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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Improved aerosol correction for OMI tropospheric NO2 retrieval over East Asia : Constraint from CALIOP aerosol vertical profile
Liu, Mengyao ; Lin, Jintai ; Folkert Boersma, K. ; Pinardi, Gaia ; Wang, Yang ; Chimot, Julien ; Wagner, Thomas ; Xie, Pinhua ; Eskes, Henk ; Roozendael, Michel Van; Hendrick, François ; Wang, Pucai ; Wang, Ting ; Yan, Yingying ; Chen, Lulu ; Ni, Ruijing - \ 2019
Atmospheric Measurement Techniques 12 (2019)1. - ISSN 1867-1381 - p. 1 - 21.

Satellite retrieval of vertical column densities (VCDs) of tropospheric nitrogen dioxide (NO2) is critical for NOx pollution and impact evaluation. For regions with high aerosol loadings, the retrieval accuracy is greatly affected by whether aerosol optical effects are treated implicitly (as additional effective clouds) or explicitly, among other factors. Our previous POMINO algorithm explicitly accounts for aerosol effects to improve the retrieval, especially in polluted situations over China, by using aerosol information from GEOS-Chem simulations with further monthly constraints by MODIS/Aqua aerosol optical depth (AOD) data. Here we present a major algorithm update, POMINO v1.1, by constructing a monthly climatological dataset of aerosol extinction profiles, based on level 2 CALIOP/CALIPSO data over 2007-2015, to better constrain the modeled aerosol vertical profiles. We find that GEOS-Chem captures the month-to-month variation in CALIOP aerosol layer height (ALH) but with a systematic underestimate by about 300-600 m (season and location dependent), due to a too strong negative vertical gradient of extinction above 1 km. Correcting the model aerosol extinction profiles results in small changes in retrieved cloud fraction, increases in cloud-top pressure (within 2 %-6 % in most cases), and increases in tropospheric NO2 VCD by 4 %-16 % over China on a monthly basis in 2012. The improved NO2 VCDs (in POMINO v1.1) are more consistent with independent ground-based MAX-DOAS observations (R2=0.80, NMB =-3.4 %, for 162 pixels in 49 days) than POMINO (R2=0.80, NMB =-9.6 %), DOMINO v2 (R2=0.68, NMB =-2.1 %), and QA4ECV (R2=0.75, NMB =-22.0 %) are. Especially on haze days, R2 reaches 0.76 for POMINO v1.1, much higher than that for POMINO (0.68), DOMINO v2 (0.38), and QA4ECV (0.34). Furthermore, the increase in cloud pressure likely reveals a more realistic vertical relationship between cloud and aerosol layers, with aerosols situated above the clouds in certain months span id=page2 instead of always below the clouds. The POMINO v1.1 algorithm is a core step towards our next public release of the data product (POMINO v2), and it will also be applied to the recently launched S5P-TROPOMI sensor.

Phytophthora infestans RXLR effectors act in concert at diverse subcellular locations to enhance host colonization
Wang, Shumei ; McLellan, Hazel ; Bukharova, Tatyana ; He, Qin ; Murphy, Fraser ; Shi, Jiayang ; Sun, Shaohui ; Weymers, Pauline van; Ren, Yajuan ; Thilliez, Gaetan ; Wang, Haixia ; Chen, Xinwei ; Engelhardt, Stefan ; Vleeshouwers, Vivianne ; Gilroy, Eleanor M. ; Whisson, Stephen C. ; Hein, Ingo ; Wang, Xiaodan ; Tian, Zhendong ; Birch, Paul R.J. ; Boevink, Petra C. - \ 2019
Journal of Experimental Botany 70 (2019)1. - ISSN 0022-0957 - p. 343 - 356.

Oomycetes such as the potato blight pathogen Phytophthora infestans deliver RXLR effectors into plant cells to manipulate host processes and promote disease. Knowledge of where they localize inside host cells is important in understanding their function. Fifty-two P. infestans RXLR effectors (PiRXLRs) up-regulated during early stages of infection were expressed as fluorescent protein (FP) fusions inside cells of the model host Nicotiana benthamiana. FP-PiRXLR fusions were predominantly nucleo-cytoplasmic, nuclear, or plasma membrane-associated. Some also localized to the endoplasmic reticulum, mitochondria, peroxisomes, or microtubules, suggesting diverse sites of subcellular activity. Seven of the 25 PiRXLRs examined during infection accumulated at sites of haustorium penetration, probably due to co-localization with host target processes; Pi16663 (Avr1), for example, localized to Sec5-associated mobile bodies which showed perihaustorial accumulation. Forty-five FP-RXLR fusions enhanced pathogen leaf colonization when expressed in Nicotiana benthamiana, revealing that their presence was beneficial to infection. Co-expression of PiRXLRs that target and suppress different immune pathways resulted in an additive enhancement of colonization, indicating the potential to study effector combinations using transient expression assays. We provide a broad platform of high confidence P. infestans effector candidates from which to investigate the mechanisms, singly and in combination, by which this pathogen causes disease.

An economic assessment of pseudorabies (Aujeszky’ disease) elimination on hog farms in China
Liu, Yumei ; Chen, Qihui ; Rao, Xudong ; Diao, Xinyu ; Yang, Lin ; Fang, Xiangming ; Hogeveen, Henk - \ 2019
Preventive Veterinary Medicine 163 (2019). - ISSN 0167-5877 - p. 24 - 30.
Aujeszky's disease - China - Economic assessment - Hog farms

Hog pseudorabies (Aujeszky's disease) can incur serious losses for farm owners and even the entire hog industry by causing infertility, abortion, and stillbirth among sows, as well as diarrhoea, respiratory failure, and death among piglets. Pseudorabies virus could be prevented, controlled, and eliminated by clean-up at both farm and regional levels through a strict procedure of vaccination, quarantine, diagnosis, elimination of positive animals, and healthy animals nurturing. Using data from 63 large-scale hog farms from nine provinces (municipalities, autonomous regions) of China, we evaluated the economic consequences of hog pseudorabies clean-up in China's hog farms based on a partial budgeting method. By comparing large-scale hog farms that have performed pseudorabies clean-up with similar farms that have not, we analysed how clean-up affected farm profit and whether there existed sufficient economic incentives for farm owners to adopt pseudorabies control measures. Further, we examined how the economic consequences varied with factors such as clean-up history and farm size. The findings showed that, on average, clean-up adopters outperformed non-adopters by 8.02 million yuan per farm per year within the four years post clean-up adoption. Also, we found that the net profit changes attributable to pseudorabies clean-up increased over time and with farm size. Although we cannot extrapolate to all Chinese hog farms, these findings suggest that the earlier a hog farm adopted pseudorabies clean-up, the larger the economic benefits would be, especially for large-scale farms.

Corrigendum to ‘Revisiting the enzymatic kinetics of pepsin using isothermal titration calorimetry’
Luo, Qi ; Chen, Dongxin ; Boom, Remko M. ; Janssen, Anja E.M. - \ 2019
Food Chemistry 278 (2019). - ISSN 0308-8146 - 1 p.

The authors regret that the wrong unit was reported for the BSA solution, which should be 300 μM instead of 300 mM. It appears in two places: 1. In the paragraph after Eq. (5); 2. In the caption of Fig. 1. The authors would like to apologise for any inconvenience caused.

Characterization of CO2 laser browning of dough
Blutinger, Jonathan David ; Meijers, Yorán ; Chen, Peter Yichen ; Zheng, Changxi ; Grinspun, Eitan ; Lipson, Hod - \ 2019
Innovative Food Science and Emerging Technologies 52 (2019). - ISSN 1466-8564 - p. 145 - 157.
Browning - CO laser - Dough - Flux - Food layered manufacture - Starch gelatinization

We study the application of laser-heating technology to browning dough, due to its potential for high-resolution spatial and surface color control. An important component of this process is the identification of how laser parameters affect browning and baking and whether desirable results can be achieved. In this study, we analyze the performance of a carbon dioxide (CO2) mid-infrared laser (operating at 10.6 μm wavelength) during the browning of dough. Dough samples—consisting of flour and water—were exposed to the infrared laser at different laser power, beam diameter, and sample exposure time. At a laser energy flux of 0.32 MW m−2 (beam diameter of 5.7 mm) and sample exposure time of 180 s we observe a maximum thermal penetration of 0.77 mm and satisfactory dough browning. These results suggest that a CO2 laser is ideal for browning thin goods as well as for food layered manufacture. Industrial relevance: A CO2 laser that operates at a wavelength of 10.6 μm (IR) was used as an alternative method for browning dough. The high-power flux of the laser and the high energy absorption of food at this wavelength allow for rapid surface browning; however, the high absorption limits thermal penetration depth. Nevertheless, accuracy of the laser beam enables high resolution spatial and thermal control of the non-enzymatic browning process. This high precision cooking makes laser-browning particularly ideal for food layered manufacture (FLM), a food processing technique that has gained increased attention in recent years. Using FLM, one can adjust the printed layer height to match cooking penetration depth. As a digital manufacturing technology, laser-browning could also enable manufacture of highly complex and customized food geometries and textures.

Drivers of tree carbon storage in subtropical forests
Li, Yin ; Bao, Weikai ; Bongers, Frans ; Chen, Bin ; Chen, Guoke ; Guo, Ke ; Jiang, Mingxi ; Lai, Jiangshan ; Lin, Dunmei ; Liu, Chunjiang ; Liu, Xiaojuan ; Liu, Yi ; Mi, Xiangcheng ; Tian, Xingjun ; Wang, Xihua ; Xu, Wubing ; Yan, Junhua ; Yang, Bo ; Zheng, Yuanrun ; Ma, Keping - \ 2019
Science of the Total Environment 654 (2019). - ISSN 0048-9697 - p. 684 - 693.
Biodiversity-ecosystem function - Environmental conditions - Mass-ratio effect - Niche complementarity - Stand age - Stand structure

Tropical and subtropical forest ecosystems play an important role in the global carbon regulation. Despite increasing evidence for effects of biodiversity (species diversity, functional diversity and functional dominance), stand structural attributes, stand age and environmental conditions (climate and topography) on tree carbon storage, the relative importance of these drivers at large scale is poorly understood. It is also still unclear whether biodiversity effects on tree carbon storage work through niche complementarity (i.e. increased tree carbon storage due to interspecific resource partitioning) or through the mass-ratio effect (tree carbon storage regulated by dominant traits within communities). Here we analyze tree carbon storage and its drivers using data of 480 plots sampled across subtropical forests in China. We use multiple regression models to test the relative effects of biodiversity, stand structural attributes, stand age and environmental conditions on tree carbon storage, and use a partial least squares path model to test how these variables directly and/or indirectly affect tree carbon storage. Our results show that tree carbon storage is most strongly affected by stand age, followed by climate, biodiversity and stand structural attributes. Stand age and climate had both direct and indirect (through species diversity, functional dominance and stand structural attributes) effects. We find that tree carbon storage correlates with both species diversity and functional dominance after stand age and environmental drivers are accounted for. Our results suggest that niche complementarity and the mass-ratio effect, not necessarily mutually exclusive, both play a role in maintaining ecosystem functioning. Our results further indicate that biodiversity conservation might be an effective way for enhancing tree carbon storage in natural, species-rich forest ecosystems.

Water resource potential for large-scale sweet sorghum production as bioenergy feedstock in Northern China
Fu, Hai Mei ; Chen, Yan Hua ; Yang, Xiao Mei ; Di, Jia Ying ; Xu, Ming Gang ; Zhang, Bao Gui - \ 2019
Science of the Total Environment 653 (2019). - ISSN 0048-9697 - p. 758 - 764.
Arid and semi-arid conditions - Bioenergy - Marginal lands - Sweet sorghum - Water resource potential

This study investigated the water resource potential for bioenergy production from sweet sorghum (Sorghum bicolor (L.)) in Northern China according to the distribution of water resources, climate conditions and the total water consumption of bioenergy based on sweet sorghum, which consisted of blue water, green water and grey water. At a case study site in Inner Mongolia, simulation with a plant phenological model was used to determine whether sweet sorghum could reach the harvestable stage for sugar juice production. The blue water in the agricultural phase was estimated according to the potential crop evapotranspiration (ETc), the drought sensitivity of sweet sorghum in different stages and the precipitation during the growing season. The results showed that the irrigation water was significantly different among the districts, ranging from 730 to 5500 m3/ha and 2060 to 6680 m3/ha for early-maturing and late-maturing varieties, respectively. To avoid the water pressure level to be exacerbated and the severe reallocation of water resources resulting in negative effects on other sectors, the maximal annual water withdrawal was set to not surpass the upper threshold of water stress level of 40%. That makes the maximum area for the production of sweet sorghum cannot exceed 1.95 × 104 ha, representing only 0.24% of the total marginal land area in Inner Mongolia. However, the economic benefits of bioenergy production from sweet sorghum would be negative due to the high labour input. Therefore, not only the availability of marginal land, the climate conditions and local water resources but also the improvement of mechanisation and agricultural production techniques should be considered to attain the sustainable development of bioenergy production and address global energy and environmental crises.

Research challenges for cultural ecosystem services and public health in (peri-)urban environments
Chen, Xianwen ; Vries, Sjerp de; Assmuth, Timo ; Dick, Jan ; Hermans, Tia ; Hertel, Ole ; Jensen, Anne ; Jones, Laurence ; Kabisch, Sigrun ; Lanki, Timo ; Lehmann, Irina ; Maskell, Lindsay ; Norton, Lisa ; Reis, Stefan - \ 2019
Science of the Total Environment 651 (2019). - ISSN 0048-9697 - p. 2118 - 2129.
Cultural ecosystem services - Nature-based solutions - Public health - Urban green/blue infrastructure

Urbanization is a global trend, and consequently the quality of urban environments is increasingly important for human health and wellbeing. Urban life-style is typically associated with low physical activity and sometimes with high mental stress, both contributing to an increasing burden of diseases. Nature-based solutions that make effective use of ecosystem services, particularly of cultural ecosystem services (CES), can provide vital building blocks to address these challenges. This paper argues that, the salutogenic, i.e. health-promoting effects of CES have so far not been adequately recognised and deserve more explicit attention in order to enhance decision making around health and wellbeing in urban areas. However, a number of research challenges will need to be addressed to reveal the mechanisms, which underpin delivery of urban CES. These include: causal chains of supply and demand, equity, and equality of public health benefits promoted. Methodological challenges in quantifying these are discussed. The paper is highly relevant for policy makers within and beyond Europe, and also serves as a review for current researchers and as a roadmap to future short- and long-term research opportunities.

Implications of crop model ensemble size and composition for estimates of adaptation effects and agreement of recommendations
Rodríguez, A. ; Ruiz-Ramos, M. ; Palosuo, T. ; Carter, T.R. ; Fronzek, S. ; Lorite, I.J. ; Ferrise, R. ; Pirttioja, N. ; Bindi, M. ; Baranowski, P. ; Buis, S. ; Cammarano, D. ; Chen, Y. ; Dumont, B. ; Ewert, F. ; Gaiser, T. ; Hlavinka, P. ; Hoffmann, H. ; Höhn, J.G. ; Jurecka, F. ; Kersebaum, K.C. ; Krzyszczak, J. ; Lana, M. ; Mechiche-Alami, A. ; Minet, J. ; Montesino, M. ; Nendel, C. ; Porter, J.R. ; Ruget, F. ; Semenov, M.A. ; Steinmetz, Z. ; Stratonovitch, P. ; Supit, I. ; Tao, F. ; Trnka, M. ; Wit, A. de; Rötter, R.P. - \ 2019
Agricultural and Forest Meteorology 264 (2019). - ISSN 0168-1923 - p. 351 - 362.
Climate change - Decision support - Outcome confidence - Response surface - Uncertainty - Wheat adaptation

Climate change is expected to severely affect cropping systems and food production in many parts of the world unless local adaptation can ameliorate these impacts. Ensembles of crop simulation models can be useful tools for assessing if proposed adaptation options are capable of achieving target yields, whilst also quantifying the share of uncertainty in the simulated crop impact resulting from the crop models themselves. Although some studies have analysed the influence of ensemble size on model outcomes, the effect of ensemble composition has not yet been properly appraised. Moreover, results and derived recommendations typically rely on averaged ensemble simulation results without accounting sufficiently for the spread of model outcomes. Therefore, we developed an Ensemble Outcome Agreement (EOA) index, which analyses the effect of changes in composition and size of a multi-model ensemble (MME) to evaluate the level of agreement between MME outcomes with respect to a given hypothesis (e.g. that adaptation measures result in positive crop responses). We analysed the recommendations of a previous study performed with an ensemble of 17 crop models and testing 54 adaptation options for rainfed winter wheat (Triticum aestivum L.) at Lleida (NE Spain) under perturbed conditions of temperature, precipitation and atmospheric CO2 concentration. Our results confirmed that most adaptations recommended in the previous study have a positive effect. However, we also showed that some options did not remain recommendable in specific conditions if different ensembles were considered. Using EOA, we were able to identify the adaptation options for which there is high confidence in their effectiveness at enhancing yields, even under severe climate perturbations. These include substituting spring wheat for winter wheat combined with earlier sowing dates and standard or longer duration cultivars, or introducing supplementary irrigation, the latter increasing EOA values in all cases. There is low confidence in recovering yields to baseline levels, although this target could be attained for some adaptation options under moderate climate perturbations. Recommendations derived from such robust results may provide crucial information for stakeholders seeking to implement adaptation measures.

Visual modeling of laser-induced dough browning
Chen, Peter Yichen ; Blutinger, Jonathan David ; Meijers, Yorán ; Zheng, Changxi ; Grinspun, Eitan ; Lipson, Hod - \ 2019
Journal of Food Engineering 243 (2019). - ISSN 0260-8774 - p. 9 - 21.
Browning - Deconvolution - Deep learning - Dough - Generative model - Infrared laser

A data-driven model that predicatively generates photorealistic RGB images of dough surface browning is proposed. This model was validated in a practical application using a CO2 laser dough browning pipeline, thus confirming that it can be employed to characterize visual appearance of browned samples, such as surface color and patterns. A supervised deep generative network takes laser speed, laser energy flux, and dough moisture as an input and outputs an image (of 64×64 pixel size) of laser-browned dough. Image generation is achieved by nonlinearly interpolating high-dimensional training data. The proposed prediction framework contributes to the development of computer-aided design (CAD) software for food processing techniques by creating more accurate photorealistic models.

Plastic film cover during the fallow season preceding sowing increases yield and water use efficiency of rain-fed spring maize in a semi-arid climate
Zhang, Zhe ; Zhang, Yanqing ; Sun, Zhanxiang ; Zheng, Jiaming ; Liu, Enke ; Feng, Liangshan ; Feng, Chen ; Si, Pengfei ; Bai, Wei ; Cai, Qian ; Yang, Ning ; Werf, Wopke van der; Zhang, Lizhen - \ 2019
Agricultural Water Management 212 (2019). - ISSN 0378-3774 - p. 203 - 210.
Film cover - Soil temperature - Water availability - Yield components

Plastic film mulch increases crop yields in rain-fed agriculture in cool semi-arid climates by warming the soil and reducing evaporative water losses. The semi-arid Khorchin area in Northeast China is an important production area for rain-fed maize. Drought stress occurs frequently, even if plastic film mulch is applied at sowing. We hypothesized that the yield and water capture of maize could be increased by reducing evaporative loss of water by use of plastic film cover during the autumn and winter preceding sowing. In this study, we compared maize growth, water uptake and yield in three film cover treatments: (1) film cover from the autumn before maize sowing until maize harvest (autumn mulching: AM), (2) film cover from maize sowing till harvest (conventional practice) (spring mulching: SM), (3) no film cover (no mulch: NM). Field experiments were conducted in Fuxin city, Khorchin region, Liaoning province, China in 2013/2014 and 2014/2015. Autumn mulching increased grain yield on average by 18% when compared to spring mulching and by 36% when compared to no mulching. The 1000-kernel weight in AM was 7% higher than in SM, and 12% higher than in NM. Soil water content in the root zone before sowing was 35 mm greater in AM than in SM and NM. Water uptake during the growing season was 34 mm greater in AM than in SM and NM. Water use efficiency for grain yield (yield per unit water uptake) in AM was on average 2.5% higher than in conventional mulching (SM) and 27% higher than in NM. Autumn mulching advanced development, with an advance of 5 days in tasseling time as compared to SM and 10 days when compared to NM. These results show that film cover during the fallow period before maize sowing can increase crop yield and water use efficiency, and reduce climate risks in rain-fed agriculture under semi-arid conditions.

Irrigation reduces the negative effect of global warming on winter wheat yield and greenhouse gas intensity
Li, Jiazhen ; Dong, Wenxu ; Oenema, Oene ; Chen, Tuo ; Hu, Chunsheng ; Yuan, Haijing ; Zhao, Liying - \ 2019
Science of the Total Environment 646 (2019). - ISSN 0048-9697 - p. 290 - 299.
Global warming potential - Greenhouse gas intensity - Greenhouse gases - Irrigation - Warming - Wheat yield

Global warming may exacerbate drought, decrease crop yield and affect greenhouse gas (GHG) emissions in semi-arid regions. However, the interactive effects of increases in temperature and water availability on winter wheat yield and GHG emissions in semi-arid climates are not well-understood. Here, we report on a two-year field experiment that examined the effects of a mean soil temperature increase of ~2 °C (at 5 cm depth) with and without additional irrigation on wheat yield and GHG emissions. Infrared heaters were placed above the crop canopy at a height of 1.8 m to simulate warming. Fluxes of CH4, CO2 and N2O were measured using closed static chamber technique once per week during the wheat growing seasons. Warming decreased wheat yield by 28% in the relatively dry year of 2015, while supplemental irrigation nullified the warming effect completely. Warming did not alter the wheat yield significantly in the relatively wet year of 2016, but supplemental irrigation with no warming decreased the wheat yield by 25%. Warming increased CO2 emissions by 28% and CH4 uptake by 24% and tended to decrease N2O emissions. Supplemental irrigation increased N2O emissions but had little effect on CO2 emissions and CH4 uptake. Evidently, warming and supplemental irrigation had interactive effects on wheat yield, GHG emissions and GHG emissions intensity. Precision irrigation appears to be a means of simultaneously increasing wheat yield and reducing GHG emissions under warming conditions in semi-arid areas.

Latitudinal adaptation and genetic insights into the origins of cannabis sativa L.
Zhang, Qingying ; Chen, Xuan ; Guo, Hongyan ; Trindade, Luisa M. ; Salentijn, Elma M.J. ; Guo, Rong ; Guo, Mengbi ; Xu, Yanping ; Yang, Ming - \ 2018
Advances in Intelligent Systems and Computing 871 (2018). - ISSN 2194-5357
Cannabaceae - CpDNA - Genetic diversity - Industrial hemp - Phylogeography

Cannabis is one of the most important industrial crops distributed worldwide. However, the phylogeographic structure and domestication knowledge of this crop remains poorly understood. In this study, sequence variations of five chloroplast DNA (cpDNA) regions were investigated to address these questions. For the 645 individuals from 52 Cannabis accessions sampled (25 wild populations and 27 domesticated populations or cultivars), three haplogroups (Haplogroup H, M, L) were identified and these lineages exhibited distinct high-middle-low latitudinal gradients distribution pattern. This pattern can most likely be explained as a consequence of climatic heterogeneity and geographical isolation. Therefore, we examined the correlations between genetic distances and geographical distances, and tested whether the climatic factors are correlated with the cpDNA haplogroup frequencies of populations. The “isolation-by-distance” models were detected for the phylogeographic structure, and the day-length was found to be the most important factor (among 20 BioClim factors) that influenced the population structures. Considering the distinctive phylogeographic structures and no reproductive isolation among members of these lineages, we recommend that Cannabis be recognized as a monotypic genus typified by Cannabis sativa L., containing three subspecies: subsp. sativa, subsp. Indica, and subsp. ruderalis. Within each haplogroup which possesses a relatively independent distribution region, the wild and domesticated populations shared the most common haplotypes, indicating that there are multiregional origins for the domesticated crop. Contrast to the prevalent Central-Asia-Origin hypothesis of C. saltiva, molecular evidence reveals for the first time that the low latitude haplogroup (Haplogroup L) is the earliest divergent lineage, implying that Cannabis is probably originated in low latitude region.

Data from: Responses of insect herbivores and their food plants to wind exposure and the importance of predation risk
Chen, C. ; Biere, Arjen ; Gols, R. ; Halfwerk, Wouter ; Oers, C.H.J. ; Harvey, J.A. - \ 2018
development - abiotic factors - plant-herbivore interactions - predator - plutella xylostella - Pieris brassicae - Parus major
1. Wind is an important abiotic factor that influences an array of biological processes, but it is rarely considered in studies on plant-herbivore interactions. 2. Here, we tested whether wind exposure could directly or indirectly affect the performance of two insect herbivores, Plutella xylostella and Pieris brassicae, feeding on Brassica nigra plants. 3. In a greenhouse study using a factorial design, B. nigra plants were exposed to different wind regimes generated by fans before and after caterpillars were introduced on plants in an attempt to separate the effects of direct and indirect wind exposure on herbivores. 4. Wind exposure delayed flowering, decreased plant height and increased leaf concentrations of amino acids and glucosinolates. 5. Plant-mediated effects of wind on herbivores, i.e., effects of exposure of plants to wind prior to herbivore feeding, were generally small. However, development time of both herbivores was extended and adult body mass of P. xylostella was reduced when they were directly exposed to wind. By contrast, wind-exposed adult P. brassicae butterflies were significantly larger, revealing a trade-off between development time and adult size. 6. Based on these results, we conducted a behavioral experiment to study preference by an avian predator, the Great Tit (Parus major) for last instar P. brassicae caterpillars on plants that were exposed to either control (no wind) or wind (fan-exposed) treatments. Tits captured significantly more caterpillars on still than on wind-exposed plants. 7. Our results suggest that P. brassicae caterpillars are able to perceive the abiotic environment and to trade off the costs of extended development time against the benefits of increased size depending on the perceived risk of predation mediated by wind exposure. Such adaptive phenotypic plasticity in insects has not yet been described in response to wind exposure.
Discovery of common and rare genetic risk variants for colorectal cancer
Huyghe, Jeroen R. ; Bien, Stephanie A. ; Harrison, Tabitha A. ; Kang, Hyun Min ; Chen, Sai ; Schmit, Stephanie L. ; Conti, David V. ; Qu, Conghui ; Jeon, Jihyoun ; Edlund, Christopher K. ; Greenside, Peyton ; Wainberg, Michael ; Schumacher, Fredrick R. ; Smith, Joshua D. ; Levine, David M. ; Nelson, Sarah C. ; Sinnott-armstrong, Nasa A. ; Albanes, Demetrius ; Alonso, M.H. ; Anderson, Kristin ; Arnau-Collell, Coral ; Arndt, Volker ; Bamia, Christina ; Banbury, Barbara L. ; Baron, John A. ; Berndt, Sonja I. ; Bézieau, Stéphane ; Bishop, D.T. ; Boehm, Juergen ; Boeing, Heiner ; Brenner, Hermann ; Brezina, Stefanie ; Buch, Stephan ; Buchanan, Daniel D. ; Burnett-hartman, Andrea ; Butterbach, Katja ; Caan, Bette J. ; Campbell, Peter T. ; Carlson, Christopher S. ; Castellví-Bel, Sergi ; Chan, Andrew T. ; Chang-Claude, Jenny ; Chanock, Stephen J. ; Chirlaque, Maria-Dolores ; Cho, Sang Hee ; Connolly, Charles M. ; Cross, Amanda J. ; Feskens, Edith J.M. ; Huang, Wen-Yi ; Li, Li - \ 2018
Nature Genetics (2018). - ISSN 1061-4036
To further dissect the genetic architecture of colorectal cancer (CRC), we performed whole-genome sequencing of 1,439 cases and 720 controls, imputed discovered sequence variants and Haplotype Reference Consortium panel variants into genome-wide association study data, and tested for association in 34,869 cases and 29,051 controls. Findings were followed up in an additional 23,262 cases and 38,296 controls. We discovered a strongly protective 0.3% frequency variant signal at CHD1. In a combined meta-analysis of 125,478 individuals, we identified 40 new independent signals at P < 5 × 10−8, bringing the number of known independent signals for CRC to ~100. New signals implicate lower-frequency variants, Krüppel-like factors, Hedgehog signaling, Hippo-YAP signaling, long noncoding RNAs and somatic drivers, and support a role for immune function. Heritability analyses suggest that CRC risk is highly polygenic, and larger, more comprehensive studies enabling rare variant analysis will improve understanding of biology underlying this risk and influence personalized screening strategies and drug development.
Sweet corn significantly increases nitrogen retention and reduces nitrogen leaching as summer catch crop in protected vegetable production systems
Guo, Ruiying ; Qin, Wei ; Jiang, Chunguang ; Kang, Lingyun ; Nendel, Claas ; Chen, Qing - \ 2018
Soil & Tillage Research 180 (2018). - ISSN 0167-1987 - p. 148 - 153.
N Isotope - Nitrogen leaching - Protected vegetable production - Soil nitrogen retention - Summer catch crop

Nitrogen (N) leaching is a commonly reported problem in protected vegetable production in China due to poor management. To minimize soil residue N and reduce N leaching, sweet corn is often used as the summer catch crop after the winter-spring growing season. However, the effectiveness of this practice has never been systematically quantified before. Here we reported the effects of sweet corn as catch crop on soil N retention and N leaching in the greenhouse vegetable system, using the data of two 15N isotope micro-plot experiments in soil-bound greenhouse. The results showed that sweet corn removed 11.5% of total residual 15N in soil profile and kept more organic 15N by 39.8% in soil profile, compared to fallow treatment. Root activity increased nitrogen retention due to temporarily immobilizing N as organic form, thereby reducing N leaching. Interestingly, sweet corn significantly reduced N leaching in the later growing stage (August), but not in the earlier stages (July). In total, dissolved organic nitrogen (DON) accounted for 63% of total N leaching. Sweet corn significantly reduced DON leaching, but not mineral N (Nmin) leaching. Hence, reducing N leaching in Chinese greenhouse must distinguish DON and Nmin sources and optimize both. Our study provides quantitative insights in N retention and leaching influenced by sweet corn as catch crop in typical Chinese greenhouse production systems, which provide guidance for searching for better catch crops in further studies.

Family size dynamics in wintering geese
Gupte, Pratik R. ; Koffijberg, Kees ; Müskens, Gerard J.D.M. ; Wikelski, Martin ; Kölzsch, Andrea - \ 2018
Journal of Ornithology (2018). - ISSN 2193-7192
Age ratio - Differential migration - Family separation - Foraging flocks - Greater White-fronted Goose Anser a. albifrons - Social status

Many bird populations are made up of social units with differences in size and social status. Of these, the family and flock structure of geese Anserini are among the better known. However, how the association of juvenile geese with their parents in families influences the migration timing and space-use of populations, as well as the events leading to juvenile independence are not well understood. We focus on family size dynamics of the Greater White-fronted Goose Anser a. albifrons on its wintering grounds in the Netherlands and northern Germany, where we gathered 17 years of observation data on foraging flocks and tracked 13 complete families with GPS transmitters. We explored how social status and family size affected wintering site choice and migration timing as well as how and why family sizes decreased. We found that family size decreased strongly during autumn migration, likely from juvenile death due to insufficient fuelling. It further decreased through the winter, here seemingly by juveniles accidentally splitting off during strong disturbance events. Different from previous findings, a large proportion of juveniles became independent during winter. Large families generally arrived later to the wintering grounds, wintered further from the breeding grounds and departed later for spring migration than adults without young. Independent young left for spring migration last. Thus, White-fronted Geese are differential migrants by social status. In combination with the observation of low breeding success in this population in recent years, our findings improve the understanding of its spatial and temporal patterns during winter, and their apparent changes. This can support conservation and management decisions for both White-fronted Geese as well as other large migrants with complex age and social structure.

Understanding the mechanisms of soil water repellency from nanoscale to ecosystem scale: a review
Mao, Jiefei ; Nierop, Klaas G.J. ; Dekker, Stefan C. ; Dekker, Louis W. ; Chen, Baoliang - \ 2018
Journal of Soils and Sediments (2018). - ISSN 1439-0108 - p. 1 - 15.
Ecosystem - Nanoscale - Organic compounds - Soil hydrophobicity - Soil moisture

Purpose: Soil water repellency (SWR) can interrupt water infiltration that may decline plant growth and potentially trigger soil erosion. Until now research has been mainly focused on understanding the mechanisms of SWR at different scales by observation and modelling studies. Materials and methods: This review systematically discusses the possible mechanisms at different scales of the occurrence and persistence of SWR from nanoscale to ecosystem scale. Results and discussion: Soil characteristics are strongly related to the severity of SWR, particularly in soil organic matter and soil moisture. The presence of a higher amount of hydrophobic organic compounds and lower soil moisture content lead to higher water repellency, suggesting that the interaction at the nanoscale between organic compounds and water molecules primarily determines the persistence of SWR. The repeated alternation of drying-wetting process largely modifies the relationship between water molecules and soil particles that impacts the possibility of SWR from hydrophilic in wet condition to hydrophobic in dry condition. Within ecosystem scale, vegetation and microbes are original sources of SWR-inducing compounds influencing the distribution and prevalence of SWR. Nevertheless, the challenge of global climate change, drought and warming can increase SWR. Extreme SWR induces more serious runoff and overland flow that is enhanced by intensive precipitation. Conclusions: We conclude that understanding the interaction of water molecules and organic compounds at soil particle surface is essential to understand SWR at the nanoscale. Expanding the mechanisms of SWR from nanoscale to a larger scale is fundamental to improve the remediation of soil pollution and mitigate global change.

Erratum to: Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study
Hellenkamp, Björn ; Schmid, Sonja ; Doroshenko, Olga ; Opanasyuk, Oleg ; Kühnemuth, Ralf ; Adariani, Soheila Rezaei ; Ambrose, Benjamin ; Aznauryan, Mikayel ; Barth, Anders ; Birkedal, Victoria ; Bowen, Mark E. ; Chen, Hongtao ; Cordes, Thorben ; Eilert, Tobias ; Fijen, Carel ; Gebhardt, Christian ; Götz, Markus ; Gouridis, Giorgos ; Gratton, Enrico ; Ha, Taekjip ; Hao, Pengyu ; Hanke, Christian A. ; Hartmann, Andreas ; Hendrix, Jelle ; Hildebrandt, Lasse L. ; Hirschfeld, Verena ; Hohlbein, Johannes ; Hua, Boyang ; Hübner, Christian G. ; Kallis, Eleni ; Kapanidis, Achillefs N. ; Kim, Jae Yeol ; Krainer, Georg ; Lamb, Don C. ; Lee, Nam Ki ; Lemke, Edward A. ; Levesque, Brié ; Levitus, Marcia ; McCann, James J. ; Naredi-Rainer, Nikolaus ; Nettels, Daniel ; Ngo, Thuy ; Qiu, Ruoyi ; Robb, Nicole C. ; Röcker, Carlheinz ; Sanabria, Hugo ; Schlierf, Michael ; Schröder, Tim ; Schuler, Benjamin ; Seidel, Henning - \ 2018
Nature Methods : techniques for life scientists and chemists 15 (2018)11. - ISSN 1548-7091 - p. 984 - 984.

This paper was originally published under standard Springer Nature copyright. As of the date of this correction, the Analysis is available online as an open-access paper with a CC-BY license. No other part of the paper has been changed.

In vitro protein digestion kinetics of protein sources for pigs
Chen, H. ; Wierenga, P.A. ; Hendriks, W.H. ; Jansman, A.J.M. - \ 2018
Animal (2018). - ISSN 1751-7311 - 11 p.
black soldier fly larvae - gastrointestinal protein degradation - plant protein sources - porcine plasma - yellow meal worm

In current feed evaluation systems, the nutritional value of protein sources in diets for pigs is based on the ileal digestibility of protein and amino acids, which does not account for the kinetics of protein digestion along the gastrointestinal tract. The objective of the present study was to determine the in vitro protein digestion kinetics of different protein sources (soya bean meal (SBM), wheat gluten (WG), rapeseed meal (RSM), whey powder (WP), dried porcine plasma protein, yellow meal worm larvae and black soldier fly larvae (BSF)). Protein sources were incubated with pepsin at pH 3.5 for 0 to 90 min and subsequently with pancreatin at pH 6.8 for 0 to 210 min at 39°C. The in vitro protein digestion kinetics were described as the kinetics of nitrogen (N) solubilisation and the release of low molecular weight peptides (LMW) (<500 Da). The N solubilisation rate ranged from 0.025 min-1 for BSF to 0.685 min-1 for WP during the incubation with pepsin, and from 0.027 min-1 for RSM to 0.343 min-1 for WP during the incubation with pancreatin. The release rate of LMW peptides ranged from 0.027 min-1 for WG to 0.093 min-1 for WP during the incubation with pepsin, and from 0.029 min-1 for SBM to 0.385 min-1 for WP. Black soldier fly larvae showed a similar release rate of LMW peptides as WP during the incubation with pancreatin. At the end of the sequential incubation with pepsin (90 min) and pancreatin (210 min), WG and WP showed the highest percentage of N present in LMW peptides relative to total N (78% and 79%, respectively), whereas SBM showed the lowest (35%). In conclusion, protein sources for pig diets show substantial differences in in vitro protein digestion kinetics as measured by the kinetics of N solubilisation and the release of LMW peptides. The rate of release of LMW peptides was not correlated to the rate of N solubilisation for each of the protein sources evaluated.

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