Staff Publications

Staff Publications

  • external user (warningwarning)
  • Log in as
  • language uk
  • About

    '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.

    We have a manual that explains all the features 

Records 1 - 20 / 185

  • help
  • print

    Print search results

  • export

    Export search results

  • alert
    We will mail you new results for this query: q=Gao
Check title to add to marked list
Optimized sowing time windows mitigate climate risks for oats production under cool semi-arid growing conditions
Zhang, Yue ; Zhang, Lizhen ; Yang, Ning ; Huth, Neil ; Wang, Enli ; Werf, Wopke van der; Evers, Jochem B. ; Wang, Qi ; Zhang, Dongsheng ; Wang, Ruonan ; Gao, Hui ; Anten, Niels P.R. - \ 2019
Agricultural and Forest Meteorology 266-267 (2019). - ISSN 0168-1923 - p. 184 - 197.
APSIM-Oats - Climate change - Cumulative probability - Optimal sowing time window - Water limited potential yield - Yield gap

Year to year variability in weather poses serious risks to crop production in the environmentally fragile agro-ecosystems of cool semi-arid areas, and future climate changes might further aggravate those risks. This study aims to quantify the contribution of altered sowing time windows to reduce climate risk for the production of oats (Avena sativa), a crop that is well adapted to short growing seasons and low rainfall. The APSIM-Oats model was calibrated and validated for phenology, above-ground dry matter and yield using data from field experiments with five sowing dates, conducted from 2009 to 2013 in Inner Mongolia, China. The model was used to determine yield trends and yield-limiting factors under rain-fed conditions using historical weather data. Changes in temperature had greater impact on crop production than changes in rainfall and the simulations indicated the importance of changed sowing windows to lengthen the growth duration and optimize water use. Delayed sowing of oats, 10 days later than current practice, ensured more secure temperature and rainfall conditions from emergence to flowering and substantially increased yields and decreased climate risk. Delayed sowing also reduced climate risk under two future climate scenarios, RCP4.5 (stabilize growth) and RCP8.5 (high greenhouse gas emission). We conclude that adaptation of sowing time of oats provides a practical strategy for enhancing yield and mitigating climate risk under climate change.

Effect of fermentation on content, molecule weight distribution and viscosity of β-glucans in oat sourdough
Lu, Jun ; Shan, Lingke ; Xie, Yiting ; Min, Fangfang ; Gao, Jinyan ; Guo, Laichun ; Ren, Changzhong ; Yuan, Juanli ; Gilissen, Luud ; Chen, Hongbing - \ 2018
International Journal of Food Science and Technology (2018). - ISSN 0950-5423
Fermentation - Lactobacillus plantarum - Oat β-glucan - Sourdough - Viscosity

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

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.

Multimodel ensembles improve predictions of crop–environment–management interactions
Wallach, Daniel ; Martre, Pierre ; Liu, Bing ; Asseng, Senthold ; Ewert, Frank ; Thorburn, Peter J. ; Ittersum, Martin van; Aggarwal, Pramod K. ; Ahmed, Mukhtar ; Basso, Bruno ; Biernath, Christian ; Cammarano, Davide ; Challinor, Andrew J. ; Sanctis, Giacomo De; Dumont, Benjamin ; Eyshi Rezaei, Ehsan ; Fereres, Elias ; Fitzgerald, Glenn J. ; Gao, Y. ; Garcia-Vila, Margarita ; Gayler, Sebastian ; Girousse, Christine ; Hoogenboom, Gerrit ; Horan, Heidi ; Izaurralde, Roberto C. ; Jones, Curtis D. ; Kassie, Belay T. ; Kersebaum, Christian C. ; Klein, Christian ; Koehler, Ann Kristin ; Maiorano, Andrea ; Minoli, Sara ; Müller, Christoph ; Naresh Kumar, Soora ; Nendel, Claas ; O'Leary, Garry J. ; Palosuo, Taru ; Priesack, Eckart ; Ripoche, Dominique ; Rötter, Reimund P. ; Semenov, Mikhail A. ; Stöckle, Claudio ; Stratonovitch, Pierre ; Streck, Thilo ; Supit, Iwan ; Tao, Fulu ; Wolf, Joost ; Zhang, Zhao - \ 2018
Global Change Biology 24 (2018)11. - ISSN 1354-1013 - p. 5072 - 5083.
climate change impact - crop models - ensemble mean - ensemble median - multimodel ensemble - prediction

A recent innovation in assessment of climate change impact on agricultural production has been to use crop multimodel ensembles (MMEs). These studies usually find large variability between individual models but that the ensemble mean (e-mean) and median (e-median) often seem to predict quite well. However, few studies have specifically been concerned with the predictive quality of those ensemble predictors. We ask what is the predictive quality of e-mean and e-median, and how does that depend on the ensemble characteristics. Our empirical results are based on five MME studies applied to wheat, using different data sets but the same 25 crop models. We show that the ensemble predictors have quite high skill and are better than most and sometimes all individual models for most groups of environments and most response variables. Mean squared error of e-mean decreases monotonically with the size of the ensemble if models are added at random, but has a minimum at usually 2–6 models if best-fit models are added first. Our theoretical results describe the ensemble using four parameters: average bias, model effect variance, environment effect variance, and interaction variance. We show analytically that mean squared error of prediction (MSEP) of e-mean will always be smaller than MSEP averaged over models and will be less than MSEP of the best model if squared bias is less than the interaction variance. If models are added to the ensemble at random, MSEP of e-mean will decrease as the inverse of ensemble size, with a minimum equal to squared bias plus interaction variance. This minimum value is not necessarily small, and so it is important to evaluate the predictive quality of e-mean for each target population of environments. These results provide new information on the advantages of ensemble predictors, but also show their limitations.

Natural genetic variation in C. elegans identified genomic loci controlling metabolite levels
Gao, Arwen W. ; Sterken, Mark G. ; De Bos, Jelmi Uit; Creij, Jelle van; Kamble, Rashmi ; Snoek, Basten L. ; Kammenga, Jan E. ; Houtkooper, Riekelt H. - \ 2018
Genome Research 28 (2018)8. - ISSN 1088-9051 - p. 1296 - 1308.
Metabolic homeostasis is sustained by complex biological networks that respond to nutrient availability. Genetic and environmental factors may disrupt this equilibrium, leading to metabolic disorders, including obesity and type 2 diabetes. To identify the genetic factors controlling metabolism, we performed quantitative genetic analysis using a population of 199 recombinant inbred lines (RILs) in the nematode Caenorhabditis elegans. We focused on the genomic regions that control metabolite levels by measuring fatty acid (FA) and amino acid (AA) composition in the RILs using targeted metabolomics. The genetically diverse RILs showed a large variation in their FA andAAlevels with a heritability ranging from 32% to 82%. We detected strongly co-correlated metabolite clusters and 36 significant metabolite QTL (mQTL). We focused on mQTL displaying highly significant linkage and heritability, including an mQTL for the FA C14:1 on Chromosome I, and another mQTL for the FA C18:2 on Chromosome IV. Using introgression lines (ILs), we were able to narrow down both mQTL to a 1.4-Mbp and a 3.6-Mbp region, respectively. RNAi-based screening focusing on the Chromosome I mQTL identified several candidate genes for the C14:1 mQTL, including lagr-1, Y87G2A.2, nhr-265, nhr-276, and nhr-81. Overall, this systems
approach provides us with a powerful platform to study the genetic basis of C. elegans metabolism. Furthermore, it allows us to investigate interventions such as nutrients and stresses that maintain or disturb the regulatory network controlling metabolic homeostasis, and identify gene-by-environment interactions.
Natural genetic variation in C. elegans identified genomic loci controlling metabolite levels
Sterken, M.G. ; Gao, Arwen W. ; Bos, Jelmi uit de; Creij, J.W. van; Kamble, Rashmi ; Snoek, L.B. ; Kammenga, J.E. ; Houtkooper, Riekelt H. - \ 2018
Metabolic homeostasis is sustained by complex biological networks responding to nutrient availability. Genetic and/or environmental perturbations can lead to metabolic disorders, including obesity and type-2 diabetes. Model organisms are particularly suited to study the interactions between genetic and environmental factors. Thus far, metabolism in C. elegans was often studied at the transcriptional level opposed to the metabolite level. Using a recently developed metabolomics platform, we were able to measure metabolites in C. elegans on a large scale. Here, we aimed to identify the genetic factors controlling metabolism using the nematode Caenorhabditis elegans.
We used a quantitative genetic approach with a C. elegans population consisting of 199 recombinant inbred lines (RILs). We measured fatty acid (FA) and amino acid (AA) composition in the RILs using targeted metabolomics. We were able to measure the metabolite levels of 56 metabolites. Subsequently, we determined transgression and heritabilities for these metabolites. We found large variation in metabolites levels and for 18 metabolites significant transgression was found, these metabolites were predominantly FAs. The heritability was significant for 51 metabolites and ranged between 32 to 82%. Using a single marker model, we found 36 significant metabolite quantitative trait loci (mQTL). Additionally, a full two-marker screen revealed interacting loci for 6 metabolites. Using introgression lines (ILs) we verified the mQTL for two FA’s, C14:1 and C18:2 mapping to chromosome I and IV respectively. We narrowed down both mQTL to a 1.4 Mbp and a 3.6 Mbp region, respectively. Focussing on the chromosome I mQTL we conducted a prioritized candidate screening, revealing several candidate genes that could affect C14:1 levels across the RILs. By RNAi based knock-down in the N2 strain we could verify that five candidate genes affect C14:1 levels: lagr-1, Y87G2A.2, nhr-265, nhr-276, and nhr-81.
In conclusion, genetic variation affecting metabolite levels in C. elegans proofed to be extensive. Natural variation in C. elegans can play an important role to dissect the mechanisms underlying the complex processes of metabolism in a natural and unbiased manner and allow us to identify factors important for gene-by-environment interactions. Therefore, our study provides the basis to investigate additional interventions, such as nutrients and stresses that maintain or disturb the regulatory network controlling metabolic homeostasis.
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.

Validation of biomarkers of food intake-critical assessment of candidate biomarkers
Dragsted, Lars O. ; Gao, Qinfeng ; Scalbert, Augustin ; Vergères, Guy ; Kolehmainen, Marjukka ; Manach, Claudine ; Brennan, Lorraine ; Afman, L.A. ; Wishart, David S. ; Lacueva, Cristina Andres ; Garcia-Aloy, Mar ; Verhagen, H. ; Feskens, E.J.M. ; Feskens, E.J.M. ; Praticò, Giulia - \ 2018
Genes & Nutrition 13 (2018). - ISSN 1555-8932
Biomarkers of food intake (BFIs) are a promising tool for limiting misclassification in nutrition research where more subjective dietary assessment instruments are used. They may also be used to assess compliance to dietary guidelines or to a dietary intervention. Biomarkers therefore hold promise for direct and objective measurement of food intake. However, the number of comprehensively validated biomarkers of food intake is limited to just a few. Many new candidate biomarkers emerge from metabolic profiling studies and from advances in food chemistry. Furthermore, candidate food intake biomarkers may also be identified based on extensive literature reviews such as described in the guidelines for Biomarker of Food Intake Reviews (BFIRev). To systematically and critically assess the validity of candidate biomarkers of food intake, it is necessary to outline and streamline an optimal and reproducible validation process. A consensus-based procedure was used to provide and evaluate a set of the most important criteria for systematic validation of BFIs. As a result, a validation procedure was developed including eight criteria, plausibility, dose-response, time-response, robustness, reliability, stability, analytical performance, and inter-laboratory reproducibility. The validation has a dual purpose: (1) to estimate the current level of validation of candidate biomarkers of food intake based on an objective and systematic approach and (2) to pinpoint which additional studies are needed to provide full validation of each candidate biomarker of food intake. This position paper on biomarker of food intake validation outlines the second step of the BFIRev procedure but may also be used as such for validation of new candidate biomarkers identified, e.g., in food metabolomic studies.
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.
Guidelines for Biomarker of Food Intake Reviews (BFIRev) : How to conduct an extensive literature search for biomarker of food intake discovery
Praticò, Giulia ; Gao, Qian ; Scalbert, Augustin ; Vergères, Guy ; Kolehmainen, Marjukka ; Manach, Claudine ; Brennan, Lorraine ; Pedapati, Sri Harsha ; Afman, Lydia A. ; Wishart, David S. ; Vázquez-Fresno, Rosa ; Lacueva, Cristina Andres ; Garcia-Aloy, Mar ; Verhagen, Hans ; Feskens, Edith J.M. ; Dragsted, Lars O. - \ 2018
Genes & Nutrition 13 (2018)1. - ISSN 1555-8932
Biomarkers - Food exposure markers - Literature search methodology - Metabolomics - Systematic review
Identification of new biomarkers of food and nutrient intake has developed fast over the past two decades and could potentially provide important new tools for compliance monitoring and dietary intake assessment in nutrition and health science. In recent years, metabolomics has played an important role in identifying a large number of putative biomarkers of food intake (BFIs). However, the large body of scientific literature on potential BFIs outside the metabolomics area should also be taken into account. In particular, we believe that extensive literature reviews should be conducted and that the quality of all suggested biomarkers should be systematically evaluated. In order to cover the literature on BFIs in the most appropriate and consistent manner, there is a need for appropriate guidelines on this topic. These guidelines should build upon guidelines in related areas of science while targeting the special needs of biomarker methodology. This document provides a guideline for conducting an extensive literature search on BFIs, which will provide the basis to systematically validate BFIs. This procedure will help to prioritize future work on the identification of new potential biomarkers and on validating these as well as other biomarker candidates, thereby providing better tools for future studies in nutrition and health.
Recommended strategies for spectral processing and post-processing of 1D 1H-NMR data of biofluids with a particular focus on urine
Emwas, Abdul Hamid ; Saccenti, Edoardo ; Gao, Xin ; McKay, Ryan T. ; Martins dos Santos, Vitor A.P. ; Roy, Raja ; Wishart, David S. - \ 2018
Metabolomics 14 (2018)3. - ISSN 1573-3882
Baseline correction - Data post-processing - Metabolomics - NMR spectroscopy - Normalization - Scaling - Spectral alignment - Spectral binning - Spectral processing - Urine
1H NMR spectra from urine can yield information-rich data sets that offer important insights into many biological and biochemical phenomena. However, the quality and utility of these insights can be profoundly affected by how the NMR spectra are processed and interpreted. For instance, if the NMR spectra are incorrectly referenced or inconsistently aligned, the identification of many compounds will be incorrect. If the NMR spectra are mis-phased or if the baseline correction is flawed, the estimated concentrations of many compounds will be systematically biased. Furthermore, because NMR permits the measurement of concentrations spanning up to five orders of magnitude, several problems can arise with data analysis. For instance, signals originating from the most abundant metabolites may prove to be the least biologically relevant while signals arising from the least abundant metabolites may prove to be the most important but hardest to accurately and precisely measure. As a result, a number of data processing techniques such as scaling, transformation and normalization are often required to address these issues. Therefore, proper processing of NMR data is a critical step to correctly extract useful information in any NMR-based metabolomic study. In this review we highlight the significance, advantages and disadvantages of different NMR spectral processing steps that are common to most NMR-based metabolomic studies of urine. These include: chemical shift referencing, phase and baseline correction, spectral alignment, spectral binning, scaling and normalization. We also provide a set of recommendations for best practices regarding spectral and data processing for NMR-based metabolomic studies of biofluids, with a particular focus on urine.
Modification of chrysanthemum odour and taste with chrysanthemol synthase induces strong dual resistance against cotton aphids
Li, Jinjin ; Delatte, Thierry ; Vervoort, Jacques ; Gao, Liping ; Verstappen, Francel ; Xiong, Wei ; Gan, Jianping ; Jongsma, Maarten A. ; Wang, Caiyun - \ 2018
Plant Biotechnology Journal 16 (2018)8. - ISSN 1467-7644 - p. 1434 - 1445.
Aphid resistance - Chrysanthemol synthase - Chrysanthemum - Double bioactivity - Glycoside - Terpene volatile
Aphids are pests of chrysanthemum that employ plant volatiles to select host plants and ingest cell contents to probe host quality before engaging in prolonged feeding and reproduction. Changes in volatile and nonvolatile metabolite profiles can disrupt aphid-plant interactions and provide new methods of pest control. Chrysanthemol synthase (CHS) from Tanacetum cinerariifolium represents the first committed step in the biosynthesis of pyrethrin ester insecticides, but no biological role for the chrysanthemol product alone has yet been documented. In this study, the TcCHS gene was over-expressed in Chrysanthemum morifolium and resulted in both the emission of volatile chrysanthemol (ca. 47 pmol/h/gFW) and accumulation of a chrysanthemol glycoside derivative, identified by NMR as chrysanthemyl-6-O-malonyl-β-D-glucopyranoside (ca. 1.1 mM), with no detrimental phenotypic effects. Dual-choice assays separately assaying these compounds in pure form and as part of the headspace and extract demonstrated independent bioactivity of both components against the cotton aphid (Aphis gossypii). Performance assays showed that the TcCHS plants significantly reduced aphid reproduction, consistent with disturbance of aphid probing activities on these plants as revealed by electropenetrogram (EPG) studies. In open-field trials, aphid population development was very strongly impaired demonstrating the robustness and high impact of the trait. The results suggest that expression of the TcCHS gene induces a dual defence system, with both repellence by chrysanthemol odour and deterrence by its nonvolatile glycoside, introducing a promising new option for engineering aphid control into plants.
Thermal regime of warm-dry permafrost in relation to ground surface temperature in the Source Areas of the Yangtze and Yellow rivers on the Qinghai-Tibet Plateau, SW China
Luo, Dongliang ; Jin, Huijun ; Wu, Qingbai ; Bense, Victor F. ; He, Ruixia ; Ma, Qiang ; Gao, Shuhui ; Jin, Xiaoying ; Lu¨, Lanzhi - \ 2018
Science of the Total Environment 618 (2018). - ISSN 0048-9697 - p. 1033 - 1045.
Ground surface temperature - Permafrost-climate relationship - Qinghai-Tibet Plateau (QTP) - The source areas of the Yangtze and Yellow rivers (SAYYR) - Warm-dry permafrost
Ecology, hydrology, and natural resources in the source areas of the Yangtze and Yellow rivers (SAYYR) are closely linked to interactions between climate and permafrost. However, a comprehensive study of the interactions is currently hampered by sparsely- and unevenly-distributed monitoring sites and limited field investigations. In this study, the thermal regime of warm-dry permafrost in the SAYYR was systematically analyzed based on extensive data collected during 2010-2016 of air temperature (T a ), ground surface temperature (GST) and ground temperature across a range of areas with contrasting land-surface characteristics. Mean annual T a (MAAT) and mean annual GST (MAGST) were regionally averaged at -3.19±0.71°C and -0.40±1.26°C. There is a close relationship between GST and T a (R 2 =0.8477) as obtained by a linear regression analysis with all available daily averages. The mean annual temperature at the bottom of the active layer (T TOP ) was regionally averaged at -0.72±1.01°C and mostly in the range of -1.0°C and 0°C except at Chalaping (~-2.0°C). Surface offset (MAGST-MAAT) was regionally averaged at 2.54±0.71°C. Thermal offset (T TOP -MAGST) was regionally averaged at -0.17±0.84°C, which was generally within -0.5°C and 0.5°C. Relatively consistent thermal conductivity between the thawed and frozen states of the soils may be responsible for the small thermal offset. Active layer thickness was generally smaller at Chalaping than that on other parts of the QTP, presumably due to smaller climatic continentality index and the thermal dampening of surface temperature variability under the presence of dense vegetation and thick peaty substrates. We conclude that the accurate mapping of permafrost on the rugged elevational QTP could be potentially obtained by correlating the parameters of GST, thermal offset, and temperature gradient in the shallow permafrost.
Nitrogen removal performance and microbial community changes in subsurface wastewater infiltration systems (SWISs) at low temperature with different bioaugmentation strategies
Liu, Chunjing ; Xie, Jianzhi ; Song, Manli ; Gao, Zhiling ; Zheng, Dongxing ; Liu, Xia ; Ning, Guohui ; Cheng, Xu ; Bruning, Harry - \ 2018
Bioresource Technology 250 (2018). - ISSN 0960-8524 - p. 603 - 610.
Aerobic denitrification - Bacterial community structure - Embedding bioaugmentation - Low temperature - Subsurface wastewater infiltration system
Poor nitrogen removal efficiency (mainly nitrate, NO3 −-N) at low temperatures strongly limits application of subsurface wastewater infiltration systems (SWISs). Seven psychrophilic strains (heterotrophic nitrifying bacteria and aerobic denitrifying bacteria) were isolated and added to SWISs to investigate the effect of embedding and direct-dosing bioaugmentation strategies on sewage treatment performance at low temperature. Both bioaugmentation strategies improved ammonium (NH4 +-N) removal efficiencies, and the embedding strategy also exhibited satisfactory NO3 −-N and total nitrogen (TN) removal efficiencies. Pyrosequencing results of the bacterial 16S rRNA gene indicated that the embedding strategy significantly decreased the indigenous soil microbial diversity (p <.05) and altered the bacterial community structure, significantly increasing the relative abundance of Clostridia, which have good nitrate-reducing activity.
Forward and reverse genetics approaches to uncover metabolic aging pathways in Caenorhabditis elegans
Gao, Arwen W. ; Bos, Jelmi uit de; Sterken, Mark G. ; Kammenga, Jan E. ; Smith, Reuben L. ; Houtkooper, Riekelt H. - \ 2018
Biochimica et Biophysica Acta. Molecular Basis of Disease 1864 (2018)9A. - ISSN 0925-4439 - p. 2697 - 2706.
The biological mechanisms of aging have been studied in depth and prominent findings in this field promote the development of new therapies for age-associated disorders. Various model organisms are used for research on aging; among these, the nematode Caenorhabditis elegans has been widely used and has provided valuable knowledge in determining the regulatory mechanisms driving the aging process. Many genes involved in lifespan regulation are associated with metabolic pathways and are influenced by genetic and environmental factors. In line with this, C. elegans provides a promising platform to study such gene by environment interactions, in either a reverse or forward genetics approach. In this review, we discuss longevity mechanisms related to metabolic networks that have been discovered in C. elegans. We also highlight the use of wild populations to study the complex genetic basis of natural variation for quantitative traits that mediate longevity.
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 - \ 2017
S22027 - linkage mapping - physical mapping - 2b-RAD approach - genotyping by sequencing - single nucleotide polymorphism - mating type loci
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.
Higher plasticity in feeding preference of a generalist than a specialist : Experiments with two closely related Helicoverpa species
Wang, Yan ; Ma, Ying ; Zhou, Dong Sheng ; Gao, Su Xia ; Zhao, Xin Cheng ; Tang, Qing Bo ; Wang, Chen Zhu ; Loon, Joop J.A. van - \ 2017
Scientific Reports 7 (2017). - ISSN 2045-2322
Herbivorous insects have been categorized as generalists or specialists depending on the taxonomic relatedness of the plants they use as food or oviposition substrates. The plasticity in host plant selection behavior of species belonging to the two categories received little attention. In the present work, fifth instar caterpillars of the generalist herbivore Helicoverpa armigera and its closely related species, the specialist Helicoverpa assulta, were fed on common host plants or artificial diet, after which their feeding preference was assessed individually by using dual - and triple- plant choice assays. Results show both the two Helicoverpa species have a preference hierarchy for host plants. Compared to the fixed preference hierarchy of the specialist H. assulta, the generalist H. armigera exhibited extensive plasticity in feeding preference depending on the host plant experienced during larval development. Whereas the specialist H. assulta exhibited a rigid preference in both dual and triple-plant choice assays, our findings demonstrate that the generalist H. armigera expressed stronger preferences in the dual-plant choice assay than in the triple-plant choice assay. Our results provide additional evidence supporting the neural constraints hypothesis which predicts that generalist herbivores make less accurate decisions than specialists when selecting plants.
A scheme for a flexible classification of dietary and health biomarkers
Gao, Qian ; Praticò, G. ; Scalbert, A. ; Vergères, Guy ; Kolehmainen, M. ; Manach, Claudine ; Brennan, L. ; Afman, L.A. ; Wishart, D.S. ; Andres-Lacueva, Cristina ; Garcia-Aloy, M. ; Verhagen, H. ; Feskens, E.J.M. ; Dragsted, L.O. - \ 2017
Genes & Nutrition 12 (2017). - ISSN 1555-8932
Biomarkers are an efficient means to examine intakes or exposures and their biological effects and to assess system susceptibility. Aided by novel profiling technologies, the biomarker research field is undergoing rapid development and new putative biomarkers are continuously emerging in the scientific literature. However, the existing concepts for classification of biomarkers in the dietary and health area may be ambiguous, leading to uncertainty about their application. In order to better understand the potential of biomarkers and to communicate their use and application, it is imperative to have a solid scheme for biomarker classification that will provide a well-defined ontology for the field. In this manuscript, we provide an improved scheme for biomarker classification based on their intended use rather than the technology or outcomes (six subclasses are suggested: food compound intake biomarkers (FCIBs), food or food component intake biomarkers (FIBs), dietary pattern biomarkers (DPBs), food compound status biomarkers (FCSBs), effect biomarkers, physiological or health state biomarkers). The application of this scheme is described in detail for the dietary and health area and is compared with previous biomarker classification for this field of research.
Universal Calibration of Computationally Predicted N 1s Binding Energies for Interpretation of XPS Experimental Measurements
Zhao, Jing Hua ; Gao, Fei ; Pujari, Sidharam P. ; Zuilhof, Han ; Teplyakov, Andrew V. - \ 2017
Langmuir 33 (2017)41. - ISSN 0743-7463 - p. 10792 - 10799.
Computationally predicted N 1s core level energies are commonly used to interpret the experimental measurements obtained with X-ray photoelectron spectroscopy. This work compares the application of Koopmans' theorem to core electrons using the B3LYP functional with two commonly used basis sets, analyzes the factors relevant to the comparison of the computational with experimental data, and presents several correlations that allow an accurate prediction of the N 1s binding energy. The first correlation is obtained with a series of known nitrogen-containing functional groups on well-characterized organic monolayers. This approach can then be reliably extended to a number of nitrogen-containing chemical systems on silicon surfaces in which the nature of the chemical environment of nitrogen atoms had only been proposed based on a number of analytical techniques. In most of those cases, the XPS analysis is consistent with the proposed structures, but is not always sufficient for conclusive assignments. Third, it was attempted to also include N-containing systems on metals. Despite the admittedly oversimplified approach taken in this case (the metal surface is approximated by a single atom), the observed correlations are still experimentally useful, although in this case significant outliers are found. Finally, previously published correlations between experimental and theoretical C 1s data were reexamined, yielding a set of correlations that allow experimentalists to predict C 1s and N 1s XPS spectra with high accuracy.
Dietary and health biomarkers-time for an update
Dragsted, L.O. ; Gao Qizian, ; Praticò, G. ; Manach, Claudine ; Wishart, D.S. ; Scalbert, A. ; Feskens, E.J.M. - \ 2017
Genes & Nutrition 12 (2017). - ISSN 1555-8932
In the dietary and health research area, biomarkers are extensively used for multiple purposes. These include biomarkers of dietary intake and nutrient status, biomarkers used to measure the biological effects of specific dietary components, and biomarkers to assess the effects of diet on health. The implementation of biomarkers in nutritional research will be important to improve measurements of dietary intake, exposure to specific dietary components, and of compliance to dietary interventions. Biomarkers could also help with improved characterization of nutritional status in study volunteers and to provide much mechanistic insight into the effects of food components and diets. Although hundreds of papers in nutrition are published annually, there is no current ontology for the area, no generally accepted classification terminology for biomarkers in nutrition and health, no systematic validation scheme for these biomarker classes, and no recent systematic review of all proposed biomarkers for food intake. While advanced databases exist for the human and food metabolomes, additional tools are needed to curate and evaluate current data on dietary and health biomarkers. The Food Biomarkers Alliance (FoodBAll) under the Joint Programming Initiative—A Healthy Diet for a Healthy Life (JPI-HDHL)—is aimed at meeting some of these challenges, identifying new dietary biomarkers, and producing new databases and review papers on biomarkers for nutritional research. This current paper outlines the needs and serves as an introduction to this thematic issue of Genes & Nutrition on dietary and health biomarkers.
Check title to add to marked list
<< previous | next >>

Show 20 50 100 records per page

 
Please log in to use this service. Login as Wageningen University & Research user or guest user in upper right hand corner of this page.