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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    Storylines for practice: a visual storytelling approach to strengthen the science-practice interface
    Cortes Arevalo, Vivian Juliette ; Verbrugge, Laura N.H. ; Sools, Anneke ; Brugnach, Marcela ; Wolterink, Rik ; Denderen, R.P. van; Candel, Jasper H.J. ; Hulscher, Suzanne J.M.H. - \ 2020
    Sustainability Science 15 (2020). - ISSN 1862-4065 - p. 1013 - 1032.
    Effectiveness evaluation - Environmental management - Narrative visualization - River research - Science communication - User-centered design

    A growing number of scientific publications is available to promote sustainable river management. However, these publications target researchers rather than water management professionals who are responsible for the implementation of management practices. To bridge this science-to-practice gap, we conceptualize and propose a series of steps to prepare effective storylines targeted at a practitioner audience. We developed this approach within a research program that supports integrated and collaborative river management. We prepared three storylines, each based on one scientific publication. The storylines combined text and interactive visuals using the ESRI StoryMaps tool to make them available online. Via focus groups with 44 participants from research and practice, we evaluated the perceived usefulness of and engagement with the content and design. We collected feedback from participants using a survey as well as via audio and screen recordings. Our findings show that we should narrow down the audience of the storylines by tailoring them to the needs of project managers rather than specialized advisors. Therefore, the content should offer more than a visual summary of the research by showing examples of the management application. A more engaging sequence with a clear protagonist is further required to better relate to the problem and the potential application. Although visuals and interactive elements were considered attractive, a multi-disciplinary editorial team is necessary to better complement the visuals’ design to the text. The level of detail of participants’ feedback shows that involving project managers to co-create storylines can be an important step for improvement.

    Impact of Xylella fastidiosa subspecies pauca in European olives
    Schneider, Kevin ; Werf, W. van der; Cendoya, Martina ; Mourits, M.C.M. ; Navas-Cortes, Juan A. ; Civera, Antonio Vicent ; Oude Lansink, A.G.J.M. - \ 2020
    Proceedings of the National Academy of Sciences of the United States of America 117 (2020)17. - ISSN 0027-8424 - p. 9250 - 9259.
    Xylella fastidiosa is the causal agent of plant diseases that cause massive economic damage. In 2013, a strain of the bacterium was, for the first time, detected in the European territory (Italy), causing the Olive Quick Decline Syndrome. We simulate future spread of the disease based on climatic-suitability modeling and radial expansion of the invaded territory. An economic model is developed to compute impact based on discounted foregone profits and losses in investment. The model projects impact for Italy, Greece, and Spain, as these countries account for around 95% of the European olive oil production. Climatic suitability modeling indicates that, depending on the suitability threshold, 95.5 to 98.9%, 99.2 to 99.8%, and 84.6 to 99.1% of the national areas of production fall into suitable territory in Italy, Greece, and Spain, respectively. For Italy, across the considered rates of radial range expansion the potential economic impact over 50 y ranges from 1.9 billion to 5.2 billion Euros for the economic worst-case scenario, in which production ceases after orchards die off. If replanting with resistant varieties is feasible, the impact ranges from 0.6 billion to 1.6 billion Euros. Depending on whether replanting is feasible, between 0.5 billion and 1.3 billion Euros can be saved over the course of 50 y if disease spread is reduced from 5.18 to 1.1 km per year. The analysis stresses the necessity to strengthen the ongoing research on cultivar resistance traits and application of phytosanitary measures, including vector control and inoculum suppression, by removing host plants
    Development of natural rubber suppliers in the Papaloapan River basin, Mexico : Progress and limitations
    González-Ramírez, María Guadalupe ; Santoyo-Cortés, Horacio ; Aguilar-Ávila, Jorge ; Aguilar-Gallegos, Norman - \ 2019
    Ciencia y Tecnologia Agropecuaria 20 (2019)2. - ISSN 0122-8706 - p. 277 - 294.
    Agricultural extension - Agroindustry - Hevea brasiliensis - Innovation adoption - Technology transfer

    Mexico has optimal conditions for the cultivation of natural rubber but imports more than 80 % of its consumption. The model of development suppliers through Innovation Management Agencies (agi, for their acronym in Spanish) was implemented to improve this situation. This work analyzed the achievements of technical assistance services provided by two agi to two rubber agro-industries (ai) and their suppliers located in the Papaloapan River Basin, Mexico. From 2011 to the beginning of 2014, the Agencies generated reports and databases about technical, productive, organizational and commercial parameters of both rubber producers and agro-industries. With this information, global databases were constructed to analyze changes in production, supply, and innovation adoption. The results show that the intervention of the Agencies was relevant and effective in improving production and post-harvest parameters. The production of coagulated rubber also increased as well as the availability of raw material to the agro-industries. Moreover, production costs were able to be reduced, and the quality of the rubber was improved. However, the fall in rubber prices at the end of 2013 caused setbacks in the adoption of innovations and the agriculture-industry integration, showing the fragility of supplier development, as well as of the ai involved serving as lead and trailblazer companies in their suppliers' networks.

    Análisis de redes en twitter para la inserción en comunidades : El caso de un producto agroindustrial
    Aguilar-Gallegos, Norman ; Valdés-López, Armando ; Muñoz-Rodríguez, Manrrubio ; Martínez-González, Enrique Genaro ; Santoyo-Cortés, Horacio ; Aguilar-Ávila, Jorge - \ 2019
    Interciencia 44 (2019)2. - ISSN 0378-1844 - p. 75 - 81.

    The hashtags and relevant content in Twitter, related to the agroindustrial product mezcal were analysed, and the so-called ‘influencers’ were also identified. For doing this, 57.362 tweets were extracted and stored; three networks were built: users-hashtags, retweets, and mentions, which were studied by using social network analysis (SNA). The application of the SNA allowed revealing certain kind of hidden patterns within the social media complex relationships, which can be useful for designing strategies aimed at positioning actors and spread information. The results allow stating that in order to get inserted in the social network, the following should be considered: the use of combined hashtags, the message content kind, including pictures attached, and mentioning the most influential accounts who are embedded in already formed communities.

    Pest categorisation of Clavibacter sepedonicus
    Bragard, C. ; Dehnen-Schmutz, Katharina ; Serio, Francesco Di; Gonthier, Paolo ; Miret, Josep Anton Jaques ; Fejer Justesen, Annemarie ; MacLeod, A. ; Magnusson, C. ; Milonas, Panagiotis ; Navas-Cortes, Juan A. ; Parnell, Stephen ; Potting, R. ; Reignault, Lucien ; Thulke, H.H. ; Werf, W. van der; Civera, Antonio Vicent ; Yuen, Jonathan ; Zappalà, Lucia ; Wolf, J.M. van der; Kaluski, Tomasz ; Pautasso, Marco ; Jacques, Marie-Agnès - \ 2019
    EFSA Journal 17 (2019)4. - ISSN 1831-4732
    bacterial ring rot of potato - European Union - pest risk - plant health - plant pest - quarantine
    Following a request from the European Commission, the EFSA Panel on Plant Health performed a pest categorisation of Clavibacter sepedonicus, a well-defined and distinguishable bacterial plant pathogen of the family Microbacteriaceae. C. sepedonicus causes bacterial ring rot of potato and is reported from North America, Asia and Europe. The bacterium is mostly tuber transmitted, but it can also enter host plants through wounds or via contaminated equipment. C. sepedonicus is regulated in Council Directive
    2000/29/EC (Annex IAII, as Clavibacter michiganensis subsp. sepedonicus) as a harmful organism whose introduction into the EU is banned. In addition, Council Directive 1993/85/EEC concerns the measures to be taken within EU Member States (MS) against C. sepedonicus to (a) detect it and determine its distribution, (b) prevent its occurrence and spread, and (c) control it with the aim of eradication. The pest is present in several EU MS, but in all cases with a restricted distribution and under official control. C. sepedonicus could enter the EU and spread primarily via host plants for planting (i.e. potato tubers).
    The pest could establish in the EU, as the main host (potato) is commonly grown and climatic conditions are favourable. Direct potato losses following infection by C. sepedonicus can be substantial and are due to the destruction of the vascular tissue, wilting of the plant and rotting of the tubers. Infected hosts can
    remain asymptomatic. The main knowledge gaps are the geographic distribution of the pest and the host range. The criteria assessed by the Panel for consideration of C. sepedonicus as a potential quarantine pest are met, while, for regulated non-quarantine pests, the criterion on the widespread presence in the EU is not met.
    Metaproteomic and 16S rRNA Gene Sequencing Analysis of the Infant Fecal Microbiome
    Cortes, Laetitia ; Wopereis, Harm ; Tartiere, Aude ; Piquenot, Julie ; Gouw, Joost W. ; Tims, Sebastian ; Knol, Jan ; Chelsky, Daniel - \ 2019
    International Journal of Molecular Sciences 20 (2019)6. - ISSN 1661-6596
    fecal - infants - intestinal - mass spectrometry - metabolism - metacluster - microbiome

    A metaproteomic analysis was conducted on the fecal microbiome of eight infants to characterize global protein and pathway expression. Although mass spectrometry-based proteomics is now a routine tool, analysis of the microbiome presents specific technical challenges, including the complexity and dynamic range of member taxa, the need for well-annotated metagenomic databases, and high inter-protein sequence redundancy and similarity. In this study, an approach was developed for assessment of biological phenotype and metabolic status, as a functional complement to DNA sequence analysis. Fecal samples were prepared and analysed by tandem mass spectrometry and a homology-based meta-clustering strategy was used to combine peptides from multiple species into representative proteins. In total, 15,250 unique peptides were sequenced and assigned to 2154 metaclusters, which were then assigned to pathways and functional groups. Differences were noted in several pathways, consistent with the dominant genera observed in different subjects. Although this study was not powered to draw conclusions from the comparisons, the results obtained demonstrate the applicability of this approach and provide the methods needed for performing semi-quantitative comparisons of human fecal microbiome composition, physiology and metabolism, as well as a more detailed assessment of microbial composition in comparison to 16S rRNA gene sequencing.

    Pest categorisation of the Ralstonia solanacearum species complex
    Bragard, C. ; Dehnen-Schmutz, Katharina ; Serio, Francesco Di; Gonthier, Paolo ; Miret, Josep Anton Jaques ; Fejer Justesen, Annemarie ; MacLeod, A. ; Magnusson, C. ; Milonas, P.G. ; Navas-Cortes, Juan A. ; Werf, W. van der; Wolf, J.M. van der - \ 2019
    EFSA Journal 17 (2019)2. - ISSN 1831-4732
    bacterial wilt - European Union - intraspecific diversity - pest risk - plant health - plant pest - quarantine
    Following a request from the European Commission, the EFSA Panel on Plant Health performed a pest categorisation of the Ralstonia solanacearum species complex (RSSC), a distinguishable cosmopolitan group of bacterial plant pathogens (including R. solanacearum, Ralstonia pseudosolanacearum and two
    subspecies of Ralstonia syzygii) of the family Burkholderiaceae. The RSSC causes bacterial wilt in solanaceous crops, such as potato, tomato and pepper, but can also cause wilts in other important food crops such as fruit banana, plantain banana and cassava. The pest survives in the soil, and a number of
    weed species can also be infected by the pest, often asymptomatically. The RSSC is regulated in Council Directive 2000/29/EC (Annex IAII) (indicated by its former name R. solanacearum, as delimited by Yabuuchi et al.) as a harmful organism whose introduction into the EU is banned. In addition, Council Directive 1998/57/EC (amended by Commission Directive 2006/63/CE) concerns the measures to be taken within EU Member States (MS) against the RSSC to (a) detect it and determine its distribution, (b) prevent its occurrence and spread, and (c) control it with the aim of eradication. The pest is present in several EU MS, but in all cases with a restricted distribution and under official control. New
    phylotypes of the RSSC could enter the EU primarily via host plants for planting (including seed tubers).
    The pest could establish in the EU, as climatic conditions are favourable, hosts are common and the pathogen has high adaptability. Spread is mainly via plants for planting. Substantial crop losses in the EU would occur in the presence of RSSC epidemics. The RSSC is regarded as one of the world’s most important phytopathogenic bacteria due to its broad geographical distribution, large host range, aggressiveness, genetic diversity and long persistence in soil and water. The list of hosts and commodities for which the pest is regulated is incomplete due to the high diversity of hosts and the lack of knowledge of the complete host range. Moreover, the comparative epidemiology of the different pathogen species has not yet been studied. The criteria assessed by the Panel for consideration of the RSSC as potential quarantine pest are met, while, for regulated non-quarantine pests, the criterion on the widespread presence in the EU is not met.
    Preferences for anuran calls in hematophagous corethrellids (Diptera Corethrellidae) from Southern Brazil
    Ambrozio-Assis, André ; Cortês Lopes, Benedito ; Amaral, André P. ; Pinho, Luiz C. ; Peeters, Edwin T.H.M. ; Neckel-Oliveira, Selvino - \ 2019
    Austral Entomology 58 (2019)3. - ISSN 2052-174X - p. 622 - 628.
    Atlantic forest - frog-biting midges - frogs - parasitism - phonotaxis

    Corethrellids are hematophagous flies that locate their frog hosts by using their calls as an auditory cue. The attractiveness of frog calls to these insects has been associated with the complexity of the vocalisation or an evolutionary relationship between the fly and frog species. We investigated the possible preferences of a local Corethrella fauna for the calls of six anurans, three species of the genus Boana (Hylidae) and three Physalaemus (Leptodactylidae) species in the Atlantic Rainforest of southern Brazil. We recorded loops of the natural advertisement calls of the different frog host species, which we broadcast from acoustic traps consisting of modified CDC (Center for Disease Control) traps fitted with a speaker under the collecting system, but without a source of light. Nine species of hematophagous flies were captured during 360 h of trapping. Three of the species captured were new to Brazil, and two could not be identified and may represent new taxa. Two corethrellid species contributed 75% of the individuals captured and were present in all the acoustic traps, while three species were attracted to only one trap. The median richness and abundance of corethrellids varied significantly in relation to the different calls broadcast by the traps. These differences in the abundance and species richness of Corethrella in the traps indicate that the frog calls vary in their attractiveness to the hematophagous flies. A model-based analysis using mvabund also indicated that the frog species and genera that produced the calls used in an acoustic trap were a significant factor determining the composition of the Corethrella assemblages captured in that trap. The variation found in the Corethrella communities of southern Brazil may be explained not only by the acoustic traits of frog vocalisations but also by differences in the morphological and ecological characteristics of the frog species.

    Evaluating online storylines to increase the accessibility, transparency and potential usefulness of RiverCare knowledge
    Cortes Arevalo, V.J. ; Sools, A. ; Verbrugge, L.N.H. ; Brugnach, M. ; Denderen, R.P. van; Candel, J.H.J. ; Gemert - Pijnen, J.E.W.C. Van; Hulscher, S.J.M.H. - \ 2018
    Geophysical Research Abstracts 20 (2018). - ISSN 1029-7006 - 1 p.
    Usefulness of storylines to increase the accessibility and transparency of RiverCare knowledge
    Sools, A. ; Cortes Arevalo, V.J. ; Verbrugge, L.N.H. ; Brugnach, M. ; Denderen, R.P. van; Candel, J.H.J. ; Gemert-Pijnen, J.E.W.C. van; Hulscher, S.J.M.H. - \ 2018
    In: The future river. - NCR (NCR 42-2018) - p. 64 - 65.
    Development and validation of IPM strategies for the cultivation of cisgenically modified late blight resistant potato
    Kessel, Geert J.T. ; Mullins, Ewen ; Evenhuis, Albartus ; Stellingwerf, Jeroen ; Cortes, Vilma Ortiz ; Phelan, Sinead ; Bosch, Trudy van den; Förch, Marieke G. ; Goedhart, Paul ; Voet, Hilko van der; Lotz, Lambertus A.P. - \ 2018
    European Journal of Agronomy 96 (2018). - ISSN 1161-0301 - p. 146 - 155.
    Cisgenic modification - GM potato - Host resistance - Integrated pest management - Phytophthora infestans
    Potato late blight disease remains the primary stressor of commercial potato production across the EU, typically requiring >10 fungicide applications per growing season to offset crop losses. In response, the goal of this study was to test and validate a novel, more durable, control strategy for potato late blight. This IPM2.0 strategy is based on the principles of Integrated Pest Management (IPM) which sees the deployment of a late blight resistant potato genotype, a cisgenically modified, Desiree based resistant potato line here, in conjunction with pathogen population monitoring for virulence to the resistance genes (R genes) deployed and a “do not spray unless”, low input fungicide spray strategy. Field evaluations were completed in the Netherlands and in Ireland in 2013, 2014 and in Ireland in 2015. Comparators used in this study included the original but susceptible potato variety Desiree and the conventional but highly resistant variety Sarpo Mira. The novel IPM2.0 strategy was compared to local common practice (fungicide applications on a near weekly basis) and an untreated control. Overall, the IPM2.0 control strategy validated here reduced the average fungicide input by 80–90% without compromising control efficacy. Corresponding environmental side-effects were reduced proportionally. The results underline the pragmatic role host resistance can provide to commercial potato production systems and to society at large if employed as part of an integrated late blight control system.
    Nitrous Oxide Abatement Coupled with Biopolymer Production As a Model GHG Biorefinery for Cost-Effective Climate Change Mitigation
    Frutos, Osvaldo D. ; Cortes, Irene ; Cantera, Sara ; Arnaiz, Esther ; Lebrero, Raquel ; Muñoz, Raúl - \ 2017
    Environmental Science and Technology 51 (2017)11. - ISSN 0013-936X - p. 6319 - 6325.

    N2O represents ∼6% of the global greenhouse gas emission inventory and the most important O3-depleting substance emitted in this 21st century. Despite its environmental relevance, little attention has been given to cost-effective and environmentally friendly N2O abatement methods. Here we examined, the potential of a bubble column (BCR) and an internal loop airlift (ALR) bioreactors of 2.3 L for the abatement of N2O from a nitric acid plant emission. The process was based on the biological reduction of N2O by Paracoccus denitrificans using methanol as a carbon/electron source. Two nitrogen limiting strategies were also tested for the coproduction of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) coupled with N2O reduction. High N2O removal efficiencies (REs) (≈87%) together with a low PHBV cell accumulation were observed in both bioreactors in excess of nitrogen. However, PHBV contents of 38-64% were recorded under N limiting conditions along with N2O-REs of ≈57% and ≈84% in the ALR and BCR, respectively. Fluorescence in situ hybridization analyses showed that P. denitrificans was dominant (>50%) after 6 months of experimentation. The successful abatement of N2O concomitant with PHBV accumulation confirmed the potential of integrating biorefinery concepts into biological gas treatment for a cost-effective GHG mitigation.

    Public good : Wheat assemblages and the revalorization of culinary and handicraft practice in Bio-Bio, Chile
    Silva, Paola ; Cortés Belmar, Maruja ; Arce, Alberto - \ 2017
    In: Food, Agriculture and Social Change: The Everyday Vitality of Latin America / Sherwood, Stephen, Arce, Alberto, Paredes, Myriam, Routledge Taylor & Francis Group - ISBN 9781138214972 - p. 153 - 168.
    This chapter approaches the landscape as a methodological reality from which to explore the livelihoods of smallholder family farmers, identifying the material characteristics of a territory for a mode of rural life, and analyzing the transformative features of agriculture as a form of existence (see Gastó and Gálvez, 2014; Dewsbury, 2015). The aim of the chapter is to address two public concerns over agricultural realities. First, externalities associated with policies that promote intensive use of the landscape (e.g., the effects of forestation policies) and second, the potential benefits of public recognition in a territory (e.g., the valuation of skills and knowledge). 1 2 In other words, it examines the material goods and services generated and brought forth in a rural landscape, in this case those related to cuisine and handicraft.
    Trading direct for indirect defense? Phytochrome B inactivation in tomato attenuates direct anti-herbivore defenses whilst enhancing volatile-mediated attraction of predators
    Cortés, Leandro E. ; Weldegergis, Berhane T. ; Boccalandro, Hernán E. ; Dicke, Marcel ; Ballaré, Carlos L. - \ 2016
    New Phytologist 212 (2016)4. - ISSN 0028-646X - p. 1057 - 1071.
    defense - indirect defense - jasmonate - phytochrome - R : FR ratio - tomato (Solanum lycopersicum) - tritrophic interaction - volatile

    Under conditions of competition for light, which lead to the inactivation of the photoreceptor phytochrome B (phyB), the growth of shade-intolerant plants is promoted and the accumulation of direct anti-herbivore defenses is down-regulated. Little is known about the effects of phyB on emissions of volatile organic compounds (VOCs), which play a major role as informational cues in indirect defense. We investigated the effects of phyB on direct and indirect defenses in tomato (Solanum lycopersicum) using two complementary approaches to inactivate phyB: illumination with a low red to far-red ratio, simulating competition, and mutation of the two PHYB genes present in the tomato genome. Inactivation of phyB resulted in low levels of constitutive defenses and down-regulation of direct defenses induced by methyl jasmonate (MeJA). Interestingly, phyB inactivation also had large effects on the blends of VOCs induced by MeJA. Moreover, in two-choice bioassays using MeJA-induced plants, the predatory mirid bug Macrolophus pygmaeus preferred VOCs from plants in which phyB was inactivated over VOCs from control plants. These results suggest that, in addition to repressing direct defense, phyB inactivation has consequences for VOC-mediated tritrophic interactions in canopies, presumably attracting predators to less defended plants, where they are likely to find more abundant prey.

    Agricultural extension in Latin America : current dynamics of pluralistic advisory systems in heterogeneous contexts
    Klerkx, Laurens ; Landini, Fernando ; Santoyo-Cortés, Horacio - \ 2016
    The Journal of Agricultural Education and Extension 22 (2016)5. - ISSN 1389-224X - p. 389 - 397.
    An expanded evaluation of protein function prediction methods shows an improvement in accuracy
    Jiang, Yuxiang ; Oron, Tal Ronnen ; Clark, Wyatt T. ; Bankapur, Asma R. ; Andrea, Daniel D'; Lepore, Rosalba ; Funk, Christopher S. ; Kahanda, Indika ; Verspoor, Karin M. ; Ben-Hur, Asa ; Koo, Da Chen Emily ; Penfold-Brown, Duncan ; Shasha, Dennis ; Youngs, Noah ; Bonneau, Richard ; Lin, Alexandra ; Sahraeian, Sayed M.E. ; Martelli, Pier Luigi ; Profiti, Giuseppe ; Casadio, Rita ; Cao, Renzhi ; Zhong, Zhaolong ; Cheng, Jianlin ; Altenhoff, Adrian ; Skunca, Nives ; Dessimoz, Christophe ; Dogan, Tunca ; Hakala, Kai ; Kaewphan, Suwisa ; Mehryary, Farrokh ; Salakoski, Tapio ; Ginter, Filip ; Fang, Hai ; Smithers, Ben ; Oates, Matt ; Gough, Julian ; Törönen, Petri ; Koskinen, Patrik ; Holm, Liisa ; Chen, Ching Tai ; Hsu, Wen Lian ; Bryson, Kevin ; Cozzetto, Domenico ; Minneci, Federico ; Jones, David T. ; Chapman, Samuel ; BKC, Dukka ; Khan, Ishita K. ; Kihara, Daisuke ; Ofer, Dan ; Rappoport, Nadav ; Stern, Amos ; Cibrian-Uhalte, Elena ; Denny, Paul ; Foulger, Rebecca E. ; Hieta, Reija ; Legge, Duncan ; Lovering, Ruth C. ; Magrane, Michele ; Melidoni, Anna N. ; Mutowo-Meullenet, Prudence ; Pichler, Klemens ; Shypitsyna, Aleksandra ; Li, Biao ; Zakeri, Pooya ; ElShal, Sarah ; Tranchevent, Léon Charles ; Das, Sayoni ; Dawson, Natalie L. ; Lee, David ; Lees, Jonathan G. ; Sillitoe, Ian ; Bhat, Prajwal ; Nepusz, Tamás ; Romero, Alfonso E. ; Sasidharan, Rajkumar ; Yang, Haixuan ; Paccanaro, Alberto ; Gillis, Jesse ; Sedeño-Cortés, Adriana E. ; Pavlidis, Paul ; Feng, Shou ; Cejuela, Juan M. ; Goldberg, Tatyana ; Hamp, Tobias ; Richter, Lothar ; Salamov, Asaf ; Gabaldon, Toni ; Marcet-Houben, Marina ; Supek, Fran ; Gong, Qingtian ; Ning, Wei ; Zhou, Yuanpeng ; Tian, Weidong ; Falda, Marco ; Fontana, Paolo ; Lavezzo, Enrico ; Toppo, Stefano ; Ferrari, Carlo ; Giollo, Manuel ; Piovesan, Damiano ; Tosatto, Silvio C.E. ; Pozo, Angela del; Fernández, José M. ; Maietta, Paolo ; Valencia, Alfonso ; Tress, Michael L. ; Benso, Alfredo ; Carlo, Stefano Di; Politano, Gianfranco ; Savino, Alessandro ; Rehman, Hafeez Ur ; Re, Matteo ; Mesiti, Marco ; Valentini, Giorgio ; Bargsten, Joachim W. ; Dijk, Aalt-Jan van; Gemovic, Branislava ; Glisic, Sanja ; Perovic, Vladmir ; Veljkovic, Veljko ; Veljkovic, Nevena ; Almeida-e-Silva, Danillo C. ; Vencio, Ricardo Z.N. ; Sharan, Malvika ; Vogel, Jörg ; Kansakar, Lakesh ; Zhang, Shanshan ; Vucetic, Slobodan ; Wang, Zheng ; Sternberg, Michael J.E. ; Wass, Mark N. ; Huntley, Rachael P. ; Martin, Maria J. ; O'Donovan, Claire ; Robinson, Peter N. ; Moreau, Yves ; Tramontano, Anna ; Babbitt, Patricia C. ; Brenner, Steven E. ; Linial, Michal ; Orengo, Christine A. ; Rost, Burkhard ; Greene, Casey S. ; Mooney, Sean D. ; Friedberg, Iddo ; Radivojac, Predrag - \ 2016
    Genome Biology 17 (2016)1. - ISSN 1474-7596
    Disease gene prioritization - Protein function prediction

    Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent.

    Influence of salinity on fungal communities in a submerged fixed bed bioreactor for wastewater treatment
    Cortés-Lorenzo, C. ; González-Martínez, A. ; Smidt, H. ; González-López, J. ; Rodelas, B. - \ 2016
    Chemical Engineering Journal 285 (2016). - ISSN 1385-8947 - p. 562 - 572.
    Fungal communities - Pyrosequencing - Saline wastewater - Submerged fixed bed bioreactor - Wastewater treatment

    Salinity is known to influence the performance of biological wastewater treatment plants. While its impact on bacterial communities has been thoroughly studied, its influence on fungal communities has been largely overlooked. To address this knowledge gap, we assessed the effect of saline influents (0, 3.7, 24.1 and 44.1. g. NaCl/L) on the community structure and diversity of fungi in a submerged fixed bed bioreactor (SFBBR). For this purpose, denaturing gradient gel electrophoresis (DGGE) and 454-pyrosequencing of PCR-amplified fungal 18S rRNA gene fragments and ITS regions, respectively, were used. Significant differences in the fungal community structure were found in relation to the NaCl concentration. Fungal diversity increased as salinity increased to a concentration up to 24.1. g. NaCl/L, but was significantly reduced at 44.1. g. NaCl/L. Basidiomycota dominated the fungal community in the absence of NaCl but decreased in relative abundance with increasing salinity, being replaced progressively by Ascomycota.

    Effect of salinity on nitrification efficiency and structure of ammonia-oxidizing bacterial communities in a submerged fixed bed bioreactor
    Cortés-Lorenzo, C. ; Rodríguez-Díaz, M. ; Sipkema, D. ; Juárez-Jiménez, B. ; Rodelas, B. ; Smidt, H. ; González-López, J. - \ 2015
    Chemical Engineering Journal 266 (2015). - ISSN 1385-8947 - p. 233 - 240.
    The effect of salt (NaCl) on biological nitrogen removal and community structure of ammonia-oxidizing bacteria (AOB) was investigated in a submerged fixed bed bioreactor (SFBBR). Influent wastewater was supplemented with NaCl at 0 (control), 3.7, 24.1 and 44.1 g/L, and the rate of ammonia removal efficiency was measured by ion chromatography. The structure of the AOB community was profiled by 454-pyrosequencing, based on the amplification of partial ammonia-monooxygenase subunit A (amoA) genes. Salinity did not inhibit nitrification at 3.7 g/L, while ammonia oxidation activity significantly decreased and nitrite was consequently accumulated in the SFBBR when the salt concentration was ¿24.1 g/L. The sequencing of amoA genes revealed that many of the OTUs found in the control experiment were still present at the full range of NaCl studied, while concentrations of 24.1 and 44.1 g of NaCl/L promoted the emergence of new OTUs phylogenetically related to AOB described in saline environments
    Information networks that generate economic value: A study on clusters of adopters of new or improved technologies and practices among oil palm growers in Mexico
    Aguilar-Gallegos, N. ; Muñoz-Rodríguez, M. ; Santoyo-Cortés, H. ; Aguilar-Ávila, J. ; Klerkx, L.W.A. - \ 2015
    Agricultural Systems 135 (2015). - ISSN 0308-521X - p. 122 - 132.
    agricultural innovation systems - sustainable agriculture - conservation practices - knowledge systems - land management - adoption - farmers - exchange - africa - kenya
    The area under cultivation of oil palm has undergone considerable growth in Mexico, but yields are far below their potential. This is related to the low rate of adoption of new or improved technologies and practices in areas such as plantation management and farm administration. This study determines the factors that have an influence on adoption of new or improved technologies and practices and their relationship with the generation of economic value of oil palm. A cluster analysis of 33 key new or improved technologies and practices adopted by 104 growers was performed, and the main adoption categories and the variables influencing adoption are described. The results indicate that three clusters of growers can be discerned that differ in terms of their levels of adoption. The highest level of adoption of new or improved technologies and practices is related to higher yields and vice versa. The new or improved technologies and practices that differentiate the cluster of the advanced adopters from the cluster of the basic adopters are those related to plantation health, grower associations and production unit management. The cluster of the intermediate adopters is outstanding for their levels of adoption of new or improved technologies and practices in the aspects of plant nutrition, harvest, and genetics and reproduction. The advanced adopters set up better links for getting information, generally fromtheir extensionists. The three clusters each exhibit a great degree of homophily, indicating little information flow between the different clusters of growers, while these can learn from each other. These results make it evident that better articulation among different clusters of growers and other actors should be encouraged, and that diversified and tailor-made extension strategies should be designed to optimally support different clusters of growers.
    Induction of phagocytosis and intracellular signaling by an inhibitory channel cathfish leukocyte immune-type receptor: evidence for immunoregulatory receptor functional plasticity in teleosts
    Cortes, H.D. ; Lillico, D.M. ; Zwozdesky, M.A. ; Pemberton, J.G. ; O'Brien, A. ; Montgomery, B.C. ; Wiersma, L.E. ; Chang, J.P. ; Stafford, J.L. - \ 2014
    Journal of Innate Immunity 6 (2014)4. - ISSN 1662-811X - p. 435 - 455.
    protein-tyrosine-phosphatase - gene-product sap/sh2d1a - ifn-gamma production - human nk cells - fc-receptors - lipid rafts - phosphoinositide 3-kinase - mediated phagocytosis - inositol phosphatase - kir2dl4 cd158d
    Immunoregulatory receptors are categorized as stimulatory or inhibitory based on their engagement of unique intracellular signaling networks. These proteins also display functional plasticity, which adds versatility to the control of innate immunity. Here we demonstrate that an inhibitory catfish leukocyte immune-type receptor (IpLITR) also displays stimulatory capabilities in a representative myeloid cell model. Previously, the receptor IpLITR 1.1b was shown to inhibit natural killer cell-mediated cytotoxicity. Here we expressed IpLITR 1.1b in rat basophilic leukemia-2H3 cells and monitored intracellular signaling and functional responses. Although IpLITR 1.1b did not stimulate cytokine secretion, activation of this receptor unexpectedly induced phagocytosis as well as extracellular signal-related kinase 1/2- and protein kinase B (Akt)-dependent signal transduction. This novel IpLITR 1.1b-mediated response was independent of an association with the FcR¿ chain and was likely due to phosphotyrosine-dependent adaptors associating with prototypical signaling motifs within the distal region of its cytoplasmic tail. Furthermore, compared to a stimulatory IpLITR, IpLITR 1.1b displayed temporal differences in the induction of intracellular signaling, and IpLITR 1.1b-mediated phagocytosis had reduced sensitivity to EDTA and cytochalasin D. Overall, this is the first demonstration of functional plasticity for teleost LITRs, a process likely important for the fine-tuning of conserved innate defenses.
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