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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    Engineering corona structure on gold nanoclusters for gastrointestinal imaging by red-shifted emissions in the second near-infrared window
    Li, Ruibin ; Wang, Weili ; Kong, Yifei ; Jiang, Jun ; Xie, Qainqian ; Huang, Yang ; Li, Guanna ; Wu, Di ; Zheng, Huizhen ; Gao, Meng ; Xu, Shujuan ; Pan, Yanxia ; Li, Wei ; Ma, Ronglin ; Wu, Mei X. ; Li, Xuehua ; Cai, Xiaoming ; Zuilhof, H. - \ 2020
    Angewandte Chemie-International Edition (2020). - ISSN 1433-7851
    Fluorescence emissions in the second near infrared window (NIR‐II) have shown extraordinary advantages for bio‐imaging. However, it’s a big challenge to exploit NIR‐II emitters for gastrointestinal (GI) tract imaging due to fluorescence quenching in digestive microenvironment. Herein, we made an interesting finding that red‐shifted emissions of Au nanoclusters (AuNCs) into NIR‐II region with improved quantum yields (QY) could be achieved by engineering a corona structure of a ribonuclease‐A (RNase‐A) on particle surfaces. RNase‐A encapsulated AuNCs (RNase‐A@AuNCs) displayed emissions at 1050 nm with a 1.9% QY. Compare to rare earth and silver based NIR‐II emitters, RNase‐A@AuNCs had excellent biocompatibility, showed >50‐fold higher sensitivity in GI tract, and homogeneously migrated during gastrointestinal peristalsis to allow visualization of the detailed structures of GI tract. Notably, RNase‐A@AuNCs could be exploited to successfully differentiate intestinal tumor mice from the healthy, indicating a potential utility for early diagnosis of intestinal tumors in clinics.
    A new TROPOMI product for tropospheric NO2 columns over East Asia with explicit aerosol corrections
    Liu, Mengyao ; Lin, Jintai ; Kong, Hao ; Boersma, K.F. ; Eskes, Henk ; Kanaya, Yugo ; He, Qin ; Tian, Xin ; Qin, Kai ; Xie, Pinhua ; Spurr, Robert ; Ni, Ruijing ; Yan, Yingying ; Weng, Hongjian ; Wang, Jingxu - \ 2020
    Atmospheric Measurement Techniques 13 (2020)8. - ISSN 1867-1381 - p. 4247 - 4259.

    We present a new product with explicit aerosol corrections, POMINO-TROPOMI, for tropospheric nitrogen dioxide (NO2) vertical column densities (VCDs) over East Asia, based on the newly launched TROPOspheric Monitoring Instrument with an unprecedented high horizontal resolution. Compared to the official TM5-MP-DOMINO (OFFLINE) product, POMINO-TROPOMI shows stronger concentration gradients near emission source locations and better agrees with MAX-DOAS measurements (R2 D 0:75; NMB D 0:8% versus R2 D 0:68, NMB D 41:9 %). Sensitivity tests suggest that implicit aerosol corrections, as in TM5-MP-DOMINO, lead to underestimations of NO2 columns by about 25%over the polluted northern East China region. Reducing the horizontal resolution of a priori NO2 profiles would underestimate the retrieved NO2 columns over isolated city clusters in western China by 35% but with overestimates of more than 50% over many offshore coastal areas. The effect of a priori NO2 profiles is more important under calm conditions.

    Pantothenic acid requirement of male White Pekin ducks from hatch to 21 days of age
    Tang, J. ; Zhang, B. ; Xue, M. ; Shi, W.B. ; Wu, Y.B. ; Feng, Y.L. ; Huang, W. ; Zhou, Z.K. ; Xie, M. ; Hou, S.S. - \ 2020
    Animal Feed Science and Technology 269 (2020). - ISSN 0377-8401
    Duck - Growth performance - Pantothenic acid - Requirement

    An experiment was conducted to determine the effects of dietary pantothenic acid levels on growth performance, carcass traits, and pantothenic acid status of male White Pekin ducks from hatch to 21 days of age, and to evaluate the requirement of this B-vitamin for starter ducks. Different levels pantothenic acid (0, 2, 4, 6, 8, 10, and 20 mg/kg) were supplemented to corn-soy isolate protein basal diet to produce 7 dietary treatments with different analyzed total pantothenic acid levels (4.65, 6.80, 8.39, 9.98, 12.04, 13.70, and 22.50 mg/kg). A total of 448 one-day-old male White Pekin ducks were allotted to 7 dietary treatments with 8 replicate pens of 8 birds per pen. At 21 days of age, body weight, average daily weight gain (ADG), average daily feed intake (ADFI), gain to feed ratio (G/F), liver pantothenic acid content, as well as percentage yield of breast meat, leg meat, and abdominal fat were examined. The growth depression, exudate on eyelids, dermatosis, poor feathering, and 100 % of mortality were observed in the ducks fed the basal diet without pantothenic acid supplementation, and these adverse effects were ameliorated by pantothenic acid supplementation. The starter ducks on the diet containing 6.80 mg/kg of pantothenic acid had a lower parameter profile of body weight, ADG, ADFI, G/F, breast meat yield, abdominal fat yield, and liver pantothenic acid content compared to the birds fed the diets with higher levels of pantothenic acid (P < 0.05). And these criteria showed a linear or quadratic response to increasing dietary pantothenic acid levels (P < 0.05). The pantothenic acid requirements (based on dietary total pantothenic acid) of starter male White Pekin ducks for body weight, ADG, ADFI, G/F, and liver pantothenic acid content were 8.95, 8.95, 8.59, 9.56, and 10.22 mg/kg based on broken-line regression, while were 10.04, 10.05, 9.18, 11.01, and 11.24 mg/kg based on quadratic broken-line regression, respectively.

    The mechanism and application of bidirectional extracellular electron transport in the field of energy and environment
    Xie, Qingqing ; Lu, Yue ; Tang, Lin ; Zeng, Guangming ; Yang, Zhaohui ; Fan, Changzheng ; Wang, Jingjing ; Atashgahi, Siavash - \ 2020
    Critical Reviews in Environmental Science and Technology (2020). - ISSN 1064-3389
    Bioremediation - energy production - extracellular electron transfer

    Bidirectional extracellular electron transfer (EET) is mediated by back and forth electron delivery between microorganisms and extracellular substances. This enables the exchange of biochemical information and energy with the surrounding environments. As a novel bioenergy strategy, bidirectional EET provides low-cost opportunities for the production of clean energy sources and carriers (e.g., hydrogen and methane) as well as the production of value-added chemicals from carbon dioxide. Electrochemically active bacteria (EAB) can also transform pollutants to less toxic or benign substances in contaminated environments, and therefore they have been widely applied in bioremediation studies. Among all the available EAB, Geobacter and Shewanella are well-known for their versatility to accept/donate electrons from/to external environments. In this review, we focus on how these model EAB generate or harvest energy through bidirectional EET, as well as recent advances in the application of EET in bioelectrochemical technology and environmental bioremediation. Finally, the challenges, perspectives and new directions in the bidirectional EET studies are discussed. (Figure presented.).

    The roles of vegetation, tide and sediment in the variability of carbon in the salt marsh dominated tidal creeks
    Tan, Li Shan ; Ge, Zhen Ming ; Fei, Bei Li ; Xie, Li Na ; Li, Ya Lei ; Li, Shi Hua ; Li, Xiu Zhen ; Ysebaert, Tom - \ 2020
    Estuarine Coastal and Shelf Science 239 (2020). - ISSN 0272-7714
    Carbon loading - Hydrological regime - Marsh creek - Seasonal variation - Vegetation type

    Combined effects of vegetation, tide and sediment on the carbon dynamics in the intertidal creek-marsh systems remain unclear. We investigated the variability of dissolved organic (DOC) and inorganic carbon (DIC), and particulate organic (POC) and inorganic carbon (PIC) in the tidal creeks within the Poaceae and Cyperaceae communities on flood-ebb cycle in a salt marsh of eastern China. In the Poaceae creek with high plant biomass and soil carbon stock, the DOC concentrations were higher by on average 1.00–1.48 times than that in the Cyperaceae creek across all seasons and spring and neap tide stages, while the difference of DIC was not notable. The POC and PIC concentrations were lower in the Poaceae creek compared to the Cyperaceae creek. Spring tides increased the carbon concentrations (except for PIC) in both creeks by on average 7–40%, relative to neap tides. Seasonal variations of sedimentary rate within the communities probably result in the discrepancy of particulate carbon loading between the creeks. The Poaceae creek functioned as a source of DOC and DIC throughout a year but as a sink of POC and PIC in summer and autumn, while it turned to a weak source of PIC in winter and spring. The Cyperaceae creek exhibited as a source of all carbon components throughout a year. We suggest that vegetation type (with soil carbon stocks), tidal regimes and sedimentary dynamics would synergistically determine the fate of carbon in the creeks. Our results are helpful in reliable estimates of carbon transport between the coastal marsh and the adjacent ocean.

    Comparative Life-Cycle Assessment of Aquifer Thermal Energy Storage Integrated with in Situ Bioremediation of Chlorinated Volatile Organic Compounds
    Ni, Zhuobiao ; Wang, Yue ; Wang, Yafei ; Chen, Shaoqing ; Xie, Manxi ; Grotenhuis, Tim ; Qiu, Rongliang - \ 2020
    Environmental Science and Technology 54 (2020)5. - ISSN 0013-936X - p. 3039 - 3049.

    Due to the increasing need for sustainable energy and environmental quality in urban areas, the combination of aquifer thermal energy storage (ATES) and in situ bioremediation (ISB) has drawn much attention as it can deliver an integrated contribution to fulfill both demands. Yet, little is known about the overall environmental impacts of ATES-ISB. Hence, we applied a life-cycle assessment (LCA) to evaluate the environmental performance of ATES-ISB, which is also compared with the conventional heating and cooling system plus ISB alone (CHC + ISB). Energy supply via electricity is revealed as the primary cause of the environmental impacts, contributing 61.26% impacts of ATES-ISB and 72.91% impacts of CHC + ISB. Specifically, electricity is responsible for over 95% of water use, global warming potential, acidification potential, and respiratory inorganics, whereas the production of the biological medium for bioremediation causes more than 85% of the eco- and human toxicity impacts in both cases. The overall environmental impact of ATES-ISB is two times smaller than that of CHC + ISB. Sensitivity analysis confirms the importance of electricity consumption and electron donor production to the environmental impacts in both energy supply and bioremediation. Thus, future studies and practical applications seeking possible optimization of the environmental performances of ATES-ISB are recommended to focus more on these two essential elements, e.g., electricity and electron donor, and their related parameters. With the comprehensive LCA, insight is obtained for better characterizing the crucial factors as well as the relevant direction for future optimization research of the ATES-ISB system.

    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.
    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.

    A second HD mating type sublocus of Flammulina velutipes is at least di-allelic and active : New primers for identification of HD - A and HD-b subloci
    Wang, Wei ; Mukhtar, Irum ; Chou, Tiansheng ; Jiang, Siyuan ; Liu, Xinrui ; Peer, Arend F. Van; Xie, Baogui - \ 2019
    PeerJ 2019 (2019)2. - ISSN 2167-8359
    Di-allelic - Flammulina velutipes - HD subloci - Homeodomain - Mating pathway - Primers

    Background: Sexual development in Flammulina velutipes is controlled by two different mating type loci (HD and PR). The HD locus contains homeodomain (Hd) genes on two separate HD subloci: HD-a and HD-b. While the functionality of the HD-b sublocus has been largely confirmed, the status and content of the HD-a sublocus has remained unclear. Methods: To examine the function of the HD-a sublocus, genome sequences of a series of F. velutipes strains were analyzed and tested through series of amplification by specific primer sets. Furthermore, activity of di-allelic HD-a locus was confirmed by crossing strains with different combinations of HD-a and HD-b subloci. Results: Sublocus HD-b contained a large variety of fixed Hd1/Hd2 gene pairs, while the HD-a sublocus either contained a conserved Hd2 gene or, a newly discovered Hd1 gene that was also conserved. Identification of whole HD loci, that is, the contents of HD-a and HD-b subloci in a strain, revealed that strains with similar HD-b subloci could still form normal dikaryons if the two genes at the HD-a sublocus differed. At least di-allelic HD-a sublocus, is thus indicated to be actively involved in mating type compatibility. Conclusions: HD-a sublocus is active and di-allelic. Using the new information on the HD subloci, primers sets were developed that specifically amplify HD-a or HD-b subloci in the majority of F. velutipes strains. In this way, unknown HD mating types of F. velutipes can now be quickly identified, and HD mating type compatibility conferred by HD-a or HD-b can be confirmed by PCR.

    Globodera pallida effector GpRbp-1 targets E3 ligase UPL3 to modulate gene expression in the host
    Diaz Granados Muñoz, A. ; Sterken, M.G. ; Overmars, H.A. ; Yuan, Yulin ; Ariaans, Roel ; Pomp, H. ; Pokare, Somnath ; Holterman, M.H.M. ; Slootweg, E.J. ; Elashry, Abdenaser ; Grundler, Florian M.W. ; Bakker, J. ; Xie, Fangming ; Goverse, A. ; Smant, G. - \ 2019
    Improved aerosol correction for OMI tropospheric NO2 retrieval over East Asia : Constraint from CALIOP aerosol vertical profile
    Liu, Mengyao ; Lin, Jintai ; Folkert Boersma, K. ; Pinardi, Gaia ; Wang, Yang ; Chimot, Julien ; Wagner, Thomas ; Xie, Pinhua ; Eskes, Henk ; Roozendael, Michel Van; Hendrick, François ; Wang, Pucai ; Wang, Ting ; Yan, Yingying ; Chen, Lulu ; Ni, Ruijing - \ 2019
    Atmospheric Measurement Techniques 12 (2019)1. - ISSN 1867-1381 - p. 1 - 21.

    Satellite retrieval of vertical column densities (VCDs) of tropospheric nitrogen dioxide (NO2) is critical for NOx pollution and impact evaluation. For regions with high aerosol loadings, the retrieval accuracy is greatly affected by whether aerosol optical effects are treated implicitly (as additional effective clouds) or explicitly, among other factors. Our previous POMINO algorithm explicitly accounts for aerosol effects to improve the retrieval, especially in polluted situations over China, by using aerosol information from GEOS-Chem simulations with further monthly constraints by MODIS/Aqua aerosol optical depth (AOD) data. Here we present a major algorithm update, POMINO v1.1, by constructing a monthly climatological dataset of aerosol extinction profiles, based on level 2 CALIOP/CALIPSO data over 2007-2015, to better constrain the modeled aerosol vertical profiles. We find that GEOS-Chem captures the month-to-month variation in CALIOP aerosol layer height (ALH) but with a systematic underestimate by about 300-600 m (season and location dependent), due to a too strong negative vertical gradient of extinction above 1 km. Correcting the model aerosol extinction profiles results in small changes in retrieved cloud fraction, increases in cloud-top pressure (within 2 %-6 % in most cases), and increases in tropospheric NO2 VCD by 4 %-16 % over China on a monthly basis in 2012. The improved NO2 VCDs (in POMINO v1.1) are more consistent with independent ground-based MAX-DOAS observations (R2=0.80, NMB =-3.4 %, for 162 pixels in 49 days) than POMINO (R2=0.80, NMB =-9.6 %), DOMINO v2 (R2=0.68, NMB =-2.1 %), and QA4ECV (R2=0.75, NMB =-22.0 %) are. Especially on haze days, R2 reaches 0.76 for POMINO v1.1, much higher than that for POMINO (0.68), DOMINO v2 (0.38), and QA4ECV (0.34). Furthermore, the increase in cloud pressure likely reveals a more realistic vertical relationship between cloud and aerosol layers, with aerosols situated above the clouds in certain months span id=page2 instead of always below the clouds. The POMINO v1.1 algorithm is a core step towards our next public release of the data product (POMINO v2), and it will also be applied to the recently launched S5P-TROPOMI sensor.

    A research roadmap for quantifying non-state and subnational climate mitigation action
    Hsu, Angel ; Höhne, Niklas ; Kuramochi, Takeshi ; Roelfsema, Mark ; Weinfurter, Amy ; Xie, Yihao ; Lütkehermöller, Katharina ; Chan, Sander ; Corfee-Morlot, Jan ; Drost, Philip ; Faria, Pedro ; Gardiner, Ann ; Gordon, David J. ; Hale, Thomas ; Hultman, Nathan E. ; Moorhead, John ; Reuvers, Shirin ; Setzer, Joana ; Singh, Neelam ; Weber, Christopher ; Widerberg, Oscar - \ 2019
    Nature Climate Change 9 (2019)1. - ISSN 1758-678X - p. 11 - 17.

    Non-state and subnational climate actors have become central to global climate change governance. Quantitatively assessing climate mitigation undertaken by these entities is critical to understand the credibility of this trend. In this Perspective, we make recommendations regarding five main areas of research and methodological development related to evaluating non-state and subnational climate actions: defining clear boundaries and terminology; use of common methodologies to aggregate and assess non-state and subnational contributions; systematically dealing with issues of overlap; estimating the likelihood of implementation; and addressing data gaps.

    Effect of fermentation on content, molecule weight distribution and viscosity of β-glucans in oat sourdough
    Lu, Jun ; Shan, Lingke ; Xie, Yiting ; Min, Fangfang ; Gao, Jinyan ; Guo, Laichun ; Ren, Changzhong ; Yuan, Juanli ; Gilissen, Luud ; Chen, Hongbing - \ 2019
    International Journal of Food Science and Technology 54 (2019)1. - ISSN 0950-5423 - p. 62 - 67.
    Fermentation - Lactobacillus plantarum - Oat β-glucan - Sourdough - Viscosity

    This study investigated the effect of fermentation on the physicochemical properties of β-glucans in oat sourdough. Sourdoughs were produced from oat using homo-fermentative lactic acid bacteria, Lactobacillus plantarum 22134. The contents of total β-glucan and soluble β-glucan, the molecular weight (MW) of β-glucan and the viscosity of the extracted β-glucans were determined at 0, 4, 8, 10 and 12 h of fermentation. The total β-glucan content decreased from 4.89% to 4.23% after 12 h of fermentation. The soluble β-glucan concentration increased from 1.89% to 2.18% and then decreased to 1.97% after 8 h of fermentation. The content of β-glucans with MW > 105 decreased from 0 to 4 h of fermentation, followed by an increase and then a decrease after 8 h. The oat sourdough fermented for 8 h had high viscosity, which could be more beneficial for health and bread texture quality, especially for gluten-free breads. International Journal of Food Science and Technology

    Three rapid methods for direct PCR of powdery mildew samples for later sequencing
    Mukhtar, Irum ; Peer, Arend F. Van; Vazquez-Marrufo, Gerardo ; Ma Vazquez-Garciduenas, Soledad ; Xie, Baogui - \ 2018
    Sydowia 70 (2018). - ISSN 0082-0598 - p. 155 - 160.
    DNA isolation - Its - Powdery mildews

    Powdery mildews are an important obligate parasitic fungal group reported in nearly all regions of the world. DNA isolation for molecular identification of powdery mildew samples is now a standard practice and is becoming more affordable but remains a lengthy process. In this study, three direct DNA isolation methods have been developed for rDNA internal transcribed spacer (ITS) amplification of different powdery mildew species. This reduces time taken for traditional DNA extraction from hours to minutes and rapid PCR means large quantities of DNA are available for sequencing in an hour. Methods proposed in this paper were found rapid and efficient for sequencing. ITS sequences obtained, were neat, clear and comparable to sequences obtained by conventional DNA extraction methods. However, ITS remains insufficient for separation of certain closely related species. In conclusion, our methods are simple, cost-effective and produced enough genomic DNA for quick and high quality sequences. Methods should be trialed further for preparation of DNA libraries of further genomic regions for rapid and accurate powdery mildew identification.

    Population and fertility by age and sex for 195 countries and territories, 1950–2017 : a systematic analysis for the Global Burden of Disease Study 2017
    Murray, Christopher J.L. ; Callender, Charlton S.K.H. ; Kulikoff, Xie Rachel ; Srinivasan, Vinay ; Geleijnse, J.M. - \ 2018
    The Lancet 392 (2018)10159. - ISSN 0140-6736 - p. 1995 - 2051.
    Background
    Population estimates underpin demographic and epidemiological research and are used to track progress on numerous international indicators of health and development. To date, internationally available estimates of population and fertility, although useful, have not been produced with transparent and replicable methods and do not use standardised estimates of mortality. We present single-calendar year and single-year of age estimates of fertility and population by sex with standardised and replicable methods.
    The red bayberry genome and genetic basis of sex determination
    Jia, Hui Min ; Jia, Hui Juan ; Cai, Qing Le ; Wang, Yan ; Zhao, Hai Bo ; Yang, Wei Fei ; Wang, Guo Yun ; Li, Ying Hui ; Zhan, Dong Liang ; Shen, Yu Tong ; Niu, Qing Feng ; Chang, Le ; Qiu, Jie ; Zhao, Lan ; Xie, Han Bing ; Fu, Wan Yi ; Jin, Jing ; Li, Xiong Wei ; Jiao, Yun ; Zhou, Chao Chao ; Tu, Ting ; Chai, Chun Yan ; Gao, Jin Long ; Fan, Long Jiang ; Weg, Eric van de; Wang, Jun Yi ; Gao, Zhong Shan - \ 2018
    Plant Biotechnology Journal 17 (2018)2. - ISSN 1467-7644 - p. 397 - 409.
    genome - Morella rubra - sex-determining region - sex-linked marker

    Morella rubra, red bayberry, is an economically important fruit tree in south China. Here, we assembled the first high-quality genome for both a female and a male individual of red bayberry. The genome size was 313-Mb, and 90% sequences were assembled into eight pseudo chromosome molecules, with 32 493 predicted genes. By whole-genome comparison between the female and male and association analysis with sequences of bulked and individual DNA samples from female and male, a 59-Kb region determining female was identified and located on distal end of pseudochromosome 8, which contains abundant transposable element and seven putative genes, four of them are related to sex floral development. This 59-Kb female-specific region was likely to be derived from duplication and rearrangement of paralogous genes and retained non-recombinant in the female-specific region. Sex-specific molecular markers developed from candidate genes co-segregated with sex in a genetically diverse female and male germplasm. We propose sex determination follow the ZW model of female heterogamety. The genome sequence of red bayberry provides a valuable resource for plant sex chromosome evolution and also provides important insights for molecular biology, genetics and modern breeding in Myricaceae family.

    Potato late blight field resistance from QTL dPI09c is conferred by the NB-LRR gene R8
    Jiang, Rui ; Li, Jingcai ; Tian, Zhendong ; Du, Juan ; Armstrong, Miles ; Baker, Katie ; Tze-Yin Lim, Joanne ; Vossen, Jack H. ; He, Huan ; Portal, Leticia ; Zhou, Jun ; Bonierbale, Merideth ; Hein, Ingo ; Lindqvist-Kreuze, Hannele ; Xie, Conghua - \ 2018
    Journal of Experimental Botany 69 (2018)7. - ISSN 0022-0957 - p. 1545 - 1555.
    dRenSeq - field resistance - late blight - map-based cloning - potato - R gene
    Following the often short-lived protection that major nucleotide binding, leucine-rich-repeat (NB-LRR) resistance genes offer against the potato pathogen Phytophthora infestans, field resistance was thought to provide a more durable alternative to prevent late blight disease. We previously identified the QTL dPI09c on potato chromosome 9 as a more durable field resistance source against late blight. Here, the resistance QTL was fine-mapped to a 186 kb region. The interval corresponds to a larger, 389 kb, genomic region in the potato reference genome of Solanum tuberosum Group Phureja doubled monoploid clone DM1-3 (DM) and from which functional NB-LRRs R8, R9a, Rpi-moc1, and Rpi-vnt1 have arisen independently in wild species. dRenSeq analysis of parental clones alongside resistant and susceptible bulks of the segregating population B3C1HP showed full sequence representation of R8. This was independently validated using long-range PCR and screening of a bespoke bacterial artificial chromosome library. The latter enabled a comparative analysis of the sequence variation in this locus in diverse Solanaceae. We reveal for the first time that broad spectrum and durable field resistance against P. infestans is conferred by the NB-LRR gene R8, which is thought to provide narrow spectrum race-specific resistance.
    An atypical R2R3 MYB transcription factor increases cold hardiness by CBF-dependent and CBF-independent pathways in apple
    Xie, Yinpeng ; Chen, Pengxiang ; Yan, Yan ; Bao, Chana ; Li, Xuewei ; Wang, Liping ; Shen, Xiaoxia ; Li, Haiyan ; Liu, Xiaofang ; Niu, Chundong ; Zhu, Chen ; Fang, Nan ; Shao, Yun ; Zhao, Tao ; Yu, Jiantao ; Zhu, Jianhua ; Xu, Lingfei ; Nocker, Steven van; Ma, Fengwang ; Guan, Qingmei - \ 2018
    New Phytologist 218 (2018)1. - ISSN 0028-646X - p. 201 - 218.
    Apple (Malus × domestica) - C-REPEAT BINDING FACTOR (CBF) - Cold hardiness - MdMYB124 - MdMYB88
    Apple (Malus × domestica) trees are vulnerable to freezing temperatures. However, there has been only limited success in developing cold-hardy cultivars. This lack of progress is due at least partly to lack of understanding of the molecular mechanisms of freezing tolerance in apple. In this study, we evaluated the potential roles for two R2R3 MYB transcription factors (TFs), MYB88 and the paralogous FLP (MYB124), in cold stress in apple and Arabidopsis. We found that MYB88 and MYB124 positively regulate freezing tolerance and cold-responsive gene expression in both apple and Arabidopsis. Chromatin-Immunoprecipitation-qPCR and electrophoretic mobility shift assays showed that MdMYB88/MdMYB124 act as direct regulators of the COLD SHOCK DOMAIN PROTEIN 3 (MdCSP3) and CIRCADIAN CLOCK ASSOCIATED 1 (MdCCA1) genes. Dual luciferase reporter assay indicated that MdCCA1 but not MdCSP3 activated the expression of MdCBF3 under cold stress. Moreover, MdMYB88 and MdMYB124 promoted anthocyanin accumulation and H2O2 detoxification in response to cold. Taken together, our results suggest that MdMYB88 and MdMYB124 positively regulate cold hardiness and cold-responsive gene expression under cold stress by C-REPEAT BINDING FACTOR (CBF)-dependent and CBF-independent pathways.
    Nitrogen removal performance and microbial community changes in subsurface wastewater infiltration systems (SWISs) at low temperature with different bioaugmentation strategies
    Liu, Chunjing ; Xie, Jianzhi ; Song, Manli ; Gao, Zhiling ; Zheng, Dongxing ; Liu, Xia ; Ning, Guohui ; Cheng, Xu ; Bruning, Harry - \ 2018
    Bioresource Technology 250 (2018). - ISSN 0960-8524 - p. 603 - 610.
    Aerobic denitrification - Bacterial community structure - Embedding bioaugmentation - Low temperature - Subsurface wastewater infiltration system
    Poor nitrogen removal efficiency (mainly nitrate, NO3 −-N) at low temperatures strongly limits application of subsurface wastewater infiltration systems (SWISs). Seven psychrophilic strains (heterotrophic nitrifying bacteria and aerobic denitrifying bacteria) were isolated and added to SWISs to investigate the effect of embedding and direct-dosing bioaugmentation strategies on sewage treatment performance at low temperature. Both bioaugmentation strategies improved ammonium (NH4 +-N) removal efficiencies, and the embedding strategy also exhibited satisfactory NO3 −-N and total nitrogen (TN) removal efficiencies. Pyrosequencing results of the bacterial 16S rRNA gene indicated that the embedding strategy significantly decreased the indigenous soil microbial diversity (p <.05) and altered the bacterial community structure, significantly increasing the relative abundance of Clostridia, which have good nitrate-reducing activity.
    Balanced N and C input recommendations for rain-fed maize production in northern China based on N balances and grain yields
    Wang, Xiaobin ; Cai, Dianxiong ; Zhao, Quansheng ; Xie, Xiaohong ; Hoogmoed, Willem B. ; Oenema, Oene - \ 2018
    Journal of the Science of Food and Agriculture 98 (2018)3. - ISSN 0022-5142 - p. 872 - 883.
    Carbon - Dryland - Maize - Nitrogen - Rain-fed farming

    BACKGROUND: This study aimed to assess longer-term (1993-2009) effects of combined applications of fertiliser, maize stover, and cattle manure on maize yields, partial nitrogen (N) and carbon (C) balances, and water and N-use efficiencies, to guide N and C input recommendations for rain-fed maize production in northern China. RESULTS: The field trial, with three factors at five levels and 12 treatments, was conducted at Shouyang Dryland-Farming Experimental Station, Shanxi, China. Data analysis revealed higher N balances but lower C balances significantly occurred in a dry year than in a wet year. Positive N balances related to higher N inputs resulted in higher soil available N, even downward to deep layers with increasing N inputs, while positive C balances due to higher C inputs could be benefit to increase soil organic C. Based on partial N balances and grain yields, N and C inputs at ranges of 100kg N ha-1 and 1.9-2.9Mg C ha-1 could be recommended for target yields of 6.7-7.2Mg ha-1 in rain-fed maize production. CONCLUSION: The study suggests that N balances close to neutral be given priority to improving N-use efficiency, and more positive C balances also be important for sustaining target yields and soil fertility levels.

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