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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Nonlinear responses of soil nematode community composition to increasing aridity
Xiong, Dan ; Wei, Cun Zheng ; Wubs, Jasper E.R. ; Veen, G.J. ; Liang, Wenju ; Wang, Xiaobo ; Li, Qi ; Putten, Wim H. Van der; Han, Xingguo - \ 2019
Global Ecology and Biogeography (2019). - ISSN 1466-822X
aridity - biodiversity - global climate change - grassland transect - nonlinear response - soil nematode community

Aim: Increasing aridity under global change is predicted to have a profound impact on the structure and functioning of terrestrial ecosystems, yet we have a poor understanding of how belowground communities respond. In order to understand the longer term responses of different trophic levels in the soil food web to increasing aridity, we investigated the abundance, richness and community similarity of the soil nematode community along a 3,200 km aridity gradient. Location: A transect across semi-arid and arid grasslands in Northern China, where the aridity ranges from.43 to.97. Time period: July and August 2012. Major taxa studied: Soil-borne Nematoda. Methods: We used generalized additive (mixed) models to analyse the abundance, richness and community similarity patterns of soil nematodes. We used structural equation modelling (SEM) to disentangle the direct and indirect environmental drivers (aridity, soil and plant variables) of the nematode community. Results: The abundance, richness and similarity of nematode communities declined nonlinearly with increasing aridity. The most pronounced decline in nematode richness and community similarity occurred in arid conditions (aridity >.80). However, the shape of the response to aridity differed among nematode feeding groups. In arid conditions, the abundance and richness of bacterial feeders were less sensitive to changes in aridity than for fungal feeders. The SEM analysis revealed that nematode community responses to aridity were not mediated via changes in plant and soil variables, but instead were affected directly by aridity. Main conclusions: Our results showed that in mesic grasslands, increasing aridity primarily caused a decline in nematode abundance, whereas increasing aridity in xeric grasslands led to a loss of nematode diversity. The nonlinear responses of nematodes to aridity could also result in nonlinear shifts in ecosystem functioning, because soil nematodes operate at various trophic levels in the soil food web, thereby influencing the performance of plants, soil biodiversity and biogeochemical cycling.

ABA-mediated regulation of leaf and root hydraulic conductance in tomato grown at elevated CO2 is associated with altered gene expression of aquaporins
Fang, Liang ; Abdelhakim, Lamis Osama Anwar ; Hegelund, Josefine Nymark ; Li, Shenglan ; Liu, Jie ; Peng, Xiaoying ; Li, Xiangnan ; Wei, Zhenhua ; Liu, Fulai - \ 2019
Horticulture Research 6 (2019)1. - ISSN 2052-7276

Elevated CO2 concentration in the air (e[CO2]) decreases stomatal density (SD) and stomatal conductance (gs) where abscisic acid (ABA) may play a role, yet the underlying mechanism remains largely elusive. We investigated the effects of e[CO2] (800 ppm) on leaf gas exchange and water relations of two tomato (Solanum lycopersicum) genotypes, Ailsa Craig (WT) and its ABA-deficient mutant (flacca). Compared to plants grown at ambient CO2 (400 ppm), e[CO2] stimulated photosynthetic rate in both genotypes, while depressed the gs only in WT. SD showed a similar response to e[CO2] as gs, although the change was not significant. e[CO2] increased leaf and xylem ABA concentrations and xylem sap pH, where the increases were larger in WT than in flacca. Although leaf water potential was unaffected by CO2 growth environment, e[CO2] lowered osmotic potential, hence tended to increase turgor pressure particularly for WT. e[CO2] reduced hydraulic conductance of leaf and root in WT but not in flacca, which was associated with downregulation of gene expression of aquaporins. It is concluded that ABA-mediated regulation of gs, SD, and gene expression of aquaporins coordinates the whole-plant hydraulics of tomato grown at different CO2 environments.

Propolis modulates the gut microbiota and improves the intestinal mucosal barrier function in diabetic rats
Xue, Meilan ; Liu, Ying ; Xu, Hongwei ; Zhou, Zhitong ; Ma, Yan ; Sun, Ting ; Liu, Man ; Zhang, Huaqi ; Liang, Hui - \ 2019
Biomedicine and Pharmacotherapy 118 (2019). - ISSN 0753-3322
16S rDNA high-throughput sequencing - Diabetes - Gut microbiota - Propolis - Short chain fatty acid

Objective: Diabetes mellitus is associated with gut microbiota disturbance and intestinal mucosal injuries. This study investigated the influence of propolis on the gut microbiota and intestinal mucosa in rats with diabetes. Methods: Sprague-Dawley (SD) rats were randomly assigned to the control group, model group, and three propolis groups (supplemented with 80, 160, and 240 mg/kg·bw propolis, respectively). A high-fat diet combined with a streptozotocin (STZ) abdominal injection were used to induce diabetes in the rats. After 4 weeks, the intestinal histopathological analysis of the ileum was observed by transmission electron microscopy. The fasting blood glucose (FBG), plasma insulin, glucose tolerance (OGTT) and glycosylated hemoglobin (HbA1c) levels were measured. The expression of tight junction (TJ) proteins in the ileum was measured using western blotting. The molecular ecology of the fecal gut microbiota was analyzed by 16S rDNA high-throughput sequencing. The contents of the short-chain fatty acids (SCFAs) in feces were measured using high-performance liquid chromatography (HPLC). Results: After propolis treatment, compared to the model group, FBG and HbA1c levels declined, while the glucose tolerance and insulin sensitivity index (ISI) increased. The levels of TJ proteins in the ileum increased in the propolis groups. The tight junctions and gap junctions of the intestinal epithelium were also improved in the propolis groups. The contents of the feces acetic acid, propionic acid and butyrate were increased in the propolis groups. 16S rDNA high-throughput sequencing revealed that the composition of the gut microbiota of rats in the propolis supplement group was significantly improved. Conclusions: Compared to the model group, propolis exerted hypoglycemic effects in diabetic rats, and it repaired intestinal mucosal damage, benefited the communities of the gut microbiota and increased SCFA levels in diabetic rats.

Interactive effects of microplastics and glyphosate on the dynamics of soil dissolved organic matter in a Chinese loess soil
Liu, Hongfei ; Yang, Xiaomei ; Liang, Chutao ; Li, Yuanze ; Qiao, Leilei ; Ai, Z. ; Xue, Sha ; Liu, Guobin - \ 2019
Catena 182 (2019). - ISSN 0341-8162
Dissolved organic carbon (DOC) - Dissolved organic nitrogen (DON) - Dissolved organic phosphorus (DOP) - Excitation-emission matrix (EEM) - Glyphosate

The increased use of plastic films and pesticides on agricultural soil leads to the accumulation of plastic debris and pesticide residues in soil. This accumulation has become a serious environmental issue, as it threatens life of earthworms, inhibits the enzyme activities and microbial diversity, and contributes to the loss of soil microbial carbon and nitrogen. However, little information is available regarding the effects of pesticides on soil dissolved organic matter (DOM). It is also unknown how plastic debris, especially small-sized particles called microplastics, influences the effects of pesticides on soil DOM. In this study, we performed a 30-day soil incubation experiment. Three levels of the common herbicide glyphosate were applied to soil: 0 (control, CK), 3.6 kg ha 1 (G1) and 7.2 kg ha 1 (G2). We also tested four levels of glyphosate and microplastics (homopolymer polypropylene powder) co-addition: 3.6 kg ha 1 + 7% (w/w) (M1G1), 3.6 kg ha 1 + 28% (w/w) (M2G1), 7.2 kg ha 1 + 7% (w/w) (M1G2), and 7.2 kg ha 1 + 28% (w/w) (M2G2). Glyphosate addition slightly increased soil fluorescein diacetate hydrolase (FDAse) and phenol oxidase (PO) activities. Although the glyphosate addition significantly promoted the accumulation of dissolved organic phosphorus (DOP) within the first 14 days, the M2 treatment decreased DOP at day 30. M2G1 and M2G2 increased soil FDAse activity and promoted the accumulation of DOC and DOP relative to G1 and G2 respectively while M1G1 and M1G2 benefited DON accumulation. Our results highlighted that the interaction between glyphosate and low microplastics content negatively affected DOC and DOP dynamics, leading to the loss of bioavailable C and P loss. The interaction between glyphosate and high content microplastics negatively affected DON compared with glyphosate addition, possibly decreasing DON.

Global 3-D Simulations of the Triple Oxygen Isotope Signature Δ17O in Atmospheric CO2
Koren, Gerbrand ; Schneider, Linda ; Velde, Ivar R. van der; Schaik, Erik van; Gromov, Sergey S. ; Adnew, Getachew A. ; Mrozek Martino, Dorota J. ; Hofmann, Magdalena E.G. ; Liang, Mao Chang ; Mahata, Sasadhar ; Bergamaschi, Peter ; Laan-Luijkx, Ingrid T. van der; Krol, Maarten C. ; Röckmann, Thomas ; Peters, Wouter - \ 2019
Journal of Geophysical Research: Atmospheres (2019). - ISSN 2169-897X
O excess (ΔO) - carbon cycle - carbon dioxide (CO) - gross primary production (GPP) - mass-independent fractionation (MIF) - stable isotopes

The triple oxygen isotope signature Δ17O in atmospheric CO2, also known as its “17O excess,” has been proposed as a tracer for gross primary production (the gross uptake of CO2 by vegetation through photosynthesis). We present the first global 3-D model simulations for Δ17O in atmospheric CO2 together with a detailed model description and sensitivity analyses. In our 3-D model framework we include the stratospheric source of Δ17O in CO2 and the surface sinks from vegetation, soils, ocean, biomass burning, and fossil fuel combustion. The effect of oxidation of atmospheric CO on Δ17O in CO2 is also included in our model. We estimate that the global mean Δ17O (defined as Δ17O = ln(δ17O+1)−λRL·ln(δ18O+1) with λRL = 0.5229) of CO2 in the lowest 500 m of the atmosphere is 39.6 per meg, which is ∼20 per meg lower than estimates from existing box models. We compare our model results with a measured stratospheric Δ17O in CO2 profile from Sodankylä (Finland), which shows good agreement. In addition, we compare our model results with tropospheric measurements of Δ17O in CO2 from Göttingen (Germany) and Taipei (Taiwan), which shows some agreement but we also find substantial discrepancies that are subsequently discussed. Finally, we show model results for Zotino (Russia), Mauna Loa (United States), Manaus (Brazil), and South Pole, which we propose as possible locations for future measurements of Δ17O in tropospheric CO2 that can help to further increase our understanding of the global budget of Δ17O in atmospheric CO2.

Author Correction: Climatic controls of decomposition drive the global biogeography of forest-tree symbioses
Steidinger, B.S. ; Crowther, T.W. ; Liang, J. ; Nuland, M.E. Van; Werner, G.D.A. ; Reich, P.B. ; Nabuurs, G.J. ; de-Miguel, S. ; Zhou, M. ; Picard, N. ; Herault, B. ; Zhao, X. ; Zhang, C. ; Routh, D. ; Peay, K.G. ; Abegg, Meinrad ; Adou Yao, C.Y. ; Alberti, Giorgio ; Almeyda Zambrano, Angelica ; Alvarez-Davila, Esteban ; Alvarez-Loayza, Patricia ; Alves, Luciana F. ; Ammer, Christian ; Antón-Fernández, Clara ; Araujo-Murakami, Alejandro ; Arroyo, Luzmila ; Avitabile, Valerio ; Aymard, Gerardo ; Baker, Timothy ; Bałazy, Radomir ; Banki, Olaf ; Barroso, Jorcely ; Bastian, Meredith ; Bastin, Jean Francois ; Birigazzi, Luca ; Birnbaum, Philippe ; Bitariho, Robert ; Boeckx, Pascal ; Bongers, Frans ; Bouriaud, Olivier ; Brancalion, Pedro H.H.S. ; Decuyper, Mathieu ; Hengeveld, Geerten ; Herold, Martin ; Lu, Huicui ; Parren, Marc ; Poorter, Lourens ; Schelhaas, Mart Jan ; Sheil, Douglas ; Zagt, Roderick - \ 2019
Nature 571 (2019)7765. - ISSN 0028-0836

In this Letter, the middle initial of author G. J. Nabuurs was omitted, and he should have been associated with an additional affiliation: ‘Forest Ecology and Forest Management Group, Wageningen University and Research, Wageningen, The Netherlands’ (now added as affiliation 182). In addition, the following two statements have been added to the Supplementary Acknowledgements. (1): ‘We would particularly like to thank The French NFI for the work of the many field teams and engineers, who have made extraordinary efforts to make forest inventory data publicly available.’ (1): ‘Sergio de Miguel benefited from a Serra- Húnter Fellowship provided by the Generalitat of Catalonia.’ Finally, the second sentence of the Methods section should have cited the French NFI, which provided a national forestry database used in our analysis, to read as follows: ‘The GFBi database consists of individual-based data that we compiled from all the regional and national GFBi forest-inventory datasets, including the French NFI (IGN—French National Forest Inventory, raw data, annual campaigns 2005 and following, https://inventaire-forestier.ign.fr/spip.php?rubrique159, site accessed on 01 January 2015)’. All of these errors have been corrected online.

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.

Addressing nutritional requirements of ageing consumers in Asia-recommendations from an expert workshop
Ong, Sherlin ; Woo, Jean ; Parikh, Panam ; Chan, Ruth ; Sun, Jianqin ; Mun, Chan Yoke ; Wee, Shiou Liang ; Thu, Nghiem Nguyet ; Thang, Pham ; Setiati, Siti ; Huang, Yi Chen ; Wahlqvist, Mark L. ; Bos, Rolf ; Groot, Lisette Cpgm de - \ 2019
Asia Pacific Journal of Clinical Nutrition 28 (2019)2. - ISSN 0964-7058 - p. 204 - 213.

The number of older persons in Asia is expected to triple by 2050. Ageing is associated with non-communicable chronic diseases, malnutrition, and geriatric syndromes, which influences the burden on the cost related to healthcare, health outcomes, and the quality of life. Experts in the field of older adult nutrition from Asia, Australia, and Europe were invited to participate in a two-day workshop to review the available data, current policies and programs for the ageing population in different countries of Asia to identify the gaps in knowledge and to develop recommendations for action. In Asia, most of the data pertaining to health status, nutritional status, and nutrient intake of the older persons were mainly obtained by conducting studies in nursing homes or hospitals and small cohort studies. There were limited country-specific data on this population. Moreover, the available data pertaining to different countries were difficult to compare due to differences in the reporting format and reference values used. Although nutrition initiatives and policies were realized and public education was conducted to support the older persons, most of these efforts targeted the general population rather than the older persons population segment. In healthcare management, a higher amount of education is required pertaining to the knowledge of nutritional requirements and appropriate feeding of the older persons to reduce underfeeding and its consequences. The expert group recommended the use of a systematic approach for reviewing data pertaining to different countries, initiatives, and programs to further evaluate the available data to underpin future research.

Climatic controls of decomposition drive the global biogeography of forest-tree symbioses
Steidinger, B.S. ; Crowther, T.W. ; Liang, J. ; Nuland, M.E. Van; Werner, G.D.A. ; Reich, P.B. ; Nabuurs, G. ; de-Miguel, S. ; Zhou, M. ; Picard, N. ; Herault, B. ; Zhao, X. ; Zhang, C. ; Routh, D. ; Peay, K.G. ; Herold, M. ; Decuyper, M. ; Avitabile, V. ; DeVries, B.R. ; Hengeveld, G.M. ; Poorter, L. ; Schelhaas, M. ; Bongers, F. - \ 2019
Nature 569 (2019)7756. - ISSN 0028-0836 - p. 404 - 408.
The identity of the dominant root-associated microbial symbionts in a forest determines the ability of trees to access limiting nutrients from atmospheric or soil pools1,2, sequester carbon3,4 and withstand the effects of climate change5,6. Characterizing the global distribution of these symbioses and identifying the factors that control this distribution are thus integral to understanding the present and future functioning of forest ecosystems. Here we generate a spatially explicit global map of the symbiotic status of forests, using a database of over 1.1 million forest inventory plots that collectively contain over 28,000 tree species. Our analyses indicate that climate variables—in particular, climatically controlled variation in the rate of decomposition—are the primary drivers of the global distribution of major symbioses. We estimate that ectomycorrhizal trees, which represent only 2% of all plant species7, constitute approximately 60% of tree stems on Earth. Ectomycorrhizal symbiosis dominates forests in which seasonally cold and dry climates inhibit decomposition, and is the predominant form of symbiosis at high latitudes and elevation. By contrast, arbuscular mycorrhizal trees dominate in aseasonal, warm tropical forests, and occur with ectomycorrhizal trees in temperate biomes in which seasonally warm-and-wet climates enhance decomposition. Continental transitions between forests dominated by ectomycorrhizal or arbuscular mycorrhizal trees occur relatively abruptly along climate-driven decomposition gradients; these transitions are probably caused by positive feedback effects between plants and microorganisms. Symbiotic nitrogen fixers—which are insensitive to climatic controls on decomposition (compared with mycorrhizal fungi)—are most abundant in arid biomes with alkaline soils and high maximum temperatures. The climatically driven global symbiosis gradient that we document provides a spatially explicit quantitative understanding of microbial symbioses at the global scale, and demonstrates the critical role of microbial mutualisms in shaping the distribution of plant species.
Phenotyping flag leaf nitrogen content in rice using a three-band spectral index
Wang, Jian Jun ; Li, Zhikang ; Jin, Xiuliang ; Liang, Guohua ; Struik, Paul C. ; Gu, Junfei ; Zhou, Yong - \ 2019
Computers and Electronics in Agriculture 162 (2019). - ISSN 0168-1699 - p. 475 - 481.
Chromosome segment substitution lines - Oryza sativa - SPAD-502plus chlorophyll meter - Spectral reflectance

Accurate, rapid and non-destructive measurements of rice flag leaf nitrogen content (LNC) are crucial for geneticists and breeders. To help design a less expensive, non-destructive, real-time LNC sensor, we developed a Three-Band Difference Ratio (TBDR) spectral index, TBDR (R 755 , R 513 , R 508 ). This spectral index could accurately and rapidly estimate rice LNC in a population of chromosome segment substitution lines with small variation in LNC. The model estimating LNC was validated using a leave-one-out cross-validation technique; the achieved root mean square error was 0.13% and the relative error was 4.74%. In comparison with SPAD-502plus chlorophyll meter readings and commonly used spectral indices, including GreenSeeker- and Crop Circle-based indices, TBDR (R 755 , R 513 , R 508 ) produced higher accuracy in LNC estimation.

Exploring optimal soil mulching to enhance maize yield and water use efficiency in dryland areas in China
Gaimei, Liang ; Yuguo, Wang ; Baoliang, Chi ; Nana, Li ; Wenliang, Chen ; Wei, Qin - \ 2018
Acta Agriculturae Scandinavica Section B-Soil and Plant Science 68 (2018)3. - ISSN 0906-4710 - p. 273 - 282.
dryland - maize yield - mulch - precipitation - Soil water

Water and nutrient availability significantly limits global crop production, especially for dryland agriculture in arid and semi-arid regions. To explore the optimal soil mulching options for the Loess Plateau in China, a 3-year field study was conducted to investigate the effects of various soil mulching practices on soil temperature and the water use and grain yield of spring maize. The treatments included traditional flat farming (CK), narrow plastic film mulch (NM), wide plastic film mulch (WM) and narrow plastic film mulch + maize straw mulch between rows (MS). The results showed that MS treatment increased consistently soil temperature during the initial stages of maize growth, and more importantly, it reduced diurnal temperature variation. MS also increased in soil water storage by 10.1%, leading to the highest water use efficiency (WUE = 30.9 kg ha−1 mm−1) over CK on 3 year average. MS significantly increased maize yield and net income of farmers by up to 20%, compared to CK. In conclusion, optimisation of soil mulching strategies significantly enhanced crop yield and water productivity in dryland agriculture in China. Our study provides important guidance for exploring better soil management practice for dryland agriculture in the other regions of the world.

Carbon storage potential in degraded forests of Kalimantan, Indonesia
Ferraz, António ; Saatchi, Sassan ; Xu, Liang ; Hagen, Stephen ; Chave, Jerome ; Yu, Yifan ; Meyer, Victoria ; Garcia, Mariano ; Silva, Carlos ; Roswintiart, Orbita ; Samboko, Ari ; Sist, Plinio ; Walker, Sarah ; Pearson, Timothy R.H. ; Wijaya, Arief ; Sullivan, Franklin B. ; Rutishauser, Ervan ; Hoekman, Dirk ; Ganguly, Sangram - \ 2018
Environmental Research Letters 13 (2018)9. - ISSN 1748-9318
aboveground biomass mapping - airborne lidar - carbon - forest degradation - Indonesia - Kalimantan - peat swamp forests

The forests of Kalimantan are under severe pressure from extensive land use activities dominated by logging, palm oil plantations, and peatland fires. To implement the forest moratorium for mitigating greenhouse gas emissions, Indonesia's government requires information on the carbon stored in forests, including intact, degraded, secondary, and peat swamp forests. We developed a hybrid approach of producing a wall-to-wall map of the aboveground biomass (AGB) of intact and degraded forests of Kalimantan at 1 ha grid cells by combining field inventory plots, airborne lidar samples, and satellite radar and optical imagery. More than 110 000 ha of lidar data were acquired to systematically capture variations of forest structure and more than 104 field plots to develop lidar-biomass models. The lidar measurements were converted into biomass using models developed for 66 439 ha of drylands and 44 250 ha of wetland forests. By combining the AGB map with the national land cover map, we found that 22.3 Mha (106 ha) of forest remain on drylands ranging in biomass from 357.2 ±12.3 Mgha-1 in relatively intact forests to 134.2 ±6.1 Mgha-1 in severely degraded forests. The remaining peat swamp forests are heterogeneous in coverage and degradation level, extending over 3.62 Mha and having an average AGB of 211.8 ±12.7 Mgha-1. Emission factors calculated from aboveground biomass only suggest that the carbon storage potential of more than 15 Mha of degraded and secondary dryland forests will be about 1.1 PgC.

Nitrate improves ammonia incorporation into rumen microbial protein in lactating dairy cows fed a low-protein diet
Wang, Rong ; Wang, Min ; Ungerfeld, Emilio M. ; Zhang, Xiu Min ; Long, Dong Lei ; Mao, Hong Xiang ; Deng, Jin Ping ; Bannink, André ; Tan, Zhi Liang - \ 2018
Journal of Dairy Science 101 (2018)11. - ISSN 0022-0302 - p. 9789 - 9799.
dissolved hydrogen - microbial protein - nitrate - rumen fermentation

Generation of ammonia from nitrate reduction is slower compared with urea hydrolysis and may be more efficiently incorporated into ruminal microbial protein. We hypothesized that nitrate supplementation could increase ammonia incorporation into microbial protein in the rumen compared with urea supplementation of a low-protein diet fed to lactating dairy cows. Eight multiparous Chinese Holstein dairy cows were used in a crossover design to investigate the effect of nitrate or an isonitrogenous urea inclusion in the basal low-protein diet on rumen fermentation, milk yield, and ruminal microbial community in dairy cows fed a low-protein diet in comparison with an isonitrogenous urea control. Eight lactating cows were blocked in 4 pairs according to days in milk, parity, and milk yield and allocated to urea (7.0 g urea/kg of dry matter of basal diet) or nitrate (14.6 g of NO3 /kg of dry matter of basal diet, supplemented as sodium nitrate) treatments, which were formulated on 75% of metabolizable protein requirements. Nitrate supplementation decreased ammonia concentration in the rumen liquids (−33.1%) and plasma (−30.6%) as well as methane emissions (−15.0%) and increased dissolved hydrogen concentration (102%), microbial N (22.8%), propionate molar percentage, milk yield, and 16S rRNA gene copies of Selenomonas ruminantium. Ruminal dissolved hydrogen was positively correlated with the molar proportion of propionate (r = 0.57), and negatively correlated with acetate-to-propionate ratio (r = −0.57) and estimated net metabolic hydrogen production relative to total VFA produced (r = −0.58). Nitrate reduction to ammonia redirected metabolic hydrogen away from methanogenesis, enhanced ammonia incorporation into rumen microbial protein, and shifted fermentation from acetate to propionate, along with increasing S. ruminantium 16S rRNA gene copies, likely leading to the increased milk yield.

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.

Edge Computing – EDGE 2018 : Second International Conference, Held as Part of the Services Conference Federation, SCF 2018, Seattle, WA, USA, June 25-30, 2018, Proceedings
Liu, Shijun ; Tekinerdogan, B. ; Aoyama, Mikio ; Zhang, Liang-Jie - \ 2018
Springer Verlag (Lecture Notes in Computer Science ) - ISBN 9783319943398 - 153 p.
Pattern based integration of internet of things systems
Tekinerdogan, Bedir ; Köksal, Ömer - \ 2018
In: Internet of Things – ICIOT 2018 - 3rd International Conference, Held as Part of the Services Conference Federation, SCF 2018, Proceedings. - Springer Verlag (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) ) - ISBN 9783319943695 - p. 19 - 33.
Architecture design patterns - Internet of Things - Smart city engineering

The Internet of Things (IoT) is the network of physical devices embedded with sensors, actuators, and connectivity which enables these objects to connect and exchange data. Cleary the IoT has a pervasive impact on the society and an increasing number of systems are now based on IoT. One of the key challenges in IoT is coping with the heterogeneous set of systems and the integration of these systems in the same communication network. Several studies have focused on this integration aspect and addressed this at different levels of abstraction. Unfortunately, the different approaches are scattered and fragmented over the different studies and it is not clear how to cope with the integration concern within a single IoT system but also across multiple IoT systems that need to be integrated. To this end this chapter provides a comprehensive and systematic approach for identifying the key integration concerns in the IoT system architecture and describing the currently provided solutions. For this we adopt a pattern-based approach in which generic architecture solution structures are provided to these recurring integration concerns. We illustrate our approach for addressing the integration of IoT based systems within the context of smart city engineering.

Real-time inverse distance weighting interpolation for streaming sensor data
Liang, Qinghan ; Nittel, Silvia ; Whittier, John C. ; Bruin, Sytze De - \ 2018
Transactions in GIS 22 (2018)5. - ISSN 1361-1682 - p. 1179 - 1204.
With advances in technology and an increasing variety of inexpensive geosensors, environmental monitoring has become increasingly sensor dense and real time. Using sensor data streams enables real‐time applications such as environmental hazard detection, or earthquake, wildfire, or radiation monitoring. In‐depth analysis of such spatial fields is often based on a continuous representation. With very large numbers of concurrent observation streams, novel algorithms are necessary that integrate streams into rasters, or other continuous representations, continuously in real time. In this article, we present an approach leveraging data stream engines (DSEs) to achieve scalable, high‐throughput inverse distance weighting (IDW). In detail, we designed and implemented a novel stream query operator framework that extends general‐purpose DSEs. The proposed framework includes a two‐panel, spatio‐temporal grid‐based index and several algorithms, namely the Shell and k‐Shell algorithms, to estimate individual grid cells efficiently and adaptively for different sampling scenarios. For our performance experiments, we generated several different spatio‐temporal stream data sets based on the radiation deposits in the Fukushima region after the nuclear accident of 2011 in Japan. Our results showed that the k‐Shell algorithm of the proposed framework produces a raster based on 250k observation streams in under 0.5 s using a state‐of‐the‐art workstation.
B Vitamins Can Reduce Body Weight Gain by Increasing Metabolism-related Enzyme Activities in Rats Fed on a High-Fat Diet
Zheng, Ying ; Ma, A. ; Zheng, Ming C. ; Wang, Qiuzhen ; Liang, Hui ; Han, Xiuxia ; Schouten, Evert G. - \ 2018
Current Medical Science 38 (2018)1. - ISSN 2096-5230 - p. 174 - 183.
B vitamins - body weight gain - enzyme activities - obesity - rats

B vitamins are enzyme cofactors that play an important role in energy metabolism. The aim of this study was to elucidate whether B vitamin administration can reduce body weight (BW) gain by improving energy metabolism-related enzyme activities in rats fed on a highfat diet. Fifty rats were randomly assigned to one of the following five groups: control group (C), including rats fed on standard rat chow; four treatment groups (HO, HI, H2, and H3), in which rats were fed on a high-fat diet. Rats in the HI group were treated daily with 100 mg/kg BW thiamine (VB1), 100 mg/kg BW riboflavin (VB2), and 250 mg/kg BW niacin (VPP); rats in the H2 group were treated daily with 100 mg/kg BW pyridoxine (VB6), 100 mg/kg BW cobalamin (VB12), and 5 mg/kg BW folate (FA); and rats in the H3 group were treated daily with all of the B vitamins administered to the HI and H2 groups. After 12 weeks, the BW gains from the initial value were 154.5±58.4 g and 159.1±53.0 g in the HI and C groups, respectively, which were significantly less than the changes in the HO group (285.2±14.8 g, P<0.05). In the HO group, the plasma total cholesterol (CHO) and triglyceride (TG) levels were 1.59±0.30 mmol/L and 1,55±0.40 mmol/L, respectively, which were significantly greater than those in the HI group (1.19±0.18 mmol/L and 0.76±0.34 mmol/L, respectively, P<0.05). The activities of transketolase (TK), glutathione reductase, and Na+/K+ adenosine triphosphatase were significantly increased in the B vitamin-treated groups and were significantly greater than those in the HO group (P<0.05). Furthermore, the glucose-6-phosphate dehydrogenase, pyruvic acid kinase, and succinate dehydrogenase activities also were increased after treatment with B vitamins. Supplementation with B vitamins could effectively reduce BW gain and plasma levels of lipids by improving energy metabolism-related enzyme activities in rats, thus possibly providing potential benefits to humans.

Preface
Liu, Shijun ; Aoyama, Mikio ; Tekinerdogan, Bedir ; Zhang, Liang Jie - \ 2018
In: Edge Computing – EDGE 2018 Springer (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 10973) - ISBN 9783319943398 - p. V - V.
Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis
Griesmann, Maximilian ; Chang, Yue ; Liu, Xin ; Song, Yue ; Haberer, Georg ; Crook, Matthew B. ; Billault-Penneteau, Benjamin ; Lauressergues, Dominique ; Keller, Jean ; Imanishi, Leandro ; Roswanjaya, Yuda Purwana ; Kohlen, Wouter ; Pujic, Petar ; Battenberg, Kai ; Alloisio, Nicole ; Liang, Yuhu ; Hilhorst, Henk ; Salgado, Marco G. ; Hocher, Valerie ; Gherbi, Hassen ; Svistoonoff, Sergio ; Doyle, Jeff J. ; He, Shixu ; Xu, Yan ; Xu, Shanyun ; Qu, Jing ; Gao, Qiang ; Fang, Xiaodong ; Fu, Yuan ; Normand, Philippe ; Berry, Alison M. ; Wall, Luis G. ; Ané, Jean Michel ; Pawlowski, Katharina ; Xu, Xun ; Yang, Huanming ; Spannagl, Manuel ; Mayer, Klaus F.X. ; Wong, Gane Ka Shu ; Parniske, Martin ; Delaux, Pierre Marc ; Cheng, Shifeng - \ 2018
Science 361 (2018)6398. - ISSN 0036-8075 - 18 p.

The root nodule symbiosis of plants with nitrogen-fixing bacteria impacts global nitrogen cycles and food production but is restricted to a subset of genera within a single clade of flowering plants. To explore the genetic basis for this scattered occurrence, we sequenced the genomes of ten plant species covering the diversity of nodule morphotypes, bacterial symbionts and infection strategies. In a genome-wide comparative analysis of a total of 37 plant species, we discovered signatures of multiple independent loss-of-function events in the indispensable symbiotic regulator NODULE INCEPTION (NIN) in ten out of 13 genomes of non-nodulating species within this clade. The discovery that multiple independent losses shaped the present day distribution of nitrogen-fixing root nodule symbiosis in plants reveals a phylogenetically wider distribution in evolutionary history and a so far underestimated selection pressure against this symbiosis.

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