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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    ReDU: a framework to find and reanalyze public mass spectrometry data
    Jarmusch, Alan K. ; Wang, Mingxun ; Aceves, Christine M. ; Advani, Rohit S. ; Aguirre, Shaden ; Aksenov, Alexander A. ; Aleti, Gajender ; Aron, Allegra T. ; Bauermeister, Anelize ; Bolleddu, Sanjana ; Bouslimani, Amina ; Caraballo Rodriguez, Andres Mauricio ; Chaar, Rama ; Coras, Roxana ; Elijah, Emmanuel O. ; Ernst, Madeleine ; Gauglitz, Julia M. ; Gentry, Emily C. ; Husband, Makhai ; Jarmusch, Scott A. ; Jones, Kenneth L. ; Kamenik, Zdenek ; Gouellec, Audrey Le; Lu, Aileen ; McCall, Laura Isobel ; McPhail, Kerry L. ; Meehan, Michael J. ; Melnik, Alexey V. ; Menezes, Riya C. ; Montoya Giraldo, Yessica Alejandra ; Nguyen, Ngoc Hung ; Nothias, Louis Felix ; Nothias-Esposito, Mélissa ; Panitchpakdi, Morgan ; Petras, Daniel ; Quinn, Robert A. ; Sikora, Nicole ; Hooft, Justin J.J. van der; Vargas, Fernando ; Vrbanac, Alison ; Weldon, Kelly C. ; Knight, Rob ; Bandeira, Nuno ; Dorrestein, Pieter C. - \ 2020
    Nature Methods : techniques for life scientists and chemists 17 (2020)9. - ISSN 1548-7091 - p. 901 - 904.

    We present ReDU (, a system for metadata capture of public mass spectrometry-based metabolomics data, with validated controlled vocabularies. Systematic capture of knowledge enables the reanalysis of public data and/or co-analysis of one’s own data. ReDU enables multiple types of analyses, including finding chemicals and associated metadata, comparing the shared and different chemicals between groups of samples, and metadata-filtered, repository-scale molecular networking.

    The long-term restoration of ecosystem complexity
    Moreno-Mateos, David ; Alberdi, Antton ; Morriën, Elly ; Putten, Wim H. van der; Rodríguez-Uña, Asun ; Montoya, Daniel - \ 2020
    Nature Ecology & Evolution 4 (2020)5. - ISSN 2397-334X - p. 676 - 685.

    Multiple large-scale restoration strategies are emerging globally to counteract ecosystem degradation and biodiversity loss. However, restoration often remains insufficient to offset that loss. To address this challenge, we propose to focus restoration science on the long-term (centuries to millennia) re-assembly of degraded ecosystem complexity integrating interaction network and evolutionary potential approaches. This approach provides insights into eco-evolutionary feedbacks determining the structure, functioning and stability of recovering ecosystems. Eco-evolutionary feedbacks may help to understand changes in the adaptive potential after disturbance of metacommunity hub species with core structural and functional roles for their use in restoration. Those changes can be studied combining a restoration genomics approach based on whole-genome sequencing with replicated space-for-time substitutions linking changes in genetic variation to functions or traits relevant to the establishment of evolutionarily resilient communities. This approach may set the knowledge basis for future tools to accelerate the restoration of ecosystems able to adapt to ongoing global changes.

    International scientists formulate a roadmap for insect conservation and recovery
    Harvey, Jeffrey A. ; Heinen, Robin ; Armbrecht, Inge ; Basset, Yves ; Baxter-Gilbert, James H. ; Bezemer, T.M. ; Böhm, Monika ; Bommarco, Riccardo ; Borges, Paulo A.V. ; Cardoso, Pedro ; Clausnitzer, Viola ; Cornelisse, Tara ; Crone, Elizabeth E. ; Dicke, Marcel ; Dijkstra, Klaas Douwe B. ; Dyer, Lee ; Ellers, Jacintha ; Fartmann, Thomas ; Forister, Mathew L. ; Furlong, Michael J. ; Garcia-Aguayo, Andres ; Gerlach, Justin ; Gols, Rieta ; Goulson, Dave ; Habel, Jan Christian ; Haddad, Nick M. ; Hallmann, Caspar A. ; Henriques, Sérgio ; Herberstein, Marie E. ; Hochkirch, Axel ; Hughes, Alice C. ; Jepsen, Sarina ; Jones, T.H. ; Kaydan, Bora M. ; Kleijn, David ; Klein, Alexandra Maria ; Latty, Tanya ; Leather, Simon R. ; Lewis, Sara M. ; Lister, Bradford C. ; Losey, John E. ; Lowe, Elizabeth C. ; Macadam, Craig R. ; Montoya-Lerma, James ; Nagano, Christopher D. ; Ogan, Sophie ; Orr, Michael C. ; Painting, Christina J. ; Pham, Thai Hong ; Potts, Simon G. ; Rauf, Aunu ; Roslin, Tomas L. ; Samways, Michael J. ; Sanchez-Bayo, Francisco ; Sar, Sim A. ; Schultz, Cheryl B. ; Soares, António O. ; Thancharoen, Anchana ; Tscharntke, Teja ; Tylianakis, Jason M. ; Umbers, Kate D.L. ; Vet, Louise E.M. ; Visser, Marcel E. ; Vujic, Ante ; Wagner, David L. ; Wallis DeVries, Michiel F. ; Westphal, Catrin ; White, Thomas E. ; Wilkins, Vicky L. ; Williams, Paul H. ; Wyckhuys, Kris A.G. ; Zhu, Zeng Rong ; Kroon, Hans de - \ 2020
    Nature Ecology & Evolution 4 (2020)4. - ISSN 2397-334X - p. 174 - 176.
    Efficacy of non-pharmacological interventions to treat malnutrition in older persons : A systematic review and meta-analysis. The SENATOR project ONTOP series and MaNuEL knowledge hub project
    Correa-Pérez, Andrea ; Abraha, Iosef ; Cherubini, Antonio ; Collinson, Avril ; Dardevet, Dominique ; Groot, Lisette C.P.G.M. de; Schueren, Marian A.E. van der; Hebestreit, Antje ; Hickson, Mary ; Jaramillo-Hidalgo, Javier ; Lozano-Montoya, Isabel ; O'Mahony, Denis ; Soiza, Roy L. ; Visser, Marjolein ; Volkert, Dorothee ; Wolters, Maike ; Jentoft, Alfonso J.C. - \ 2019
    Ageing Research Reviews 49 (2019). - ISSN 1568-1637 - p. 27 - 48.
    Elderly, dietary supplementation - Protein energy malnutrition - Review, systematic

    Introduction: We aimed to perform a review of SRs of non-pharmacological interventions in older patients with well-defined malnutrition using relevant outcomes agreed by a broad panel of experts. Methods: PubMed, Cochrane, EMBASE, and CINHAL databases were searched for SRs. Primary studies from those SRs were included. Quality assessment was undertaken using Cochrane and GRADE criteria. Results: Eighteen primary studies from seventeen SRs were included. Eleven RCTs compared oral nutritional supplementation (ONS) with usual care. No beneficial effects of ONS treatment, after performing two meta-analysis in body weight changes (six studies), mean difference: 0.59 (95%CI -0.08, 1.96) kg, and in body mass index changes (two studies), mean difference: 0.31 (95%CI -0.17, 0.79) kg/m2 were found. Neither in MNA scores, muscle strength, activities of daily living, timed Up&Go, quality of life and mortality. Results of other intervention studies (dietary counselling and ONS, ONS combined with exercise, nutrition delivery systems) were inconsistent. The overall quality of the evidence was very low due to risk of bias and small sample size. Conclusions: This review has highlighted the lack of high quality evidence to indicate which interventions are effective in treating malnutrition in older people. High quality research studies are urgently needed in this area.

    Erratum to: The sponge microbiome project
    Moitinho-Silva, Lucas ; Nielsen, Shaun ; Amir, Amnon ; Gonzalez, Antonio ; Ackermann, Gail L. ; Cerrano, Carlo ; Astudillo-Garcia, Carmen ; Easson, Cole ; Sipkema, Detmer ; Liu, Fang ; Steinert, Georg ; Kotoulas, Giorgos ; McCormack, Grace P. ; Feng, Guofang ; Bell, James J. ; Vicente, Jan ; Björk, Johannes R. ; Montoya, Jose M. ; Olson, Julie B. ; Reveillaud, Julie ; Steindler, Laura ; Pineda, Mari Carmen ; Marra, Maria V. ; Ilan, Micha ; Taylor, Michael W. ; Polymenakou, Paraskevi ; Erwin, Patrick M. ; Schupp, Peter J. ; Simister, Rachel L. ; Knight, Rob ; Thacker, Robert W. ; Costa, Rodrigo ; Hill, Russell T. ; Lopez-Legentil, Susanna ; Dailianis, Thanos ; Ravasi, Timothy ; Hentschel, Ute ; Li, Zhiyong ; Webster, Nicole S. ; Thomas, Torsten - \ 2018
    GigaScience 7 (2018)12. - ISSN 2047-217X
    Ecological networks in managed ecosystems: Connecting structure to services
    Mulder, Christian ; Sechi, Valentina ; Woodward, Guy ; Bohan, David Andrew - \ 2017
    In: Adaptive Food Webs Cambridge University Press - ISBN 9781107182110 - p. 214 - 227.

    Introduction Ecological networks represent a cornerstone of ecology: they describe and evaluate the links between form and function in multispecies systems, such as food-web structure and dynamics, and they connect different scales and levels of biological organization (Moore and de Ruiter, 2012; Wall et al., 2015). These properties of being able to elucidate both the structure within complex systems and their scaling indicate that ecological networks and network theory could be widely applied to practical problems, including management decision-making processes such as the design of nature reserves and the preservation of ecosystem services. While the study of networks – initially food-web compartments, then community assemblages, and more recently mutualistic networks – is now firmly embedded in ecology (Levins, 1974; Cohen, 1978; Hunt et al., 1987; Beare et al., 1992; Solé and Montoya, 2001; Berlow et al., 2004; Moore et al., 2004; Cohen and Carpenter, 2005; Thébault and Fontaine, 2010; Moore and de Ruiter, 2012; Pocock et al., 2012; Neutel and Thorne, 2014), the application of such approaches to managed ecosystems has lagged far behind. There are many explanations for this disconnection between agro-ecology and ecology, not least the pervasive view that because they are human managed and disturbed agro-systems are fundamentally “unnatural” and different from natural ecosystems: most ecologists prefer to study so-called natural ecosystems, even though most of these have in fact been heavily influenced by mankind for centuries either directly by local activity or indirectly by long-distance pollution. Network approaches have rarely been applied to agriculture and forestry, which is perhaps surprising given that much of the early, integrated management research (e.g., from the seminal works by Von Carlowitz, 1713, and Von Liebig, 1840, onwards) and the study of networks that stimulated major advances in ecological theory was grounded in attempts to improve agricultural and timber production (Wardle, 2002; Schröter et al., 2003; Coleman et al., 2004; Moore and de Ruiter, 2012, and the references therein). The last two decades have seen a hiatus in advances in agro-ecology in this area, while new network theory and empirical studies have elucidated the roles of body size in ecosystems and the study of plant–pollinator networks and other mutualistic webs have redefined our understanding of general ecology.

    The sponge microbiome project
    Moitinho-Silva, Lucas ; Nielsen, Shaun ; Amir, Amnon ; Gonzalez, Antonio ; Ackermann, Gail L. ; Cerrano, Carlo ; Astudillo-Garcia, Carmen ; Easson, Cole ; Sipkema, Detmer ; Liu, Fang ; Steinert, Georg ; Kotoulas, Giorgos ; McCormack, Grace P. ; Feng, Guofang ; Bell, James J. ; Vicente, Jan ; Björk, Johannes R. ; Montoya, Jose M. ; Olson, Julie B. ; Reveillaud, Julie ; Steindler, Laura ; Pineda, Mari Carmen ; Marra, Maria V. ; Ilan, Micha ; Taylor, Michael W. ; Polymenakou, Paraskevi ; Erwin, Patrick M. ; Schupp, Peter J. ; Simister, Rachel L. ; Knight, Rob ; Thacker, Robert W. ; Costa, Rodrigo ; Hill, Russell T. ; Lopez-Legentil, Susanna ; Dailianis, Thanos ; Ravasi, Timothy ; Hentschel, Ute ; Li, Zhiyong ; Webster, Nicole S. ; Thomas, Torsten - \ 2017
    GigaScience 6 (2017)10. - ISSN 2047-217X
    16S rRNA gene - Archaea - Bacteria - Marine sponges - Microbial diversity - Microbiome - Symbiosis
    Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal, and environmental scales. Samples from marine sponges (n = 3569 specimens), seawater (n = 370), marine sediments (n = 65) and other environments (n = 29) were collected from different locations across the globe. This dataset incorporates at least 268 different sponge species, including several yet unidentified taxa. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA using standardised procedures. Raw sequences (total of 1.1 billion sequences) were processed and clustered with (i) a standard protocol using QIIME closed-reference picking resulting in 39 543 operational taxonomic units (OTU) at 97% sequence identity, (ii) a de novo clustering using Mothur resulting in 518 246 OTUs, and (iii) a new high-resolution Deblur protocol resulting in 83 908 unique bacterial sequences. Abundance tables, representative sequences, taxonomic classifications, and metadata are provided. This dataset represents a comprehensive resource of sponge-associated microbial communities based on 16S rRNA gene sequences that can be used to address overarching hypotheses regarding host-associated prokaryotes, including host specificity, convergent evolution, environmental drivers of microbiome structure, and the sponge-associated rare biosphere.
    Influence of Age and Dose of African Swine Fever Virus Infections on Clinical Outcome and Blood Parameters in Pigs
    Post, Jacob ; Weesendorp, Eefke ; Montoya, Maria ; Loeffen, Willie L. - \ 2017
    Viral Immunology 30 (2017)1. - ISSN 0882-8245 - p. 58 - 69.
    African swine fever - IL-10 - peripheral blood cells - serum cytokines - γδ T cells

    African swine fever (ASF) is a fatal disease for domestic pigs, leading to serious economic losses in countries where ASF is endemic. Despite extensive research, efficient vaccines against ASF are lacking. Since peripheral blood cells are important mediators for vaccines, we study the impact of ASF on blood parameters in pigs with different ages and infected with different doses of ASF virus. Four different groups were studied: (1) 12 weeks of age/low virus dose; (2) 12 weeks of age/high virus dose; (3) 18 weeks of age/low virus dose; and (4) 18 weeks of age/high virus dose. By varying in age and/or ASFV inoculation dose, we monitor blood parameters during different degrees of disease. Thirty percent of the pigs survived the infection with a moderately virulent strain of African swine fever virus (ASFV). Animals that did survive infection were generally older, independent from the inoculation dose used. A firm reduction in many different cell types at 3-5 days postinfection (DPI) was accompanied by an increase in body temperature, followed by clinical signs and mortality from day 6 PI. While blood parameters generally normalized in survivors, γδ T cells and IL-10 levels could be related to mortality. These conclusions should be considered in new approaches for protection against ASF.

    Decision Support Tools and Strategies to Simulate Forest Landscape Evolutions Integrating Forest Owner Behaviour: A Review from the Case Studies of the European Project, INTEGRAL
    Orazio, Christophe ; Montoya, Rebeca ; Régolini, Margot ; Borges, José ; Garcia-Gonzalo, Jordi ; Barreiro, Susana ; Botequim, Brigite ; Marques, Susete ; Sedmák, Róbert ; Smreček, Róbert ; Brodrechtová, Yvonne ; Brukas, Vilis ; Chirici, Gherardo ; Marchetti, Marco ; Moshammer, Ralf ; Biber, Peter ; Corrigan, Edwin ; Eriksson, Ljusk ; Favero, Matteo ; Galev, Emil ; Hengeveld, Geerten ; Kavaliauskas, Marius ; Mozgeris, Gintautas ; Navrátil, Rudolf ; Nieuwenhuis, Maarten ; Paligorov, Ivan ; Pettenella, Davide ; Stanislovaitis, Andrius ; Tomé, Margarida ; Trubins, Renats ; Tuček, Ján ; Vizzarri, Matteo ; Wallin, Ida ; Pretzsch, Hans ; Sallnäs, Ola - \ 2017
    Sustainability 9 (2017)4. - ISSN 2071-1050
    For forest sustainability and vulnerability assessment, the landscape scale is considered to be more and more relevant as the stand level approaches its known limitations. This review, which describes the main forest landscape simulation tools used in the 20 European case studies of the European project “Future-oriented integrated management of European forest landscapes” (INTEGRAL), gives an update on existing decision support tools to run landscape simulation from Mediterranean to boreal ecosystems. The main growth models and software available in Europe are described, and the strengths and weaknesses of different approaches are discussed. Trades-offs between input efforts and output are illustrated. Recommendations for the selection of a forest landscape simulator are given. The paper concludes by describing the need to have tools that are able to cope with climate change and the need to build more robust indicators for assessment of forest landscape sustainability and vulnerability.
    Seasonal drought limits tree species across the Neotropics
    Esquivel-Muelbert, Adriane ; Baker, Timothy R. ; Dexter, Kyle G. ; Lewis, Simon L. ; Steege, Hans ter; Lopez-Gonzalez, Gabriela ; Monteagudo Mendoza, Abel ; Brienen, Roel ; Feldpausch, Ted R. ; Pitman, Nigel ; Alonso, Alfonso ; Heijden, Geertje van der; Peña-Claros, Marielos ; Ahuite, Manuel ; Alexiaides, Miguel ; Álvarez Dávila, Esteban ; Murakami, Alejandro Araujo ; Arroyo, Luzmila ; Aulestia, Milton ; Balslev, Henrik ; Barroso, Jorcely ; Boot, Rene ; Cano, Angela ; Chama Moscoso, Victor ; Comiskey, James A. ; Cornejo, Fernando ; Dallmeier, Francisco ; Daly, Douglas C. ; Dávila, Nallarett ; Duivenvoorden, Joost F. ; Duque Montoya, Alvaro Javier ; Erwin, Terry ; Fiore, Anthony Di; Fredericksen, Todd ; Fuentes, Alfredo ; García-Villacorta, Roosevelt ; Gonzales, Therany ; Guevara Andino, Juan Ernesto ; Honorio Coronado, Euridice N. ; Huamantupa-Chuquimaco, Isau ; Killeen, Timothy J. ; Malhi, Yadvinder ; Mendoza, Casimiro ; Mogollón, Hugo ; Jørgensen, Peter Møller ; Montero, Juan Carlos ; Mostacedo, Bonifacio ; Nauray, William ; Neill, David ; Vargas, Percy Núñez ; Palacios, Sonia ; Palacios Cuenca, Walter ; Pallqui Camacho, Nadir Carolina ; Peacock, Julie ; Phillips, Juan Fernando ; Pickavance, Georgia ; Quesada, Carlos Alberto ; Ramírez-Angulo, Hirma ; Restrepo, Zorayda ; Reynel Rodriguez, Carlos ; Paredes, Marcos Ríos ; Sierra, Rodrigo ; Silveira, Marcos ; Stevenson, Pablo ; Stropp, Juliana ; Terborgh, John ; Tirado, Milton ; Toledo, Marisol ; Torres-Lezama, Armando ; Umaña, María Natalia ; Urrego, Ligia Estela ; Vasquez Martinez, Rodolfo ; Gamarra, Luis Valenzuela ; Vela, César I.A. ; Vilanova Torre, Emilio ; Vos, Vincent ; Hildebrand, Patricio von; Vriesendorp, Corine ; Wang, Ophelia ; Young, Kenneth R. ; Zartman, Charles Eugene ; Phillips, Oliver L. - \ 2017
    Ecography 40 (2017)5. - ISSN 0906-7590 - p. 618 - 629.
    Within the tropics, the species richness of tree communities is strongly and positively associated with precipitation. Previous research has suggested that this macroecological pattern is driven by the negative effect of water-stress on the physiological processes of most tree species. This implies that the range limits of inventory plots of closed canopy forest distributed across the western Neotropics taxa are defined by their ability to occur under dry conditions, and thus in terms of species distributions predicts a nested pattern of taxa distribution from wet to dry areas. However, this 'dry-tolerance' hypothesis has yet to be adequately tested at large spatial and taxonomic scales. Here, using a dataset of 531 we investigated how precipitation, evaluated both as mean annual precipitation and as the maximum climatological water deficit, influences the distribution of tropical tree species, genera and families. We find that the distributions of tree taxa are indeed nested along precipitation gradients in the western Neotropics. Taxa tolerant to seasonal drought are disproportionally widespread across the precipitation gradient, with most reaching even the wettest climates sampled; however, most taxa analysed are restricted to wet areas. Our results suggest that the 'dry tolerance' hypothesis has broad applicability in the world's most species-rich forests. In addition, the large number of species restricted to wetter conditions strongly indicates that an increased frequency of drought could severely threaten biodiversity in this region. Overall, this study establishes a baseline for exploring how tropical forest tree composition may change in response to current and future environmental changes in this region.
    In vivo and in vitro effects of a blend of essential oils on rumen methane mitigation
    Castro-Montoya, J. ; Peiren, N. ; Cone, J.W. ; Zweifel, B. ; Fievez, V. ; Campeneere, S. De - \ 2015
    Livestock Science 180 (2015). - ISSN 1871-1413 - p. 134 - 142.
    The effect of Agolin Ruminant, a blend of essential oils, on methane (CH4) emissions were investigated in two in vivo experiments and in four in vitro experiments. In the in vivo experiments, four lactating dairy cows and four beef heifers were supplemented 0.2 g/d of the essential oils (ca. 2–4 ppm m/v) during an eight-weeks period, where the first two weeks served as control (no essential oils supplementation). In dairy cattle, essential oils tended to decrease the daily CH4 emissions (g/d) and CH4 relative to dry matter intake (g/kg DMI) by 15% and 14%, respectively, after 6 weeks of supplementation (P=0.07), but no difference was observed for CH4 relative to milk production (g/kg milk) (P=0.64) or CH4 relative to bodyweight (g/kg BW) (P=0.12). In the in vivo experiment with beef cattle daily CH4 emissions and CH4 relative to DMI did not change when supplemented the essential oils at a dose of 0.2 g/d (numerical decreases of 10 and 11% for g CH4/d and g CH4/kg DMI, respectively) but CH4 relative to body weight tended to decrease by 20% after 6 weeks of supplementation (P=0.07). The in vitro experiments were expected to replicate the results observed in vivo. However, no decrease in CH4 production was observed in 24 h batch incubations at concentrations up to 30 ppm (m/v). A longer contact time between the essential oils (15 and 30 ppm) and the feedstuff (essential oils added ca. 16 h prior the start of the incubation) did not elicit any effect on CH4 production and was not different from addition immediately prior to the start of the incubation. Longer incubation time (96 h and 14 d) and regular supply of both substrate and additive in a consecutive batch incubation system did not induce CH4 inhibition up to essential oils doses of 30 ppm (m/v) and hence, also were not able to replicate in vivo results. Using the gas production technique (GPT) methane was inhibited by 17% with an essential oils dose of 30 ppm after 24 h, but this decrease was not constant across all times during the 72 h incubation. The blend of essential oil was effective reducing daily emissions of methane in dairy cattle and emissions relative to body weight in beef cattle, interestingly, these effects were not observed in vitro regardless of the techniques used to replicate in vivo results. This might be due to differences in the mode of action of the essential oils in vitro and in vivo, which merits attention for future research.
    Identifying paths of SME pursuing international buyers, and the influence of third parties: A promising tool for Latin American Agri-Food SMEs
    Solorzano, M. ; Dentoni, D. ; Montoya, D. - \ 2013
    Fortalecimiento de la capacidad de innovación agrícola: ¿los gestores sistémicos de innovación son la respuesta?
    Klerkx, L.W.A. ; Hall, A. ; Leeuwis, C. - \ 2013
    In: Escalando innovaciones rurales / Paz, A., Paz Montoya, M., Asensio, R.H., Lima, Peru : IEP Instituto de Estudios Peruanos - ISBN 9789972513893 - p. 87 - 108.
    A novel approach to analysing the regimes of temporary streams in relation to their controls on the composition and structure of aquatic biota
    Gallart, F. ; Prat, N. ; Garcia-Roger, E.M. ; Latron, J. ; Rieradevall, M. ; Liorens, P. ; Barbera, G.G. ; Brito, D. ; Girolamo, A. De; Porto, A. Lo; Buffagni, A. ; Erba, S. ; Neves, R. ; Nikolaidis, N.P. ; Perrin, L. ; Querner, E.P. ; Quinonero, J.M. ; Tournoud, M.G. ; Tzoraki, O. ; Skoulikidis, N. ; Gomez, R. ; Sanchez-Montoya, M.M. ; Froebrich, J. - \ 2012
    Hydrology and Earth System Sciences 16 (2012)9. - ISSN 1027-5606 - p. 3165 - 3182.
    benthic macroinvertebrate assemblages - mediterranean streams - intermittent streams - community structure - ephemeral channels - habitat features - fish assemblages - flow permanence - river health - drought
    Temporary streams are those water courses that undergo the recurrent cessation of flow or the complete drying of their channel. The structure and composition of biological communities in temporary stream reaches are strongly dependent on the temporal changes of the aquatic habitats determined by the hydrological conditions. Therefore, the structural and functional characteristics of aquatic fauna to assess the ecological quality of a temporary stream reach cannot be used without taking into account the controls imposed by the hydrological regime. This paper develops methods for analysing temporary streams' aquatic regimes, based on the definition of six aquatic states that summarize the transient sets of mesohabitats occurring on a given reach at a particular moment, depending on the hydrological conditions: Hyperrheic, Eurheic, Oligorheic, Arheic, Hyporheic and Edaphic. When the hydrological conditions lead to a change in the aquatic state, the structure and composition of the aquatic community changes according to the new set of available habitats. We used the water discharge records from gauging stations or simulations with rainfall-runoff models to infer the temporal patterns of occurrence of these states in the Aquatic States Frequency Graph we developed. The visual analysis of this graph is complemented by the development of two metrics which describe the permanence of flow and the seasonal predictability of zero flow periods. Finally, a classification of temporary streams in four aquatic regimes in terms of their influence over the development of aquatic life is updated from the existing classifications, with stream aquatic regimes defined as Permanent, Temporary-pools, Temporary-dry and Episodic. While aquatic regimes describe the long-term overall variability of the hydrological conditions of the river section and have been used for many years by hydrologists and ecologists, aquatic states describe the availability of mesohabitats in given periods that determine the presence of different biotic assemblages. This novel concept links hydrological and ecological conditions in a unique way. All these methods were implemented with data from eight temporary streams around the Mediterranean within the MIRAGE project. Their application was a precondition to assessing the ecological quality of these streams.
    Normative, cultural and cognitive aspects of modelling policies
    Dignum, V. ; Dignum, F. ; Osinga, S.A. ; Hofstede, G.J. - \ 2010
    In: Proceedings Winter simulation conference 2010, Baltimore, Maryland, USA, 5 - 8 December, 2010. - Baltimore : - ISBN 9781424498642 - p. 720 - 732.
    Induction of ovarian maturation and spawning by combined treatment of serotonin and a dopamine antagonist, spiperone in Litopenaeus stylirostris and Litopenaeus vannamei
    Alfaro Montoya, J. ; Zuniga, G. ; Komen, J. - \ 2004
    Aquaculture 236 (2004)1-4. - ISSN 0044-8486 - p. 511 - 522.
    red swamp crayfish - penaeus-vannamei - libinia-emarginata - methyl farnesoate - white shrimp - procambarus-clarkii - spider crab - steroids - release - growth
    The study was designed to develop a reliable technique for inducing ovarian maturation and spawning in Litopenaeus stylirostris and Litopenaeus vannamei, as an alternative to the traditional and destructive eyestalk ablation. Two combinations of molecules were evaluated: (a) serotonin (5-HT) at 50 ¿g g¿1 body weight (b.w.)+juvenile hormone (JH III) at 227 ng g¿1 b.w., and (b) 5-HT at 25 ¿g g¿1 b.w.+1.5 or 5 ¿g g¿1 b.w. spiperone. Combination (a) was tested in wild L. stylirostris, generating no ovarian maturation. Combination (b) did induce maturation and spawning in wild L. stylirostris and pond-grown L. vannamei. Maturation was observed in both 5-HT/spiperone treated females, as well as in vehicle injected females and in non-treated non-injected neighboring females, at rates similar to those obtained with eyestalk ablation. There was no significant difference in the quality of spawns between treatment groups. It is proposed that the combined injection of 5-HT and spiperone not only induces maturation and spawning, but also stimulates the release of maturation promoting pheromones into the water. The technique should be further tested at private facilities to define its commercial relevance for nauplii production
    Induction of sperm activation in open and closed thelycum penaeoid shrimps
    Alfaro Montoya, J. ; Munoz, N. ; Vargas, M. ; Komen, J. - \ 2003
    Aquaculture 216 (2003). - ISSN 0044-8486 - p. 371 - 382.
    sicyonia-ingentis - marine shrimp - setiferus - hybridization - decapoda
    A modified egg water (EW) technique for in vitro induction of sperm activation was applied to Trachypenaeus byrdi, Xiphopenaeus riveti (closed thelycum shrimps), and Litopenaeus occidentalis (open thelycum) from a tropical estuary, Golfo de Nicoya, Costa Rica. The study was designed to investigate the changes that occur in the sperm following contact with egg water, and to determine the potential of the technique for the assessment of differences in quality between sperm from spermatophores and sperm taken from the seminal receptacles. The modified technique induced activation of sperm removed from females' seminal receptacles, and demonstrated that sperm from males of T byrdi and X riveti do not react against conspecific EW, indicating that further maturation is required in seminal receptacles. Sperm from wild males of L. occidentalis reacted against conspecific EW, but at a low rate, suggesting that further maturation may be required in the external surface of the thelycum. Activation rates were low or variable between individuals in each species despite the expected high sperm quality from wild shrimp, indicating that the technique is not yet an useful sperm quality assay for the captive reproduction industry. The interspecific interaction between T byrdi sperm (seminal receptacles) and EW from X riveti and L. occidentalis generated no acrosome reaction, which may be an indication that molecular recognition is missing. (C) 2003 Elsevier Science B.V. All rights reserved.
    Controlled reproduction of penaeid shrimp: a contribution to its improvement
    Alfaro Montoya, J. - \ 2001
    Wageningen University. Promotor(en): E.A. Huisman; J. Komen. - S.l. : S.n. - ISBN 9789058084002 - 149
    aquacultuur - dierfysiologie - garnalen - penaeus - geslachtelijke voortplanting - gametogenese - schaal- en schelpdierenteelt - aquaculture - animal physiology - shrimps - penaeus - sexual reproduction - gametogenesis - shellfish culture

    This dissertation deals with controlled reproduction of penaeid shrimp. New knowledge about natural reproductive activity of Penaeus occidentalis in Gulf of Nicoya, Costa Rica, is presented. Since in vitro fertilization of open thelycum shrimp proved unsuccessful, a hypothesis is given to explain experimental results. In P. setiferus , the Male Reproductive Blackening Disease was studied, and bacterial infection was found to be associated with the male's condition. Production of spermatophores in captivity was explored in two species, P. stylirostris and P. vannamei . Adequate husbandry as well as successive ejaculation improved spermatophore quality. Deterioration of spermatophores was observed as part of a normal process for renewal in P. vannamei , without pathological implications. In order to further improve spermatophore quality, the injection of 17-alpha-methyltestosterone and 17-alpha-hydroxyprogesterone at 0.01 and 0.1 µg g -1 body weight was evaluated. 17-alpha-methyltestosterone significantly improved the quality of spermatophores, whereas 17-alpha-hydroxyprogesterone did not. Serotonin injection was evaluated as an alternative to female's eyestalk ablation for induction of ovarian maturation and spawning in P. vannamei . This neurotransmitter induced lower maturation and spawning with 3 doses of 50 µg g -1 body weight, than eyestalk ablation. In other to lay a basis for cryopreservation, penaeid embryos were evaluated in terms of their tolerance to cooling, cryoprotectants, and hypersaline solutions. T. byrdi morulae and advanced embryos (10 h) were tolerant to cooling at 10 °C, but were very sensitive to 0 °C. Embryos showed high tolerance to methanol and intermediate tolerance to dimethyl sulfoxide. Morulae were more resistant to hypersaline treatment at 55 ppt than advanced embryos.

    Cooling, cryporitectant and hypersaline sensitivity of Penaeid shrimp embryos and nauplii larvae
    Alfaro Montoya, J. ; Komen, J. ; Huisman, E.A. - \ 2001
    Aquaculture 195 (2001). - ISSN 0044-8486 - p. 353 - 366.
    The sensitivity of embryos of the penaeid shrimp, Trachypenaeus byrdi, to cooling, cryoprotectant exposure (dimethyl sulfoxide : DMSO, sucrose, methanol and glycerol), and hypersaline treatment was assessed in order to gain basic knowledge for cryopreservation procedures. In addition, cooling and DMSO exposure was evaluated in Penaeus stylirostris and T. byrdi nauplii. Morulae and advanced embryos (setae development stage) showed tolerance to cooling at 10°C, but were very sensitive to 0°C exposure. Methanol exposure at 12°C up to 2 M, was non-toxic for advanced embryos. DMSO toxicity was intermediate; no statistical decrease in survival (P>0.05) was measured at 0.5 M. Sucrose and glycerol were toxic to both embryo stages over 0.25 and 0.5 M, respectively. Morulae were more resistant to hypersaline treatment at 55 ppt than advanced embryos. Nauplii showed a better tolerance to cooling and DMSO exposure than embryos. These findings are being applied to develop a cryogenic protocol for penaeid embryos.
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