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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    Lymphoid tissue in teleost gills : Variations on a theme
    Rességuier, Julien ; Dalum, Alf S. ; Pasquier, Louis Du; Zhang, Yaqing ; Koppang, Erling Olaf ; Boudinot, Pierre ; Wiegertjes, Geert F. - \ 2020
    Biology - open access biological sciences journal 9 (2020)6. - ISSN 2079-7737 - p. 1 - 14.
    Evolution - Fish - Gills - Ilt - Zap70

    In bony fish, the gill filaments are essential for gas exchanges, but also are vulnerable to infection by water‐borne microorganisms. Omnipresent across fish, gill‐associated lymphoid tissues (GIALT) regulate interactions with local microbiota and halt infection by pathogens. A special GIALT structure has recently been found in Salmonids, the interbranchial lymphoid tissue (ILT). However, the structural variation of GIALT across bony fish remains largely unknown. Here, we show how this critical zone of interaction evolved across fishes. By labeling a conserved T‐cell epitope on tissue sections, we find that several basal groups of teleosts possess typical ILT, while modern teleosts have lymphoepithelium of different shape and size at the base of primary gill filaments. Within Cypriniformes, neither body size variation between two related species, zebrafish and common carp, nor morphotype variation, did have a drastic effect on the structure of ILT. Thereby this study is the first to describe the presence of ILT in zebrafish. The ILT variability across fish orders seems to represent different evolutionary solutions to balancing trade‐offs between multiple adaptations of jaws and pharyngeal region, and immune responses. Our data point to a wide structural variation in gill immunity between basal groups and modern teleosts.

    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.

    Light from below matters: Quantifying the consequences of responses to far‐red light reflected upwards for plant performance in heterogeneous canopies
    Zhang, Ningyi ; Westreenen, Arian Van; He, Lizhong ; Evers, Jochem B. ; Anten, Niels P.R. ; Marcelis, Leo F.M. - \ 2020
    Plant, Cell & Environment (2020). - ISSN 0140-7791
    In vegetation stands, plants receive red to far‐red ratio (R:FR) signals of varying strength from all directions. However, plant responses to variations in R:FR reflected from below have been largely ignored despite their potential consequences for plant performance. Using a heterogeneous rose canopy, which consists of bent shoots down in the canopy and vertically growing upright shoots, we quantified upward far‐red reflection by bent shoots and its consequences for upright shoot architecture. With a three‐dimensional plant model, we assessed consequences of responses to R:FR from below for plant photosynthesis. Bent shoots reflected substantially more far‐red than red light, causing reduced R:FR in light reflected upwards. Leaf inclination angles increased in upright shoots which received low R:FR reflected from below. The increased leaf angle led to an increase in simulated plant photosynthesis only when this low R:FR was reflected off their own bent shoots and not when it reflected off neighbour bent shoots. We conclude that plant response to R:FR from below is an under‐explored phenomenon which may have contrasting consequences for plant performance depending on the type of vegetation or crop system. The responses are beneficial for performance only when R:FR is reflected by lower foliage of the same plants.
    Sel1L-Hrd1 ER-associated degradation maintains β cell identity via TGF-β signaling
    Shrestha, Neha ; Liu, Tongyu ; Ji, Yewei ; Reinert, Rachel B. ; Torres, Mauricio ; Li, Xin ; Zhang, Maria ; Tang, Chih-Hang Anthony ; Hu, Chih-Chi Andrew ; Liu, Chengyang ; Naji, Ali ; Liu, Ming ; Lin, Jiandie D. ; Kersten, Sander ; Arvan, Peter ; Qi, Ling - \ 2020
    The Journal of Clinical Investigation 130 (2020)7. - ISSN 0021-9738 - p. 3499 - 3510.
    β Cell apoptosis and dedifferentiation are 2 hotly debated mechanisms underlying β cell loss in type 2 diabetes; however, the molecular drivers underlying such events remain largely unclear. Here, we performed a side-by-side comparison of mice carrying β cell-specific deletion of ER-associated degradation (ERAD) and autophagy. We reported that, while autophagy was necessary for β cell survival, the highly conserved Sel1L-Hrd1 ERAD protein complex was required for the maintenance of β cell maturation and identity. Using single-cell RNA-Seq, we demonstrated that Sel1L deficiency was not associated with β cell loss, but rather loss of β cell identity. Sel1L-Hrd1 ERAD controlled β cell identity via TGF-β signaling, in part by mediating the degradation of TGF-β receptor 1. Inhibition of TGF-β signaling in Sel1L-deficient β cells augmented the expression of β cell maturation markers and increased the total insulin content. Our data revealed distinct pathogenic effects of 2 major proteolytic pathways in β cells, providing a framework for therapies targeting distinct mechanisms of protein quality control
    ER-associated degradation is required for the maintenance of β cell identity via TGFβ signaling
    Shrestha, Neha ; Liu, T. ; Ji, Yewei ; Reinert, Rachel B. ; Torres, Mauricio ; Zhang, M. ; Tang, C.A. ; Hu, C.A. ; Liu, Chengyang ; Naji, Ali ; Lin, Jiandie D. ; Kersten, Sander ; Arvan, Peter ; Qi, Ling ; Hooiveld, Guido - \ 2020
    Wageningen University & Research
    Mus musculus - GSE143757 - PRJNA601502
    β cell apoptosis and dedifferentiation are two hotly-debated mechanisms underlying β cell loss in type 2 diabetes (T2D); however, the molecular drivers underlying such events remain largely unclear. Here, by performing a side-by-side comparison of mice carrying β cell-specific deletion of endoplasmic reticulum (ER)-associated degradation (ERAD) and autophagy, we report that while autophagy appears necessary for β cell survival, the highly conserved Sel1L-Hrd1 ERAD protein complex is required for the maintenance of β cell maturation and identity. Notably, SEL1L expression is significantly reduced in human T2D islets compared to healthy human islets. At the single cell level, we demonstrate that Sel1L deficiency is not associated with β cell loss, but rather loss of β cell identity. Mechanistically, we find that Sel1L-Hrd1 ERAD controls β cell identity via TGFβ signaling, in part by mediating the degradation of TGF-β receptor 1 (TGFβRI). Inhibition of TGFβ signaling in Sel1L-deficient β cells augments the expression of β cell maturation markers and increases the total insulin content. Our data reveal profound but distinct pathogenic effects of two major proteolytic pathways in β cells, providing a new framework for therapies targeting distinct mechanisms of protein quality control
    Replication Data for: The stove, dome, and umbrella effects of pollutant aerosol on the planetary boundary layer: a large-eddy simulation and observations in Beijing
    Ma, Yongjing ; Ye, Jianhuai ; Xin, Jinyuan ; Zhang, Wenyu ; Vila-Guerau de Arellano, Jordi ; Zhao, Dandan ; Dai, Lindong ; Ma, Yongxiang ; Wu, Xiaoyan ; Xia, Xiangao ; Tang, Guiqian ; Shen, Pengke ; Lei, Yali ; Martin, Scot T. - \ 2020
    Harvard University
    Dataset for campaign observations and LES input file for the reference case.
    The Stove, Dome, and Umbrella Effects of Atmospheric Aerosol on the Development of the Planetary Boundary Layer in Hazy Regions
    Ma, Yongjing ; Ye, Jianhuai ; Xin, Jinyuan ; Zhang, Wenyu ; Vilà‐Guerau de Arellano, Jordi ; Wang, Shigong ; Zhao, Dandan ; Dai, Lindong ; Ma, Yongxiang ; Wu, Xiaoyan ; Xia, Xiangao ; Tang, Guiqian ; Wang, Yuesi ; Shen, Pengke ; Lei, Yali ; Martin, Scot T. - \ 2020
    Geophysical Research Letters 47 (2020)13. - ISSN 0094-8276
    Atmospheric aerosol plays critical roles in suppressing planetary boundary layer (PBL) and deteriorating air quality. However, comprehensive understanding on how aerosol optical properties (absorption and scattering) affect PBL remains lacking. Utilizing a large‐eddy simulation model incorporated with in situ observations, we demonstrate distinct impacts of absorption aerosol on PBL development when it is present below (stove effect and promotion) or above morning residual layer (dome effect and strong inhibition) and similar inhibition umbrella effects of scattering aerosol on PBL regardless of its vertical locations. There exists a transition height, above which absorption aerosol is more effective in suppressing PBL and below which scattering aerosol dominates the suppression. This height is highly related to the height of morning residual layer. Aerosol stove, dome, and umbrella effects enrich our knowledge on aerosol‐PBL interactions and the latter two can be interpreted as “double inhibitions” in promoting haze episodes in the North China Plain.
    Effect of dietary fiber fermentation on short-chain fatty acid production and microbial composition in vitro
    Bai, Yu ; Zhao, Jin Biao ; Tao, Shi Yu ; Zhou, Xing Jian ; Pi, Yu ; Gerrits, Walter J.J. ; Johnston, Lee J. ; Zhang, Shi Yi ; Yang, Hong Jian ; Liu, Ling ; Zhang, Shuai ; Wang, Jun Jun - \ 2020
    Journal of the Science of Food and Agriculture 100 (2020)11. - ISSN 0022-5142 - p. 4282 - 4291.
    fiber-rich co-products - gas production - in vitro fermentation - microbial community - short chain fatty acid

    BACKGROUND: The efficient utilization of fiber-rich co-products is important for optimizing feed resource utilization and animal health. This study was conducted to evaluate the fermentation characteristics of fiber-rich co-products, which had equal quantities of total dietary fiber (TDF), at different time points using batch in vitro methods. It considered their gas production, short-chain fatty acid (SCFA) production, and microbial composition. RESULTS: The fermentation of wheat bran (WB) and oat bran (OB) showed higher and faster (P < 0.05) gas and SCFA production than corn bran (CB), sugar beet pulp (SBP), and soybean hulls (SH). The α-diversity was higher in the CB, SBP, and SH groups than in the WB and OB groups (P < 0.05). At the phylum level, OB and WB fermentation showed lower (P < 0.05) relative abundance of Actinobacteria than the CB, SBP, and SH groups. At the genus level, OB and WB fermentation increased the Enterococcus population in comparison with the CB, SBP, and SH groups, whereas CB and SBP fermentation improved the relative abundance of the Christensenellaceae R-7 group more than the WB, OB, and SH groups (P < 0.05). CONCLUSION: Overall, WB and OB were rapidly fermented by fecal microbiota, in contrast with SBP, SH, and CB. Fermentation of different fiber-rich co-products with an equal TDF content gives different responses in terms of microbial composition and SCFA production due to variations in their physicochemical properties and molecular structure.

    Population Genomic Analysis Reveals a Highly Conserved Mitochondrial Genome in Fusarium asiaticum
    Yang, Meixin ; Zhang, Hao ; Lee, T.A.J. van der; Waalwijk, C. ; Diepeningen, A.D. van; Feng, Jie ; Brankovics, Balázs ; Chen, Wanquan - \ 2020
    Frontiers in Microbiology 11 (2020). - ISSN 1664-302X
    Fusarium asiaticum is one of the pivotal members of the Fusarium graminearum species complex (FGSC) causing Fusarium head blight (FHB) on wheat, barley and rice in large parts of Asia. Besides resulting in yield losses, FHB also causes the accumulation of mycotoxins such as nivalenol (NIV) and deoxynivalenol (DON). The aim of this study was to conduct population studies on F. asiaticum from Southern China through mitochondrial genome analyses. All strains were isolated from wheat or rice from several geographic areas in seven provinces in Southern China. Based on geographic location and host, 210 isolates were selected for next generation sequencing, and their mitogenomes were assembled by GRAbB and annotated to explore the mitochondrial genome variability of F. asiaticum. The F. asiaticum mitogenome proves extremely conserved and variation is mainly caused by absence/presence of introns harboring homing endonuclease genes. These variations could be utilized to develop molecular markers for track and trace of migrations within and between populations. This study illustrates how mitochondrial introns can be used as markers for population genetic analysis. SNP analysis demonstrate the occurrence of mitochondrial recombination in F. asiaticum as was previously found for F. oxysporum and implied for F. graminearum. Furthermore, varying degrees of genetic diversity and recombination showed a high association with different geographic regions as well as with cropping systems. The mitogenome of F. graminearum showed a much higher SNP diversity while the interspecies intron variation showed no evidence of gene flow between the two closely related and sexual compatible species
    Fertilization changes soil microbiome functioning, especially phagotrophic protists
    Zhao, Zhi Bo ; He, Ji Zheng ; Quan, Zhi ; Wu, Chuan Fa ; Sheng, Rong ; Zhang, Li Mei ; Geisen, Stefan - \ 2020
    Soil Biology and Biochemistry 148 (2020). - ISSN 0038-0717
    Fertilization - High-throughput sequencing - Microbiome functioning - Nitrogen - Phagotrophic protists

    The soil microbiome determines crop production and drives nutrient cycling, functions that are altered by fertilization. Yet, we have only begun to understand the effects of fertilization on taxonomic changes on soil microorganisms, while impacts on functional groups across the microbiome and therefore potential soil functioning have never been assessed. Here, using a range of methods including high-throughput sequencing, we identified 77 functional parameters of the main microbiome groups including bacteria, fungi, and protists in three common agricultural soil types in China (black, fluvo-aquic, and red soil), which were fertilized in the same way over two years. We show that fertilization most strongly and generally throughout soil types reduced the relative abundance of the main microbial predators, phagotrophic protists, by 31%. Ten functional groups within the microbiome showed soil type-specific responses to fertilization. For example, ammonia-oxidizing bacteria, and predatory/exoparasitic bacteria were reduced by fertilization in the acidic black and the red soils, while, no other microbial functional group than phagotrophic protists was suppressed by fertilization in the alkaline fluvo-aquic soil. The significant reductions in microbial functional groups especially in acidic soils could be explained by nitrogen enrichment, increased soil acidification and potential biotic links between the functional groups within the microbiome. Together, we show that the fertilization-induced abiotic changes alter microbial functions that depend on the soil and environmental conditions. Particularly the most profound changes on the group of microbial predators might subsequently affect other soil functions performed by bacteria and fungi.

    Impacts of nitrogen fertilizer type and application rate on soil acidification rate under a wheat-maize double cropping system
    Hao, Tianxiang ; Zhu, Qichao ; Zeng, Mufan ; Shen, Jianbo ; Shi, Xiaojun ; Liu, Xuejun ; Zhang, Fusuo ; Vries, Wim de - \ 2020
    Journal of Environmental Management 270 (2020). - ISSN 0301-4797
    Ammonium chloride - Cropland - Soil acidification - Soil pH - Urea

    Nitrogen (N) fertilizer-induced soil acidification in Chinese croplands is well-known, but insight in the impacts of different N fertilizer management approaches (fertilizer type and rate) on soil acidification rates is very limited. Here, we conducted a field experiment on a moderate acid soil to quantify soil acidification rates in response to N fertilization by different fertilizer types and N rates through monitoring the fate of elements (mainly nutrients) related to H+ production and consumption. Two N fertilizer types (urea and NH4Cl) and three N rates (control, optimized and conventional, 0/120/240 kg N ha−1 for wheat, 0/160/320 kg N ha−1 for maize) were included. Nitrogen addition led to an average H+ production of 4.0, 8.7, 11.4, 29.7 and 52.6 keq ha−1 yr−1, respectively, for the control, optimized urea, conventional urea, optimized NH4Cl and conventional NH4Cl plots. This was accompanied with a decline in soil base saturation of 1–10% and in soil pH of 0.1–0.7 units in the topsoil (0–20 cm). Removal of base cations by crop harvesting and N transformations contributed ~70% and ~20% to the H+ production in the urea treated plots, being ~20% and ~75% in the NH4Cl treated plots, respectively. The large NH4+ input via fertilization in the NH4Cl treated plots strongly enhanced the H+ production induced by N transformations. The low contribution of N transformations to the H+ production in the urea treated plots was due to the limited NO3 leaching, induced by the high N losses to air caused by denitrification. Increased N addition by urea, however, strongly increased H+ production by enhanced plant uptake of base cations, mainly due to a large potassium uptake in straw. Our results highlight the important role of optimizing fertilizer form and N rate as well as straw return to the field in alleviating soil acidification.

    Protein A-mesoporous silica composites for chromatographic purification of immunoglobulin G
    Huang, Si ; Cheng, Si Yuan ; Zhang, Shu Yuan ; Yan, Yi Lun ; Cai, Song Liang ; Li, Xin Le ; Zheng, Sheng Run ; Fan, Jun ; Zhang, Wei Guang - \ 2020
    New Journal of Chemistry 44 (2020)19. - ISSN 1144-0546 - p. 7884 - 7890.

    The development of a robust and efficient stationary phase for chromatographic biopharmaceutical purification is of prime importance but remains challenging. Herein, we have developed a series of protein A-mesoporous silica composites for the first time by covalently coupling protein A with the tagged carbonyl imidazole moieties in the column, which constitutes a facile and efficient route for the preparation of protein A immunoaffinity materials. The resultant composites are employed as the stationary phase for chromatographic purification of immunoglobulin G (IgG). The effect of silica's pore size and coupled protein A on the antibody purification is systematically investigated. When the pore size of silica increased from 100 to 1000 Å, the amount of coupled protein A decreased, and the surface coverage on the silica significantly improved, accompanied by an increase in the amount of purified rabbit IgG. With an increasing coupled protein A, the surface coverage increased at first and decreased subsequently, which shows a similar trend to the amount of purified IgG and specific activity. When practically implemented for purifying several immunoglobulins that are central for commercial ELISA Kits, the protein A-mesoporous silica composite exhibited superior performance compared to the GE-Mabselcetxtra rProtein A column, particularly in the purification of immunoglobulin M (IgM), which cannot be realized by the GE-Mabselcetxtra rProtein A column. This study sheds new light on the rational development of protein-affinity chromatography for biopharmaceutical purification.

    Late-spring frost risk between 1959 and 2017 decreased in North America but increased in Europe and Asia
    Zohner, Constantin M. ; Mo, Lidong ; Renner, Susanne S. ; Svenning, Jens Christian ; Vitasse, Yann ; Benito, Blas M. ; Ordonez, Alejandro ; Baumgarten, Frederik ; Bastin, Jean François ; Sebald, Veronica ; Reich, Peter B. ; Liang, Jingjing ; Nabuurs, Gert Jan ; De-Migueln, Sergio ; Alberti, Giorgio ; Antón-Fernández, Clara ; Balazy, Radomir ; Brändli, Urs Beat ; Chen, Han Y.H. ; Chisholm, Chelsea ; Cienciala, Emil ; Dayanandan, Selvadurai ; Fayle, Tom M. ; Frizzera, Lorenzo ; Gianelle, Damiano ; Jagodzinski, Andrzej M. ; Jaroszewicz, Bogdan ; Jucker, Tommaso ; Kepfer-Rojas, Sebastian ; Khan, Mohammed Latif ; Kim, Hyun Seok ; Korjus, Henn ; Johannsen, Vivian Kvist ; Laarmann, Diana ; Langn, Mait ; Zawila-Niedzwiecki, Tomasz ; Niklaus, Pascal A. ; Paquette, Alain ; Pretzsch, Hans ; Saikia, Purabi ; Schall, Peter ; Seben, Vladimír ; Svoboda, Miroslav ; Tikhonova, Elena ; Viana, Helder ; Zhang, Chunyu ; Zhao, Xiuhai ; Crowther, Thomas W. - \ 2020
    Proceedings of the National Academy of Sciences of the United States of America 117 (2020)22. - ISSN 0027-8424
    Climate change - Freezing damage - Late frost - Phenology - Spring leaf-out

    Late-spring frosts (LSFs) affect the performance of plants and animals across the world's temperate and boreal zones, but despite their ecological and economic impact on agriculture and forestry, the geographic distribution and evolutionary impact of these frost events are poorly understood. Here, we analyze LSFs between 1959 and 2017 and the resistance strategies of Northern Hemisphere woody species to infer trees' adaptations for minimizing frost damage to their leaves and to forecast forest vulnerability under the ongoing changes in frost frequencies. Trait values on leaf-out and leaf-freezing resistance come from up to 1,500 temperate and boreal woody species cultivated in common gardens. We find that areas in which LSFs are common, such as eastern North America, harbor tree species with cautious (late-leafing) leaf-out strategies. Areas in which LSFs used to be unlikely, such as broad-leaved forests and shrublands in Europe and Asia, instead harbor opportunistic tree species (quickly reacting to warming air temperatures). LSFs in the latter regions are currently increasing, and given species' innate resistance strategies, we estimate that ∼35% of the European and ∼26% of the Asian temperate forest area, but only ∼10% of the North American, will experience increasing late-frost damage in the future. Our findings reveal region-specific changes in the spring-frost risk that can inform decision-making in land management, forestry, agriculture, and insurance policy.

    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.

    Gut dysbacteriosis and intestinal disease: mechanism and treatment
    Meng, X. ; Zhang, G. ; Cao, H. ; Yu, D. ; Fang, X. ; Vos, W.M. de; Wu, H. - \ 2020
    Journal of Applied Microbiology (2020). - ISSN 1364-5072
    gut microbiome - immune response - intestinal diseases - prebiotics - probiotics

    The gut microbiome functions like an endocrine organ, generating bioactive metabolites, enzymes or small molecules that can impact host physiology. Gut dysbacteriosis is associated with many intestinal diseases including (but not limited to) inflammatory bowel disease, primary sclerosing cholangitis-IBD, irritable bowel syndrome, chronic constipation, osmotic diarrhoea and colorectal cancer. The potential pathogenic mechanism of gut dysbacteriosis associated with intestinal diseases includes the alteration of composition of gut microbiota as well as the gut microbiota–derived signalling molecules. The many correlations between the latter and the susceptibility for intestinal diseases has placed a spotlight on the gut microbiome as a potential novel target for therapeutics. Currently, faecal microbial transplantation, dietary interventions, use of probiotics, prebiotics and drugs are the major therapeutic tools utilized to impact dysbacteriosis and associated intestinal diseases. In this review, we systematically summarized the role of intestinal microbiome in the occurrence and development of intestinal diseases. The potential mechanism of the complex interplay between gut dysbacteriosis and intestinal diseases, and the treatment methods are also highlighted.

    Steering protein and salt ad- and desorption by an electrical switch applied to polymer-coated electrodes
    Fritz, P.A. ; Zhang, P. ; Bruschinski, Tom ; Sahin, S. ; Smet, L.C.P.M. de; Chan-Park, M.B. ; Boom, R.M. ; Schroën, C.G.P.H. - \ 2020
    Separation and Purification Technology 250 (2020). - ISSN 1383-5866
    Although solid-phase chromatography is a well-established method for protein separation, chemically intensive and often costly regeneration steps are needed to make reuse of the adsorbent possible. Here, we demonstrate the use of electrochemical principles as sustainable alternative. We make use of spontaneous adsorption of proteins to solid electrodes and reverse this process by applying an electric potential to regenerate the interface. This allows for adsorption of proteins to take place at 0 V difference between the electrodes, due to electrostatic interactions between the protein and the electrode surface. The desorption is then triggered by applying a potential difference (−1.2 V) between the electrodes.

    It is demonstrated that the incorporation of negatively charged polystyrene sulfonate (PSS) or positively charged polydiallyldimethylammonium chloride (PDMAC) in or on top of the respective activated carbon electrodes increases the amount of exchanged protein from 1 to 10 mg g−1, as compared to simple activated carbon electrodes. Interestingly, salt ad- and desorption occurs in opposite cycles compared to protein ad- and desorption, resulting in simultaneous concentration and desalting of the protein when 0 V is applied. On top of that, we also found that an enrichment in β-lactoglobulin could be achieved starting from whey protein isolate. These results clearly demonstrate that electrochemical technologies can be used not only for protein separation (including removal of salt), but also for protein fractionation, while not requiring solvent use.
    Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing
    Lieven, Christian ; Beber, Moritz E. ; Olivier, Brett G. ; Bergmann, Frank T. ; Ataman, Meric ; Babaei, Parizad ; Bartell, Jennifer A. ; Blank, Lars M. ; Chauhan, Siddharth ; Correia, Kevin ; Diener, Christian ; Dräger, Andreas ; Ebert, Birgitta E. ; Edirisinghe, Janaka N. ; Faria, José P. ; Feist, Adam M. ; Fengos, Georgios ; Fleming, Ronan M.T. ; García-Jiménez, Beatriz ; Hatzimanikatis, Vassily ; Helvoirt, Wout van; Henry, Christopher S. ; Hermjakob, Henning ; Herrgård, Markus J. ; Kaafarani, Ali ; Kim, Hyun Uk ; King, Zachary ; Klamt, Steffen ; Klipp, Edda ; Koehorst, Jasper J. ; König, Matthias ; Lakshmanan, Meiyappan ; Lee, Dong Yup ; Lee, Sang Yup ; Lee, Sunjae ; Lewis, Nathan E. ; Liu, Filipe ; Ma, Hongwu ; Machado, Daniel ; Mahadevan, Radhakrishnan ; Maia, Paulo ; Mardinoglu, Adil ; Medlock, Gregory L. ; Monk, Jonathan M. ; Nielsen, Jens ; Nielsen, Lars Keld ; Nogales, Juan ; Nookaew, Intawat ; Palsson, Bernhard O. ; Papin, Jason A. ; Patil, Kiran R. ; Poolman, Mark ; Price, Nathan D. ; Resendis-Antonio, Osbaldo ; Richelle, Anne ; Rocha, Isabel ; Sánchez, Benjamín J. ; Schaap, Peter J. ; Malik Sheriff, Rahuman S. ; Shoaie, Saeed ; Sonnenschein, Nikolaus ; Teusink, Bas ; Vilaça, Paulo ; Vik, Jon Olav ; Wodke, Judith A.H. ; Xavier, Joana C. ; Yuan, Qianqian ; Zakhartsev, Maksim ; Zhang, Cheng - \ 2020
    Nature Biotechnology 38 (2020)4. - ISSN 1087-0156 - 1 p.

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    Genome-wide identification of small G protein ROPs and their potential roles in Solanaceous family
    Yang, Shuqing ; Yan, Ningning ; Bouwmeester, Klaas ; Na, Ren ; Zhang, Zhiwei ; Zhao, Jun - \ 2020
    Gene 753 (2020). - ISSN 0378-1119
    Genome-wide screening - Phylogenetic analysis - Plant growth and development - Plant immunity - Small GTPase ROPs - Solanaceous family

    Small GTPases function as molecular switches to active or inactive signaling cascades via binding or hydrolyzing GTP. A type of plant specific small GTPases, the ROPs are known to be involved in plant growth, development and immunity. We determined whether ROPs are conserved in Solanaceous species and whether they are involved in plant growth, development and resistance against Phytophthora capsisi. In genome-wide screening, a total of 66 ROPs in six Solanaceous species (SolROPs) were identified, including 16 ROPs in Solanum tuberosum L. (potato), 9 in Solanum lycopersicum L. (tomato), 5 in Solanum melongena L. (eggplant), 9 in Capsicum annuum L. (pepper), 13 in Nicotiana benthamiana Domin and 14 in Nicotiana tabacum L. (tobacco). Phylogenetic analysis revealed that 11 AtROPs and 66 SolROPs fall into five distinct clades (I-V) and hence a novel and systematic gene nomenclature was proposed. In addition, a comprehensive expression analysis was performed by making use of an online database. This revealed that ROP genes are differentially expressed during plant growth and development. Moreover, gene expression of SlROP-II.1 in S. lycopersicum could be significantly induced by P. capsici. Subsequently, SlROP-II.1 and its homologues in N. benthamiana and C. annuum (NbROP-II.1 and CaROP-II.1) were selected for functional analysis using virus-induced gene silencing. Infection assays with P. capsici on silenced plants revealed that SlROP-II.1, NbROP-II.1 and CaROP-II.1 play a role in P. capsici resistance, suggesting conserved function of ROP-II clade across different Solanaceous species. In addition, NbROP-II.1 is also involved in regulating plant growth and development. This study signified the diversity of Solanaceous ROPs and their potential roles in plant growth, development and immunity.

    Substantial differences occur between canopy and ambient climate : Quantification of interactions in a greenhouse-canopy system
    Westreenen, A. van; Zhang, N. ; Douma, J.C. ; Evers, J.B. ; Anten, N.P.R. ; Marcelis, L.F.M. - \ 2020
    PLoS ONE 15 (2020)5. - ISSN 1932-6203 - p. e0233210 - e0233210.

    Organ temperature and variation therein plays a key role in plant functioning and its responses to e.g. climate change. There is a strong feedback between organ, especially leaf, temperature and the climate within the canopy (canopy climate), which in turn interacts with the climate outside the canopy (ambient climate). For greenhouses, the determinants of this interplay and how they drive differences between canopy and ambient climate are poorly understood. Yet, as many experiments on both regular greenhouse crops and field crops are done in greenhouses, this is crucial to know. Therefore, we designed an experiment to quantify the differences between ambient and canopy climate and leaf temperature. A path analysis was performed to quantify the interactions between components of the greenhouse canopy-climate system. We found that with high radiation the canopy climate can be up to 5°C cooler than the ambient climate, while for cloudy days this was only 2°C. Canopy relative humidity (RH) was up to 25% higher compared to ambient RH. We showed that radiation is very important for these climate differences, but that this effect could be partly counteracted by turning off supplementary light (i.e. due to its indirect effects e.g. changing light distribution). Leaf temperature was substantially different, both higher and lower, from the canopy air temperature. This difference was determined by leaf area index (LAI), temperature of the heating pipe and the use of supplementary light, which all strongly influence radiation, either shortwave or thermal radiation. The difference between leaf and ambient air temperature could be decreased by decreasing the LAI or increasing the temperature of the heating pipe.

    Improvement in municipal wastewater treatment alters lake nitrogen to phosphorus ratios in populated regions
    Tong, Yindong ; Wang, Mengzhu ; Peñuelas, Josep ; Liu, Xueyan ; Paerl, Hans W. ; Elser, James J. ; Sardans, Jordi ; Couture, Raoul Marie ; Larssen, Thorjørn ; Hu, Hongying ; Dong, Xin ; He, Wei ; Zhang, Wei ; Wang, Xuejun ; Zhang, Yang ; Liu, Yi ; Zeng, Siyu ; Kong, Xiangzhen ; Janssen, Annette B.G. ; Lin, Yan - \ 2020
    Proceedings of the National Academy of Sciences of the United States of America 117 (2020)21. - ISSN 0027-8424
    Anthropogenic source - Aquatic ecosystem - Nutrient balance - Wastewater treatment - Water quality change

    Large-scale and rapid improvement in wastewater treatment is common practice in developing countries, yet this influence on nutrient regimes in receiving waterbodies is rarely examined at broad spatial and temporal scales. Here, we present a study linking decadal nutrient monitoring data in lakes with the corresponding estimates of five major anthropogenic nutrient discharges in their surrounding watersheds over time. Within a continuous monitoring dataset covering the period 2008 to 2017, we find that due to different rates of change in TN and TP concentrations, 24 of 46 lakes, mostly located in China's populated regions, showed increasing TN/TP mass ratios; only 3 lakes showed a decrease. Quantitative relationships between in-lake nutrient concentrations (and their ratios) and anthropogenic nutrient discharges in the surrounding watersheds indicate that increase of lake TN/TP ratios is associated with the rapid improvement in municipal wastewater treatment. Due to the higher removal efficiency of TP compared with TN, TN/TP mass ratios in total municipal wastewater discharge have continued to increase from a median of 10.7 (95% confidence interval, 7.6 to 15.1) in 2008 to 17.7 (95% confidence interval, 13.2 to 27.2) in 2017. Improving municipal wastewater collection and treatment worldwide is an important target within the 17 sustainable development goals set by the United Nations. Given potential ecological impacts on biodiversity and ecosystem function of altered nutrient ratios in wastewater discharge, our results suggest that long-term strategies for domestic wastewater management should not merely focus on total reductions of nutrient discharges but also consider their stoichiometric balance.

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