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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    Twenty-three unsolved problems in hydrology (UPH)–a community perspective
    Blöschl, Günter ; Bierkens, Marc F.P. ; Chambel, Antonio ; Cudennec, Christophe ; Destouni, Georgia ; Fiori, Aldo ; Kirchner, James W. ; McDonnell, Jeffrey J. ; Savenije, Hubert H.G. ; Sivapalan, Murugesu ; Stumpp, Christine ; Toth, Elena ; Volpi, Elena ; Carr, Gemma ; Lupton, Claire ; Salinas, Josè ; Széles, Borbála ; Viglione, Alberto ; Aksoy, Hafzullah ; Allen, Scott T. ; Amin, Anam ; Andréassian, Vazken ; Arheimer, Berit ; Aryal, Santosh K. ; Baker, Victor ; Bardsley, Earl ; Barendrecht, Marlies H. ; Bartosova, Alena ; Batelaan, Okke ; Berghuijs, Wouter R. ; Beven, Keith ; Blume, Theresa ; Bogaard, Thom ; Borges de Amorim, Pablo ; Böttcher, Michael E. ; Boulet, Gilles ; Breinl, Korbinian ; Brilly, Mitja ; Brocca, Luca ; Buytaert, Wouter ; Castellarin, Attilio ; Castelletti, Andrea ; Chen, Xiaohong ; Chen, Yangbo ; Chen, Yuanfang ; Chifflard, Peter ; Claps, Pierluigi ; Clark, Martyn P. ; Collins, Adrian L. ; Croke, Barry ; Dathe, Annette ; David, Paula C. ; Barros, Felipe P.J. de; Rooij, Gerrit de; Baldassarre, Giuliano Di; Driscoll, Jessica M. ; Duethmann, Doris ; Dwivedi, Ravindra ; Eris, Ebru ; Farmer, William H. ; Feiccabrino, James ; Ferguson, Grant ; Ferrari, Ennio ; Ferraris, Stefano ; Fersch, Benjamin ; Finger, David ; Foglia, Laura ; Fowler, Keirnan ; Gartsman, Boris ; Gascoin, Simon ; Gaume, Eric ; Gelfan, Alexander ; Geris, Josie ; Gharari, Shervan ; Gleeson, Tom ; Glendell, Miriam ; Gonzalez Bevacqua, Alena ; González-Dugo, María P. ; Grimaldi, Salvatore ; Gupta, A.B. ; Guse, Björn ; Han, Dawei ; Hannah, David ; Harpold, Adrian ; Haun, Stefan ; Heal, Kate ; Helfricht, Kay ; Herrnegger, Mathew ; Hipsey, Matthew ; Hlaváčiková, Hana ; Hohmann, Clara ; Holko, Ladislav ; Hopkinson, Christopher ; Hrachowitz, Markus ; Illangasekare, Tissa H. ; Inam, Azhar ; Innocente, Camyla ; Istanbulluoglu, Erkan ; Jarihani, Ben ; Kalantari, Zahra ; Kalvans, Andis ; Khanal, Sonu ; Khatami, Sina ; Kiesel, Jens ; Kirkby, Mike ; Knoben, Wouter ; Kochanek, Krzysztof ; Kohnová, Silvia ; Kolechkina, Alla ; Krause, Stefan ; Kreamer, David ; Kreibich, Heidi ; Kunstmann, Harald ; Lange, Holger ; Liberato, Margarida L.R. ; Lindquist, Eric ; Link, Timothy ; Liu, Junguo ; Loucks, Daniel Peter ; Luce, Charles ; Mahé, Gil ; Makarieva, Olga ; Malard, Julien ; Mashtayeva, Shamshagul ; Maskey, Shreedhar ; Mas-Pla, Josep ; Mavrova-Guirguinova, Maria ; Mazzoleni, Maurizio ; Mernild, Sebastian ; Misstear, Bruce Dudley ; Montanari, Alberto ; Müller-Thomy, Hannes ; Nabizadeh, Alireza ; Nardi, Fernando ; Neale, Christopher ; Nesterova, Nataliia ; Nurtaev, Bakhram ; Odongo, Vincent O. ; Panda, Subhabrata ; Pande, Saket ; Pang, Zhonghe ; Papacharalampous, Georgia ; Perrin, Charles ; Pfister, Laurent ; Pimentel, Rafael ; Polo, María J. ; Post, David ; Prieto Sierra, Cristina ; Ramos, Maria Helena ; Renner, Maik ; Reynolds, José Eduardo ; Ridolfi, Elena ; Rigon, Riccardo ; Riva, Monica ; Robertson, David E. ; Rosso, Renzo ; Roy, Tirthankar ; Sá, João H.M. ; Salvadori, Gianfausto ; Sandells, Mel ; Schaefli, Bettina ; Schumann, Andreas ; Scolobig, Anna ; Seibert, Jan ; Servat, Eric ; Shafiei, Mojtaba ; Sharma, Ashish ; Sidibe, Moussa ; Sidle, Roy C. ; Skaugen, Thomas ; Smith, Hugh ; Spiessl, Sabine M. ; Stein, Lina ; Steinsland, Ingelin ; Strasser, Ulrich ; Su, Bob ; Szolgay, Jan ; Tarboton, David ; Tauro, Flavia ; Thirel, Guillaume ; Tian, Fuqiang ; Tong, Rui ; Tussupova, Kamshat ; Tyralis, Hristos ; Uijlenhoet, Remko ; Beek, Rens van; Ent, Ruud J. van der; Ploeg, Martine van der; Loon, Anne F. Van; Meerveld, Ilja van; Nooijen, Ronald van; Oel, Pieter R. van; Vidal, Jean Philippe ; Freyberg, Jana von; Vorogushyn, Sergiy ; Wachniew, Przemyslaw ; Wade, Andrew J. ; Ward, Philip ; Westerberg, Ida K. ; White, Christopher ; Wood, Eric F. ; Woods, Ross ; Xu, Zongxue ; Yilmaz, Koray K. ; Zhang, Yongqiang - \ 2019
    Hydrological Sciences Journal 64 (2019)10. - ISSN 0262-6667 - p. 1141 - 1158.
    hydrology - interdisciplinary - knowledge gaps - research agenda - science questions

    This paper is the outcome of a community initiative to identify major unsolved scientific problems in hydrology motivated by a need for stronger harmonisation of research efforts. The procedure involved a public consultation through online media, followed by two workshops through which a large number of potential science questions were collated, prioritised, and synthesised. In spite of the diversity of the participants (230 scientists in total), the process revealed much about community priorities and the state of our science: a preference for continuity in research questions rather than radical departures or redirections from past and current work. Questions remain focused on the process-based understanding of hydrological variability and causality at all space and time scales. Increased attention to environmental change drives a new emphasis on understanding how change propagates across interfaces within the hydrological system and across disciplinary boundaries. In particular, the expansion of the human footprint raises a new set of questions related to human interactions with nature and water cycle feedbacks in the context of complex water management problems. We hope that this reflection and synthesis of the 23 unsolved problems in hydrology will help guide research efforts for some years to come.

    Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen
    Pais, Marina ; Yoshida, Kentaro ; Giannakopoulou, Artemis ; Pel, M. ; Cano, Liliana M. ; Oliva, Ricardo F. ; Witek, Kamil ; Lindqvist-Kreuze, Hannele ; Vleeshouwers, V.G.A.A. ; Kamoun, Sophien - \ 2018
    The Sainsbury Laboratory
    asexual reproduction - clonal lineage - Phytophthora infestans - emergent pathogen - evolution - immunity - phenotypic plasticity - expression polymorphism - structural variation - copy number variation - loss of heterozygosity
    Background Outbreaks caused by asexual lineages of fungal and oomycete pathogens are a continuing threat to crops, wild animals and natural ecosystems (Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, Gurr SJ, Nature 484:186–194, 2012; Kupferschmidt K, Science 337:636–638, 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl MF, Thomma BP, BioEssays 36:335–345, 2014). Ever since the 19th century Irish famine, the oomycete Phytophthora infestans has caused recurrent outbreaks on potato and tomato crops that have been primarily caused by the successive rise and migration of pandemic asexual lineages (Goodwin SB, Cohen BA, Fry WE, Proc Natl Acad Sci USA 91:11591–11595, 1994; Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10:e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Cooke DEL, Cano LM, Raffaele S, Bain RA, Cooke LR, Etherington GJ, Deahl KL, Farrer RA, Gilroy EM, Goss EM, et al. PLoS Pathog 8:e1002940, 2012). However, the dynamics of genome evolution within these clonal lineages have not been determined. The objective of this study was to use a comparative genomics and transcriptomics approach to determine the molecular mechanisms that underpin phenotypic variation within a clonal lineage of P. infestans. Results Here, we reveal patterns of genomic and gene expression variation within a P. infestans asexual lineage by comparing strains belonging to the South American EC-1 clone that has dominated Andean populations since the 1990s (Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Delgado RA, Monteros-Altamirano AR, Li Y, Visser RGF, van der Lee TAJ, Vosman B, Plant Pathol 62:1081–1088, 2013; Forbes GA, Escobar XC, Ayala CC, Revelo J, Ordonez ME, Fry BA, Doucett K, Fry WE, Phytopathology 87:375–380, 1997; Oyarzun PJ, Pozo A, Ordonez ME, Doucett K, Forbes GA, Phytopathology 88:265–271, 1998). We detected numerous examples of structural variation, nucleotide polymorphisms and loss of heterozygosity within the EC-1 clone. Remarkably, 17 genes are not expressed in one of the two EC-1 isolates despite apparent absence of sequence polymorphisms. Among these, silencing of an effector gene was associated with evasion of disease resistance conferred by a potato immune receptor. Conclusions Our findings highlight the molecular changes underpinning the exceptional genetic and phenotypic plasticity associated with host adaptation in a pandemic clonal lineage of a eukaryotic plant pathogen. We observed that the asexual P. infestans lineage EC-1 can exhibit phenotypic plasticity in the absence of apparent genetic mutations resulting in virulence on a potato carrying the Rpi-vnt1.1 gene. Such variant alleles may be epialleles that arose through epigenetic changes in the underlying genes.
    Towards sustainable European grassland farming with Inno4Grass: an infrastructure for innovation and knowledge sharing
    Krause, A. ; Becker, Talea ; Feindt, Peter H. ; Huyghe, C. ; O'Donovan, Michael ; Peeters, A. ; Pol, A. van den - \ 2018
    In: Sustainable meat and milk production from grasslands. - Zürich : European Grassland Federation EGF (Grassland Science in Europe ) - ISBN 9781841706436 - p. 925 - 936.
    European agriculture is facing tremendous challenges related to the rapid decrease of farm populations, competitiveness on open markets and the preservation of natural resources on finite areas. Grasslands, which are highly significant for nature conservation, often face land-use competition with arable cropping, urbanisation and other uses. Farmers need dedicated innovations to improve grasslands economic performance and their effective implementation in practice. This requires co-creation of knowledge between researchers and farmland practitioners, as was broadly pointed out by the European Commission. This paper describes a novel approach to create a collaborative space for grassland innovations contributing to profitability of European grassland farms while preserving environmental benefits. Innovative modes of collaboration between practice and science are enabled by an international thematic network across eight European member states. A methodolog y serves to collect farmers’ innovative ideas and to stimulate collaboration among various stakeholders (farmers’ groups, extension services, education and research) including cross-border collaborations, where grassland-related knowledge is made available for local conditions. This interactive innovation model fosters knowledge exchange and establishes a farmland-specific Information Management System. The aim is to stimulate a renewed, collaborative innovation culture for EU grasslands. The methods are conceptualised and put into practice by the Thematic Network project Inno4Grass funded under Horizon 2020.
    A protocol for an intercomparison of biodiversity and ecosystem services models using harmonized land-use and climate scenarios
    Kim, Hyejin ; Rosa, Isabel M.D. ; Alkemade, Rob ; Leadley, Paul ; Hurtt, George ; Popp, Alexander ; Vuuren, Detlef P. van; Anthoni, Peter ; Arneth, Almut ; Baisero, Daniele ; Caton, Emma ; Chaplin-Kramer, Rebecca ; Chini, Louise ; Palma, Adriana De; Fulvio, Fulvio Di; Marco, Moreno Di; Espinoza, Felipe ; Ferrier, Simon ; Fujimori, Shinichiro ; Gonzalez, Ricardo E. ; Gueguen, Maya ; Guerra, Carlos ; Harfoot, Mike ; Harwood, Thomas D. ; Hasegawa, Tomoko ; Haverd, Vanessa ; Havlík, Petr ; Hellweg, Stefanie ; Hill, Samantha L.L. ; Hirata, Akiko ; Hoskins, Andrew J. ; Janse, Jan H. ; Jetz, Walter ; Johnson, Justin A. ; Krause, Andreas ; Leclère, David ; Martins, Ines S. ; Matsui, Tetsuya ; Merow, Cory ; Obersteiner, Michael ; Ohashi, Haruka ; Poulter, Benjamin ; Purvis, Andy ; Quesada, Benjamin ; Rondinini, Carlo ; Schipper, Aafke M. ; Sharp, Richard ; Takahashi, Kiyoshi ; Thuiller, Wilfried ; Titeux, Nicolas - \ 2018
    Geoscientific Model Development 11 (2018)11. - ISSN 1991-959X - p. 4537 - 4562.

    To support the assessments of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES), the IPBES Expert Group on Scenarios and Models is carrying out an intercomparison of biodiversity and ecosystem services models using harmonized scenarios (BES-SIM). The goals of BES-SIM are (1) to project the global impacts of land-use and climate change on biodiversity and ecosystem services (i.e., nature's contributions to people) over the coming decades, compared to the 20th century, using a set of common metrics at multiple scales, and (2) to identify model uncertainties and research gaps through the comparisons of projected biodiversity and ecosystem services across models. BES-SIM uses three scenarios combining specific Shared Socio-economic Pathways (SSPs) and Representative Concentration Pathways (RCPs)-SSP1xRCP2.6, SSP3xRCP6.0, SSP5xRCP8.6-to explore a wide range of land-use change and climate change futures. This paper describes the rationale for scenario selection, the process of harmonizing input data for land use, based on the second phase of the Land Use Harmonization Project (LUH2), and climate, the biodiversity and ecosystem services models used, the core simulations carried out, the harmonization of the model output metrics, and the treatment of uncertainty. The results of this collaborative modeling project will support the ongoing global assessment of IPBES, strengthen ties between IPBES and the Intergovernmental Panel on Climate Change (IPCC) scenarios and modeling processes, advise the Convention on Biological Diversity (CBD) on its development of a post-2020 strategic plans and conservation goals, and inform the development of a new generation of nature-centred scenarios.

    Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen
    Pais, Marina ; Yoshida, Kentaro ; Giannakopoulou, Artemis ; Pel, Mathieu A. ; Cano, Liliana M. ; Oliva, Ricardo F. ; Witek, Kamil ; Lindqvist-Kreuze, Hannele ; Vleeshouwers, Vivianne G.A.A. ; Kamoun, Sophien - \ 2018
    BMC Evolutionary Biology 18 (2018)1. - ISSN 1471-2148
    Asexual reproduction - Clonal lineage - Copy number variation - Emergent pathogen - Evolution - Expression polymorphism - Immunity - Loss of heterozygosity - Phenotypic plasticity - Phytophthora infestans - Structural variation

    Background: Outbreaks caused by asexual lineages of fungal and oomycete pathogens are a continuing threat to crops, wild animals and natural ecosystems (Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, Gurr SJ, Nature 484:186-194, 2012; Kupferschmidt K, Science 337:636-638, 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl MF, Thomma BP, BioEssays 36:335-345, 2014). Ever since the 19th century Irish famine, the oomycete Phytophthora infestans has caused recurrent outbreaks on potato and tomato crops that have been primarily caused by the successive rise and migration of pandemic asexual lineages (Goodwin SB, Cohen BA, Fry WE, Proc Natl Acad Sci USA 91:11591-11595, 1994; Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10:e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Cooke DEL, Cano LM, Raffaele S, Bain RA, Cooke LR, Etherington GJ, Deahl KL, Farrer RA, Gilroy EM, Goss EM, et al. PLoS Pathog 8:e1002940, 2012). However, the dynamics of genome evolution within these clonal lineages have not been determined. The objective of this study was to use a comparative genomics and transcriptomics approach to determine the molecular mechanisms that underpin phenotypic variation within a clonal lineage of P. infestans. Results: Here, we reveal patterns of genomic and gene expression variation within a P. infestans asexual lineage by comparing strains belonging to the South American EC-1 clone that has dominated Andean populations since the 1990s (Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Delgado RA, Monteros-Altamirano AR, Li Y, Visser RGF, van der Lee TAJ, Vosman B, Plant Pathol 62:1081-1088, 2013; Forbes GA, Escobar XC, Ayala CC, Revelo J, Ordonez ME, Fry BA, Doucett K, Fry WE, Phytopathology 87:375-380, 1997; Oyarzun PJ, Pozo A, Ordonez ME, Doucett K, Forbes GA, Phytopathology 88:265-271, 1998). We detected numerous examples of structural variation, nucleotide polymorphisms and loss of heterozygosity within the EC-1 clone. Remarkably, 17 genes are not expressed in one of the two EC-1 isolates despite apparent absence of sequence polymorphisms. Among these, silencing of an effector gene was associated with evasion of disease resistance conferred by a potato immune receptor. Conclusions: Our findings highlight the molecular changes underpinning the exceptional genetic and phenotypic plasticity associated with host adaptation in a pandemic clonal lineage of a eukaryotic plant pathogen. We observed that the asexual P. infestans lineage EC-1 can exhibit phenotypic plasticity in the absence of apparent genetic mutations resulting in virulence on a potato carrying the Rpi-vnt1.1 gene. Such variant alleles may be epialleles that arose through epigenetic changes in the underlying genes.

    Is Low-field NMR a Complementary Tool to GC-MS in Quality Control of Essential Oils? A Case Study : Patchouli Essential Oil *
    Krause, Andre ; Wu, Yu ; Tian, Runtao ; Beek, Teris A. van - \ 2018
    Planta Medica 84 (2018)12/13. - ISSN 0032-0943 - p. 953 - 963.
    60 MHz H-NMR - adulteration - chemometrics - essential oil - fingerprinting - patchouli - quality control
    High-field NMR is an expensive and important quality control technique. In recent years, cheaper and simpler low-field NMR has become available as a new quality control technique. In this study, 60 MHz 1 H-NMR was compared with GC-MS and refractometry for the detection of adulteration of essential oils, taking patchouli essential oil as a test case. Patchouli essential oil is frequently adulterated, even today. In total, 75 genuine patchouli essential oils, 10 commercial patchouli essential oils, 10 other essential oils, 17 adulterants, and 1 patchouli essential oil, spiked at 20% with those adulterants, were measured. Visual inspection of the NMR spectra allowed for easy detection of 14 adulterants, while gurjun and copaiba balsams proved difficult and one adulterant could not be detected. NMR spectra of 10 random essential oils differed not only strongly from patchouli essential oil but also from one another, suggesting that fingerprinting by low-field NMR is not limited to patchouli essential oil. Automated chemometric evaluation of NMR spectra was possible by similarity analysis (Mahalanobis distance) based on the integration from 0.1 – 8.1 ppm in 0.01 ppm increments. Good quality patchouli essential oils were recognised as well as 15 of 17 deliberate adulterations. Visual qualitative inspection by GC-MS allowed for the detection of all volatile adulterants. Nonvolatile adulterants, and all but one volatile adulterant, could be detected by semiquantitation. Different chemometric approaches showed satisfactory results. Similarity analyses were difficult with nonvolatile adulterants. Refractive index measurements could detect only 8 of 17 adulterants. Due to advantages such as simplicity, rapidity, reproducibility, and ability to detect nonvolatile adulterants, 60 MHz 1 H-NMR is complimentary to GC-MS for quality control of essential oils.
    Natural attenuation of chlorinated ethenes in hyporheic zones : A review of key biogeochemical processes and in-situ transformation potential
    Weatherill, John J. ; Atashgahi, Siavash ; Schneidewind, Uwe ; Krause, Stefan ; Ullah, Sami ; Cassidy, Nigel ; Rivett, Michael O. - \ 2018
    Water Research 128 (2018). - ISSN 0043-1354 - p. 362 - 382.
    Biogeochemistry - Biotransformation - Chlorinated ethenes - Heterogeneity - Hyporheic zone - Natural attenuation
    Chlorinated ethenes (CEs) are legacy contaminants whose chemical footprint is expected to persist in aquifers around the world for many decades to come. These organohalides have been reported in river systems with concerning prevalence and are thought to be significant chemical stressors in urban water ecosystems. The aquifer-river interface (known as the hyporheic zone) is a critical pathway for CE discharge to surface water bodies in groundwater baseflow. This pore water system may represent a natural bioreactor where anoxic and oxic biotransformation process act in synergy to reduce or even eliminate contaminant fluxes to surface water. Here, we critically review current process understanding of anaerobic CE respiration in the competitive framework of hyporheic zone biogeochemical cycling fuelled by in-situ fermentation of natural organic matter. We conceptualise anoxic-oxic interface development for metabolic and co-metabolic mineralisation by a range of aerobic bacteria with a focus on vinyl chloride degradation pathways. The superimposition of microbial metabolic processes occurring in sediment biofilms and bulk solute transport delivering reactants produces a scale dependence in contaminant transformation rates. Process interpretation is often confounded by the natural geological heterogeneity typical of most riverbed environments. We discuss insights from recent field experience of CE plumes discharging to surface water and present a range of practical monitoring technologies which address this inherent complexity at different spatial scales. Future research must address key dynamics which link supply of limiting reactants, residence times and microbial ecophysiology to better understand the natural attenuation capacity of hyporheic systems.
    Variation in Reproductive Success Across Captive Populations: Methodological Differences, Potential Biases and Opportunities
    Griffith, Simon C. ; Crino, Ondi L. ; Andrew, Samuel C. ; Nomano, Fumiaki Y. ; Adkins-Regan, Elizabeth ; Alonso-Alvarez, Carlos ; Bailey, Ida E. ; Bittner, Stephanie S. ; Bolton, Peri E. ; Boner, Winnie ; Boogert, Neeltje ; Boucaud, Ingrid C.A. ; Briga, Michael ; Buchanan, Katherine L. ; Caspers, Barbara A. ; Cichoń, Mariusz ; Clayton, David F. ; Derégnaucourt, Sebastien ; Forstmeier, Wolfgang ; Guillette, Lauren M. ; Hartley, Ian R. ; Healy, Susan D. ; Hill, Davina L. ; Holveck, Marie Jeanne ; Hurley, Laura L. ; Ihle, Malika ; Tobias Krause, E. ; Mainwaring, Mark C. ; Marasco, Valeria ; Mariette, Mylene M. ; Martin-Wintle, Meghan S. ; McCowan, Luke S.C. ; McMahon, Maeve ; Monaghan, Pat ; Nager, Ruedi G. ; Naguib, Marc ; Nord, Andreas ; Potvin, Dominique A. ; Prior, Nora H. ; Riebel, Katharina ; Romero-Haro, Ana A. ; Royle, Nick J. ; Rutkowska, Joanna ; Schuett, Wiebke ; Swaddle, John P. ; Tobler, Michael ; Trompf, Larissa ; Varian-Ramos, Claire W. ; Vignal, Clémentine ; Villain, Avelyne S. ; Williams, Tony D. - \ 2017
    Ethology 123 (2017)1. - ISSN 0179-1613 - p. 1 - 29.
    captive breeding - captivity - domestication - husbandry - model species - reproductive failure - Taeniopygia guttata - zebra finch

    Our understanding of fundamental organismal biology has been disproportionately influenced by studies of a relatively small number of ‘model’ species extensively studied in captivity. Laboratory populations of model species are commonly subject to a number of forms of past and current selection that may affect experimental outcomes. Here, we examine these processes and their outcomes in one of the most widely used vertebrate species in the laboratory – the zebra finch (Taeniopygia guttata). This important model species is used for research across a broad range of fields, partly due to the ease with which it can be bred in captivity. However despite this perceived amenability, we demonstrate extensive variation in the success with which different laboratories and studies bred their subjects, and overall only 64% of all females that were given the opportunity, bred successfully in the laboratory. We identify and review several environmental, husbandry, life-history and behavioural factors that potentially contribute to this variation. The variation in reproductive success across individuals could lead to biases in experimental outcomes and drive some of the heterogeneity in research outcomes across studies. The zebra finch remains an excellent captive animal system and our aim is to sharpen the insight that future studies of this species can provide, both to our understanding of this species and also with respect to the reproduction of captive animals more widely. We hope to improve systematic reporting methods and that further investigation of the issues we raise will lead both to advances in our fundamental understanding of avian reproduction as well as to improvements in future welfare and experimental efficiency.

    Spacer capture and integration by a type I-F Cas1-Cas2-3 CRISPR adaptation complex
    Fagerlund, Robert D. ; Wilkinson, Max E. ; Klykov, Oleg ; Barendregt, Arjan ; Pearce, F.G. ; Kieper, Sebastian N. ; Maxwell, Howard W.R. ; Capolupo, Angela ; Heck, Albert J.R. ; Krause, Kurt L. ; Bostina, Mihnea ; Scheltema, Richard A. ; Staals, Raymond H.J. ; Fineran, Peter C. - \ 2017
    Proceedings of the National Academy of Sciences of the United States of America 114 (2017)26. - ISSN 0027-8424 - p. E5122 - E5128.
    Crispr-cas - Horizontal gene transfer - Mass spectrometry - Phage resistance - Spacer acquisition

    CRISPR-Cas adaptive immune systems capture DNA fragments from invading bacteriophages and plasmids and integrate them as spacers into bacterial CRISPR arrays. In type I-E and II-A CRISPR-Cas systems, this adaptation process is driven by Cas1-Cas2 complexes. Type I-F systems, however, contain a unique fusion of Cas2, with the type I effector helicase and nuclease for invader destruction, Cas3. By using biochemical, structural, and biophysical methods, we present a structural model of the 400-kDa Cas14-Cas2-32 complex from Pectobacterium atrosepticum with bound protospacer substrate DNA. Two Cas1 dimers assemble on a Cas2 domain dimeric core, which is flanked by two Cas3 domains forming a groove where the protospacer binds to Cas1-Cas2. We developed a sensitive in vitro assay and demonstrated that Cas1-Cas2-3 catalyzed spacer integration into CRISPR arrays. The integrase domain of Cas1 was necessary, whereas integration was independent of the helicase or nuclease activities of Cas3. Integration required at least partially duplex protospacers with free 3′-OH groups, and leader-proximal integration was stimulated by integration host factor. In a coupled capture and integration assay, Cas1-Cas2-3 processed and integrated protospacers independent of Cas3 activity. These results provide insight into the structure of protospacer-bound type I Cas1-Cas2-3 adaptation complexes and their integration mechanism.

    Shared Innovation Space for Sustainable Productivity of Grasslands in Europe : Inno4Grass deliverable no. 3.1
    Golinski, P. ; Pol, A. van den; Golinska, B. ; Paszkowski, A. ; Nilsdotter-Linde, N. ; O'Donovan, M. ; Porqueddu, C. ; Czerwińska, A. ; Delaite, B. ; Bauer, A. ; Florian, C. ; Baste, F. ; Fradin, J. ; Gauder, P. ; Kort, H. de; Krause, A. - \ 2017
    Inno4Grass - 17 p.
    Towards systematic analyses of ecosystem service trade-offs and synergies : Main concepts, methods and the road ahead
    Cord, Anna F. ; Bartkowski, Bartosz ; Beckmann, Michael ; Dittrich, Andreas ; Hermans, Kathleen ; Kaim, Andrea ; Lienhoop, Nele ; Locher-Krause, Karla ; Priess, Jörg ; Schröter-Schlaack, Christoph ; Schwarz, Nina ; Seppelt, Ralf ; Strauch, Michael ; Václavík, Tomáš ; Volk, Martin - \ 2017
    Ecosystem Services 28 (2017)part C. - ISSN 2212-0416 - p. 264 - 272.
    Ecosystem service bundles - Ecosystem service demand - Ecosystem service supply - Optimization - Spatio-temporal scales - Stakeholders

    Ecosystem services (ES), the benefits that humans obtain from nature, are of great importance for human well-being. The challenge of meeting the growing human demands for natural resources while sustaining essential ecosystem functions and resilience requires an in-depth understanding of the complex relationships between ES. These conflicting ('trade-offs') or synergistic ('synergies') relationships mean that changes in one ES can cause changes in other ES. By synthesizing the growing body of literature on ES relationships, we identified the following four main study objectives: (i) the identification and characterization of co-occurrences of ES, (ii) the identification of drivers that shape ES relationships, (iii) the exploration of biophysical constraints of landscapes and limitations to their multifunctionality, and (iv) the support of environmental planning, management and policy decisions. For each of these objectives we here describe the key concepts, including viewpoints of different disciplines, and highlight the major challenges that need to be addressed. We identified three cross-cutting themes being relevant to all four main types of studies. To help guiding researchers towards more systematic analyses of ES trade-offs and synergies, we conclude with an outlook on suggested future research priorities.

    Implications of nutritional stress as nestling or fledgling on subsequent attractiveness and fecundity in zebra finches (Taeniopygia guttata)
    Honarmand, Mariam ; Krause, E.T. ; Naguib, Marc - \ 2017
    PeerJ 5 (2017). - ISSN 2167-8359 - 18 p.
    Early developmental stress - Female choice - Male choice - Mate choice - Zebra finch

    The conditions an organism experiences during early development can have profound and long lasting effects on its subsequent behavior, attractiveness, and life history decisions. Most previous studies have exposed individuals to different conditions throughout development until nutritional independence. Yet under natural conditions, individuals may experience limitations for much shorter periods due to transient environmental fluctuations. Here, we used zebra finches (Taeniopygia guttata) in captivity to determine if conditions experienced during distinctly different early developmental phases contribute differently to male and female attractiveness and subsequent reproduction. We conducted a breeding experiment in which offspring were exposed to food regimes with (a) low quality food provided only during the nestling period, (b) low quality food provided only during the fledgling period, or (c) high quality food throughout early development. We show that despite short-term effects on biometry and physiology, there were no effects on either male or female attractiveness, as tested in two-way mate choice free-flight aviary experiments. In a subsequent breeding experiment, the offspring from the initial experiment were allowed to breed themselves. The next generation offspring from mothers raised under lower quality nutrition as either nestling or fledging were lighter at hatching compared to offspring from mothers raised under higher quality nutrition whereas paternal early nutrition had no such effects. The lack of early developmental limitations on attractiveness suggests that attractiveness traits were not affected or that birds compensated for any such effects. Furthermore, maternal trans-generational effects of dietary restrictions emphasize the importance of role of limited periods of early developmental stress in the expression of environmentally determined fitness components.

    Le pâturage en France et en Europe : État des lieux et enjeux
    Huyghe, C. ; Pol-van Dasselaar, A. van den; Krause, A. - \ 2017
    Fourrages (2017)229. - ISSN 0429-2766 - p. 1 - 10.
    Basic diet - Change in time - Economic aspect - Estimation method - Europe - Forecast - Grassland - Grazing - New-Zealand - Seasonal variations

    Livestock grazing is central to many important agricultural and dietary issues. However, its use has been declining as both farm size and climate-related variability in forage have increased. Foresight studies examining food security have found that grasslands play an important role in allowing adjustments under different circumstances. Grazing can be used to ensure farm economic performance, address environmental challenges, and respond to consumer expectations. It is drawing ever increasing attention from the dairy industry and product distributors, as well as from legislators in certain countries. However, we currently lack a proper method for quantifying grazing practices (here, we describe a potential way to estimate the maximum contribution made by grazing to livestock production). We also need to establish shared European-level standards (in Germany and the Netherlands, to be considered grass fed, livestock must graze at least 6 h/day and 120 days/year).

    Desert agricultural systems at EBA Jawa (Jordan): Integrating archaeological and paleoenvironmental records
    Meister, Julia ; Krause, J. ; Müller-Neuhofb, B. ; Portillo, M. ; Reimann, T. ; Schütt, B. - \ 2017
    Quaternary International 434 (2017). - ISSN 1040-6182 - p. 33 - 50.
    Ancient agricultural terraces; Early Bronze Age;Terrace fill sediments;Multi-proxy approach;Phytoliths; OSL dating
    Located in the arid basalt desert of northeastern Jordan, the settlement of Jawa is by far the largest and best-preserved archaeological site in the region. The Early Bronze Age (EBA) settlement phase of Jawa (3500–3000 BCE) is characterized by a highly sophisticated water storage system made of a series of pools, dams, and canals. In addition, recent archaeological and geoarchaeological surveys have uncovered agricultural terrace systems in the nearby vicinity.
    In this study, four of these runoff terrace systems were investigated by detailed mapping. Additionally, thirteen sediment profiles from inside and outside the terrace systems were recorded and sampled. The examined samples were analyzed for bulk chemistry, texture, phytoliths, diatoms, and dung spherulites to supply information on the environmental and depositional conditions. The terrace systems were dated using optically stimulated luminescence (OSL).
    Ancient terrace agriculture was practiced on slopes, small plateaus, and valleys close to Jawa through the use of surface canals, which collected and diverted floodwater from nearby wadis or runoff from adjacent slopes. The terraced fields were usually arranged in cascades and comprised a system of risers, canals, and spillways. The terrace fills investigated yield OSL ages of around 3300 BCE, indicating that the terraces were constructed in the Early Bronze Age. The terrace fill sequences are composed of mixed unstratified fine sediments of local origin, reflecting low-energy fluvial deposition regimes. The phytolith record is dominated by Pooid grasses that include the most common Near Eastern cereals, such as wheat and barley. Increased phytolith concentrations in terrace fill sediments, as compared to samples from non-terrace deposits nearby, suggest increased plant growth and water availability within the terraces. Whether the terrace systems were used for growing food crops only or whether they were additionally used for grazing cannot be ascertained. Overall, quantitative phytolith analyses in arid environments are well suited to investigate temporal and spatial distributions of plant microfossil concentrations and their relation to human activity or paleoenvironmental conditions.
    Distributed Temperature Sensing as a downhole tool in hydrogeology
    Bense, V.F. ; Read, T. ; Bour, O. ; Borgne, T. Le; Coleman, T. ; Krause, S. ; Chalari, A. ; Mondanos, M. ; Ciocca, F. ; Selker, J.S. - \ 2016
    Water Resources Research 52 (2016)12. - ISSN 0043-1397 - p. 9259 - 9273.
    Distributed Temperature Sensing - Subsurface hydrology

    Distributed Temperature Sensing (DTS) technology enables downhole temperature monitoring to study hydrogeological processes at unprecedentedly high frequency and spatial resolution. DTS has been widely applied in passive mode in site investigations of groundwater flow, in-well flow, and subsurface thermal property estimation. However, recent years have seen the further development of the use of DTS in an active mode (A-DTS) for which heat sources are deployed. A suite of recent studies using A-DTS downhole in hydrogeological investigations illustrate the wide range of different approaches and creativity in designing methodologies. The purpose of this review is to outline and discuss the various applications and limitations of DTS in downhole investigations for hydrogeological conditions and aquifer geological properties. To this end, we first review examples where passive DTS has been used to study hydrogeology via downhole applications. Secondly, we discuss and categorize current A-DTS borehole methods into three types. These are thermal advection tests, hybrid cable flow logging, and heat pulse tests. We explore the various options with regards to cable installation, heating approach, duration, and spatial extent in order to improve their applicability in a range of settings. These determine the extent to which each method is sensitive to thermal properties, vertical in-well flow, or natural gradient flow. Our review confirms that the application of DTS has significant advantages over discrete point temperature measurements, particularly in deep wells, and highlights the potential for further method developments in conjunction with other emerging hydrogeophysical tools.

    An overview of the adequacy of Arctic sea basin data
    Kater, Belinda ; Heuvel-Greve, M.J. van den; Thijsse, Peter ; Beegle-Krause, C.J. ; Bos, O.G. ; Grasmeijer, B.T. ; Griffin, L. ; Jak, R.G. ; Onselen, Eline van; Overzee, H.M.J. van; Piet, G.J. ; Tamis, J.E. ; Tuijnder, Arjan ; Vries, P. de; Wal, J.T. van der; Steins, N.A. - \ 2016
    - 1 p.
    Structural plasticity and in vivo activity of Cas1 from the type I-F CRISPR-Cas system
    Wilkinson, Max E. ; Nakatani, Yoshio ; Staals, Raymond H.J. ; Kieper, Sebastian N. ; Opel-Reading, Helen K. ; McKenzie, Rebecca E. ; Fineran, Peter C. ; Krause, Kurt L. - \ 2016
    Biochemical Journal 473 (2016)8. - ISSN 0264-6021 - p. 1063 - 1072.
    Adaptation - Bacteriophages - Csy - Horizontal gene transfer - Plasmids - Protein structure

    CRISPR-Cas systems are adaptive immune systems in prokaryotes that provide protection against viruses and other foreign DNA. In the adaptation stage, foreign DNA is integrated into CRISPR (clustered regularly interspaced short palindromic repeat) arrays as new spacers. These spacers are used in the interference stage to guide effector CRISPR associated (Cas) protein(s) to target complementary foreign invading DNA. Cas1 is the integrase enzyme that is central to the catalysis of spacer integration. There are many diverse types of CRISPR-Cas systems, including type I-F systems, which are typified by a unique Cas1-Cas2-3 adaptation complex. In the present study we characterize the Cas1 protein of the potato phytopathogen Pectobacterium atrosepticum, an important model organism for understanding spacer acquisition in type I-F CRISPR-Cas systems. We demonstrate by mutagenesis that Cas1 is essential for adaptation in vivo and requires a conserved aspartic acid residue. By X-ray crystallography, we show that although P. atrosepticum Cas1 adopts a fold conserved among other Cas1 proteins, it possesses remarkable asymmetry as a result of structural plasticity. In particular, we resolve for the first time a flexible, asymmetric loop that may be unique to type I-F Cas1 proteins, and we discuss the implications of these structural features for DNA binding and enzymatic activity.

    Patient Parents : Do Offspring Decide on the Timing of Fledging in Zebra Finches?
    Trillmich, Fritz ; Spiller, Inka ; Naguib, Marc ; Krause, Eike Tobias - \ 2016
    Ethology (2016). - ISSN 0179-1613 - p. 411 - 418.
    Parent-offspring conflict - Parental care - Timing of fledging - Transition to independence - Weaning
    Parent-offspring conflict over parental care is predicted to become most pronounced during offspring transition to independence when offspring are predicted to attempt to extend care for longer than parents are selected to provide it. However, on the proximate level, it is difficult to determine who plays the most important role in this process, parents or offspring. For several vertebrate taxa, it has been documented that parents end brood care by abandoning offspring after a fixed period or else show high flexibility in the duration of care, but teasing apart the role of offspring and parents underlying this flexibility has been difficult. Here, we studied the decision to fledge in captive zebra finches (Taeniopygia guttata), an altricial songbird. We experimentally delayed the time of fledging to determine who decides about the end of feeding inside the nest, parents or offspring. The experiment indicates that parents do not primarily rely on phenotypic offspring traits in their decision to feed offspring in the nest, but appear to adjust the duration of parental care as long as offspring are in the nest which parents may take as an indicator of offspring need and locomotor abilities. Delayed-fledging offspring appeared not to suffer a disadvantage in terms of age at the onset of independent feeding. Our study suggests that, in zebra finches, offspring play a major role in determining the time of fledging and leave the nest on their own, possibly to reduce the risk of nest predation, or to evade sibling competition in the nest.
    Upgrading Marine Ecosystem Restoration Using Ecological-Social Concepts
    Abelson, Avigdor ; Halpern, Benjamin S. ; Reed, Daniel C. ; Orth, Robert J. ; Kendrick, Gary A. ; Beck, Michael W. ; Belmaker, Jonathan ; Krause, Gesche ; Edgar, Graham J. ; Airoldi, Laura ; Brokovich, Eran ; France, Robert ; Shashar, Nadav ; Blaeij, Arianne De; Stambler, Noga ; Salameh, Pierre ; Shechter, Mordechai ; Nelson, Peter A. - \ 2016
    Bioscience 66 (2016)2. - ISSN 0006-3568 - p. 156 - 163.
    conservation - marine ecosystems - marine spatial planning (MSP) - Ocean Health Index (OHI) - social-ecological restoration

    Conservation and environmental management are principal countermeasures to the degradation of marine ecosystems and their services. However, in many cases, current practices are insufficient to reverse ecosystem declines. We suggest that restoration ecology, the science underlying the concepts and tools needed to restore ecosystems, must be recognized as an integral element for marine conservation and environmental management. Marine restoration ecology is a young scientific discipline, often with gaps between its application and the supporting science. Bridging these gaps is essential to using restoration as an effective management tool and reversing the decline of marine ecosystems and their services. Ecological restoration should address objectives that include improved ecosystem services, and it therefore should encompass social-ecological elements rather than focusing solely on ecological parameters. We recommend using existing management frameworks to identify clear restoration targets, to apply quantitative tools for assessment, and to make the re-establishment of ecosystem services a criterion for success.

    Information transmission via movement behaviour improves decision accuracy in human groups
    Clément, R.J.G. ; Wolf, Max ; Snijders, Lysanne ; Krause, Jens ; Kurvers, R.H.J.M. - \ 2015
    Animal Behaviour 105 (2015). - ISSN 0003-3472 - p. 85 - 93.
    Collective behaviour - Decision accuracy - Group decision making - Locomotion - Swarm intelligence

    A major advantage of group living is increased decision accuracy. In animal groups information is often transmitted via movement. For example, an individual quickly moving away from its group may indicate approaching predators. However, individuals also make mistakes which can initiate information cascades. How responsive should individuals then be to escaping group members? Increasing responsiveness increases true positives (i.e. escape when a predator is present) but at the cost of increased false positives (i.e. escape when a predator is absent). Conversely, reducing responsiveness decreases not only false positives but also true positives, resulting in a fundamental trade-off in decision accuracy. Here we investigated how socially responsive individuals are to information transmission via movement. We performed a simulated predator detection task using human groups in which humans stepped forward if they wanted to escape. We confirm that this simple movement mechanism allows individuals in groups to simultaneously increase true positives and decrease false positives. The increase in the number of escapees over time during collective decisions depended on the personal information of the group members. Individual predator detection by only a few group members rarely resulted in anyone stepping forward. Individual predator detection by a quarter of the group often resulted in the entire group escaping. Finally, individual predator detection by at least half of the group led to a rapid escape of the whole group. Overall, the increase in the number of escapees over time followed a linear response. Since information transmission via movement is widespread in animal groups, this mechanism is expected to be relevant for many animal groups to improve decision accuracy.

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