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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    Metabolomics of Milk Reflects a Negative Energy Balance in Cows
    Xu, Wei ; Knegsel, Ariette Van; Saccenti, Edoardo ; Hoeij, Renny Van; Kemp, Bas ; Vervoort, Jacques - \ 2020
    Journal of Proteome Research 19 (2020)8. - ISSN 1535-3893 - p. 2942 - 2949.
    energy balance - integrated analysis - LC-MS - metabolic status - metabolomics - milk - NMR

    Dairy cows can experience a negative energy balance (NEB) in early lactation when feed intake is too low to meet the energy requirements for body maintenance and milk production. Metabolic changes occur in mammary gland cells of animals experiencing a negative energy balance. We studied these metabolic changes in milk samples from dairy cows in relation to energy balance status using liquid chromatography-mass spectrometry (QQQ-LC-MS) and nuclear magnetic resonance (1H NMR). NMR and LC-MS techniques are complementary techniques that enabled a comprehensive overview of milk metabolites in our study. Energy balance and milk samples were obtained from 87 dairy cows. A total of 55 milk metabolites were reliably detected, of which 15 metabolites were positively correlated to energy balance and 20 were negatively correlated to energy balance. Cows in NEB produced more milk with increased milk fat yield and higher concentrations of citrate, cis-aconitate, creatinine, glycine, phosphocreatine, galactose-1-phosphate, glucose-1-phosphate, UDP-N-acetyl-galactosamine, UDP-N-acetyl-glucosamine, and phosphocholine but lower concentrations of choline, ethanolamine, fucose, N-acetyl-neuraminic acid, N-acetyl-glucosamine, and N-acetyl-galactosamine. During NEB, we observed an increased leakage of cellular content, increased synthesis of nucleic acids and cell membrane phospholipids, an increase in one-carbon metabolic processes, and an increase in lipid-triglyceride anabolism. Overall, both apoptosis combined with cellular renewal is paramount in the mammary gland in cows in NEB.

    Towards a comprehensive and consistent global aquatic land cover characterization framework addressing multiple user needs
    Xu, Panpan ; Herold, Martin ; Tsendbazar, Nandin Erdene ; Clevers, Jan G.P.W. - \ 2020
    Remote Sensing of Environment 250 (2020). - ISSN 0034-4257
    Aquatic land cover monitoring - Characterization framework - Global aquatic land cover dataset - LCCS - User needs

    Aquatic land cover represents the land cover type that is significantly influenced by the presence of water over an extensive part of a year. Monitoring global aquatic land cover types plays an essential role in preserving aquatic ecosystems and maintaining the ecosystem service they provide for humans, while at the same time their accurate and consistent monitoring for multiple purposes (e.g. climate modelling, biodiversity conservation, water resource management) remains challenging. Although a number of global aquatic land cover (GALC) datasets are available for use to monitor aquatic ecosystems, there are prominent variabilities among these datasets, which is primarily caused by the inconsistency between different land versus water-related monitoring approaches and characterization schemes. As aquatic land cover exists in many different forms on Earth (e.g. wetland, open water) and can be mapped by different approaches, it is necessary to consider a much more consistent and comprehensive characterization framework that not only ensures the consistency in the monitoring of aquatic land cover but also serves the needs of multiple users (e.g. climate users, agricultural users) interested in different aspects of aquatic lands. In this study, we addressed this issue by 1) reviewing 33 GALC datasets and user needs identified from the citing papers of current datasets and international conventions, policies and agreements in relation to aquatic ecosystems, 2) proposing a global characterization framework for aquatic land cover based on the Land Cover Classification System (LCCS) classifier principles and the identified user needs, and 3) highlighting the opportunities and challenges provided by remote sensing techniques for the implementation of the proposed framework. Results show that users require or prefer various kinds of information on aquatic types including vegetation type, water persistence, the artificiality of cover (i.e. artificial vs natural), water salinity, and the accessibility to the sea (i.e. coastal vs inland). Datasets with medium to high spatial resolution, intra-annual dynamics and inter-annual changes are needed by many users. However, none of the existing datasets can meet all these requirements and a rigorous quantitative accuracy assessment is lacking to evaluate its quality for most of the GALC datasets. The proposed framework has three levels and users are allowed to derive their aquatic land cover types of interest by combining different levels and classifiers of information. This comprehensive mapping framework can help to bridge the gap between user needs and current GALC datasets as well as the gap between generic and aquatic land cover monitoring. The implementation of the framework can benefit from evolving satellite-data availability, improved computation capability and open-source machine learning algorithms, although at the same time it faces challenges mainly coming from the complexity of aquatic ecosystems. The framework proposed in this study provides insights for future operational aquatic land cover monitoring initiatives and will support better understanding and monitoring of complex aquatic ecosystems.

    Quantitative comparison between the rhizosphere effect of Arabidopsis thaliana and co-occurring plant species with a longer life history
    Schneijderberg, Martinus ; Cheng, Xu ; Franken, Carolien ; Hollander, Mattias de; Velzen, Robin van; Schmitz, Lucas ; Heinen, Robin ; Geurts, Rene ; Putten, Wim H. van der; Bezemer, Martijn T. ; Bisseling, Ton - \ 2020
    ISME Journal (2020). - ISSN 1751-7362

    As a model for genetic studies, Arabidopsis thaliana (Arabidopsis) offers great potential to unravel plant genome-related mechanisms that shape the root microbiome. However, the fugitive life history of this species might have evolved at the expense of investing in capacity to steer an extensive rhizosphere effect. To determine whether the rhizosphere effect of Arabidopsis is different from other plant species that have a less fugitive life history, we compared the root microbiome of Arabidopsis to eight other, later succession plant species from the same habitat. The study included molecular analysis of soil, rhizosphere, and endorhizosphere microbiome both from the field and from a laboratory experiment. Molecular analysis revealed that the rhizosphere effect (as quantified by the number of enriched and depleted bacterial taxa) was ~35% lower than the average of the other eight species. Nevertheless, there are numerous microbial taxa differentially abundant between soil and rhizosphere, and they represent for a large part the rhizosphere effects of the other plants. In the case of fungal taxa, the number of differentially abundant taxa in the Arabidopsis rhizosphere is 10% of the other species’ average. In the plant endorhizosphere, which is generally more selective, the rhizosphere effect of Arabidopsis is comparable to other species, both for bacterial and fungal taxa. Taken together, our data imply that the rhizosphere effect of the Arabidopsis is smaller in the rhizosphere, but equal in the endorhizosphere when compared to plant species with a less fugitive life history.

    Chemical structure predicts the effect of plant‐derived low molecular weight compounds on soil microbiome structure and pathogen suppression
    Gu, Yian ; Wang, Xiaofang ; Yang, Tianjie ; Friman, Ville Petri ; Geisen, Stefan ; Wei, Zhong ; Xu, Yangchun ; Jousset, Alexandre ; Shen, Qirong - \ 2020
    Functional Ecology (2020). - ISSN 0269-8463


    1. Plant‐derived low molecular weight compounds play a crucial role in shaping soil microbiome functionality. While various compounds have been demonstrated to affect soil microbes, mout data are case‐specific and do not provide generalizable predictions on their effects. Here we show that the chemical structural affiliation of low molecular weight compounds typically secreted by plant roots – sugars, amino acids, organic acids and phenolic acids – can predictably affect microbiome diversity, composition and functioning in terms of plant disease suppression.

    2. We amended soil with single or mixtures of representative compounds, mimicking carbon deposition by plants. We then assessed how different classes of compounds, or their combinations, affected microbiome composition and the protection of tomato plants from the soil‐borne Ralstonia solanacearum bacterial pathogen.

    3. We found that chemical class predicted well the changes in microbiome composition and diversity. Organic and amino acids generally decreased the microbiome diversity compared to sugars and phenolic acids. These changes were also linked to disease incidence, with amino acids and nitrogen‐containing compound mixtures inducing more severe disease symptoms connected with a reduction in bacterial community diversity.

    4. Together, our results demonstrate that low molecular weight compounds can predictably steer rhizosphere microbiome functioning providing guidelines to engineer microbiomes based on root exudation patterns by specific plant cultivars or crop regimes.
    Temperature-Induced Annual Variation in Microbial Community Changes and Resulting Metabolome Shifts in a Controlled Fermentation System
    Wang, Shilei ; Xiong, Wu ; Wang, Yuqiao ; Nie, Yao ; Wu, Qun ; Xu, Yan ; Geisen, Stefan - \ 2020
    mSystems 5 (2020)4. - ISSN 2379-5077
    We are rapidly increasing our understanding on the spatial distribution of microbial communities. However, microbial functioning, as well as temporal differences and mechanisms causing microbial community shifts, remains comparably little explored. Here, using Chinese liquor fermentation as a model system containing a low microbial diversity, we studied temporal changes in microbial community structure and functioning. For that, we used high-throughput sequencing to analyze the composition of bacteria and fungi and analyzed the microbially derived metabolome throughout the fermentation process in all four seasons in both 2018 and 2019. We show that microbial communities and the metabolome changed throughout the fermentation process in each of the four seasons, with metabolome diversity increasing throughout the fermentation process. Across seasons, bacterial and fungal communities as well as the metabolome driven by 10 indicator microorganisms and six metabolites varied even more. Daily average temperature in the external surroundings was the primary determinant of the observed temporal microbial community and metabolome changes. Collectively, our work reveals critical insights into patterns and processes determining temporal changes of microbial community composition and functioning. We highlight the importance of linking taxonomic to functional changes in microbial ecology to enable predictions of human-relevant applications.
    Plant architectural responses in simultaneous maize/soybean strip intercropping do not lead to a yield advantage
    Li, Shuangwei ; Evers, Jochem B. ; Werf, Wopke van der; Wang, Ruili ; Xu, Zhaoli ; Guo, Yan ; Li, Baoguo ; Ma, Yuntao - \ 2020
    Annals of Applied Biology 177 (2020)2. - ISSN 0003-4746 - p. 195 - 210.
    architectural response - border row effect - growth - intercropping - land equivalent ratio

    Maize/soybean strip intercropping is a commonly used system throughout China with high crop yields at reduced nutrient input compared to sole maize. Maize is the taller crop, and due to its dominance in light capture over soybean in the intercrop, maize is expected to outperform maize in sole cropping. Conversely, soybean is the subordinate crop and intercropped soybean plants are expected to perform worse than sole soybean. Crop plants show plastic responses in plant architecture to their growing conditions to forage for light and avoid shading. There is little knowledge on plant architectural responses to growing conditions in simultaneous (non-relay) intercropping and their relationship to species yields. A two-year field experiment with two simultaneous maize/soybean intercropping systems with narrow and wide strips was conducted to characterise architectural traits of maize and soybean plants grown as intercrop and sole crops. Intercropped maize plants, especially those in border rows, had substantially greater leaf area, biomass and yield than maize plants in sole crops. Intercropped soybean plants, especially those in border rows, had lower leaf area, biomass and yield than sole soybean plants. Overall intercrop performance was similar to that of sole crops, with the land equivalent ratio (LER) being only slightly greater than one (1.03–1.08). Soybean displayed typical shade avoidance responses in the intercrop, such as greater internode elongation and changes in specific leaf area, but these responses could not overcome the consequences of the competition with the taller maize plants. Therefore, in contrast to relay intercrop systems, in the studied simultaneous maize/soybean system, plastic responses did not contribute to practically relevant increases in resource capture and yield at whole system (i.e., intercrop) level.

    Disentangling the direct and indirect effects of cropland abandonment on soil microbial activity in grassland soil at different depths
    Xu, Hongwei ; Qu, Qing ; Chen, Yanhua ; Wang, Minggang ; Liu, Guobin ; Xue, Sha ; Yang, Xiaomei - \ 2020
    Catena 194 (2020). - ISSN 0341-8162
    Plant-soil interactions - Soil enzyme activity - Soil nutrients - Structural equation models - Vegetation restoration

    Cropland abandonment strongly affects plant-soil interactions. However, knowledge remains limited about how the production and diversity of plants and soil physicochemical parameters drive changes in soil microbial activity (such as microbial biomass, respiration, and enzyme activity) after cropland abandonment. Here, we investigated a grassland restoration chronosequence (0–30 years) to determine the dynamics of soil microbial biomass, respiration, and enzyme activity in the Loess Hilly, Region (China). Overall, cropland abandonment caused an increase in soil microbial activity primarily in the 0–20 cm soil layers. The metabolic quotient in the 0–10 cm layer decreased linearly with time since abandonment (recovery years). Structural equation models showed that recovery years directly and indirectly affected changes to soil microbial activity. Plant species richness, aboveground biomass, and soil organic carbon explained a large proportion of the variability in soil microbial activity in the 0–20 cm layer. However, the variability in soil microbial activity was mostly explained by plant species richness, belowground biomass, and soil total nitrogen in the 20–50 cm layers. Our results indicate that during recovery after cropland abandonment, changes in soil microbial activity are driven by plant characteristics and soil physicochemical parameters, with different drivers at different soil depths.

    Estimation of nitrogen supply for winter wheat production through a long-term field trial in China
    Huang, Shaohui ; Ding, Wencheng ; Yang, Junfang ; Zhang, Jiajia ; Ullah, Sami ; Xu, Xinpeng ; Liu, Yingxia ; Yang, Yunma ; Liu, Mengchao ; He, Ping ; Jia, Liangliang - \ 2020
    Journal of Environmental Management 270 (2020). - ISSN 0301-4797
    Nitrogen use efficiency - Relative yield - Total nitrogen supply - Winter wheat

    Excessive synthetic nitrogen (N) applications, high mineral N accumulation and low N use efficiency (NUE) are current issues in intensively cultivated winter wheat production system impeding the sustainable development of agriculture in China. To solve these problems, soil accumulated N in the top 1 m of the soil profile before sowing (Nsoil), returned straw-N from the previous maize crop (Nstraw) and fertilizer N application (Nfertilizer) should be comprehensively considered N supply sources in N management. As such, the objective of this research was to determine the optimal total N supply (TNsupply) level needed to meet crop requirements while minimizing environmental impacts. A 9-year on-farm experiment was conducted in accordance with a split-plot design involving two different fertilizer management systems (main treatments) and three N application strategies (sub treatments). Extensive TNsupply levels (ranging from 61 kg ha−1 to 813 kg ha−1) were detected, and relative yield (RY), N input and N output in response to the TNsupply were measured. The relationships between TNsupply and RY, N input, and N output strongly fit linear-plateau, linear, and linear-plateau models, respectively. The minimum TNsupply levels needed to achieve the maximum RY and N output were 325 and 392 kg ha−1, respectively. On the basis of N supply capacity, the TNsupply was removed from the growing system by 61% (N input). As the N input increased past 209 kg ha−1, the NUE declined, at which point the TNsupply reached 433 kg ha−1. Therefore, the suitable TNsupply should range from 325 kg ha−1 (ensuring a total N supply for high yield and N uptake) to 433 kg ha−1 (obtaining a relatively higher NUE and less N loss to the environment). The TNsupply was highlighted to be an indicator for use in N management recommendations. Considering the average high N accumulation in winter wheat production systems, N management should essentially take into account the consumption of Nsoil, the levels of Nstraw and the minimum application of Nfertilizer to obtain high yields while minimizing environmental impacts under suitable TNsupply levels.

    Increasing yield and nitrogen use efficiency of spring maize in Northeast China through ecological intensification management
    Xu, Rui ; Xu, Rui ; Xu, Xin Peng ; Hou, Yun Peng ; Zhang, Jia Jia ; Huang, Shao Hui ; Ding, Wen Cheng ; Liu, Ying Xia ; He, Ping - \ 2020
    Journal of Plant Nutrition and Fertilizers 26 (2020)3. - ISSN 1008-505X - p. 461 - 471.
    Ecological intensive nutrient management - Nitrogen balance - Nitrogen use efficiency - Spring maize

    [Objectives] In view of the problems in ecological environment and sustainable agricultural development caused by excessive and unreasonable fertilizer application in spring maize production in China, the effects of ecological intensive nutrient management on spring maize yield, nitrogen use efficiency and nitrogen balance in Northeast China were studied in order to make full use of resources, increase production efficiency and ensure national food security scientifically and rationally. [Methods] A long-term experiment was conducted from 2009 to 2017 in Gongzhuling City, Jilin Province. Two factors of split plot were designed in the experiment. The main plot was two fertilization managements: the ecological intensive nutrient management (EI) and farmer practice management (FP). The sub-plot was three N application methods, including no N application treatment (N0), N application in two of three years (N2/3) and in three years (N3/3). In EI treatment, P2O575 kg/hm2, K2O 90 kg/hm2, S 30 kg/hm2, Zn 5 kg/hm2and 1/4 of N (180 kg/hm2in 2009-2014, 200 kg/hm2in 2015-2017) applied as basal, 1/2 N top dressed at jointing stage and 1/4 N at tassel stage. In the treatment of FP, N 251 kg/hm2, P2O5145 kg/hm2and K2O 100 kg/hm2were applied once as basal. The yield, N uptake and accumulation of maize and the balance of soil N were investigated. [Results] In N0 treatment, the yield and N uptake showed a downward trend since 2010. In N2/3 treatment, the yield and N uptake decreased in the year without N application, and increased to the level of N3/3 treatment in the case of N application in the following year. In EI treatment, the average yield of N3/3 treatment was 11505 kg/hm2in 9 years, while that of FP treatment was significantly lower, which was 10764 kg/hm2. Compared with FP treatment, EI treatment significantly increased nitrogen agronomic efficiency (AEN), recovery efficiency (REN) and partial factor productivity (PFPN) by 47.4%, 39.6% and 43.8%, respectively. The residual N and apparent loss of N in EI treatment were 49.2% and 63.9% lower than those in FP treatment, respectively. [Conclusions] Ecological intensive nutrient management, including right fertilization rate and time, and suitable cultivar and plant density, is proved to be effective in increasing spring maize yield and N utilization, reducing residue and apparent loss of N in soil. The experiment also confirms that continuous appropriate N fertilizer application is essential for high and stable yield of maize in Northeast China.

    Neighbourhood-dependent root distributions and the consequences on root separation in arid ecosystems
    Chen, Bin J.W. ; Xu, Chi ; Liu, Mao Song ; Huang, Zheng Y.X. ; Zhang, Ming Juan ; Tang, Jian ; Anten, Niels P.R. - \ 2020
    Journal of Ecology 108 (2020)4. - ISSN 0022-0477 - p. 1635 - 1648.
    dryland - growth form - niche partitioning - plant–plant interactions - root competition - root distribution - root separation - species coexistence

    Interspecific root separation is an important example of spatial niche differentiation that drives species coexistence in many ecosystems. Particularly under water-stressed conditions, it is believed to be an inevitable outcome of species interactions. However, evidence for and against this idea has been found. So far, studies aiming at reconciling the debate have mainly focused on abiotic determinants. It remains unclear if and to what extent root separation depends on the type and growth form of interacting plants. We conducted a detailed field study in three adjacently located (with pairwise distances <500 m) arid patchy communities where a common tussock grass species Achnatherum splendens grew in association with either a tree Elaeagnus angustifolia, a shrub Nitraria tangutorum or a perennial forb species Sophora alopecuroides. In each community, roots and soils were sampled along the soil layers from five depths (0–10, 10–30, 30–60, 60–100 and 100–150 cm) in the patches and in the adjacent bare ground outside the patches. Significant vertical interspecific root separation occurred in the species-association patches of tree-grass and forb-grass communities, but not in the shrub-grass community. As the neighbour changed going from trees to shrubs and to forbs, rooting profiles of the grass Achnatherum became progressively deeper, with progressively less roots allocated in the upmost 10 cm soil layer and more in the subsequent two layers. After controlling for the differences in soil water and nutrient conditions among the three communities, the effects of neighbour type on grass rooting profiles remained robust. Synthesis. We found that the root distributions of plants in the dryland strongly depend on the type of neighbour plants, which can, at least partially, determine the extent of interspecific root separation at the community scale. Our work poses new questions about plasticity in root distribution and helps to better understand species interactions and coexistence under stressful conditions.

    Short communication : Prediction of hyperketonemia in dairy cows in early lactation using on-farm cow data and net energy intake by partial least square discriminant analysis
    Xu, Wei ; Saccenti, Edoardo ; Vervoort, Jacques ; Kemp, Bas ; Bruckmaier, Rupert M. ; Knegsel, Ariette T.M. van - \ 2020
    Journal of Dairy Science 103 (2020)7. - ISSN 0022-0302 - p. 6576 - 6582.
    metabolic status - partial least square discriminant analysis - subclinical ketosis

    The objectives of this study were (1) to evaluate if hyperketonemia in dairy cows (defined as plasma β-hydroxybutyrate ≥1.0 mmol/L) can be predicted using on-farm cow data either in current or previous lactation week, and (2) to study if adding individual net energy intake (NEI) can improve the predictive ability of the model. Plasma β-hydroxybutyrate concentration, on-farm cow data (milk yield, percentage of fat, protein and lactose, fat- and protein-corrected milk yield, body weight, body weight change, dry period length, parity, and somatic cell count), and NEI of 424 individual cows were available weekly through lactation wk 1 to 5 postpartum. To predict hyperketonemia in dairy cows, models were first trained by partial least square discriminant analysis, using on-farm cow data in the same or previous lactation week. Second, NEI was included in models to evaluate the improvement of the predictability of the models. Through leave-one trial-out cross-validation, models were evaluated by accuracy (the ratio of the sum of true positive and true negative), sensitivity (68.2% to 84.9%), specificity (61.5% to 98.7%), positive predictive value (57.7% to 98.7%), and negative predictive value (66.2% to 86.1%) to predict hyperketonemia of dairy cows. Through lactation wk 1 to 5, the accuracy to predict hyperketonemia using data in the same week was 64.4% to 85.5% (on-farm cow data only), 66.1% to 87.0% (model including NEI), and using data in the previous week was 58.5% to 82.0% (on-farm cow data only), 59.7% to 85.1% (model including NEI). An improvement of the accuracy of the model due to including NEI ranged among lactation weeks from 1.0% to 4.4% when using data in the same lactation week and 0.2% to 6.6% when using data in the previous lactation week. In conclusion, trained models via partial least square discriminant analysis have potential to predict hyperketonemia in dairy cows not only using data in the current lactation week, but also using data in the previous lactation week. Net energy intake can improve the accuracy of the model, but only to a limited extent. Besides NEI, body weight, body weight change, milk fat, and protein content were important variables to predict hyperketonemia, but their rank of importance differed across lactation weeks.

    Chain conformation and physicochemical properties of polysaccharide (glucuronoxylomannan) from Fruit Bodies of Tremella fuciformis
    Xu, Xiaoqi ; Chen, Aijun ; Ge, Xinyan ; Li, Sha ; Zhang, Tao ; Xu, Hong - \ 2020
    Carbohydrate Polymers 245 (2020). - ISSN 0144-8617
    Chain conformation - Glucuronoxylomannan - Moisture absorption and retention capacity - Rheological properties - Tremella fuciformis - Wormlike cylinder model

    Based on its potential bioactivities and sustainable source, polysaccharide (glucuronoxylomannan) from fruit bodies of Tremella fuciformis (TFP) aroused attention in food, pharmaceutical and cosmetic industry. The present study aimed at revealing its chain conformational and physicochemical properties. By using HPSEC-MALLS-Visc-RI measurement, worm-like cylinder model calculation and AFM observation, we manifested that TFP existed as flexible chains in 0.15 M NaCl (pH 7.4) solution, with the persistence length of 9.20 nm and chain diameter of 0.97 nm. Meanwhile, TFP solution exhibited shear-thinning behavior with C* at 5.3 mg mL−1, owning the feature of entangled polysaccharide. TFP solution changed from liquid-like to solid-like behavior as frequency increases, and the crossover points shifted to lower frequencies with concentration increasing. Besides, the strong moisture retention ability of TFP was evaluated. These characteristics indicated that TFP could be utilized to design microstructure system and applied as stabilizer or moisture holding ingredient in food, pharmaceutical and cosmetic system.

    MicroRNA-204-5p modulates mitochondrial biogenesis in C2C12 myotubes and associates with oxidative capacity in humans
    Houzelle, Alexandre ; Dahlmans, Dennis ; Nascimento, Emmani B.M. ; Schaart, Gert ; Jörgensen, Johanna A. ; Moonen-Kornips, Esther ; Kersten, Sander ; Wang, Xu ; Hoeks, Joris - \ 2020
    Journal of Cellular Physiology (2020). - ISSN 0021-9541
    C2C12 - microRNA - mitochondria - mitophagy - skeletal muscle

    Using an unbiased high-throughput microRNA (miRNA)-silencing screen combined with functional readouts for mitochondrial oxidative capacity in C2C12 myocytes, we previously identified 19 miRNAs as putative regulators of skeletal muscle mitochondrial metabolism. In the current study, we highlight miRNA-204-5p, identified from this screen, and further studied its role in the regulation of skeletal muscle mitochondrial function. Following silencing of miRNA-204-5p in C2C12 myotubes, gene and protein expression were assessed using quantitative polymerase chain reaction, microarray analysis, and western blot analysis, while morphological changes were studied by confocal microscopy. In addition, miRNA-204-5p expression was quantified in human skeletal muscle biopsies and associated with in vivo mitochondrial oxidative capacity. Transcript levels of PGC-1α (3.71-fold; p <.01), predicted as an miR-204-5p target, as well as mitochondrial DNA copy number (p <.05) and citrate synthase activity (p =.06) were increased upon miRNA-204-5p silencing in C2C12 myotubes. Silencing of miRNA-204-5p further resulted in morphological changes, induced gene expression of autophagy marker light chain 3 protein b (LC3B; q =.05), and reduced expression of the mitophagy marker FUNDC1 (q =.01). Confocal imaging revealed colocalization between the autophagosome marker LC3B and the mitochondrial marker OxPhos upon miRNA-204-5p silencing. Finally, miRNA-204-5p was differentially expressed in human subjects displaying large variation in oxidative capacity and its expression levels associated with in vivo measures of skeletal muscle mitochondrial function. In summary, silencing of miRNA-204-5p in C2C12 myotubes stimulated mitochondrial biogenesis, impacted on cellular morphology, and altered expression of markers related to autophagy and mitophagy. The association between miRNA-204-5p and in vivo mitochondrial function in human skeletal muscle further identifies miRNA-204-5p as an interesting modulator of skeletal muscle mitochondrial metabolism.

    Future of the human climate niche
    Xu, Chi ; Kohler, Timothy A. ; Lenton, Timothy M. ; Svenning, Jens Christian ; Scheffer, Marten - \ 2020
    Proceedings of the National Academy of Sciences of the United States of America 117 (2020)21. - ISSN 0027-8424
    Climate - Migration - Societies

    All species have an environmental niche, and despite technological advances, humans are unlikely to be an exception. Here, we demonstrate that for millennia, human populations have resided in the same narrow part of the climatic envelope available on the globe, characterized by a major mode around ~11 °C to 15 °C mean annual temperature (MAT). Supporting the fundamental nature of this temperature niche, current production of crops and livestock is largely limited to the same conditions, and the same optimum has been found for agricultural and nonagricultural economic output of countries through analyses of year-to-year variation. We show that in a business-as-usual climate change scenario, the geographical position of this temperature niche is projected to shift more over the coming 50 y than it has moved since 6000 BP. Populations will not simply track the shifting climate, as adaptation in situ may address some of the challenges, and many other factors affect decisions to migrate. Nevertheless, in the absence of migration, one third of the global population is projected to experience a MAT >29 °C currently found in only 0.8% of the Earth's land surface, mostly concentrated in the Sahara. As the potentially most affected regions are among the poorest in the world, where adaptive capacity is low, enhancing human development in those areas should be a priority alongside climate mitigation.

    Agriculture green development : A model for China and the world
    Shen, Jianbo ; Zhu, Qichao ; Jiao, Xiaoqiang ; Ying, Hao ; Wang, Hongliang ; Wen, Xin ; Xu, Wen ; Li, Tingyu ; Cong, Wenfeng ; Liu, Xuejun ; Hou, Yong ; Cui, Zhenling ; Oenema, Oene ; Davies, William J. ; Zhang, Fusuo - \ 2020
    Frontiers of Agricultural Science and Engineering 7 (2020)1. - ISSN 2095-7505 - p. 5 - 13.
    Agriculture green development - Food security - Interdisciplinary innovations - Resource use efficiency - Sustainable development - Sustainable intensification - Whole industry chain

    Realizing sustainable development has become a global priority. This holds, in particular, for agriculture. Recently, the United Nations launched the Sustainable Development Goals (SDGs), and the Nineteenth National People's Congress has delivered a national strategy for sustainable development in China-realizing green development. The overall objective of Agriculture Green Development (AGD) is to coordinate "green" with "development" to realize the transformation of current agriculture with high resource consumption and high environmental costs into a green agriculture and countryside with high productivity, high resource use efficiency and low environmental impact. This is a formidable task, requiring joint efforts of government, farmers, industry, educators and researchers. The innovative concept for AGD will focus on reconstructing the whole crop-animal production and food production-consumption system, with the emphasis on high thresholds for environmental standards and food quality as well as enhanced human well-being. This paper addresses the significance, challenges, framework, pathways and potential solutions for realizing AGD in China, and highlights the potential changes that will lead to a more sustainable agriculture in the future. Proposals include interdisciplinary innovations, whole food chain improvement and regional solutions. The implementation of AGD in China will provide important implications for the countries in developmental transition, and contribute to global sustainable development.

    Visual assessment of the impact of agricultural management practices on soil quality
    Alaoui, Abdallah ; Barão, Lúcia ; Ferreira, Carla S.S. ; Schwilch, Gudrun ; Basch, Gottlieb ; Garcia-Orenes, Fuensanta ; Morugan, Alicia ; Mataix-Solera, Jorge ; Kosmas, Costas ; Glavan, Matjaž ; Szabó, Brigitta ; Hermann, Tamás ; Vizitiu, Olga Petrutza ; Lipiec, Jerzy ; Frąc, Magdalena ; Reintam, Endla ; Xu, Minggang ; Di, Jiaying ; Fan, Hongzhu ; Sukkel, Wijnand ; Lemesle, Julie ; Geissen, Violette ; Fleskens, Luuk - \ 2020
    Agronomy Journal 112 (2020)4. - ISSN 0002-1962 - p. 2608 - 2623.

    The intensification of agricultural practices to increase food and feed outputs is a pressing challenge causing deterioration of soil quality and soil functions. Such a challenge demands provision of empirical evidence to provide context-sensitive guidance on agricultural management practices (AMPs) that may enhance soil quality. The objectives of this study are to identify the most promising AMPs (and their combinations) applied by farmers with the most positive effects on soil quality and to evaluate the sensitivity of the soil quality indicators to the applied AMPs. The effect of selected AMPs on soil quality was assessed using a visual soil assessment tool in a total of 138 pairs of plots spread across 14 study site areas in Europe and China covering representative pedo-climatic zones. The inventory and scoring of soil quality were conducted together with landowners. Results show that 104 pairs show a positive effect of AMPs on soil quality. Higher effects of the AMPs were observed in lower fertile soils (i.e., Podzols and Calcisols) as opposed to higher fertile soils (i.e., Luvisols and Fluvisols). For the single use applications, the AMPs with positive effects were crop rotation; manuring, composting, and no-tillage; followed by organic agriculture and residue maintenance. Cluster analysis showed that the most promising combinations of AMPs with the most positive effects on soil quality are composed of crop rotation, mulching, and min-till. The agreement between scientific skills and empirical knowledge in the field identified by the farmers confirm our findings and ensures their applicability.

    Pathogen manipulation of chloroplast function triggers a light-dependent immune recognition
    Gao, Chuyun ; Xu, Huawei ; Huang, Jie ; Sun, Biying ; Zhang, Fan ; Savage, Zachary ; Duggan, Cian ; Yan, Tingxiu ; Wu, Chih Hang ; Wang, Yuanchao ; Vleeshouwers, Vivianne G.A.A. ; Kamoun, Sophien ; Bozkurt, Tolga O. ; Dong, Suomeng - \ 2020
    Proceedings of the National Academy of Sciences of the United States of America 117 (2020)17. - ISSN 0027-8424 - p. 9613 - 9620.
    Chloroplast - Disease resistance - Light - NLR - Potato blight

    In plants and animals, nucleotide-binding leucine-rich repeat (NLR) proteins are intracellular immune sensors that recognize and eliminate a wide range of invading pathogens. NLR-mediated immunity is known to be modulated by environmental factors. However, how pathogen recognition by NLRs is influenced by environmental factors such as light remains unclear. Here, we show that the agronomically important NLR Rpi-vnt1.1 requires light to confer disease resistance against races of the Irish potato famine pathogen Phytophthora infestans that secrete the effector protein AVRvnt1. The activation of Rpi-vnt1.1 requires a nuclear-encoded chloroplast protein, glycerate 3-kinase (GLYK), implicated in energy production. The pathogen effector AVRvnt1 binds the full-length chloroplast-targeted GLYK isoform leading to activation of Rpi-vnt1.1. In the dark, Rpi-vnt1.1-mediated resistance is compromised because plants produce a shorter GLYK-lacking the intact chloroplast transit peptide-that is not bound by AVRvnt1. The transition between full-length and shorter plant GLYK transcripts is controlled by a light-dependent alternative promoter selection mechanism. In plants that lack Rpi-vnt1.1, the presence of AVRvnt1 reduces GLYK accumulation in chloroplasts counteracting GLYK contribution to basal immunity. Our findings revealed that pathogen manipulation of chloroplast functions has resulted in a light-dependent immune response.

    Prevalence of coeliac disease in Northwest China: heterogeneity across Northern Silk road ethnic populations
    Zhou, Chunyan ; Gao, Feng ; Gao, Jinyan ; Yuan, Juanli ; Lu, Jiajie ; Sun, Zhenzhu ; Xu, Mengyu ; Engel, J. ; Hui, Wenjia ; Gilissen, L.J.W.J. ; Chen, Hongbing - \ 2020
    Alimentary Pharmacology and Therapeutics 51 (2020)11. - ISSN 0269-2813 - p. 1116 - 1129.
    Background: Epidemiological data of coeliac disease are lacking from the central Asian region. Aims: To verify the occurrence of coeliac disease amongst four major ethnic groups of Xinjiang Uyghur Autonomus Region, China. Methods: 2277 in-patients with gastrointestinal symptoms (1391 Han, 608 Uyghur, 146 Kazakh and 132 Hui; mean age: 54 ± 12.8 years) were included. Total IgA, anti-deamidated gliadin peptide (DGP)-IgG, and anti-tissue transglutaminase (anti-tTG)-IgA were analysed. All antibody-positive subjects were further tested for endomysial (EMA) antibodies and were HLA genotyped. All subjects with antibody positivity were asked to undergo intestinal biopsy. In addition, a subset of antibody-negative subjects were tested for HLA-DQA1and DQB1. Results: Among the 2277 subjects, 29 subjects were defined as coeliac disease au-toimmune (positive results for anti-tTG IgA and EMA-IgA) (1.27%; 95% confidence interval, 0.81%-1.73%), eight of them underwent biopsy and all showed coeliac dis-ease histology (0.35%; 95% Cl, 0.11%-0.59%). The frequency of coeliac disease au-toimmunity was lowest among the Han (0.79%), followed by the Uyghur (1.81%), the Kazakh (2.05%) and the Hui (3.03%). The frequency of the HLA-DQ2 and/or DQ8 haplotype was highest in the Uyghur (52.1%), followed by the Hui (44.4%), the Kazakh (40.0%) and the Han (39.4%). Besides, a three times higher frequency of coeliac dis-ease autoimmunity was found among rural living subjects with significantly higher wheat consumption compared to urban living subjects (3.16% vs 0.97%, P < 0.01). Conclusions: In Xinjiang, coeliac disease does occur, especially in the rural area. The HLA haplotype and environment play key roles in the development of coeliac disease.
    Dynamic balancing of intestinal short-chain fatty acids: the crucial role of bacterial metabolism
    Xu, Youqiang ; Zhu, Yang ; Li, Xiuting ; Sun, Baoguo - \ 2020
    Trends in Food Science and Technology 100 (2020). - ISSN 0924-2244 - p. 118 - 130.
    Background: Short-chain fatty acids (SCFAs) play important physiological roles in human health. Adverse effects on health are known with a low or excessive concentration of SCFAs although the optimal level of SCFAs in the body is unknown yet. The level of endogenous SCFAs is affected by many factors of which gut bacteria are the most important one. However, how gut bacteria and a dietary intervention affect SCFA balance in the gut still needs to be clarified.
    Scope and approach: In addition to addressing the importance of a dynamic balance of SCFAs for health, we discuss the factors affecting the dynamic balance of SCFAs, especially the gut SCFA-producing bacteria, including the classification of the bacteria, their response to diet, the SCFAs metabolic pathways and the catalytic mechanisms of the main rate-limiting enzymes.
    Key findings and conclusions: SCFAs levels can be regulated endogenously and exogenously. Exogenous regulation delivers SCFAs to gut by esterification with dietary fibres. Endogenous regulation like diet, directly or indirectly affect gut microbiota, including their abundance, fitness and SCFAs production. Until now, 74 bacterial species are reported to produce SCFAs, the metabolic pathways are classified into 4 categories, and the 4 rate-limiting enzymes in the metabolic pathways are summarized. We also propose methods for long-lasting endogenous SCFAs balancing, including identifying the minimum sets of SCFA-producing bacterial group, and possible dietary intervention to form a minimum group of gut microbiota for SCFAs synthesis. An integrated approach will help realize the rational regulation of balanced SCFAs levels to benefit human health.
    Modeling of industrial-scale anaerobic solid-state fermentation for Chinese liquor production
    Jin, Guangyuan ; Uhl, Philipp ; Zhu, Yang ; Wijffels, René H. ; Xu, Yan ; Rinzema, Arjen - \ 2020
    Chemical Engineering Journal 394 (2020). - ISSN 1385-8947
    Chinese liquor - Heat transfer - Mathematical modeling - Product inhibition - Solid-state fermentation - Temperature modeling

    Traditional solid-state fermentation processes can give fluctuating product quality and quantity due to difficulties in control and scale up. This paper describes an engineering study of an industrial-scale anaerobic solid-state fermentation process for Chinese liquor (Baijiu) production, aimed at better understanding of the traditional process, as an initial step for future optimization. This mixed-culture fermentation is done in 0.44-m3 vessels embedded in the soil. At this scale, the fermentation is limited by product inhibition. We developed mathematical models based on the Han-Levenspiel equation for product inhibition, with parameters derived from measured data. The models accurately predicted the concentrations of starch and dry matter. A model with radial conduction into a small soil volume around the fermenter and consecutive vertical conduction into the underlying soil accurately predicted the pit temperature in the heating and cooling phases. This model is very sensitive to the values used for the enthalpies of combustion, meaning that direct measurement of the heat production rate would be preferable. In the industry practice, the fermenter volume can be from around 0.20 to 15.00 m3. The model predicts that overheating will occur not only in larger fermenters, but also in the 0.44-m3 fermenters when the soil temperature is high in summer. Our model predictions are consistent with observed behavior in the industry. Our findings can be used to improve this traditional process, as well as similar systems.

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