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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Embolism resistance drives the distribution of Amazonian rainforest tree species along hydro-topographic gradients
Oliveira, Rafael S. ; Costa, Flavia R.C. ; Baalen, Emma van; Jonge, Arjen de; Bittencourt, Paulo R. ; Almanza, Yanina ; V. Barros, Fernanda de; Cordoba, Edher C. ; Fagundes, Marina V. ; Garcia, Sabrina ; Guimaraes, Zilza T.T.M. ; Hertel, Mariana ; Schietti, Juliana ; Rodrigues-Souza, Jefferson ; Poorter, Lourens - \ 2018
New Phytologist (2018). - ISSN 0028-646X - 9 p.
drought vulnerability - forest resilience - functional ecology - hydrological niches - P - phosphorus - tropical forests - water table

Species distribution is strongly driven by local and global gradients in water availability but the underlying mechanisms are not clear. Vulnerability to xylem embolism (P50) is a key trait that indicates how species cope with drought and might explain plant distribution patterns across environmental gradients. Here we address its role on species sorting along a hydro-topographical gradient in a central Amazonian rainforest and examine its variance at the community scale. We measured P50 for 28 tree species, soil properties and estimated the hydrological niche of each species using an indicator of distance to the water table (HAND). We found a large hydraulic diversity, covering as much as 44% of the global angiosperm variation in P50. We show that P50: contributes to species segregation across a hydro-topographic gradient in the Amazon, and thus to species coexistence; is the result of repeated evolutionary adaptation within closely related taxa; is associated with species tolerance to P-poor soils, suggesting the evolution of a stress-tolerance syndrome to nutrients and drought; and is higher for trees in the valleys than uplands. The large observed hydraulic diversity and its association with topography has important implications for modelling and predicting forest and species resilience to climate change.

Participation through place-based e-tools : A valuable resource for urban green infrastructure governance?
Steen Møller, Maja ; Olafsson, Anton ; Vierikko, Kati ; Sehested, Karina ; Elands, Birgit ; Buijs, Arjen ; Konijnendijk van den Bosch, Cecil - \ 2018
Urban Forestry and Urban Greening (2018). - ISSN 1618-8667 - 9 p.
Digital tools - E-tools - Participatory governance - Place - Urban Green space

Digital communication tools for information sharing are being increasingly used in governance, including green space governance and natural resource management and planning. Citizens’ resources in the form of knowledge, skills, as well as their collaboration with authorities have been identified in the governance literature as crucial elements in sustainable development. Technical advancement in internet communication technology (ICT) presents novel opportunities for engaging and leveraging civic knowledge and skills into different levels of governance. These options are still largely unexplored in governance research on urban green infrastructure (UGI). In this paper, we analyse three different digital tools (e-tools) from the perspective of a Scandinavian planning context. We explore how e-tools can support UGI governance and the perceived barriers. The e-tools explored are three digital platforms with a focus on public participation related to UGI. The three e-tools are map-based, i.e., users share information on digital maps: so-called Volunteered Geographic Information. Here, we call them place-based e-tools. We explore and analyse their adoption into UGI governance, the institutional contexts that affect them and also discuss potential of e-tools in place-based governance. Our findings indicate that the analysed tools all facilitate UGI governance in terms of engaging citizens in use, management, and planning of UGI. However, there are challenges to be aware of, such as the digital divide and the importance of clear participatory frameworks. We conclude that place-based e-tools have potential for UGI governance and that there is potential to strengthen links to ‘place’, while continuously testing and challenging new opportunities as technology rapidly develops.

Persistent Organic Pollutants in two species of migratory birds from Rothera Point, Adelaide Island, Antarctica
Krasnobaev, A. ; Dam, G. ten; Leeuwen, S.P.J. van; Peck, L.S. ; Brink, N.W. van den - \ 2018
Marine Pollution Bulletin 137 (2018). - ISSN 0025-326X - p. 113 - 118.
Antarctica - Birds - OCPs - PBDEs - PCBs - POPs

Carcasses of South Polar Skuas (Catharacta maccormicki) and Kelp gulls (Larus dominicanus) were opportunistically collected around of Rothera Research station (67°35′8″S and 68°7′59″W) during the 2016/2017 austral summer. Samples of their tissues (muscle, liver and subcutaneous fat) were analysed for Persistent Organic Pollutants (POPs). Organochlorine pesticides (OCPs) showed the highest concentrations, notably for pp′-DDE and HCB. The Polychlorinated biphenyls (PCBs)-profiles demonstrated a clear dominance of hexa- and hepta-CBs, while concentrations of polybrominated diphenyl ethers (PBDEs) remained low. The concentrations of some POPs (e.g. HCB) were lower than in past studies on similar species, however others were within the previous range (PCBs) or even higher than previous reported values (DDE). Although no major interspecific differences in the absolute concentrations of POPs were detected, their profiles varied, being likely related to feeding and migration patterns of each species. The current study provides important baseline data for future monitoring of POPs in Antarctica.

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

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

Complex rice systems to improve rice yield and yield stability in the face of variable weather conditions
Khumairoh, Uma ; Lantinga, Egbert A. ; Schulte, Rogier P.O. ; Suprayogo, Didik ; Groot, Jeroen C.J. - \ 2018
Scientific Reports 8 (2018)1. - ISSN 2045-2322

Extreme weather events and pest outbreaks decrease rice yields and increase their variability, presenting challenges for the agricultural agenda to increase rice productivity and yield stability in Asia. The integration of azolla, fish and ducks has been shown to create robust systems that maintain high yields under heavy rainfall, but no clear evidence exists that rice yields in these systems are stable across locations and throughout time under divergent weather conditions. We show that the introduction of additional elements into the rice cropping system enhanced the adaptive capacity to extreme weather events across four locations and three cropping cycles. The complex system showed both static and dynamic stability, and had the highest reliability index, thereby outperforming the conventional and organic monoculture systems. The complex rice system design provides a promising example for resilience towards the impacts of climate change on rice production and for safeguarding food security in Asia and beyond.

UAV based soil salinity assessment of cropland
Ivushkin, Konstantin ; Bartholomeus, Harm ; Bregt, Arnold K. ; Pulatov, Alim ; Franceschini, Marston H.D. ; Kramer, Henk ; Loo, Eibertus N. van; Jaramillo Roman, Viviana ; Finkers, Richard - \ 2018
Geoderma (2018). - ISSN 0016-7061 - 11 p.
Hyperspectral - LiDAR - Quinoa - Remote sensing - Soil salinity - Thermography - UAV

Increased soil salinity is a significant agricultural problem that decreases yields for common agricultural crops. Its dynamics require cost and labour effective measurement techniques and widely acknowledged methods are not present yet. We investigated the potential of Unmanned Aerial Vehicle (UAV) remote sensing to measure salt stress in quinoa plants. Three different UAV sensors were used: a WIRIS thermal camera, a Rikola hyperspectral camera and a Riegl VUX-SYS Light Detection and Ranging (LiDAR) scanner. Several vegetation indices, canopy temperature and LiDAR measured plant height were derived from the remote sensing data and their relation with ground measured parameters like salt treatment, stomatal conductance and actual plant height is analysed. The results show that widely used multispectral vegetation indices are not efficient in discriminating between salt affected and control quinoa plants. The hyperspectral Physiological Reflectance Index (PRI) performed best and showed a clear distinction between salt affected and treated plants. This distinction is also visible for LiDAR measured plant height, where salt treated plants were on average 10 cm shorter than control plants. Canopy temperature was significantly affected, though detection of this required an additional step in analysis – Normalised Difference Vegetation Index (NDVI) clustering. This step assured temperature comparison for equally vegetated pixels. Data combination of all three sensors in a Multiple Linear Regression model increased the prediction power and for the whole dataset R2 reached 0.46, with some subgroups reaching an R2 of 0.64. We conclude that UAV borne remote sensing is useful for measuring salt stress in plants and a combination of multiple measurement techniques is advised to increase the accuracy.

Impacto de las variables ambientales en los niveles de PCDD/F y dl-PCB en la leche de la región agrícola de Chile
Pizarro-Aránguiz, Nicolás ; García-Mendoza, Diego ; Muñoz, Rubén ; San Martín, Betty ; Morales, Rodrigo - \ 2018
Ciencia e Investigacion Agraria 45 (2018)2. - ISSN 0304-5609 - p. 109 - 119.
Dioxin-like polychlorinated biphenyls - Environmental variables - Food contamination - Persistent organic pollutants - Polychlorinated dibenzo-p-dioxins - Polychlorinated dibenzofurans

According to a One Health perspective, the importance of persistent organic pollutants (POPs) must be assessed because of their impact on the environment, food chain and human health. However, information on these toxic compounds is limited in Latin America and the Caribbean region. Chile is no exception; therefore, this work aimed to explain previously reported dioxin levels in cow-milk samples by utilizing regression with meteorological/geographical data that were collected over a three-year survey. To accomplish this aim, a stepwise general multiple regression analysis was carried out for polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs), and dioxin-like polychlorinated biphenyls (dl-PCBs). The best statistical adjustments were achieved only for highly present congeners. Regarding PCDD/F congeners, the most relevant and significant (P <0.05) factors were the year (mostly a negative coefficient), the season, and the hectares affected by forest fires. In the case of dl-PCB congeners, there was a clear, positive relationship with the geographic parameter (UTM), and this result was consistent with previous findings that dl-PCB congeners show a trend with latitude. In contrast, wind speed was a significant negative coefficient for dl-PCBs. Despite existing knowledge on pollutant levels in milk, this study is relevant to better understand these findings in the Latin America and Caribbean regions.

Data from: Increased transgenerational epigenetic variation, but not predictable epigenetic variants, after environmental exposure in two apomictic dandelion lineages
Preite, Veronica ; Oplaat, Carla ; Biere, Arjen ; Kirschner, Jan ; Putten, W.H. van der; Verhoeven, Koen J.F. - \ 2018
DNA methylation - stress memory - drought - salicylic acid
DNA methylation is one of the mechanisms underlying epigenetic modifications. DNA methylations can be environmentally induced and such induced modifications can at times be transmitted to successive generations. However, it remains speculative how common such environmentally induced transgenerational DNA methylation changes are and if they persist for more than one offspring generation. We exposed multiple accessions of two different apomictic dandelion lineages of the Taraxacum officinale group (Taraxacum alatum and T. hemicyclum) to drought and salicylic acid (SA) treatment. Using methylation-sensitive amplified fragment length polymorphism markers (MS-AFLPs) we screened anonymous methylation changes at CCGG restriction sites throughout the genome after stress treatments and assessed the heritability of induced changes for two subsequent unexposed offspring generations. Irrespective of the initial stress treatment, a clear buildup of heritable DNA methylation variation was observed across three generations, indicating a considerable background rate of heritable epimutations. Less evidence was detected for environmental effects. Drought stress showed some evidence for accession-specific methylation changes, but only in the exposed generation and not in their offspring. By contrast, SA treatment caused an increased rate of methylation change in offspring of treated plants. These changes were seemingly undirected resulting in increased transgenerational epigenetic variation between offspring individuals, but not in predictable epigenetic variants. While the functional consequences of these MS-AFLP-detected DNA methylation changes remain to be demonstrated, our study shows that (1) stress-induced transgenerational DNA methylation modification in dandelions is genotype and context-specific; and (2) inherited environmental DNA methylation effects are mostly undirected and not targeted to specific loci.
Tracking the Transport of Silver Nanoparticles in Soil : a Saturated Column Experiment
Mahdi, Karrar N.M. ; Peters, Ruud ; Ploeg, Martine van der; Ritsema, Coen ; Geissen, Violette - \ 2018
Water Air and Soil Pollution 229 (2018)10. - ISSN 0049-6979
Leaching - Silver nanoparticles - Soil - Transport

Silver nanoparticles (AgNPs) can enter the environment when released from products containing them. As AgNPs enter soil, they are often retained in the soil profile and/or leached to the groundwater. This research assessed the transport of AgNPs in their “particle form” through the soil profile using a series of columns. Three soil types were put into soil columns: LSH (loam with high organic matter (OM)), LSL (loam with low OM), and Sand (no OM). The results showed that AgNP transport and retention in soil as well as particle size changes are affected by soil organic matter (OM) and the cation exchange capacity (CEC) of soil. OM affected the transport and retention of AgNPs. This was evident in the LSH columns where the OM concentration was the highest and the AgNP content the lowest in the soil layers and in the effluent water. The highest transported AgNP content was detected in the Sand columns where OM was the lowest. CEC had an impact on the particle size of the AgNPs that were retained in the soil layers. This was clear in columns packed with high CEC-containing soils (LSL and LSH) where AgNP particle size decreased more substantially than in the columns packed with sand. However, the decrease in AgNP sizes in the effluent water was less than the decrease in particle size of AgNPs transported through but retained in the soil. This means that the AgNPs that reached the effluent were transported directly from the first layer through the soil macropores. This work highlights the ability to track AgNPs at low concentrations (50 μg kg−1) and monitor the changes in particle size potential as the particles leach through soil all of which increases our knowledge about AgNP transport mechanisms in porous media.

Identifying anti-HSV compounds from unrelated plants using NMR and LC–MS metabolomic analysis
Prinsloo, Gerhard ; Vervoort, Jacques - \ 2018
Metabolomics 14 (2018)10. - ISSN 1573-3882
Anti-viral - Chlorogenic acids - CMV - HIV - HSV - Metabolomics

Introduction: Plants have been used to treat various ailments and diseases, including viral infections. Often activity is reported after screening plants traditionally used, without identifying the active principles. Objectives: This study investigated the use of metabolomics to identify common compound groups or compounds from unrelated plants, but with similar reported biological activity. Plants with anti-viral activities against Herpes Simplex Virus (HSV), Cytomegalovirus (CMV) and Human Immunodeficiency Virus (HIV) were collected and analysed. A few non-active plants, with no reported anti-viral activity were included as control samples. Methods: 1H-NMR and LC–MS metabolomic analysis were conducted, to determine the chemical similarity between plants with similar activity using SIMCA and XCMS online. Results: Plants with anti-HSV, anti-HIV and anti-CMV activity, presented specific clusters, with the non-active samples separating from the active samples. The anti-HSV group presented a clear contribution plot and chlorogenic acid was identified by NMR. LC–MS metabolomic analysis confirmed the NMR results and furthermore identified several chlorogenic acid isomers including the main substructures of chlorogenic acids. Conclusion: Metabolomic analysis on unrelated plants with similar activity can be used to identify the active compound groups or compounds, thereby eliminating the need for screening of plants to determine biological activity, additionally providing information on possible active principles. The two analytical methods identified chlorogenic acids and its building blocks as common and important compounds within plants with anti-HSV activity. Intensified research on plants containing chlorogenic acids should be the focus of future research for development of accessible anti-HSV treatments.

Sustainable development goal 2: Improved targets and indicators for agriculture and food security
Gil, Juliana Dias Bernardes ; Reidsma, Pytrik ; Giller, Ken ; Todman, Lindsay ; Whitmore, Andrew ; Ittersum, Martin van - \ 2018
Ambio (2018). - ISSN 0044-7447 - 14 p.
The pursuit of global food security and agricultural sustainability, the dual aim of the second sustainable development goal (SDG-2), requires urgent and concerted action from developing and developed countries. This, in turn, depends on clear and universally applicable targets and indicators which are partially lacking. The novel and complex nature of the SDGs poses further challenges to their implementation on the ground, especially in the face of interlinkages across SDG objectives and scales. Here we review the existing SDG-2 indicators, propose improvements to facilitate their operationalization, and illustrate their practical implementation in Nigeria, Brazil and the Netherlands. This exercise provides insights into the concrete actions needed to achieve SDG-2 across contrasting development contexts and highlights the challenges of addressing the links between targets and indicators within and beyond SDG-2. Ultimately, it underscores the need for integrated policies and reveals opportunities to leverage the fulfillment of SDG-2 worldwide.
A systematic review of research on biodiversity in European livestock systems
Kok, A. ; Boer, I.J.M. de; Ripoll Bosch, R. - \ 2018
In: Book of Abstracts of the 69th Annual Meeting of the European Federation of Animal Science. - Wageningen Academic Publishers (EAAP Book of Abstracts ) - ISBN 9789086863235 - p. 342 - 342.
The decline of biodiversity is a major concern to scientists, society, and policy makers in the European union (EU). The EU Biodiversity Strategy (2010) aims to halt the loss of biodiversity in the EU by 2020. One target to reach this aim is to increase the contribution of agriculture to maintain and enhance biodiversity. According to reports, however, no significant overall progress has been made to meet this target. Moreover, agriculture is both reported to reduce and to enhance biodiversity. To enhance biodiversity in agriculture, we need to understand how biodiversity is measured in the existing studies, and to map relations between agricultural land use and biodiversity. We aimed to
(1) review indicators used in science to measure biodiversity in EU livestock systems, and (2) to review described effects of livestock on biodiversity. We conducted a systematic review in Scopus and Web of Science. The search for research articles that assessed impacts of livestock on biodiversity yielded 857 articles after deduplication, which was narrowed down to 163 relevant articles. Species abundance and species diversity were commonly used state indicators of biodiversity across scales. Modelling studies also used aggregated indicators with biodiversity values that were directly linked to land use. Most studies focussed on the impact of grazing ruminants on biodiversity, either for food production or nature conservation purposes. Pigs and poultry were mainly studied in relation to local ammonia emissions. Only few studies considered impacts of land use for feed production on biodiversity. We argue that the traditional pressure-state-response framework to categorize indicators of biodiversity does not provide clear actions to enhance biodiversity in agriculture. Instead, we propose the use of comparators (e.g. grazing intensity levels) in relation with state measures of biodiversity. This review can help to identify commonly used indicators of biodiversity, and provide insight in quantitative relations between agricultural land use and biodiversity.
Deleterious alleles in the context of domestication, inbreeding, and selection
Bosse, Mirte ; Megens, Hendrik-Jan ; Derks, Martijn F.L. ; Cara, Ángeles M.R. de; Groenen, Martien A.M. - \ 2018
Evolutionary Applications (2018). - ISSN 1752-4563
deleterious alleles - domestication - genetic load - inbreeding - selection

Each individual has a certain number of harmful mutations in its genome. These mutations can lower the fitness of the individual carrying them, dependent on their dominance and selection coefficient. Effective population size, selection, and admixture are known to affect the occurrence of such mutations in a population. The relative roles of demography and selection are a key in understanding the process of adaptation. These are factors that are potentially influenced and confounded in domestic animals. Here, we hypothesize that the series of events of bottlenecks, introgression, and strong artificial selection associated with domestication increased mutational load in domestic species. Yet, mutational load is hard to quantify, so there are very few studies available revealing the relevance of evolutionary processes. The precise role of artificial selection, bottlenecks, and introgression in further increasing the load of deleterious variants in animals in breeding and conservation programmes remains unclear. In this paper, we review the effects of domestication and selection on mutational load in domestic species. Moreover, we test some hypotheses on higher mutational load due to domestication and selective sweeps using sequence data from commercial pig and chicken lines. Overall, we argue that domestication by itself is not a prerequisite for genetic erosion, indicating that fitness potential does not need to decline. Rather, mutational load in domestic species can be influenced by many factors, but consistent or strong trends are not yet clear. However, methods emerging from molecular genetics allow discrimination of hypotheses about the determinants of mutational load, such as effective population size, inbreeding, and selection, in domestic systems. These findings make us rethink the effect of our current breeding schemes on fitness of populations.

Indicators of resilience during the transition period in dairy cows : A case study
Dixhoorn, I.D.E. van; Mol, R.M. de; Werf, J.T.N. van der; Mourik, S. van; Reenen, C.G. van - \ 2018
Journal of Dairy Science (2018). - ISSN 0022-0302 - 12 p.
behavior - dairy cow - dynamic indicator - resilience - transition period
The transition period is a demanding phase in the life of dairy cows. Metabolic and infectious disorders frequently occur in the first weeks after calving. To identify cows that are less able to cope with the transition period, physiologic or behavioral signals acquired with sensors might be useful. However, it is not yet clear which signals or combination of signals and which signal properties are most informative with respect to disease severity after calving. Sensor data on activity and behavior measurements as well as rumen and ear temperature data from 22 dairy cows were collected during a period starting 2 wk before expected parturition until 6 wk after parturition. During this period, the health status of each cow was clinically scored daily. A total deficit score (TDS) was calculated based on the clinical assessment, summarizing disease length and intensity for each cow. Different sensor data properties recorded during the period before calving as well as the period after calving were tested as a predictor for TDS using univariate analysis of covariance. To select the model with the best combination of signals and signal properties, we quantified the prediction accuracy for TDS in a multivariate model. Prediction accuracy for TDS increased when sensors were combined, using static and dynamic signal properties. Statistically, the most optimal linear combination of predictors consisted of average eating time, variance of daily ear temperature, and regularity of daily behavior patterns in the dry period. Our research indicates that a combination of static and dynamic sensor data properties could be used as indicators of cow resilience.
Unravelling the relative roles of physical processes in modelling the life cycle of a warm radiation fog
Steeneveld, G.J. ; Bode, M. de - \ 2018
Quarterly Journal of the Royal Meteorological Society (2018). - ISSN 0035-9009
This study evaluates the representation of the life cycle of a radiation fog case study observed at the Cabauw 213‐m tower (Netherlands) facility by the WRF single‐column model, and aims to advance the understanding of the model behaviour, which will assist to set research priorities for the future. First an ensemble of sixteen WRF configurations that vary in parameterization schemes for the PBL, land surface, longwave radiation, and microphysics are evaluated. Next, we perform a sensitivity study to examine which physical process is most crucial in modelling the fog, i.e. soil heat diffusivity, the CO2 concentration (representing clear‐sky longwave radiation), the vapour diffusion to droplets, and the turbulent mixing. Subsequently, we study whether these perturbations can improve the model representation, and on the other hand whether they can explain the model behaviour of the sixteen ensemble members. Results are displayed in process diagrams. We find that behaviour of the ensemble can be explained by a variations in the soil heat diffusivity and the turbulent mixing. However their sensitivities orient in approximately the same direction, and as such, errors in the formulation of the boundary‐layer scheme can be hidden by compensating errors in the land‐surface scheme. In addition, we find that simultaneous perturbations in the soil heat diffusivity and turbulent mixing do not result in the same results as superpositioning of the individual perturbations.
Mechanisms of allergen-specific immunotherapy : Diverse mechanisms of immune tolerance to allergens
Głobińska, Anna ; Boonpiyathad, Tadech ; Satitsuksanoa, Pattraporn ; Kleuskens, Mirelle ; Veen, Willem van de; Sokolowska, Milena ; Akdis, Mübeccel - \ 2018
Annals of Allergy, Asthma and Immunology 121 (2018)3. - ISSN 1081-1206 - p. 306 - 312.

Objective: The aim of this review is to provide an overview of the current knowledge on the mechanisms of allergen immunotherapy based on the recent publications and clinical trials. Data sources: PubMed literature review. Study selections: In this review, we focus on diverse mechanisms of AIT and provide an insight into alternative routes of administration. Additionally, we review and discuss the most recent studies investigating potential biomarkers and highlight their role in clinical settings. Results: Successful allergen-specific immunotherapy (AIT) induces the reinstatement of tolerance toward allergens and represents a disease-modifying treatment. In the last decades, substantial progress in understanding the mechanisms of AIT has been achieved. Establishment of long-term clinical tolerance to allergens engages a complex network of interactions, modulating the functions of basophils, mast cells, allergen-specific regulatory T and B cells, and production of specific antibodies. The reduction of symptoms and clinical improvement is achieved by skewing the immune response away from allergic inflammation. Conclusion: Although the complex nature of AIT mechanisms is becoming more clear, the need to discover reliable biomarkers to define patients likely to respond to the treatment is emerging.

Differences in infectivity and pathogenicity of two Plantago asiatica mosaic virus isolates in lilies
Tanaka, Masashi ; Verbeek, Martin ; Takehara, Miki ; Pham, Khanh ; Lemmers, Miriam ; Slootweg, Casper ; Arie, Tsutomu ; Komatsu, Ken - \ 2018
European Journal of Plant Pathology (2018). - ISSN 0929-1873
Environmental effects - Infectivity - Necrosis - Ornamental lily - Pathogenicity - Plantago asiatica mosaic virus

Plantago asiatica mosaic virus (PlAMV) is a member of the genus Potexvirus in the family Alphaflexiviridae and has been isolated from a variety of host plants. In particular, PlAMV isolates from ornamental lilies (Lilium spp.) cause necrotic symptoms in these plants, which significantly reduces their commercial value. However, it has not been clear whether PlAMV isolates from other host plants differ in their infectivity and/or pathogenicity to ornamental lilies, and whether growth conditions affect infectivity and pathogenicity. In this study, we inoculated an edible lily species (Lilium leichtlinii) and seven varieties of ornamental lilies with two PlAMV isolates, an isolate from ornamental lily (PlAMV-OL) and an isolate from edible lily (PlAMV-Li1). We found that PlAMV-OL showed higher infection rates and exhibited necrotic symptoms more frequently in lilies than PlAMV-Li1. Moreover, we observed higher infection rates of PlAMV-OL in open field than in greenhouse, and higher rates of necrotic symptoms in autumn test than in spring test, suggesting that growth conditions and season affect infectivity and pathogenicity of PlAMV in lilies. Our study would provide important information for estimating the risk of necrotic disease caused by PlAMV, as well as for cultivation management preventing the occurrence of the disease.

Data from: Increased transgenerational epigenetic variation, but not predictable epigenetic variants, after environmental exposure in two apomictic dandelion lineages
Preite, Veronica ; Oplaat, Carla ; Biere, Arjen ; Kirschner, Jan ; Putten, W.H. van der; Verhoeven, Koen J.F. - \ 2018
DNA methylation - stress memory - drought - salicylic acid - Taraxacum officinale
DNA methylation is one of the mechanisms underlying epigenetic modifications. DNA methylations can be environmentally induced and such induced modifications can at times be transmitted to successive generations. However, it remains speculative how common such environmentally induced transgenerational DNA methylation changes are and if they persist for more than one offspring generation. We exposed multiple accessions of two different apomictic dandelion lineages of the Taraxacum officinale group (Taraxacum alatum and T. hemicyclum) to drought and salicylic acid (SA) treatment. Using methylation-sensitive amplified fragment length polymorphism markers (MS-AFLPs) we screened anonymous methylation changes at CCGG restriction sites throughout the genome after stress treatments and assessed the heritability of induced changes for two subsequent unexposed offspring generations. Irrespective of the initial stress treatment, a clear buildup of heritable DNA methylation variation was observed across three generations, indicating a considerable background rate of heritable epimutations. Less evidence was detected for environmental effects. Drought stress showed some evidence for accession-specific methylation changes, but only in the exposed generation and not in their offspring. By contrast, SA treatment caused an increased rate of methylation change in offspring of treated plants. These changes were seemingly undirected resulting in increased transgenerational epigenetic variation between offspring individuals, but not in predictable epigenetic variants. While the functional consequences of these MS-AFLP-detected DNA methylation changes remain to be demonstrated, our study shows that (1) stress-induced transgenerational DNA methylation modification in dandelions is genotype and context-specific; and (2) inherited environmental DNA methylation effects are mostly undirected and not targeted to specific loci.
Unravelling the mechanisms underlying health and productivity promoting agricultural practices by fine-mapping rhizosphere communities
Harkes, Paula - \ 2018
The impact of soil pathogens on crops has been studied for decades as if this was a multitude of bilateral interactions. For a long time, it has been realised that crops and soil-borne pathogens are interacting in a densely inhabited environment, the rhizosphere. A more versatile approach was hampered because of technical limitations: it was just impracticable to take major and highly diverse organismal groups such as bacteria, fungi and protists into consideration. Here we monitored the (plant-parasitic) nematode community in the rhizosphere of barley under three distinct soil management regimes, for two developmental stages of the crop, in two different locations. Total DNA and RNA was isolated from rhizosphere samples - 104 rhizosphere samples, for each sample DNA and cDNA was analysed separately - using home-made extraction and purification protocols. Targeted (ribosomal DNA) Illumina MiSeq sequencing was used to characterise the nematode, protist, fungal and bacterial community. First of all, very significant location effects were observed for all four organismal groups. Superimposed on the location effects, clear effects of organic, integrated and conventional soil management could be pinpointed. To the best of our knowledge, this is the first time four major key organismal groups players of the soil food web are simultaneously mapped in order to obtain insight in the effects of soil management practices on plant-parasitic nematodes taking a major part of the rhizobiome into consideration.
Madeiran Arabidopsis thaliana reveals ancient long-range colonization and clarifies demography in Eurasia
Fulgione, Andrea ; Koornneef, Maarten ; Roux, Fabrice ; Hermisson, Joachim ; Hancock, Angela M. - \ 2018
Molecular Biology and Evolution 35 (2018)3. - ISSN 0737-4038 - p. 564 - 574.
Admixture - Arabidopsis thaliana - Demography - Island - Population genetics - Relict

The study of model organisms on islands may shed light on rare long-range dispersal events, uncover signatures of local evolutionary processes, and inform demographic inference on the mainland. Here, we sequenced the genomes of Arabidopsis thaliana samples from the oceanic island of Madeira. These samples include the most diverged worldwide, likely a result of long isolation on the island. We infer that colonization of Madeira happened between 70 and 85 ka, consistent with a propagule dispersal model (of size 10), or with an ecological window of opportunity. This represents a clear example of a natural long-range dispersal event in A. thaliana. Long-term effective population size on the island, rather than the founder effect, had the greatest impact on levels of diversity, and rates of coalescence. Our results uncover a selective sweep signature on the ancestral haplotype of a known translocation in Eurasia, as well as the possible importance of the low phosphorous availability in volcanic soils, and altitude, in shaping early adaptations to the island conditions. Madeiran genomes, sheltered from the complexities of continental demography, help illuminate ancient demographic events in Eurasia. Our data support a model in which two separate lineages of A. thaliana, one originating in Africa and the other from the Caucasus expanded and met in Iberia, resulting in a secondary contact zone there. Although previous studies inferred that the westward expansion of A. thaliana coincided with the spread of human agriculture, our results suggest that it happened much earlier (20-40 ka).

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