Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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A historic perspective from a molecular view
Gent-Pelzer, Marga van; Vossenberg, Bart van de; Rijswick, Patricia van; Lee, Theo van der - \ 2019
Integrative pangenome analysis of the Pectobacterium genus
Jonkheer, Eef ; Brankovics, Balázs ; Houwers, I.M. ; Wolf, J.M. van der; Bonants, P.J.M. ; Vreeburg, R.A.M. ; Sheikhizadeh Anari, S. ; Ridder, D. de; Smit, S. ; Lee, T.A.J. van der - \ 2019
WGS of pygmy hog and Babyrousa babyrussa
Liu, Langqing ; Bosse, Mirte ; Megens, Hendrik-Jan ; Frantz, Laurent A.F. ; Lee, Young Lim ; Irving-Pease, Evan K. ; Narayan, Goutam ; Groenen, Martien ; Madsen, Ole - \ 2019
Wageningen University & Research
PRJEB30129 - ERP112560 - Babyrousa babyrussa - Porcula salvania
An alternative bioassay for Synchytrium endobioticum demonstrates the expression of potato wart resistance in aboveground plant parts
Vossenberg, Bart van de; Gent-Pelzer, Marga van; Boerma, M. ; Gouw, Lucas P. van der; Lee, Theo van der; Vossen, Jack - \ 2019
Wageningen University and Research
PRJEB30662 - ERP113139 - Synchytrium endobioticum
The obligate biotrophic chytrid species Synchytrium endobioticum is the causal agent of potato wart disease. Currently 39 pathotypes have been described based on their interaction with a differential set of potato varieties. Wart resistance and pathotyping is performed using bioassays in which etiolated tuber sprouts are inoculated. Here we describe an alternative method in which aboveground plant parts are inoculated. Susceptible plants produced typical wart symptoms in developing, but not in fully expanded, aboveground organs. Colonization of the host by S endobioticum was verified by screening for resting spores by microscopy and by molecular techniques using TaqMan PCR and RNAseq analysis. When applied to resistant plants, none of these symptoms were detectable. Recognition of S. endobioticum pathotypes by differentially resistant potato varieties was identical in aboveground plant parts and the tuber-based bioassays. This suggests that S. endobioticum resistance genes are expressed both in etiolated “belowground” sprouts and green aboveground organs. RNAseq analysis demonstrated that the symptomatic aboveground materials contain less contaminants compared to resting spores extracted from tuber-based assays. This reduced microbial contamination in the aboveground bioassay could be an important advantage to study this obligate biotrophic plant-pathogen interaction. As wart resistance is active in both below and above ground organs, the aboveground bioassay can potentially speed up screening for S. endobioticum resistance in potato breeding programs as it omits the requirement for tuber formation. In addition, possibilities arise to express S. endobioticum effectors in potato leaves through agroinfiltration, thereby providing additional phenotyping tools for research and breeding.
The Synchytrium endobioticum AvrSen1 triggers a Hypersensitive Response in Sen1 potatoes while natural variants evade detection
Vossenberg, Bart van de; Prodhomme, Charlotte ; Arkel, G. van; Gent-Pelzer, M.P.E. van; Bergervoet-van Deelen, J.E.M. ; Brankovics, Balázs ; Przetakiewicz, J. ; Visser, R.G.F. ; Lee, T.A.J. van der; Vossen, J.H. - \ 2019
Molecular Plant-Microbe Interactions 32 (2019)11. - ISSN 0894-0282 - p. 1536 - 1546.
avirulence factors - cell death - chytridiomycota - effector - fungus-plant interactions - Genomics - hypersensitive response - metabolomics - plant-pathogen interactions - population genetics - proteomics - resistance genes
Synchytrium endobioticum is an obligate biotrophic fungus of the phylum Chytridiomycota. It causes potato wart disease, has a world-wide quarantine status and is included on the HHS and USDA Select Agent list. S. endobioticum isolates are grouped in pathotypes based on their ability to evade host-resistance in a set of differential potato varieties. So far, thirty-nine pathotypes are reported. A single dominant gene (Sen1) governs pathotype 1 resistance and we anticipated that the underlying molecular model would involve a pathogen effector (AvrSen1) that is recognized by the host. The S. endobioticum specific secretome of fourteen isolates representing six different pathotypes was screened for effectors specifically present in pathotype 1(D1) isolates but absent in others. We identified a single AvrSen1 candidate. Expression of this candidate in potato Sen1 plants showed a specific hypersensitive response, which co-segregated with the Sen1 resistance in potato populations. No HR was obtained with truncated genes found in pathotypes that evaded recognition by Sen1. These findings established that our candidate gene was indeed Avrsen1. The S. endobioticum AvrSen1 is a single copy gene and encodes a 376 amino acid protein without predicted function or functional domains, and is the first effector gene identified in Chytridiomycota, an extremely diverse yet underrepresented basal lineage of fungi.
Creation of a new genus in the family Secoviridae substantiated by sequence variation of newly identified strawberry latent ringspot
Dullemans, A.M. ; Botermans, M. ; Kock, M.J.D. de; Krom, C.E. de; Lee, T.A.J. van der; Roenhorst, J.W. ; Stulemeijer, I.J.E. ; Verbeek, M. ; Westenberg, M. ; Vlugt, R.A.A. van der - \ 2019
Archives of Virology (2019). - ISSN 0304-8608 - 11 p.
To obtain insight into the sequence diversity of strawberry latent ringspot virus (SLRSV), isolates from collections and diagnostic samples were sequenced by high-throughput sequencing. For five SLRSV isolates, the complete genome sequences were determined, and for 18 other isolates nearly complete genome sequences were determined. The sequence data were analysed in relation to sequences of SLRSV and related virus isolates available in the NCBI GenBank database. The genome sequences were annotated, and sequences of the protease-polymerase (Pro-Pol) region and coat proteins (CPs) (large and small CP together) were used for phylogenetic analysis. The amino acid sequences of the Pro-Pol region were very similar, whereas the nucleotide sequences of this region were more variable. The amino acid sequences of the CPs were less similar, which was corroborated by the results of a serological comparison performed using antisera raised against different isolates of SLRSV. Based on these results, we propose that SLRSV and related unassigned viruses be assigned to a new genus within the family Secoviridae, named “Stralarivirus”. Based on the phylogenetic analysis, this genus should include at least three viruses, i.e., SLRSV-A, SLRSV-B and lychnis mottle virus. The newly generated sequence data provide a basis for designing molecular tests to screen for SLRSV.
The fertilization effect of global dimming on crop yields is not attributed to an improved light interception
Shao, Liping ; Li, Gang ; Zhao, Qiannan ; Li, Yabing ; Sun, Yutong ; Wang, Weinan ; Cai, Chuang ; Chen, Weiping ; Liu, Ronghua ; Luo, Weihong ; Yin, Xinyou ; Lee, Xuhui - \ 2019
Global Change Biology (2019). - ISSN 1354-1013
acclimation - diffuse radiation - fertilization effect - global dimming - radiation use efficiency - rice - wheat - yield

Global dimming, a decadal decrease in incident global radiation, is often accompanied with an increase in the diffuse radiation fraction, and, therefore, the impact of global dimming on crop production is hard to predict. A popular approach to quantify this impact is the statistical analysis of historical climate and crop data, or use of dynamic crop simulation modelling approach. Here, we show that statistical analysis of historical data did not provide plausible values for the effect of diffuse radiation versus direct radiation on rice or wheat yield. In contrast, our field experimental study of 3 years demonstrated a fertilization effect of increased diffuse radiation fraction, which partly offset yield losses caused by decreased global radiation, in both crops. The fertilization effect was not attributed to any improved canopy light interception but mainly to the increased radiation use efficiency (RUE). The increased RUE was explained not only by the saturating shape of photosynthetic light response curves but also by plant acclimation to dimming that gradually increased leaf nitrogen concentration. Crop harvest index slightly decreased under dimming, thereby discounting the fertilization effect on crop yields. These results challenge existing modelling paradigms, which assume that the fertilization effect on crop yields is mainly attributed to an improved light interception. Further studies on the physiological mechanism of plant acclimation are required to better quantify the global dimming impact on agroecosystem productivity under future climate change.

NODULE INCEPTION Recruits the Lateral Root Developmental Program for Symbiotic Nodule Organogenesis in Medicago truncatula
Schiessl, Katharina ; Lilley, Jodi L.S. ; Lee, Tak ; Tamvakis, Ioannis ; Kohlen, Wouter ; Bailey, Paul C. ; Thomas, Aaron ; Luptak, Jakub ; Ramakrishnan, Karunakaran ; Carpenter, Matthew D. ; Mysore, Kirankumar S. ; Wen, Jiangqi ; Ahnert, Sebastian ; Grieneisen, Veronica A. ; Oldroyd, Giles E.D. - \ 2019
Current Biology 29 (2019)21. - ISSN 0960-9822 - p. 3657 - 3668.e5.
auxin - CYTOKININ RESPONSE FACTOR - endosymbiosis - LATERAL ORGAN BOUNDARIES DOMAIN - lateral root/nodule organogenesis - Medicago truncatula - nitrogen - NODULE INCEPTION - rhizobia - YUCCA

To overcome nitrogen deficiencies in the soil, legumes enter symbioses with rhizobial bacteria that convert atmospheric nitrogen into ammonium. Rhizobia are accommodated as endosymbionts within lateral root organs called nodules that initiate from the inner layers of Medicago truncatula roots in response to rhizobial perception. In contrast, lateral roots emerge from predefined founder cells as an adaptive response to environmental stimuli, including water and nutrient availability. CYTOKININ RESPONSE 1 (CRE1)-mediated signaling in the pericycle and in the cortex is necessary and sufficient for nodulation, whereas cytokinin is antagonistic to lateral root development, with cre1 showing increased lateral root emergence and decreased nodulation. To better understand the relatedness between nodule and lateral root development, we undertook a comparative analysis of these two root developmental programs. Here, we demonstrate that despite differential induction, lateral roots and nodules share overlapping developmental programs, with mutants in LOB-DOMAIN PROTEIN 16 (LBD16) showing equivalent defects in nodule and lateral root initiation. The cytokinin-inducible transcription factor NODULE INCEPTION (NIN) allows induction of this program during nodulation through activation of LBD16 that promotes auxin biosynthesis via transcriptional induction of STYLISH (STY) and YUCCAs (YUC). We conclude that cytokinin facilitates local auxin accumulation through NIN promotion of LBD16, which activates a nodule developmental program overlapping with that induced during lateral root initiation.

Supporting Information for: Scale-dependent evanescence of river dunes during discharge extremes
Naqshband, Suleyman ; Hoitink, Ton - \ 2019
Wageningen University & Research
river dunes - sediment transport - upper stage plane bed
Data contains dune slipface angles (steepest part of the dune lee-face) for different experimental conditions as shown in figure 4 of the submitted manuscript. The slipface angles are derived using a widely used bedform tracking tool.
The Impact of Genomic and Traditional Selection on the Contribution of Mutational Variance to Long-Term Selection Response and Genetic Variance
Mulder, Herman A. ; Lee, Sang Hong ; Clark, Sam ; Hayes, Ben J. ; Werf, Julius H.J. van der - \ 2019
Genetics 213 (2019)2. - ISSN 0016-6731 - p. 361 - 378.
de novo mutation - genetic variance - genomic selection - response to selection - selection strategies

De novo mutations (DNM) create new genetic variance and are an important driver for long-term selection response. We hypothesized that genomic selection exploits mutational variance less than traditional selection methods such as mass selection or selection on pedigree-based breeding values, because DNM in selection candidates are not captured when the selection candidates' own phenotype is not used in genomic selection, DNM are not on SNP chips and DNM are not in linkage disequilibrium with the SNP on the chip. We tested this hypothesis with Monte Carlo simulation. From whole-genome sequence data, a subset of ∼300,000 variants was used that served as putative markers, quantitative trait loci or DNM. We simulated 20 generations with truncation selection based on breeding values from genomic best linear unbiased prediction without (GBLUP_no_OP) or with own phenotype (GBLUP_OP), pedigree-based BLUP without (BLUP_no_OP) or with own phenotype (BLUP_OP), or directly on phenotype. GBLUP_OP was the best strategy in exploiting mutational variance, while GBLUP_no_OP and BLUP_no_OP were the worst in exploiting mutational variance. The crucial element is that GBLUP_no_OP and BLUP_no_OP puts no selection pressure on DNM in selection candidates. Genetic variance decreased faster with GBLUP_no_OP and GBLUP_OP than with BLUP_no_OP, BLUP_OP or mass selection. The distribution of mutational effects, mutational variance, number of DNM per individual and nonadditivity had a large impact on mutational selection response and mutational genetic variance, but not on ranking of selection strategies. We advocate that more sustainable genomic selection strategies are required to optimize long-term selection response and to maintain genetic diversity.

3R Kenya (Robust, Reliable and Resilient) - From aid to trade project : Annual report 2018
Koge, Jessica ; Kilelu, Catherine ; Coninx, I. ; Vugt, S.M. van; Lee, J. van der; Koomen, I. ; Soma, K. ; Obwanga, Benson ; Gema, Joyce ; Omedo Bebe, Bockline - \ 2019
Wageningen Centre for Development Innovation (WCDI-19-057 )
Selection and gene flow shape niche-associated variation in pheromone response
Lee, Daehan ; Zdraljevic, Stefan ; Cook, Daniel E. ; Frézal, Lise ; Hsu, Jung-Chen ; Sterken, Mark G. ; Riksen, Joost A.G. ; Wang, John ; Kammenga, Jan E. ; Braendle, Christian ; Félix, Marie-Anne ; Schroeder, Frank C. ; Andersen, Erik C. - \ 2019
Nature Ecology & Evolution 3 (2019). - ISSN 2397-334X - p. 1455 - 1463.
From quorum sensing in bacteria to pheromone signalling in social insects, chemical communication mediates interactions among individuals in local populations. In Caenorhabditis elegans, ascaroside pheromones can dictate local population density; high levels of pheromones inhibit the reproductive maturation of individuals. Little is known about how natural genetic diversity affects the pheromone responses of individuals from diverse habitats. Here, we show that a niche-associated variation in pheromone receptor genes contributes to natural differences in pheromone responses. We identified putative loss-of-function deletions that impair duplicated pheromone receptor genes (srg-36 and srg-37), which were previously shown to be lost in population-dense laboratory cultures. A common natural deletion in srg-37 arose recently from a single ancestral population that spread throughout the world; this deletion underlies reduced pheromone sensitivity across the global C. elegans population. We found that many local populations harbour individuals with a wild-type or a deletion allele of srg-37, suggesting that balancing selection has maintained the recent variation in this pheromone receptor gene. The two srg-37 genotypes are associated with niche diversity underlying boom-and-bust population dynamics. We hypothesize that human activities likely contributed to the gene flow and balancing selection of srg-37 variation through facilitating the migration of species and providing a favourable niche for the recently arisen srg-37 deletion.

FgPex3, a Peroxisome Biogenesis Factor, Is Involved in Regulating Vegetative Growth, Conidiation, Sexual Development, and Virulence in Fusarium graminearum
Kong, Xiangjiu ; Zhang, Hao ; Wang, Xiaoliang ; Lee, T.A.J. van der; Waalwijk, C. ; Diepeningen, A.D. van; Brankovics, Balázs ; Xu, Jin ; Xu, Jingsheng ; Chen, Wanquan ; Feng, Jie - \ 2019
Frontiers in Microbiology 10 (2019). - ISSN 1664-302X
Peroxisomes are involved in a wide range of important cellular functions. Here, the role of the peroxisomal membrane protein PEX3 in the plant-pathogen and mycotoxin producer Fusarium graminearum was studied using knock-out and complemented strains. To fluorescently label peroxisomes’ punctate structures, GFP and RFP fusions with the PTS1 and PTS2 localization signal were transformed into the wild type PH- 1 and 1FgPex3 knock-out strains. The GFP and RFP transformants in the 1FgPex3 background showed a diffuse fluorescence pattern across the cytoplasm suggesting the absence of mature peroxisomes. The 1FgPex3 strain showed a minor, non-significant reduction in growth on various sugar carbon sources. In contrast, deletion of FgPex3 affected fatty acid b-oxidation in F. graminearum and significantly reduced the utilization of fatty acids. Furthermore, the 1FgPex3 mutant was sensitive to osmotic stressors
as well as to cell wall-damaging agents. Reactive oxygen species (ROS) levels in the mutant had increased significantly, which may be linked to the reduced longevity of cultured strains. The mutant also showed reduced production of conidiospores, while sexual reproduction was completely impaired. The pathogenicity of 1FgPex3, especially during the process of systemic infection, was strongly reduced on both tomato and on wheat, while to production of deoxynivalenol (DON), an important factor for virulence, appeared to be unaffected.
Assessment of policy instruments for pesticide use reduction in Europe; Learning from a systematic literature review
Lee, Rhiannon ; Uyl, Roos den; Runhaar, Hens - \ 2019
Crop Protection 126 (2019). - ISSN 0261-2194
Agrochemicals - Biodiversity - Environmental Governance - IPM (Integrated Pest Management) - Sustainable Agriculture

Intensive and worldwide usage of conventional pesticides on arable land has led to varying problems for the environment and human health. Consequently, many governments and several private actors actively stimulate reduction of pesticide use. This paper focuses on the effectiveness of public and private policy instruments in terms of reducing pesticide use by farmers via a systematic literature review of 78 articles published between 1967 and 2017. The geographical focus area was Europe. The review determined that no specific instrument is guaranteed to reduce pesticide use. Instead, characteristics comprising an instrument were confirmed to be beneficial to reducing pesticide use. In particular, mixes of instruments, with varying degrees of authoritative force, applied at multiple scales with stakeholder collaboration were identified as beneficial to reducing farmer pesticide use. It is implied within the literature that instruments comprised of such characteristics aid reducing pesticide use due to facilitating consideration of heterogeneous farm and farmer characteristics.

Enhancing knowledge and skills for the agri-food sector: The emerging market-led extension and advisory services in Kenya
Kilelu, C.W. ; Lee, J. van der; Opola, Felix - \ 2019
Wageningen University & Research (3R Kenya Issue Brief 002) - 7 p.
An Alternative Bioassay for Synchytrium endobioticum Demonstrates the Expression of Potato Wart Resistance in Aboveground Plant Parts
Vossenberg, B.T.L.H. van de; Gent-Pelzer, M.P.E. van; Boerma, M. ; Gouw, L.P. van der; Lee, T.A.J. van der; Vossen, J.H. - \ 2019
Phytopathology 109 (2019)6. - ISSN 0031-949X - p. 1043 - 1052.
Genetics and resistance - Molecular verification - Mycology - Pathogen proliferation - Plant–pathogen interaction - RNAseq - Species richness - Techniques

The obligate biotrophic chytrid species Synchytrium endobioticum is the causal agent of potato wart disease. Currently, 39 pathotypes have been described based on their interaction with a differential set of potato varieties. Wart resistance and pathotyping is performed using bioassays in which etiolated tuber sprouts are inoculated. Here, we describe an alternative method in which aboveground plant parts are inoculated. Susceptible plants produced typical wart symptoms in developing but not in fully expanded aboveground organs. Colonization of the host by S. endobioticum was verified by screening for resting spores by microscopy and by molecular techniques using TaqMan polymerase chain reaction and RNAseq analysis. When applied to resistant plants, none of these symptoms were detectable. Recognition of S. endobioticum pathotypes by differentially resistant potato varieties was identical in axillary buds and the tuber-based bioassays. This suggests that S. endobioticum resistance genes are expressed in both etiolated “belowground” sprouts and green aboveground organs. RNAseq analysis demonstrated that the symptomatic aboveground materials contain less contaminants compared with resting spores extracted from tuber-based assays. This reduced microbial contamination in the aboveground bioassay could be an important advantage to study this obligate biotrophic plant–pathogen interaction. Because wart resistance is active in both below- and aboveground organs, the aboveground bioassay can potentially speed up screening for S. endobioticum resistance in potato breeding programs because it omits the requirement for tuber formation. In addition, possibilities arise to express S. endobioticum effectors in potato leaves through agroinfiltration, thereby providing additional phenotyping tools for research and breeding.

National Reference Laboratories WFSR : annual report 2018
Noordam, M.Y. ; Silletti, E. ; Alewijn, A. ; Scholtens, I.M.J. ; Jong, J. de; Raamsdonk, L. aan; Lasaroms, J.J.P. ; Gerssen, A. ; Lee, M.K. van der; Mol, J.G.J. ; Leeuwen, S.P.J. van - \ 2019
Wageningen : Wageningen University & Research (WFSR-report 2018.011) - 51
Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
Bolyen, Evan ; Rideout, Jai Ram ; Dillon, Matthew R. ; Bokulich, Nicholas A. ; Abnet, Christian C. ; Al-Ghalith, Gabriel A. ; Alexander, Harriet ; Alm, Eric J. ; Arumugam, Manimozhiyan ; Asnicar, Francesco ; Bai, Yang ; Bisanz, Jordan E. ; Bittinger, Kyle ; Brejnrod, Asker ; Brislawn, Colin J. ; Brown, C.T. ; Callahan, Benjamin J. ; Caraballo-Rodríguez, Andrés Mauricio ; Chase, John ; Cope, Emily K. ; Silva, Ricardo Da; Diener, Christian ; Dorrestein, Pieter C. ; Douglas, Gavin M. ; Durall, Daniel M. ; Duvallet, Claire ; Edwardson, Christian F. ; Ernst, Madeleine ; Estaki, Mehrbod ; Fouquier, Jennifer ; Gauglitz, Julia M. ; Gibbons, Sean M. ; Gibson, Deanna L. ; Gonzalez, Antonio ; Gorlick, Kestrel ; Guo, Jiarong ; Hillmann, Benjamin ; Holmes, Susan ; Holste, Hannes ; Huttenhower, Curtis ; Huttley, Gavin A. ; Janssen, Stefan ; Jarmusch, Alan K. ; Jiang, Lingjing ; Kaehler, Benjamin D. ; Kang, Kyo Bin ; Keefe, Christopher R. ; Keim, Paul ; Kelley, Scott T. ; Knights, Dan ; Koester, Irina ; Kosciolek, Tomasz ; Kreps, Jorden ; Langille, Morgan G.I. ; Lee, Joslynn ; Ley, Ruth ; Liu, Yong Xin ; Loftfield, Erikka ; Lozupone, Catherine ; Maher, Massoud ; Marotz, Clarisse ; Martin, Bryan D. ; McDonald, Daniel ; McIver, Lauren J. ; Melnik, Alexey V. ; Metcalf, Jessica L. ; Morgan, Sydney C. ; Morton, Jamie T. ; Naimey, Ahmad Turan ; Navas-Molina, Jose A. ; Nothias, Louis Felix ; Orchanian, Stephanie B. ; Pearson, Talima ; Peoples, Samuel L. ; Petras, Daniel ; Preuss, Mary Lai ; Pruesse, Elmar ; Rasmussen, Lasse Buur ; Rivers, Adam ; Robeson, Michael S. ; Rosenthal, Patrick ; Segata, Nicola ; Shaffer, Michael ; Shiffer, Arron ; Sinha, Rashmi ; Song, Se Jin ; Spear, John R. ; Swafford, Austin D. ; Thompson, Luke R. ; Torres, Pedro J. ; Trinh, Pauline ; Tripathi, Anupriya ; Turnbaugh, Peter J. ; Ul-Hasan, Sabah ; Hooft, Justin J.J. van der; Vargas, Fernando ; Vázquez-Baeza, Yoshiki ; Vogtmann, Emily ; Hippel, Max von; Walters, William ; Wan, Yunhu ; Wang, Mingxun ; Warren, Jonathan ; Weber, Kyle C. ; Williamson, Charles H.D. ; Willis, Amy D. ; Xu, Zhenjiang Zech ; Zaneveld, Jesse R. ; Zhang, Yilong ; Zhu, Qiyun ; Knight, Rob ; Caporaso, J.G. - \ 2019
Nature Biotechnology (2019). - ISSN 1087-0156

In the version of this article initially published, some reference citations were incorrect. The three references to Jupyter Notebooks should have cited Kluyver et al. instead of Gonzalez et al. The reference to Qiita should have cited Gonzalez et al. instead of Schloss et al. The reference to mothur should have cited Schloss et al. instead of McMurdie & Holmes. The reference to phyloseq should have cited McMurdie & Holmes instead of Huber et al. The reference to Bioconductor should have cited Huber et al. instead of Franzosa et al. And the reference to the biobakery suite should have cited Franzosa et al. instead of Kluyver et al. The errors have been corrected in the HTML and PDF versions of the article.

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
Bolyen, Evan ; Rideout, Jai Ram ; Dillon, Matthew R. ; Bokulich, Nicholas A. ; Abnet, Christian C. ; Al-Ghalith, Gabriel A. ; Alexander, Harriet ; Alm, Eric J. ; Arumugam, Manimozhiyan ; Asnicar, Francesco ; Bai, Yang ; Bisanz, Jordan E. ; Bittinger, Kyle ; Brejnrod, Asker ; Brislawn, Colin J. ; Brown, Titus C. ; Callahan, Benjamin J. ; Caraballo-Rodríguez, Andrés Mauricio ; Chase, John ; Cope, Emily K. ; Silva, Ricardo da; Diener, Christian ; Dorrestein, Pieter C. ; Douglas, Gavin M. ; Durall, Daniel M. ; Duvallet, Claire ; Edwardson, Christian F. ; Ernst, Madeleine ; Estaki, Mehrbod ; Fouquier, Jennifer ; Gauglitz, Julia M. ; Gibbons, Sean M. ; Gibson, Deanna L. ; Gonzalez, Antonio ; Gorlick, Kestrel ; Guo, Jiarong ; Hillmann, Benjamin ; Holmes, Susan ; Holste, Hannes ; Huttenhower, Curtis ; Huttley, Gavin A. ; Janssen, Stefan ; Jarmusch, Alan K. ; Jiang, Lingjing ; Kaehler, Benjamin D. ; Kang, Kyo Bin ; Keefe, Christopher R. ; Keim, Paul ; Kelley, Scott T. ; Knights, Dan ; Koester, Irina ; Kosciolek, Tomasz ; Kreps, Jorden ; Langille, Morgan G.I. ; Lee, Joslynn ; Ley, Ruth ; Liu, Yong Xin ; Loftfield, Erikka ; Lozupone, Catherine ; Maher, Massoud ; Marotz, Clarisse ; Martin, Bryan D. ; McDonald, Daniel ; McIver, Lauren J. ; Melnik, Alexey V. ; Metcalf, Jessica L. ; Morgan, Sydney C. ; Morton, Jamie T. ; Naimey, Ahmad Turan ; Navas-Molina, Jose A. ; Nothias, Louis Felix ; Orchanian, Stephanie B. ; Pearson, Talima ; Peoples, Samuel L. ; Petras, Daniel ; Preuss, Mary Lai ; Pruesse, Elmar ; Rasmussen, Lasse Buur ; Rivers, Adam ; Robeson, Michael S. ; Rosenthal, Patrick ; Segata, Nicola ; Shaffer, Michael ; Shiffer, Arron ; Sinha, Rashmi ; Song, Se Jin ; Spear, John R. ; Swafford, Austin D. ; Thompson, Luke R. ; Torres, Pedro J. ; Trinh, Pauline ; Tripathi, Anupriya ; Turnbaugh, Peter J. ; Ul-Hasan, Sabah ; Hooft, Justin J.J. van der; Vargas, Fernando ; Vázquez-Baeza, Yoshiki ; Vogtmann, Emily ; Hippel, Max von; Walters, William ; Wan, Yunhu ; Wang, Mingxun ; Warren, Jonathan ; Weber, Kyle C. ; Williamson, Charles H.D. ; Willis, Amy D. ; Xu, Zhenjiang Zech ; Zaneveld, Jesse R. ; Zhang, Yilong ; Zhu, Qiyun ; Knight, Rob ; Caporaso, J.G. - \ 2019
Nature Biotechnology 37 (2019)8. - ISSN 1087-0156 - p. 852 - 857.
antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline
Blin, Kai ; Shaw, Simon ; Steinke, Katharina ; Villebro, Rasmus ; Ziemert, Nadine ; Lee, Sang Yup ; Medema, Marnix H. ; Weber, Tilmann - \ 2019
Nucleic acids research 47 (2019)W1. - ISSN 0305-1048 - p. W81 - W87.

Secondary metabolites produced by bacteria and fungi are an important source of antimicrobials and other bioactive compounds. In recent years, genome mining has seen broad applications in identifying and characterizing new compounds as well as in metabolic engineering. Since 2011, the 'antibiotics and secondary metabolite analysis shell-antiSMASH' (https://antismash.secondarymetabolites.org) has assisted researchers in this, both as a web server and a standalone tool. It has established itself as the most widely used tool for identifying and analysing biosynthetic gene clusters (BGCs) in bacterial and fungal genome sequences. Here, we present an entirely redesigned and extended version 5 of antiSMASH. antiSMASH 5 adds detection rules for clusters encoding the biosynthesis of acyl-amino acids, β-lactones, fungal RiPPs, RaS-RiPPs, polybrominated diphenyl ethers, C-nucleosides, PPY-like ketones and lipolanthines. For type II polyketide synthase-encoding gene clusters, antiSMASH 5 now offers more detailed predictions. The HTML output visualization has been redesigned to improve the navigation and visual representation of annotations. We have again improved the runtime of analysis steps, making it possible to deliver comprehensive annotations for bacterial genomes within a few minutes. A new output file in the standard JavaScript object notation (JSON) format is aimed at downstream tools that process antiSMASH results programmatically.

Quantitative trait loci analysis of hormone levels in Arabidopsis roots
Lee, Sangseok ; Sergeeva, Lidiya I. ; Vreugdenhil, Dick - \ 2019
PLoS ONE 14 (2019)6. - ISSN 1932-6203

Quantitative trait loci (QTL) analyses for five groups of hormones, including cytokinins in Arabidopsis roots were performed using recombinant inbred lines (Ler×Cvi). Significant QTLs were detected for cytokinins, jasmonic acid and salicylic acid. Separate analysis of two sub-populations, viz., vegetative and flowering plants revealed that many of the QTLs were development-specific. Using near-isogenic lines, several significant QTLs were confirmed; three co-localized QTL regions were responsible for determining several cytokinin metabolites. Using a knock-out plant, a functional role of zeatin N-glucosyltransferase gene (UGT76C2) underlying a large-effect QTL for levels of tZ-N-glucosides and tZRMP was evaluated in the metabolism of cytokinins. Pleotropic effects of this gene were found for cytokinin levels in both roots and leaves, but significant changes of morphological traits were observed only in roots. Hormone QTL analysis reveals development-specific and organ-dependent aspects of the regulation of plant hormone content and metabolism.

Comparative genomics of chytrid fungi reveal insights into the obligate biotrophic and pathogenic lifestyle of Synchytrium endobioticum
Vossenberg, Bart T.L.H. van de; Warris, Sven ; Nguyen, Hai D.T. ; Gent-Pelzer, Marga P.E. van; Joly, David L. ; Geest, Henri C. van de; Bonants, Peter J.M. ; Smith, Donna S. ; Lévesque, André C. ; Lee, Theo A.J. van der - \ 2019
Scientific Reports 9 (2019)1. - ISSN 2045-2322

Synchytrium endobioticum is an obligate biotrophic soilborne Chytridiomycota (chytrid) species that causes potato wart disease, and represents the most basal lineage among the fungal plant pathogens. We have chosen a functional genomics approach exploiting knowledge acquired from other fungal taxa and compared this to several saprobic and pathogenic chytrid species. Observations linked to obligate biotrophy, genome plasticity and pathogenicity are reported. Essential purine pathway genes were found uniquely absent in S. endobioticum, suggesting that it relies on scavenging guanine from its host for survival. The small gene-dense and intron-rich chytrid genomes were not protected for genome duplications by repeat-induced point mutation. Both pathogenic chytrids Batrachochytrium dendrobatidis and S. endobioticum contained the largest amounts of repeats, and we identified S. endobioticum specific candidate effectors that are associated with repeat-rich regions. These candidate effectors share a highly conserved motif, and show isolate specific duplications. A reduced set of cell wall degrading enzymes, and LysM protein expansions were found in S. endobioticum, which may prevent triggering plant defense responses. Our study underlines the high diversity in chytrids compared to the well-studied Ascomycota and Basidiomycota, reflects characteristic biological differences between the phyla, and shows commonalities in genomic features among pathogenic fungi.

Disease-free monoculture farming by fungus-growing termites
Otani, Saria ; Challinor, Victoria L. ; Kreuzenbeck, Nina B. ; Kildgaard, Sara ; Krath Christensen, Søren ; Larsen, Louise Lee Munk ; Aanen, Duur K. ; Rasmussen, Silas Anselm ; Beemelmanns, Christine ; Poulsen, Michael - \ 2019
Scientific Reports 9 (2019)1. - ISSN 2045-2322

Fungus-growing termites engage in an obligate mutualistic relationship with Termitomyces fungi, which they maintain in monocultures on specialised fungus comb structures, without apparent problems with infectious diseases. While other fungi have been reported in the symbiosis, detailed comb fungal community analyses have been lacking. Here we use culture-dependent and -independent methods to characterise fungus comb mycobiotas from three fungus-growing termite species (two genera). Internal Transcribed Spacer (ITS) gene analyses using 454 pyrosequencing and Illumina MiSeq showed that non-Termitomyces fungi were essentially absent in fungus combs, and that Termitomyces fungal crops are maintained in monocultures as heterokaryons with two or three abundant ITS variants in a single fungal strain. To explore whether the essential absence of other fungi within fungus combs is potentially due to the production of antifungal metabolites by Termitomyces or comb bacteria, we performed in vitro assays and found that both Termitomyces and chemical extracts of fungus comb material can inhibit potential fungal antagonists. Chemical analyses of fungus comb material point to a highly complex metabolome, including compounds with the potential to play roles in mediating these contaminant-free farming conditions in the termite symbiosis.

Patterns of nitrogen-fixing tree abundance in forests across Asia and America
Menge, Duncan N.L. ; Chisholm, Ryan A. ; Davies, Stuart J. ; Abu Salim, Kamariah ; Allen, David ; Alvarez, Mauricio ; Bourg, Norm ; Brockelman, Warren Y. ; Bunyavejchewin, Sarayudh ; Butt, Nathalie ; Cao, Min ; Chanthorn, Wirong ; Chao, Wei Chun ; Clay, Keith ; Condit, Richard ; Cordell, Susan ; Silva, João Batista da; Dattaraja, H.S. ; Andrade, Ana Cristina Segalin de; Oliveira, Alexandre A. de; Ouden, Jan den; Drescher, Michael ; Fletcher, Christine ; Giardina, Christian P. ; Savitri Gunatilleke, C.V. ; Gunatilleke, I.A.U.N. ; Hau, Billy C.H. ; He, Fangliang ; Howe, Robert ; Hsieh, Chang Fu ; Hubbell, Stephen P. ; Inman-Narahari, Faith M. ; Jansen, Patrick A. ; Johnson, Daniel J. ; Kong, Lee Sing ; Král, Kamil ; Ku, Chen Chia ; Lai, Jiangshan ; Larson, Andrew J. ; Li, Xiankun ; Li, Yide ; Lin, Luxiang ; Lin, Yi Ching ; Liu, Shirong ; Lum, Shawn K.Y. ; Lutz, James A. ; Ma, Keping ; Malhi, Yadvinder ; McMahon, Sean ; McShea, William ; Mi, Xiangcheng ; Morecroft, Michael ; Myers, Jonathan A. ; Nathalang, Anuttara ; Novotny, Vojtech ; Ong, Perry ; Orwig, David A. ; Ostertag, Rebecca ; Parker, Geoffrey ; Phillips, Richard P. ; Abd. Rahman, Kassim ; Sack, Lawren ; Sang, Weiguo ; Shen, Guochun ; Shringi, Ankur ; Shue, Jessica ; Su, Sheng Hsin ; Sukumar, Raman ; Fang Sun, I. ; Suresh, H.S. ; Tan, Sylvester ; Thomas, Sean C. ; Toko, Pagi S. ; Valencia, Renato ; Vallejo, Martha I. ; Vicentini, Alberto ; Vrška, Tomáš ; Wang, Bin ; Wang, Xihua ; Weiblen, George D. ; Wolf, Amy ; Xu, Han ; Yap, Sandra ; Zhu, Li ; Fung, Tak - \ 2019
Journal of Ecology 107 (2019)6. - ISSN 0022-0477 - p. 2598 - 2610.
forest - legume - nitrogen fixation - nutrient limitation - Smithsonian ForestGEO - symbiosis

Symbiotic nitrogen (N)-fixing trees can provide large quantities of new N to ecosystems, but only if they are sufficiently abundant. The overall abundance and latitudinal abundance distributions of N-fixing trees are well characterised in the Americas, but less well outside the Americas. Here, we characterised the abundance of N-fixing trees in a network of forest plots spanning five continents, ~5,000 tree species and ~4 million trees. The majority of the plots (86%) were in America or Asia. In addition, we examined whether the observed pattern of abundance of N-fixing trees was correlated with mean annual temperature and precipitation. Outside the tropics, N-fixing trees were consistently rare in the forest plots we examined. Within the tropics, N-fixing trees were abundant in American but not Asian forest plots (~7% versus ~1% of basal area and stems). This disparity was not explained by mean annual temperature or precipitation. Our finding of low N-fixing tree abundance in the Asian tropics casts some doubt on recent high estimates of N fixation rates in this region, which do not account for disparities in N-fixing tree abundance between the Asian and American tropics. Synthesis. Inputs of nitrogen to forests depend on symbiotic nitrogen fixation, which is constrained by the abundance of N-fixing trees. By analysing a large dataset of ~4 million trees, we found that N-fixing trees were consistently rare in the Asian tropics as well as across higher latitudes in Asia, America and Europe. The rarity of N-fixing trees in the Asian tropics compared with the American tropics might stem from lower intrinsic N limitation in Asian tropical forests, although direct support for any mechanism is lacking. The paucity of N-fixing trees throughout Asian forests suggests that N inputs to the Asian tropics might be lower than previously thought.

From metagenome to gene : Identification of the first Synchytrium endobioticum effector through comparative genomics
Vossenberg, Bartholomeus Theodorus Leonardus Henricus van de - \ 2019
Wageningen University. Promotor(en): R.G.F. Visser, co-promotor(en): T.A.J. van der Lee; J.H. Vossen. - Wageningen : Wageningen University - ISBN 9789463439640 - 290
Brominated flame retardants in animal derived foods in the Netherlands between 2009 and 2014
Gebbink, Wouter A. ; Lee, Martijn K. van der; Peters, Ruud J.B. ; Traag, Wim A. ; Dam, Guillaume ten; Hoogenboom, Ron L.A.P. ; Leeuwen, Stefan P.J. van - \ 2019
Chemosphere 234 (2019). - ISSN 0045-6535 - p. 171 - 178.
Eggs - Fish - HBCDD - Meat - Milk - PBDE

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

Prediction of enteric methane production, yield and intensity of beef cattle using an intercontinental database
Lingen, Henk J. van; Niu, Mutian ; Kebreab, Ermias ; Valadares Filho, Sebastião C. ; Rooke, John A. ; Duthie, Carol Anne ; Schwarm, Angela ; Kreuzer, Michael ; Hynd, Phil I. ; Caetano, Mariana ; Eugène, Maguy ; Martin, Cécile ; McGee, Mark ; O'Kiely, Padraig ; Hünerberg, Martin ; McAllister, Tim A. ; Berchielli, Telma T. ; Messana, Juliana D. ; Peiren, Nico ; Chaves, Alex V. ; Charmley, Ed ; Cole, N.A. ; Hales, Kristin E. ; Lee, Sang Suk ; Berndt, Alexandre ; Reynolds, Christopher K. ; Crompton, Les A. ; Bayat, Ali R. ; Yáñez-Ruiz, David R. ; Yu, Zhongtang ; Bannink, André ; Dijkstra, Jan ; Casper, David P. ; Hristov, Alexander N. - \ 2019
Agriculture, Ecosystems and Environment 283 (2019). - ISSN 0167-8809
Dietary variables - Empirical modeling - Forage content - Geographical region - Methane emission

Enteric methane (CH4) production attributable to beef cattle contributes to global greenhouse gas emissions. Reliably estimating this contribution requires extensive CH4 emission data from beef cattle under different management conditions worldwide. The objectives were to: 1) predict CH4 production (g d−1 animal−1), yield [g (kg dry matter intake; DMI)−1] and intensity [g (kg average daily gain)−1] using an intercontinental database (data from Europe, North America, Brazil, Australia and South Korea); 2) assess the impact of geographic region, and of higher- and lower-forage diets. Linear models were developed by incrementally adding covariates. A K-fold cross-validation indicated that a CH4 production equation using only DMI that was fitted to all available data had a root mean square prediction error (RMSPE; % of observed mean) of 31.2%. Subsets containing data with ≥25% and ≤18% dietary forage contents had an RMSPE of 30.8 and 34.2%, with the all-data CH4 production equation, whereas these errors decreased to 29.3 and 28.4%, respectively, when using CH4 prediction equations fitted to these subsets. The RMSPE of the ≥25% forage subset further decreased to 24.7% when using multiple regression. Europe- and North America-specific subsets predicted by the best performing ≥25% forage multiple regression equation had RMSPE of 24.5 and 20.4%, whereas these errors were 24.5 and 20.0% with region-specific equations, respectively. The developed equations had less RMSPE than extant equations evaluated for all data (22.5 vs. 23.2%), for higher-forage (21.2 vs. 23.1%), but not for the lower-forage subsets (28.4 vs. 27.9%). Splitting the dataset by forage content did not improve CH4 yield or intensity predictions. Predicting beef cattle CH4 production using energy conversion factors, as applied by the Intergovernmental Panel on Climate Change, indicated that adequate forage content-based and region-specific energy conversion factors improve prediction accuracy and are preferred in national or global inventories.

Oyster breakwater reefs promote adjacent mudflat stability and salt marsh growth in a monsoon dominated subtropical coast
Chowdhury, Mohammed Shah Nawaz ; Walles, Brenda ; Sharifuzzaman, Sm ; Shahadat Hossain, M. ; Ysebaert, Tom ; Smaal, Aad C. - \ 2019
Scientific Reports 9 (2019)1. - ISSN 2045-2322

Oyster reefs have the potential as eco-engineers to improve coastal protection. A field experiment was undertaken to assess the benefit of oyster breakwater reefs to mitigate shoreline erosion in a monsoon-dominated subtropical system. Three breakwater reefs with recruited oysters were deployed on an eroding intertidal mudflat at Kutubdia Island, the southeast Bangladesh coast. Data were collected on wave dissipation by the reef structures, changes in shoreline profile, erosion-accretion patterns, and lateral saltmarsh movement and related growth. This was done over four seasons, including the rainy monsoon period. The observed wave heights in the study area ranged 0.1–0.5 m. The reefs were able to dissipate wave energy and act as breakwaters for tidal water levels between 0.5–1.0 m. Waves were totally blocked by the vertical relief of the reefs at water levels <0.5 m. On the lee side of the reefs, there was accretion of 29 cm clayey sediments with erosion reduction of 54% as compared to control sites. The changes caused by the deployed reefs also facilitated seaward expansion of the salt marsh. This study showed that breakwater oyster reefs can reduce erosion, trap suspended sediment, and support seaward saltmarsh expansion demonstrating the potential as a nature-based solution for protecting the subtropical coastlines.

Glucosinolate variability between turnip organs during development
Bonnema, Guusje ; Lee, Jun Gu ; Shuhang, Wang ; Lagarrigue, David ; Bucher, Johan ; Wehrens, Ron ; Vos, Ric De; Beekwilder, Jules - \ 2019
PLoS ONE 14 (2019)6. - ISSN 1932-6203

Turnip (Brassica rapa spp. rapa) is an important vegetable species, with a unique physiology. Several plant parts, including both the turnip tubers and leaves, are important for human consumption. During the development of turnip plants, the leaves function as metabolic source tissues, while the tuber first functions as a sink, while later the tuber turns into a source for development of flowers and seeds. In the present study, chemical changes were determined for two genotypes with different genetic background, and included seedling, young leaves, mature leaves, tuber surface, tuber core, stalk, flower and seed tissues, at seven different time points during plant development. As a basis for understanding changes in glucosinolates during plant development, the profile of glucosinolates was analysed using liquid chromatography (LC) coupled to mass spectrometry (MS). This analysis was complemented by a gene expression analysis, focussed on GLS biosynthesis, which could explain part of the observed variation, pointing to important roles of specific gene orthologues for defining the chemical differences. Substantial differences in glucosinolate profiles were observed between above-ground tissues and turnip tuber, reflecting the differences in physiological role. In addition, differences between the two genotypes and between tissues that were harvested early or late during the plant lifecycle. The importance of the observed differences in glucosinolate profile for the ecophysiology of the turnip and for breeding turnips with optimal chemical profiles is discussed.

Making milk quality assurance work on an unlevel playing field : Lessons from the Happy Cow pilot
Ndambi, Asaah ; Kilelu, Catherine W. ; Lee, Jan van der; Njiru, Ruth ; Koge, Jessica - \ 2019
Wageningen : Wageningen Livestock Research (Wageningen Livestock Research report 1165) - 72
This report describes and assesses a milk quality assurance innovation, the milk quality tracking andtracing system (MQT&T) and Quality-Based Milk Payment System (QBMPS) project. The project was piloted by Happy Cow Ltd (HC), a medium-scale processor in Nakuru, Kenya, and its milk suppliers.The objective of the pilot project was to offer a proof of concept to track and trace milk quality within a smallholder-dominated supply chain and to develop and implement a payment system based on the quality of raw milk delivered. The assessment adapted the PPPLab Scaling Scan as the mainframework to enumerate the various project investments, interventions and achievements and toreflect on the success factors, shortcomings and preconditions required for QBMPS scalability.
Enhanced nutrient supply and intestinal microbiota development in very low birth weight infants
Blakstad, Elin W. ; Korpela, Katri ; Lee, Sindre ; Nakstad, Britt ; Moltu, Sissel J. ; Strømmen, Kenneth ; Rønnestad, Arild E. ; Brække, Kristin ; Iversen, Per O. ; Vos, Willem M. de; Drevon, Christian A. - \ 2019
Pediatric Research 86 (2019). - ISSN 0031-3998 - p. 323 - 332.

Background: Promoting a healthy intestinal microbiota may have positive effects on short- and long-term outcomes in very low birth weight (VLBW; BW < 1500 g) infants. Nutrient supply influences the intestinal microbiota. Methods: Fifty VLBW infants were randomized to an intervention group receiving enhanced nutrient supply or a control group. Fecal samples from 45 infants collected between birth and discharge were analyzed using 16S ribosomal RNA (rRNA) amplicon sequencing. Results: There was considerable individual variation in microbiota development. Microbial richness decreased towards discharge in the controls compared to the intervention group. In the intervention group, there was a greater increase in diversity among moderately/very preterm (MVP, gestational age ≥ 28 weeks) infants and a steeper decrease in relative Staphylococcus abundance in extremely preterm (EP, gestational age < 28 weeks) infants as compared to controls. Relative Bifidobacterium abundance tended to increase more in MVP controls compared to the intervention group. Abundance of pathogens was not increased in the intervention group. Higher relative Bifidobacterium abundance was associated with improved weight gain. Conclusion: Nutrition may affect richness, diversity, and microbiota composition. There was no increase in relative abundance of pathogens among infants receiving enhanced nutrient supply. Favorable microbiota development was associated with improved weight gain.

Blood and urine analyses after radioembolization of liver malignancies with [166Ho]Ho-acetylacetonate-poly(L-lactic acid) microspheres
Bakker, Robbert C. ; Roos, Remmert de; Tessa Ververs, F.F. ; Lam, Marnix G.E.H. ; Lee, Martijn K. van der; Zonnenberg, Bernard A. ; Krijger, Gerard C. - \ 2019
Nuclear medicine and biology 71 (2019). - ISSN 0969-8051 - p. 11 - 18.
Blood - Holmium - Radioisotope - SIRT - Urine

Background: [ 166 Ho]Ho-acetylacetonate-poly(L-lactic acid) microspheres were used in radioembolization of liver malignancies by intra-arterial administration. The primary aim of this study was to assess the stability and biodistribution of these microspheres. Materials and methods: Peripheral blood and urine samples were obtained from two clinical studies. Patient and in vitro experiment samples were analyzed using inductively coupled plasma mass spectrometry (ICP-MS), gamma-ray spectroscopy, light microscopy, Coulter particle counting, and high performance liquid chromatography (HPLC). Results: The median percentage holmium compared to the total amount injected into the hepatic artery was 0.19% (range 0.08–2.8%) and 0.32% (range 0.03–1.8%) in the 1 h blood plasma and 24 h urine, respectively. Both the blood plasma and urine were correlated with the neutron irradiation exposure required for [ 166 Ho]Ho-AcAc-PLLA microsphere production (ρ = 0.616, p = 0.002). After a temporary interruption of the phase 2 clinical study, the resuspension medium was replaced to precipitate [ 166 Ho]Ho 3+ pre-administration using phosphate. The in vitro near-maximum neutron irradiation experiments showed significant [ 166 Ho]Ho-AcAc-PLLA microsphere damage. Conclusion: The amount of holmium in the peripheral blood and urine samples after [ 166 Ho]Ho-AcAc-PLLA microsphere intrahepatic infusion was low. A further decrease was observed after reformulation of the resuspension solution but minimization of production damage is necessary.

Genomic analysis on pygmy hog reveals extensive interbreeding during wild boar expansion
Liu, Langqing ; Bosse, Mirte ; Megens, Hendrik-Jan ; Frantz, Laurent A.F. ; Lee, Young Lim ; Irving-Pease, Evan K. ; Narayan, Goutam ; Groenen, Martien A.M. ; Madsen, Ole - \ 2019
Nature Communications 10 (2019). - ISSN 2041-1723

Wild boar (Sus scrofa) drastically colonized mainland Eurasia and North Africa, most likely from East Asia during the Plio-Pleistocene (2–1Mya). In recent studies, based on genome-wide information, it was hypothesized that wild boar did not replace the species it encountered, but instead exchanged genetic materials with them through admixture. The highly endangered pygmy hog (Porcula salvania) is the only suid species in mainland Eurasia known to have outlived this expansion, and therefore provides a unique opportunity to test this hybridization hypothesis. Analyses of pygmy hog genomes indicate that despite large phylogenetic divergence (~2 My), wild boar and pygmy hog did indeed interbreed as the former expanded across Eurasia. In addition, we also assess the taxonomic placement of the donor of another introgression, pertaining to a now-extinct species with a deep phylogenetic placement in the Suidae tree. Altogether, our analyses indicate that the rapid spread of wild boar was facilitated by inter-specific/inter-generic admixtures.

sPlot – A new tool for global vegetation analyses
Bruelheide, Helge ; Dengler, Jürgen ; Jiménez-Alfaro, Borja ; Purschke, Oliver ; Hennekens, Stephan M. ; Chytrý, Milan ; Pillar, Valério D. ; Jansen, Florian ; Kattge, Jens ; Sandel, Brody ; Aubin, Isabelle ; Biurrun, Idoia ; Field, Richard ; Haider, Sylvia ; Jandt, Ute ; Lenoir, Jonathan ; Peet, Robert K. ; Peyre, Gwendolyn ; Sabatini, Francesco Maria ; Schmidt, Marco ; Schrodt, Franziska ; Winter, Marten ; Aćić, Svetlana ; Agrillo, Emiliano ; Alvarez, Miguel ; Ambarlı, Didem ; Angelini, Pierangela ; Apostolova, Iva ; Arfin Khan, Mohammed A.S. ; Arnst, Elise ; Attorre, Fabio ; Baraloto, Christopher ; Beckmann, Michael ; Berg, Christian ; Bergeron, Yves ; Bergmeier, Erwin ; Bjorkman, Anne D. ; Bondareva, Viktoria ; Borchardt, Peter ; Botta-Dukát, Zoltán ; Boyle, Brad ; Breen, Amy ; Brisse, Henry ; Byun, Chaeho ; Cabido, Marcelo R. ; Casella, Laura ; Cayuela, Luis ; Černý, Tomáš ; Chepinoga, Victor ; Csiky, János ; Curran, Michael ; Ćušterevska, Renata ; Dajić Stevanović, Zora ; Bie, Els De; Ruffray, Patrice de; Sanctis, Michele De; Dimopoulos, Panayotis ; Dressler, Stefan ; Ejrnæs, Rasmus ; El-Sheikh, Mohamed A.E.R.M. ; Enquist, Brian ; Ewald, Jörg ; Fagúndez, Jaime ; Finckh, Manfred ; Font, Xavier ; Forey, Estelle ; Fotiadis, Georgios ; García-Mijangos, Itziar ; Gasper, André Luis de; Golub, Valentin ; Gutierrez, Alvaro G. ; Hatim, Mohamed Z. ; He, Tianhua ; Higuchi, Pedro ; Holubová, Dana ; Hölzel, Norbert ; Homeier, Jürgen ; Indreica, Adrian ; Işık Gürsoy, Deniz ; Jansen, Steven ; Janssen, John ; Jedrzejek, Birgit ; Jiroušek, Martin ; Jürgens, Norbert ; Kącki, Zygmunt ; Kavgacı, Ali ; Kearsley, Elizabeth ; Kessler, Michael ; Knollová, Ilona ; Kolomiychuk, Vitaliy ; Korolyuk, Andrey ; Kozhevnikova, Maria ; Kozub, Łukasz ; Krstonošić, Daniel ; Kühl, Hjalmar ; Kühn, Ingolf ; Kuzemko, Anna ; Küzmič, Filip ; Landucci, Flavia ; Lee, Michael T. ; Levesley, Aurora ; Li, Ching Feng ; Liu, Hongyan ; Lopez-Gonzalez, Gabriela ; Lysenko, Tatiana ; Macanović, Armin ; Mahdavi, Parastoo ; Manning, Peter ; Marcenò, Corrado ; Martynenko, Vassiliy ; Mencuccini, Maurizio ; Minden, Vanessa ; Moeslund, Jesper Erenskjold ; Moretti, Marco ; Müller, Jonas V. ; Munzinger, Jérôme ; Niinemets, Ülo ; Nobis, Marcin ; Noroozi, Jalil ; Nowak, Arkadiusz ; Onyshchenko, Viktor ; Overbeck, Gerhard E. ; Ozinga, Wim A. ; Pauchard, Anibal ; Pedashenko, Hristo ; Peñuelas, Josep ; Pérez-Haase, Aaron ; Peterka, Tomáš ; Petřík, Petr ; Phillips, Oliver L. ; Prokhorov, Vadim ; Rašomavičius, Valerijus ; Revermann, Rasmus ; Rodwell, John ; Ruprecht, Eszter ; Rūsiņa, Solvita ; Samimi, Cyrus ; Schaminée, Joop H.J. ; Schmiedel, Ute ; Šibík, Jozef ; Šilc, Urban ; Škvorc, Željko ; Smyth, Anita ; Sop, Tenekwetche ; Sopotlieva, Desislava ; Sparrow, Ben ; Stančić, Zvjezdana ; Svenning, Jens Christian ; Swacha, Grzegorz ; Tang, Zhiyao ; Tsiripidis, Ioannis ; Turtureanu, Pavel Dan ; Uğurlu, Emin ; Uogintas, Domas ; Valachovič, Milan ; Vanselow, Kim André ; Vashenyak, Yulia ; Vassilev, Kiril ; Vélez-Martin, Eduardo ; Venanzoni, Roberto ; Vibrans, Alexander Christian ; Violle, Cyrille ; Virtanen, Risto ; Wehrden, Henrik von; Wagner, Viktoria ; Walker, Donald A. ; Wana, Desalegn ; Weiher, Evan ; Wesche, Karsten ; Whitfeld, Timothy ; Willner, Wolfgang ; Wiser, Susan ; Wohlgemuth, Thomas ; Yamalov, Sergey ; Zizka, Georg ; Zverev, Andrei - \ 2019
Journal of Vegetation Science 30 (2019)2. - ISSN 1100-9233 - p. 161 - 186.
biodiversity - community ecology - ecoinformatics - functional diversity - global scale - macroecology - phylogenetic diversity - plot database - sPlot - taxonomic diversity - vascular plant - vegetation relevé

Aims: Vegetation-plot records provide information on the presence and cover or abundance of plants co-occurring in the same community. Vegetation-plot data are spread across research groups, environmental agencies and biodiversity research centers and, thus, are rarely accessible at continental or global scales. Here we present the sPlot database, which collates vegetation plots worldwide to allow for the exploration of global patterns in taxonomic, functional and phylogenetic diversity at the plant community level. Results: sPlot version 2.1 contains records from 1,121,244 vegetation plots, which comprise 23,586,216 records of plant species and their relative cover or abundance in plots collected worldwide between 1885 and 2015. We complemented the information for each plot by retrieving climate and soil conditions and the biogeographic context (e.g., biomes) from external sources, and by calculating community-weighted means and variances of traits using gap-filled data from the global plant trait database TRY. Moreover, we created a phylogenetic tree for 50,167 out of the 54,519 species identified in the plots. We present the first maps of global patterns of community richness and community-weighted means of key traits. Conclusions: The availability of vegetation plot data in sPlot offers new avenues for vegetation analysis at the global scale.

Consumer acceptance measurement focusing on a specified sensory attribute of products : Can the attribute-specified degree of satisfaction-difference (DOSD) method replace hedonic scaling?
Kim, Min A. ; Hout, Danielle van; Zandstra, Elizabeth H. ; Lee, Hye Seong - \ 2019
Food Quality and Preference 75 (2019). - ISSN 0950-3293 - p. 198 - 208.
Consumer sensory segmentation - Degree of satisfaction-difference (DOSD) - Sensory attribute-specified acceptance test - Signal detection theory

A specific attribute can play an important role in determining consumers’ perceived quality and acceptance of a product. Kim, van Hout, Dessirier, and Lee (2018) proposed a new affective method, the degree of satisfaction-difference (DOSD) method, to study consumer acceptance in terms of overall satisfaction with products. In the present study, this DOSD method was further developed to assess satisfaction for a specified attribute of products rather than overall satisfaction, and this modification is referred to as the attribute-specified DOSD method. To test its applicability, 11 bouillon products (including a reference product) varying in viscosity were used as stimuli. Satisfaction with the perceived mouthfeel thickness, which is a viscosity-related sensory attribute, was evaluated with the attribute-specified DOSD method and with a 10-point category scale for overall liking as the control method. Two groups of consumers performed either the attribute-specified DOSD method or hedonic scaling over two repeated sessions. Results showed that the satisfaction patterns of the attribute-specified DOSD method were similar to those of the hedonic scaling across products, confirming that the mouthfeel thickness was a determinant of consumer acceptance for bouillon products. Examining the test reliability in terms of consistency of consumers’ responses for the same stimulus in different sessions, both groups showed consistent results. The subjects who performed the attribute-specified DOSD method were also segmented based on the degree of satisfaction with the reference product. Here, each consumer sensory segment showed different patterns on satisfaction with other test products. These findings demonstrate the potential of the attribute-specified DOSD method for measuring the consumer responses to the level/quality of an important attribute/dimension and highlight its usefulness for consumer sensory segmentation.

Transcriptional profiling of PPARα-/- and CREB3L3-/- livers reveals disparate regulation of hepatoproliferative and metabolic functions of PPARα
Ruppert, P.M.M. ; Park, Jong-Gil ; Xu, Xu ; Hur, Kyu Yeon ; Kersten, A.H. ; Lee, Ann-Hwee - \ 2019
GSE121096 - Mus musculus - PRJNA495632
Peroxisome Proliferator-Activated receptor α (PPARα) and cAMP-Responsive Element Binding Protein 3-Like 3 (CREB3L3) are transcription factors involved in the regulation of lipid metabolism in the liver. The aim of the present study was to characterize the interrelationship between PPARα and CREB3L3 in regulating hepatic gene expression. Male wildtype, PPARα-/-, CREB3L3-/- and combined PPARα/CREB3L3-/- mice were subjected to a 16-hour fast or 4 days of ketogenic diet. Whole genome expression analysis was performed on liver samples. Under conditions of overnight fasting, the effects of PPARα ablation and CREB3L3 ablation on plasma triglyceride, plasma β-hydroxybutyrate, and hepatic gene expression were largely disparate, and showed only limited interdependence. Gene and pathway analysis underscored the importance of CREB3L3 in regulating (apo)lipoprotein metabolism, and of PPARα as master regulator of intracellular lipid metabolism. A small number of genes, including Fgf21 and Mfsd2a, were under dual control of PPARα and CREB3L3. By contrast, a strong interaction between PPARα and CREB3L3 ablation was observed during ketogenic diet feeding. Specifically, the pronounced effects of CREB3L3 ablation on liver damage and hepatic gene expression during ketogenic diet were almost completely abolished by the simultaneous ablation of PPARα. Loss of CREB3L3 influenced PPARα signalling in two major ways. Firstly, it reduced expression of PPARα and its target genes involved in fatty acid oxidation and ketogenesis. In stark contrast, the hepatoproliferative function of PPARα was markedly activated by loss of CREB3L3. These data indicate that CREB3L3 ablation uncouples the hepatoproliferative and lipid metabolic effects of PPARα. Overall, except for the shared regulation of a very limited number of genes, the roles of PPARα and CREB3L3 in hepatic lipid metabolism are clearly distinct and are highly dependent on dietary status.
Transcriptional profiling of PPARα−/− and CREB3L3−/− livers reveals disparate regulation of hepatoproliferative and metabolic functions of PPARα
Ruppert, Philip M.M. ; Park, Jong-Gil ; Xu, Xu ; Hur, Kyu Yeon ; Lee, Ann-Hwee ; Kersten, Sander - \ 2019
BMC Genomics 20 (2019). - ISSN 1471-2164
Background: Peroxisome Proliferator-Activated receptor α (PPARα) and cAMP-Responsive Element Binding Protein 3-Like 3 (CREB3L3) are transcription factors involved in the regulation of lipid metabolism in the liver. The aim of the present study was to characterize the interrelationship between PPARα and CREB3L3 in regulating hepatic gene expression. Male wild-type, PPARα−/−, CREB3L3−/− and combined PPARα/CREB3L3−/− mice were subjected to a 16-h fast or 4 days of ketogenic diet. Whole genome expression analysis was performed on liver samples. Results: Under conditions of overnight fasting, the effects of PPARα ablation and CREB3L3 ablation on plasma triglyceride, plasma β-hydroxybutyrate, and hepatic gene expression were largely disparate, and showed only limited interdependence. Gene and pathway analysis underscored the importance of CREB3L3 in regulating (apo)lipoprotein metabolism, and of PPARα as master regulator of intracellular lipid metabolism. A small number of genes, including Fgf21 and Mfsd2a, were under dual control of PPARα and CREB3L3. By contrast, a strong interaction between PPARα and CREB3L3 ablation was observed during ketogenic diet feeding. Specifically, the pronounced effects of CREB3L3 ablation on liver damage and hepatic gene expression during ketogenic diet were almost completely abolished by the simultaneous ablation of PPARα. Loss of CREB3L3 influenced PPARα signalling in two major ways. Firstly, it reduced expression of PPARα and its target genes involved in fatty acid oxidation and ketogenesis. In stark contrast, the hepatoproliferative function of PPARα was markedly activated by loss of CREB3L3. Conclusions: These data indicate that CREB3L3 ablation uncouples the hepatoproliferative and lipid metabolic effects of PPARα. Overall, except for the shared regulation of a very limited number of genes, the roles of PPARα and CREB3L3 in hepatic lipid metabolism are clearly distinct and are highly dependent on dietary status.
Dystrophin is required for normal synaptic gain in the Drosophila olfactory circuit
Jantrapirom, Salinee ; Cao, De Shou ; Wang, Jing W. ; Hing, Huey ; Tabone, Christopher J. ; Lantz, Kathryn ; Belle, J.S. de; Qiu, Yu Tong ; Smid, Hans M. ; Yamaguchi, Masamitsu ; Fradkin, Lee G. ; Noordermeer, Jasprina N. ; Potikanond, Saranyapin - \ 2019
Brain Research 1712 (2019). - ISSN 0006-8993 - p. 158 - 166.
Antennal lobe - Behavior - Drosophila melanogaster - Dystrophin - Olfaction - Olfactory receptor neurons - Projection neurons

The Drosophila olfactory system provides an excellent model to elucidate the neural circuits that control behaviors elicited by environmental stimuli. Despite significant progress in defining olfactory circuit components and their connectivity, little is known about the mechanisms that transfer the information from the primary antennal olfactory receptor neurons to the higher order brain centers. Here, we show that the Dystrophin Dp186 isoform is required in the olfactory system circuit for olfactory functions. Using two-photon calcium imaging, we found the reduction of calcium influx in olfactory receptor neurons (ORNs) and also the defect of GABA A mediated inhibitory input in the projection neurons (PNs) in Dp186 mutation. Moreover, the Dp186 mutant flies which display a decreased odor avoidance behavior were rescued by Dp186 restoration in the Drosophila olfactory neurons in either the presynaptic ORNs or the postsynaptic PNs. Therefore, these results revealed a role for Dystrophin, Dp 186 isoform in gain control of the olfactory synapse via the modulation of excitatory and inhibitory synaptic inputs to olfactory projection neurons.

Development and evaluation of a triplex TaqMan assay and Next Generation Sequence Analysis for improved detection of Xylella in plant material
Bonants, P.J.M. ; Griekspoor, Y. ; Houwers, I.M. ; Krijger, M.C. ; Zouwen, P.S. van der; Lee, T.A.J. van der; Wolf, J.M. van der - \ 2019
Plant Disease 103 (2019)4. - ISSN 0191-2917 - 36 p.
Xylella fastidiosa is a heterogenous gram-negative bacterial plant pathogen with a wide host range covering over 300 plant species. Since 2013, in Europe, the presence of the pathogen is increasing in a part of the Mediterranean area, but causes in particular severe disease problems in olive orchards in the Southern part of Italy. Various subspecies of the pathogen were also diagnosed in natural outbreaks and intercepted ornamental plants in Europe, among them Olea europaea, Coffea arabica and Nerium oleander. The host range of the pathogen can vary, depending on the subspecies and even the strain. The availability of fast and reliable diagnostic tools are indispensable in management strategies to control diseases caused by X. fastidiosa. To improve the reliability of the TaqMan assay, currently widely used in surveys, a triplex TaqMan assay was developed in which two specific and sensitive TaqMan assays, previously designed for X. fastidiosa, were combined with an internal control. The triplex assay exhibited the same diagnostic sensitivity as the simplex assays. In addition, the usefulness of a metagenomic approach using next generation sequencing (NGS) was demonstrated, in which total DNA extracted from plant material was sequenced. DNA extracts from plant material free of X. fastidiosa, from artificially inoculated hosts plants or from naturally infected plants sampled in France, Spain and Italy, or intercepted in Austria and The Netherlands, were analysed for the presence of X. fastidiosa using the metagenomic approach. In all samples, even in samples with a low infection level, but not in the pathogen-free samples, DNA reads were detected specific for X. fastidiosa. In most cases, the pathogen could be identified up to the subspecies level and for one sample even the whole genome could be assembled and the sequence type could be determined. All results of NGS analysed samples were confirmed with the triplex TaqMan PCR and LAMP.
Homoeostatic maintenance of nonstructural carbohydrates during the 2015–2016 El Niño drought across a tropical forest precipitation gradient
Dickman, Lee Turin ; McDowell, Nate G. ; Grossiord, Charlotte ; Collins, Adam D. ; Wolfe, Brett T. ; Detto, Matteo ; Wright, S.J. ; Medina-Vega, José A. ; Goodsman, Devin ; Rogers, Alistair ; Serbin, Shawn P. ; Wu, Jin ; Ely, Kim S. ; Michaletz, Sean T. ; Xu, Chonggang ; Kueppers, Lara ; Chambers, Jeffrey Q. - \ 2019
Plant, Cell & Environment 42 (2019)5. - ISSN 0140-7791 - p. 1705 - 1714.
climate - ENSO - NSC - Panama - storage - sugars - tropics - vegetation

Nonstructural carbohydrates (NSCs) are essential for maintenance of plant metabolism and may be sensitive to short- and long-term climatic variation. NSC variation in moist tropical forests has rarely been studied, so regulation of NSCs in these systems is poorly understood. We measured foliar and branch NSC content in 23 tree species at three sites located across a large precipitation gradient in Panama during the 2015–2016 El Niño to examine how short- and long-term climatic variation impact carbohydrate dynamics. There was no significant difference in total NSCs as the drought progressed (leaf P = 0.32, branch P = 0.30) nor across the rainfall gradient (leaf P = 0.91, branch P = 0.96). Foliar soluble sugars decreased while starch increased over the duration of the dry period, suggesting greater partitioning of NSCs to storage than metabolism or transport as drought progressed. There was a large variation across species at all sites, but total foliar NSCs were positively correlated with leaf mass per area, whereas branch sugars were positively related to leaf temperature and negatively correlated with daily photosynthesis and wood density. The NSC homoeostasis across a wide range of conditions suggests that NSCs are an allocation priority in moist tropical forests.

What agricultural practices are most likely to deliver “sustainable intensification” in the UK?
Dicks, Lynn V. ; Rose, David C. ; Ang, Frederic ; Aston, Stephen ; Birch, A.N.E. ; Boatman, Nigel ; Bowles, Elizabeth L. ; Chadwick, David ; Dinsdale, Alex ; Durham, Sam ; Elliott, John ; Firbank, Les ; Humphreys, Stephen ; Jarvis, Phil ; Jones, Dewi ; Kindred, Daniel ; Knight, Stuart M. ; Lee, Michael R.F. ; Leifert, Carlo ; Lobley, Matt ; Matthews, Kim ; Midmer, Alice ; Moore, Mark ; Morris, Carol ; Mortimer, Simon ; Murray, T.C. ; Norman, Keith ; Ramsden, Stephen ; Roberts, Dave ; Smith, Laurence G. ; Soffe, Richard ; Stoate, Chris ; Taylor, Bryony ; Tinker, David ; Topliff, Mark ; Wallace, John ; Williams, Prysor ; Wilson, Paul ; Winter, Michael ; Sutherland, William J. - \ 2019
Food and Energy Security 8 (2019)1. - ISSN 2048-3694

Sustainable intensification is a process by which agricultural productivity is enhanced whilst also creating environmental and social benefits. We aimed to identify practices likely to deliver sustainable intensification, currently available for UK farms but not yet widely adopted. We compiled a list of 18 farm management practices with the greatest potential to deliver sustainable intensification in the UK, following a well-developed stepwise methodology for identifying priority solutions, using a group decision-making technique with key agricultural experts. The list of priority management practices can provide the focal point of efforts to achieve sustainable intensification of agriculture, as the UK develops post-Brexit agricultural policy, and pursues the second Sustainable Development Goal, which aims to end hunger and promote sustainable agriculture. The practices largely reflect a technological, production-focused view of sustainable intensification, including for example, precision farming and animal health diagnostics, with less emphasis on the social and environmental aspects of sustainability. However, they do reflect an integrated approach to farming, covering many different aspects, from business organization and planning, to soil and crop management, to landscape and nature conservation. For a subset of 10 of the priority practices, we gathered data on the level of existing uptake in English and Welsh farms through a stratified survey in seven focal regions. We find substantial existing uptake of most of the priority practices, indicating that UK farming is an innovative sector. The data identify two specific practices for which uptake is relatively low, but which some UK farmers find appealing and would consider adopting. These practices are: prediction of pest and disease outbreaks, especially for livestock farms; staff training on environmental issues, especially on arable farms.

A review of environmental enrichment for laying hens during rearing in relation to their behavioral and physiological development
Campbell, D.L.M. ; Haas, E.N. de; Lee, Caroline - \ 2019
Poultry Science 98 (2019)1. - ISSN 0032-5791 - p. 9 - 28.
Globally, laying hen production systems are a focus of concern for animal welfare. Recently, the impacts of rearing environments have attracted attention, particularly with the trend toward more complex production systems including aviaries, furnished cages, barn, and free-range. Enriching the rearing environments with physical, sensory, and stimulatory additions can optimize the bird's development but commercial-scale research is limited. In this review, “enrichment” is defined as anything additional added to the bird's environment including structurally complex rearing systems. The impacts of enrichments on visual development, neurobehavioral development, auditory stimulation, skeletal development, immune function, behavioral development of fear and pecking, and specifically pullets destined for free-range systems are summarized and areas for future research identified. Visual enrichment and auditory stimulation may enhance neural development but specific mechanisms of impact and suitable commercial enrichments still need elucidating. Enrichments that target left/right brain hemispheres/behavioral traits may prepare birds for specific types of adult housing environments (caged, indoor, outdoor). Similarly, structural enrichments are needed to optimize skeletal development depending on the adult layer system, but specific physiological processes resulting from different types of exercise are poorly understood. Stimulating appropriate pecking behavior from hatch is critical but producers will need to adapt to different flock preferences to provide enrichments that are utilized by each rearing group. Enrichments have potential to enhance immune function through the application of mild stressors that promote adaptability, and this same principle applies to free-range pullets destined for variable outdoor environments. Complex rearing systems may have multiple benefits, including reducing fear, that improve the transition to the layer facility. Overall, there is a need to commercially validate positive impacts of cost-effective enrichments on bird behavior and physiology.
The antiSMASH database version 2 : a comprehensive resource on secondary metabolite biosynthetic gene clusters
Blin, Kai ; Pascal Andreu, Victòria ; Los Santos, Emmanuel L.C. de; Carratore, Francesco Del; Lee, Sang Yup ; Medema, Marnix H. ; Weber, Tilmann - \ 2019
Nucleic acids research 47 (2019)D1. - ISSN 0305-1048 - p. D625 - D630.

Natural products originating from microorganisms are frequently used in antimicrobial and anticancer drugs, pesticides, herbicides or fungicides. In the last years, the increasing availability of microbial genome data has made it possible to access the wealth of biosynthetic clusters responsible for the production of these compounds by genome mining. antiSMASH is one of the most popular tools in this field. The antiSMASH database provides pre-computed antiSMASH results for many publicly available microbial genomes and allows for advanced cross-genome searches. The current version 2 of the antiSMASH database contains annotations for 6200 full bacterial genomes and 18,576 bacterial draft genomes and is available at https://antismash-db.secondarymetabolites.org/.

Unexpected role of canonical aerobic methanotrophs in upland agricultural soils
Ho, Adrian ; Lee, Hyo Jung ; Reumer, Max ; Meima-Franke, Marion ; Raaijmakers, Ciska ; Zweers, Hans ; Boer, Wietse de; Putten, Wim H. Van der; Bodelier, Paul L.E. - \ 2019
Soil Biology and Biochemistry 131 (2019). - ISSN 0038-0717 - p. 1 - 8.
C labelling - High-affinity methane oxidation - Methylocystaceae - PLFA analysis/ land-use change - pmoA

Aerobic oxidation of methane at (circum-)atmospheric concentrations (<40 ppmv) has long been assumed to be catalyzed by the as-yet-uncultured high-affinity methanotrophs in well-aerated, non-wetland (upland) soils, the only known biological methane sink globally. Although the low-affinity canonical methanotrophs with cultured representatives have been detected along with the high-affinity ones, their role as a methane sink in upland soils remains enigmatic. Here, we show that canonical methanotrophs can contribute to (circum-)atmospheric methane uptake in agricultural soils. We performed a stable-isotope 13C–CH4 labelling incubation in the presence and absence of bio-based residues that were added to the soil to track the flow of methane. Residue amendment transiently stimulated methane uptake rate (<50 days). Soil methane uptake was sustained throughout the incubation (130 days), concomitant to the enrichment of 13C–CO2. The 13C-enriched phospholipid fatty acids (PLFAs) were distinct in both soils, irrespective of amendments, and were unambiguously assigned almost exclusively to canonical alphaproteobacterial methanotrophs with cultured representatives. 16S rRNA and pmoA gene sequence analyses revealed that the as-yet-uncultured high-affinity methanotrophs were virtually absent in these soils. The stable-isotope labelling approach allowed to attribute soil methane uptake to canonical methanotrophs, whereas these were not expected to consume (circum-)atmospheric methane. Our findings thus revealed an overlooked reservoir of high-affinity methane-oxidizers represented by the canonical methanotrophs in agriculture-impacted upland soils. Given that upland agricultural soils have been thought to marginally or do not contribute to atmospheric methane consumption due to the vulnerability of the high-affinity methanotrophs, our findings suggest a thorough revisiting of the contribution of agricultural soils, and the role of agricultural management to mitigation of climate change.

Comparative transcriptome analysis of Ethiopian indigenous chickens from low and high altitudes under heat stress condition reveals differential immune response
Park, W. ; Srikanth, K. ; Lim, D. ; Park, M. ; Hur, T. ; Kemp, S. ; Dessie, T. ; Kim, M.S. ; Lee, S.R. ; Pas, M.F.W. te; Kim, J.M. ; Park, J.E. - \ 2019
Animal Genetics 50 (2019)1. - ISSN 0268-9146 - p. 42 - 53.
highlands - lowlands - RNA-seq - thermal tolerance

Ethiopia is an ecologically diverse country; the low altitude regions are hot and humid whereas the high altitude regions are cooler. In this study we analyzed the transcriptome response of high altitude (Addis Ababa) and low altitude (Awash) chickens to heat stress conditions that are prevalent in the low altitude regions. The chickens were free ranged for 20 h in an enclosure in Awash, and then the heart, breast muscle and spleen tissues were collected at 6:00 am, 12:00 noon and 6:00 pm to follow a daily circadian cycle. Through RNA-sequencing analysis, we identified differentially expressed genes (DEGs) that were significant (q < 0.05). These DEGs were subjected to protein–protein interaction (PPI) network and gene co-expression network (GCN) analyses to understand their role. KEGG pathway analysis and Gene Ontology analysis of all the identified DEGs and the genes identified from the PPI network and GCN analyses revealed that several immune-related pathways, such as proteasome, focal adhesion, influenza A, the ErbB signaling pathway and glycerophospholipid metabolism, were enriched in response to heat stress. These results suggest that the high altitude chickens were under heat stress and might be immunologically susceptible. Our findings will help in developing a genetic approach to mitigate production loss due to heat stress.

Does the knowledge economy advance the green economy? An evaluation of green jobs in the 100 largest metropolitan regions in the United States
Lee, Taedong ; Heijden, Jeroen van der - \ 2019
Energy & Environment 30 (2019)1. - ISSN 0958-305X - p. 141 - 155.
climate action - green economy - Green jobs - institutions of higher education - knowledge economy

Institutions of higher education are significant economic engines and innovative places in local economies: they directly employ large numbers of people, often with well-paying jobs; they are magnets for businesses that service the student population; they educate and often assist students in securing first jobs; and they partner with local organizations and businesses to provide students with hands-on experiences while “giving-back” to the community. In this article, we examine the impact that institutions of higher education have as an engine of growth for the green economy and, specifically, assess their impact on the development of green jobs. Green jobs have been touted as an important strategy to simultaneously address both the economic downturn and environmental degradation. This article empirically assesses the impact that the knowledge economy has on the presence of green jobs in the 100 largest metropolitan regions in the United States. Our findings suggest that enhanced higher education and sustainability-oriented departments and centers have a positive impact on green job development in urban regions.

Pangenome analysis and its application on Pectobacterium
Jonkheer, Eef ; Smit, S. ; Ridder, D. de; Brankovics, Balázs ; Houwers, I.M. ; Wolf, J.M. van der; Bonants, P.J.M. ; Vreeburg, R.A.M. ; Lee, T.A.J. van der - \ 2018
The linear mitochondrial genome of the quarantine chytrid Synchytrium endobioticum; insights into the evolution and recent history of an obligate biotrophic plant pathogen
Vossenberg, Bart van de; Brankovics, Balázs ; Nguyen, H.D.T. ; Gent-Pelzer, Marga van; Smith, D. ; Przetakiewicz, J. ; Kreuze, J.F. ; Boerma, M. ; Leeuwen, G.C.M. van; André Lévesque, C. ; Lee, Theo van der - \ 2018
Wageningen University and Research
PRJEB24465 - ERP106293 - Synchytrium endobioticum
Species of the Chytridiomycota, also known as chytrids, belong to a basal lineage in the fungal kingdom inhabiting terrestrial and aquatic environments. Most of the described chytrids are free-living saprophytes, but several species cause important diseases. Examples are Batrachochytrium dendrobatidis responsible for the world wide amphibian decline and Synchytrium endobioticum the causal agent of potato wart disease. Synchytrium endobioticum has an obligate biotrophic lifestyle and isolates can be differentiated based on their virulence on a differential set of potato cultivars, referred to as pathotypes. Quarantine measures have been implemented worldwide to control the disease and to prevent its spread. To determine taxonomical relationships, and to gain insights into the evolution and recent history of introductions of this plant pathogen we assembled and annotated the complete mitochondrial genome of S. endobioticum and generated mitochondrial genomes for five additional chytrid species. The mitochondrial genome of S. endobioticum pathotype 1(D1) strain MB42 is a linear 72,865 bp molecule with terminal inverted repeats that encodes 14 core genes typically found on fungal mitochondrial genomes. Based on single nucleotide polymorphisms the 30 S. endobioticum isolates sequenced could be clustered in four distinct mitochondrial lineages, indicating multiple introductions of the pest to the European main land. These lineages comprise different pathotypes suggesting that pathotypes 2(G1) and 6(O1) have emerged at least twice independently. Variations for polymorphic sites within a strain were observed demonstrating that S. endobioticum strains represent in fact a community of different genotypes. Such a community was shown to be complex and stable over time, but we also demonstrate that the population may shift rapidly based on selection for virulence on a specific R gene from the host.
Assessment of the genetic and clinical determinants of fracture risk : Genome wide association and mendelian randomisation study
Trajanoska, Katerina ; Morris, John A. ; Oei, Ling ; Zheng, Hou Feng ; Evans, David M. ; Kiel, Douglas P. ; Ohlsson, Claes ; Richards, J.B. ; Rivadeneira, Fernando ; Forgett, V. ; Leong, A. ; Ahmad, O.S. ; Laurin, C. ; Mokry, L.E. ; Ross, S. ; Elks, C.E. ; Bowden, J. ; Warrington, N.M. ; Kleinman, A. ; Willems, S.M. ; Wright, D. ; Day, F.R. ; Murray, A. ; Ruth, K.S. ; Tsilidis, K.K. ; Ackert-Bicknell, C.L. ; Bassett, J.H.D. ; Eerden, B.C.J. van der; Gautvik, K. ; Reppe, S. ; Williams, G.R. ; Medina-Gómez, C. ; Estrada, K. ; Amin, N. ; Enneman, A.W. ; Li, G. ; Liu, C.T. ; Liu, Y. ; Xiao, S.M. ; Lee, S.H. ; Koh, J.M. ; Tang, N.L.S. ; Cummings, S.R. ; Brown, M. ; Groot, L. de; Jukema, J.W. ; Lips, P. ; Meurs, J.B.J. van; Smith, A.V. ; Tian, S. - \ 2018
BMJ: British Medical Journal 362 (2018). - ISSN 0959-8146

Objectives To identify the genetic determinants of fracture risk and assess the role of 15 clinical risk factors on osteoporotic fracture risk. Design Meta-analysis of genome wide association studies (GWAS) and a two-sample mendelian randomisation approach. Setting 25 cohorts from Europe, United States, east Asia, and Australia with genome wide genotyping and fracture data. Participants A discovery set of 37 857 fracture cases and 227 116 controls; with replication in up to 147 200 fracture cases and 150 085 controls. Fracture cases were defined as individuals (>18 years old) who had fractures at any skeletal site confirmed by medical, radiological, or questionnaire reports. Instrumental variable analyses were performed to estimate effects of 15 selected clinical risk factors for fracture in a two-sample mendelian randomisation framework, using the largest previously published GWAS meta-analysis of each risk factor. Results Of 15 fracture associated loci identified, all were also associated with bone mineral density and mapped to genes clustering in pathways known to be critical to bone biology (eg, SOST, WNT16, and ESR1) or novel pathways (FAM210A, GRB10, and ETS2). Mendelian randomisation analyses showed a clear effect of bone mineral density on fracture risk. One standard deviation decrease in genetically determined bone mineral density of the femoral neck was associated with a 55% increase in fracture risk (odds ratio 1.55 (95% confidence interval 1.48 to 1.63; P=1.5×10'68). Hand grip strength was inversely associated with fracture risk, but this result was not significant after multiple testing correction. The remaining clinical risk factors (including vitamin D levels) showed no evidence for an effect on fracture. Conclusions This large scale GWAS meta-analysis for fracture identified 15 genetic determinants of fracture, all of which also influenced bone mineral density. Among the clinical risk factors for fracture assessed, only bone mineral density showed a major causal effect on fracture. Genetic predisposition to lower levels of vitamin D and estimated calcium intake from dairy sources were not associated with fracture risk.

Resource Recovery From Wastes and Wastewaters Using Bioelectrochemical Systems.
Seelam, Jai Sankar ; Maesara, Sausan A. ; Mohanakrishna, Gunda ; Patil, S.A. ; Heijne, A. ter; Pant, Deepak - \ 2018
In: Waste Biorefinery / Bhaskar, Thallada, Pandey, Ashok, Venkata Mohan, S., Duu-Jong Lee,, Kumar Khanal, Samir, Elsevier B.V. - ISBN 9780444639929 - p. 535 - 570.
Resource recovery - Bioelectrochemical systems - Waste valorization - Wastewater feedstocks - Metals - Bioenergy - Nutrients
Recent scientific and technological advancements in bioelectrochemical system (BES) research have opened up several avenues for realizing the concept of bio-based economy. Current research within this area has been directed toward exploring their applicability to generate a wastewater biorefinery. Valorization of resources in the form of energy, nutrients, metals, and chemicals has been actively exhibited using this technology. This chapter highlights the fundamentals and technological aspects of bioelectrochemical resource recovery from wastes and wastewaters with detailed emphasis on the latest trends of bioelectrorecovery systems (BERSs). Several wastes and wastewater feedstocks are enlisted and classified based on their prospects for resource and energy recovery. Two representative case studies, existing challenges, and a brief overview of the relative advantages and disadvantages of BERSs over alternative resource recovery options are also included. Further, an outlook is given for realizing resource recovery using BESs as a sustainable technology in the domain of energy and resource management.
Milk Retailing Innovation in Kenya and Consumers Perceptions of Safety : 3R Kenya Project Practice Brief 010
Bebe, B.O. ; Lee, J. van der; Kilelu, Catherine W. - \ 2018
Wageningen : Wageningen Livestock Research
Milk Retailing Practices and Quality compliance in Urban Kenya
Bebe, B.O. ; Lee, J. van der; Kilelu, C.W. - \ 2018
The Grand Transformation: A Food System Approach to Transform the African Dairy Sector
Lee, Jan van der - \ 2018
Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen
Pais, Marina ; Yoshida, Kentaro ; Giannakopoulou, Artemis ; Pel, M. ; Cano, Liliana M. ; Oliva, Ricardo F. ; Witek, Kamil ; Lindqvist-Kreuze, Hannele ; Vleeshouwers, V.G.A.A. ; Kamoun, Sophien - \ 2018
asexual reproduction - clonal lineage - Phytophthora infestans - emergent pathogen - evolution - immunity - phenotypic plasticity - expression polymorphism - structural variation - copy number variation - loss of heterozygosity
Background Outbreaks caused by asexual lineages of fungal and oomycete pathogens are a continuing threat to crops, wild animals and natural ecosystems (Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, Gurr SJ, Nature 484:186–194, 2012; Kupferschmidt K, Science 337:636–638, 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl MF, Thomma BP, BioEssays 36:335–345, 2014). Ever since the 19th century Irish famine, the oomycete Phytophthora infestans has caused recurrent outbreaks on potato and tomato crops that have been primarily caused by the successive rise and migration of pandemic asexual lineages (Goodwin SB, Cohen BA, Fry WE, Proc Natl Acad Sci USA 91:11591–11595, 1994; Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10:e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Cooke DEL, Cano LM, Raffaele S, Bain RA, Cooke LR, Etherington GJ, Deahl KL, Farrer RA, Gilroy EM, Goss EM, et al. PLoS Pathog 8:e1002940, 2012). However, the dynamics of genome evolution within these clonal lineages have not been determined. The objective of this study was to use a comparative genomics and transcriptomics approach to determine the molecular mechanisms that underpin phenotypic variation within a clonal lineage of P. infestans. Results Here, we reveal patterns of genomic and gene expression variation within a P. infestans asexual lineage by comparing strains belonging to the South American EC-1 clone that has dominated Andean populations since the 1990s (Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Delgado RA, Monteros-Altamirano AR, Li Y, Visser RGF, van der Lee TAJ, Vosman B, Plant Pathol 62:1081–1088, 2013; Forbes GA, Escobar XC, Ayala CC, Revelo J, Ordonez ME, Fry BA, Doucett K, Fry WE, Phytopathology 87:375–380, 1997; Oyarzun PJ, Pozo A, Ordonez ME, Doucett K, Forbes GA, Phytopathology 88:265–271, 1998). We detected numerous examples of structural variation, nucleotide polymorphisms and loss of heterozygosity within the EC-1 clone. Remarkably, 17 genes are not expressed in one of the two EC-1 isolates despite apparent absence of sequence polymorphisms. Among these, silencing of an effector gene was associated with evasion of disease resistance conferred by a potato immune receptor. Conclusions Our findings highlight the molecular changes underpinning the exceptional genetic and phenotypic plasticity associated with host adaptation in a pandemic clonal lineage of a eukaryotic plant pathogen. We observed that the asexual P. infestans lineage EC-1 can exhibit phenotypic plasticity in the absence of apparent genetic mutations resulting in virulence on a potato carrying the Rpi-vnt1.1 gene. Such variant alleles may be epialleles that arose through epigenetic changes in the underlying genes.
3R Kenya Issue Brief 001 : Targeting medium-sized commercial family farms: A pathway for development
Koomen, I. ; Lee, J. van der; Obwanga, Benson - \ 2018
Wageningen : Wageningen University & Research - 7 p.
Development of an extraction method for selenium speciation in feed
Brust, Hanneke ; Frankhuizen, Sjoerd ; Lee, M.K. van der - \ 2018
First steps towards mitochondrial pan-genomics: Detailed analysis of Fusarium graminearum mitogenomes
Brankovics, Balázs ; Kulik, Tomasz ; Sawicki, J. ; Bilska, K. ; Zhang, Hao ; Hoog, G.S. de; Lee, T.A.J. van der; Waalwijk, C. ; Diepeningen, A.D. van - \ 2018
PeerJ 6 (2018). - ISSN 2167-8359
There is a gradual shift from representing a species’ genome by a single reference genome sequence to a pan-genome representation. Pan-genomes are the abstract representations of the genomes of all the strains that are present in the population or species. In this study, we employed a pan-genomic approach to analyze the intraspecific mitochondrial genome diversity of Fusarium graminearum. We present an improved reference mitochondrial genome for F. graminearum with an intron-exon annotation that was verified using RNA-seq data. Each of the 24 studied isolates had a distinct mitochondrial sequence. Length variation in the F. graminearum mitogenome was found to be largely due to variation of intron regions (99.98%). The “intronless” mitogenome length was found to be quite stable and could be informative when comparing species. The coding regions showed high conservation, while the variability of intergenic regions was highest. However, the most important variable parts are the intron regions, because they contain approximately half of the variable sites, make up more than half of the mitogenome, and show presence/absence variation. Furthermore, our analyses show that the mitogenome of F. graminearum is recombining, as was previously shown in F. oxysporum, indicating that mitogenome recombination is a common phenomenon in Fusarium. The majority of mitochondrial introns in F. graminearum belongs to group I introns, which are associated with homing endonuclease genes (HEGs). Mitochondrial introns containing HE genes may spread within populations through homing, where the endonuclease recognizes and cleaves the recognition site in the target gene. After cleavage of the “host” gene, it is replaced by the gene copy containing the intron with HEG. We propose to use introns unique to a population for tracking the spread of the given population, because introns can spread through vertical inheritance, recombination as well as via horizontal transfer. We demonstrate how pooled sequencing of strains can be used for mining mitogenome data. The usage of pooled sequencing offers a scalable solution for population analysis and for species level comparisons studies. This study may serve as a basis for future mitochondrial genome variability studies and representations.
National Reference Laboratories RIKILT : annual report 2017
Leeuwen, S.P.J. van; Mol, J.G.J. ; Lee, M.K. van der; Gerssen, A. ; Lasaroms, J.J.P. ; Sterk, S.S. ; Raamsdonk, L. aan; Jong, J. de; Scholtens, I.M.J. ; Alewijn, A. ; Silletti, E. ; Ginkel, L. van; Noordam, M.Y. ; Meijer, N. - \ 2018
Wageningen : RIKILT Wageningen University & Research (RIKILT-report 2018.009) - 51
Enhancing milk quality and safety: : Towards milk quality-based milk payments in Kenya
Ndambi, O.A. ; Njiru, Ruth ; Knippenberg, Camee van; Lee, J. van der; Kilelu, C.W. ; Ngigi, M. ; Mulwa, R.M. ; Asher, D. ; Mbera, Gloria - \ 2018
Wageningen University & Research (3R Kenya Project Research Brief 001)
The Dairy Feed Advancing Model - a Value Chain Innovation in the Ethiopian Dairy Sector
Lee, J. van der; Dirbaba, D. ; Minuye, S. ; Workneh, M.T. - \ 2018
Wageningen University & Research (ADIAS Research Brief 001) - 6 p.
The fate of new mutations: genomic selection exploits new mutation variance to a much smaller degree than traditional selection
Mulder, H.A. ; Lee, S.H. ; Hayes, B.J. ; Werf, J.H.J. van der - \ 2018
In: Proceedings of the 11th World Congress on Genetics Applied to Livestock Production. - WCGALP - 5 p.
New mutations create new genetic variance in populations and contribute to long-term response to selection. We hypothesize that genomic selection exploits new mutational variance much less than traditional selection methods, because new mutations are not in linkage disequilibrium with markers on the current SNP chips, while animals with a favourable mutation have a selective advantage with mass and pedigree-based BLUP selection. We used Monte Carlo simulation using real sequence data to generate the base generation to test this hypothesis. Genomic selection increased response to selection due to old QTL by 33% and 1% in generation 5 and 20 compared to mass selection, respectively, while response to selection from new mutations was 65-85% and 61% lower than with mass selection in generation 5 and 20, respectively. In genomic selection, genetic variance due to old QTL was much faster eroded, while new mutational variance did not increase much, resulting in a 65% and 43% lower total genetic variance in generation 20 with genomic selection, compared to mass and pedigree-based BLUP selection. In summary, we showed that genomic selection hardly exploits new mutational variance and erodes genetic variance much faster than mass and BLUP selection. Future research should focus on developing sustainable genomic selection strategies to optimize long-term response to selection, exploiting new mutational variance. Keywords: de novo mutation, genomic selection, long-term selection response, selection
Dairy Input Service Delivery System By Lead Farm To Dairy Farmers For The Improvement Of Dairying In Three Zones Of Oromia, Ethiopia
Tolera, Degu ; Merera, Chala ; Gelmessa, U. ; Lee, J. van der; Ndambi, O.A. - \ 2018
International Journal of Advanced Research and Publications (2018). - ISSN 2456-9992 - p. 12 - 19.
The Grand Transfromation - A Food System Approach to Transform the African Dairy Sector
Lee, Jan van der - \ 2018
The linear mitochondrial genome of the quarantine chytrid Synchytrium endobioticum; insights into the evolution and recent history of an obligate biotrophic plant pathogen
Vossenberg, Bart T.L.H. van de; Brankovics, Balázs ; Nguyen, H.D.T. ; Gent-Pelzer, M.P.E. van; Smith, D. ; Dadej, K. ; Przetakiewicz, J. ; Kreuze, J.F. ; Boerma, M. ; Leeuwen, G.C.M. van; André Lévesque, C. ; Lee, T.A.J. van der - \ 2018
BMC Evolutionary Biology 18 (2018). - ISSN 1471-2148
Background: Chytridiomycota species (chytrids) belong to a basal lineage in the fungal kingdom. Inhabiting terrestrial and aquatic environments, most are free-living saprophytes but several species cause important diseases: e.g. Batrachochytrium dendrobatidis, responsible for worldwide amphibian decline; and Synchytrium endobioticum, causing potato wart disease. S. endobioticum has an obligate biotrophic lifestyle and isolates can be further characterized as pathotypes based on their virulence on a differential set of potato cultivars. Quarantine measures have been implemented globally to control the disease and prevent its spread. We used a comparative approach using chytrid mitogenomes to determine taxonomical relationships and to gain insights into the evolution and recent history of introductions of this plant pathogen. Results: We assembled and annotated the complete mitochondrial genome of 30 S. endobioticum isolates and generated mitochondrial genomes for five additional chytrid species. The mitochondrial genome of S. endobioticum is linear with terminal inverted repeats which was validated by tailing and PCR amplifying the telomeric ends. Surprisingly, no conservation in organisation and orientation of mitochondrial genes was observed among the Chytridiomycota except for S. endobioticum and its sister species Synchytrium microbalum. However, the mitochondrial genome of S. microbalum is circular and comprises only a third of the 72.9 Kbp found for S. endobioticum suggesting recent linearization and expansion. Four mitochondrial lineages were identified in the S. endobioticum mitochondrial genomes. Several pathotypes occur in different lineages, suggesting that these have emerged independently. In addition, variations for polymorphic sites in the mitochondrial genome of individual isolates were observed demonstrating that S. endobioticum isolates represent a community of different genotypes. Such communities were shown to be complex and stable over time, but we also demonstrate that the use of semi-resistant potato cultivars triggers a rapid shift in the mitochondrial haplotype associated with increased virulence. Conclusions: Mitochondrial genomic variation shows that S. endobioticum has been introduced into Europe multiple times, that several pathotypes emerged multiple times, and that isolates represent communities of different genotypes. Our study represents the most comprehensive dataset of chytrid mitogenomes, which provides new insights into the extraordinary dynamics and evolution of mitochondrial genomes involving linearization, expansion and reshuffling.
Professional, easy to use and robust bioinformatic tools
Warris, S. ; Lee, T.A.J. van der - \ 2018
- 1 p.
Mitochondrial genomes and species boundaries in the genus Fusarium
Brankovics, Balázs ; Waalwijk, C. ; Lee, T.A.J. van der; Hoog, G.S. de; Diepeningen, A.D. van - \ 2018
Towards improved methods for detection of Xylella fastidiosa in plant material using triplex TaqMan PCR and NGS analysis
Bonants, P.J.M. ; Griekspoor, Y. ; Houwers, I.M. ; Krijger, M.C. ; Zouwen, P.S. van der; Lee, T.A.J. van der; Wolf, J.M. van der - \ 2018
Innovative detection methods to support plant health diagnostics
Bonants, P.J.M. ; Houwers, I.M. ; Dullemans, A.M. ; Griekspoor, Y. ; Mendes, O. ; Gent-Pelzer, M.P.E. van; Vlugt, R.A.A. van der; Bergervoet, J.H.W. ; Schoen, C.D. ; Wolf, J.M. van der; Lee, T.A.J. van der - \ 2018
Conjectural ‘Landscape Cities’ and the Gap of Imagination
Abbott, Mick ; Roncken, P.A. ; Lee, Woody ; Pickett, Tenille - \ 2018
Landscape Review 18 (2018)1. - ISSN 2253-1440 - 11 p.
This report discusses the results and layout of a design research studio focused on applying methods related to speculation and imagination. Three main findings are presented: a review of six methods that can direct designerly speculations; development of 11 'landscape city' scenarios; and a discussion of the role design 'challenges' can play in studio research settings. These outcomes reveal that creative discoveries are not bound to elaborative final outcomes only. Some of the intermediate results, particularly those with explicit habit-breaking effects on the imagination of the designers involved, and the process-driven materials produced, are equally valuable. This report seeks a reconsideration of the presentation and sharing of research results through designing, moving from the familiar focus on high-end, 'glossy' finalisations towards those more revealing of intermediate and abstract products of inquiry. In conclusion, an argument is made as to what can be framed as an 'imagination gap' that suggests possibility operates as a counterpoint to empiricism. L andscape architecture has a speculative role in imagining diverse, innovative and environmentally responsive futures (Waldheim, 2012; Weller, 2009). In its research, the discipline is prone to critique by a scientific community that either disqualifies speculative approaches or does not know how to assess the associative imaginations on which most design processes depend. Such critique is constructive as it urges clarification of what is both unique and systematic about design-directed research.
Erratum to: Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study
Hellenkamp, Björn ; Schmid, Sonja ; Doroshenko, Olga ; Opanasyuk, Oleg ; Kühnemuth, Ralf ; Adariani, Soheila Rezaei ; Ambrose, Benjamin ; Aznauryan, Mikayel ; Barth, Anders ; Birkedal, Victoria ; Bowen, Mark E. ; Chen, Hongtao ; Cordes, Thorben ; Eilert, Tobias ; Fijen, Carel ; Gebhardt, Christian ; Götz, Markus ; Gouridis, Giorgos ; Gratton, Enrico ; Ha, Taekjip ; Hao, Pengyu ; Hanke, Christian A. ; Hartmann, Andreas ; Hendrix, Jelle ; Hildebrandt, Lasse L. ; Hirschfeld, Verena ; Hohlbein, Johannes ; Hua, Boyang ; Hübner, Christian G. ; Kallis, Eleni ; Kapanidis, Achillefs N. ; Kim, Jae Yeol ; Krainer, Georg ; Lamb, Don C. ; Lee, Nam Ki ; Lemke, Edward A. ; Levesque, Brié ; Levitus, Marcia ; McCann, James J. ; Naredi-Rainer, Nikolaus ; Nettels, Daniel ; Ngo, Thuy ; Qiu, Ruoyi ; Robb, Nicole C. ; Röcker, Carlheinz ; Sanabria, Hugo ; Schlierf, Michael ; Schröder, Tim ; Schuler, Benjamin ; Seidel, Henning - \ 2018
Nature Methods : techniques for life scientists and chemists 15 (2018)11. - ISSN 1548-7091 - p. 984 - 984.
Targeting medium size commercial family farms : A pathway for development
Koomen, I. ; Lee, J. van der; Obwanga, B. ; Coninx, I. - \ 2018
Intensification and upgrading dynamics in emerging dairy clusters in the East African highlands
Lee, Jan van der; Klerkx, Laurens ; Bebe, Bockline Omedo ; Mengistu, Ashenafi ; Oosting, Simon - \ 2018
Sustainability 10 (2018)11. - ISSN 2071-1050
Agribusiness cluster - Commercialization - Dairy value chain - Ethiopia - Farming system - Kenya - Service arrangements - Sustainable intensification

Based on farmer and value chain actor interviews, this comparative study of five emerging dairy clusters elaborates on the upgrading of farming systems, value chains, and context shapes transformations from semi-subsistent to market-oriented dairy farming. The main results show unequal cluster upgrading along two intensification dimensions: dairy feeding system and cash cropping. Intensive dairy is competing with other high-value cash crop options that resource-endowed farmers specialize in, given conducive support service arrangements and context conditions. A large number of drivers and co-dependencies between technical, value chain, and institutional upgrading build up to system jumps. Transformation may take decades when market and context conditions remain sub-optimal. Clusters can be expected to move further along initial intensification pathways, unless actors consciously redirect course. The main theoretical implications for debate about cluster upgrading are that co-dependencies between farming system, market, and context factors determine upgrading outcomes; the implications for the debate about intensification pathways are that they need to consider differences in farmer resource endowments, path dependency, concurrency, and upgrading investments. Sustainability issues for consideration include enabling a larger proportion of resource-poor farmers to participate in markets; enabling private input and service provision models; attention for food safety; and climate smartness.

Higher Mediterranean Diet scores are not cross-sectionally associated with better cognitive scores in 20- to 70-year-old Dutch adults: The NQplus study
Brouwer, E.M. ; Benati, Anita ; Wiel, A.M. van de; Lee, L. van; Vries, J.H.M. de; Feskens, E.J.M. ; Rest, O. van de - \ 2018
Nutrition Research 59 (2018). - ISSN 0271-5317 - p. 80 - 89.
Adherence to the Mediterranean Diet (MedDiet) has been suggested to reduce
the risk of age-related cognitive decline. Therefore, we hypothesized that
adults consuming a more Mediterranean-like diet were more likely to have
better cognitive scores. We investigated cross-sectional associations between
MedDiet adherence and cognitive performance using data of 1607 Dutch men
and women aged 20–70 years. Dietary intake was assessed using a 183-item
Food Frequency Questionnaire. MedDiet adherence was defined by a 0–9 point
scale; which was based on intakes of vegetables, legumes, fruits/nuts, cereals,
fish/seafood, meat/poultry, dairy, ethanol and the MUFA:SFA ratio. Cognitive
function was assessed with a neuropsychological test battery. Linear regression
analyses adjusted for relevant covariates showed a significant inverse association
between MedDiet adherence and everyday memory: specifically β = −0.107
± 0.046 points (P = .02) for the total population and β = −0.139 ± 0.055 points
(P = .01) for those aged ≥50 years. Further exploration of the individual MedDiet
food groups suggested that the association between MedDiet and everyday
memory was predominantly driven by the MUFA:SFA ratio. Moreover, associations were observed between higher ethanol intake better semantic memory and language production (β = 0.016 ± 0.008 P = .05), higher
vegetable intake with better processing speed (β = 0.005 ± 0.002, P = .02), and
higher legumes intake with poorer processing speed (β = −0.014 ±0.006, P = 03). Thus, in this Dutch cohort, higher MedDiet adherence was associated with poorer everyday memory.
The role of pasture in the diet of ruminant livestock
Lee, Michael R.F. ; Jordana Rivero, M. ; Cone, J.W. - \ 2018
In: Improving grassland and pasture management in temperature agriculture / Marshall, Athole, Collins, Rosemary, Burleigh Dodds Science Publishing Limited - ISBN 9781786762009
Grazed pasture is the single most important forage feed for ruminants due to its low unit cost and widespread global availability. However, there is a growing use of arable crops in ruminant rations, which may exceed that used by humans by 2050. This chapter describes the ways in which grazed pasture provides the energy, proteins, minerals and vitamins and other nutritional factors required by ruminants. The chapter shows that the use of pasture and its by-products underpins the possibility of sustainably delivering future ruminant livestock production systems and ensuring their future role in food security.
The Bruce Lee statue in Mostar : 'Heritage from below' experiments in a divided city
Aceska, Ana ; Minca, C. - \ 2018
In: After Heritage / Muzaini, Hamzah, Minca, Claudio, London : Edward Elgar - ISBN 9781788110730 - p. 64 - 85.
Focusing on the practices and politics of heritage-making at the individual and the local level, this book uses a wide array of international case studies to argue for their potential not only to disrupt but also to complement formal heritage-making in public spaces. Providing a much-needed clarion call to reinsert the individual as well as the transient into more collective heritage processes and practices, this strong contribution to the field of Critical Heritage Studies offers insight into benefits of the ‘heritage from below approach’ for researchers, policy makers and practitioners.
The SPLENDID eating detection sensor : Development and feasibility study
Boer, Janet van den; Lee, Annemiek van der; Zhou, Lingchuan ; Papapanagiotou, Vasileios ; Diou, Christos ; Delopoulos, Anastasios ; Mars, Monica - \ 2018
Journal of Medical Internet Research 6 (2018)9. - ISSN 1438-8871
Chewing sensor - In-ear microphone - Mobile phone - Obesity prevention - Overweight - PPG sensor - Weight management

Background: The available methods for monitoring food intake-which for a great part rely on self-report-often provide biased and incomplete data. Currently, no good technological solutions are available. Hence, the SPLENDID eating detection sensor (an ear-worn device with an air microphone and a photoplethysmogram [PPG] sensor) was developed to enable complete and objective measurements of eating events. The technical performance of this device has been described before. To date, literature is lacking a description of how such a device is perceived and experienced by potential users. Objective: The objective of our study was to explore how potential users perceive and experience the SPLENDID eating detection sensor. Methods: Potential users evaluated the eating detection sensor at different stages of its development: (1) At the start, 12 health professionals (eg, dieticians, personal trainers) were interviewed and a focus group was held with 5 potential end users to find out their thoughts on the concept of the eating detection sensor. (2) Then, preliminary prototypes of the eating detection sensor were tested in a laboratory setting where 23 young adults reported their experiences. (3) Next, the first wearable version of the eating detection sensor was tested in a semicontrolled study where 22 young, overweight adults used the sensor on 2 separate days (from lunch till dinner) and reported their experiences. (4) The final version of the sensor was tested in a 4-week feasibility study by 20 young, overweight adults who reported their experiences. Results: Throughout all the development stages, most individuals were enthusiastic about the eating detection sensor. However, it was stressed multiple times that it was critical that the device be discreet and comfortable to wear for a longer period. In the final study, the eating detection sensor received an average grade of 3.7 for wearer comfort on a scale of 1 to 10. Moreover, experienced discomfort was the main reason for wearing the eating detection sensor <2 hours a day. The participants reported having used the eating detection sensor on 19/28 instructed days on average. Conclusions: The SPLENDID eating detection sensor, which uses an air microphone and a PPG sensor, is a promising new device that can facilitate the collection of reliable food intake data, as shown by its technical potential. Potential users are enthusiastic, but to be successful wearer comfort and discreetness of the device need to be improved.

Dissolved oxygen dynamics in drainage ditches along a eutrophication gradient
Lee, Gea H. van der; Verdonschot, Ralf C.M. ; Kraak, Michiel H.S. ; Verdonschot, Piet F.M. - \ 2018
Limnologica 72 (2018). - ISSN 0075-9511 - p. 28 - 31.
Dissolved oxygen saturation - Ecosystem functioning - Monitoring - Primary production - Respiration - Water quality

The impact of eutrophication on the functioning of drainage ditch ecosystems is understudied. Therefore, we performed a field study to quantify the dissolved oxygen dynamics of ditches at different depths and seasons along a eutrophication gradient. During summer, a clear distinction in daily variation in dissolved oxygen saturation of the top water layer was observed between the trophic states. We recommend including dissolved oxygen dynamics as a functional parameter in drainage ditch monitoring programmes.

Experimental investigation of low-angle dune morphodynamics
Naqshband, Suleyman ; Wullems, Bas ; Ruijsscher, Timo de; Hoitink, Ton - \ 2018
In: River Flow 2018 - Ninth International Conference on Fluvial Hydraulics. - EDP Sciences (E3S Web of Conferences ) - 5 p.

Dunes commonly dominate the bed of sandy rivers and they are of central importance in predicting flow resistance and water levels. In the present study, we show that by using light-weight polystyrene particles as substrate in a laboratory setting, promising morphodynamic similarity is obtained between dunes in shallow flow (flume) and deep flow (field) conditions. In particular, results from our flume experiments show that dune lee-side angles, which are crucial in turbulence production and energy dissipation, better approximate dune lee-side angles observed in natural channels. Furthermore, dune height evolution towards upper stage plane bed observed in the present experimental study, closely follows dune height evolution as observed in world's large rivers.

Biocatalytic C=C Bond Reduction through Carbon Nanodot-Sensitized Regeneration of NADH Analogues
Kim, Jinhyun ; Lee, Sahng Ha ; Tieves, Florian ; Choi, Da Som ; Hollmann, Frank ; Paul, Caroline E. ; Park, Chan Beum - \ 2018
Angewandte Chemie-International Edition 57 (2018)42. - ISSN 1433-7851 - p. 13825 - 13828.
alkene hydrogenation - asymmetric catalysis - carbon nanodot - NADH analogues - photobiocatalysis

Light-driven activation of redox enzymes is an emerging route for sustainable chemical synthesis. Among redox enzymes, the family of Old Yellow Enzyme (OYE) dependent on the nicotinamide adenine dinucleotide cofactor (NADH) catalyzes the stereoselective reduction of α,β-unsaturated hydrocarbons. Here, we report OYE-catalyzed asymmetric hydrogenation through light-driven regeneration of NADH and its analogues (mNADHs) by N-doped carbon nanodots (N-CDs), a zero-dimensional photocatalyst. Our spectroscopic and photoelectrochemical analyses verified the transfer of photo-induced electrons from N-CDs to an organometallic electron mediator (M) for highly regioselective regeneration of cofactors. Light triggered the reduction of NAD+ and mNAD+s with the cooperation of N-CDs and M, and the reduction behaviors of cofactors were dependent on their own reduction peak potentials. The regenerated cofactors subsequently delivered hydrides to OYE for stereoselective conversions of a broad range of substrates with excellent biocatalytic efficiencies.

Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study
Hellenkamp, Björn ; Schmid, Sonja ; Doroshenko, Olga ; Opanasyuk, Oleg ; Kühnemuth, Ralf ; Rezaei Adariani, Soheila ; Ambrose, Benjamin ; Aznauryan, Mikayel ; Barth, Anders ; Birkedal, Victoria ; Bowen, Mark E. ; Chen, Hongtao ; Cordes, Thorben ; Eilert, Tobias ; Fijen, Carel ; Gebhardt, Christian ; Götz, Markus ; Gouridis, Giorgos ; Gratton, Enrico ; Ha, Taekjip ; Hao, Pengyu ; Hanke, Christian A. ; Hartmann, Andreas ; Hendrix, Jelle ; Hildebrandt, Lasse L. ; Hirschfeld, Verena ; Hohlbein, Johannes ; Hua, Boyang ; Hübner, Christian G. ; Kallis, Eleni ; Kapanidis, Achillefs N. ; Kim, Jae Yeol ; Krainer, Georg ; Lamb, Don C. ; Lee, Nam Ki ; Lemke, Edward A. ; Levesque, Brié ; Levitus, Marcia ; McCann, James J. ; Naredi-Rainer, Nikolaus ; Nettels, Daniel ; Ngo, Thuy ; Qiu, Ruoyi ; Robb, Nicole C. ; Röcker, Carlheinz ; Sanabria, Hugo ; Schlierf, Michael ; Schröder, Tim ; Schuler, Benjamin ; Seidel, Henning ; Streit, Lisa ; Thurn, Johann ; Tinnefeld, Philip ; Tyagi, Swati ; Vandenberk, Niels ; Vera, Andrés Manuel ; Weninger, Keith R. ; Wünsch, Bettina ; Yanez-Orozco, Inna S. ; Michaelis, Jens ; Seidel, Claus A.M. ; Craggs, Timothy D. ; Hugel, Thorsten - \ 2018
Nature Methods : techniques for life scientists and chemists 15 (2018)9. - ISSN 1548-7091 - p. 669 - 676.

Single-molecule Förster resonance energy transfer (smFRET) is increasingly being used to determine distances, structures, and dynamics of biomolecules in vitro and in vivo. However, generalized protocols and FRET standards to ensure the reproducibility and accuracy of measurements of FRET efficiencies are currently lacking. Here we report the results of a comparative blind study in which 20 labs determined the FRET efficiencies (E) of several dye-labeled DNA duplexes. Using a unified, straightforward method, we obtained FRET efficiencies with s.d. between ±0.02 and ±0.05. We suggest experimental and computational procedures for converting FRET efficiencies into accurate distances, and discuss potential uncertainties in the experiment and the modeling. Our quantitative assessment of the reproducibility of intensity-based smFRET measurements and a unified correction procedure represents an important step toward the validation of distance networks, with the ultimate aim of achieving reliable structural models of biomolecular systems by smFRET-based hybrid methods.

Phenotypic trait variation measured on european genetic trials of fagus sylvatica L
Robson, Matthew T. ; Garzón, Marta Benito ; Miranda, Ricardo Alia ; Egido, Diana Barba ; Bogdan, Saša ; Borovics, Attila ; Božič, Gregor ; Brendel, Oliver ; Clark, Jo ; Vries, Sven M.G. de; Delehan, Ivan I. ; Ducousso, Alexis ; Fady, Bruno ; Fennessy, John ; Forstreuter, Manfred ; Frýdl, Josef ; Geburek, Thomas ; Gömöry, Dušan ; Hauke-Kowalska, Maria ; Huber, Gerhard ; Ibañez, Juan Ignacio ; Ioniţă, Lucia ; Ivankovič, Mladen ; Hansen, Jon Kehlet ; Kóczán-Horváth, Anikó ; Kraigher, Hojka ; Lee, Steve ; Liesebach, Mirko ; Mátyás, Csaba ; Mertens, Patrick ; Muhs, Hans Jakob ; Novotný, Petr ; Parnuţa, Gheorghe ; Paule, Ladislav ; Picardo, Alvaro ; Rasztovics, Ervin ; Rogge, Martin ; Stener, Lars Göran ; Sułkowska, Małgorzata ; Urban, Otmar ; Wuehlisch, Georg Von; Vendramin, Giovanni G. ; Vettori, Cristina ; Wesoły, Wojciech - \ 2018
Scientific Data 5 (2018). - ISSN 2052-4463
We present BeechCOSTe52; a database of European beech (Fagus sylvatica) phenotypic measurements for several traits related to fitness measured in genetic trials planted across Europe. The dataset was compiled and harmonized during the COST-Action E52 (2006-2010), and subsequently cross-validated to ensure consistency of measurement data among trials and provenances. Phenotypic traits (height, diameter at breast height, basal diameter, mortality, phenology of spring bud burst and autumn-leaf discoloration) were recorded in 38 trial sites where 217 provenances covering the entire distribution of European beech were established in two consecutive series (1993/95 and 1996/98). The recorded data refer to 862,095 measurements of the same trees aged from 2 to 15 years old over multiple years. This dataset captures the considerable genetic and phenotypic intra-specific variation present in European beech and should be of interest to researchers from several disciplines including quantitative genetics, ecology, biogeography, macroecology, adaptive management of forests and bioeconomy.
The functional change and deletion of FLC homologs contribute to the evolution of rapid flowering in Boechera stricta
Lee, Cheng-Ruei ; Hsieh, Jo-Wei ; Schranz, M.E. ; Mitchell-Olds, Thomas - \ 2018
Frontiers in Plant Science 9 (2018). - ISSN 1664-462X
Differences in the timing of vegetative-to-reproductive phase transition have evolved independently and repeatedly in different plant species. Due to their specific biological functions and positions in pathways, some genes are important targets of repeated evolution – independent mutations on these genes caused the evolution of similar phenotypes in distantly related organisms. While many studies have investigated these genes, it remains unclear how gene duplications influence repeated phenotypic evolution. Here we characterized the genetic architecture underlying a novel rapid-flowering phenotype in Boechera stricta and investigated the candidate genes BsFLC1 and BsFLC2. The expression patterns of BsFLC1 suggested its function in flowering time suppression, and the deletion of BsFLC1 is associated with rapid flowering and loss of vernalization requirement. In contrast, BsFLC2 did not appear to be associated with flowering and had accumulated multiple amino acid substitutions in the relatively short evolutionary timeframe after gene duplication. These non-synonymous substitutions greatly changed the physicochemical properties of the original amino acids, concentrated non-randomly near a protein-interacting domain, and had greater substitution rate than synonymous changes. Here we suggested that, after recent gene duplication of the FLC gene, the evolution of rapid phenology was made possible by the change of BsFLC2 expression pattern or protein sequences and the deletion of BsFLC1.
Nutrition Questionnaires plus (NQplus) study, a prospective study on dietary determinants and cardiometabolic health in Dutch adults
Brouwer-Brolsma, Elske Maria ; Lee, Linde Van; Streppel, Martinette T. ; Sluik, Diewertje ; De Wiel, Anne M. Van; Vries, Jeanne H.M. De; Geelen, Anouk ; Feskens, Edith J.M. - \ 2018
BMJ Open 8 (2018)7. - ISSN 2044-6055
Purpose
During the past decades, the number of people with cardiometabolic conditions substantially increased. To identify dietary factors that may be responsible for this increase in cardiometabolic conditions, the Nutrition Questionnaires plus (NQplus) study was initiated. The aim of this article is to provide an overview of the study design and baseline characteristics of the NQplus population.
Participants
The NQplus study is a prospective cohort study among 2048 Dutch men (52%) and women (48%) aged 20–70 years. Findings to date At baseline, we assessed habitual dietary intake, conducted physical examinations (measuring, eg, anthropometrics, body composition, blood pressure, pulse wave velocity, advanced glycation end product accumulation, cognitive performance), collected blood and 24-hour urine and administered a variety of validated demographic, health and lifestyle questionnaires. Participants had a mean BMI of 26.0±4.2 kg/m2, were mostly highly educated (63%), married or having a registered partnership (72%) and having a paid job (72%). Estimated daily energy and macronutrient intakes (mean±SD) were 8581±2531 kJ, 15±2energy (en%) of protein, 43±6 en% of carbohydrates, 36±5 en% of fat and 11±13 g of alcohol. Mean systolic blood pressure was 126±15 mm Hg, total cholesterol 5.3±1.1 mmol/L and haemoglobin A1c 36±5 mmol/mol. A total of 24% of the participants reported to be diagnosed with hypertension, 18% with hypercholesterolaemia and 4% with diabetes mellitus. All measurements were repeated after 1 and 2 years of follow-up.
Future plans
We endeavour to continue measurements on the long-term. Moreover, dietary assessment methods used in the NQplus study will be extensively validated, that is, Food Frequency Questionnaires, 24-hour recalls and urinary and blood biomarkers of exposure. As such, the NQplus study will provide a unique opportunity to study many cross-sectional and longitudinal associations between diet and cardiometabolic health outcomes using the best dietary assessment methods available so far.
Economic diversification in Mongolia: Import substitution and expert orientation
Dagys, K. ; Lee, Song Kun ; Dries, L.K.E. ; Agipar, Bakey ; Heijman, W.J.M. - \ 2018
China’s livestock transition : Driving forces, impacts, and consequences
Bai, Zhaohai ; Ma, Wenqi ; Ma, Lin ; Velthof, Gerard L. ; Wei, Zhibiao ; Havlík, Petr ; Oenema, Oene ; Lee, Michael R.F. ; Zhang, Fusuo - \ 2018
Science Advances 4 (2018)7. - ISSN 2375-2548

China’s livestock industry has experienced a vast transition during the last three decades, with profound effects on domestic and global food provision, resource use, nitrogen and phosphorus losses, and greenhouse gas (GHG) emissions. We provide a comprehensive analysis of the driving forces around this transition and its national and global consequences. The number of livestock units (LUs) tripled in China in less than 30 years, mainly through the growth of landless industrial livestock production systems and the increase in monogastric livestock (from 62 to 74% of total LUs). Changes were fueled through increases in demand as well as, supply of new breeds, new technology, and government support. Production of animal source protein increased 4.9 times, nitrogen use efficiency at herd level tripled, and average feed use and GHG emissions per gram protein produced decreased by a factor of 2 between 1980 and 2010. In the same period, animal feed imports have increased 49 times, total ammonia and GHG emissions to the atmosphere doubled, and nitrogen losses to watercourses tripled. As a consequence, China’s livestock transition has significant global impact. Forecasts for 2050, using the Shared Socio-economic Pathways scenarios, indicate major further changes in livestock production and impacts. On the basis of these possible trajectories, we suggest an alternative transition, which should be implemented by government, processing industries, consumers, and retailers. This new transition is targeted to increase production efficiency and environmental performance at system level, with coupling of crop-livestock production, whole chain manure management, and spatial planning as major components.

Satellite DNA in Paphiopedilum subgenus Parvisepalum as revealed by high-throughput sequencing and fluorescent in situ hybridization
Lee, Yung I. ; Yap, Jing Wei ; Izan, Shairul ; Leitch, Ilia J. ; Fay, Michael F. ; Lee, Yi Ching ; Hidalgo, Oriane ; Dodsworth, Steven ; Smulders, Marinus J.M. ; Gravendeel, Barbara ; Leitch, Andrew R. - \ 2018
BMC Genomics 19 (2018)1. - ISSN 1471-2164
FISH - Fluorescent in situ hybridization - Karyotype - Paphiopedilum - Satellite DNA

Background: Satellite DNA is a rapidly diverging, largely repetitive DNA component of many eukaryotic genomes. Here we analyse the evolutionary dynamics of a satellite DNA repeat in the genomes of a group of Asian subtropical lady slipper orchids (Paphiopedilum subgenus Parvisepalum and representative species in the other subgenera/sections across the genus). A new satellite repeat in Paphiopedilum subgenus Parvisepalum, SatA, was identified and characterized using the RepeatExplorer pipeline in HiSeq Illumina reads from P. armeniacum (2n = 26). Reconstructed monomers were used to design a satellite-specific fluorescent in situ hybridization (FISH) probe. The data were also analysed within a phylogenetic framework built using the internal transcribed spacer (ITS) sequences of 45S nuclear ribosomal DNA. Results: SatA comprises c. 14.5% of the P. armeniacum genome and is specific to subgenus Parvisepalum. It is composed of four primary monomers that range from 230 to 359 bp and contains multiple inverted repeat regions with hairpin-loop motifs. A new karyotype of P. vietnamense (2n = 28) is presented and shows that the chromosome number in subgenus Parvisepalum is not conserved at 2n = 26, as previously reported. The physical locations of SatA sequences were visualised on the chromosomes of all seven Paphiopedilum species of subgenus Parvisepalum (2n = 26-28), together with the 5S and 45S rDNA loci using FISH. The SatA repeats were predominantly localisedin the centromeric, peri-centromeric and sub-telocentric chromosome regions, but the exact distribution pattern was species-specific. Conclusions: We conclude that the newly discovered, highly abundant and rapidly evolving satellite sequence SatA is specific to Paphiopedilum subgenus Parvisepalum. SatA and rDNA chromosomal distributions are characteristic of species, and comparisons between species reveal that the distribution patterns generate a strong phylogenetic signal. We also conclude that the ancestral chromosome number of subgenus Parvisepalum and indeed of all Paphiopedilum could be either 2n = 26 or 28, if P. vietnamense is sister to all species in the subgenus as suggested by the ITS data.

Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen
Pais, Marina ; Yoshida, Kentaro ; Giannakopoulou, Artemis ; Pel, Mathieu A. ; Cano, Liliana M. ; Oliva, Ricardo F. ; Witek, Kamil ; Lindqvist-Kreuze, Hannele ; Vleeshouwers, Vivianne G.A.A. ; Kamoun, Sophien - \ 2018
BMC Evolutionary Biology 18 (2018)1. - ISSN 1471-2148
Asexual reproduction - Clonal lineage - Copy number variation - Emergent pathogen - Evolution - Expression polymorphism - Immunity - Loss of heterozygosity - Phenotypic plasticity - Phytophthora infestans - Structural variation

Background: Outbreaks caused by asexual lineages of fungal and oomycete pathogens are a continuing threat to crops, wild animals and natural ecosystems (Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, Gurr SJ, Nature 484:186-194, 2012; Kupferschmidt K, Science 337:636-638, 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl MF, Thomma BP, BioEssays 36:335-345, 2014). Ever since the 19th century Irish famine, the oomycete Phytophthora infestans has caused recurrent outbreaks on potato and tomato crops that have been primarily caused by the successive rise and migration of pandemic asexual lineages (Goodwin SB, Cohen BA, Fry WE, Proc Natl Acad Sci USA 91:11591-11595, 1994; Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10:e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Cooke DEL, Cano LM, Raffaele S, Bain RA, Cooke LR, Etherington GJ, Deahl KL, Farrer RA, Gilroy EM, Goss EM, et al. PLoS Pathog 8:e1002940, 2012). However, the dynamics of genome evolution within these clonal lineages have not been determined. The objective of this study was to use a comparative genomics and transcriptomics approach to determine the molecular mechanisms that underpin phenotypic variation within a clonal lineage of P. infestans. Results: Here, we reveal patterns of genomic and gene expression variation within a P. infestans asexual lineage by comparing strains belonging to the South American EC-1 clone that has dominated Andean populations since the 1990s (Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Delgado RA, Monteros-Altamirano AR, Li Y, Visser RGF, van der Lee TAJ, Vosman B, Plant Pathol 62:1081-1088, 2013; Forbes GA, Escobar XC, Ayala CC, Revelo J, Ordonez ME, Fry BA, Doucett K, Fry WE, Phytopathology 87:375-380, 1997; Oyarzun PJ, Pozo A, Ordonez ME, Doucett K, Forbes GA, Phytopathology 88:265-271, 1998). We detected numerous examples of structural variation, nucleotide polymorphisms and loss of heterozygosity within the EC-1 clone. Remarkably, 17 genes are not expressed in one of the two EC-1 isolates despite apparent absence of sequence polymorphisms. Among these, silencing of an effector gene was associated with evasion of disease resistance conferred by a potato immune receptor. Conclusions: Our findings highlight the molecular changes underpinning the exceptional genetic and phenotypic plasticity associated with host adaptation in a pandemic clonal lineage of a eukaryotic plant pathogen. We observed that the asexual P. infestans lineage EC-1 can exhibit phenotypic plasticity in the absence of apparent genetic mutations resulting in virulence on a potato carrying the Rpi-vnt1.1 gene. Such variant alleles may be epialleles that arose through epigenetic changes in the underlying genes.

The unforeseen evolutionary history of Fusarium mitochondrial genomes
Brankovics, B. ; Kulik, T. ; Lee, T.A.J. van der; Waalwijk, C. ; Hoog, G.S. de; Diepeningen, A.D. van - \ 2018
Gewasbescherming 48 (2018)4/5/6. - ISSN 0166-6495 - p. 120 - 121.
The Fusarium graminearum Histone Acetyltransferases Are Important for Morphogenesis, DON Biosynthesis, and Pathogenicity
Kong, Xiangjiu ; Diepeningen, A.D. van; Lee, T.A.J. van der; Waalwijk, C. ; Xu, Jingsheng ; Xu, Jin ; Zhang, Hao ; Chen, Wanquan ; Feng, Jie - \ 2018
Frontiers in Microbiology 9 (2018). - ISSN 1664-302X
Post-translational modifications of chromatin structure by histone acetyltransferase (HATs) play a central role in the regulation of gene expression and various biological processes in eukaryotes. Although HAT genes have been studied in many fungi, few of them have been functionally characterized. In this study, we identified and characterized four putative HATs (FgGCN5, FgRTT109, FgSAS2, FgSAS3) in the plant pathogenic ascomycete Fusarium graminearum, the causal agent of Fusarium head blight of wheat and barley. We replaced the genes and all mutant strains showed reduced growth of F. graminearum. The ΔFgSAS3 and ΔFgGCN5 mutant increased sensitivity to oxidative and osmotic stresses. Additionally, ΔFgSAS3 showed reduced conidia sporulation and perithecium formation. Mutant ΔFgGCN5 was unable to generate any conidia and lost its ability to form perithecia. Our data showed also that FgSAS3 and FgGCN5 are pathogenicity factors required for infecting wheat heads as well as tomato fruits. Importantly, almost no Deoxynivalenol (DON) was produced either in ΔFgSAS3 or ΔFgGCN5 mutants, which was consistent with a significant downregulation of TRI genes expression. Furthermore, we discovered for the first time that FgSAS3 is indispensable for the acetylation of histone site H3K4, while FgGCN5 is essential for the acetylation of H3K9, H3K18, and H3K27. H3K14 can be completely acetylated when FgSAS3 and FgGCN5 were both present. The RNA-seq analyses of the two mutant strains provide insight into their functions in development and metabolism. Results from this study clarify the functional divergence of HATs in F. graminearum, and may provide novel targeted strategies to control secondary metabolite expression and infections of F. graminearum.
Host and Cropping System Shape the Fusarium Population: 3ADON-Producers Are Ubiquitous in Wheat Whereas NIV-Producers Are More Prevalent in Rice
Yang, Meixin ; Zhang, Hao ; Kong, Xiangjiu ; Lee, T.A.J. van der; Waalwijk, C. ; Diepeningen, A.D. van; Xu, Jin ; Xu, Jingsheng ; Chen, Wanquan ; Feng, Jie - \ 2018
Toxins 10 (2018)3. - ISSN 2072-6651
In recent years, Fusarium head blight (FHB) outbreaks have occurred much more frequently in China. The reduction of burning of the preceding crop residues is suggested to contribute to more severe epidemics as it may increase the initial inoculum. In this study, a large number of Fusarium isolates was collected from blighted wheat spikes as well as from rice stubble with perithecia originating from nine sampling sites in five provinces in Southern China. Fusarium asiaticum dominated both wheat and rice populations, although rice populations showed a higher species diversity. Chemotype analysis showed that rice is the preferred niche for NIV mycotoxin producers that were shown to be less virulent on wheat. In contrast, 3ADON producers are more prevalent on wheat and in wheat producing areas. The 3ADON producers were shown to be more virulent on wheat, revealing the selection pressure of wheat on 3ADON producers. For the first time, members of the Incarnatum-clade of Fusarium Incarnatum-Equiseti Species Complex (FIESC) were found to reproduce sexually on rice stubble. The pathogenicity of FIESC isolates on wheat proved very low and this may cause the apparent absence of this species in the main wheat producing provinces. This is the first report of the Fusarium population structure including rice stubble as well as a direct comparison with the population on wheat heads in the same fields. Our results confirm that the perithecia on rice stubble are the primary inoculum of FHB on wheat and that cropping systems affect the local Fusarium population.
Private and public costs and benefits of implementing a quality-based milk payment system in Kenya
Ndambi, O.A. ; Njiru, Ruth ; Knippenberg, Camee van; Lee, J. van der; Kilelu, C.W. ; Ngigi, M. - \ 2018
Wageningen : Wageningen University & Research (3R Kenya Project Research Brief 001) - 14 p.
Promises and challenges in insect-plant interactions
Giron, David ; Dubreuil, Géraldine ; Bennett, Alison ; Dedeine, Franck ; Dicke, Marcel ; Dyer, Lee A. ; Erb, Matthias ; Harris, Marion O. ; Huguet, Elisabeth ; Kaloshian, Isgouhi ; Kawakita, Atsushi ; Lopez-Vaamonde, Carlos ; Palmer, Todd M. ; Petanidou, Theodora ; Poulsen, Michael ; Sallé, Aurélien ; Simon, Jean Christophe ; Terblanche, John S. ; Thiéry, Denis ; Whiteman, Noah K. ; Woods, H.A. ; Pincebourde, Sylvain - \ 2018
Entomologia Experimentalis et Applicata 166 (2018)5. - ISSN 0013-8703 - p. 319 - 343.
Community ecology - Ecological networks - Evolutionary genomics - Forests and agroecosystems - Global change - Insect effectors - Multitrophic interactions - Phylogenetics - Plant response - Symbionts - Thermal ecology

There is tremendous diversity of interactions between plants and other species. These relationships range from antagonism to mutualism. Interactions of plants with members of their ecological community can lead to a profound metabolic reconfiguration of the plants' physiology. This reconfiguration can favour beneficial organisms and deter antagonists like pathogens or herbivores. Determining the cellular and molecular dialogue between plants, microbes, and insects, and its ecological and evolutionary implications is important for understanding the options for each partner to adopt an adaptive response to its biotic environment. Moving forward, understanding how such ecological interactions are shaped by environmental change and how we potentially mitigate deleterious effects will be increasingly important. The development of integrative multidisciplinary approaches may provide new solutions to the major ecological and societal issues ahead of us. The rapid evolution of technology provides valuable tools and opens up novel ways to test hypotheses that were previously unanswerable, but requires that scientists master these tools, understand potential ethical problems flowing from their implementation, and train new generations of biologists with diverse technical skills. Here, we provide brief perspectives and discuss future promise and challenges for research on insect-plant interactions building on the 16th International Symposium on Insect-Plant interactions (SIP) meeting that was held in Tours, France (2-6 July 2017). Talks, posters, and discussions are distilled into key research areas in insect-plant interactions, highlighting the current state of the field and major challenges, and future directions for both applied and basic research.

Assimilation of Streamflow Observations
Noh, Seong Jin ; Weerts, Albrecht H. ; Rakovec, Oldrich ; Lee, Haksu ; Seo, Dong-Jun - \ 2018
In: Handbook of Hydrometeorological Ensemble Forecasting / Duan, Qingyun, Pappenberger, Florian, Thielen, Jutta, Wood, Andy, Cloke, Hannah L., Schaake, John C., Springer Verlag - ISBN 9783642404573 - p. 1 - 36.
Streamflow is arguably the most important predictor in operational hydrologic forecasting and water resources management. Assimilation of streamflow observations into hydrologic models has received growing attention in recent decades as a cost-effective means to improve prediction accuracy. Whereas the methods used for streamflow data assimilation (DA) originated and were popularized in atmospheric and ocean sciences, the nature of streamflow DA is significantly different from that of atmospheric or oceanic DA. Compared to the atmospheric processes modeled in weather forecasting, the hydrologic processes for surface and groundwater flow operate over a much wider range of time scales. Also, most hydrologic systems are severely under-observed. The purpose of this chapter is to provide a review on streamflow measurements and associated uncertainty and to share the latest advances, experiences gained, and science issues and challenges in streamflow DA. Toward this end, we discuss the following aspects of streamflow observations and assimilation methods: (1) measurement methods and uncertainty of streamflow observations, (2) streamflow assimilation applications, and (3) benefits and challenges streamflow DA with regard to large-scale DA, multi-data assimilation, and dealing with timing errors.
Evolution and diversity of biosynthetic gene clusters in Fusarium
Hoogendoorn, Koen ; Barra, Lena ; Waalwijk, Cees ; Dickschat, Jeroen S. ; Lee, Theo A.J. van der; Medema, Marnix H. - \ 2018
Frontiers in Microbiology 9 (2018). - ISSN 1664-302X
Ancestral state reconstruction (ASR) - Biosynthetic gene cluster - Fusarium - Koraiol - Supernumary chromosome

Plant pathogenic fungi in the Fusarium genus cause severe damage to crops, resulting in great financial losses and health hazards. Specialized metabolites synthesized by these fungi are known to play key roles in the infection process, and to provide survival advantages inside and outside the host. However, systematic studies of the evolution of specialized metabolite-coding potential across Fusarium have been scarce. Here, we apply a combination of bioinformatic approaches to identify biosynthetic gene clusters (BGCs) across publicly available genomes from Fusarium, to group them into annotated families and to study gain/loss events of BGC families throughout the history of the genus. Comparison with MIBiG reference BGCs allowed assignment of 29 gene cluster families (GCFs) to pathways responsible for the production of known compounds, while for 57 GCFs, the molecular products remain unknown. Comparative analysis of BGC repertoires using ancestral state reconstruction raised several new hypotheses on how BGCs contribute to Fusarium pathogenicity or host specificity, sometimes surprisingly so: for example, a gene cluster for the biosynthesis of hexadehydro-astechrome was identified in the genome of the biocontrol strain Fusarium oxysporum Fo47, while being absent in that of the tomato pathogen F. oxysporum f.sp. lycopersici. Several BGCs were also identified on supernumerary chromosomes; heterologous expression of genes for three terpene synthases encoded on the Fusarium poae supernumerary chromosome and subsequent GC/MS analysis showed that these genes are functional and encode enzymes that each are able to synthesize koraiol; this observed functional redundancy supports the hypothesis that localization of copies of BGCs on supernumerary chromosomes provides freedom for evolutionary innovations to occur, while the original function remains conserved. Altogether, this systematic overview of biosynthetic diversity in Fusarium paves the way for targeted natural product discovery based on automated identification of species-specific pathways as well as for connecting species ecology to the taxonomic distributions of BGCs.

A comparison of VMS and AIS data : The effect of data coverage and vessel position recording frequency on estimates of fishing footprints
Shepperson, Jennifer L. ; Hintzen, Niels T. ; Szostek, Claire L. ; Bell, Ewen ; Murray, Lee G. ; Kaiser, Michel J. - \ 2018
ICES Journal of Marine Science 75 (2018)3. - ISSN 1054-3139 - p. 988 - 998.
automatic identification system - extent - fisheries - footprint - scallop dredging - vessel monitoring system

Understanding the distribution of fishing activity is fundamental to quantifying its impact on the seabed. Vessel monitoring system (VMS) data provides a means to understand the footprint (extent and intensity) of fishing activity. Automatic Identification System (AIS) data could offer a higher resolution alternative to VMS data, but differences in coverage and interpretation need to be better understood. VMS and AIS data were compared for individual scallop fishing vessels. There were substantial gaps in the AIS data coverage; AIS data only captured 26% of the time spent fishing compared to VMS data. The amount of missing data varied substantially between vessels (45-99% of each individuals' AIS data were missing). A cubic Hermite spline interpolation of VMS data provided the greatest similarity between VMS and AIS data. But the scale at which the data were analysed (size of the grid cells) had the greatest influence on estimates of fishing footprints. The present gaps in coverage of AIS may make it inappropriate for absolute estimates of fishing activity. VMS already provides a means of collecting more complete fishing position data, shielded from public view. Hence, there is an incentive to increase the VMS poll frequency to calculate more accurate fishing footprints.

Nu inzetten op groen voor leefbare stad
Snep, Robbert - \ 2018
The Shifting Structure of Agricultural R&D : Worldwide Investment Patterns and Payoffs
Pardey, Philip G. ; Alston, Julian M. ; Chang-Kang, Connie ; Hurley, Terrance M. ; Andrade, Robert S. ; Dehmer, Steven P. ; Lee, Kyuseon ; Rao, X. - \ 2018
In: From Agriscience to Agribusiness / Kalaitzandonakes, N., Carayannis, E.G., Grigoroudis, E., Rozakis, S., Springer (Innovation, Technology, and Knowledge Management ) - ISBN 9783319679570 - p. 13 - 39.
The future path and pace of agricultural productivity growth areinextricably intertwined with investments in food and agricultural research and development (R&D). Looking back over half a century of evidence, we find that the lay of the global food and agricultural R&D land is changing, with indications that we are in the midst of an historic transition. The more notable trends are as follows: (1) for the first time in modern history (in purchasing power parity, PPP, terms), the middle-income countries now outspend the rich countries in terms of public-sector investments in food and agricultural R&D; (2) the shifting public shares reflect a continuing decline in the rate of growth of food and agricultural R&D spending by the rich countries, along with a generally sustained and substantial growth in spending by the middle-income countries (especially China, India, and Brazil); (3) in PPP terms, China now spends more than the United States on both public- and private-sector food and agricultural R&D; (4) the global share of food and agricultural R&D being conducted by the private sector has increased, especially in the high- and rapidly growing middle-income countries; and (5) the low-income countries are losing ground and account for an exceptionally small share of global spending. The mean and median values of the reported rates of return to food and agricultural R&D based on the IRR are high and remain so, with no signs of a diminution in the payoffs to more recent (compared with earlier) investments in R&D. But the available evidence on the returns to food and agricultural R&D is not fully representative of the institutional (i.e., public versus private), locational, or commodity orientation of the research and the agricultural sector itself. The Shifting Structure of Agricultural R&D: Worldwide.... Available from: https://www.researchgate.net/publication/321253196_The_Shifting_Structure_of_Agricultural_RD_Worldwide_Investment_Patterns_and_Payoffs [accessed May 15 2018].
Performance of emerging dairy services agri-enterprises: a case study of youth-led service provider enterprises (SPE)
Kilelu, Catherine W. ; Koge, Jessica ; Kabuga, Cyrus ; Lee, Jan van der - \ 2018
Wageningen : Wageningen Livestock Research (Wageningen Livestock Research report 1094) - 39
Benchmarking of Dairy Processors’ Associations : actors and their activities in The Netherlands, Zambia and South Africa
Houwers, Wim ; Lee, Jan van der - \ 2018
Wageningen : Wageningen Livestock Research (Wageningen Livestock Research report 1096) - 33
This report describes a study of dairy processors’ associations in three countries. As the dairy sectors in these countries are at different stages of development, the challenges these associations face are very different indeed, and so are their functions and structures. Learnings from these cases are drawn for the situation in Kenya.
Detection of titanium particles in human liver and spleen and possible health implications
Heringa, M.B. ; Peters, R.J.B. ; Bleys, R.L.A.W. ; Lee, M.K. van der; Tromp, P.C. ; Kesteren, P.C.E. van; Eijkeren, J.C.H. van; Undas, A.K. ; Oomen, A.G. ; Bouwmeester, H. - \ 2018
Particle and Fibre Toxicology 15 (2018)1. - ISSN 1743-8977
Human liver - Human spleen - Nanoparticle - Quantification - Risk assessment - Sp-ICP-HRMS - Tissue level - Titanium dioxide
Background: Titanium dioxide (TiO2) is produced at high volumes and applied in many consumer and food products. Recent toxicokinetic modelling indicated the potential of TiO2 to accumulate in human liver and spleen upon daily oral exposure, which is not routinely investigated in chronic animal studies. A health risk from nanosized TiO2 particle consumption could not be excluded then. Results: Here we show the first quantification of both total titanium (Ti) and TiO2 particles in 15 post-mortem human livers and spleens. These low-level analyses were enabled by the use of fully validated (single particle) inductively coupled plasma high resolution mass spectrometry ((sp)ICP-HRMS) detection methods for total Ti and TiO2 particles. The presence of TiO2 in the particles in tissues was confirmed by Scanning Electron Microscopy with energy dispersive X-ray spectrometry. Conclusions: These results prove that TiO2 particles are present in human liver and spleen, with ≥24% of nanosize (< 100 nm). The levels are below the doses regarded as safe in animals, but half are above the dose that is deemed safe for liver damage in humans when taking into account several commonly applied uncertainty factors. With these new and unique human data, we remain with the conclusion that health risks due to oral exposure to TiO2 cannot be excluded.
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