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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Food allergy : From molecular mechanisms to control strategies
Fu, Linglin ; Cherayil, Bobby J. ; Shi, Haining ; Wang, Yanbo ; Zhu, Yang - \ 2019
Springer Nature Singapore - ISBN 9789811369278 - 214 p.

This book addresses the molecular mechanisms of food allergies and related control strategies. To do so, it covers a broad range of topics, including: the basic immunology of food allergies, including crosstalk between gut mucosal immunity and allergens; types of food allergens, structure of food allergen epitopes and cross-reactivity; detection and quantification methods for food allergens; in vitro and in vivo models for evaluating allergenicity; novel food processing methods for the development of hypoallergenic foods; bioactive natural compounds and functional foods for alleviating allergic reactions; modulation of the microbiota in food allergies and use of probiotics in allergic response regulation; and risk assessment and control strategies for food allergens. The information provided will enable food scientists/specialists to design safer and more functional food products, and will help regulatory agencies identify and label food allergens (and thus help consumers avoid allergic reactions). It will help clinicians and public health investigators prevent or treat outbreaks of food allergies, and will provide food producers and processors, as well as government inspectors, with valuable insights into evaluation, risk assessment and control strategies for allergens. Lastly, it will benefit upper-level undergraduate and graduate students in food science and safety, public health, medicine, nutrition and related fields.

CCDC 1904736: Experimental Crystal Structure Determination
Demay-Drouhard, Paul ; Du, Ke ; Samanta, Kushal ; Wan, Xintong ; Yang, Weiwei ; Srinivasan, Rajavel ; Sue, Andrew C.H. ; Zuilhof, Han - \ 2019
Tianjin University
BODJAI : 2,2',2'',2''',2''''-{[26,28,30,32,34-pentamethoxyhexacyclo[21.2.2.23,6.28,11.213,16.218,21]pentatriaconta-1(25),3,5,8,10,13,15,18,20,23,26,28,30,32,34-pentadecaene-4,9,14,19,24-pentayl]pentakis(oxy)}penta-acetonitrile unknown solvate Space Group: P 1 (2), Cell: a 12.1203(2)Å b 13.2138(2)Å c 17.0854(3)Å, α 89.7350(10)° β 81.9010(10)° γ 75.3150(10)°
CCDC 1904933: Experimental Crystal Structure Determination
Demay-Drouhard, Paul ; Du, Ke ; Samanta, Kushal ; Wan, Xintong ; Yang, Weiwei ; Srinivasan, Rajavel ; Sue, Andrew C.H. ; Zuilhof, Han - \ 2019
Tianjin University
BODJEM : 26,28,30,32,34-pentakis([1,1'-biphenyl]-4-yl)hexacyclo[21.2.2.23,6.28,11.213,16.218,21]pentatriaconta-1(25),3,5,8,10,13,15,18,20,23,26,28,30,32,34-pentadecaene-4,9,14,19,24-pentol acetone unknown solvate Space Group: P 1 (2), Cell: a 16.63130(10)Å b 19.13610(10)Å c 25.19360(10)Å, α 94.5000(10)° β 96.8560(10)° γ 98.2260(10)° BODJEM : 26,28,30,32,34-pentakis([1,1'-biphenyl]-4-yl)hexacyclo[21.2.2.23,6.28,11.213,16.218,21]pentatriaconta-1(25),3,5,8,10,13,15,18,20,23,26,28,30,32,34-pentadecaene-4,9,14,19,24-pentol acetone unknown solvate Space Group: P 1 (2), Cell: a 16.63130(10)Å b 19.13610(10)Å c 25.19360(10)Å, α 94.5000(10)° β 96.8560(10)° γ 98.2260(10)°
High dose of dietary nicotinamide riboside induces glucose intolerance and white adipose tissue dysfunction in mice fed a mildly obesogenic diet
Shi, Wenbiao ; Hegeman, Maria A. ; Doncheva, Atanaska ; Bekkenkamp-Grovenstein, Melissa ; Boer, Vincent C.J. de; Keijer, Jaap - \ 2019
Nutrients 11 (2019)10. - ISSN 2072-6643
Adipose tissue - Glucose tolerance - NAD - Nnt - Supplementation - Vitamin B3

Nicotinamide riboside (NR) is a nicotinamide adenine dinucleotide (NAD+) precursor vitamin. The scarce reports on the adverse effects on metabolic health of supplementation with high-dose NR warrant substantiation. Here, we aimed to examine the physiological responses to high-dose NR supplementation in the context of a mildly obesogenic diet and to substantiate this with molecular data. An 18-week dietary intervention was conducted in male C57BL/6JRccHsd mice, in which a diet with 9000 mg NR per kg diet (high NR) was compared to a diet with NR at the recommended vitamin B3 level (control NR). Both diets were mildly obesogenic (40 en% fat). Metabolic flexibility and glucose tolerance were analyzed and immunoblotting, qRT-PCR and histology of epididymal white adipose tissue (eWAT) were performed. Mice fed with high NR showed a reduced metabolic flexibility, a lower glucose clearance rate and aggravated systemic insulin resistance. This was consistent with molecular and morphological changes in eWAT, including sirtuin 1 (SIRT1)-mediated PPARγ (proliferator-activated receptor γ) repression, downregulated AKT/glucose transporter type 4 (GLUT4) signaling, an increased number of crown-like structures and macrophages, and an upregulation of pro-inflammatory gene markers. In conclusion, high-dose NR induces the onset of WAT dysfunction, which may in part explain the deterioration of metabolic health.

Optimum leaf defoliation: A new agronomic approach for increasing nutrient uptake and land equivalent ratio of maize soybean relay intercropping system
Raza, Muhammad Ali ; Feng, Ling Yang ; Werf, Wopke van der; Iqbal, Nasir ; Khan, Imran ; Hassan, Muhammad Jawad ; Ansar, Muhammad ; Chen, Yuan Kai ; Xi, Zeng Jin ; Shi, Jian Yi ; Ahmed, Mukhtar ; Yang, Feng ; Yang, Wenyu - \ 2019
Field Crops Research 244 (2019). - ISSN 0378-4290
Defoliation - Economics - LER - Nutrient - Relay-intercropping

Upper canopy leaves of maize decrease the light-transmittance at middle-strata-leaves of maize and soybean canopy in maize-soybean relay-intercropping systems (MS). This affects the uptake of nutrients and distribution patterns in various plant organs of intercrop species in MS. Judicious defoliation of maize plants in MS could help to alleviate this problem and improve nutrient uptake and intercrop yields. In a two-year field experiment with MS, including the measurements of biomass production, nutrients uptake, and distribution at the organ level, and grain yields of intercrop species, maize plants were subjected to four-leaf defoliation treatments to improve the light-transmittance of maize and soybean plants. Defoliation of the topmost two-leaves (T2), four-leaves (T4), six-leaves (T6) was compared to no defoliation (T0). Compared to T0, treatment T2 improved the uptake of nitrogen (N), phosphorus (P), and potassium (K) in each plant part of maize by 23, 12, and 11% (grain), 22, 19, and 13% (straw), and 28, 14, and 18% (root), respectively. Defoliation also enhanced the uptake of N, P, and K in each plant part of soybean by 5, 5, and 10% (grain), 10, 17, and 13% (straw), and 14, 11, and 11% (root), respectively. The improved nutrient uptake in T2 increased the total biomass and its distribution in the root, straw, and grain of soybean and maize by 15 and 13%, and 21 and 15%, 20 and 14%, 7 and 10%, respectively compared to T0. On average, over two years, under T2, relay-cropped maize obtained 107% of the sole-yield, and relay-cropped soybean obtained 65% of the sole-yield. The T2 defoliation treatment also achieved the highest land equivalent ratio of 1.69 and 1.77, with a net profit of 1301.6 $ ha−1 and 1293.4 $ ha−1 in 2017 and 2018, respectively. Following the optimum defoliation treatment of maize in maize-soybean intercrops, i.e., defoliation of the topmost two-leaves, the nutrient uptake can be increased, and the nutrient partitioning over plant organs be better balanced. Optimum defoliation, therefore, enhances the productivity of maize-soybean intercropping systems.

Cohesion-driven mixing and segregation of dry granular media
Jarray, Ahmed ; Shi, Hao ; Scheper, Bert J. ; Habibi, Mehdi ; Luding, Stefan - \ 2019
Scientific Reports 9 (2019)1. - ISSN 2045-2322 - 1 p.

Granular segregation is a common, yet still puzzling, phenomenon encountered in many natural and engineering processes. Here, we experimentally investigate the effect of particles cohesion on segregation in dry monodisperse and bidisperse systems using a rotating drum mixer. Chemical silanization, glass surface functionalization via a Silane coupling agent, is used to produce cohesive dry glass particles. The cohesive force between the particles is controlled by varying the reaction duration of the silanization process, and is measured using an in-house device specifically designed for this study. The effects of the cohesive force on flow and segregation are then explored and discussed. For monosized particulate systems, while cohesionless particles perfectly mix when tumbled, highly cohesive particles segregate. For bidisperse mixtures of particles, an adequate cohesion-tuning reduces segregation and enhances mixing. Based on these results, a simple scheme is proposed to describe the system's mixing behaviour with important implications for the control of segregation or mixing in particulate industrial processes.

Plant-part segmentation using deep learning and multi-view vision
Shi, Weinan ; Zedde, Rick van de; Jiang, Huanyu ; Kootstra, Gert - \ 2019
Biosystems Engineering 187 (2019). - ISSN 1537-5110 - p. 81 - 95.
2D images and 3D point clouds - digital plant phenotyping - instance segmentation - semantic segmentation

To accelerate the understanding of the relationship between genotype and phenotype, plant scientists and plant breeders are looking for more advanced phenotyping systems that provide more detailed phenotypic information about plants. Most current systems provide information on the whole-plant level and not on the level of specific plant parts such as leaves, nodes and stems. Computer vision provides possibilities to extract information from plant parts from images. However, the segmentation of plant parts is a challenging problem, due to the inherent variation in appearance and shape of natural objects. In this paper, deep-learning methods are proposed to deal with this variation. Moreover, a multi-view approach is taken that allows the integration of information from the two-dimensional (2D) images into a three-dimensional (3D) point-cloud model of the plant. Specifically, a fully convolutional network (FCN) and a masked R-CNN (region-based convolutional neural network) were used for semantic and instance segmentation on the 2D images. The different viewpoints were then combined to segment the 3D point cloud. The performance of the 2D and multi-view approaches was evaluated on tomato seedling plants. Our results show that the integration of information in 3D outperforms the 2D approach, because errors in 2D are not persistent for the different viewpoints and can therefore be overcome in 3D.

Dynamic virulence-related regions of the plant pathogenic fungus Verticillium dahliae display enhanced sequence conservation
Depotter, Jasper R.L. ; Shi-Kunne, Xiaoqian ; Missonnier, Hélène ; Liu, Tingli ; Faino, Luigi ; Berg, Grardy C.M. van den; Wood, Thomas A. ; Zhang, Baolong ; Jacques, Alban ; Seidl, Michael F. ; Thomma, Bart P.H.J. - \ 2019
Molecular Ecology 28 (2019)15. - ISSN 0962-1083 - p. 3482 - 3495.
comparative genomics - effector - genome evolution - mutagenesis - two-speed genome - Verticillium wilt

Plant pathogens continuously evolve to evade host immune responses. During host colonization, many fungal pathogens secrete effectors to perturb such responses, but these in turn may become recognized by host immune receptors. To facilitate the evolution of effector repertoires, such as the elimination of recognized effectors, effector genes often reside in genomic regions that display increased plasticity, a phenomenon that is captured in the two-speed genome hypothesis. The genome of the vascular wilt fungus Verticillium dahliae displays regions with extensive presence/absence polymorphisms, so-called lineage-specific regions, that are enriched in in planta-induced putative effector genes. As expected, comparative genomics reveals differential degrees of sequence divergence between lineage-specific regions and the core genome. Unanticipated, lineage-specific regions display markedly higher sequence conservation in coding as well as noncoding regions than the core genome. We provide evidence that disqualifies horizontal transfer to explain the observed sequence conservation and conclude that sequence divergence occurs at a slower pace in lineage-specific regions of the V. dahliae genome. We hypothesize that differences in chromatin organisation may explain lower nucleotide substitution rates in the plastic, lineage-specific regions of V. dahliae.

The future of intercropping under growing resource scarcity and declining grain prices - A model analysis based on a case study in Northwest China
Hong, Yu ; Berentsen, Paul ; Heerink, Nico ; Shi, Minjun ; Werf, Wopke van der - \ 2019
Agricultural Systems 176 (2019). - ISSN 0308-521X
China - Intercropping - Labor - Maize price - Water

Intercropping, i.e. mixed crop species cultivation on a field, can potentially reduce pressure on land and water resources by generating higher resource use efficiencies and crop yields through exploitation of complementarities between species. Intercropping systems in China and elsewhere have come under pressure through labor migration, growing water scarcity, changing crop prices and other factors. However, little hard evidence is available on how these socio-economic factors interplay and affect the prevalence of intercropping systems now and in the near future. The objective of this study is to explore the effect of growing scarcity of (water and labor) resources and declining (maize) grain prices on the share of intercropping in the optimal cropping plan and on associated agricultural income levels in an intercropping-dominated agricultural system in China. To undertake this analysis, we developed a mathematical programming model to simulate crop production for a model village in Gaotai county in the Hexi Corridor in northwest China, for given resources and economic conditions in 2013 and possible changes (scenarios) in the future. In the Hexi Corridor, conventional wheat/maize intercropping contributed greatly to rising food production while cash crops integrated with maize provided important cash income. With the introduction of seed crops and stricter water regulations, intercropping has become less prevalent in this area in recent years. In the absence of water constraints and at price levels and labor availability in 2013, our model results indicate that an optimal land use would entail that all land would be devoted to intercropping. Sole cumin and sole cotton enter the optimal cropping plan when water becomes scarce and the maize price declines substantially, while increases in hired labor wages have a strong negative impact on intercropping only when on-farm labor becomes scarce.

The impacts of the eco-environmental policy on grassland degradation and livestock production in Inner Mongolia, China : An empirical analysis based on the simultaneous equation model
Liu, Min ; Dries, Liesbeth ; Huang, Jikun ; Min, Shi ; Tang, Jianjun - \ 2019
Land Use Policy 88 (2019). - ISSN 0264-8377
Eco-environmental program - Grassland condition - Livestock production - Pastoral area - Simultaneous equation model

Grassland degradation has been deteriorating while the demands for meat products have been surging in China over the past few decades, leading to multiple policy initiatives to balance the grassland ecosystem and livestock production of the pastoral areas. This paper investigates the impacts of a prevailing eco-environmental program, i.e. Subsidy and Incentive System for Grassland Conservation (SISGC), in the pastoral areas of Inner Mongolia, on grassland condition and livestock production. The Normalized Difference Vegetation Index (NDVI), measured with remote sensing technology, is used to quantify grassland condition. Our empirical analysis was based on the data of 52 counties across a 15-year timespan covering 10 years before the introduction of SISGC and 5 years after its implementation. Simultaneous equation models are employed to study the mutual relationship between grassland condition and livestock production. The results suggest that the SISGC has significantly improved grassland condition. The total livestock population, especially the sheep population, has decreased due to SISGC, but the large animal population has not been impacted. On the other hand, growing meat prices (market demands) have resulted in an increase in the population of sheep, large animals, and total livestock. Implications are that the SISGC has been successful in preventing grassland degradation by controlling the increase in livestock population of the pastoral areas. Other policy initiatives need to consider how to prevent grassland degradation not only by controlling the livestock population given the soaring meat demand by the Chinese population and to address the high level of poverty among pastoralists.

Decisions by Chinese households regarding renting in arable land—The impact of tenure security perceptions and trust
Ma, Xianlei ; Heerink, Nico ; Ierland, Ekko van; Lang, Hairu ; Shi, Xiaoping - \ 2019
China Economic Review (2019). - ISSN 1043-951X
China - Land rental market - Property rights - Tenure security - Trust

Policies aimed at strengthening tenure security through the elimination of land reallocations and provision of land certificates have been implemented with different degrees of success in rural China. In this study, we examine the impact of tenure security perceptions and trust on household decisions to rent in land in a region where tenure security is high and in a region where households face much lower land tenure security. Our regression results suggest that when land tenure is less secure, household perceptions of tenure security positively affect decisions to rent in additional land and the size of the rented land, whereas trust is important for the choice between oral and written contracts. When land tenure is relatively secure, household tenure security perceptions are less relevant, and trust becomes more important for land rental decisions. However, tenure security perceptions do seem to play a role in the choice between oral and written contracts in such high tenure security environments.

Transcriptome analysis of virulence-differentiated Fusarium oxysporum f. Sp. Cucumerinum isolates during cucumber colonisation reveals pathogenicity profiles
Huang, Xiao Qing ; Lu, Xiao Hong ; Sun, Man Hong ; Guo, Rong Jun ; Diepeningen, Anne D. Van; Li, Shi Dong - \ 2019
BMC Genomics 20 (2019)1. - ISSN 1471-2164
Cucumber Fusarium wilt - Differentially expressed genes - Fusarium oxysporum f. Sp. Cucumerinum - Transposon - Virulence variation

Background: Cucumber Fusarium wilt, caused by Fusarium oxysporum f. Sp. Cucumerinum (Foc), is one of the most notorious diseases in cucumber production. Our previous research showed the virulence of Foc significantly increases over consecutive rounds of infection in a resistant cultivar. To understand the virulence variation of Foc under host pressure, the mildly virulent strain foc-3b (WT) and its virulence-enhanced variant Ra-4 (InVir) were selected and their transcriptome profiles in infected cucumber roots were analyzed at 24 h after inoculation (hai) and 120 hai. Results: A series of differentially expressed genes (DEGs) potentially involved in fungal pathogenicity and pathogenicity variation were identified and prove mainly involved in metabolic, transport, oxidation-reduction, cell wall degradation, macromolecules modification, and stress and defense. Among these DEGs, 190 up- and 360 down-regulated genes were expressed in both strains, indicating their importance in Foc infection. Besides, 286 and 366 DEGs showed up-regulated expression, while 492 and 214 showed down-regulated expression in InVir at 24 and 120 hai, respectively. These DEGs may be involved in increased virulence. Notably, transposases were more active in InVir than WT, indicating transposons may contribute to adaptive evolution. Conclusions: By a comparative transcriptome analysis of the mildly and highly virulent strains of Foc during infection of cucumber, a series of DEGs were identified that may be associated with virulence. Hence, this study provides new insight into the transcriptomic profile underlying pathogenicity and virulence differentiation of Foc.

Immunogenicity in Rabbits of Virus-Like Particles from a Contemporary Rabbit Haemorrhagic Disease Virus Type 2 (GI.2/RHDV2/b) Isolated in The Netherlands
Miao, Qiuhong ; Qi, Ruibing ; Veldkamp, Luut ; Ijzer, Jooske ; Kik, Marja L. ; Zhu, Jie ; Tang, Aoxing ; Dong, Dandan ; Shi, Yonghong ; Oers, Monique M. van; Liu, Guangqing ; Pijlman, Gorben P. - \ 2019
Viruses 11 (2019)6. - ISSN 1999-4915
baculovirus expression - immunogenicity - insect cells - Netherlands - rabbit haemorrhagic disease virus 2 (GI.2/RHDV2/b) - virus-like particles - VP60

Rabbit haemorrhagic disease virus (RHDV) type 2 (GI.2/RHDV2/b) is an emerging pathogen in wild rabbits and in domestic rabbits vaccinated against RHDV (GI.1). Here we report the genome sequence of a contemporary RHDV2 isolate from the Netherlands and investigate the immunogenicity of virus-like particles (VLPs) produced in insect cells. RHDV2 RNA was isolated from the liver of a naturally infected wild rabbit and the complete viral genome sequence was assembled from sequenced RT-PCR products. Phylogenetic analysis based on the VP60 capsid gene demonstrated that the RHDV2 NL2016 isolate clustered with other contemporary RHDV2 strains. The VP60 gene was cloned in a baculovirus expression vector to produce VLPs in Sf9 insect cells. Density-gradient purified RHDV2 VLPs were visualized by transmission electron microscopy as spherical particles of around 30 nm in diameter with a morphology resembling authentic RHDV. Immunization of rabbits with RHDV2 VLPs resulted in high production of serum antibodies against VP60, and the production of cytokines (IFN-γ and IL-4) was significantly elevated in the immunized rabbits compared to the control group. The results demonstrate that the recombinant RHDV2 VLPs are highly immunogenic and may find applications in serological detection assays and might be further developed as a vaccine candidate to protect domestic rabbits against RHDV2 infection.

Gender in climate change, agriculture, and natural resource policies: insights from East Africa
Ampaire, Edidah L. ; Acosta, Mariola ; Huyer, Sofia ; Kigonya, Ritah ; Muchunguzi, Perez ; Muna, Rebecca ; Jassogne, Laurence - \ 2019
Climatic Change (2019). - ISSN 0165-0009

Gender mainstreaming was acknowledged as an indispensable strategy for achieving gender equality at the 1995 Beijing Platform for Action. Since then, governments have made substantial efforts in developing gender-responsive policies and implementation strategies. The advent of climate change and its effects, which have continued to impact rural livelihoods and especially food security, demands that gender mainstreaming efforts are accelerated. Effective gender mainstreaming requires that gender is sufficiently integrated in policies, development plans, and implementation strategies, supported by budgetary allocations. This study analyzes the extent of gender integration in agricultural and natural resource policies in Uganda and Tanzania, and how gender is budgeted for in implementation plans at district and lower governance levels. A total of 155 policy documents, development plans, and annual action plans from national, district, and sub-county/ward levels were reviewed. In addition, district and sub-county budgets for four consecutive financial years from 2012/2013 to 2015/2016 were analyzed for gender allocations. Results show that whereas there is increasing gender responsiveness in both countries, (i) gender issues are still interpreted as “women issues,” (ii) there is disharmony in gender mainstreaming across governance levels, (iii) budgeting for gender is not yet fully embraced by governments, (iii) allocations to gender at sub-national level remain inconsistently low with sharp differences between estimated and actual budgets, and (iv) gender activities do not address any structural inequalities. We propose approaches that increase capacity to develop and execute gender-responsive policies, implementation plans, and budgets.

In silico prediction and characterisation of secondary metabolite clusters in the plant pathogenic fungus Verticillium dahliae
Shi-Kunne, Xiaoqian ; Pedro Jové, Roger de; Depotter, Jasper R.L. ; Ebert, Malaika K. ; Seidl, Michael F. ; Thomma, Bart P.H.J. - \ 2019
FEMS Microbiology Letters 366 (2019)7. - ISSN 0378-1097
fungi - genomics - natural product - pathogen - Verticillium

Fungi are renowned producers of natural compounds, also known as secondary metabolites (SMs) that display a wide array of biological activities. Typically, the genes that are involved in the biosynthesis of SMs are located in close proximity to each other in so-called secondary metabolite clusters. Many plant-pathogenic fungi secrete SMs during infection in order to promote disease establishment, for instance as cytocoxic compounds. Verticillium dahliae is a notorious plant pathogen that can infect over 200 host plants worldwide. However, the SM repertoire of this vascular pathogen remains mostly uncharted. To unravel the potential of V. dahliae to produce SMs, we performed in silico predictions and in-depth analyses of its secondary metabolite clusters. Using distinctive traits of gene clusters and the conserved signatures of core genes 25 potential SM gene clusters were identified. Subsequently, phylogenetic and comparative genomics analyses were performed, revealing that two putative siderophores, ferricrocin and TAFC, DHN-melanin and fujikurin may belong to the SM repertoire of V. dahliae.

The white adipose tissue transcriptional response to withdrawal of vitamin B3
Shi, W. ; Boer, V.C.J. de; Schothorst, E.M. van; Stelt, I. van der; Keijer, J. - \ 2019
GSE116483 - PRJNA478790 - Mus musculus
Distinct markers for early, mild vitamin B3 deficiency are lacking. To identify these, we examined the molecular responses of white adipose tissue to vitamin B3 withdrawal. We performed a dietary intervention in male C57Bl/6JRcc mice. A diet with a low but adequate level of tryptophan without nicotinamide riboside (NR) was compared to the same diet with NR at the recommended vitamin B3 (30 mg NR per kg diet). Physiological and circulating parameters were determined and global transcriptomics, qRT-PCR and histology of epididymal white adipose tissue (eWAT) were done. We observed a decreased insulin sensitivity and a shift from carbohydrate to fatty acid oxidation. This was consistent with molecular changes in eWAT, where we observed an altered MEK/ERK signalling, a lowering of glucose utilization markers and an increase in makers of fatty acid catabolism, which may be related to the consistent reduction of mitochondrial OXPHOS Complex I (mRNAs and protein). The synthesis pathway of tetrahydropteridine (BH4), an essential cofactor for neurotransmitter synthesis, was found to be increased. Based on our results, we propose the technically validated downregulation of Anp32a, Tnk2 and the upregulation of Mapk1, Map2k1, Mthfs, Mthfsl and Qdpr as a WAT transcriptional signature marker for mild vitamin B3 deficiency
Transcriptional Response of White Adipose Tissue to Withdrawal of Vitamin B3
Shi, Wenbiao ; Hegeman, Maria A. ; Doncheva, Atanaska ; Stelt, Inge van der; Bekkenkamp‐Grovenstein, Melissa ; Schothorst, Evert M. van; Brenner, Charles ; Boer, Vincent C.J. ; Keijer, Jaap - \ 2019
Molecular Nutrition & Food Research (2019). - ISSN 1613-4125
SCOPE: Distinct markers for mild vitamin B3 deficiency are lacking. To identify these, the molecular responses of white adipose tissue (WAT) to vitamin B3 withdrawal are examined.
METHODS AND RESULTS: A dietary intervention is performed in male C57BL/6JRccHsd mice, in which a diet without nicotinamide riboside (NR) is compared to a diet with NR at the recommended vitamin B3 level. Both diets contain low but adequate level of tryptophan. Metabolic flexibility and systemic glucose tolerance are analyzed and global transcriptomics, qRT-PCR, and histology of epididymal WAT (eWAT) are performed. A decreased insulin sensitivity and a shift from carbohydrate to fatty acid oxidation in response to vitamin B3 withdrawal are observed. This is consistent with molecular changes in eWAT, including an activated MEK/ERK signaling, a lowering of glucose utilization markers, and an increase in makers of fatty acid catabolism, possibly related to the consistent lower expression of mitochondrial electron transport complexes. The synthesis pathway of tetrahydropteridine (BH4), an essential cofactor for neurotransmitter synthesis, is transcriptionally activated. Genes marking these processes are technically validated.
CONCLUSION: The downregulation of Anp32a, Tnk2 and the upregulation of Mapk1, Map2k1, Qdpr, Mthfs, and Mthfsl are proposed as a WAT transcriptional signature marker for mild vitamin B3 deficiency
Comparative genomics of the fungal genus Verticillium
Shi, Xiaoqian - \ 2019
Wageningen University. Promotor(en): B.P.H.J. Thomma, co-promotor(en): M.F. Seidl. - Wageningen : Wageningen University - ISBN 9789463434218 - 194
Seasonality in river export of nitrogen : A modelling approach for the Yangtze River
Chen, Xuanjing ; Strokal, Maryna ; Kroeze, Carolien ; Ma, Lin ; Shen, Zhenyao ; Wu, Jiechen ; Chen, Xinping ; Shi, Xiaojun - \ 2019
Science of the Total Environment 671 (2019). - ISSN 0048-9697 - p. 1282 - 1292.
Diffuse and point sources - MARINA model - Nitrogen - Sub-basins - Water quality - Yangtze River

In China, many estuaries suffer from eutrophication problems such as green tides and hypoxia. This is often a result of human activities on land leading to increased nutrient exports by rivers. River pollution shows seasonal trends that are not well understood. Therefore, the main objective of this study is to improve our understanding of the seasonal variation in river export of dissolved inorganic nitrogen (DIN) by source and at the sub-basin scale. To this end, we modified the existing MARINA model 1.0 (Model to Assess River Input of Nutrient to seAs) to account for seasonality in river export of DIN, and applied it to the Yangtze River. The resulting MARINA model version 1.1 takes a mass-balance approach and accounts for seasonality in human activities (e.g., crop planting and fertilization) and meteorology. The model distinguishes four seasons: winter (December–February), spring (March–May), summer (June–August) and fall (September–November). Our results for Yangtze indicate that N inputs to land and river export of DIN to sea are higher in summer and lower in winter. In spring, summer and fall, diffuse sources from agriculture contribute 43–85% to DIN export. In spring and fall, use of synthetic N fertilizers in cropland is an important source of DIN. In summer, both atmospheric N deposition and synthetic N fertilizers dominate. Animal manure is typically applied on land in spring and fall, contributing then to DIN. In winter, point sources of animal manure are responsible for 34–74% of DIN river export. In general, more DIN is exported to the sea from activities in middlestream and downstream sub-basins. Our results can serve as an example for other large rivers worldwide, and support the formulation of effective strategies to reduce seasonal eutrophication.

The Genome of the Fungal Pathogen Verticillium dahliae Reveals Extensive Bacterial to Fungal Gene Transfer
Shi-Kunne, Xiaoqian ; Kooten, Mathijs van; Depotter, Jasper R.L. ; Thomma, Bart P.H.J. ; Seidl, Michael F. - \ 2019
Genome Biology and Evolution 11 (2019)3. - ISSN 1759-6653 - p. 855 - 868.
Verticillium - ascomycete - bacteria - fungus - horizontal gene transfer

Horizontal gene transfer (HGT) involves the transmission of genetic material between distinct evolutionary lineages and can be an important source of biological innovation. Reports of interkingdom HGT to eukaryotic microbial pathogens have accumulated over recent years. Verticillium dahliae is a notorious plant pathogen that causes vascular wilt disease on hundreds of plant species, resulting in high economic losses every year. Previously, the effector gene Ave1 and a glucosyltransferase-encoding gene were identified as virulence factor-encoding genes that were proposed to be horizontally acquired from a plant and a bacterial donor, respectively. However, to what extent HGT contributed to the overall genome composition of V. dahliae remained elusive. Here, we systematically searched for evidence of interkingdom HGT events in the genome of V. dahliae and provide evidence for extensive horizontal gene acquisition from bacterial origin.

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