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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    Control over the fibrillization yield by varying the oligomeric nucleation propensities of self-assembling peptides
    Lau, Chun Yin Jerry ; Fontana, Federico ; Mandemaker, Laurens D.B. ; Wezendonk, Dennie ; Vermeer, Benjamin ; Bonvin, Alexandre M.J.J. ; Vries, Renko de; Zhang, Heyang ; Remaut, Katrien ; Dikkenberg, Joep van den; Medeiros-Silva, João ; Hassan, Alia ; Perrone, Barbara ; Kuemmerle, Rainer ; Gelain, Fabrizio ; Hennink, Wim E. ; Weingarth, Markus ; Mastrobattista, Enrico - \ 2020
    Communications Chemistry 3 (2020). - ISSN 2399-3669

    Self-assembling peptides are an exemplary class of supramolecular biomaterials of broad biomedical utility. Mechanistic studies on the peptide self-assembly demonstrated the importance of the oligomeric intermediates towards the properties of the supramolecular biomaterials being formed. In this study, we demonstrate how the overall yield of the supramolecular assemblies are moderated through subtle molecular changes in the peptide monomers. This strategy is exemplified with a set of surfactant-like peptides (SLPs) with different β-sheet propensities and charged residues flanking the aggregation domains. By integrating different techniques, we show that these molecular changes can alter both the nucleation propensity of the oligomeric intermediates and the thermodynamic stability of the fibril structures. We demonstrate that the amount of assembled nanofibers are critically defined by the oligomeric nucleation propensities. Our findings offer guidance on designing self-assembling peptides for different biomedical applications, as well as insights into the role of protein gatekeeper sequences in preventing amyloidosis.

    Applications of anodized TiO2 nanotube arrays on the removal of aqueous contaminants of emerging concern: A review
    Feng, Yanyue ; Rijnaarts, Huub H.M. ; Yntema, Doekle ; Gong, Zhengjun ; Dionysiou, Dionysios D. ; Cao, Zhourong ; Miao, Shiyu ; Chen, Yanlong ; Ye, Yin ; Wang, Yuheng - \ 2020
    Water Research 186 (2020). - ISSN 0043-1354
    Contaminants of emerging concern - Photocatalysis - Photoelectrocatalysis - TiO nanotube arrays - Water treatment

    The presence of contaminants of emerging concern (CECs) in various water bodies and the associated threats to eco-system and human society have raised increasing concerns. To fight against such a problem, TiO2 photocatalysis is considered to be a powerful tool. In recent decades, TiO2 nanotube array (TNA) fabricated by electrochemical anodization emerged as a viable immobilized catalyst and its applications on CECs removal have gained a considerable amount of research interest. We herein present a critical review on the development of TNA and its applications on the removal of aqueous CECs. In this work, the CECs removal in different TNA based processes, the CECs removal mechanisms, the role of TNA properties, the role of operational parameters, and the role of water matrices are discussed. Moreover, perspectives on the current research progress are presented and recommendations on future research are elaborated.

    The case for improving crop carbon sink strength or plasticity for a CO2-rich future
    Dingkuhn, Michael ; Luquet, Delphine ; Fabre, Denis ; Muller, Bertrand ; Yin, Xinyou ; Paul, Matthew J. - \ 2020
    Current Opinion in Plant Biology 56 (2020). - ISSN 1369-5266 - p. 259 - 272.

    Atmospheric CO2 concentration [CO2] has increased from 260 to 280 μmol mol−1 (level during crop domestication up to the industrial revolution) to currently 400 and will reach 550 μmol mol−1 by 2050. C3 crops are expected to benefit from elevated [CO2] (e-CO2) thanks to photosynthesis responsiveness to [CO2] but this may require greater sink capacity. We review recent literature on crop e-CO2 responses, related source-sink interactions, how abiotic stresses potentially interact, and prospects to improve e-CO2 response via breeding or genetic engineering. Several lines of evidence suggest that e-CO2 responsiveness is related either to sink intrinsic capacity or adaptive plasticity, for example, involving enhanced branching. Wild relatives and old cultivars mostly showed lower photosynthetic rates, less downward acclimation of photosynthesis to e-CO2 and responded strongly to e-CO2 due to greater phenotypic plasticity. While reverting to such archaic traits would be an inappropriate strategy for breeding, we argue that substantial enhancement of vegetative sink vigor, inflorescence size and/or number and root sinks will be necessary to fully benefit from e-CO2. Potential ideotype features based on enhanced sinks are discussed. The generic ‘feast-famine’ sugar signaling pathway may be suited to engineer sink strength tissue-specifically and stage-specifically and help validate ideotype concepts. Finally, we argue that models better accounting for acclimation to e-CO2 are needed to predict which trait combinations should be targeted by breeders for a CO2-rich world.

    Effects of migration network configuration and migration synchrony on infection prevalence in geese
    Yin, Shenglai ; Knegt, Henrik J. de; Jong, Mart C.M. de; Si, Yali ; Prins, Herbert H.T. ; Huang, Zheng Y.X. ; Boer, Willem F. de - \ 2020
    Journal of Theoretical Biology 502 (2020). - ISSN 0022-5193
    Avian influenza - Cumulative infection - Environmental transmission - SIR model - Stopover site

    Migration can influence dynamics of pathogen-host interactions. However, it is not clearly known how migration pattern, in terms of the configuration of the migration network and the synchrony of migration, affects infection prevalence. We therefore applied a discrete-time SIR model, integrating environmental transmission and migration, to various migration networks, including networks with serial, parallel, or both serial and parallel stopover sites, and with various levels of migration synchrony. We applied the model to the infection of avian influenza virus in a migratory geese population. In a network with only serial stopover sites, increasing the number of stopover sites reduced infection prevalence, because with every new stopover site, the amount of virus in the environment was lower than that in the previous stopover site, thereby reducing the exposure of the migratory population. In a network with parallel stopover sites, both increasing the number and earlier appearance of the stopover sites led to an earlier peak of infection prevalence in the migratory population, because the migratory population is exposed to larger total amount of virus in the environment, speeding-up the infection accumulation. Furthermore, higher migration synchrony reduced the average number of cumulative infection, because the majority of the population can fly to a new stopover site where the amount of virus is still relatively low and has not been increased due to virus shedding of infected birds. Our simulations indicate that a migration pattern with multiple serial stopover sites and with highly synchronized migration reduces the infection prevalence.

    Comparisons with wheat reveal root anatomical and histochemical constraints of rice under water-deficit stress
    Ouyang, Wenjing ; Yin, Xinyou ; Yang, Jianchang ; Struik, Paul C. - \ 2020
    Plant and Soil 452 (2020). - ISSN 0032-079X - p. 547 - 568.
    Lignin - Rice - Root anatomy - Root morphology - Suberin - Water deficit - Wheat

    Aims: To face the challenge of decreasing freshwater availability for agriculture, it is important to explore avenues for developing rice genotypes that can be grown like dryland cereals. Roots play a key role in plant adaptation to dry environments. Methods: We examined anatomical and histochemical root traits that affect water acquisition in rice (Oryza sativa) and wheat (Triticum aestivum). These traits and root growth were measured at two developmental stages for three rice and two wheat cultivars that were grown in pots under three water regimes. Results: Wheat roots had larger xylem sizes than rice roots, which potentially led to a higher axial conductance, especially under water-deficit conditions. Suberization, lignification and thickening of the endodermis in rice roots increased with increasing water deficit, resulting in stronger radial barriers for water flow in rice than in wheat, especially near the root apex. In addition, water deficit strongly impeded root growth and lateral root proliferation in rice, but only slightly in wheat, and cultivars within a species differed little in these responses. The stress sensitivity of rice attributes was slightly more prominent at vegetative than at flowering stages. Conclusions: Rice root characteristics, which are essential for growth under inundated conditions, are not conducive to growth under water deficit. Although rice roots show considerable plasticity under different watering regimes, improving root xylem size and reducing the radial barriers would be required if rice is to grow like dryland cereals.

    Responses of Lowland, Upland and Aerobic Rice Genotypes to Water Limitation During Different Phases
    Vijayaraghavareddy, Preethi ; Xinyou, Yin ; Struik, Paul C. ; Makarla, Udayakumar ; Sreeman, Sheshshayee - \ 2020
    Rice Science 27 (2020)4. - ISSN 1672-6308 - p. 345 - 354.
    Aerobic - Oryza sativa - Phenology - Upland - Water limitation - yield

    Rice yield reduction due to water limitation depends on its severity and duration and on the phenological stage of its occurrence. We exposed three contrasting rice genotypes, IR64, UPLRi7 and Apo (adapted to lowland, upland and aerobic conditions, respectively), to three water regimes (puddle, 100% and 60% field capacity) in pots during the vegetative (GSI), flowering (GSII) and grain filling (GSIII) stages. Stress at all the three stages significantly reduced yield especially in lowland genotype IR64. Effect of water limitation was more severe at GSII than at the other two stages. Stress at GSI stage reduced both source activity (leaf area and photosynthetic rate) and sink capacity (tiller number or panicle number per pot). When stress was imposed at GSII, spikelet fertility was most affected in all the three genotypes. In both GSII and GSIII, although leaf area was constant in all the three water regimes, estimated relative whole-plant photosynthesis was strongly associated with yield reduction. Reduced photosynthesis due to stress at any given stage was found to have direct impact on yield. Compared to the other genotypes, Apo had deeper roots and maintained a better water relation, thus, higher carbon gain and spikelet viability, and ultimately, higher biomass and productivity under water-limited conditions. Therefore, screening for these stage-dependent adaptive mechanisms is crucial in breeding for sustained rice production under water limitation.

    The Kok effect revisited
    Yin, Xinyou ; Niu, Yuxi ; Putten, Peter E.L. van der; Struik, Paul C. - \ 2020
    New Phytologist 227 (2020)6. - ISSN 0028-646X - p. 1764 - 1775.
    day respiration - Kok method - photorespiration - photosystem II efficiency - reassimilation - Yin method

    The Kok effect refers to the abrupt decrease around the light compensation point in the slope of net photosynthetic rate vs irradiance. Arguably, this switch arises from light inhibition of respiration, allowing the Kok method to estimate day respiration (Rd). Recent analysis suggests that increasing proportions of photorespiration (quantified as Γ*/Cc, the ratio of CO2 compensation point Γ* to chloroplast CO2 concentration, Cc) with irradiance explain much of the Kok effect. Also, the Kok method has been modified to account for the decrease in PSII photochemical efficiency (Φ2) with irradiance. Using a model that illustrates how varying Rd, Γ*/Cc, Φ2 and proportions of alternative electron transport could engender the Kok effect, we quantified the contribution of these parameters to the Kok effect measured in sunflower across various O2 and CO2 concentrations and various temperatures. Overall, the decreasing Φ2 with irradiance explained c. 12%, and the varying Γ*/Cc explained c. 25%, of the Kok effect. Maximum real light inhibition of Rd was much lower than the inhibition derived from the Kok method, but still increased with photorespiration. Photorespiration had a dual contribution to the Kok effect, one via the varying Γ*/Cc and the other via its participation in light inhibition of Rd.

    Towards a multiscale crop modelling framework for climate change adaptation assessment
    Peng, Bin ; Guan, Kaiyu ; Tang, Jinyun ; Ainsworth, Elizabeth A. ; Asseng, Senthold ; Bernacchi, Carl J. ; Cooper, Mark ; Delucia, Evan H. ; Elliott, Joshua W. ; Ewert, Frank ; Grant, Robert F. ; Gustafson, David I. ; Hammer, Graeme L. ; Jin, Zhenong ; Jones, James W. ; Kimm, Hyungsuk ; Lawrence, David M. ; Li, Yan ; Lombardozzi, Danica L. ; Marshall-Colon, Amy ; Messina, Carlos D. ; Ort, Donald R. ; Schnable, James C. ; Vallejos, C.E. ; Wu, Alex ; Yin, Xinyou ; Zhou, Wang - \ 2020
    Nature Plants 6 (2020)4. - ISSN 2055-026X - p. 338 - 348.

    Predicting the consequences of manipulating genotype (G) and agronomic management (M) on agricultural ecosystem performances under future environmental (E) conditions remains a challenge. Crop modelling has the potential to enable society to assess the efficacy of G × M technologies to mitigate and adapt crop production systems to climate change. Despite recent achievements, dedicated research to develop and improve modelling capabilities from gene to global scales is needed to provide guidance on designing G × M adaptation strategies with full consideration of their impacts on both crop productivity and ecosystem sustainability under varying climatic conditions. Opportunities to advance the multiscale crop modelling framework include representing crop genetic traits, interfacing crop models with large-scale models, improving the representation of physiological responses to climate change and management practices, closing data gaps and harnessing multisource data to improve model predictability and enable identification of emergent relationships. A fundamental challenge in multiscale prediction is the balance between process details required to assess the intervention and predictability of the system at the scales feasible to measure the impact. An advanced multiscale crop modelling framework will enable a gene-to-farm design of resilient and sustainable crop production systems under a changing climate at regional-to-global scales.

    A high throughput method for quantifying number and size distribution of Arabidopsis seeds using large particle flow cytometry
    Morales, Alejandro ; Teapal, J. ; Ammerlaan, J.M.H. ; Yin, X. ; Evers, J.B. ; Anten, N.P.R. ; Sasidharan, R. ; Zanten, M. Van - \ 2020
    Plant Methods 16 (2020)1. - ISSN 1746-4811
    Arabidopsis thaliana - BioSorter - Machine learning - Phenotyping - R package - Seed number - Seed size - SeedSorter

    Background: Seed size and number are important plant traits from an ecological and horticultural/agronomic perspective. However, in small-seeded species such as Arabidopsis thaliana, research on seed size and number is limited by the absence of suitable high throughput phenotyping methods. Results: We report on the development of a high throughput method for counting seeds and measuring individual seed sizes. The method uses a large-particle flow cytometer to count individual seeds and sort them according to size, allowing an average of 12,000 seeds/hour to be processed. To achieve this high throughput, post harvested seeds are first separated from remaining plant material (dust and chaff) using a rapid sedimentation-based method. Then, classification algorithms are used to refine the separation process in silico. Accurate identification of all seeds in the samples was achieved, with relative errors below 2%. Conclusion: The tests performed reveal that there is no single classification algorithm that performs best for all samples, so the recommended strategy is to train and use multiple algorithms and use the median predictions of seed size and number across all algorithms. To facilitate the use of this method, an R package (SeedSorter) that implements the methodology has been developed and made freely available. The method was validated with seed samples from several natural accessions of Arabidopsis thaliana, but our analysis pipeline is applicable to any species with seed sizes smaller than 1.5 mm.

    Cumulative Burden of Colorectal Cancer–Associated Genetic Variants Is More Strongly Associated With Early-Onset vs Late-Onset Cancer
    Archambault, Alexi N. ; Su, Yu Ru ; Jeon, Jihyoun ; Thomas, Minta ; Lin, Yi ; Conti, David V. ; Win, Aung Ko ; Sakoda, Lori C. ; Lansdorp-Vogelaar, Iris ; Peterse, Elisabeth F.P. ; Zauber, Ann G. ; Duggan, David ; Holowatyj, Andreana N. ; Huyghe, Jeroen R. ; Brenner, Hermann ; Cotterchio, Michelle ; Bézieau, Stéphane ; Schmit, Stephanie L. ; Edlund, Christopher K. ; Southey, Melissa C. ; MacInnis, Robert J. ; Campbell, Peter T. ; Chang-Claude, Jenny ; Slattery, Martha L. ; Chan, Andrew T. ; Joshi, Amit D. ; Song, Mingyang ; Cao, Yin ; Woods, Michael O. ; White, Emily ; Weinstein, Stephanie J. ; Ulrich, Cornelia M. ; Hoffmeister, Michael ; Bien, Stephanie A. ; Harrison, Tabitha A. ; Hampe, Jochen ; Li, Christopher I. ; Schafmayer, Clemens ; Offit, Kenneth ; Pharoah, Paul D. ; Moreno, Victor ; Lindblom, Annika ; Wolk, Alicja ; Wu, Anna H. ; Li, Li ; Gunter, Marc J. ; Gsur, Andrea ; Keku, Temitope O. ; Pearlman, Rachel ; Bishop, D.T. ; Castellví-Bel, Sergi ; Moreira, Leticia ; Vodicka, Pavel ; Kampman, Ellen ; Giles, Graham G. ; Albanes, Demetrius ; Baron, John A. ; Berndt, Sonja I. ; Brezina, Stefanie ; Buch, Stephan ; Buchanan, Daniel D. ; Trichopoulou, Antonia ; Severi, Gianluca ; Chirlaque, María Dolores ; Sánchez, Maria José ; Palli, Domenico ; Kühn, Tilman ; Murphy, Neil ; Cross, Amanda J. ; Burnett-Hartman, Andrea N. ; Chanock, Stephen J. ; Chapelle, Albert de la; Easton, Douglas F. ; Elliott, Faye ; English, Dallas R. ; Feskens, Edith J.M. ; FitzGerald, Liesel M. ; Goodman, Phyllis J. ; Hopper, John L. ; Hudson, Thomas J. ; Hunter, David J. ; Jacobs, Eric J. ; Joshu, Corinne E. ; Küry, Sébastien ; Markowitz, Sanford D. ; Milne, Roger L. ; Platz, Elizabeth A. ; Rennert, Gad ; Rennert, Hedy S. ; Schumacher, Fredrick R. ; Sandler, Robert S. ; Seminara, Daniela ; Tangen, Catherine M. ; Thibodeau, Stephen N. ; Toland, Amanda E. ; Duijnhoven, Franzel J.B. van; Visvanathan, Kala ; Vodickova, Ludmila ; Potter, John D. ; Männistö, Satu ; Weigl, Korbinian ; Figueiredo, Jane ; Martín, Vicente ; Larsson, Susanna C. ; Parfrey, Patrick S. ; Huang, Wen Yi ; Lenz, Heinz Josef ; Castelao, Jose E. ; Gago-Dominguez, Manuela ; Muñoz-Garzón, Victor ; Mancao, Christoph ; Haiman, Christopher A. ; Wilkens, Lynne R. ; Siegel, Erin ; Barry, Elizabeth ; Younghusband, Ban ; Guelpen, Bethany Van; Harlid, Sophia ; Zeleniuch-Jacquotte, Anne ; Liang, Peter S. ; Du, Mengmeng ; Casey, Graham ; Lindor, Noralane M. ; Marchand, Loic Le; Gallinger, Steven J. ; Jenkins, Mark A. ; Newcomb, Polly A. ; Gruber, Stephen B. ; Schoen, Robert E. ; Hampel, Heather ; Corley, Douglas A. ; Hsu, Li ; Peters, Ulrike ; Hayes, Richard B. - \ 2020
    Gastroenterology 158 (2020)5. - ISSN 0016-5085 - p. 1274 - 1286.e12.
    Colon Cancer - EOCRC - Penetrance - SNP

    Background & Aims: Early-onset colorectal cancer (CRC, in persons younger than 50 years old) is increasing in incidence; yet, in the absence of a family history of CRC, this population lacks harmonized recommendations for prevention. We aimed to determine whether a polygenic risk score (PRS) developed from 95 CRC-associated common genetic risk variants was associated with risk for early-onset CRC. Methods: We studied risk for CRC associated with a weighted PRS in 12,197 participants younger than 50 years old vs 95,865 participants 50 years or older. PRS was calculated based on single nucleotide polymorphisms associated with CRC in a large-scale genome-wide association study as of January 2019. Participants were pooled from 3 large consortia that provided clinical and genotyping data: the Colon Cancer Family Registry, the Colorectal Transdisciplinary Study, and the Genetics and Epidemiology of Colorectal Cancer Consortium and were all of genetically defined European descent. Findings were replicated in an independent cohort of 72,573 participants. Results: Overall associations with CRC per standard deviation of PRS were significant for early-onset cancer, and were stronger compared with late-onset cancer (P for interaction = .01); when we compared the highest PRS quartile with the lowest, risk increased 3.7-fold for early-onset CRC (95% CI 3.28–4.24) vs 2.9-fold for late-onset CRC (95% CI 2.80–3.04). This association was strongest for participants without a first-degree family history of CRC (P for interaction = 5.61 × 10–5). When we compared the highest with the lowest quartiles in this group, risk increased 4.3-fold for early-onset CRC (95% CI 3.61–5.01) vs 2.9-fold for late-onset CRC (95% CI 2.70–3.00). Sensitivity analyses were consistent with these findings. Conclusions: In an analysis of associations with CRC per standard deviation of PRS, we found the cumulative burden of CRC-associated common genetic variants to associate with early-onset cancer, and to be more strongly associated with early-onset than late-onset cancer, particularly in the absence of CRC family history. Analyses of PRS, along with environmental and lifestyle risk factors, might identify younger individuals who would benefit from preventive measures.

    Sediment toxicity of the fungicide fludioxonil to benthic macroinvertebrates -evaluation of the tiered effect assessment procedure
    Brock, Theo C.M. ; Romão, João ; Yin, Xiao ; Osman, Rima ; Roessink, Ivo - \ 2020
    Ecotoxicology and Environmental Safety 195 (2020). - ISSN 0147-6513
    Fungicide exposure - Sediment ecotoxicology - Species sensitivity distributions - Standard test species - Weight of evidence approach

    28-Day sediment-spiked laboratory toxicity tests with eight benthic macroinvertebrates and the lipophilic fungicide fludioxonil were conducted to verify the proposed tiered sediment effect assessment procedure as recommended by the European Food Safety Authority (EFSA). The test species were the oligochaetes Lumbriculus variegatus and Tubifex tubifex, the insects Chironomus riparius and Caenis horaria, the crustaceans Hyalella azteca and Asellus aquaticus and the bivalves Corbicula fluminalis and Pisidium amnicum. Toxicity estimates were expressed in terms of total concentration of dry sediment as well as in pore water concentration. Field-collected sediment, also used in a previously performed sediment-spiked microcosm experiment, was used in tests with all species. L. variegatus and C. riparius had similar lowest 28d-L(E)C10 values when expressed in terms of total sediment concentration, but in terms of pore water concentration L. variegatus was more sensitive. Three of the six additional benthic test species (A. aquaticus, C. horaria, C. fluminalis) had 28d-EC10 values a factor of 2–6 lower than that of L. variegatus. Comparing different effect assessment tiers for sediment organisms, i.e. Tier-0 (Modified Equilibrium Partitioning approach), Tier-1 (Standard Test Species approach), Tier-2 (Species Sensitivity Distribution (SSD) approach) and Tier-3 (Model Ecosystem approach), it is concluded that the tiers based on sediment-spiked laboratory toxicity tests provide sufficient protection when compared with the Tier-3 Regulatory Acceptable Concentration (RAC). Differences between Tier-1 and Tier-2 RACs, however, appear to be relatively small and not always consistent, irrespective of expressing the RAC in terms of total sediment or pore water concentration. Derivation of RACs by means of the SSD approach may be a challenge, because it is difficult obtaining a sufficient number of valid chronic EC10 values with appropriate 95% confidence bands for sediment-dwelling macroinvertebrates. Therefore, this paper proposes a Tier-2 Weight-of-Evidence approach to be used in case an insufficient number of valid additional toxicity data is made available. Similar studies with pesticides that differ in fate properties and toxic mode-of-action are necessary for further validation of the tiered effect assessment approach for sediment organisms.

    Using photorespiratory oxygen response to analyse leaf mesophyll resistance
    Yin, Xinyou ; Putten, Peter E.L. van der; Belay, Daniel ; Struik, Paul C. - \ 2020
    Photosynthesis Research 144 (2020). - ISSN 0166-8595 - p. 85 - 99.
    CO compensation point - CO transfer - Internal conductance - O response - Re-assimilation - Resistance

    Classical approaches to estimate mesophyll conductance ignore differences in resistance components for CO2 from intercellular air spaces (IAS) and CO2 from photorespiration (F) and respiration (Rd). Consequently, mesophyll conductance apparently becomes sensitive to (photo)respiration relative to net photosynthesis, (F + Rd)/A. This sensitivity depends on several hard-to-measure anatomical properties of mesophyll cells. We developed a method to estimate the parameter m (0 ≤ m ≤ 1) that lumps these anatomical properties, using gas exchange and chlorophyll fluorescence measurements where (F + Rd)/A ratios vary. This method was applied to tomato and rice leaves measured at five O2 levels. The estimated m was 0.3 for tomato but 0.0 for rice, suggesting that classical approaches implying m = 0 work well for rice. The mesophyll conductance taking the m factor into account still responded to irradiance, CO2, and O2 levels, similar to response patterns of stomatal conductance to these variables. Largely due to different m values, the fraction of (photo)respired CO2 being refixed within mesophyll cells was lower in tomato than in rice. But that was compensated for by the higher fraction via IAS, making the total re-fixation similar for both species. These results, agreeing with CO2 compensation point estimates, support our method of effectively analysing mesophyll resistance.

    Feed types driven differentiation of microbial community and functionality in marine integrated multitrophic aquaculture system
    Deng, Yale ; Zhou, Fan ; Ruan, Yunjie ; Ma, Bin ; Ding, Xueyan ; Yue, Xiaomei ; Ma, Wenjun ; Yin, Xuwang - \ 2020
    Water 12 (2020)1. - ISSN 2073-4441
    Formulated diet - Functionality - Integrated multitrophic aquaculture - Microbial community - Sustainability

    Integrated multi trophic aquaculture (IMTA) improves the production of aquatic animals by promoting nutrient utilization through different tropical levels. Microorganisms play an important role in elements cycling, energy flow and farmed-species health. The aim of this study was to evaluate how feed types, fresh frozen fish diet (FFD) or formulated diet (FD), influence the microbial community diversity and functionality in both water and sediment in a marine IMTA system. Preferable water quality, higher animal yields and higher cost efficiency were achieved in the FD pond. Feed types changed the pond bacterial community distribution, especially in the rearing water. The FFD pond was dominated with Cyanobacteria in the water, which played an important role in nitrogen fixation through photosynthesis due to the high nitrogen input of the frozen fish diet. The high carbohydrate composition in the formulated diet triggered higher metabolic pathways related to carbon and lipid metabolism in the water of the FD pond. Sediment had significantly higher microbial diversity than the rearing water. In sediment, the dominating genus, Sulfurovum and Desulfobulbus, were found to be positively correlated by network analysis, which had similar functionality in sulfur transformation. The relatively higher rates of antibiotic biosynthesis in the FFD sediment might be related to the pathogenic bacteria introduced by the trash fish diet. The difference in microbial community composition and metabolic pathways may be associated with the different pathways for nutrient cycling and animal growth performance. The formulated diet was determined to be more ecologically and economically sustainable than the frozen fish diet for marine IMTA pond systems.

    Genotypic variation in source and sink traits affects the response of photosynthesis and growth to elevated atmospheric CO2
    Fabre, Denis ; Dingkuhn, Michael ; Yin, Xinyou ; Clément-Vidal, Anne ; Roques, Sandrine ; Soutiras, Armelle ; Luquet, Delphine - \ 2020
    Plant, Cell & Environment 43 (2020)3. - ISSN 0140-7791 - p. 579 - 593.
    carbon assimilation - climate change - CO - enrichment - L. phenotypic plasticity - local source–sink ratio - Oryza sativa - sink limitation - triose phosphate utilization

    This study aimed to understand the response of photosynthesis and growth to e-CO2 conditions (800 vs. 400 μmol mol−1) of rice genotypes differing in source–sink relationships. A proxy trait called local C source–sink ratio was defined as the ratio of flag leaf area to the number of spikelets on the corresponding panicle, and five genotypes differing in this ratio were grown in a controlled greenhouse. Differential CO2 resources were applied either during the 2 weeks following heading (EXP1) or during the whole growth cycle (EXP2). Under e-CO2, low source–sink ratio cultivars (LSS) had greater gains in photosynthesis, and they accumulated less nonstructural carbohydrate in the flag leaf than high source–sink ratio cultivars (HSS). In EXP2, grain yield and biomass gain was also greater in LSS probably caused by their strong sink. Photosynthetic capacity response to e-CO2 was negatively correlated across genotypes with local C source–sink ratio, a trait highly conserved across environments. HSS were sink-limited under e-CO2, probably associated with low triose phosphate utilization (TPU) capacity. We suggest that the local C source–sink ratio is a potential target for selecting more CO2-responsive cultivars, pending validation for a broader genotypic spectrum and for field conditions.

    Dynamic process-based modelling of crop growth and competitive water extraction in relay strip intercropping: Model development and application to wheat-maize intercropping
    Tan, Meixiu ; Gou, Fang ; Stomph, Tjeerd Jan ; Wang, Jing ; Yin, Wen ; Zhang, Lizhen ; Chai, Qiang ; Werf, Wopke van der - \ 2020
    Field Crops Research 246 (2020). - ISSN 0378-4290
    AquaCrop - LER - Water use efficiency - WER

    Strip intercropping increases land use efficiency but the effect on water use efficiency is less well-known. Here we develop a modelling method to simulate the growth of an intercrop taking into account the acquisition of light and water by the component species in order to calculate the efficacy of light and water acquisition in an intercropping system as compared to sole crops. The model is parameterized, calibrated and validated using data on wheat-maize intercropping in Gansu province, Northwest China. Observed above-ground biomass was 1630 g m−2 for sole wheat and 1334 g m−2 for intercropped wheat while it was 3023 g m−2 for sole maize and 2259 g m−2 for intercropped maize. The average water use was 405 mm in sole wheat, 595 mm in sole maize and 711 mm in wheat-maize intercropping. Based on observed yields, the land equivalent ratio (LER) was 1.59 and the water equivalent ratio (WER) was 1.14, where LER and WER express the relative amounts of land and water needed to achieve the yields obtained in a unit area of intercrop using sole crops. These results indicate that relay strip intercropping of wheat and maize achieves an increase of land use efficiency of 59% and of water use efficiency of 14%. Overall the intercrop model gave satisfactory predictions, with coefficients of efficiency (CE) in validation of 0.86–0.97, 0.90–0.95, 0.85–0.91 and 0.98 for biomass of sole wheat, sole maize, intercropped wheat, and intercropped maize, respectively. Overall CE of water use was 0.95. Simulated LER and WER were similar to observed LER and WER. The results show that intercropping could be used to obtain more yield on less land with less water. Policies that limit water use per unit land and prohibit the use of intercropping on the basis of its high water use per unit area may therefore be counter-productive. The model for intercrop growth and development under water limitation may be used for exploring production possibilities under land and water constraints.

    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 - \ 2020
    Global Change Biology 26 (2020)3. - ISSN 1354-1013 - p. 1697 - 1713.
    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.

    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 - \ 2020
    Global Change Biology 26 (2020)2. - ISSN 1354-1013 - p. 539 - 556.
    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.

    A network approach to prioritize conservation efforts for migratory birds
    Xu, Yanjie ; Si, Yali ; Takekawa, John ; Liu, Qiang ; Prins, Herbert H.T. ; Yin, Shenglai ; Prosser, Diann J. ; Gong, Peng ; Boer, Willem F. de - \ 2020
    Conservation Biology 34 (2020)2. - ISSN 0888-8892 - p. 416 - 426.
    bird migration - connectivity - conservation designation - habitat loss - network

    Habitat loss can trigger migration network collapse by isolating migratory bird breeding grounds from nonbreeding grounds. Theoretically, habitat loss can have vastly different impacts depending on the site's importance within the migratory corridor. However, migration-network connectivity and the impacts of site loss are not completely understood. We used GPS tracking data on 4 bird species in the Asian flyways to construct migration networks and proposed a framework for assessing network connectivity for migratory species. We used a node-removal process to identify stopover sites with the highest impact on connectivity. In general, migration networks with fewer stopover sites were more vulnerable to habitat loss. Node removal in order from the highest to lowest degree of habitat loss yielded an increase of network resistance similar to random removal. In contrast, resistance increased more rapidly when removing nodes in order from the highest to lowest betweenness value (quantified by the number of shortest paths passing through the specific node). We quantified the risk of migration network collapse and identified crucial sites by first selecting sites with large contributions to network connectivity and then identifying which of those sites were likely to be removed from the network (i.e., sites with habitat loss). Among these crucial sites, 42% were not designated as protected areas. Setting priorities for site protection should account for a site's position in the migration network, rather than only site-specific characteristics. Our framework for assessing migration-network connectivity enables site prioritization for conservation of migratory species.

    Large expert-curated database for benchmarking document similarity detection in biomedical literature search
    Brown, Peter ; Zhou, Yaoqi ; Tan, Aik Choon ; El-Esawi, Mohamed A. ; Liehr, Thomas ; Blanck, Oliver ; Gladue, Douglas P. ; Almeida, Gabriel M.F. ; Cernava, Tomislav ; Sorzano, Carlos O. ; Yeung, Andy W.K. ; Engel, Michael S. ; Chandrasekaran, Arun R. ; Muth, Thilo ; Staege, Martin S. ; Daulatabad, Swapna V. ; Widera, Darius ; Zhang, Junpeng ; Meule, Adrian ; Honjo, Ken ; Pourret, Olivier ; Yin, Cong Cong ; Zhang, Zhongheng ; Cascella, Marco ; Flegel, Willy A. ; Goodyear, Carl S. ; Raaij, Mark J. van; Bukowy-Bieryllo, Zuzanna ; Campana, Luca G. ; Kurniawan, Nicholas A. ; Lalaouna, David ; Hüttner, Felix J. ; Ammerman, Brooke A. ; Ehret, Felix ; Cobine, Paul A. ; Tan, Ene Choo ; Han, Hyemin ; Xia, Wenfeng ; McCrum, Christopher ; Dings, Ruud P.M. ; Marinello, Francesco ; Nilsson, Henrik ; Nixon, Brett ; Voskarides, Konstantinos ; Yang, Long ; Costa, Vincent D. ; Bengtsson-Palme, Johan ; Bradshaw, William ; Smeets, Paul A.M. ; Heijne, Marloes - \ 2019
    Database : the Journal of Biological Databases and Curation 2019 (2019). - ISSN 1758-0463 - p. 1 - 67.

    Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical science.

    Handhavingsprotocol Hokverrijking : Praktische uitwerking van open normen in wetgeving helpt varkenswelzijn vooruit
    Jonge, Francien de; Nieuwenhuizen, Jeroen van den; Ekkelboom, Myra ; Ernst, Kristi ; Kerssen, Nynke ; Smeets, Sharine ; Sun, Yan ; Yin, Xuetong ; Blaauw, Xana ; He, Zhengxiao ; Jong, Mandy de; Nauta, Charlotte ; Verdaasdonk, Marleen ; Kanhailal, Sharita - \ 2019
    Wageningen : Wageningen University & Research, Wetenschapswinkel (Rapport / Wageningen University & Research, Wetenschapswinkel 353) - ISBN 9789463951685 - 27
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