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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Flower movement balances pollinator needs and pollen protection
Haverkamp, Alexander ; Li, Xiang ; Hansson, Bill S. ; Baldwin, Ian T. ; Knaden, Markus ; Yon, Felipe - \ 2019
Ecology 100 (2019)1. - ISSN 0012-9658
flower handling - flower orientation - Manduca - Nicotiana - pollen viability - pollination

Flower signaling and orientation are key characteristics that determine a flower's pollinator guild. However, many flowers actively move during their daily cycle, changing both their detectability and accessibility to pollinators. The flowers of the wild tobacco Nicotiana attenuata orientate their corolla upward at sunset and downward after sunrise. Here, we investigated the effect of different flower orientations on a major pollinator of N. attenuata, the hawkmoth Manduca sexta. We found that although flower orientation influenced the flight altitude of the moth in respect to the flower, it did not alter the moth's final flower choice. These behavioral observations were consistent with the finding that orientation did not systematically change the spatial distribution of floral volatiles, which are major attractants for the moths. Moreover, hawkmoths invested the same amount of time into probing flowers at different orientations, even though they were only able to feed and gather pollen from horizontally and upward-oriented flowers, but not from downward-facing flowers. The orientation of the flower was hence crucial for a successful interaction between N. attenuata and its hawkmoth pollinator. Additionally, we also investigated potential adverse effects of exposing flowers at different orientations to natural daylight levels, finding that anther temperature of upward-oriented flowers was more than 7°C higher than for downward-oriented flowers. This increase in temperature likely caused the significantly reduced germination success that was observed for pollen grains from upward-oriented flowers in comparison to those of downward and horizontally oriented flowers. These results highlight the importance of flower reorientation to balance pollen protection and a successful interaction of the plant with its insect pollinators by maintaining the association between flower volatiles and flower accessibility to the pollinator.

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.

Revealing microbial processes and nutrient limitation in soil through ecoenzymatic stoichiometry and glomalin-related soil proteins in a retreating glacier forefield
Jiang, Yonglei ; Lei, Yanbao ; Qin, Wei ; Korpelainen, Helena ; Li, Chunyang - \ 2019
Geoderma 338 (2019). - ISSN 0016-7061 - p. 313 - 324.
Bacterial and fungal community structure - Glomalin-related soil protein - Hailuogou Glacier Chronosequence - Soil extracellular enzymes

The glacial retreat is observed and predicted to increase in intensity especially in high-elevation areas as a result of global warming, which leaves behind a primary succession along soil chronosequences. Although soil microbes have been recognized as main drivers of ecological and evolutionary processes, our understanding of their effects on nutrient biogeochemistry during primary succession remains limited. In this study, we investigated changes in the microbial community structure, ecoenzymatic stoichiometry, and glomalin-related soil protein (GRSP) accumulation in the Hailuogou Glacier Chronosequence, located on the eastern Tibetan Plateau. We wanted to reveal the effects of nutrient limitation on soil microbes and the relative contributions of edaphic and biotic factors. The results showed that with an increasing soil age, there was a steady increase in the microbial biomass and a shift from a bacterial to fungal dominated pattern. Soil enzyme stoichiometry and analyses on threshold elemental ratios revealed that microbial activities are limited by carbon and nitrogen during the early successional stage (3–52 years), while phosphorus was the main limiting factor during later stages (80–120 years). Moreover, the redundancy analysis and structural equation modeling suggested that during early stages edaphic factors had a greater impact on microbial processes, while the vegetation factors were most influential during the last two stages. Overall, these results highlighted the importance of integrating knowledge of the microbial community structure, soil enzyme activities and GRSP to gain a holistic view of soil-plant-microbe interactions during ecosystem successions.

Conflation of expert and crowd reference data to validate global binary thematic maps
Waldner, François ; Schucknecht, Anne ; Lesiv, Myroslava ; Gallego, Javier ; See, Linda ; Pérez-Hoyos, Ana ; andrimont, Raphaël D'; Maet, Thomas De; Bayas, Juan Carlos Laso ; Fritz, Steffen ; Leo, Olivier ; Kerdiles, Hervé ; Díez, Mónica ; Tricht, Kristof Van; Gilliams, Sven ; Shelestov, Andrii ; Lavreniuk, Mykola ; Simões, Margareth ; Ferraz, Rodrigo ; Bellón, Beatriz ; Bégué, Agnès ; Hazeu, Gerard ; Stonacek, Vaclav ; Kolomaznik, Jan ; Misurec, Jan ; Verón, Santiago R. ; Abelleyra, Diego De; Plotnikov, Dmitry ; Mingyong, Li ; Singha, Mrinal ; Patil, Prashant ; Zhang, Miao ; Defourny, Pierre - \ 2019
Remote Sensing of Environment 221 (2019). - ISSN 0034-4257 - p. 235 - 246.
With the unprecedented availability of satellite data and the rise of global binary maps, the collection of shared reference data sets should be fostered to allow systematic product benchmarking and validation. Authoritative global reference data are generally collected by experts with regional knowledge through photo-interpretation. During the last decade, crowdsourcing has emerged as an attractive alternative for rapid and relatively cheap data collection, beckoning the increasingly relevant question: can these two data sources be combined to validate thematic maps? In this article, we compared expert and crowd data and assessed their relative agreement for cropland identification, a land cover class often reported as difficult to map. Results indicate that observations from experts and volunteers could be partially conflated provided that several consistency checks are performed. We propose that conflation, i.e., replacement and augmentation of expert observations by crowdsourced observations, should be carried out both at the sampling and data analytics levels. The latter allows to evaluate the reliability of crowdsourced observations and to decide whether they should be conflated or discarded. We demonstrate that the standard deviation of crowdsourced contributions is a simple yet robust indicator of reliability which can effectively inform conflation. Following this criterion, we found that 70% of the expert observations could be crowdsourced with little to no effect on accuracy estimates, allowing a strategic reallocation of the spared expert effort to increase the reliability of the remaining 30% at no additional cost. Finally, we provide a collection of evidence-based recommendations for future hybrid reference data collection campaigns.
Modeling nutrients in Lake Dianchi (China) and its watershed
Li, Xiaolin ; Janssen, Annette B.G. ; Klein, Jeroen J.M. de; Kroeze, Carolien ; Strokal, Maryna ; Ma, Lin ; Zheng, Yi - \ 2019
Agricultural Water Management 212 (2019). - ISSN 0378-3774 - p. 48 - 59.
Critical loading - MARINA nutrient model - Mining - PCLake ecosystem model - River export of nutrients

Lake Dianchi suffered from severe eutrophication for decades. Past efforts to reduce the eutrophication were not very effective. The objective of this study is to improve our understanding of nitrogen (N) and phosphorus (P) loadings and to analyze to what extent they exceed critical nutrient loadings of Lake Dianchi. To this end, we applied the nutrient MARINA model and the ecosystem model PCLake. Results show that river export of dissolved N and P was high in 2012. About 6 209 ton of total dissolved N (TDN) was exported to the lake (i.e. 23.6 kg ha−1), of which more than two-thirds in the form of dissolved inorganic N. For total dissolved P, this export was about 413 ton (i.e. 1.6 kg ha−1), of which 75% dissolved inorganic P. Urban sewage is a major source of nutrients in rivers in the northern sub-basins. In southern sub-basins, agriculture is an important source of both N and P, while P mining and processing is a major source of dissolved inorganic P. Nutrient inputs to the lake are particularly high from urbanization sub-basins draining into the northern part of the lake (Caohai). Critical nutrient loadings for the northern part of the lake (Caohai) are 0.34 mg P m−2d−1 (3.06 mg N m−2d−1) and for the southern part (Waihai) 0.38 mg P m−2d−1 (3.42 mg N m−2d−1). Actual loadings exceed the critical nutrient loadings by 82 times and 17 times of Caohai and Waihai, respectively. Our study illustrates how linking MARINA with PCLake helped to quantify the causes of lake eutrophication and to identify critical loadings for N and P in the lake. Our study can assist local authorities to formulate management options to reduce nutrient pollution in Lake Dianchi in the future.

Causal relationship in the interaction between land cover change and underlying surface climate in the grassland ecosystems in China
Li, Zhouyuan ; Wang, Zezhong ; Liu, Xuehua ; Fath, Brian D. ; Liu, Xiaofei ; Xu, Yanjie ; Hutjes, Ronald ; Kroeze, Carolien - \ 2019
Science of the Total Environment 647 (2019). - ISSN 0048-9697 - p. 1080 - 1087.
Cause-effect - Correlation analysis - Eco-climatology - Grassland - Land-climate - Remote sensing

Land-climate interactions are driven by causal relations that are difficult to ascertain given the complexity and high dimensionality of the systems. Many methods of statistical and mechanistic models exist to identify and quantify the causality in such highly-interacting systems. Recent advances in remote sensing development allowed people to investigate the land-climate interaction with spatially and temporally continuous data. In this study, we present a new approach to measure how climatic factors interact with each other under land cover change. The quantification method is based on the correlation analysis of the different order derivatives, with the canonical mathematical definitions developed from the theories of system dynamics and practices of the macroscopic observations. We examined the causal relationship between the interacting variables on both spatial and temporal dimensions based on macroscopic observations of land cover change and surface climatic factors through a comparative study in the different grassland ecosystems of China. The results suggested that the interaction of land-climate could be used to explain the temporal lag effect in the comparison of the three grassland ecosystems. Significant spatial correlations between the vegetation and the climatic factors confirmed feedback mechanisms described in the theories of eco-climatology, while the uncertain temporal synchronicity reflects the causality among the key indicators. This has been rarely addressed before. Our research show that spatial correlations and the temporal synchronicity among key indicators of the land surface and climatic factors can be explained by a novel method of causality quantification using derivative analysis.

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.

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.
Red/blue light ratio strongly affects steady-state photosynthesis, but hardly affects photosynthetic induction in tomato (Solanum lycopersicum)
Zhang, Yuqi ; Kaiser, Elias ; Zhang, Yating ; Yang, Qichang ; Li, Tao - \ 2018
Physiologia Plantarum (2018). - ISSN 0031-9317

Plants are often subjected to rapidly alternating light intensity and quality. While both short- and long-term changes in red and blue light affect leaf photosynthesis, their impact on dynamic photosynthesis is not well documented. It was tested how dynamic and steady-state photosynthetic traits were affected by red/blue ratios, either during growth or during measurements, in tomato leaves. Four red/blue ratios were used: monochromatic red (R100), monochromatic blue (B100), a red/blue light ratio of 9:1 (R90B10) and a red/blue light ratio of 7:3 (R70B30). R100 grown leaves showed decreased photosynthetic capacity (maximum rates of light-saturated photosynthesis, carboxylation, electron transport and triose phosphate use), leaf thickness and nitrogen concentrations. Acclimation to various red/blue ratios had limited effects on photosynthetic induction in dark-adapted leaves. B100-grown leaves had a approximately 15% larger initial NPQ transient than the other treatments, which may be beneficial for photoprotection under fluctuating light. B100-grown leaves also showed faster stomatal closure when exposed to low light intensity, which likely resulted from smaller stomata and higher stomatal density. When measured under different red/blue ratios, stomatal opening rate and photosynthetic induction rate were hardly accelerated by increased fractions of blue light in both growth chamber-grown leaves and greenhouse-grown leaves. However, steady-state photosynthesis rate 30 min after photosynthetic induction was strongly reduced in leaves exposed to B100 during the measurement. We conclude that varying red/blue light ratios during growth and measurement strongly affects steady-state photosynthesis, but has limited effects on photosynthetic induction rate.

Review: Selecting for improved feed efficiency and reduced methane emissions in dairy cattle
Løvendahl, P. ; Difford, G.F. ; Li, B. ; Chagunda, M.G.G. ; Huhtanen, P. ; Lidauer, M.H. ; Lassen, J. ; Lund, P. - \ 2018
Animal 12 (2018)s2. - ISSN 1751-7311 - p. s336 - s349.
digestibility - genetics - holobiont - microbiome - ranking

It may be possible for dairy farms to improve profitability and reduce environmental impacts by selecting for higher feed efficiency and lower methane (CH4) emission traits. It remains to be clarified how CH4 emission and feed efficiency traits are related to each other, which will require direct and accurate measurements of both of these traits in large numbers of animals under the conditions in which they are expected to perform. The ranking of animals for feed efficiency and CH4 emission traits can differ depending upon the type and duration of measurement used, the trait definitions and calculations used, the period in lactation examined and the production system, as well as interactions among these factors. Because the correlation values obtained between feed efficiency and CH4 emission data are likely to be biased when either or both are expressed as ratios, therefore researchers would be well advised to maintain weighted components of the ratios in the selection index. Nutrition studies indicate that selecting low emitting animals may result in reduced efficiency of cell wall digestion, that is NDF, a key ruminant characteristic in human food production. Moreover, many interacting biological factors that are not measured directly, including digestion rate, passage rate, the rumen microbiome and rumen fermentation, may influence feed efficiency and CH4 emission. Elucidating these mechanisms may improve dairy farmers ability to select for feed efficiency and reduced CH4 emission.

Legacy of land use history determines reprogramming of plant physiology by soil microbiome
Li, Xiaogang ; Jousset, Alexandre ; Boer, Wietse de; Carrión, Víctor J. ; Zhang, Taolin ; Wang, Xingxiang ; Kuramae, Eiko E. - \ 2018
ISME Journal (2018). - ISSN 1751-7362

Microorganisms associated with roots are thought to be part of the so-called extended plant phenotypes with roles in the acquisition of nutrients, production of growth hormones, and defense against diseases. Since the crops selectively enrich most rhizosphere microbes out of the bulk soil, we hypothesized that changes in the composition of bulk soil communities caused by agricultural management affect the extended plant phenotype. In the current study, we performed shotgun metagenome sequencing of the rhizosphere microbiome of the peanut (Arachis hypogaea) and metatranscriptome analysis of the roots of peanut plants grown in the soil with different management histories, peanut monocropping and crop rotation. We found that the past planting record had a significant effect on the assembly of the microbial community in the peanut rhizosphere, indicating a soil memory effect. Monocropping resulted in a reduction of the rhizosphere microbial diversity, an enrichment of several rare species, and a reduced representation of traits related to plant performance, such as nutrients metabolism and phytohormone biosynthesis. Furthermore, peanut plants in monocropped soil exhibited a significant reduction in growth coinciding with a down-regulation of genes related to hormone production, mainly auxin and cytokinin, and up-regulation of genes related to the abscisic acid, salicylic acid, jasmonic acid, and ethylene pathways. These findings suggest that land use history affects crop rhizosphere microbiomes and plant physiology.

Preantral follicular atresia occurs mainly through autophagy, while antral follicles degenerate mostly through apoptosis
Meng, Li ; Jan, Sabrina Z. ; Hamer, Geert ; Pelt, Ans M. van; Stelt, Inge van der; Keijer, Jaap ; Teerds, Katja J. - \ 2018
Biology of Reproduction 99 (2018)4. - ISSN 0006-3363 - p. 853 - 863.

There is a general agreement that granulosa cell apoptosis is the cause of antral follicle attrition. Less clear is whether this pathway is also activated in case of preantral follicle degeneration, as several reports mention that the incidence of granulosa cell apoptosis in preantral follicles is negligible. Our objective is therefore to determine which cell-death pathways are involved in preantral and antral follicular degeneration.Atretic preantal and antral follicles were investigated using immunohistochemistry and laser-capture microdissection followed by quantitative real-time reverse transcription polymerase chain reaction. Microtubule-associated light-chain protein 3 (LC3), sequestosome 1 (SQSTM1/P62), Beclin1, autophagy-related protein 7 (ATG7), and cleaved caspase 3 (cCASP3) were used as markers for autophagy and apoptosis, respectively. P62 immunostaining was far less intense in granulosa cells of atretic compared to healthy preantral follicles, while no difference in LC3 and BECLIN1 immunostaining intensity was observed. This difference in P62 immunostaining was not observed in atretic antral follicles. mRNA levels of LC3 and P62 were not different between healthy and atretic (pre)antral follicles. ATG7 immunostaining was observed in granulosa cells of preantral atretic follicles, not in granulosa cells of degenerating antral follicles. The number of cCASP3-positive cells was negligible in preantral atretic follicles, while numerous in atretic antral follicles. Taken together, we conclude that preantral and antral follicular atresia is the result of activation of different cell-death pathways as antral follicular degeneration is initiated by massive granulosa cell apoptosis, while preantral follicular atresia occurs mainly via enhanced granulosa cell autophagy.

Substrate binding by the second sialic acid-binding site of influenza a virus N1 neuraminidase contributes to enzymatic activity
Du, Wenjuan ; Dai, Meiling ; Li, Zeshi ; Boons, Geert-Jan ; Peeters, Ben ; Kuppeveld, Frank J.M. van; Vries, Erik de; Haan, Cornelis A.M. de - \ 2018
Journal of Virology 92 (2018)20. - ISSN 0022-538X
Influenza A virus - Neuraminidase - Second SIA-binding site - Sialic acid

The influenza A virus (IAV) neuraminidase (NA) protein plays an essential role in the release of virus particles from cells and decoy receptors. The NA enzymatic activity presumably needs to match the activity of the IAV hemagglutinin (HA) attachment protein and the host sialic acid (SIA) receptor repertoire. We analyzed the enzymatic activities of N1 NA proteins derived from avian (H5N1) and human (H1N1) IAVs and analyzed the role of the second SIA-binding site, located adjacent to the conserved catalytic site, therein. SIA contact residues in the second SIAbinding site of NA are highly conserved in avian, but not human, IAVs. All N1 proteins preferred cleaving α2,3- over α2,6-linked SIAs even when their corresponding HA proteins displayed a strict preference for α2,6-linked SIAs, indicating that the specificity of the NA protein does not need to fully match that of the corresponding HA protein. NA activity was affected by substitutions in the second SIA-binding site that are observed in avian and human IAVs, at least when multivalent rather than monovalent substrates were used. These mutations included both SIA contact residues and residues that do not directly interact with SIA in all three loops of the second SIA-binding site. Substrate binding via the second SIA-binding site enhanced the catalytic activity of N1. Mutation of the second SIA-binding site was also shown to affect virus replication in vitro. Our results indicate an important role for the N1 second SIA-binding site in binding to and cleavage of multivalent substrates. IMPORTANCE Avian and human influenza A viruses (IAVs) preferentially bind α2,3- and α2,6-linked sialic acids (SIAs), respectively. A functional balance between the hemagglutinin (HA) attachment and neuraminidase (NA) proteins is thought to be important for host tropism. What this balance entails at the molecular level is, however, not well understood. We now show that N1 proteins of both avian and human viruses prefer cleaving avian- over human-type receptors although human viruses were relatively better in cleavage of the human-type receptors. In addition, we show that substitutions at different positions in the second SIA-binding site found in NA proteins of human IAVs have a profound effect on binding and cleavage of multivalent, but not monovalent, receptors and affect virus replication. Our results indicate that the HA-NA balance can be tuned via modification of substrate binding via this site and suggest an important role of the second SIA-binding site in host tropism.

Resistance to tomato yellow leaf curl virus in tomato germplasm
Yan, Zhe ; Pérez-de-Castro, Ana ; Díez, Maria J. ; Hutton, Samuel F. ; Visser, Richard G.F. ; Wolters, Anne-Marie A. ; Bai, Yuling ; Li, Junming - \ 2018
Frontiers in Plant Science 9 (2018). - ISSN 1664-462X
Begomovirus - Resistance - S. chilense - S. peruvianum - Solanum lycopersicum - Tomato - TYLCV

Tomato yellow leaf curl virus (TYLCV) is a virus species causing epidemics in tomato (Solanum lycopersicum) worldwide. Many efforts have been focused on identification of resistance sources by screening wild tomato species. In many cases, the accession numbers were either not provided in publications or not provided in a consistent manner, which led to redundant screenings. In the current study, we summarized efforts on the screenings of wild tomato species for TYLCV resistance from various publications. In addition, we screened 708 accessions from 13 wild tomato species using different inoculation assays (i.e., whitefly natural infection and Agrobacterium-mediated inoculation) from which 138 accessions exhibited no tomato yellow leaf curl disease (TYLCD) symptoms. These symptomless accessions include 14 accessions from S. arcanum, 43 from S. chilense, 1 from S. chmielewskii, 28 from S. corneliomulleri, 5 from S. habrochaites, 4 from S. huaylasense, 2 from S. neorickii, 1 from S. pennellii, 39 from S. peruvianum, and 1 from S. pimpinellifolium. Most of the screened S. chilense accessions remained symptomless. Many symptomless accessions were also identified in S. arcanum, S. corneliomulleri, and S. peruvianum. A large number of S. pimpinellifolium accessions were screened. However, almost all of the tested accessions showed TYLCD symptoms. Further, we studied allelic variation of the Ty-1/Ty-3 gene in few S. chilense accessions by applying virus-induced gene silencing and allele mining, leading to identification of a number of allele-specific polymorphisms. Taken together, we present a comprehensive overview on TYLCV resistance and susceptibility in wild tomato germplasm, and demonstrate how to study allelic variants of the cloned Ty-genes in TYLCV-resistant accessions.

The potential of osmolytes and their precursors to alleviate osmotic stress of anaerobic granular sludge.
Sudmalis, D. ; Millah, S.K. ; Gagliano, M.C. ; Butré, C.I. ; Plugge, C.M. ; Rijnaarts, H.H.M. ; Zeeman, G. ; Temmink, H. - \ 2018
Water Research 147 (2018). - ISSN 0043-1354 - p. 142 - 151.
Anaerobic granular sludge - Methanogenic activity - Osmolytes - Saline wastewater

Increasing amounts of saline (waste)water with high concentrations of organic pollutants are generated globally. In the anaerobic (waste)water treatment domain, high salt concentrations are repeatedly reported to inhibit methanogenic activity and strategies to overcome this toxicity are needed. Current research focuses on the use of potential osmolyte precursor compounds for osmotic stress alleviation in granular anaerobic sludges upon exposure to hypersalinity shocks. Glutamic acid, aspartic acid, lysine, potassium, gelatine, and tryptone were tested for their potential to alleviate osmotic stress in laboratory grown and full – scale granular sludge. The laboratory grown granular sludge was adapted to 5 (R5) and 20 (R20) g Na+/L. Full-scale granular sludge was obtained from internal circulation reactors treating tannery (waste)water with influent conductivity of 29.2 (Do) and 14.1 (Li) mS/cm. In batch experiments which focused on specific methanogenic activity (SMA), R5 granular sludge was exposed to a hypersalinity shock of 20 g Na+/L. The granular sludge of Do and Li was exposed to a hypersalinity shock of 10 g Na+/L with sodium acetate as the sole carbon source. The effects on R20 granular sludge were studied at the salinity level to which the sludge was already adapted, namely 20 g Na+/L. Dosing of glutamic acid, aspartic acid, gelatine, and tryptone resulted in increased SMA compared to only acetate fed batches. In batches with added glutamic acid, the SMA increased by 115% (Li), 35% (Do) and 9% (R20). With added aspartic acid, SMA increased by 72% (Li), 26% (Do), 12% (R5) and 7% (R20). The addition of tryptone resulted in SMA increases of 36% (R5), 17% (R20), 179% (Li), and 48% (Do), whereas added gelatine increased the SMA by 30% (R5), 14% (R20), 23% (Li), and 13% (Do). The addition of lysine, meanwhile, gave negative effects on SMA of all tested granular sludges. Potassium at sea water Na/K ratio (27.8 w/w) had a slight positive effect on SMA of Do (7.3%) and Li (10.1%), whereas at double the sea water ratio (13.9% w/w) had no pronounced positive effect. R20 granular sludge was also exposed to hyposalinity shock from 20 down to 5 g Na+/L. Glutamate and N-acetyl-β-lysine were excreted by microbial consortium in anaerobic granular sludge adapted to 20 g Na+/L upon this exposure to hyposalinity. A potential consequence when applying these results is that saline streams containing specific and hydrolysable proteins can be anaerobically treated without additional dosing of osmolytes.

Correction to: New traits in crops produced by genome editing techniques based on deletions
Wiel, C.C.M. van de; Schaart, J.G. ; Lotz, L.A.P. ; Smulders, M.J.M. - \ 2018
Plant Biotechnology Reports 12 (2018)5. - ISSN 1863-5466 - p. 375 - 375.

In the original publication of the article, Li et al. has been incorrectly cited in the following sentence “Interestingly, a complex trait par excellence, yield, was also shown to be amenable to an SDN-1 approach. Li et al. (2017) used CRISPR-Cas9 in rice to mutate the regulatory genes Gna1, DEP1, and GS3 and obtained plants with increased grain numbers, dense erect panicles plus semi-dwarf phenotype, and larger grains, respectively.”.

Purified Dietary Red and White Meat Proteins Show Beneficial Effects on Growth and Metabolism of Young Rats Compared to Casein and Soy Protein
Song, Shangxin ; Hua, Chun ; Zhao, Fan ; Li, Mengjie ; Fu, Qingquan ; Hooiveld, Guido J.E.J. ; Muller, Michael ; Li, Chunbao ; Zhou, Guanghong - \ 2018
Journal of Agricultural and Food Chemistry 66 (2018)38. - ISSN 0021-8561 - p. 9942 - 9951.
molecular nutrition - protein quality - proteomics - red meat - white meat

This study compared the effects of casein, soy protein (SP), red (RMP), and white meat (WMP) proteins on growth and metabolism of young rats. Compared to casein, the ratio of daily feed intake to daily body weight gain of rats was not changed by meat protein but reduced by SP by 93.3% (P < 0.05). Feeding RMP and WMP reduced the liver total cholesterol (TC) contents by 24.3% and 17.8%, respectively (P < 0.05). Only RMP increased plasma HDL-cholesterol concentrations (by 12.7%, P < 0.05), whereas SP increased plasma triacylglycerol, TC, and LDL-cholesterol concentrations by 23.7%, 19.5%, and 61.5%, respectively (P < 0.05). Plasma essential and total amino acid concentrations were increased by WMP (by 18.8% and 12.4%, P < 0.05) but reduced by SP (by 28.3% and 37.7%, P < 0.05). Twenty-five liver proteins were differentially expressed in response to different protein sources. Therefore, meat proteins were beneficial for growth and metabolism of young rats compared to casein and SP.

Interleukin-37 treatment of mice with metabolic syndrome improves insulin sensitivity and reduces pro-inflammatory cytokine production in adipose tissue
Ballak, Dov B. ; Li, Suzhao ; Cavalli, Giulio ; Stahl, Jonathan L. ; Tengesdal, Isak W. ; Diepen, Janna A. van; Klück, Viola ; Swartzwelter, Benjamin ; Azam, Tania ; Tack, Cees J. ; Stienstra, Rinke ; Mandrup-Poulsen, Thomas ; Seals, Douglas R. ; Dinarello, Charles A. - \ 2018
Journal of Biological Chemistry 293 (2018)37. - ISSN 0021-9258 - p. 14224 - 14236.

Obesity and the metabolic syndrome are characterized by chronic, low-grade inflammation mainly originating from expanding adipose tissue and resulting in inhibition of insulin signaling and disruption of glycemic control.Transgenic mice expressing human interleukin 37 (IL-37),an anti-inflammatory cytokine of the IL-1 family,are protected against metabolic syndrome when fed a high-fat diet (HFD) containing 45% fat. Here, we examined whether treatment with recombinant IL-37 ameliorates established insulin resistance and obesity-induced inflammation. WT mice were fed a HFD for 22 weeks and then treated daily with IL-37 (1 ug/mouse) during the last 2 weeks. Compared with vehicle only-treated mice, IL-37-treated mice exhibited reduced insulin in the plasma and had significant improvements in glucose tolerance and in insulin content of the islets.The IL-37 treatment also increased the levels of circulating IL-1 receptor antagonist. Cultured adipose tissues revealed that IL-37 treatment significantly decreases spontaneous secretions of IL-1β, tumor necrosis factor α (TNFα), and CXC motif chemokine ligand 1 (CXCL-1). We also fed mice a 60% fat diet with concomitant daily IL-37 for 2 weeks and observed decreased secretion of IL-1β, TNFα, and IL-6 and reduced intracellular levels of IL-1β in the liver and adipose tissue, along with improved plasma glucose clearance. Compared with vehicle treatment, these IL-37-treated mice had no apparent weight gain. In human adipose tissue cultures, the presence of 50 pM IL-37 reduced spontaneous release of TNF and 50% of lipopolysaccharide-induced TNFα. These findings indicate that IL-37's anti-inflammatory effects can ameliorate established metabolic disturbances during obesity.

Waterbird Communities in Subsidence Wetlands Created by Underground Coal Mining in China : Effects of Multi-Scale Environmental and Anthropogenic Variables
Li, Chunlin ; Yang, Sen ; Zha, Daode ; Zhang, Yong ; Boer, Willem F. de - \ 2018
Environmental Conservation (2018). - ISSN 0376-8929 - 9 p.
Habitat loss - subsidence wetland - waterbird - wetland degradation

SummaryUnderground coal mining in the North China Plain has created large-scale subsidence wetlands that may attract waterbirds that use them as complementary habitats. However, no study has been conducted to understand avian use of these created wetlands, inhibiting the formulation of effective management plans. Here, we carried out 12 semi-monthly surveys in 55 subsidence wetlands during the 2016-2017 migration and wintering period and performed direct multivariate analyses, combined with variance partitioning, to test the effects of multi-scale habitat variables on the waterbird assemblages. A total of 89 349 waterbirds representing 60 species were recorded, with seasonal fluctuations in species richness and bird abundance. Waterbird community structures were shaped by four groups of variables at local, landscape and human levels with different effects among seasons. Anthropogenic disturbance was the most important factor group, negatively affecting most guilds. Waterbirds in this human-dominated environment are under a variety of potential threats that should be further studied. The subsidence wetlands are still expanding, and if managed effectively, may provide important complementary habitats for a wide array of waterbird species, particularly for those migrating along the East Asian-Australasian Flyway. Our study provides key baseline data regarding the waterbird communities and may help with the designing of effective management and conservation plans.

Denitrification-potential evaluation and nitrate-removal-pathway analysis of aerobic denitrifier strain Marinobacter hydrocarbonoclasticus RAD-2
Kong, Dedong ; Li, Wenbing ; Deng, Yale ; Ruan, Yunjie ; Chen, Guangsuo ; Yu, Jianhai ; Lin, Fucheng - \ 2018
Water 10 (2018)10. - ISSN 2073-4441
Aerobic denitrification - Denitrifying gene expression - Marinobacter hydrocarbonoclasticus RAD-2 - Nitrogen removal - Wastewater treatment

An aerobic denitrifier was isolated from a long-term poly (3-hydroxybutyrate-co-3- hydroxyvalerate) PHBV-supported denitrification reactor that operated under alternate aerobic/anoxic conditions. The strain was identified as Marinobacter hydrocarbonoclasticus RAD-2 based on 16S rRNA-sequence phylogenetic analysis. Morphology was observed by scanning electron microscopy (SEM), and phylogenetic characteristics were analyzed with the API 20NE test. Strain RAD-2 showed efficient aerobic denitrification ability when using NO3 - -N or NO2 --N as its only nitrogen source, while heterotrophic nitrification was not detected. The average NO3 --N and NO2 --N removal rates were 6.47 mg/(L·h)and 6.32 mg/(L·h), respectively. Single-factor experiments indicated that a 5:10 C/N ratio, 25-40 °C temperature, and 100-150 rpm rotation speed were the optimal conditions for aerobic denitrification. Furthermore, the denitrifying gene napA had the highest expression on a transcriptional level, followed by the denitrifying genes nirS and nosZ. The norB gene was found to have significantly low expression during the experiment. Overall, great aerobic denitrification ability makes the RAD-2 strain a potential alternative in enhancing nitrate management for marine recirculating aquaculture system (RAS) practices.

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