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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Quantitative proteomics reveals the crucial role of YbgC for Salmonella enterica serovar Enteritidis survival in egg white
Qin, Xiaojie ; He, Shoukui ; Zhou, Xiujuan ; Cheng, Xu ; Huang, Xiaozhen ; Wang, Yanyan ; Wang, Siyun ; Cui, Yan ; Shi, Chunlei ; Shi, Xianming - \ 2019
International Journal of Food Microbiology 289 (2019). - ISSN 0168-1605 - p. 115 - 126.
Chicken egg white - iTRAQ - Salmonella - Survival mechanisms - YbgC

Salmonella enterica serovar Enteritidis (S. Enteritidis) is a food-borne bacterial pathogen that can cause human salmonellosis predominately by contamination of eggs and egg products. However, its survival mechanisms in egg white are not fully understood, especially from a proteomic point of view. In this study, the proteomic profiles of S. Enteritidis in Luria-Bertani (LB) broth containing 50% and 80% egg white, and in whole egg white were compared with the profile in LB broth using iTRAQ technology to identify key proteins that were involved in S. Enteritidis survival in egg white. It was found that there were 303, 284 and 273 differentially expressed proteins in S. Enteritidis after 6 h exposure to whole, 80% and 50% egg white, respectively. Most of up-regulated proteins were primarily associated with iron acquisition, cofactor and amino acid biosynthesis, transporter, regulation and stress responses, whereas down-regulated proteins were mainly involved in energy metabolism, virulence as well as motility and chemotaxis. Three stress response-related proteins (YbgC, TolQ, TolA) of the tol-pal system responsible for maintaining cell membrane stability of Gram-negative bacteria were up-regulated in S. Enteritidis in response to whole egg white. Interestingly, deletion of ybgC resulted in a decreased resistance of S. Enteritidis to egg white. Compared with the wild type and complementary strains, a 3-log population reduction was observed in △ybgC mutant strain after incubation in whole egg white for 24 h. Cellular morphology of △ybgC mutant strain was altered from rods to spheres along with cell lysis in whole egg white. Furthermore, deletion of ybgC decreased the expression of tol-pal system-related genes (tolR, tolA). Collectively, these proteomic and mutagenic analysis reveal that YbgC is essential for S. Enteritidis survival in egg white.

DeepGlobe 2018: A Challenge to Parse the Earth through Satellite Images
Demir, I. ; Koperski, K. ; Lindenbaum, D. ; Pang, G. ; Huang, J. ; Basu, S. ; Hughes, F. ; Tuia, D. ; Raska, R. - \ 2018
In: Proceedings 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops CVPRW 2018. - IEEE - ISBN 9781538661017 - p. 17200 - 17209.
We present the DeepGlobe 2018 Satellite Image Understanding Challenge, which includes three public competitions for segmentation, detection, and classification tasks on satellite images (Figure 1). Similar to other challenges in computer vision domain such as DAVIS[21] and COCO[33], DeepGlobe proposes three datasets and corresponding evaluation methodologies, coherently bundled in three competitions with a dedicated workshop co-located with CVPR 2018. We observed that satellite imagery is a rich and structured source of information, yet it is less investigated than everyday images by computer vision researchers. However, bridging modern computer vision with remote sensing data analysis could have critical impact to the way we understand our environment and lead to major breakthroughs in global urban planning or climate change research. Keeping such bridging objective in mind, DeepGlobe aims to bring together researchers from different domains to raise awareness of remote sensing in the computer vision community and vice-versa. We aim to improve and evaluate state-of-the-art satellite image understanding approaches, which can hopefully serve as reference benchmarks for future research in the same topic. In this paper, we analyze characteristics of each dataset, define the evaluation criteria of the competitions, and provide baselines for each task.
Discovery of common and rare genetic risk variants for colorectal cancer
Huyghe, Jeroen R. ; Bien, Stephanie A. ; Harrison, Tabitha A. ; Kang, Hyun Min ; Chen, Sai ; Schmit, Stephanie L. ; Conti, David V. ; Qu, Conghui ; Jeon, Jihyoun ; Edlund, Christopher K. ; Greenside, Peyton ; Wainberg, Michael ; Schumacher, Fredrick R. ; Smith, Joshua D. ; Levine, David M. ; Nelson, Sarah C. ; Sinnott-armstrong, Nasa A. ; Albanes, Demetrius ; Alonso, M.H. ; Anderson, Kristin ; Arnau-Collell, Coral ; Arndt, Volker ; Bamia, Christina ; Banbury, Barbara L. ; Baron, John A. ; Berndt, Sonja I. ; Bézieau, Stéphane ; Bishop, D.T. ; Boehm, Juergen ; Boeing, Heiner ; Brenner, Hermann ; Brezina, Stefanie ; Buch, Stephan ; Buchanan, Daniel D. ; Burnett-hartman, Andrea ; Butterbach, Katja ; Caan, Bette J. ; Campbell, Peter T. ; Carlson, Christopher S. ; Castellví-Bel, Sergi ; Chan, Andrew T. ; Chang-Claude, Jenny ; Chanock, Stephen J. ; Chirlaque, Maria-Dolores ; Cho, Sang Hee ; Connolly, Charles M. ; Cross, Amanda J. ; Feskens, Edith J.M. ; Huang, Wen-Yi ; Li, Li - \ 2018
Nature Genetics (2018). - ISSN 1061-4036
To further dissect the genetic architecture of colorectal cancer (CRC), we performed whole-genome sequencing of 1,439 cases and 720 controls, imputed discovered sequence variants and Haplotype Reference Consortium panel variants into genome-wide association study data, and tested for association in 34,869 cases and 29,051 controls. Findings were followed up in an additional 23,262 cases and 38,296 controls. We discovered a strongly protective 0.3% frequency variant signal at CHD1. In a combined meta-analysis of 125,478 individuals, we identified 40 new independent signals at P < 5 × 10−8, bringing the number of known independent signals for CRC to ~100. New signals implicate lower-frequency variants, Krüppel-like factors, Hedgehog signaling, Hippo-YAP signaling, long noncoding RNAs and somatic drivers, and support a role for immune function. Heritability analyses suggest that CRC risk is highly polygenic, and larger, more comprehensive studies enabling rare variant analysis will improve understanding of biology underlying this risk and influence personalized screening strategies and drug development.
Relationship between socioeconomic status and weight gain during infancy : The BeeBOFT study
Wang, Lu ; Grieken, Amy van; Yang-Huang, Junwen ; Vlasblom, Eline ; L’Hoir, Monique P. ; Boere-Boonekamp, Magda M. ; Raat, Hein - \ 2018
PLoS One 13 (2018)11. - ISSN 1932-6203

Background Increased weight gain during infancy is a risk factor for obesity and related diseases in later life. The aim of the present study was to investigate the association between socioeconomic status (SES) and weight gain during infancy, and to identify the factors mediating the association between SES and infant weight gain. Methods Subjects were 2513 parent-child dyads participating in a cluster randomized controlled intervention study. Family SES was indexed by maternal education level. Weight gain in different time windows (infant age 0–3, 0–6, and 6–12 months) was calculated by subtracting the weight for age z-score (WAZ) between the two time-points. Path analysis was performed to examine the mediating pathways linking SES and infant weight gain. Results On average, infants of low-educated mothers had a lower birth weight and caught-up at approximately 6 months. In the period of 0–6 months, infants with low-educated mothers had an 0.42 (95% CI 0.27–0.57) higher gain in weight for age z-score compared to children with high-educated mothers. The association between maternal education level and increased infant weight gain in the period of 0–6 months can be explained by infant birth weight, gestational age at child birth, duration of breastfeeding, and age at introduction of complementary foods. After adjusting all the mediating factors, there was no association between maternal education level and infant weight gain. Conclusion Infants with lower SES had an increased weight gain during the first 6 months of infancy, and the effect can be explained by infant birth weight, gestational age at child birth, and infant feeding practices.

Modern Magnetic Resonance
Webb, G.A. ; Craik, David J. ; Martin, Gary ; Saito, Hazime ; Standal, Inger B. ; Duynhoven, John van; Aursand, Marit ; Bardet, Michel ; So, Po-Wah ; Utz, Marcel ; Huang, Yining - \ 2018
Springer Science - ISBN 9783319283876
Multidecadal, county-level analysis of the effects of land use, Bt cotton, and weather on cotton pests in China
Zhang, Wei ; Lu, Yanhui ; Werf, Wopke van der; Huang, Jikun ; Wu, Feng ; Zhou, Ke ; Deng, Xiangzheng ; Jiang, Yuying ; Wu, Kongming ; Rosegrant, Mark W. - \ 2018
Proceedings of the National Academy of Sciences of the United States of America 115 (2018)33. - ISSN 0027-8424 - p. E7700 - E7709.
Bt-cotton - Climate change - Insecticide use - Integrated pest management - Land use diversity

Long-term changes in land use, climate, and agricultural technologies may affect pest severity and management. The influences of these major drivers can only be identified by analyzing long-term data. This study examines panel data on land use, adoption of genetically modified Bacillus thuringiensis (Bt) insect-resistant cotton, weather, pest severity, and insecticide use on three major cotton pests for 51 counties in China during 1991–2015. Bt cotton had pervasive effects on the whole pest complex in cotton and its management. Adoption resulted in major reductions in insecticide use for bollworm control. The resulting restoration of aphid biological control decreased aphid severity. However, mirid bugs, which have few effective natural enemies in cotton, increased in severity with warming May and reduced insecticide spraying against bollworm. The effects of landscape on pest severity were pest specific. The severity of cotton aphid and mirid bugs decreased with higher land use diversity, but the severity of highly polyphagous cotton bollworm was unrelated to land use diversity. Shares of forest, water body, and unused land area were negatively associated with the severity of mirid bugs, whereas cotton bollworm responded positively to the shares of water body and unused land area. Farmers sprayed insecticides at mild infestation levels and responded aggressively to severe bollworm outbreaks. Findings support the usefulness of Bt-based plant resistance as a component of integrated pest management (IPM) but highlight the potential for unexpected outcomes resulting from agro-ecosystem feedback loops as well as the importance of climate.

Rethinking care through transnational health and long-term care practices
Ormond, M.E. ; Toyota, Mika - \ 2018
In: Routledge Handbook of Health Geography / Crooks, Valorie, Pearce, Jamie, Andrews, Gavin, London : Routledge - ISBN 9781138098046 - p. 237 - 243.
With more people living longer than ever before, populations’ medical and long-term care needs are increasingly placing strain on individual and collective resources and capacities. National governments are gradually withdrawing from responsibility for direct welfare provision for their citizenries and adopting neoliberal policies that facilitate and expand market-based involvement in health and social care. This has profoundly (re-)structured care relations by (re-)domesticating, individualizing, and commoditizing responsibility (Huang, Thang and Toyota, 2012; Raghuram, Madge and Noxolo, 2009). Yet, while much earlier research focused on this (re-)distribution of care responsibility within countries, a growing literature traces how formal and informal health- and social-care provision extends well beyond the national. The transnational (i.e., spanning of international borders) dimension of health and long-term care has been significantly heightened not only by neoliberal trade policies facilitating transnational flows of people, goods, and services, but also by advancements in communication technologies and biotechnological innovation (Gatrell, 2011; Sparke, 2009).
Uncovering the economic value of natural enemies and true costs of chemical insecticides to cotton farmers in China
Huang, Jikun ; Zhou, Ke ; Zhang, Wei ; Deng, Xiangzheng ; Der Werf, Wopke van; Lu, Yanhui ; Wu, Kongming ; Rosegrant, Mark W. - \ 2018
Environmental Research Letters 13 (2018)6. - ISSN 1748-9318
biological control - economic value - insecticides - natural enemies - smallholder farming

Little empirical evidence on the economic value of biological control of pests at farm level is available to improve economic decision-making by farmers and policy makers. Using insect sampling and household survey in an integrated bio-economic analysis framework, this paper studies farmers' crop management practices in cotton in the North China Plain, and estimates the marginal value of natural enemies and costs of chemical insecticides to farmers. Ladybeetles (mainly Harmonia axyridis, Propylea japonica, and Coccinella septempunctata), the dominant natural enemy group that controls the primary pest (aphid) in cotton in our study area, provide a significant economic benefit that is unknown to the farmers. Even at the current high levels of insecticide use, an additional ladybeetle provides an economic benefit of 0.05 CNY (almost USD 0.01) to farmers. The use of broad-spectrum insecticides by farmers is alarmingly excessive, not only undermining farmers' cotton profitability but also inducing social costs as well as disruption of the natural pest suppression system. Doubling current ladybeetle density in cotton field could gain an estimated USD 300 million for cotton farmers in China, providing a strong economic case for policies to move the pest control system towards a more ecologically-based regime, with positive consequences for farm income and environmental health. With rising use of biological control service provided by natural enemies such as ladybeetles in cotton fields, significant falls in farmers' insecticide use would be expected, which could raise the value of ladybeetles and other natural enemies even further. The results indicate that there is an urgent need to rationalize inputs and move forward to improved agro-ecosystem management in smallholder farming system. Raising knowledge and awareness on the costs and value of biological pest control versus insecticides among farmers and policy makers and having effective extension service, are priorities towards achieving a more ecologically-based approach to crop protection on smallholder farms.

Regulation of myostatin expression is associated with growth and muscle development in commercial broiler and DMC muscle
Dou, Tengfei ; Li, Zhengtian ; Wang, Kun ; Liu, Lixian ; Rong, Hua ; Xu, Zhiqiang ; Huang, Ying ; Gu, Dahai ; Chen, Xiaobo ; Hu, Wenyuan ; Zhang, Jiarong ; Zhao, Sumei ; Jois, Markandeya ; Li, Qihua ; Ge, Changrong ; Pas, Marinus F.W. te; Jia, Junjing - \ 2018
Molecular Biology Reports 45 (2018)4. - ISSN 0301-4851 - p. 511 - 522.
Commercial broiler chicken - Daweishan mini chicken - Growth rate - mRNA expression - Muscle weight - Myostatin
Myostatin is a negative regulator of skeletal muscle growth. Muscle tissue is the largest tissue in the body and influences body growth. Commercial Avian broiler chickens are selected for high growth rate and muscularity. Daweishan mini chickens are a slow growing small-sized chicken breed. We investigated the relations between muscle (breast and leg) myostatin mRNA expression and body and muscle growth. Twenty chickens per breed were slaughtered at 0, 30, 60, 90, 120, and 150 days of age. Body and muscle weights were higher at all times in Avian chickens. Breast muscle myostatin expression was higher in Avian chickens than in Daweishan mini chickens at day 30. Myostatin expression peaked at day 60 in Daweishan mini chickens and expression remained higher in breast muscle. Daweishan mini chickens myostatin expression correlated positively with carcass weight, breast and leg muscle weight from day 0 to 60, and correlated negatively with body weight from day 90 to 150, while myostatin expression in Avian chickens was negatively correlated with carcass and muscle weight from day 90 to 150. The results suggest that myostatin expression is related to regulation of body growth and muscle development, with two different regulatory mechanisms that switch between days 30 and 60.
Improving the energy efficiency of a pilot-scale UASB-digester for low temperature domestic wastewater treatment
Xu, Shengnan ; Zhang, Lei ; Huang, Shengle ; Zeeman, Grietje ; Rijnaarts, Huub ; Liu, Yang - \ 2018
Biochemical Engineering Journal 135 (2018). - ISSN 1369-703X - p. 71 - 78.
Anaerobic domestic wastewater treatment - Energy saving - Low temperature - Methanogenic activity - UASB-digester

A pilot-scale UASB-Settler-Digester (USD) system was utilized to treat raw municipal wastewater collected from a sewer system at 10 °C. During the reactor operation, UASB sludge was continuously transferred from the UASB to a settler; concentrated sludge in the settler was then transferred to a digester operated at 35 °C. The results showed that the settler with a hydraulic retention time (HRT) of 3 h increased UASB sludge chemical oxygen demand (COD) concentration from 14.5 ± 2.5 g/L to 29.9 ± 4.1 g/L. With an HRT of 6 h, the USD system achieved a mean COD removal of 49.2%; and 23.9% influent COD was converted to methane. The specific methanogenic activities at 35 °C of the UASB and the digester sludge were 0.26 and 0.24 g CH4 COD/(g VSS d), respectively, and the stability values were 0.21 and 0.16 g CH4 COD/g COD, respectively. The stability of the settled sludge was similar to that of the recirculated UASB sludge. Compared to a UASB-digester system, the system with an added settler achieved similar COD removal and methane production, but reduced sludge recirculation rate (from 16% to 8% of the influent flow rate), which led to a 50% heating energy saving in the digester of the UASB-digester.

Exploring Future Water Shortage for Large River Basins under Different Water Allocation Strategies
Yan, Dan ; Yao, Mingtian ; Ludwig, Fulco ; Kabat, Pavel ; Huang, He Qing ; Hutjes, Ronald W.A. ; Werners, Saskia E. - \ 2018
Water Resources Management 32 (2018)9. - ISSN 0920-4741 - p. 3071 - 3086.
Climate change - Pearl River basin - Socio-economic development - Water resources allocation - Water shortage
Climate change and socio-economic development increase variations in water availability and water use in the Pearl River Basin (PRB), China. This can potentially result in conflicts over water resources between water users, and cause water shortage in the dry season. To assess and manage water shortage in the PRB, we first explored two water availability and three water use scenarios. Next, four different strategies to allocate water were defined. These water allocation strategies prioritized upstream water use, Pearl River Delta water use, irrigation water use, and manufacturing water use, respectively. The impact of the four strategies on water use and related economic output was assessed under different water availability and water use scenarios. Results show that almost all the regions in the PRB are likely to face water shortage under the four strategies. The increasing water demand contributes twice as much as the decreasing water availability to water shortage. All four water allocation strategies are insufficient to solve the water scarcity in the PRB. The economic losses differ greatly under the four water allocation strategies. Prioritizing the delta region or manufacturing production would result in lower economic losses than the other two strategies. However, all of them are rather extreme strategies. Development of water resources management strategies requires a compromise between different water users.
Selection for growth rate and body size have altered the expression profiles of somatotropic axis genes in chickens
Jia, Junjing ; Ahmed, Irfan ; Liu, Lixian ; Liu, Yong ; Xu, Zhiqiang ; Duan, Xiaohua ; Li, Qihua ; Dou, Tengfei ; Gu, Dahai ; Rong, Hua ; Wang, Kun ; Li, Zhengtian ; Talpur, Mir Zulqarnain ; Huang, Ying ; Wang, Shanrong ; Yan, Shixiong ; Tong, Huiquan ; Zhao, Sumei ; Zhao, Guiping ; Pas, Marinus F.W. te; Su, Zhengchang ; Ge, Changrong - \ 2018
PLoS One 13 (2018)4. - ISSN 1932-6203
The growth hormone / insulin-like growth factor-1 (GH/IGF-1) pathway of the somatotropic axis is the major controller for growth rate and body size in vertebrates, but the effect of selection on the expression of GH/IGF-1 somatotropic axis genes and their association with body size and growth performance in farm animals is not fully understood. We analyzed a time series of expression profiles of GH/IGF-1 somatotropic axis genes in two chicken breeds, the Daweishan mini chickens and Wuding chickens, and the commercial Avian broilers hybrid exhibiting markedly different body sizes and growth rates. We found that growth rate and feed conversion efficiency in Daweishan mini chickens were significantly lower than those in Wuding chickens and Avian broilers. The Wuding and Daweishan mini chickens showed higher levels of plasma GH, pituitary GH mRNA but lower levels of hepatic growth hormone receptor (GHR) mRNA than in Avian broilers. Daweishan mini chickens showed significantly lower levels of plasma IGF-1, thigh muscle and hepatic IGF-1 mRNA than did Avian broilers and Wuding chickens. These results suggest that the GH part of the somatotropic axis is the main regulator of growth rate, while IGF-1 may regulate both growth rate and body weight. Selection for growth performance and body size have altered the expression profiles of somatotropic axis genes in a breed-, age-, and tissue-specific manner, and manner, and alteration of regulatory mechanisms of these genes might play an important role in the developmental characteristics of chickens.
Information with a smile – Does it increase recycling?
Huang, Y.Y. ; Tamas, P.A. ; Harder, M.K. - \ 2018
Journal of Cleaner Production 178 (2018). - ISSN 0959-6526 - p. 947 - 953.
This work investigates the impact of human-human interaction on a target behaviour change by comparing the effect of programme delivery of a fixed set of tailored information via proximate but trivial interaction between subjects and volunteers, a set of well-produced single-topic colour leaflets, and a control on behaviour in a real world setting. The behaviour targeted was householder sorting of food waste into specialised bins in high-rise apartment buildings in Shanghai, China, measured by discreet direct daily weighing of waste fractions. The unit of analysis was the set of households in each building. Two versions of the volunteer delivery were trialled: one neutral in tone and action, and the second slightly positive in tone and action. Despite the existence of tens of theories about behaviour change and hundreds of empirical case studies of pro-environmental behaviour change programs, human-human interaction is not mentioned as a predictor and is only rarely as possibly moderating subsequent conduct. Results suggest that human-human interaction is not likely to be a key explanatory factor but that a positive human-human interaction may be an important factor. Furthermore, these effects were observed when the six social influence mechanisms suggested in current behaviour theory were eliminated, suggesting new mechanisms need to be proposed. For practitioner waste managers the results indicate that funding programmes with human interaction may not be sufficient for greater results: the humans may need training for positive interaction. In addition, the results indicate that currently held opinions by theorists and practitioners on the relative usefulness of tailored information may need revising, since most compound it with human interaction. Explanatory studies are thus called for at programme and individual levels.
Genetically engineering Crambe abyssinica- A potentially high-value oil crop for salt land improvement
Qi, W. ; Tinnenbroek-Capel, I.E.M. ; Salentijn, E.M.J. ; Zhang, Zhao ; Huang, Bangquan ; Cheng, Jihua ; Shao, Hongbo ; Visser, R.G.F. ; Krens, F.A. ; Loo, E.N. van - \ 2018
Land Degradation and Development 29 (2018)4. - ISSN 1085-3278 - p. 1096 - 1106.
Crambe abyssinica (crambe) is a new industrial oil crop that can grow on saline soil and tolerates salty water irrigation. Genetically engineered crambe in which the seed‐oil composition is manipulated for more erucic acid and less polyunsaturated fatty acid (PUFA) would be highly beneficial to industry. In this research, lysophosphatidic acid acyltransferase 2 RNA interference (CaLPAT2‐RNAi) was introduced into the crambe genome to manipulate its oil composition. The result showed in comparison with wild type, CaLPAT2‐RNAi could significantly reduce linoleic and linolenic acid content, simultaneously increasing erucic acid content. Systematic metabolism engineering was then carried out to further study CaLPAT2‐RNAi, combined with the overexpression of Brassica napus fatty acid elongase (BnFAE), Limnanthes douglasii LPAT (LdLPAT), and RNAi of endogenous fatty acid desaturase 2 (CaFAD2‐RNAi). Oil composition analysis on the tranformants' seeds showed that (a) with CaFAD2‐RNAi, PUFA content could be dramatically decreased, in comparison with BnFAE + LdLPAT + CaFAD2‐RNAi, and BnFAE + LdLPAT + CaFAD2‐RNAi + CaLPAT2‐RNAi seeds showed lower linolenic acid content; (b) BnFAE + LdLPAT + CaFAD2‐RNAi + CaLPAT2‐RNAi could increase the erucic acid content in crambe seed oil from less than 66.6% to 71.6%, whereas the highest erucic acid content of BnFAE + LdLPAT + CaFAD2‐RNAi was 79.2%; (c) although the four‐gene combination could not increase the erucic acid content of seed oil to a higher level than the others, it led to increased carbon resource deposited into C22:1 and C18:1 moieties and lower PUFA. Summarily, the present research indicates that suppression of LPAT2 is a new, promising strategy for seed‐oil biosynthesis pathway engineering, which would increase the value of crambe oil.
A genetic linkage map of Pleurotus tuoliensis integrated with physical mapping of the de novo sequenced genome and the mating type loci
Gao, Wei ; Qu, Jibin ; Zhang, Jinxia ; Sonnenberg, A.S.M. ; Chen, Qiang ; Zhang, Yan ; Huang, Chenyang - \ 2018
BMC Genomics 19 (2018). - ISSN 1471-2164
Background Pleurotus tuoliensis (Bailinggu) is a commercially cultivated mushroom species with an increasing popularity in China and other Asian countries. Commercial profits are now low, mainly due to a low yield, long cultivation period and sensitivity to diseases. Breeding efforts are thus required to improve agronomical important traits. Developing saturated genetic linkage and physical maps is a start for applying genetic and molecular approaches to accelerate the precise breeding programs. Results Here we present a genetic linkage map for P. tuoliensis constructed by using 115 haploid monokaryons derived from a hybrid strain H6. One thousand one hundred and eighty-two SNP markers developed by 2b–RAD (type IIB restriction-site associated DNA) approach were mapped to 12 linkage groups. The map covers 1073 cM with an average marker spacing of 1.0 cM. The genome of P. tuoliensis was de novo sequenced as 40.8 Mb and consisted of 500 scaffolds (>500 bp), which showed a high level of colinearity to the genome of P. eryngii var. eryngii. A total of 97.4% SNP markers (1151) were physically localized on 78 scaffolds, and the physical length of these anchored scaffolds were 33.9 Mb representing 83.1% of the whole genome. Mating type loci A and B were mapped on separate linkage groups and identified physically on the assembled genomes. Five putative pheromone receptors and two putative pheromone precursors were identified for the mating type B locus. Conclusions This study reported a first genetic linkage map integrated with physical mapping of the de novo sequenced genome and the mating type loci of an important cultivated mushroom in China, P. tuoliensis. The de novo sequenced and annotated genome, assembled using a 2b–RAD generated linkage map, provides a basis for marker-assisted breeding of this economic important mushroom species.
The Impact of Ecological Construction Programs on Grassland Conservation in Inner Mongolia, China
Liu, Min ; Dries, Liesbeth ; Heijman, Wim ; Huang, Jikun ; Zhu, Xueqin ; Hu, Yuanning ; Chen, Haibin - \ 2018
Land Degradation and Development 29 (2018)2. - ISSN 1085-3278 - p. 326 - 336.
Ecological Construction Programs - fixed effects model - grassland degradation - Inner Mongolia - NDVI
A series of Ecological Construction Programs have been initiated to protect the condition of grasslands in China during recent decades. However, grassland degradation is still severe, and conditions have not been restored as intended. This paper aims to empirically examine the effectiveness of these programs for protecting the grassland condition in the extensive pastoral areas of China. We focus on one major program that has been implemented widely on the grasslands, the Subsidy and Incentive System for Grassland Conservation (SISGC). The normalized difference vegetation index, measured with remote sensing technology, is used to quantify the grassland condition between 2001 and 2014. With data from 54 counties in the pastoral areas of Inner Mongolia, we estimate the impact of SISGC on the grassland condition. A fixed effects model is employed to control for livestock production, climate, time trends, and time-invariant heterogeneity between counties. The model results provide quantitative evidence that the condition of the grasslands has improved significantly because of SISGC; but that the effectiveness of SISGC was offset to some extent by other socio-economic and climate factors, such as increased producer prices and high temperature. This may explain why the actual grassland degradation has not been prevented as effectively as was expected. In addition, the impact of SISGC was stronger in counties with worse initial grassland condition. Furthermore, the effects of producer prices and climate changes were also more pronounced in these counties.
Genome-wide association study in 79,366 European-ancestry individuals informs the genetic architecture of 25-hydroxyvitamin D levels
Jiang, Xia ; O'Reilly, Paul F. ; Aschard, Hugues ; Hsu, Yi Hsiang ; Richards, J.B. ; Dupuis, Josée ; Ingelsson, Erik ; Karasik, David ; Pilz, Stefan ; Berry, Diane ; Kestenbaum, Bryan ; Zheng, Jusheng ; Luan, Jianan ; Sofianopoulou, Eleni ; Streeten, Elizabeth A. ; Albanes, Demetrius ; Lutsey, Pamela L. ; Yao, Lu ; Tang, Weihong ; Econs, Michael J. ; Wallaschofski, Henri ; Völzke, Henry ; Zhou, Ang ; Power, Chris ; McCarthy, Mark I. ; Michos, Erin D. ; Boerwinkle, Eric ; Weinstein, Stephanie J. ; Freedman, Neal D. ; Huang, Wen Yi ; Schoor, Natasja M. van; Velde, Nathalie van der; Groot, Lisette C.P.G.M. de; Enneman, Anke ; Cupples, L.A. ; Booth, Sarah L. ; Vasan, Ramachandran S. ; Liu, Ching Ti ; Zhou, Yanhua ; Ripatti, Samuli ; Ohlsson, Claes ; Vandenput, Liesbeth ; Lorentzon, Mattias ; Eriksson, Johan G. ; Shea, M.K. ; Houston, Denise K. ; Kritchevsky, Stephen B. ; Liu, Yongmei ; Lohman, Kurt K. ; Ferrucci, Luigi ; Peacock, Munro ; Gieger, Christian ; Beekman, Marian ; Slagboom, Eline ; Deelen, Joris ; Deelen, Joris ; Heemst, Diana van; Kleber, Marcus E. ; März, Winfried ; Boer, Ian H. De; Wood, Alexis C. ; Rotter, Jerome I. ; Rich, Stephen S. ; Robinson-Cohen, Cassianne ; Heijer, Martin Den; Jarvelin, Marjo Riitta ; Jarvelin, Marjo Riitta ; Cavadino, Alana ; Cavadino, Alana ; Joshi, Peter K. ; Wilson, James F. ; Hayward, Caroline ; Lind, Lars ; Michaëlsson, Karl ; Trompet, Stella ; Zillikens, M.C. ; Uitterlinden, Andre G. ; Rivadeneira, Fernando - \ 2018
Nature Communications 9 (2018)1. - ISSN 2041-1723
Vitamin D is a steroid hormone precursor that is associated with a range of human traits and diseases. Previous GWAS of serum 25-hydroxyvitamin D concentrations have identified four genome-wide significant loci (GC, NADSYN1/DHCR7, CYP2R1, CYP24A1). In this study, we expand the previous SUNLIGHT Consortium GWAS discovery sample size from 16,125 to 79,366 (all European descent). This larger GWAS yields two additional loci harboring genome-wide significant variants (P = 4.7×10 -9 at rs8018720 in SEC23A, and P = 1.9×10 -14 at rs10745742 in AMDHD1). The overall estimate of heritability of 25-hydroxyvitamin D serum concentrations attributable to GWAS common SNPs is 7.5%, with statistically significant loci explaining 38% of this total. Further investigation identifies signal enrichment in immune and hematopoietic tissues, and clustering with autoimmune diseases in cell-type-specific analysis. Larger studies are required to identify additional common SNPs, and to explore the role of rare or structural variants and gene-gene interactions in the heritability of circulating 25-hydroxyvitamin D levels.
Hydroxy-interlayered minerals in the Holocene paleosol on the southernmost Loess Plateau, China
Huang, Chuan Qin ; Wang, Mi Nan ; Tan, Wen Feng ; Wang, Ming Kuang ; Koopal, Luuk K. - \ 2018
Applied Clay Science 153 (2018). - ISSN 0169-1317 - p. 70 - 77.
Chinese Loess Plateau - Clay minerals - Holocene paleosol - Hydroxy-interlayered minerals - Hydroxy-interlayered vermiculite
The presence and formation of hydroxy-interlayered minerals in the Holocene paleosol at the Wugong profile on the southernmost Chinese Loess Plateau were investigated by examining the < 1 μm and 1–2 μm clay fractions of the 50–150 cm horizon by Fourier-transform infrared spectroscopy (FTIR) and X-ray diffraction (XRD). Prior to the analyses free Al and Fe phases were removed by dithionite-citric-bicarbonate (DCB) extraction. XRD patterns were obtained with air-dried, Mg-saturated, Mg-saturated with glycerol solvation (Mg-glycerol) and K-saturated and heated at 110, 250, 350, 450 and 550 °C samples both before and after hydroxy-interlayered materials removal by sodium citrate extraction. The absorption bands at 3699 and 3430 cm− 1 in the FTIR spectra of both sub-fractions indicated the presence of hydroxy-interlayered minerals. The K-saturated and heated XRD patterns confirmed this by the progressive collapse of the 1.4 nm reflection to a 1.0 nm reflection. After removal of the hydroxy-interlayered materials no obvious increase of the relative XRD intensity of the 1.8 nm reflection in Mg-glycerol pattern was observed and the 1.4 nm reflection exhibited a stronger collapse to 1.0 nm after K-saturation and increasing temperature treatment. This indicated that the hydroxy-interlayered minerals in the Holocene paleosol were mainly composed of hydroxyl-interlayer vermiculite. The hydroxyl-interlayer vermiculite was formed by the polymerization of Al/Fe-hydroxy materials within the interlayer space of vermiculite. Shoulder-like reflection at 1.2 nm in the K-550 °C pattern of the 1–2 μm fraction indicated a higher degree of Al/Fe-hydroxylation in the coarse fraction than in the fine fraction, which was consistent with the lower extractable Al and Fe in the coarse fraction. The reflection at 1.38 nm in the K-550 °C pattern could be interpreted as pedogenic chlorite. Thus, transformation of vermiculite into hydroxy-interlayered vermiculite and finally into a chlorite-like mineral (pedogenic chlorite) has occurred in the Holocene paleosol on the southernmost Chinese Loess Plateau.
More money, better performance? The effects of student loans and need-based grants in China's higher education
Huang, Wei ; Li, Fan ; Liao, Xiaowei ; Hu, Pingping - \ 2018
China Economic Review 51 (2018). - ISSN 1043-951X - p. 208 - 227.
China - Financial aid - Higher education - Need-based grants - Student achievement - Student loans

The goal of this study is to examine the effect of student loans and need-based grants on financially disadvantaged student academic performance in China's higher education. We used a large sampled data from 101 universities to conduct our study. By employing different matching methods, we found that receiving a student loan did not improve student academic performance, but slightly increased students' likelihood of doing a part-time job. Likewise, receiving a need-based grant had no significant effect on student academic performance. We argue that current financial aid programs do not yield any measurable improvement on student performance. Reform and more rigorous evaluations are needed to design an effective financial aid program to promote the development of higher education in China.

The phylogeny of Galerucinae (Coleoptera: Chrysomelidae) and the performance of mitochondrial genomes in phylogenetic inference compared to nuclear rRNA genes
Nie, Rui E. ; Breeschoten, Thijmen ; Timmermans, Martijn J.T.N. ; Nadein, Konstantin ; Xue, Huai Jun ; Bai, Ming ; Huang, Yuan ; Yang, Xing Ke ; Vogler, Alfried P. - \ 2018
Cladistics-The International Journal of the Willi Hennig Society 34 (2018)2. - ISSN 0748-3007 - p. 113 - 130.

With efficient sequencing techniques, full mitochondrial genomes are rapidly replacing other widely used markers, such as the nuclear rRNA genes, for phylogenetic analysis but their power to resolve deep levels of the tree remains controversial. We studied phylogenetic relationships of leaf beetles (Chrysomelidae) in the tribes Galerucini and Alticini (root worms and flea beetles) based on full mitochondrial genomes (103 newly sequenced), and compared their performance to the widely sequenced nuclear rRNA genes (full 18S, partial 28S). Our results show that: (i) the mitogenome is phylogenetically informative from subtribe to family level, and the per-nucleotide contribution to nodal support is higher than that of rRNA genes, (ii) the Galerucini and Alticini are reciprocally monophyletic sister groups, if the classification is adjusted to accommodate several 'problematic genera' that do not fit the dichotomy of lineages based on the presence (Alticini) or absence (Galerucini) of the jumping apparatus, and (iii) the phylogenetic results suggest a new classification system of Galerucini with eight subtribes: Oidina, Galerucina, Hylaspina, Metacyclina, Luperina, Aulacophorina, Diabroticina and Monoleptina.

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