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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The effect of urban 2D and 3D morphology on air temperature in residential neighborhoods
Tian, Yunyu ; Zhou, Weiqi ; Qian, Yuguo ; Zheng, Zhong ; Yan, Jingli - \ 2019
Landscape Ecology 34 (2019)5. - ISSN 0921-2973 - p. 1161 - 1178.
Context: Both urban two-dimensional (2D) and three-dimensional (3D) morphology can affect air and land surface temperature. While many studies have looked at the impact of horizontal morphology, few have explored the relationship between vertical morphology and temperature, especially at the neighborhood scale. Objectives: This study aims to answer two questions: (1) Does air temperature vary in neighborhoods with different morphology? (2) If so, how does the 2D (horizontal) and 3D (vertical) morphology affect air temperature? Methods: We examined the relationship between morphology and air temperature for 24 residential neighborhoods in Beijing, using correlation analysis, regression analysis, and structural equation modeling. Morphological indicators were derived from remotely sensed land cover and light detecting and ranging (LiDAR) point cloud data. Air temperature was continuously measured using HOBO data loggers during the summer of 2014. Results

Nighttime air temperature was higher in neighborhoods dominated by high-rise structures compared to neighborhoods dominated by low-rise structures suggesting that 3D morphology is more important than 2D morphology in predicting air temperature. The ratio of vegetation volume to building volume negatively correlated with average air temperature and daytime temperature, while the mean distance among adjacent buildings had a positive effect. Building height was the most important predictor of nighttime air temperature. The major determinants of air temperature in high-rise and low-rise neighborhoods were different. Conclusions: Both 2D and 3D morphology can affect air temperature in residential neighborhoods. Increasing vegetation volume relative to building volume and decreasing the distance among buildings can reduce daytime air temperatures.
CENTRORADIALIS Interacts with FLOWERING LOCUS T-Like Genes to Control Floret Development and Grain Number
Bi, Xiaojing ; Esse, Wilma van; Mulki, Mohamed Aman ; Kirschner, Gwendolyn ; Zhong, Jinshun ; Simon, Rüdiger ; Korff, Maria von - \ 2019
Plant Physiology 180 (2019)2. - ISSN 0032-0889 - p. 1013 - 1030.

CENTRORADIALIS (CEN) is a key regulator of flowering time and inflorescence architecture in plants. Natural variation in the barley (Hordeum vulgare) homolog HvCEN is important for agricultural range expansion of barley cultivation, but its effects on shoot and spike architecture and consequently yield have not yet been characterized. Here, we evaluated 23 independent hvcen, also termed mat-c, mutants to determine the pleiotropic effects of HvCEN on developmental timing and shoot and spike morphologies of barley under outdoor and controlled conditions. All hvcen mutants flowered early and showed a reduction in spikelet number per spike, tiller number, and yield in the outdoor experiments. Mutations in hvcen accelerated spikelet initiation and reduced axillary bud number in a photoperiod-independent manner but promoted floret development only under long days (LDs). The analysis of a flowering locus t3 (hvft3) hvcen double mutant showed that HvCEN interacts with HvFT3 to control spikelet initiation. Furthermore, early flowering3 (hvelf3) hvcen double mutants with high HvFT1 expression levels under short days suggested that HvCEN interacts with HvFT1 to repress floral development. Global transcriptome profiling in developing shoot apices and inflorescences of mutant and wild-type plants revealed that HvCEN controlled transcripts involved in chromatin remodeling activities, cytokinin and cell cycle regulation and cellular respiration under LDs and short days, whereas HvCEN affected floral homeotic genes only under LDs. Understanding the stage and organ-specific functions of HvCEN and downstream molecular networks will allow the manipulation of different shoot and spike traits and thereby yield.

Convergent xylem widening among organs across diverse woody seedlings
Zhong, Mengying ; Castro-Díez, Pilar ; Puyravaud, Jean Philippe ; Sterck, Frank J. ; Cornelissen, Johannes H.C. - \ 2019
New Phytologist 222 (2019)4. - ISSN 0028-646X - p. 1873 - 1882.
leaf area - organs - plant size - stem height - tissue density - vessel diameter - xylem anatomy

Xylem conduit diameter (D max ) of woody angiosperm adults scales with plant size and widens from the stem apex downwards. We hypothesized that, notwithstanding relative growth rate (RGR), growth form or leaf habit, woody seedling conduit D max scales linearly with plant size across species; this scaling should be applicable to all vegetative organs, with consistent conduit widening from leaf via stem to main root and coupling with whole-leaf area and whole-stem xylem area. To test these hypotheses, organ-specific xylem anatomy traits and size-related traits in laboratory-grown seedlings were analyzed across 55 woody European species from cool-temperate and Mediterranean climates. As hypothesized, conduit D max of each organ showed similar scaling with plant size and consistent basipetal widening from the leaf midvein via the stem to the main root across species, independently of growth form, RGR and leaf habit. We also found a strong correlation between D max and average leaf area, and between stem xylem area and whole-plant leaf area. We conclude that seedlings of ecologically wide-ranging woody species converge in their allometric scaling of conduit diameters within and across plant organs. These relationships will contribute to modeling of water transport in woody vegetation that accounts for the whole life history from the trees’ regeneration phase to adulthood.

Dietary microbial exposure assessment in adults from China and the Netherlands
Zhong, Q. ; Vlieg-Boerstra, Berber ; Helvoort, A. van; Vries, J.H.M. de; Zwietering, M.H. - \ 2018
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.

Vertical coordination and cooperative member benefits : Case studies of four dairy farmers' cooperatives in China
Zhong, Zhen ; Zhang, Chen ; Jia, Fu ; Bijman, Jos - \ 2018
Journal of Cleaner Production 172 (2018). - ISSN 0959-6526 - p. 2266 - 2277.
Agricultural cooperatives - Case studies - China - Dairy industry - Member benefits - Vertical coordination
Agricultural cooperatives have grown exponentially in the past few decades. There is anecdotal evidence showing that vertical coordination of cooperatives with upstream and downstream supply chain bring benefits to cooperative members; however this relationship is far from clear. In particular, the common measurements for member benefits may not accurately represent cooperative practice in the literature. To fill this gap and using an ethnographic multiple case study method, 32 interviews were carried out with four dairy cooperatives in China. It is found that (1) there is a linear relationship between vertical coordination and cooperative performance; (2) Vertical coordination is associated with benefits distribution within the dairy cooperative, showing an inverted U-shaped relationship; (3) Member benefits are a function of both cooperative performance and benefits distribution.
Developing a Research Strategy to Better Understand, Observe, and Simulate Urban Atmospheric Processes at Kilometer to Subkilometer Scales
Barlow, J. ; Best, M. ; Bohnenstengel, S. ; Clark, P. ; Grimmond, S. ; Lean, H. ; Christen, A. ; Emeis, S. ; Haeffelin, M. ; Harman, I.N. ; Lemonsu, A. ; Martilli, A. ; Pardyjak, E. ; Rotach, M.W. ; Ballard, S. ; Boutle, I. ; Brown, A. ; Cai, X. ; Carpentieri, M. ; Coceal, O. ; Crawford, B. ; Sabatino, S. Di; Dou, J. ; Drew, D.R. ; Edwards, J.M. ; Fallmann, J. ; Fortuniak, K. ; Gornall, J. ; Gronemeier, T. ; Halios, C.H. ; Hertwig, D. ; Hirano, K. ; Holtslag, A.A.M. ; Luo, Z. ; Mills, G. ; Nakayoshi, M. ; Pain, K. ; Schlünzen, K.H. ; Smith, S. ; Soulhac, L. ; Steeneveld, G.J. ; Sun, T. ; Theeuwes, N.E. ; Thomson, D. ; Voogt, J.A. ; Ward, H.C. ; Xie, Z.T. ; Zhong, J. - \ 2017
Bulletin of the American Meteorological Society 98 (2017)10. - ISSN 0003-0007 - p. ES261 - ES264.
Erratum to : Performance evaluation of operational atmospheric correction algorithms over the East China Seas (Chinese Journal of Oceanology and Limnology, (2017), 35, 1, (1-22), 10.1007/s00343-016-5170-6)
He, Shuangyan ; He, Mingxia ; Fischer, Jürgen ; Yuan, Dongliang ; Xu, Peng ; Xu, Tengfei ; Yang, Xianping ; Sokoletsky, Leonid ; Wei, Xiaodao ; Shen, Fang ; Zou, Juhong ; Guo, Maohua ; Cui, Songxue ; Zhou, Wu ; Gao, Dalu ; Jin, Guangzhen ; Lü, Xianqing ; Qiu, Fuwen ; Fang, Wendong ; Pan, Aijun ; Cha, Jing ; Zhang, Shanwu ; Huang, Jiang ; Wang, Tao ; Cheng, Yongzhou ; Chen, Xiaoyan ; Liu, Zhaopu ; Long, Xiaohua ; Hou, Zhishuai ; Wen, Haishen ; Li, Jifang ; He, Feng ; Liu, Qun ; Wang, Jinhuan ; Guan, Biao ; Wang, Qinglong ; Shahjahan, Md ; Kabir, Md Farajul ; Sumon, Kizar Ahmed ; Bhowmik, Lipi Rani ; Rashid, Harunur ; Li, Shu ; Yu, Kefu ; Zhao, Jianxin ; Feng, Yuexing ; Chen, Tianran ; Zhou, Shun ; Ren, Yichao ; Pearce, Christopher M. ; Dong, Shuanglin ; Tian, Xiangli ; Gao, Qinfeng ; Wang, Fang ; Liu, Liming ; Du, Rongbin ; Zhang, Xiaoling ; Dong, Shuanglin ; Sun, Shichun ; Feng, Song ; Lin, Jianing ; Sun, Song ; Zhang, Fang ; Zhang, Zhipeng ; Tang, Xuexi ; Tang, Haitian ; Song, Jingjing ; Zhou, Jian ; Liu, Hongjun ; Wang, Qixiang ; Qian, Kuimei ; Liu, Xia ; Chen, Yuwei ; Sun, Chengjun ; Jiang, Fenghua ; Gao, Wei ; Li, Xiaoyun ; Yu, Yanzhen ; Yin, Xiaofei ; Wang, Yong ; Ding, Haibing ; Sun, Zhongmin ; Wang, Yongqiang ; Yan, Pengcheng ; Guo, Hui ; Yao, Jianting ; Tanaka, Jiro ; Kawai, Hiroshi ; Song, Na ; Chen, Muyan ; Gao, Tianxiang ; Yanagimoto, Takashi ; Lu, Xia ; Luan, Sheng ; Kong, Jie ; Hu, Longyang ; Mao, Yong ; Zhong, Shengping ; Liu, Yan ; Zhao, Weihong ; Li, Caiyan ; Miao, Hui - \ 2017
Chinese Journal of Oceanology and Limnology 35 (2017)2. - ISSN 0254-4059 - p. 466 - 467.
Unfortunately for all articles of Vol. 35 No. 1 the future journal title “Journal of Oceanology and Limnology” was used instead of the current journal title “Chinese Journal of Oceanology and Limnology”. All articles in the issue are aff ected. Please make sure to cite the articles with the following Vol. and No. info: Chinese Journal of Oceanology and Limnology, Vol. 35 No. 1, [page range].
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
Jiang, Yuxiang ; Oron, Tal Ronnen ; Clark, Wyatt T. ; Bankapur, Asma R. ; Andrea, Daniel D'; Lepore, Rosalba ; Funk, Christopher S. ; Kahanda, Indika ; Verspoor, Karin M. ; Ben-Hur, Asa ; Koo, Da Chen Emily ; Penfold-Brown, Duncan ; Shasha, Dennis ; Youngs, Noah ; Bonneau, Richard ; Lin, Alexandra ; Sahraeian, Sayed M.E. ; Martelli, Pier Luigi ; Profiti, Giuseppe ; Casadio, Rita ; Cao, Renzhi ; Zhong, Zhaolong ; Cheng, Jianlin ; Altenhoff, Adrian ; Skunca, Nives ; Dessimoz, Christophe ; Dogan, Tunca ; Hakala, Kai ; Kaewphan, Suwisa ; Mehryary, Farrokh ; Salakoski, Tapio ; Ginter, Filip ; Fang, Hai ; Smithers, Ben ; Oates, Matt ; Gough, Julian ; Törönen, Petri ; Koskinen, Patrik ; Holm, Liisa ; Chen, Ching Tai ; Hsu, Wen Lian ; Bryson, Kevin ; Cozzetto, Domenico ; Minneci, Federico ; Jones, David T. ; Chapman, Samuel ; BKC, Dukka ; Khan, Ishita K. ; Kihara, Daisuke ; Ofer, Dan ; Rappoport, Nadav ; Stern, Amos ; Cibrian-Uhalte, Elena ; Denny, Paul ; Foulger, Rebecca E. ; Hieta, Reija ; Legge, Duncan ; Lovering, Ruth C. ; Magrane, Michele ; Melidoni, Anna N. ; Mutowo-Meullenet, Prudence ; Pichler, Klemens ; Shypitsyna, Aleksandra ; Li, Biao ; Zakeri, Pooya ; ElShal, Sarah ; Tranchevent, Léon Charles ; Das, Sayoni ; Dawson, Natalie L. ; Lee, David ; Lees, Jonathan G. ; Sillitoe, Ian ; Bhat, Prajwal ; Nepusz, Tamás ; Romero, Alfonso E. ; Sasidharan, Rajkumar ; Yang, Haixuan ; Paccanaro, Alberto ; Gillis, Jesse ; Sedeño-Cortés, Adriana E. ; Pavlidis, Paul ; Feng, Shou ; Cejuela, Juan M. ; Goldberg, Tatyana ; Hamp, Tobias ; Richter, Lothar ; Salamov, Asaf ; Gabaldon, Toni ; Marcet-Houben, Marina ; Supek, Fran ; Gong, Qingtian ; Ning, Wei ; Zhou, Yuanpeng ; Tian, Weidong ; Falda, Marco ; Fontana, Paolo ; Lavezzo, Enrico ; Toppo, Stefano ; Ferrari, Carlo ; Giollo, Manuel ; Piovesan, Damiano ; Tosatto, Silvio C.E. ; Pozo, Angela del; Fernández, José M. ; Maietta, Paolo ; Valencia, Alfonso ; Tress, Michael L. ; Benso, Alfredo ; Carlo, Stefano Di; Politano, Gianfranco ; Savino, Alessandro ; Rehman, Hafeez Ur ; Re, Matteo ; Mesiti, Marco ; Valentini, Giorgio ; Bargsten, Joachim W. ; Dijk, Aalt-Jan van; Gemovic, Branislava ; Glisic, Sanja ; Perovic, Vladmir ; Veljkovic, Veljko ; Veljkovic, Nevena ; Almeida-e-Silva, Danillo C. ; Vencio, Ricardo Z.N. ; Sharan, Malvika ; Vogel, Jörg ; Kansakar, Lakesh ; Zhang, Shanshan ; Vucetic, Slobodan ; Wang, Zheng ; Sternberg, Michael J.E. ; Wass, Mark N. ; Huntley, Rachael P. ; Martin, Maria J. ; O'Donovan, Claire ; Robinson, Peter N. ; Moreau, Yves ; Tramontano, Anna ; Babbitt, Patricia C. ; Brenner, Steven E. ; Linial, Michal ; Orengo, Christine A. ; Rost, Burkhard ; Greene, Casey S. ; Mooney, Sean D. ; Friedberg, Iddo ; Radivojac, Predrag - \ 2016
Genome Biology 17 (2016)1. - ISSN 1474-7596
Disease gene prioritization - Protein function prediction

Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent.

Regime Shifts and Resilience in Fisheries Management : A Case Study of the Argentinean Hake fishery
Li, Chuan Zhong ; Villasante, Sebastian ; Zhu, Xueqin - \ 2016
Environmental and Resource Economics 65 (2016)3. - ISSN 0924-6460 - p. 623 - 637.
Argentinean hake fishery (Merluccius hubbsi) - Corrective tax - Marine ecosystems - Regime shifts - Resilience

We investigate the role of potential regime shifts in Argentinean hake fishery and the inter-linkage between ecological and economic resilience. We develop a theoretical model incorporated with the hazard function for resource management under alternative conditions, and derive the corrective tax. Applying the model to the case of Argentinean hake fishery, we obtain insights for fishery management in the presence of risk for a regime shift. Based on three value functions, our model simulation indicates that the higher the relative loss from the fishery collapse, the more important the risk management would be with the resilience value taken into account. A higher level of fish stock leads to a higher optimized value and a lower corrective tax rate. When the stock level is lower, we need to introduce a higher tax rate to best avoid the fishery collapse. Decomposing the marginal value of the fish stock into a stock service value for fish production and a resilience value for flip risk reduction, we find that a higher fish stock leads to a lower tax rate because of the higher resilience of the fish stock, and hence the corrective tax rate as an instrument for managing fishery becomes less important.

Genetic diversity of male and female Chinese bayberry (Myrica rubra) populations and identification of sex-associated markers
Jia, Hui Min ; Jiao, Yun ; Wang, Guo Yun ; Li, Ying Hui ; Jia, Hui Juan ; Wu, Hong Xia ; Chai, Chun Yan ; Dong, Xiao ; Guo, Yanping ; Zhang, Liping ; Gao, Qi Kang ; Chen, Wei ; Song, Li Juan ; Weg, Eric van de; Gao, Zhong Shan - \ 2015
BMC Genomics 16 (2015). - ISSN 1471-2164

Background: Chinese bayberry (Myrica rubra Sieb. & Zucc.) is an important subtropical evergreen fruit tree in southern China. Generally dioecious, the female plants are cultivated for fruit and have been studied extensively, but male plants have received very little attention. Knowledge of males may have a major impact on conservation and genetic improvement as well as on breeding. Using 84 polymorphic SSRs, we genotyped 213 M. rubra individuals (99 male individuals, 113 female varieties and 1 monoecious) and compared the difference in genetic diversity between the female and the male populations. Results: Neighbour-joining cluster analysis separated M. rubra from three related species, and the male from female populations within M. rubra. By structure analysis, 178 M. rubra accessions were assigned to two subpopulations: Male dominated (98) and Female dominated (80). The well-known cultivars 'Biqi' and 'Dongkui', and the landraces 'Fenhong' are derived from three different gene pools. Female population had a slightly higher values of genetic diversity parameters (such as number of alleles and heterozygosity) than the male population, but not significantly different. The SSR loci ZJU062 and ZJU130 showed an empirical Fst value of 0.455 and 0.333, respectively, which are significantly above the 95 % confidence level, indicating that they are outlier loci related to sex separation. Conclusion: The male and female populations of Chinese bayberry have similar genetic diversity in terms of average number of alleles and level of heterozygosity, but were clearly separated by genetic structure analysis due to two markers associated with sex type, ZJU062 and ZJU130. Zhejiang Province China could be the centre of diversity of M. rubra in China, with wide genetic diversity coverage; and the two representative cultivars 'Biqi' and 'Dongkui', and one landrace 'Fenhong' in three female subpopulations. This research provides genetic information on male and female Chinese bayberry and will act as a reference for breeding programs.

1H NMR-based metabolomics approach for understanding the fermentation behaviour of Bacillus licheniformis
Yan, Zheng ; Zheng, Xiaowei ; Han, Bei Zhong ; Yan, Yin Zhuo ; Zhang, Xin ; Chen, Jing Yu - \ 2015
Journal of the Institute of Brewing 121 (2015)3. - ISSN 0046-9750 - p. 425 - 431.
<sup>1</sup>H NMR - Bacillus licheniformis - Daqu - Fermentation - Metabolic profile

Bacillus licheniformis has been found to be one of the persistent dominant microorganisms in Daqu, which is a traditional fermentation starter, and it has been used to intensify certain strains. To understand the impact of B. licheniformis on Daqu, the fermentation behaviour of B. licheniformis was studied using 1H NMR-based non-targeted analysis and principal component analysis. During the fermentation, 53 compounds were identified. Among them, seven compounds were largely consumed and 17 metabolites were largely accumulated. The macromolecular starch and cellulose were degraded by B. licheniformis, and then utilized to produce acetic acid, lactic acid, propionic acid, succinate acid, etc. Principal component analysis was carried out to study the variations of analytes during the fermentation. Samples collected at each time point could be clearly discriminated and the biomarkers of each time point were defined. A variety of biochemical compounds (such as acetate, ethanol, lactate, pyruvate, malate, maltose and sucrose) were changed during the fermentation of B. licheniformis. The results are useful to reveal how and why B. licheniformis becomes dominant in Daqu, and to reveal its impact on the aroma formation of Daqu and its derived products.

Growth regulation, imprinting, and epigenetic transcription-related gene expression differs in lung of deceased transgenic cloned and normal goats
Meng, L. ; Jia, R.X. ; Sun, Y. ; Wang, Z.Y. ; Wan, Y.J. ; Zhang, Y.L. ; Zhong, B.S. ; Wang, F. - \ 2014
Theriogenology 81 (2014)3. - ISSN 0093-691X - p. 459 - 466.
cell nuclear transfer - dna methylation - nationwide survey - tumor-suppressor - bovine clones - aberrant - calves - mice - cdkn1c - cattle
Somatic cell nuclear transfer (SCNT) is a promising technique to produce mammalian transgenic clones. Only a small proportion of manipulated embryos, however, can develop into viable offspring. The abnormal growth and development of cloned animals, furthermore, are accompanied by aberrant lung development. Our objective was to investigate molecular background of lung developmental problems in transgenic (random insertion of exogenous DNA) cloned goats. We examined expression of 15 genes involved in growth regulation, imprinting, and epigenetic transcription in lung tissue of deceased transgenic cloned and normal goats of various ages. Compared with normal goats of the same age from conventional reproduction, expression of 13 genes (BMP4, FGF10, GHR, HGFR, PDGFR, RABP, VEGF, H19, CDKNIC, PCAF, MeCP2, HDAC1, and Dnmt3b) decreased in transgenic cloned goats that died at or shortly after birth; Expression of eight genes (FGF10, PDGFR, RABP, VEGF, PCAF, HDAC1, MeCP2, and Dnmt3b) decreased in fetal death of transgenic cloned goats. Expression of two epigenetic transcription genes (PCAF and Dnmt3b) decreased in disease death of transgenic cloned goats (1-4 months old). Disruptions in gene expression might be associated with the high neonatal mortality in transgenic cloned animals. These findings have implications in understanding the low efficiency of transgenic cloning. (C) 2014 Elsevier Inc. All rights reserved.
An integrated catalog of reference genes in the human gut microbiome
Li, J. ; Jia, H. ; Cai, X. ; Zhong, H. ; Feng, Q. ; Sunagawa, S. ; Arumugam, M. ; Kultima, J.R. ; Prifti, E. ; Nielsen, T. ; Juncker, A.S. ; Manichanh, C. ; Chen, B. ; Zhang, W. ; Levenez, F. ; Xu, X. ; Xiao, L. ; Liang, S. ; Zhang, D. ; Zhang, Z. ; Chen, W. ; Zhao, H. ; Al-Aama, J.Y. ; Edris, S. ; Yang, H. ; Hansen, H. ; Nielsen, H.B. ; Brunak, S. ; Kristiansen, K. ; Guarner, F. ; Pedersen, O. ; Doré, J. ; Ehrlich, S.D. ; Bork, P. ; Wang, J. ; Vos, W.M. de; Tims, S. ; Zoetendal, E.G. ; Kleerebezem, M. - \ 2014
Nature Biotechnology 32 (2014)8. - ISSN 1087-0156 - p. 834 - 841.
eukaryotic diversity - fecal microbiota - population-size - metagenome - sequences - genomes - tool - alignment - impact - twins
Many analyses of the human gut microbiome depend on a catalog of reference genes. Existing catalogs for the human gut microbiome are based on samples from single cohorts or on reference genomes or protein sequences, which limits coverage of global microbiome diversity. Here we combined 249 newly sequenced samples of the Metagenomics of the Human Intestinal Tract (MetaHit) project with 1,018 previously sequenced samples to create a cohort from three continents that is at least threefold larger than cohorts used for previous gene catalogs. From this we established the integrated gene catalog (IGC) comprising 9,879,896 genes. The catalog includes close-to-complete sets of genes for most gut microbes, which are also of considerably higher quality than in previous catalogs. Analyses of a group of samples from Chinese and Danish individuals using the catalog revealed country-specific gut microbial signatures. This expanded catalog should facilitate quantitative characterization of metagenomic, metatranscriptomic and metaproteomic data from the gut microbiome to understand its variation across populations in human health and disease.
What are the socio-economic impacts of genetically modified crops worldwide? A systematic map protocol
Garcia-Yi, J. ; Lapikanonth, T. ; Vionita, H. ; Vu, H. ; Yang, S. ; Zhong, Y. ; Li, Y. ; Nagelschneider, V. ; Schlindwein, B. ; Wesseler, J.H.H. - \ 2014
Environmental Evidence 3 (2014). - ISSN 2047-2382 - 35 p.
Genetically modified (GM) crops have generated a great deal of controversy. Since commercially introduced to farmers in 1996, the global area cultivated with GM crops has increased 94-fold. The rapid adoption of GM technology has had substantial socio-economic impacts which a vast amount of technical and non-technical literature has addressed in the last two decades. However, contradictory results between individual studies abound. Extensive and transparent reviews concerning this contentious and complex issue could help promote evidence-based dialogue among the diverse parties involved. This protocol specifies the methodology for identifying, evaluating, and mapping evidence related to the main review question: what are the socio-economic impacts of genetically modified crops worldwide? This question has been subdivided into the following topics: (a) farm-level impacts; (b) impacts of coexistence regulations; (c) impacts along the supply chain; (d) consumer-level impacts; (e) impacts on food security; and (f) environmental economic impacts. The search strategy includes the identification of primary studies from general scientific databases; global, regional, and national specialist databases; an on-line search engine; institutional websites; journal websites; subject experts/researchers; and serendipity. Searches will be conducted in six languages (Chinese, English, French, German, Portuguese, and Spanish). Identified studies will be screened for inclusion/exclusion criteria by a group of multi-language reviewers. Finally, pre-defined data from the studies will be extracted, mapped, and presented in a report. Potential research gaps will be identified and discussed, and the review process will be documented in an open-access database (i.e. CADIMA, http://www.cadima.info/).
Multidisciplinary approaches to allergies
Gilissen, L.J.W.J. ; Frewer, L.J. ; Zhong-Shan, G. - \ 2013
Food Science & Technology (IFST) 27 (2013)2. - ISSN 1475-3324 - p. 27 - 30.
Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi
Ohm, R.A. ; Feau, N. ; Henrissat, B. ; Schoch, C.L. ; Horwitz, B.A. ; Bradshaw, R.E. ; Ciuffetti, L. ; Hamelin, R.C. ; Kema, G.H.J. ; Lawrence, C. ; Scott, J.A. ; Spatafora, J.W. ; Turgeon, B.G. ; Wit, P.J.G.M. de; Zhong, S. ; Goodwin, S.B. ; Grigoriev, I.V. - \ 2013
In: Book of Abstracts 27th Fungal Genetics Conference, Asilomar, Pacific Grove, California, USA, 12-17 March 2013. - - p. 203 - 203.
The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than 280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appears to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, the Capnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, including oxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting a possible function in response to oxidative stress.
Bending in cut Gerbera jamesonii flowers relates to adverse water relations and lack of stem sclerenchyma development, not to expansion of the stem central cavity or stem elongation
Perik, R.R.J. ; Raze, D. ; Harkema, H. ; Zhong, Y. ; Doorn, W.G. van - \ 2012
Postharvest Biology and Technology 74 (2012). - ISSN 0925-5214 - p. 11 - 18.
keeping-quality - bacteria
We studied stem bending in cut Gerbera flowers (Gerbera jamesonii cv. Tamara). Bending might be due to turgor loss. During vase life water uptake decreased more rapidly than transpiration, hence the flowers lost water. Net water loss did not occur in the floral head, but was found in the stem. It was largest in the segment (10-15 cm below the floral head) where bending was localised. When comparing flowers that showed stem bending with those that did not, on day 7 of vase life, the fresh weight loss of 5 cm stem segments was higher in the stems that had bent. Covering the stems with a flexible, thin sleeve of polypropylene plastic reduced transpiration and increased the time to stem bending from d 7 to d 14 of vase life. Additionally, stem bending might relate to stem elongation and to stem morphology and anatomy. Stems elongated by 1-1.5 cm, in the uppermost 10 cm, during the first two days of vase life. No relationship was found between stem elongation and bending. At harvest, the stems contained a large central cavity, starting at about 5 cm from the root-shoot junction, and ending about 10 cm below the floral head. The cavity extended upwards and laterally during vase life, but no relationship was found between cavity formation and stem bending. A cylinder of sclerenchyma in the stems was found to end about 20 cm below the floral head, in summer. Bending was correlated with the extent of sclerenchyma formation and stem lignin levels. It is concluded that stem bending is due to net water loss from the stem. particularly in the area of bending, and to low mechanical strength in the upper part of the stems, which lack a sclerenchyma cylinder.
Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi
Ohm, R.A. ; Feau, N. ; Henrissat, B. ; Schoch, C.L. ; Horwitz, B.A. ; Barry, K.W. ; Condon, B.J. ; Copeland, A.C. ; Dhillon, B. ; Glaser, F. ; Hesse, C.N. ; Kosti, I. ; LaButti, K. ; Lindquist, E.A. ; Lucas, S. ; Salamov, A.A. ; Bradshaw, R.E. ; Ciuffetti, L. ; Hamelin, R.C. ; Kema, G.H.J. ; Lawrence, C. ; Scott, J.A. ; Spatafora, J.W. ; Turgeon, B.G. ; Wit, P.J.G.M. de; Zhong, S. ; Goodwin, S.B. ; Grigoriev, I.V. - \ 2012
PLoS Pathogens 8 (2012)12. - ISSN 1553-7366
ascomycete leptosphaeria-maculans - nonribosomal peptide synthetases - induced point mutations - polyketide synthase - cochliobolus-heterostrophus - colletotrichum-graminicola - fusarium-graminearum - stagonospora-nodorum - phylogenetic trees - neurospora-crassa
The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than 280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appears to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, the Capnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, including oxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting a possible function in response to oxidative stress.
Integrating and Prioritizing Environmental Risks in China's Risk Management Discourse
Zhang, L. ; Zhong, L. - \ 2010
Journal of Contemporary China 19 (2010)63. - ISSN 1067-0564 - p. 119 - 136.
Human society faces a growing number of risks, including both natural disasters and risks that stem from human behavior. This is particularly true in China, which is experiencing rapid social, economic and political transitions. Since the 1970s, China's modernization process has been accompanied by the emergence of an increasing number of man-made risks, in particular environmental pollution, but until very recently, a risk management system did not exist in China. Society was woken up by a series of disasters and accidents, including SARS in 2003, followed by the explosion of avian flu and the chemical spill in the Songhua River in 2005. The last incident in particular finally kicked off the development of a national risk management system (specifically an emergency response system) in China. This paper analyses the status quo of the legislation, institutions and mechanisms for risk management in China and identifies opportunities and strategies for prioritizing and integrating environmental and health risks into the emerging system. The study concludes that although a series of alarming incidents have succeeded in putting risk management issues at the top of the public and political agenda, currently risk management in China can be characterized as reactive and compartmentalized, with a lack of prioritization and integration of policy efforts and resources. There is also a danger that the traditional state-centered approach may fail to create an effective risk management system, which requires improved transparency, accountability, and cross-sectoral coordination. The paper concludes with the proposal of strategies that might enable the environmental authorities to be more effective and reduce their marginalization and isolation.
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