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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    The Continuous Hotelling Pure Location Game with Elastic Demand Revisited
    Mouche, Pierre von - \ 2020
    In: Mathematical Optimization Theory and Operations Research - 19th International Conference, MOTOR 2020, Proceedings. - Springer (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) ) - ISBN 9783030499877 - p. 246 - 262.
    Hotelling game - Potential game - Principle of Minimum Differentiation - Pure Nash equilibrium existence

    The Hotelling pure location game has been revisited. It is assumed that there are two identical players, strategy sets are one-dimensional, and demand as a function of distance is constant or strictly decreasing. Besides qualitative properties of conditional payoff functions, attention is given to the structure of the equilibrium set, best-response correspondences and the existence of potentials.

    The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data
    Pastorello, Gilberto ; Trotta, Carlo ; Canfora, Eleonora ; Chu, Housen ; Christianson, Danielle ; Cheah, You Wei ; Poindexter, Cristina ; Chen, Jiquan ; Elbashandy, Abdelrahman ; Humphrey, Marty ; Isaac, Peter ; Polidori, Diego ; Ribeca, Alessio ; Ingen, Catharine van; Zhang, Leiming ; Amiro, Brian ; Ammann, Christof ; Arain, M.A. ; Ardö, Jonas ; Arkebauer, Timothy ; Arndt, Stefan K. ; Arriga, Nicola ; Aubinet, Marc ; Aurela, Mika ; Baldocchi, Dennis ; Barr, Alan ; Beamesderfer, Eric ; Marchesini, Luca Belelli ; Bergeron, Onil ; Beringer, Jason ; Bernhofer, Christian ; Berveiller, Daniel ; Billesbach, Dave ; Black, Thomas Andrew ; Blanken, Peter D. ; Bohrer, Gil ; Boike, Julia ; Bolstad, Paul V. ; Bonal, Damien ; Bonnefond, Jean Marc ; Bowling, David R. ; Bracho, Rosvel ; Brodeur, Jason ; Brümmer, Christian ; Buchmann, Nina ; Burban, Benoit ; Burns, Sean P. ; Buysse, Pauline ; Cale, Peter ; Cavagna, Mauro ; Cellier, Pierre ; Chen, Shiping ; Chini, Isaac ; Christensen, Torben R. ; Cleverly, James ; Collalti, Alessio ; Consalvo, Claudia ; Cook, Bruce D. ; Cook, David ; Coursolle, Carole ; Cremonese, Edoardo ; Curtis, Peter S. ; Andrea, Ettore D'; Rocha, Humberto da; Dai, Xiaoqin ; Davis, Kenneth J. ; Cinti, Bruno De; Grandcourt, Agnes de; Ligne, Anne De; Oliveira, Raimundo C. De; Delpierre, Nicolas ; Desai, Ankur R. ; Bella, Carlos Marcelo Di; Tommasi, Paul di; Dolman, Han ; Domingo, Francisco ; Dong, Gang ; Dore, Sabina ; Duce, Pierpaolo ; Dufrêne, Eric ; Dunn, Allison ; Dušek, Jiří ; Eamus, Derek ; Eichelmann, Uwe ; ElKhidir, Hatim Abdalla M. ; Eugster, Werner ; Ewenz, Cacilia M. ; Ewers, Brent ; Famulari, Daniela ; Fares, Silvano ; Feigenwinter, Iris ; Feitz, Andrew ; Fensholt, Rasmus ; Filippa, Gianluca ; Fischer, Marc ; Frank, John ; Galvagno, Marta ; Gharun, Mana ; Gianelle, Damiano ; Gielen, Bert ; Gioli, Beniamino ; Gitelson, Anatoly ; Goded, Ignacio ; Goeckede, Mathias ; Goldstein, Allen H. ; Gough, Christopher M. ; Goulden, Michael L. ; Graf, Alexander ; Griebel, Anne ; Gruening, Carsten ; Grünwald, Thomas ; Hammerle, Albin ; Han, Shijie ; Han, Xingguo ; Hansen, Birger Ulf ; Hanson, Chad ; Hatakka, Juha ; He, Yongtao ; Hehn, Markus ; Heinesch, Bernard ; Hinko-Najera, Nina ; Hörtnagl, Lukas ; Hutley, Lindsay ; Ibrom, Andreas ; Ikawa, Hiroki ; Jackowicz-Korczynski, Marcin ; Janouš, Dalibor ; Jans, Wilma ; Jassal, Rachhpal ; Jiang, Shicheng ; Kato, Tomomichi ; Khomik, Myroslava ; Klatt, Janina ; Knohl, Alexander ; Knox, Sara ; Kobayashi, Hideki ; Koerber, Georgia ; Kolle, Olaf ; Kosugi, Yoshiko ; Kotani, Ayumi ; Kowalski, Andrew ; Kruijt, Bart ; Kurbatova, Julia ; Kutsch, Werner L. ; Kwon, Hyojung ; Launiainen, Samuli ; Laurila, Tuomas ; Law, Bev ; Leuning, Ray ; Li, Yingnian ; Liddell, Michael ; Limousin, Jean Marc ; Lion, Marryanna ; Liska, Adam J. ; Lohila, Annalea ; López-Ballesteros, Ana ; López-Blanco, Efrén ; Loubet, Benjamin ; Loustau, Denis ; Lucas-Moffat, Antje ; Lüers, Johannes ; Ma, Siyan ; Macfarlane, Craig ; Magliulo, Vincenzo ; Maier, Regine ; Mammarella, Ivan ; Manca, Giovanni ; Marcolla, Barbara ; Margolis, Hank A. ; Marras, Serena ; Massman, William ; Mastepanov, Mikhail ; Matamala, Roser ; Matthes, Jaclyn Hatala ; Mazzenga, Francesco ; McCaughey, Harry ; McHugh, Ian ; McMillan, Andrew M.S. ; Merbold, Lutz ; Meyer, Wayne ; Meyers, Tilden ; Miller, Scott D. ; Minerbi, Stefano ; Moderow, Uta ; Monson, Russell K. ; Montagnani, Leonardo ; Moore, Caitlin E. ; Moors, Eddy ; Moreaux, Virginie ; Moureaux, Christine ; Munger, J.W. ; Nakai, Taro ; Neirynck, Johan ; Nesic, Zoran ; Nicolini, Giacomo ; Noormets, Asko ; Northwood, Matthew ; Nosetto, Marcelo ; Nouvellon, Yann ; Novick, Kimberly ; Oechel, Walter ; Olesen, Jørgen Eivind ; Ourcival, Jean Marc ; Papuga, Shirley A. ; Parmentier, Frans Jan ; Paul-Limoges, Eugenie ; Pavelka, Marian ; Peichl, Matthias ; Pendall, Elise ; Phillips, Richard P. ; Pilegaard, Kim ; Pirk, Norbert ; Posse, Gabriela ; Powell, Thomas ; Prasse, Heiko ; Prober, Suzanne M. ; Rambal, Serge ; Rannik, Üllar ; Raz-Yaseef, Naama ; Reed, David ; Dios, Victor Resco de; Restrepo-Coupe, Natalia ; Reverter, Borja R. ; Roland, Marilyn ; Sabbatini, Simone ; Sachs, Torsten ; Saleska, Scott R. ; Sánchez-Cañete, Enrique P. ; Sanchez-Mejia, Zulia M. ; Schmid, Hans Peter ; Schmidt, Marius ; Schneider, Karl ; Schrader, Frederik ; Schroder, Ivan ; Scott, Russell L. ; Sedlák, Pavel ; Serrano-Ortíz, Penélope ; Shao, Changliang ; Shi, Peili ; Shironya, Ivan ; Siebicke, Lukas ; Šigut, Ladislav ; Silberstein, Richard ; Sirca, Costantino ; Spano, Donatella ; Steinbrecher, Rainer ; Stevens, Robert M. ; Sturtevant, Cove ; Suyker, Andy ; Tagesson, Torbern ; Takanashi, Satoru ; Tang, Yanhong ; Tapper, Nigel ; Thom, Jonathan ; Tiedemann, Frank ; Tomassucci, Michele ; Tuovinen, Juha Pekka ; Urbanski, Shawn ; Valentini, Riccardo ; Molen, Michiel van der; Gorsel, Eva van; Huissteden, Ko van; Varlagin, Andrej ; Verfaillie, Joseph ; Vesala, Timo ; Vincke, Caroline ; Vitale, Domenico ; Vygodskaya, Natalia ; Walker, Jeffrey P. ; Walter-Shea, Elizabeth ; Wang, Huimin ; Weber, Robin ; Westermann, Sebastian ; Wille, Christian ; Wofsy, Steven ; Wohlfahrt, Georg ; Wolf, Sebastian ; Woodgate, William ; Li, Yuelin ; Zampedri, Roberto ; Zhang, Junhui ; Zhou, Guoyi ; Zona, Donatella ; Agarwal, Deb ; Biraud, Sebastien ; Torn, Margaret ; Papale, Dario - \ 2020
    Scientific Data 7 (2020)1. - ISSN 2052-4463 - 1 p.

    The FLUXNET2015 dataset provides ecosystem-scale data on CO2, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible.

    Relative brain size is predicted by the intensity of intrasexual competition in frogs
    Mai, Chun Lan ; Liao, Wen Bo ; Lüpold, Stefan ; Kotrschal, Alexander - \ 2020
    American Naturalist 196 (2020)2. - ISSN 0003-0147 - p. 169 - 179.
    Anurans - Cognitive abilities - Male-male competition - Operational sex ratio - Spawning-site group size

    Competition over mates is a powerful force shaping trait evolution. For instance, better cognitive abilities may be beneficial in male-male competition and thus be selected for by intrasexual selection. Alternatively, investment in physical attributes favoring male performance in competition for mates may lower the resources available for brain development, and more intense male mate competition would coincide with smaller brains. To date, only indirect evidence for such relationships exists, and most studies are heavily biased toward primates and other homoeothermic vertebrates. We tested the association between male brain size (relative to body size) and male-male competition across N = 30 species of Chinese anurans. Three indicators of the intensity of male mate competition—operational sex ratio (OSR), spawningsite density, and male forelimb muscle mass—were positively associated with relative brain size, whereas the absolute spawning group size was not. The relationship with the OSR and male forelimb muscle mass was stronger for the male than for the female brains. Taken together, our findings suggest that the increased cognitive abilities of larger brains are beneficial in male-male competition. This study adds taxonomic breadth to the mounting evidence for a prominent role of sexual selection in vertebrate brain evolution.

    GeoFood: An example of circular economy by using geothermal heat, RAS and horticulture to produce fish and vegetables.
    Boedijn, Alexander - \ 2020
    Energietransitie: geothermie voor productie van vis en groenten met aquaponics
    Boedijn, Alexander - \ 2020
    WUR Lecture: Greenhouse Horticulture in the Circular Economy
    Boedijn, Alexander - \ 2020
    An efficient single-cell transcriptomics workflow for microbial eukaryotes benchmarked on Giardia intestinalis cells
    Onsbring, Henning ; Tice, Alexander K. ; Barton, Brandon T. ; Brown, Matthew W. ; Ettema, Thijs J.G. - \ 2020
    BMC Genomics 21 (2020)1. - ISSN 1471-2164 - 1 p.
    Giardia intestinalis - Microbial diversity - Microbial eukaryotes - Protists - RNAseq - Single cell genomics - Single-cell RNA sequencing - Smart-seq2 - Transcriptome - Transcriptomics

    BACKGROUND: Most diversity in the eukaryotic tree of life is represented by microbial eukaryotes, which is a polyphyletic group also referred to as protists. Among the protists, currently sequenced genomes and transcriptomes give a biased view of the actual diversity. This biased view is partly caused by the scientific community, which has prioritized certain microbes of biomedical and agricultural importance. Additionally, some protists remain difficult to maintain in cultures, which further influences what has been studied. It is now possible to bypass the time-consuming process of cultivation and directly analyze the gene content of single protist cells. Single-cell genomics was used in the first experiments where individual protists cells were genomically explored. Unfortunately, single-cell genomics for protists is often associated with low genome recovery and the assembly process can be complicated because of repetitive intergenic regions. Sequencing repetitive sequences can be avoided if single-cell transcriptomics is used, which only targets the part of the genome that is transcribed. RESULTS: In this study we test different modifications of Smart-seq2, a single-cell RNA sequencing protocol originally developed for mammalian cells, to establish a robust and more cost-efficient workflow for protists. The diplomonad Giardia intestinalis was used in all experiments and the available genome for this species allowed us to benchmark our results. We could observe increased transcript recovery when freeze-thaw cycles were added as an extra step to the Smart-seq2 protocol. Further we reduced the reaction volume and purified the amplified cDNA with alternative beads to test different cost-reducing changes of Smart-seq2. Neither improved the procedure, and reducing the volumes by half led to significantly fewer genes detected. We also added a 5' biotin modification to our primers and reduced the concentration of oligo-dT, to potentially reduce generation of artifacts. Except adding freeze-thaw cycles and reducing the volume, no other modifications lead to a significant change in gene detection. Therefore, we suggest adding freeze-thaw cycles to Smart-seq2 when working with protists and further consider our other modification described to improve cost and time-efficiency. CONCLUSIONS: The presented single-cell RNA sequencing workflow represents an efficient method to explore the diversity and cell biology of individual protist cells.

    Transdisciplinary knowledge management : A key but underdeveloped skill in EBM decision-making
    Giebels, Diana ; Carus, Jana ; Paul, Maike ; Kleyer, Michael ; Siebenhüner, Bernd ; Arns, Arne ; Bartholomä, Alexander ; Carlow, Vanessa ; Jensen, Jürgen ; Tietjen, Britta ; Wehrmann, Achim ; Schröder, Boris - \ 2020
    Marine Policy 119 (2020). - ISSN 0308-597X

    The ecosystem-based management (EBM) philosophy draws upon the principle that holistic understanding of the system to be governed needs to guide the decision-making process. However, empirical evidence is growing that knowledge integration is still a main bottleneck for EBM decision-makers. This paper argues that transdisciplinary knowledge management (TKM) is a key competence in achieving knowledge integration, while simultaneously it represents an underdeveloped research area in EBM if understood as a process of human interaction. Based on a literature review, this article summarizes and reflects upon the most recent development in the field of TKM. The paper presents a detailed definition and in-depth description of TKM as a process of human interaction and a diversity of organizational structures that effectuate TKM. Theoretically discussed premises are furthermore illuminated and evaluated by a case study that exemplifies pro-active development and implementation of TKM. Deviating case observations are presented as novel contributions to the field. They suggest new ideas and inspiration for future EBM research and policy agendas.

    Welkom bij de Kaskieswijzer: Wiki
    Boedijn, Alexander ; Franken, Geert ; Swinkels, G.L.A.M. ; Kempkes, F.L.K. - \ 2020
    Wageningen : Wageningen University & Research, BU Glastuinbouw
    De Kaskieswijzer is een interactief naslagwerk op het gebied van daglichtbenutting in de glastuinbouw. Om zonne-energie optimaal te kunnen benutten is veel onderzoek uitgevoerd naar factoren die de toetreding van licht in de kas bepalen. Deze factoren hebben onder andere betrekking op kasontwerp, kasconstructie, kasdekmateriaal en schermen. Het doel van de Kaskieswijzer is om deze kennis toegankelijk en interpreteerbaar te maken voor ondernemers binnen de glastuinbouwsector met plannen voor nieuwbouw of verbouw. Zodoende biedt de Kaskieswijzer ondersteuning tijdens het ontwerpproces.
    A generic framework to assess the representation and protection of benthic ecosystems in European marine protected areas
    Greathead, Clare ; Magni, Paolo ; Vanaverbeke, Jan ; Buhl‐Mortensen, Lene ; Janas, Urszula ; Blomqvist, Mats ; Craeymeersch, Johan A. ; Dannheim, Jennifer ; Darr, Alexander ; Degraer, Steven ; Desroy, Nicolas ; Donnay, Annick ; Griffiths, Yessica ; Guala, Ivan ; Guerin, Laurent ; Hinchen, Hayley ; Labrune, Celine ; Reiss, Henning ; Hoey, Gert Van; Birchenough, Silvana N.R. - \ 2020
    Aquatic conservation: marine and freshwater ecosystems 30 (2020)7. - ISSN 1052-7613 - p. 1253 - 1275.
    There is concern across the International Council for the Exploration of the Sea (ICES) region that a consideration of vulnerable components and the wider support mechanisms underpinning benthic marine ecosystems may be lacking from the process of marine protected area (MPA) designation, management and monitoring. In this study, MPAs across six European ecoregions were assessed from a benthic ecology perspective. The study included 102 MPAs, designated by 10 countries, and focused on three aspects regarding the role of the benthos in: (i) the designation of MPAs; (ii) the management measures used in MPAs; and (iii) the monitoring and assessment of MPAs. Qualitative entries to a questionnaire based on an existing framework (EU project ‘Monitoring Evaluation of Spatially Managed Areas’, (MESMA) were collected by 19 benthic experts of the ICES Benthic Ecology Working Group. A pedigree matrix was used to apply a numerical scale (score) to these entries. The results showed clear differences in scores between ecoregions and between criteria. The designation‐phase criteria generally achieved higher scores than the implementation‐phase criteria. Poor designation‐phase scores were generally reiterated in the implementation‐phase scores, such as scores for assessment and monitoring. Over 70% of the MPA case studies were found to consider the benthos to some extent during selection and designation; however, this was not followed up with appropriate management measures and good practice during the implementation phase.
    Poor spatial and temporal coverage of monitoring and ineffective indicators is unlikely to pick up changes caused by management measures in the MPA. There is concern that without adequate monitoring and adaptive management frameworks, the MPAs will be compromised. Also, there could be an increased likelihood that, with regard to the benthos, they will fail to meet their conservation objectives. This assessment was successful in highlighting issues related to the representation and protection of the benthos in MPAs and where changes need to be made, such as expanding the characterization and monitoring of benthic species or habitats of interest. These issues could be attributable to an ongoing process and/or an indication that some MPAs only have ‘paper protection’.
    Roadmap for naming uncultivated Archaea and Bacteria
    Murray, Alison E. ; Freudenstein, John ; Gribaldo, Simonetta ; Hatzenpichler, Roland ; Hugenholtz, Philip ; Kämpfer, Peter ; Konstantinidis, Konstantinos T. ; Lane, Christopher E. ; Papke, R.T. ; Parks, Donovan H. ; Rossello-Mora, Ramon ; Stott, Matthew B. ; Sutcliffe, Iain C. ; Thrash, J.C. ; Venter, Stephanus N. ; Whitman, William B. ; Acinas, Silvia G. ; Amann, Rudolf I. ; Anantharaman, Karthik ; Armengaud, Jean ; Baker, Brett J. ; Barco, Roman A. ; Bode, Helge B. ; Boyd, Eric S. ; Brady, Carrie L. ; Carini, Paul ; Chain, Patrick S.G. ; Colman, Daniel R. ; DeAngelis, Kristen M. ; Rios, Maria Asuncion de los; Estrada-de los Santos, Paulina ; Dunlap, Christopher A. ; Eisen, Jonathan A. ; Emerson, David ; Ettema, Thijs J.G. ; Eveillard, Damien ; Girguis, Peter R. ; Hentschel, Ute ; Hollibaugh, James T. ; Hug, Laura A. ; Inskeep, William P. ; Ivanova, Elena P. ; Klenk, Hans Peter ; Li, Wen Jun ; Lloyd, Karen G. ; Löffler, Frank E. ; Makhalanyane, Thulani P. ; Moser, Duane P. ; Nunoura, Takuro ; Palmer, Marike ; Parro, Victor ; Pedrós-Alió, Carlos ; Probst, Alexander J. ; Smits, Theo H.M. ; Steen, Andrew D. ; Steenkamp, Emma T. ; Spang, Anja ; Stewart, Frank J. ; Tiedje, James M. ; Vandamme, Peter ; Wagner, Michael ; Wang, Feng Ping ; Hedlund, Brian P. ; Reysenbach, Anna Louise - \ 2020
    Nature Microbiology 5 (2020). - ISSN 2058-5276 - p. 987 - 994.

    The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as ‘type material’, thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.

    Diversity of Mobile Genetic Elements in the Mitogenomes of Closely Related Fusarium culmorum and F. graminearum sensu stricto Strains and Its Implication for Diagnostic Purposes
    Kulik, Tomasz ; Brankovics, Balázs ; Diepeningen, A.D. van; Bilska, K. ; Zelechowski, Maciej ; Myszczynski, Kamil ; Molcan, Tomasz ; Stakheev, Alexander ; Stenglein, Sebastian ; Beyer, Marco ; Pasquali, Matias ; Sawicki, Jakub ; Wyrebek, Joanne ; Baturo-Ciesniewska, Anna - \ 2020
    Frontiers in Microbiology 11 (2020). - ISSN 1664-302X
    Much of the mitogenome variation observed in fungal lineages seems driven by mobile genetic elements (MGEs), which have invaded their genomes throughout evolution. The variation in the distribution and nucleotide diversity of these elements appears to be the main distinction between different fungal taxa, making them promising candidates for diagnostic purposes. Fungi of the genus Fusarium display a high variation in MGE content, from MGE-poor (Fusarium oxysporum and Fusarium fujikuroi species complex) to MGE-rich mitogenomes found in the important cereal pathogens F. culmorum and F. graminearum sensu stricto. In this study, we investigated the MGE variation in these latter two species by mitogenome analysis of geographically diverse strains. In addition, a smaller set of F. cerealis and F. pseudograminearum strains was included for comparison. Forty-seven introns harboring from 0 to 3 endonucleases (HEGs) were identified in the standard set of mitochondrial protein-coding genes. Most of them belonged to the group I intron family and harbored either LAGLIDADG or GIY-YIG HEGs. Among a total of 53 HEGs, 27 were shared by all fungal strains. Most of the optional HEGs were irregularly distributed among fungal strains/species indicating ancestral mosaicism in MGEs. However, among optional MGEs, one exhibited species-specific conservation in F. culmorum. While in F. graminearum s.s. MGE patterns in cox3 and in the intergenic spacer between cox2 and nad4L may facilitate the identification of this species. Thus, our results demonstrate distinctive traits of mitogenomes for diagnostic purposes of Fusaria.
    Off-target activity inhibitors for guided endonucleases
    Notebaart, Richard Alexander ; Künne, Tim Andreas ; Brouns, Stan Johan Jozef ; Oost, John Van Der - \ 2020
    Octrooinummer: WO2020065062, gepubliceerd: 2020-04-02.

    Incidence of off-target DNA cleavage when using CRISPR Cas systems for gene modification are lessened or avoided by using oligonucleotides of rational design and which are antisense to target sequence of the guide RNA or other targeting nucleic acid sequence. Whether in vitro or in vivo, a target nucleic acid comprising a targeted sequence is exposed to the CRISPR enzyme and relevant guiding RNA (or ribonucleoprotein complex) with the antisense oligonucleotide. The antisense oligonucleotide is exposed to the target nucleic acid substantially simultaneously, separately or sequentially together with the CRISPR enzyme or ribonucleoprotein complex.

    Body mass variation is negatively associated with brain size: Evidence for the fat-brain trade-off in anurans
    Huang, Yan ; Mai, Chun Lan ; Liao, Wen Bo ; Kotrschal, Alexander - \ 2020
    Evolution 74 (2020)7. - ISSN 0014-3820 - p. 1551 - 1557.
    body mass - Brain size - fat storage - trade-off

    Species can evolve diverse strategies to survive periods of uncertainty. Animals may either invest in energy storage, allowing them to decrease foraging costs, such as locomotion or risk of predation, or they may invest in better cognitive abilities helping them to flexibly adapt their behavior to meet novel challenges. Here, we test this idea of a fat-brain trade-off in 38 species of Chinese anurans by relating the coefficient of variation of body mass (CVbodymass; as an indicator of how much animals invest into storage over the season) to brain anatomical features. After correcting for shared ancestry and body mass, we found a negative relationship between relative brain size and CVbodymass. This indicates that anurans seem to trade-off physiological and cognitive buffering during energy shortages. As similar patterns have been reported in arboreal mammals and primates our findings suggest that the fat-brain trade-off, where animals either invest into physiological or cognitive strategies to survive harsh conditions, may be a general pattern across vertebrates.

    The C-Termini of the baculovirus per os infectivity factors 1 and 2 mediate ODV oral infectivity by facilitating the binding of PIF0 and PIF8 to the core of the entry complex
    Boogaard, Bob ; Ortega Murillo, Fabiola D. ; Sminia, Alexander L. ; Theilmann, David A. ; Lent, Jan W.M. Van; Oers, Monique M. Van - \ 2020
    Journal of General Virology 101 (2020)5. - ISSN 0022-1317 - p. 553 - 564.
    AcMNPV. - Baculovirus - Oral Infectivity - PIF - PIF complex

    Oral infection of caterpillars by baculoviruses is initiated by occlusion-derived virus particles (ODVs) that infect midgut epithelium cells. The ODV envelope therefore contains at least ten different proteins, which are called per os infectivity factors (PIFs). Nine of these PIFs form the so-called ODV entry complex that consists of a stable core formed by PIF1, 2, 3 and 4, to which the other PIFs [PIF0, 6, 7, 8 and 9 (ac108)] bind with lower affinity. PIF1 and 2 are not only essential for complex formation, but also mediate ODV-binding to the epithelial brush border, probably via the C-Termini. To study the involvement of these PIFs during midgut infection in greater detail, we assessed the oral infectivity and the ability to form the complex of a series of PIF1 and PIF2 C-Terminal truncation mutants of Autographa californica multiple nucleopolyhedrovirus (AcMNPV), which were constructed in this study. Limited truncation of either PIF1 or 2 already severely impaired the ODV oral infectivity, but did not affect the formation of the core complex. However, the entry complex as a whole was not assembled in these mutants as PIF0 and 8 failed to bind to the core. This suggests that the interactions between the core and the loosely associated PIFs are important for the ODV infectivity and that complex formation complicates the determination of the exact roles of PIF1 and 2 during midgut infection. We also showed that the presence of PIF0, 6 and the ZF-domain of PIF8 are crucial for complex formation.

    The Benefit of Using an Ensemble of Global Hydrological Models in Surface Water Availability for Irrigation Area Planning
    Kaune, Alexander ; López, Patricia ; Gevaert, Anouk ; Veldkamp, Ted ; Werner, Micha ; Fraiture, Charlotte de - \ 2020
    Water Resources Management 34 (2020). - ISSN 0920-4741 - p. 2221 - 2240.
    Hydrological information - Irrigated agriculture - Irrigation demand - Water allocation decisions

    Hydrological data and information on the availability of water are essential to support water allocation decisions in irrigated agriculture, especially under increasingly water scarce conditions. However, in many agricultural regions hydrological information is scarce, leading to sub-optimal water allocation decisions and crop yield reduction. Here we assess the benefit of using surface water availability estimates derived from an ensemble of global hydrological models for establishing the potential area that can be irrigated; where the size is determined based on agreed water supply reliability targets. Risky outcomes of the annual agricultural production due to the true occurrence of water scarcity are generated for both the reference and established irrigation areas, resulting in a Relative Utility Value (RUV) that expresses the utility of the information used. Results show that using an ensemble of global hydrological models provides more robust estimates of the planned area compared to using any of the single global models that constitutes the ensemble. A comparison of the information content in the ensemble shows that an ensemble with a period of record of 15 years has an information content equivalent to a single model of 30 years.

    Modelling food security : Bridging the gap between the micro and the macro scale
    Müller, Birgit ; Hoffmann, Falk ; Heckelei, Thomas ; Müller, Christoph ; Hertel, Thomas W. ; Polhill, J.G. ; Wijk, Mark van; Achterbosch, Thom ; Alexander, Peter ; Brown, Calum ; Kreuer, David ; Ewert, Frank ; Ge, Jiaqi ; Millington, James D.A. ; Seppelt, Ralf ; Verburg, Peter H. ; Webber, Heidi - \ 2020
    Global environmental change : human and policy dimensions 63 (2020). - ISSN 0959-3780
    Agent-based models - Crop models - Economic equilibrium models - Food security - Land use - Model integration - Multi-scale interactions - Social-ecological feedbacks

    Achieving food and nutrition security for all in a changing and globalized world remains a critical challenge of utmost importance. The development of solutions benefits from insights derived from modelling and simulating the complex interactions of the agri-food system, which range from global to household scales and transcend disciplinary boundaries. A wide range of models based on various methodologies (from food trade equilibrium to agent-based) seek to integrate direct and indirect drivers of change in land use, environment and socio-economic conditions at different scales. However, modelling such interaction poses fundamental challenges, especially for representing non-linear dynamics and adaptive behaviours. We identify key pieces of the fragmented landscape of food security modelling, and organize achievements and gaps into different contextual domains of food security (production, trade, and consumption) at different spatial scales. Building on in-depth reflection on three core issues of food security – volatility, technology, and transformation – we identify methodological challenges and promising strategies for advancement. We emphasize particular requirements related to the multifaceted and multiscale nature of food security. They include the explicit representation of transient dynamics to allow for path dependency and irreversible consequences, and of household heterogeneity to incorporate inequality issues. To illustrate ways forward we provide good practice examples using meta-modelling techniques, non-equilibrium approaches and behavioural-based modelling endeavours. We argue that further integration of different model types is required to better account for both multi-level agency and cross-scale feedbacks within the food system.

    Long-term thermal sensitivity of Earth's tropical forests
    Sullivan, Martin J.P. ; Lewis, Simon L. ; Affum-Baffoe, Kofi ; Castilho, Carolina ; Costa, Flávia ; Sanchez, Aida Cuni ; Ewango, Corneille E.N. ; Hubau, Wannes ; Marimon, Beatriz ; Monteagudo-Mendoza, Abel ; Qie, Lan ; Sonké, Bonaventure ; Martinez, Rodolfo Vasquez ; Baker, Timothy R. ; Brienen, Roel J.W. ; Feldpausch, Ted R. ; Galbraith, David ; Gloor, Manuel ; Malhi, Yadvinder ; Aiba, Shin Ichiro ; Alexiades, Miguel N. ; Almeida, Everton C. ; Oliveira, Edmar Almeida de; Dávila, Esteban Álvarez ; Loayza, Patricia Alvarez ; Andrade, Ana ; Vieira, Simone Aparecida ; Aragão, Luiz E.O.C. ; Araujo-Murakami, Alejandro ; Arets, Eric J.M.M. ; Arroyo, Luzmila ; Ashton, Peter ; Aymard C, Gerardo ; Baccaro, Fabrício B. ; Banin, Lindsay F. ; Baraloto, Christopher ; Camargo, Plínio Barbosa ; Barlow, Jos ; Barroso, Jorcely ; Bastin, Jean François ; Batterman, Sarah A. ; Beeckman, Hans ; Begne, Serge K. ; Bennett, Amy C. ; Berenguer, Erika ; Berry, Nicholas ; Blanc, Lilian ; Boeckx, Pascal ; Bogaert, Jan ; Bonal, Damien ; Bongers, Frans ; Bradford, Matt ; Brearley, Francis Q. ; Brncic, Terry ; Brown, Foster ; Burban, Benoit ; Camargo, José Luís ; Castro, Wendeson ; Céron, Carlos ; Ribeiro, Sabina Cerruto ; Moscoso, Victor Chama ; Chave, Jerôme ; Chezeaux, Eric ; Clark, Connie J. ; Souza, Fernanda Coelho de; Collins, Murray ; Comiskey, James A. ; Valverde, Fernando Cornejo ; Medina, Massiel Corrales ; Costa, Lola da; Dančák, Martin ; Dargie, Greta C. ; Davies, Stuart ; Cardozo, Nallaret Davila ; Haulleville, Thales de; Medeiros, Marcelo Brilhante de; Aguila Pasquel, Jhon Del; Derroire, Géraldine ; Fiore, Anthony Di; Doucet, Jean Louis ; Dourdain, Aurélie ; Droissant, Vincent ; Duque, Luisa Fernanda ; Ekoungoulou, Romeo ; Elias, Fernando ; Erwin, Terry ; Esquivel-Muelbert, Adriane ; Fauset, Sophie ; Ferreira, Joice ; Llampazo, Gerardo Flores ; Foli, Ernest ; Ford, Andrew ; Gilpin, Martin ; Hall, Jefferson S. ; Hamer, Keith C. ; Hamilton, Alan C. ; Harris, David J. ; Hart, Terese B. ; Hédl, Radim ; Herault, Bruno ; Herrera, Rafael ; Higuchi, Niro ; Hladik, Annette ; Coronado, Eurídice Honorio ; Huamantupa-Chuquimaco, Isau ; Huasco, Walter Huaraca ; Jeffery, Kathryn J. ; Jimenez-Rojas, Eliana ; Kalamandeen, Michelle ; Djuikouo, Marie Noël Kamdem ; Kearsley, Elizabeth ; Umetsu, Ricardo Keichi ; Kho, Lip Khoon ; Killeen, Timothy ; Kitayama, Kanehiro ; Klitgaard, Bente ; Koch, Alexander ; Labrière, Nicolas ; Laurance, William ; Laurance, Susan ; Leal, Miguel E. ; Levesley, Aurora ; Lima, Adriano J.N. ; Lisingo, Janvier ; Lopes, Aline P. ; Lopez-Gonzalez, Gabriela ; Lovejoy, Tom ; Lovett, Jon C. ; Lowe, Richard ; Magnusson, William E. ; Malumbres-Olarte, Jagoba ; Manzatto, Ângelo Gilberto ; Marimon, Ben Hur ; Marshall, Andrew R. ; Marthews, Toby ; Almeida Reis, Simone Matias de; Maycock, Colin ; Melgaço, Karina ; Mendoza, Casimiro ; Metali, Faizah ; Mihindou, Vianet ; Milliken, William ; Mitchard, Edward T.A. ; Morandi, Paulo S. ; Mossman, Hannah L. ; Nagy, Laszlo ; Nascimento, Henrique ; Neill, David ; Nilus, Reuben ; Vargas, Percy Núñez ; Palacios, Walter ; Camacho, Nadir Pallqui ; Peacock, Julie ; Pendry, Colin ; Peñuela Mora, Maria Cristina ; Pickavance, Georgia C. ; Pipoly, John ; Pitman, Nigel ; Playfair, Maureen ; Poorter, Lourens ; Poulsen, John R. ; Poulsen, Axel Dalberg ; Preziosi, Richard ; Prieto, Adriana ; Primack, Richard B. ; Ramírez-Angulo, Hirma ; Reitsma, Jan ; Réjou-Méchain, Maxime ; Correa, Zorayda Restrepo ; Sousa, Thaiane Rodrigues de; Bayona, Lily Rodriguez ; Roopsind, Anand ; Rudas, Agustín ; Rutishauser, Ervan ; Abu Salim, Kamariah ; Salomão, Rafael P. ; Schietti, Juliana ; Sheil, Douglas ; Silva, Richarlly C. ; Espejo, Javier Silva ; Valeria, Camila Silva ; Silveira, Marcos ; Simo-Droissart, Murielle ; Simon, Marcelo Fragomeni ; Singh, James ; Soto Shareva, Yahn Carlos ; Stahl, Clement ; Stropp, Juliana ; Sukri, Rahayu ; Sunderland, Terry ; Svátek, Martin ; Swaine, Michael D. ; Swamy, Varun ; Taedoumg, Hermann ; Talbot, Joey ; Taplin, James ; Taylor, David ; Steege, Hans Ter; Terborgh, John ; Thomas, Raquel ; Thomas, Sean C. ; Torres-Lezama, Armando ; Umunay, Peter ; Gamarra, Luis Valenzuela ; Heijden, Geertje van der; Hout, Peter van der; Meer, Peter van der; Nieuwstadt, Mark van; Verbeeck, Hans ; Vernimmen, Ronald ; Vicentini, Alberto ; Vieira, Ima Célia Guimarães ; Torre, Emilio Vilanova ; Vleminckx, Jason ; Vos, Vincent ; Wang, Ophelia ; White, Lee J.T. ; Willcock, Simon ; Woods, John T. ; Wortel, Verginia ; Young, Kenneth ; Zagt, Roderick ; Zemagho, Lise ; Zuidema, Pieter A. ; Zwerts, Joeri A. ; Phillips, Oliver L. - \ 2020
    Science 368 (2020)6493. - ISSN 0036-8075 - p. 869 - 874.

    The sensitivity of tropical forest carbon to climate is a key uncertainty in predicting global climate change. Although short-term drying and warming are known to affect forests, it is unknown if such effects translate into long-term responses. Here, we analyze 590 permanent plots measured across the tropics to derive the equilibrium climate controls on forest carbon. Maximum temperature is the most important predictor of aboveground biomass (-9.1 megagrams of carbon per hectare per degree Celsius), primarily by reducing woody productivity, and has a greater impact per °C in the hottest forests (>32.2°C). Our results nevertheless reveal greater thermal resilience than observations of short-term variation imply. To realize the long-term climate adaptation potential of tropical forests requires both protecting them and stabilizing Earth's climate.

    Effects of climate and land-use changes on fish catches across lakes at a global scale
    Kao, Yu Chun ; Rogers, Mark W. ; Bunnell, David B. ; Cowx, Ian G. ; Qian, Song S. ; Anneville, Orlane ; Beard, T.D. ; Brinker, Alexander ; Britton, J.R. ; Chura-Cruz, René ; Gownaris, Natasha J. ; Jackson, James R. ; Kangur, Külli ; Kolding, Jeppe ; Lukin, Anatoly A. ; Lynch, Abigail J. ; Mercado-Silva, Norman ; Moncayo-Estrada, Rodrigo ; Njaya, Friday J. ; Ostrovsky, Ilia ; Rudstam, Lars G. ; Sandström, Alfred L.E. ; Sato, Yuichi ; Siguayro-Mamani, Humberto ; Thorpe, Andy ; Zwieten, Paul A.M. van; Volta, Pietro ; Wang, Yuyu ; Weiperth, András ; Weyl, Olaf L.F. ; Young, Joelle D. - \ 2020
    Nature Communications 11 (2020)1. - ISSN 2041-1723

    Globally, our knowledge on lake fisheries is still limited despite their importance to food security and livelihoods. Here we show that fish catches can respond either positively or negatively to climate and land-use changes, by analyzing time-series data (1970–2014) for 31 lakes across five continents. We find that effects of a climate or land-use driver (e.g., air temperature) on lake environment could be relatively consistent in directions, but consequential changes in a lake-environmental factor (e.g., water temperature) could result in either increases or decreases in fish catch in a given lake. A subsequent correlation analysis indicates that reductions in fish catch was less likely to occur in response to potential climate and land-use changes if a lake is located in a region with greater access to clean water. This finding suggests that adequate investments for water-quality protection and water-use efficiency can provide additional benefits to lake fisheries and food security.

    Integrated urban hydrometeorological, climate and environmental services : Concept, methodology and key messages
    Grimmond, Sue ; Bouchet, Veronique ; Molina, Luisa T. ; Baklanov, Alexander ; Tan, Jianguo ; Schlünzen, K.H. ; Mills, Gerald ; Golding, Brian ; Masson, Valery ; Ren, Chao ; Voogt, James ; Miao, Shiguang ; Lean, Humphrey ; Heusinkveld, Bert ; Hovespyan, Anahit ; Teruggi, Giacomo ; Parrish, Patrick ; Joe, Paul - \ 2020
    Urban Climate 33 (2020). - ISSN 2212-0955

    Integrated Urban hydrometeorological, climate and environmental Services (IUS) is a World Meteorological Organization (WMO) initiative to aid development of science-based services to support safe, healthy, resilient and climate friendly cities. Guidance for Integrated Urban Hydrometeorological, Climate and Environmental Services (Volume I) has been developed with the intent to provide an overview of the concept, methods and good practices for producing and providing these services to respond to urban hazards across a range of time scales (weather to climate). This involves combining (dense) heterogeneous observation networks, high-resolution forecasts, multi-hazard early warning systems and climate services to assist cities in setting and implementing mitigation and adaptation strategies for the management and building of resilient and sustainable cities. IUS includes research, evaluation and delivery with a wide participation from city governments, national hydrometeorological services, international organizations, universities, research institutions and private sector stakeholders. An overview of the IUS concept with key messages, examples of good practice and recommendations are provided. The research community will play an important role to: identify critical research challenges; develop impact forecasts and warnings; promote and deliver IUS internationally, and; support national and local communities in the implementation of IUS thereby contributing to the United Nations' Sustainable Development Goals at all scales.

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