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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Salutogenic health promotion program for migrant women at risk of social exclusion
Bonmatí-tomas, A. ; Malagón-aguilera, M.C. ; Gelabert-Vilella, S. ; Bosch-farré, C. ; Vaandrager, L. ; García-Gil, M.M. ; Juvinyà-canal, D. - \ 2019
International Journal for Equity in Health 18 (2019). - ISSN 1475-9276
Background Migrant women at risk of social exclusion often experience health inequities based on gender, country of origin or socioeconomic status. Traditional health promotion programs designed for this population have focused on covering their basic needs or modifying lifestyle behaviors. The salutogenic model of health could offer a new perspective enabling health promotion programs to reduce the impact of health inequities. This study evaluated the effectiveness of a salutogenic health promotion program focused on the empowerment of migrant women at risk of social exclusion. Methods A four-session salutogenic health promotion program was conducted over a period of 6 months. In a quasi-experimental pre-test post-test design, an ad hoc questionnaire was administered to 26 women to collect sociodemographic data, together with 5 validated instruments: Antonovsky’s Sense of Coherence (SOC-13), Duke-UNC-11 (perceived social support), Quality of Life Short Form-36 (SF-36), Rosenberg’s Self-Esteem Scale, and the Cohen et al. Perceived Stress Scale (PSS-10). Descriptive analysis and multiple linear regression models were performed. Statistical tests were considered significant with a two-tailed p value < 0.05. Results Participants had a low initial SOC-13 score (60.36; SD 8.16), which did not show significant change after the health promotion program. Perceived social support (37.07; SD 6.28) and mental quality of life also remained unchanged, while physical quality of life increased from 50.84 (SD 4.60) to 53.08 (SD 5.31) (p = 0.049). Self-esteem showed an increasing trend from 30.14 (SD 4.21) to 31.92 (SD 4.38) (p = 0.120). Perceived stress decreased from 20.57 (SD 2.91) to 18.38 (SD 3.78) (p = 0.016). A greater effect was observed at the end of the program in women with lower initial scores for SOC-13 and quality of life and higher initial scores of perceived stress. Conclusions The health promotion program reduced perceived stress, increased physical quality of life and showed a trend toward increased self-esteem, especially among migrant women with multiple vulnerability factors. The salutogenic model of health should be considered as a good practice to apply in health promotion programs and to be included in national policies to reduce health inequity in migrant populations.
AVR2-induced immunity to Phytophthora infestans by unrelated resistance genes of Solanum species
Aguilera Galvez, Carolina - \ 2019
Wageningen University. Promotor(en): R.G.F. Visser, co-promotor(en): V.G.A.A. Vleeshouwers. - Wageningen : Wageningen University - ISBN 9789463439916 - 145
EFSA Scientific Colloquium 24 – 'omics in risk assessment: state of the art and next steps
Aguilera, Jaime ; Aguilera‐gomez, Margarita ; Barrucci, Federica ; Cocconcelli, Pier Sandro ; Davies, Howard ; Denslow, Nancy ; Lou Dorne, Jean ; Grohmann, Lutz ; Herman, Lieve ; Hogstrand, Christer ; Kass, George E.N. ; Kille, Peter ; Kleter, Gijs ; Nogué, Fabien ; Plant, Nick J. ; Ramon, Matthew ; Schoonjans, Reinhilde ; Waigmann, Elisabeth ; Wright, Matthew C. - \ 2018
EFSA Supporting Publications 15 (2018)11. - ISSN 2397-8325
In recent years, the development of innovative tools in genomics, transcriptomics, proteomics and metabolomics (designated collectively as 'omics technologies) has opened up new possibilities for applications in scientific research and led to the availability of vast amounts of analytical data. The interpretation and integration of 'omics data can provide valuable information on the functional status of an organism and on the effect of external factors such as stressors. The European Food Safety Authority's (EFSA) 24th Scientific Colloquium on 'omics in risk assessment: state of the art and next steps explored the opportunities for integration of datasets produced via specific 'omics tools within the remit of EFSA's risk assessment approaches and tried to build further towards concrete paths of implementation. Discussions focused on genomics in microbial strain characterisation, metabolomics for the comparative assessment of GM plants and the use of 'omics for toxicological and environmental risk assessment. From the Colloquium it became clear that 'omics technologies are a valuable addition in some aspects of risk assessment of food and feed products and the environment, especially now that this technology is almost mature and stable. However, a consistent reporting framework for data collection, processing, interpretation, storage and curation should be further drawn up together with national and international organisations before 'omics technologies can be routinely used in risk assessment. For 'omics datasets in chemical and environmental risk assessments, the use of 'omics technologies alongside current toxicological or environmental risk assessment approaches is needed to re‐inforce confidence and expertise before implementation of these datasets as a standalone tool in risk assessment. Test cases could be worked out to enhance confidence in the use of 'omics datasets in risk assessment.
Biomarkers of food intake for cocoa and liquorice (products) : A systematic review
Michielsen, Charlotte C.J.R. ; Almanza-Aguilera, Enrique ; Brouwer-Brolsma, Elske M. ; Urpi-Sarda, Mireia ; Afman, L.A. - \ 2018
Genes & Nutrition 13 (2018)1. - ISSN 1555-8932
Biomarkers - Cacao - Chocolate - Cocoa - Licorice - Liquorice - Metabolites - Metabolomics

Background: To unravel true links between diet and health, it is important that dietary exposure is accurately measured. Currently, mainly self-reporting methods (e.g. food frequency questionnaires and 24-h recalls) are used to assess food intake in epidemiological studies. However, these traditional instruments are subjective measures and contain well-known biases. Especially, estimating the intake of the group of confectionary products, such as products containing cocoa and liquorice, remains a challenge. The use biomarkers of food intake (BFIs) may provide a more objective measurement. However, an overview of current candidate biomarkers and their validity is missing for both cocoa- and liquorice-containing foods. Objective: The purpose of the current study was to (1) identify currently described candidate BFIs for cocoa (products) and liquorice, (2) to evaluate the validity of these identified candidate BFIs and (3) to address further validation and/or identification work to be done. Methods: This systematic review was based on a comprehensive literature search of three databases (PubMed, Scopus and ISI web of Science), to identify candidate BFIs. Via a second search step in the Human Metabolome Database (HMDB), the Food Database (FooDB) and Phenol-Explorer, the specificity of the candidate BFIs was evaluated, followed by an evaluation of the validity of the specific candidate BFIs, via pre-defined criteria. Results: In total, 37 papers were included for cocoa and 8 papers for liquorice. For cocoa, 164 unique candidate BFIs were obtained, and for liquorice, four were identified in total. Despite the high number of identified BFIs for cocoa, none of the metabolites was specific. Therefore, the validity of these compounds was not further examined. For liquorice intake, 18-glycyrrhetinic acid (18-GA) was found to have the highest assumed validity. Conclusions: For cocoa, specific BFIs were missing, mainly because the individual BFIs were also found in foods having a similar composition, such as tea (polyphenols) or coffee (caffeine). However, a combination of individual BFIs might lead to discriminating profiles between cocoa (products) and foods with a similar composition. Therefore, studies directly comparing the consumption of cocoa to these similar products are needed, enabling efforts to find a unique profile per product. For liquorice, we identified 18-GA as a promising BFI; however, important information on its validity is missing; thus, more research is necessary. Our findings indicate a need for more studies to determine acceptable BFIs for both cocoa and liquorice.

Two different R gene loci co-evolved with Avr2 of Phytophthora infestans and confer distinct resistance specificities in potato
Aguilera-Galvez, C. ; Champouret, N. ; Rietman, H. ; Lin, X. ; Wouters, D. ; Chu, Z. ; Jones, J.D.G. ; Vossen, J.H. ; Visser, R.G.F. ; Wolters, P.J. ; Vleeshouwers, V.G.A.A. - \ 2018
Studies in Mycology 89 (2018). - ISSN 0166-0616 - p. 105 - 115.
Avr gene - Co-evolution - Late blight - Phytophthora infestans - Potato - R gene - Resistance - Solanum
Late blight, caused by the oomycete pathogen Phytophthora infestans, is the most devastating disease in potato. For sustainable management of this economically important disease, resistance breeding relies on the availability of resistance (R) genes. Such R genes against P. infestans have evolved in wild tuber-bearing Solanum species from North, Central and South America, upon co-evolution with cognate avirulence (Avr) genes. Here, we report how effectoromics screens with Avr2 of P. infestans revealed defense responses in diverse Solanum species that are native to Mexico and Peru. We found that the response to AVR2 in the Mexican Solanum species is mediated by R genes of the R2 family that resides on a major late blight locus on chromosome IV. In contrast, the response to AVR2 in Peruvian Solanum species is mediated by Rpi-mcq1, which resides on chromosome IX and does not belong to the R2 family. The data indicate that AVR2 recognition has evolved independently on two genetic loci in Mexican and Peruvian Solanum species, respectively. Detached leaf tests on potato cultivar ‘Désirée’ transformed with R genes from either the R2 or the Rpi-mcq1 locus revealed an overlapping, but distinct resistance profile to a panel of 18 diverse P. infestans isolates. The achieved insights in the molecular R – Avr gene interaction can lead to more educated exploitation of R genes and maximize the potential of generating more broad-spectrum, and potentially more durable control of the late blight disease in potato.
High resolution full scan liquid chromatography mass spectrometry comprehensive screening in sports antidoping urine analysis
Abushareeda, Wadha ; Vonaparti, Ariadni ; Saad, Khadija Al ; Almansoori, Moneera ; Meloug, Mbarka ; Saleh, Amal ; Aguilera, Rodrigo ; Angelis, Yiannis ; Horvatovich, Peter L. ; Lommen, Arjen ; Alsayrafi, Mohammed ; Georgakopoulos, Costas - \ 2018
Journal of Pharmaceutical and Biomedical Analysis 151 (2018). - ISSN 0731-7085 - p. 10 - 24.
Full scan high-resolution - Human urine - Liquid chromatography - Mass spectrometry - Small molecule prohibited substances - Sulfo-conjugate steroids
The aim of this paper is to present the development and validation of a high-resolution full scan (HR-FS) electrospray ionization (ESI) liquid chromatography coupled to quadrupole Orbitrap mass spectrometer (LC/Q/Orbitrap MS) platform for the screening of prohibited substances in human urine according to World Antidoping Agency (WADA) requirements. The method was also validated for quantitative analysis of six endogenous steroids (epitestosterone, testosterone, 5α-dihydrotestosterone, dehydroepiandrosterone, androsterone and etiocholanolone) in their intact sulfates form. The sample preparation comprised a combination of a hydrolyzed urine liquid–liquid extraction and the dilute & shoot addition of original urine in the extracted aliquot. The HR-FS MS acquisition mode with Polarity Switching was applied in combination of the Quadrupole-Orbitrap mass filter. The HR-FS acquisition of analytical signal, for known and unknown small molecules, allows the inclusion of all analytes detectable with LC–MS for antidoping investigations to identify the use of known or novel prohibited substances and metabolites after electronic data files’ reprocessing. The method has been validated to be fit-for-purpose for the antidoping analysis.
Sistema multipropósito de agua Jaime Roldós Aguilera: el territorio hidrosocial como escenario de disputa y resistencia
Hidalgo, Juan Pablo ; Boelens, R.A. ; Isch Lôpez, E. - \ 2017
In: Los Caminos del Agua / Artoyo, Aline, Isch Lopez, Edgar, Quito : Abya Yala - ISBN 9789942094230 - p. 109 - 132.
Effectoromics-based identification of cell surface receptors in potato
Domazakis, Emmanouil ; Lin, Xiao ; Aguilera-Galvez, Carolina ; Wouters, Doret ; Bijsterbosch, Gerard ; Wolters, Pieter J. ; Vleeshouwers, Vivianne G.A.A. - \ 2017
In: Plant Pattern Recognition Receptors / Shan, Libo, He, Ping, Humana Press Inc. (Methods in Molecular Biology ) - ISBN 9781493968596 - p. 337 - 353.
Agroinfiltration - Apoplastic effector - Effectoromics - Genetic mapping - Pattern recognition receptors (PRRs) - Protein infiltration - PVX agroinfection - Solanum - Yeast protein production

In modern resistance breeding, effectors have emerged as tools for accelerating and improving the identification of immune receptors. Effector-assisted breeding was pioneered for identifying resistance genes (R genes) against Phytophthora infestans in potato (Solanum tuberosum). Here we show that effectoromics approaches are also well suitable for identifying pathogen recognition receptors (PRRs) that recognize apoplastic effectors. To detect genotypes that recognize apoplastic proteins of P. infestans, routine agroinfiltration and potato virus X (PVX) agroinfection methods can be applied. In addition, protein infiltrations are feasible for assessing responses to apoplastic effectors and aid in confirming results obtained from the aforementioned methods. Protocols for the effectoromics pipeline are provided, starting from phenotyping for effector responses, up to genotyping and PRR gene identification.

Strategies for greenhouse gas emissions mitigation in Mediterranean agriculture: A review
Sanz-Cobena, A. ; Lassaletta, L. ; Aguilera, E. ; Prado, A. Del; Garnier, J. ; Billen, G. ; Iglesias, A. ; Sánchez, B. ; Guardia, G. ; Abalos Rodriguez, Diego ; Plaza-Bonilla, D. ; Puigdueta-bartolomé, I. ; Moral, R. ; Galán, E. ; Arriaga, H. ; Merino, P. ; Infante-Amate, J. ; Meijide, A. ; Pardo, G. ; Álvaro-Fuentes, J. ; Gilsanz, C. ; Báez, D. ; Doltra, J. ; González-Ubierna, S. ; Cayuela, M.L. ; Menéndez, S. ; Díaz-Pinés, E. ; Le-Noë, J. ; Quemada, M. ; Estellés, F. ; Calvet, S. ; Grinsven, H.J.M. Van; Westhoek, H. ; Sanz, M.J. ; Gimeno, B.S. ; Vallejo, A. ; Smith, P. - \ 2017
Agriculture, Ecosystems and Environment 238 (2017). - ISSN 0167-8809 - p. 5 - 24.
An integrated assessment of the potential of different management practices for mitigating specific components of the total GHG budget (N2O and CH4 emissions and C sequestration) of Mediterranean agrosystems was performed in this study. Their suitability regarding both yield and environmental (e.g. nitrate leaching and ammonia volatilization) sustainability, and regional barriers and opportunities for their implementation were also considered. Based on its results best strategies to abate GHG emissions in Mediterranean agro-systems were proposed. Adjusting N fertilization to crop needs in both irrigated and rain-fed systems could reduce N2O emissions up to 50% compared with a non-adjusted practice. Substitution of N synthetic fertilizers by solid manure can be also implemented in those systems, and may abate N2O emissions by about 20% under Mediterranean conditions, with additional indirect benefits associated to energy savings and positive effects in crop yields. The use of urease and nitrification inhibitors enhances N use efficiency of the cropping systems and may mitigate N2O emissions up to 80% and 50%, respectively. The type of irrigation may also have a great mitigation potential in the Mediterranean region. Drip-irrigated systems have on average 80% lower N2O emissions than sprinkler systems and drip-irrigation combined with optimized fertilization showed a reduction in direct N2O emissions up to 50%. Methane fluxes have a relatively small contribution to the total GHG budget of Mediterranean crops, which can mostly be controlled by careful management of the water table and organic inputs in paddies. Reduced soil tillage, improved management of crop residues and agro-industry by-products, and cover cropping in orchards, are the most suitable interventions to enhance organic C stocks in Mediterranean agricultural soils. The adoption of the proposed agricultural practices will require farmers training. The global analysis of life cycle emissions associated to irrigation type (drip, sprinkle and furrow) and N fertilization rate (100 and 300 kg N ha−1 yr−1) revealed that these factors may outweigh the reduction in GHG emissions beyond the plot scale. The analysis of the impact of some structural changes on top-down mitigation of GHG emissions revealed that 3–15% of N2O emissions could be suppressed by avoiding food waste at the end-consumer level. A 40% reduction in meat and dairy consumption could reduce GHG emissions by 20–30%. Reintroducing the Mediterranean diet (i.e. ∼35% intake of animal protein) would therefore result in a significant decrease of GHG emissions from agricultural production systems under Mediterranean conditions.
Direct nitrous oxide emissions in Mediterranean climate cropping systems : Emission factors based on a meta-analysis of available measurement data
Cayuela, Maria L. ; Aguilera, Eduardo ; Sanz-Cobena, Alberto ; Adams, Dean C. ; Abalos Rodriguez, Diego ; Barton, Louise ; Ryals, Rebecca ; Silver, Whendee L. ; Alfaro, Marta A. ; Pappa, Valentini A. ; Bouwman, Lex ; Lassaletta, Luis - \ 2017
Agriculture, Ecosystems and Environment 238 (2017). - ISSN 0167-8809 - p. 25 - 35.
Field studies - Greenhouse gases - Mitigation - NO - Systematic review

Many recent reviews and meta-analyses of N2O emissions do not include data from Mediterranean studies. In this paper we present a meta-analysis of the N2O emissions from Mediterranean cropping systems, and propose a more robust and reliable regional emission factor (EF) for N2O, distinguishing the effects of water management, crop type, and fertilizer management. The average overall EF for Mediterranean agriculture (EFMed) was 0.5%, which is substantially lower than the IPCC default value of 1%. Soil properties had no significant effect on EFs for N2O. Increasing the N fertilizer rate led to higher EFs; when N was applied at rates greater than 400kgNha-1, the EF did not significantly differ from the 1% default value (EF: 0.82%). Liquid slurries led to emissions that did not significantly differ from 1%; the other fertilizer types were lower but did not significantly differ from each other. Rain-fed crops in Mediterranean regions have lower EFs (EF: 0.27%) than irrigated crops (EF: 0.63%). Drip irrigation systems (EF: 0.51%) had 44% lower EF than sprinkler irrigation methods (EF: 0.91%). Extensive crops, such as winter cereals (wheat, oat and barley), had lower EFs (EF: 0.26%) than intensive crops such as maize (EF: 0.83%). For flooded rice, anaerobic conditions likely led to complete denitrification and low EFs (EF: 0.19%). Our results indicate that N2O emissions from Mediterranean agriculture are overestimated in current national greenhouse gas inventories and that, with the new EF determined from this study, the effect of mitigation strategies such as drip irrigation or the use of nitrification inhibitors, even if highly significant, may be smaller in absolute terms.

Nine things to know about elicitins
Derevnina, Lida ; Dagdas, Yasin F. ; Concepcion, Juan Carlos De la; Bialas, Aleksandra ; Kellner, Ronny ; Petre, Benjamin ; Domazakis, Emmanouil ; Du, Juan ; Wu, Chih Hang ; Lin, Xiao ; Aguilera-Galvez, Carolina ; Cruz-Mireles, Neftaly ; Vleeshouwers, Vivianne G.A.A. ; Kamoun, Sophien - \ 2016
New Phytologist 212 (2016)4. - ISSN 0028-646X - p. 888 - 895.
Cell death - Elicitin response (ELR) - Elicitor - Hypersensitive response (HR) - INF1 - Microbe-associated molecular patterns (MAMPs) - Oomycetes

Elicitins are structurally conserved extracellular proteins in Phytophthora and Pythium oomycete pathogen species. They were first described in the late 1980s as abundant proteins in Phytophthora culture filtrates that have the capacity to elicit hypersensitive (HR) cell death and disease resistance in tobacco. Later, they became well-established as having features of microbe-associated molecular patterns (MAMPs) and to elicit defences in a variety of plant species. Research on elicitins culminated in the recent cloning of the elicitin response (ELR) cell surface receptor-like protein, from the wild potato Solanum microdontum, which mediates response to a broad range of elicitins. In this review, we provide an overview on elicitins and the plant responses they elicit. We summarize the state of the art by describing what we consider to be the nine most important features of elicitin biology.

Soil moisture prediction to support management in semiarid wetlands during drying episodes
Aguilera, Héctor ; Moreno, Luis ; Wesseling, Jan G. ; Jiménez-Hernández, María E. ; Castaño, Silvino - \ 2016
Catena 147 (2016). - ISSN 0341-8162 - p. 709 - 724.
Critical soil moisture - Peat fires - Soil functional types - SWAP model - Wetland management

Wetlands supported by groundwater in semiarid regions are extremely vulnerable to the impacts of droughts, particularly anthropized systems. During drying periods, soil water content arises as the controlling factor for environmental and ecological disturbances such as the spread of invasive plant species, the combustibility of organic soils, nutrient redistribution or soil physical disruption. The presented management tool for semiarid wetlands is supported by the Soil-Water-Atmosphere-Plant (SWAP) model for soil moisture modeling and simulation. Main input data are experimental values of soil physical and hydraulic characteristics, soil moisture measurements, vegetation growth parameters and climatic records. Decision-makers can use the calibrated datasets to predict the evolution of soil moisture under different drying scenarios in order to choose the most efficient management options for preventing soil moisture to reach critical values. The approach has been tested in the anthropized Mediterranean semiarid wetland area of Las Tablas de Daimiel National Park in central Spain. Ten vadose zone water models were successfully calibrated and validated for different soil units. Critical soil moisture conditions for invasive reed overgrowth and peat combustibility have been estimated. Simulations of a typical 2-year drought scenario indicated that critical soil moisture conditions for reed overgrowth are attained 9–10 months after flooding ceased and that peat areas colonized by reed plants become combustible (even 50% probability chance) by the end of the simulated period.

An efficient flat-surface collar-free grafting method for Arabidopsis thaliana seedlings
Marsch-Martinez, N. ; Franken, J. ; Gonzalez-Aguilera, K.L. ; Folter, S. de; Angenent, G.C. ; Alvarez-Buylla, E.R. - \ 2013
Plant Methods 9 (2013). - ISSN 1746-4811
ft protein - shoot - transport - cotyledon - movement - plants - rnas - root
Background: Grafting procedures are an excellent tool to study long range signalling processes within a plant. In the last decade, suitable flat-surface grafting procedures for young Arabidopsis seedlings using a collar to support the graft have been developed, allowing the study of long-range signals from a molecular perspective. Results: In the modification presented here, scion and stock are put together on the medium without supporting elements, while cotyledons are removed from the scion, resulting in increased grafting success that can reach up to 100%. At the same time, the protocol enables to process as many as 36 seedlings per hour, which combined with the high success percentage represents increased efficiency per time unit. Conclusions: Growing cotyledons usually push the scion and the rootstock away in the absence of a supporting element. Removing them at the grafting step greatly improved success rate and reduced post-grafting manipulations.
Validation of a new phytotoxicity test (phytotoxkit) against an established four-week growing test with pre-grown plant plugs
Blok, C. ; Aguilera, M. ; Os, E.A. van - \ 2009
Acta Horticulturae 819 (2009). - ISSN 0567-7572 - p. 209 - 214.
The aim of the studies was to correlate results of a fast extract-based toxicity test with results of an established growing test with mostly pre-grown plants. A standard white peat was contaminated with four levels of TCA (trichloroacetic acid), a known toxic substance. A range was composed of five levels of TCA, including zero, 0.0013, 0.013, 0.13, and 1.3 g/L of peat. Part of the material was entered in Phytotoxkit containers and covered with a filter paper. At the other side of the filter paper two dicotyledonous species, garden cress (Lepidium sativum) and mustard (Sinapis alba) and one monocotyledon, Sorghum (Sorghum saccharatum) were allowed to germinate for a three day period on the extract from the substrate in a climate-controlled cabinet. The same range of amended peats was used in the standard test to grow transplanted lettuce (Lactuca sativa), Chinese cabbage (Brassica rapa subsp. pekinensis) and directly sown barley (Hordeum vulgare). For the Phytotoxkit the above ground length and root length were recorded, and for the standard test the fresh weight and dry weight of the above ground parts were recorded. Results showed a growth reduction for all levels of TCA when using the standard method. When using the Phytotoxkit only the two highest concentrations of TCA reduced growth. For screenings of product alternatives or dissolution series the Phytotoxkit is a faster and cheaper alternative
A Cultural Algorithm for POMDPs from Stochastic Inventory Control
Prestwich, S. ; Tarim, S.A. ; Rossi, R. ; Hnich, B. - \ 2008
In: Hybrid Metaheuristics / Blesa Aguilera, M.J., Blum, C., Cotta, C., Fernández Leiva, A.J., Gallardo Ruiz, J.E., Sampels, M., Springer Berlin/Heidelberg (Lecture Notes in Computer Science 5296) - ISBN 9783540884385 - p. 16 - 28.
Reinforcement Learning algorithms such as SARSA with an eligibility trace, and Evolutionary Computation methods such as genetic algorithms, are competing approaches to solving Partially Observable Markov Decision Processes (POMDPs) which occur in many fields of Artificial Intelligence. A powerful form of evolutionary algorithm that has not previously been applied to POMDPs is the cultural algorithm, in which evolving agents share knowledge in a belief space that is used to guide their evolution. We describe a cultural algorithm for POMDPs that hybridises SARSA with a noisy genetic algorithm, and inherits the latter¿s convergence properties. Its belief space is a common set of state-action values that are updated during genetic exploration, and conversely used to modify chromosomes. We use it to solve problems from stochastic inventory control by finding memoryless policies for nondeterministic POMDPs. Neither SARSA nor the genetic algorithm dominates the other on these problems, but the cultural algorithm outperforms the genetic algorithm, and on highly non-Markovian instances also outperforms SARSA
Assembly of Structures in Foods
Linden, E. van der - \ 2008
In: Food Materials Science. Principles and Practice / Aguilera, J.M., Lillford, P.J., New York : Springer (Food Engineering Series ) - ISBN 9780387719467 - p. 145 - 168.
Halomonas indalinina sp.nov., a moderately halophilic bacterium isolated from a solar saltern in Cabo de Gata, Al,eria, southern Spain
Cabrera, A. ; Aguilera, M. ; Fuentes Enriquez de Salamanca, S. ; Incerti, C. ; Russell, N.J. ; Ramos-Cormenzana, A. ; Monteoliva-Sanchez, M. - \ 2007
International Journal of Systematic and Evolutionary Microbiology 57 (2007)2. - ISSN 1466-5026 - p. 376 - 380.
gram-negative rods - numerical taxonomy - sequence alignment - exopolysaccharide - microorganisms - biotechnology - halotolerant - phylogeny - strains - atacama
moderately halophilic bacterium, strain CG2.1T, isolated from a solar saltern at Cabo de Gata, a wildlife reserve located in the province of Almería, southern Spain, was subjected to a polyphasic taxonomic study. This organism was an aerobic, motile, Gram-negative rod that produced orange-pigmented colonies. Strain CG2.1T was able to grow at salinities of 3¿25 % (w/v) and at temperatures of 15¿40 °C. The pH range for growth was 5¿9. Strain CG2.1T was a heterotroph capable of utilizing various carbohydrates as carbon sources. The organism reduced nitrate and showed phenylalanine deaminase activity. The major fatty acids were C18 : 17c, C16 : 0 and C19 : 0 cyclo 8c. The DNA G+C content was 60.9 mol%. On the basis of the phenotypic and phylogenetic data, strain CG2.1T appeared to be a member of the genus Halomonas and clustered closely with Halomonas marisflavi (97.1 % 16S rRNA gene sequence similarity). However, the level of DNA¿DNA relatedness between the novel isolate and the most closely related Halomonas species was low. On the basis of these data, strain CG2.1T represents a novel member of the genus Halomonas, for which the name Halomonas indalinina is proposed. The type strain is CG2.1T (=CECT 5902T=LMG 23625T).
Quantitative resistance and its components in 16 barley cultivars to yellow rust, Puccinia striiformis f.sp. hordei
Sandoval-Islas, J.S. ; Broers, L.H.M. ; Mora-Aguilera, G. ; Parlevliet, J.E. ; Osada-Kawasoe, S. ; Vivar, H.E. - \ 2007
Euphytica 153 (2007)3. - ISSN 0014-2336 - p. 295 - 308.
wheat leaf rust - adult-plant resistance - stripe rust - spring wheat - development stage - latent period - growth stages - epidemics
Sixteen barley cultivars with a susceptible infection type (IT = 7-8) in the seedling stage to an isolate of race 24 of Puccinia striiformis f. sp. hordei were planted at two locations in México. Disease severity (DS) parameters were assessed for the flag leaf and for the upper three leaves. The cultivars represented at least five levels of quantitative resistance ranging from very susceptible to quite resistant. ¿Granado¿, ¿Gloria/Copal¿ and ¿Calicuchima-92¿ represented the most resistant group and had an IT of 7 or 8. The cultivar × environment interaction variance, although significant, was very small compared with the cultivar variance. The disease severity parameters were highly correlated. The monocyclic parameter DSm, measured when the most susceptible cultivar had reached its maximum DS, was very highly correlated with the area under the disease progress curve (AUDPC), r being 0.98. Components of quantitative resistance were evaluated in two plant stages. In the seedling stage small cultivar effects for the latency period were observed, which were not correlated with the quantitative resistance measured in the field. In the adult plant stage the latency period (LP), infection frequency (IF) and colonization rate (CR) were measured in the upper two leaves. The LP was much longer than in the seedling stage and differed strongly between cultivars. The differences in IF were too large, those in CR varied much less. The components showed association with one another. The LP and IF were well correlated with the AUDPC (r = 0.7-0.8).
Beet mosaic virus : epidemiology and damage
Dusi, A. - \ 1999
Agricultural University. Promotor(en): R.W. Goldbach; D. Peters; W. van der Werf. - S.l. : Dusi - ISBN 9789058080752 - 137
bietenmozaïekvirus - plantenvirussen - plantenziekteverwekkers - plantenziekten - epidemiologie - oogstschade - simulatiemodellen - Beet mosaic virus - plant viruses - plant pathogens - plant diseases - epidemiology - crop damage - simulation models

Overview:

The aim of the studies described in this thesis was to obtain a thorough understanding of the main factors determining the spread of a potyvirus in a high plant density crop. The factors studied included the relationships between virus, host and vector, the spread of the virus around an initial virus source consisting of one or more infected plants, the spread of the virus by the prevailing aphid population, and the effect of plant density on the spread of the virus. A time-save sampling technique was developed and the damage caused was estimated. This study was made with the system beet - beet mosaic virus (BtMV), a potyvirus infecting sugar beet, as a model pathosystem. Sugar beet is a herbaceous plant widely cultivated in The Netherlands. The crop, which has a cycle of approximately 8 months, is cultivated in fields at a density of 7 to 10 plants/m 2. The disease in this crop is polycyclic, as several infection cycles occur during the growing season.

The spread of a potyvirus in a crop starts with a primary infection, either introduced by migrating aphids from sources outside the field or by the use of infected seed or propagative plant material. These plants form the sources from which the virus is spread secondarily in the field. The primary infections are in most cases scattered over the field, whereas secondary infections are aggregated around early-infected plants. Studies on the spread of a virus from a known source are few, as primary introductions are difficult to prevent in many crop virus system. Primary infections are frequently introduced at erratic moments and increase in virus incidence, due to plants infected from outside sources is superimposed on the secondary spread ongoing within the field. As BtMV is only rarely encountered in The Netherlands and not seed transmitted, this pathosystem is a good model to analyze secondary spread using a known virus source in the experimental plots. Spread was expected only to occur from these sources and not from outside sources.

Development of a time saving transect sampling method:

Spread of BtMV occurred around the virus source in a clustered isotropic pattern with a negative exponential gradient. Such a spread is common for polycyclic epidemics of potyviruses in annual crops (Dahal, 1992; Eckel and Lampert, 1993; Nelson and Campbell, 1993; Perring et al., 1992). The isotropic spatial pattern of spread found in all plots showed that a simple sampling method, called transect sampling method, could be developed and used to monitor the development of the infection. This method consisted of monitoring the plants on two orthogonal transects extending diagonally across the rows from the source plants in the plot. In the analysis of transect data, the uneven representation of the sampled plants at each distance class must be taken into consideration. The temporal and spatial spread of the BtMV disease could be described as reliably using the transect method, as by monitoring the whole plot, provided that a lower precision per repetition is compensated by raising the number of repetitions. This result suggests that by using this less labor intensive and less time consuming sampling method, more sites or more treatments can be studied.

This sampling method can also be applied to study the spread in other pathosystems such as Papayaringspotvirus (PRSV) in cucurbits, Potato vi r us Y (PVY) in crops of various solanaceous species, and Soybean mosaic virus (SMV) in soybeans, when the virus source is known or can be found. This sampling method can potentially also be applied to semi-persistently and persistently transmitted viruses such as Beet yellows virus ( BYV and Beet mild yellowing virus (BMYV) (van der Werf, personal communication), which form usually clusters with an isotropic spatial pattern around the primarily infected virus source, in a similar fashion as BtMV.

Modeling spread as a function of migrating aphid flights:

Under natural conditions, aphids transmit potyviruses in a non-persistent manner. Although the interaction between the virus and the vector is specific (Shukla et al., 1994), apparent specificities in the epidemiological relationships between potyviruses and aphid species have not been elucidated. The role of the individual aphid species in the spread of potyviruses has been analyzed by different analytical methods. The simplest approach is to plot virus incidence and number of aphids counted on plants or collected with traps on a common time axis and to subjectively compare the curves obtained for the spread and the number of aphids obtained for each individual species or the total aphid population. Eckel and Lampert (1993), van Hoof (1977) and Karl et al. (1983) used this approach but could not find any relation between the species and the spread of the potyviruses studied. A pitfall of this approach is that population trends of different aphid species over time may be collinear (Chapter 4). Thus, the role of one species might not be isolated from the other. Correlation and regression analysis also usually fail to relate spread to aphid species or total counts (Madden et al., 1987; Mora-Aguilera et al., 1992; Watson and Healy, 1953).

Garrett (1988) demonstrated that, in lupine, Clover yellow vein virus was mostly spread by two aphid species ( Aphis craccivora and Myzus persicae ) using multiple regression analysis to relate the rate of spread of this potyvirus to the species that compose the aphid population. In the studies described here, no single species could be associated with the spread applying correlation or regression analyses. A good correlation could be detected between the total daily number of alatae caught and the spread of BtMV.

Based on the collected data, a deterministic simulation model was developed to study the spread as a function of the migrating aphid population (Chapter 4). This model was based on a logistic population growth applied to plant diseases (van der Plank, 1963). The rate of the disease was, in this model, proportional to the virus sources, healthy plants, latent and incubation periods of the virus in the plant, the total number of aphids caught in a suction trap (not discriminating species) and a parameter ( r ) that represented all aspects of vector activity relevant to virus spread (Jeger et al. 1998). This parameter r , describing the relationship between the daily catches of aphids and the number of newly infected plants, was quite robust among experiments. Remarkably, r appeared to be independent of the moments at which the primary inoculum sources were introduced, confirming that the chosen model and common parameter value give a seasonable mechanistic description of epidemics started at different dates. These results confirm and extend the conclusions of Di Fonzo et al. (1997), Madden et al. (1987), Mora-Aguilera et al. (1992) and Nemecek (1993), that migrating aphids, regardless of the species, play a major role in the spread of non-persistently transmitted viruses.

The simulation model used in this study only accounted for secondary spread as introductions from external virus sources rarely occur in the Netherlands. The absence of any spread from outside sources allowed inoculating the field at different dates. This simulation model could simulate the final number of plants showing symptoms. A rough approximation, using the averaged obtained value for r and aphid catches showed that the number of infected plants to occur could be predicted two weeks in advance. The use of this model as a predictive tool for the whole crop cycle is premature because it does not model the development of the aphid population. Although r was conserved between the inoculation dates in each experiment, it varied between experiments. The species composition of the aphid population varies each year. Although the total number of aphids caught could be related to virus spread, the rate by which the virus will be spread will differ among years and among locations. In more elaborate models, r must be decomposed into different components representing the behavior of the aphid population such as the acquisition and inoculation rates, the infectious period of the virus in the vector, the vector turn over, the feeding time per vector per day, and the distance hopped by aphids (Jeger et al., 1998).

The simulation models used by Nemecek (1993) and Sigvald (1992), to predict Potato virus Y spread in potatoes, included some behavioral characteristics and a more detailed description of the aphid species composition. These models could be used to simulate the final disease incidence in crops, which were initially infected with different numbers of virus sources. The studies in Soybean mosaic virus presented by Ruesink and Irwin (1986) also included some behavioral aspects of the vector and could be used to predict yield and level of seed transmission. The complementary information added by the present study was an experimentally demonstration that spread of BtMV is related to the major migrating aphid flight. The calibration studies using a simulation model confirmed that this spread could be described by one absolute rate parameter. It can be concluded that management strategies to control virus spread have to be focused on a delay of virus introductions in the field, or alternatively, to restrain aphid dispersal early in the season.

The deterministic model developed in Chapter 4 was adapted to include a factor that describes the effect of plant density in the rate equation. This factor could be included on the assumption that plant density would affect the spread by affecting the number of aphids per plant, and the number of available plants, while the other parameters related to spread would remain constant. The spread was indeed inversely proportional to the plant density in the first weeks after the virus started to spread. However, analyzing the incidence for the whole growing season, the model failed to explain the observed spread. Values of r estimated by calibration, to experimental field data, showed that the rate of spread in low-density plots was lower than the rate expected by the hypothesis that spread is proportional to the number of aphids per plant. The factors that lead to the strong aggregation of the infected plants around the primarily infected plant might have affected the rate of spread in these low-density plots.

The contrast between bare soil and plants will be larger in low-density plots than in plots with standard density. By the middle of July, when most of the aphid migration occurred in both years, the canopy was closed in the standard density plots while bare soil was still visible in the low-density plots. An attraction exerted on the aphids by the contrast between plants and bare soil might have affected the mobility of the aphids within the plot, reducing the distance hopped between plants and, consequently, the spread of the disease as the infected plants might be re-inoculated frequently. A factor considering this distance and/or the spatial pattern of the spread must be included to improve the model. Improvements of this model must, therefore, concentrate on the inclusion of a set of equations representing the vector behavioral components and the spatial pattern of spread.

BtMV and damage in sugar beet:

Experiments to determine damage due to virus infections are laborious. It is assumed that yield will depend on date of inoculation, initial inoculum levels, rate at which the virus spreads, disease incidence at the moment of harvest, and others. Since many factors will affect the yield, it will be difficult to estimate the crop losses caused by a pathogen. The use of a crop growth model can overcome these difficulties, assuming that the parameters related to damage can be determined and incorporated in the model. Information on damage caused by BtMV is rare in the literature, but it is generally accepted that this disease has little impact on yield of sugar beet (Watson and Watson, 1953).

The effect of BtMV infections on the yield of the sugar beet crop was evaluated by simulation using a crop growth model (SUCROS). This analysis was experimentally grounded by determination of the light response curve, light absorption and transmission, and other parameters on healthy and BtMV infected leaves showing mosaic symptoms. The model dynamically simulates the carbon budget and growth of the crop by integrating leaf photosynthesis over time and leaf area, taking into account incident light, leaf area index, proportion of mosaic-affected leaf area, and optical characteristics of the leaves and the canopy. The damage simulated for early-infected crops was estimated to be, under the most extreme situation, approximately 20%. However, as the infection usually starts to spread in the second half of the growing season, the estimated damage in a fully infected crop after July was less than 3%. This value can be neglected considering the damage due to other diseases, harvesting and processing of the roots. Injury component analyses indicated that the direct effect due to both reduction in maximum rate of photosynthesis ( Pm ) and increase in dark respiration ( Rd ) were the major causes of the simulated damage (Chapter 6).

The simulation studies demonstrated that the usually observed negligible damaging effect of BtMV is due to the late occurrence of the spread of the disease under field conditions (Chapters 3 and 4). When infection takes place, the crop has already a large enough area of healthy leaves to sustain the yield, even if all plants in the field were infected after the middle of the growing season (Chapter 6). This study is probably the first which simulates crop damage caused by a potyvirus, and it is certainly the first simulation study of the damage caused by BtMV in sugar beet.

Concluding remarks:

As a model is a simplification of reality, perfection is not expected (Ruesink and Irvin, 1986). Several improvements can be made to the simulation model presented in this study to describe the disease incidence. The present version allowed to test the raised hypothesis that spread was a function of the migrating aphid population, for every date at which the inoculum source was introduced. The results of the analysis of the rate of spread of the field experiments, together with the modeling studies, could indicate the model has to be improved by including an aphid population sub-model that describes vector behavior. It suggested also that the spatial characteristics of spread must be taken in account.

Differences in energy metabolism between chickens of white leghorn laying hens selected for high and low residual feed consumption.
Boekholt, H.A. ; Luiting, P. - \ 1994
In: Proc. 13th Symp. Energy Metabolism of Farm Animals, J.F. Aguilera (ed.). Mojacar, Spain, EEAP publ. 76 - p. 281 - 284.
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