W. ; Boersma, Klaas Folkert ; Douros, John ; Williams, Jason E. ; Eskes, Henk ; Liu, Fei ; Beirle, Steffen ; Delcloo, Andy - \ 2018
Sensors 18 (2018)9. - ISSN 1424-8220
LOTOS-EUROS CTM - OMI data - Surface NO emissions - Tropospheric NO column

Top-down estimates of surface NOX emissions were derived for 23 European cities based on the downwind plume decay of tropospheric nitrogen dioxide (NO2) columns from the LOTOS-EUROS (Long Term Ozone Simulation-European Ozone Simulation) chemistry transport model (CTM) and from Ozone Monitoring Instrument (OMI) satellite retrievals, averaged for the summertime period (April–September) during 2013. Here we show that the top-down NOX emissions derived from LOTOS-EUROS for European urban areas agree well with the bottom-up NOX emissions from the MACC-III inventory data (R2 = 0.88) driving the CTM demonstrating the potential of this method. OMI top-down NOX emissions over the 23 European cities are generally lower compared with the MACC-III emissions and their correlation is slightly lower (R2 = 0.79). The uncertainty on the derived NO2 lifetimes and NOX emissions are on average ~55% for OMI and ~63% for LOTOS-EUROS data. The downwind NO2 plume method applied on both LOTOS-EUROS and OMI tropospheric NO2 columns allows to estimate NOX emissions from urban areas, demonstrating that this is a useful method for real-time updates of urban NOX emissions with reasonable accuracy.

Designing Vulnerable Zones of Nitrogen and Phosphorus Transfers to Control Water Pollution in China
Bai, Zhaohai ; Lu, Jie ; Zhao, Hao ; Velthof, Gerard L. ; Oenema, Oene ; Chadwick, Dave ; Williams, John R. ; Jin, Shuqin ; Liu, Hongbin ; Wang, Mengru ; Strokal, Maryna ; Kroeze, Carolien ; Hu, Chunsheng ; Ma, Lin - \ 2018
Environmental Science and Technology 52 (2018)16. - ISSN 0013-936X - p. 8987 - 8988.
Arabidopsis phospholipase C3 is involved in lateral root initiation and ABA responses in seed germination and stomatal closure
Zhang, Qianqian ; Wijk, Ringo van; Shahbaz, Muhammad ; Roels, Wendy ; Schooten, Bas Van; Vermeer, Joop E.M. ; Zarza, Xavier ; Guardia, Aisha ; Scuffi, Denise ; García-Mata, Carlos ; Laha, Debabrata ; Williams, Phoebe ; Willems, Leo A.J. ; Ligterink, Wilco ; Hoffmann-Benning, Susanne ; Gillaspy, Glenda ; Schaaf, Gabriel ; Haring, Michel A. ; Laxalt, Ana M. ; Munnik, Teun - \ 2018
Plant and Cell Physiology 59 (2018)3. - ISSN 0032-0781 - p. 469 - 486.
ABA - Arabidopsis - Drought tolerance - Lateral root formation - Seed germination - Stomatal closure

Phospholipase C (PLC) is well known for its role in animal signaling, where it generates the second messengers, inositol 1,4,5-trisphosphate (IP3) and diacylglycerol (DAG), by hydrolyzing the minor phospholipid, phosphatidylinositol 4,5-bisphosphate (PIP2), upon receptor stimulation. In plants, PLC's role is still unclear, especially because the primary targets of both second messengers are lacking, i.e. the ligand-gated Ca2+ channel and protein kinase C, and because PIP2 levels are extremely low. Nonetheless, the Arabidopsis genome encodes nine PLCs. We used a reversed-genetic approach to explore PLC's function in Arabidopsis, and report here that PLC3 is required for proper root development, seed germination and stomatal opening. Two independent knock-down mutants, plc3-2 and plc3-3, were found to exhibit reduced lateral root densities by 10-20%. Mutant seeds germinated more slowly but were less sensitive to ABA to prevent germination. Guard cells of plc3 were also compromised in ABA-dependent stomatal closure. Promoter-b-glucuronidase (GUS) analyses confirmed PLC3 expression in guard cells and germinating seeds, and revealed that the majority is expressed in vascular tissue, most probably phloem companion cells, in roots, leaves and flowers. In vivo 32Pi labeling revealed that ABA stimulated the formation of PIP2 in germinating seeds and guard cell-enriched leaf peels, which was significantly reduced in plc3 mutants. Overexpression of PLC3 had no effect on root system architecture or seed germination, but increased the plant's tolerance to drought. Our results provide genetic evidence for PLC's involvement in plant development and ABA signaling, and confirm earlier observations that overexpression increases drought tolerance. Potential molecular mechanisms for the above observations are discussed.

Problemshed or watershed? Participatory modeling towards IWRM in North Ghana
Daré, Williams ; Venot, Jean Philippe ; Page, Christophe Le ; Aduna, Aaron - \ 2018
Water 10 (2018)6. - ISSN 2073-4441
Agent-based model - Companion modeling - Role-playing game - Sub-Saharan Africa - Water resources

This paper is a reflexive analysis of a three-year participatory water research project conducted in the Upper East Region (UER) of Ghana, whose explicit objective was to initiate a multi-level dialogue to support the national Integrated Water Resources Management (IWRM) policy framework. The transdisciplinary team adopted the Companion Modeling approach (ComMod), using role-playing games and a computerized agent-based model to support the identification of a problemshed centered on issues of river bank cultivation, erosion, and flooding, and initiate a multi-level dialogue on ways that this problemshed could be tackled. On the basis of this experience, we identify three key criteria for transdisciplinary research to support innovative water governance: (1) the iterative adaptation of tools and facilitation techniques based on feedback from participants; (2) a common understanding of the objectives pursued and the approach used among researchers, who need to explicit their posture, and crucially; (3) the co-identification of a problemshed that diverse stakeholders are interested in tackling. Finally, we argue that the context in which research is funded and conducted in the development sector constitutes a challenge for researchers to be "participants like any other" in the projects they coordinate, which constitutes a barrier to true transdisciplinarity.

Ten essentials for action-oriented and second order energy transitions, transformations and climate change research
Fazey, Ioan ; Schäpke, Niko ; Caniglia, Guido ; Patterson, James ; Hultman, Johan ; Mierlo, Barbara Van; Säwe, Filippa ; Wiek, Arnim ; Wittmayer, Julia ; Aldunce, Paulina ; Waer, Husam Al; Battacharya, Nandini ; Bradbury, Hilary ; Carmen, Esther ; Colvin, John ; Cvitanovic, Christopher ; D’Souza, Marcella ; Gopel, Maja ; Goldstein, Bruce ; Hämäläinen, Timo ; Harper, Gavin ; Henfry, Tom ; Hodgson, Anthony ; Howden, Mark S. ; Kerr, Andy ; Klaes, Matthias ; Lyon, Christopher ; Midgley, Gerald ; Moser, Susanne ; Mukherjee, Nandan ; Müller, Karl ; O’brien, Karen ; O’Connell, Deborah A. ; Olsson, Per ; Page, Glenn ; Reed, Mark S. ; Searle, Beverley ; Silvestri, Giorgia ; Spaiser, Viktoria ; Strasser, Tim ; Tschakert, Petra ; Uribe-Calvo, Natalia ; Waddell, Steve ; Rao-Williams, Jennifer ; Wise, Russel ; Wolstenholme, Ruth ; Woods, Mel ; Wyborn, Carina - \ 2018
Energy Research & Social Science 40 (2018). - ISSN 2214-6296 - p. 54 - 70.
The most critical question for climate research is no longer about the problem, but about how to facilitate the transformative changes necessary to avoid catastrophic climate-induced change. Addressing this question, however, will require massive upscaling of research that can rapidly enhance learning about transformations. Ten essentials for guiding action-oriented transformation and energy research are therefore presented, framed in relation to second-order science. They include: (1) Focus on transformations to low-carbon, resilient living; (2) Focus on solution processes; (3) Focus on ‘how to’ practical knowledge; (4) Approach research as occurring from within the system being intervened; (5) Work with normative aspects; (6) Seek to transcend current thinking; (7) Take a multi-faceted approach to understand and shape change; (8) Acknowledge the value of alternative roles of researchers; (9) Encourage second-order experimentation; and (10) Be reflexive. Joint application of the essentials would create highly adaptive, reflexive, collaborative and impact-oriented research able to enhance capacity to respond to the climate challenge. At present, however, the practice of such approaches is limited and constrained by dominance of other approaches. For wider transformations to low carbon living and energy systems to occur, transformations will therefore also be needed in the way in which knowledge is produced and used.
Reviewing research priorities in weed ecology, evolution and management: a horizon scan
Neve, P. ; Barney, J.N. ; Buckley, Y. ; Cousens, R.D. ; Graham, S. ; Jordan, N.R. ; Lawton-Rauh, A. ; Liebman, M. ; Mesgaran, M.B. ; Shaw, J. ; Storkey, J. ; Baraibar, B. ; Baucom, R.S. ; Chalak, M. ; Childs, D.Z. ; Christensen, S. ; Eizenberg, H. ; Fernández-Quintanilla, C. ; French, K. ; Harsch, M. ; Heijting, S. ; Harrison, L. ; Loddo, D. ; Macel, M. ; Maczey, N. ; Merotto, A. ; Mortensen, D. ; Necajeva, J. ; Peltzer, D.A. ; Recasens, J. ; Renton, M. ; Riemens, M. ; Sønderskov, M. ; Williams, M. ; Rew, Lisa - \ 2018
Weed Research 58 (2018)4. - ISSN 0043-1737 - p. 250 - 258.
Weedy plants pose a major threat to food security, biodiversity, ecosystem services and consequently to human health and wellbeing. However, many currently used weed management approaches are increasingly unsustainable. To address this knowledge and practice gap, in June 2014, 35 weed and invasion ecologists, weed scientists, evolutionary biologists and social scientists convened a workshop to explore current and future perspectives and approaches in weed ecology and management. A horizon scanning exercise ranked a list of 124 pre‐submitted questions to identify a priority list of 30 questions. These questions are discussed under seven themed headings that represent areas for renewed and emerging focus for the disciplines of weed research and practice. The themed areas considered the need for transdisciplinarity, increased adoption of integrated weed management and agroecological approaches, better understanding of weed evolution, climate change, weed invasiveness and finally, disciplinary challenges for weed science. Almost all the challenges identified rested on the need for continued efforts to diversify and integrate agroecological, socio‐economic and technological approaches in weed management. These challenges are not newly conceived, though their continued prominence as research priorities highlights an ongoing intransigence that must be addressed through a more system‐oriented and transdisciplinary research agenda that seeks an embedded integration of public and private research approaches. This horizon scanning exercise thus set out the building blocks needed for future weed management research and practice; however, the challenge ahead is to identify effective ways in which sufficient research and implementation efforts can be directed towards these needs.
Monoterpene chemical speciation in a tropical rainforest : variation with season, height, and time of dayat the Amazon Tall Tower Observatory (ATTO)
Maria Yanez-Serrano, Ana ; Christine Nölscher, Anke ; Bourtsoukidis, Efstratios ; Gomes Alves, Eliane ; Ganzeveld, Laurens ; Bonn, Boris ; Wolff, Stefan ; Sa, Marta ; Yamasoe, Marcia ; Williams, Jonathan ; Andreae, Meinrat O. - \ 2018
Atmospheric Chemistry and Physics 18 (2018)5. - ISSN 1680-7316 - p. 3403 - 3418.
Speciated monoterpene measurements in rainforest air are scarce, but they are essential for understanding the contribution of these compounds to the overall reactivity of volatile organic compound (VOC) emissions towards the main atmospheric oxidants, such as hydroxyl radicals (OH), ozone (O3) and nitrate radicals (NO3). In this study, we present the chemical speciation of gas-phase monoterpenes measured in the tropical rainforest at the Amazon Tall Tower Observatory (ATTO, Amazonas, Brazil). Samples of VOCs were collected by two automated sampling systems positioned on a tower at 12 and 24ĝ€-m height and analysed using gas chromatography-flame ionization detection. The samples were collected in October 2015, representing the dry season, and compared with previous wet and dry season studies at the site. In addition, vertical profile measurements (at 12 and 24ĝ€-m) of total monoterpene mixing ratios were made using proton-transfer-reaction mass spectrometry. The results showed a distinctly different chemical speciation between day and night. For instance, α-pinene was more abundant during the day, whereas limonene was more abundant at night. Reactivity calculations showed that higher abundance does not generally imply higher reactivity. Furthermore, inter- and intra-annual results demonstrate similar chemodiversity during the dry seasons analysed. Simulations with a canopy exchange modelling system show simulated monoterpene mixing ratios that compare relatively well with the observed mixing ratios but also indicate the necessity of more experiments to enhance our understanding of in-canopy sinks of these compounds.
Phylogenetic classification of the world's tropical forests
Slik, J.W.F. ; Franklin, Janet ; Arroyo-Rodríguez, Víctor ; Field, Richard ; Aguilar, Salomon ; Aguirre, Nikolay ; Ahumada, Jorge ; Aiba, Shin Ichiro ; Alves, Luciana F. ; Anitha, K. ; Avella, Andres ; Mora, Francisco ; Aymard, Gerardo A.C. ; Báez, Selene ; Balvanera, Patricia ; Bastian, Meredith L. ; Bastin, Jean François ; Bellingham, Peter J. ; Berg, Eduardo Van Den; Conceição Bispo, Polyanna Da; Boeckx, Pascal ; Boehning-Gaese, Katrin ; Bongers, Frans ; Boyle, Brad ; Brambach, Fabian ; Brearley, Francis Q. ; Brown, Sandra ; Chai, Shauna Lee ; Chazdon, Robin L. ; Chen, Shengbin ; Chhang, Phourin ; Chuyong, George ; Ewango, Corneille ; Coronado, Indiana M. ; Cristóbal-Azkarate, Jurgi ; Culmsee, Heike ; Damas, Kipiro ; Dattaraja, H.S. ; Davidar, Priya ; DeWalt, Saara J. ; Din, Hazimah ; Drake, Donald R. ; Duque, Alvaro ; Durigan, Giselda ; Eichhorn, Karl ; Eler, Eduardo Schmidt ; Enoki, Tsutomu ; Ensslin, Andreas ; Fandohan, Adandé Belarmain ; Farwig, Nina ; Feeley, Kenneth J. ; Fischer, Markus ; Forshed, Olle ; Garcia, Queila Souza ; Garkoti, Satish Chandra ; Gillespie, Thomas W. ; Gillet, Jean Francois ; Gonmadje, Christelle ; Granzow-De La Cerda, Iñigo ; Griffith, Daniel M. ; Grogan, James ; Hakeem, Khalid Rehman ; Harris, David J. ; Harrison, Rhett D. ; Hector, Andy ; Hemp, Andreas ; Homeier, Jürgen ; Hussain, M.S. ; Ibarra-Manríquez, Guillermo ; Hanum, I.F. ; Imai, Nobuo ; Jansen, Patrick A. ; Joly, Carlos Alfredo ; Joseph, Shijo ; Kartawinata, Kuswata ; Kearsley, Elizabeth ; Kelly, Daniel L. ; Kessler, Michael ; Killeen, Timothy J. ; Kooyman, Robert M. ; Laumonier, Yves ; Laurance, Susan G. ; Laurance, William F. ; Lawes, Michael J. ; Letcher, Susan G. ; Lindsell, Jeremy ; Lovett, Jon ; Lozada, Jose ; Lu, Xinghui ; Lykke, Anne Mette ; Mahmud, Khairil Bin; Mahayani, Ni Putu Diana ; Mansor, Asyraf ; Marshall, Andrew R. ; Martin, Emanuel H. ; Matos, Darley Calderado Leal ; Meave, Jorge A. ; Melo, Felipe P.L. ; Mendoza, Zhofre Huberto Aguirre ; Metali, Faizah ; Medjibe, Vincent P. ; Metzger, Jean Paul ; Metzker, Thiago ; Mohandass, D. ; Munguía-Rosas, Miguel A. ; Muñoz, Rodrigo ; Nurtjahy, Eddy ; Oliveira, Eddie Lenza De; Onrizal, ; Parolin, Pia ; Parren, Marc ; Parthasarathy, N. ; Paudel, Ekananda ; Perez, Rolando ; Pérez-García, Eduardo A. ; Pommer, Ulf ; Poorter, Lourens ; Qi, Lan ; Piedade, Maria Teresa F. ; Pinto, José Roberto Rodrigues ; Poulsen, Axel Dalberg ; Poulsen, John R. ; Powers, Jennifer S. ; Prasad, Rama Chandra ; Puyravaud, Jean Philippe ; Rangel, Orlando ; Reitsma, Jan ; Rocha, Diogo S.B. ; Rolim, Samir ; Rovero, Francesco ; Rozak, Andes ; Ruokolainen, Kalle ; Rutishauser, Ervan ; Rutten, Gemma ; Mohd Said, Mohd Nizam ; Saiter, Felipe Z. ; Saner, Philippe ; Santos, Braulio ; Santos, João Roberto Dos; Sarker, Swapan Kumar ; Schmitt, Christine B. ; Schoengart, Jochen ; Schulze, Mark ; Sheil, Douglas ; Sist, Plinio ; Souza, Alexandre F. ; Spironello, Wilson Roberto ; Sposito, Tereza ; Steinmetz, Robert ; Stevart, Tariq ; Suganuma, Marcio Seiji ; Sukri, Rahayu ; Sultana, Aisha ; Sukumar, Raman ; Sunderland, Terry ; Supriyadi, S. ; Suresh, H.S. ; Suzuki, Eizi ; Tabarelli, Marcelo ; Tang, Jianwei ; Tanner, Ed V.J. ; Targhetta, Natalia ; Theilade, Ida ; Thomas, Duncan ; Timberlake, Jonathan ; Morisson Valeriano, Márcio De; Valkenburg, Johan Van; Do, Tran Van; Sam, Hoang Van; Vandermeer, John H. ; Verbeeck, Hans ; Vetaas, Ole Reidar ; Adekunle, Victor ; Vieira, Simone A. ; Webb, Campbell O. ; Webb, Edward L. ; Whitfeld, Timothy ; Wich, Serge ; Williams, John ; Wiser, Susan ; Wittmann, Florian ; Yang, Xiaobo ; Yao, C.Y.A. ; Yap, Sandra L. ; Zahawi, Rakan A. ; Zakaria, Rahmad ; Zang, Runguo - \ 2018
Proceedings of the National Academy of Sciences of the United States of America 115 (2018)8. - ISSN 0027-8424 - p. 1837 - 1842.
Biogeographic legacies - Forest classification - Forest functional similarity - Phylogenetic community distance - Tropical forests

Knowledge about the biogeographic affinities of the world's tropical forests helps to better understand regional differences in forest structure, diversity, composition, and dynamics. Such understanding will enable anticipation of region-specific responses to global environmental change. Modern phylogenies, in combination with broad coverage of species inventory data, now allow for global biogeographic analyses that take species evolutionary distance into account. Here we present a classification of the world's tropical forests based on their phylogenetic similarity. We identify five principal floristic regions and their floristic relationships: (i) Indo-Pacific, (ii) Subtropical, (iii) African, (iv) American, and (v) Dry forests. Our results do not support the traditional neo- versus paleotropical forest division but instead separate the combined American and African forests from their Indo-Pacific counterparts. We also find indications for the existence of a global dry forest region, with representatives in America, Africa, Madagascar, and India. Additionally, a northern-hemisphere Subtropical forest region was identified with representatives in Asia and America, providing support for a link between Asian and American northernhemisphere forests.

Rapid evolution of phenology during range expansion with recent climate change
Lustenhouwer, Nicky ; Wilschut, Rutger A. ; Williams, Jennifer L. ; Putten, Wim H. van der; Levine, Jonathan M. - \ 2018
Global Change Biology 24 (2018)2. - ISSN 1354-1013 - p. e534 - e544.
Although climate warming is expected to make habitat beyond species’ current cold range edge suitable for future colonization, this new habitat may present an array of biotic or abiotic conditions not experienced within the current range. Species’ ability to shift their range with climate change may therefore depend on how populations evolve in response to such novel environmental conditions. However, due to the recent nature of thus far observed range expansions, the role of rapid adaptation during climate change migration is only beginning to be understood. Here, we evaluated evolution during the recent native range expansion of the annual plant Dittrichia graveolens, which is spreading northward in Europe from the Mediterranean region. We examined genetically based differentiation between core and edge populations in their phenology, a trait that is likely under selection with shorter growing seasons and greater seasonality at northern latitudes. In parallel common garden experiments at range edges in Switzerland and the Netherlands, we grew plants from Dutch, Swiss, and central and southern French populations. Population genetic analysis following RAD-sequencing of these populations supported the hypothesized central France origins of the Swiss and Dutch range edge populations. We found that in both common gardens, northern plants flowered up to 4 weeks earlier than southern plants. This differentiation in phenology extended from the core of the range to the Netherlands, a region only reached from central France over approximately the last 50 years. Fitness decreased as plants flowered later, supporting the hypothesized benefits of earlier flowering at the range edge. Our results suggest that native range expanding populations can rapidly adapt to novel environmental conditions in the expanded range, potentially promoting their ability to spread.
The ALFAM2 database on ammonia emission from field-applied manure : Description and illustrative analysis
Hafner, Sasha D. ; Pacholski, Andreas ; Bittman, Shabtai ; Burchill, William ; Bussink, Wim ; Chantigny, Martin ; Carozzi, Marco ; Génermont, Sophie ; Häni, Christoph ; Hansen, Martin N. ; Huijsmans, Jan ; Hunt, Derek ; Kupper, Thomas ; Lanigan, Gary ; Loubet, Benjamin ; Misselbrook, Tom ; Meisinger, John J. ; Neftel, Albrecht ; Nyord, Tavs ; Pedersen, Simon V. ; Sintermann, Jörg ; Thompson, Rodney B. ; Vermeulen, Bert ; Voylokov, Polina ; Williams, John R. ; Sommer, Sven G. - \ 2018
Agricultural and Forest Meteorology 258 (2018). - ISSN 0168-1923 - p. 66 - 79.
Ammonia - Cattle - Emission - Manure - Pig - Slurry
Ammonia (NH3) emission from animal manure contributes to air pollution and ecosystem degradation, and the loss of reactive nitrogen (N) from agricultural systems. Estimates of NH3 emission are necessary for national inventories and nutrient management, and NH3 emission from field-applied manure has been measured in many studies over the past few decades. In this work, we facilitate the use of these data by collecting and organizing them in the ALFAM2 database. In this paper we describe the development of the database and summarise its contents, quantify effects of application methods and other variables on emission using a data subset, and discuss challenges for data analysis and model development. The database contains measurements of emission, manure and soil properties, weather, application technique, and other variables for 1895 plots from 22 research institutes in 12 countries. Data on five manure types (cattle, pig, mink, poultry, mixed, as well as sludge and "other") applied to three types of crops (grass, small grains, maize, as well as stubble and bare soil) are included. Application methods represented in the database include broadcast, trailing hose, trailing shoe (narrow band application), and open slot injection. Cattle manure application to grassland was the most common combination, and analysis of this subset (with dry matter (DM) limited to <15%) was carried out using mixed- and fixed-effects models in order to quantify effects of management and environment on ammonia emission, and to highlight challenges for use of the database. Measured emission in this subset ranged from <1% to 130% of applied ammonia after 48 h. Results showed clear, albeit variable, reductions in NH3 emission due to trailing hose, trailing shoe, and open slot injection of slurry compared to broadcast application. There was evidence of positive effects of air temperature and wind speed on NH3 emission, and limited evidence of effects of slurry DM. However, random-effects coefficients for differences among research institutes were among the largest model coefficients, and showed a deviation from the mean response by more than 100% in some cases. The source of these institute differences could not be determined with certainty, but there is some evidence that they are related to differences in soils, or differences in application or measurement methods. The ALFAM2 database should be useful for development and evaluation of both emission factors and emission models, but users need to recognize the limitations caused by confounding variables, imbalance in the dataset, and dependence among observations from the same institute. Variation among measurements and in reported variables highlights the importance of international agreement on how NH3 emission should be measured, along with necessary types of supporting data and standard protocols for their measurement. Both are needed in order to produce more accurate and useful ammonia emission measurements. Expansion of the ALFAM2 database will continue, and readers are invited to contact the corresponding author for information on data submission. The latest version of the database is available at
Non-Chemical Weed Management
Melander, Bo ; Liebman, Matt ; Davis, Adam S. ; Gallandt, Eric R. ; Bàrberi, Paolo ; Moonen, Anna Camilla ; Rasmussen, Jesper ; Weide, Rommie van der; Vidotto, Francesco - \ 2017
In: Weed Research / Hatcher, Paul E., Froud-Williams, Robert J., Wiley - ISBN 9781119969143 - p. 245 - 270.
Crop competition - Cultural methods - European weed research - Non-chemical weed management - North America - Organic crop production - Weed control methods - Weed germination

Non-chemical weed management covers all management practices that influence weeds except herbicides. This chapter summarises the major achievements in European research, as well as work undertaken in North America. Research groups from both continents have interacted strongly on the topic over the years and shared common interests on the development of non-chemical tactics. The chapter encompasses preventive, cultural and direct weed control methods, explaining the basic principles and the integration of these tactics in weed management strategies for agricultural and horticultural crops and in some cases amenity areas as well. Preventive methods reduce weed germination, cultural methods improve crop competition and direct physical weed control reduces weed survival. Non-chemical weed management is mainly adopted in organic crop production, as conventional growers still perceive it as more costly and less reliable than herbicide-based weed control programmes.

Dataset supplementing Lichtenberg et al. (2017) A global synthesis of the effects of diversified farming systems on arthropod diversity within fields and across agricultural landscapes. Global Change Biology
Lichtenberg, Elinor M. ; Kennedy, Christina M. ; Kremen, Claire ; Batáry, Péter ; Berendse, F. ; Bommarco, Riccardo ; Bosque-Pérez, Nilsa A. ; Carvalheiro, Luísa G. ; Snyder, William E. ; Williams, Neal M. - \ 2017
agricultural management schemes - arthropod diversity - functional groups - landscape complexity - meta-analysis - evenness - biodiversity - organic farming - plant diversity
This dataset contains data and scripts that supplement the publication
Automated assembly of species metabolomes through data submission into a public repository
Salek, Reza ; Conesa, Pablo ; Cochrane, Keeva ; Haug, Kenneth ; Williams, M. ; Kale, Namrata ; Moreno, P. ; Jayaseelan, Kalai Vanii ; Macias, Jose Ramon ; Nainala, Venkata Chandrasekhar ; Hall, R.D. ; Reed, Laura ; Viant, Mark ; Donovan, C. ; Steinbeck, Christoph - \ 2017
GigaScience 6 (2017)8. - ISSN 2047-217X - p. 1 - 4.
Following similar global efforts to exchange genomic and other biomedical data, global databases in metabolomics have now been established. MetaboLights, the first general purpose, publically available, cross-species, cross-application database in metabolomics, has become the fastest growing data repository at the European Bioinformatics Institute in terms of data volume. Here we present the automated assembly of species metabolomes in MetaboLights, a crucial reference for chemical biology, which is growing through user submissions.
The value and opportunities of community- and citizen-based approaches to tropical forest biodiversity monitoring
Chandler, Mark ; See, Linda ; Andrianandrasana, Herizo ; Becker, Dusti ; Berardi, Andrea ; Bodmer, Richard ; Brofeldt, S. ; Araujo Lima Constantino, Pedro de; Cousins, Jenny ; Crimmins, Theresa M. ; Danielsen, Finn ; Giorgi, Ana Paula ; Huxham, Mark ; Leslie, Alison ; Mistry, Jayalaxshmi ; Mora, B. ; Nelson, M. ; Poulsen, Michael ; Pratihast, A.K. ; Theilade, I. ; Vakil, Thrity ; Williams, John N. - \ 2017
In: A Sourcebook of Methods and Procedures for Monitoring Essential Biodiversity Variables in Tropical Forests with Remote Sensing / Gill, Mike, Jongman, Rob, Luque, Sandra, Mora, Brice, Paganini, Marc, Szantoi, Zoltan, Wageningen : GOFC-GOLD Land Cover Project Office, Wageningen University, The Netherlands (Report version UNCBD COP-13 ) - p. 223 - 281.
Sustainable intensification of agriculture for human prosperity and global sustainability
Rockstrom, J. ; Williams, J. ; Daily, G. ; Noble, A. ; Matthews, N. ; Gordon, L. ; Wetterstrand, H. ; DeClerck, F. ; Fraiture, C.M.S. de - \ 2017
Ambio 46 (2017)1. - ISSN 0044-7447 - p. 4 - 17.
There is an ongoing debate on what constitutes sustainable intensification of agriculture (SIA). In this paper, we propose that a paradigm for sustainable intensification can be defined and translated into an operational framework for agricultural development. We argue that this paradigm must now be defined—at all scales—in the context of rapidly rising global environmental changes in the Anthropocene, while focusing on eradicating poverty and hunger and contributing to human wellbeing. The criteria and approach we propose, for a paradigm shift towards sustainable intensification of agriculture, integrates the dual and interdependent goals of using sustainable practices to meet rising human needs while contributing to resilience and sustainability of landscapes, the biosphere, and the Earth system. Both of these, in turn, are required to sustain the future viability of agriculture. This paradigm shift aims at repositioning world agriculture from its current role as the world’s single largest driver of global environmental change, to becoming a key contributor of a global transition to a sustainable world within a safe operating space on Earth.
Time series livestock diet optimization : cost-effective broiler feed substitution using the commodity price spread approach
Alqaisi, Othman ; Ndambi, Oghaiki Asaah ; Williams, Ryan Blake - \ 2017
Agricultural and food economics 5 (2017)1. - ISSN 2193-7532
Broiler diet - Byproducts - Feed industry - Multi-stage linear-programming - Price spread - Trading
Sustainable feed formulation (defined here as nutritional and economic feed optimization) is substantial in feed chain production from crop farmers to livestock producers. Diet formulation employing a static linear programming (LP) approach, which is widely used in trading firms and feed production facilities, does not allow for intertemporal flexibility. Our approach allows the interaction between feed components over time, considering the volatile global feed prices, thereby improving sustainability in feed formulation and feed availability. The objectives of this study were to (1) develop a multi-stage LP feed model, (2) demonstrate its potential use in broiler feeding, and (3) illustrate the impact of feed input price spread (variation) on the composition of broiler diets. Modeling resulted in reciprocal relationships between conventional feeds and byproducts at different rates. Based on the price spreads expressed as a percentage of DDGS (distiller’s dried grains with solubles) price compared to corn price, three positions of dietary switch were identified; corn-DDGS price spreads of higher than 94%, between 76 and 94%, and lower than 76% corresponding to limited/no inclusion, partial inclusion, and maximum replacement of corn by DDGS, respectively. Rapeseed meal inclusion was 4, 5, and 6% in the corn-based starter, grower, and finisher diets, respectively, and its potential to replace soybean meal was limited by its higher fiber content. Based on the simulated compound feed prices, the global broiler feed industry could gain 1.7 billion USD through improved resources planning.
Mapping local and global variability in plant trait distributions
Butler, Ethan E. ; Datta, Abhirup ; Flores-Moreno, Habacuc ; Chen, Ming ; Wythers, Kirk R. ; Fazayeli, Farideh ; Banerjee, Arindam ; Atkin, Owen K. ; Kattge, Jens ; Amiaud, Bernard ; Blonder, Benjamin ; Boenisch, Gerhard ; Bond-Lamberty, Ben ; Brown, Kerry A. ; Byun, Chaeho ; Campetella, Giandiego ; Cerabolini, Bruno E.L. ; Cornelissen, Johannes H.C. ; Craine, Joseph M. ; Craven, Dylan ; Vries, Franciska T. De; Díaz, Sandra ; Domingues, Tomas F. ; Forey, Estelle ; González-Melo, Andrés ; Gross, Nicolas ; Han, Wenxuan ; Hattingh, Wesley N. ; Hickler, Thomas ; Jansen, Steven ; Kramer, Koen ; Kraft, Nathan J.B. ; Kurokawa, Hiroko ; Laughlin, Daniel C. ; Meir, Patrick ; Minden, Vanessa ; Niinemets, Ülo ; Onoda, Yusuke ; Peñuelas, Josep ; Read, Quentin ; Sack, Lawren ; Schamp, Brandon ; Soudzilovskaia, Nadejda A. ; Spasojevic, Marko J. ; Sosinski, Enio ; Thornton, Peter E. ; Valladares, Fernando ; Bodegom, Peter M. Van; Williams, Mathew ; Wirth, Christian ; Reich, Peter B. ; Schlesinger, William H. - \ 2017
Proceedings of the National Academy of Sciences of the United States of America 114 (2017)51. - ISSN 0027-8424 - p. E10937 - E10946.
Bayesian modeling - Climate - Global - Plant traits - Spatial statistics
Our ability to understand and predict the response of ecosystems to a changing environment depends on quantifying vegetation functional diversity. However, representing this diversity at the global scale is challenging. Typically, in Earth system models, characterization of plant diversity has been limited to grouping related species into plant functional types (PFTs), with all trait variation in a PFT collapsed into a single mean value that is applied globally. Using the largest global plant trait database and state of the art Bayesian modeling, we created fine-grained global maps of plant trait distributions that can be applied to Earth system models. Focusing on a set of plant traits closely coupled to photosynthesis and foliar respiration - specific leaf area (SLA) and dry mass-based concentrations of leaf nitrogen (Nm) and phosphorus (Pm), we characterize how traits vary within and among over 50,000 ∼50×50-km cells across the entire vegetated land surface. We do this in several ways - without defining the PFT of each grid cell and using 4 or 14 PFTs; each model's predictions are evaluated against out-of-sample data. This endeavor advances prior trait mapping by generating global maps that preserve variability across scales by using modern Bayesian spatial statistical modeling in combination with a database over three times larger than that in previous analyses. Our maps reveal that the most diverse grid cells possess trait variability close to the range of global PFT means.
Descriptive and mechanistic models of crop–weed competition
Bastiaans, L. ; Storkey, J. - \ 2017
In: Weed Research / Hatcher, Paul E., Froud-Williams, Robert J., Wiley-Blackwell - ISBN 9781119969143 - p. 33 - 60.
Crop-weed competitive relations are an important element of agroecosystems. Quantifying and understanding them helps to design appropriate weed management at operational, tactical and strategic level. This chapter presents and discusses simple descriptive and more mechanistic models for crop-weed interaction. Along with an elaboration of underlying principles, attention is on application of the models in support of research, management and policy development. The main purpose of mechanistic crop-weed competition models is to obtain a better quantitative understanding of crop-weed interactions and to identify how species characteristics, management interventions and environmental factors such as resource availability and climate change influence the competitive relations between crop and weed. The use of mechanistic models for crop-weed competition not only allows the ranking of genotypes on weed-suppressive ability, but also allows identification of appropriate traits capable of increasing weed suppressiveness without penalising yielding ability in the absence of weeds.
Predicting gene regulatory networks by combining spatial and temporal gene expression data in Arabidopsis root stem cells
Balaguer, Maria Angels De Luis ; Fisher, Adam P. ; Clark, Natalie M. ; Fernandez-Espinosa, Maria Guadalupe ; Möller, Barbara K. ; Weijers, Dolf ; Lohmann, Jan U. ; Williams, Cranos ; Lorenzo, Oscar ; Sozzani, Rosangela - \ 2017
Proceedings of the National Academy of Sciences of the United States of America 114 (2017)36. - ISSN 0027-8424 - p. E7632 - E7640.
Cell-type expression profile - Gene regulatory network - Modeling - Root development - Root stem cell
Identifying the transcription factors (TFs) and associated networks involved in stem cell regulation is essential for understanding the initiation and growth of plant tissues and organs. Although many TFs have been shown to have a role in the Arabidopsis root stem cells, a comprehensive view of the transcriptional signature of the stem cells is lacking. In this work, we used spatial and temporal transcriptomic data to predict interactions among the genes involved in stem cell regulation. To accomplish this, we transcriptionally profiled several stem cell populations and developed a gene regulatory network inference algorithm that combines clustering with dynamic Bayesian network inference. We leveraged the topology of our networks to infer potential major regulators. Specifically, through mathematical modeling and experimental validation, we identified PERIANTHIA (PAN) as an important molecular regulator of quiescent center function. The results presented in this work show that our combination of molecular biology, computational biology, and mathematical modeling is an efficient approach to identify candidate factors that function in the stem cells.
Large meta-analysis of genome-wide association studies identifies five loci for lean body mass
Zillikens, M.C. ; Demissie, Serkalem ; Hsu, Yi Hsiang ; Yerges-Armstrong, Laura M. ; Chou, Wen Chi ; Stolk, Lisette ; Livshits, Gregory ; Broer, Linda ; Johnson, Toby ; Koller, Daniel L. ; Kutalik, Zoltán ; Luan, J.A. ; Malkin, Ida ; Ried, Janina S. ; Smith, Albert V. ; Thorleifsson, Gudmar ; Vandenput, Liesbeth ; Hua Zhao, Jing ; Zhang, Weihua ; Aghdassi, Ali ; Åkesson, Kristina ; Amin, Najaf ; Baier, Leslie J. ; Barroso, Inês ; Bennett, David A. ; Bertram, Lars ; Biffar, Rainer ; Bochud, Murielle ; Boehnke, Michael ; Borecki, Ingrid B. ; Buchman, Aron S. ; Byberg, Liisa ; Campbell, Harry ; Campos Obanda, Natalia ; Cauley, Jane A. ; Cawthon, Peggy M. ; Cederberg, Henna ; Chen, Zhao ; Cho, Nam H. ; Jin Choi, Hyung ; Claussnitzer, Melina ; Collins, Francis ; Cummings, Steven R. ; Jager, Philip L. De; Demuth, Ilja ; Dhonukshe-Rutten, Rosalie A.M. ; DIatchenko, Luda ; Eiriksdottir, Gudny ; Enneman, Anke W. ; Erdos, Mike ; Eriksson, Johan G. ; Eriksson, Joel ; Estrada, Karol ; Evans, Daniel S. ; Feitosa, Mary F. ; Fu, Mao ; Garcia, Melissa ; Gieger, Christian ; Girke, Thomas ; Glazer, Nicole L. ; Grallert, Harald ; Grewal, Jagvir ; Han, Bok Ghee ; Hanson, Robert L. ; Hayward, Caroline ; Hofman, Albert ; Hoffman, Eric P. ; Homuth, Georg ; Hsueh, Wen Chi ; Hubal, Monica J. ; Hubbard, Alan ; Huffman, Kim M. ; Husted, Lise B. ; Illig, Thomas ; Ingelsson, Erik ; Ittermann, Till ; Jansson, John Olov ; Jordan, Joanne M. ; Jula, Antti ; Karlsson, Magnus ; Khaw, Kay Tee ; Kilpelaïnen, Tuomas O. ; Klopp, Norman ; Kloth, Jacqueline S.L. ; Koistinen, Heikki A. ; Kraus, William E. ; Kritchevsky, Stephen ; Kuulasmaa, Teemu ; Kuusisto, Johanna ; Laakso, Markku ; Lahti, Jari ; Lang, Thomas ; Langdahl, Bente L. ; Launer, Lenore J. ; Lee, Jong Young ; Lerch, Markus M. ; Lewis, Joshua R. ; Lind, Lars ; Lindgren, Cecilia M. ; Liu, Yongmei ; Liu, Tian ; Liu, Youfang ; Ljunggren, Östen ; Lorentzon, Mattias ; Luben, Robert N. ; Maixner, William ; McGuigan, Fiona E. ; Medina-Gomez, Carolina ; Meitinger, Thomas ; Melhus, Håkan ; Mellström, Dan ; Melov, Simon ; Michaëlsson, Karl ; Mitchell, Braxton D. ; Morris, Andrew P. ; Mosekilde, Leif ; Newman, Anne ; Nielson, Carrie M. ; O'Connell, Jeffrey R. ; Oostra, Ben A. ; Orwoll, Eric S. ; Palotie, Aarno ; Parker, Stephan ; Peacock, Munro ; Perola, Markus ; Peters, Annette ; Polasek, Ozren ; Prince, Richard L. ; Raïkkönen, Katri ; Ralston, Stuart H. ; Ripatti, Samuli ; Robbins, John A. ; Rotter, Jerome I. ; Rudan, Igor ; Salomaa, Veikko ; Satterfield, Suzanne ; Schadt, Eric E. ; Schipf, Sabine ; Scott, Laura ; Sehmi, Joban ; Shen, Jian ; Soo Shin, Chan ; Sigurdsson, Gunnar ; Smith, Shad ; Soranzo, Nicole ; Stančáková, Alena ; Steinhagen-Thiessen, Elisabeth ; Streeten, Elizabeth A. ; Styrkarsdottir, Unnur ; Swart, Karin M.A. ; Tan, Sian Tsung ; Tarnopolsky, Mark A. ; Thompson, Patricia ; Thomson, Cynthia A. ; Thorsteinsdottir, Unnur ; Tikkanen, Emmi ; Tranah, Gregory J. ; Tuomilehto, Jaakko ; Schoor, Natasja M. van; Verma, Arjun ; Vollenweider, Peter ; Völzke, Henry ; Wactawski-Wende, Jean ; Walker, Mark ; Weedon, Michael N. ; Welch, Ryan ; Wichman, H.E. ; Widen, Elisabeth ; Williams, Frances M.K. ; Wilson, James F. ; Wright, Nicole C. ; Xie, Weijia ; Yu, Lei ; Zhou, Yanhua ; Chambers, John C. ; Döring, Angela ; Duijn, Cornelia M. Van; Econs, Michael J. ; Gudnason, Vilmundur ; Kooner, Jaspal S. ; Psaty, Bruce M. ; Spector, Timothy D. ; Stefansson, Kari ; Rivadeneira, Fernando ; Uitterlinden, André G. ; Wareham, Nicholas J. ; Ossowski, Vicky ; Waterworth, Dawn M. ; Loos, Ruth J.F. ; Karasik, David ; Harris, Tamara B. ; Ohlsson, Claes ; Kiel, Douglas P. - \ 2017
Nature Communications 8 (2017)1. - ISSN 2041-1723
Lean body mass, consisting mostly of skeletal muscle, is important for healthy aging. We performed a genome-wide association study for whole body (20 cohorts of European ancestry with n = 38,292) and appendicular (arms and legs) lean body mass (n = 28,330) measured using dual energy X-ray absorptiometry or bioelectrical impedance analysis, adjusted for sex, age, height, and fat mass. Twenty-one single-nucleotide polymorphisms were significantly associated with lean body mass either genome wide (p < 5 × 10-8) or suggestively genome wide (p < 2.3 × 10-6). Replication in 63,475 (47,227 of European ancestry) individuals from 33 cohorts for whole body lean body mass and in 45,090 (42,360 of European ancestry) subjects from 25 cohorts for appendicular lean body mass was successful for five single-nucleotide polymorphisms in/near HSD17B11, VCAN, ADAMTSL3, IRS1, and FTO for total lean body mass and for three single-nucleotide polymorphisms in/near VCAN, ADAMTSL3, and IRS1 for appendicular lean body mass. Our findings provide new insight into the genetics of lean body mass.
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