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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    Phylogenomic analysis sheds light on the evolutionary pathways towards acoustic communication in Orthoptera
    Song, Hojun ; Béthoux, Olivier ; Shin, Seunggwan ; Donath, Alexander ; Letsch, Harald ; Liu, Shanlin ; McKenna, Duane D. ; Meng, Guanliang ; Misof, Bernhard ; Podsiadlowski, Lars ; Zhou, Xin ; Wipfler, Benjamin ; Simon, Sabrina - \ 2020
    Nature Communications 11 (2020)1. - ISSN 2041-1723

    Acoustic communication is enabled by the evolution of specialised hearing and sound producing organs. In this study, we performed a large-scale macroevolutionary study to understand how both hearing and sound production evolved and affected diversification in the insect order Orthoptera, which includes many familiar singing insects, such as crickets, katydids, and grasshoppers. Using phylogenomic data, we firmly establish phylogenetic relationships among the major lineages and divergence time estimates within Orthoptera, as well as the lineage-specific and dynamic patterns of evolution for hearing and sound producing organs. In the suborder Ensifera, we infer that forewing-based stridulation and tibial tympanal ears co-evolved, but in the suborder Caelifera, abdominal tympanal ears first evolved in a non-sexual context, and later co-opted for sexual signalling when sound producing organs evolved. However, we find little evidence that the evolution of hearing and sound producing organs increased diversification rates in those lineages with known acoustic communication.

    Response of common bean (Phaseolus vulgaris L.) growth to soil contaminated with microplastics
    Meng, Fanrong ; Yang, Xiaomei ; Riksen, Michel ; Xu, Minggang ; Geissen, Violette - \ 2020
    Science of the Total Environment 755 (2020)2. - ISSN 0048-9697
    Biodegradable microplastics - Microplastics - Plant growth - Soil-plant system

    Although concerns surrounding microplastics (MPs) in terrestrial ecosystems have been growing in recent years, little is known about the responses of plant growth to MPs pollution. Here, we conducted a pot experiment in a net house under natural condition by adding two types of MPs, low-density polyethylene (LDPE-MPs) and polylactic acid (PLA) mixed with poly-butylene-adipate-co-terephthalate (PBAT, Bio-MPs), to sandy soil at 5 doses (0.5%, 1.0%, 1.5%, 2.0%, 2.5% ω/ω dry soil weight). The effects of LDPE-MPs and Bio-MPs on common bean (Phaseolus vulgaris L) were tested. Compared to control (no MPs addition), LDPE-MPs showed no significant effects on shoot, root and fruit biomass while ≥1.0% LDPE-MPs showed significant higher specific root nodules (n·g−1 dry root biomass) and only 2.5% LDPE-MPs showed significant higher specific root length (cm·g−1 dry root biomass). 1.0% LDPE-MPs caused significant higher leaf area and 0.5% LDPE-MPs caused significant lower leaf relative chlorophyll content. For Bio-MPs treatment, compared to control, ≥1.5% Bio-MPs showed significant lower shoot and root biomass. ≥2.0% Bio-MPs showed significant lower leaf area and fruit biomass. All Bio-MPs treatments showed significant higher specific root length and specific root nodules as compared to control. The results of the current research show that both MPs induced the responses of common bean growth, and ≥1.5% Bio-MPs exerted stronger effects. Further studies of their ecological impacts on soil-plant systems are urgently needed.

    Highly Stable Perovskite Supercrystals via Oil-in-Oil Templating
    Tang, Yingying ; Gomez, Leyre ; Lesage, Arnon ; Marino, Emanuele ; Kodger, Thomas E. ; Meijer, Janne Mieke ; Kolpakov, Paul ; Meng, Jie ; Zheng, Kaibo ; Gregorkiewicz, Tom ; Schall, Peter - \ 2020
    Nano Letters 20 (2020)8. - ISSN 1530-6984 - p. 5997 - 6004.
    assembly - emulsion-droplet templating - perovskite films - stability - supercrystals

    Inorganic perovskites display an enticing foreground for their wide range of optoelectronic applications. Recently, supercrystals (SCs) of inorganic perovskite nanocrystals (NCs) have been reported to possess highly ordered structure as well as novel collective optical properties, opening new opportunities for efficient films. Here, we report the large-scale assembly control of spherical, cubic, and hexagonal SCs of inorganic perovskite NCs through templating by oil-in-oil emulsions. We show that an interplay between the roundness of the cubic NCs and the tension of the confining droplet surface sets the superstructure morphology, and we exploit this interplay to design dense hyperlattices of SCs. The SC films show strongly enhanced stability for at least two months without obvious structural degradation and minor optical changes. Our results on the controlled large-scale assembly of perovskite NC superstructures provide new prospects for the bottom-up production of optoelectronic devices based on the microfluidic production of mesoscopic building blocks.

    Update: proposed reference sequences for subtypes of hepatitis E virus (species Orthohepevirus A)
    Smith, Donald B. ; Izopet, Jacques ; Nicot, Florence ; Simmonds, Peter ; Jameel, Shahid ; Meng, Xiang Jin ; Norder, Heléne ; Okamoto, Hiroaki ; Poel, Wim H.M. van der; Reuter, Gábor ; Purdy, Michael A. - \ 2020
    Journal of General Virology 101 (2020)7. - ISSN 0022-1317 - p. 692 - 698.
    hepatitis E virus - Hepeviridae - Orthohepevirus A

    In this recommendation, we update our 2016 table of reference sequences of subtypes of hepatitis E virus (HEV; species Orthohepevirus A, family Hepeviridae) for which complete genome sequences are available (Smith et al., 2016). This takes into account subsequent publications describing novel viruses and additional proposals for subtype names; there are now eight genotypes and 36 subtypes. Although it remains difficult to define strict criteria for distinguishing between virus subtypes, and is not within the remit of the International Committee on Taxonomy of Viruses (ICTV), the use of agreed reference sequences will bring clarity and stability to researchers, epidemiologists and clinicians working with HEV.

    Morphological and reproductive responses of coastal pioneer sedge vegetation to inundation intensity
    Li, Shi Hua ; Ge, Zhen Ming ; Tan, Li Shan ; Hu, Meng Yao ; Li, Ya Lei ; Li, Xiu Zhen ; Ysebaert, Tom - \ 2020
    Estuarine Coastal and Shelf Science 244 (2020). - ISSN 0272-7714
    Intraspecific traits - Inundation stresses - Phenotypic plasticity - Pioneer plant - Reproductive strategy - Salt marsh

    Coastal plants have unique adaptability to cope with strong hydrological stresses in tidal wetlands. A fundamental understanding of the establishment and maintenance of coastal plants is needed for conservation and restoration. In the Yangtze Estuary, the plasticity of the morphological and reproductive traits of a pioneer Scirpus species (sedge), in terms of phenotypic growth, biomass allocation, and sexual and asexual reproductive traits, was investigated with increasing flooding intensity (elevation gradient) in a tidal flat. The varying response extents (thresholds) of plant zonation and morphological and reproductive traits to multiscale environmental heterogeneity were also assessed. Our results showed that plant colonization and performance at coastal frontiers are sensitive to the microtopography of elevation and reflect the ecological adaptability at both the landscape and individual scales. Sedge species typically exhibit morphological and reproductive flexibility across the inundation intensity. The plants allocated more biomass to belowground tissues in response to decreasing elevation. The elevation thresholds for the yield of reproductive organs were higher (2.38–2.50 m based on the local Wusong datum) than those for morphology (2.05–2.14 m). The thresholds for the yield of asexual reproductive organs shifted to a lower elevation by approximately 0.15 m relative to that of the sexual reproductive organs. The increasing corm: spike ratios of plants with longer inundation durations also indicated this reproductive plasticity. This study revealed that the combination of morphological and reproductive responses of pioneer sedges contributed to survival and colonization at the foremost coastal flat. Our results are useful for developing restoration strategies for the native Scirpus species on China's coast.

    Biofuel burning and human respiration bias on satellite estimates of fossil fuel CO2emissions
    Ciais, P. ; Wang, Y. ; Andrew, R. ; Bréon, F.M. ; Chevallier, F. ; Broquet, G. ; Nabuurs, G.J. ; Peters, G. ; Mcgrath, M. ; Meng, W. ; Zheng, B. ; Tao, S. - \ 2020
    Environmental Research Letters 15 (2020)7. - ISSN 1748-9318
    biofuels - fossil fuel emissions - satellites

    The satellites that have been designed to support the monitoring of fossil fuel CO2 emissions aim to systematically measure atmospheric CO2 plumes generated by intense emissions from large cities, power plants and industrial sites. These data can be assimilated into atmospheric transport models in order to estimate the corresponding emissions. However, plumes emitted by cities and powerplants contain not only fossil fuel CO2 but also significant amounts of CO2 released by human respiration and by the burning of biofuels. We show that these amounts represent a significant proportion of the fossil fuel CO2 emissions, up to 40% for instance in cities of Nordic countries, and will thus leave some ambiguity in the retrieval of fossil fuel CO2 emissions from satellite concentration observations. Auxiliary information such as biofuel use statistics and radiocarbon measurement could help reduce the ambiguity and improve the framework of monitoring fossil fuel CO2 emissions from space.

    Characteristics of circular rna expression profiles of porcine granulosa cells in healthy and atretic antral follicles
    Meng, Li ; Teerds, Katja ; Tao, Jian ; Wei, Hengxi ; Jaklofsky, Marcel ; Zhao, Zhihong ; Liang, Yaodi ; Li, Li ; Wang, Chi Chiu ; Zhang, Shouquan - \ 2020
    International Journal of Molecular Sciences 21 (2020)15. - ISSN 1661-6596 - p. 1 - 25.
    Antral follicular atresia - CircRNA expression profiles - Granulosa cell apoptosis

    Circular RNAs (circRNAs) are thought to play essential roles in multiple biological processes, including apoptosis, an important process in antral follicle atresia. We aimed to investigate the potential involvement of circRNAs in granulosa cell apoptosis and thus antral follicle atresia. CircRNA expression profiles were generated from porcine granulosa cells isolated from healthy antral (HA) and atretic antral (AA) follicles. Over 9632 circRNAs were identified, of which 62 circRNAs were differentially expressed (DE-circRNAs). Back-splicing, RNase R resistance, and stability of DE-circRNAs were validated, and miRNA binding sites and related target genes were predicted. Two exonic circRNAs with low false discovery rate (FDR) high fold change, miRNA binding sites, and relevant biological functions—circ_CBFA2T2 and circ_KIF16B—were selected for further characterization. qRT-PCR and linear regression analysis confirmed expression and correlation of the targeted genes—the antioxidant gene GCLC (potential target of circ_CBFA2T2) and the apoptotic gene TP53 (potential target of circ_KIF16B). Increased mRNA content of TP53 in granulosa cells of AA follicles was further confirmed by strong immunostaining of both p53 and its downstream target pleckstrin homology like domain family a member 3 (PHLDA3) in AA follicles compared to negligible staining in granulosa cells of HA follicles. Therefore, we concluded that aberrantly expressed circRNAs presumably play a potential role in antral follicular atresia.

    A systems analysis of microplastic pollution in Laizhou Bay, China
    Teng, Jia ; Zhao, Jianmin ; Zhang, C. ; Cheng, Bo ; Koelmans, A.A. ; Wu, Di ; Gao, Meng ; Sun, Xiyan ; Wang, Qing - \ 2020
    Science of the Total Environment 745 (2020). - ISSN 0048-9697
    Microplastic contamination is attracting increasing attention worldwide. In this study, the patterns of microplastic contamination in surface water and sediment from 58 sites, and living fish from 31 sites were investigated in a semi-closed bay (Laizhou Bay, China). Microplastics in Laizhou Bay were pervasively distributed, particularly in the form of fibers. Microplastic abundance exhibited no significant differences among regions in either surface waters or sediments, indicating multiple sources of microplastics pollution in the bay. Spatial hotspot (Getis-Ord Gi*) analysis demonstrated that microplastic pollution was mainly concentrated in the Laizhou-Weifang area, which in turn was mainly affected by ocean current dynamics. Although the spatial distribution of microplastics in sediments was different from surface water, it was also affected by geology, hydrogeology, and anthropogenic activities. The most common polymer in the surface waters was polyethylene terephthalate (PET), while cellophane (CP) was the most frequently observed polymer in sediment, suggesting different sinking behaviors of these microplastics. The proportion of low-density microplastics (PE and PP) in surface water was approximately 19.9%, but these microplastics accounted for only approximately 1.7% in the sediment, suggesting that low-density microplastic particles preferentially migrate to open sea. There were significant differences in shape, size and polymer type of the microplastics among surface water, sediment and biota (p < 0.05). Cluster analysis suggested that the Gudong, Yellow River Estuary and Laizhou-Weifang regions are three sources of microplastics, which might originate from river input, plastic recycling and marine raft aquaculture. Furthermore, microplastic particle diversity was greater in sediment at offshore sites, suggesting that these sites receive microplastics from multiple sources. Our results characterize the microplastic pollution pattern, clarify the possible transfer mechanisms between different environmental media, and will provide important information for risk evaluation and pollution control in this area.
    Gut dysbacteriosis and intestinal disease: mechanism and treatment
    Meng, X. ; Zhang, G. ; Cao, H. ; Yu, D. ; Fang, X. ; Vos, W.M. de; Wu, H. - \ 2020
    Journal of Applied Microbiology (2020). - ISSN 1364-5072
    gut microbiome - immune response - intestinal diseases - prebiotics - probiotics

    The gut microbiome functions like an endocrine organ, generating bioactive metabolites, enzymes or small molecules that can impact host physiology. Gut dysbacteriosis is associated with many intestinal diseases including (but not limited to) inflammatory bowel disease, primary sclerosing cholangitis-IBD, irritable bowel syndrome, chronic constipation, osmotic diarrhoea and colorectal cancer. The potential pathogenic mechanism of gut dysbacteriosis associated with intestinal diseases includes the alteration of composition of gut microbiota as well as the gut microbiota–derived signalling molecules. The many correlations between the latter and the susceptibility for intestinal diseases has placed a spotlight on the gut microbiome as a potential novel target for therapeutics. Currently, faecal microbial transplantation, dietary interventions, use of probiotics, prebiotics and drugs are the major therapeutic tools utilized to impact dysbacteriosis and associated intestinal diseases. In this review, we systematically summarized the role of intestinal microbiome in the occurrence and development of intestinal diseases. The potential mechanism of the complex interplay between gut dysbacteriosis and intestinal diseases, and the treatment methods are also highlighted.

    Factors affecting the creaming of human milk
    Meng, F. ; Uniacke-Lowe, T. ; Lanfranchi, E. ; Meehan, G. ; O'Shea, C.A. ; Fox, P.F. ; Huppertz, T. ; Ryan, C.A. ; Kelly, A.L. - \ 2020
    International Dairy Journal 108 (2020). - ISSN 0958-6946

    The creaming properties of human milk have not been widely studied to date, and a mechanism for this phenomenon is not known. Here, the natural creaming of human milk, as affected by temperature and pre-treatments, was studied using dynamic light-scattering. The creaming rate of human milk increased with temperature in the range 5 °C–40 °C. Freezing human milk at −20 °C and thawing at room temperature had little influence on creaming. Compared with bovine milk, human milk showed a faster creaming rate at 40 °C, but a slower rate at 5 °C, suggesting a lack of cold agglutination; the mechanisms of creaming were also shown to differ in response to heat treatment. This study expands the current knowledge on milk creaming, and may have potential application to storage and handling of human milk in hospitals or homes, therefore supporting optimal nutrition of infants.

    Litter cover promotes biocrust decomposition and surface soil functions in sandy ecosystem
    Wu, Gao Lin ; Zhang, Meng Qi ; Liu, Yu ; López‐Vicente, Manuel - \ 2020
    Geoderma 374 (2020). - ISSN 0016-7061
    Ecological restoration - Sandy ecosystem - Soil crust - Soil nutrient - Soil organic matter - Soil particle size

    Ecological restoration of sandy inland ecosystems is important for achieving global sustainability. In the world's semi-arid regions, soil crusts play crucial roles in maintaining ecosystem functioning. However, the true extent of soil quality improvement during the development of crusts is an issue not solved. In this study, four development stages of natural soil crusts, i.e., physical crusts (PC), biocrusts (BC), litter covered biocrusts (LBC) and litter crusts (LC) were selected in a semi-arid sandy ecosystem, along with a bare sandy land (BSL) as control area, to evaluate soil physicochemical properties at different soil depths. The coverage of litter (mainly leaves of Populus simonii) increased soil moisture and reduced soil bulk density. Compared with BC, the content of total soil organic matter (SOM) decreased in LBC by 13.83% and increased in LC by 36.57%. In contrast with BC, LC promoted a significant increase in soil nutrients, such as total nitrogen (30.30%), total phosphorus (46.89%) and available potassium (34.40%) in the topsoil layer (0–2 cm). Besides, LC contained higher clay and silt contents (10.47% and 29.81%) and lower sand content (−1.02%) than BC. In the 0–10 cm soil layer, the D (fractal dimension of the soil particle size distribution) of LC was the largest, with a value 5.71%, 6.1%, 2.44% and 0.93% higher than D in BSL, PC, BC and LBC, respectively. These findings reveal that litter covering facilitate the disintegration of BC, which further forms LC, and these processes clearly promote the enhancement of soil quality under sandy semi-arid conditions. Our findings are particularly important for predicting the transformation processes of sandy soil crusts and are of interest in ecological restoration programs.

    Neighbourhood fast food exposure and consumption: the mediating role of neighbourhood social norms
    Rongen, Sofie Van; Poelman, Maartje P. ; Thornton, Lukar ; Abbott, Gavin ; Lu, Meng ; Kamphuis, Carlijn B.M. ; Verkooijen, Kirsten ; Vet, Emely De - \ 2020
    International journal of behavioral nutrition and physical activity 17 (2020)1. - ISSN 1479-5868
    Background: The association between the residential fast food environment and diet has gained growing attention. However, why the food environment affects food consumption is under-examined. This study aimed to investigate neighbourhood social norms with respect to fast food consumption as a potential mediating pathway between residential fast food outlet exposure and residents’ fast food consumption.

    Methods: A correlational study was conducted in which a nationwide sample of 1038 respondents living across The Netherlands completed a survey. Respondents reported their fast food consumption (amount/week) as well as perceived descriptive and injunctive norms regarding fast food consumption in their neighbourhood. Fast food outlet exposure was measured by the average count of fast food outlets within a 400 m walking distance buffer around the zip-codes of the respondents, using a retail outlet database. Regression models were used to assess associations between residential fast food outlet exposure, fast food consumption, and social norm perceptions, and a bootstrapping procedure was used to test the indirect -mediation- effect. Separate analyses were performed for descriptive norms and injunctive norms.

    Results: There was no overall or direct association between residential fast food outlet exposure and residents’ fast food consumption. However, fast food outlet exposure was positively associated with neighbourhood social norms (descriptive and injunctive) regarding fast food consumption, which in turn were positively associated with the odds of consuming fast food. Moreover, results of the bootstrapped analysis provided evidence of indirect effects of fast food outlet exposure on fast food consumption, via descriptive norms and injunctive norms.

    Conclusions: In neighbourhoods with more fast food outlets, residents were more likely to perceive fast food consumption in the neighbourhood as more common and appropriate. In turn, stronger neighbourhood social norms were associated with higher fast food consumption. Acknowledging the correlational design, this study is the first that implies that neighbourhood social norms may be a mediating pathway in the relation between the residential fast food environment and fast food consumption. Future research may examine the role of neighbourhood social norms in other contexts and explore how the changing food environment may shift our consumption norms.
    Valuation of Wetland Ecosystem Services in National Nature Reserves in China’s Coastal Zones
    Li, Xiaowei ; Yu, Xiubo ; Hou, Xiyong ; Liu, Yubin ; Li, Hui ; Zhou, Yangming ; Xia, Shaoxia ; Liu, Yu ; Duan, Houlang ; Wang, Yuyu ; Dou, Yuehan ; Yang, Meng ; Zhang, Li - \ 2020
    Sustainability 12 (2020)8. - ISSN 2071-1050
    Wetlands provide ecosystem services for regional development, and, thus, have considerable economic value. In this study, a combination of evaluation methods was carried out to evaluate the wetland ecosystem services provided by national nature reserves in 11 coastal provinces/municipalities in China. We constructed a literature database containing 808observations (over 170 papers) on field-scale research for wetlands in China’s coastal zones. Using this literature database, as well as land use (LU) data, net primary productivity (NPP), and statistical data, and digital elevation model (DEM) data, we established a valuation framework and database for nine important ecosystem services of the 13 wetland types in the study area. After the large-scale academic literature review, the ordinary kriging offered by Geostatistical Analyst tools was used to interpolate the physical dimensions of the unmeasured locations. The results showed that: 1) the wetland ecosystem services in 35 national nature reserves have a total value of 33.168billion USD/year; 2) the values of wetland ecosystem services revealed considerable spatial variability along China’s coastal zones; and 3) assessments provide additional insights into the trade-offs between different ecosystem services and wetland types. The valuation framework and database established in this study can contribute to the mapping of wetland ecosystem services in coastal zones.
    Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation
    Daly, Paul ; Peng, Mao ; Mitchell, Hugh D. ; Kim, Young Mo ; Ansong, Charles ; Brewer, Heather ; Gijsel, Peter de; Lipton, Mary S. ; Markillie, Lye Meng ; Nicora, Carrie D. ; Orr, Galya ; Wiebenga, Ad ; Hildén, Kristiina S. ; Kabel, Mirjam A. ; Baker, Scott E. ; Mäkelä, Miia R. ; Vries, Ronald P. de - \ 2020
    Environmental Microbiology 22 (2020)3. - ISSN 1462-2912 - p. 1154 - 1166.

    Saprobic fungi, such as Aspergillus niger, grow as colonies consisting of a network of branching and fusing hyphae that are often considered to be relatively uniform entities in which nutrients can freely move through the hyphae. In nature, different parts of a colony are often exposed to different nutrients. We have investigated, using a multi-omics approach, adaptation of A. niger colonies to spatially separated and compositionally different plant biomass substrates. This demonstrated a high level of intra-colony differentiation, which closely matched the locally available substrate. The part of the colony exposed to pectin-rich sugar beet pulp and to xylan-rich wheat bran showed high pectinolytic and high xylanolytic transcript and protein levels respectively. This study therefore exemplifies the high ability of fungal colonies to differentiate and adapt to local conditions, ensuring efficient use of the available nutrients, rather than maintaining a uniform physiology throughout the colony.

    Land use regression models revealing spatiotemporal co-variation in NO2, NO, and O3 in the Netherlands
    Lu, Meng ; Soenario, Ivan ; Helbich, Marco ; Schmitz, Oliver ; Hoek, Gerard ; Molen, Michiel van der; Karssenberg, Derek - \ 2020
    Atmospheric Environment 223 (2020). - ISSN 1352-2310

    Land use regression (LUR) modeling has been applied to study the spatiotemporal patterns of air pollution, which when combined with human space-time activity, is important in understanding the health effects of air pollution. However, most of these studies focus either on the temporal or the spatial domain and do not consider the variability in both space and time. A temporally aggregated model does not reflect the temporal variability caused by traffic and atmospheric conditions and leads to inaccurate estimation of personal exposure. Besides, most studies focus on a single air pollutant (e.g., O3, NO2, or NO). These pollutants have a strong interaction due to photochemical processes. For studying relations between spatial and temporal patterns in these pollutants it is preferable to use a uniform data source and modelling approach which makes comparison of pollution surfaces between pollutants more reliable as they are produced with the same methodology. We developed temporal land use regression models of O3, NO2 and NO to study the co-variability of these pollutants and the relations with typical weather conditions over the year. We use hourly concentrations from the measurement network of the Dutch National Institute for Public Health and the Environment and aggregate them by hour, for weekday/weekend and month, and fit a regression model for each hour of the day. 70 candidate predictors that are known to have a strong relationship with combustion-related emissions are evaluated in the LUR modelling process. For all pollutants, the optimal LUR was identified with 4 predictors and the temporal variability was determined by the explained variance of each temporal model. Our temporal models for O3, NO2, and NO strongly reflect the photochemical processes in space and time. O3 shows a high background value throughout the day and only dips in the (close) vicinity of roads. The diminishing rate is affected by traffic intensity. The NO2 LUR is validated against NO2 measurements from the Traffic-Related Air pollution and Children's respiratory HEalth and Allergies (TRACHEA) study, resulting in an R2 of 0.61.

    Systematic meta-Analyses, field synopsis and global assessment of the evidence of genetic association studies in colorectal cancer
    Montazeri, Zahra ; Li, Xue ; Nyiraneza, Christine ; Ma, Xiangyu ; Timofeeva, Maria ; Svinti, Victoria ; Meng, Xiangrui ; He, Yazhou ; Bo, Yacong ; Morgan, Samuel ; Castellví-Bel, Sergi ; Ruiz-Ponte, Clara ; Fernández-Rozadilla, Ceres ; Carracedo, Ángel ; Castells, Antoni ; Bishop, Timothy ; Buchanan, Daniel ; Jenkins, Mark A. ; Keku, Temitope O. ; Lindblom, Annika ; Duijnhoven, Fränzel J.B. Van; Wu, Anna ; Farrington, Susan M. ; Dunlop, Malcolm G. ; Campbell, Harry ; Theodoratou, Evropi ; Zheng, Wei ; Little, Julian - \ 2020
    Gut 69 (2020). - ISSN 0017-5749 - p. 1460 - 1471.
    colorectal cancer

    Objective: To provide an understanding of the role of common genetic variations in colorectal cancer (CRC) risk, we report an updated field synopsis and comprehensive assessment of evidence to catalogue all genetic markers for CRC (CRCgene2). Design: We included 869 publications after parallel literature review and extracted data for 1063 polymorphisms in 303 different genes. Meta-Analyses were performed for 308 single nucleotide polymorphisms (SNPs) in 158 different genes with at least three independent studies available for analysis. Scottish, Canadian and Spanish data from genome-wide association studies (GWASs) were incorporated for the meta-Analyses of 132 SNPs. To assess and classify the credibility of the associations, we applied the Venice criteria and Bayesian False-Discovery Probability (BFDP). Genetic associations classified as â € positive' and â € less-credible positive' were further validated in three large GWAS consortia conducted in populations of European origin. Results: We initially identified 18 independent variants at 16 loci that were classified as â € positive' polymorphisms for their highly credible associations with CRC risk and 59 variants at 49 loci that were classified as â € less-credible positive' SNPs; 72.2% of the â € positive' SNPs were successfully replicated in three large GWASs and the ones that were not replicated were downgraded to â € less-credible' positive (reducing the â € positive' variants to 14 at 11 loci). For the remaining 231 variants, which were previously reported, our meta-Analyses found no evidence to support their associations with CRC risk. Conclusion: The CRCgene2 database provides an updated list of genetic variants related to CRC risk by using harmonised methods to assess their credibility.

    Long-term fertilization alters microbial community but fails to reclaim soil organic carbon stocks in a land-use changed soil of the Tibetan Plateau
    Li, Meng ; Wang, Guoxi ; Kang, Xiaoming ; Hu, Hualing ; Wang, Yan ; Zhang, Xiangru ; Sun, Xiaolei ; Zhang, Hui ; Hu, Zhengyi ; Xi, Beidou - \ 2020
    Land Degradation and Development 31 (2020)4. - ISSN 1085-3278 - p. 531 - 524.
    16S rRNA sequencing - aggregates - manure compost - meadow - soil organic fractions

    The microbial community and soil organic carbon (SOC), which play vital roles in soil fertility and the global C cycle, have been heavily altered due to land-use changes and long-term fertilization. However, the effect of long-term fertilization on the microbial community and SOC in land-use changed soil is still unclear. In this study, a 26-year field experiment is conducted to detect the bacterial community and SOC stocks in the soils from meadow grasslands (M), croplands without fertilization (NF), and croplands with fertilization for 13 (F13a) and 26 years (F26a) in the Tibetan Plateau. The results show that land-use change from meadow grassland to cropland induced a decrease in the SOC stocks of total (TOC), free (FOC) and permanganate-oxidizable OC (POxC) by 61.8–85.0, 51.1–82.8, and 78.4–95.8%, respectively. Long-term fertilization increased the SOC stocks by 124.4–419.0%, which was still lower than those in the M soils. In addition, macroaggregates (MAA) and bacterial diversity displayed reductions when the land-use was changed from grassland to cropland, but they were enhanced after long-term fertilization. Land-use change and long-term fertilization both altered the microbial community. MAA served as a habitat for the microbial community and physical protection for SOC. This may be a key driver of changes in the bacterial community and SOC. This study demonstrates that long-term fertilization alters the microbial community but fails to restore SOC stocks to the level of uncropped meadow soils. Long-term fertilization integrated with macroaggregates are required to improve OC sequestration for developing sustainable agriculture and mitigating global climate change.

    Yield and nitrogen uptake of sole and intercropped maize and peanut in response to N fertilizer input
    Gao, Huaxin ; Meng, Weiwei ; Zhang, Chaochun ; Werf, Wopke van der; Zhang, Zheng ; Wan, Shubo ; Zhang, Fusuo - \ 2020
    Food and Energy Security 9 (2020)1. - ISSN 2048-3694
    intercropping - land equivalent ratio - N input - N uptake - yield

    Chinese agriculture needs to become less dependent on fertilizer inputs to enhance sustainability. Cereal/legume intercropping is a potential pathway to lower fertilizer inputs, but there is insufficient knowledge on the nitrogen (N) response in species mixtures. Here, we investigated N response in maize/peanut intercropping. Maize showed a stronger yield response to N input than peanut both in sole cropping and in intercropping, and so did sole crops relative to intercrops. Maize yield was the highest at the maximum level tested: 360 kg N/ha. Agronomic efficiency (AE) of sole maize was 7.8 kg/kg N input, averaged across five N levels (0, 90, 180, 270, and 360 kg/ha). Partial land equivalent ratios (pLERs) for maize decreased with N input, from 0.70 at zero to 0.64 at 360 kg/ha. Sole peanut showed an optimum yield response to N input, with the highest yield at 270 kg/ha and lower yield at 360 kg/ha. The average AE of sole peanut was 1.3 kg/kg. The pLER of peanut declined from 0.43 at zero to 0.32 at 360 kg/ha while the overall LER decreased from 1.13 to 0.96, indicating relative better performance of intercropping at low than at high N input. Apparent recovery (RE) for N was 27.2% for sole maize, 12.4% for sole peanut, and 7.2% for intercrops. Mean N uptake was 179 kg/ha in sole maize, 199 kg/ha in intercropping, and 264 kg/ha in sole peanut. Partial economic budgeting indicated that with the current low Chinese N fertilizer prices, gross margin is maximized with high N input in sole crops; however, for intercropping, the highest gross margin was attained at intermediate N inputs of 180 or 270 kg/ha. Fertilizer price incentives may facilitate a transition to intercropping at moderate N input in China.

    Sulfur controlled cadmium dissolution in pore water of cadmium-contaminated soil as affected by DOC under waterlogging
    Wang, Guoxi ; Hu, Zhengyi ; Li, Songyan ; Wang, Yan ; Sun, Xiaolei ; Zhang, Xiangru ; Li, Meng - \ 2020
    Chemosphere 240 (2020). - ISSN 0045-6535
    Cadmium - DOC - Paddy soil - Sulfate oxidizing bacteria - Sulfur

    Cadmium (Cd) precipitation and dissolution in pore water is associated with dissolved organic carbon (DOC)-induced reduction-oxidation of sulfur (S) under waterlogging and is vital for controlling the bioavailability in paddy soil. A 120-day soil incubation experiment, including application of sulfur (S, 30 mg kg−1) and wheat straw (W, 1.0%) alone or in combination (W + S) into Cd-contaminated paddy soil under waterlogging, was conducted to investigate the dynamic of dissolved Cd and its relationship with DOC, S2−, Fe2+, pH, Eh and pe + pH in soil pore water. The results showed that the lowest dissolved Cd concentration was observed in the W + S-treated soil pore water among all treatments when the soil Eh remained at lower values during the period of 15–60 days of incubation, which could be attributed to CdS precipitation and/or co-precipitation of Cd absorbed by FeS2 because of the reduction in sulfur. The application of S resulted in a Cd rebound in the pore water irrespective of W addition when the Eh began to increase from its lowest values during the period of 45–75 days of incubation, and SOB genera were observed in the S added soil. This could be attributed to re-dissolution of the precipitated Cd in soils under the SOB-driven oxidation of sulfide such as CdS and FeS2. In conclusion, DOC-driven reduction-oxidation of sulfur controls Cd dissolution in the pore water of Cd-contaminated paddy soil under waterlogging conditions. Further studies are required to investigate the interaction of sulfur and SOM-induced DOC on Cd bioavailability in rice-planted paddy soils.

    Process simulation and life cycle assessment of converting autoclaved municipal solid waste into butanol and ethanol as transport fuels
    Meng, Fanran ; Ibbett, Roger ; Vrije, Truus de; Metcalf, Pete ; Tucker, Gregory ; McKechnie, Jon - \ 2019
    Waste Management 89 (2019). - ISSN 0956-053X - p. 177 - 189.
    ABE fermentation - Enzymatic hydrolysis - Life cycle assessment - Municipal solid waste - Waste autoclaving

    In 2015/2016, the total municipal solid waste (MSW) collected by local authority in the U.K. was 26 million tonnes and over 57% is still put into landfill or incinerated. MSW is a promising feedstock for bio-butanol production as it has a high lignocellulosic fibre content such as paper, wood, and food waste, about 50 wt% of a typical MSW stream. The study evaluates acetone, butanol, ethanol and hydrogen production from autoclaved municipal solid waste feedstock. Life cycle assessment is undertaken to evaluate the acetone, butanol, ethanol and hydrogen production process, considering cogeneration of heat and power from residual biogenic waste based on experimental data and process modelling. Acetone, butanol, and ethanol product yield can be achieved at 12.2 kg butanol, 1.5 kg ethanol, 5.7 kg acetone, and 0.9 kg hydrogen per tonne MSW. The product yield is relatively low compared to other lignocellulosic feedstocks primarily because of the lower hydrolysis yield (38% for glucose) achieved in this study; however, hydrolysis yields could be improved in future optimisation work. The conversion shows a net primary energy demand of −1.11 MJ/MJ liquid biofuels (butanol and ethanol) and net greenhouse gas emission of −12.57 g CO 2 eq/MJ liquid biofuels, achieving a greenhouse gas reduction of 115% compared to gasoline comparator.

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