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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Fostering the development of climate services through Copernicus Climate Change Service (C3S) for agriculture applications
Buontempo, Carlo ; Hutjes, Ronald ; Beavis, Philip ; Berckmans, Julie ; Cagnazzo, Chiara ; Vamborg, Freja ; Thépaut, Jean Noël ; Bergeron, Cedric ; Almond, Samuel ; Amici, Alessandro ; Ramasamy, Selvaraju ; Dee, Dick - \ 2019
Weather and Climate Extremes (2019). - ISSN 2212-0947
Agriculture sector - Climate Data Store (CDS) - Copernicus Climate Change Services (C3S) - User-driven applications

To better understand and manage climate risks in climate-sensitive sectors such as agriculture, it is essential to have access to consistent and reliable data and information products. Tailoring these products to the needs of the users they want to serve facilitate informed decision-making and downstream applications. This requires an in-depth understanding of users' needs and the context in which these users operate. Considering the diversity of the economic sectors and their actors it is extremely challenging if not outright impossible to promote the emergence of climate services without empowering a plethora of intermediate users who can act as one of the steps in a potential long knowledge brokers chain that connect the climate data providers and the end-users. In this context, Copernicus Climate Change Service (C3S) has been designed around the Climate Data Store (CDS), a unique entry point to a huge variety of quality-controlled climate data and high-level utilities to process that data to develop user-driven applications. Through the Sectoral Information System, C3S has then developed a series of sector specific applications, which show how the infrastructure can be used to address specific users’ needs. This paper presents the key elements of the CDS and selected cases of sectoral application of C3S in agriculture.

N2Africa Annual Report 2019
Dontsop-Nguezet, Paul M. ; Ampadu-Boakye, Theresa ; Ronner, E. ; Baars, Edward ; Kanampiu, Fred ; Giller, K.E. ; Vanlauwe, B. ; Adjei-nsiah, Samuel ; Wolde-Meskel, E. ; Ebanyat, Peter ; Baijukya, Frederick ; Dianda, M. ; Sanginga, Jean-Marie ; Woomer, P.L. ; Chikowo, Regis ; Phiphira, Lloyd ; Kantengwa, Speciose ; Leonardo, W. ; Kamai, Nkeki ; Thuijsman, E.C. ; Schilt-van Ettekoven, C. - \ 2019
Wageningen : N2Africa (N2Africa project report 120) - 78 p.
Annual report, Key milestones, objectives, progress, biological nitrogen fixation, grain legumes, Nigeria, Borno State, Ghana, Tanzania, Ethiopia, Uganda, DR Congo, Rwanda, Kenya, Malawi, Zimbabwe, Mozambique
Genetically modified and biofortified crops and food security in developing countries: A review
Adeyeye, Samuel Ayofemi Olalekan ; Idowu-Adebayo, Folake - \ 2019
Nutrition & Food Science 49 (2019)5. - ISSN 0034-6659
Biofortified crops - Developing countries - Food security - Genetically modified crops - Review

Purpose: In recent times, science and technology has taken a front seat in revolutionizing agricultural production and food processing globally with noticeable impact on food, nutrition and family health. This study was carried out to have a critical review of genetically modified (GM) foods and the use of GM and biofortified crops for food security in developing countries where foods are not adequately available and people are not food secured. Design/methodology/approach: A critical review of GM foods was undertaken and the use of GM and biofortified crops for food security in developing countries where foods are not adequately available and people are not food secured was carried out. Findings: Currently, there are no recent patents on GM and biofortified crops and this shows that there are more works to be done by policymakers, regulatory agencies, consumers and right organizations on environmental, health and biosafety of GM and biofortified crops. Advances in science and technology have changed our relationship with nature which enables crops to be modified and improved through selective breeding to obtain more stronger and productive crops. However, despite the benefits and improvements from GM and biofortified crops, controversy and arguments have continued to trail the consumption of GM and biofortified crops because of the perceived safety issues. Although genetic engineering has helped in developing fast-growing and pest-resistant crops, as well as reduction in use of pesticides, however, its impact on the environment and the consumers cannot be overemphasized. In conclusion, this study showed that the role of GM and biofortified crops for food security is the subject of public controversy; however, genetic engineering has the potential to improve world food production, increase food availability and influence farmers’ income and thus their economic access to food but the attendance potential risks related to food safety and avoidable environmental hazards should not be overlooked. There is need for comprehensive information on the impact of GM and biofortified crops on environment, human health and biosafety of the crops. Research limitations/implications: Few available literatures on the subject matter were critically reviewed. Practical implications: The paper helps in creating awareness for more in-depth research on GM and biofortified crops and their impacts on food security in developing countries where foods are not adequately available and people are not food secured. Originality/value: This research is of value to the researchers, policymakers and regulatory agencies in developing countries on food safety.

Effectiveness of Panama as an intercontinental land bridge for large mammals
Meyer, Ninon F.V. ; Moreno, Ricardo ; Sutherland, Christopher ; Torre, J.A. de la; Esser, Helen J. ; Jordan, Christopher A. ; Olmos, Melva ; Ortega, Josué ; Reyna-Hurtado, Rafael ; Valdes, Samuel ; Jansen, Patrick A. - \ 2019
Conservation Biology (2019). - ISSN 0888-8892
Bayesian statistics - community-level distribution - hierarchical occupancy modeling - landscape connectivity - Mesoamerican Biological Corridor - Neotropical forest

Habitat fragmentation is a primary driver of wildlife loss, and establishment of biological corridors is a common strategy to mitigate this problem. A flagship example is the Mesoamerican Biological Corridor (MBC), which aims to connect protected forest areas between Mexico and Panama to allow dispersal and gene flow of forest organisms. Because forests across Central America have continued to degrade, the functioning of the MBC has been questioned, but reliable estimates of species occurrence were unavailable. Large mammals are suitable indicators of forest functioning, so we assessed their conservation status across the Isthmus of Panama, the narrowest section of the MBC. We used large-scale camera-trap surveys and hierarchical multispecies occupancy models in a Bayesian framework to estimate the occupancy of 9 medium to large mammals and developed an occupancy-weighted connectivity metric to evaluate species-specific functional connectivity. White-lipped peccary (Tayassu pecari), jaguar (Panthera onca), giant anteater (Myrmecophaga tridactyla), white-tailed deer (Odocoileus virginianus), and tapir (Tapirus bairdii) had low expected occupancy along the MBC in Panama. Puma (Puma concolor), red brocket deer (Mazama temama), ocelot (Leopardus pardalis), and collared peccary (Pecari tajacu), which are more adaptable, had higher occupancy, even in areas with low forest cover near infrastructure. However, the majority of species were subject to ≥1 gap that was larger than their known dispersal distances, suggesting poor connectivity along the MBC in Panama. Based on our results, forests in Darien, Donoso–Santa Fe, and La Amistad International Park are critical for survival of large terrestrial mammals in Panama and 2 areas need restoration.

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.

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.
Astin C Production by the Endophytic Fungus Cyanodermella asteris in Planktonic and Immobilized Culture Conditions
Vassaux, Antoine ; Tarayre, Cédric ; Arguëlles-Arias, Anthony ; Compère, Philippe ; Delvigne, Frank ; Fickers, Patrick ; Jahn, Linda ; Lang, Alexander ; Leclère, Valérie ; Ludwig-Müller, Jutta ; Ongena, Marc ; Schafhauser, Thomas ; Telek, Samuel ; Théatre, Ariane ; Berkel, Willem J.H. van; Vandenbol, Micheline ; Pée, Karl Heinz van; Willems, Luc ; Wohlleben, Wolfgang ; Jacques, Philippe - \ 2019
Biotechnology Journal 14 (2019)8. - ISSN 1860-6768
astin C - biofilms - Cyanodermella asteris - immobilized-cell cultures - secondary metabolites

The fungal endophyte Cyanodermella asteris (C. asteris) has been recently isolated from the medicinal plant Aster tataricus (A. tataricus). This fungus produces astin C, a cyclic pentapeptide with anticancer and anti-inflammatory properties. The production of this secondary metabolite is compared in immobilized and planktonic conditions. For immobilized cultures, a stainless steel packing immersed in the culture broth is used as a support. In these conditions, the fungus exclusively grows on the packing, which provides a considerable advantage for astin C recovery and purification. C. asteris metabolism is different according to the culture conditions in terms of substrate consumption rate, cell growth, and astin C production. Immobilized-cell cultures yield a 30% increase of astin C production, associated with a 39% increase in biomass. The inoculum type as spores rather than hyphae, and a pre-inoculation washing procedure with sodium hydroxide, turns out to be beneficial both for astin C production and fungus development onto the support. Finally, the influence of culture parameters such as pH and medium composition on astin C production is evaluated. With optimized culture conditions, astin C yield is further improved reaching a five times higher final specific yield compared to the value reported with astin C extraction from A. tataricus (0.89 mg g−1 and 0.16 mg g−1 respectively).

Identifying Dietary Strategies to Improve Nutrient Adequacy among Ethiopian Infants and Young Children Using Linear Modelling
Samuel, Aregash ; Osendarp, Saskia J.M. ; Ferguson, Elaine ; Borgonjen, Karin ; Alvarado, Brenda M. ; Neufeld, Lynnette M. ; Adish, Abdulaziz ; Kebede, Amha ; Brouwer, Inge D. - \ 2019
Nutrients 11 (2019)6. - ISSN 2072-6643
complementary food - Ethiopia - food-based dietary recommendations - nutrient adequacy - Optifood analysis

Nutrient adequacy of young children's diet and best possible strategies to improve nutrient adequacy were assessed. Data from the Ethiopian National Food Consumption Survey were analysed using Optifood (software for linear programming) to identify nutrient gaps in diets for children (6-8, 9-11 and 12-23 months), and to formulate feasible Food-Based Dietary Recommendations (FBDRs) in four regions which differ in culture and food practices. Alternative interventions including a local complementary food, micronutrient powders (MNPs), Small quantity Lipid-based Nutrient Supplement (Sq-LNS) and combinations of these were modelled in combination with the formulated FBDRs to compare their relative contributions. Risk of inadequate and excess nutrient intakes was simulated using the Estimated Average Requirement cut-point method and the full probability approach. Optimized local diets did not provide adequate zinc in all regions and age groups, iron for infants <12 months of age in all regions, and calcium, niacin, thiamine, folate, vitamin B12 and B6 in some regions and age-groups. The set of regional FBDRs, considerably different for four regions, increased nutrient adequacy but some nutrients remained sub-optimal. Combination of regional FBDRs with daily MNP supplementation for 6-12 months of age and every other day for 12-23 months of age, closed the identified nutrient gaps without leading to a substantial increase in the risk of excess intakes.

Measuring P deficiency in maize leaves: comparing spectral and wet chemical measurements under tropical conditions
Ravensbergen, Paul ; Hijbeek, R. ; Njoroge, Samuel ; Carstensen, A. ; Berge, H.F.M. ten; Ittersum, M.K. van - \ 2019
Bioturbation of Ag2S-NPs in soil columns by earthworms
Baccaro, Marta ; Harrison, Samuel ; Berg, Hans van den; Sloot, Laura ; Hermans, Davy ; Cornelis, Geert ; Gestel, Cornelis A.M. van; Brink, Nico W. van den - \ 2019
Environmental Pollution 252 (2019). - ISSN 0269-7491 - p. 155 - 162.
Bioturbation - Earthworms - Nanoparticles - Soil - Transport

Sewage sludge contains Ag2S-NPs causing NP exposure of soil fauna when sludge is applied as soil amendment. Earthworm bioturbation is an important process affecting many soil functions. Bioturbation may be affected by the presence of Ag2S-NPs, but the earthworm activity itself may also influence the displacement of these NPs that otherwise show little transport in the soil. The aim of this study was to determine effects of Ag2S-NPs on earthworm bioturbation and effect of this bioturbation on the vertical distribution of Ag2S-NPs. Columns (12 cm) of a sandy loamy soil with and without Lumbricus rubellus were prepared with and without 10 mg Ag kg−1, applied as Ag2S-NPs in the top 2 cm of the soil, while artificial rainwater was applied at ∼1.2 mm day−1. The soil columns were sampled at three depths weekly for 28 days and leachate collected from the bottom. Total Ag measurements showed more displacement of Ag to deeper soil layers in the columns with earthworms. The application of rain only did not significantly affect Ag transport in the soil. No Ag was detected in column leachates. X-ray tomography showed that changes in macro porosity and pore size distribution as a result of bioturbation were not different between columns with and without Ag2S-NPs. Earthworm activity was therefore not affected by Ag2S-NPs at the used exposure concentration. Ag concentrations along the columns and the earthworm density allowed the calculation of the bioturbation rate. The effect on the Ag transport in the soil shows that earthworm burrowing activity is a relevant process that must be taken into account when studying the fate of nanoparticles in soils. Earthworm bioturbation plays a more important role than rainfall in the vertical transport of Ag2S-NPs in soil.

N2Africa Annual Report 2018
Ampadu-Boakye, Theresa ; Ronner, E. ; Kanampiu, Fred ; Giller, K.E. ; Baars, Edward ; Vanlauwe, B. ; Adjei-nsiah, Samuel ; Wolde-Meskel, E. ; Ebanyat, Peter ; Baijukya, Frederick ; Sanginga, Jean-Marie ; Woomer, P.L. ; Chikowo, Regis ; Phiphira, Lloyd ; Kantengwa, Speciose ; Leonardo, W. ; Kamai, Nkeki ; Thuijsman, E.C. ; Schilt-van Ettekoven, C. - \ 2019
Wageningen : N2Africa (N2Africa project report 111) - 77 p.
Annual report, Key milestones, objectives, progress, biological nitrogen fixation, grain legumes, Nigeria, Borno State, Ghana, Tanzania, Ethiopia, Uganda, DR Congo, Rwanda, Kenya, Malawi, Zimbabwe, Mozambique
Can yield variability be explained? Integrated assessment of maize yield gaps across smallholders in Ghana
Loon, Marloes P. van; Adjei-Nsiah, Samuel ; Descheemaeker, Katrien ; Akotsen-Mensah, Clement ; Dijk, Michiel van; Morley, Tom ; Ittersum, Martin K. van; Reidsma, Pytrik - \ 2019
Field Crops Research 236 (2019). - ISSN 0378-4290 - p. 132 - 144.
Crop experiments - Crop modelling - Farm household survey - Integrated assessment - Smallholder farms - Yield gaps - Yield potential

Agricultural production in Ghana should more than double to fulfil the estimated food demand in 2050, but this is a challenge as the productivity of food crops has been low, extremely variable and prone to stagnation. Yield gap estimations and explanations can help to identify the potential for intensification on existing agricultural land. However, to date most yield gap analyses had a disciplinary focus. The objective of this paper is to assess the impact of crop management, soil and household factors on maize (Zea mays) yields in two major maize growing regions in Ghana through an integrated approach. We applied a variety of complementary methods to study sites in the Brong Ahafo and Northern region. Farm household surveys, yield measurements and soil sampling were undertaken in 2015 and 2016. Water-limited potential yield (Y w ) was estimated with a crop growth simulation model, and two different on-farm demonstration experiments were carried out in 2016 and 2017. There is great potential to increase maize yields across the study sites. Estimated yield gaps ranged between 3.8 Mg ha −1 (67% of Y w ) and 13.6 Mg ha −1 (84% of Y w ). However, there was no consistency in factors affecting maize yield and yield gaps when using complementary methods. Demonstration experiments showed the potential of improved varieties, fertilizers and improved planting densities, with yields up to 9 Mg ha −1 . This was not confirmed in the analysis of the household surveys, as the large yield variation across years on the same farms impeded the disclosure of effects of management, soil and household factors. The low-input nature of the farming system and the incidence of fall armyworm led to relatively uniform and low yields across the entire population. So, farmers’ yields were determined by interacting, and strongly varying, household, soil and management factors. We found that for highly variable and complex smallholder farming systems there is a danger in drawing oversimplified conclusions based on results from a single methodological approach. Integrating household surveys, crop growth simulation modelling and demonstration experiments can add value to yield gap analysis. However, the challenge remains to improve upon this type of integrated assessment to be able to satisfactorily disentangle the interacting factors that can be managed by farmers in order to increase crop yields.

Correlating farmers' perception and sheep preference with the nutritional quality of grain legume fodders stored under different conditions
Akakpo, Daniel ; Oosting, S.J. ; Adjei-nsiah, Samuel ; Duncan, A. ; Boer, I.J.M. de; Giller, K.E. - \ 2019
In: Trade-Offs in Science - Keeping the balance. - Wageningen University & Research - p. 20 - 20.
The objective of the present study was to correlate farmers’ perception (FP), sheep preference (SP) and laboratory analysis (LA) of nutritional quality of stored grain legume fodders (GLFs). The GLFs of cowpea, groundnut and soybean were stored at 3-locations (rooftop, room and treefork) in -packaging types (polythene sacks or tied with ropes) for 120 days. FP was assessed by scoring the perceived quality of GLFs on a scale of 1 to 10 (1=bad and 0=good) based on physical appraisal by a group of farmers. SP was assessed by cafeteria feeding trial based on dry matter intake (DMI) of GLFs by a flock of 12 sheep during a 14 hr period. For LA, Organic Matter Digestibility (OMD) and Crude Protein (CP) content were assessed by Near Infra-Red Spectroscopy (NIRS). Cowpea scored higher FP (6.3) and SP (66 g DMI/14hr/sheep) than
groundnut (FP 5.5 and SP 59 g DMI/14hr/sheep) and soybean had lowest FP (2.3) and SP (39 g DMI/14hr/sheep). However, LA indicated that groundnut had higher CP content (140 g kg DM) than cowpea (115 g kg DM) and soybean (98 g kg DM). OMD, on the other hand, was higher in cowpea (686 g kg DM) than groundnut (659 g kg DM) and soybean (574 g kg DM). CP was positively orrelated with FP (r=0.35) and with SP (r=0.48). Similarly, OMD was positively correlated with FP (r=0.50) and with SP (r=0.70). Room storage had higher FP and SP than rooftop and treefork. Sack storage scored higher than tied on FP, SP and LA. The present study demonstrated that it is possible to used FP and SP to predict the nutritional quality of GLFs.
Learning from the soil's memory : Tailoring of fertilizer application based on past manure applications increases fertilizer use efficiency and crop productivity on Kenyan smallholder farms
Njoroge, Samuel ; Schut, Antonius G.T. ; Giller, Ken E. ; Zingore, Shamie - \ 2019
European Journal of Agronomy 105 (2019). - ISSN 1161-0301 - p. 52 - 61.
Past manure application - Sub-Saharan Africa - Yield response to fertilizers

The large uncertainty in yield response to fertilizer application within smallholder cropping systems in sub-Saharan Africa (SSA) limits efforts aimed at intensifying crop production based on increased fertilizer application. We assessed the key field-scale cause of variability in maize (Zea mays) grain yield response to fertilizer nitrogen (N), phosphorus (P) and potassium (K) in the Sidindi area of Western Kenya based on past manure application, distance from the homestead, and clay and silt contents. We used data from nutrient omission trials conducted on 23 farms over seven consecutive cropping seasons covering the period 2013–2016, without changing treatments or plot location. Treatments included a control and PK, NK, NP and NPK. Accounting for past manure application increased the explained variability in maize yield, and yield response to N, P, and K application. Mean treatment maize grain yield in the control, PK, NK, NP and NPK treatments were 1.0, 2.2, 1.5, 2.9 and 4.5 t ha −1 at 88% dry matter respectively in fields without past manure application, and 2.4, 2.7, 4.4, 4.9 and 5.4 t ha -1 in fields which had received animal manure in at least two out of three seasons prior to the start of the trials. Mean maize yield response to N, P and K application was 2.3, 3.0 and 1.6 t ha −1 respectively in fields without past manure application, and 2.8, 1.1 and 0.6 t ha −1 in fields with past manure application. In the seventh cropping season, past animal manure application contributed a fertilizer equivalent of 28.3, 29.8 and 31.5 kg ha −1 of N, P and K, respectively. At both the onset and at the start of the last season, fields with past animal manure application had on average higher contents of SOC, available P and exchangeable K, yet differences were not always significant within treatments. Accounting for past animal manure application reduces crop fertilizer requirements for P and K as well as decreasing uncertainty in yield response to fertilizer. We conclude that the strong influence of past animal manure application on yield response to fertilizer application merits the inclusion of past manure application as a co-variate in analysis of yield response data from smallholder cropping systems of SSA.

Soil parameters, land use, and geographical distance drive soil bacterial communities along a European transect
Plassart, Pierre ; Prévost-Bouré, Nicolas Chemidlin ; Uroz, Stéphane ; Dequiedt, Samuel ; Stone, Dorothy ; Creamer, Rachel ; Griffiths, Robert I. ; Bailey, Mark J. ; Ranjard, Lionel ; Lemanceau, Philippe - \ 2019
Scientific Reports 9 (2019). - ISSN 2045-2322

To better understand the relationship between soil bacterial communities, soil physicochemical properties, land use and geographical distance, we considered for the first time ever a European transect running from Sweden down to Portugal and from France to Slovenia. We investigated 71 sites based on their range of variation in soil properties (pH, texture and organic matter), climatic conditions (Atlantic, alpine, boreal, continental, Mediterranean) and land uses (arable, forest and grassland). 16S rRNA gene amplicon pyrosequencing revealed that bacterial communities highly varied in diversity, richness, and structure according to environmental factors. At the European scale, taxa area relationship (TAR) was significant, supporting spatial structuration of bacterial communities. Spatial variations in community diversity and structure were mainly driven by soil physicochemical parameters. Within soil clusters (k-means approach) corresponding to similar edaphic and climatic properties, but to multiple land uses, land use was a major driver of the bacterial communities. Our analyses identified specific indicators of land use (arable, forest, grasslands) or soil conditions (pH, organic C, texture). These findings provide unprecedented information on soil bacterial communities at the European scale and on the drivers involved; possible applications for sustainable soil management are discussed.

Trained immunity and diabetic vascular disease
Thiem, Kathrin ; Stienstra, Rinke ; Riksen, Niels P. ; Keating, Samuel T. - \ 2019
Clinical science 133 (2019)2. - ISSN 0143-5221 - p. 195 - 203.
Cardiovascular disease - Diabetes - Immunometabolism - Macrophage - Monocyte - Trained immunity

Trained immunity is a recently described phenomenon whereby innate immune cells undergo functional reprogramming in response to microbial products, vaccines, or other stimuli, leading them to mount a sensitized nonspecific response to subsequent stimulation. While it is essential for the host response to pathogens, many diseases are the product of excessive or chronic inflammation. Atherosclerosis is a disease characterized by chronic low-grade inflammation of the arterial wall leading to plaque formation, where macrophages are the most abundant cell regulating plaque progression and stability. Recent studies have revealed a role for endogenous compounds related to atherosclerosis in the induction of trained immunity, which can enhance the expression of genes implicated in atherosclerosis and associated cardiovascular disease. Accelerated atherosclerosis remains the principal cause of morbidity and premature mortality in patients with diabetes, and the burden of vascular complications is greatly enhanced by prior periods of inadequate control of blood glucose. Recent findings suggest that long-term changes in bone marrow myeloid progenitors, similar to those induced by microbial products or high cholesterol diets in mice, may help to explain the chronic inflammatory state driving atherosclerosis and cardiovascular risk that exists for patients with diabetes despite improved metabolic control. From an immunometabolic perspective, we speculate that changes supporting the trained macrophage phenotype, such as up-regulation of glycolysis, indicate that a high glucose environment could enhance the pro-inflammatory consequences of trained immunity thereby contributing to the accelerated progression of atherosclerosis in patients with diabetes.

Accelerating Metabolite Identification in Natural Product Research : Toward an Ideal Combination of Liquid Chromatography-High-Resolution Tandem Mass Spectrometry and NMR Profiling, in Silico Databases, and Chemometrics
Wolfender, Jean Luc ; Nuzillard, Jean Marc ; Hooft, Justin J.J. Van Der; Renault, Jean Hugues ; Bertrand, Samuel - \ 2019
Analytical Chemistry 91 (2019)1. - ISSN 0003-2700 - p. 704 - 742.
FEMA GRAS assessment of natural flavor complexes : Citrus-derived flavoring ingredients
Cohen, Samuel M. ; Eisenbrand, Gerhard ; Fukushima, Shoji ; Gooderham, Nigel J. ; Guengerich, F.P. ; Hecht, Stephen S. ; Rietjens, Ivonne M.C.M. ; Bastaki, Maria ; Davidsen, Jeanne M. ; Harman, Christie L. ; McGowen, Margaret ; Taylor, Sean V. - \ 2019
Food and Chemical Toxicology 124 (2019). - ISSN 0278-6915 - p. 192 - 218.
Botanical - Citrus - GRAS - Natural flavor complex - Safety evaluation

In 2015, the Expert Panel of the Flavor and Extract Manufacturers Association (FEMA) initiated a re-evaluation of the safety of over 250 natural flavor complexes (NFCs) used as flavoring ingredients. This publication is the first in a series and summarizes the evaluation of 54 Citrus-derived NFCs using the procedure outlined in Smith et al. (2005) and updated in Cohen et al. (2018) to evaluate the safety of naturally-occurring mixtures for their intended use as flavoring ingredients. The procedure relies on a complete chemical characterization of each NFC intended for commerce and organization of each NFC's chemical constituents into well-defined congeneric groups. The safety of the NFC is evaluated using the well-established and conservative threshold of toxicological concern (TTC) concept in addition to data on absorption, metabolism and toxicology of members of the congeneric groups and the NFC under evaluation. As a result of the application of the procedure, 54 natural flavor complexes derived from botanicals of the Citrus genus were affirmed as generally recognized as safe (GRAS) under their conditions of intended use as flavoring ingredients based on an evaluation of each NFC and the constituents and congeneric groups therein.

Models for assessing engineered nanomaterial fate and behaviour in the aquatic environment
Williams, Richard J. ; Harrison, Samuel ; Keller, Virginie ; Kuenen, Jeroen ; Lofts, Stephen ; Praetorius, Antonia ; Svendsen, Claus ; Vermeulen, Lucie C. ; Wijnen, Jikke van - \ 2019
Current Opinion in Environmental Sustainability 36 (2019). - ISSN 1877-3435 - p. 105 - 115.

Engineered nanomaterials (ENMs, material containing particles with at least one dimension less than 100 nm) are present in a range of consumer products and could be released into the environment from these products during their production, use or end-of-life. The high surface to volume ratio of nanomaterials imparts a high reactivity, which is of interest for novel applications but may raise concern for the environment. In the absence of measurement methods, there is a need for modelling to assess likely concentrations and fate arising from current and future releases. To assess the capability that exists to do such modelling, progress in modelling ENM fate since 2011 is reviewed. ENM-specific processes represented in models are mainly limited to aggregation and, in some instances, dissolution. Transformation processes (e.g. sulphidation), the role of the manufactured coatings, particle size distribution and particle form and state are still usually excluded. Progress is also being made in modelling ENMs at larger scales. Currently, models can give a reasonable assessment of the fate of ENMs in the environment, but a full understanding will likely require fuller inclusion of these ENM-specific processes.

Spatial variation of carbon and nutrients stocks in Amazonian Dark Earth
Brazao Vieira Alho, C.F. ; Samuel Rosa, A. ; Coimbra Martins, Gilvan ; Hiemstra, T. ; Kuijper, T.W.M. ; Teixeira, Wenceslau G. - \ 2019
Geoderma 337 (2019). - ISSN 0016-7061 - p. 322 - 332.
Amazonian Dark Earths (ADE) are anthropic soils that are enriched in carbon (C) and several nutrients, particularly calcium (Ca) and phosphorus (P), when compared to adjacent soils from the Amazon basin. Studies on ADE empower the understanding of complex pre-Columbian cultural development in the Amazon and may also provide insights for future sustainable agricultural practices in the tropics. ADE are highly variable in size, depth and soil physico-chemical characteristics. Nonetheless, the differentiation between ADE and the adjacent soils is not standardized and is commonly done based on visual field observations. In this regard, the pretic horizon has been recently proposed as an attempt to classify ADE systematically. Spatial modelling techniques can be of great use to study the structure of the spatial variation of soil properties in highly variable areas. Here, we predicted the carbon and nutrients stocks in ADE by applying spatial modelling techniques using an environmental covariate (i.e. expected anthropic enrichment gradient) in our model. In addition, we used the pretic horizon criteria to classify pretic and non-pretic areas and evaluate their relative contribution to the total stocks. In this study, we collected soil samples from five 20-cm soil layers at n = 53 georeferenced points placed in a grid of about 10 to 60 m spacing in a study area located in Central Amazon (~9.4 ha). Ceramic fragments were weighed and quantified. Samples were analysed for: Total C, Total Ca, Total P, Exchangeable Ca + Mg, Extractable P, soil pH, potential CEC (pH = 7.0) and the clay content. The use of the pretic horizon criteria allowed us to clearly distinguish two unambiguous areas with a sharp transition, rather than a smooth continuum, in contrast to previous studies in ADE. Depth- and profile-wise linear regression model parameters indicated a greater importance of the chosen environmental covariate (i.e. expected anthropic enrichment gradient) to explain the spatial variation of Total Ca and Total P stocks than Total C stocks. The overall Total Ca and Total P stocks were twice as large in the pretic area when compared to the non-pretic area.
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