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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    Challenges for Rural Livelihoods, Participatory Agroforestry, and Biodiversity Conservation in a Neotropical Biosphere Reserve in Mexico
    García-Barrios, Luis ; Cruz-Morales, Juana ; Braasch, Marco ; Dechnik-Vázquez, Yanus A. ; Gutiérrez-Navarro, Alonso ; Meza-Jiménez, Amayrani ; Rivera-Núñez, Tlacaelel ; Speelman, E.N. ; Trujillo-Díaz, Gabriela ; Valencia, Vivian ; Zabala, Aiora - \ 2020
    In: Participatory Biodiversity Conversation / Baldauf, Cristina, Springer - ISBN 9783030416850 - p. 69 - 89.
    Man and the Biosphere Programme - Participatory research - Rural livelihoods - Rural domestic groups (RDGs)
    We report on 10 years of participatory research processes linking livelihoods, agroforestry, and conservation in the La Sepultura Man and the Biosphere (MAB) Reserve in Chiapas, Mexico. These processes entail both cooperation and conflict between farmers and external actors who try to create and/or prevent the collapse of “nature-friendly” land uses. We developed a multidimensional research agenda with the participation of 12 communities and many graduate students. This agenda began with the promotion and monitoring of experimental fodder-tree plantations to counter dry season livestock starvation and forest degradation. Poor adoption of fodder trees motivated us to explore the history, conditions, needs, and motivations of farmers in this territory, and how these play out in their interaction with other actors when implementing agroforestry projects linked explicitly with biodiversity conservation. We report an analysis of three processes: (1) efforts to promote fodder-tree plantations as a means to intensify and move livestock production away from forest browsing; (2) “conservation” shade-coffee production in which benefits for farmers and forests are dubious, which also might collapse due to recent rust epidemics; (3) Pinus oocarpa resin extraction in pine-grass rangelands, where cattle exclusion, fire use prohibition, and unfavorable market deals could render this activity unsustainable. We reflect on how silvopastoral and agroforestry projects constitute an unstable balancing act among actors in this MAB reserve (and probably in similar ones). We discuss what participatory processes seem promising and need to be developed for the sake of long-term decent rural livelihoods and high-quality conservation landscapes.
    2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales
    Kuhn, Jens H. ; Adkins, Scott ; Alioto, Daniela ; Alkhovsky, Sergey V. ; Amarasinghe, Gaya K. ; Anthony, Simon J. ; Avšič-Županc, Tatjana ; Ayllón, María A. ; Bahl, Justin ; Balkema-Buschmann, Anne ; Ballinger, Matthew J. ; Bartonička, Tomáš ; Basler, Christopher ; Bavari, Sina ; Beer, Martin ; Bente, Dennis A. ; Bergeron, Éric ; Bird, Brian H. ; Blair, Carol ; Blasdell, Kim R. ; Bradfute, Steven B. ; Breyta, Rachel ; Briese, Thomas ; Brown, Paul A. ; Buchholz, Ursula J. ; Buchmeier, Michael J. ; Bukreyev, Alexander ; Burt, Felicity ; Buzkan, Nihal ; Calisher, Charles H. ; Cao, Mengji ; Casas, Inmaculada ; Chamberlain, John ; Chandran, Kartik ; Charrel, Rémi N. ; Chen, Biao ; Chiumenti, Michela ; Choi, Ryong ; Clegg, J.C.S. ; Crozier, Ian ; Graça, John V. da; Bó, Elena Dal; Dávila, Alberto M.R. ; Torre, Juan Carlos de la; Lamballerie, Xavier de; Swart, Rik L. de; Bello, Patrick L. Di; Paola, Nicholas Di; Serio, Francesco Di; Dietzgen, Ralf G. ; Digiaro, Michele ; Dolja, Valerian V. ; Dolnik, Olga ; Drebot, Michael A. ; Drexler, Jan Felix ; Dürrwald, Ralf ; Dufkova, Lucie ; Dundon, William G. ; Duprex, W.P. ; Dye, John M. ; Easton, Andrew J. ; Ebihara, Hideki ; Elbeaino, Toufic ; Ergünay, Koray ; Fernandes, Jorlan ; Fooks, Anthony R. ; Formenty, Pierre B.H. ; Forth, Leonie F. ; Fouchier, Ron A.M. ; Freitas-Astúa, Juliana ; Gago-Zachert, Selma ; Gāo, George Fú ; García, María Laura ; García-Sastre, Adolfo ; Garrison, Aura R. ; Gbakima, Aiah ; Goldstein, Tracey ; Gonzalez, Jean Paul J. ; Griffiths, Anthony ; Groschup, Martin H. ; Günther, Stephan ; Guterres, Alexandro ; Hall, Roy A. ; Hammond, John ; Hassan, Mohamed ; Hepojoki, Jussi ; Hepojoki, Satu ; Hetzel, Udo ; Hewson, Roger ; Hoffmann, Bernd ; Hongo, Seiji ; Höper, Dirk ; Horie, Masayuki ; Hughes, Holly R. ; Hyndman, Timothy H. ; Jambai, Amara ; Jardim, Rodrigo ; Jiāng, Dàohóng ; Jin, Qi ; Jonson, Gilda B. ; Junglen, Sandra ; Karadağ, Serpil ; Keller, Karen E. ; Klempa, Boris ; Klingström, Jonas ; Kobinger, Gary ; Kondō, Hideki ; Koonin, Eugene V. ; Krupovic, Mart ; Kurath, Gael ; Kuzmin, Ivan V. ; Laenen, Lies ; Lamb, Robert A. ; Lambert, Amy J. ; Langevin, Stanley L. ; Lee, Benhur ; Lemos, Elba R.S. ; Leroy, Eric M. ; Li, Dexin ; Lǐ, Jiànróng ; Liang, Mifang ; Liú, Wénwén ; Liú, Yàn ; Lukashevich, Igor S. ; Maes, Piet ; Marciel de Souza, William ; Marklewitz, Marco ; Marshall, Sergio H. ; Martelli, Giovanni P. ; Martin, Robert R. ; Marzano, Shin Yi L. ; Massart, Sébastien ; McCauley, John W. ; Mielke-Ehret, Nicole ; Minafra, Angelantonio ; Minutolo, Maria ; Mirazimi, Ali ; Mühlbach, Hans Peter ; Mühlberger, Elke ; Naidu, Rayapati ; Natsuaki, Tomohide ; Navarro, Beatriz ; Navarro, José A. ; Netesov, Sergey V. ; Neumann, Gabriele ; Nowotny, Norbert ; Nunes, Márcio R.T. ; Nylund, Are ; Økland, Arnfinn L. ; Oliveira, Renata C. ; Palacios, Gustavo ; Pallas, Vicente ; Pályi, Bernadett ; Papa, Anna ; Parrish, Colin R. ; Pauvolid-Corrêa, Alex ; Pawęska, Janusz T. ; Payne, Susan ; Pérez, Daniel R. ; Pfaff, Florian ; Radoshitzky, Sheli R. ; ul Rahman, Aziz ; Ramos-González, Pedro L. ; Resende, Renato O. ; Reyes, Carina A. ; Rima, Bertus K. ; Romanowski, Víctor ; Robles Luna, Gabriel ; Rota, Paul ; Rubbenstroth, Dennis ; Runstadler, Jonathan A. ; Ruzek, Daniel ; Sabanadzovic, Sead ; Salát, Jiří ; Sall, Amadou Alpha ; Salvato, Maria S. ; Sarpkaya, Kamil ; Sasaya, Takahide ; Schwemmle, Martin ; Shabbir, Muhammad Z. ; Shí, Xiǎohóng ; Shí, Zhènglì ; Shirako, Yukio ; Simmonds, Peter ; Širmarová, Jana ; Sironi, Manuela ; Smither, Sophie ; Smura, Teemu ; Song, Jin Won ; Spann, Kirsten M. ; Spengler, Jessica R. ; Stenglein, Mark D. ; Stone, David M. ; Straková, Petra ; Takada, Ayato ; Tesh, Robert B. ; Thornburg, Natalie J. ; Tomonaga, Keizō ; Tordo, Noël ; Towner, Jonathan S. ; Turina, Massimo ; Tzanetakis, Ioannis ; Ulrich, Rainer G. ; Vaira, Anna Maria ; Hoogen, Bernadette van den; Varsani, Arvind ; Vasilakis, Nikos ; Verbeek, Martin ; Wahl, Victoria ; Walker, Peter J. ; Wang, Hui ; Wang, Jianwei ; Wang, Xifeng ; Wang, Lin Fa ; Wèi, Tàiyún ; Wells, Heather ; Whitfield, Anna E. ; Williams, John V. ; Wolf, Yuri I. ; Wú, Zhìqiáng ; Yang, Xin ; Yáng, Xīnglóu ; Yu, Xuejie ; Yutin, Natalya ; Zerbini, Murilo ; Zhang, Tong ; Zhang, Yong Zhen ; Zhou, Guohui ; Zhou, Xueping - \ 2020
    Archives of Virology (2020). - ISSN 0304-8608

    In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

    Multiparental QTL analysis: can we do it in polyploids?
    Thérèse Navarro, A. ; Tumino, G. ; Visser, R.G.F. ; Voorrips, R.E. ; Weg, W.E. van de; Maliepaard, C. - \ 2020
    Acta Horticulturae 1283 (2020). - ISSN 0567-7572 - p. 55 - 64.
    Breeding populations - Family-based analysis - GWAS - IBD - Pedigree-based analysis

    Many ornamental crops are polyploid or even exist at different ploidy levels. Polyploid QTL analysis tools have been developed in recent years, yet they are limited in the population types they accept. Biparental populations are nowadays being regarded as a limited tool for QTL discovery, as only a limited number of QTLs occurs in an experimental cross and their effects might not be stable across genetic backgrounds. Genome-Wide Association Studies include more genetic diversity but suffer from (hidden) genetic structure and low frequency of QTL alleles. Both factors influence QTL detection and effect estimation, decreasing the sensitivity of QTL analysis. Alternatively, multiparental populations (MPP) can be used, potentially combining multiple QTLs and QTL alleles with known population structure and balanced allele frequencies. Breeding populations of interconnected crosses also constitute a form of MPP and QTLs identified in them might be more applicable to commercial cultivars. To perform QTL analysis in polyploids, mixed models or Bayesian approaches that consider pedigree information are recommended. During the analysis, QTL effects are ideally estimated using Identity by Descent (IBD) alleles (genomic regions that originate from the same ancestor) which can be obtained through haplotype estimation. Although MPPs could thus be a powerful set-up to estimate polyploid haplotypes, a software gap was identified as no current polyploid haplotyping tools are able to utilize MPP pedigree information to obtain haplotypes across an MPP. In order to utilize MPPs to their full extent and expand polyploid QTL analyses to encompass typical breeding populations, new haplotyping tools must be developed.

    Effect of mineral and vitamin C mix on growth performance and blood corticosterone concentrations in heat-stressed broilers
    Saiz del Barrio, A. ; Mansilla, W.D. ; Navarro-Villa, A. ; Mica, J.H. ; Smeets, J.H. ; Hartog, L.A. den; García-Ruiz, A.I. - \ 2020
    Journal of Applied Poultry Research 29 (2020)1. - ISSN 1056-6171 - p. 23 - 33.
    broilers - heat stress - mineral - nutrition - vitamin-C

    Heat stress is a major problem in the poultry industry, especially during summer months and when birds are raised under high-density conditions. Previous studies have reported that vitamin C or electrolyte supplementation could palliate the effects of heat stress in broiler chickens. The present study evaluated the effect of a mineral and vitamin mix (AHS) added to drinking water on the performance of broiler chickens. In total, 1,824 one-day-old birds were randomly allocated to 48 pens. Maximum animal density was 26.5 kg/m2. The control group received no additive; AHS-1 and -2 groups received the AHS mix at a concentration of 1 and 2 kg/1,000 L in drinking water, respectively; and the Vit-C group received vitamin C in drinking water at 200 g/1,000 L. All birds were fed the same diets based on a 3-phase feeding program; feed and water were given on ad libitum basis. To mimic heat stress conditions, temperature in the barn was raised to 35 C from 08:00 to 14:00 h each day. For the overall growing period (0 to 35 D), adding AHS to drinking water increased final BW, ADG, and ADFI linearly (PLinear < 0.05); FCR was decreased linearly with AHS supplementation (PLinear < 0.05). Final BW, ADG, and FCR for the Vit-C group were intermediate between AHS-2 and the control groups (P > 0.10). No significant effect on mortality were found (8.77%; P > 0.10). Relative to control, all the treatments tested reduced (P < 0.05) corticosterone concentration in blood serum. In conclusion, the combined use of supplementary levels of minerals and vitamins could alleviate the effects of heat stress on broilers chickens.

    Effects of an artificial hay aroma and compound feed formulation on feed intake pattern, rumen function and milk production in lactating dairy cows
    Binti Abd Rahim, Sholeha ; Laar, Harmen van; Dijkstra, J. ; Navarro-Villa, A. ; Fowers, R. ; Hendriks, W.H. ; Pellikaan, W.F. ; Leen, F. ; Martín-Tereso, J. - \ 2020
    Animal 14 (2020)3. - ISSN 1751-7311 - p. 529 - 537.
    The Kempen system is a dairy feeding system in which diet is provided in the form of a compound feed (CF) and hay offered ad libitum. Ad libitum access to CF and hay allows cows in this system to achieve a high DM intake (DMI). Out of physiological concerns, the voluntary hay intake could be increased and the consumption pattern of CF could be manipulated to maintain proper rumen functioning and health. This study investigated the effects of an artificial hay aroma and CF formulation on feed intake pattern, rumen function and milk production in mid- to late-lactating dairy cows. Twenty Holstein–Friesian cows were assigned to four treatments in a 4 × 4 Latin square design. Diet consisted of CF and grass hay (GH), fed separately, and both offered ad libitum, although CF supply was restricted in maximum meal size and speed of supply by an electronic system. Treatments were the combination of two CF formulations – high in starch (CHS) and fibre (CHF); and two GH – untreated (UGH) and the same hay treated with an artificial aroma (TGH). Meal criteria were determined using three-population Gaussian–Gaussian–Weibull density functions. No GH × CF interaction effects on feed intake pattern characteristics were found. Total DMI and CF intake, but not GH intake, were greater (P < 0.01) in TGH treatment, and feed intake was not affected by type of CF. Total visits to feeders per day, visits to the GH feeder, visits to the CF feeder and CF eating time (all P < 0.01) were significantly greater in cows fed with TGH. Meal frequency, meal size and meal duration were unaffected by treatments. Cows fed CHF had a greater milk fat (P = 0.02), milk urea content (P < 0.01) and a greater milk fat yield (P < 0.01). Cows fed TGH had a greater milk lactose content and lactose yield (P < 0.05), and milk urea content (P < 0.01). Cows fed TGH had smaller molar proportions of acetic acid and greater molar proportions of propionic acid compared with UGH. In conclusion, treatment of GH with an artificial aroma increased CF intake and total DMI, but did not affect hay intake. Additionally, GH treatment increased the frequency of visits to both feeders, and affected rumen volatile fatty acid profile. Type of CF did not affect meal patterns, ruminal pH, nor fermentation profiles.
    MIBiG 2.0: a repository for biosynthetic gene clusters of known function
    Kautsar, S.A. ; Blin, Kai ; Shaw, Simon ; Navarro Munoz, J.C. ; Terlouw, Barbara ; Hooft, J.J.J. van der; Santen, Jeffrey A. Van; Tracanna, V. ; Suarez Duran, Hernando ; Pascal Andreu, V. ; Selem Mojica, Nelly ; Alanjary, Mohammad ; Robinson, Serina ; Lund, George ; Epstein, Samuel C. ; Sisto, Ashley C. ; Charkoudian, Louise K. ; Collemare, Jérôme ; Linington, Roger G. ; Weber, Tilmann ; Medema, M.H. - \ 2020
    Nucleic acids research 48 (2020)D1. - ISSN 0305-1048 - p. D454 - D458.
    Fueled by the explosion of (meta)genomic data, genome mining of specialized metabolites has become a major technology for drug discovery and studying microbiome ecology. In these efforts, computational tools like antiSMASH have played a central role through the analysis of Biosynthetic Gene Clusters (BGCs). Thousands of candidate BGCs from microbial genomes have been identified and stored in public databases. Interpreting the function and novelty of these predicted BGCs requires comparison with a well-documented set of BGCs of known function. The MIBiG (Minimum Information about a Biosynthetic Gene Cluster) Data Standard and Repository was established in 2015 to enable curation and storage of known BGCs. Here, we present MIBiG 2.0, which encompasses major updates to the schema, the data, and the online repository itself. Over the past five years, 851 new BGCs have been added. Additionally, we performed extensive manual data curation of all entries to improve the annotation quality of our repository. We also redesigned the data schema to ensure the compliance of future annotations. Finally, we improved the user experience by adding new features such as query searches and a statistics page, and enabled direct link-outs to chemical structure databases. The repository is accessible online at https://mibig.secondarymetabolites.org/.
    How to measure, report and verify soil carbon change to realize the potential of soil carbon sequestration for atmospheric greenhouse gas removal
    Smith, Pete ; Soussana, Jean Francois ; Angers, Denis ; Schipper, Louis ; Chenu, Claire ; Rasse, Daniel P. ; Batjes, Niels H. ; Egmond, Fenny van; McNeill, Stephen ; Kuhnert, Matthias ; Arias-Navarro, Cristina ; Olesen, Jorgen E. ; Chirinda, Ngonidzashe ; Fornara, Dario ; Wollenberg, Eva ; Álvaro-Fuentes, Jorge ; Sanz-Cobena, Alberto ; Klumpp, Katja - \ 2020
    Global Change Biology 26 (2020)1. - ISSN 1354-1013 - p. 219 - 241.
    measurement - monitoring - MRV - reporting - soil organic carbon - soil organic matter - verification

    There is growing international interest in better managing soils to increase soil organic carbon (SOC) content to contribute to climate change mitigation, to enhance resilience to climate change and to underpin food security, through initiatives such as international ‘4p1000’ initiative and the FAO's Global assessment of SOC sequestration potential (GSOCseq) programme. Since SOC content of soils cannot be easily measured, a key barrier to implementing programmes to increase SOC at large scale, is the need for credible and reliable measurement/monitoring, reporting and verification (MRV) platforms, both for national reporting and for emissions trading. Without such platforms, investments could be considered risky. In this paper, we review methods and challenges of measuring SOC change directly in soils, before examining some recent novel developments that show promise for quantifying SOC. We describe how repeat soil surveys are used to estimate changes in SOC over time, and how long-term experiments and space-for-time substitution sites can serve as sources of knowledge and can be used to test models, and as potential benchmark sites in global frameworks to estimate SOC change. We briefly consider models that can be used to simulate and project change in SOC and examine the MRV platforms for SOC change already in use in various countries/regions. In the final section, we bring together the various components described in this review, to describe a new vision for a global framework for MRV of SOC change, to support national and international initiatives seeking to effect change in the way we manage our soils.

    A computational framework to explore large-scale biosynthetic diversity
    Navarro-Muñoz, Jorge C. ; Selem-Mojica, Nelly ; Mullowney, Michael W. ; Kautsar, Satria A. ; Tryon, James H. ; Parkinson, Elizabeth I. ; Los Santos, Emmanuel L.C. De; Yeong, Marley ; Cruz-Morales, Pablo ; Abubucker, Sahar ; Roeters, Arne ; Lokhorst, Wouter ; Fernandez-Guerra, Antonio ; Cappelini, Luciana Teresa Dias ; Goering, Anthony W. ; Thomson, Regan J. ; Metcalf, William W. ; Kelleher, Neil L. ; Barona-Gomez, Francisco ; Medema, Marnix H. - \ 2019
    Nature Chemical Biology 16 (2019). - ISSN 1552-4450 - p. 60 - 68.

    Genome mining has become a key technology to exploit natural product diversity. Although initially performed on a single-genome basis, the process is now being scaled up to mine entire genera, strain collections and microbiomes. However, no bioinformatic framework is currently available for effectively analyzing datasets of this size and complexity. In the present study, a streamlined computational workflow is provided, consisting of two new software tools: the ‘biosynthetic gene similarity clustering and prospecting engine’ (BiG-SCAPE), which facilitates fast and interactive sequence similarity network analysis of biosynthetic gene clusters and gene cluster families; and the ‘core analysis of syntenic orthologues to prioritize natural product gene clusters’ (CORASON), which elucidates phylogenetic relationships within and across these families. BiG-SCAPE is validated by correlating its output to metabolomic data across 363 actinobacterial strains and the discovery potential of CORASON is demonstrated by comprehensively mapping biosynthetic diversity across a range of detoxin/rimosamide-related gene cluster families, culminating in the characterization of seven detoxin analogues.

    Nutritional dietary supplements to reduce the incidence of fatty liver syndrome in laying hens and the use of spectrophotometry to predict liver fat content
    Navarro-Villa, A. ; Mica, J.H. ; Mozos, J. de los; Hartog, L.A. den; Garcia Ruiz, A.I. - \ 2019
    Journal of Applied Poultry Research 28 (2019)2. - ISSN 1056-6171 - p. 435 - 446.
    Fatty liver syndrome (FLS) in laying hens is a metabolic disease that can potentially reduce egg production while compromising the health status of the bird. This study assessed the combined use of B vitamins via the feed (FLS-MIX) or the drinking water (FLS-LIQ) to reduce FLS and the use of spectrophotometry to estimate liver fat content. Individually, caged Hy-line brown hens (n = 288) underwent a pre-experimental period (from week 66 to 67, both included) receiving a Standard diet or a Challenge diet (high energy–low protein) to nutritionally induce the FLS. Subsequently, hens followed a 2 diets (Standard; Challenge) × 3 dietary supplements (NONE; FLS-MIX; and FLS-LIQ) factorial arrangement of treatments from 68 to 73 wk old, both included. Compared to the Standard, the Challenge diet increased liver fat (188 vs. 270 g/kg DM) and reduced feed consumption, lay percentage, and egg mass production (P < 0.05). No differences in lay performance or eggshell quality were observed among dietary supplements; however, FLS-MIX significantly increased (P < 0.05) feed intake relative to NONE. On birds subjected to the Challenge diet, the use of FLS-MIX and FLS-LIQ led to lower (P < 0.05) liver fat relative to NONE. Regression analysis between the L, a+, and b+ values and liver fat content provided significant (P < 0.001) regression equations to estimate liver fat content (R2 = 0.62). Results of this study suggest that B vitamin supplements could be an effective means to reduce liver fat deposition when hens are susceptible of suffering FLS, and that spectrometry could be a reliable tool to estimate liver fat content.
    The NEWA Ferry Lidar Benchmark: Comparing mesoscale models with lidar measurements along a ship rout
    Witha, B. ; Dörenkämper, M. ; Frank, H. ; Hawbecker, P. ; Navarro, J. ; Schneider, M. ; Steeneveld, G.J. ; Svensson, N. ; Gottschall, J. - \ 2019
    - 1 p.
    Effects of inclusion rate of high fiber dietary ingredients on apparent ileal, hindgut, and total tract digestibility of dry matter and nutrients in ingredients fed to growing pigs
    Navarro, D.M.D.L. ; Bruininx, E.M.A.M. ; Jong, L. de; Stein, H.H. - \ 2019
    Animal Feed Science and Technology 248 (2019). - ISSN 0377-8401 - p. 1 - 9.
    Digestibility - Fiber - Pigs

    An experiment was conducted to determine if values for the coefficient of ileal apparent digestibility (CIAD), the coefficient of hindgut apparent disappearance (CHAD), and the coefficient of total tract apparent digestibility (CTTAD) of dry matter (DM) and nutrients in high-fiber ingredients measured at 150 g/kg inclusion are also accurate if measured at 300 g/kg inclusion in diets fed to pigs. The second objective was to confirm that most of the insoluble dietary fiber (IDF) is not fermented by growing pigs. Twenty ileal-cannulated pigs (BW: 30.64 ± 2.09 kg) were allotted to a replicated 10 × 4 incomplete Latin Square design with 10 diets and four 26-d periods. There were 2 pigs per diet in each period for a total of 8 replications per diet. A corn and soybean meal (SBM) basal diet and a corn-SBM diet with 300 g/kg corn starch were formulated. Six diets were formulated by replacing 150 or 300 g/kg corn starch by 150 or 300 g/kg corn germ meal (CGM), sugar beet pulp (SBP), or wheat middlings (WM). Two additional diets were formulated by adding 150 or 300 g/kg canola meal (CM) to the diet containing corn, SBM, and 300 g/kg corn starch at the expense of corn and SBM. Effects of inclusion rate of each fiber source in the diet on CIAD, CHAD, and CTTAD of DM and nutrients were analyzed using orthogonal contrasts. Independent t-tests were used to compare inclusion rates within each ingredient. Results indicated that CIAD and CHAD of CP, acid hydrolyzed ether extract (AEE), and most fiber fractions in CM decreased (P<0.05) as inclusion level increased from 150 to 300 g/kg, but that was not the case for CGM, SBP, or WM. The CTTAD of DM, organic matter (OM), AEE, and soluble dietary fiber (SDF) in CGM increased (P<0.05) if 300 g/kg rather than 150 g/kg was included in the diet and CTTAD of DM, OM, acid detergent fiber, and SDF in WM increased (P<0.05) as inclusion level increased. No differences in CTTAD of DM and nutrients in CM and SBP were observed between inclusion rates. The CTTAD of IDF ranged from 0.529 in WM included at 150 g/kg to 0.862 in SBP included at 300 g/kg in the diet. In conclusion, CIAD, CHAD, and CTTAD of most nutrients in test ingredients is not different between 150 and 300 g/kg inclusion rate. Under the conditions of this experiment, there was relatively high digestibility of IDF.

    Corrigendum: ICTV Virus Taxonomy Profile: Ophioviridae
    García, María Laura ; Bó, Elena Dal ; Graça, John V. Da; Gago-Zachert, Selma ; Hammond, John ; Moreno, Pedro ; Natsuaki, Tomohide ; Pallás, Vicente ; Navarro, Jose A. ; Reyes, Carina A. ; Luna, Gabriel Robles ; Sasaya, Takahide ; Tzanetakis, Ioannis E. ; Vaira, Anna María ; Verbeek, Martin - \ 2018
    Journal of General Virology 99 (2018)7. - ISSN 0022-1317 - p. 949 - 949.
    The International Committee on Taxonomy of Viruses has ratified a taxonomic proposal to change the name of the family Ophioviridae to Aspiviridae, and to change the names of species in the family to Blueberry mosaic associated ophiovirus, Citrus psorosis ophiovirus, Freesia sneak ophiovirus, Lettuce ring necrosis ophiovirus, Mirafiori lettuce big-vein ophiovirus, Ranunculus white mottle ophiovirus and Tulip mild mottle mosaic ophiovirus. These species are all members of the genus Ophiovirus, the genus name being unchanged.
    Implementation of PROMETHEUS 4‐step approach for evidence use in EFSA scientific assessments: benefits, issues, needs and solutions
    Aiassa, Elisa ; Martino, Laura ; Barizzone, Fulvio ; Ciccolallo, Laura ; Garcia, Ana ; Georgiadis, Marios ; Guajardo, Irene Muñoz ; Tomcikova, Daniela ; Alexander, Jan ; Calistri, Paolo ; Gundert‐remy, Ursula ; Hart, Andrew David ; Hoogenboom, Ron Laurentius ; Messean, Antoine ; Naska, Androniki ; Navarro, Maria Navajas ; Noerrung, Birgit ; Ockleford, Colin ; Wallace, Robert John ; Younes, Maged ; Abuntori, Blaize ; Alvarez, Fernando ; Aryeetey, Monica ; Baldinelli, Francesca ; Barrucci, Federica ; Bau, Andrea ; Binaglia, Marco ; Broglia, Alessandro ; Castoldi, Anna Federica ; Christoph, Eugen ; Sesmaisons‐Lecarré, Agnes De; Georgiadis, Nikolaos ; Gervelmeyer, Andrea ; Istace, Frederique ; López‐Gálvez, Gloria ; Manini, Paola ; Maurici, Daniela ; Merten, Caroline ; Messens, Winy ; Mosbach‐Schulz, Olaf ; Putzu, Claudio ; Bordajandi, Luisa Ramos ; Smeraldi, Camilla ; Tiramani, Manuela ; Martínez, Silvia Valtueña ; Sybren, Vos ; Hardy, Anthony Richard ; Hugas, Marta ; Kleiner, Juliane ; Seze, Guilhem De - \ 2018
    EFSA Supporting Publications 15 (2018)4. - ISSN 2397-8325
    In 2014, the European Food Safety Authority (EFSA) started the PROMETHEUS (PROmoting METHods for Evidence Use in Scientific assessments) project to improve further and increase the consistency of the methods it uses in its scientific assessments. The project defined a set of principles for the scientific assessment process and a 4‐step approach (plan/carry out/verify/report) for their fulfilment, which was tested in ten case studies, one from each EFSA panel. The present report describes the benefits, issues, needs and solutions related to the implementation of the 4‐step approach in EFSA, identified in a dedicated workshop in October 2017. The key benefits of the approach, which was deemed applicable to all types of EFSA scientific assessment including assessments of regulated products, are: 1) increased ‘scientific value’ of EFSA outputs, i.e. the extent of impartiality, methodological rigour, transparency and engagement; 2) guarantee of fitness‐for‐purpose, as it implies tailoring the methods to the specificities of each assessment; 3) efficiency gain, since preparing a protocol for the assessment upfront helps more streamlined processes throughout the implementation phase; 4) innovation, as the approach promotes the pioneering practice of ‘planning before doing’ (well established in primary research) for broad scientific assessments in regulatory science; and 5) increased harmonisation and consistency of EFSA assessments. The 4‐step approach was also considered an effective system for detecting additional methodological and/or expertise needs and a useful basis for further defining a quality management system for EFSA's scientific processes. The identified issues and solutions related to the implementation of the approach are: a) lack of engagement and need for effective communication on benefits and added value; b) need for further advances especially in the field of problem formulation/protocol development, evidence appraisal and evidence integration; c) need for specialised expertise in the previous aspects; and specific needs for d) assessments of regulated products and e) outsourced projects.
    Effects of inclusion rate of high fiber dietary ingredients on concentration of digestible and metabolizable energy in mixed diets fed to growing pigs
    Bruininx, E.M.A.M. ; Navarro, D.M.D.L. ; Jong, Lineke de; Stein, Hans H. - \ 2018
    Effects of Inclusion Rate of High Fiber Dietary Ingredients on Apparent Ileal, Hindgut, and Total Tract Digestibility of Dry Matter and Nutrients in ingredients fed to growing pigs
    Bruininx, E.M.A.M. ; Navarro, D.M.D.L. ; Jong, Lineke de; Stein, Hans H. - \ 2018
    Effects of physicochemical characteristics of feed ingredients on the apparent total tract digestibility of energy, DM, and nutrients by growing pigs
    Navarro, Diego M.D.L. ; Bruininx, Erik M.A.M. ; Jong, Lineke de; Stein, Hans H. - \ 2018
    Journal of Animal Science 96 (2018)6. - ISSN 0021-8812 - p. 2265 - 2277.
    Correlation - Digestibility - Energy - Physicochemical characteristics - Pigs - Total dietary fiber

    Effects of physicochemical characteristics of feed ingredients on DE and ME and apparent total tract digestibility (ATTD) of GE, DM, and nutrients were determined in growing pigs using ingredients with different ratios between insoluble dietary fiber (IDF) and soluble dietary fiber (SDF). Eighty growing barrows (BW: 48.41 ± 1.50 kg) were allotted to a randomized complete block design with 10 diets and eight replicate pigs per diet. Dietary treatments included a corn-based diet, a wheat-based diet, a corn–soybean meal (SBM) diet, and seven diets based on a mixture of the corn–SBM diet and canola meal, distillers dried grains with solubles (DDGS), corn germ meal (CGM), copra expellers, sugar beet pulp (SBP), synthetic cellulose, or pectin. Values for the ATTD of DM and nutrients were also compared with the in vitro digestibility of GE, DM, and nutrients. Results indicated that the ATTD of GE was greater (P < 0.05) in wheat than in canola meal, DDGS, CGM, copra expellers, SBP, and synthetic cellulose, but not different from corn, SBM, or pectin. SBM had greater (P < 0.05) DE and ME (DM basis) compared with all other ingredients. The concentration of ME (DM basis) was greater (P < 0.05) in wheat than in canola meal, DDGS, CGM, copra expellers, SBP, synthetic cellulose, and pectin, but not different from corn. Stronger correlations between total dietary fiber (TDF) and DE and ME than between ADF or NDF and DE and ME were observed, indicating that TDF can be used to more accurately predict DE and ME than values for NDF or ADF. The DE, ME, and the ATTD of DM in ingredients were positively correlated (P < 0.05) with in vitro ATTD of DM, indicating that the in vitro procedure may be used to estimate DE and ME in feed ingredients. Swelling and water-binding capacity were positively correlated (P < 0.05) with the ATTD of IDF, TDF, non-starch polysaccharides (NSP), and insoluble NSP, and viscosity was positively correlated (P < 0.05) with the ATTD of NDF, IDF, and insoluble NSP, indicating that some physical characteristics may influence digestibility of fiber. However, physical characteristics of feed ingredients were not correlated with the concentration of DE and ME, which indicates that these parameters do not influence in vivo energy digestibility in feed ingredients. It is concluded that the DE and ME in feed ingredients may be predicted from some chemical constituents and from in vitro digestibility of DM, but not from physical characteristics.

    Addressing climate change in Responsible Research and Innovation : Recommendations for its operationalization
    Ligardo-Herrera, Ivan ; Gómez-Navarro, Tomás ; Inigo, Edurne A. ; Blok, Vincent - \ 2018
    Sustainability 10 (2018)6. - ISSN 2071-1050
    Climate change - Corporate social responsibility - Responsible research and innovation - Sustainable innovation

    Responsible Research and Innovation (RRI) has only lately included environmental sustainability as a key area for the social desirability of research and innovation. That is one of the reasons why just a few RRI projects and proposals include environmental sustainability, and Climate Change (CC) in particular. CC is one of the grand challenges of our time and, thus, this paper contributes to the operationalization of CC prevention in RRI. To this end, the tools employed against CC were identified. Tools originated in corporate social responsibility and sustainable innovation which help to operationalize strategies against CC in RRI practice. Complementarily, the latest proposals by RRI projects and actors related to CC were reviewed. The findings of the document analysis and the web review were arranged in a framework intended for research and innovation that has an indirect but relevant negative impact due to CC. Thus, four main strategies for CC prevention in RRI were determined: a voluntary integration of the aims, a life cycle perspective, open access databases and key performance indicators, and stakeholder management. The article is finished acknowledging diverse barriers hindering the operationalization of CC prevention in RRI, and we introduce future avenues for research in this area.

    The contribution of digestible and metabolizable energy from high-fiber dietary ingredients is not affected by inclusion rate in mixed diets fed to growing pigs
    Navarro, D.M.D.L. ; Bruininx, E.M.A.M. ; Jong, L. de; Stein, H.H. - \ 2018
    Journal of Animal Science 96 (2018)5. - ISSN 0021-8812 - p. 1860 - 1868.
    Digestibility - Energy - Fiber - Inclusion rate - Passage rate - Pigs

    Effects of inclusion rate of fiber-rich ingredients on apparent ileal digestibility (AID) and apparent total tract digestibility (ATTD) of GE and on the concentration of DE and ME in mixed diets fed to growing pigs were determined. The hypothesis was that increasing the inclusion rate of fiber decreases digestibility of GE, and thus, the contribution of DE and ME from hindgut fermentation because greater concentrations may reduce the ability of microbes to ferment fiber. Twenty ileal-cannulated pigs (BW: 30.64 ± 2.09 kg) were allotted to a replicated 10 × 4 incomplete Latin Square design with 10 diets and four 26-d periods. There were 2 pigs per diet in each period for a total of 8 replications per diet. A basal diet based on corn and soybean meal (SBM) and a corn-SBM diet with 30% corn starch were formulated. Six additional diets were formulated by replacing 15% or 30% corn starch by 15% or 30% corn germ meal, sugar beet pulp, or wheat middlings, and 2 diets were formulated by including 15% or 30% canola meal in a diet containing corn, SBM, and 30% corn starch. Effects of adding 15% or 30% of each fiber source to experimental diets were analyzed using orthogonal contrasts and t-tests were used to compare inclusion rates within each ingredient. The AID and ATTD of GE and concentration of DE and ME in diets decreased (P < 0.05) with the addition of 15% or 30% canola meal, corn germ meal, sugar beet pulp, or wheat middlings compared with the corn starch diet. However, inclusion rate did not affect the calculated DE and ME or AID and ATTD of GE in any of the ingredients indicating that concentration of DE and ME in ingredients was independent of inclusion rate and utilization of energy from test ingredients was equally efficient between diets with 15% and 30% inclusion. Increased inclusion of fiber in the diet did not influence transit time in the small intestine, but reduced the time of first appearance of digesta in the feces indicating that transit time was reduced in the hindgut of pigs fed high-fiber diets. However, this had no impact on DE and ME or ATTD of GE in test ingredients. In conclusion, fiber reduced the DE and ME in the diet. However, inclusion rate of fiber-rich ingredients in diets did not affect calculated values for DE and ME in feed ingredients indicating that microbial capacity for fermentation of fiber in pigs is not overwhelmed by inclusion of 30% high-fiber ingredients in the diets.

    Taxonomy of the family Arenaviridae and the order Bunyavirales : update 2018
    Maes, Piet ; Alkhovsky, Sergey V. ; Bào, Yīmíng ; Beer, Martin ; Birkhead, Monica ; Briese, Thomas ; Buchmeier, Michael J. ; Calisher, Charles H. ; Charrel, Rémi N. ; Choi, Il Ryong ; Clegg, Christopher S. ; Torre, Juan Carlos de la; Delwart, Eric ; DeRisi, Joseph L. ; Bello, Patrick L. Di; Serio, Francesco Di; Digiaro, Michele ; Dolja, Valerian V. ; Drosten, Christian ; Druciarek, Tobiasz Z. ; Du, Jiang ; Ebihara, Hideki ; Elbeaino, Toufic ; Gergerich, Rose C. ; Gillis, Amethyst N. ; Gonzalez, Jean Paul J. ; Haenni, Anne Lise ; Hepojoki, Jussi ; Hetzel, Udo ; Hồ, Thiện ; Hóng, Ní ; Jain, Rakesh K. ; Jansen van Vuren, Petrus ; Jin, Qi ; Jonson, Miranda Gilda ; Junglen, Sandra ; Keller, Karen E. ; Kemp, Alan ; Kipar, Anja ; Kondov, Nikola O. ; Koonin, Eugene V. ; Kormelink, Richard ; Korzyukov, Yegor ; Krupovic, Mart ; Lambert, Amy J. ; Laney, Alma G. ; LeBreton, Matthew ; Lukashevich, Igor S. ; Marklewitz, Marco ; Markotter, Wanda ; Martelli, Giovanni P. ; Martin, Robert R. ; Mielke-Ehret, Nicole ; Mühlbach, Hans Peter ; Navarro, Beatriz ; Ng, Terry Fei Fan ; Nunes, Márcio Roberto Teixeira ; Palacios, Gustavo ; Pawęska, Janusz T. ; Peters, Clarence J. ; Plyusnin, Alexander ; Radoshitzky, Sheli R. ; Romanowski, Víctor ; Salmenperä, Pertteli ; Salvato, Maria S. ; Sanfaçon, Hélène ; Sasaya, Takahide ; Schmaljohn, Connie ; Schneider, Bradley S. ; Shirako, Yukio ; Siddell, Stuart ; Sironen, Tarja A. ; Stenglein, Mark D. ; Storm, Nadia ; Sudini, Harikishan ; Tesh, Robert B. ; Tzanetakis, Ioannis E. ; Uppala, Mangala ; Vapalahti, Olli ; Vasilakis, Nikos ; Walker, Peter J. ; Wáng, Guópíng ; Wáng, Lìpíng ; Wáng, Yànxiăng ; Wèi, Tàiyún ; Wiley, Michael R. ; Wolf, Yuri I. ; Wolfe, Nathan D. ; Wú, Zhìqiáng ; Xú, Wénxìng ; Yang, Li ; Yāng, Zuòkūn ; Yeh, Shyi Dong ; Zhāng, Yǒng Zhèn ; Zhèng, Yàzhōu ; Zhou, Xueping ; Zhū, Chénxī ; Zirkel, Florian ; Kuhn, Jens H. - \ 2018
    Archives of Virology 163 (2018)8. - ISSN 0304-8608 - p. 2295 - 2310.
    In 2018, the family Arenaviridae was expanded by inclusion of 1 new genus and 5 novel species. At the same time, the recently established order Bunyavirales was expanded by 3 species. This article presents the updated taxonomy of the family Arenaviridae and the order Bunyavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV) and summarizes additional taxonomic proposals that may affect the order in the near future.
    Analysis for low-molecular-weight carbohydrates is needed to account for all energy-contributing nutrients in some feed ingredients, but physical characteristics do not predict in vitro digestibility of dry matter
    Navarro, D.M.D.L. ; Bruininx, E.M.A.M. ; Jong, L. de; Stein, H.H. - \ 2018
    Journal of Animal Science 96 (2018)2. - ISSN 0021-8812 - p. 532 - 544.
    Energy - In vitro digestibility - Physicochemical characteristics - Total dietary fiber
    An experiment was conducted to quantify nutrient and fiber fractions of feed ingredients and to determine in vitro apparent ileal digestibility (IVAID) and in vitro apparent total tract digestibility (IVATTD) of DM and OM in each ingredient. Ten ingredients that vary in fiber concentration and composition were used: corn, wheat, soybean meal (SBM), canola meal, distillers dried grains with solubles (DDGS), corn germ meal, copra expellers, sugar beet pulp (SBP), synthetic cellulose (SF), and pectin. Correlations between chemical and physical characteristics of ingredients and IVAID and IVATTD of DM and OM were determined. The physical characteristics measured included bulk density, water-binding capacity (WBC), swelling, and viscosity. The analyzed GE was compared with values for GE calculated from all energy-contributing components. Results indicated that the analyzed chemical composition of most ingredients added to 100% or greater, except for DDGS, SBP, and SF, where nutrients added to only 94.29%, 88.90%, and 96.09%, respectively. The difference between the sum of the calculated GE of the analyzed components and the analyzed GE of the ingredients ranged from −2.25 MJ/kg in DDGS to 1.74 MJ/kg in pectin. No correlation was observed between swelling, WBC, or viscosity and IVAID or IVATTD of DM or OM. The concentration of insoluble dietary fiber (IDF) and total dietary fiber (TDF) was negatively correlated (P < 0.05) with IVAID and IVATTD of DM and OM. There was a tendency for NDF (r = −0.60) and ADF (r = −0.61) to be negatively correlated (P < 0.10) with IVAID of DM. However, no correlation was observed between the concentration of CP, GE, acid-hydrolyzed ether extract, lignin, or soluble dietary fiber and IVAID and IVATTD of DM and OM. The stronger correlations between IDF, TDF, and insoluble non-starch polysaccharides and IVAID and IVATTD of DM and OM than between ADF and NDF and IVAID and IVATTD of DM and OM indicate that the concentration of TDF in feed ingredients is a better predictor of the digestibility of DM and OM than values for NDF and ADF. In conclusion, the calculated GE of some feed ingredients was in agreement with the analyzed GE, which gives confidence that energy-contributing components were accounted for, but for DDGS and SBP, it was not possible to account for all analyzed GE. Concentrations of IDF and TDF, but not the physical characteristics of feed ingredients, may be used to estimate IVAID and IVATTD of DM and OM in feed ingredients.
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