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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Modeling phosphorus in rivers at the global scale : recent successes, remaining challenges, and near-term opportunities
Harrison, John A. ; Beusen, Arthur H.W. ; Fink, Gabriel ; Tang, Ting ; Strokal, Maryna ; Bouwman, Alexander F. ; Metson, Geneviève S. ; Vilmin, Lauriane - \ 2019
Current Opinion in Environmental Sustainability 36 (2019). - ISSN 1877-3435 - p. 68 - 77.

Understanding and mitigating the effects of phosphorus (P) overenrichment of waters globally, including the evaluation of the global Sustainability Development Goals, requires the use of global models. Such models quantitatively link land use, global population growth and climate to aquatic nutrient loading and biogeochemical cycling. Here we describe, compare, and contrast the existing global models capable of predicting P transport by rivers at a global scale. We highlight important insights gained from the development and application of these models, and identify important near-term opportunities for model improvements as well as additional insight to be gained through new model analysis.

Bridging global, basin and local-scale water quality modeling towards enhancing water quality management worldwide
Tang, Ting ; Strokal, Maryna ; Vliet, Michelle T.H. van; Seuntjens, Piet ; Burek, Peter ; Kroeze, Carolien ; Langan, Simon ; Wada, Yoshihide - \ 2019
Current Opinion in Environmental Sustainability 36 (2019). - ISSN 1877-3435 - p. 39 - 48.

Global water quality (WQ) modeling is an emerging field. In this article, we identify the missing linkages between global and basin/local-scale WQ models, and discuss the possibilities to fill these gaps. We argue that WQ models need stronger linkages across spatial scales. This would help to identify effective scale-specific WQ management options and contribute to future development of global WQ models. Two directions are proposed to improve the linkages: nested multiscale WQ modeling towards enhanced water management, and development of next-generation global WQ models based-on basin/local-scale mechanistic understanding. We highlight the need for better collaboration among WQ modelers and policy-makers in order to deliver responsive water policies and management strategies across scales.

Global multi-pollutant modelling of water quality: scientific challenges and future directions
Strokal, M. ; Spanier, Emiel ; Kroeze, C. ; Koelmans, A.A. ; Florke, Martina ; Franssen, W.H.P. ; Hofstra, N. ; Langan, Simon ; Ting, Tang ; Vliet, M.T.H. van; Wada, Yoshihide ; Wang, M. ; Wijnen, Jikke van; Williams, R. - \ 2019
Current Opinion in Environmental Sustainability 36 (2019). - ISSN 1877-3435 - p. 116 - 125.
Assessing global water quality issues requires a multi-pollutant modelling approach. We discuss scientific challenges and future directions for such modeling. Multi-pollutant river models need to integrate information on sources of pollutants such as plastic debris, nutrients, chemicals, pathogens, their effects and possible solutions. In this paper, we first explain what we consider multi-pollutant modelling. Second, we discuss scientific challenges in multi-pollutant modelling relating to consistent model inputs, modelling approaches and model evaluation. Next, we illustrate the potential of global multi-pollutant modelling for hotspot analyses. We show hotspots of river pollution with microplastics, nutrients, triclosan and Cryptosporidium in many sub-basins of Europe, North America and South Asia. Finally, we reflect on future directions for multi-pollutant modelling, and for linking model results to policy-making.
Nucleolin mediates the internalization of rabbit hemorrhagic disease virus through clathrin-dependent endocytosis
Zhu, Jie ; Miao, Qiuhong ; Tang, Jingyu ; Wang, Xiaoxue ; Dong, Dandan ; Liu, Teng ; Qi, Ruibin ; Yang, Zhibiao ; Liu, Guangqing - \ 2018
PLoS Pathogens 14 (2018)10. - ISSN 1553-7366

Rabbit hemorrhagic disease virus (RHDV) is an important member of the Caliciviridae family and a highly lethal pathogen in rabbits. Although the cell receptor of RHDV has been identified, the mechanism underlying RHDV internalization remains unknown. In this study, the entry and post-internalization of RHDV into host cells were investigated using several biochemical inhibitors and RNA interference. Our data demonstrate that rabbit nucleolin (NCL) plays a key role in RHDV internalization. Further study revealed that NCL specifically interacts with the RHDV capsid protein (VP60) through its N-terminal residues (aa 285-318), and the exact position of the VP60 protein for the interaction with NCL is located in a highly conserved region (472Asp-Val-Asn474; DVN motif). Following competitive blocking of the interaction between NCL and VP60 with an artificial DVN peptide (RRTGDVNAAAGSTNGTQ), the internalization efficiency of the virus was markedly reduced. Moreover, NCL also interacts with the C-terminal residues of clathrin light chain A, which is an important component in clathrin-dependent endocytosis. In addition, the results of animal experiments also demonstrated that artificial DVN peptides protected most rabbits from RHDV infection. These findings demonstrate that NCL is involved in RHDV internalization through clathrin-dependent endocytosis.

Phase II study of ERC1671 plus bevacizumab versus bevacizumab plus placebo in recurrent glioblastoma : interim results and correlations with CD4+ T-lymphocyte counts
Bota, Daniela A. ; Chung, Jinah ; Dandekar, Manisha ; Carrillo, Jose A. ; Kong, Xiao Tang ; Fu, Beverly D. ; Hsu, Frank Pk ; Schönthal, Axel H. ; Hofman, Florence M. ; Chen, Thomas C. ; Zidovetzki, Raphael ; Pretto, Chrystel ; Strik, Ankie ; Schijns, Virgil E.J.C. ; Stathopoulos, Apostolos - \ 2018
JAMA Oncology 7 (2018)3. - ISSN 2374-2437 - p. CNS22 - CNS22.
allogeneic - autologous - bevacizumab - CD4+ T lymphocyte - ERC1671 - GBM - GBM vaccine - glioma surgery - immunotherapy

AIM: ERC1671 is an allogeneic/autologous therapeutic glioblastoma (GBM) vaccine - composed of whole, inactivated tumor cells mixed with tumor cell lysates derived from the patient and three GBM donors.

METHODS: In this double-blinded, randomized, Phase II study bevacizumab-naive patients with recurrent GBM were randomized to receive either ERC1671 in combination with granulocyte-macrophage colony-stimulating factor (GM-CSF) (Leukine® or sargramostim) and cyclophosphamide plus bevacizumab, or placebo plus bevacizumab. Interim results: Median overall survival (OS) of patients treated with ERC1671 plus bevacizumab was 12 months. In the placebo plus bevacizumab group, median OS was 7.5 months. The maximal CD4+ T-lymphocyte count correlated with OS in the ERC1671 but not in the placebo group.

CONCLUSION: The addition of ERC1671/GM-CSF/cyclophosphamide to bevacizumab resulted in a clinically meaningful survival benefit with minimal additional toxicity.

A Mediterranean-like dietary pattern with Vitamin D3 (10 μg/d) supplements reduced the rate of bone loss in older Europeans with osteoporosis at baseline : Results of a 1-y randomized controlled trial
Jennings, Amy ; Cashman, Kevin D. ; Gillings, Rachel ; Cassidy, Aedin ; Tang, Jonathan ; Fraser, William ; Dowling, Kirsten G. ; Hull, George L.J. ; Berendsen, Agnes A.M. ; Groot, Lisette C.P.G.M. de; Pietruszka, Barbara ; Wierzbicka, Elzbieta ; Ostan, Rita ; Bazzocchi, Alberto ; Battista, Giuseppe ; Caumon, Elodie ; Meunier, Nathalie ; Malpuech-Brugère, Corinne ; Franceschi, Claudio ; Santoro, Aurelia ; Fairweather-Tait, Susan J. - \ 2018
American Journal of Clinical Nutrition 108 (2018)3. - ISSN 0002-9165 - p. 633 - 640.
bone - Mediterranean diet - older adults - Osteoporosis - Vitamin D supplementation

Background: The Mediterranean diet (MD) is widely recommended for the prevention of chronic disease, but evidence for a beneficial effect on bone health is lacking. Objective: The aim of this study was to examine the effect of a Mediterranean-like dietary pattern [NU-AGE (New Dietary Strategies Addressing the Specific Needs of the Elderly Population for Healthy Aging in Europe)] on indexes of inflammation with a number of secondary endpoints, including bone mineral density (BMD) and biomarkers of bone and collagen degradation in a 1-y multicenter randomized controlled trial (RCT; NU-AGE) in elderly Europeans. Design: An RCT was undertaken across 5 European centers. Subjects in the intervention group consumed the NU-AGE diet for 1 y by receiving individually tailored dietary advice, coupled with supplies of foods including whole-grain pasta, olive oil, and a vitamin D3 supplement (10 μg/d). Participants in the control group were provided with leaflets on healthy eating available in their country. Results: A total of 1294 participants (mean ± SD age: 70.9 ±4.0 y; 44% male) were recruited to the study and 1142 completed the 1-y trial. The Mediterranean-like dietary pattern had no effect on BMD (site-specific or whole-body); the inclusion of compliance to the intervention in the statistical model did not change the findings. There was also no effect of the intervention on the urinary biomarkers free pyridinoline or free deoxypyridinoline. Serum 25-hydroxyvitamin D significantly increased and parathyroid hormone decreased (P < 0.001) in the MD compared with the control group. Subgroup analysis of individuals with osteoporosis at baseline (site-specific BMD T-score ≤ -2.5 SDs) showed that the MD attenuated the expected decline in femoral neck BMD (n = 24 and 30 in MD and control groups, respectively; P = 0.04) but had no effect on lumbar spine or whole-body BMD. Conclusions: A 1-y intervention of the Mediterranean-like diet together with vitamin D3 supplements (10 μg/d) had no effect on BMD in the normal age-related range, but it significantly reduced the rate of loss of bone at the femoral neck in individuals with osteoporosis. The NU-AGE trial is registered at clinicaltrials.gov as NCT01754012.

Therapeutic immunization against glioblastoma
Schijns, Virgil E.J.C. ; Pretto, Chrystel ; Strik, Anna M. ; Gloudemans-Rijkers, Rianne ; Deviller, Laurent ; Pierre, Denis ; Chung, Jinah ; Dandekar, Manisha ; Carrillo, Jose A. ; Kong, Xiao Tang ; Fu, Beverly D. ; Hsu, Frank P.K. ; Hofman, Florence M. ; Chen, Thomas C. ; Zidovetzki, Raphael ; Bota, Daniela A. ; Stathopoulos, Apostolos - \ 2018
International Journal of Molecular Sciences 19 (2018)9. - ISSN 1661-6596
Allogenic - Autologous - Brain tumor - Glioma tumor - Immunotherapy - Therapeutic vaccine
Glioblastoma is the most common form of brain cancer in adults that produces severe damage to the brain leading to a very poor survival prognosis. The standard of care for glioblastoma is usually surgery, as well as radiotherapy followed by systemic temozolomide chemotherapy, resulting in a median survival time of about 12 to 15 months. Despite these therapeutic efforts, the tumor returns in the vast majority of patients. When relapsing, statistics suggest an imminent death dependent on the size of the tumor, the Karnofsky Performance Status, and the tumor localization. Following the standard of care, the administration of Bevacizumab, inhibiting the growth of the tumor vasculature, is an approved medicinal treatment option approved in the United States, but not in the European Union, as well as the recently approved alternating electric fields (AEFs) generator NovoTTF/Optune. However, it is clear that regardless of the current treatment regimens, glioma patients continue to have dismal prognosis and novel treatments are urgently needed. Here, we describe different approaches of recently developed therapeutic glioma brain cancer vaccines, which stimulate the patient’s immune system to recognize tumor-associated antigens (TAA) on cancer cells, aiming to instruct the immune system to eventually attack and destroy the brain tumor cells, with minimal bystander damage to normal brain cells. These distinct immunotherapies may target particular glioma TAAs which are molecularly defined, but they may also target broad patient-derived tumor antigen preparations intentionally evoking a very broad polyclonal antitumor immune stimulation.
Water-and nitrogen-use efficiencies of hemp (Cannabis sativa L.) based on whole-canopy measurements and modeling
Tang, Kailei ; Fracasso, Alessandra ; Struik, Paul C. ; Yin, Xinyou ; Amaducci, Stefano - \ 2018
Frontiers in Plant Science 9 (2018). - ISSN 1664-462X
Cannabis sativa L. - Canopy gas exchange - Hemp - Nitrogen use efficiency - Water use efficiency

Interest in hemp (Cannabis sativa L.) as a crop for the biobased economy is growing worldwide because hemp produces a high and valuable biomass while requiring low inputs. To understand the physiological basis of hemp’s resource-use efficiency, canopy gas exchange was assessed using a chamber technique on canopies exposed to a range of nitrogen (N) and water levels. Since canopy transpiration and carbon assimilation were very sensitive to variations in microclimate among canopy chambers, observations were adjusted for microclimatic differences using a physiological canopy model, with leaf-level parameters estimated for hemp from our previous study. Canopy photosynthetic water-use efficiency (PWUEc), defined as the ratio of gross canopy photosynthesis to canopy transpiration, ranged from 4.0 mmol CO2 (mol H2 O)−1 to 7.5 mmol CO2 (mol H2 O)−1. Canopy photosynthetic nitrogen-use efficiency (PNUEc), the ratio of the gross canopy photosynthesis to canopy leaf-N content, ranged from 0.3mol CO2 d−1 (g N)−1 to 0.7mol CO2 d−1 (g N)−1. The effect of N-input levels on PWUEc and PNUEc was largely determined by the N effect on canopy size or leaf area index (LAI), whereas the effect of water-input levels differed between short-and long-term stresses. The effect of short-term water stress was reflected by stomatal regulation. The long-term stress increased leaf senescence, decreased LAI but retained total canopy N content; however, the increased average leaf-N could not compensate for the lost LAI, leading to a decreased PNUEc. Although hemp is known as a resource-use efficient crop, its final biomass yield and nitrogen use efficiency may be restricted by water limitation during growth. Our results also suggest that crop models should take stress-induced senescence into account in addition to stomatal effects if crops experience a prolonged water stress during growth.

Atmosphere-vegetation-soil interactions in a climate change context; Impact of changing conditions on engineered transport infrastructure slopes in Europe
Tang, A.M. ; Hughes, P.N. ; Dijkstra, T.A. ; Askarinejad, A. ; Brenčič, M. ; Cui, Y.J. ; Diez, J.J. ; Firgi, T. ; Gajewska, B. ; Gentile, F. ; Grossi, G. ; Jommi, C. ; Kehagia, F. ; Koda, E. ; Maat, H.W. Ter; Lenart, S. ; Lourenco, S. ; Oliveira, M. ; Osinski, P. ; Springman, S.M. ; Stirling, R. ; Toll, D.G. ; Beek, V. Van - \ 2018
Quarterly Journal of Engineering Geology and Hydrogeology 51 (2018)2. - ISSN 1470-9236 - p. 156 - 168.

In assessing the impact of climate change on infrastructure, it is essential to consider the interactions between the atmosphere, vegetation and the near-surface soil. This paper presents an overview of these processes, focusing on recent advances from the literature and those made by members of COST Action TU1202 - Impacts of climate change on engineered slopes for infrastructure. Climate- and vegetation-driven processes (suction generation, erosion, desiccation cracking, freeze- thaw effects) are expected to change in incidence and severity, which will affect the stability of new and existing infrastructure slopes. This paper identifies the climate- and vegetation-driven processes that are of greatest concern, the suite of known unknowns that require further research, and lists key aspect that should be considered for the design of engineered transport infrastructure slopes in the context of climate change.

HEx : A heterologous expression platform for the discovery of fungal natural products
Harvey, Colin J.B. ; Tang, Mancheng ; Schlecht, Ulrich ; Horecka, Joe ; Fischer, Curt R. ; Lin, Hsiao Ching ; Li, Jian ; Naughton, Brian ; Cherry, James ; Miranda, Molly ; Li, Yong Fuga ; Chu, Angela M. ; Hennessy, James R. ; Vandova, Gergana A. ; Inglis, Diane ; Aiyar, Raeka S. ; Steinmetz, Lars M. ; Davis, Ronald W. ; Medema, Marnix H. ; Sattely, Elizabeth ; Khosla, Chaitan ; Onge, Robert P.S. ; Tang, Yi ; Hillenmeyer, Maureen E. - \ 2018
Science Advances 4 (2018)4. - ISSN 2375-2548
For decades, fungi have been a source of U.S. Food and Drug Administration-approved natural products such as penicillin, cyclosporine, and the statins. Recent breakthroughs in DNA sequencing suggest that millions of fungal species exist on Earth, with each genome encoding pathways capable of generating as many as dozens of natural products. However, the majority of encoded molecules are difficult or impossible to access because the organisms are uncultivable or the genes are transcriptionally silent. To overcome this bottleneck in natural product discovery, we developed the HEx (Heterologous EXpression) synthetic biology platform for rapid, scalable expression of fungal biosynthetic genes and their encoded metabolites in Saccharomyces cerevisiae. We applied this platform to 41 fungal biosynthetic gene clusters from diverse fungal species from around the world, 22 of which produced detectable compounds. These included novel compounds with unexpected biosynthetic origins, particularly from poorly studied species. This result establishes the HEx platform for rapid discovery of natural products from any fungal species, even those that are uncultivable, and opens the door to discovery of the next generation of natural products.
Brassicales phylogeny inferred from 72 plastid genes : A reanalysis of the phylogenetic localization of two paleopolyploid events and origin of novel chemical defenses
Edger, Patrick P. ; Hall, Jocelyn C. ; Harkess, Alex ; Tang, Michelle ; Coombs, Jill ; Mohammadin, Setareh ; Schranz, Eric ; Xiong, Zhiyong ; Leebens-Mack, James ; Meyers, Blake C. ; Sytsma, Kenneth J. ; Koch, Marcus A. ; Al-Shehbaz, Ihsan A. ; Pires, J.C. - \ 2018
American Journal of Botany 105 (2018)3. - ISSN 0002-9122 - p. 463 - 469.
Evolutionary novelties - Glucosinolates - Phylogenomics - Secondary metabolites
PREMISE OF THE STUDY: Previous phylogenetic studies employing molecular markers have yielded various insights into the evolutionary history across Brassicales, but many relationships between families remain poorly supported or unresolved. A recent phylotranscriptomic approach utilizing 1155 nuclear markers obtained robust estimates for relationships among 14 of 17 families. Here we report a complete family-level phylogeny estimated using the plastid genome. METHODS: We conducted phylogenetic analyses on a concatenated data set comprising 44,926 bp from 72 plastid genes for species distributed across all 17 families. Our analysis includes three additional families, Tovariaceae, Salvadoraceae, and Setchellanthaceae, that were omitted in the previous phylotranscriptomic study. KEY RESULTS: Our phylogenetic analyses obtained fully resolved and strongly supported estimates for all nodes across Brassicales. Importantly, these findings are congruent with the topology reported in the phylotranscriptomic study. This consistency suggests that future studies could utilize plastid genomes as markers for resolving relationships within some notoriously difficult clades across Brassicales. We used this new phylogenetic framework to verify the placement of the At-α event near the origin of Brassicaceae, with median date estimates of 31.8 to 42.8 million years ago and restrict the At-β event to one of two nodes with median date estimates between 85 to 92.2 million years ago. These events ultimately gave rise to novel chemical defenses and are associated with subsequent shifts in net diversification rates. CONCLUSIONS: We anticipate that these findings will aid future comparative evolutionary studies across Brassicales, including selecting candidates for whole-genome sequencing projects.
Risk assessment of genotoxic and carcinogenic alkenylbenzenes in botanical containing products present on the Chinese market
Ning, Jia ; Cui, Xin Yue ; Kong, Xiang Nan ; Tang, Yi Fei ; Wulandari, Riana ; Chen, Lu ; Wesseling, Sebas ; Rietjens, Ivonne M.C.M. - \ 2018
Food and Chemical Toxicology 115 (2018). - ISSN 0278-6915 - p. 344 - 357.
Alkenylbenzenes - Chinese market - Herbal teas - Margin of Exposure (MOE) - Plant food supplement (PFS) - Traditional Chinese medicine (TCM)
In the present study, a risk assessment of plant food supplements (PFS), traditional Chinese medicines (TCM) and herbal teas containing alkenylbenzenes was performed using the Margin of Exposure (MOE) approach. The levels of alkenylbenzenes in botanical preparations collected on the Chinese market were quantified and the combined estimated daily intake (EDI) was determined using dose additivity. The combined EDI values obtained assuming equal potency of all alkenylbenzenes detected in the PFS, TCM and herbal teas were 0.3 to 14.3, 0.05 to 539.4 and 0.04 to 42.5 μg/kg bw/day, respectively. Calculating combined EDI values taking into account the toxic equivalency (TEQ) approach, the values for PFS, TCM and herbal teas were 0.3 to 7.7, 0.05 to 278.0 and 0.02 to 16.5 μg estragole equivalents/kg bw/day, respectively. The MOE values resulting from consumption of these PFS, TCM and one cup of herbal tea per day during life-time were generally lower than 10 000, suggesting a potential priority for risk management. For short-term exposure such as two weeks consumption, applying Haber's rule, only one TCM 6 (四神丸) still had an MOE value below 10 000. It is concluded that selected consumption of Chinese botanical preparations raise a concern because of exposure to alkenylbenzenes, especially when exposure is for longer periods of time.
Bridging global and basin scale water quality modeling towards enhancing global water quality modeling and management
Tang, Ting ; Wada, Yoshihide ; Strokal, M. ; Burek, P. ; Langan, Simon - \ 2018
Geophysical Research Abstracts 20 (2018). - ISSN 1029-7006 - 1 p.
abstract
Agronomy and photosynthesis physiology of hemp (Cannabis sativa L.)
Tang, Kailei - \ 2018
Wageningen University. Promotor(en): Paul Struik, co-promotor(en): Xinyou Yin; S. Amaducci. - Wageningen : Wageningen University - ISBN 9789463438841 - 174

Hemp (Cannabis sativa L.) is a sustainable high-yielding crop that delivers valuable fibres, seeds and psychoactive substances. However, there is a lack of field experimental data on the cultivation of hemp because its production was largely abandoned in the last century. Hemp is now considered as an ideal crop to produce innovative biomaterials, and in particular, the dual-purpose hemp production (fibre + seed) is now the norm in European countries, driven by the shift of a rapidly expanding market for hemp seeds coupled with lower quality fibre requirements for innovative biomaterials. This study brought new information on the agronomy and photosynthesis physiology for the resurging production of hemp, particularly for dual-purpose production in Europe.

The effects of important agronomic factors, i.e. cultivar, planting density, and nitrogen fertilization, on the performance of the hemp crop were investigated under contrasting European environments. Based on the experimental data, for dual-purpose hemp production, a planting density of 90–150 plants m-2 is recommended for a monoecious cultivar that gives a long vegetative phase while leaving enough time for seed growth. A nitrogen fertilization rate of 60 kg N ha-1 was generally sufficient in the tested environments whereas further optimization of nitrogen fertilization requires accurate and precise assessment of plant nutritional status. To facilitate assessing plant nutritional status, a critical nitrogen dilution curve was determined for hemp.

The responses of leaf photosynthesis to nitrogen content and temperature were quantified using a biochemical model of C3 leaf photosynthesis, based on a complete set of photosynthetic measurements for hemp leaves. Then, by combining measurements and modelling, an upscaling was made from the leaf to the canopy level to analyse hemp’s photosynthetic nitrogen-use efficiency (NUE) and water-use efficiency (WUE) in response to water and nitrogen supply. The effect of nitrogen supply level on hemp’s NUE and WUE was largely determined by its effect on canopy size or leaf area index (LAI). The effect of short-term water stress on WUE and NUE was reflected in the stomatal regulation, whereas long-term water stress enhanced leaf senescence, reduced LAI but retained total canopy nitrogen content, and thus resulted in a further increase in WUE.

Findings in this thesis provided an improved understanding of the agronomy and photosynthesis physiology of hemp, particularly in relation to the dual-purpose production of hemp in Europe. Such understanding not only provides additional evidence that hemp can be grown as a sustainable crop over a wide range of climatic and agronomic conditions, but also provides essential information for parameterizing crop growth models. Prospects for further research were discussed in view of using the findings in this thesis in combination with a crop growth model to develop strategies for optimization of hemp cultivation and breeding.

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.

Genome-wide association study in 79,366 European-ancestry individuals informs the genetic architecture of 25-hydroxyvitamin D levels
Jiang, Xia ; O'Reilly, Paul F. ; Aschard, Hugues ; Hsu, Yi Hsiang ; Richards, J.B. ; Dupuis, Josée ; Ingelsson, Erik ; Karasik, David ; Pilz, Stefan ; Berry, Diane ; Kestenbaum, Bryan ; Zheng, Jusheng ; Luan, Jianan ; Sofianopoulou, Eleni ; Streeten, Elizabeth A. ; Albanes, Demetrius ; Lutsey, Pamela L. ; Yao, Lu ; Tang, Weihong ; Econs, Michael J. ; Wallaschofski, Henri ; Völzke, Henry ; Zhou, Ang ; Power, Chris ; McCarthy, Mark I. ; Michos, Erin D. ; Boerwinkle, Eric ; Weinstein, Stephanie J. ; Freedman, Neal D. ; Huang, Wen Yi ; Schoor, Natasja M. van; Velde, Nathalie van der; Groot, Lisette C.P.G.M. de; Enneman, Anke ; Cupples, L.A. ; Booth, Sarah L. ; Vasan, Ramachandran S. ; Liu, Ching Ti ; Zhou, Yanhua ; Ripatti, Samuli ; Ohlsson, Claes ; Vandenput, Liesbeth ; Lorentzon, Mattias ; Eriksson, Johan G. ; Shea, M.K. ; Houston, Denise K. ; Kritchevsky, Stephen B. ; Liu, Yongmei ; Lohman, Kurt K. ; Ferrucci, Luigi ; Peacock, Munro ; Gieger, Christian ; Beekman, Marian ; Slagboom, Eline ; Deelen, Joris ; Deelen, Joris ; Heemst, Diana van; Kleber, Marcus E. ; März, Winfried ; Boer, Ian H. De; Wood, Alexis C. ; Rotter, Jerome I. ; Rich, Stephen S. ; Robinson-Cohen, Cassianne ; Heijer, Martin Den; Jarvelin, Marjo Riitta ; Jarvelin, Marjo Riitta ; Cavadino, Alana ; Cavadino, Alana ; Joshi, Peter K. ; Wilson, James F. ; Hayward, Caroline ; Lind, Lars ; Michaëlsson, Karl ; Trompet, Stella ; Zillikens, M.C. ; Uitterlinden, Andre G. ; Rivadeneira, Fernando - \ 2018
Nature Communications 9 (2018)1. - ISSN 2041-1723
Vitamin D is a steroid hormone precursor that is associated with a range of human traits and diseases. Previous GWAS of serum 25-hydroxyvitamin D concentrations have identified four genome-wide significant loci (GC, NADSYN1/DHCR7, CYP2R1, CYP24A1). In this study, we expand the previous SUNLIGHT Consortium GWAS discovery sample size from 16,125 to 79,366 (all European descent). This larger GWAS yields two additional loci harboring genome-wide significant variants (P = 4.7×10 -9 at rs8018720 in SEC23A, and P = 1.9×10 -14 at rs10745742 in AMDHD1). The overall estimate of heritability of 25-hydroxyvitamin D serum concentrations attributable to GWAS common SNPs is 7.5%, with statistically significant loci explaining 38% of this total. Further investigation identifies signal enrichment in immune and hematopoietic tissues, and clustering with autoimmune diseases in cell-type-specific analysis. Larger studies are required to identify additional common SNPs, and to explore the role of rare or structural variants and gene-gene interactions in the heritability of circulating 25-hydroxyvitamin D levels.
The impact of water hyacinth (Eichhornia crassipes) on greenhouse gas emission and nutrient mobilization depends on rooting and plant coverage
Oliveira-Junior, Ernandes Sobreira ; Tang, Yingying ; Berg, Sanne J.P. van den; Cardoso, Simone J. ; Lamers, Leon P.M. ; Kosten, Sarian - \ 2018
Aquatic Botany 145 (2018). - ISSN 0304-3770 - p. 1 - 9.
Carbon dioxide - Eutrophication - Floating plant - Invasive species - Methane - Nutrient dynamics
Water hyacinth stands are known to affect both nutrient concentrations in the water and carbon exchange with the atmosphere. However, both enhanced and reduced greenhouse gas (GHG) emissions have been reported in relation to water hyacinth presence. This controversy may be explained by variation in plant density and rooting. High growth rates indicate its capacity to mobilize and store nutrients in the tissues, and assimilate large amounts of carbon dioxide (CO2). Simultaneously the plant can stimulate methane (CH4) emission. This may occur when plants are rooting in the sediment due to CH4 shuttling from the sediment, through the plant, into the atmosphere. To unravel the potential influences of water hyacinth on nutrient dynamics and GHG fluxes, we performed an experiment in which plant coverage and root access to the sediment were manipulated. Plants reduced phosphorus concentrations in water and pore-water, independent of coverage and rooting, also rooting plants grown at high coverage showed higher plant N:P ratios. CH4 emissions were highest at high coverage and were further increased by rooting, indicating that plant-mediated transport indeed takes place. However, the overall GHG budget in terms of CO2 equivalents still resulted in the water hyacinth vegetation being near neutral, or even a net sink with respect to GHG exchange. The plant-induced enhancement of CH4 emissions suggests that the plant can be an effective CO2-to-biomass-to-CH4 converter. Our results show that plant coverage and water depth – regulating sediment-root contact – should be taken into account when estimating water hyacinth's effect on GHG emissions.
Effect of butyrate release location on cecal microbiota composition of broilers
Moquet, P.C.A. ; Tang, C. ; Onrust, L. ; Kwakkel, R.P. - \ 2017
Higher plasticity in feeding preference of a generalist than a specialist : Experiments with two closely related Helicoverpa species
Wang, Yan ; Ma, Ying ; Zhou, Dong Sheng ; Gao, Su Xia ; Zhao, Xin Cheng ; Tang, Qing Bo ; Wang, Chen Zhu ; Loon, Joop J.A. van - \ 2017
Scientific Reports 7 (2017). - ISSN 2045-2322
Herbivorous insects have been categorized as generalists or specialists depending on the taxonomic relatedness of the plants they use as food or oviposition substrates. The plasticity in host plant selection behavior of species belonging to the two categories received little attention. In the present work, fifth instar caterpillars of the generalist herbivore Helicoverpa armigera and its closely related species, the specialist Helicoverpa assulta, were fed on common host plants or artificial diet, after which their feeding preference was assessed individually by using dual - and triple- plant choice assays. Results show both the two Helicoverpa species have a preference hierarchy for host plants. Compared to the fixed preference hierarchy of the specialist H. assulta, the generalist H. armigera exhibited extensive plasticity in feeding preference depending on the host plant experienced during larval development. Whereas the specialist H. assulta exhibited a rigid preference in both dual and triple-plant choice assays, our findings demonstrate that the generalist H. armigera expressed stronger preferences in the dual-plant choice assay than in the triple-plant choice assay. Our results provide additional evidence supporting the neural constraints hypothesis which predicts that generalist herbivores make less accurate decisions than specialists when selecting plants.
Combining hyperspectral UAV and multispectral Formosat-2 imagery for precision agriculture applications
Gevaert, C.M. ; Tang, J. ; García-Haro, F.J. ; Suomalainen, J. ; Kooistra, L. - \ 2017
In: 6th Workshop on Hyperspectral Image and Signal Processing. - IEEE computer society - ISBN 9781467390132 - 4 p.
precision agriculture - STARFM - UAV - unmixing-based data fusion - WDVI

Remote sensing is a key tool for precision agriculture applications as it is capable of capturing spatial and temporal variations in crop status. However, satellites often have an inadequate spatial resolution for precision agriculture applications. High-resolution Unmanned Aerial Vehicles (UAV) imagery can be obtained at flexible dates, but operational costs may limit the collection frequency. The current study utilizes data fusion to create a dataset which benefits from the temporal resolution of Formosat-2 imagery and the spatial resolution of UAV imagery with the purpose of monitoring crop growth in a potato field. The correlation of the Weighted Difference Vegetation Index (WDVI) from fused imagery to measured crop indicators at field level and added value of the enhanced spatial and temporal resolution are discussed. The results of the STARFM method were restrained by the requirement of same-day base imagery. However, the unmixing-based method provided a high correlation to the field data and accurately captured the WDVI temporal variation at field level (r=0.969).

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