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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CD-MUSIC-EDL modeling of Pb2+ adsorption on birnessites : Role of vacant and edge sites
Zhao, Wei ; Tan, Wenfeng ; Wang, Mingxia ; Xiong, Juan ; Liu, Fan ; Weng, Liping ; Koopal, Luuk K. - \ 2018
Environmental Science and Technology 52 (2018)18. - ISSN 0013-936X - p. 10522 - 10531.
adsorption - Birnessite - CD-MUSIC Modeling - Electrical double layer model - External surface - Interlayer space - Manganese oxide - Mn average oxidation state - Pb - Rietveld refinement

The surface complexation modeling of metal adsorption to birnessites is in its infancy compared to the charge-distribution multi-site ion complexation (CD-MUSIC) models for iron/aluminum (hydr)oxides. Therefore, using X-ray diffraction with Rietveld refinement to obtain the reactive sites and their densities, a CD-MUSIC model combined with a Stern-Gouy-Chapman electrical double layer (EDL) model for the external surface and a Donnan model for the interlayer surface is developed for birnessites with different Mn average oxidation state (MnAOS). Proton affinity constants and the charge distributions of Pb surface complexes were calculated a priory. By fitting Pb adsorption data to the model the obtained equilibrium constants (logKPb) of Pb complexes were 6.9-10.9 for the double-corner-sharing and double-edge-sharing Pb2+ complexes on the edge sites and 2.2-6.5 for the triple-corner-sharing Pb2+ complex on the vacancies. The larger logKPb value was obtained for higher MnAOS. Speciation calculations showed that with increasing MnAOS from 3.67 to 3.92 the interlayer surface contribution to the total Pb2+ adsorption increased from 43.2% to 48.6%, and the vacancy contribution increased from 43.9% to 54.7%. The vacancy contribution from interlayer surface was predominant. The present CD-MUSIC-EDL model contributes to understand better the difference in metal adsorption mechanism between birnessite and iron/aluminum (hydr)oxides.

Modelling strategies for assessing and increasing the effectiveness of new phenotyping techniques in plant breeding
Eeuwijk, Fred A. van; Bustos-Korts, Daniela ; Millet, Emilie J. ; Boer, Martin P. ; Kruijer, Willem ; Thompson, Addie ; Malosetti, Marcos ; Iwata, Hiroyoshi ; Quiroz, Roberto ; Kuppe, Christian ; Muller, Onno ; Blazakis, Konstantinos N. ; Yu, Kang ; Tardieu, Francois ; Chapman, Scott C. - \ 2018
Plant Science (2018). - ISSN 0168-9452
Crop growth model - Genomic prediction - Genotype-by-environment-interaction - Genotype-to-phenotype model - Mixed model - Multi-environment model - Multi-trait model - Phenotyping - Phenotyping platform - Physiology - Plant breeding - Prediction - Reaction norm - Response surface - Statistical genetics

New types of phenotyping tools generate large amounts of data on many aspects of plant physiology and morphology with high spatial and temporal resolution. These new phenotyping data are potentially useful to improve understanding and prediction of complex traits, like yield, that are characterized by strong environmental context dependencies, i.e., genotype by environment interactions. For an evaluation of the utility of new phenotyping information, we will look at how this information can be incorporated in different classes of genotype-to-phenotype (G2P) models. G2P models predict phenotypic traits as functions of genotypic and environmental inputs. In the last decade, access to high-density single nucleotide polymorphism markers (SNPs) and sequence information has boosted the development of a class of G2P models called genomic prediction models that predict phenotypes from genome wide marker profiles. The challenge now is to build G2P models that incorporate simultaneously extensive genomic information alongside with new phenotypic information. Beyond the modification of existing G2P models, new G2P paradigms are required. We present candidate G2P models for the integration of genomic and new phenotyping information and illustrate their use in examples. Special attention will be given to the modelling of genotype by environment interactions. The G2P models provide a framework for model based phenotyping and the evaluation of the utility of phenotyping information in the context of breeding programs.

Toward sustainable environmental quality : Priority research questions for Europe
Brink, Paul J. Van den; Boxall, Alistair B.A. ; Maltby, Lorraine ; Brooks, Bryan W. ; Rudd, Murray A. ; Backhaus, Thomas ; Spurgeon, David ; Verougstraete, Violaine ; Ajao, Charmaine ; Ankley, Gerald T. ; Apitz, Sabine E. ; Arnold, Kathryn ; Brodin, Tomas ; Cañedo-Argüelles, Miguel ; Chapman, Jennifer ; Corrales, Jone ; Coutellec, Marie Agnès ; Fernandes, Teresa F. ; Fick, Jerker ; Ford, Alex T. ; Giménez Papiol, Gemma ; Groh, Ksenia J. ; Hutchinson, Thomas H. ; Kruger, Hank ; Kukkonen, Jussi V.K. ; Loutseti, Stefania ; Marshall, Stuart ; Muir, Derek ; Ortiz-Santaliestra, Manuel E. ; Paul, Kai B. ; Rico, Andreu ; Rodea-Palomares, Ismael ; Römbke, Jörg ; Rydberg, Tomas ; Segner, Helmut ; Smit, Mathijs ; Gestel, Cornelis A.M. van; Vighi, Marco ; Werner, Inge ; Zimmer, Elke I. ; Wensem, Joke van - \ 2018
Environmental Toxicology and Chemistry 37 (2018)9. - ISSN 0730-7268 - p. 2281 - 2295.
Chemical management - Environmental risk assessment - Global megatrends - Key questions exercise - Sustainability

The United Nations' Sustainable Development Goals have been established to end poverty, protect the planet, and ensure prosperity for all. Delivery of the Sustainable Development Goals will require a healthy and productive environment. An understanding of the impacts of chemicals which can negatively impact environmental health is therefore essential to the delivery of the Sustainable Development Goals. However, current research on and regulation of chemicals in the environment tend to take a simplistic view and do not account for the complexity of the real world, which inhibits the way we manage chemicals. There is therefore an urgent need for a step change in the way we study and communicate the impacts and control of chemicals in the natural environment. To do this requires the major research questions to be identified so that resources are focused on questions that really matter. We present the findings of a horizon-scanning exercise to identify research priorities of the European environmental science community around chemicals in the environment. Using the key questions approach, we identified 22 questions of priority. These questions covered overarching questions about which chemicals we should be most concerned about and where, impacts of global megatrends, protection goals, and sustainability of chemicals; the development and parameterization of assessment and management frameworks; and mechanisms to maximize the impact of the research. The research questions identified provide a first-step in the path forward for the research, regulatory, and business communities to better assess and manage chemicals in the natural environment.

Groei en productie van populier in Nederland
Jansen, J.J. ; Mohren, G.M.J. ; Schmidt, P. ; Goudzwaard, L. ; Oosterbaan, A. ; Ouden, J. den - \ 2018
Wageningen : Wageningen University & Research (FEM Groei en Productie rapport 2018-8) - 127
Between 1947 and 2000, growth and yield of Poplar was studied in the Netherlands. To the permanent plots measured by Becking and De Dorschkamp/IBN, the permanent sample plots from HOSP were added, resulting in 235 plots and 1808 recordings.The development of the mean height hm with age t was found to be best described by a Chapman-Richards-model, with adjustment factors for dense stand and for different parameters for forest stands, line plantings, and for aspen, using site index h25. The diameter development up to a height of 7 m was best described with a Gompertz-model in t, hm and the initial spacing (SP0).The basal area increment IG was best explained by a power function in which hm, age, h25 and the Becking-Hart spacing index S% are included. For S% > 29.2 the basal area increment dropped with a non-linear function in S%. For dense spacing and for line plantings, other models fitted best.Combining all models, a stand projection model was constructed, which described the plot develop-ment as measured reasonably well.Yield tables were made for forests with different spacing, for forests with a wide stand with and with-out systematically thinning, for forest with very dense spacing including mortality, for line plantings without thinning, and for aspen with heavy thinning from below
Mechanism and structural diversity of exoribonuclease-resistant RNA structures in flaviviral RNAs
Macfadden, Andrea ; O’Donoghue, Zoe ; Silva, Patricia A.G.C. ; Chapman, Erich G. ; Olsthoorn, René C. ; Sterken, Mark G. ; Pijlman, Gorben P. ; Bredenbeek, Peter J. ; Kieft, Jeffrey S. - \ 2018
Nature Communications 9 (2018)1. - ISSN 2041-1723
Flaviviruses such as Yellow fever, Dengue, West Nile, and Zika generate disease-linked viral noncoding RNAs called subgenomic flavivirus RNAs. Subgenomic flavivirus RNAs result when the 5′–3′ progression of cellular exoribonuclease Xrn1 is blocked by RNA elements called Xrn1-resistant RNAs located within the viral genome’s 3′-untranslated region that operate without protein co-factors. Here, we show that Xrn1-resistant RNAs can halt diverse exoribonucleases, revealing a mechanism in which they act as general mechanical blocks that ‘brace’ against an enzyme’s surface, presenting an unfolding problem that confounds further enzyme progression. Further, we directly demonstrate that Xrn1-resistant RNAs exist in a diverse set of flaviviruses, including some specific to insects or with no known arthropod vector. These Xrn1-resistant RNAs comprise two secondary structural classes that mirror previously reported phylogenic analysis. Our discoveries have implications for the evolution of exoribonuclease resistance, the use of Xrn1-resistant RNAs in synthetic biology, and the development of new therapies.
Campylobacter pinnipediorum sp. Nov., isolated from pinnipeds, comprising Campylobacter pinnipediorum subsp. pinnipediorum subsp. nov. and Campylobacter pinnipediorum subsp. caledonicus subsp. nov
Gilbert, Maarten J. ; Miller, William G. ; St. Leger, Judy ; Chapman, Mary H. ; Timmerman, Arjen J. ; Duim, Birgitta ; Foster, Geoffrey ; Wagenaar, Jaap A. - \ 2017
International Journal of Systematic and Evolutionary Microbiology 67 (2017)6. - ISSN 1466-5026 - p. 1961 - 1968.
Average nucleotide identity - Campylobacter - Novel species - Pinnipeds - Urease - Whole genome sequencing

During independent diagnostic screenings of otariid seals in California (USA) and phocid seals in Scotland (UK), Campylobacter-like isolates, which differed from the established taxa of the genus Campylobacter, were cultured from abscesses and internal organs of different seal species. A polyphasic study was undertaken to determine the taxonomic position of these six isolates. The isolates were characterized by 16S rRNA gene and AtpA sequence analysis and by conventional phenotypic testing. The whole-genome sequences were determined for all isolates, and the average nucleotide identity (ANI) was determined. The isolates formed a separate phylogenetic clade, divergent from all other taxa of the genus Campylobacter and most closely related to Campylobactermucosalis. Although all isolates showed 100 % 16S rRNA gene sequence homology, AtpA and ANI analyses indicated divergence between the otariid isolates from California and the phocid isolates from Scotland, which warrants subspecies status for each clade. The two subspecies could also be distinguished phenotypically on the basis of catalase activity. This study shows clearly that the isolates obtained from pinnipeds represent a novel species within the genus Campylobacter, for which the name Campylobacter pinnipediorum sp. nov. is proposed. Within this novel species, the Californian isolates represent a separate subspecies, for which the name C. pinnipediorum subsp. pinnipediorum subsp. nov. is proposed. The type strain for both this novel species and subspecies is RM17260T (=LMG 29472T=CCUG 69570T). The Scottish isolates represent another subspecies, for which the name C. pinnipediorum subsp. caledonicus subsp. nov. is proposed. The type strain of this subspecies is M302/10/6T (=LMG 29473T=CCUG 68650T).

Denial of long-term issues with agriculture on tropical peatlands will have devastating consequences
Wijedasa, Lahiru S. ; Jauhiainen, Jyrki ; Könönen, Mari ; Lampela, Maija ; Vasander, Harri ; Leblanc, Marie-Claire ; Evers, Stephanie ; Smith, Thomas E.L. ; Yule, Catherine M. ; Varkkey, Helena ; Lupascu, Massimo ; Parish, Faizal ; Singleton, Ian ; Clements, Gopalasamy R. ; Aziz, Sheema Abdul ; Harrison, Mark E. ; Cheyne, Susan ; Anshari, Gusti Z. ; Meijaard, Erik ; Goldstein, Jenny E. ; Waldron, Susan ; Hergoualc'h, Kristell ; Dommain, Rene ; Frolking, Steve ; Evans, Christopher D. ; Posa, Mary Rose C. ; Glaser, Paul H. ; Suryadiputra, Nyoman ; Lubis, Reza ; Santika, Truly ; Padfield, Rory ; Kurnianto, Sofyan ; Hadisiswoyo, Panut ; Lim, Teck Wyn ; Page, Susan E. ; Gauci, Vincent ; Meer, Peter J. Van Der; Buckland, Helen ; Garnier, Fabien ; Samuel, Marshall K. ; Choo, Liza Nuriati Lim Kim ; O'reilly, Patrick ; Warren, Matthew ; Suksuwan, Surin ; Sumarga, Elham ; Jain, Anuj ; Laurance, William F. ; Couwenberg, John ; Joosten, Hans ; Vernimmen, Ronald ; Hooijer, Aljosja ; Malins, Chris ; Cochrane, Mark A. ; Perumal, Balu ; Siegert, Florian ; Peh, Kelvin S.H. ; Comeau, Louis-Pierre ; Verchot, Louis ; Harvey, Charles F. ; Cobb, Alex ; Jaafar, Zeehan ; Wösten, Henk ; Manuri, Solichin ; Müller, Moritz ; Giesen, Wim ; Phelps, Jacob ; Yong, Ding Li ; Silvius, Marcel ; Wedeux, Béatrice M.M. ; Hoyt, Alison ; Osaki, Mitsuru ; Hirano, Takashi ; Takahashi, Hidenori ; Kohyama, Takashi S. ; Haraguchi, Akira ; Nugroho, Nunung P. ; Coomes, David A. ; Quoi, Le Phat ; Dohong, Alue ; Gunawan, Haris ; Gaveau, David L.A. ; Langner, Andreas ; Lim, Felix K.S. ; Edwards, David P. ; Giam, Xingli ; Werf, Guido Van Der; Carmenta, Rachel ; Verwer, Caspar C. ; Gibson, Luke ; Gandois, Laure ; Graham, Laura Linda Bozena ; Regalino, Jhanson ; Wich, Serge A. ; Rieley, Jack ; Kettridge, Nicholas ; Brown, Chloe ; Pirard, Romain ; Moore, Sam ; Capilla, B.R. ; Ballhorn, Uwe ; Ho, Hua Chew ; Hoscilo, Agata ; Lohberger, Sandra ; Evans, Theodore A. ; Yulianti, Nina ; Blackham, Grace ; Onrizal, O. ; Husson, Simon ; Murdiyarso, Daniel ; Pangala, Sunita ; Cole, Lydia E.S. ; Tacconi, Luca ; Segah, Hendrik ; Tonoto, Prayoto ; Lee, Janice S.H. ; Schmilewski, Gerald ; Wulffraat, Stephan ; Putra, Erianto Indra ; Cattau, Megan E. ; Clymo, R.S. ; Morrison, Ross ; Mujahid, Aazani ; Miettinen, Jukka ; Liew, Soo Chin ; Valpola, Samu ; Wilson, David ; Arcy, Laura D'; Gerding, Michiel ; Sundari, Siti ; Thornton, Sara A. ; Kalisz, Barbara ; Chapman, Stephen J. ; Su, Ahmad Suhaizi Mat ; Basuki, Imam ; Itoh, Masayuki ; Traeholt, Carl ; Sloan, Sean ; Sayok, Alexander K. ; Andersen, Roxane - \ 2017
Global Change Biology 23 (2017)3. - ISSN 1354-1013 - p. 977 - 982.
The first International Peat Congress (IPC) held in the tropics – in Kuching (Malaysia) – brought together over 1000 international peatland scientists and industrial partners from across the world (“International Peat Congress with over 1000 participants!,” 2016). The congress covered all aspects of peatland ecosystems and their management, with a strong focus on the environmental, societal and economic challenges associated with contemporary large-scale agricultural conversion of tropical peat.
Improvement of Predictive Ability by Uniform Coverage of the Target Genetic Space
Bustos-Korts, D. ; Malosetti Zunin, Marcos ; Chapman, S. ; Biddulph, B. ; Eeuwijk, F. Van - \ 2016
G3 : Genes Genomes Genetics 6 (2016)11. - ISSN 2160-1836 - p. 3733 - 3747.
Genome enabled prediction provides breeders with the means to increase the number of genotypes that can be evaluated for selection. One of the major challenges in genome enabled prediction is how to construct a training set of genotypes from a calibration set that represents the target population of genotypes, where the calibration set is composed of a training and validation set. A random sampling protocol of genotypes from the calibration set will lead to low quality coverage of the total genetic space by the training set when the calibration set contains population structure. As a consequence, predictive ability will be affected negatively, because some parts of the genotypic diversity in the target population will be under represented in the training set, whereas other parts will be over represented. Therefore, we propose a training set construction method that uniformly samples the genetic space spanned by the target population of genotypes, thereby increasing predictive ability. To evaluate our method, we constructed training sets alongside with the identification of corresponding genomic prediction models for four genotype panels that differed in the amount of population structure they contained (maize Flint, maize Dent, wheat, and rice). Training sets were constructed using uniform sampling, stratified-uniform sampling, stratified sampling and random sampling. We compared these methods with a method that maximizes the generalized coefficient of determination (CD), proposed by Rincent et al. (2012). Several training set sizes were considered. We investigated four genomic prediction models: multi-locus QTL models, GBLUP models, combinations of QTLs and GBLUPs, and Reproducing Kernel Hilbert Spaces (RKHS) models. For the maize and wheat panels, construction of the training set under uniform sampling led to a larger predictive ability than under stratified and random sampling. The results of our methods were similar to those of the CD method. For the rice panel, all training set construction methods led to similar predictive ability, a reflection of the very strong population structure in this panel.
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
Jiang, Yuxiang ; Oron, Tal Ronnen ; Clark, Wyatt T. ; Bankapur, Asma R. ; Andrea, Daniel D'; Lepore, Rosalba ; Funk, Christopher S. ; Kahanda, Indika ; Verspoor, Karin M. ; Ben-Hur, Asa ; Koo, Da Chen Emily ; Penfold-Brown, Duncan ; Shasha, Dennis ; Youngs, Noah ; Bonneau, Richard ; Lin, Alexandra ; Sahraeian, Sayed M.E. ; Martelli, Pier Luigi ; Profiti, Giuseppe ; Casadio, Rita ; Cao, Renzhi ; Zhong, Zhaolong ; Cheng, Jianlin ; Altenhoff, Adrian ; Skunca, Nives ; Dessimoz, Christophe ; Dogan, Tunca ; Hakala, Kai ; Kaewphan, Suwisa ; Mehryary, Farrokh ; Salakoski, Tapio ; Ginter, Filip ; Fang, Hai ; Smithers, Ben ; Oates, Matt ; Gough, Julian ; Törönen, Petri ; Koskinen, Patrik ; Holm, Liisa ; Chen, Ching Tai ; Hsu, Wen Lian ; Bryson, Kevin ; Cozzetto, Domenico ; Minneci, Federico ; Jones, David T. ; Chapman, Samuel ; BKC, Dukka ; Khan, Ishita K. ; Kihara, Daisuke ; Ofer, Dan ; Rappoport, Nadav ; Stern, Amos ; Cibrian-Uhalte, Elena ; Denny, Paul ; Foulger, Rebecca E. ; Hieta, Reija ; Legge, Duncan ; Lovering, Ruth C. ; Magrane, Michele ; Melidoni, Anna N. ; Mutowo-Meullenet, Prudence ; Pichler, Klemens ; Shypitsyna, Aleksandra ; Li, Biao ; Zakeri, Pooya ; ElShal, Sarah ; Tranchevent, Léon Charles ; Das, Sayoni ; Dawson, Natalie L. ; Lee, David ; Lees, Jonathan G. ; Sillitoe, Ian ; Bhat, Prajwal ; Nepusz, Tamás ; Romero, Alfonso E. ; Sasidharan, Rajkumar ; Yang, Haixuan ; Paccanaro, Alberto ; Gillis, Jesse ; Sedeño-Cortés, Adriana E. ; Pavlidis, Paul ; Feng, Shou ; Cejuela, Juan M. ; Goldberg, Tatyana ; Hamp, Tobias ; Richter, Lothar ; Salamov, Asaf ; Gabaldon, Toni ; Marcet-Houben, Marina ; Supek, Fran ; Gong, Qingtian ; Ning, Wei ; Zhou, Yuanpeng ; Tian, Weidong ; Falda, Marco ; Fontana, Paolo ; Lavezzo, Enrico ; Toppo, Stefano ; Ferrari, Carlo ; Giollo, Manuel ; Piovesan, Damiano ; Tosatto, Silvio C.E. ; Pozo, Angela del; Fernández, José M. ; Maietta, Paolo ; Valencia, Alfonso ; Tress, Michael L. ; Benso, Alfredo ; Carlo, Stefano Di; Politano, Gianfranco ; Savino, Alessandro ; Rehman, Hafeez Ur ; Re, Matteo ; Mesiti, Marco ; Valentini, Giorgio ; Bargsten, Joachim W. ; Dijk, Aalt-Jan van; Gemovic, Branislava ; Glisic, Sanja ; Perovic, Vladmir ; Veljkovic, Veljko ; Veljkovic, Nevena ; Almeida-e-Silva, Danillo C. ; Vencio, Ricardo Z.N. ; Sharan, Malvika ; Vogel, Jörg ; Kansakar, Lakesh ; Zhang, Shanshan ; Vucetic, Slobodan ; Wang, Zheng ; Sternberg, Michael J.E. ; Wass, Mark N. ; Huntley, Rachael P. ; Martin, Maria J. ; O'Donovan, Claire ; Robinson, Peter N. ; Moreau, Yves ; Tramontano, Anna ; Babbitt, Patricia C. ; Brenner, Steven E. ; Linial, Michal ; Orengo, Christine A. ; Rost, Burkhard ; Greene, Casey S. ; Mooney, Sean D. ; Friedberg, Iddo ; Radivojac, Predrag - \ 2016
Genome Biology 17 (2016)1. - ISSN 1474-7596
Disease gene prioritization - Protein function prediction

Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent.

Biochemical characterization of the tomato phosphatidylinositol-specific phospholipase C (PI-PLC) family and its role in plant immunity
Abd-El-Haliem, Ahmed ; Vossen, J.H. ; Zeijl, Arjan van; Dezhsetan, Sara ; Testerink, Christa ; Seidl, M.F. ; Beck, Martina ; Strutt, James ; Robatzek, Silke ; Joosten, M.H.A.J. - \ 2016
Biochimica et Biophysica Acta. Molecular and Cell Biology of Lipids 1861 (2016)9 Part B. - ISSN 1388-1981 - p. 1365 - 1378.
Defence response - Immune receptors - Phospholipids - PLC enzymes - Signal transduction

Plants possess effective mechanisms to quickly respond to biotic and abiotic stresses. The rapid activation of phosphatidylinositol-specific phospholipase C (PLC) enzymes occurs early after the stimulation of plant immune-receptors. Genomes of different plant species encode multiple PLC homologs belonging to one class, PLCζ. Here we determined whether all tomato homologs encode active enzymes and whether they can generate signals that are distinct from one another. We searched the recently completed tomato (Solanum lycopersicum) genome sequence and identified a total of seven PLCs. Recombinant proteins were produced for all tomato PLCs, except for SlPLC7. The purified proteins showed typical PLC activity, as different PLC substrates were hydrolysed to produce diacylglycerol. We studied SlPLC2, SlPLC4 and SlPLC5 enzymes in more detail and observed distinct requirements for Ca2+ ions and pH, for both their optimum activity and substrate preference. This indicates that each enzyme could be differentially and specifically regulated in vivo, leading to the generation of PLC homolog-specific signals in response to different stimuli. PLC overexpression and specific inhibition of PLC activity revealed that PLC is required for both specific effector- and more general "pattern"-triggered immunity. For the latter, we found that both the flagellin-triggered response and the internalization of the corresponding receptor, Flagellin Sensing 2 (FLS2) of Arabidopsis thaliana, are suppressed by inhibition of PLC activity. Altogether, our data support an important role for PLC enzymes in plant defence signalling downstream of immune receptors.This article is part of a Special Issue entitled: Plant Lipid Biology edited by Kent D. Chapman and Ivo Feussner.

Modelling of Genotype by Environment Interaction and Prediction of Complex Traits across Multiple Environments as a Synthesis of Crop Growth Modelling, Genetics and Statistics
Bustos Korts, Daniela ; Malosetti, M. ; Chapman, S. ; Eeuwijk, Fred van - \ 2016
In: Crop Systems Biology : Narrowing the Gaps Between Crop Modelling and Genetics / Yin, X., Struik, P.C., Springer International Publishing - ISBN 9783319205618 - p. 55 - 82.
Selection processes in plant breeding depend critically on the quality of phenotype predictions. The phenotype is classically predicted as a function of genotypic and environmental information. Models for phenotype prediction contain a mixture of statistical, genetic and physiological elements. In this chapter, we discuss prediction from linear mixed models (LMMs), with an emphasis on statistics, and prediction from crop growth models (CGMs), with an emphasis on physiology. Three modalities of prediction are distinguished: predictions for new genotypes under known environmental conditions, predictions for known genotypes under new environmental conditions, and predictions for new genotypes under new environmental conditions. For LMMs, the genotypic input information includes molecular marker variation, while the environmental input can consist of meteorological, soil and management variables. However, integrated types of environmental characterizations obtained from CGMs can also serve as environmental covariable in LMMs. LMMs consist of a fixed part, corresponding to the mean for a particular genotype in a particular environment, and a random part defined by genotypic and environmental variances and correlations. For prediction via the fixed part, genotypic and/or environmental covariables are required as in classical regression. For predictions via the random part, correlations need to be estimated between observed and new genotypes, between observed and new environments, or both. These correlations can be based on similarities calculated from genotypic and environmental covariables. A simple type of covariable assigns genotypes to sub-populations and environments to regions. Such groupings can improve phenotype prediction. For a second type of phenotype prediction, we consider CGMs. CGMs predict a target phenotype as a non-linear function of underlying intermediate phenotypes. The intermediate phenotypes are outcomes of functions defined on genotype dependent CGM parameters and classical environmental descriptors. While the intermediate phenotypes may still show some genotype by environment interaction, the genotype dependent CGM parameters should be consistent across environmental conditions. The CGM parameters are regressed on molecular marker information to allow phenotype prediction from molecular marker information and standard physiologically relevant environmental information. Both LMMs and CGMs require extensive characterization of genotypes and environments. High-throughput technologies for genotyping and phenotyping provide new opportunities for upscaling phenotype prediction and increasing the response to selection in the breeding process.
Olfactory responses of western flower thrips (Frankliniella occidentalis) populations to a non-pheromone lure
Nielsen, M.C. ; Worner, S.P. ; Rostás, M. ; Chapman, R.B. ; Butler, R.C. ; Kogel, W.J. de; Teulon, D.A.J. - \ 2015
Entomologia Experimentalis et Applicata 156 (2015)3. - ISSN 0013-8703 - p. 254 - 262.
Attractant - Feeding history - Genotype - Host plant - Kairomone - Methyl isonicotinate - Rearing conditions - Semiochemicals - Thripidae - Thysanoptera - Y-tube olfactometer

Western flower thrips (WFT), Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae), is a major pest of horticultural crops worldwide. The search for alternative pest management techniques has resulted in increasing interest in the use of kairomones and other behaviour-modifying chemicals to mitigate the impact of this pest. In this study, we determined whether the origin of populations, feeding history, and/or genotype influence the response of WFT to the thrips kairomone lure methyl isonicotinate (MI) in a Y-tube olfactometer study. Four New Zealand thrips populations were tested: (1) from a commercial glasshouse capsicum crop, (2) from a long-established laboratory colony (>222 generations) kept on chrysanthemums, (3) from a laboratory colony (6-9 generations) kept on French dwarf beans, and (4) thought to be a separate cryptic non-pest species from outdoor yellow tree lupins, Lupinus arboreus Sims (Fabaceae). In the laboratory tests, significantly more WFT from all four populations chose the MI-laden arm of a Y-tube olfactometer when it contained 1 μl methyl isonicotinate (61.3-73.2%) compared with the blank no-odour arm. No differences in response to MI were found between the two laboratory and the one glasshouse WFT populations. Both laboratory populations and the greenhouse population belonged to the 'glasshouse pest' genotype of WFT. However, the cryptic non-pest WFT genotype responded more strongly to MI than any of the other populations, although the response was only significantly stronger than that of the long-established laboratory population. Significant differences were also found among populations in the average time taken for thrips to make a choice to enter either arm of the Y-tube olfactometer, with the cryptic non-pest lupin genotype taking the shortest time, followed by thrips from the capsicum glasshouse. The results are discussed with respect to the variability in olfactory perception and olfactory behaviour within a species and the relevance to the use of such a kairomone lure in pest management programmes.

Crowdsourcing for climate and atmospheric sciences: current status and future potential
Muller, C.L. ; Chapman, L. ; Johnston, S. ; Kidd, C. ; Illingworth, S. ; Foody, G. ; Overeem, A. ; Leigh, R.R. - \ 2015
International Journal of Climatology 35 (2015)11. - ISSN 0899-8418 - p. 3185 - 3203.
Crowdsourcing is traditionally defined as obtaining data or information by enlisting the services of a (potentially large) number of people. However, due to recent innovations, this definition can now be expanded to include ‘and/or from a range of public sensors, typically connected via the Internet.’ A large and increasing amount of data is now being obtained from a huge variety of non-traditional sources – from smart phone sensors to amateur weather stations to canvassing members of the public. Some disciplines (e.g. astrophysics, ecology) are already utilizing crowdsourcing techniques (e.g. citizen science initiatives, web 2.0 technology, low-cost sensors), and while its value within the climate and atmospheric science disciplines is still relatively unexplored, it is beginning to show promise. However, important questions remain; this paper introduces and explores the wide-range of current and prospective methods to crowdsource atmospheric data, investigates the quality of such data and examines its potential applications in the context of weather, climate and society. It is clear that crowdsourcing is already a valuable tool for engaging the public, and if appropriate validation and quality control procedures are adopted and implemented, it has much potential to provide a valuable source of high temporal and spatial resolution, real-time data, especially in regions where few observations currently exist, thereby adding value to science, technology and society.
Carbon nanotube yarns as strong flexible conductive capacitive electrodes
Liu, F. ; Wagterveld, R.M. ; Gebben, B. ; Otto, M.J. ; Biesheuvel, P.M. ; Hamelers, H.V.M. - \ 2015
Colloids and Interface Science Communications 3 (2015). - ISSN 2215-0382 - p. 9 - 12.
Carbon nanotube (CNT) yarn, consisting of 23 µm diameter CNT filaments, can be used as capacitive electrodes that are long, flexible, conductive and strong, for applications in energy and electrochemical water treatment. We measure the charge storage capacity as function of salt concentration, and use Gouy–Chapman–Stern theory to describe the data. CNT yarn can also be used as conductive scaffold for the application of a porous activated carbon (AC) layer. We show the potential of CNT yarn for the generation of electrical energy from environmental entropy differences, by coating yarn (both with and without AC coating) with ion-exchange membranes (IEMs) and generating power from the salt concentration difference between river water and seawater. The use of flexible and conductive CNT yarns as capacitive electrodes and electrode scaffolds breaks with the paradigm of planar static electrodes, and opens up a range of alternative designs for electrochemical cells with enhanced performance.
Linking effects of anthropogenic debris to ecological impacts
Browne, M.A. ; Underwood, A.J. ; Chapman, M.G. ; Williams, R. ; Thompson, R.C. ; Franeker, J.A. van - \ 2015
Proceedings of the Royal Society. B: Biological Sciences 282 (2015)1807. - ISSN 0962-8452
mytilus-edulis l. - marine debris - southern california - plastic ingestion - oxidative stress - atlantic-ocean - oil-spills - seabirds - particles - pacific
Accelerated contamination of habitats with debris has caused increased effort to determine ecological impacts. Strikingly, most work on organisms focuses on sublethal responses to plastic debris. This is controversial because (i) researchers have ignored medical insights about the mechanisms that link effects of debris across lower levels of biological organization to disease and mortality, and (ii) debris is considered non-hazardous by policy-makers, possibly because individuals can be injured or removed from populations and assemblages without ecological impacts. We reviewed the mechanisms that link effects of debris across lower levels of biological organization to assemblages and populations. Using plastic, we show microplastics reduce the ‘health’, feeding, growth and survival of ecosystem engineers. Larger debris alters assemblages because fishing-gear and tyres kill animals and damage habitat-forming plants, and because floating bottles facilitate recruitment and survival of novel taxa. Where ecological linkages are not known, we show how to establish hypothetical links by synthesizing studies to assess the likelihood of impacts. We also consider how population models examine ecological linkages and guide management of ecological impacts. We show that by focusing on linkages to ecological impacts rather than the presence of debris and its sublethal impacts, we could reduce threats posed by debris.
Coupled human and natural system dynamics as key to the sustainability of Lake Victoria’s ecosystem services
Downing, A.S. ; Nes, E.H. van; Balirwa, J.S. ; Beuving, J. ; Bwathondi, P.O.J. ; Chapman, L.J. ; Cornelissen, I.J.M. ; Cowx, I.G. ; Goudswaard, P.C. ; Hecky, R.E. ; Janse, J.H. ; Janssen, A.B.G. ; Kaufman, L. ; Kishe-Machumu, M.A. ; Kolding, J. ; Ligtvoet, W. ; Mbabazi, D. ; Medard, M. ; Mkumbo, O.C. ; Mlaponi, E. ; Munyaho, A.T. ; Nagelkerke, L.A.J. ; Ogutu-Ohwayo, R. ; Ojwang, W.O. ; Peter, H.K. ; Schindler, D.E. ; Seehausen, O. ; Sharpe, D. ; Silsbe, G.M. ; Sitoki, L. ; Tumwebaze, R. ; Tweddle, D. ; Wolfshaar, K.E. van de; Dijk, J.W.M. van; Donk, E. van; Rijssel, J.C. van; Zwieten, P.A.M. van; Wanink, J. ; Witte, F. ; Mooij, W.M. - \ 2014
Ecology and Society 19 (2014)4. - ISSN 1708-3087
cyprinid rastrineobola-argentea - perch lates-niloticus - nile perch - east-africa - water hyacinth - mwanza gulf - oreochromis-niloticus - morphological-changes - introduced predator - biological-control
East Africa’s Lake Victoria provides resources and services to millions of people on the lake’s shores and abroad. In particular, the lake’s fisheries are an important source of protein, employment, and international economic connections for the whole region. Nonetheless, stock dynamics are poorly understood and currently unpredictable. Furthermore, fishery dynamics are intricately connected to other supporting services of the lake as well as to lakeshore societies and economies. Much research has been carried out piecemeal on different aspects of Lake Victoria’s system; e.g., societies, biodiversity, fisheries, and eutrophication. However, to disentangle drivers and dynamics of change in this complex system, we need to put these pieces together and analyze the system as a whole. We did so by first building a qualitative model of the lake’s social-ecological system. We then investigated the model system through a qualitative loop analysis, and finally examined effects of changes on the system state and structure. The model and its contextual analysis allowed us to investigate system-wide chain reactions resulting from disturbances. Importantly, we built a tool that can be used to analyze the cascading effects of management options and establish the requirements for their success. We found that high connectedness of the system at the exploitation level, through fisheries having multiple target stocks, can increase the stocks’ vulnerability to exploitation but reduce society’s vulnerability to variability in individual stocks. We describe how there are multiple pathways to any change in the system, which makes it difficult to identify the root cause of changes but also broadens the management toolkit. Also, we illustrate how nutrient enrichment is not a self-regulating process, and that explicit management is necessary to halt or reverse eutrophication. This model is simple and usable to assess system-wide effects of management policies, and can serve as a paving stone for future quantitative analyses of system dynamics at local scales.
Transcriptional control of fleshy fruit development and ripening
Karlova, R.B. ; Chapman, N. ; David, K. ; Angenent, G.C. ; Seymour, G.B. ; Maagd, R.A. de - \ 2014
Journal of Experimental Botany 65 (2014)16. - ISSN 0022-0957 - p. 4527 - 4541.
mads-box gene - tomato fruit - abscisic-acid - draft genome - carotenoid accumulation - climacteric fruit - down-regulation - anthocyanin accumulation - ethylene biosynthesis - hormonal-regulation
Fleshy fruits have evolved to be attractive to frugivores in order to enhance seed dispersal, and have become an indispensable part of the human diet. Here we review the recent advances in the understanding of transcriptional regulation of fleshy fruit development and ripening with a focus on tomato. While aspects of fruit development are probably conserved throughout the angiosperms, including the model plant Arabidopsis thaliana, it is shown that the likely orthologues of Arabidopsis genes have distinct functions in fleshy fruits. The model for the study of fleshy fruit development is tomato, because of the availability of single gene mutants and transgenic knock-down lines. In other species, our knowledge is often incomplete or absent. Tomato fruit size and shape are co-determined by transcription factors acting during formation of the ovary. Other transcription factors play a role in fruit chloroplast formation, and upon ripening impact quality aspects such as secondary metabolite content. In tomato, the transcription factors NON-RIPENING (NOR), COLORLESS NON-RIPENING (CNR), and RIPENING INHIBITOR (MADS-RIN) in concert with ethylene signalling regulate ripening, possibly in response to a developmental switch. Additional components include TOMATO AGAMOUS-LIKE1 (TAGL1), APETALA2a (AP2a), and FRUITFULL (FUL1 and FUL2). The links between this highly connected regulatory network and downstream effectors modulating colour, texture, and flavour are still relatively poorly understood. Intertwined with this network is post-transcriptional regulation by fruit-expressed micro-RNAs targeting several of these transcription factors. This important developmental process is also governed by changes in DNA methylation levels and possibly chromatin remodelling.
History of canonical correspondence analysis
Braak, C.J.F. ter - \ 2014
In: Visualization and verbalization of Data / Blasius, J., Greenacre, M., Londen : Chapman and Hall/CRC (Chapman & Hall/CRC Computer Science & Data Analysis ) - ISBN 9781466589803 - p. 61 - 75.
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies
Katayama, T. ; Wilkinson, D.W. ; Micklem, G. ; Kawashima, S. ; Yamaguchi, A. ; Nakao, M. ; Yamamoto, T. ; Okamoto, S. ; Oouchida, K. ; Chung, H. ; Aerts, J. ; Afzal, H. ; Antezana, E. ; Arakawa, K. ; Aranda, B. ; Belleau, F. ; Bolleman, J. ; Bonnal, R.J.P. ; Chapman, B. ; Cock, P.J.A. ; Eriksson, T. ; Gordon, P.M.K. ; Goto, N. ; Hayashida, K. ; Horn, H. ; Ishiwata, R. ; Kaminuma, E. ; Kasprzyk, A. ; Kawaji, H. ; Kido, N. ; Kim, Y. ; Kinjo, A.R. ; Konishi, F. ; Kwon, K.H. ; Labarga, A. ; Lamprecht, A. ; Lin, Y. ; Lindenbaum, P. ; McCarthy, L. ; Morita, H. ; Murakami, K. ; Nagao, K. ; Nishida, K. ; Nishimura, K. ; Nishizawa, T. ; Ogishima, S. ; Ono, K. ; Oshita, K. ; Park, K. ; Prins, J.C.P. ; Saito, T. ; Samwald, M. ; Satagopam, V.P. ; Shigemoto, Y. ; Smith, R. ; Splendiani, A. ; Sugawara, H. ; Taylor, J. ; Vos, R.A. ; Withers, D. ; Yamasaki, C. ; Zmasek, C.M. ; Kawamoto, S. ; Okubo, K. ; Asai, K. ; Takagi, T. - \ 2013
Journal of Biomedical Semantics 4 (2013). - ISSN 2041-1480
protein-interaction database - systems biology - ontology - bioinformatics - tool - representation - services - language - framework - networks
Background: BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. Results: The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. Conclusion: We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer. source provider, through middleware, to the end-consumer.
Recent switch by the Great Blue Heron (Ardea herodias fannini) in the Pacific northwest to associative nesting with Bald Eagles (Haliaeetus leucocephalus) to gain predator protection
Jones, I.M. ; Butler, R.W. ; Ydenberg, R.C. - \ 2013
Canadian Journal of Zoology 91 (2013)7. - ISSN 0008-4301 - p. 489 - 495.
colonies - advantages - habitat - magpies
The Great Blue Heron (Ardea herodias fannini Chapman, 1901) in the Pacific northwest appears to have modified nesting behaviour in response to the strong recent recovery of the Bald Eagle (Haliaeetus leucocephalus (L., 1766)) population. Previously undescribed, herons now often nest in close association with some breeding eagles, even though eagles depredate heron nestlings, are implicated in the recent reproductive decline of herons, and may induce abandonment of heron breeding colonies. We tested the hypothesis that breeding herons gain protection from the territorial behaviour of eagles. Natural observations and simulated incursions showed that nesting eagles actively repel other eagles within at least 250 m around the nest site, thereby establishing a relatively safe place for herons to nest. Surveys showed that 70% of heron nests and 19% of heron colonies were located within 200 m of eagle nests with high reproductive success. These herons had greater reproductive success than those nesting far from eagle nests.
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