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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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.

Abscisic acid influences tillering by modulation of strigolactones in barley
Wang, Hongwen ; Chen, Wanxin ; Eggert, Kai ; Charnikhova, Tatsiana ; Bouwmeester, Harro ; Schweizer, Patrick ; Hajirezaei, Mohammad R. ; Seiler, Christiane ; Sreenivasulu, Nese ; Wirén, Nicolaus von; Kuhlmann, Markus - \ 2018
Journal of Experimental Botany 69 (2018)16. - ISSN 0022-0957 - p. 3883 - 3898.
Abscisic acid - barley - cereals - hormone regulation - phytohormone cross-talk - shoot branching - strigolactone biosynthesis - tillering

Strigolactones (SLs) represent a class of plant hormones that are involved in inhibiting shoot branching and in promoting abiotic stress responses. There is evidence that the biosynthetic pathways of SLs and abscisic acid (ABA) are functionally connected. However, little is known about the mechanisms underlying the interaction of SLs and ABA, and the relevance of this interaction for shoot architecture. Based on sequence homology, four genes (HvD27, HvMAX1, HvCCD7, and HvCCD8) involved in SL biosynthesis were identified in barley and functionally verified by complementation of Arabidopsis mutants or by virus-induced gene silencing. To investigate the influence of ABA on SLs, two transgenic lines accumulating ABA as a result of RNAi-mediated down-regulation of HvABA 8'-hydroxylase 1 and 3 were employed. LC-MS/MS analysis confirmed higher ABA levels in root and stem base tissues in these transgenic lines. Both lines showed enhanced tiller formation and lower concentrations of 5-deoxystrigol in root exudates, which was detected for the first time as a naturally occurring SL in barley. Lower expression levels of HvD27, HvMAX1, HvCCD7, and HvCCD8 indicated that ABA suppresses SL biosynthesis, leading to enhanced tiller formation in barley.

Milking exopolysaccharides from Botryococcus braunii CCALA778 by membrane filtration
Cubero, Rafael ; Wang, Weiliang ; Martín, Judit ; Bermejo, Elisabeth ; Sijtsma, Lolke ; Togtema, Arnoud ; Barbosa, María J. ; Kleinegris, Dorinde M.M. - \ 2018
Algal Research 34 (2018). - ISSN 2211-9264 - p. 175 - 181.

The aim of this work was to optimize the efficiency of extraction and recovery, also known as ‘milking’ of exopolysaccharides (excreted polysaccharides, EPS) from continuous cultures of Botryococcus braunii CCALA778. First, an indoor process was developed and optimised, ensuring the highest milking efficiency without compromising culture viability. For this, photobioreactors were operated in a photo-chemostat mode under simulated outdoor conditions of a typical summer at AlgaePARC (51°59′44.1”N 5°39′26.2″E) in Wageningen, The Netherlands. Once a steady state was reached, areal productivities of 23 g m−2 d−1 and 3 g m−2 d−1 for biomass and EPS were achieved. EPS milking was done by membrane filtration of one reactor volume at the beginning of the dark period. After optimization, the maximum recovery of EPS, without damaging the cells, was 12%; yielding a daily EPS extraction rate of 0.36 g m−2 d−1. The optimised process was scaled-up and applied outdoors during the summer (at AlgaePARC facilities). Outdoor cultures showed 25% lower biomass productivity (17 g m−2 d−1) but an 25% higher EPS productivity (4 g m−2 d−1). The efficiency in the milking, however, decreased as compared to indoor results. Only 3% of the total content of EPS produced outdoors was milked (0.12 g m−2 d−1). To improve the EPS milking process, future research should focus on increasing the EPS extraction yield without negatively influencing its production by Botryococcus braunii.

Influence of humic acid on transport, deposition and activity of lysozyme in quartz sand
Li, Yan ; Koopal, Luuk K. ; Xiong, Juan ; Wang, Mingxia ; Yang, Chenfeng ; Tan, Wenfeng - \ 2018
Environmental Pollution 242 (2018). - ISSN 0269-7491 - p. 298 - 306.
Deposition - Enzyme activity - Humic acid - Lysozyme - Protein - Transport

Increasing humic acid concentration reduced the mobility of proteins with opposite charges, and the increased activity of effluent proteins could bring potential environmental hazards.

Human Milk Oligosaccharides in Colostrum and Mature Milk of Chinese Mothers : Lewis Positive Secretor Subgroups
Elwakiel, M. ; Hageman, J.A. ; Wang, W. ; Szeto, I.M. ; Goudoever, J.B. van; Hettinga, K.A. ; Schols, H.A. - \ 2018
Journal of Agricultural and Food Chemistry 66 (2018)27. - ISSN 0021-8561 - p. 7036 - 7043.
carbohydrates - genetic polymorphisms - lactation stage - variability

To study the variability in human milk oligosaccharide (HMO) composition of Chinese human milk over a 20-wk lactation period, HMO profiles of 30 mothers were analyzed using CE-LIF. This study showed that total HMO concentrations in Chinese human milk decreased significantly over a 20-wk lactation period, independent of the mother's SeLe status, although with individual variations. In addition, total acidic and neutral HMO concentrations in Chinese human milk decreased over lactation, and levels are driven by their mother's SeLe status. Analysis showed that total neutral fucosylated HMO concentrations in Chinese human milk were higher in the two secretor groups as compared to the nonsecretor group. On the basis of the total neutral fucosylated HMO concentrations in Chinese human milk, HMO profiles within the Se+Le+ group can be divided into two subgroups. HMOs that differed in level between Se+Le+ subgroups were 2′FL, DF-L, LNFP I, and F-LNO. HMO profiles in Dutch human milk also showed Se+Le+ subgroup division, with 2′FL, LNT, and F-LNO as the driving force.

Comparing OMI-based and EPA AQS in situ NO2 trends: towards understanding surface NOx emission changes
Zhang, R. ; Wang, Y. ; Smeltzer, C. ; Qu, Hang ; Koshak, W. ; Boersma, K.F. - \ 2018
Atmospheric Measurement Techniques 11 (2018)7. - ISSN 1867-1381 - p. 3955 - 3967.
With the improved spatial resolution of the Ozone Monitoring Instrument (OMI) over earlier instruments and more than 10 years of service, tropospheric NO2 retrievals from OMI have led to many influential studies on the relationships between socioeconomic activities and NOx emissions. Previous studies have shown that the OMI NO2 data show different relative trends compared to in situ measurements. However, the sources of the discrepancies need further investigations. This study focuses on how to appropriately compare relative trends derived from OMI and in situ measurements. We retrieve OMI tropospheric NO2 vertical column densities (VCDs) and obtain the NO2 seasonal trends over the United States, which are compared with coincident in situ surface NO2 measurements from the Air Quality System (AQS) network. The Mann–Kendall method with Sen's slope estimator is applied to derive the NO2 seasonal and annual trends for four regions at coincident sites during 2005–2014. The OMI-based NO2 seasonal relative decreasing trends are generally biased low compared to the in situ trends by up to 3.7%yr−1, except for the underestimation in the US Midwest and Northeast during December, January, and February (DJF). We improve the OMI retrievals for trend analysis by removing the ocean trend, using the Moderate Resolution Imaging Spectroradiometer (MODIS) albedo data in air mass factor (AMF) calculation. We apply a lightning flash filter to exclude lightning-affected data to make proper comparisons. These data processing procedures result in close agreement (within 0.3%yr−1) between in situ and OMI-based NO2 regional annual relative trends. The remaining discrepancies may result from inherent difference between trends of NO2 tropospheric VCDs and surface concentrations, different spatial sampling of the measurements, chemical nonlinearity, and tropospheric NO2 profile changes. We recommend that future studies apply these procedures (ocean trend removal and MODIS albedo update) to ensure the quality of satellite-based NO2 trend analysis and apply the lightning filter in studying surface NOx emission changes using satellite observations and in comparison with the trends derived from in situ NO2 measurements. With these data processing procedures, we derive OMI-based NO2 regional annual relative trends using all available data for the US West (−2.0%±0.3yr−1), Midwest (−1.8%±0.4yr−1), Northeast (−3.1%±0.5yr−1), and South (−0.9%±0.3yr−1). The OMI-based annual mean trend over the contiguous United States is −1.5%±0.2yr−1. It is a factor of 2 lower than that of the AQS in situ data (−3.9%±0.4yr−1); the difference is mainly due to the fact that the locations of AQS sites are concentrated in urban and suburban regions
Roles of nitrogen and cytokinin signals in root and shoot communications in maximizing of plant productivity and their agronomic applications
Gu, Junfei ; Li, Zhikang ; Mao, Yiqi ; Struik, Paul C. ; Zhang, Hao ; Liu, Lijun ; Wang, Zhiqin ; Yang, Jianchang - \ 2018
Plant Science 274 (2018). - ISSN 0168-9452 - p. 320 - 331.
Cytokinin transport - Long-distance signaling - Nitrogen status - Root - shoot relationship - Source-sink relationship

Nitrogen is an essential, often limiting, factor in plant growth and development. To regulate growth under limited nitrogen supply, plants sense the internal and external nitrogen status, and coordinate various metabolic processes and developmental programs accordingly. This coordination requires the transmission of various signaling molecules that move across the entire plant. Cytokinins, phytohormones derived from adenine and synthesized in various parts of the plant, are considered major local and long-distance messengers. Cytokinin metabolism and signaling are closely associated with nitrogen availability. They are systemically transported via the vasculature from plant roots to shoots, and vice versa, thereby coordinating shoot and root development. Tight linkage exists between the nitrogen signaling network and cytokinins during diverse developmental and physiological processes. However, the cytokinin-nitrogen interactions and the communication systems involved in sensing rhizospheric nitrogen status and in regulating canopy development remain obscure. We review current knowledge on cytokinin biosynthesis, transport and signaling, nitrogen acquisition, metabolism and signaling, and their interactive roles in regulating root-shoot morphological and physiological characteristics. We also discuss the role of spatio-temporal regulation of cytokinins in enhancing beneficial crop traits of yield and nitrogen use efficiency.

Predicting individual differences in viral susceptibility caused by natural genetic variation within species
Sluijs, L. van; Sterken, M.G. ; Wang, Yiru ; Ritmahan, Wannisa ; Gultom, Mitra ; Pankok, Frederik ; Blokhina, T. ; Riksen, J.A.G. ; Volkers, J.M. ; Snoek, L.B. ; Pijlman, G.P. ; Kammenga, J.E. - \ 2018
Natural genetic variation within species can underlie different individual susceptibilities upon viral infection. The molecular mechanisms by which genetic variation affects the viral susceptibility are currently poorly understood. Here we use Caenorhabditis elegans as a model organism to identify which polymorphisms alter the viral susceptibility. Moreover, we predict how the molecular mechanisms behind altered susceptibilities may work. The viral susceptibility towards Orsay virus of the commonly used lab strain, N2, is higher than that of the Hawaiian isolate CB4856. The phenotype of N2xCB4856 recombinant inbred strains was obtained by measuring the viral load upon infection and these viral loads were correlated to the genotypes by quantitative trait locus (QTL) mapping. A region on chromosome IV was found to correlate with changes in the viral susceptibility. This QTL region, containing hundreds of candidate polymorphisms, was fine mapped using two introgression line panels. The first introgression line panel contained an introgression of N2 into the genome of CB4856, whereas the second panel contained an introgression of CB4856 into the genome of N2. Using these two panels the QTL region was fine mapped to a region containing about 30 polymorphisms. Using known protein structures we predicted possible effects of candidate polymorphisms. An example is a single nucleotide polymorphism in a conserved region of the known antiviral defence gene cul-6. This polymorphism may be responsible for an altered stability of the SCF complex that targets viral particles for degradation. A causal relationship could be experimentally verified by exchanging the polymorphism of the resistant and susceptible strain, an approach we are currently taking.
Genetic variation causes differential viral susceptibilities in the model organism Caenorhabditis elegans
Sluijs, L. van; Sterken, M.G. ; Wang, Yiru ; Ritmahan, Wannisa ; Gultom, Mitra ; Pankok, Frederik ; Blokhina, T. ; Riksen, J.A.G. ; Volkers, J.M. ; Snoek, L.B. ; Pijlman, G.P. ; Kammenga, J.E. - \ 2018
Individual genetic variation in the same species can cause different susceptibilities upon viral infection. Causal polymorphisms that underlie susceptibility differences can be identified by mapping the susceptibility of individuals to the genetic variants the individuals carry. Genetic mapping usually indicates a locus containing multiple candidate polymorphisms that may be the causal one. Here, we used three independent mapping populations of the nematode Caenorhabditis elegans to find a small group of candidate polymorphisms that determine the susceptibility to infection by a natural virus. Homozygous mapping populations of C. elegans were previously obtained by crossing two strains with a different viral susceptibility: the susceptible strain N2 and the more resistant strain CB4856. A recombinant inbred panel was used for quantitative trait locus (QTL) mapping to identify a region containing hundreds of candidate genes. Two introgression line panels experimentally confirmed the causal region and fine mapped the candidate region to about 30 potentially causal polymorphisms. One of these polymorphisms, the known antiviral defence gene cul-6, contains a single nucleotide polymorphism in a conserved region. We hypothesise that this polymorphism may be responsible for the difference in viral susceptibility and we are currently trying to exchange polymorphisms between the susceptible and resistant strain using CRISPR/Cas9. In the end, finding how polymorphisms in viral response pathways alter the molecular mechanisms upon viral infection can contribute to a better understanding of the close interactions between host and virus.

The intelligent delivery systems for bioactive compounds in foods : Physicochemical and physiological conditions, absorption mechanisms, obstacles and responsive strategies
Chai, Jingjing ; Jiang, Ping ; Wang, Pengjie ; Jiang, Yumeng ; Li, Dan ; Bao, Weier ; Liu, Bingxue ; Liu, Bin ; Zhao, Liyun ; Norde, Willem ; Yuan, Qipeng ; Ren, Fazheng ; Li, Yuan - \ 2018
Trends in Food Science and Technology 78 (2018). - ISSN 0924-2244 - p. 144 - 154.
Bioaccessibility - Bioactive compounds - Bioavailability - Delivery barriers - Encapsulation - Intelligent delivery systems

Background: Bioactive natural compounds have received considerable attention due to their health benefits, including anti-oxidant, anti-cancer, anti-diabetes and cardiovascular disease-preventing functions. However, the stability of these sensitive compounds can be influenced by unfavourable environmental conditions during processing and storage. In addition, delivery of bioactive compounds via the oral route is restricted by various physiological barriers, including a harsh pH, gastrointestinal enzymes, the mucus layer, and the epithelium. Intelligent delivery systems are a promising method to protect bioactive molecules from degradation and improve their bioavailability. Scope and approach: We have demonstrated the physicochemical and physiological GI conditions. The structural composition of the epithelium and transport mechanisms of bioactives and nanoparticles across the intestinal epithelium were discussed. The effects of enhanced aqueous solubility, stability, bioaccessibility and bioavailability after encapsulation were illustrated. Furthermore, novel intelligent carriers that are responsive to the oral route, pH, enzymes and cell receptors were also discussed. Key findings and conclusions: This comprehensive multidisciplinary review provides useful guidelines for the application of bioactive compounds in the food industry. Intelligent carrier systems are designed to improve the low solubility, poor stability and low permeability of the gastrointestinal tract, and they have the potential to improve oral bioavailability.

An integrated method for calculating DEM-based RUSLE LS
Wang, Meng ; Baartman, Jantiene E.M. ; Zhang, Hongming ; Yang, Qinke ; Li, Shuqin ; Yang, Jiangtao ; Cai, Cheng ; Wang, Meili ; Ritsema, Coen J. ; Geissen, Violette - \ 2018
Earth Science Informatics (2018). - ISSN 1865-0473 - 12 p.
Geographic information system (GIS) - LS factor - Revised universal soil loss equation (RUSLE) - Soil erosion

The improvement of resolution of digital elevation models (DEMs) and the increasing application of the Revised Universal Soil Loss Equation (RUSLE) over large areas have created problems for the efficiency of calculating the LS factor for large data sets. The pretreatment for flat areas, flow accumulation, and slope-length calculation have traditionally been the most time-consuming steps. However, obtaining these features are generally usually considered as separate steps, and calculations still tend to be time-consuming. We developed an integrated method to improve the efficiency of calculating the LS factor. The calculation model contains algorithms for calculating flow direction, flow accumulation, slope length, and the LS factor. We used the Deterministic 8 method to develop flow-direction octrees (FDOTs), flat matrices (FMs) and first-in-first-out queues (FIFOQs) tracing the flow path. These data structures were much more time-efficient for calculating the slope length inside the flats, the flow accumulation, and the slope length linearly by traversing the FDOTs from their leaves to their roots, which can reduce the search scope and data swapping. We evaluated the accuracy and effectiveness of this integrated algorithm by calculating the LS factor for three areas of the Loess Plateau in China and SRTM DEM of China. The results indicated that this tool could substantially improve the efficiency of LS-factor calculations over large areas without reducing accuracy.

The tomato MAX1 homolog, SlMAX1, is involved in the biosynthesis of tomato strigolactones from carlactone
Zhang, Yanxia ; Cheng, Xi ; Wang, Yanting ; Díez-Simón, Carmen ; Flokova, Kristyna ; Bimbo, Andrea ; Bouwmeester, Harro J. ; Ruyter-Spira, Carolien - \ 2018
New Phytologist 219 (2018)1. - ISSN 0028-646X - p. 297 - 309.
cytochrome P450 (CYP) - didehydro-orobanchol isomers - MORE AXILLARY GROWTH 1 (MAX1) - orobanchol - solanacol - tomato strigolactones
Strigolactones (SLs) are rhizosphere signalling molecules exuded by plants that induce seed germination of root parasitic weeds and hyphal branching of arbuscular mycorrhiza. They are also phytohormones regulating plant architecture. MORE AXILLARY GROWTH 1 (MAX1) and its homologs encode cytochrome P450 (CYP) enzymes that catalyse the conversion of the strigolactone precursor carlactone to canonical strigolactones in rice (Oryza sativa), and to an SL-like compound in Arabidopsis. Here, we characterized the tomato (Solanum lycopersicum) MAX1 homolog, SlMAX1. The targeting induced local lesions in genomes method was used to obtain Slmax1 mutants that exhibit strongly reduced production of orobanchol, solanacol and didehydro-orobanchol (DDH) isomers. This results in a severe strigolactone mutant phenotype in vegetative and reproductive development. Transient expression of SlMAX1 – together with SlD27, SlCCD7 and SlCCD8 – in Nicotiana benthamiana showed that SlMAX1 catalyses the formation of carlactonoic acid from carlactone. Plant feeding assays showed that carlactone, but not 4-deoxy-orobanchol, is the precursor of orobanchol, which in turn is the precursor of solanacol and two of the three DDH isomers. Inhibitor studies suggest that a 2-oxoglutarate-dependent dioxygenase is involved in orobanchol biosynthesis from carlactone and that the formation of solanacol and DDH isomers from orobanchol is catalysed by CYPs.
Microscopic Origins of Shear Jamming for 2D Frictional Grains
Wang, Dong ; Ren, Jie ; Dijksman, Joshua A. ; Zheng, Hu ; Behringer, Robert P. - \ 2018
Physical Review Letters 120 (2018)20. - ISSN 0031-9007

Shear jamming (SJ) occurs for frictional granular materials with packing fractions φ in φS<φ<φJ0, when the material is subject to shear strain γ starting from a force-free state. Here, φJμ is the isotropic jamming point for particles with a friction coefficient μ. SJ states have mechanically stable anisotropic force networks, e.g., force chains. Here, we investigate the origins of SJ by considering small-scale structures - trimers and branches - whose response to shear leads to SJ. Trimers are any three grains where the two outer grains contact a center one. Branches occur where three or more quasilinear force chain segments intersect. Certain trimers respond to shear by compressing and bending; bending is a nonlinear symmetry-breaking process that can push particles in the dilation direction faster than the affine dilation. We identify these structures in physical experiments on systems of two-dimensional frictional discs, and verify their role in SJ. Trimer bending and branch creation both increase Z above Ziso≃3 needed for jamming 2D frictional grains, and grow the strong force network, leading to SJ.

The functional oligomeric state of tegument protein GP41 is essential for baculovirus budded virion and occlusion-derived virion assembly
Li, Yimeng ; Shen, Shu ; Hu, Liangbo ; Deng, Fei ; Vlak, Just M. ; Hu, Zhihong ; Wang, Hualin ; Wang, Manli - \ 2018
Journal of Virology 92 (2018)12. - ISSN 0022-538X
Baculovirus - Function - GP41 - Leucine zipper - Oligomerization - Tegument protein - Virion assembly
gp41, one of the baculovirus core genes, encodes the only recognized tegument (O-glycosylated) protein of the occlusion-derived virion (ODV) phenotype so far. A previous study using a temperature-sensitive Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) mutant showed that GP41 plays a crucial role in budded virion (BV) formation. However, the precise function of GP41 in the baculovirus replication cycle remains unclear. In this study, AcMNPV GP41 was found to accumulate around the ring zone (RZ) region within the infected nucleus and finally assembled into both BVs and ODVs. Deletion of gp41 from the AcMNPV genome showed that BVs were no longer formed and ODVs were no longer assembled, suggesting the essential role of this gene in baculovirus virion morphogenesis. In infected cells, besides the 42-kDa monomers, dimers and trimers were detected under nonreducing conditions, whereas only trimeric GP41 forms were selectively incorporated into BVs or ODVs. Mutations of all five cysteines in GP41 individually had minor effects on GP41 oligomer formation, albeit certain mutations impaired infectious BV production, suggesting flexibility in the intermolecular disulfide bonding. Single mutations of key leucines within two predicted leucine zipper-like motifs did not interfere with GP41 oligomerization or BV and ODV formation, but double leucine mutations completely blocked oligomerization of GP41 and progeny BV production. In the latter case, the usual subcellular localization, especially RZ accumulation, of GP41 was abolished. The above findings clearly point out a close correlation between GP41 oligomerization and function and therefore highlight the oligomeric state as the functional form of GP41 in the baculovirus replication cycle.
Perception of Urban Environmental Risks and the Effects of Urban Green Infrastructures (UGIs) on Human Well-being in Four Public Green Spaces of Guangzhou, China
Duan, Junya ; Wang, Yafei ; Fan, Chen ; Xia, Beicheng ; Groot, Rudolf de - \ 2018
Environmental Management (2018). - ISSN 0364-152X - 18 p.
Environmental risks - Human well-being - Perception - Questionnaire survey - UGI

Cities face many challenging environmental problems that affect human well-being. Environmental risks can be reduced by Urban Green Infrastructures (UGIs). The effects of UGIs on the urban environment have been widely studied, but less attention has been given to the public perception of these effects. This paper presents the results of a study in Guangzhou, China, on UGI users’ perceptions of these effects and their relationship with sociodemographic variables. A questionnaire survey was conducted in four public green spaces. Descriptive statistics, a binary logistic regression model and cross-tabulation analysis were applied on the data from 396 valid questionnaires. The results show that UGI users were more concerned about poor air quality and high temperature than about flooding events. Their awareness of environmental risks was partly in accordance with official records. Regarding the perception of the impacts of environmental risks on human well-being, elderly and female respondents with higher education levels were the most sensitive to these impacts. The respondents’ perceptions of these impacts differed among the different green spaces. The effects of UGIs were well perceived and directly observed by the UGI users, but were not significantly influenced by most sociodemographic variables. Moreover, tourists had a lower perception of the impacts of environmental risks and the effects of UGI than residents did. This study provides strong support for UGIs as an effective tool to mitigate environmental risks. Local governments should consider the role of UGIs in environmental risk mitigation and human well-being with regard to urban planning and policy making.

Transcriptome analysis reveals the genetic foundation for the dynamics of starch and lipid production in Ettlia oleoabundans
Sturme, Mark H.J. ; Gong, Yanhai ; Heinrich, Josué Miguel ; Klok, Anne J. ; Eggink, Gerrit ; Wang, Dongmei ; Xu, Jian ; Wijffels, Rene H. - \ 2018
Algal Research 33 (2018). - ISSN 2211-9264 - p. 142 - 155.
Carbon-partitioning - Lipids - Microalgae - Nitrogen starvation - Starch - Transcriptome

The oleaginous microalga Ettlia oleoabundans accumulates both starch and lipids to high levels under stress conditions such as nitrogen starvation (N−). To steer biosynthesis towards starch or lipids only, it is important to understand the regulatory mechanisms involved. Here physiological and transcriptional changes under nitrogen starvation were analysed in controlled flat-panel photobioreactors at both short and long time-scales. Starch accumulation was transient and occurred rapidly within 24 h upon starvation, while lipid accumulation was gradual and reached a maximum after 4 days. The major fraction of accumulated lipids was composed of de novo synthesized neutral lipids - triacylglycerides (TAG) - and was characterized by a decreased composition of the polyunsaturated fatty acids (PUFAs) C18:3 and C16:3 and an increased composition of the mono-unsaturated (MUFAs) and saturated (SFAs) fatty acids C18:1/C16:1 and C18:0/C16:0, respectively. RNA-sequencing revealed that starch biosynthesis and degradation genes show different expression dynamics from lipid biosynthesis ones. An immediate rapid increase in starch synthetic transcripts was followed by an increase in starch degrading transcripts and a decrease in the starch synthetic ones. In contrast, increased gene expression for fatty acid and TAG synthesis was initiated later and occurred more gradually. Expression of several fatty acid desaturase (FAD) genes was decreased upon starvation, which corresponds to the observed changes to higher levels of MUFAs and SFAs. Moreover, several homologs of transcription regulators that were implicated in controlling starch and lipid metabolism in other microalgae showed differential gene expression and might be key regulators of starch and lipid metabolism in E. oleoabundans as well. Our data provide insights into the genetic foundation of starch and lipid metabolism in E. oleoabundans under nitrogen starvation and should facilitate metabolic engineering towards tailored strains with desired storage compound composition.

Air bubbles in fibrous caseinate gels investigated by neutron refraction, X-ray tomography and refractive microscope
Tian, Bei ; Wang, Zhaojun ; Goot, Atze Jan van der; Bouwman, Wim G. - \ 2018
Food Hydrocolloids 83 (2018). - ISSN 0268-005X - p. 287 - 295.
Bubble morphology - Calcium caseinate - Isotope effect - Meat analogue - Neutron refraction - X-ray tomography

Fibrous protein gels have the potential to form the basis for the next-generation of meat analogue. It is suggested that fibre anisotropy is related to air bubbles present in the gel. Given the complexity and heterogeneity of the samples, several quantitative techniques are needed to ensure a comprehensive understanding of the air bubbles. We performed neutron refraction experiments to study the size and shape of the air bubbles in three calcium caseinate samples containing different H2O to D2O ratios. Refractive microscopy and X-ray tomography (XRT) analysis were done on the same samples to provide complementary information. The deformation degree and average width of the air bubbles were obtained from both the XRT and neutron refraction experiment. A neutron refraction model calculates the average area and volume of a single air bubble, which correspond to the largest area and volume fractions of all the air bubbles from the XRT analysis. Additionally, we found that the H2O to D2O ratios in the sample largely influence the size, number distribution and deformation degree of the air bubbles. The neutron refraction technique can be a simple and complementary method to help understanding the role of air bubbles in the meat analogue.

Regulation of myostatin expression is associated with growth and muscle development in commercial broiler and DMC muscle
Dou, Tengfei ; Li, Zhengtian ; Wang, Kun ; Liu, Lixian ; Rong, Hua ; Xu, Zhiqiang ; Huang, Ying ; Gu, Dahai ; Chen, Xiaobo ; Hu, Wenyuan ; Zhang, Jiarong ; Zhao, Sumei ; Jois, Markandeya ; Li, Qihua ; Ge, Changrong ; Pas, Marinus F.W. te; Jia, Junjing - \ 2018
Molecular Biology Reports 45 (2018)4. - ISSN 0301-4851 - p. 511 - 522.
Commercial broiler chicken - Daweishan mini chicken - Growth rate - mRNA expression - Muscle weight - Myostatin
Myostatin is a negative regulator of skeletal muscle growth. Muscle tissue is the largest tissue in the body and influences body growth. Commercial Avian broiler chickens are selected for high growth rate and muscularity. Daweishan mini chickens are a slow growing small-sized chicken breed. We investigated the relations between muscle (breast and leg) myostatin mRNA expression and body and muscle growth. Twenty chickens per breed were slaughtered at 0, 30, 60, 90, 120, and 150 days of age. Body and muscle weights were higher at all times in Avian chickens. Breast muscle myostatin expression was higher in Avian chickens than in Daweishan mini chickens at day 30. Myostatin expression peaked at day 60 in Daweishan mini chickens and expression remained higher in breast muscle. Daweishan mini chickens myostatin expression correlated positively with carcass weight, breast and leg muscle weight from day 0 to 60, and correlated negatively with body weight from day 90 to 150, while myostatin expression in Avian chickens was negatively correlated with carcass and muscle weight from day 90 to 150. The results suggest that myostatin expression is related to regulation of body growth and muscle development, with two different regulatory mechanisms that switch between days 30 and 60.
Propagating annotations of molecular networks using in silico fragmentation
Silva, Ricardo R. da; Wang, Mingxun ; Nothias, Louis Félix ; Hooft, Justin J.J. van der; Caraballo-Rodríguez, Andrés Mauricio ; Fox, Evan ; Balunas, Marcy J. ; Klassen, Jonathan L. ; Lopes, Norberto Peporine ; Dorrestein, Pieter C. - \ 2018
PLoS Computational Biology 14 (2018)4. - ISSN 1553-734X

The annotation of small molecules is one of the most challenging and important steps in untargeted mass spectrometry analysis, as most of our biological interpretations rely on structural annotations. Molecular networking has emerged as a structured way to organize and mine data from untargeted tandem mass spectrometry (MS/MS) experiments and has been widely applied to propagate annotations. However, propagation is done through manual inspection of MS/MS spectra connected in the spectral networks and is only possible when a reference library spectrum is available. One of the alternative approaches used to annotate an unknown fragmentation mass spectrum is through the use of in silico predictions. One of the challenges of in silico annotation is the uncertainty around the correct structure among the predicted candidate lists. Here we show how molecular networking can be used to improve the accuracy of in silico predictions through propagation of structural annotations, even when there is no match to a MS/MS spectrum in spectral libraries. This is accomplished through creating a network consensus of re-ranked structural candidates using the molecular network topology and structural similarity to improve in silico annotations. The Network Annotation Propagation (NAP) tool is accessible through the GNPS web-platform https://gnps.ucsd.edu/ProteoSAFe/static/gnps-theoretical.jsp.

Hotspots for Nitrogen and Phosphorus Losses from Food Production in China : A County-Scale Analysis
Wang, M. ; Ma, L. ; Strokal, M. ; Ma, Wenqi ; Liu, Xuejun ; Kroeze, C. - \ 2018
Environmental Science and Technology 52 (2018)10. - ISSN 0013-936X - p. 5782 - 5791.
Food production in China results in large losses of nitrogen (N) and phosphorus (P) to the environment. Our objective is to identify hotspots for N and P losses to the environment from food production in China at the county scale. To do this, we used the NUFER (Nutrient flows in Food chains, Environment and Resources use) model. Between 1990 and 2012, the hotspot area expanded by a factor of 3 for N, and 24 for P. In 2012 most hotspots were found in the North China Plain. Hotspots covered less than 10% of the Chinese land area, but contributed by more than half to N and P losses to the environment. Direct discharge of animal manure to rivers was an important cause of N and P losses. Food production was found to be more intensive in hotspots than in other counties. Synthetic fertilizer use and animal numbers in hotspots were a factor of 4–5 higher than in other counties in 2012. Also the number of people working in food production and the incomes of farmers are higher in hotspots than in other counties. This study concludes with suggestions for region-specific pollution control technologies for food production in China.
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