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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    Ecological insights from three decades of animal movement tracking across a changing Arctic
    Davidson, Sarah C. ; Bohrer, Gil ; Gurarie, Eliezer ; LaPoint, Scott ; Mahoney, Peter J. ; Boelman, Natalie T. ; Eitel, Jan U.H. ; Prugh, Laura R. ; Vierling, Lee A. ; Jennewein, Jyoti ; Grier, Emma ; Couriot, Ophélie ; Kelly, Allicia P. ; Meddens, Arjan J.H. ; Oliver, Ruth Y. ; Kays, Roland ; Wikelski, Martin ; Aarvak, Tomas ; Ackerman, Joshua T. ; Alves, José A. ; Bayne, Erin ; Bedrosian, Bryan ; Belant, Jerrold L. ; Berdahl, Andrew M. ; Berlin, Alicia M. ; Berteaux, Dominique ; Bêty, Joël ; Boiko, Dmitrijs ; Booms, Travis L. ; Borg, Bridget L. ; Boutin, Stan ; Boyd, Sean ; Brides, Kane ; Brown, Stephen ; Bulyuk, Victor N. ; Burnham, Kurt K. ; Cabot, David ; Casazza, Michael ; Christie, Katherine ; Craig, Erica H. ; Davis, Shanti E. ; Davison, Tracy ; Demma, Dominic ; DeSorbo, Christopher R. ; Dixon, Andrew ; Domenech, Robert ; Eichhorn, Götz ; Elliott, Kyle ; Evenson, Joseph R. ; Exo, Klaus Michael ; Ferguson, Steven H. ; Fiedler, Wolfgang ; Fisk, Aaron ; Fort, Jérôme ; Franke, Alastair ; Fuller, Mark R. ; Garthe, Stefan ; Gauthier, Gilles ; Gilchrist, Grant ; Glazov, Petr ; Gray, Carrie E. ; Grémillet, David ; Griffin, Larry ; Hallworth, Michael T. ; Harrison, Autumn Lynn ; Hennin, Holly L. ; Hipfner, Mark ; Hodson, James ; Johnson, James A. ; Joly, Kyle ; Jones, Kimberly ; Katzner, Todd E. ; Kidd, Jeff W. ; Knight, Elly C. ; Kochert, Michael N. ; Kölzsch, Andrea ; Kruckenberg, Helmut ; Lagassé, Benjamin J. ; Lai, Sandra ; Lamarre, Jean François ; Lanctot, Richard B. ; Larter, Nicholas C. ; Latham, A.D.M. ; Latty, Christopher J. ; Lawler, James P. ; Léandri-Breton, Don Jean ; Lee, Hansoo ; Lewis, Stephen B. ; Love, Oliver P. ; Madsen, Jesper ; Maftei, Mark ; Mallory, Mark L. ; Mangipane, Buck ; Markovets, Mikhail Y. ; Marra, Peter P. ; McGuire, Rebecca ; McIntyre, Carol L. ; McKinnon, Emily A. ; Miller, Tricia A. ; Moonen, Sander ; Mu, Tong ; Müskens, Gerhard J.D.M. ; Ng, Janet ; Nicholson, Kerry L. ; Øien, Ingar Jostein ; Overton, Cory ; Owen, Patricia A. ; Patterson, Allison ; Petersen, Aevar ; Pokrovsky, Ivan ; Powell, Luke L. ; Prieto, Rui ; Quillfeldt, Petra ; Rausch, Jennie ; Russell, Kelsey ; Saalfeld, Sarah T. ; Schekkerman, Hans ; Schmutz, Joel A. ; Schwemmer, Philipp ; Seip, Dale R. ; Shreading, Adam ; Silva, Mónica A. ; Smith, Brian W. ; Smith, Fletcher ; Smith, Jeff P. ; Snell, Katherine R.S. ; Sokolov, Aleksandr ; Sokolov, Vasiliy ; Solovyeva, Diana V. ; Sorum, Mathew S. ; Tertitski, Grigori ; Therrien, J.F. ; Thorup, Kasper ; Tibbitts, Lee ; Tulp, Ingrid ; Uher-Koch, Brian D. ; Bemmelen, Rob S.A. van; Wilgenburg, Steven Van; Duyke, Andrew L. Von; Watson, Jesse L. ; Watts, Bryan D. ; Williams, Judy A. ; Wilson, Matthew T. ; Wright, James R. ; Yates, Michael A. ; Yurkowski, David J. ; Žydelis, Ramūnas ; Hebblewhite, Mark - \ 2020
    Science 370 (2020)6517. - ISSN 0036-8075 - p. 712 - 715.

    The Arctic is entering a new ecological state, with alarming consequences for humanity. Animal-borne sensors offer a window into these changes. Although substantial animal tracking data from the Arctic and subarctic exist, most are difficult to discover and access. Here, we present the new Arctic Animal Movement Archive (AAMA), a growing collection of more than 200 standardized terrestrial and marine animal tracking studies from 1991 to the present. The AAMA supports public data discovery, preserves fundamental baseline data for the future, and facilitates efficient, collaborative data analysis. With AAMA-based case studies, we document climatic influences on the migration phenology of eagles, geographic differences in the adaptive response of caribou reproductive phenology to climate change, and species-specific changes in terrestrial mammal movement rates in response to increasing temperature.

    Erratum : Author Correction: The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms (Communications biology (2020) 3 1 (303))
    Kallscheuer, Nicolai ; Jeske, Olga ; Sandargo, Birthe ; Boedeker, Christian ; Wiegand, Sandra ; Bartling, Pascal ; Jogler, Mareike ; Rohde, Manfred ; Petersen, Jörn ; Medema, Marnix H. ; Surup, Frank ; Jogler, Christian - \ 2020
    Communications Biology 3 (2020). - ISSN 2399-3642

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    Erratum: The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms
    Kallscheuer, Nicolai ; Jeske, Olga ; Sandargo, Birthe ; Boedeker, Christian ; Wiegand, Sandra ; Bartling, Pascal ; Jogler, Mareike ; Rohde, Manfred ; Petersen, Jörn ; Medema, Marnix H. ; Surup, Frank ; Jogler, Christian - \ 2020
    Communications Biology 3 (2020)1. - ISSN 2399-3642 - 1 p.


    The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms
    Kallscheuer, Nicolai ; Jeske, Olga ; Sandargo, Birthe ; Boedeker, Christian ; Wiegand, Sandra ; Bartling, Pascal ; Jogler, Mareike ; Rohde, Manfred ; Petersen, Jörn ; Medema, Marnix H. ; Surup, Frank ; Jogler, Christian - \ 2020
    Communications Biology 3 (2020)1. - ISSN 2399-3642

    Bacterial strains of the phylum Planctomycetes occur ubiquitously, but are often found on surfaces of aquatic phototrophs, e.g. alga. Despite slower growth, planctomycetes are not outcompeted by faster-growing bacteria in biofilms on such surfaces; however, strategies allowing them to compensate for slower growth have not yet been investigated. Here, we identified stieleriacines, a class of N-acylated tyrosines produced by the novel planctomycete Stieleria maiorica Mal15T, and analysed their effects on growth of the producing strain and bacterial species likely co-occurring with strain Mal15T. Stieleriacines reduced the lag phase of Mal15T and either stimulated or inhibited biofilm formation of two bacterial competitors, indicating that Mal15T employs stieleriacines to specifically alter microbial biofilm composition. The genetic organisation of the putative stieleriacine biosynthetic cluster in strain Mal15T points towards a functional link of stieleriacine biosynthesis to exopolysaccharide-associated protein sorting and biofilm formation.

    A novel alphaproteobacterium with a small genome identified from the digestive gland of multiple species of abalone
    Huang, Zhaobin ; Petersen, Jillian M. ; Martijn, Joran ; Ettema, Thijs J.G. ; Shao, Zongze - \ 2020
    Environmental Microbiology Reports 12 (2020)4. - ISSN 1758-2229 - p. 387 - 395.

    We identified an alphaproteobacterium in the digestive gland of the abalone species Haliotis discus hannai. This phylotype dominated our 16S rRNA clone libraries from the digestive gland of H. discus hannai. Diversity surveys revealed that this phylotype was associated with H. discus hannai and also in another host species, H. gigantea. Whole genome phylogenies placed this bacterium as a new member affiliated with the family Rhodospirillaceae in Alphaproteobacteria. Gene annotation revealed a nearly complete glycolysis pathway but no TCA cycle, but the presence of anaerobic ribonucleoside-triphosphate reductase and oxygen-insensitive NAD(P)H-dependent nitroreductase, which show the genomic potential for anaerobic metabolism. A large cluster of genes encoding ankyrin repeat proteins (ANK) of eukaryotic-like repeat domains and a large gene set for the flagellar system were also detected. Alginate-binding periplasmic proteins and key genes responsible for alginate assimilation were found in the genome, which could potentially contribute to the breakdown of the host's alginate-rich macroalgal diet. These results raise the possibility that this novel alphaproteobacterium is a widespread member of the abalone microbiome that may use polysaccharides derived from its host's macroalgal diet.

    “Candidatus Galacturonibacter soehngenii” Shows Acetogenic Catabolism of Galacturonic Acid but Lacks a Canonical Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase Complex
    Valk, Laura C. ; Diender, Martijn ; Stouten, Gerben R. ; Petersen, Jette F. ; Nielsen, Per H. ; Dueholm, Morten S. ; Pronk, Jack T. ; Loosdrecht, Mark C.M. van - \ 2020
    Frontiers in Microbiology 11 (2020). - ISSN 1664-302X
    C-labeling - acetogenesis - chemostat enrichment culture - meta-transcriptomics - Wood-Ljungdahl pathway

    Acetogens have the ability to fixate carbon during fermentation by employing the Wood-Ljungdahl pathway (WLP), which is highly conserved across Bacteria and Archaea. In a previous study, product stoichometries in galacturonate-limited, anaerobic enrichment cultures of “Candidatus Galacturonibacter soehngenii,” from a novel genus within the Lachnospiraceae, suggested the simultaneous operation of a modified Entner-Doudoroff pathway for galacturonate fermentation and a WLP for acetogenesis. However, a draft metagenome-assembled genome (MAG) based on short reads did not reveal homologs of genes encoding a canonical WLP carbon-monoxide-dehydrogenase/acetyl-Coenzyme A synthase (CODH/ACS) complex. In this study, NaH13CO3 fed to chemostat-grown, galacturonate-limited enrichment cultures of “Ca. G. soehngenii” was shown to be incorporated into acetate. Preferential labeling of the carboxyl group of acetate was consistent with acetogenesis via a WLP in which the methyl group of acetate was predominately derived from formate. This interpretation was further supported by high transcript levels of a putative pyruvate-formate lyase gene and very low transcript levels of a candidate gene for formate dehydrogenase. Reassembly of the “Ca. G. soehngenii” MAG with support from long-read nanopore sequencing data produced a single-scaffold MAG, which confirmed the absence of canonical CODH/ACS-complex genes homologs. However, high CO-dehydrogenase activities were measured in cell extracts of “Ca. G. soehngenii” enrichment cultures, contradicting the absence of corresponding homologs in the MAG. Based on the highly conserved amino-acid motif associated with anaerobic Ni-CO dehydrogenase proteins, a novel candidate was identified which could be responsible for the observed activities. These results demonstrate operation of an acetogenic pathway, most probably as a yet unresolved variant of the Wood-Ljungdahl pathway, in anaerobic, galacturonate-limited cultures of “Ca. G. soehngenii.”

    Collective Choices Affecting Natural Hazards Governance, Risk, and Vulnerability
    Thaler, Thomas ; Shively, David ; Petersen-Perlman, Jacob ; Slavikova, Lenka ; Hartmann, Thomas - \ 2019
    In: Oxford Research Encyclopedia of Natural Hazard Science Oxford University Press - ISBN 9780199389407
    The frequency and severity of extreme weather events are expected to increase due to climate change. These developments and challenges have focused the attention of policymakers on the question of how to manage natural hazards. The main political discourse revolves around the questions of how we can make our society more resilient for possible future events. A central challenge reflects collective choices, which affect natural hazards governance, risk, and individual and societal vulnerability. In particular, transboundary river basins present difficult and challenging decisions at local, regional, national, and international levels as they involve and engage large numbers of stakeholders. Each of these groups has different perspectives and interests in how to design and organize flood risk management, which often hinder transnational collaborations in terms of upstream–downstream or different riverbed cooperation. Numerous efforts to resolve these conflicts have historically been tried across the world, particularly in relation to institutional cooperation. Consequently, greater engagement of different countries in management of natural hazards risks could decrease international conflicts and increase capacity at regional and local levels to adapt to future hazard events. Better understanding of the issues, perspectives, choices, and potential for conflict, and clear sharing of responsibilities, is crucial for reducing impacts of future events at the transboundary level.
    Evaluation of calcium lignosulfonate as a acceptable previous cargo for edible fats and oils
    Schrenk, Dieter ; Bignami, Margherita ; Bodin, Laurent ; Chipman, James Kevin ; Mazo, Jesús del; Grasl-Kraupp, Bettina ; Hogstrand, Christer ; Hoogenboom, Laurentius ; Leblanc, Jean Charles ; Nebbia, Carlo Stefano ; Nielsen, Elsa ; Ntzani, Evangelia ; Petersen, Annette ; Sand, Salomon ; Schwerdtle, Tanja ; Wallace, Heather ; Grob, Konrad ; Castle, Laurence ; Christodoulidou, Anna ; Vleminckx, Christiane - \ 2019
    EFSA Journal 17 (2019)12. - ISSN 1831-4732
    acceptable previous cargo - calcium lignosulfonate - edible fats and oils - sea transport

    Shipping of edible fats and oils into Europe is permitted in bulk tanks, provided that the previous cargo is included in a positive list. The European Commission requested EFSA to evaluate the acceptability of calcium lignosulfonate as previous cargo for fats and oils. The evaluation was based on the same criteria as those used for the evaluation of the substances currently on the list in the Annex to Commission Directive 96/3/EC as a acceptable previous cargoes for edible fats and oils. In 2017, the EFSA Panel on Contaminants in the Food Chain (CONTAM Panel) concluded that calcium lignosulfonate did not meet the acceptability criteria, due to uncertainties as regards the composition and toxicity of its low-molecular weight fraction (LMWF) below 1,000 Da. In the current evaluation, new information, showing lack of genotoxicity of the LMWF isolated from a technical grade of calcium lignosulfonate was provided. Due to uncertainties regarding the presence of lignosulfonate components below 200 Da in this LMWF tested for genotoxicity, the CONTAM Panel concluded that the information provided was insufficient to assess the acceptability of calcium lignosulfonate as previous cargo. The Panel recommends a better analysis of the LMWF and a new genotoxicity test using this LMWF, including components < 200 Da, and evidence that the tested material is representative of the LMWF in products intended to be shipped as previous cargo for edible fat and oils.

    Evaluation of the health risks related to the presence of cyanogenic glycosides in foods other than raw apricot kernels
    Schrenk, Dieter ; Bignami, Margherita ; Bodin, Laurent ; Chipman, James Kevin ; Mazo, Jesús del; Grasl-Kraupp, Bettina ; Hogstrand, Christer ; Hoogenboom, Laurentius ; Leblanc, Jean Charles ; Nebbia, Carlo Stefano ; Nielsen, Elsa ; Ntzani, Evangelia ; Petersen, Annette ; Sand, Salomon ; Vleminckx, Christiane ; Wallace, Heather ; Benford, Diane ; Brimer, Leon ; Mancini, Francesca Romana ; Metzler, Manfred ; Viviani, Barbara ; Altieri, Andrea ; Arcella, Davide ; Steinkellner, Hans ; Schwerdtle, Tanja - \ 2019
    EFSA Journal 17 (2019)4. - ISSN 1831-4732
    cyanide - cyanogenic glycosides - health-based guidance values - risk assessment

    In 2016, the EFSA Panel on Contaminants in the Food Chain (CONTAM) published a scientific opinion on the acute health risks related to the presence of cyanogenic glycosides (CNGs) in raw apricot kernels in which an acute reference dose (ARfD) of 20 μg/kg body weight (bw) was established for cyanide (CN). In the present opinion, the CONTAM Panel concluded that this ARfD is applicable for acute effects of CN regardless the dietary source. To account for differences in cyanide bioavailability after ingestion of certain food items, specific factors were used. Estimated mean acute dietary exposures to cyanide from foods containing CNGs did not exceed the ARfD in any age group. At the 95th percentile, the ARfD was exceeded up to about 2.5-fold in some surveys for children and adolescent age groups. The main contributors to exposures were biscuits, juice or nectar and pastries and cakes that could potentially contain CNGs. Taking into account the conservatism in the exposure assessment and in derivation of the ARfD, it is unlikely that this estimated exceedance would result in adverse effects. The limited data from animal and human studies do not allow the derivation of a chronic health-based guidance value (HBGV) for cyanide, and thus, chronic risks could not be assessed.

    Scientific opinion on the risks for animal and human health related to the presence of quinolizidine alkaloids in feed and food, in particular in lupins and lupin-derived products
    Schrenk, Dieter ; Bodin, Laurent ; Chipman, James Kevin ; Mazo, Jesús del; Grasl-Kraupp, Bettina ; Hogstrand, Christer ; Hoogenboom, Laurentius ; Leblanc, Jean Charles ; Nebbia, Carlo Stefano ; Nielsen, Elsa ; Ntzani, Evangelia ; Petersen, Annette ; Sand, Salomon ; Schwerdtle, Tanja ; Vleminckx, Christiane ; Wallace, Heather ; Alexander, Jan ; Cottrill, Bruce ; Dusemund, Birgit ; Mulder, Patrick ; Arcella, Davide ; Baert, Katleen ; Cascio, Claudia ; Steinkellner, Hans ; Bignami, Margherita - \ 2019
    EFSA Journal 17 (2019)11. - ISSN 1831-4732
    feed - food - lupanine - Lupin - margin of exposure (MOE) - quinolizidine alkaloid - sparteine

    The European Commission asked EFSA for a scientific opinion on the risks for animal and human health related to the presence of quinolizidine alkaloids (QAs) in feed and food. This risk assessment is limited to QAs occurring in Lupinus species/varieties relevant for animal and human consumption in Europe (i.e. Lupinus albus L., Lupinus angustifolius L., Lupinus luteus L. and Lupinus mutabilis Sweet). Information on the toxicity of QAs in animals and humans is limited. Following acute exposure to sparteine (reference compound), anticholinergic effects and changes in cardiac electric conductivity are considered to be critical for human hazard characterisation. The CONTAM Panel used a margin of exposure (MOE) approach identifying a lowest single oral effective dose of 0.16 mg sparteine/kg body weight as reference point to characterise the risk following acute exposure. No reference point could be identified to characterise the risk of chronic exposure. Because of similar modes of action for QAs, the CONTAM Panel used a group approach assuming dose additivity. For food, the highest mean concentration of Total QAs (TotQAs) (i.e. the 6 most abundant QAs) was found in lupin seed samples classified as ‘Lupins (dry) and similar-’. Due to the limited data on occurrence and consumption, dietary exposure was calculated for some specific scenarios and no full human health risk characterisation was possible. The calculated margin of exposures (MOEs) may indicate a risk for some consumers. For example, when lupin seeds are consumed without a debittering step, or as debittered lupin seeds high in QA content and when ‘lupin-based meat imitates’ are consumed. For horses, companion and farm animals, other than salmonids, the available database on adverse effects was too limited to identify no-observed-adverse-effect levels and/or lowest-observed-adverse-effect levels and no risk characterisation was possible. For salmonids, the CONTAM Panel considers the risk for adverse effects to be low.

    A multi-parent recombinant inbred line population of C. elegans allows identification of novel QTLs for complex life history traits
    Snoek, Basten ; Volkers, Rita ; Nijveen, Harm ; Petersen, Carola ; Dirksen, Philipp ; Sterken, Mark ; Nakad, Rania ; Riksen, Joost ; Rosenstiel, P.C. ; Stastna, J.J. ; Braekman, B.P. ; Harvey, S.C. ; Schulenburg, Hinrich ; Kammenga, Jan - \ 2019
    Wageningen University & Research
    Multi-parent RILs - Caenorhabditis elegans - QTL - life-history - natural variation - genetic map
    Background The nematode Caenorhabditis elegans has been extensively used to explore the relationships between complex traits, genotypes, and environments. Complex traits can vary across different genotypes of a species, and the genetic regulators of trait variation can be mapped on the genome using quantitative trait locus (QTL) analysis of recombinant inbred lines (RILs) derived from genetically and phenotypically divergent parents. Most RILs have been derived from crossing two parents from globally distant locations. However, the genetic diversity between local C. elegans populations can be as diverse as between global populations and could thus provide means of identifying genetic variation associated with complex traits relevant on a broader scale. Results To investigate the effect of local genetic variation on heritable traits, we developed a new RIL population derived from 4 parental wild isolates collected from 2 closely located sites in France: Orsay and Santeuil. We crossed these 4 genetically diverse parental isolates to generate a population of 200 multi-parental RILs and used RNA-seq to obtain sequence polymorphisms identifying almost 9000 SNPs variable between the 4 genotypes with an average spacing of 11Â kb, doubling the mapping resolution relative to currently available RIL panels for many loci. The SNPs were used to construct a genetic map to facilitate QTL analysis. We measured life history traits such as lifespan, stress resistance, developmental speed, and population growth in different environments, and found substantial variation for most traits. We detected multiple QTLs for most traits, including novel QTLs not found in previous QTL analysis, including those for lifespan and pathogen responses. This shows that recombining genetic variation across C. elegans populations that are in geographical close proximity provides ample variation for QTL mapping. Conclusion Taken together, we show that using more parents than the classical two parental genotypes to construct a RIL population facilitates the detection of QTLs and that the use of wild isolates facilitates the detection of QTLs. The use of multi-parent RIL populations can further enhance our understanding of local adaptation and life history trade-offs.
    Genome-Wide association studies in apple reveal loci for aroma volatiles, sugar composition, and harvest Date
    Larsen, Bjarne ; Migicovsky, Zoë ; Jeppesen, Anne Aae ; Gardner, Kyle M. ; Toldam-Andersen, Torben Bo ; Myles, Sean ; Ørgaard, Marian ; Petersen, Mikael Agerlin ; Pedersen, Carsten - \ 2019
    The Plant Genome 12 (2019)2. - ISSN 1940-3372

    Understanding the genetic architecture of fruit quality traits is crucial to target breeding of apple (Malus domestica L.) cultivars. We linked genotype and phenotype information by combining genotyping-by-sequencing (GBS) generated single nucleotide polymorphism (SNP) markers with fruit flavor volatile data, sugar and acid content, and historical trait data from a gene bank collection. Using gas chromatography–mass spectrometry (GC-MS) analysis of apple juice samples, we identified 49 fruit volatile organic compounds (VOCs). We found a very variable content of VOCs, especially for the esters, among 149 apple cultivars. We identified convincing associations for the acetate esters especially butyl acetate and hexyl acetate on chromosome 2 in a region of several alcohol acyl-transferases including AAT1. For sucrose content and for fructose and sucrose in percentage of total sugars, we revealed significant SNP associations. Here, we suggest a vacuolar invertase close to significant SNPs for this association as candidate gene. Harvest date was in strong SNP association with a NAC transcription factor gene and sequencing identified two haplotypes associated with harvest date. The study shows that SNP marker characterization of a gene bank collection can be successfully combined with new and historical trait data for association studies. Suggested candidate genes may contribute to an improved understanding of the genetic basis for important traits and simultaneously provide tools for targeted breeding using marker-assisted selection (MAS).

    Strategies for robust and accurate experimental approaches to quantify nanomaterial bioaccumulation across a broad range of organisms
    Petersen, Elijah J. ; Mortimer, Monika ; Burgess, Robert M. ; Handy, Richard ; Hanna, Shannon ; Ho, Kay T. ; Johnson, Monique ; Loureiro, Susana ; Selck, Henriette ; Scott-Fordsmand, Janeck J. ; Spurgeon, David ; Unrine, Jason ; Brink, Nico W. Van Den; Wang, Ying ; White, Jason ; Holden, Patricia - \ 2019
    Environmental Science: Nano covers the benefits... 6 (2019)6. - ISSN 2051-8153 - p. 1619 - 1656.

    One of the key components for environmental risk assessment of engineered nanomaterials (ENMs) is data on bioaccumulation potential. Accurately measuring bioaccumulation can be critical for regulatory decision-making regarding material hazard and risk, and for understanding the mechanism of toxicity. This perspective provides expert guidance for performing ENM bioaccumulation measurements across a broad range of test organisms and species. To accomplish this aim, we critically evaluated ENM bioaccumulation within three categories of organisms: single-celled species, multicellular species excluding plants, and multicellular plants. For aqueous exposures of suspended single-celled and small multicellular species, it is critical to perform a robust procedure to separate suspended ENMs and small organisms to avoid overestimating bioaccumulation. For many multicellular organisms, it is essential to differentiate between the ENMs adsorbed to external surfaces or in the digestive tract and the amount absorbed across epithelial tissues. For multicellular plants, key considerations include how exposure route and the role of the rhizosphere may affect the quantitative measurement of uptake, and that the efficiency of washing procedures to remove loosely attached ENMs to the roots is not well understood. Within each organism category, case studies are provided to illustrate key methodological considerations for conducting robust bioaccumulation experiments for different species within each major group. The full scope of ENM bioaccumulation measurements and interpretations are discussed including conducting the organism exposure, separating organisms from the ENMs in the test media after exposure, analytical methods to quantify ENMs in the tissues or cells, and modeling the ENM bioaccumulation results. One key finding to improve bioaccumulation measurements was the critical need for further analytical method development to identify and quantify ENMs in complex matrices. Overall, the discussion, suggestions, and case studies described herein will help improve the robustness of ENM bioaccumulation studies.

    Evaluation of academic legal publications in Germany
    Purnhagen, K. ; Petersen, Niels - \ 2019
    In: Evaluating academic legal research in Europe / van Gestel, Rob, Lienhard, Andreas, Elgar - ISBN 9781788115490 - p. 88 - 103.
    Legal research has a longstanding and proud tradition in Germany. German academia has always had assessment procedures in place to ensure the quality of legal research and teaching. However, there has been little study of legal research evaluation itself, its effectiveness and ‘fit[ness] for purpose’. A general evaluation of the state of legal scholarship in Germany has been conducted by the Wissenschaftsrat: a group of scientists and politicians which advises the German federal government and the state (Länder) governments on the structure and development of higher education and research. In 2012 the Wissenschaftsrat published a widely discussed analysis of legal scholarship in Germany, which also reflected on the evaluation of the quality of legal research in Germany. In response to this analysis, a number of publications have developed a specific vision of what legal research in Germany is and what it should look like. However, there is still very little discussion in German legal academia on what constitutes good legal research. As a consequence, unfortunately, little data exists on which to base this chapter. The most comprehensive evaluation is still the 2012 publication of the Wissenschaftsrat and publicly available official statistics on the matter. In light of this research gap, the analysis in this chapter is based mainly on these publications, as well as anecdotal evidence acquired from the authors’ own experiences and confidential open interviews with colleagues working at German universities.
    A Migratory Divide Among Red-Necked Phalaropes in the Western Palearctic Reveals Contrasting Migration and Wintering Movement Strategies
    Bemmelen, Rob S.A. van; Kolbeinsson, Yann ; Ramos, Raül ; Gilg, Olivier ; Alves, José A. ; Smith, Malcolm ; Schekkerman, Hans ; Lehikoinen, Aleksi ; Petersen, Ib Krag ; Þórisson, Böðvar ; Sokolov, Aleksandr A. ; Välimäki, Kaisa ; Meer, Tim Van Der; Okill, J.D. ; Bolton, Mark ; Moe, Børge ; Hanssen, Sveinn Are ; Bollache, Loïc ; Petersen, Aevar ; Thorstensen, Sverrir ; González-Solís, Jacob ; Klaassen, Raymond H.G. ; Tulp, Ingrid - \ 2019
    Frontiers in Ecology and Evolution 7 (2019). - ISSN 2296-701X - 17 p.
    flexibility - itinerancy - migration strategy - Phalaropus lobatus - red-necked phalarope
    Non-breeding movement strategies of migratory birds may be expected to be flexibly adjusted to the distribution and quality of habitat, but few studies compare movement strategies among populations using distinct migration routes and wintering areas. In our study, individual movement strategies of red-necked phalaropes (Phalaropus lobatus), a long-distance migratory wader which uses saline waters in the non-breeding period, were studied using light-level geolocators. Results revealed a migratory divide between two populations with distinct migration routes and wintering areas: one breeding in the north-eastern North Atlantic and migrating ca. 10,000 km oversea to the tropical eastern Pacific Ocean, and the other breeding in Fennoscandia and Russia migrating
    ca. 6,000 km—largely over land—to the Arabian Sea (Indian Ocean). In line with our expectations, the transoceanic migration between the North Atlantic and the Pacific was associated with proportionately longer wings, a more even spread of stopovers in autumn and a higher migration speed in spring compared to the migration between Fennoscandian-Russian breeding grounds and the Arabian Sea. In the wintering period, van Bemmelen et al. Contrasting Movement Strategies in Phalaropes birds wintering in the Pacific were stationary in roughly a single area, whereas individuals wintering in the Arabian Sea moved extensively between different areas, reflecting differences in spatio-temporal variation in primary productivity between the two wintering areas. Our study is unique in showing how habitat distribution shapes movement strategies over the entire non-breeding period within a species.
    Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage
    Hendriksen, Rene S. ; Munk, Patrick ; Njage, Patrick ; Bunnik, Bram Van; Mcnally, Luke ; Lukjancenko, Oksana ; Röder, Timo ; Nieuwenhuijse, David ; Pedersen, Susanne Karlsmose ; Kjeldgaard, Jette ; Kaas, Rolf S. ; Clausen, Philip Thomas Lanken Conradsen ; Vogt, Josef Korbinian ; Leekitcharoenphon, Pimlapas ; De Schans, Milou G.M. Van; Zuidema, Tina ; Roda Husman, Ana Maria De; Rasmussen, Simon ; Petersen, Bent ; Amid, Clara ; Cochrane, Guy ; Sicheritz-ponten, Thomas ; Schmitt, Heike ; Alvarez, Jorge Raul Matheu ; Aidara-kane, Awa ; Pamp, Sünje J. ; Lund, Ole ; Hald, Tine ; Woolhouse, Mark ; Koopmans, Marion P. ; Vigre, Håkan ; Petersen, Thomas Nordahl ; Aarestrup, Frank M. - \ 2019
    Nature Communications 10 (2019)1. - ISSN 2041-1723 - 12 p.
    Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use meta-genomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.
    A multi-parent recombinant inbred line population of C. elegans allows identification of novel QTLs for complex life history traits
    Snoek, B.L. ; Volkers, J.M. ; Nijveen, H. ; Petersen, Carola ; Dirksen, Philipp ; Sterken, M.G. ; Nakad, Rania ; Riksen, J.A.G. ; Rosenstiel, P.C. ; Stastna, J.J. ; Braekman, B.P. ; Harvey, S.C. ; Schulenburg, Hinrich ; Kammenga, J.E. - \ 2019
    BMC Biology 17 (2019). - ISSN 1741-7007 - 17 p.
    Background - The nematode Caenorhabditis elegans has been extensively used to explore the relationships between complex traits, genotypes, and environments. Complex traits can vary across different genotypes of a species, and the genetic regulators of trait variation can be mapped on the genome using quantitative trait locus (QTL) analysis of recombinant inbred lines (RILs) derived from genetically and phenotypically divergent parents. Most RILs have been derived from crossing two parents from globally distant locations. However, the genetic diversity between local C. elegans populations can be as diverse as between global populations and could thus provide means of identifying genetic variation associated with complex traits relevant on a broader scale.
    Results - To investigate the effect of local genetic variation on heritable traits, we developed a new RIL population derived from 4 parental wild isolates collected from 2 closely located sites in France: Orsay and Santeuil. We crossed these 4 genetically diverse parental isolates to generate a population of 200 multi-parental RILs and used RNA-seq to obtain sequence polymorphisms identifying almost 9000 SNPs variable between the 4 genotypes with an average spacing of 11 kb, doubling the mapping resolution relative to currently available RIL panels for many loci. The SNPs were used to construct a genetic map to facilitate QTL analysis. We measured life history traits such as lifespan, stress resistance, developmental speed, and population growth in different environments, and found substantial variation for most traits. We detected multiple QTLs for most traits, including novel QTLs not found in previous QTL analysis, including those for lifespan and pathogen responses. This shows that recombining genetic variation across C. elegans populations that are in geographical close proximity provides ample variation for QTL mapping.
    Conclusion -Taken together, we show that using more parents than the classical two parental genotypes to construct a RIL population facilitates the detection of QTLs and that the use of wild isolates facilitates the detection of QTLs. The use of multi-parent RIL populations can further enhance our understanding of local adaptation and life history trade-offs.
    Sameness and difference in delta planning
    Zegwaard, Arjen ; Zwarteveen, Margreet ; Halsema, Gerardo van; Petersen, Arthur - \ 2019
    Environmental Science & Policy 94 (2019). - ISSN 1462-9011 - p. 237 - 244.
    Coevolution - Delta planning - Dutch delta knowledge - Masterplanning

    Triggered by an increased awareness of the possible effects of climate change, many deltaic regions around the world are undertaking planning initiatives to address the problems they expect to face in the future. Dutch delta planning knowledge and expertise figure prominently in some of these initiatives. We use this article to ask why this is so. What makes Dutch delta knowledge special, and how does it become generic enough to travel to other places? The pertinence of these questions stems from the realization that deltas do not pre-exist human interventions, but are as much the effect of different planning cultures, trajectories and objectives, as they are their cause. Through a discussion of some telling anecdotes of delta planning, our analysis shows that while the Dutchness of delta planning expertise is a powerful branding, this expertise can only travel through a conscious and simultaneous process of un-Dutching: by packaging and scientizing Dutch Delta planning to turn it into a more generic Adaptive Delta Management approach.

    Correction to: In Vitro Seeding Activity of Glycoform-Deficient Prions from Variably Protease-Sensitive Prionopathy and Familial CJD Associated with PrPV180I Mutation
    Wang, Zerui ; Yuan, Jue ; Shen, Pingping ; Abskharon, Romany ; Lang, Yue ; Dang, Johnny ; Adornato, Alise ; Xu, Ling ; Chen, Jiafeng ; Feng, Jiachun ; Moudjou, Mohammed ; Kitamoto, Tetsuyuki ; Langeveld, Jan ; Appleby, Brian ; Ma, Jiyan ; Kong, Qingzhong ; Petersen, Robert B. ; Zou, Wen Quan ; Cui, Li - \ 2019
    Molecular Neurobiology 56 (2019)8. - ISSN 0893-7648 - p. 5470 - 5470.

    The original version of this article unfortunately contained a mistake. The email address Dr. Wen-Quan Zou, one of the corresponding authors should be written as “wxz6@case.edu” instead of “wxz@case.edu”.

    The Role and Need for Space-Based Forest Biomass-Related Measurements in Environmental Management and Policy
    Herold, Martin ; Carter, Sarah ; Avitabile, Valerio ; Espejo, Andrés B. ; Jonckheere, Inge ; Lucas, Richard ; McRoberts, Ronald E. ; Næsset, Erik ; Nightingale, Joanne ; Petersen, Rachael ; Reiche, Johannes ; Romijn, Erika ; Rosenqvist, Ake ; Rozendaal, Danaë M.A. ; Seifert, Frank Martin ; Sanz, María J. ; Sy, V. de - \ 2019
    Surveys in Geophysics 40 (2019)4. - ISSN 0169-3298 - p. 757 - 778.
    The achievement of international goals and national commitments related to forest conservation and management, climate change, and sustainable development requires credible, accurate, and reliable monitoring of stocks and changes in forest biomass and carbon. Most prominently, the Paris Agreement on Climate Change and the United Nations’ Sustainable Development Goals in particular require data on biomass to monitor progress. Unprecedented opportunities to provide forest biomass data are created by a series of upcoming space-based missions, many of which provide open data targeted at large areas and better spatial resolution biomass monitoring than has previously been achieved. We assess various policy needs for biomass data and recommend a long-term collaborative effort among forest biomass data producers and users to meet these needs. A gap remains, however, between what can be achieved in the research domain and what is required to support policy making and meet reporting requirements. There is no single biomass dataset that serves all users in terms of definition and type of biomass measurement, geographic area, and uncertainty requirements, and whether there is need for the most recent up-to-date biomass estimate or a long-term biomass trend. The research and user communities should embrace the potential strength of the multitude of upcoming missions in combination to provide for these varying needs and to ensure continuity for long-term data provision which one-off research missions cannot provide. International coordination bodies such as Global Forest Observations Initiative (GFOI), Committee on Earth Observation Satellites (CEOS), and Global Observation of Forest Cover and Land Dynamics (GOFC‐GOLD) will be integral in addressing these issues in a way that fulfils these needs in a timely fashion. Further coordination work should particularly look into how space-based data can be better linked with field reference data sources such as forest plot networks, and there is also a need to ensure that reference data cover a range of forest types, management regimes, and disturbance regimes worldwide.
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