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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Transparent experiments: releasing data from mechanical tests on three dimensional hydrogel sphere packings
Barés, Jonathan ; Brodu, Nicolas ; Zheng, Hu ; Dijksman, Joshua A. - \ 2020
Granular Matter 22 (2020)1. - ISSN 1434-5021
3D packing - Calibration - Force networks - Hydrogel particles - Image analysis

We describe here experiments on the mechanics of hydrogel particle packings from the Behringer lab, performed between 2012 and 2015. These experiments quantify the evolution of all contact forces inside soft particle packings exposed to compression, shear, and the intrusion of a large intruder. The experimental set-ups and processes are presented and the data are concomitantly published in a repository (Barés et al. in Dryad, Dataset, 2019).

Nonlinear responses of soil nematode community composition to increasing aridity
Xiong, Dan ; Wei, Cun Zheng ; Wubs, Jasper E.R. ; Veen, G.J. ; Liang, Wenju ; Wang, Xiaobo ; Li, Qi ; Putten, Wim H. Van der; Han, Xingguo - \ 2020
Global Ecology and Biogeography 29 (2020)1. - ISSN 1466-822X - p. 117 - 126.
aridity - biodiversity - global climate change - grassland transect - nonlinear response - soil nematode community

Aim: Increasing aridity under global change is predicted to have a profound impact on the structure and functioning of terrestrial ecosystems, yet we have a poor understanding of how belowground communities respond. In order to understand the longer term responses of different trophic levels in the soil food web to increasing aridity, we investigated the abundance, richness and community similarity of the soil nematode community along a 3,200 km aridity gradient. Location: A transect across semi-arid and arid grasslands in Northern China, where the aridity ranges from.43 to.97. Time period: July and August 2012. Major taxa studied: Soil-borne Nematoda. Methods: We used generalized additive (mixed) models to analyse the abundance, richness and community similarity patterns of soil nematodes. We used structural equation modelling (SEM) to disentangle the direct and indirect environmental drivers (aridity, soil and plant variables) of the nematode community. Results: The abundance, richness and similarity of nematode communities declined nonlinearly with increasing aridity. The most pronounced decline in nematode richness and community similarity occurred in arid conditions (aridity >.80). However, the shape of the response to aridity differed among nematode feeding groups. In arid conditions, the abundance and richness of bacterial feeders were less sensitive to changes in aridity than for fungal feeders. The SEM analysis revealed that nematode community responses to aridity were not mediated via changes in plant and soil variables, but instead were affected directly by aridity. Main conclusions: Our results showed that in mesic grasslands, increasing aridity primarily caused a decline in nematode abundance, whereas increasing aridity in xeric grasslands led to a loss of nematode diversity. The nonlinear responses of nematodes to aridity could also result in nonlinear shifts in ecosystem functioning, because soil nematodes operate at various trophic levels in the soil food web, thereby influencing the performance of plants, soil biodiversity and biogeochemical cycling.

Longitudinal RNA-seq Analysis of Tissue Development Reveals the Hub genes that Influencing the Chicken Intramuscular Fat and Abdominal Fat Deposition
Xing, Siyuan ; Liu, Ranran ; Crooijmans, Richard ; Liu, Lu ; Madsen, Ole ; Zhou, Wu ; Cui, Huanxian ; Li, Qinghe ; Zheng, Maiqing ; Zhao, Guiping ; Groenen, Martien ; Wen, Jie - \ 2019
Powerpoint presentation
Protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soils
Zhao, Zhi Bo ; He, Ji Zheng ; Geisen, Stefan ; Han, Li Li ; Wang, Jun Tao ; Shen, Ju Pei ; Wei, Wen Xue ; Fang, Yun Ting ; Li, Pei Pei ; Zhang, Li Mei - \ 2019
Microbiome 7 (2019)1. - ISSN 2049-2618
High-throughput sequencing - Microbiome - Nitrogen fertilizers - Soil protists - Soil type

Background: Agricultural food production is at the base of food and fodder, with fertilization having fundamentally and continuously increased crop yield over the last decades. The performance of crops is intimately tied to their microbiome as they together form holobionts. The importance of the microbiome for plant performance is, however, notoriously ignored in agricultural systems as fertilization disconnects the dependency of plants for often plant-beneficial microbial processes. Moreover, we lack a holistic understanding of how fertilization regimes affect the soil microbiome. Here, we examined the effect of a 2-year fertilization regime (no nitrogen fertilization control, nitrogen fertilization, and nitrogen fertilization plus straw amendment) on entire soil microbiomes (bacteria, fungi, and protist) in three common agricultural soil types cropped with maize in two seasons. Results: We found that the application of nitrogen fertilizers more strongly affected protist than bacterial and fungal communities. Nitrogen fertilization indirectly reduced protist diversity through changing abiotic properties and bacterial and fungal communities which differed between soil types and sampling seasons. Nitrogen fertilizer plus straw amendment had greater effects on soil physicochemical properties and microbiome diversity than nitrogen addition alone. Moreover, nitrogen fertilization, even more together with straw, increased soil microbiome network complexity, suggesting that the application of nitrogen fertilizers tightened soil microbiomes interactions. Conclusions: Together, our results suggest that protists are the most susceptible microbiome component to the application of nitrogen fertilizers. As protist communities also exhibit the strongest seasonal dynamics, they serve as the most sensitive bioindicators of soil changes. Changes in protist communities might have long-term effects if some of the key protist hubs that govern microbiome complexities as top microbiome predators are altered. This study serves as the stepping stone to promote protists as promising agents in targeted microbiome engineering to help in reducing the dependency on exogenous unsustainably high fertilization and pesticide applications.

Subtidal Flow Reversal Associated With Sediment Accretion in a Delta Channel
Zhang, Wei ; Feng, Haochuan ; Zhu, Yuliang ; Zheng, Jinhai ; Hoitink, A.J.F. - \ 2019
Water Resources Research (2019). - ISSN 0043-1397
deltas tidal networks salt intrusion bifurcation Yangtze Delta Stokes transport

In branching delta channel networks, tides intrude into parallel river outlets causing complex tidal behavior. The tidal motion can impact the division of river discharge over distributary channels. Under some circumstances, the discharge averaged over a tidal cycle may even reverse, drawing ocean water intox the delta, such as observed in the Yangtze Delta, the Fly Delta and the Colorado Delta. Here, we study the flow reversal associated with sediment accumulation of a distributary channel in terms of tidal propagation and subtidal discharge dynamics, by focusing on the Yangtze Delta. The Yangtze Delta channel configuration represents a deep and wide main channel and a smaller side channel that has rapidly accreted over the past decades. A new mechanism is presented, which results in seawater transport across the shallow side channel, posing a risk to freshwater availability. The shallowest section in the side channel nearly acts as a tidal divide. In this section, the tide has the character of a standing wave, which implies that Stokes transport converges from opposite sides of the channel. This leads to significant variation of the total water storage in the side channel and subtidal water levels in the side channel being elevated above that in the main channel. The bulge of water that is stored during spring tide leaves the side channel toward neap tide, explaining reversal of the tide-averaged discharge and seawater intrusion when the river discharge is low.

Combining Crop Growth Modeling and Statistical Genetic Modeling to Evaluate Phenotyping Strategies
Bustos-Korts, Daniela ; Boer, Martin P. ; Malosetti, Marcos ; Chapman, Scott ; Chenu, Karine ; Zheng, Bangyou ; Eeuwijk, Fred A. van - \ 2019
Frontiers in Plant Science 10 (2019). - ISSN 1664-462X
APSIM model - crop growth model - dynamic traits - genomic prediction - genotype to phenotype - P-spline - trait hierarchy - wheat

Genomic prediction of complex traits, say yield, benefits from including information on correlated component traits. Statistical criteria to decide which yield components to consider in the prediction model include the heritability of the component traits and their genetic correlation with yield. Not all component traits are easy to measure. Therefore, it may be attractive to include proxies to yield components, where these proxies are measured in (high-throughput) phenotyping platforms during the growing season. Using the Agricultural Production Systems Simulator (APSIM)-wheat cropping systems model, we simulated phenotypes for a wheat diversity panel segregating for a set of physiological parameters regulating phenology, biomass partitioning, and the ability to capture environmental resources. The distribution of the additive quantitative trait locus effects regulating the APSIM physiological parameters approximated the same distribution of quantitative trait locus effects on real phenotypic data for yield and heading date. We use the crop growth model APSIM-wheat to simulate phenotypes in three Australian environments with contrasting water deficit patterns. The APSIM output contained the dynamics of biomass and canopy cover, plus yield at the end of the growing season. Each water deficit pattern triggered different adaptive mechanisms and the impact of component traits differed between drought scenarios. We evaluated multiple phenotyping schedules by adding plot and measurement error to the dynamics of biomass and canopy cover. We used these trait dynamics to fit parametric models and P-splines to extract parameters with a larger heritability than the phenotypes at individual time points. We used those parameters in multi-trait prediction models for final yield. The combined use of crop growth models and multi-trait genomic prediction models provides a procedure to assess the efficiency of phenotyping strategies and compare methods to model trait dynamics. It also allows us to quantify the impact of yield components on yield prediction accuracy even in different environment types. In scenarios with mild or no water stress, yield prediction accuracy benefitted from including biomass and green canopy cover parameters. The advantage of the multi-trait model was smaller for the early-drought scenario, due to the reduced correlation between the secondary and the target trait. Therefore, multi-trait genomic prediction models for yield require scenario-specific correlated traits.

From QTLs to Adaptation Landscapes: Using Genotype-To-Phenotype Models to Characterize G×E Over Time
Bustos-Korts, Daniela ; Malosetti, Marcos ; Chenu, Karine ; Chapman, Scott ; Boer, Martin P. ; Zheng, Bangyou ; Eeuwijk, Fred A. van - \ 2019
Frontiers in Plant Science 10 (2019). - ISSN 1664-462X
adaptation - APSIM model - crop growth model - G×E interaction - QTL (quantitative trait loci) - reaction norm - wheat

Genotype by environment interaction (G×E) for the target trait, e.g. yield, is an emerging property of agricultural systems and results from the interplay between a hierarchy of secondary traits involving the capture and allocation of environmental resources during the growing season. This hierarchy of secondary traits ranges from basic traits that correspond to response mechanisms/sensitivities, to intermediate traits that integrate a larger number of processes over time and therefore show a larger amount of G×E. Traits underlying yield differ in their contribution to adaptation across environmental conditions and have different levels of G×E. Here, we provide a framework to study the performance of genotype to phenotype (G2P) modeling approaches. We generate and analyze response surfaces, or adaptation landscapes, for yield and yield related traits, emphasizing the organization of the traits in a hierarchy and their development and interactions over time. We use the crop growth model APSIM-wheat with genotype-dependent parameters as a tool to simulate non-linear trait responses over time with complex trait dependencies and apply it to wheat crops in Australia. For biological realism, APSIM parameters were given a genetic basis of 300 QTLs sampled from a gamma distribution whose shape and rate parameters were estimated from real wheat data. In the simulations, the hierarchical organization of the traits and their interactions over time cause G×E for yield even when underlying traits do not show G×E. Insight into how G×E arises during growth and development helps to improve the accuracy of phenotype predictions within and across environments and to optimize trial networks. We produced a tangible simulated adaptation landscape for yield that we first investigated for its biological credibility by statistical models for G×E that incorporate genotypic and environmental covariables. Subsequently, the simulated trait data were used to evaluate statistical genotype-to-phenotype models for multiple traits and environments and to characterize relationships between traits over time and across environments, as a way to identify traits that could be useful to select for specific adaptation. Designed appropriately, these types of simulated landscapes might also serve as a basis to train other, more deep learning methodologies in order to transfer such network models to real-world situations.

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 - \ 2019
Gut (2019). - ISSN 0017-5749
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.

Genetic Variants in Group-Specific Component (GC) Gene Are Associated with Breast Cancer Risk among Chinese Women
Chen, Fuxing ; Zhu, Zheng ; Duijnhoven, Fränzel J.B. Van; Dong, Meihua ; Qian, Yun ; Yu, Hao ; Yang, Jie ; Cui, Lan ; Han, Renqiang ; Su, Jian ; Du, Wencong ; Zhou, Jinyi ; Wu, Ming - \ 2019
BioMed Research International 2019 (2019). - ISSN 2314-6133

The group-specific component (GC) gene, one of the vitamin D pathway genes, seems to play an important role in cancer development. A population-based breast cancer study including 818 cases and 935 controls in a Chinese population was carried out to evaluate the potential associations of four polymorphisms (rs16847024, rs17467825, rs2298850, and rs3755967) in the GC gene with risk of breast cancer. We detected three SNPs with statistically significant effects on breast cancer development after adjusting for age, menopausal status, body mass index (BMI), family history of breast cancer, income, waist circumference, and education (rs17467825: adjusted OR = 0.80, 95% CI = 0.65-0.99; rs2298850: adjusted OR = 0.80, 95% CI = 0.65-0.98; rs3755967: adjusted OR = 0.80, 95% CI = 0.65-0.98). Stratified analysis found that when an individual had a waist circumference <80 cm, rs17467825, rs2298850, and rs3755967 could markedly reduce the risk of breast cancer. Significant interactions between polymorphisms of rs2298850 and rs3755967 and waist circumference were also observed for breast cancer risk. Combined analysis revealed a significant association among the allele numbers of protective effects with decreased breast cancer risk (Ptrend=0.043). These results indicated that, in the GC gene, genetic mutations might be related to breast cancer susceptibility in Chinese women.

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 - \ 2019
Food and Energy Security (2019). - 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.

Negative effects of urbanization on agricultural soil easily oxidizable organic carbon down the profile of the Chengdu Plain, China
Luo, Youlin ; Li, Qiquan ; Wang, Changquan ; Li, Bing ; Stomph, Tjeerd Jan ; Yang, Juan ; Tao, Qi ; Yuan, Shu ; Tang, Xiaoyan ; Ge, Jinru ; Yu, Xuelian ; Peng, Yueyue ; Xu, Qiang ; Zheng, Gangxun - \ 2019
Land Degradation and Development (2019). - ISSN 1085-3278
easily oxidized organic carbon - impact factors - negative effects - rapid urbanization - soil profile

Soil easily oxidizable organic carbon (EOC) is directly related to CO2 density; dynamics in subsurface EOC have been observed globally in relation to rapid urbanization. However, in the context of rapid urbanization, the factors related to EOC and the response of the EOC pool to urbanization down the profile remain elusive. The aim of the current paper is to investigate possible changes in the distribution of EOC over the soil profile and the impact of land use, socioeconomic, and natural factors on these. The study used samples from 182 soil profiles (0–100 cm) taken in the peri-urban areas of the megacity Chengdu (a typical megacity with rapid urbanization). Main drivers of changes in soil EOC were analyzed by using spatial and regression analyses. Closer to the centre of the city, soil EOC levels were lower and land-use factors and socioeconomic factors contributed more to explaining variation in EOC levels in the 0–40-cm layer, whereas natural factors were most important at larger distance from the city. The effect of land-use factors and socioeconomic factors on EOC reached down to 60-cm depths. Moreover, an estimated 20% loss of EOC stock was observed close to the city in comparison with the surroundings, suggesting that the rapid process of urbanization was accompanied by a loss of EOC stock down the profile to depths of 60 cm, and the negative effects on EOC stock became more intensive as the distance to the city decreased.

Analytical model captures intratidal variation in salinity in a convergent, well-mixed estuary
Xu, Yanwen ; Hoitink, Antonius J.F. ; Zheng, Jinhai ; Kästner, Karl ; Zhang, Wei - \ 2019
Hydrology and Earth System Sciences 23 (2019)10. - ISSN 1027-5606 - p. 4309 - 4322.

Knowledge of the processes governing salt intrusion in estuaries is important, since it influences the eco-environment of estuaries as well as its water resource potential in many ways. Analytical models of salinity variation offer a simple and efficient method for studying salt intrusion in estuaries. In this paper, an unsteady analytical solution is presented to predict the spatio-temporal variation in salinity in convergent estuaries. It is derived from a one-dimensional advection-diffusion equation for salinity, adopting a constant mixing coefficient and a single-frequency tidal wave, which can directly reflect the influence of the tidal motion and the interaction between the tide and runoff. The deduced analytical solution is illustrated with an application to the Humen estuary of the Pearl River Delta (PRD) and proves to be an efficient and accurate approach for predicting the salt intrusion in convergent estuaries. The unsteady analytical solution is tested against observations from six study sites to validate its capability to predict intratidal variation in salt intrusion. The results show that the proposed unsteady analytical solution can be successfully used to reproduce the spatial distribution and temporal processes governing salinity dynamics in convergent, well-mixed estuaries. The proposed method provides a quick and convenient approach for deciding on water-fetching methods to make good use of water resources.

Forest connectivity, host assemblage characteristics of local and neighboring counties, and temperature jointly shape the spatial expansion of lyme disease in United States
Wang, Yingying X.G. ; Matson, Kevin D. ; Xu, Yanjie ; Prins, Herbert H.T. ; Huang, Zheng Y.X. ; Boer, Willem F. de - \ 2019
Remote Sensing 11 (2019)20. - ISSN 2072-4292
Assemblage similarity - Disease spread - Forest cover - Host assemblage composition - Infection intensity

Understanding risk factors for the spread of infectious diseases over time and across the landscape is critical for managing disease risk. While habitat connectivity and characteristics of local and neighboring animal (i.e., host) assemblages are known to influence the spread of diseases, the interactions among these factors remain poorly understood. In this study, we conducted a county-level analysis to test the effects of forest connectivity, together with the suitability of local assemblage (measured by the similarity of local host assemblage with neighboring assemblages) and the infection intensity of neighboring counties on the spatial expansion of Lyme disease in the United States. Our results suggested that both the similarity of local host assemblage and the infection intensity of neighboring counties were positively correlated with the probability of disease spread. Moreover, we found that increasing forest connectivity could facilitate the positive effect of neighbor infection intensity. In contrast, the effect size of the host assemblage similarity decreased with increasing connectivity, suggesting that host assemblage similarity was less effective in well-connected habitats. Our results thus indicate that habitat connectivity can indirectly influence disease spread by mediating the effects of other risk factors.

The effect of urban 2D and 3D morphology on air temperature in residential neighborhoods
Tian, Yunyu ; Zhou, Weiqi ; Qian, Yuguo ; Zheng, Zhong ; Yan, Jingli - \ 2019
Landscape Ecology 34 (2019)5. - ISSN 0921-2973 - p. 1161 - 1178.
Context: Both urban two-dimensional (2D) and three-dimensional (3D) morphology can affect air and land surface temperature. While many studies have looked at the impact of horizontal morphology, few have explored the relationship between vertical morphology and temperature, especially at the neighborhood scale. Objectives: This study aims to answer two questions: (1) Does air temperature vary in neighborhoods with different morphology? (2) If so, how does the 2D (horizontal) and 3D (vertical) morphology affect air temperature? Methods: We examined the relationship between morphology and air temperature for 24 residential neighborhoods in Beijing, using correlation analysis, regression analysis, and structural equation modeling. Morphological indicators were derived from remotely sensed land cover and light detecting and ranging (LiDAR) point cloud data. Air temperature was continuously measured using HOBO data loggers during the summer of 2014. Results

Nighttime air temperature was higher in neighborhoods dominated by high-rise structures compared to neighborhoods dominated by low-rise structures suggesting that 3D morphology is more important than 2D morphology in predicting air temperature. The ratio of vegetation volume to building volume negatively correlated with average air temperature and daytime temperature, while the mean distance among adjacent buildings had a positive effect. Building height was the most important predictor of nighttime air temperature. The major determinants of air temperature in high-rise and low-rise neighborhoods were different. Conclusions: Both 2D and 3D morphology can affect air temperature in residential neighborhoods. Increasing vegetation volume relative to building volume and decreasing the distance among buildings can reduce daytime air temperatures.
Joint toxicity of binary complexes of cartap, spirotetramat, copper, and cadmium to Vibrio fischeri
Yin, Hong Yang ; Zhao, Yuan ; Zheng, Yi ; Bao, Cong ; Huang, Xin Xin ; Ding, Ying Jie ; Cai, Qiang - \ 2019
Journal of Agro-Environment Science 38 (2019)9. - ISSN 1672-2043 - p. 2080 - 2085.
Acute toxicity - Heavy metals - Joint toxicity evaluation - Pesticide - Vibrio fischeri

In view of the widespread use of cartap, spirotetramat, and common heavy metal pollutants, such as copper and cadmium in agri? cultural activities, the joint toxicity of their complexes on Vibrio fischeri was studied. The EC50(median effective concentration)was calcu? lated with the acute toxic effects of binary complex contamination on Vibrio fischeri employing different exposure times. The Mixtures Toxic? ity Index method was employed to evaluate the joint toxicity. The acute toxicity experiments showed that the EC50 of copper, cadmium, car? tap, and spirotetramat on Vibrio fischeri at 15 mins was 0.53, 0.74, 79.06 mg·L-1, and 116.67 mg·L-1, respectively. The joint toxicity of car? tap and heavy metals on Vibrio fischeri was mainly additive. When the spirotetramat accounted for a low proportion in the binary mixtures, the joint toxicity was partially additive. The presence of cartap and spirotetramat may slow down the rate of metal ions entering the cell. Therefore, the study of exposure time for joint toxicity on Vibrio fischeri should be extended to 45 mins.

Enlightening force chains: a review of photoelasticimetry in granular matter
Abed Zadeh, Aghil ; Barés, Jonathan ; Brzinski, Theodore A. ; Daniels, Karen E. ; Dijksman, Joshua ; Docquier, Nicolas ; Everitt, Henry O. ; Kollmer, Jonathan E. ; Lantsoght, Olivier ; Wang, Dong ; Workamp, Marcel ; Zhao, Yiqiu ; Zheng, Hu - \ 2019
Granular Matter 21 (2019). - ISSN 1434-5021
Experimental methods - Force chains - Image post-processing - Photoelasticimetry - Protocols

A photoelastic material will reveal its internal stresses when observed through polarizing filters. This eye-catching property has enlightened our understanding of granular materials for over half a century, whether in the service of art, education, or scientific research. In this review article in honor of Robert Behringer, we highlight both his pioneering use of the method in physics research, and its reach into the public sphere through museum exhibits and outreach programs. We aim to provide clear protocols for artists, exhibit-designers, educators, and scientists to use in their own endeavors. It is our hope that this will build awareness about the ubiquitous presence of granular matter in our lives, enlighten its puzzling behavior, and promote conversations about its importance in environmental and industrial contexts. To aid in this endeavor, this paper also serves as a front door to a detailed wiki containing open, community-curated guidance on putting these methods into practice (Abed-Zadeh et al. in Photoelastic methods wiki, 2019).

Construction of Genetic Linkage Maps in Multiparental Populations
Zheng, Chaozhi ; Boer, Martin P. ; Eeuwijk, Fred A. van - \ 2019
Genetics 212 (2019)4. - ISSN 0016-6731 - p. 1031 - 1044.
cross-pollinated (CP) - genetic map construction - hidden Markov model (HMM) - MPP - multiparent advanced generation intercross (MAGIC) - multiparental populations - nested association mapping (NAM)

Construction of genetic linkage maps has become a routine step for mapping quantitative trait loci (QTL), particularly in animal and plant breeding populations. Many multiparental populations have recently been produced to increase genetic diversity and QTL mapping resolution. However, few software packages are available for map construction in these populations. In this paper, we build a general framework for the construction of genetic linkage maps from genotypic data in diploid populations, including bi- and multiparental populations, cross-pollinated (CP) populations, and breeding pedigrees. The framework is implemented as an automatic pipeline called magicMap, where the maximum multilocus likelihood approach utilizes genotypic information efficiently. We evaluate magicMap by extensive simulations and eight real datasets: one biparental, one CP, four multiparent advanced generation intercross (MAGIC), and two nested association mapping (NAM) populations, the number of markers ranging from a few hundred to tens of thousands. Not only is magicMap the only software capable of accommodating all of these designs, it is more accurate and robust to missing genotypes and genotyping errors than commonly used packages.

A Medicago truncatula SWEET transporter implicated in arbuscule maintenance during arbuscular mycorrhizal symbiosis
An, Jianyong ; Zeng, Tian ; Ji, Chuanya ; Graaf, Sanne de; Zheng, Zijun ; Xiao, Ting Ting ; Deng, Xiuxin ; Xiao, Shunyuan ; Bisseling, Ton ; Limpens, Erik ; Pan, Zhiyong - \ 2019
New Phytologist 224 (2019)1. - ISSN 0028-646X - p. 396 - 408.
arbuscular mycorrhiza (AM) - glucose - Medicago truncatula - sugar export - SWEET - symbiosis

Plants form a mutualistic symbiosis with arbuscular mycorrhizal (AM) fungi, which facilitates the acquisition of scarce minerals from the soil. In return, the host plants provide sugars and lipids to its fungal partner. However, the mechanism by which the AM fungi obtain sugars from the plant has remained elusive. In this study we investigated the role of potential SWEET family sugar exporters in AM symbiosis in Medicago truncatula. We show that M. truncatula SWEET1b transporter is strongly upregulated in arbuscule-containing cells compared to roots and localizes to the peri-arbuscular membrane, across which nutrient exchange takes place. Heterologous expression of MtSWEET1b in a yeast hexose transport mutant showed that it mainly transports glucose. Overexpression of MtSWEET1b in M. truncatula roots promoted the growth of intraradical mycelium during AM symbiosis. Surprisingly, two independent Mtsweet1b mutants, which are predicted to produce truncated protein variants impaired in glucose transport, exhibited no significant defects in AM symbiosis. However, arbuscule-specific overexpression of MtSWEET1bY57A/G58D, which are considered to act in a dominant-negative manner, resulted in enhanced collapse of arbuscules. Taken together, our results reveal a (redundant) role for MtSWEET1b in the transport of glucose across the peri-arbuscular membrane to maintain arbuscules for a healthy mutually beneficial symbiosis.

Correction to: Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer
Bien, Stephanie A. ; Su, Yu Ru ; Conti, David V. ; Harrison, Tabitha A. ; Qu, Conghui ; Guo, Xingyi ; Lu, Yingchang ; Albanes, Demetrius ; Auer, Paul L. ; Banbury, Barbara L. ; Berndt, Sonja I. ; Bézieau, Stéphane ; Brenner, Hermann ; Buchanan, Daniel D. ; Caan, Bette J. ; Campbell, Peter T. ; Carlson, Christopher S. ; Chan, Andrew T. ; Chang-Claude, Jenny ; Chen, Sai ; Connolly, Charles M. ; Easton, Douglas F. ; Feskens, Edith J.M. ; Gallinger, Steven ; Giles, Graham G. ; Gunter, Marc J. ; Hampe, Jochen ; Huyghe, Jeroen R. ; Hoffmeister, Michael ; Hudson, Thomas J. ; Jacobs, Eric J. ; Jenkins, Mark A. ; Kampman, Ellen ; Kang, Hyun Min ; Kühn, Tilman ; Küry, Sébastien ; Lejbkowicz, Flavio ; Marchand, Loic Le; Milne, Roger L. ; Li, Li ; Li, Christopher I. ; Lindblom, Annika ; Lindor, Noralane M. ; Martín, Vicente ; McNeil, Caroline E. ; Melas, Marilena ; Moreno, Victor ; Newcomb, Polly A. ; Offit, Kenneth ; Pharaoh, Paul D.P. ; Potter, John D. ; Qu, Chenxu ; Riboli, Elio ; Rennert, Gad ; Sala, Núria ; Schafmayer, Clemens ; Scacheri, Peter C. ; Schmit, Stephanie L. ; Severi, Gianluca ; Slattery, Martha L. ; Smith, Joshua D. ; Trichopoulou, Antonia ; Tumino, Rosario ; Ulrich, Cornelia M. ; Duijnhoven, Fränzel J.B. van; Guelpen, Bethany Van; Weinstein, Stephanie J. ; White, Emily ; Wolk, Alicja ; Woods, Michael O. ; Wu, Anna H. ; Abeçasis, Goncalo R. ; Casey, Graham ; Nickerson, Deborah A. ; Gruber, Stephen B. ; Hsu, Li ; Zheng, Wei ; Peters, Ulrike - \ 2019
Human Genetics 138 (2019)7. - ISSN 0340-6717 - p. 789 - 791.

Every author has erroneously been assigned to the affiliation “62”. The affiliation 62 belongs to the author Graham Casey.

Nature and mental health: An ecosystem service perspective
Bratman, Gregory N. ; Anderson, Christopher B. ; Berman, Marc G. ; Cochran, Bobby ; Vries, Sjerp De; Flanders, Jon ; Folke, Carl ; Frumkin, Howard ; Gross, James J. ; Hartig, Terry ; Kahn, Peter H. ; Kuo, Ming ; Lawler, Joshua J. ; Levin, Phillip S. ; Lindahl, Therese ; Meyer-lindenberg, Andreas ; Mitchell, Richard ; Ouyang, Zhiyun ; Roe, Jenny ; Scarlett, Lynn ; Smith, Jeffrey R. ; Bosch, Matilda Van Den; Wheeler, Benedict W. ; White, Mathew P. ; Zheng, Hua ; Daily, Gretchen C. - \ 2019
Science Advances 5 (2019)7. - ISSN 2375-2548 - 15 p.
A growing body of empirical evidence is revealing the value of nature experience for mental health. With rapid urbanization and declines in human contact with nature globally, crucial decisions must be made about how to preserve and enhance opportunities for nature experience. Here, we first provide points of consensus across the natural, social, and health sciences on the impacts of nature experience on cognitive functioning, emotional well-being, and other dimensions of mental health. We then show how ecosystem service assessments can be expanded to include mental health, and provide a heuristic, conceptual model for doing so.
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