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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Risk perception and management strategies in farming systems of southern Mali
Huet, E.K. ; Adam, Myriam ; Giller, K.E. ; Traore, Bouba ; Coulibaly, S. ; Descheemaeker, K.K.E. - \ 2019
Land–atmosphere interactions in the tropics – a review
Gentine, Pierre ; Massmann, Adam ; Lintner, Benjamin R. ; Hamed Alemohammad, Sayed ; Fu, Rong ; Green, Julia K. ; Kennedy, Daniel ; Vilà-Guerau De Arellano, Jordi - \ 2019
Hydrology and Earth System Sciences 23 (2019)10. - ISSN 1027-5606 - p. 4171 - 4197.
The continental tropics play a leading role in the terrestrial energy, water, and carbon cycles. Land–atmosphere interactions are integral in the regulation of these fluxes across multiple spatial and temporal scales over tropical continents. We review here some of the important characteristics of tropical continental climates and how land–atmosphere interactions regulate them. Along with a wide range of climates, the tropics manifest a diverse array of land–atmosphere interactions. Broadly speaking, in tropical rainforest climates, light and energy are typically more limiting than precipitation and water supply for photosynthesis and evapotranspiration (ET), whereas in savanna and semi-arid climates, water is the critical regulator of surface fluxes and land–atmosphere interactions. We discuss the impact of the land surface, how it affects shallow and deep clouds, and how these clouds in turn can feed back to the surface by modulating surface radiation and precipitation. Some results from recent research suggest that shallow clouds may be especially critical to land–atmosphere interactions. On the other hand, the impact of land-surface conditions on deep convection appears to occur over larger, nonlocal scales and may be a more relevant land–atmosphere feedback mechanism in transitional dry-to-wet regions and climate regimes.
Dawn of the pyrocene
Stoof, Cathelijne - \ 2019
Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
Bolyen, Evan ; Rideout, Jai Ram ; Dillon, Matthew R. ; Bokulich, Nicholas A. ; Abnet, Christian C. ; Al-Ghalith, Gabriel A. ; Alexander, Harriet ; Alm, Eric J. ; Arumugam, Manimozhiyan ; Asnicar, Francesco ; Bai, Yang ; Bisanz, Jordan E. ; Bittinger, Kyle ; Brejnrod, Asker ; Brislawn, Colin J. ; Brown, C.T. ; Callahan, Benjamin J. ; Caraballo-Rodríguez, Andrés Mauricio ; Chase, John ; Cope, Emily K. ; Silva, Ricardo Da; Diener, Christian ; Dorrestein, Pieter C. ; Douglas, Gavin M. ; Durall, Daniel M. ; Duvallet, Claire ; Edwardson, Christian F. ; Ernst, Madeleine ; Estaki, Mehrbod ; Fouquier, Jennifer ; Gauglitz, Julia M. ; Gibbons, Sean M. ; Gibson, Deanna L. ; Gonzalez, Antonio ; Gorlick, Kestrel ; Guo, Jiarong ; Hillmann, Benjamin ; Holmes, Susan ; Holste, Hannes ; Huttenhower, Curtis ; Huttley, Gavin A. ; Janssen, Stefan ; Jarmusch, Alan K. ; Jiang, Lingjing ; Kaehler, Benjamin D. ; Kang, Kyo Bin ; Keefe, Christopher R. ; Keim, Paul ; Kelley, Scott T. ; Knights, Dan ; Koester, Irina ; Kosciolek, Tomasz ; Kreps, Jorden ; Langille, Morgan G.I. ; Lee, Joslynn ; Ley, Ruth ; Liu, Yong Xin ; Loftfield, Erikka ; Lozupone, Catherine ; Maher, Massoud ; Marotz, Clarisse ; Martin, Bryan D. ; McDonald, Daniel ; McIver, Lauren J. ; Melnik, Alexey V. ; Metcalf, Jessica L. ; Morgan, Sydney C. ; Morton, Jamie T. ; Naimey, Ahmad Turan ; Navas-Molina, Jose A. ; Nothias, Louis Felix ; Orchanian, Stephanie B. ; Pearson, Talima ; Peoples, Samuel L. ; Petras, Daniel ; Preuss, Mary Lai ; Pruesse, Elmar ; Rasmussen, Lasse Buur ; Rivers, Adam ; Robeson, Michael S. ; Rosenthal, Patrick ; Segata, Nicola ; Shaffer, Michael ; Shiffer, Arron ; Sinha, Rashmi ; Song, Se Jin ; Spear, John R. ; Swafford, Austin D. ; Thompson, Luke R. ; Torres, Pedro J. ; Trinh, Pauline ; Tripathi, Anupriya ; Turnbaugh, Peter J. ; Ul-Hasan, Sabah ; Hooft, Justin J.J. van der; Vargas, Fernando ; Vázquez-Baeza, Yoshiki ; Vogtmann, Emily ; Hippel, Max von; Walters, William ; Wan, Yunhu ; Wang, Mingxun ; Warren, Jonathan ; Weber, Kyle C. ; Williamson, Charles H.D. ; Willis, Amy D. ; Xu, Zhenjiang Zech ; Zaneveld, Jesse R. ; Zhang, Yilong ; Zhu, Qiyun ; Knight, Rob ; Caporaso, J.G. - \ 2019
Nature Biotechnology (2019). - ISSN 1087-0156

In the version of this article initially published, some reference citations were incorrect. The three references to Jupyter Notebooks should have cited Kluyver et al. instead of Gonzalez et al. The reference to Qiita should have cited Gonzalez et al. instead of Schloss et al. The reference to mothur should have cited Schloss et al. instead of McMurdie & Holmes. The reference to phyloseq should have cited McMurdie & Holmes instead of Huber et al. The reference to Bioconductor should have cited Huber et al. instead of Franzosa et al. And the reference to the biobakery suite should have cited Franzosa et al. instead of Kluyver et al. The errors have been corrected in the HTML and PDF versions of the article.

Characterisation of the effect of day length, and associated differences in dietary intake, on the gut microbiota of Soay sheep
Thomas, Nadine A. ; Olvera-Ramírez, Andrea M. ; Abecia, Leticia ; Adam, Clare L. ; Edwards, Joan E. ; Cox, Georgina F. ; Findlay, Patricia A. ; Destables, Elodie ; Wood, Tracy A. ; McEwan, Neil R. - \ 2019
Archives of Microbiology 201 (2019)7. - ISSN 0302-8933 - p. 889 - 896.
Anaerobic fungi - Bacteria - Ciliated protozoa - Day length - Digestive tract - Soay sheep

Differences in the rumen bacterial community have been previously reported for Soay sheep housed under different day length conditions. This study extends this previous investigation to other organs of the digestive tract, as well as the analysis of ciliated protozoa and anaerobic fungi. The detectable concentrations of ciliated protozoa and anaerobic fungi decreased with increased day length in both the rumen and large colon, unlike those of bacteria where no effect was observed. Conversely, bacterial community composition was affected by day length in both the rumen and large colon, but the community composition of the detectable ciliated protozoa and anaerobic fungi was not affected. Day length-associated differences in the bacterial community composition extended to all of the organs examined, with the exception of the duodenum and the jejunum. It is proposed that differences in rumen fill and ruminal ‘by-pass’ nutrients together with endocrinological changes cause the observed effects of day length on the different gut microbial communities.

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
Bolyen, Evan ; Rideout, Jai Ram ; Dillon, Matthew R. ; Bokulich, Nicholas A. ; Abnet, Christian C. ; Al-Ghalith, Gabriel A. ; Alexander, Harriet ; Alm, Eric J. ; Arumugam, Manimozhiyan ; Asnicar, Francesco ; Bai, Yang ; Bisanz, Jordan E. ; Bittinger, Kyle ; Brejnrod, Asker ; Brislawn, Colin J. ; Brown, Titus C. ; Callahan, Benjamin J. ; Caraballo-Rodríguez, Andrés Mauricio ; Chase, John ; Cope, Emily K. ; Silva, Ricardo da; Diener, Christian ; Dorrestein, Pieter C. ; Douglas, Gavin M. ; Durall, Daniel M. ; Duvallet, Claire ; Edwardson, Christian F. ; Ernst, Madeleine ; Estaki, Mehrbod ; Fouquier, Jennifer ; Gauglitz, Julia M. ; Gibbons, Sean M. ; Gibson, Deanna L. ; Gonzalez, Antonio ; Gorlick, Kestrel ; Guo, Jiarong ; Hillmann, Benjamin ; Holmes, Susan ; Holste, Hannes ; Huttenhower, Curtis ; Huttley, Gavin A. ; Janssen, Stefan ; Jarmusch, Alan K. ; Jiang, Lingjing ; Kaehler, Benjamin D. ; Kang, Kyo Bin ; Keefe, Christopher R. ; Keim, Paul ; Kelley, Scott T. ; Knights, Dan ; Koester, Irina ; Kosciolek, Tomasz ; Kreps, Jorden ; Langille, Morgan G.I. ; Lee, Joslynn ; Ley, Ruth ; Liu, Yong Xin ; Loftfield, Erikka ; Lozupone, Catherine ; Maher, Massoud ; Marotz, Clarisse ; Martin, Bryan D. ; McDonald, Daniel ; McIver, Lauren J. ; Melnik, Alexey V. ; Metcalf, Jessica L. ; Morgan, Sydney C. ; Morton, Jamie T. ; Naimey, Ahmad Turan ; Navas-Molina, Jose A. ; Nothias, Louis Felix ; Orchanian, Stephanie B. ; Pearson, Talima ; Peoples, Samuel L. ; Petras, Daniel ; Preuss, Mary Lai ; Pruesse, Elmar ; Rasmussen, Lasse Buur ; Rivers, Adam ; Robeson, Michael S. ; Rosenthal, Patrick ; Segata, Nicola ; Shaffer, Michael ; Shiffer, Arron ; Sinha, Rashmi ; Song, Se Jin ; Spear, John R. ; Swafford, Austin D. ; Thompson, Luke R. ; Torres, Pedro J. ; Trinh, Pauline ; Tripathi, Anupriya ; Turnbaugh, Peter J. ; Ul-Hasan, Sabah ; Hooft, Justin J.J. van der; Vargas, Fernando ; Vázquez-Baeza, Yoshiki ; Vogtmann, Emily ; Hippel, Max von; Walters, William ; Wan, Yunhu ; Wang, Mingxun ; Warren, Jonathan ; Weber, Kyle C. ; Williamson, Charles H.D. ; Willis, Amy D. ; Xu, Zhenjiang Zech ; Zaneveld, Jesse R. ; Zhang, Yilong ; Zhu, Qiyun ; Knight, Rob ; Caporaso, J.G. - \ 2019
Nature Biotechnology 37 (2019)8. - ISSN 1087-0156 - p. 852 - 857.
The potential for pre-, pro- and synbiotics in the management of infants at risk of cow's milk allergy or with cow's milk allergy: An exploration of the rationale, available evidence and remaining questions
Fox, Adam ; Bird, J.A. ; Fiocchi, Alessandro ; Knol, Jan ; Meyer, Rosan ; Salminen, Seppo ; Sitang, Gong ; Szajewska, Hania ; Papadopoulos, Nikolaos - \ 2019
World Allergy Organization Journal 12 (2019)5. - ISSN 1939-4551
Allergy - Anaphylaxis - Bifidobacteria - Cow's milk allergy - Dysbiosis - IgE - Lactobacilli - Microbiota - Prebiotic - Probiotic - Synbiotic - World Allergy Organization

Cow's milk allergy is one of the most commonly reported childhood food allergies, with increasing incidence, persistence and severity in many countries across the world. The World Allergy Organization Special Committee on Food Allergy has identified cow's milk allergy as an area in need of a rationale-based approach in order to make progress against what it considered an onerous problem, with worldwide public health impact. There is growing interest in the potential role of the gut microbiota in the early programming and development of immune responses and allergy. This discussion paper considers the rationale and available evidence for modulation of the gut microbiota and for the use of synbiotics in the management of infants at risk of, or living with cow's milk allergy and summarizes remaining research questions that need to be answered for the development of evidence-based recommendations.

The in vivo developmental toxicity of diethylstilbestrol (DES) in rat evaluated by an alternative testing strategy
Adam, Aziza Hussein Bakheit ; Zhang, Mengying ; Haan, Laura H.J. de; Ravenzwaay, Bennard van; Louisse, Jochem ; Rietjens, Ivonne M.C.M. - \ 2019
Archives of Toxicology 93 (2019)7. - ISSN 0340-5761 - p. 2021 - 2033.
Developmental toxicity - Diethylstilbestrol - Estrogen receptor alpha (ERα) - Physiologically based kinetic modelling - Reverse dosimetry

In the present study, we evaluated an alternative testing strategy to quantitatively predict the in vivo developmental toxicity of the synthetic hormone diethylstilbestrol (DES). To this end, a physiologically based kinetic (PBK) model was defined that was subsequently used to translate concentration–response data for the in vitro developmental toxicity of DES, obtained in the ES-D3 cell differentiation assay, into predicted in vivo dose–response data for developmental toxicity. The previous studies showed that the PBK model-facilitated reverse dosimetry approach is a useful approach to quantitatively predict the developmental toxicity of several developmental toxins. The results obtained in the present study show that the PBK model adequately predicted DES blood concentrations in rats. Further studies revealed that DES tested positive in the ES-D3 differentiation assay and that DES-induced inhibition of the ES-D3 cell differentiation could be counteracted by the estrogen receptor alpha (ERα) antagonist fulvestrant, indicating that the in vitro ES-D3 cell differentiation assay was able to mimic the role of ERα reported in the mode of action underlying the developmental toxicity of DES in vivo. In spite of this, combining these in vitro data with the PBK model did not adequately predict the in vivo developmental toxicity of DES in a quantitative way. It is concluded that although the EST qualifies DES as a developmental toxin and detects the role of ERα in this process, the ES-D3 cell differentiation assay of the EST apparently does not adequately capture the processes underlying DES-induced developmental toxicity in vivo.

A specific synbiotic-containing amino acid-based formula restores gut microbiota in non-IgE mediated cow's milk allergic infants: A randomized controlled trial
Wopereis, Harm ; Ampting, Marleen T.J. Van; Cetinyurek-Yavuz, Aysun ; Slump, Rob ; Candy, David C.A. ; Butt, Assad M. ; Peroni, Diego G. ; Vandenplas, Yvan ; Fox, Adam T. ; Shah, Neil ; Roeselers, Guus ; Harthoorn, Lucien F. ; Michaelis, Louise J. ; Knol, Jan ; West, Christina E. - \ 2019
Clinical and Translational Allergy 9 (2019)1. - ISSN 2045-7022
Cow's milk allergy - Gut microbiota - Pediatrics - Prebiotics - Probiotics

Background: Altered gut microbiota is implicated in cow's milk allergy (CMA) and differs markedly from healthy, breastfed infants. Infants who suffer from severe CMA often rely on cow's milk protein avoidance and, when breastfeeding is not possible, on specialised infant formulas such as amino-acid based formulas (AAF). Herein, we report the effects of an AAF including specific synbiotics on oral and gastrointestinal microbiota of infants with non-IgE mediated CMA with reference to healthy, breastfed infants. Methods: In this prospective, randomized, double-blind controlled study, infants with suspected non-IgE mediated CMA received test or control formula. Test formula was AAF with synbiotics (prebiotic fructo-oligosaccharides and probiotic Bifidobacterium breve M-16V). Control formula was AAF without synbiotics. Healthy, breastfed infants were used as a separate reference group (HBR). Bacterial compositions of faecal and salivary samples were analysed by 16S rRNA-gene sequencing. Faecal analysis was complemented with the analysis of pH, short-chain fatty acids (SCFAs) and lactic acids. Results: The trial included 35 test subjects, 36 controls, and 51 HBR. The 16S rRNA-gene sequencing revealed moderate effects of test formula on oral microbiota. In contrast, the gut microbiota was substantially affected across time comparing test with control. In both groups bacterial diversity increased over time but was characterised by a more gradual increment in test compared to control. Compositionally this reflected an enhancement of Bifidobacterium spp. and Veillonella sp. in the test group. In contrast, the control-fed infants showed increased abundance of adult-like species, mainly within the Lachnospiraceae family, as well as within the Ruminococcus and Alistipes genus. The effects on Bifidobacterium spp. and Lachnospiraceae spp. were previously confirmed through enumeration by fluorescent in situ hybridization and were shown for test to approximate the proportions observed in the HBR. Additionally, microbial activity was affected as evidenced by an increase of l-lactate, a decrease of valerate, and reduced concentrations of branched-chain SCFAs in test versus control. Conclusions: The AAF including specific synbiotics effectively modulates the gut microbiota and its metabolic activity in non-IgE mediated CMA infants bringing it close to a healthy breastfed profile. Trial registration Registered on 1 May 2013 with Netherlands Trial Register Number NTR3979.

Enzyme promiscuity shapes adaptation to novel growth substrates
Guzmán, Gabriela I. ; Sandberg, Troy E. ; LaCroix, Ryan A. ; Nyerges, Ákos ; Papp, Henrietta ; Raad, Markus de; King, Zachary A. ; Hefner, Ying ; Northen, Trent R. ; Notebaart, Richard A. ; Pál, Csaba ; Palsson, Bernhard O. ; Papp, Balázs ; Feist, Adam M. - \ 2019
Molecular Systems Biology 15 (2019)4. - ISSN 1744-4292 - p. e8462 - e8462.
adaptive evolution - enzyme promiscuity - genome‐scale modeling - systems biology

Evidence suggests that novel enzyme functions evolved from low-level promiscuous activities in ancestral enzymes. Yet, the evolutionary dynamics and physiological mechanisms of how such side activities contribute to systems-level adaptations are not well characterized. Furthermore, it remains untested whether knowledge of an organism's promiscuous reaction set, or underground metabolism, can aid in forecasting the genetic basis of metabolic adaptations. Here, we employ a computational model of underground metabolism and laboratory evolution experiments to examine the role of enzyme promiscuity in the acquisition and optimization of growth on predicted non-native substrates in Escherichia coli K-12 MG1655. After as few as approximately 20 generations, evolved populations repeatedly acquired the capacity to grow on five predicted non-native substrates-D-lyxose, D-2-deoxyribose, D-arabinose, m-tartrate, and monomethyl succinate. Altered promiscuous activities were shown to be directly involved in establishing high-efficiency pathways. Structural mutations shifted enzyme substrate turnover rates toward the new substrate while retaining a preference for the primary substrate. Finally, genes underlying the phenotypic innovations were accurately predicted by genome-scale model simulations of metabolism with enzyme promiscuity.

Forest decision support systems for the analysis of ecosystem services provisioning at the landscape scale under global climate and market change scenarios
Nordström, Eva-Maria ; Nieuwenhuis, Maarten ; Başkent, Emin Zeki ; Biber, Peter ; Black, Kevin ; Borges, Jose G. ; Bugalho, Miguel N. ; Corradini, Giulia ; Corrigan, Edwin ; Eriksson, Ljusk Ola ; Felton, Adam ; Forsell, Nicklas ; Hengeveld, Geerten ; Hoogstra-Klein, Marjanke ; Korosuo, Anu ; Lindbladh, Matts ; Lodin, Isak ; Lundholm, Anders ; Marto, Marco ; Masiero, Mauro ; Mozgeris, Gintautas ; Pettenella, Davide ; Poschenrieder, Werner ; Sedmak, Robert ; Tucek, Jan ; Zoccatelli, Davide - \ 2019
European Journal of Forest Research 138 (2019)4. - ISSN 1612-4669 - p. 561 - 581.
Sustainable forest management is driving the development of forest decision support systems (DSSs) to include models and methods concerned with climate change, biodiversity and various ecosystem services (ESs). The future development of forest landscapes is very much dependent on how forest owners act and what goes on in the wider world; thus, models are needed that incorporate these aspects. The objective of this study is to assess how nine European state-of-the-art forest DSSs cope with these issues. The assessment focuses on the ability of these DSSs to generate landscape-level scenarios to explore the output of current and alternative forest management models (FMMs) in terms of a range of ESs and the robustness of these FMMs in the face of increased risks and uncertainty. Results show that all DSSs assessed in this study can be used to quantify the impacts of both stand- and landscape-level FMMs on the provision of a range of ESs over a typical planning horizon. DSSs can be used to assess how timber price trends may impact that provision over time. The inclusion of forest owner behavior as reflected by the adoption of specific FMMs seems to be also in the reach of all DSSs. Nevertheless, some DSSs need more data and development of models to estimate the impacts of climate change on biomass production and other ESs. Spatial analysis functionality needs to be further developed for a more accurate assessment of the landscape-level output of ESs from both current and alternative FMMs.
The shufflon of IncI1 plasmids is rearranged constantly during different growth conditions
Brouwer, Michael S.M. ; Jurburg, Stephanie D. ; Harders, Frank ; Kant, Arie ; Mevius, Dik J. ; Roberts, Adam P. ; Bossers, Alex - \ 2019
Plasmid 102 (2019). - ISSN 0147-619X - p. 51 - 55.

One of the factors that can affect conjugation of IncI1 plasmids, amongst others, is the genetic region known as the shufflon. This multiple inversion system modifies the pilus tip proteins used during conjugation, thus affecting the affinity for different recipient cells. Although recombination is known to occur in in vitro conditions, little is known about the regulation and the extent of recombination that occurs. To measure the recombination of the shufflon, we have amplified the entire shufflon region and sequenced the amplicons using nanopore long-read sequencing. This method was effective to determine the order of the segments of the shufflon and allow for the analysis of the shufflon variants that are present in a heterogeneous pool of templates. Analysis was performed over different growth phases and after addition of cefotaxime. Furthermore, analysis was performed in different E. coli host cells to determine if recombination is likely to be influenced. Recombination of the shufflon was constantly ongoing in all conditions that were measured, although no differences in the amount of different shufflon variants or the rate at which novel variants were formed could be found. As previously reported, some variants were abundant in the population while others were scarce. This leads to the conclusion that the shufflon is continuously recombining at a constant rate, or that the method used here was not sensitive enough to detect differences in this rate. For one of the plasmids, the host cell appeared to have an effect on the specific shufflon variants that were formed which were not predominant in another host, indicating that host factors may be involved. As previously reported, the pilV-A and pilV-A' ORFs are formed at higher frequencies than other pilV ORFs. These results demonstrate that the recombination that occurs within the shufflon is not random. While any regulation of the shufflon affected by these in vitro conditions could not be revealed, the method of amplifying large regions for long-read sequencing for the analysis of multiple inversion systems proved effective.

A model to examine farm household trade-offs and synergies with an application to smallholders in Vietnam
Ditzler, Lenora ; Komarek, Adam M. ; Chiang, Tsai Wei ; Alvarez, Stéphanie ; Chatterjee, Shantonu Abe ; Timler, Carl ; Raneri, Jessica E. ; Carmona, Natalia Estrada ; Kennedy, Gina ; Groot, Jeroen C.J. - \ 2019
Agricultural Systems 173 (2019). - ISSN 0308-521X - p. 49 - 63.
FarmDESIGN model - Farmer livelihoods - Labor - Multi-objective optimization - Nutrition - Soil organic matter

Farm models have the potential to describe farming systems and livelihoods, identify trade-offs and synergies, and provide ex-ante assessments of agricultural technologies and policies. We developed three new modules related to budget, labor, and human nutrition for the bio-economic whole-farm model ‘FarmDESIGN’. The expanded model positions the farming enterprise within the farm household. We illustrate the model's new capabilities for farm households in two villages in Northwest Vietnam, where we conducted multi-objective optimization to identify options for improving the farm households' current performance on key sustainability and livelihood indicators. Modeling results suggest trade-offs between environmental, economic, and social objectives are common, although not universal. The new modules increase the scope for modeling flows of resources (namely cash, labor, and food) between the farm enterprise and the farm household, as well as beyond the farm gate. This allows conducting modeling explorations, optimization routines, and scenario analyses in farming systems research.

Homoeostatic maintenance of nonstructural carbohydrates during the 2015–2016 El Niño drought across a tropical forest precipitation gradient
Dickman, Lee Turin ; McDowell, Nate G. ; Grossiord, Charlotte ; Collins, Adam D. ; Wolfe, Brett T. ; Detto, Matteo ; Wright, S.J. ; Medina-Vega, José A. ; Goodsman, Devin ; Rogers, Alistair ; Serbin, Shawn P. ; Wu, Jin ; Ely, Kim S. ; Michaletz, Sean T. ; Xu, Chonggang ; Kueppers, Lara ; Chambers, Jeffrey Q. - \ 2019
Plant, Cell & Environment 42 (2019)5. - ISSN 0140-7791 - p. 1705 - 1714.
climate - ENSO - NSC - Panama - storage - sugars - tropics - vegetation

Nonstructural carbohydrates (NSCs) are essential for maintenance of plant metabolism and may be sensitive to short- and long-term climatic variation. NSC variation in moist tropical forests has rarely been studied, so regulation of NSCs in these systems is poorly understood. We measured foliar and branch NSC content in 23 tree species at three sites located across a large precipitation gradient in Panama during the 2015–2016 El Niño to examine how short- and long-term climatic variation impact carbohydrate dynamics. There was no significant difference in total NSCs as the drought progressed (leaf P = 0.32, branch P = 0.30) nor across the rainfall gradient (leaf P = 0.91, branch P = 0.96). Foliar soluble sugars decreased while starch increased over the duration of the dry period, suggesting greater partitioning of NSCs to storage than metabolism or transport as drought progressed. There was a large variation across species at all sites, but total foliar NSCs were positively correlated with leaf mass per area, whereas branch sugars were positively related to leaf temperature and negatively correlated with daily photosynthesis and wood density. The NSC homoeostasis across a wide range of conditions suggests that NSCs are an allocation priority in moist tropical forests.

High-Resolution Mapping of Nitrogen Dioxide With TROPOMI : First Results and Validation Over the Canadian Oil Sands
Griffin, Debora ; Zhao, Xiaoyi ; McLinden, Chris A. ; Boersma, Folkert ; Bourassa, Adam ; Dammers, Enrico ; Degenstein, Doug ; Eskes, Henk ; Fehr, Lukas ; Fioletov, Vitali ; Hayden, Katherine ; Kharol, Shailesh K. ; Li, Shao Meng ; Makar, Paul ; Martin, Randall V. ; Mihele, Cristian ; Mittermeier, Richard L. ; Krotkov, Nickolay ; Sneep, Maarten ; Lamsal, Lok N. ; Linden, Mark ter; Geffen, Jos van; Veefkind, Pepijn ; Wolde, Mengistu - \ 2019
Geophysical Research Letters 46 (2019)2. - ISSN 0094-8276 - p. 1049 - 1060.
nitrogen dioxide - OMI - TROPOMI

TROPOspheric Monitoring Instrument (TROPOMI), on-board the Sentinel-5 Precurser satellite, is a nadir-viewing spectrometer measuring reflected sunlight in the ultraviolet, visible, near-infrared, and shortwave infrared. From these spectra several important air quality and climate-related atmospheric constituents are retrieved, including nitrogen dioxide (NO2) at unprecedented spatial resolution from a satellite platform. We present the first retrievals of TROPOMI NO2 over the Canadian Oil Sands, contrasting them with observations from the Ozone Monitoring Instrument satellite instrument, and demonstrate TROPOMI's ability to resolve individual plumes and highlight its potential for deriving emissions from individual mining facilities. Further, the first TROPOMI NO2 validation is presented, consisting of aircraft and surface in situ NO2 observations, and ground-based remote-sensing measurements between March and May 2018. Our comparisons show that the TROPOMI NO2 vertical column densities are highly correlated with the aircraft and surface in situ NO2 observations, and the ground-based remote-sensing measurements with a low bias (15–30 %); this bias can be reduced by improved air mass factors.

The Effect of Psyllium Husk on Intestinal Microbiota in Constipated Patients and Healthy Controls
Jalanka, Jonna ; Major, Giles ; Murray, Kathryn ; Singh, Gulzar ; Nowak, Adam ; Kurtz, Caroline ; Silos-Santiago, Inmaculada ; Johnston, Jeffrey M. ; Vos, Willem M. de; Spiller, Robin - \ 2019
International Journal of Molecular Sciences 20 (2019)2. - ISSN 1661-6596
constipation - ispaghula - microbiome - prebiotics - transit

Psyllium is a widely used treatment for constipation. It traps water in the intestine increasing stool water, easing defaecation and altering the colonic environment. We aimed to assess the impact of psyllium on faecal microbiota, whose key role in gut physiology is being increasingly recognised. We performed two randomised, placebo-controlled, double-blinded trials comparing 7 days of psyllium with a placebo (maltodextrin) in 8 healthy volunteers and 16 constipated patients respectively. We measured the patients' gastrointestnal (GI) transit, faecal water content, short-chain fatty acid (SCFA) and the stool microbiota composition. While psyllium supplement had a small but significant effect on the microbial composition of healthy adults (increasing Veillonella and decreasing Subdoligranulum), in constipated subjects there were greater effects on the microbial composition (increased Lachnospira, Faecalibacterium, Phascolarctobacterium, Veillonella and Sutterella and decreased uncultured Coriobacteria and Christensenella) and alterations in the levels of acetate and propionate. We found several taxa to be associated with altered GI transit, SCFAs and faecal water content in these patients. Significant increases in three genera known to produce butyrate, Lachnospira, Roseburia and Faecalibacterium, correlated with increased faecal water. In summary, psyllium supplementation increased stool water and this was associated with significant changes in microbiota, most marked in constipated patients.

A specific synbiotic-containing amino acid-based formula in dietary management of cow's milk allergy : A randomized controlled trial
Fox, Adam T. ; Wopereis, Harm ; Ampting, Marleen T.J. van; Oude Nijhuis, Manon M. ; Butt, Assad M. ; Peroni, Diego G. ; Vandenplas, Yvan ; Candy, David C.A. ; Shah, Neil ; West, Christina E. ; Garssen, Johan ; Harthoorn, Lucien F. ; Knol, Jan ; Michaelis, Louise J. - \ 2019
Clinical and Translational Allergy 9 (2019)1. - ISSN 2045-7022
Bifidobacterium breve M-16V - Cow's milk allergy - Gut microbiota - Prebiotic - Probiotic - Symptoms

Background: Here we report follow-up data from a double-blind, randomized, controlled multicenter trial, which investigated fecal microbiota changes with a new amino acid-based formula (AAF) including synbiotics in infants with non-immunoglobulin E (IgE)-mediated cow's milk allergy (CMA). Methods: Subjects were randomized to receive test product (AAF including fructo-oligosaccharides and Bifidobacterium breve M-16V) or control product (AAF) for 8 weeks, after which infants could continue study product until 26 weeks. Fecal percentages of bifidobacteria and Eubacterium rectale/Clostridium coccoides group (ER/CC) were assessed at 0, 8, 12, and 26 weeks. Additional endpoints included stool markers of gut immune status, clinical symptoms, and safety assessments including adverse events and medication use. Results: The trial included 35 test subjects, 36 controls, and 51 in the healthy reference group. Study product was continued by 86% and 92% of test and control subjects between week 8-12, and by 71% and 80%, respectively until week 26. At week 26 median percentages of bifidobacteria were significantly higher in test than control [47.0% vs. 11.8% (p < 0.001)], whereas percentages of ER/CC were significantly lower [(13.7% vs. 23.6% (p = 0.003)]. Safety parameters were similar between groups. Interestingly use of dermatological medication and reported ear infections were lower in test versus control, p = 0.019 and 0.011, respectively. Baseline clinical symptoms and stool markers were mild (but persistent) and low, respectively. Symptoms reduced towards lowest score in both groups. Conclusion: Beneficial effects of this AAF including specific synbiotics on microbiota composition were observed over 26 weeks, and shown suitable for dietary management of infants with non-IgE-mediated CMA.

Rejoinder to Comments on Minasny et al., 2017 Soil carbon 4 per mille Geoderma 292, 59–86
Minasny, Budiman ; Arrouays, Dominique ; McBratney, Alex B. ; Angers, Denis A. ; Chambers, Adam ; Chaplot, Vincent ; Chen, Zueng Sang ; Cheng, Kun ; Das, Bhabani S. ; Field, Damien J. ; Gimona, Alessandro ; Hedley, Carolyn ; Hong, Suk Young ; Mandal, Biswapati ; Malone, Brendan P. ; Marchant, Ben P. ; Martin, Manuel ; McConkey, Brian G. ; Mulder, Vera Leatitia ; O'Rourke, Sharon ; Richer-de-Forges, Anne C. ; Odeh, Inakwu ; Padarian, José ; Paustian, Keith ; Pan, Genxing ; Poggio, Laura ; Savin, Igor ; Stolbovoy, Vladimir ; Stockmann, Uta ; Sulaeman, Yiyi ; Tsui, Chun Chih ; Vågen, Tor Gunnar ; Wesemael, Bas van; Winowiecki, Leigh - \ 2018
Geoderma 309 (2018). - ISSN 0016-7061 - p. 124 - 129.
Tailoring Agroecological Intensification to the context of Southern Mali: Co-learning Through Agronomic Experiments with Farmers
Huet, E.K. ; Descheemaeker, K.K.E. ; Adam, Myriam ; Dembélé, Ousmane ; Giller, K.E. - \ 2018
- 1 p.
Co-learning Through Agronomic Experiments with Farmers: Tailoring Agroecological Intensification to the context of Southern Mali
Huet, E.K. ; Descheemaeker, K.K.E. ; Adam, Myriam ; Dembélé, Ousmane ; Giller, K.E. - \ 2018
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