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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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 (2018). - ISSN 1467-7644
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 (2018). - 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.

Auxin transport, metabolism, and signalling during nodule initiation: indeterminate and determinate nodules
Kohlen, W. ; Ng, Jason Liang Pin ; Deinum, E.E. ; Mathesius, Ulrike - \ 2018
Journal of Experimental Botany 69 (2018)2. - ISSN 0022-0957 - p. 229 - 244.
Most legumes can form a unique type of lateral organ on their roots: root nodules. These structures host symbiotic nitrogen-fixing bacteria called rhizobia. Several different types of nodules can be found in nature, but the two best-studied types are called indeterminate and determinate nodules. These two types differ with respect to the presence or absence of a persistent nodule meristem, which consistently correlates with the cortical cell layers giving rise to the nodule primordia. Similar to other plant developmental processes, auxin signalling overlaps with the site of organ initiation and meristem activity. Here, we review how auxin contributes to early nodule development. We focus on changes in auxin transport, signalling, and metabolism during nodule initiation, describing both experimental evidence and computer modelling. We discuss how indeterminate and determinate nodules may differ in their mechanisms for generating localized auxin response maxima and highlight outstanding questions for future research.
Developing a water and nitrogen management model for greenhouse vegetable production in China : Sensitivity analysis and evaluation
Liang, Hao ; Hu, Kelin ; Batchelor, William D. ; Qin, Wei ; Li, Baoguo - \ 2018
Ecological Modelling 367 (2018). - ISSN 0304-3800 - p. 24 - 33.
Auto-calibration - Greenhouse vegetable - Sensitivity analysis - Water and nitrogen management - WHCNS-Veg model
Excessive water and fertilizer inputs have led to a series of environmental problems in vegetable production areas in China. Identifying the fates of water and nutrients is crucial to develop best management strategies in intensive vegetable production systems. The objectives of this study were to (i) develop a scientific water and nitrogen (N) management tool for intensive greenhouse vegetable production in China, and (ii) evaluate the model performance in the simulating the fate of water and N, and vegetable growth under different water and N management practices in China. A vegetable growth component was added to the field soil-crop system model WHCNS (soil Water Heat Carbon Nitrogen Simulator), named WHCNS_Veg. Parameters for the model were estimated and a sensitivity analysis was conducted by coupling the model with the model-independent parameter estimation program (PEST). Data used to test the model came from two years of cucumber and tomato experiments with various water and N combinations in Shandong province, China. The results of sensitivity analysis showed that the soil hydraulic parameters and vegetable genetic parameters had a relatively higher sensitivity compared with those of N transformation parameters. The saturated soil water content had the highest sensitivity among soil hydraulic parameters, and the total available accumulated temperature, crop coefficient and maximum root depth had higher sensitivity for both vegetable crops. Among the N transformation parameters, the parameters related to nitrification had the highest sensitivity. The automatic optimization algorithm performed well in adjusting soil hydraulic parameters, vegetable genetic parameters and N transformation parameters. The normalized root mean square error for soil water content, soil nitrate concentration, marketable fresh yield and vegetable N uptake were 5.7%, 28.0%, 2.7% and 8.3%, respectively, and indices of agreement were 0.727, 0.730, 0.997 and 0.832, respectively. The results indicated that the WHCNS_Veg model has great potential to simulate and analyze water and N fates, and vegetable growth for the intensive greenhouse vegetable production in China.
Data and analysis of diet-induced and obesity-associated alterations of gut microbiota of 129S6/Sv and C57BL/6J mice
Xiao, Liang ; Sonne, Si Brask ; Feng, Qiang ; Chen, Ning ; Xia, Zhongkui ; Li, Xiaoping ; Fang, Zhiwei ; Fjære, Even ; Derrien, M.M.N. ; Hugenholtz, F. ; Kleerebezem, M. - \ 2017
PRJEB10308 - ERP011540 - C57BL/6J mice - 129S6/Sv mice - obesity - high fat feeding - microbiota - indomethacin
High fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice. It is well known that the microbiota of high fat (HF) diet-induced obese mice differs from that of lean mice, but to what extent this difference reflects the obese state or the diet is unclear. To dissociate changes in the gut microbiota associated with high HF feeding from those associated with obesity, we took advantage of the different susceptibility of C57BL/6JBomTac (BL6) and 129S6/SvEvTac (Sv129) mice to diet-induced obesity and of their different responses to inhibition of cyclooxygenase (COX) activity, where inhibition of COX activity in BL6 mice prevents HF diet-induced obesity, but in Sv129 mice accentuates obesity. Using HiSeq-based whole genome sequencing we identified taxonomic and functional differences in the gut microbiota of the two mouse strains fed regular low fat or HF diets with or without supplementation with the COX-inhibitor, indomethacin. Here we present the sequence assemblies and annotations for those 54 samples, together with the gene catalogue and relevative abundance levels of both genes and OTUs. It is hoped these data can be used for comparison in future studies of a similar design.
A microbiomic analysis in African Americans with colonic lesions reveals streptococcus sp.VT162 as a marker of neoplastic transformation
Brim, Hassan ; Yooseph, Shibu ; Lee, Edward ; Sherif, Zaki ; Abbas, Muneer ; Laiyemo, Adeyinka O. ; Varma, Sudhir ; Torralba, Manolito ; Dowd, Scot E. ; Nelson, Karen E. ; Pathmasiri, Wimal ; Sumner, Susan ; Vos, Willem De; Liang, Qiaoyi ; Yu, Jun ; Zoetendal, Erwin ; Ashktorab, Hassan - \ 2017
Genes 8 (2017)11. - ISSN 2073-4425
AfricanAmericans - Colorectal cancer - Metabolomics - Metagenomic linkage groups - Microbiota
Increasing evidence suggests a role of the gut microbiota in colorectal carcinogenesis (CRC). To detect bacterial markers of colorectal cancer in African Americans a metabolomic analysis was performed on fecal water extracts. DNA from stool samples of adenoma and healthy subjects and from colon cancer and matched normal tissues was analyzed to determine the microbiota composition (using 16S rDNA) and genomic content (metagenomics). Metagenomic functions with discriminative power between healthy and neoplastic specimens were established. Quantitative Polymerase Chain Reaction (q-PCR) using primers and probes specific to Streptococcus sp. VT_162 were used to validate this bacterium association with neoplastic transformation in stool samples from two independent cohorts of African Americans and Chinese patients with colorectal lesions. The metabolomic analysis of adenomas revealed low amino acids content. The microbiota in both cancer vs. normal tissues and adenoma vs. normal stool samples were different at the 16S rRNA gene level. Cross-mapping of metagenomic data led to 9 markers with significant discriminative power between normal and diseased specimens. These markers identified with Streptococcus sp. VT_162. Q-PCR data showed a statistically significant presence of this bacterium in advanced adenoma and cancer samples in an independent cohort of CRC patients. We defined metagenomic functions from Streptococcus sp. VT_162 with discriminative power among cancers vs. matched normal and adenomas vs. healthy subjects’ stools. Streptococcus sp. VT_162 specific 16S rDNA was validated in an independent cohort. These findings might facilitate non-invasive screening for colorectal cancer.
Causes of variation among rice models in yield response to CO2 examined with Free-Air CO2 Enrichment and growth chamber experiments
Hasegawa, Toshihiro ; Li, Tao ; Yin, Xinyou ; Zhu, Yan ; Boote, Kenneth ; Baker, Jeffrey ; Bregaglio, Simone ; Buis, Samuel ; Confalonieri, Roberto ; Fugice, Job ; Fumoto, Tamon ; Gaydon, Donald ; Kumar, Soora Naresh ; Lafarge, Tanguy ; Marcaida, Manuel ; Masutomi, Yuji ; Nakagawa, Hiroshi ; Oriol, Philippe ; Ruget, Françoise ; Singh, Upendra ; Tang, Liang ; Tao, Fulu ; Wakatsuki, Hitomi ; Wallach, Daniel ; Wang, Yulong ; Wilson, Lloyd Ted ; Yang, Lianxin ; Yang, Yubin ; Yoshida, Hiroe ; Zhang, Zhao ; Zhu, Jianguo - \ 2017
Scientific Reports 7 (2017). - ISSN 2045-2322 - 13 p.

The CO2 fertilization effect is a major source of uncertainty in crop models for future yield forecasts, but coordinated efforts to determine the mechanisms of this uncertainty have been lacking. Here, we studied causes of uncertainty among 16 crop models in predicting rice yield in response to elevated [CO2] (E-[CO2]) by comparison to free-air CO2 enrichment (FACE) and chamber experiments. The model ensemble reproduced the experimental results well. However, yield prediction in response to E-[CO2] varied significantly among the rice models. The variation was not random: models that overestimated at one experiment simulated greater yield enhancements at the others. The variation was not associated with model structure or magnitude of photosynthetic response to E-[CO2] but was significantly associated with the predictions of leaf area. This suggests that modelled secondary effects of E-[CO2] on morphological development, primarily leaf area, are the sources of model uncertainty. Rice morphological development is conservative to carbon acquisition. Uncertainty will be reduced by incorporating this conservative nature of the morphological response to E-[CO2] into the models. Nitrogen levels, particularly under limited situations, make the prediction more uncertain. Improving models to account for [CO2] × N interactions is necessary to better evaluate management practices under climate change.

Estimation of high-resolution terrestrial evapotranspiration from Landsat data using a simple Taylor skill fusion method
Yao, Yunjun ; Liang, Shunlin ; Li, Xianglan ; Zhang, Yuhu ; Chen, Jiquan ; Jia, Kun ; Zhang, Xiaotong ; Fisher, Joshua B. ; Wang, Xuanyu ; Zhang, Lilin ; Xu, Jia ; Shao, Changliang ; Posse, Gabriela ; Li, Yingnian ; Magliulo, Vincenzo ; Varlagin, Andrej ; Moors, Eddy J. ; Boike, Julia ; Macfarlane, Craig ; Kato, Tomomichi ; Buchmann, Nina ; Billesbach, D.P. ; Beringer, Jason ; Wolf, Sebastian ; Papuga, Shirley A. ; Wohlfahrt, Georg ; Montagnani, Leonardo ; Ardö, Jonas ; Paul-Limoges, Eugénie ; Emmel, Carmen ; Hörtnagl, Lukas ; Sachs, Torsten ; Gruening, Carsten ; Gioli, Beniamino ; López-Ballesteros, Ana ; Steinbrecher, Rainer ; Gielen, Bert - \ 2017
Journal of Hydrology 553 (2017). - ISSN 0022-1694 - p. 508 - 526.
Eddy covariance - Fusion method - High-resolution products - Landsat data - Terrestrial evapotranspiration

Estimation of high-resolution terrestrial evapotranspiration (ET) from Landsat data is important in many climatic, hydrologic, and agricultural applications, as it can help bridging the gap between existing coarse-resolution ET products and point-based field measurements. However, there is large uncertainty among existing ET products from Landsat that limit their application. This study presents a simple Taylor skill fusion (STS) method that merges five Landsat-based ET products and directly measured ET from eddy covariance (EC) to improve the global estimation of terrestrial ET. The STS method uses a weighted average of the individual ET products and weights are determined by their Taylor skill scores (S). The validation with site-scale measurements at 206 EC flux towers showed large differences and uncertainties among the five ET products. The merged ET product exhibited the best performance with a decrease in the averaged root-mean-square error (RMSE) by 2–5 W/m2 when compared to the individual products. To evaluate the reliability of the STS method at the regional scale, the weights of the STS method for these five ET products were determined using EC ground-measurements. An example of regional ET mapping demonstrates that the STS-merged ET can effectively integrate the individual Landsat ET products. Our proposed method provides an improved high-resolution ET product for identifying agricultural crop water consumption and providing a diagnostic assessment for global land surface models.

Response of soil dissolved organic matter to microplastic addition in Chinese loess soil
Liu, Hongfei ; Yang, Xiaomei ; Liu, Guobin ; Liang, Chutao ; Xue, Sha ; Chen, Hao ; Ritsema, Coen J. ; Geissen, Violette - \ 2017
Chemosphere 185 (2017). - ISSN 0045-6535 - p. 907 - 917.
Dissolved organic carbon (DOC) - Dissolved organic nitrogen (DON) - Dissolved organic phosphorus (DOP) - Excitation-emission matrix (EEM) - Microplastic
Plastic debris is accumulating in agricultural land due to the increased use of plastic mulches, which is causing serious environmental problems, especially for biochemical and physical properties of the soil. Dissolved organic matter (DOM) plays a central role in driving soil biogeochemistry, but little information is available on the effects of plastic residues, especially microplastic, on soil DOM. We conducted a soil-incubation experiment in a climate-controlled chamber with three levels of microplastic added to loess soil collected from the Loess Plateau in China: 0% (control, CK), 7% (M1) and 28% (M2) (w/w). We analysed the soil contents of dissolved organic carbon (DOC), dissolved organic nitrogen (DON), NH4 +, NO3 −, dissolved organic phosphorus (DOP), and PO4 3− and the activities of fluorescein diacetate hydrolase (FDAse) and phenol oxidase. The higher level of microplastic addition significantly increased the nutrient contents of the DOM solution. The lower level of addition had no significant effect on the DOM solution during the first seven days, but the rate of DOM decomposition decreased in M1 between days 7 and 30, which increased the nutrient contents. The microplastic facilitated the accumulation of high-molecular-weight humic-like material between days 7 and 30. The DOM solutions were mainly comprised of high-molecular-weight humic-like material in CK and M1 and of high-molecular-weight humic-like material and tyrosine-like material in M2. The Microplastic stimulated the activities of both enzymes. Microplastic addition thus stimulated enzymatic activity, activated pools of organic C, N, and P, and was beneficial for the accumulation of dissolved organic C, N and P.
High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice
Xiao, Liang ; Sonne, Si Brask ; Feng, Qiang ; Chen, Ning ; Xia, Zhongkui ; Li, Xiaoping ; Fang, Zhiwei ; Zhang, Dongya ; Fjære, Even ; Midtbø, Lisa Kolden ; Derrien, Muriel ; Hugenholtz, Floor ; Tang, Longqing ; Li, Junhua ; Zhang, Jianfeng ; Liu, Chuan ; Hao, Qin ; Vogel, Ulla Birgitte ; Mortensen, Alicja ; Kleerebezem, Michiel ; Licht, Tine Rask ; Yang, Huanming ; Wang, Jian ; Li, Yingrui ; Arumugam, Manimozhiyan ; Wang, Jun ; Madsen, Lise ; Kristiansen, Karsten - \ 2017
Microbiome 5 (2017). - ISSN 2049-2618 - p. 43 - 43.
129S6/Sv mice - C57BL/6J mice - High-fat feeding - Indomethacin - Microbiome - Microbiota - Obesity

BACKGROUND: It is well known that the microbiota of high-fat (HF) diet-induced obese mice differs from that of lean mice, but to what extent, this difference reflects the obese state or the diet is unclear. To dissociate changes in the gut microbiota associated with high HF feeding from those associated with obesity, we took advantage of the different susceptibility of C57BL/6JBomTac (BL6) and 129S6/SvEvTac (Sv129) mice to diet-induced obesity and of their different responses to inhibition of cyclooxygenase (COX) activity, where inhibition of COX activity in BL6 mice prevents HF diet-induced obesity, but in Sv129 mice accentuates obesity.

RESULTS: Using HiSeq-based whole genome sequencing, we identified taxonomic and functional differences in the gut microbiota of the two mouse strains fed regular low-fat or HF diets with or without supplementation with the COX-inhibitor, indomethacin. HF feeding rather than obesity development led to distinct changes in the gut microbiota. We observed a robust increase in alpha diversity, gene count, abundance of genera known to be butyrate producers, and abundance of genes involved in butyrate production in Sv129 mice compared to BL6 mice fed either a LF or a HF diet. Conversely, the abundance of genes involved in propionate metabolism, associated with increased energy harvest, was higher in BL6 mice than Sv129 mice.

CONCLUSIONS: The changes in the composition of the gut microbiota were predominantly driven by high-fat feeding rather than reflecting the obese state of the mice. Differences in the abundance of butyrate and propionate producing bacteria in the gut may at least in part contribute to the observed differences in obesity propensity in Sv129 and BL6 mice.

Genome-wide identification, cloning and functional analysis of the Zinc/Iron-regulated transporter-like protein (ZIP) gene family in trifoliate orange (poncirus trifoliata L. Raf.)
Fu, Xing Zheng ; Zhou, Xue ; Xing, Fei ; Ling, Li Li ; Chun, Chang Pin ; Cao, Li ; Aarts, Mark G.M. ; Peng, Liang Zhi - \ 2017
Frontiers in Plant Science 8 (2017). - ISSN 1664-462X
Citrus - Iron deficiency - Yeast complementation - Zinc deficiency - ZIP gene

Zinc (Zn) and iron (Fe) deficiency are widespread among citrus plants, but the molecular mechanisms regarding uptake and transport of these two essential metal ions in citrus are still unclear. In the present study, 12 members of the Zn/Fe-regulated transporter (ZRT/IRT)-related protein (ZIP) gene family were identified and isolated from a widely used citrus rootstock, trifoliate orange (Poncirus trifoliata L. Raf.), and the genes were correspondingly named as PtZIPs according to the sequence and functional similarity to Arabidopsis thaliana ZIPs. The 12 PtZIP genes were predicted to encode proteins of 334-419 amino acids, harboring 6-9 putative transmembrane (TM) domains. All of the PtZIP proteins contained the highly conserved ZIP signature sequences in TM-IV, and nine of them showed a variable region rich in histidine residues between TM-III and TM-IV. Phylogenetic analysis subdivided the PtZIPs into four groups, similar as found for the ZIP family of A. thaliana, with clustered PtZIPs sharing a similar gene structure. Expression analysis showed that the PtZIP genes were very differently induced in roots and leaves under conditions of Zn, Fe and Mn deficiency. Yeast complementation tests indicated that PtIRT1, PtZIP1, PtZIP2, PtZIP3, and PtZIP12 were able to complement the zrt1zrt2 mutant, which was deficient in Zn uptake; PtIRT1 and PtZIP7 were able to complement the fet3fet4 mutant, which was deficient in Fe uptake, and PtIRT1 was able to complement the smf1 mutant, which was deficient in Mn uptake, suggesting their respective functions in Zn, Fe, and Mn transport. The present study broadens our understanding of metal ion uptake and transport and functional divergence of the various PtZIP genes in citrus plants.

Data on the effect of boiling on the organosulfides and the hydrogen sulfide-releasing activity of garlic
Tocmo, Restituto ; Wu, Yuchen ; Liang, Dong ; Fogliano, Vincenzo ; Huang, Dejian - \ 2017
Data in Brief 10 (2017). - ISSN 2352-3409 - p. 221 - 226.

This article contains experimental data on the identification and quantification of the organosulfides on boiled garlic extracts. Data included are related to the research article “Boiling enriches the linear polysulfides and the hydrogen sulfide-releasing activity of garlic” (R. Tocmo, Y. Wu, D. Liang, V. Fogliano, D. Huang, 2016) [1]. Characterization was carried out by GC–MS and HPLC. Dose-response curves obtained from the cell-based H2S-releasing capacity assay of allicin transformation products, namely vinyl dithiins and ajoene are also included. DATS-E values were calculated from these dose-response curves to quantify the contribution of the individual polysulfides to the H2S-releasing capacity of boiled extracts.

Is low serum 25-hydroxyvitamin D a possible link between pulmonary tuberculosis and type 2 diabetes?
Wang, Qiuzhen ; Ma, Aiguo ; Han, Xiuxia ; Zhang, Huizhen ; Zhao, Shanliang ; Liang, Hui ; Cai, Jing ; Kok, Frans J. ; Schouten, Evert G. - \ 2017
Asia Pacific Journal of Clinical Nutrition 26 (2017)2. - ISSN 0964-7058 - p. 241 - 246.
25-hydroxyvitamin D - Body mass index - Link - Pulmonary tuberculosis - Type 2 diabetes
Background and Objectives: Although vitamin D is implicated in the generation of anti-microbial peptide cathelicidin, which plays a key role against pulmonary tuberculosis (PTB), and may have an inverse association with the risk of type 2 diabetes (DM), its role in the co-existence of these two diseases (PTB-DM) is still uncertain. This study explored the association of vitamin D status with prevalent PTB, PTB-DM and DM. Methods and Study Design: We randomly selected 130 PTB patients, 90 PTB-DM, 91 DM and 134 controls. Serum 25(OH)D was determined. A structured questionnaire and anthropometric measurements were administered. Results: Serum 25(OH)D in PTB and PTB-DM were 12.2±2.2 ng/mL and 12.9±2.5 ng/mL, respectively, which were lower than those in DM and control groups. Odds ratios of PTB and PTB-DM comparing extreme quartiles of 25(OH)D (lower than 8.6 ng/mL versus ≥26.6 ng/mL) were 3.26 and 2.27, respectively. These associations remained after adjustment for possible risk factors [OR (95% CI)=4.73 (2.04-10.9) and 2.50 (1.04-6.02), respectively]. A synergistic interaction was observed between low 25(OH)D and underweight in respect to prevalent PTB-DM [OR=24.6 vs 2.50 for lowest quartile of 25(OH) D and 4.59 for underweight]. Conclusions: Odds ratios of low serum 25(OH)D for PTB and PTB-DM were greater than 1.0, and were even much greater when combined with underweight. However, since the association of serum 25(OH)D with PTB was stronger than with PTB-DM, we could not draw the conclusion that vitamin D is a link between PTB and DM.
Organosulphide profile and hydrogen sulphide-releasing activity of garlic fermented by Lactobacillus plantarum
Tocmo, Restituto ; Lai, Abigail Nianci ; Wu, Yuchen ; Liang, Dong ; Fogliano, Vincenzo ; Huang, Dejian - \ 2017
Journal of Functional Foods 30 (2017). - ISSN 1756-4646 - p. 254 - 259.
Diallyl trisulphide - Fermented garlic - Hydrogen sulphide-releasing capacity - Lactobacillus plantarum
Blanched and unblanched garlic were fermented using L. plantarum for investigation of organosulphide profiles, hydrogen sulphide-releasing activity, pH, titratable activity and microbial growth. Both raw and blanched garlic preparations allowed growth of L. plantarum with corresponding lowering of pH below 4.0 and an increase in titratable acidity from an initial value of less 0.05% to 0.3 and 0.5%, respectively. Fermentation, alone, decreased allicin and vinyl dithiins, but increased the concentration of DATS. The H2S-releasing activity, expressed as DATS-E (mmol DATS/g oil), of raw-fermented (2.91) garlic was not significantly different to that of raw (4.74) garlic, but values in blanched (0.41) and blanched-fermented (0.71) samples significantly decreased. Reductions in DATS-E values in blanched and blanched-fermented garlic corresponded well with the negative effect of blanching on the organosulphide concentrations of the products. Fermentation with L. plantarum retains H2S-releasing activity by increasing DATS, despite notable losses in allicin and allicin transformation products.
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