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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The fertilization effect of global dimming on crop yields is not attributed to an improved light interception
Shao, Liping ; Li, Gang ; Zhao, Qiannan ; Li, Yabing ; Sun, Yutong ; Wang, Weinan ; Cai, Chuang ; Chen, Weiping ; Liu, Ronghua ; Luo, Weihong ; Yin, Xinyou ; Lee, Xuhui - \ 2019
Global Change Biology (2019). - ISSN 1354-1013
acclimation - diffuse radiation - fertilization effect - global dimming - radiation use efficiency - rice - wheat - yield

Global dimming, a decadal decrease in incident global radiation, is often accompanied with an increase in the diffuse radiation fraction, and, therefore, the impact of global dimming on crop production is hard to predict. A popular approach to quantify this impact is the statistical analysis of historical climate and crop data, or use of dynamic crop simulation modelling approach. Here, we show that statistical analysis of historical data did not provide plausible values for the effect of diffuse radiation versus direct radiation on rice or wheat yield. In contrast, our field experimental study of 3 years demonstrated a fertilization effect of increased diffuse radiation fraction, which partly offset yield losses caused by decreased global radiation, in both crops. The fertilization effect was not attributed to any improved canopy light interception but mainly to the increased radiation use efficiency (RUE). The increased RUE was explained not only by the saturating shape of photosynthetic light response curves but also by plant acclimation to dimming that gradually increased leaf nitrogen concentration. Crop harvest index slightly decreased under dimming, thereby discounting the fertilization effect on crop yields. These results challenge existing modelling paradigms, which assume that the fertilization effect on crop yields is mainly attributed to an improved light interception. Further studies on the physiological mechanism of plant acclimation are required to better quantify the global dimming impact on agroecosystem productivity under future climate change.

Simulated heatwave conditions associated with global warming affect development and competition between hyperparasitoids
Chen, Cong ; Donner, Helena ; Biere, Arjen ; Gols, Rieta ; Harvey, Jeffrey A. - \ 2019
Oikos (2019). - ISSN 0030-1299
Acrolyta nens - climate warming - Cotesia glomerata - host–parasitoid interactions intrinsic competition - Lysibia nana - temperature

Anthropogenic global warming and attendant effects like heatwaves affect the biology and ecology of both individuals and species within and across different trophic levels. Here, we examined the effects of a simulated heatwave on development of and competition between two hyperparasitoid wasps, Lysibia nana and Acrolyta nens when attacking the same host, cocoons of the primary parasitoid, Cotesia glomerata. Parasitized hosts were exposed to three different day and night temperature regimes (low, medium and high) that reflect cool, normal and heatwave conditions in the Netherlands. We found that higher temperatures decreased survival to eclosion more strongly in the hyperparasitoids than in their host. Heatwave conditions also shortened development time and led to the production of smaller adult wasps of both hyperparasitoid species in singly parasitized hosts. In multiparasitized hosts, L. nana won most of the contests when it oviposited first, irrespective of the time interval between the first and second parasitism, whereas A. nens only dominated when it had a 24 h head start or longer. Most importantly, our results show that L. nana in particular benefited in competition at higher temperatures, perhaps due to an increase in the metabolic rate and more rapid egg and/or larval development. This may potentially reduce opportunities for coexistence following heat waves. Our results suggest that heatwaves associated with global warming will enhance the rate of development, but negatively affect survival and other fitness-related traits in (hyper)parasitoids. Moreover, the outcome of larval competition may be determined via physiological responses that are species-specific and thus influence phenology.

The acclimation of leaf photosynthesis of wheat and rice to seasonal temperature changes in T-FACE environments
Cai, Chuang ; Li, Gang ; Di, Lijun ; Ding, Yunjie ; Fu, Lin ; Guo, Xuanhe ; Struik, Paul C. ; Pan, Genxing ; Li, Haozheng ; Chen, Weiping ; Luo, Weihong ; Yin, Xinyou - \ 2019
Global Change Biology (2019). - ISSN 1354-1013
climate change - free-air CO enrichment - growth temperature - leaf nitrogen content - Oryza sativa L. - photosynthesis model - stomatal conductance - Triticum aestivum L.

Crops show considerable capacity to adjust their photosynthetic characteristics to seasonal changes in temperature. However, how photosynthesis acclimates to changes in seasonal temperature under future climate conditions has not been revealed. We measured leaf photosynthesis (An) of wheat (Triticum aestivum L.) and rice (Oryza sativa L.) grown under four combinations of two levels of CO2 (ambient and enriched up to 500 µmol/mol) and two levels of canopy temperature (ambient and increased by 1.5–2.0°C) in temperature by free-air CO2 enrichment (T-FACE) systems. Parameters of a biochemical C3-photosynthesis model and of a stomatal conductance (gs) model were estimated for the four conditions and for several crop stages. Some biochemical parameters related to electron transport and most gs parameters showed acclimation to seasonal growth temperature in both crops. The acclimation response did not differ much between wheat and rice, nor among the four treatments of the T-FACE systems, when the difference in the seasonal growth temperature was accounted for. The relationships between biochemical parameters and leaf nitrogen content were consistent across leaf ranks, developmental stages, and treatment conditions. The acclimation had a strong impact on gs model parameters: when parameter values of a particular stage were used, the model failed to correctly estimate gs values of other stages. Further analysis using the coupled gs–biochemical photosynthesis model showed that ignoring the acclimation effect did not result in critical errors in estimating leaf photosynthesis under future climate, as long as parameter values were measured or derived from data obtained before flowering.

Earthworms Coordinate Soil Biota to Improve Multiple Ecosystem Functions
Liu, Ting ; Chen, Xiaoyun ; Gong, Xin ; Lubbers, Ingrid M. ; Jiang, Yangyang ; Feng, Wen ; Li, Xianping ; Whalen, Joann K. ; Bonkowski, Michael ; Griffiths, Bryan S. ; Hu, Feng ; Liu, Manqiang - \ 2019
Current Biology 29 (2019)20. - ISSN 0960-9822 - p. 3420 - 3429.
bacterial-dominated channel - earthworm - ecosystem engineer - ecosystem service - soil fauna - soil microbe - sustainable agriculture

Liu et al. study a 13-year-old field experiment to show that earthworms are beneficial to agroecosystems from a multifunctional perspective. This work incorporates the concerns of negative effects of earthworms in recently published syntheses and highlights the potential pathways in which earthworms contribute to sustainable agriculture.

Optimum leaf defoliation: A new agronomic approach for increasing nutrient uptake and land equivalent ratio of maize soybean relay intercropping system
Raza, Muhammad Ali ; Feng, Ling Yang ; Werf, Wopke van der; Iqbal, Nasir ; Khan, Imran ; Hassan, Muhammad Jawad ; Ansar, Muhammad ; Chen, Yuan Kai ; Xi, Zeng Jin ; Shi, Jian Yi ; Ahmed, Mukhtar ; Yang, Feng ; Yang, Wenyu - \ 2019
Field Crops Research 244 (2019). - ISSN 0378-4290
Defoliation - Economics - LER - Nutrient - Relay-intercropping

Upper canopy leaves of maize decrease the light-transmittance at middle-strata-leaves of maize and soybean canopy in maize-soybean relay-intercropping systems (MS). This affects the uptake of nutrients and distribution patterns in various plant organs of intercrop species in MS. Judicious defoliation of maize plants in MS could help to alleviate this problem and improve nutrient uptake and intercrop yields. In a two-year field experiment with MS, including the measurements of biomass production, nutrients uptake, and distribution at the organ level, and grain yields of intercrop species, maize plants were subjected to four-leaf defoliation treatments to improve the light-transmittance of maize and soybean plants. Defoliation of the topmost two-leaves (T2), four-leaves (T4), six-leaves (T6) was compared to no defoliation (T0). Compared to T0, treatment T2 improved the uptake of nitrogen (N), phosphorus (P), and potassium (K) in each plant part of maize by 23, 12, and 11% (grain), 22, 19, and 13% (straw), and 28, 14, and 18% (root), respectively. Defoliation also enhanced the uptake of N, P, and K in each plant part of soybean by 5, 5, and 10% (grain), 10, 17, and 13% (straw), and 14, 11, and 11% (root), respectively. The improved nutrient uptake in T2 increased the total biomass and its distribution in the root, straw, and grain of soybean and maize by 15 and 13%, and 21 and 15%, 20 and 14%, 7 and 10%, respectively compared to T0. On average, over two years, under T2, relay-cropped maize obtained 107% of the sole-yield, and relay-cropped soybean obtained 65% of the sole-yield. The T2 defoliation treatment also achieved the highest land equivalent ratio of 1.69 and 1.77, with a net profit of 1301.6 $ ha−1 and 1293.4 $ ha−1 in 2017 and 2018, respectively. Following the optimum defoliation treatment of maize in maize-soybean intercrops, i.e., defoliation of the topmost two-leaves, the nutrient uptake can be increased, and the nutrient partitioning over plant organs be better balanced. Optimum defoliation, therefore, enhances the productivity of maize-soybean intercropping systems.

Recently duplicated sesterpene (C25) gene clusters in Arabidopsis thaliana modulate root microbiota.
Chen, Qingwen ; Jiang, Ting ; Liu, Yong-Xiu ; Haili, Liu ; Zhao, T. ; Liu, Zhixi ; Gan, Xiangchao ; Hallab, Asis ; Wang, Xuemei ; He, Juan ; Ma, Yihua ; Zhang, Fengxia ; Jin, Tao ; Schranz, M.E. ; Wang, Yong ; Yang, Bai - \ 2019
Science in China Series C-Life Sciences 62 (2019)7. - ISSN 1006-9305 - p. 947 - 958.
Quantifying Localized Macromolecular Dynamics within Hydrated Cellulose Fibril Aggregates
Chen, Pan ; Terenzi, Camilla ; Furó, István ; Berglund, Lars A. ; Wohlert, Jakob - \ 2019
Macromolecules (2019). - ISSN 0024-9297 - p. 7278 - 7288.

Molecular dynamics (MD) simulations of 13C NMR longitudinal relaxation (T1) distributions were recently established as a powerful tool for characterizing moisture adsorption in natural amorphous polymers. Here, such computational-experimental synergy is demonstrated in a system with intrinsically high structural heterogeneity, namely crystalline cellulose nanofibrils (CNFs) in highly hydrated aggregated state. In such a system, structure-function properties on the nanoscale remain largely uncovered by experimental means alone. In this work, broadly polydispersed experimental 13C NMR T1 distributions could be successfully reproduced in simulations and, for the first time, were decomposed into contributions from distinct molecular sources within the aggregated CNFs, namely, (i) the core and (ii) the less-accessible and accessible surface regions of the CNFs. Furthermore, within the surface groups structurally different sites such as (iii) residues with different hydroxymethyl orientations and (iv) center and origin chains could be discerned based on their distinct molecular dynamics. The MD simulations unravel a direct correlation between dynamical and structural heterogeneity at an atomistic-level resolution that cannot be accessed by NMR experiments. The proposed approach holds the potential to enable quantitative interpretation of NMR data from a range of multicomponent high-performance nanocomposites with significantly heterogeneous macromolecular structure.

Maize leaf-removal: A new agronomic approach to increase dry matter, flower number and seed-yield of soybean in maize soybean relay intercropping system
Raza, Muhammad Ali ; Feng, Ling Yang ; Werf, Wopke van der; Iqbal, Nasir ; Khalid, Muhammad Hayder Bin ; Chen, Yuan Kai ; Wasaya, Allah ; Ahmed, Shoaib ; Ud Din, Atta Mohi ; Khan, Ahsin ; Ahmed, Saeed ; Yang, Feng ; Yang, Wenyu - \ 2019
Scientific Reports 9 (2019)1. - ISSN 2045-2322 - 1 p.

Shading conditions adversely affect flower-number and pod-number of soybeans under maize-soybean relay-intercropping (MSR). Here we reveal that leaf-removal from maize-canopy improves the photosynthetically active radiation (PAR) transmittance and dry-matter production (DMP) of soybean (especially during the co-growth phase), and compensates the maize seed-yield loss by considerably increasing soybean seed-yield. In a two-year experiment with MSR, maize-plants were subjected to different leaf-removal treatments to increase the PAR-transmittance of soybean; removal of the topmost two-leaves (R2), four-leaves (R4), six-leaves (R6), with no-removal of leaves (R0). Leaf-removal treatments improved the PAR-transmittance, photosynthetic-rate, and morphological-characteristics of soybean under MSR. At 90 days after sowing, the dry-matter of pods, and seeds was increased by 25%, and 32%, respectively under R6 than R0. Importantly, enhanced PAR-transmittance and DMP under R6 enabled soybean to initiate a greater number of flowers 182.2 plant-1 compared to 142.7 plant-1 under R0, and it also decreased the flower-abscission (by 13%, from 54.9% under R0 to 47.6% under R6). These positive responses increased the pod-number by 49% and seed-number by 28% under R6 than R0. Overall, under R6, relay-intercropped soybean produced 78% of sole-soybean seed-yield, and relay-intercropped maize produced 81% of sole-maize seed-yield and achieved the land equivalent ratio of 1.59.

Selection and gene flow shape niche-associated variation in pheromone response
Lee, Daehan ; Zdraljevic, Stefan ; Cook, Daniel E. ; Frézal, Lise ; Hsu, Jung-Chen ; Sterken, Mark G. ; Riksen, Joost A.G. ; Wang, John ; Kammenga, Jan E. ; Braendle, Christian ; Félix, Marie-Anne ; Schroeder, Frank C. ; Andersen, Erik C. - \ 2019
Nature Ecology & Evolution 3 (2019). - ISSN 2397-334X - p. 1455 - 1463.
From quorum sensing in bacteria to pheromone signalling in social insects, chemical communication mediates interactions among individuals in local populations. In Caenorhabditis elegans, ascaroside pheromones can dictate local population density; high levels of pheromones inhibit the reproductive maturation of individuals. Little is known about how natural genetic diversity affects the pheromone responses of individuals from diverse habitats. Here, we show that a niche-associated variation in pheromone receptor genes contributes to natural differences in pheromone responses. We identified putative loss-of-function deletions that impair duplicated pheromone receptor genes (srg-36 and srg-37), which were previously shown to be lost in population-dense laboratory cultures. A common natural deletion in srg-37 arose recently from a single ancestral population that spread throughout the world; this deletion underlies reduced pheromone sensitivity across the global C. elegans population. We found that many local populations harbour individuals with a wild-type or a deletion allele of srg-37, suggesting that balancing selection has maintained the recent variation in this pheromone receptor gene. The two srg-37 genotypes are associated with niche diversity underlying boom-and-bust population dynamics. We hypothesize that human activities likely contributed to the gene flow and balancing selection of srg-37 variation through facilitating the migration of species and providing a favourable niche for the recently arisen srg-37 deletion.

FgPex3, a Peroxisome Biogenesis Factor, Is Involved in Regulating Vegetative Growth, Conidiation, Sexual Development, and Virulence in Fusarium graminearum
Kong, Xiangjiu ; Zhang, Hao ; Wang, Xiaoliang ; Lee, T.A.J. van der; Waalwijk, C. ; Diepeningen, A.D. van; Brankovics, Balázs ; Xu, Jin ; Xu, Jingsheng ; Chen, Wanquan ; Feng, Jie - \ 2019
Frontiers in Microbiology 10 (2019). - ISSN 1664-302X
Peroxisomes are involved in a wide range of important cellular functions. Here, the role of the peroxisomal membrane protein PEX3 in the plant-pathogen and mycotoxin producer Fusarium graminearum was studied using knock-out and complemented strains. To fluorescently label peroxisomes’ punctate structures, GFP and RFP fusions with the PTS1 and PTS2 localization signal were transformed into the wild type PH- 1 and 1FgPex3 knock-out strains. The GFP and RFP transformants in the 1FgPex3 background showed a diffuse fluorescence pattern across the cytoplasm suggesting the absence of mature peroxisomes. The 1FgPex3 strain showed a minor, non-significant reduction in growth on various sugar carbon sources. In contrast, deletion of FgPex3 affected fatty acid b-oxidation in F. graminearum and significantly reduced the utilization of fatty acids. Furthermore, the 1FgPex3 mutant was sensitive to osmotic stressors
as well as to cell wall-damaging agents. Reactive oxygen species (ROS) levels in the mutant had increased significantly, which may be linked to the reduced longevity of cultured strains. The mutant also showed reduced production of conidiospores, while sexual reproduction was completely impaired. The pathogenicity of 1FgPex3, especially during the process of systemic infection, was strongly reduced on both tomato and on wheat, while to production of deoxynivalenol (DON), an important factor for virulence, appeared to be unaffected.
Robustness of trait connections across environmental gradients and growth forms
Flores-Moreno, Habacuc ; Fazayeli, Farideh ; Banerjee, Arindam ; Datta, Abhirup ; Kattge, Jens ; Butler, Ethan E. ; Atkin, Owen K. ; Wythers, Kirk ; Chen, Ming ; Anand, Madhur ; Bahn, Michael ; Byun, Chaeho ; Cornelissen, Hans C. ; Craine, Joseph ; Gonzalez-Melo, Andres ; Hattingh, Wesley N. ; Jansen, Steven ; Kraft, Nathan J.B. ; Kramer, Koen ; Laughlin, Daniel C. ; Minden, Vanessa ; Niinemets, Ülo ; Onipchenko, Vladimir ; Peñuelas, Josep ; Soudzilovskaia, Nadejda A. ; Dalrymple, Rhiannon L. ; Reich, Peter B. - \ 2019
Global Ecology and Biogeography (2019). - ISSN 1466-822X
leaf traits - plant functional traits - plant strategy integration - seed traits - stem traits - trait interdependence - trait networks

Aim: Plant trait databases often contain traits that are correlated, but for whom direct (undirected statistical dependency) and indirect (mediated by other traits) connections may be confounded. The confounding of correlation and connection hinders our understanding of plant strategies, and how these vary among growth forms and climate zones. We identified the direct and indirect connections across plant traits relevant to competition, resource acquisition and reproductive strategies using a global database and explored whether connections within and between traits from different tissue types vary across climates and growth forms. Location: Global. Major taxa studied: Plants. Time period: Present. Methods: We used probabilistic graphical models and a database of 10 plant traits (leaf area, specific leaf area, mass- and area-based leaf nitrogen and phosphorous content, leaf life span, plant height, stem specific density and seed mass) with 16,281 records to describe direct and indirect connections across woody and non-woody plants across tropical, temperate, arid, cold and polar regions. Results: Trait networks based on direct connections are sparser than those based on correlations. Land plants had high connectivity across traits within and between tissue types; leaf life span and stem specific density shared direct connections with all other traits. For both growth forms, two groups of traits form modules of more highly connected traits; one related to resource acquisition, the other to plant architecture and reproduction. Woody species had higher trait network modularity in polar compared to temperate and tropical climates, while non-woody species did not show significant differences in modularity across climate regions. Main conclusions: Plant traits are highly connected both within and across tissue types, yet traits segregate into persistent modules of traits. Variation in the modularity of trait networks suggests that trait connectivity is shaped by prevailing environmental conditions and demonstrates that plants of different growth forms use alternative strategies to cope with local conditions.

The consequences of seabird habitat loss from offshore wind turbines, version 2 : Displacement and population level effects in 5 selected species
Kooten, Tobias van; Soudijn, Floor ; Tulp, Ingrid ; Chen, Chun ; Benden, Daniel ; Leopold, Mardik - \ 2019
IJmuiden : Wageningen Marine Research (Wageningen Marine Research report C063/19) - 116
Rain downpours affect survival and development of insect herbivores: the specter of climate change?
Chen, Cong ; Harvey, Jeffrey A. ; Biere, Arjen ; Gols, Rieta - \ 2019
Ecology 100 (2019)11. - ISSN 0012-9658
climate change - development - global warming - glucosinolates - insect herbivores - phytochemistry - plant–insect interactions - rain - secondary plant metabolites

Changes in the frequency, duration, and intensity of rainfall events are among the abiotic effects predicted under anthropogenic global warming. Heavy downpours may profoundly affect the development and survival of small organisms such as insects. Here, we examined direct (physically on the insects) and indirect (plant-mediated) effects of simulated downpours on the performance of caterpillars of two lepidopteran herbivores (Plutella xylostella and Pieris brassicae) feeding on black mustard (Brassica nigra) plants. Host plants were exposed to different rainfall regimes both before and while caterpillars were feeding on the plants in an attempt to separate direct and indirect (plant-mediated) effects of rainfall on insect survival and development. In two independent experiments, downpours were simulated as a single long (20 min) or as three short (5 min) daily events. Downpours had a strong negative direct effect on the survival of P. xylostella, but not on that of P. brassicae. Direct effects of downpours consistently increased development time of both herbivore species, whereas effects on body mass depended on herbivore species and downpour frequency. Caterpillar disturbance by rain and recorded microclimatic cooling by 5°C may explain extended immature development. Indirect, plant-mediated effects of downpours on the herbivores were generally small, despite the fact that sugar concentrations were reduced and herbivore induction of secondary metabolites (glucosinolates) was enhanced in plants exposed to rain. Changes in the frequency of precipitation events due to climate change may impact the survival and development of insect herbivores differentially. Broader effects of downpours on insects and other arthropods up the food chain could seriously impair and disrupt trophic interactions, ultimately destabilizing communities.

Novel strategies for risk assessment of pyrrolizidine alkaloids
Chen, Lu - \ 2019
Wageningen University. Promotor(en): I.M.C.M. Rietjens, co-promotor(en): A.A.C.M. Peijnenburg. - Wageningen : Wageningen University - ISBN 9789463950374 - 245
Improving accuracy of direct and maternal genetic effects in genomic evaluations using pooled boar semen: a simulation study
Maiorano, Amanda M. ; Assen, Alula ; Bijma, Piter ; Chen, Ching Yi ; Silva, Josineudson Augusto Ii Vasconcelos ; Herring, William O. ; Tsuruta, Shogo ; Misztal, Ignacy ; Lourenco, Daniela A.L. - \ 2019
Journal of Animal Science 97 (2019)8. - ISSN 0021-8812 - p. 3237 - 3245.
genomic prediction - maternal ability - multiple sire - prediction accuracy

Pooling semen of multiple boars is commonly used in swine production systems. Compared with single boar systems, this technique changes family structure creating maternal half-sib families. The aim of this simulation study was to investigate how pooling semen affects the accuracy of estimating direct and maternal effects for individual piglet birth weight, in purebred pigs. Different scenarios of pooling semen were simulated by allowing the same female to mate from 1 to 6 boars, per insemination, whereas litter size was kept constant (N = 12). In each pooled boar scenario, genomic information was used to construct either the genomic relationship matrix (G) or to reconstruct pedigree in addition to G. Genotypes were generated for 60,000 SNPs evenly distributed across 18 autosomes. From the 5 simulated generations, only animals from generations 3 to 5 were genotyped (N = 36,000). Direct and maternal true breeding values (TBV) were computed as the sum of the effects of the 1,080 QTLs. Phenotypes were constructed as the sum of direct TBV, maternal TBV, an overall mean of 1.25 kg, and a residual effect. The simulated heritabilities for direct and maternal effects were 0.056 and 0.19, respectively, and the genetic correlation between both effects was -0.25. All simulations were replicated 5 times. Variance components and direct and maternal heritability were estimated using average information REML. Predictions were computed via pedigree-based BLUP and single-step genomic BLUP (ssGBLUP). Genotyped littermates in the last generation were used for validation. Prediction accuracies were calculated as correlations between EBV and TBV for direct (accdirect) and maternal (accmat) effects. When boars were known, accdirect were 0.21 (1 boar) and 0.26 (6 boars) for BLUP, whereas for ssGBLUP, they were 0.38 (1 boar) and 0.43 (6 boars). When boars were unknown, accdirect was lower in BLUP but similar in ssGBLUP. For the scenario with known boars, accmat was 0.58 and 0.63 for 1 and 6 boars, respectively, under ssGBLUP. For unknown boars, accmat was 0.63 for 2 boars and 0.62 for 6 boars in ssGBLUP. In general, accdirect and accmat were lower in the single-boar scenario compared with pooled semen scenarios, indicating that a half-sib structure is more adequate to estimate direct and maternal effects. Using pooled semen from multiple boars can help us to improve accuracy of predicting maternal and direct effects when maternal half-sib families are larger than 2.

Seed maturation and post-harvest ripening negatively affect arabidopsis somatic embryogenesis
Wu, Han ; Chen, Baojian ; Fiers, Martijn ; Wróbel-Marek, Justyna ; Kodde, Jan ; Groot, Steven P.C. ; Angenent, Gerco ; Feng, Hui ; Bentsink, Leónie ; Boutilier, Kim - \ 2019
Plant Cell, Tissue and Organ Culture: an international journal on in vitro culture of higher plants 139 (2019)1. - ISSN 0167-6857 - p. 17 - 27.
ABA - Arabidopsis - Auxin - Post-harvest ripening - ROS - Seed maturation - Somatic embryogenesis

Plant development is highly malleable, as evidenced by the ability of cultured cells, tissues and organs to regenerate into whole plants in vitro. The ability of plants to regenerate in vitro is influenced by many different factors, including the donor plant growth conditions and the type of explant. Empirical trial and error manipulation of these and other culture parameters is the basis for improving plant regeneration protocols, but the mechanisms underlying the effects of these parameters on plant regeneration are unknown. Somatic embryogenesis (SE) is a type of in vitro plant regeneration where somatic/vegetative cells are induced to form embryos. Here we show that seed maturation is one of the parameters that affects the ability of germinating embryos to undergo auxin-induced somatic embryogenesis in Arabidopsis thaliana. Late maturation stage seeds harvested from yellow siliques have a higher capacity for somatic embryogenesis than seeds harvested later from brown siliques, a process that can be mimicked by post-harvest storage. Physiological and genetic analyses suggest that an oxidizing environment and ABA metabolism enhance the rate at which germinating embryos lose capacity to reactivate embryogenic growth. Our data suggest that there is a narrow window during late seed maturation in which embryogenic competence is reduced, and that this process also takes place, albeit more slowly, during seed storage. This knowledge provides a framework for identifying new plant totipotency factors and for directing efficient SE in systems that make use of mature seed explants.

Super-resolution land cover mapping based on the convolutional neural network
Jia, Yuanxin ; Ge, Yong ; Chen, Yuehong ; Li, Sanping ; Heuvelink, Gerard B.M. ; Ling, Feng - \ 2019
Remote Sensing 11 (2019)15. - ISSN 2072-4292
Convolutional neural network - Land cover - Remote sensing imagery - Super-resolution mapping

Super-resolution mapping (SRM) is used to obtain fine-scale land cover maps from coarse remote sensing images. Spatial attraction, geostatistics, and using prior geographic information are conventional approaches used to derive fine-scale land cover maps. As the convolutional neural network (CNN) has been shown to be effective in capturing the spatial characteristics of geographic objects and extrapolating calibrated methods to other study areas, it may be a useful approach to overcome limitations of current SRM methods. In this paper, a new SRM method based on the CNN (SRMCNN) is proposed and tested. Specifically, an encoder-decoder CNN is used to model the nonlinear relationship between coarse remote sensing images and fine-scale land cover maps. Two real-image experiments were conducted to analyze the effectiveness of the proposed method. The results demonstrate that the overall accuracy of the proposed SRMCNN method was 3% to 5% higher than that of two existing SRM methods. Moreover, the proposed SRMCNN method was validated by visualizing output features and analyzing the performance of different geographic objects.

Molnetenhancer: Enhanced molecular networks by integrating metabolome mining and annotation tools
Ernst, Madeleine ; Kang, Kyo Bin ; Caraballo-Rodríguez, Andrés Mauricio ; Nothias, Louis Felix ; Wandy, Joe ; Chen, Christopher ; Wang, Mingxun ; Rogers, Simon ; Medema, Marnix H. ; Dorrestein, Pieter C. ; Hooft, Justin J.J. van der - \ 2019
Metabolites 9 (2019)7. - ISSN 2218-1989
Chemical classification - In silico workflows - Metabolite annotation - Metabolite identification - Metabolome mining - Molecular families - Networking - Substructures

Metabolomics has started to embrace computational approaches for chemical interpretation of large data sets. Yet, metabolite annotation remains a key challenge. Recently, molecular networking and MS2LDA emerged as molecular mining tools that find molecular families and substructures in mass spectrometry fragmentation data. Moreover, in silico annotation tools obtain and rank candidate molecules for fragmentation spectra. Ideally, all structural information obtained and inferred from these computational tools could be combined to increase the resulting chemical insight one can obtain from a data set. However, integration is currently hampered as each tool has its own output format and efficient matching of data across these tools is lacking. Here, we introduce MolNetEnhancer, a workflow that combines the outputs from molecular networking, MS2LDA, in silico annotation tools (such as Network Annotation Propagation or DEREPLICATOR), and the automated chemical classification through ClassyFire to provide a more comprehensive chemical overview of metabolomics data whilst at the same time illuminating structural details for each fragmentation spectrum. We present examples from four plant and bacterial case studies and show how MolNetEnhancer enables the chemical annotation, visualization, and discovery of the subtle substructural diversity within molecular families. We conclude that MolNetEnhancer is a useful tool that greatly assists the metabolomics researcher in deciphering the metabolome through combination of multiple independent in silico pipelines.

A predictive strategy for mapping locations where future MOSSFA events are expected
Murk, A.J. ; Hollander, D.J. ; Chen, S. ; Hu, C. ; Liu, Y. ; Vonk, S.M. ; Schwing, Patrick T. ; Gilbert, S. ; Foekema, E.M. - \ 2019
In: Scenarios and Responses to Future Deep Oil Spills / Murawski, S.A., Ainsworth, C.H., Gilbert, S., Hollander, D.J., Paris, C.B., Schlueter, M., Wetzel, D.L., - p. 355 - 368.
A MOSSFA (marine oil snow sedimentation and flocculent accumulation) event was the reason that substantial amounts of the spilled oil were transported to the seafloor during the Deepwater Horizon (DWH) oil well blowout. The region-wide sinking and flocculent accumulation of marine oil snow on the sediment surface changed redox conditions, slowed down the biodegradation of the oil, and increased the spatial and temporal impacts on the benthic community and habitat suitability. Recent field research has confirmed that, in addition to the DWH MOSSFA event in the northern Gulf of Mexico (nGoM), another extensive MOSSFA event occurred in a biologically sensitive area in the southern Gulf of Mexico (sGoM) during the 1979 - 1980 Ixtoc I oil well blowout. Thus, MOSSFA events are not unexpected and have the potential to not only alter sediment chemical conditions but also to extend, expand, and intensify the ecological impact of an oil spill. Consequently this risk should be taken into consideration when preparing response...
Toward the improvement of total nitrogen deposition budgets in the United States
Walker, J.T. ; Beachley, G. ; Amos, H.M. ; Baron, J.S. ; Bash, J. ; Baumgardner, R. ; Bell, M.D. ; Benedict, K.B. ; Chen, X. ; Clow, D.W. ; Cole, A. ; Coughlin, J.G. ; Cruz, K. ; Daly, R.W. ; Decina, S.M. ; Elliott, E.M. ; Fenn, M.E. ; Ganzeveld, L. ; Gebhart, K. ; Isil, S.S. ; Kerschner, B.M. ; Larson, R.S. ; Lavery, T. ; Lear, G.G. ; Macy, T. ; Mast, M.A. ; Mishoe, K. ; Morris, K.H. ; Padgett, P.E. ; Pouyat, R.V. ; Puchalski, M. ; Pye, H.O.T. ; Rea, A.W. ; Rhodes, M.F. ; Rogers, C.M. ; Saylor, R. ; Scheffe, R. ; Schichtel, B.A. ; Schwede, D.B. ; Sexstone, G.A. ; Sive, B.C. ; Sosa, R. ; Templer, P.H. ; Thompson, T. ; Tong, D. ; Wetherbee, G.A. ; Whitlow, T.H. ; Wu, Z. ; Yu, Z. ; Zhang, L. - \ 2019
Science of the Total Environment 691 (2019). - ISSN 0048-9697 - p. 1328 - 1352.
Ammonia - Dry deposition - Organic nitrogen - Oxidized nitrogen - Reactive nitrogen - Wet deposition

Frameworks for limiting ecosystem exposure to excess nutrients and acidity require accurate and complete deposition budgets of reactive nitrogen (Nr). While much progress has been made in developing total Nr deposition budgets for the U.S., current budgets remain limited by key data and knowledge gaps. Analysis of National Atmospheric Deposition Program Total Deposition (NADP/TDep) data illustrates several aspects of current Nr deposition that motivate additional research. Averaged across the continental U.S., dry deposition contributes slightly more (55%) to total deposition than wet deposition and is the dominant process (>90%) over broad areas of the Southwest and other arid regions of the West. Lack of dry deposition measurements imposes a reliance on models, resulting in a much higher degree of uncertainty relative to wet deposition which is routinely measured. As nitrogen oxide (NOx) emissions continue to decline, reduced forms of inorganic nitrogen (NHx = NH3 + NH4 +) now contribute >50% of total Nr deposition over large areas of the U.S. Expanded monitoring and additional process-level research are needed to better understand NHx deposition, its contribution to total Nr deposition budgets, and the processes by which reduced N deposits to ecosystems. Urban and suburban areas are hotspots where routine monitoring of oxidized and reduced Nr deposition is needed. Finally, deposition budgets have incomplete information about the speciation of atmospheric nitrogen; monitoring networks do not capture important forms of Nr such as organic nitrogen. Building on these themes, we detail the state of the science of Nr deposition budgets in the U.S. and highlight research priorities to improve deposition budgets in terms of monitoring and flux measurements, leaf- to regional-scale modeling, source apportionment, and characterization of deposition trends and patterns.

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