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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Combining multi-population datasets for joint genome-wide association and meta-analyses: The case of bovine milk fat composition traits
Gebreyesus, G. ; Buitenhuis, A.J. ; Poulsen, N.A. ; Visker, M.H.P.W. ; Zhang, Q. ; Valenberg, H.J.F. van; Sun, D. ; Bovenhuis, H. - \ 2019
Journal of Dairy Science 102 (2019)12. - ISSN 0022-0302 - p. 11124 - 11141.
mega-analysis - meta-analysis - multi-population GWAS

In genome-wide association studies (GWAS), sample size is the most important factor affecting statistical power that is under control of the investigator, posing a major challenge in understanding the genetics underlying difficult-to-measure traits. Combining data sets available from different populations for joint or meta-analysis is a promising alternative to increasing sample sizes available for GWAS. Simulation studies indicate statistical advantages from combining raw data or GWAS summaries in enhancing quantitative trait loci (QTL) detection power. However, the complexity of genetics underlying most quantitative traits, which itself is not fully understood, is difficult to fully capture in simulated data sets. In this study, population-specific and combined-population GWAS as well as a meta-analysis of the population-specific GWAS summaries were carried out with the objective of assessing the advantages and challenges of different data-combining strategies in enhancing detection power of GWAS using milk fatty acid (FA) traits as examples. Gas chromatography (GC) quantified milk FA samples and high-density (HD) genotypes were available from 1,566 Dutch, 614 Danish, and 700 Chinese Holstein Friesian cows. Using the joint GWAS, 28 additional genomic regions were detected, with significant associations to at least 1 FA, compared with the population-specific analyses. Some of these additional regions were also detected using the implemented meta-analysis. Furthermore, using the frequently reported variants of the diacylglycerol acyltransferase 1 (DGAT1) and stearoyl-CoA desaturase (SCD1) genes, we show that significant associations were established with more FA traits in the joint GWAS than the remaining scenarios. However, there were few regions detected in the population-specific analyses that were not detected using the joint GWAS or the meta-analyses. Our results show that combining multi-population data set can be a powerful tool to enhance detection power in GWAS for seldom-recorded traits. Detection of a higher number of regions using the meta-analysis, compared with any of the population-specific analyses also emphasizes the utility of these methods in the absence of raw multi-population data sets to undertake joint GWAS.

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.

Improving environmental risk assessments of chemicals: Steps towards evidence-based ecotoxicology
Martin, Olwenn V. ; Adams, Julie ; Beasley, Amy ; Belanger, Scott ; Breton, Roger L. ; Brock, Theo C.M. ; Buonsante, Vito A. ; Galay Burgos, Malyka ; Green, John ; Guiney, Patrick D. ; Hall, Tilghman ; Hanson, Mark ; Harris, Meagan J. ; Henry, Tala R. ; Huggett, Duane ; Junghans, Marion ; Laskowski, Ryszard ; Maack, Gerd ; Moermond, Caroline T.A. ; Panter, Grace ; Pease, Anita ; Poulsen, Veronique ; Roberts, Mike ; Rudén, Christina ; Schlekat, Christian E. ; Schoeters, Ilse ; Solomon, Keith R. ; Staveley, Jane ; Stubblefield, Bill ; Sumpter, John P. ; Warne, Michael S.J. ; Wentsel, Randall ; Wheeler, James R. ; Wolff, Brian A. ; Yamazaki, Kunihiko ; Zahner, Holly ; Ågerstrand, Marlene - \ 2019
Environment International 128 (2019). - ISSN 0160-4120 - p. 210 - 217.
Chemical safety - Decision-making - Ecological risk assessment - Ecotoxicology - Environmental risk assessment - Evidence-based
Reliability of genomic prediction for milk fatty acid composition by using a multi-population reference and incorporating GWAS results
Gebreyesus, Grum ; Bovenhuis, Henk ; Lund, Mogens S. ; Poulsen, Nina A. ; Sun, Dongxiao ; Buitenhuis, Bart - \ 2019
Genetics, Selection, Evolution 51 (2019)1. - ISSN 0999-193X

Background: Large-scale phenotyping for detailed milk fatty acid (FA) composition is difficult due to expensive and time-consuming analytical techniques. Reliability of genomic prediction is often low for traits that are expensive/difficult to measure and for breeds with a small reference population size. An effective method to increase reference population size could be to combine datasets from different populations. Prediction models might also benefit from incorporation of information on the biological underpinnings of quantitative traits. Genome-wide association studies (GWAS) show that genomic regions on Bos taurus chromosomes (BTA) 14, 19 and 26 underlie substantial proportions of the genetic variation in milk FA traits. Genomic prediction models that incorporate such results could enable improved prediction accuracy in spite of limited reference population sizes. In this study, we combine gas chromatography quantified FA samples from the Chinese, Danish and Dutch Holstein populations and implement a genomic feature best linear unbiased prediction (GFBLUP) model that incorporates variants on BTA14, 19 and 26 as genomic features for which random genetic effects are estimated separately. Prediction reliabilities were compared to those estimated with traditional GBLUP models. Results: Predictions using a multi-population reference and a traditional GBLUP model resulted in average gains in prediction reliability of 10% points in the Dutch, 8% points in the Danish and 1% point in the Chinese populations compared to predictions based on population-specific references. Compared to the traditional GBLUP, implementation of the GFBLUP model with a multi-population reference led to further increases in prediction reliability of up to 38% points in the Dutch, 23% points in the Danish and 13% points in the Chinese populations. Prediction reliabilities from the GFBLUP model were moderate to high across the FA traits analyzed. Conclusions: Our study shows that it is possible to predict genetic merits for milk FA traits with reasonable accuracy by combining related populations of a breed and using models that incorporate GWAS results. Our findings indicate that international collaborations that facilitate access to multi-population datasets could be highly beneficial to the implementation of genomic selection for detailed milk composition traits.

Multi-population GWAS and enrichment analyses reveal novel genomic regions and promising candidate genes underlying bovine milk fatty acid composition
Gebreyesus, G. ; Buitenhuis, A.J. ; Poulsen, N.A. ; Visker, M.H.P.W. ; Zhang, Q. ; Valenberg, H.J.F. Van; Sun, D. ; Bovenhuis, H. - \ 2019
BMC Genomics 20 (2019)1. - ISSN 1471-2164
Candidate genes - Milk fatty acids - Multi-population GWAS - Pathway analysis

Background: The power of genome-wide association studies (GWAS) is often limited by the sample size available for the analysis. Milk fatty acid (FA) traits are scarcely recorded due to expensive and time-consuming analytical techniques. Combining multi-population datasets can enhance the power of GWAS enabling detection of genomic region explaining medium to low proportions of the genetic variation. GWAS often detect broader genomic regions containing several positional candidate genes making it difficult to untangle the causative candidates. Post-GWAS analyses with data on pathways, ontology and tissue-specific gene expression status might allow prioritization among positional candidate genes. Results: Multi-population GWAS for 16 FA traits quantified using gas chromatography (GC) in sample populations of the Chinese, Danish and Dutch Holstein with high-density (HD) genotypes detects 56 genomic regions significantly associated to at least one of the studied FAs; some of which have not been previously reported. Pathways and gene ontology (GO) analyses suggest promising candidate genes on the novel regions including OSBPL6 and AGPS on Bos taurus autosome (BTA) 2, PRLH on BTA 3, SLC51B on BTA 10, ABCG5/8 on BTA 11 and ALG5 on BTA 12. Novel genes in previously known regions, such as FABP4 on BTA 14, APOA1/5/7 on BTA 15 and MGST2 on BTA 17, are also linked to important FA metabolic processes. Conclusion: Integration of multi-population GWAS and enrichment analyses enabled detection of several novel genomic regions, explaining relatively smaller fractions of the genetic variation, and revealed highly likely candidate genes underlying the effects. Detection of such regions and candidate genes will be crucial in understanding the complex genetic control of FA metabolism. The findings can also be used to augment genomic prediction models with regions collectively capturing most of the genetic variation in the milk FA traits.

A probabilistic approach for risk-benefit assessment of food substitutions : A case study on substituting meat by fish
Thomsen, Sofie Theresa ; Boer, Waldo de; Pires, Sara M. ; Devleesschauwer, Brecht ; Fagt, Sisse ; Andersen, Rikke ; Poulsen, Morten ; Voet, Hilko van der - \ 2019
Food and Chemical Toxicology 126 (2019). - ISSN 0278-6915 - p. 79 - 96.
Disability-Adjusted Life Year(DALY) - Food-based dietary guidelines - Health impact - Risk-benefit assessment (RBA) - Substitution - Usual intake difference model

Accounting for substitution of foods is inevitable when evaluating health impact of dietary changes. But substitution behavior and the associated health impact may vary between individuals. We therefore propose the use of probabilistic methods to model substitution and assess health impact distributions in risk-benefit assessment (RBA) of foods. We investigated the health impact of substituting red and processed meat with fish in the Danish adult population and the variability in health impact. We applied probabilistic approaches in modeling the substitution to reflect variability between individual substitution behaviors. Furthermore, when multiple intake scenarios are compared, we propose a method for adjusting intake differences for individual day-to-day variability. We estimated that 134 (95% UI: 102; 169) Disability-Adjusted Life Years/100,000 were averted per year by the substitution. The health impact varied considerably by age and sex, with the largest health benefit of the substitution observed for young women in the child-bearing age and for the older generation, mainly men. This study provides further insight in how the health impact of substituting meat by fish varies between individuals and suggests a framework to be applied in RBAs of other food substitutions. Our results are relevant for policy makers in defining targeted public health strategies.

Reviewing the taxonomy of Podaxis : Opportunities for understanding extreme fungal lifestyles
Conlon, Benjamin H. ; Aanen, Duur K. ; Beemelmanns, Christine ; Beer, Z.W. de; Fine Licht, Henrik H. De; Gunde-Cimerman, Nina ; Schiøtt, Morten ; Poulsen, Michael - \ 2019
Fungal Biology 123 (2019)3. - ISSN 1878-6146 - p. 183 - 187.
Basidiomycota - Drought - Extremophile - Low water activity - Termite

There are few environments more hostile and species-poor than deserts and the mounds of Nasutitermitinae termites. However, despite the very different adaptations required to survive in such extreme and different environments, the fungal genus Podaxis is capable of surviving in both: where few other fungi are reported to grow. Despite their prominence in the landscape and their frequent documentation by early explorers, there has been relatively little research into the genus. Originally described by Linnaeus in 1771, in the early 20th Century, the then ∼25 species of Podaxis were almost entirely reduced into one species: Podaxis pistillaris. Since this reduction, several new species of Podaxis have been described but without consideration of older descriptions. This has resulted in 44 recognised species names in Index Fungorum but the vast majority of studies and fungarium specimens still refer to P. pistillaris. Studies of Podaxis' extremely different lifestyles is hampered by its effective reduction to a single-species genus. Here we examine the history of the taxonomy of Podaxis before focusing on its extreme lifestyles. From this, we consider how the muddled taxonomy of Podaxis may be resolved; opening up further avenues for future research into this enigmatic fungal genus.

Can interaction specificity in the fungus-farming termite symbiosis be explained by nutritional requirements of the fungal crop?
Costa, Rafael R. da; Vreeburg, Sabine M.E. ; Shik, Jonathan Z. ; Aanen, Duur K. ; Poulsen, Michael - \ 2019
Fungal Ecology 38 (2019). - ISSN 1754-5048 - p. 54 - 61.
Biomass - Carbohydrates - Geometric framework - Interaction specificity - Macrotermes - Nutrition - Odontotermes - Protein - Symbiosis - Termitomyces

Fungus-growing termites are associated with genus-specific fungal symbionts, which they acquire via horizontal transmission. Selection of specific symbionts may be explained by the provisioning of specific, optimal cultivar growth substrates by termite farmers. We tested whether differences in in vitro performance of Termitomyces cultivars from nests of three termite species on various substrates are correlated with the interaction specificity of their hosts. We performed single-factor growth assays (varying carbon sources), and a two-factor geometric framework experiment (simultaneously varying carbohydrate and protein availability). Although we did not find qualitative differences between Termitomyces strains in carbon-source use, there were quantitative differences, which we analysed using principal component analysis. This showed that growth of Termitomyces on different carbon sources was correlated with termite host genus, rather than host species, while growth on different ratios and concentrations of protein and carbohydrate was correlated with termite host species. Our findings corroborate the interaction specificity between fungus-growing termites and Termitomyces cultivars and indicate that specificity between termite hosts and fungi is reflected both nutritionally and physiologically. However, it remains to be demonstrated whether those differences contribute to selection of specific fungal cultivars by termites at the onset of colony foundation.

External scientific report: Data collection for the estimation of ecological data (specific focal species, time spent in treated areas collecting food, composition of diet), residue level and residue decline on food items to be used in the risk assessment for birds and mammals
Lahr, J. ; Kramer, Wolfgang ; Mazerolles, Vanessa ; Poulsen, Veronique ; Jölli, Daniela ; Müller, Marc ; McVey, Emily ; Wassenberg, J. ; Derkx, M.P.M. ; Brouwer, J.H.D. ; Deneer, J.W. ; Beltman, W.H.J. ; Lammertsma, D.R. ; Jansman, H.A.H. ; Buij, R. - \ 2018
EFSA (EFSA Supporting Publications 5)
The study described in this report was conducted with the aim of developing an unified database of ecological data and residue data to be used for the risk assessment of plant protection products for birds and mammals. The main sources of data were the information submitted in the context of approval of active substances and authorization of products and and additional information retrieved through a systematic literature review. The data were screened and organised in three Excel databases, one for birds, one for mammals and one for residue studies. The ecological information for birds and mammal risk assessment consisted of data that is used for the determination of focal species, estimation of the proportion of an animal's daily diet obtained in a treated habitat (PT) and assessment of the composition of the diet obtained from a treated area (PD). The information gathered on residues focussed on (initial) residue levels after treatment and on residue decline (the reported half‐life or DT50 and the DT90)
Searching for Podaxis on the trails of early explorers in southern Africa
Buys, M. ; Conlon, B. ; Fine Licht, Henrik H. De; Aanen, D.K. ; Poulsen, M. ; Beer, Z.W. de - \ 2018
South African Journal of Botany 115 (2018). - ISSN 0254-6299 - p. 317 - 317.
Podaxis pistillaris is the name often given to the torpedo-shaped mushrooms forming on termite mounds across southern Africa during the rainy season. Linnaeus described the species in 1871 based on a specimen from India. In 1881, he described a second species as Lycoperdon carcinomale from a South African specimen he received from Thunberg. In 1812, Burchell made a painting of the fungus during his exploration of southern Africa. In 1933, all 33 Podaxis species described by that time from Africa, Asia, Australia and the USA, were lumped as synonyms of P. pistillaris. Another 12 species were subsequently described, but most authors treated all these fungi as P. pistillaris. In a quest to resolve the taxonomy of the fungus, we studied Southern African specimens from various herbaria, and some specimens from the USA, Mexico, India, and Africa. We also visited the sites where Thunberg collected his specimen (Western Cape) and where Burchell made his painting (Northern Cape), but could not find fresh specimens. We distributed flyers to local communities in these areas and requested that they contact us should Podaxis be observed. Within six weeks we received specimens from a farm close to Burchell’s camp site, and more from the Northern and Eastern Cape. Ribosomal DNA sequences were successfully obtained from all the fresh and almost all herbarium specimens, including some older than 100 years. Phylogenetic analyses showed that the southern African specimens separate in at least five distinct species, some of which might represent novel taxa
Genome-wide association study of the de novo synthesized milk fatty acids based on Dutch, Danish and Chinese Holstein Friesians
Gebreyesus, Grum ; Buitenhuis, Bart ; Poulsen, Nina A. ; Visker, M.H.P.W. ; Zhang, Qianqian ; Valenberg, H.J.F. van; Sun, D. ; Bovenhuis, H. - \ 2018
In: Proceedings of the World Congress on Genetics Applied to Livestock Production. - WCGALP - 6 p.
Data for the de novo synthesized milk fatty acids (FAs) were obtained from milk samples of 1736 Dutch, 675 Danish and 784 Chinese Holstein Friesian cows and combined for multipopulation genome-wide association study (GWAS) using a mixed linear model. Results were compared with population specific GWAS undertaken for each population. In the combined analysis, QTL regions spread across 16 chromosomes were found significantly associated with the de novo synthesized FAs. Compared to the population-specific analyses, our multipopulation GWAS resulted in more regions showing significant associations for the de novo synthesized FAs, some of which were not previously reported.
Interleukin-37 treatment of mice with metabolic syndrome improves insulin sensitivity and reduces pro-inflammatory cytokine production in adipose tissue
Ballak, Dov B. ; Li, Suzhao ; Cavalli, Giulio ; Stahl, Jonathan L. ; Tengesdal, Isak W. ; Diepen, Janna A. van; Klück, Viola ; Swartzwelter, Benjamin ; Azam, Tania ; Tack, Cees J. ; Stienstra, Rinke ; Mandrup-Poulsen, Thomas ; Seals, Douglas R. ; Dinarello, Charles A. - \ 2018
Journal of Biological Chemistry 293 (2018)37. - ISSN 0021-9258 - p. 14224 - 14236.

Obesity and the metabolic syndrome are characterized by chronic, low-grade inflammation mainly originating from expanding adipose tissue and resulting in inhibition of insulin signaling and disruption of glycemic control.Transgenic mice expressing human interleukin 37 (IL-37),an anti-inflammatory cytokine of the IL-1 family,are protected against metabolic syndrome when fed a high-fat diet (HFD) containing 45% fat. Here, we examined whether treatment with recombinant IL-37 ameliorates established insulin resistance and obesity-induced inflammation. WT mice were fed a HFD for 22 weeks and then treated daily with IL-37 (1 ug/mouse) during the last 2 weeks. Compared with vehicle only-treated mice, IL-37-treated mice exhibited reduced insulin in the plasma and had significant improvements in glucose tolerance and in insulin content of the islets.The IL-37 treatment also increased the levels of circulating IL-1 receptor antagonist. Cultured adipose tissues revealed that IL-37 treatment significantly decreases spontaneous secretions of IL-1β, tumor necrosis factor α (TNFα), and CXC motif chemokine ligand 1 (CXCL-1). We also fed mice a 60% fat diet with concomitant daily IL-37 for 2 weeks and observed decreased secretion of IL-1β, TNFα, and IL-6 and reduced intracellular levels of IL-1β in the liver and adipose tissue, along with improved plasma glucose clearance. Compared with vehicle treatment, these IL-37-treated mice had no apparent weight gain. In human adipose tissue cultures, the presence of 50 pM IL-37 reduced spontaneous release of TNF and 50% of lipopolysaccharide-induced TNFα. These findings indicate that IL-37's anti-inflammatory effects can ameliorate established metabolic disturbances during obesity.

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.

Phylogenetic classification of the world's tropical forests
Slik, J.W.F. ; Franklin, Janet ; Arroyo-Rodríguez, Víctor ; Field, Richard ; Aguilar, Salomon ; Aguirre, Nikolay ; Ahumada, Jorge ; Aiba, Shin Ichiro ; Alves, Luciana F. ; Anitha, K. ; Avella, Andres ; Mora, Francisco ; Aymard, Gerardo A.C. ; Báez, Selene ; Balvanera, Patricia ; Bastian, Meredith L. ; Bastin, Jean François ; Bellingham, Peter J. ; Berg, Eduardo Van Den; Conceição Bispo, Polyanna Da; Boeckx, Pascal ; Boehning-Gaese, Katrin ; Bongers, Frans ; Boyle, Brad ; Brambach, Fabian ; Brearley, Francis Q. ; Brown, Sandra ; Chai, Shauna Lee ; Chazdon, Robin L. ; Chen, Shengbin ; Chhang, Phourin ; Chuyong, George ; Ewango, Corneille ; Coronado, Indiana M. ; Cristóbal-Azkarate, Jurgi ; Culmsee, Heike ; Damas, Kipiro ; Dattaraja, H.S. ; Davidar, Priya ; DeWalt, Saara J. ; Din, Hazimah ; Drake, Donald R. ; Duque, Alvaro ; Durigan, Giselda ; Eichhorn, Karl ; Eler, Eduardo Schmidt ; Enoki, Tsutomu ; Ensslin, Andreas ; Fandohan, Adandé Belarmain ; Farwig, Nina ; Feeley, Kenneth J. ; Fischer, Markus ; Forshed, Olle ; Garcia, Queila Souza ; Garkoti, Satish Chandra ; Gillespie, Thomas W. ; Gillet, Jean Francois ; Gonmadje, Christelle ; Granzow-De La Cerda, Iñigo ; Griffith, Daniel M. ; Grogan, James ; Hakeem, Khalid Rehman ; Harris, David J. ; Harrison, Rhett D. ; Hector, Andy ; Hemp, Andreas ; Homeier, Jürgen ; Hussain, M.S. ; Ibarra-Manríquez, Guillermo ; Hanum, I.F. ; Imai, Nobuo ; Jansen, Patrick A. ; Joly, Carlos Alfredo ; Joseph, Shijo ; Kartawinata, Kuswata ; Kearsley, Elizabeth ; Kelly, Daniel L. ; Kessler, Michael ; Killeen, Timothy J. ; Kooyman, Robert M. ; Laumonier, Yves ; Laurance, Susan G. ; Laurance, William F. ; Lawes, Michael J. ; Letcher, Susan G. ; Lindsell, Jeremy ; Lovett, Jon ; Lozada, Jose ; Lu, Xinghui ; Lykke, Anne Mette ; Mahmud, Khairil Bin; Mahayani, Ni Putu Diana ; Mansor, Asyraf ; Marshall, Andrew R. ; Martin, Emanuel H. ; Matos, Darley Calderado Leal ; Meave, Jorge A. ; Melo, Felipe P.L. ; Mendoza, Zhofre Huberto Aguirre ; Metali, Faizah ; Medjibe, Vincent P. ; Metzger, Jean Paul ; Metzker, Thiago ; Mohandass, D. ; Munguía-Rosas, Miguel A. ; Muñoz, Rodrigo ; Nurtjahy, Eddy ; Oliveira, Eddie Lenza De; Onrizal, ; Parolin, Pia ; Parren, Marc ; Parthasarathy, N. ; Paudel, Ekananda ; Perez, Rolando ; Pérez-García, Eduardo A. ; Pommer, Ulf ; Poorter, Lourens ; Qi, Lan ; Piedade, Maria Teresa F. ; Pinto, José Roberto Rodrigues ; Poulsen, Axel Dalberg ; Poulsen, John R. ; Powers, Jennifer S. ; Prasad, Rama Chandra ; Puyravaud, Jean Philippe ; Rangel, Orlando ; Reitsma, Jan ; Rocha, Diogo S.B. ; Rolim, Samir ; Rovero, Francesco ; Rozak, Andes ; Ruokolainen, Kalle ; Rutishauser, Ervan ; Rutten, Gemma ; Mohd Said, Mohd Nizam ; Saiter, Felipe Z. ; Saner, Philippe ; Santos, Braulio ; Santos, João Roberto Dos; Sarker, Swapan Kumar ; Schmitt, Christine B. ; Schoengart, Jochen ; Schulze, Mark ; Sheil, Douglas ; Sist, Plinio ; Souza, Alexandre F. ; Spironello, Wilson Roberto ; Sposito, Tereza ; Steinmetz, Robert ; Stevart, Tariq ; Suganuma, Marcio Seiji ; Sukri, Rahayu ; Sultana, Aisha ; Sukumar, Raman ; Sunderland, Terry ; Supriyadi, S. ; Suresh, H.S. ; Suzuki, Eizi ; Tabarelli, Marcelo ; Tang, Jianwei ; Tanner, Ed V.J. ; Targhetta, Natalia ; Theilade, Ida ; Thomas, Duncan ; Timberlake, Jonathan ; Morisson Valeriano, Márcio De; Valkenburg, Johan Van; Do, Tran Van; Sam, Hoang Van; Vandermeer, John H. ; Verbeeck, Hans ; Vetaas, Ole Reidar ; Adekunle, Victor ; Vieira, Simone A. ; Webb, Campbell O. ; Webb, Edward L. ; Whitfeld, Timothy ; Wich, Serge ; Williams, John ; Wiser, Susan ; Wittmann, Florian ; Yang, Xiaobo ; Yao, C.Y.A. ; Yap, Sandra L. ; Zahawi, Rakan A. ; Zakaria, Rahmad ; Zang, Runguo - \ 2018
Proceedings of the National Academy of Sciences of the United States of America 115 (2018)8. - ISSN 0027-8424 - p. 1837 - 1842.
Biogeographic legacies - Forest classification - Forest functional similarity - Phylogenetic community distance - Tropical forests

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

Enzyme activities at different stages of plant biomass decomposition in three species of fungusgrowing termites
Costa, Rafael R. da; Hu, Haofu ; Pilgaard, Bo ; Sabine, Sabine M. ; Schückel, Julia ; Pedersen, Kristine S.K. ; Kračun, Stjepan K. ; Busk, Peter K. ; Harholt, Jesper ; Sapountzis, Panagiotis ; Lange, Lene ; Aanen, Duur K. ; Poulsen, Michael - \ 2018
Applied and Environmental Microbiology 84 (2018)5. - ISSN 0099-2240
AZCL - Chromogenic substrates - HPLC - Macrotermes - Odontotermes - Peptide pattern recognition - Plant substrate - RNA-seq - Symbiosis - Termitomyces
Fungus-growing termites rely on mutualistic fungi of the genus Termitomyces and gut microbes for plant biomass degradation. Due to a certain degree of symbiont complementarity, this tripartite symbiosis has evolved as a complex bioreactor, enabling decomposition of nearly any plant polymer, likely contributing to the success of the termites as one of the main plant decomposers in the Old World. In this study, we evaluated which plant polymers are decomposed and which enzymes are active during the decomposition process in two major genera of fungus-growing termites. We found a diversity of active enzymes at different stages of decomposition and a consistent decrease in plant components during the decomposition process. Furthermore, our findings are consistent with the hypothesis that termites transport enzymes from the older mature parts of the fungus comb through young worker guts to freshly inoculated plant substrate. However, preliminary fungal RNA sequencing (RNA-seq) analyses suggest that this likely transport is supplemented with enzymes produced in situ. Our findings support that the maintenance of an external fungus comb, inoculated with an optimal mixture of plant material, fungal spores, and enzymes, is likely the key to the extraordinarily efficient plant decomposition in fungus-growing termites.
Critical review of methods for risk ranking of food related hazards, based on risks for human health
Fels-Klerx, H.J. van der; Asselt, E.D. van; Raley, M. ; Poulsen, M. ; Marvin, H.J.P. - \ 2018
Critical Reviews in Food Science and Nutrition 58 (2018)2. - ISSN 1040-8398 - p. 178 - 193.
This study aimed to critically review methods for ranking risks related to food safety and dietary hazards on the basis of their anticipated human health impacts. A literature review was performed to identify and characterize methods for risk ranking from the fields of food, environmental science and socio-economic sciences. The review used a predefined search protocol, and covered the bibliographic databases Scopus, CAB Abstracts, Web of Sciences, and PubMed over the period 1993–2013.

All references deemed relevant, on the basis of of predefined evaluation criteria, were included in the review, and the risk ranking method characterized. The methods were then clustered – based on their characteristics - into eleven method categories. These categories included: risk assessment, comparative risk assessment, risk ratio method, scoring method, cost of illness, health adjusted life years, multi-criteria decision analysis, risk matrix, flow charts/decision trees, stated preference techniques and expert synthesis. Method categories were described by their characteristics, weaknesses and strengths, data resources, and fields of applications.

It was concluded there is no single best method for risk ranking. The method to be used should be selected on the basis of risk manager/assessor requirements, data availability, and the characteristics of the method. Recommendations for future use and application are provided.
The value and opportunities of community- and citizen-based approaches to tropical forest biodiversity monitoring
Chandler, Mark ; See, Linda ; Andrianandrasana, Herizo ; Becker, Dusti ; Berardi, Andrea ; Bodmer, Richard ; Brofeldt, S. ; Araujo Lima Constantino, Pedro de; Cousins, Jenny ; Crimmins, Theresa M. ; Danielsen, Finn ; Giorgi, Ana Paula ; Huxham, Mark ; Leslie, Alison ; Mistry, Jayalaxshmi ; Mora, B. ; Nelson, M. ; Poulsen, Michael ; Pratihast, A.K. ; Theilade, I. ; Vakil, Thrity ; Williams, John N. - \ 2017
In: A Sourcebook of Methods and Procedures for Monitoring Essential Biodiversity Variables in Tropical Forests with Remote Sensing / Gill, Mike, Jongman, Rob, Luque, Sandra, Mora, Brice, Paganini, Marc, Szantoi, Zoltan, Wageningen : GOFC-GOLD Land Cover Project Office, Wageningen University, The Netherlands (Report version UNCBD COP-13 ) - p. 223 - 281.
An ecosystem services approach to pesticide risk assessment and risk management of non-target terrestrial plants: recommendations from a 1st SETAC Europe workshop
Arts, G.H.P. ; Dollinger, M. ; Kohlschmid, Eva ; Maltby, Lorraine ; Ochoa-Acuna, H. ; Poulsen, V. - \ 2017
Brussels : SETAC - 55 p.
An ecosystem services approach to pesticide risk assessment and risk management of non-target terrestrial plants: recommendations from a 2nd SETAC Europe workshop
Arts, G.H.P. ; Kohlschmid, Eva ; Maltby, Lorraine ; Mayer, C. ; Meregalli, G. ; Poulsen, Veronique ; Streissl, F. - \ 2017
Brussels : SETAC - 80 p.
Modeling heterogeneous (co)variances from adjacent-SNP groups improves genomic prediction for milk protein composition traits
Gebreyesus, Grum ; Lund, Mogens S. ; Buitenhuis, Bart ; Bovenhuis, Henk ; Poulsen, Nina A. ; Janss, Luc G. - \ 2017
Genetics, Selection, Evolution 49 (2017)1. - ISSN 0999-193X
Background: Accurate genomic prediction requires a large reference population, which is problematic for traits that are expensive to measure. Traits related to milk protein composition are not routinely recorded due to costly procedures and are considered to be controlled by a few quantitative trait loci of large effect. The amount of variation explained may vary between regions leading to heterogeneous (co)variance patterns across the genome. Genomic prediction models that can efficiently take such heterogeneity of (co)variances into account can result in improved prediction reliability. In this study, we developed and implemented novel univariate and bivariate Bayesian prediction models, based on estimates of heterogeneous (co)variances for genome segments (BayesAS). Available data consisted of milk protein composition traits measured on cows and de-regressed proofs of total protein yield derived for bulls. Single-nucleotide polymorphisms (SNPs), from 50K SNP arrays, were grouped into non-overlapping genome segments. A segment was defined as one SNP, or a group of 50, 100, or 200 adjacent SNPs, or one chromosome, or the whole genome. Traditional univariate and bivariate genomic best linear unbiased prediction (GBLUP) models were also run for comparison. Reliabilities were calculated through a resampling strategy and using deterministic formula. Results: BayesAS models improved prediction reliability for most of the traits compared to GBLUP models and this gain depended on segment size and genetic architecture of the traits. The gain in prediction reliability was especially marked for the protein composition traits β-CN, κ-CN and β-LG, for which prediction reliabilities were improved by 49 percentage points on average using the MT-BayesAS model with a 100-SNP segment size compared to the bivariate GBLUP. Prediction reliabilities were highest with the BayesAS model that uses a 100-SNP segment size. The bivariate versions of our BayesAS models resulted in extra gains of up to 6% in prediction reliability compared to the univariate versions. Conclusions: Substantial improvement in prediction reliability was possible for most of the traits related to milk protein composition using our novel BayesAS models. Grouping adjacent SNPs into segments provided enhanced information to estimate parameters and allowing the segments to have different (co)variances helped disentangle heterogeneous (co)variances across the genome.
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