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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Details of plastic ingestion and fibre contamination in North Sea fishes
Kühn, Susanne ; Franeker, Jan A. van; O’donoghue, Anastasia M. ; Swiers, Ailynn ; Starkenburg, Marrit ; Werven, Bernike van; Foekema, Edwin ; Hermsen, Enya ; Egelkraut-holtus, Marion ; Lindeboom, Han - \ 2019
Environmental Pollution (2019). - ISSN 0269-7491
This study combines published datasets with unpublished data on plastic ingestion in several North Sea fish species. The combined dataset of 4389 individuals from 15 species allows the analysis of spatial distribution and temporal variability of plastic uptake in fish. Airborne fibre contamination was observed to be the main contributor to fibres encountered in the samples. The number of fibres in samples was strongly related to the time needed to process a sample, not to the number of individual fishes in the sample. Accurate correction for secondary fibre contamination was not possible, but corrections required would be similar to fibre numbers observed in the samples. Consequently, all fibres were omitted from further analysis. The frequency of occurrence and the average number of plastics in fish is generally low (1.8% and 0.022 pieces per organism respectively), with only cod having a higher prevalence (12.3%). While latitude of catch locations influences plastic uptake in fish, no correlation with the distance to the coast was found. Slightly less plastics were ingested in winter, and a decrease in plastics ingested was observed between 2009 and 2018. These factors should be considered when fish species, catch location and time are discussed as indicators for plastic pollution in the European Marine Strategy Framework Directive. We recommend considering demersal cod and pelagic sprat as two species suitable for monitoring plastic ingestion in biota, both on the seafloor and in the water column.
Sea ice production and ecology study (SIPES2)
Castellani, G. ; Meiners, K. ; Kuhn, S. ; Milnes, M. ; M., Vortkamp ; Meijboom, A. ; Feij, B. ; Dorssen, M. van; Flores, H. ; Putte, A.P. van de; Schaafsma, F.L. ; Franeker, J.A. van - \ 2019
In: The expedition PS117 of the research vessel Polarstern to the Weddell Sea / Boebel, O., Bremerhaven : AWI Alfred-Wegener-Institut (Berichte zur Polar- und Meeresforschung ) - p. 132 - 146.
The FAIR Funder pilot programme to make it easy for funders to require and for grantees to produce FAIR Data
Wittenburg, Peter ; Sustkova, Hana Pergl ; Montesanti, Annalisa ; Bloemers, Margreet ; Waard, S.H. de; Musen, Mark A. ; Graybeal, John ; Hettne, Kristina M. ; Jacobsen, Annika ; Pergl, Robert ; Hooft, Rob W.W. ; Staiger, Christine ; Gelder, Celia W.G. van; Knijnenburg, Sebastiaan L. ; Arkel, A.C. van; Meerman, Bert ; Wilkinson, Mark D. ; Sansone, S.A. ; Rocca-Serra, Philippe ; McQuilton, Peter ; Gonzalez-Beltran, Alejandra N. ; Aben, G.J.C. ; Henning, P. ; Menezes Alencar, Maria Simone de; Ribeiro, C. ; Silva, C.R.L. ; Sayao, Luis ; Sales, Luana ; Veiga, Viviane ; Lima, Jefferson ; Dib, Simone ; Xavier dos Santos, Paula dos; Murtinho, R. ; Tendel, Jakob ; Schaap, B.F. ; Brouwer, P.M. ; Gavai, A.K. ; Bouzembrak, Yamine ; Marvin, Hans J.P. ; Mons, Albert ; Kuhn, Tobias ; Gambardella, A.A. ; Miranda Azevedo, Ricardo de; Muhonen, Vesa ; Naald, Mira van der; Smit, N.W. ; Buys, M.J. ; Bruin, Taco F. de; Schoots, Fieke ; Goodson, H.J.E. ; Rzepa, Henry S. ; Jeffery, Keith G. ; Shanahan, Hugh P. ; Axton, M. ; Tkachenko, Veniamin ; Deslattes Maya, Anne ; Meyers, Natalie ; Conlon, Michael ; Haak, Laurel L. ; Schultes, Erik - \ 2019
arXiv - 13 p.
There is a growing acknowledgement in the scientific community of the importance of making experimental data machine findable, accessible, interoperable, and reusable (FAIR). Recognizing that high quality metadata are essential to make datasets FAIR, members of the GO FAIR Initiative and the Research Data Alliance (RDA) have initiated a series of workshops to encourage the creation of Metadata for Machines (M4M), enabling any self-identified stakeholder to define and promote the reuse of standardized, comprehensive machine-actionable metadata. The funders of scientific research recognize that they have an important role to play in ensuring that experimental results are FAIR, and that high quality metadata and careful planning for FAIR data stewardship are central to these goals. We describe the outcome of a recent M4M workshop that has led to a pilot programme involving two national science funders, the Health Research Board of Ireland (HRB) and the Netherlands Organisation for Health Research and Development (ZonMW). These funding organizations will explore new technologies to define at the time that a request for proposals is issued the minimal set of machine-actionable metadata that they would like investigators to use to annotate their datasets, to enable investigators to create such metadata to help make their data FAIR, and to develop data-stewardship plans that ensure that experimental data will be managed appropriately abiding by the FAIR principles. The FAIR Funders design envisions a data-management workflow having seven essential stages, where solution providers are openly invited to participate. The initial pilot programme will launch using existing computer-based tools of those who attended the M4M Workshop.
Vitamin D-related genes, blood vitamin D levels and colorectal cancer risk in western european populations
Fedirko, Veronika ; Mandle, Hannah B. ; Zhu, Wanzhe ; Hughes, David J. ; Siddiq, Afshan ; Ferrari, Pietro ; Romieu, Isabelle ; Riboli, Elio ; Bueno-de-Mesquita, Bas ; Duijnhoven, Fränzel J.B. Van; Siersema, Peter D. ; Tjønneland, Anne ; Olsen, Anja ; Perduca, Vittorio ; Carbonnel, Franck ; Boutron-Ruault, Marie Christine ; Kühn, Tilman ; Johnson, Theron ; Krasimira, Aleksandrova ; Trichopoulou, Antonia ; Makrythanasis, Periklis ; Thanos, Dimitris ; Panico, Salvatore ; Krogh, Vittorio ; Sacerdote, Carlotta ; Skeie, Guri ; Weiderpass, Elisabete ; Colorado-Yohar, Sandra ; Sala, Núria ; Barricarte, Aurelio ; Sanchez, Maria Jose ; Quirós, Ramón ; Amiano, Pilar ; Gylling, Björn ; Harlid, Sophia ; Perez-Cornago, Aurora ; Heath, Alicia K. ; Tsilidis, Konstantinos K. ; Aune, Dagfinn ; Freisling, Heinz ; Murphy, Neil ; Gunter, Marc J. ; Jenab, Mazda - \ 2019
Nutrients 11 (2019)8. - ISSN 2072-6643
Colorectal neoplasms - Incidence - Single nucleotide polymorphism (SNP) - Vitamin D

Higher circulating 25-hydroxyvitamin D levels (25(OH)D) have been found to be associated with lower risk for colorectal cancer (CRC) in prospective studies. Whether this association is modified by genetic variation in genes related to vitamin D metabolism and action has not been well studied in humans. We investigated 1307 functional and tagging single-nucleotide polymorphisms (SNPs; individually, and by gene/pathway) in 86 vitamin D-related genes in 1420 incident CRC cases matched to controls from the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort. We also evaluated the association between these SNPs and circulating 25(OH)D in a subset of controls. We confirmed previously reported CRC risk associations between SNPs in the VDR, GC, and CYP27B1 genes. We also identified additional associations with 25(OH)D, as well as CRC risk, and several potentially novel SNPs in genes related to vitamin D transport and action (LRP2, CUBN, NCOA7, and HDAC9). However, none of these SNPs were statistically significant after Benjamini-Hochberg (BH) multiple testing correction. When assessed by a priori defined functional pathways, tumor growth factor β(TGFβ) signaling was associated with CRC risk (P ≤ 0.001), with most statistically significant genes being SMAD7 (PBH = 0.008) and SMAD3 (PBH = 0.008), and 18 SNPs in the vitamin D receptor (VDR) binding sites (P = 0.036). The 25(OH)D-gene pathway analysis suggested that genetic variants in the genes related to VDR complex formation and transcriptional activity are associated with CRC depending on 25(OH)D levels (interaction P = 0.041). Additional studies in large populations and consortia, especially with measured circulating 25(OH)D, are needed to confirm our findings.

Wageningen University Research: Northern Fulmar and plastics - monitoring report 2018
Franeker, J.A. van; Kuhn, S. - \ 2019
Fulmar Litter EcoQO monitoring in the Netherlands: update 2018
Franeker, J.A. van; Kühn, S. - \ 2019
Den Helder : Wageningen Marine Research (Wageningen Marine Research report C077/19) - 60
Correction to: Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer
Bien, Stephanie A. ; Su, Yu Ru ; Conti, David V. ; Harrison, Tabitha A. ; Qu, Conghui ; Guo, Xingyi ; Lu, Yingchang ; Albanes, Demetrius ; Auer, Paul L. ; Banbury, Barbara L. ; Berndt, Sonja I. ; Bézieau, Stéphane ; Brenner, Hermann ; Buchanan, Daniel D. ; Caan, Bette J. ; Campbell, Peter T. ; Carlson, Christopher S. ; Chan, Andrew T. ; Chang-Claude, Jenny ; Chen, Sai ; Connolly, Charles M. ; Easton, Douglas F. ; Feskens, Edith J.M. ; Gallinger, Steven ; Giles, Graham G. ; Gunter, Marc J. ; Hampe, Jochen ; Huyghe, Jeroen R. ; Hoffmeister, Michael ; Hudson, Thomas J. ; Jacobs, Eric J. ; Jenkins, Mark A. ; Kampman, Ellen ; Kang, Hyun Min ; Kühn, Tilman ; Küry, Sébastien ; Lejbkowicz, Flavio ; Marchand, Loic Le; Milne, Roger L. ; Li, Li ; Li, Christopher I. ; Lindblom, Annika ; Lindor, Noralane M. ; Martín, Vicente ; McNeil, Caroline E. ; Melas, Marilena ; Moreno, Victor ; Newcomb, Polly A. ; Offit, Kenneth ; Pharaoh, Paul D.P. ; Potter, John D. ; Qu, Chenxu ; Riboli, Elio ; Rennert, Gad ; Sala, Núria ; Schafmayer, Clemens ; Scacheri, Peter C. ; Schmit, Stephanie L. ; Severi, Gianluca ; Slattery, Martha L. ; Smith, Joshua D. ; Trichopoulou, Antonia ; Tumino, Rosario ; Ulrich, Cornelia M. ; Duijnhoven, Fränzel J.B. van; Guelpen, Bethany Van; Weinstein, Stephanie J. ; White, Emily ; Wolk, Alicja ; Woods, Michael O. ; Wu, Anna H. ; Abeçasis, Goncalo R. ; Casey, Graham ; Nickerson, Deborah A. ; Gruber, Stephen B. ; Hsu, Li ; Zheng, Wei ; Peters, Ulrike - \ 2019
Human Genetics 138 (2019)7. - ISSN 0340-6717 - p. 789 - 791.

Every author has erroneously been assigned to the affiliation “62”. The affiliation 62 belongs to the author Graham Casey.

Recommended best practices for plastic and litter ingestion studies in marine birds: Collection, processing, and reporting
Provencher, Jennifer F. ; Borrelle, Stephanie B. ; Bond, Alexander L. ; Lavers, Jennifer L. ; Franeker, Jan A. Van; Kühn, Susanne ; Hammer, Sjúrður ; Avery-Gomm, Stephanie ; Mallory, Mark L. ; Favaro, Brett - \ 2019
FACETS 4 (2019)1. - ISSN 2371-1671 - p. 111 - 130.
bird - bolus - diet analysis - marine debris - method standardization - necropsy - plastic debris - plastic ingestion
Marine plastic pollution is an environmental contaminant of significant concern. There is a lack of consistency in sample collection and processing that continues to impede meta-analyses and largescale comparisons across time and space. This is true for most taxa, including seabirds, which are the most studied megafauna group with regards to plastic ingestion research. Consequently, it is difficult to evaluate the impacts and extent of plastic contamination in seabirds fully and accurately, and to make inferences about species for which we have little or no data. We provide a synthesized set of recommendations specific for seabirds and plastic ingestion studies that include best practices in relation to sample collection, processing, and reporting, as well as highlighting some
“cross-cutting” methods. We include guidance for how carcasses, regurgitations, and pellets should be handled and treated to prevent cross-contamination, and a discussion of what size class of microplastics can be assessed in each sample type. Although we focus on marine bird samples, we also include standardized techniques to remove sediment and biological material that are generalizable
to other taxa. Lastly, metrics and data presentation of ingested plastics are briefly reviewed in the context of seabird studies.
sPlot – A new tool for global vegetation analyses
Bruelheide, Helge ; Dengler, Jürgen ; Jiménez-Alfaro, Borja ; Purschke, Oliver ; Hennekens, Stephan M. ; Chytrý, Milan ; Pillar, Valério D. ; Jansen, Florian ; Kattge, Jens ; Sandel, Brody ; Aubin, Isabelle ; Biurrun, Idoia ; Field, Richard ; Haider, Sylvia ; Jandt, Ute ; Lenoir, Jonathan ; Peet, Robert K. ; Peyre, Gwendolyn ; Sabatini, Francesco Maria ; Schmidt, Marco ; Schrodt, Franziska ; Winter, Marten ; Aćić, Svetlana ; Agrillo, Emiliano ; Alvarez, Miguel ; Ambarlı, Didem ; Angelini, Pierangela ; Apostolova, Iva ; Arfin Khan, Mohammed A.S. ; Arnst, Elise ; Attorre, Fabio ; Baraloto, Christopher ; Beckmann, Michael ; Berg, Christian ; Bergeron, Yves ; Bergmeier, Erwin ; Bjorkman, Anne D. ; Bondareva, Viktoria ; Borchardt, Peter ; Botta-Dukát, Zoltán ; Boyle, Brad ; Breen, Amy ; Brisse, Henry ; Byun, Chaeho ; Cabido, Marcelo R. ; Casella, Laura ; Cayuela, Luis ; Černý, Tomáš ; Chepinoga, Victor ; Csiky, János ; Curran, Michael ; Ćušterevska, Renata ; Dajić Stevanović, Zora ; Bie, Els De; Ruffray, Patrice de; Sanctis, Michele De; Dimopoulos, Panayotis ; Dressler, Stefan ; Ejrnæs, Rasmus ; El-Sheikh, Mohamed A.E.R.M. ; Enquist, Brian ; Ewald, Jörg ; Fagúndez, Jaime ; Finckh, Manfred ; Font, Xavier ; Forey, Estelle ; Fotiadis, Georgios ; García-Mijangos, Itziar ; Gasper, André Luis de; Golub, Valentin ; Gutierrez, Alvaro G. ; Hatim, Mohamed Z. ; He, Tianhua ; Higuchi, Pedro ; Holubová, Dana ; Hölzel, Norbert ; Homeier, Jürgen ; Indreica, Adrian ; Işık Gürsoy, Deniz ; Jansen, Steven ; Janssen, John ; Jedrzejek, Birgit ; Jiroušek, Martin ; Jürgens, Norbert ; Kącki, Zygmunt ; Kavgacı, Ali ; Kearsley, Elizabeth ; Kessler, Michael ; Knollová, Ilona ; Kolomiychuk, Vitaliy ; Korolyuk, Andrey ; Kozhevnikova, Maria ; Kozub, Łukasz ; Krstonošić, Daniel ; Kühl, Hjalmar ; Kühn, Ingolf ; Kuzemko, Anna ; Küzmič, Filip ; Landucci, Flavia ; Lee, Michael T. ; Levesley, Aurora ; Li, Ching Feng ; Liu, Hongyan ; Lopez-Gonzalez, Gabriela ; Lysenko, Tatiana ; Macanović, Armin ; Mahdavi, Parastoo ; Manning, Peter ; Marcenò, Corrado ; Martynenko, Vassiliy ; Mencuccini, Maurizio ; Minden, Vanessa ; Moeslund, Jesper Erenskjold ; Moretti, Marco ; Müller, Jonas V. ; Munzinger, Jérôme ; Niinemets, Ülo ; Nobis, Marcin ; Noroozi, Jalil ; Nowak, Arkadiusz ; Onyshchenko, Viktor ; Overbeck, Gerhard E. ; Ozinga, Wim A. ; Pauchard, Anibal ; Pedashenko, Hristo ; Peñuelas, Josep ; Pérez-Haase, Aaron ; Peterka, Tomáš ; Petřík, Petr ; Phillips, Oliver L. ; Prokhorov, Vadim ; Rašomavičius, Valerijus ; Revermann, Rasmus ; Rodwell, John ; Ruprecht, Eszter ; Rūsiņa, Solvita ; Samimi, Cyrus ; Schaminée, Joop H.J. ; Schmiedel, Ute ; Šibík, Jozef ; Šilc, Urban ; Škvorc, Željko ; Smyth, Anita ; Sop, Tenekwetche ; Sopotlieva, Desislava ; Sparrow, Ben ; Stančić, Zvjezdana ; Svenning, Jens Christian ; Swacha, Grzegorz ; Tang, Zhiyao ; Tsiripidis, Ioannis ; Turtureanu, Pavel Dan ; Uğurlu, Emin ; Uogintas, Domas ; Valachovič, Milan ; Vanselow, Kim André ; Vashenyak, Yulia ; Vassilev, Kiril ; Vélez-Martin, Eduardo ; Venanzoni, Roberto ; Vibrans, Alexander Christian ; Violle, Cyrille ; Virtanen, Risto ; Wehrden, Henrik von; Wagner, Viktoria ; Walker, Donald A. ; Wana, Desalegn ; Weiher, Evan ; Wesche, Karsten ; Whitfeld, Timothy ; Willner, Wolfgang ; Wiser, Susan ; Wohlgemuth, Thomas ; Yamalov, Sergey ; Zizka, Georg ; Zverev, Andrei - \ 2019
Journal of Vegetation Science 30 (2019)2. - ISSN 1100-9233 - p. 161 - 186.
biodiversity - community ecology - ecoinformatics - functional diversity - global scale - macroecology - phylogenetic diversity - plot database - sPlot - taxonomic diversity - vascular plant - vegetation relevé

Aims: Vegetation-plot records provide information on the presence and cover or abundance of plants co-occurring in the same community. Vegetation-plot data are spread across research groups, environmental agencies and biodiversity research centers and, thus, are rarely accessible at continental or global scales. Here we present the sPlot database, which collates vegetation plots worldwide to allow for the exploration of global patterns in taxonomic, functional and phylogenetic diversity at the plant community level. Results: sPlot version 2.1 contains records from 1,121,244 vegetation plots, which comprise 23,586,216 records of plant species and their relative cover or abundance in plots collected worldwide between 1885 and 2015. We complemented the information for each plot by retrieving climate and soil conditions and the biogeographic context (e.g., biomes) from external sources, and by calculating community-weighted means and variances of traits using gap-filled data from the global plant trait database TRY. Moreover, we created a phylogenetic tree for 50,167 out of the 54,519 species identified in the plots. We present the first maps of global patterns of community richness and community-weighted means of key traits. Conclusions: The availability of vegetation plot data in sPlot offers new avenues for vegetation analysis at the global scale.

Mogelijke ecologische gevolgen containerramp MSC Zoe voor Waddenzee en Noordzee: een quickscan
Baptist, M.J. ; Brasseur, S.M.J.M. ; Foekema, E.M. ; Franeker, J.A. van; Kuhn, S. ; Leopold, M.F. - \ 2019
Den Helder : Wageningen Marine Research (Wageningen Marine Research rapport C029/19) - 18
De Zoe en de zeekoet : een onderzoek naar de doodsoorzaak en de herkomst van de zeekoeten die massaal strandden op de Nederlandse kust in januari en februari 2019
Leopold, Mardik F. ; Kik, Marja ; Tulden, Peter van; Franeker, Jan Andries van; Kühn, Suzanne ; Rijks, Jolianne - \ 2019
Den Helder : Wageningen Marine Research (Wageningen Marine Research rapport C026/19) - 59
Addendum: The FAIR Guiding Principles for scientific data management and stewardship
Wilkinson, Mark D. ; Dumontier, Michel ; Aalbersberg, Ijsbrand Jan ; Appleton, Gabrielle ; Axton, Myles ; Baak, Arie ; Blomberg, Niklas ; Boiten, Jan Willem ; Silva Santos, Luiz Bonino Da; Bourne, Philip E. ; Bouwman, Jildau ; Brookes, Anthony J. ; Clark, Tim ; Crosas, Mercè ; Dillo, Ingrid ; Dumon, Olivier ; Edmunds, Scott ; Evelo, Chris T. ; Finkers, Richard ; Gonzalez-Beltran, Alejandra ; Gray, Alasdair J.G. ; Groth, Paul ; Goble, Carole ; Grethe, Jeffrey S. ; Heringa, Jaap ; Hoen, Peter A.C. 't; Hooft, Rob ; Kuhn, Tobias ; Kok, Ruben ; Kok, Joost ; Lusher, Scott J. ; Martone, Maryann E. ; Mons, Albert ; Packer, Abel L. ; Persson, Bengt ; Rocca-Serra, Philippe ; Roos, Marco ; Schaik, Rene van; Sansone, Susanna Assunta ; Schultes, Erik ; Sengstag, Thierry ; Slater, Ted ; Strawn, George ; Swertz, Morris A. ; Thompson, Mark ; Lei, Johan van der; Mulligen, Erik van; Velterop, Jan ; Waagmeester, Andra ; Wittenburg, Peter ; Wolstencroft, Katherine ; Zhao, Jun ; Mons, Barend - \ 2019
Scientific Data 6 (2019). - ISSN 2052-4463

Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer
Bien, Stephanie A. ; Su, Yu-Ru ; Conti, David V. ; Harrison, Tabitha A. ; Qu, Conghui ; Guo, Xingyi ; Lu, Yingchang ; Albanes, Demetrius ; Auer, Paul L. ; Banbury, Barbara L. ; Berndt, Sonja I. ; Bézieau, Stéphane ; Brenner, Hermann ; Buchanan, Daniel D. ; Caan, Bette J. ; Campbell, Peter T. ; Carlson, Christopher S. ; Chan, Andrew T. ; Chang-Claude, Jenny ; Chen, Sai ; Connolly, Charles M. ; Easton, Douglas F. ; Feskens, Edith J.M. ; Gallinger, Steven ; Giles, Graham G. ; Gunter, Marc J. ; Hampe, Jochen ; Huyghe, Jeroen R. ; Hoffmeister, Michael ; Hudson, Thomas J. ; Jacobs, Eric J. ; Jenkins, Mark A. ; Kampman, Ellen ; Kang, Hyun Min ; Kühn, Tilman ; Küry, Sébastien ; Lejbkowicz, Flavio ; Marchand, Loic Le; Milne, Roger L. ; Li, Christopher I. ; Lindblom, Annika ; Lindor, Noralane M. ; Martín, Vicente ; McNeil, Caroline E. ; Melas, Marilena ; Moreno, Victor ; Newcomb, Polly A. ; Offit, Kenneth ; Pharaoh, Paul D.P. ; Potter, John D. ; Qu, Chenxu ; Riboli, Elio ; Rennert, Gad ; Sala, Núria ; Schafmayer, Clemens ; Scacheri, Peter C. ; Schmit, Stephanie L. ; Severi, Gianluca ; Slattery, Martha L. ; Smith, Joshua D. ; Trichopoulou, Antonia ; Tumino, Rosario ; Ulrich, Cornelia M. ; Duijnhoven, Fränzel J.B. van; Guelpen, Bethany Van; Weinstein, Stephanie J. ; White, Emily ; Wolk, Alicja ; Woods, Michael O. ; Wu, Anna H. ; Abecasis, Goncalo R. ; Casey, Graham ; Nickerson, Deborah A. ; Gruber, Stephen B. ; Hsu, Li ; Zheng, Wei ; Peters, Ulrike - \ 2019
Human Genetics 138 (2019)4. - ISSN 0340-6717 - p. 307 - 326.
Genome-wide association studies have reported 56 independently associated colorectal cancer (CRC) risk variants, most of which are non-coding and believed to exert their effects by modulating gene expression. The computational method PrediXcan uses cis-regulatory variant predictors to impute expression and perform gene-level association tests in GWAS without directly measured transcriptomes. In this study, we used reference datasets from colon (n = 169) and whole blood (n = 922) transcriptomes to test CRC association with genetically determined expression levels in a genome-wide analysis of 12,186 cases and 14,718 controls. Three novel associations were discovered from colon transverse models at FDR ≤ 0.2 and further evaluated in an independent replication including 32,825 cases and 39,933 controls. After adjusting for multiple comparisons, we found statistically significant associations using colon transcriptome models with TRIM4 (discovery P = 2.2 × 10− 4, replication P = 0.01), and PYGL (discovery P = 2.3 × 10− 4, replication P = 6.7 × 10− 4). Interestingly, both genes encode proteins that influence redox homeostasis and are related to cellular metabolic reprogramming in tumors, implicating a novel CRC pathway linked to cell growth and proliferation. Defining CRC risk regions as one megabase up- and downstream of one of the 56 independent risk variants, we defined 44 non-overlapping CRC-risk regions. Among these risk regions, we identified genes associated with CRC (P < 0.05) in 34/44 CRC-risk regions. Importantly, CRC association was found for two genes in the previously reported 2q25 locus, CXCR1 and CXCR2, which are potential cancer therapeutic targets. These findings provide strong candidate genes to prioritize for subsequent laboratory follow-up of GWAS loci. This study is the first to implement PrediXcan in a large colorectal cancer study and findings highlight the utility of integrating transcriptome data in GWAS for discovery of, and biological insight into, risk loci.
Monitoring van paraffine-achtige stoffen op Nederlandse stranden en in magen van Noordse Stormvogels
Franeker, Jan Andries van; Kühn, Susanne ; Kotterman, Michiel ; Kwadijk, Christiaan - \ 2019
Den Helder : Wageningen Marine Research (Wageningen Marine Research rapport C001/19) - 32
Within the KB-Program System Earth Management 2018 (KB-24-002-036) a pilot study was conducted into options to monitor of paraffin- or palmfat-like substances on Dutch beaches and in stomachs of corpses of beached Northern Fulmars. Such substances are, in part legally, discharged by tanker ships cleaning their tanks at sea.Paraffin was chemically identified by the presence of alkanes in the samples. It remains to be investigated in detail which other mineral oil derivatives may show similar alkane patterns. In the absence of alkanes further analyses were conducted to assess the type of material involved.Samples taken from beaches showed to be paraffin in 30 of 32 analyses (94%). One sample contained palmoil related substances, one sample remained unclear but contained phthalates (eg used as plastic softeners). The materials from bird stomachs proved to be different. Paraffin was only found in 31% of 32 samples. In 41% of the stomachs vegetable fatty substances were demonstrated, usually palm oil related. The remainder of samples had an uncertain mix of vegetable and animal fats. The difference between beaches and bird stomachs may have several backgrounds, including attraction for wildlife, melting points, and biodegradability.Over 20% of fulmars found in the Netherlands has chemical suspect materials in the stomach. Not much is known about potential health impacts. Over the years no clear changes can be detected. Quantities of material ingested are highly variable. Frequency of occurrence may slightly reduce over the more recent years, but there is no statistically significant trend. It would make sense to add records on chemical suspect materials in fulmar stomachs to the existing monitoring of plastics in the framework of OSPAR and the EU Marine Strategy Framework Directive. Clearly chemical analyses of substances encountered on beaches and in birds is additionally recommended.
Reacties zeevogels in windparken bij doorvaart
Leopold, Mardik ; Geelhoed, Steve ; Verdaat, Hans ; Kühn, Susanne ; Puijenbroek, Marinka van - \ 2018
Den Helder : Wageningen Marine Research (Wageningen Marine Research rapport C066/18a) - 129
Selektion von Antagonisten für die biologische Bekämpfung von Pflanzenkrankheiten.
Kohl, Jurgen - \ 2018
The potential role of gut microbiota and its modulators in the management of propionic and methylmalonic acidemia
Burlina, Alberto ; Tims, Sebastian ; Spronsen, Francjan van; Sperl, Wolfgang ; Burlina, Alessandro P. ; Kuhn, Mirjam ; Knol, Jan ; Rakhshandehroo, Maryam ; Coşkun, Turgay ; Singh, Rani H. ; MacDonald, Anita - \ 2018
Expert Opinion on Orphan Drugs 6 (2018)11. - ISSN 2167-8707 - p. 683 - 692.
methylmalonic acid - microbiota - prebiotic - probiotic - Propionic acid

Introduction: Propionic and methylmalonic acidemia (PA/MMA) are rare inborn errors of metabolism characterized by accumulation of propionyl CoA and/or methylmalonyl CoA, resulting in potentially serious metabolic crises and clinical complications. The gut microbiota contributes a significant proportion of total propionate production and provides a potentially modifiable target. Empiric use of oral antibiotics to reduce propionate production is a common approach but is hampered by possible drug resistance, perturbation of normal gut microbiota, and toxicity. Moreover, constipation, associated with low fiber intake, inadequate fluid intake, low gut motility, and other factors, is a chronic problem in this patient population and may influence propionate production. Newer management techniques that reduce the burden of propionate and address these clinical challenges are needed. Areas covered: This paper summarizes the potential contribution of gut-related factors in PA/MMA and considers modifying gut microbiota as a management approach. Expert opinion: Dietary management of PA/MMA may be improved by specific prebiotics that modify gut microbiota to stabilize or possibly reduce PA production.

Fulmar Litter EcoQO monitoring in the Netherlands : Update 2017
Franeker, J.A. van; Kühn, S. - \ 2018
Den Helder : Wageningen Marine Research (Wageningen Marine Research report C060/18) - 60
Marine microplastic: Preparation of relevant test materials for laboratory assessment of ecosystem impacts
Kühn, Susanne ; Oyen, Albert Van; Booth, Andy M. ; Meijboom, André ; Franeker, Jan A. Van - \ 2018
Chemosphere 213 (2018). - ISSN 0045-6535 - p. 103 - 113.
Reference material - Microplastic - Characterisation - Cryo-milling - Impact assessment - Marine debris
Studies investigating the effects of plastic litter on marine biota have almost exclusively utilised pristine plastic materials that are homogeneous in polymer type, size, shape and chemical composition. This is particularly the case for microplastics (<5 mm), where collecting sufficient quantities from the marineenvironment for use in laboratory impacts studies is simply not feasible. Weathered plastics collected from the marine environment show considerable physical and chemical differences to pristine and postproduction consumer plastics. For this study, macroplastic litter was collected on a Dutch beach andcryo-milled to create a microplastic mixture for environmental impact assessments. The sample composition followed proportions of marine plastic litter types observed in an earlier large beach cleanup. Polymer composition of the sample was assessed by infrared spectroscopy (ATR-FTIR) and differentialscanning calorimetry analysis (DSC). The particle size distribution of the cryo-milled microplastics showed that particles 0.5e2.0mm represented 68% of mass, but smaller sizes (<2 mm) strongly dominated numerically. Inductively coupled plasma spectroscopy (ICP-MS and ICP-OES) analysis of the microplastic mixture revealed a broad range of metals and other elements (e.g. Al, Cd, Cr, Fe, Mg, Pb, S and Zn), representing common inorganic additives used as colorants, fillers and stabilisers. GC-MS analysis identified a broad range of organic plasticisers, stabilisers, antioxidants and flame retardants. Comparison of different analytical approaches showed that creation of a homogeneous microplastic mixture is possible, representing a first step in closing the gap between laboratory studies with pristine materials and realistic scenarios with weathered microplastic.
Prediagnostic serum Vitamin D levels and the risk of Crohn's disease and ulcerative colitis in european populations : A nested case-control study
Opstelten, Jorrit L. ; Chan, Simon S.M. ; Hart, Andrew R. ; Schaik, Fiona D.M. Van; Siersema, Peter D. ; Lentjes, Eef G.W.M. ; Khaw, Kay Tee ; Luben, Robert ; Key, Timothy J. ; Boeing, Heiner ; Bergmann, Manuela M. ; Overvad, Kim ; Palli, Domenico ; Masala, Giovanna ; Racine, Antoine ; Carbonnel, Franck ; Boutron-Ruault, Marie Christine ; Tjønneland, Anne ; Olsen, Anja ; Andersen, Vibeke ; Kaaks, Rudolf ; Kuhn, Tilman ; Tumino, Rosario ; Trichopoulou, Antonia ; Peeters, Petra H.M. ; Verschuren, W.M.M. ; Witteman, Ben J.M. ; Oldenburg, Bas - \ 2018
Inflammatory Bowel Diseases 24 (2018)3. - ISSN 1078-0998 - p. 633 - 640.
Crohn's disease - etiology - inflammatory bowel disease - ulcerative colitis - Vitamin D

Background A low vitamin D status has been put forward as a potential risk factor for the development of inflammatory bowel disease (IBD). This study investigated the association between prediagnostic circulating vitamin D concentrations and dietary intakes of vitamin D, and the risk of Crohn's disease (CD) and ulcerative colitis (UC). Methods Among 359,728 participants of the European Prospective Investigation into Cancer and Nutrition cohort, individuals who developed CD or UC after enrollment were identified. Each case was matched with2 controls by center, gender, age, date of recruitment, and follow-up time. At cohort entry, blood samples were collected and dietary vitamin D intakes were obtained from validated food frequency questionnaires. Serum 25-hydroxyvitamin D levels were measured using liquid chromatography-tandem mass spectrometry. Conditional logistic regression was performed to determine the odds of CD and UC. Results Seventy-two participants developed CD and 169 participants developed UC after a median follow-up of 4.7 and 4.1 years, respectively. Compared with the lowest quartile, no associations with the 3 higher quartiles of vitamin D concentrations were observed for CD (p trend = 0.34) or UC (p trend = 0.66). Similarly, no associations were detected when serum vitamin D levels were analyzed as a continuous variable. Dietary vitamin D intakes were not associated with CD (p trend = 0.39) or UC (p trend = 0.83). Conclusions Vitamin D status was not associated with the development of CD or UC. This does not suggest a major role for vitamin D deficiency in the etiology of IBD, although larger studies are needed to confirm these findings.

Under-ice fauna, zoöplankton and endotherms
Flores, Hauke ; Ehrlich, Julia ; Lange, Benjamin ; Sulanke, Erik ; Niehoff, Barabara ; Hildebrandt, Nicole ; Doble, Martin ; Schaafsma, F.L. ; Meijboom, A. ; Fey, Bram ; Kuhn, S. ; Bravo Rebolledo, Elisa ; Dorssen, Michiel van; Gradinger, Rolf ; Hassett, Brandon ; Kunisch, Erin ; Kohlbach, Doreen ; Graeve, Martin ; Franeker, J.A. van; Bluhm, Bodil - \ 2018
In: The expeditions PS106/1 and 2 of the research vessel Polarstern to the Arctic Ocean in 2017 / Macke, Andreas, Flores, Hauke, Helmholtz : AWI Alfred-Wegener-Institut (Berichte zur Polar- und Meeresforschung ) - p. 123 - 133.
Multigram Scale Enzymatic Synthesis of (R)-1-(4′-Hydroxyphenyl)ethanol Using Vanillyl Alcohol Oxidase
Ewing, Tom A. ; Kühn, Jasmin ; Segarra, Silvia ; Tortajada, Marta ; Zuhse, Ralf ; Berkel, Willem J.H. van - \ 2018
Advanced Synthesis and Catalysis 360 (2018)12. - ISSN 1615-4150 - p. 2370 - 2376.
Alcohols - Alkylphenols - Enantioselectivity - Flavoprotein - Hydroxylation - Oxidoreductases

The enantioselective oxyfunctionalisation of C−H bonds is a highly interesting reaction, as it provides access to chiral alcohols that are important pharmaceutical building blocks. However, it is hard to achieve using traditional methods. One way in which it can be achieved is through the action of oxidative enzymes. Although many reports of the oxyfunctionalisation capabilities of enzymes at an analytical scale have been published, reports on the use of enzymes to achieve oxyfunctionalisation on a synthetically relevant scale are fewer. Here, we describe the scale-up of the conversion of 4-ethylphenol to (R)-1-(4′-hydroxyphenyl)ethanol using the flavin-dependent enzyme vanillyl alcohol oxidase. The process was optimised by testing different reaction media and substrate and enzyme concentrations and by performing it under an oxygen atmosphere. Under optimised reaction conditions, 4.10 g (R)-1-(4′-hydroxyphenyl)ethanol at 97% ee was obtained from 10 g 4-ethylphenol (isolated yield 36%). These results highlight some of the challenges that can be encountered during scale-up of an enzymatic oxyfunctionalisation process to a synthetically relevant scale and will be of use for the development of enzymatic processes for the synthesis of industrially relevant compounds. (Figure presented.).

Vissen in de Noordzee
Kühn, Suse - \ 2018
Leaching and degradation kinetics of glucosinolates during boiling of Brassica oleracea vegetables and the formation of their breakdown products
Hanschen, Franziska S. ; Kühn, Carla ; Nickel, Marie ; Rohn, Sascha ; Dekker, Matthijs - \ 2018
Food Chemistry 263 (2018). - ISSN 0308-8146 - p. 240 - 250.
Brassica - Epithionitriles - Epithiospecifier protein - Glucosinolates - Isothiocyanates - Modeling - Nitriles - Processing
Domestic processing methods, such as boiling, significantly affect the glucosinolate content and the formation of breakdown products in Brassica vegetables. Here, we comprehensively describe the effect of aqueous heat treatment on the degradation and leaching kinetics of glucosinolates on the formation of their enzymatic and non-enzymatic hydrolysis and breakdown products. The results were correlated with the inactivation kinetics of myrosinase and epithiospecifier protein activity in the Brassica oleracea vegetables kohlrabi, white cabbage, and red cabbage. Short-term heating increased isothiocyanate formation due to inactivation of the epithiospecifier protein. Myrosinase was inactivated shortly after that. Boiling led to leaching of glucosinolates and their hydrolysis products into the boiling water. Heating to 99 °C resulted in thermally-induced glucosinolate breakdown and nitrile formation, both in vegetables and boiling water. Finally, kinetic modeling not only revealed differences in myrosinase inactivation among the vegetables, but also glucosinolate leaching and degradation kinetics differed between individual glucosinolates and vegetables.
Taxonomy of the family Arenaviridae and the order Bunyavirales : update 2018
Maes, Piet ; Alkhovsky, Sergey V. ; Bào, Yīmíng ; Beer, Martin ; Birkhead, Monica ; Briese, Thomas ; Buchmeier, Michael J. ; Calisher, Charles H. ; Charrel, Rémi N. ; Choi, Il Ryong ; Clegg, Christopher S. ; Torre, Juan Carlos de la; Delwart, Eric ; DeRisi, Joseph L. ; Bello, Patrick L. Di; Serio, Francesco Di; Digiaro, Michele ; Dolja, Valerian V. ; Drosten, Christian ; Druciarek, Tobiasz Z. ; Du, Jiang ; Ebihara, Hideki ; Elbeaino, Toufic ; Gergerich, Rose C. ; Gillis, Amethyst N. ; Gonzalez, Jean Paul J. ; Haenni, Anne Lise ; Hepojoki, Jussi ; Hetzel, Udo ; Hồ, Thiện ; Hóng, Ní ; Jain, Rakesh K. ; Jansen van Vuren, Petrus ; Jin, Qi ; Jonson, Miranda Gilda ; Junglen, Sandra ; Keller, Karen E. ; Kemp, Alan ; Kipar, Anja ; Kondov, Nikola O. ; Koonin, Eugene V. ; Kormelink, Richard ; Korzyukov, Yegor ; Krupovic, Mart ; Lambert, Amy J. ; Laney, Alma G. ; LeBreton, Matthew ; Lukashevich, Igor S. ; Marklewitz, Marco ; Markotter, Wanda ; Martelli, Giovanni P. ; Martin, Robert R. ; Mielke-Ehret, Nicole ; Mühlbach, Hans Peter ; Navarro, Beatriz ; Ng, Terry Fei Fan ; Nunes, Márcio Roberto Teixeira ; Palacios, Gustavo ; Pawęska, Janusz T. ; Peters, Clarence J. ; Plyusnin, Alexander ; Radoshitzky, Sheli R. ; Romanowski, Víctor ; Salmenperä, Pertteli ; Salvato, Maria S. ; Sanfaçon, Hélène ; Sasaya, Takahide ; Schmaljohn, Connie ; Schneider, Bradley S. ; Shirako, Yukio ; Siddell, Stuart ; Sironen, Tarja A. ; Stenglein, Mark D. ; Storm, Nadia ; Sudini, Harikishan ; Tesh, Robert B. ; Tzanetakis, Ioannis E. ; Uppala, Mangala ; Vapalahti, Olli ; Vasilakis, Nikos ; Walker, Peter J. ; Wáng, Guópíng ; Wáng, Lìpíng ; Wáng, Yànxiăng ; Wèi, Tàiyún ; Wiley, Michael R. ; Wolf, Yuri I. ; Wolfe, Nathan D. ; Wú, Zhìqiáng ; Xú, Wénxìng ; Yang, Li ; Yāng, Zuòkūn ; Yeh, Shyi Dong ; Zhāng, Yǒng Zhèn ; Zhèng, Yàzhōu ; Zhou, Xueping ; Zhū, Chénxī ; Zirkel, Florian ; Kuhn, Jens H. - \ 2018
Archives of Virology 163 (2018)8. - ISSN 0304-8608 - p. 2295 - 2310.
In 2018, the family Arenaviridae was expanded by inclusion of 1 new genus and 5 novel species. At the same time, the recently established order Bunyavirales was expanded by 3 species. This article presents the updated taxonomy of the family Arenaviridae and the order Bunyavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV) and summarizes additional taxonomic proposals that may affect the order in the near future.
Plastic ingestion by juvenile polar cod (Boreogadus saida) in the Arctic Ocean
Kühn, Susanne ; Schaafsma, Fokje L. ; Werven, Bernike van; Flores, Hauke ; Bergmann, Melanie ; Egelkraut-Holtus, Marion ; Tekman, Mine B. ; Franeker, Jan A. van - \ 2018
Polar Biology 41 (2018)6. - ISSN 0722-4060 - p. 1269 - 1278.
Airborne micro-fibre contamination - Arctic - Microplastic - Polar cod (Boreogadus saida)
One of the recently recognised stressors in Arctic ecosystems concerns plastic litter. In this study, juvenile polar cod (Boreogadus saida) were investigated for the presence of plastics in their stomachs. Polar cod is considered a key species in the Arctic ecosystem. The fish were collected both directly from underneath the sea ice in the Eurasian Basin and in open waters around Svalbard. We analysed the stomachs of 72 individuals under a stereo microscope. Two stomachs contained non-fibrous microplastic particles. According to µFTIR analysis, the particles consisted of epoxy resin and a mix of Kaolin with polymethylmethacrylate (PMMA). Fibrous objects were excluded from this analysis to avoid bias due to contamination with airborne micro-fibres. A systematic investigation of the risk for secondary micro-fibre contamination during analytical procedures showed that precautionary measures in all procedural steps are critical. Based on the two non-fibrous objects found in polar cod stomachs, our results show that ingestion of microplastic particles by this ecologically important fish species is possible. With increasing human activity, plastic ingestion may act as an increasing stressor on polar cod in combination with ocean warming and sea-ice decline in peripheral regions of the Arctic Ocean. To fully assess the significance of this stressor and its spatial and temporal variability, future studies must apply a rigorous approach to avoid secondary pollution.
Plastic ingestion by harbour porpoises Phocoena phocoena in the Netherlands: Establishing a standardised method
Franeker, Jan A. van; Bravo Rebolledo, Elisa L. ; Hesse, Eileen ; IJsseldijk, Lonneke L. ; Kühn, Susanne ; Leopold, Mardik ; Mielke, Lara - \ 2018
Ambio 47 (2018)4. - ISSN 0044-7447 - p. 387 - 397.
harbour porpoise - marine litter monitoring - marine strategy framework directive - MSFD - North Sea - Phocoena phocoena - Plastic ingestion
Stomach contents of harbour porpoises (Phocoena phocoena) collected in the Netherlands between 2003 and 2013 were inspected for the presence of plastic and other man-made litter. In 654 stomach samples the frequency of occurrence of plastic litter was 7% with less than 0.5% additional presence of nonsynthetic
man-made litter. However, we show that when a dedicated standard protocol for the detection of litter is followed, a considerably higher percentage (15% of 81
harbour porpoise stomachs from the period 2010–2013) contained plastic litter. Results thus strongly depended on methods used and time period considered. Occurrence of litter in the stomach was correlated to the presence of other
non-food remains like stones, shells, bog-wood, etc., suggesting that litter was often ingested accidentally when the animals foraged close to the bottom. Most
items were small and were not considered to have had a major health impact. No evident differences in ingestion were found between sexes or age groups, with the exception that neonates contained no litter. Polyethylene and polypropylene were the most common plastic types encountered. Compared to earlier literature on the harbour porpoise and related species, our results suggest higher
levels of ingestion of litter. This is largely due to the lack of dedicated protocols to investigate marine litter ingestion in previous studies. Still, the low frequency of ingestion, and minor number and mass of litter items found in harbour
porpoises in the relatively polluted southern North Sea indicates that the species is not a strong candidate for annual monitoring of marine litter trends under the EU marine strategy framework directive. However, for longerterm
comparisons and regional differences, with proper dedicated protocols applied, the harbour porpoise has specific use in quantifying litter presence in the, for that specific objective, poorly studied benthic marine habitat.
Circulating concentrations of vitamin D in relation to pancreatic cancer risk in European populations
Duijnhoven, Fränzel J.B. van; Jenab, Mazda ; Hveem, Kristian ; Siersema, Peter D. ; Fedirko, Veronika ; Duell, Eric J. ; Kampman, Ellen ; Halfweeg, Anouk ; Kranen, Henk J. van; Ouweland, Jody M.W. van den; Weiderpass, Elisabete ; Murphy, Neil ; Langhammer, Arnulf ; Ness-Jensen, Eivind ; Olsen, Anja ; Tjønneland, Anne ; Overvad, Kim ; Cadeau, Claire ; Kvaskoff, Marina ; Boutron-Ruault, Marie Christine ; Katzke, Verena A. ; Kühn, Tilman ; Boeing, Heiner ; Trichopoulou, Antonia ; Kotanidou, Anastasia ; Kritikou, Maria ; Palli, Domenico ; Agnoli, Claudia ; Tumino, Rosario ; Panico, Salvatore ; Matullo, Giuseppe ; Peeters, Petra ; Brustad, Magritt ; Olsen, Karina Standahl ; Lasheras, Cristina ; Obón-Santacana, Mireia ; Sánchez, María José ; Dorronsoro, Miren ; Chirlaque, Maria Dolores ; Barricarte, Aurelio ; Manjer, Jonas ; Almquist, Martin ; Renström, Frida ; Ye, Weimin ; Wareham, Nick ; Khaw, Kay Tee ; Bradbury, Kathryn E. ; Freisling, Heinz ; Aune, Dagfinn ; Norat, Teresa ; Riboli, Elio ; Bueno-de-Mesquita, H.B. - \ 2018
International Journal of Cancer 142 (2018)6. - ISSN 0020-7136 - p. 1189 - 1201.
Cancer epidemiology - Nested case-control study - Pancreatic cancer - Vitamin D
Evidence from in vivo, in vitro and ecological studies are suggestive of a protective effect of vitamin D against pancreatic cancer (PC). However, this has not been confirmed by analytical epidemiological studies. We aimed to examine the association between pre-diagnostic circulating vitamin D concentrations and PC incidence in European populations. We conducted a pooled nested case-control study within the European Prospective Investigation into Cancer and Nutrition (EPIC) and the Nord-Trøndelag Health Study's second survey (HUNT2) cohorts. In total, 738 primary incident PC cases (EPIC n=626; HUNT2 n=112; median follow-up=6.9 years) were matched to 738 controls. Vitamin D [25(OH)D2 and 25(OH)D3 combined] concentrations were determined using isotope-dilution liquid chromatography-tandem mass spectrometry. Conditional logistic regression models with adjustments for body mass index and smoking habits were used to estimate incidence rate ratios (IRRs) and 95% confidence intervals (95%CI). Compared with a reference category of >50 to 75 nmol/L vitamin D, the IRRs (95% CIs) were 0.71 (0.42-1.20); 0.94 (0.72-1.22); 1.12 (0.82-1.53) and 1.26 (0.79-2.01) for clinically pre-defined categories of ≤25; >25 to 50; >75 to 100; and >100 nmol/L vitamin D, respectively (p for trend=0.09). Corresponding analyses by quintiles of season-standardized vitamin D concentrations also did not reveal associations with PC risk (p for trend=0.23). Although these findings among participants from the largest combination of European cohort studies to date show increasing effect estimates of PC risk with increasing pre-diagnostic concentrations of vitamin D, they are not statistically significant.
Sterk verband tussen arctische kabeljauw en het zee-ijs van de Arctische Oceaan
Kühn, Suse - \ 2017
Hoe groot is het probleem met plastic?
Kühn, Suse - \ 2017
We eten plastic, we ademen plastic en het regent plastic
Kühn, Suse - \ 2017
Predicting habitat affinities of plant species using commonly measured functional traits
Shipley, B. ; Belluau, M. ; Kuhn, I. ; Soudzilovskaia, N.A. ; Bahn, M. ; Penuelas, J. ; Kattge, J. ; Sack, L. ; Cavender-Bares, J. ; Ozinga, W.A. ; Blonders, B. ; Bodegom, P.M. van; Manning, P. ; Hickler, T. ; Sosinski, E. ; Pillar, V.D. ; Onipchenko, V.G. ; Poschlod, P. - \ 2017
Journal of Vegetation Science 28 (2017)5. - ISSN 1100-9233 - p. 1082 - 1095.
Questions Heinz Ellenberg classically defined “indicator” scores for species representing their typical positions along gradients of key environmental variables, and these have proven very useful for designating ecological distributions. We tested a key tenent of trait-based ecology, i.e. the ability to predict ecological preferences from species’ traits. More specifically, can we predict Ellenberg indicator scores for soil nutrients, soil moisture and irradiance from four well-studied traits: leaf area, leaf dry matter content, specific leaf area (SLA) and seed mass? Can we use such relationships to estimate Ellenberg scores for species never classified by Ellenberg? Location Global. Methods Cumulative link models were developed to predict Ellenberg nutrients, irradiance and moisture values from Ln-transformed trait values using 922, 981 and 988 species, respectively. We then independently tested these prediction equations using the trait values of 423 and 421 new species that occurred elsewere in Europe, North America and Morocco, and whose habitat affinities we could classify from independent sources as three-level ordinal ranks related to soil moisture and irradiance. The traits were SLA, leaf dry matter content, leaf area and seed mass. Results The four functional traits predicted the Ellenberg indicator scores of site fertility, light and moisture with average error rates of <2 Ellenberg ranks out of nine. We then used the trait values of 423 and 421 species, respectively, that occurred (mostly) outside of Germany but whose habitat affinities we could classify as three-level ordinal ranks related to soil moisture and irradiance. The predicted positions of the new species, given the equations derived from the Ellenberg indices, agreed well with their independent habitat classifications, although our equation for Ellenberg irrandiance levels performed poorly on the lower ranks. Conclusions These prediction equations, and their eventual extensions, could be used to provide approximate descriptions of habitat affinities of large numbers of species worldwide.
Association between plasma phospholipid saturated fatty acids and metabolic markers of lipid, hepatic, inflammation and glycaemic pathways in eight European countries: a cross-sectional analysis in the EPIC-InterAct study
Zheng, Ju-Sheng ; Sharp, Stephen J. ; Imamura, Fumiaki ; Koulman, Albert ; Schulze, Matthias B. ; Ye, Zheng ; Griffin, Jules ; Guevara, Marcela ; Huerta, José María ; Kröger, Janine ; Sluijs, Ivonne ; Agudo, Antonio ; Barricarte, Aurelio ; Boeing, Heiner ; Colorado-Yohar, Sandra ; Dow, Courtney ; Dorronsoro, Miren ; Dinesen, Pia T. ; Fagherazzi, Guy ; Franks, Paul W. ; Feskens, Edith J.M. ; Kühn, Tilman ; Katzke, Verena Andrea ; Key, Timothy J. ; Khaw, Kay-Tee ; Magistris, Maria Santucci De; Mancini, Francesca Romana ; Molina-Portillo, Elena ; Nilsson, Peter M. ; Olsen, Anja ; Overvad, Kim ; Palli, Domenico ; Quirós, Jose Ramón ; Rolandsson, Olov ; Ricceri, Fulvio ; Spijkerman, Annemieke M.W. ; Slimani, Nadia ; Tagliabue, Giovanna ; Tjonneland, Anne ; Tumino, Rosario ; Schouw, Yvonne T. Van Der; Langenberg, Claudia ; Riboli, Elio ; Forouhi, Nita G. ; Wareham, Nicholas J. - \ 2017
BMC Medicine 15 (2017)1. - ISSN 1741-7015
Background
Accumulating evidence suggests that individual circulating saturated fatty acids (SFAs) are heterogeneous in their associations with cardio-metabolic diseases, but evidence about associations of SFAs with metabolic markers of different pathogenic pathways is limited. We aimed to examine the associations between plasma phospholipid SFAs and the metabolic markers of lipid, hepatic, glycaemic and inflammation pathways.
Methods
We measured nine individual plasma phospholipid SFAs and derived three SFA groups (odd-chain: C15:0 + C17:0, even-chain: C14:0 + C16:0 + C18:0, and very-long-chain: C20:0 + C22:0 + C23:0 + C24:0) in individuals from the subcohort of the European Prospective Investigation into Cancer and Nutrition (EPIC)-InterAct case-cohort study across eight European countries. Using linear regression in 15,919 subcohort members, adjusted for potential confounders and corrected for multiple testing, we examined cross-sectional associations of SFAs with 13 metabolic markers. Multiplicative interactions of the three SFA groups with pre-specified factors, including body mass index (BMI) and alcohol consumption, were tested.
Results
Higher levels of odd-chain SFA group were associated with lower levels of major lipids (total cholesterol (TC), triglycerides, apolipoprotein A-1 (ApoA1), apolipoprotein B (ApoB)) and hepatic markers (alanine transaminase (ALT), aspartate transaminase (AST), gamma-glutamyl transferase (GGT)). Higher even-chain SFA group levels were associated with higher levels of low-density lipoprotein cholesterol (LDL-C), TC/high-density lipoprotein cholesterol (HDL-C) ratio, triglycerides, ApoB, ApoB/A1 ratio, ALT, AST, GGT and CRP, and lower levels of HDL-C and ApoA1. Very-long-chain SFA group levels showed inverse associations with triglycerides, ApoA1 and GGT, and positive associations with TC, LDL-C, TC/HDL-C, ApoB and ApoB/A1. Associations were generally stronger at higher levels of BMI or alcohol consumption.
Conclusions
Subtypes of SFAs are associated in a differential way with metabolic markers of lipid metabolism, liver function and chronic inflammation, suggesting that odd-chain SFAs are associated with lower metabolic risk and even-chain SFAs with adverse metabolic risk, whereas mixed findings were obtained for very-long-chain SFAs. The clinical and biochemical implications of these findings may vary by adiposity and alcohol intake.
Fulmar Litter EcoQO monitoring in the Netherlands : update 2016
Franeker, J.A. van; Kühn, S. ; Meijboom, A. - \ 2017
Den Helder : Wageningen Marine Research (Wageningen Marine Research report C053/17) - 52
Key components of different plant defense pathways are dispensable for powdery mildew resistance of the arabidopsis mlo2 mlo6 mlo12 triple mutant
Kuhn, Hannah ; Lorek, Justine ; Kwaaitaal, Mark ; Consonni, Chiara ; Becker, Katia ; Micali, Cristina ; Themaat, Emiel Ver Loren Van; Bednarek, Paweł ; Raaymakers, Tom M. ; Appiano, Michela ; Bai, Yuling ; Feussner, Ivo - \ 2017
Frontiers in Plant Science 8 (2017). - ISSN 1664-462X
Camalexin - Indole glucosinolates - Jasmonic acid - Microarray analysis - MLO - Plant defense - Powdery mildew - Tryptophan

Loss of function mutations of particular plant MILDEW RESISTANCE LOCUS O (MLO) genes confer durable and broad-spectrum penetration resistance against powdery mildew fungi. Here, we combined genetic, transcriptomic and metabolomic analyses to explore the defense mechanisms in the fully resistant Arabidopsis thaliana mlo2 mlo6 mlo12 triple mutant. We found that this genotype unexpectedly overcomes the requirement for indolic antimicrobials and defense-related secretion, which are critical for incomplete resistance of mlo2 single mutants. Comparative microarray-based transcriptome analysis of mlo2 mlo6 mlo12 mutants and wild type plants upon Golovinomyces orontii inoculation revealed an increased and accelerated accumulation of many defense-related transcripts. Despite the biotrophic nature of the interaction, this included the non-canonical activation of a jasmonic acid/ethylene-dependent transcriptional program. In contrast to a non-adapted powdery mildew pathogen, the adapted powdery mildew fungus is able to defeat the accumulation of defense-relevant indolic metabolites in a MLO protein-dependent manner. We suggest that a broad and fast activation of immune responses in mlo2 mlo6 mlo12 plants can compensate for the lack of single or few defense pathways. In addition, our results point to a role of Arabidopsis MLO2, MLO6, and MLO12 in enabling defense suppression during invasion by adapted powdery mildew fungi.

Consensus statement : Virus taxonomy in the age of metagenomics
Simmonds, Peter ; Adams, Mike J. ; Benk, Mária ; Breitbart, Mya ; Brister, J.R. ; Carstens, Eric B. ; Davison, Andrew J. ; Delwart, Eric ; Gorbalenya, Alexander E. ; Harrach, Balázs ; Hull, Roger ; King, Andrew M.Q. ; Koonin, Eugene V. ; Krupovic, Mart ; Kuhn, Jens H. ; Lefkowitz, Elliot J. ; Nibert, Max L. ; Orton, Richard ; Roossinck, Marilyn J. ; Sabanadzovic, Sead ; Sullivan, Matthew B. ; Suttle, Curtis A. ; Tesh, Robert B. ; Vlugt, René A. Van Der; Varsani, Arvind ; Murilo Zerbini, F. - \ 2017
Nature Reviews Microbiology 15 (2017)3. - ISSN 1740-1526 - p. 161 - 168.
The number and diversity of viral sequences that are identified in metagenomic data far exceeds that of experimentally characterized virus isolates. In a recent workshop, a panel of experts discussed the proposal that, with appropriate quality control, viruses that are known only from metagenomic data can, and should be, incorporated into the official classification scheme of the International Committee on Taxonomy of Viruses (ICTV). Although a taxonomy that is based on metagenomic sequence data alone represents a substantial departure from the traditional reliance on phenotypic properties, the development of a robust framework for sequence-based virus taxonomy is indispensable for the comprehensive characterization of the global virome. In this Consensus Statement article, we consider the rationale for why metagenomic sequence data should, and how it can, be incorporated into the ICTV taxonomy, and present proposals that have been endorsed by the Executive Committee of the ICTV.
The use of potassium hydroxide (KOH) solution as a suitable approach to isolate plastics ingested by marine organisms
Kühn, Susanne ; Werven, Bernike Van; Oyen, Albert Van; Meijboom, André ; Bravo Rebolledo, Elisa L. ; Franeker, Jan A. Van - \ 2017
Marine Pollution Bulletin 115 (2017)1-2. - ISSN 0025-326X - p. 86 - 90.
Marine debris - Plastic - Potassium hydroxide (KOH) - Extraction method
In studies of plastic ingestion by marine wildlife, visual separation of plastic particles from gastrointestinal tracts or their dietary content can be challenging. Earlier studies have used solutions to dissolve organic materials leaving synthetic particles unaffected. However, insufficient tests have been conducted to ensure that different categories of consumer products partly degraded in the environment and/or in gastrointestinal tracts were not affected. In this study 63 synthetic materials and 11 other dietary items and non-plastic marine debris were tested. Irrespective of shape or preceding environmental history, most polymers resisted potassium hydroxide (KOH) solution, with the exceptions of cellulose acetate from cigarette filters, some biodegradable plastics and a single polyethylene sheet. Exposure of hard diet components and other marine debris showed variable results. In conclusion, the results confirm that usage of KOH solutions can be a useful approach in general quantitative studies of plastic ingestion by marine wildlife.
Quantifying ingested debris in marine megafauna: a review and recommendations for standardization
Provencher, Jennifer F. ; Bond, Alexander L. ; Avery-gomm, Stephanie ; Borrelle, Stephanie B. ; Bravo Rebolledo, Elisa L. ; Hammer, Sjúrður ; Kühn, Suse ; Lavers, Jennifer L. ; Mallory, Mark L. ; Trevail, Alice ; Franeker, Jan A. van - \ 2017
Analytical Methods 9 (2017)9. - ISSN 1759-9660 - p. 1454 - 1469.
Plastic pollution has become one of the largest environmental challenges we currently face. The United Nations Environment Program (UNEP) has listed it as a critical problem, comparable to climate change, demonstrating both the scale and degree of the environmental problem. Mortalities due to entanglement
in plastic fishing nets and bags have been reported for marine mammals, turtles and seabirds, and to date over 690 marine species have been reported to ingest plastics. The body of literature documenting plastic ingestion by marine megafauna (i.e. seabirds, turtles, fish and marine mammals) has grown rapidly over the last decade, and it is expected to continue grow as researchers explore the ecological impacts of marine pollution. Unfortunately, a cohesive approach by the scientific community to quantify plastic ingestion by wildlife is lacking, which is now hindering spatial and temporal comparisons between and among species/ organisms. Here, we discuss and propose standardized techniques, approaches and metrics for reporting debris ingestion that are applicable to most large marine vertebrates. As a case study, we examine how the use of standardized methods to report ingested debris in Northern Fulmars (Fulmarus glacialis) has enabled long term and spatial trends in plastic pollution to be studied. Lastly, we outline standardized metric recommendations for reporting ingested plastics in marine megafauna, with the aim to harmonize the data
that are available to facilitate large-scale comparisons and meta-analyses of plastic accumulation in a variety of taxa. If standardized methods are adopted, future plastic ingestion research will be better able to inform questions related to the impacts of plastics across taxonomic, ecosystem and spatial scales.
Pre-diagnostic meat and fibre intakes in relation to colorectal cancer survival in the European Prospective Investigation into Cancer and Nutrition
Ward, Heather A. ; Norat, Teresa ; Overvad, Kim ; Dahm, Christina C. ; Bueno-de-Mesquita, H.B. ; Jenab, Mazda ; Fedirko, Veronika ; Duijnhoven, Fränzel J.B. Van; Skeie, Guri ; Romaguera-Bosch, Dora ; Tjonneland, Anne ; Olsen, Anja ; Carbonnel, Franck ; Affret, Aurélie ; Boutron-Ruault, Marie Christine ; Katzke, Verena ; Kühn, Tilman ; Aleksandrova, Krassimira ; Boeing, Heiner ; Trichopoulou, Antonia ; Lagiou, Pagona ; Bamia, Christina ; Palli, Domenico ; Sieri, Sabina ; Tumino, Rosario ; Naccarati, Alessio ; Mattiello, Amalia ; Peeters, Petra H. ; Weiderpass, Elisabete ; Åsli, Lene Angell ; Jakszyn, Paula ; Ramón Quirós, J. ; Sánchez, María José ; Dorronsoro, Miren ; Huerta, José María ; Barricarte, Aurelio ; Jirström, Karin ; Ericson, Ulrika ; Johansson, Ingegerd ; Gylling, Björn ; Bradbury, Kathryn E. ; Khaw, Kay Tee ; Wareham, Nicholas J. ; Stepien, Magdalena ; Freisling, Heinz ; Murphy, Neil ; Cross, Amanda J. ; Riboli, Elio - \ 2016
The British journal of nutrition 116 (2016)2. - ISSN 0007-1145 - p. 316 - 325.
Cancer survival - Cohorts - Colorectal cancers - Diets - European Prospective Investigation into Cancer and Nutrition
Improvements in colorectal cancer (CRC) detection and treatment have led to greater numbers of CRC survivors, for whom there is limited evidence on which to provide dietary guidelines to improve survival outcomes. Higher intake of red and processed meat and lower intake of fibre are associated with greater risk of developing CRC, but there is limited evidence regarding associations with survival after CRC diagnosis. Among 3789 CRC cases in the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort, pre-diagnostic consumption of red meat, processed meat, poultry and dietary fibre was examined in relation to CRC-specific mortality (n 1008) and all-cause mortality (n 1262) using multivariable Cox regression models, adjusted for CRC risk factors. Pre-diagnostic red meat, processed meat or fibre intakes (defined as quartiles and continuous grams per day) were not associated with CRC-specific or all-cause mortality among CRC survivors; however, a marginal trend across quartiles of processed meat in relation to CRC mortality was detected (P 0·053). Pre-diagnostic poultry intake was inversely associated with all-cause mortality among women (hazard ratio (HR)/20 g/d 0·92; 95 % CI 0·84, 1·00), but not among men (HR 1·00; 95 % CI 0·91, 1·09) (P for heterogeneity=0·10). Pre-diagnostic intake of red meat or fibre is not associated with CRC survival in the EPIC cohort. There is suggestive evidence of an association between poultry intake and all-cause mortality among female CRC survivors and between processed meat intake and CRC-specific mortality; however, further research using post-diagnostic dietary data is required to confirm this relationship.
Data from: The evolutionary legacy of diversification predicts ecosystem function
Yguel, Benjamin ; Jactel, H. ; Pearse, Ian S. ; Moen, Daniel ; Winter, M. de; Hortal, J. ; Helmus, Matthew R. ; Kühn, I. ; Pavoine, S. ; Purschke, Oliver ; Weiher, Evan ; Violle, C. ; Ozinga, W.A. ; Brändle, Martin ; Bartish, I. ; Prinzing, Andreas - \ 2016
community ecology - evolutionary history - lineage-through-time plots - phylogenetic diversity - productivity - species coexistence
The Rdata files are simulated phylogenies and lineage through time plot of these simulated phylogenies, used in Yguel et al. 2016 AmNat. The code to extract the LTT plot from the phylogenies is given in the Appendices of the article as well as the method used to make these simulations.The name of the Rdata file indicates which simulation the file is refering to. The Excel files contain measures of phylogenetic structure of these simulated phylogenies (Measure phylogenetic structure parameters on simulated phylogenies.xlsx) and phylogenies of the experimental communities used in the article (Measure phylogenetic structure parameters on Cadotte Zanne phylog.xlsx). The code to calculate a1, a2, a3, and to measure S1 and S2 are given in the method of the article. In all excel files, a1 a2 a3 are the polynomial parameters fitted on the LTT plots. S1 and S2 are respectively ES1 and ES2, the "elderness surface" presented in the article. MPD, MNTD, gamma, and Colless are the common phylogenetic structure measurement (see also method), and invNRI and invNTI the standardized version of MPD and MNTD. RichSpe or Sps correspond to the species richness. PlotID corresponds to the identification of the plot. Mean19962007 corresponds to the mean productivity from 1996 to 2007.
Plastic and restricted heavy metals
Oyen, Albert Van; Kühn, Suse ; Franeker, J.A. van; Ortlieb, M. ; Egelkraut-Holtus, M. - \ 2016
- 13 p.
Characteristics of plastic in stomachs of Northern Fulmars (Fulmarus glacialis)
Kühn, Suse ; Franeker, J.A. van - \ 2016
Daytime formation of nitrous acid at a coastal remote site in Cyprus indicating a common ground source of atmospheric HONO and NO
Meusel, Hannah ; Kuhn, Uwe ; Reiffs, Andreas ; Mallik, Chinmay ; Harder, Hartwig ; Martinez, Monica ; Schuladen, Jan ; Bohn, Birger ; Parchatka, Uwe ; Crowley, John N. ; Fischer, Horst ; Tomsche, Laura ; Novelli, Anna ; Hoffmann, Thorsten ; Janssen, Ruud H.H. ; Hartogensis, Oscar ; Pikridas, Michael ; Vrekoussis, Mihalis ; Bourtsoukidis, Efstratios ; Weber, Bettina ; Lelieveld, Jos ; Williams, Jonathan ; Pöschl, Ulrich ; Cheng, Yafang ; Su, Hang - \ 2016
Atmospheric Chemistry and Physics 16 (2016)22. - ISSN 1680-7316 - p. 14475 - 14493.

Characterization of daytime sources of nitrous acid (HONO) is crucial to understand atmospheric oxidation and radical cycling in the planetary boundary layer. HONO and numerous other atmospheric trace constituents were measured on the Mediterranean island of Cyprus during the CYPHEX (Cyprus PHotochemical EXperiment) campaign in summer 2014. Average volume mixing ratios of HONO were 35 pptv (±25 pptv) with a HONO/NOx ratio of 0.33, which was considerably higher than reported for most other rural and urban regions. Diel profiles of HONO showed peak values in the late morning (60 ± 28 pptv around 09:00 local time) and persistently high mixing ratios during daytime (45 ± 18 pptv), indicating that the photolytic loss of HONO is compensated by a strong daytime source. Budget analyses revealed unidentified sources producing up to 3.4 × 106 molecules cm-3 s-1 of HONO and up to 2.0 × 107 molecules cm-3 s-1 NO. Under humid conditions (relative humidity 2 Combining double low line 0.72), suggesting a common source that may be attributable to emissions from microbial communities on soil surfaces.

Fulmar Litter EcoQO monitoring in the Netherlands : update 2015
Franeker, J.A. van; Kühn, S. ; Bravo Rebolledo, E.L. - \ 2016
Den Helder : Wageningen Marine Research (Wageningen Marine Research report C091/16) - 50
fulmarus - sea birds - wastes - water pollution - marine environment - monitoring - netherlands - zeevogels - afval - waterverontreiniging - marien milieu - nederland
The evolutionary legacy of diversification predicts ecosystem function
Yguel, Benjamin ; Jactel, Hervé ; Pearse, Ian S. ; Moen, Daniel ; Winter, Marten ; Hortal, Joaquin ; Helmus, Matthew R. ; Kühn, Ingolf ; Pavoine, Sandrine ; Purschke, Oliver ; Weiher, Evan ; Violle, Cyrille ; Ozinga, Wim ; Brändle, Martin ; Bartish, Igor ; Prinzing, Andreas - \ 2016
American Naturalist 188 (2016)4. - ISSN 0003-0147 - p. 398 - 410.
Community ecology - Evolutionary history - Lineage-throughtime plots - Phylogenetic diversity - Productivity - Species coexistence

Theory suggests that the structure of evolutionary history represented in a species community may affect its functioning, but phylogenetic diversity metrics do not allow for the identification of major differences in this structure. Here we propose a new metric, ELDERness (for Evolutionary Legacy of DivERsity) to estimate evolutionary branching patterns within communities by fitting a polynomial function to lineage-through-time (LTT) plots. We illustrate how real and simulated community branching patterns can be more correctly described by ELDERness and can successfully predict ecosystem functioning. In particular, the evolutionary history of branching patterns can be encapsulated by the parameters of third-order polynomial functions and further measured through only two parameters, the “ELDERness surfaces.” These parameters captured variation in productivity of a grassland community better than existing phylogenetic diversity or diversification metrics and independent of species richness or presence of nitrogen fixers. Specifically, communitieswith small ELDERness surfaces (constant accumulation of lineages through time in LTT plots) were more productive, consistent with increased productivity resulting from complementary lineages combined with niche filling within lineages. Overall, while existing phylogenetic diversity metrics remain useful in many contexts, we suggest that our ELDERness approach better enables testing hypotheses that relate complex patterns of macroevolutionary history represented in local communities to ecosystem functioning.

Comparison of phenotyping methods for resistance to stem rot and aggregated sheath spot in rice
Rosas, Juan E. ; Martínez, Sebastián ; Bonnecarrère, Victoria ; Pérez de Vida, Fernando ; Blanco, Pedro ; Malosetti Zunin, Marcos ; Jannink, Jean Luc ; Gutiérrez, Lucía - \ 2016
Crop Science 56 (2016)4. - ISSN 0011-183X - p. 1619 - 1627.

Stem and sheath diseases caused by Sclerotium oryzae Cattaneo (SCL) and Rhizoctonia oryzae-sativae Sawada Mordue (ROS) can severely reduce rice (Oryza sativa L.) yield and grain quality. Genetic resistance is the best strategy to control them. Phenotypic selection for resistance is hampered due to a heterogeneous distribution of the inoculum in the soil that generates high environmental variability and decreases genetic gain. To have higher selection accuracy it is necessary to develop phenotyping methods with high repeatability and discriminative power. Comparison of greenhouse methods have been reported for Rhizoctonia solani Kühn, a more invasive pathogen than SCL and ROS, and for SCL, but no such comparisons are reported for ROS. Our study compares five inoculation methods for SCL and ROS to identify the more discriminant and repeatable method and to apply it for high-throughput phenotyping of hundreds of rice lines. A method that uses an agar disc with growing mycelium attached to the base of stems was found to have the best balance between discrimination among genotypes and variability among replicates of the same genotype for both pathogens. This method was used in five greenhouse experiments for phenotyping resistance to SCL and ROS in a population of 641 rice advanced breeding lines. Heritabilities of resistance ranged from 0.36 to 0.71 in these experiments. These findings have a direct application in screening for resistance of rice to SCL and ROS, and in high-throughput phenotyping for mapping loci associated to disease resistance.

Developments in physical weed control in Northwest Europe
Riemens, M.M. - \ 2016
In: Proceedings 27th German Conference on Weed Biology and Weed Control. - Julius Kühn-Institut - p. 24 - 26.
In North West Europe there is an increasing need for advanced weed control methods. This paper gives an overview of the developments in physical weed control methods. Current innovations in interrow weeding focus on systems that take over the steering function of the driver in order to make them more precise and reduce crop lasses. The latest developments in intrarow weeding techniques involve technologies that automatically detect and classify crop and weed plants and use this information to guide a weeding device. Several commercially available examples are presented.
Taxonomy of the order Mononegavirales : update 2016
Afonso, Claudio L. ; Amarasinghe, Gaya K. ; Bányai, Krisztián ; Bào, Yīmíng ; Basler, Christopher F. ; Bavari, Sina ; Bejerman, Nicolás ; Blasdell, Kim R. ; Briand, François Xavier ; Briese, Thomas ; Bukreyev, Alexander ; Calisher, Charles H. ; Chandran, Kartik ; Chéng, Jiāsēn ; Clawson, Anna N. ; Collins, Peter L. ; Dietzgen, Ralf G. ; Dolnik, Olga ; Domier, Leslie L. ; Dürrwald, Ralf ; Dye, John M. ; Easton, Andrew J. ; Ebihara, Hideki ; Farkas, Szilvia L. ; Freitas-Astúa, Juliana ; Formenty, Pierre ; Fouchier, Ron A.M. ; Fù, Yànpíng ; Ghedin, Elodie ; Goodin, Michael M. ; Hewson, Roger ; Horie, Masayuki ; Hyndman, Timothy H. ; Jiāng, Dàohóng ; Kitajima, Elliot W. ; Kobinger, Gary P. ; Kondo, Hideki ; Kurath, Gael ; Lamb, Robert A. ; Lenardon, Sergio ; Leroy, Eric M. ; Li, Ci Xiu ; Lin, Xian Dan ; Liú, Lìjiāng ; Longdon, Ben ; Marton, Szilvia ; Maisner, Andrea ; Mühlberger, Elke ; Netesov, Sergey V. ; Nowotny, Norbert ; Patterson, Jean L. ; Payne, Susan L. ; Paweska, Janusz T. ; Randall, Rick E. ; Rima, Bertus K. ; Rota, Paul ; Rubbenstroth, Dennis ; Schwemmle, Martin ; Shi, Mang ; Smither, Sophie J. ; Stenglein, Mark D. ; Stone, David M. ; Takada, Ayato ; Terregino, Calogero ; Tesh, Robert B. ; Tian, Jun Hua ; Tomonaga, Keizo ; Tordo, Noël ; Towner, Jonathan S. ; Vasilakis, Nikos ; Verbeek, Martin ; Volchkov, Viktor E. ; Wahl-Jensen, Victoria ; Walsh, John A. ; Walker, Peter J. ; Wang, David ; Wang, Lin Fa ; Wetzel, Thierry ; Whitfield, Anna E. ; Xiè, Jiǎtāo ; Yuen, Kwok Yung ; Zhang, Yong Zhen ; Kuhn, Jens H. - \ 2016
Archives of Virology 161 (2016)8. - ISSN 0304-8608 - p. 2351 - 2360.

In 2016, the order Mononegavirales was emended through the addition of two new families (Mymonaviridae and Sunviridae), the elevation of the paramyxoviral subfamily Pneumovirinae to family status (Pneumoviridae), the addition of five free-floating genera (Anphevirus, Arlivirus, Chengtivirus, Crustavirus, and Wastrivirus), and several other changes at the genus and species levels. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).

Genome-wide association mapping and genomic prediction elucidate the genetic architecture of morphological traits in arabidopsis
Kooke, Rik ; Kruijer, Willem ; Bours, Ralph ; Becker, Frank ; Kuhn, A. ; Geest, Henri van de; Buntjer, Jaap ; Doeswijk, Timo ; Guerra, José ; Bouwmeester, Harro ; Vreugdenhil, Dick ; Keurentjes, Joost J.B. - \ 2016
Plant Physiology 170 (2016)4. - ISSN 0032-0889 - p. 2187 - 2203.

Quantitative traits in plants are controlled by a large number of genes and their interaction with the environment. To disentangle the genetic architecture of such traits, natural variation within species can be explored by studying genotype-phenotype relationships. Genome-wide association studies that link phenotypes to thousands of single nucleotide polymorphism markers are nowadays common practice for such analyses. In many cases, however, the identified individual loci cannot fully explain the heritability estimates, suggesting missing heritability. We analyzed 349 Arabidopsis accessions and found extensive variation and high heritabilities for different morphological traits. The number of significant genome-wide associations was, however, very low. The application of genomic prediction models that take into account the effects of all individual loci may greatly enhance the elucidation of the genetic architecture of quantitative traits in plants. Here, genomic prediction models revealed different genetic architectures for the morphological traits. Integrating genomic prediction and association mapping enabled the assignment of many plausible candidate genes explaining the observed variation. These genes were analyzed for functional and sequence diversity, and good indications that natural allelic variation in many of these genes contributes to phenotypic variation were obtained. For ACS11, an ethylene biosynthesis gene, haplotype differences explaining variation in the ratio of petiole and leaf length could be identified.

The FAIR Guiding Principles for scientific data management and stewardship : Comment
Wilkinson, Mark D. ; Dumontier, Michel ; Aalbersberg, Ijsbrand Jan ; Appleton, Gabrielle ; Axton, Myles ; Baak, Arie ; Blomberg, Niklas ; Boiten, Jan Willem ; Silva Santos, Luiz Bonino Da; Bourne, Philip E. ; Bouwman, Jildau ; Brookes, Anthony J. ; Clark, Tim ; Crosas, Mercè ; Dillo, Ingrid ; Dumon, Olivier ; Edmunds, Scott ; Evelo, Chris T. ; Finkers, Richard ; Gonzalez-Beltran, Alejandra ; Gray, Alasdair J.G. ; Groth, Paul ; Goble, Carole ; Grethe, Jeffrey S. ; Heringa, Jaap ; Hoen, Peter A.C. 't; Hooft, Rob ; Kuhn, Tobias ; Kok, Ruben ; Kok, Joost ; Lusher, Scott J. ; Martone, Maryann E. ; Mons, Albert ; Packer, Abel L. ; Persson, Bengt ; Rocca-Serra, Philippe ; Roos, Marco ; Schaik, Rene van; Sansone, Susanna Assunta ; Schultes, Erik ; Sengstag, Thierry ; Slater, Ted ; Strawn, George ; Swertz, Morris A. ; Thompson, Mark ; Lei, Johan van der; Mulligen, Erik van; Velterop, Jan ; Waagmeester, Andra ; Wittenburg, Peter ; Wolstencroft, Katherine ; Zhao, Jun ; Mons, Barend - \ 2016
Scientific Data 3 (2016). - ISSN 2052-4463

There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders-representing academia, industry, funding agencies, and scholarly publishers-have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.

Avr4 promotes Cf-4 receptor-like protein association with the BAK1/SERK3 receptor-like kinase to initiate receptor endocytosis and plant immunity
Postma, Jelle ; Liebrand, Thomas ; Bi, Guozhi ; Evrard, Alexandre ; Bye, Ruby R. ; Mbengue, Malick ; Kuhn, Hannah ; Joosten, Matthieu H.A.J. ; Robatzek, Silke - \ 2016
New Phytologist (2016). - ISSN 0028-646X - p. 642 - 672.
Avr4 effector - BAK1/SERK3 - Cf-4 receptor-like protein (RLP) - Immunity - Receptor endocytosis - Subcellular trafficking - SUPPRESSOR OF BIR1 (SOBIR1)

The first layer of plant immunity is activated by cell surface receptor-like kinases (RLKs) and proteins (RLPs) that detect infectious pathogens. Constitutive interaction with the SUPPRESSOR OF BIR1 (SOBIR1) RLK contributes to RLP stability and kinase activity. As RLK activation requires transphosphorylation with a second associated RLK, it remains elusive how RLPs initiate downstream signaling. We employed live-cell imaging, gene silencing and coimmunoprecipitation to investigate the requirement of associated kinases for functioning and ligand-induced subcellular trafficking of Cf RLPs that mediate immunity of tomato against Cladosporium fulvum. Our research shows that after elicitation with matching effector ligands Avr4 and Avr9, BRI1-ASSOCIATED KINASE 1/SOMATIC EMBRYOGENESIS RECEPTOR KINASE 3 (BAK1/SERK3) associates with Cf-4 and Cf-9. BAK1/SERK3 is required for the effector-triggered hypersensitive response and resistance of tomato against C. fulvum. Furthermore, Cf-4 interacts with SOBIR1 at the plasma membrane and is recruited to late endosomes upon Avr4 trigger, also depending on BAK1/SERK3. These observations indicate that RLP-mediated resistance and endocytosis require ligand-induced recruitment of BAK1/SERK3, reminiscent of BAK1/SERK3 interaction and subcellular fate of the FLAGELLIN SENSING 2 (FLS2) RLK. This reveals that diverse classes of cell surface immune receptors share common requirements for initiation of resistance and endocytosis.

Simulating the viability of water institutions under volatile rainfall conditions - The case of the Lake Naivasha Basin
Kuhn, A. ; Britz, W. ; Kyalo Willy, D. ; Oel, P.R. van - \ 2016
Environmental Modelling & Software 75 (2016). - ISSN 1364-8152 - p. 373 - 387.
This study views the Lake Naivasha Basin in Kenya's Rift Valley as a hydro-economic system with slowly emerging basin-wide water management institutions. Possible institutions face two interlinked challenges. Firstly, large scale horticultural activities as a core economic activity in the basin require substantial and regular amounts of irrigation water, abstracted from the lake and its aquifer. The lake level and thus irrigation water availability reveal a falling trend over the last two decades, which calls for institutions aimed at restricting further expansion in water use. Secondly, the region is characterized by volatile weather conditions where periods of average and above average rainfall have alternated with prolonged droughts for centuries. That leads to highly volatile water inflows into the lake. The two challenges combined thus call for water management institutions that support sustainable water use in both the short and the long run. This study therefore investigates the effect of water institutions already existing or proposed by local stakeholder organizations on preserving target lake levels against a background of highly volatile water availability which negatively affects the economic viability of institutions. To take the absence of functioning basin-wide coordination mechanisms for water allocation into account, we employ the solution format of Multiple Optimization Problems with Equilibrium Constraints (MOPEC) in our integrated hydro-economic model. Stochastic scenario simulations with the model reveal that compliance to water regulations and thus the viability of water institutions in the Naivasha Basin would require very high penalties which are not likely to be accepted by users.
Elevated levels of plastic ingestion in a high-Arctic seabird
Trevail, A.M. ; Gabrielsen, G.W. ; Kuhn, S. ; Franeker, J.A. van - \ 2015
- 1 p.
Plastic pollution is of worldwide concern, however increases in international commercial activity in the Arctic are occurring without knowledge of the existing threat posted to the local marine environment by plastic litter. Here, we quantify plastic ingestion by northern fulmars, Fulmarus glacialis, from Svalbard, at the gateway to future shipping routes in the high Arctic. Plastic ingestion by Svalbard fulmars does not follow the established decreasing trend away from human marine impact. Of 40 sampled individuals, 35 {87.5%) had plastic in their stomachs, averaging at 0.08g or 15.3 pieces per individual. Critically, plastic ingestion levels on Svalbard exceed the ecological quality objective defined by OSPAR for European seas. Furthermore we present analytica! results that
suggest a tissue chemica! burden that results from plastic ingestion. Such chemicals may cause disruption to the endocrine and immune system of birds, and thus the potential for population-scale effects are evident. This highlights an urgent need for mitigation of plastic pollution in the Arctic as well as international regulation of future commercial activity. The picture attached shows an example of the stomach plastic content from one fulmar on Svalbard. Scale bar is lcm.
Measuring the canopy development of fruit trees for direct spray volume adjustment
Michielsen, J.G.P. ; Zande, J.C. van de; Wenneker, M. - \ 2015
In: Proceedings of the SuproFruit 2015 13th Workshop on Spray Applications in fruit growing, 15.-18. July 2015 Lindau/Lake Constance, Germany. - Julius Kühn-Institut (Julius-Kühn-Archiv ) - p. 78 - 79.
Improving spray deposition and reducing spray drift in orchard spraying by multiple row sprayers
Zande, J.C. van de; Wenneker, M. ; Michielsen, J.G.P. ; Stallinga, H. - \ 2015
In: Suprofruit 2015 - 13th Workshop on Spray Application in Fruit Growing, Lindau, Germany. - Julius Kühn-Institut (Julius-Kühn-Archiv ) - p. 85 - 86.
Spray drift and resident risk in orchard spraying: reference and spray drift reducing techniques
Zande, J.C. van de; Wenneker, M. ; Michielsen, J.G.P. ; Stallinga, H. - \ 2015
In: Suprofruit 2015 - 13th Workshop on Spray Application in Fruit Growing, Lindau, Germany. - Julius Kühn-Institut (Julius-Kühn-Archiv ) - p. 40 - 41.
Non-alcoholic fatty liver disease (NAFLD) is associated with a distinct fecal microbiome signature–a case control study
Schulz, C. ; Lerch, M. ; Lahti, L.M. ; Kühn, J. ; Schütte, K. ; Weiss, F. ; Völzke, H. ; Baumeister, S. ; Fuentes Enriquez de Salamanca, S. ; Fluhr, G. ; Vos, W.M. de; Mayerle, J. - \ 2015
Background: Nonalcoholic fatty liver disease is now being recognized as the most common liver disorder worldwide. The majority of NAFLD patients are characterized by mere liver steatosis but up to one third progresses to non-alcoholic steatohepatitis (NASH). The underlying pathophysiology is poorly understood but changes in the gut microbiome have been suggested to be involved. Design: Using a case control design we recruited 84 subjects with liver steatosis and 83 controls from the population-based Study of Health in Pommerania. Subjects with diabetes mellitus, BMI > 25 kg/m2, immoderate alcohol intake or gallstone disease were excluded. Liver fat content was quantitated by confounder corrected chemical shift encoded MRI sequence at 1.5T. Cases with steatosis were defined as subjects with a mean liver fat content of 24.9% and controls with 2.2%. NAFLD and NASH were distinguished by using the FIB-4 score (Cut-off 1.3). Phylogenetic profiling of fecal samples was performed using the Human intestinal tract Chip (HITChip). For phenotypic correlation of the gut microbiome signature up to 224 host variables, including diet, were available and 38 reached significance. Results: By study design the extent of steatosis on liver MRI differed significantly between cases and controls (p <10 – 6). Hierarchical clustering showed a clustering tendency. Random Forrest analysis revealed 69%± 14% 95CI classification accuracy on 130 genus-level taxa. Diet did not affect the classification accuracy. Reduced Shannon diversity (p = 0.046) and richness (p = 0.007) in cases were detected. PCA cluster analysis identified 4 out of 130 taxa discriminating between cases and controls (Prevotella oralis and P. melaninogenica, Sutterella wadsworthia, Uncultured Clostridiales) all of those with bimodal distribution. NASH cases showed a significantly increased abundancy of Gram-positive taxa as well as several Bacteroides spp. that could be used as a classifier. Conclusion: In the absence of metabolic syndrome NAFLD is associated with a distinct gut microbiome signature, which is unaffected by diet. Decreased abundancy of taxa, previously defined as tipping elements, points to a pathophysiological relevance. Progression to NASH is correlated with additional distinct changes in the microbiome.
A statistical framework to model the meeting-in-the-middle principle using metabolic data: application to hepatocellular carcinoma in the EPIC study
Assi, N. ; Fages, A. ; Vineis, P. ; Chadeau-Hyam, M. ; Stepien, M. ; Duarte-Salles, T. ; Byrnes, G. ; Boumaza, H. ; Knüppel, S. ; Kühn, T. ; Palli, D. ; Boshuizen, H.C. - \ 2015
Mutagenesis 30 (2015)6. - ISSN 0267-8357 - p. 743 - 753.
Metabolomics is a potentially powerful tool for identification of biomarkers associated with lifestyle exposures and risk of various diseases. This is the rationale of the ‘meeting-in-the-middle’ concept, for which an analytical framework was developed in this study. In a nested case–control study on hepatocellular carcinoma (HCC) within the European Prospective Investigation into Cancer and nutrition (EPIC), serum 1H nuclear magnetic resonance (NMR) spectra (800 MHz) were acquired for 114 cases and 222 matched controls. Through partial least square (PLS) analysis, 21 lifestyle variables (the ‘predictors’, including information on diet, anthropometry and clinical characteristics) were linked to a set of 285 metabolic variables (the ‘responses’). The three resulting scores were related to HCC risk by means of conditional logistic regressions. The first PLS factor was not associated with HCC risk. The second PLS metabolomic factor was positively associated with tyrosine and glucose, and was related to a significantly increased HCC risk with OR = 1.11 (95% CI: 1.02, 1.22, P = 0.02) for a 1SD change in the responses score, and a similar association was found for the corresponding lifestyle component of the factor. The third PLS lifestyle factor was associated with lifetime alcohol consumption, hepatitis and smoking, and had negative loadings on vegetables intake. Its metabolomic counterpart displayed positive loadings on ethanol, glutamate and phenylalanine. These factors were positively and statistically significantly associated with HCC risk, with 1.37 (1.05, 1.79, P = 0.02) and 1.22 (1.04, 1.44, P = 0.01), respectively. Evidence of mediation was found in both the second and third PLS factors, where the metabolomic signals mediated the relation between the lifestyle component and HCC outcome. This study devised a way to bridge lifestyle variables to HCC risk through NMR metabolomics data. This implementation of the ‘meeting-in-the-middle’ approach finds natural applications in settings characterised by high-dimensional data, increasingly frequent in the omics generation.
Ems-Dollard primary production research: Full data report
Brinkman, A.G. ; Riegman, R. ; Jacobs, P. ; Kuhn, S. ; Meijboom, A. - \ 2015
IJmuiden : IMARES Wageningen UR (Report / IMARES Wageningen UR C160/14) - 297
kaderrichtlijn water - richtlijnen (directives) - waterbeleid - waterkwaliteit - modder - troebelheid - ecologie - eems - eems-dollard - water framework directive - directives - water policy - water quality - mud - turbidity - ecology - river ems
The Water Framework Directive (WFD) requires EU member states to achieve good ecological and chemical status of all designated water bodies (rivers, lakes, transitional and coastal waters) by 2015. Therefore Rijkswaterstaat Waterdienst has initiated the project ‘Research mud dynamics Ems Estuary’ . The aim of this project, carried out by Deltares and IMARES, is to (1) improve our knowledge on the mud dynamics in the Ems Estuary, (2) to identify the reasons for the increase in turbidity and (3) to quantify measures to improve the ecological status of the estuary.
Traffic Control for Plant Immunity and Receptor Kinases
Kuhn, H. ; Beck, M. ; Khaled, S. Ben; Bourdais, G. ; Mbengue, M. ; Kopischke, M. ; Postma, J. ; Spallek, T. ; Joosten, M. ; Robatzek, S. - \ 2015
In: Book of Abstracts Keystone Symposia on Molecular and Cellular Biology. - - p. 32 - 32.
In our attempts to understand the full nature of the interactions that occur between a potential pathogen and its host, we are elucidating the transport processes that are engaged by the plant’s immune system. Our main research focus has been how transport processes regulate defence activation. Combining genetic, molecular and biochemical approaches with cell biology we have comprehensively dissected the subcellular transport pathways dependent upon microbial stimulation. Our studies have revealed that clathrin- and ESCRT-mediated endosomal trafficking is required for plant defence and is important for stomatal immunity. To identify mechanistic and functional elements of transport-regulated immunity, we focus on how the pattern recognition receptors (PRRs), the primary sensors of the plant’s immune system, are transported through the cell. PRRs are receptor kinases and receptor-like proteins that must be presented at the plasma membrane to recognize potentially infectious pathogens and trigger immunity. We found that PRRs representing different protein families are endocytosed in a ligand-induced and BAK1/SERK3 co-receptor dependent manner. Together with the finding that activated PRRs (FLS2, EFR, PEPR1) traffic via a common endosomal pathway, this suggests a role of endocytosis in the regulation of receptor abundance at the plasma membrane triggered by ligand perception. Furthermore, endocytosis of activated FLS2 is mediated by clathrin and involves sorting by the ESCRT machinery. This indicates a link between transport processes involved in defence and PRR trafficking. Understanding these mechanisms is providing novel insights into the regulation of plant immunity. This work is supported by the Gatsby Charitable Foundation and a grant by the European Research Council (ERC).
Microplastic in a macro filter feeder: humpback whale Megaptera novaeangliae
Besseling, E. ; Foekema, E.M. ; Franeker, J.A. van; Leopold, M.F. ; Bravo Rebolledo, E. ; Kühn, S. ; Mielke, L. ; Heberle-Bors, E. ; Ijzer, J. ; Kamminga, P. ; Koelmans, A.A. - \ 2015
Marine Pollution Bulletin 95 (2015)1. - ISSN 0025-326X - p. 248 - 252.
marine-environment - plastic ingestion - balaenoptera-physalus - mediterranean sea - north-sea - debris - identification - pollutants - particles - additives
Marine filter feeders are exposed to microplastic because of their selection of small particles as food source. Baleen whales feed by filtering small particles from large water volumes. Macroplastic was found in baleen whales before. This study is the first to show the presence of microplastic in intestines of a baleen whale (Megaptera novaeangliae). Contents of its gastrointestinal tract were sieved, dissolved in 10% potassium hydroxide and washed. From the remaining dried material, potential synthetic polymer particles were selected based on density and appearance, and analysed by Fourier transform infrared (FTIR) spectroscopy. Several polymer types (polyethylene, polypropylene, polyvinylchloride, polyethylene terephthalate, nylon) were found, in varying particle shapes: sheets, fragments and threads with a size of 1 mm to 17 cm. This diversity in polymer types and particle shapes, can be interpreted as a representation of the varying characteristics of marine plastic and the unselective way of ingestion by M. novaeangliae.
Deleterious effects of litter on marine life
Kuhn, S. ; Bravo Rebolledo, E. ; Franeker, J.A. van - \ 2015
In: Marine Anthropogenic Litter / Bergmann, M., Gutow, L., Klages, M., Springer International Publishing - ISBN 9783319165103 - p. 75 - 116.
In this review we report new findings concerning interaction between marine debris and wildlife. Deleterious effects and consequences of entanglement, consumption and smothering are highlighted and discussed. The number of species known to have been affected by either entanglement or ingestion of plastic debris has doubled since 1997, from 267 to 557 species among all groups of wildlife. For marine turtles the number of affected species increased from 86 to 100 % (now 7 of 7 species), for marine mammals from 43 to 66 % (now 81 of 123 species) and for seabirds from 44 to 50 % of species (now 203 of 406 species). Strong increases in records were also listed for fish and invertebrates, groups that were previously not considered in detail. In future records of interactions between marine debris and wildlife we recommend to focus on standardized data on frequency of occurrence and quantities of debris ingested. In combination with dedicated impact studies in the wild or experiments, this will allow more detailed assessments of the deleterious effects of marine debris on individuals and populations.
Elevated levels of ingested plastic in a high Arctic seabird, the northern fulmar (Fulmarus glacialis)
Trevail, A.M. ; Gabrielsen, G.W. ; Kühn, S. ; Franeker, J.A. van - \ 2015
Polar Biology 38 (2015)7. - ISSN 0722-4060 - p. 975 - 981.
atlantic-ocean - sea - debris - biodiversity - pacific - chicks
Plastic pollution is of worldwide concern; however, increases in international commercial activity in the Arctic are occurring without the knowledge of the existing threat posed to the local marine environment by plastic litter. Here, we quantify plastic ingestion by northern fulmars, Fulmarus glacialis, from Svalbard, at the gateway to future shipping routes in the high Arctic. Plastic ingestion by Svalbard fulmars does not follow the established decreasing trend away from human marine impact. Of 40 sampled individuals, 35 fulmars (87.5 %) had plastic in their stomachs, averaging at 0.08 g or 15.3 pieces per individual. Plastic ingestion levels on Svalbard exceed the ecological quality objective defined by OSPAR for European seas. This highlights an urgent need for mitigation of plastic pollution in the Arctic as well as international regulation of future commercial activity.
Plastic Ingestion by Northern Fulmars, Fulmarus glacialis, in Svalbard and Iceland, and Relationships between Plastic Ingestion and Contaminant Uptake
Trevail, A.M. ; Gabrielsen, G.W. ; Kuhn, S. ; Bock, A. ; Franeker, J.A. van - \ 2014
Tromsoe : Norsk Polarinstitutt (Brief report series / Norwegian Polar Institute 029) - 24
BIOCOMES (EU-Projekt 612713) entwickelt neue biologische Pflanzenschutzmittel für IPM in Land- und Forstwirtschaft (BIOCOMES (EU project 612713) develops new biological control products for IPM in agriculture and forestry)
Köhl, J. ; Zingg, D. ; Benuzzi, M. ; Ehlers, R.U. ; Perdrix, V. ; Eiben, U. ; Rosemeyer, V. ; Wikström, M. ; Azzaro, A. ; Glazer, I. ; O'Tuama, P. ; Tomanovic, Z. ; Tamm, L. ; Hauschild, R. ; Antonakou, M. ; Skrzecz, I. ; Cal, A. De; Teixidó, N. ; Jehle, J. ; Griffin, C. ; Beliën, T. ; Birnstingl, B. ; Berg, G. ; Simões, N. ; Causin, R. ; Muñoz, D. ; Eibl, R. - \ 2014
In: Poster Biologischer Pflanzenschutz. 59. Deutsche Pflanzenschutztagung "Forschen – Wissen – Pflanzen schützen: Ernährung sichern!" 23. bis 26. September 2014, Freiburg. - Germany : Julius Kühn-Institut - p. 458 - 459.
Anwendung des Antagonisten Cladosporium cladosporioides H39 zur biologischen Bekämpfung von Apfelschorf
Köhl, J. ; Scheer, C. ; Holb, I.J. ; Masny, S. ; Molhoek, W.M.L. - \ 2014
In: 59. Deutsche Pflanzenschutztagung "Forschen – Wissen – Pflanzen schützen: Ernährung sichern!" 23. bis 26. September 2014, Freiburg. - Julius Kühn-Institut - p. 328 - 328.
Der durch Venturia inaequalis verursachte Apfelschorf führt zu hohen Ertragsausfällen im Apfelanbau. Die Krankheit wird in der Regel durch intensive Fungizidapplikationen bekämpft. Für ein Selektionsprogramm von Antagonisten wurden Apfelblätter mit Schorfsymptomen aus Obstanlagen gesammelt und pilzliche Isolate aus sporulierenden Kolonien des Erregers gewonnen (Köhl et al., 2009). Das Isolat Cladosporium cladosporioides H39 zeigte in Versuchen auf Apfelsämlingen ein hohes Potenzial die Sporulation des Erregers zu reduzieren sowie weitere günstige Eigenschaften für die Entwicklung eines biologischen Bekämpfungsmittels (Köhl et al., 2011). Insgesamt wurden mit dem Antagonisten Cladosporium cladosporioides H39 in 2012 und 2013 acht Feldversuche in Obstanlagen in Eperjeske (Ungarn), Dabrowice (Polen) und Bavendorf (Deutschland) durchgeführt. Behandlungen erfolgten während der Primärsaison oder der Sommersaison. In zusätzlichen Versuchen in Randwijk (Niederlande) wurde der Effekt unterschiedlicher Positionierung der Behandlung vor oder nach Infektionsmomenten gemessen. Die Gesamtergebnisse der Versuchsreihe zeigen, dass der Apfelschorfbefall auf Blättern und auf Früchten durch wiederholte Applikationen des Antagonisten reduziert werden kann. Diese Ergebnisse wurden sowohl in Versuchen in Obstanlagen mit integrierten als auch mit biologischen Anbauverfahren erzielt. Die Bekämpfungserfolge lagen teilweise in Bereichen, die mit chemischen Verfahren erzielt wurden. Die Verminderung des Blattbefalls lag zwischen 42 und 98%, die des Fruchtbefalls zwischen 41 und 94 %. Der Antagonist war auch wirksam, wenn er einen oder sogar mehrere Tage nach einem Infektionsmoment appliziert wurde. Cladosporium cladosporioides H39 kann nun in komplexeren Spritzfolgen getestet werden, die auf die Bekämpfung des Gesamtkomplexes von Krankheitserregern und Schädlingen im Apfelanbau abzielen.
Importing food into the EU
Kühn, M.C. ; Montanari, F. - \ 2014
In: EU Food Law Handbook / van der Meulen, B.M.J., Wageningen : Wageningen Academic Publishers - ISBN 9789086862467 - p. 443 - 470.
Particles decorated by an ionizable thermoresponsive polymer brush in water: Experiments and self-consistent field modeling
Alves, S.P.C. ; Pinheiro, J.P. ; Farinha, J.P.S. ; Leermakers, F.A.M. - \ 2014
The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical 118 (2014). - ISSN 1520-6106 - p. 3192 - 3206.
star-branched polyelectrolytes - n-isopropylacrylamide - nanoparticles - shell - conformations - microgels
We have synthesized anionic multistimuli responsive core–shell polymer nanoparticles with low size dispersity composed of glassy poly(methyl methacrylate) (PMMA) cores of ca. 40 nm radius and poly(N-isopropylacrylamide) (PNIPAM) anionic brush-like shells with methacrylic acid comonomers. Using dynamic light scattering, we observed a volume phase transition upon an increase in temperature and this response was pH and ionic strength dependent. Already at room temperature we observed a pronounced polyelectrolyte effect, that is, a shift of the apparent pKa extracted from the degree of dissociation of the acids as a function of the pH. The multiresponsive behavior of the hydrophobic polyelectrolyte brush has been modeled using the Scheutjens–Fleer self-consistent field (SF-SCF) approach. Using a phenomenological relation between the Flory–Huggins ¿ parameter and the temperature, we confront the predicted change in the brush height with the observed change of the hydrodynamic radius and degree of dissociation and obtain estimates for the average chain lengths (number of Kuhn segments) of the corona chains, the grafting density and charge density distributions. The theory reveals a rich internal structure of the hydrophobic polyelectrolyte brush, especially near the collapse transition, where we find a microphase segregated structure. Considering this complexity, it is fair to state that the theoretical predictions follow the experimental data semiquantitatively, and it is attractive to attribute the observed disparity between theory and experiments to the unknown polydispersity of the chains, the unknown distribution of the charges, or other experimental complications. More likely, however, the deviations point to significant problems of the mean field theory, which focuses solely on the radial distributions and ignores the possibility of the formation of lateral (local) inhomogeneities in partially collapsed polyelectrolyte brushes. We argue that the PNIPAM brush at room temperature is already behaving nonideally.
Fulmar Litter EcoQO monitoring in the Netherlands - Update 2012 and 2013
Franeker, J.A. van; Kuhn, S. ; Bravo Rebolledo, E. ; Meijboom, A. - \ 2014
Den Burg : IMARES (Report / IMARES Wageningen UR C122/14) - 56
fulmarus - zeevogels - afval - waterverontreiniging - nadelige gevolgen - microplastics - mariene gebieden - monitoring - sea birds - wastes - water pollution - adverse effects - marine areas
Fulmars are purely offshore foragers that ingest all sorts of litter from the sea surface and do not regurgitate poorly degradable diet components like plastics. Initial size of ingested debris is usually in the range of millimetres to centimeters, but may be considerably larger for flexible items as for instance threadlike or sheetlike materials. Items must gradually wear down in the muscular stomach to a size small enough for passage to the intestines. During this process, plastics accumulate in the stomach to a level that integrates litter levels encountered in their foraging area for a period of probably up to a few weeks. The Dutch monitoring approach using beached fulmars was developed for international implementation by OSPAR.
Diagnosing the unknown - advancing the taxonomy of aquatic invertebrate viruses
Bateman, K.S. ; Stentiford, G.D. ; Oers, M.M. van - \ 2014
In: Proceeding of the 2014 IC on Invertebrate Pathology and Microbial Control & 47th Annual Meeting of the Society for Invertebrate Pathology. - Julius Kühn-Institut - p. 127 - 127.
The essential baculovirus protein VP1054 is a hijacked cellular PURa, a nucleic-acid-binding protein specific for GGN repeats
Marek, M. ; Romier, C. ; Galibert, L. ; Merten, O.W. ; Oers, M.M. van - \ 2014
In: Proceedings of the 47th annual meeting of the society for invertebrate pathology and int. congress on invertebrate pathology and microbial control, August 3 - 7, 2014, Mainz, Germany. - Julius Kühn-Institut - p. 143 - 143.
Mechanism underlying virus-induced hyperactive behavior: Substrate identification of the baculovirus protein tyrosine phosphatase, August 3 - 7, 2014, Mainz, Germany
Houte, S. van; Embregts, C.W.E. ; Andel, E. van; Ros, V.I.D. ; Vlak, J.M. ; Oers, M.M. van - \ 2014
In: Proceedings of the IC on Invertebrate Pathology and Microbial Control & 47th Annual Meeting of the Society for Invertebrate Pathology. - Julius Kühn-Institut - p. 143 - 143.
Mechanisms of tree-top disease induced by the specialist baculovirus SeMNPV
Han, Y. ; Houte, S. van; Ros, V.I.D. ; Vlak, J.M. ; Oers, M.M. van - \ 2014
In: Proceedings of the IC on Invertebrate Pathology and Microbial Control & 47th Annual Meeting of the Society for Invertebrate Pathology. - Julius Kühn-Institut - p. 142 - 142.
Construction and Characterization of a Recombinant Invertebrate Iridovirus
Ozgen, A. ; Muratoglu, H. ; Demirbag, Z. ; Vlak, J.M. ; Oers, M.M. van; Nalcacioglu, R. - \ 2014
In: Book of abstracts of the 47th Annual Meeting of the Society for Invertebrate Pathology and International Congress on Invertebrate Pathology and Microbial Control. - Julius Kühn-Institut - p. 132 - 132.
Induction and suppression of tick cell antiviral RNAi responses by tick-borne flaviviruses
Schnettler, E. ; Tykalova, H. ; Watson, M. ; Sharma, M. ; Sterken, M.G. ; Obbard, D.J. ; Lewis, S.H. ; McFarlane, M. ; Bell-Sakyi, L. ; Barry, G. ; Weisheit, S. ; Best, S.M. ; Kuhn, R.J. ; Pijlman, G.P. ; Chase-Topping, M.E. ; Gould, E.A. ; Grubhoffer, L. ; Fazakerley, J.K. ; Kohl, A. - \ 2014
Nucleic acids research 42 (2014)14. - ISSN 0305-1048 - p. 9436 - 9446.
forest-virus replicon - interferon antagonist - arbovirus infection - immunity - replication - drosophila - identification - alphavirus - mosquitos - origin
Arboviruses are transmitted by distantly related arthropod vectors such as mosquitoes (class Insecta) and ticks (class Arachnida). RNA interference (RNAi) is the major antiviral mechanism in arthropods against arboviruses. Unlike in mosquitoes, tick antiviral RNAi is not understood, although this information is important to compare arbovirus/host interactions in different classes of arbovirus vectos. Using an Ixodes scapularis-derived cell line, key Argonaute proteins involved in RNAi and the response against tick-borne Langat virus (Flaviviridae) replication were identified and phylogenetic relationships characterized. Analysis of small RNAs in infected cells showed the production of virus-derived small interfering RNAs (viRNAs), which are key molecules of the antiviral RNAi response. Importantly, viRNAs were longer (22 nucleotides) than those from other arbovirus vectors and mapped at highest frequency to the termini of the viral genome, as opposed to mosquito-borne flaviviruses. Moreover, tick-borne flaviviruses expressed subgenomic flavivirus RNAs that interfere with tick RNAi. Our results characterize the antiviral RNAi response in tick cells including phylogenetic analysis of genes encoding antiviral proteins, and viral interference with this pathway. This shows important differences in antiviral RNAi between the two major classes of arbovirus vectors, and our data broadens our understanding of arthropod antiviral RNAi.
The recent occurrence of humpback whales in the southern North Sea: a range expansion
Leopold, M.F. ; Bemmelen, R.S.A. van; Bravo Rebolledo, E. ; Franeker, J.A. van; Hesse, E. ; Kuhn, S. ; Mielke, L. ; Strietman, W.J. ; Camphuysen, K. - \ 2014
Comparative measurements with seven rainfall simulators on uniform bare fallow land
Iserloh, T. ; Ries, J.B. ; Cerda, A. ; Echeverria, M.T. ; Fister, W. ; Geissler, C. ; Kuhn, N.J. ; Leon, F.J. ; Peters, P. ; Schindewolf, M. ; Schmidt, J. ; Scholten, T. ; Seeger, K.M. - \ 2013
Zeitschrift für Geomorphologie 57 (2013)1. - ISSN 0372-8854 - p. 11 - 26.
portable wind - soil-erosion
To assess the influence of rainfall simulator type and plot dimensions on runoff and erosion, seven small portable rainfall simulators from Freiberg, Tubingen, Trier (all Germany), Valencia, Zaragoza (both Spain), Basel (Switzerland) and Wageningen (the Netherlands) were compared on a prepared bare fallow field. The experiments were carried out during an international rainfall simulator workshop, organized at Trier University (Germany) from 30th of June to 1st of July 2011. The tested rainfall simulators differ in design, rainfall intensities, rain spectra, etc. and represent most of the devices which have been used over the last decade in Europe. The plots for the different rainfall simulators were selected as similar as possible concerning soil physical and chemical properties, aspect and inclination and were chosen to be placed side by side in horizontal direction. Test procedure was standardized in order to examine the influence of the rainfall simulator and plot dimension only. The results show a clear and consistent relationship in runoff, erosion and infiltration behaviour of the different used rainfall simulators. With all the devices total soil loss is measurable, but different plot sizes, intensities and kinetic energies of the simulated rainfall caused differences in soil loss and runoff quantities per unit of area. Regarding course characteristics over runs, similarities could be observed especially in runoff behaviour. The rainfall simulators (= 1 m(2)), rill-erosion will be also reflected. Therefore it can be concluded that up to a certain plot size, the results of the different simulators are comparable and depend in their magnitude on the properties of the applied rainfall. The increase in process complexity with increasing plot size shows, that the scale of the simulation is one of the most important parameters to be taken into account when comparing values of erosion and runoff.
Plasma 25(OH)vitamin D and the risk of breast cancer in the european prospective investigation into cancer and nutrition (EPIC): A nested case-control study
Kühn, T. ; Kaaks, R. ; Becker, S. ; Eomois, P.P. ; Clavel-Chapelon, F. ; Kvaskoff, M. ; Dossus, L. ; Duijnhoven, F.J.B. van - \ 2013
International Journal of Cancer 133 (2013)7. - ISSN 0020-7136 - p. 1689 - 1700.
d-binding protein - circulating vitamin-d - french e3n cohort - postmenopausal women - nurses health - serum-levels - association - prevention - calcium - time
Experimental evidence suggests that vitamin D might play a role in the development of breast cancer. Although the results of case–control studies indicate that circulating 25-hydroxyvitamin D [25(OH)D] is inversely associated with the risk of breast cancer, the results of prospective studies are inconsistent. A case–control study embedded in the European Prospective Investigation into Cancer and Nutrition (EPIC) was carried out comprising 1,391 incident breast cancer cases and 1,391 controls. Multivariable conditional logistic regression models did not reveal a significant overall association between season-standardized 25(OH)D levels and the risk of breast cancer (ORQ4–Q1 [95% CI]: 1.07 [0.85–1.36], ptrend = 0.67). Moreover, 25(OH)D levels were not related to the risks of estrogen receptor positive tumors (ORQ4–Q1 [95% CI]: 0.97 [0.67–1.38], ptrend = 0.90) and estrogen receptor negative tumors (ORQ4–Q1 [95% CI]: 0.97 [0.66–1.42], ptrend = 0.98). In hormone replacement therapy (HRT) users, 25(OH)D was significantly inversely associated with incident breast cancer (ORlog2 [95% CI]: 0.62 [0.42–0.90], p = 0.01), whereas no significant association was found in HRT nonusers (ORlog2 [95% CI]: 1.14 [0.80–1.62], p = 0.48). Further, a nonsignificant inverse association was found in women with body mass indices (BMI) <25 kg/m2 (ORlog2 [95% CI]: 0.83 [0.67–1.03], p = 0.09), as opposed to a borderline significant positive association in women with BMI = 25 kg/m2 (ORlog2 [95% CI]: 1.30 [1.0–1.69], p = 0.05). Overall, prediagnostic levels of circulating 25(OH)D were not related to the risk of breast cancer in the EPIC study. This result is in line with findings in the majority of prospective studies and does not support a role of vitamin D in the development of breast cancer
Temporal variations in natural attenuation of chlorinated aliphatic hydrocarbons in eutrophic river sediments impacted by a contaminated groundwater plume
Hamonts, K. ; Kuhn, T. ; Vos, J. ; Maesen, M. ; Kalka, H. ; Smidt, H. ; Springael, D. ; Meckenstock, R.U. ; Dejonghe, W. - \ 2012
Water Research 46 (2012)6. - ISSN 0043-1354 - p. 1873 - 1888.
dehalococcoides sp strain - isotope fractionation analysis - vinyl-chloride reductase - bearing soil minerals - surface-water - degradation - aquifer - biodegradation - dechlorination - identification
Chlorinated aliphatic hydrocarbons (CAHs) often discharge into rivers as contaminated groundwater base flow. Biotrans formation, sorption and dilution of CAHs in the impacted river sediments have been reported to reduce discharge, but the effect of temporal variations in environmental conditions on the occurrence and extent of those processes in river sediments is largely unknown. We monitored the reduction of CAH discharge into the Zenne River during a 21-month period. Despite a relatively stable influx of CAHs from the groundwater, the total reduction in CAH discharge from 120 to 20 cm depth in the river sediments, on average 74 +/- 21%, showed moderate to large temporal variations, depending on the riverbed location. High organic carbon and anaerobic conditions in the river sediments allowed microbial reductive dechlorination of both chlorinated ethenes and chlorinated ethanes. delta C-13 values of the CAHs showed that this biotransformation was remarkably stable over time, despite fluctuating pore water temperatures. Daughter products of the CAHs, however, were not detected in stoichiometric amounts and suggested the co-occurrence of a physical process reducing the concentrations of CAHs in the riverbed. This process was the main process causing temporal variations in natural attenuation of the CAHs and was most likely dilution by surface water-mixing. However, higher spatial resolution monitoring of flow transients in the riverbed is required to prove dilution contributions due to dynamic surface water-groundwater flow exchanges. delta C-13 values and a site-specific isotope enrichment factor for reductive dechlorination of the main groundwater pollutant vinyl chloride (VC) allowed assessment of changes over time in the extent of both biotransformation and dilution of VC for different scenarios in which those processes either occurred consecutively or simultaneously between 120 and 20 cm depth in the riverbed. The extent of reductive dechlorination of VC ranged from 27 to 89% and differed spatially but was remarkably stable over time, whereas the extent of VC reduction by dilution ranged from 6 to 94%, showed large temporal variations, and was often the main process contributing to the reduction of VC discharge into the river.
Impact of the Manaus urban plume on trace gas mixing ratios near the surface in the Amazon Basin: Implications for the NO-NO2-O-3 photostationary state and peroxy radical levels
Trebs, I. ; Mayol-Bracero, O.L. ; Pauliquevis, T. ; Kuhn, U. ; Sander, R. ; Ganzeveld, L.N. ; Meixner, F.X. ; Kesselmeier, J. ; Artaxo, P. ; Andreae, M.O. - \ 2012
Journal of Geophysical Research: Atmospheres 117 (2012). - ISSN 2169-897X - 16 p.
volatile organic-compounds - photochemical steady-state - reactive nitrogen-oxides - tropical rain-forest - chemistry box model - boundary-layer - atmospheric chemistry - dry season - airborne measurements - hydroxyl radicals
We measured the mixing ratios of NO, NO2, O-3, and volatile organic carbon as well as the aerosol light-scattering coefficient on a boat platform cruising on rivers downwind of the city of Manaus (Amazonas State, Brazil) in July 2001 (Large-Scale Biosphere-Atmosphere Experiment in Amazonia-Cooperative LBA Airborne Regional Experiment-2001). The dispersion and impact of the Manaus plume was investigated by a combined analysis of ground-based (boat platform) and airborne trace gas and aerosol measurements as well as by meteorological measurements complemented by dispersion calculations (Hybrid Single-Particle Lagrangian Integrated Trajectory model). For the cases with the least anthropogenic influence (including a location in a so far unexplored region similar to 150 km west of Manaus on the Rio Manacapuru), the aerosol scattering coefficient, sigma(s), was below 11 Mm(-1), NOx mixing ratios remained below 0.6 ppb, daytime O-3 mixing ratios were mostly below 20 ppb and maximal isoprene mixing ratios were about 3 ppb in the afternoon. The photostationary state (PSS) was not established for these cases, as indicated by values of the Leighton ratio, Phi, well above unity. Due to the influence of river breeze systems and other thermally driven mesoscale circulations, a change of the synoptic wind direction from east-northeast to south-southeast in the afternoon often caused a substantial increase of ss and trace gas mixing ratios (about threefold for sigma(s), fivefold for NOx, and twofold for O-3), which was associated with the arrival of the Manaus pollution plume at the boat location. The ratio F reached unity within its uncertainty range at NOx mixing ratios of about 3 ppb, indicating "steady-state" conditions in cases when radiation variations, dry deposition, emissions, and reactions mostly involving peroxy radicals (XO2) played a minor role. The median midday/afternoon XO2 mixing ratios estimated using the PSS method range from 90 to 120 parts per trillion (ppt) for the remote cases (sigma(s) <11 Mm(-1) and NOx <0.6 ppb), while for the polluted cases our estimates are 15 to 60 ppt. These values are within the range of XO2 estimated by an atmospheric chemistry box model (Chemistry As A Box model Application-Module Efficiently Calculating the Chemistry of the Atmosphere (CAABA/MECCA)-3.0).
Friese Front Alk / Zeekoet: Oktober / November 2012, cruise rapport
Leopold, M.F. ; Bemmelen, R.S.A. van; Kuhn, S. ; Lagerveld, S. - \ 2012
Den Burg : IMARES (Rapport / IMARES Wageningen UR C150/12) - 27
vogels - monitoring - natura 2000 - inventarisaties - waddenzee - birds - inventories - wadden sea
Het Friese Front, zoals omschreven en geografisch aangeduid in het rapport van Lindeboom et al. (2005) zal binnenkort worden aangewezen als Natura 2000 gebied. Vanwege de bijzondere status van het gebied is het belangrijk om te weten welke aantallen Zeekoeten het gebied bezoeken. De aantallen moeten daarom worden gevolgd, maar een monitoringsprogramma dat de benodigde gegevens kan aanleveren is er nog niet. Daarbij is het niet uitgesloten dat ook de aantallen Alken die het Friese Front bezoeken van internationale betekenis zijn. Alken arriveren later in de herfst dan Zeekoeten, die al vanaf juli in grote aantallen op het Friese Front arriveren
Plastic ingestion by the northern fulmar (Fulmarus glacialis) in Iceland
Kühn, S. ; Franeker, J.A. van - \ 2012
Marine Pollution Bulletin 64 (2012)6. - ISSN 0025-326X - p. 1252 - 1254.
marine-environment - debris
In 2011, northern fulmars (Fulmarus glacialis) from Iceland were used to test the hypothesis that plastic debris decreases at northern latitudes in the Atlantic when moving away from major human centres of coastal and marine activities. Stomach analyses of Icelandic fulmars confirm that plastic pollution levels in the North Atlantic tend to decrease towards higher latitudes. Levels of pollution thus appear to link to regions of intense human coastal and marine activities, suggesting substantial current inputs in those areas
Editorial: Experiments in Earth surface process research
Seeger, K.M. ; Quinton, J. ; Kuhn, N.J. - \ 2012
Catena 91 (2012)april. - ISSN 0341-8162 - p. 1 - 3.
agricultural soil-erosion - carbon-cycle
Within this Editorial, we put the articles included in the Special Issue into a historical and actual context of experimental research in Earth system sciences.
Depletion profiles for dilute solutions of linear chains, stars and H-branched molecules by self-consistent field calculations and Monte Carlo simulations
Preisler, Z. ; Kosovan, P. ; Kuldova, J. ; Uhlik, F. ; Limpouchova, Z. ; Prochazka, K. ; Leermakers, F.A.M. - \ 2011
Soft Matter 7 (2011)21. - ISSN 1744-683X - p. 10258 - 10265.
polymer-chains - adsorption
We have performed self-consistent field (SCF) calculations and Monte Carlo (MC) simulations to analyse the depletion profiles for isolated linear, star-like and H-shaped polymers in good solvent using lattice approximations in both methods. In the SCF approach the intra-molecular excluded-volume effects are accounted for using an approach that resembles Flory's method that leads to the Flory size of the chains. This gives a major improvement over the classical tanh profile, and becomes much closer to the MC results, provided that a Kuhn length of 1.5 is implemented.
TRY - a global database of plant traits
Kattge, J. ; Diaz, S. ; Lavorel, S. ; Prentices, I.C. ; Leadley, P. ; Bönisch, G. ; Garnier, E. ; Westobys, M. ; Reich, P.B. ; Wrights, I.J. ; Cornelissen, C. ; Violle, C. ; Harisson, S.P. ; Bodegom, P.M. van; Reichstein, M. ; Enquist, B.J. ; Soudzilovskaia, N.A. ; Ackerly, D.D. ; Anand, M. ; Atkin, O. ; Bahn, M. ; Baker, T.R. ; Baldochi, D. ; Bekker, R. ; Blanco, C.C. ; Blonders, B. ; Bond, W.J. ; Bradstock, R. ; Bunker, D.E. ; Casanoves, F. ; Cavender-Bares, J. ; Chambers, J.Q. ; Chapin III, F.S. ; Chave, J. ; Coomes, D. ; Cornwell, W.K. ; Craine, J.M. ; Dobrin, B.H. ; Duarte, L. ; Durka, W. ; Elser, J. ; Esser, G. ; Estiarte, M. ; Fagan, W.F. ; Fang, J. ; Fernadez-Mendez, F. ; Fidelis, A. ; Finegan, B. ; Flores, O. ; Ford, H. ; Frank, D. ; Freschet, T. ; Fyllas, N.M. ; Gallagher, R.V. ; Green, W.A. ; Gutierrez, A.G. ; Hickler, T. ; Higgins, S.I. ; Hodgson, J.G. ; Jalili, A. ; Jansen, S. ; Joly, C.A. ; Kerkhoff, A.J. ; Kirkup, D. ; Kitajima, K. ; Kleyer, M. ; Klotz, S. ; Knops, J.M.H. ; Kramer, K. ; Kühn, I. ; Kurokawa, H. ; Laughlin, D. ; Lee, T.D. ; Leishman, M. ; Lens, F. ; Lewis, S.L. ; Lloyd, J. ; Llusia, J. ; Louault, F. ; Ma, S. ; Mahecha, M.D. ; Manning, P. ; Massad, T. ; Medlyn, B.E. ; Messier, J. ; Moles, A.T. ; Müller, S.C. ; Nadrowski, K. ; Naeem, S. ; Niinemets, Ü. ; Nöllert, S. ; Nüske, A. ; Ogaya, R. ; Oleksyn, J. ; Onipchenko, V.G. ; Onoda, Y. ; Ordonez Barragan, J.C. ; Ozinga, W.A. ; Poorter, L. - \ 2011
Global Change Biology 17 (2011)9. - ISSN 1354-1013 - p. 2905 - 2935.
relative growth-rate - tropical rain-forest - hawaiian metrosideros-polymorpha - litter decomposition rates - leaf economics spectrum - old-field succession - sub-arctic flora - functional traits - wide-range - terrestrial biosphere
Plant traits – the morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs – determine how primary producers respond to environmental factors, affect other trophic levels, influence ecosystem processes and services and provide a link from species richness to ecosystem functional diversity. Trait data thus represent the raw material for a wide range of research from evolutionary biology, community and functional ecology to biogeography. Here we present the global database initiative named TRY, which has united a wide range of the plant trait research community worldwide and gained an unprecedented buy-in of trait data: so far 93 trait databases have been contributed. The data repository currently contains almost three million trait entries for 69 000 out of the world's 300 000 plant species, with a focus on 52 groups of traits characterizing the vegetative and regeneration stages of the plant life cycle, including growth, dispersal, establishment and persistence. A first data analysis shows that most plant traits are approximately log-normally distributed, with widely differing ranges of variation across traits. Most trait variation is between species (interspecific), but significant intraspecific variation is also documented, up to 40% of the overall variation. Plant functional types (PFTs), as commonly used in vegetation models, capture a substantial fraction of the observed variation – but for several traits most variation occurs within PFTs, up to 75% of the overall variation. In the context of vegetation models these traits would better be represented by state variables rather than fixed parameter values. The improved availability of plant trait data in the unified global database is expected to support a paradigm shift from species to trait-based ecology, offer new opportunities for synthetic plant trait research and enable a more realistic and empirically grounded representation of terrestrial vegetation in Earth system models.
Bayesian image restoration models for combining expert knowledge on recording activity with species distribution data
Bierman, S.M. ; Butler, A. ; Marion, G. ; Kuhn, I. - \ 2010
Ecography 33 (2010)3. - ISSN 0906-7590 - p. 451 - 460.
pseudo-absence data - biodiversity databases - plant diversity - habitat - abundance - patterns - wildlife - europe - rates - bias
Biological atlases are, for many species, the only source of information on their distribution over large geographical areas, and are widely used to inform models of the environmental distribution of species. Such data are not collected using standardized survey techniques, however, and spatial variations in coverage (the relative extent or completeness of records) may lead to variations in the probability that the species will be recorded at locations where it is present (the "recording probability"). If spatial patterns in recording probabilities are correlated with key environmental variables, then biased estimates of the relationships between environmental variables and species distributions may be obtained. We outline a general statistical framework for modelling the environmental distribution of species using, known as Bayesian Image Restoration (BIR). BIR can be used in combination with any species distribution model, but in addition allows us to account for spatial heterogeneity in recording probabilities by utilizing expert knowledge on spatial patterns in coverage. We illustrate the methodology by applying it to maps of the recorded distribution of two plant species in Germany, taken from the German atlas of vascular plants. We find that estimated spatial patterns in recording probabilities for both species are correlated with key environmental variables. Consequently, different relationships between the probability of presence of a species and environmental variables were obtained when the species distribution models were parameterised within a BIR framework. Care must be taken in the application of BIR, since the resulting inferences can depend strongly upon the modelling assumptions that are adopted. Nevertheless, we conclude that BIR has the potential to make better use of uncertain information on species distributions than conventional methods, and can be used to formally investigate the robustness of inferences on the environmental distribution of species to assumptions concerning spatial patterns in recording probabilities
Impact of Manaus City on the Amazon Green Ocean atmosphere: Ozone production, precursor sensitivity and aerosol load
Kuhn, U. ; Ganzeveld, L.N. - \ 2010
Atmospheric Chemistry and Physics 10 (2010). - ISSN 1680-7316 - p. 9251 - 9282.
secondary organic aerosol - cloud condensation nuclei - biomass-burning emissions - power-plant plumes - tropical south-atlantic - trace gas exchanges - rain-forest - tropospheric ozone - dry season - physical-properties
As a contribution to the Large-Scale Biosphere-Atmosphere Experiment in Amazonia – Cooperative LBA Airborne Regional Experiment (LBA-CLAIRE-2001) field campaign in the heart of the Amazon Basin, we analyzed the temporal and spatial dynamics of the urban plume of Manaus City during the wet-to-dry season transition period in July 2001. During the flights, we performed vertical stacks of crosswind transects in the urban outflow downwind of Manaus City, measuring a comprehensive set of trace constituents including O3, NO, NO2, CO, VOC, CO2, and H2O. Aerosol loads were characterized by concentrations of total aerosol number (CN) and cloud condensation nuclei (CCN), and by light scattering properties. Measurements over pristine rainforest areas during the campaign showed low levels of pollution from biomass burning or industrial emissions, representative of wet season background conditions. The urban plume of Manaus City was found to be joined by plumes from power plants south of the city, all showing evidence of very strong photochemical ozone formation. One episode is discussed in detail, where a threefold increase in ozone mixing ratios within the atmospheric boundary layer occurred within a 100 km travel distance downwind of Manaus. Observation-based estimates of the ozone production rates in the plume reached 15 ppb h-1. Within the plume core, aerosol concentrations were strongly enhanced, with ¿CN/¿CO ratios about one order of magnitude higher than observed in Amazon biomass burning plumes. ¿CN/¿CO ratios tended to decrease with increasing transport time, indicative of a significant reduction in particle number by coagulation, and without substantial new particle nucleation occurring within the time/space observed. While in the background atmosphere a large fraction of the total particle number served as CCN (about 60–80% at 0.6% supersaturation), the CCN/CN ratios within the plume indicated that only a small fraction (16±12%) of the plume particles were CCN. The fresh plume aerosols showed relatively weak light scattering efficiency. The CO-normalized CCN concentrations and light scattering coefficients increased with plume age in most cases, suggesting particle growth by condensation of soluble organic or inorganic species. We used a Single Column Chemistry and Transport Model (SCM) to infer the urban pollution emission fluxes of Manaus City, implying observed mixing ratios of CO, NOx and VOC. The model can reproduce the temporal/spatial distribution of ozone enhancements in the Manaus plume, both with and without accounting for the distinct (high NOx) contribution by the power plants; this way examining the sensitivity of ozone production to changes in the emission rates of NOx. The VOC reactivity in the Manaus region was dominated by a high burden of biogenic isoprene from the background rainforest atmosphere, and therefore NOx control is assumed to be the most effective ozone abatement strategy. Both observations and models show that the agglomeration of NOx emission sources, like power plants, in a well-arranged area can decrease the ozone production efficiency in the near field of the urban populated cores. But on the other hand remote areas downwind of the city then bear the brunt, being exposed to increased ozone production and N-deposition. The simulated maximum stomatal ozone uptake fluxes were 4 nmol m-2 s-1 close to Manaus, and decreased only to about 2 nmol m-2 s-1 within a travel distance >1500 km downwind from Manaus, clearly exceeding the critical threshold level for broadleaf trees. Likewise, the simulated N deposition close to Manaus was ~70 kg N ha-1 a-1 decreasing only to about 30 kg N ha-1 a-1 after three days of simulation.
Evaluation of biofumigation crops for the control of Pratylenchus penetrans and Verticilium dahliae
Korthals, G.W. ; Visser, J.H.M. ; Thoden, T.C. ; Molendijk, L.P.G. - \ 2010
Berichte aus dem Julius Kühn-Institut (2010)155. - ISSN 1866-590X - p. 54 - 59.
Improvement and monitoring of soil health
Thoden, T.C. ; Molendijk, L.P.G. ; Visser, J.H.M. ; Korthals, G.W. - \ 2010
Berichte aus dem Julius Kühn-Institut 155 (2010). - ISSN 1866-590X - p. 48 - 53.
Concurrent bio-electricity and biomass production in three Plant-Microbial Fuel Cells using Spartina anglica, Arundinella anomala and Arundo donax
Helder, M. ; Strik, D.P.B.T.B. ; Hamelers, H.V.M. ; Kuhn, A.J. ; Blok, C. ; Buisman, C.J.N. - \ 2010
Bioresource Technology 101 (2010)10. - ISSN 0960-8524 - p. 3541 - 3547.
giant reed - growth - dynamics - stress
In a Plant Microbial Fuel Cell (P-MFC) three plants were tested for concurrent biomass and bio-electricity production and maximization of power output. Spartina anglica and Arundinella anomala concurrently produced biomass and bio-electricity for six months consecutively. Average power production of the P-MFC with S. anglica during 13 weeks was 16% of the theoretical maximum power and 8% during 7 weeks for A. anomala. The P-MFC with Arundo donax, did not produce electricity with a stable output, due to break down of the system. The highest obtained power density in a P-MFC was 222 mW/m2 membrane surface area with S. anglica, over twice as high as the highest reported power density in a P-MFC. High biomass yields were obtained in all P-MFC’s, with a high root:shoot ratio, probably caused nutrient availability and anaerobia in the soil. Power output maximization via adjusting load on the system lead to unstable performance of the P-MFC
How species traits and affinity to urban land use control large-scale species frequency
Knapp, S. ; Kuhn, I. ; Bakker, J.P. ; Kleyer, M. ; Klotz, S. ; Ozinga, W.A. ; Poschlod, P. ; Thompson, K. ; Thuiller, W. ; Romermann, C. - \ 2009
Diversity and Distributions 15 (2009)3. - ISSN 1366-9516 - p. 533 - 546.
life-history traits - indicator values - spatial autocorrelation - plant ecology - models - patterns - europe - areas - flora - biodiversity
Although urban areas only occupy c. 2.8% of the earth's land surface, urbanization threatens biodiversity as areas of high human population density often coincide with high biodiversity. Therefore, nature conservation should concentrate on both remote areas and densely populated regions. Protecting rare plant species in rural and urban areas can contribute to the protection of biodiversity. We therefore need to understand why species are rare. Studies on causes of rarity often concentrate on either plant traits or extrinsic threats (such as habitat fragmentation or nitrogen enrichment). However, there are only a few studies that combine traits and extrinsic threats, although such analyses might clarify causes of rarity. We assessed how the affinity of vascular plant species to urban land use ('urbanity') interacts with plant traits in determining species frequency. Germany, resolution c. 12 km x 11 km. Species with a low frequency may be rare because they occur in rare habitats or because of other reasons, although their habitat is frequent. Therefore, we calculated the frequency of species corrected for habitat frequency, i.e. relative species frequency. We explained relative species frequency by the interactions of species traits and species affinity to urban land use using generalized linear models. Simultaneous autoregressive error models controlled for phylogenetic relationships of species. Relative species frequency depends on species affinity to urban land use, independent of the different interactions between traits and urbanity used as predictors. The higher the urbanity the higher is species frequency. Urbanity interacts with species preferences towards temperature and soil acidity. Moreover, dispersal, nitrogen preferences and origin explain relative species frequency, amongst others. Many rare species, especially those preferring cool or acidic habitats might already have disappeared from urban areas. Analyses that combine species traits and environmental effects can explain the causes of rarity and help to derive better conservation strategies.
A new estimator for trade costs and its small sample
Jansson, T.G. ; Heckelei, T. - \ 2009
Economic Modelling 26 (2009)2. - ISSN 0264-9993 - p. 489 - 498.
spatial equilibrium
This paper discusses the estimation of parameters of a traditional transportation model, as it is typically present in so-called Takayama¿Judge type spatial price equilibrium models. In contrast to previously used estimation methods, observations of regional prices as well as of trade costs are used in a direct estimation of the first order conditions. The proposed method uses bi-level programming techniques to minimize a weighted least squares criterion under the restriction that the estimated parameters satisfy the Kuhn¿Tucker conditions for an optimal solution of the transport model. A penalty function and a smooth reformulation are used to iteratively approximate the complementary slackness conditions. Monte-Carlo simulations are used to trace out some properties of the estimator and compare it with a traditional calibration method. The analysis shows that the proposed technique estimates prices as well as trade costs more precisely than the traditional calibration method. It is suggested to apply the same method to a range of linear and quadratic models.
Urbanization causes shifts in species' trait state frequencies
Knapp, S. ; Kühn, I. ; Wittig, R. ; Ozinga, W.A. ; Poschlod, P. ; Klotz, S. - \ 2008
Preslia 80 (2008). - ISSN 0032-7786 - p. 375 - 388.
plant functional types - compositional data - leaf traits - urban - dispersal - biodiversity - habitats - richness - patterns - flora
Urbanization is one of the most extreme forms of land transformation. It is supposed to change the frequencies of species trait states in species assemblages.We hypothesize that the flora of urban and rural areas differs in the frequency of trait states and ask which traits enable a plant to cope with the urban environment. We tested our hypothesis in Germany, which was divided into grid-cells of ca 130 km2. We distinguished urbanized (with more than 33% urban land use; n = 59), agricultural (with more than 50% agricultural land use; n = 1365) and semi-natural (with more than 50% forest and semi-natural land use; n = 312) grid-cells and calculated the proportions of plant species per trait state in each grid-cell. Multiple linear regressions explained the log-transformed ratio of one proportion to another with land use (urban, agricultural, semi-natural) and the environmental parameters (climate, topography, soils and geology). Additionally, linear mixed effect models accounted for the effects of land use and biogeography and differences in sample size of the three grid-cell types. Urbanized and rural areas showed clear differences in the proportion of trait states. Urbanized grid-cells had e.g., higher proportions of wind-pollinated plants, plants with scleromorphic leaves or plants dispersed by animals, and lower proportions of insect-pollinated plants, plants with hygromorphic leaves or plants dispersed by wind than other grid-cells. Our study shows that shifts in land use can change the trait state composition of plant assemblages. Far-reach
The LEDA Traitbase: a database of life-history traits of the Northwest European flora
Kleyer, M. ; Bekker, R.M. ; Knevel, I.C. ; Bakker, J.P. ; Thompson, K. ; Sonnenschein, M. ; Poschlod, P. ; Groenendael, J.M. van; Klimes, L. ; Klimesova, J. ; Klotz, S. ; Rusch, G.M. ; Hermy, M. ; Adriaens, D. ; Boedeltje, G. ; Bossuyt, B. ; Dannemann, A. ; Endels, P. ; Götzenberger, L. ; Hodgson, J.G. ; Jackel, A.K. ; Kühn, L. ; Kunzmann, D. ; Ozinga, W.A. ; Römermann, C. ; Stadler, M. ; Schlegelmilch, J. ; Steendam, H.J. ; Tackenberg, O. ; Wilmann, B. ; Cornelissen, J.H.C. ; Eriksson, O. ; Garnier, E. ; Peco, B. - \ 2008
Journal of Ecology 96 (2008). - ISSN 0022-0477 - p. 1266 - 1274.
plant functional traits - trade-off - communities - dispersal - mechanisms - consequences - regeneration - biodiversity - divergence - attributes
An international group of scientists has built an open internet data base of life-history traits of the Northwest European flora (the LEDA-Traitbase) that can be used as a data source for fundamental research on plant biodiversity and coexistence, macro-ecological patterns and plant functional responses. The species-trait matrix comprises referenced information under the control of an editorial board, for ca. 3000 species of the Northwest European flora, combining existing information and additional measurements. The data base currently contains data on 26 plant traits that describe three key features of plant dynamics: persistence, regeneration and dispersal. The LEDA-Traitbase is freely available at http://www.leda-traitbase.org. We present the structure of the data base and an overview of the trait information available. Synthesis. The LEDA Traitbase is useful for large-scale analyses of functional responses of communities to environmental change, effects of community trait composition on ecosystem properties and patterns of rarity and invasiveness, as well as linkages between traits as expressions of fundamental trade-offs in plants.
Plant functional group composition and large-scale species richness in European agricultural landscapes
Liira, J. ; Schmidt, T. ; Aavik, T. ; Arens, P.F.P. ; Augenstein, I. ; Bailey, D. ; Billeter, R. ; Bukacek, R. ; Burel, F. ; Blust, G. de; Cock, R. de; Dirksen, J. ; Edwards, P.J. ; Hamersky, R. ; Herzog, F. ; Klotz, S. ; Kuhn, I. ; Coeur, D. Le; Miklova, P. ; Roubalova, M. ; Schweiger, O. ; Smulders, M.J.M. ; Wingerden, W.K.R.E. van; Bugter, R.J.F. ; Zobel, M. - \ 2008
Journal of Vegetation Science 19 (2008)1. - ISSN 1100-9233 - p. 3 - 14.
habitat fragmentation - boundary vegetation - grassland plants - biodiversity - traits - conservation - connectivity - diversity - land - area
Question: Which are the plant functional groups responding most clearly to agricultural disturbances? Which are the relative roles of habitat availability, landscape configuration and agricultural land use intensity in affecting the functional composition and diversity of vascular plants in agricultural landscapes? Location: 25 agricultural landscape areas in seven European countries. Methods: We examined the plant species richness and abundance in 4 km x 4 km landscape study sites. The plant functional group classification was derived from the BIOLFLOR database. Factorial decomposition of functional groups was applied. Results: Natural habitat availability and low land use intensity supported the abundance and richness of perennials, sedges, pteridophytes and high nature quality indicator species. The abundance of clonal species, C and S strategists was also correlated with habitat area. An increasing density of field edges explained a decrease in richness of high nature quality species and an increase in richness of annual graminoids. Intensive agriculture enhanced the richness of annuals and low nature quality species. Conclusions: Habitat patch availability and habitat quality are the main drivers of functional group composition and plant species richness in European agricultural landscapes. Linear elements do not compensate for the loss of habitats, as they mostly support disturbance tolerant generalist species. In order to conserve vascular plant species diversity in agricultural landscapes, the protection and enlargement of existing patches of ( semi-) natural habitats appears to be more effective than relying on the rescue effect of linear elements. This should be done in combination with appropriate agricultural management techniques to limit the effect of agrochemicals to the fields.
Optimization of simulated systems: OptQuest and alternatives
Kleijnen, J.P.C. ; Wan, J. - \ 2007
Simulation Modelling Practice and Theory 15 (2007)3. - ISSN 1569-190X - p. 354 - 362.
This article illustrates the general problem known as `simulation optimization¿ through an (s, S) inventory management system. In this system, the goal function to be minimized is the expected value of specific inventory costs. Moreover, specific constraints must be satisfied for some random simulation responses, namely the service or fill rate, and for some deterministic simulation inputs, namely the constraint s
Isoprene and monoterpene fluxes from Central Amazonian rainforest inferred from tower-based and airborne measurements, and implications on the atmospheric chemistry and the local carbon budget
Kuhn, U. ; Andreae, M.O. ; Ammann, C. ; Araújo, A.C. ; Brancaleoni, E. ; Ciccioli, P. ; Dindorf, T. ; Frattoni, M. ; Gatti, L.V. ; Ganzeveld, L.N. ; Kruijt, B. ; Lelieveld, J. ; Lloyd, J. ; Meixner, F.X. ; Nobre, A.D. ; Pöschl, U. ; Spirig, C. ; Stefani, P. ; Thielmann, A. ; Valentini, R. ; Kesselmeier, J. - \ 2007
Atmospheric Chemistry and Physics 7 (2007)11. - ISSN 1680-7316 - p. 2855 - 2879.
volatile organic-compounds - boundary-layer - art. - emissions - aerosols - dependence - exchange - biomass - site - nox
We estimated the isoprene and monoterpene source strengths of a pristine tropical forest north of Manaus in the central Amazon Basin using three different micrometeorological flux measurement approaches. During the early dry season campaign of the Cooperative LBA Airborne Regional Experiment (LBA-CLAIRE-2001), a tower-based surface layer gradient (SLG) technique was applied simultaneously with a relaxed eddy accumulation (REA) system. Airborne measurements of vertical profiles within and above the convective boundary layer (CBL) were used to estimate fluxes on a landscape scale by application of the mixed layer gradient (MLG) technique. The mean daytime fluxes of organic carbon measured by REA were 2.1 mg C m¿2 h¿1 for isoprene, 0.20 mg C m¿2 h¿1 for ¿-pinene, and 0.39 mg C m¿2 h¿1 for the sum of monoterpenes. These values are in reasonable agreement with fluxes determined with the SLG approach, which exhibited a higher scatter, as expected for the complex terrain investigated. The observed VOC fluxes are in good agreement with simulations using a single-column chemistry and climate model (SCM). In contrast, the model-derived mixing ratios of VOCs were by far higher than observed, indicating that chemical processes may not be adequately represented in the model. The observed vertical gradients of isoprene and its primary degradation products methyl vinyl ketone (MVK) and methacrolein (MACR) suggest that the oxidation capacity in the tropical CBL is much higher than previously assumed. A simple chemical kinetics model was used to infer OH radical concentrations from the vertical gradients of (MVK+MACR)/isoprene. The estimated range of OH concentrations during the daytime was 3¿8×106 molecules cm¿3, i.e., an order of magnitude higher than is estimated for the tropical CBL by current state-of-the-art atmospheric chemistry and transport models. The remarkably high OH concentrations were also supported by results of a simple budget analysis, based on the flux-to-lifetime relationship of isoprene within the CBL. Furthermore, VOC fluxes determined with the airborne MLG approach were only in reasonable agreement with those of the tower-based REA and SLG approaches after correction for chemical decay by OH radicals, applying a best estimate OH concentration of 5.5×106 molecules cm¿3. The SCM model calculations support relatively high OH concentration estimates after specifically being constrained by the mixing ratios of chemical constituents observed during the campaign. The relevance of the VOC fluxes for the local carbon budget of the tropical rainforest site during the measurements campaign was assessed by comparison with the concurrent CO2 fluxes, estimated by three different methods (eddy correlation, Lagrangian dispersion, and mass budget approach). Depending on the CO2 flux estimate, 1¿6% or more of the carbon gained by net ecosystem productivity appeared to be re-emitted through VOC emissions
An airborne regional carbon balance for Central Amazonia
Lloyd, J. ; Kolle, O. ; Fritsch, H. ; Freitas, S.R. de; Silva Dias, M.A.F. ; Artaxo, P. ; Nobre, A.D. ; Araújo, A.C. de; Kruijt, B. ; Sogacheva, L. ; Fisch, G. ; Thielmann, A. ; Kuhn, U. ; Andreae, M.O. - \ 2007
Biogeosciences 4 (2007)5. - ISSN 1726-4170 - p. 759 - 768.
atmospheric co2 concentrations - plant-growth responses - boundary-layer budgets - soil nutrient status - rain-forest - tropical forest - water-vapor - eddy covariance - central siberia - dioxide uptake
We obtained regional estimates of surface CO2 exchange rates using atmospheric boundary layer budgeting techniques above tropical forest near Manaus, Brazil. Comparisons were made with simultaneous measurements from two eddy covariance towers below. Although there was good agreement for daytime measurements, large differences emerged for integrating periods dominated by the night-time fluxes. These results suggest that a systematic underestimation of night time respiratory effluxes may be responsible for the high Amazonian carbon sink suggested by several previous eddy covariance studies. Large CO2 fluxes from riverine sources or high respiratory losses from recently disturbed forests do not need to be invoked in order to balance the carbon budget of the Amazon. Our results do not, however, discount some contribution of these processes to the overall Amazon carbon budget.
Stress induced VOC emissions
Miebach, M. ; Beauchamp, J. ; Hansel, A. ; Heiden, A.C. ; Jansen, R.M.C. ; Kesselmeier, J. ; Kleist, E. ; Kuhn, U. ; Roese, U. ; Steindel, F. ; Uerlings, R. ; Wisthaler, A. ; Wildt, J. - \ 2007
Significant light and temperature dependent monoterpene emissions from European beech (fagus sylvatiga L.) and their potential impact on the European VOC budget
Dindorf, T. ; Kuhn, U. ; Ganzeveld, L.N. ; Schebeske, G. ; Ciccioli, P. ; Holzke, C. ; Köble, R. ; Seufert, G. ; Kesselmeier, J. - \ 2006
Journal of Geophysical Research: Atmospheres 111 (2006)10. - ISSN 2169-897X
quercus-ilex l - biogenic voc emissions - amazonian rain-forest - in-field conditions - isoprene emission - pinus-pinea - atmospheric chemistry - synthase activities - mass-spectrometry - flux measurements
By using a dynamic branch enclosure system the emission of monoterpenes from European beech (Fagus sylvatica L.) was investigated during two consecutive summer vegetation periods in the years of 2002 and 2003 in Germany. All measurements were performed under field conditions within the framework of the ECHO project (Emission and Chemical Transformation of Biogenic Volatile Organic Compounds, AFO 2000). European beech was characterized as a substantial emitter of monoterpenes, with sabinene being the predominant compound released. The monoterpene emission from European beech was shown to be a function of light and temperature and agreed well to emission algorithms that consider a light and temperature dependent release of volatile organics. Standard emission factors that were measured from these sunlit leaves of European beech ranged up to 4–13 µg g-1 h-1 (normalized to 1000 µmol m-2 s-1, 30°C) in the years of 2003 and 2002, respectively. The nighttime emission of monoterpene compounds was negligible. Also the artificial darkening of the sunlit branch during daylight conditions led to an immediate cessation of monoterpene emission. European beech is the dominating deciduous tree species in Europe. To demonstrate the effect of an updated monoterpene emission factor for European beech in combination with the consideration of a light and temperature dependent monoterpene emission, we applied a species based model simulation on a European scale. With respect to conventional estimates of the European volatile organic compound budget, the latter simulation resulted in relative increases of 16% by taking solely this tree species into account. On local scales these increases exceeded even more than 100% depending on the respective vegetation area coverage of European beech
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