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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    UVA radiation promotes tomato growth through morphological adaptation leading to increased light interception
    Zhang, Yating ; Kaiser, Elias ; Zhang, Yuqi ; Zou, Jie ; Bian, Zhonghua ; Yang, Qichang ; Li, Tao - \ 2020
    Environmental and Experimental Botany 176 (2020). - ISSN 0098-8472
    Blue light - Leaf photosynthesis - Phenolics - Photomorphogenesis - Red light syndrome - UVA radiation

    UVA radiation (315−400 nm) is the main component of solar UV radiation. Although it shares photoreceptors (i.e. cryptochromes and phototropins) with blue light (400−500 nm), its function in plant biology is unclear to a large extent. This study aimed at exploring how UVA radiation affects plant morphology and physiology, and at distinguishing to what extent these effects differ from those of blue light. Tomato plants were grown under monochromatic red (R), dichromatic red and blue (R/B = 7:1), as well as red and two different levels of UVA radiation (R/UVA = 7:1 and 15:1, respectively), with identical photon flux density (250 μmol⋅m−2⋅s−1). Peak intensities of UVA, B and R were 370, 450 and 660 nm, respectively. We showed that replacing blue by UVA (in a background of red light) induced plant morphological modifications, as reflected by larger leaf area, steeper leaf angles, flatter leaves and longer stems. UVA had reduced effects on leaf secondary metabolism compared to blue light, resulting in significantly lower total phenolics and flavonoid contents, as well as concentrations of UV-absorbing compounds. In addition, UVA had a similar function as blue light in shaping the development of the photosynthetic apparatus, as both wavebands alleviated the ‘red light syndrome’ (i.e. low photosynthetic capacity, reduced photosynthetic electron transport, and unresponsive stomata). We conclude that: 1) UVA promotes tomato growth through morphological adaptation leading to increased light interception; 2) UVA affects leaf secondary metabolite accumulation less strongly than blue light; 3) UVA functions similarly to blue light in maintaining leaf photosynthetic functioning. Thus, unlike previously suggested, UVA cannot be unequivocally considered as an abiotic stress factor. This research adds to the understanding of plant processes in response to UVA radiation and provides a basis for future recipes for growing plants with artificial light.

    Corncob cellulose nanosphere as an eco-friendly detergent
    Liu, Bin ; Li, Tao ; Wang, Wenya ; Sagis, Leonard M.C. ; Yuan, Qipeng ; Lei, Xingen ; Cohen Stuart, Martien A. ; Li, Dan ; Bao, Cheng ; Bai, Jie ; Yu, Zhengquan ; Ren, Fazheng ; Li, Yuan - \ 2020
    Nature Sustainability (2020). - ISSN 2398-9629

    The daily use of synthetic detergents at a global scale is responsible for substantial environmental impacts but managerial and policy strategies to address them are largely inadequate. More sustainable and eco-friendly detergents are an appealing solution to reduce environmental impacts. Here, we developed a detergent based on cellulose nanospheres (CNSs) from agricultural waste corncob, an overlooked abundant and cheap natural source that is often discarded. Compared with conventional surfactants, CNSs stabilize at oil–water interfaces and form Pickering emulsions with enhanced stability and antiredeposition properties. CNSs show higher cleaning efficiency in removing stains from various surfaces compared with powder and liquid commercial detergents. In contrast to high toxicity of commercial detergents, CNSs are non-toxic to several mammalian cell lines, zebrafish and hydroponic lettuce. Overall, our results demonstrated the feasibility of using agriculturally derived waste CNSs as a safer, more cost-effective and sustainable alternative to commercial synthetic detergents.

    High-Speed Super-Resolution Imaging Using Protein-Assisted DNA-PAINT
    Filius, Mike ; Cui, Tao Ju ; Ananth, Adithya N. ; Docter, Margreet W. ; Hegge, Jorrit W. ; Oost, John van der; Joo, Chirlmin - \ 2020
    Nano Letters 20 (2020)4. - ISSN 1530-6984 - p. 2264 - 2270.
    Ago-PAINT - Argonaute - DNA origami - DNA-PAINT - single-molecule FRET - super-resolution microscopy

    Super-resolution imaging allows for the visualization of cellular structures on a nanoscale level. DNA-PAINT (DNA point accumulation in nanoscale topology) is a super-resolution method that depends on the binding and unbinding of DNA imager strands. The current DNA-PAINT technique suffers from slow acquisition due to the low binding rate of the imager strands. Here we report on a method where imager strands are loaded into a protein, Argonaute (Ago), which allows for faster binding. Ago preorders the DNA imager strand into a helical conformation, allowing for 10 times faster target binding. Using a 2D DNA origami structure, we demonstrate that Ago-assisted DNA-PAINT (Ago-PAINT) can speed up the current DNA-PAINT technique by an order of magnitude, while maintaining the high spatial resolution. We envision this tool to be useful for super-resolution imaging and other techniques that rely on nucleic acid interactions.

    Accelerated grain-filling rate increases seed size and grain yield of recent naked oat cultivars under well-watered and water-deficit conditions
    Wang, Tao ; Li, Feng Min ; Turner, Neil C. ; Wang, Bing Ru ; Wu, Fan ; Anten, Niels P.R. ; Du, Yan Lei - \ 2020
    European Journal of Agronomy 116 (2020). - ISSN 1161-0301
    abscisic acid concentration - endosperm cell number - fertile spike number - starch synthesis - water stress

    Increased seed size has greater contribution in yield improvement in recent naked oat (Avena sativa L. subsp. nudisativa) cultivars than cultivars derived from landraces. However, the underlying grain-filling mechanisms associated with seed size and grain yield in naked oat have received limited study. Two field experiments and a pot experiment compared grain-filling mechanisms, seed size and grain yield of ten naked oat cultivars, including old (landraces, released before 1950s) and new (released since 2008) cultivars. In both well-watered and water-deficit conditions, the new cultivars had higher grain yields, higher thousand kernel weights (TKW) and higher grain numbers per spike, but fewer fertile spikes per unit area or per plant, and no significant differences in grain number per unit area or per plant, than old cultivars. The findings in both the field and pot experiments demonstrated that increased grain-filling rate, rather than duration, enhanced seed size (TKW) and grain yield in the new cultivars. The increased grain-filling rate in a new cultivar was associated with higher rates of endosperm cell division and higher number of endosperm cells, compared to that in an old cultivar, but there were no significant differences in starch synthesis enzyme activity and ABA concentration between the old and new cultivars. As a result of current breeding and selection, the increased the grain yield of new cultivars of naked oat is primarily due to increased seed size (increased sink size) arising from a greater number of endosperm cells per grain, and not because of increased enzyme or phytohormonal activity. The larger seed size is important in the production of oats for food rather than for forage.

    Rescue of tomato spotted wilt virus entirely fromcomplementary DNA clones
    Feng, Mingfeng ; Cheng, Ruixiang ; Chen, Minglong ; Guo, Rong ; Li, Luyao ; Feng, Zhike ; Wu, Jianyan ; Xie, Li ; Hong, Jian ; Zhang, Zhongkai ; Kormelink, R.J.M. ; Tao, Xiaorong - \ 2020
    Proceedings of the National Academy of Sciences of the United States of America 117 (2020)2. - ISSN 0027-8424BioRxiv - p. 1181 - 1190.
    Negative-stranded/ambisense RNA viruses (NSVs) include not only dangerous pathogens of medical importance but also serious plant pathogens of agronomic importance. Tomato spotted wilt virus (TSWV) is one of the most important plant NSVs, infecting more than 1,000 plant species, and poses major threats to global food security. The segmented negative-stranded/ambisense RNA genomes of TSWV, however, have been a major obstacle to molecular genetic manipulation. In this study, we report the complete recovery of infectious TSWV entirely from complementary DNA (cDNA) clones. First, a replication- and transcription-competent minigenome replication system was established based on 35S-driven constructs of the S(−)-genomic (g) or S(+)-antigenomic (ag) RNA template, flanked by the 5′ hammerhead and 3′ ribozyme sequence of hepatitis delta virus, a nucleocapsid (N) protein gene and codon-optimized viral RNA-dependent RNA polymerase (RdRp) gene. Next, a movement-competent minigenome replication system was developed based on M(−)-gRNA, which was able to complement cell-to-cell and systemic movement of reconstituted ribonucleoprotein complexes (RNPs) of S RNA replicon. Finally, infectious TSWV and derivatives carrying eGFP reporters were rescued in planta via simultaneous expression of full-length cDNA constructs coding for S(+)-agRNA, M(−)-gRNA, and L(+)-agRNA in which the glycoprotein gene sequence of M(−)-gRNA was optimized. Viral rescue occurred with the addition of various RNAi suppressors including P19, HcPro, and γb, but TSWV NSs interfered with the rescue of genomic RNA. This reverse genetics system for TSWV now allows detailed molecular genetic analysis of all aspects of viral infection cycle and pathogenicity.
    Cellular RNA Hubs: Friends and Foes of Plant Viruses
    Xu, Min ; Mazur, Magdalena J. ; Tao, Xiaorong ; Kormelink, Richard - \ 2020
    Molecular Plant-Microbe Interactions 33 (2020)1. - ISSN 0894-0282 - p. 40 - 54.
    RNA granules are dynamic cellular foci that are widely spread in eukaryotic cells and play essential roles in cell growth and development, and immune and stress responses. Different types of granules can be distinguished, each with a specific function and playing a role in, for example, RNA transcription, modification, processing, decay, translation, and arrest. By means of communication and exchange of (shared) components, they form a large regulatory network in cells. Viruses have been reported to interact with one or more of these either cytoplasmic or nuclear granules, and act either proviral, to enable and support viral infection and facilitate viral movement, or antiviral, protecting or clearing hosts from viral infection. This review describes an overview and recent progress on cytoplasmic and nuclear RNA granules and their interplay with virus infection, first in animal systems and as a prelude to the status and current developments on plant viruses, which have been less well studied on this thus far.
    Benefits and trade-offs of replacing synthetic fertilizers by animal manures in crop production in China: A meta-analysis
    Zhang, Xiaoying ; Fang, Qunchao ; Zhang, Tao ; Ma, Wenqi ; Velthof, Gerard L. ; Hou, Yong ; Oenema, Oene ; Zhang, Fusuo - \ 2020
    Global Change Biology 26 (2020)2. - ISSN 1354-1013 - p. 888 - 900.
    ammonia emissions - crop yield - fertilizers - greenhouse gases - livestock manure - meta-analysis - soil type - trade-offs

    Recycling of livestock manure to agricultural land may reduce the use of synthetic fertilizer and thereby enhance the sustainability of food production. However, the effects of substitution of fertilizer by manure on crop yield, nitrogen use efficiency (NUE), and emissions of ammonia (NH3), nitrous oxide (N2O) and methane (CH4) as function of soil and manure properties, experimental duration and application strategies have not been quantified systematically and convincingly yet. Here, we present a meta-analysis of these effects using results of 143 published studies in China. Results indicate that the partial substitution of synthetic fertilizers by manure significantly increased the yield by 6.6% and 3.3% for upland crop and paddy rice, respectively, but full substitution significantly decreased yields (by 9.6% and 4.1%). The response of crop yields to manure substitution varied with soil pH and experimental durations, with relatively large positive responses in acidic soils and long-term experiments. NUE increased significantly at a moderate ratio (<40%) of substitution. NH3 emissions were significantly lower with full substitution (62%–77%), but not with partial substitution. Emissions of CH4 from paddy rice significantly increased with substitution ratio (SR), and varied by application rates and manure types, but N2O emissions decreased. The SR did not significantly influence N2O emissions from upland soils, and a relative scarcity of data on certain manure characteristic was found to hamper identification of the mechanisms. We derived overall mean N2O emission factors (EF) of 0.56% and 0.17%, as well as NH3 EFs of 11.1% and 6.5% for the manure N applied to upland and paddy soils, respectively. Our study shows that partial substitution of fertilizer by manure can increase crop yields, and decrease emissions of NH3 and N2O, but depending on site-specific conditions. Manure addition to paddy rice soils is recommended only if abatement strategies for CH4 emissions are also implemented.

    Negative effects of urbanization on agricultural soil easily oxidizable organic carbon down the profile of the Chengdu Plain, China
    Luo, Youlin ; Li, Qiquan ; Wang, Changquan ; Li, Bing ; Stomph, Tjeerd Jan ; Yang, Juan ; Tao, Qi ; Yuan, Shu ; Tang, Xiaoyan ; Ge, Jinru ; Yu, Xuelian ; Peng, Yueyue ; Xu, Qiang ; Zheng, Gangxun - \ 2020
    Land Degradation and Development 31 (2020)3. - ISSN 1085-3278 - p. 404 - 416.
    easily oxidized organic carbon - impact factors - negative effects - rapid urbanization - soil profile

    Soil easily oxidizable organic carbon (EOC) is directly related to CO2 density; dynamics in subsurface EOC have been observed globally in relation to rapid urbanization. However, in the context of rapid urbanization, the factors related to EOC and the response of the EOC pool to urbanization down the profile remain elusive. The aim of the current paper is to investigate possible changes in the distribution of EOC over the soil profile and the impact of land use, socioeconomic, and natural factors on these. The study used samples from 182 soil profiles (0–100 cm) taken in the peri-urban areas of the megacity Chengdu (a typical megacity with rapid urbanization). Main drivers of changes in soil EOC were analyzed by using spatial and regression analyses. Closer to the centre of the city, soil EOC levels were lower and land-use factors and socioeconomic factors contributed more to explaining variation in EOC levels in the 0–40-cm layer, whereas natural factors were most important at larger distance from the city. The effect of land-use factors and socioeconomic factors on EOC reached down to 60-cm depths. Moreover, an estimated 20% loss of EOC stock was observed close to the city in comparison with the surroundings, suggesting that the rapid process of urbanization was accompanied by a loss of EOC stock down the profile to depths of 60 cm, and the negative effects on EOC stock became more intensive as the distance to the city decreased.

    Ground cover rice production system reduces water consumption and nitrogen loss and increases water and nitrogen use efficiencies
    Liang, Hao ; Hu, Kelin ; Qin, Wei ; Zuo, Qiang ; Guo, Lin ; Tao, Yueyue ; Lin, Shan - \ 2019
    Field Crops Research 233 (2019). - ISSN 0378-4290 - p. 70 - 79.
    Conventional flooding paddy systems consume large amounts of water and results in water body pollution due to low water (WUE) and nitrogen use efficiencies (NUE). Therefore, rice production systems with water-saving and high resource use efficiencies need to be developed. A two-year field experiment was conducted in Fangxian County of Hubei Province in Central China. The experiment consisted of a conventional flooding paddy system (Paddy) and ground cover rice production system (GCRPS) with two different water management practices (i.e., GCRPSsat and GCRPS80%), factorially combined with three different N management practices (N1, no N fertilizer; N2, 150 kg urea N ha−1; and N3, 75 kg urea N ha−1 plus 75 kg N ha−1 as manure). In this study, we applied soil-crop system model (WHCNS, soil water heat carbon nitrogen simulator) coupled with simplified net mineralization model (LIXIM) to quantitatively evaluate water consumption, N fates, and rice growth under different N management practices for both Paddy and GCRPS. Results showed that the simulated soil water storage, soil mineral N content, leaf area index, dry matter, crop N uptake, and yield agreed well with the measured values. The Nash-Sutcliffe efficiency and index of agreement were greater than 0.51 and 0.86, respectively. Compared with Paddy, GCRPS significantly reduced the quantities of irrigation water (78.1%), nonproductive water consumption (evaporation, drainage, and runoff) (69.3%), and nitrate leaching (74.5%), and significantly enhanced yield (12.6%), WUE (42.8%), and NUE (20.0%). The WUE was ranked as follows: GCRPS80% > GCRPSsat > Paddy. In GCRPSs, GCRPS80% further decreased the nonproductive water consumption by 20.6% and did not reduce the yield compared with GCRPSsat. For different N management practices, no significant differences were found between the N2 and N3 treatments in terms of yields and NUEs. Meanwhile, the WUE of N3 (1.50 kg m-3) was significantly higher than that of N2 (1.41 kg m-3) in GCRPS. Hence, GCRPS80%_N3 was recommended as the best management practice for achieving high yield and high resource use efficiencies with the least environmental impact in the study region.
    Modelling groundwater level dynamics under different cropping systems and developing groundwater neutral systems in the North China Plain
    Liang, Hao ; Qin, Wei ; Hu, Kelin ; Tao, Hongbing ; Li, Baoguo - \ 2019
    Agricultural Water Management 213 (2019). - ISSN 0378-3774 - p. 732 - 741.
    Over-exploitation of groundwater for irrigation has led to a series of ecological and environmental problems in the North China Plain (NCP). Identifying the water consumption and groundwater level dynamics under different cropping systems can help to develop groundwater neutral system in the NCP. The WHCNS (soil Water, Heat, Carbon and Nitrogen Simulator) model was applied to quantify the effects of different cropping systems (2H1Y, two harvests in one year; 3H2Y, three harvests in two years; and 1H1Y, one harvest in one year) on groundwater use and crop growth, and to explore the trade-offs of possible scenarios on the decline of groundwater level and cereal yield. Results showed that WHCNS performed well in simulating soil water content, leaf area index, dry matter and crop yield, as well as groundwater level dynamics, with the Nash and Sutcliffe Efficiency > 0.4 and index of agreement > 0.8. The simulated results indicated that the groundwater levels of 2H1Y decreased faster than those of other cropping systems, at a decline rate of 0.33 m yr−1. Irrigation of 300 mm yr−1 for the remaining high yield of winter wheat mainly resulted in the decline of groundwater level in the NCP. Scenario analyses showed that the groundwater levels would stop decreasing when the current planting area of winter wheat decreased by 76%. However, the reduction of wheat planting area (scenario 1) will also decrease the annual yield by 27% (from 13,547 to 9909 kg ha−1). Fallowing (scenario 2) may reduce annual yield by 50% (from 13,547 to 6834 kg ha−1) in order to maintain groundwater level. The SNWT (South to North Water Transfer) project (scenario 3) may have to provide 50% of irrigation water (130 mm yr−1), to prevent groundwater decline while maintaining the current yield. Scenario 3 could be better than scenario 1 only if the water price was less than 8 ¥m-3. In the future, reducing winter wheat planting area (especially for low-yield cropland) may be a good option to mitigate groundwater decline while maintaining relatively high yield and income for local farmers in the NCP.
    Protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soils
    Zhao, Zhi Bo ; He, Ji Zheng ; Geisen, Stefan ; Han, Li Li ; Wang, Jun Tao ; Shen, Ju Pei ; Wei, Wen Xue ; Fang, Yun Ting ; Li, Pei Pei ; Zhang, Li Mei - \ 2019
    Microbiome 7 (2019)1. - ISSN 2049-2618
    High-throughput sequencing - Microbiome - Nitrogen fertilizers - Soil protists - Soil type

    Background: Agricultural food production is at the base of food and fodder, with fertilization having fundamentally and continuously increased crop yield over the last decades. The performance of crops is intimately tied to their microbiome as they together form holobionts. The importance of the microbiome for plant performance is, however, notoriously ignored in agricultural systems as fertilization disconnects the dependency of plants for often plant-beneficial microbial processes. Moreover, we lack a holistic understanding of how fertilization regimes affect the soil microbiome. Here, we examined the effect of a 2-year fertilization regime (no nitrogen fertilization control, nitrogen fertilization, and nitrogen fertilization plus straw amendment) on entire soil microbiomes (bacteria, fungi, and protist) in three common agricultural soil types cropped with maize in two seasons. Results: We found that the application of nitrogen fertilizers more strongly affected protist than bacterial and fungal communities. Nitrogen fertilization indirectly reduced protist diversity through changing abiotic properties and bacterial and fungal communities which differed between soil types and sampling seasons. Nitrogen fertilizer plus straw amendment had greater effects on soil physicochemical properties and microbiome diversity than nitrogen addition alone. Moreover, nitrogen fertilization, even more together with straw, increased soil microbiome network complexity, suggesting that the application of nitrogen fertilizers tightened soil microbiomes interactions. Conclusions: Together, our results suggest that protists are the most susceptible microbiome component to the application of nitrogen fertilizers. As protist communities also exhibit the strongest seasonal dynamics, they serve as the most sensitive bioindicators of soil changes. Changes in protist communities might have long-term effects if some of the key protist hubs that govern microbiome complexities as top microbiome predators are altered. This study serves as the stepping stone to promote protists as promising agents in targeted microbiome engineering to help in reducing the dependency on exogenous unsustainably high fertilization and pesticide applications.

    Formation and Morphology Evolution from Ferrihydrite to Hematite in the Presence of Tartaric Acid
    Wang, Mingxia ; Tao, Zhengxing ; Xiong, Juan ; Wang, Xiaoming ; Hou, Jingtao ; Koopal, Luuk K. ; Tan, Wenfeng - \ 2019
    ACS Earth and Space Chemistry 3 (2019)4. - ISSN 2472-3452 - p. 562 - 570.
    dissolution-crystallization - hematite - iron oxide - low molecular organic acids - morphology - transformation

    Hematite, with ferrihydrite as the common precursor, is the most stable iron oxide in soils and sediments and has many applications in environmental systems. As a common reducing agent in soils, tartaric acid (L-TA) can reduce Fe3+ to Fe2+ and template the formation of hematite from ferrihydrite. Here, the formation of hematite in the presence of L-TA was investigated under different L-TA concentrations, initial suspension pH, and aging time. The products were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), and high- resolution transmission electron microscopy (HRTEM). Both the transformation process and the particle morphology of hematite were affected by the initial suspension pHi at which the L-TA was added to the suspension. Optimal pHi values at a L-TA/Fe(III) molar ratio of 1.0% and an aging time of 10 h at 100 °C were pHi 7 and pHi 11. At pHi 7, the optimal L-TA/Fe(III) molar ratio for the transformation was 1.0% and aging at 100 °C was completed after about 20 h. The transformation occurred through a dissolution-crystallization process. Crystalline corn-like particles (84 m2/g) were obtained through an oriented attachment mechanism. At a L-TA/Fe(III) molar ratio of 3.0% the ferrihydrite surface was saturated with L-TA and the transformation was inhibited. At pHi 11, L-TA/Fe(III) of 1.0% and aging for 10 h (100 °C), subrounded crystalline particles (24 m2/g) were obtained by solid-phase transformation, oriented attachment, and Ostwald ripening mechanism.

    Comparison of smoking-related DNA methylation between newborns from prenatal exposure and adults from personal smoking
    Sikdar, Sinjini ; Joehanes, Roby ; Joubert, Bonnie R. ; Xu, Cheng Jian ; Vives-Usano, Marta ; Rezwan, Faisal I. ; Felix, Janine F. ; Ward, James M. ; Guan, Weihua ; Richmond, Rebecca C. ; Brody, Jennifer A. ; Küpers, Leanne K. ; Baïz, Nour ; Håberg, Siri E. ; Smith, Jennifer A. ; Reese, Sarah E. ; Aslibekyan, Stella ; Hoyo, Cathrine ; Dhingra, Radhika ; Markunas, Christina A. ; Xu, Tao ; Reynolds, Lindsay M. ; Just, Allan C. ; Mandaviya, Pooja R. ; Ghantous, Akram ; Bennett, Brian D. ; Wang, Tianyuan ; Consortium, The Bios ; Bakulski, Kelly M. ; Melen, Erik ; Zhao, Shanshan ; Jin, Jianping ; Herceg, Zdenko ; Meurs, Joyce Van; Taylor, Jack A. ; Baccarelli, Andrea A. ; Murphy, Susan K. ; Liu, Yongmei ; Munthe-Kaas, Monica Cheng ; Deary, Ian J. ; Nystad, Wenche ; Waldenberger, Melanie ; Annesi-Maesano, Isabella ; Conneely, Karen ; Jaddoe, Vincent W.V. ; Arnett, Donna ; Snieder, Harold ; Kardia, Sharon L.R. ; Relton, Caroline L. ; Ong, Ken K. ; Ewart, Susan ; Moreno-Macias, Hortensia ; Romieu, Isabelle ; Sotoodehnia, Nona ; Fornage, Myriam ; Motsinger-Reif, Alison ; Koppelman, Gerard H. ; Bustamante, Mariona ; Levy, Daniel ; London, Stephanie J. - \ 2019
    Epigenomics 11 (2019)13. - ISSN 1750-1911 - p. 1487 - 1500.
    cigarette smoking - epigenetics - infant - maternal exposure - methylation

    Aim: Cigarette smoking influences DNA methylation genome wide, in newborns from pregnancy exposure and in adults from personal smoking. Whether a unique methylation signature exists for in utero exposure in newborns is unknown. Materials & methods: We separately meta-analyzed newborn blood DNA methylation (assessed using Illumina450k Beadchip), in relation to sustained maternal smoking during pregnancy (9 cohorts, 5648 newborns, 897 exposed) and adult blood methylation and personal smoking (16 cohorts, 15907 participants, 2433 current smokers). Results & conclusion: Comparing meta-analyses, we identified numerous signatures specific to newborns along with many shared between newborns and adults. Unique smoking-associated genes in newborns were enriched in xenobiotic metabolism pathways. Our findings may provide insights into specific health impacts of prenatal exposure on offspring.

    Argonaute bypasses cellular obstacles without hindrance during target search
    Cui, Tao Ju ; Klein, Misha ; Hegge, Jorrit W. ; Chandradoss, Stanley D. ; Oost, John van der; Depken, Martin ; Joo, Chirlmin - \ 2019
    Nature Communications 10 (2019). - ISSN 2041-1723

    Argonaute (Ago) proteins are key players in both gene regulation (eukaryotes) and host defense (prokaryotes). Acting on single-stranded nucleic-acid substrates, Ago relies on base pairing between a small nucleic-acid guide and its complementary target sequences for specificity. To efficiently scan nucleic-acid chains for targets, Ago diffuses laterally along the substrate and must bypass secondary structures as well as protein barriers. Using single-molecule FRET in conjunction with kinetic modelling, we reveal that target scanning is mediated through loose protein-nucleic acid interactions, allowing Ago to slide short distances over secondary structures, as well as to bypass protein barriers via intersegmental transfer. Our combined single-molecule experiment and kinetic modelling approach may serve as a platform to dissect search processes and study the effect of sequence on search kinetics for other nucleic acid-guided proteins.

    Paving the Way to Tospovirus Infection: Multilined Interplays with Plant Innate Immunity
    Zhu, Min ; Grinsven, Irene Louise Van; Kormelink, Richard ; Tao, Xiaorong - \ 2019
    Annual Review of Phytopathology 57 (2019). - ISSN 0066-4286 - p. 41 - 62.
    Antiviral RNAi - Effector/avirulence determinant - NLR - R gene - tospovirus - Viral RNA silencing suppressor

    Tospoviruses are among the most important plant pathogens and cause serious crop losses worldwide. Tospoviruses have evolved to smartly utilize the host cellular machinery to accomplish their life cycle. Plants mount two layers of defense to combat their invasion. The first one involves the activation of an antiviral RNA interference (RNAi) defense response. However, tospoviruses encode an RNA silencing suppressor that enables them to counteract antiviral RNAi. To further combat viral invasion, plants also employ intracellular innate immune receptors (e.g., Sw-5b and Tsw) to recognize different viral effectors (e.g., NSm and NSs). This leads to the triggering of a much more robust defense against tospoviruses called effector-Triggered immunity (ETI). Tospoviruses have further evolved their effectors and can break Sw-5b-/Tsw-mediated resistance. The arms race between tospoviruses and both layers of innate immunity drives the coevolution of host defense and viral genes involved in counter defense. In this review, a state-of-The-Art overview is presented on the tospoviral life cycle and the multilined interplays between tospoviruses and the distinct layers of defense.

    Contribution of methylation regulation of MpDREB2A promoter to drought resistance of Mauls prunifolia
    Li, Xuewei ; Xie, Yinpeng ; Lu, Liyuan ; Yan, Mingjia ; Fang, Nan ; Xu, Jidi ; Wang, Liping ; Yan, Yan ; Zhao, Tao ; Nocker, Steve van; Ma, Fengwang ; Liang, Dong ; Guan, Qingmei - \ 2019
    Plant and Soil 441 (2019)1-2. - ISSN 0032-079X - p. 15 - 32.
    ChIP-seq - DNA methylation - DREB2A - Drought resistance - Gene expression - Malus

    Background and aims: Malus prunifolia (Chinese name: Fu Ping Qiu Zi), a wild relative of cultivated apple (Malus x domestica Borkh), is extremely resistant to drought compared with domesticated cultivars, such as ‘Golden Delicious’. However, the molecular mechanisms underlying drought resistance of M. prunifolia have not been characterized. This study investigates a new regulatory mechanism to improve apple drought resistance. Methods: M. prunifolia and ‘Golden Delicious’ were each grafted on M. hupehensis for gene expression analysis. The methylation level of the DREB2A promoter was determined by bisulfite sequencing and ChIP-qPCR. Chromatin immunoprecipitation sequencing (ChIP-seq) was used to identify target genes of MpDREB2A in apple. Results: The exposure to drought stress stimulated the expression level of DREB2A gene more than 100-fold in M. prunifolia, but only 16-fold in ‘Golden Delicious’. This difference in gene expression could not be explained in terms of difference in leaf relative water content. Correspondingly, the methylation level of M. prunifolia DREB2A (MpDREB2A) promoter region was significantly reduced. Additionally, MpDREB2A conferred enhanced drought resistance when ectopically expressed in Arabidopsis. Over 2800 potential downstream target genes of MpDREB2A were identified by ChIP-seq and these downstream genes have diverse potential functions related to stress resistance. Conclusions: Methylation regulation in promoter of MpDREB2A may contribute to the drought resistance of M. prunifolia.

    DNA-guided DNA cleavage at moderate temperatures by Clostridium butyricum Argonaute
    Hegge, Jorrit W. ; Swarts, Daan C. ; Chandradoss, Stanley D. ; Cui, Tao Ju ; Kneppers, Jeroen ; Jinek, Martin ; Joo, Chirlmin ; Oost, John van der - \ 2019
    Nucleic acids research 47 (2019)11. - ISSN 0305-1048 - p. 5809 - 5821.

    Prokaryotic Argonaute proteins (pAgos) constitute a diverse group of endonucleases of which some mediate host defense by utilizing small interfering DNA guides (siDNA) to cleave complementary invading DNA. This activity can be repurposed for programmable DNA cleavage. However, currently characterized DNA-cleaving pAgos require elevated temperatures (≥65°C) for their activity, making them less suitable for applications that require moderate temperatures, such as genome editing. Here, we report the functional and structural characterization of the siDNA-guided DNA-targeting pAgo from the mesophilic bacterium Clostridium butyricum (CbAgo). CbAgo displays a preference for siDNAs that have a deoxyadenosine at the 5'-end and thymidines at nucleotides 2-4. Furthermore, CbAgo mediates DNA-guided DNA cleavage of AT-rich double stranded DNA at moderate temperatures (37°C). This study demonstrates that certain pAgos are capable of programmable DNA cleavage at moderate temperatures and thereby expands the scope of the potential pAgo-based applications.

    Recently duplicated sesterterpene (C25) gene clusters in Arabidopsis thaliana modulate root microbiota
    Chen, Quingwen ; Jiang, Ting ; Liu, Yong-Xin ; Liu, Haili ; Zhao, T. ; Liu, Zhixi ; Gan, Xiangchao ; Hallab, Asis ; Wang, Xuemei ; He, Juan ; Ma, Yihua ; Zhang, Fengxia ; Jin, Tao ; Schranz, M.E. ; Wang, Yong ; Bai, Yang ; Wang, Guodong - \ 2019
    Science in China Series C-Life Sciences 62 (2019)7. - ISSN 1006-9305 - p. 947 - 958.
    Land plants co-speciate with a diversity of continually expanding plant specialized metabolites (PSMs) and root microbial communities (microbiota). Homeostatic interactions between plants and root microbiota are essential for plant survival in natural environments. A growing appreciation of microbiota for plant health is fuelling rapid advances in genetic mechanisms of controlling microbiota by host plants. PSMs have long been proposed to mediate plant and single microbe interactions. However, the effects of PSMs, especially those evolutionarily new PSMs, on root microbiota at community level remain to be elucidated. Here, we discovered sesterterpenes in Arabidopsis thaliana, produced by recently duplicated prenyltransferase-terpene synthase (PT-TPS) gene clusters, with neo-functionalization. A single-residue substitution played a critical role in the acquisition of sesterterpene synthase (sesterTPS) activity in Brassicaceae plants. Moreover, we found that the absence of two root-specific sesterterpenoids, with similar chemical structure, significantly affected root microbiota assembly in similar patterns. Our results not only demonstrate the sensitivity of plant microbiota to PSMs but also establish a complete framework of host plants to control root microbiota composition through evolutionarily dynamic PSMs.
    Baculovirus per os infectivity factor complex : Components and assembly
    Wang, Xi ; Shang, Yu ; Chen, Cheng ; Liu, Shurui ; Chang, Meng ; Zhang, Nan ; Hu, Hengrui ; Zhang, Fenghua ; Zhang, Tao ; Wang, Zhiying ; Liu, Xijia ; Lin, Zhe ; Deng, Fei ; Wang, Hualin ; Zou, Zhen ; Vlak, Just M. ; Wang, Manli ; Hu, Zhihong - \ 2019
    Journal of Virology 93 (2019)6. - ISSN 0022-538X
    Baculovirus - Entry - Per os infectivity factor - PIF complex - PIF9

    Baculovirus entry into insect midgut cells is dependent on a multiprotein complex of per os infectivity factors (PIFs) on the envelopes of occlusion-derived virions (ODVs). The structure and assembly of the PIF complex are largely unknown. To reveal the complete members of the complex, a combination of blue native polyacrylamide gel electrophoresis, liquid chromatography-tandem mass spectrometry, and Western blotting was conducted on three different baculoviruses. The results showed that the PIF complex has a molecular mass of ~500 kDa and consists of nine PIFs, including a newly discovered member (PIF9). To decipher the assembly process, each pif gene was knocked out from the Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) genome individually by use of synthetic baculovirus technology, and the impact on PIF complex formation was investigated. Deletion of pif8 resulted in the formation of an ~400-kDa subcomplex. Deletion of pif0, -4, -6, -7, or -9 resulted in a subcomplex of ~230 kDa, but deletion of pif1, -2, or -3 abolished formation of any complex. Taken together, our data identified a core complex of ~230 kDa, consisting of PIF1, -2, and -3. This revised the previous knowledge that the core complex was about 170 kDa and contained PIF1 to -4. Analysis of the PIF complex in cellular fractions suggested that it is assembled in the cytoplasm before being transported to the nucleus and subsequently incorporated into the envelopes of ODVs. Only the full complex, not the subcomplex, is resistant to proteolytic attack, indicating the essentiality of correct complex assembly for oral infection. IMPORTANCE Entry of baculovirus into host insects is mediated by a per os infectivity factor (PIF) complex on the envelopes of occlusion-derived viruses (ODVs). Knowledge of the composition and structure of the PIF complex is fundamental to understanding its mode of action. By using multiple approaches, we determined the complete list of proteins (nine) in the PIF complex. In contrast to previous knowledge in the field, the core complex is revised to ~230 kDa and consists of PIF1 to -3 but not PIF4. Interestingly, our results suggest that the PIF complex is formed in the cytoplasm prior to its transport to the nucleus and subsequent incorporation into ODVs. Only the full complex is resistant to proteolytic degradation in the insect midgut, implying the critical role of the entire complex. These findings provide the baseline for future studies on the ODV entry mechanism mediated by the multiprotein complex.

    Global wheat production with 1.5 and 2.0°C above pre‐industrial warming
    Liu, B. ; Martre, P. ; Ewert, F. ; Porter, J.R. ; Challinor, A.J. ; Muller, G. ; Ruane, A.C. ; Waha, K. ; Thorburn, Peter J. ; Aggarwal, P.K. ; Ahmed, M. ; Balkovic, Juraj ; Basso, B. ; Biernath, C. ; Bindi, M. ; Cammarano, D. ; Sanctis, Giacomo De; Dumont, B. ; Espadafor, M. ; Eyshi Rezaei, Ehsan ; Ferrise, Roberto ; Garcia-Vila, M. ; Gayler, S. ; Gao, Y. ; Horan, H. ; Hoogenboom, G. ; Izaurralde, Roberto C. ; Jones, C.D. ; Kassie, Belay T. ; Kersebaum, K.C. ; Klein, C. ; Koehler, A.K. ; Maiorano, Andrea ; Minoli, Sara ; Montesino San Martin, M. ; Kumar, S.N. ; Nendel, C. ; O'Leary, G.J. ; Palosuo, T. ; Priesack, E. ; Ripoche, D. ; Rötter, R.P. ; Semenov, M.A. ; Stockle, Claudio ; Streck, T. ; Supit, I. ; Tao, F. ; Velde, M. van der; Wallach, D. ; Wang, E. ; Webber, H. ; Wolf, J. ; Xiao, L. ; Zhang, Z. ; Zhao, Z. ; Zhu, Y. ; Asseng, S. - \ 2019
    Global Change Biology 25 (2019)4. - ISSN 1354-1013 - p. 1428 - 1444.
    Efforts to limit global warming to below 2°C in relation to the pre-industrial level are under way, in accordance with the 2015 Paris Agreement. However, most impact research on agriculture to date has focused on impacts of warming >2°C on mean crop yields, and many previous studies did not focus sufficiently on extreme events and yield interannual variability. Here, with the latest climate scenarios from the Half a degree Additional warming, Prognosis and Projected Impacts (HAPPI) project, we evaluated the impacts of the 2015 Paris Agreement range of global warming (1.5°C and 2.0°C warming above the pre-industrial period) on global wheat production and local yield variability. A multi-crop and multi-climate model ensemble over a global network of sites developed by the Agricultural Model Intercomparison and Improvement Project (AgMIP) for Wheat was used to represent major rainfed and irrigated wheat cropping systems. Results show that projected global wheat production will change by -2.3% to 7.0% under the 1.5 °C scenario and -2.4% to 10.5% under the 2.0 °C scenario, compared to a baseline of 1980-2010, when considering changes in local temperature, rainfall and global atmospheric CO2 concentration, but no changes in management or wheat cultivars. The projected impact on wheat production varies spatially; a larger increase is projected for temperate high rainfall regions than for moderate hot low rainfall and irrigated regions. Grain yields in warmer regions are more likely to be reduced than in cooler regions. Despite mostly positive impacts on global average grain yields, the frequency of extremely low yields (bottom 5 percentile of baseline distribution) and yield inter-annual variability will increase under both warming scenarios for some of the hot growing locations, including locations from the second largest global wheat producer -India, which supplies more than 14% of global wheat. The projected global impact of warming <2°C on wheat production are therefore not evenly distributed and will affect regional food security across the globe as well as food prices and trade.
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