Staff Publications

Staff Publications

  • external user (warningwarning)
  • Log in as
  • language uk
  • About

    '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.

    We have a manual that explains all the features 

    Records 1 - 78 / 78

    • help
    • print

      Print search results

    • export

      Export search results

    Check title to add to marked list
    Two decades of forest-related legislation changes in European countries analysed from a property rights perspective
    Nichiforel, Liviu ; Deuffic, Philippe ; Thorsen, Bo Jellesmark ; Weiss, G. ; Hujala, Teppo ; Keary, Kevin ; Lawrence, A. ; Avdibegović, Mersudin ; Dobšinská, Zuzana ; Feliciano, Diana ; Gorriz Mifsud, Elena ; Hoogstra-Klein, M.A. ; Hrib, Michal ; Jarský, Vilém ; Jodłowski, Krzysztof ; Lukmine, Diana ; Pezdevšek Malovrh, Špela ; Nedeljković, Jelena ; Bouriaud, Laura - \ 2020
    Forest Policy and Economics 115 (2020). - ISSN 1389-9341
    In the last two decades, attention on forests and ownership rights has increased in different domains of international policy, particularly in relation to achieving the global sustainable development goals. This paper looks at the changes in forest-specific legislation applicable to regular productive forests, across 28 European countries. We compare the legal framework applicable in the mid-1990s with that applicable in 2015, using the Property Rights Index in Forestry (PRIF) to measure changes across time and space.
    Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age
    Merid, Simon Kebede ; Novoloaca, Alexei ; Sharp, Gemma C. ; Küpers, Leanne K. ; Kho, Alvin T. ; Roy, Ritu ; Gao, Lu ; Annesi-Maesano, Isabella ; Jain, Pooja ; Plusquin, Michelle ; Kogevinas, Manolis ; Allard, Catherine ; Vehmeijer, Florianne O. ; Kazmi, Nabila ; Salas, Lucas A. ; Rezwan, Faisal I. ; Zhang, Hongmei ; Sebert, Sylvain ; Czamara, Darina ; Rifas-Shiman, Sheryl L. ; Melton, Phillip E. ; Lawlor, Debbie A. ; Pershagen, Göran ; Breton, Carrie V. ; Huen, Karen ; Baiz, Nour ; Gagliardi, Luigi ; Nawrot, Tim S. ; Corpeleijn, Eva ; Perron, Patrice ; Duijts, Liesbeth ; Nohr, Ellen Aagaard ; Bustamante, Mariona ; Ewart, Susan L. ; Karmaus, Wilfried ; Zhao, Shanshan ; Page, Christian M. ; Herceg, Zdenko ; Jarvelin, Marjo Riitta ; Lahti, Jari ; Baccarelli, Andrea A. ; Anderson, Denise ; Kachroo, Priyadarshini ; Relton, Caroline L. ; Bergström, Anna ; Eskenazi, Brenda ; Soomro, Munawar Hussain ; Vineis, Paolo ; Snieder, Harold ; Bouchard, Luigi ; Jaddoe, Vincent W. ; Sørensen, Thorkild I.A. ; Vrijheid, Martine ; Arshad, S.H. ; Holloway, John W. ; Håberg, Siri E. ; Magnus, Per ; Dwyer, Terence ; Binder, Elisabeth B. ; Demeo, Dawn L. ; Vonk, Judith M. ; Newnham, John ; Tantisira, Kelan G. ; Kull, Inger ; Wiemels, Joseph L. ; Heude, Barbara ; Sunyer, Jordi ; Nystad, Wenche ; Munthe-Kaas, Monica C. ; Raïkkönen, Katri ; Oken, Emily ; Huang, Rae Chi ; Weiss, Scott T. ; Antó, Josep Maria ; Bousquet, Jean ; Kumar, Ashish ; Söderhäll, Cilla ; Almqvist, Catarina ; Cardenas, Andres ; Gruzieva, Olena ; Xu, Cheng Jian ; Reese, Sarah E. ; Kere, Juha ; Brodin, Petter ; Solomon, Olivia ; Wielscher, Matthias ; Holland, Nina ; Ghantous, Akram ; Hivert, Marie France ; Felix, Janine F. ; Koppelman, Gerard H. ; London, Stephanie J. ; Melén, Erik - \ 2020
    Genome Medicine 12 (2020)1. - ISSN 1756-994X
    Development - Epigenetics - Gestational age - Preterm birth - Transcriptomics

    Background: Preterm birth and shorter duration of pregnancy are associated with increased morbidity in neonatal and later life. As the epigenome is known to have an important role during fetal development, we investigated associations between gestational age and blood DNA methylation in children. Methods: We performed meta-analysis of Illumina's HumanMethylation450-array associations between gestational age and cord blood DNA methylation in 3648 newborns from 17 cohorts without common pregnancy complications, induced delivery or caesarean section. We also explored associations of gestational age with DNA methylation measured at 4-18 years in additional pediatric cohorts. Follow-up analyses of DNA methylation and gene expression correlations were performed in cord blood. DNA methylation profiles were also explored in tissues relevant for gestational age health effects: Fetal brain and lung. Results: We identified 8899 CpGs in cord blood that were associated with gestational age (range 27-42 weeks), at Bonferroni significance, P < 1.06 × 10-7, of which 3343 were novel. These were annotated to 4966 genes. After restricting findings to at least three significant adjacent CpGs, we identified 1276 CpGs annotated to 325 genes. Results were generally consistent when analyses were restricted to term births. Cord blood findings tended not to persist into childhood and adolescence. Pathway analyses identified enrichment for biological processes critical to embryonic development. Follow-up of identified genes showed correlations between gestational age and DNA methylation levels in fetal brain and lung tissue, as well as correlation with expression levels. Conclusions: We identified numerous CpGs differentially methylated in relation to gestational age at birth that appear to reflect fetal developmental processes across tissues. These findings may contribute to understanding mechanisms linking gestational age to health effects.

    Environmental footprint family to address local to planetary sustainability and deliver on the SDGs
    Vanham, Davy ; Leip, Adrian ; Galli, Alessandro ; Kastner, Thomas ; Bruckner, Martin ; Uwizeye, Aimable ; Dijk, Kimo Van; Ercin, Ertug ; Dalin, Carole ; Brandão, Miguel ; Bastianoni, Simone ; Fang, Kai ; Leach, Allison ; Chapagain, Ashok ; Velde, Marijn Van Der; Sala, Serenella ; Pant, Rana ; Mancini, Lucia ; Monforti-ferrario, Fabio ; Carmona-garcia, Gema ; Marques, Alexandra ; Weiss, Franz ; Hoekstra, Arjen Y. - \ 2019
    Science of the Total Environment 693 (2019). - ISSN 0048-9697
    The number of publications on environmental footprint indicators has been growing rapidly, but with limited efforts to integrate different footprints into a coherent framework. Such integration is important for comprehensive understanding of environmental issues, policy formulation and assessment of trade-offs between different environmental concerns. Here, we systematize published footprint studies and define a family of footprints that can be used for the assessment of environmental sustainability. We identify overlaps between different footprints and analyse how they relate to the nine planetary boundaries and visualize the crucial information they provide for local and planetary sustainability. In addition, we assess how the footprint family delivers on measuring progress towards Sustainable Development Goals (SDGs), considering its ability to quantify environmental pressures along the supply chain and relating them to the water-energy-food-ecosystem (WEFE) nexus and ecosystem services. We argue that the footprint family is a flexible framework where particular members can be included or excluded according to the context or area of concern. Our paper is based upon a recent workshop bringing together global leading experts on existing environmental footprint indicators.
    A method to lead discussion groups for the analysis of grassland innovations
    Mairhofer, Franziska van den; Weiss, A. ; Pfeifer, A. ; Plitzner, C. ; Prünster, T. ; Pol, A. van den; Peratoner, Giovanni - \ 2019
    In: Improving sown grasslands through breeding and management / Huguenin-Elie, O., Studer, B., Kölliker, R., Reheul, D., Probo, M., Barre, P., Feuerstein, U., Roldán-Ruiz, I., Mariotte, P., Hopkins, A., Eucarpia (Grassland Science in Europe ) - ISBN 9783033072787 - p. 500 - 502.
    Rarity of monodominance in hyperdiverse Amazonian forests
    Steege, Hans Ter; Henkel, Terry W. ; Helal, Nora ; Marimon, Beatriz S. ; Marimon-Junior, Ben Hur ; Huth, Andreas ; Groeneveld, Jürgen ; Sabatier, Daniel ; Souza Coelho, Luiz de; Andrade Lima Filho, Diogenes de; Salomão, Rafael P. ; Amaral, Iêda Leão ; Almeida Matos, Francisca Dionízia de; Castilho, Carolina V. ; Phillips, Oliver L. ; Guevara, Juan Ernesto ; Jesus Veiga Carim, Marcelo de; Cárdenas López, Dairon ; Magnusson, William E. ; Wittmann, Florian ; Irume, Mariana Victória ; Martins, Maria Pires ; Silva Guimarães, José Renan da; Molino, Jean François ; Bánki, Olaf S. ; Piedade, Maria Teresa Fernandez ; Pitman, Nigel C.A. ; Mendoza, Abel Monteagudo ; Ramos, José Ferreira ; Luize, Bruno Garcia ; Moraes de Leão Novo, Evlyn Márcia ; Núñez Vargas, Percy ; Silva, Thiago Sanna Freire ; Venticinque, Eduardo Martins ; Manzatto, Angelo Gilberto ; Reis, Neidiane Farias Costa ; Terborgh, John ; Casula, Katia Regina ; Honorio Coronado, Euridice N. ; Montero, Juan Carlos ; Feldpausch, Ted R. ; Duque, Alvaro ; Costa, Flávia R.C. ; Arboleda, Nicolás Castaño ; Schöngart, Jochen ; Killeen, Timothy J. ; Vasquez, Rodolfo ; Mostacedo, Bonifacio ; Demarchi, Layon O. ; Assis, Rafael L. ; Baraloto, Chris ; Engel, Julien ; Petronelli, Pascal ; Castellanos, Hernán ; Medeiros, Marcelo Brilhante de; Quaresma, Adriano ; Simon, Marcelo Fragomeni ; Andrade, Ana ; Camargo, José Luís ; Laurance, Susan G.W. ; Laurance, William F. ; Rincón, Lorena M. ; Schietti, Juliana ; Sousa, Thaiane R. ; Sousa Farias, Emanuelle de; Lopes, Maria Aparecida ; Magalhães, José Leonardo Lima ; Mendonça Nascimento, Henrique Eduardo ; Lima de Queiroz, Helder ; Aymard C, Gerardo A. ; Brienen, Roel ; Revilla, Juan David Cardenas ; Vieira, Ima Célia Guimarães ; Cintra, Bruno Barçante Ladvocat ; Stevenson, Pablo R. ; Feitosa, Yuri Oliveira ; Duivenvoorden, Joost F. ; Mogollón, Hugo F. ; Araujo-Murakami, Alejandro ; Ferreira, Leandro Valle ; Lozada, José Rafael ; Comiskey, James A. ; Toledo, José Julio de; Damasco, Gabriel ; Dávila, Nállarett ; Draper, Freddie ; García-Villacorta, Roosevelt ; Lopes, Aline ; Vicentini, Alberto ; Alonso, Alfonso ; Dallmeier, Francisco ; Gomes, Vitor H.F. ; Lloyd, Jon ; Neill, David ; Aguiar, Daniel Praia Portela de; Arroyo, Luzmila ; Carvalho, Fernanda Antunes ; Souza, Fernanda Coelho de; Amaral, Dário Dantas do; Feeley, Kenneth J. ; Gribel, Rogerio ; Pansonato, Marcelo Petratti ; Barlow, Jos ; Berenguer, Erika ; Ferreira, Joice ; Fine, Paul V.A. ; Guedes, Marcelino Carneiro ; Jimenez, Eliana M. ; Licona, Juan Carlos ; Peñuela Mora, Maria Cristina ; Villa, Boris ; Cerón, Carlos ; Maas, Paul ; Silveira, Marcos ; Stropp, Juliana ; Thomas, Raquel ; Baker, Tim R. ; Daly, Doug ; Dexter, Kyle G. ; Huamantupa-Chuquimaco, Isau ; Milliken, William ; Pennington, Toby ; Ríos Paredes, Marcos ; Fuentes, Alfredo ; Klitgaard, Bente ; Pena, José Luis Marcelo ; Peres, Carlos A. ; Silman, Miles R. ; Tello, J.S. ; Chave, Jerome ; Cornejo Valverde, Fernando ; Fiore, Anthony Di; Hilário, Renato Richard ; Phillips, Juan Fernando ; Rivas-Torres, Gonzalo ; Andel, Tinde R. van; Hildebrand, Patricio von; Noronha, Janaína Costa ; Barbosa, Edelcilio Marques ; Barbosa, Flávia Rodrigues ; Matos Bonates, Luiz Carlos de; Sá Carpanedo, Rainiellen de; Dávila Doza, Hilda Paulette ; Fonty, Émile ; GómeZárate Z, Ricardo ; Gonzales, Therany ; Gallardo Gonzales, George Pepe ; Hoffman, Bruce ; Junqueira, André Braga ; Malhi, Yadvinder ; Andrade Miranda, Ires Paula de; Pinto, Linder Felipe Mozombite ; Prieto, Adriana ; Jesus Rodrigues, Domingos de; Rudas, Agustín ; Ruschel, Ademir R. ; Silva, Natalino ; Vela, César I.A. ; Vos, Vincent Antoine ; Zent, Egleé L. ; Zent, Stanford ; Weiss Albuquerque, Bianca ; Cano, Angela ; Carrero Márquez, Yrma Andreina ; Correa, Diego F. ; Costa, Janaina Barbosa Pedrosa ; Flores, Bernardo Monteiro ; Galbraith, David ; Holmgren, Milena ; Kalamandeen, Michelle ; Nascimento, Marcelo Trindade ; Oliveira, Alexandre A. ; Ramirez-Angulo, Hirma ; Rocha, Maira ; Scudeller, Veridiana Vizoni ; Sierra, Rodrigo ; Tirado, Milton ; Umaña Medina, Maria Natalia ; Heijden, Geertje van der; Vilanova Torre, Emilio ; Vriesendorp, Corine ; Wang, Ophelia ; Young, Kenneth R. ; Ahuite Reategui, Manuel Augusto ; Baider, Cláudia ; Balslev, Henrik ; Cárdenas, Sasha ; Casas, Luisa Fernanda ; Farfan-Rios, William ; Ferreira, Cid ; Linares-Palomino, Reynaldo ; Mendoza, Casimiro ; Mesones, Italo ; Torres-Lezama, Armando ; Giraldo, Ligia Estela Urrego ; Villarroel, Daniel ; Zagt, Roderick ; Alexiades, Miguel N. ; Oliveira, Edmar Almeida de; Garcia-Cabrera, Karina ; Hernandez, Lionel ; Palacios Cuenca, Walter ; Pansini, Susamar ; Pauletto, Daniela ; Ramirez Arevalo, Freddy ; Sampaio, Adeilza Felipe ; Valderrama Sandoval, Elvis H. ; Valenzuela Gamarra, Luis ; Levesley, Aurora ; Pickavance, Georgia ; Melgaço, Karina - \ 2019
    Scientific Reports 9 (2019). - ISSN 2045-2322

    Tropical forests are known for their high diversity. Yet, forest patches do occur in the tropics where a single tree species is dominant. Such "monodominant" forests are known from all of the main tropical regions. For Amazonia, we sampled the occurrence of monodominance in a massive, basin-wide database of forest-inventory plots from the Amazon Tree Diversity Network (ATDN). Utilizing a simple defining metric of at least half of the trees ≥ 10 cm diameter belonging to one species, we found only a few occurrences of monodominance in Amazonia, and the phenomenon was not significantly linked to previously hypothesized life history traits such wood density, seed mass, ectomycorrhizal associations, or Rhizobium nodulation. In our analysis, coppicing (the formation of sprouts at the base of the tree or on roots) was the only trait significantly linked to monodominance. While at specific locales coppicing or ectomycorrhizal associations may confer a considerable advantage to a tree species and lead to its monodominance, very few species have these traits. Mining of the ATDN dataset suggests that monodominance is quite rare in Amazonia, and may be linked primarily to edaphic factors.

    Mapping Geospatial Processes Affecting the Environmental Fate of Agricultural Pesticides in Africa
    Hendriks, Chantal M.J. ; Gibson, Harry S. ; Trett, Anna ; Python, André ; Weiss, Daniel J. ; Vrieling, Anton ; Coleman, Michael ; Gething, Peter W. ; Hancock, Penny A. ; Moyes, Catherine L. - \ 2019
    International Journal of Environmental Research and Public Health 16 (2019)19. - ISSN 1660-4601
    artificial compound - crop protection - environmental data - insecticide residue - satellite data - tropics

    The application of agricultural pesticides in Africa can have negative effects on human health and the environment. The aim of this study was to identify African environments that are vulnerable to the accumulation of pesticides by mapping geospatial processes affecting pesticide fate. The study modelled processes associated with the environmental fate of agricultural pesticides using publicly available geospatial datasets. Key geospatial processes affecting the environmental fate of agricultural pesticides were selected after a review of pesticide fate models and maps for leaching, surface runoff, sedimentation, soil storage and filtering capacity, and volatilization were created. The potential and limitations of these maps are discussed. We then compiled a database of studies that measured pesticide residues in Africa. The database contains 10,076 observations, but only a limited number of observations remained when a standard dataset for one compound was extracted for validation. Despite the need for more in-situ data on pesticide residues and application, this study provides a first spatial overview of key processes affecting pesticide fate that can be used to identify areas potentially vulnerable to pesticide accumulation.

    Supplementary material from "Stress behaviour and physiology of developing Arctic barnacle goslings (Branta leucopsis) is affected by legacy trace contaminants"
    Scheiber, Isabella B.R. ; Weiß, Brigitte M. ; Jong, Margje E. de; Braun, Anna ; Brink, Nico van den; Loonen, Maarten J.J.E. ; Millesi, Eva ; Komdeur, Jan - \ 2018
    Wageningen University and Research
    legacy trace metal contamination - stress coping - acute stress behaviour - HPA corticosterone metabolites - Arctic - barnacle goosse (Branta leucopsis)
    Natural populations are persistently exposed to environmental pollution, which may adversely impact animal physiology and behaviour and even compromise survival. Responding appropriately to any stressor, ultimately might tip the scales for survival, as mistimed behaviour and inadequate physiological responses may be detrimental. Yet, effects of legacy contamination on immediate physiological and behavioural stress coping abilities during acute stress are virtually unknown. Here, we assessed these effects in barnacle goslings (Branta leucopsis) at a historical coal mine site in the Arctic. For three weeks we led human-imprinted goslings, collected from nests in unpolluted areas, to feed in an abandoned coal mining area, where they were exposed to trace metals. As control we led their siblings to feed on clean grounds. After submitting both groups to three well-established stress tests (group isolation, individual isolation, on-back restraint), control goslings behaved calmer and excreted lower levels of corticosterone metabolites. Thus, legacy contamination may decisively change stress physiology and behaviour in long-lived vertebrates exposed at a young age.
    Stress behaviour and physiology of developing Arctic barnacle goslings (Branta leucopsis) is affected by legacy trace contaminants
    Scheiber, Isabella B.R. ; Weiß, Brigitte M. ; Jong, Margje E. De; Braun, Anna ; Brink, Nico W. Van Den; Loonen, Maarten J.J.E. ; Millesi, Eva ; Komdeur, Jan - \ 2018
    Proceedings of the Royal Society. B: Biological Sciences 285 (2018)1893. - ISSN 0962-8452
    acute stress behaviour - Arctic - barnacle goose (Branta leucopsis) - HPA corticosterone metabolites - legacy trace metal contamination - stress coping

    Natural populations are persistently exposed to environmental pollution, which may adversely impact animal physiology and behaviour and even compromise survival. Responding appropriately to any stressor ultimately might tip the scales for survival, as mistimed behaviour and inadequate physiological responses may be detrimental. Yet effects of legacy contamination on immediate physiological and behavioural stress coping abilities during acute stress are virtually unknown. Here, we assessed these effects in barnacle goslings (Branta leucopsis) at a historical coal mine site in the Arctic. For three weeks we led human-imprinted goslings, collected from nests in unpolluted areas, to feed in an abandoned coal mining area, where they were exposed to trace metals. As control we led their siblings to feed on clean grounds. After submitting both groups to three well-established stress tests (group isolation, individual isolation, on-back restraint), control goslings behaved calmer and excreted lower levels of corticosterone metabolites. Thus, legacy contamination may decisively change stress physiology and behaviour in long-lived vertebrates exposed at a young age.

    Enhancing vector refractoriness to trypanosome infection : achievements, challenges and perspectives
    Kariithi, Henry M. ; Meki, Irene K. ; Schneider, Daniela I. ; Vooght, Linda De; Khamis, Fathiya M. ; Geiger, Anne ; Demirbaş-Uzel, Guler ; Vlak, Just M. ; iNCE, Ikbal Agah ; Kelm, Sorge ; Njiokou, Flobert ; Wamwiri, Florence N. ; Malele, Imna I. ; Weiss, Brian L. ; Abd-Alla, Adly M.M. - \ 2018
    BMC Microbiology 18 (2018). - ISSN 1471-2180
    Glossina - Hytrosaviridae - Microbiota - Paratransgenesis - Trypanosoma-refractoriness, sterile insect technique - Vector competence

    With the absence of effective prophylactic vaccines and drugs against African trypanosomosis, control of this group of zoonotic neglected tropical diseases depends the control of the tsetse fly vector. When applied in an area-wide insect pest management approach, the sterile insect technique (SIT) is effective in eliminating single tsetse species from isolated populations. The need to enhance the effectiveness of SIT led to the concept of investigating tsetse-trypanosome interactions by a consortium of researchers in a five-year (2013-2018) Coordinated Research Project (CRP) organized by the Joint Division of FAO/IAEA. The goal of this CRP was to elucidate tsetse-symbiome-pathogen molecular interactions to improve SIT and SIT-compatible interventions for trypanosomoses control by enhancing vector refractoriness. This would allow extension of SIT into areas with potential disease transmission. This paper highlights the CRP's major achievements and discusses the science-based perspectives for successful mitigation or eradication of African trypanosomosis.

    Identification of Chaoborus kairomone chemicals that induce defences in Daphnia
    Weiss, Linda C. ; Albada, Bauke ; Becker, Sina M. ; Meckelmann, Sven W. ; Klein, Julia ; Meyer, Martin ; Schmitz, Oliver J. ; Sommer, Ulf ; Leo, Markus ; Zagermann, Johannes ; Metzler-Nolte, Nils ; Tollrian, Ralph - \ 2018
    Nature Chemical Biology 14 (2018). - ISSN 1552-4450 - p. 1133 - 1139.

    Infochemicals play important roles in aquatic ecosystems. They even modify food web interactions, such as by inducing defenses in prey. In one classic but still not fully understood example, the planktonic freshwater crustacean Daphnia pulex forms specific morphological defenses (neckteeth) induced by chemical cues (kairomones) released from its predator, the phantom midge larva Chaoborus. On the basis of liquid chromatography, mass spectrometry, and chemical synthesis, we report here the chemical identity of the Chaoborus kairomone. The biologically active cues consist of fatty acids conjugated to the amino group of glutamine via the N terminus. These cues are involved in Chaoborus digestive processes, which explains why they are consistently released despite the disadvantage for its emitter. The identification of the kairomone may allow in-depth studies on multiple aspects of this inducible defense system.

    How private are Europe’s private forests? A comparative property rights analysis
    Nichiforel, Liviu ; Keary, Kevin ; Deuffic, Philippe ; Weiss, Gerhard ; Thorsen, Bo Jellesmark ; Winkel, Georg ; Avdibegović, Mersudin ; Dobšinská, Zuzana ; Feliciano, Diana ; Gatto, Paola ; Gorriz Mifsud, Elena ; Hoogstra-klein, Marjanke ; Hrib, Michal ; Hujala, Teppo ; Jager, Laszlo ; Jarský, Vilém ; Jodłowski, Krzysztof ; Lawrence, Anna ; Lukmine, Diana ; Pezdevšek Malovrh, Špela ; Nedeljković, Jelena ; Nonić, Dragan ; Krajter Ostoić, Silvija ; Pukall, Klaus ; Rondeux, Jacques ; Samara, Theano ; Sarvašová, Zuzana ; Scriban, Ramona Elena ; Šilingienė, Rita ; Sinko, Milan ; Stojanovska, Makedonka ; Stojanovski, Vladimir ; Stoyanov, Nickola ; Teder, Meelis ; Vennesland, Birger ; Vilkriste, Lelde ; Wilhelmsson, Erik ; Wilkes-Allemann, Jerylee ; Bouriaud, Laura - \ 2018
    Land Use Policy 76 (2018). - ISSN 0264-8377 - p. 535 - 552.
    Private forests are widespread in Europe providing a range of ecosystem services of significant value to society, and there are calls for novel policies to enhance their provision and to face the challenges of environmental changes. Such policies need to acknowledge the importance of private forests, and importantly they need to be based on a deep understanding of how property rights held by private forest owners vary across Europe. We collected and analysed data on the content of property rights based on formal legal requirements existing in 31 European jurisdictions. To allow a comparison across jurisdictions, we constructed an original Property Rights Index for Forestry encompassing five rights domains (access, withdrawal, management, exclusion and alienation). We documented substantial variation of the private forest owners’ rights, and notably to i) make decisions in operational management and the formulation of management goals, ii) withdraw timber resources from their forest, and iii) exclude others from the use of forest resources. We identified broad relations between the scope for decision making of private forest owners and jurisdictions’ former socio-political background and geographical distribution. The variation in the content of property rights has implications for the implementation of international environmental policies, and stresses the need for tailored policy instruments, when addressing European society’s rural development, the bioeconomy, climate change mitigation measures and nature protection strategies.
    Major challenges of integrating agriculture into climate change mitigation policy frameworks
    Fellmann, T. ; Witzke, P. ; Weiss, F. ; Doorslaer, B. van; Drabik, D. ; Huck, I. ; Salputra, G. ; Jansson, T. ; Leip, A. - \ 2018
    Mitigation and Adaptation Strategies for Global Change 23 (2018)3. - ISSN 1381-2386 - p. 451 - 468.
    Agriculture - Climate change - Emissions - Mitigation - Policy
    Taking the European Union (EU) as a case study, we simulate the application of non-uniform national mitigation targets to achieve a sectoral reduction in agricultural non-carbon dioxide (CO2) greenhouse gas (GHG) emissions. Scenario results show substantial impacts on EU agricultural production, in particular, the livestock sector. Significant increases in imports and decreases in exports result in rather moderate domestic consumption impacts but induce production increases in non-EU countries that are associated with considerable emission leakage effects. The results underline four major challenges for the general integration of agriculture into national and global climate change mitigation policy frameworks and strategies, as they strengthen requests for (1) a targeted but flexible implementation of mitigation obligations at national and global level and (2) the need for a wider consideration of technological mitigation options. The results also indicate that a globally effective reduction in agricultural emissions requires (3) multilateral commitments for agriculture to limit emission leakage and may have to (4) consider options that tackle the reduction in GHG emissions from the consumption side.
    Transdisciplinary understanding of SI in MRAs
    Kluvankova, Tatiana ; Gežik, Veronika ; Špaček, Martin ; Brnkalakova, Stanislava ; Slee, Bill ; Polman, N.B.P. ; Valero, Diana ; Bryce, Rosalind ; Alkhaled, Sophie ; Secco, Laura ; Burlando, Catie ; Kozova, Maria ; Miller, David ; Nijnik, Maria ; Perlik, Manfred ; Pisani, Elena ; Price, Martin ; Sarkki, Simo ; Weiss, Gerhard - \ 2017
    SIMRA - 53 p.
    Set of Methods to Assess SI Implications at Different Levels
    Secco, Laura ; Pisani, Elena ; Burlando, Catie ; Re, Riccardo Da; Gatto, Paola ; Pettenella, Davide ; Vassilopoulos, Achilleas ; Akinsete, Ebun ; Koundouri, Phoebe ; Lopolito, Antonio ; Prosperi, Maurizio ; Tuomasiukka, Diana ; Herde, Micheal Den; Lovric, Marko ; Polman, N.B.P. ; Dijkshoorn-Dekker, M.W.C. ; Soma, K. ; Ludvig, Alice ; Weiss, Gerhard ; Zivojinovic, Ivana ; Sarkki, Simo ; Ravazzoli, Elisa ; Torre, Cristina Dalla; Streifeneder, Thomas ; Slee, Bill ; Nijnik, Maria ; Miller, David ; Barlagne, Carla ; Prokofieva, Irina - \ 2017
    SIMRA - 203 p.
    Deliverable No. D9.4: Enhanced modelling of sustainable food and nutrition security: the agri-food commodity and nutrient flows and the food supply chains
    Carmona-Garcia, G. ; Leip, A. ; Weiss, F. ; Witzke, P. ; Verma, M. ; Philippidis, George ; Kuiper, M.H. - \ 2017
    SUSFANS - 86 p.
    Affairs happen-To whom? A study on extrapair paternity in common nightingales
    Landgraf, Conny ; Wilhelm, Kerstin ; Wirth, Jutta ; Weiss, Michael ; Kipper, Silke - \ 2017
    Current Zoology 63 (2017)4. - ISSN 1674-5507 - p. 421 - 431.
    Common nightingale - Direct fitness - Extrapair paternity - Luscinia megarhynchos - Repertoire size - Territorial settlement
    Most birds engage in extrapair copulations despite great differences across and within species. Besides cost and benefit considerations of the two sex environmental factors have been found to alter mating strategies within or between populations and/or over time. For socially monogamous species, the main advantage that females might gain from mating with multiple males is probably increasing their offspring's genetic fitness. Since male (genetic) quality is mostly not directly measurable for female birds, (extrapair) mate choice is based on male secondary traits. In passerines male song is such a sexual ornament indicating male phenotypic and/or genetic quality and song repertoires seem to affect female mate choice in a number of species. Yet their role in extrapair mating behavior is not well understood. In this study, we investigated the proportion of extrapair paternity (EPP) in a population of common nightingales Luscinia megarhynchos. We found that EPP rate was rather high (21.5% of all offspring tested) for a species without sexual dimorphism and high levels of paternal care. Furthermore, the occurrence of EPP was strongly related to the spatial distribution of male territories with males settling in densely occupied areas having higher proportions of extrapair young within their own brood. Also, song repertoire size affected EPP: here larger repertoires of social mates were negatively related to the probability of being cuckolded. When directly comparing repertoires sizes of social and extrapair mates, extrapair mates tended to have larger repertoires. We finally discuss our results as a hint for a flexible mating strategy in nightingales where several factors-including ecological as well as male song features- need to be considered when studying reproductive behavior in monogamous species with complex song.
    The challenge of financing the implementation of Natura 2000 – Empirical evidence from six European Union Member States
    Geitzenauer, Maria ; Blondet, Marieke ; Koning, Jessica De; Ferranti, Francesca ; Sotirov, Metodi ; Weiss, Gerhard ; Winkel, Georg - \ 2017
    Forest Policy and Economics 82 (2017). - ISSN 1389-9341 - p. 3 - 13.
    Natura 2000, which is the core pillar of the European Union's biodiversity conservation policy, is an ambitious and complex venture that requires funding to be successful. A major challenge is said to be a lack of available funding, and a low uptake of allocated funds is also reported. However, in in-depth analysis has still not been produced to assess the approaches to funding, the reasons for these approaches and their impact regarding the achievement of the aims of Natura 2000. Thus, with this article, we intend to fill this gap. To accomplish this, a case study analysis was carried out in six selected EU Member States: Austria, France, Germany, the Netherlands, Spain, and the UK.

    In our study, we perceived different approaches which we sum up to two main types of approaches that were present in the Member States to different degrees. The first type was to find the funding necessary for the required activities, and the second was to delay the implementation of Natura 2000. The major reasons for the different approaches were related to domestic political power realities. The funding approaches impacted onto the attractiveness of EU co-financing instruments, and the sustainability of the schemes. Alternative approaches were either absent or declining in importance. The economic benefits were not perceived on the ground.

    We conclude that neither a “one size fits all” approach to funding Natura 2000 will work nor will a universal claim for “more money”. Therefore, a successful funding strategy ultimately necessitates effective interventions at institutional levels, the business environment and the local level.
    Participation in the implementation of Natura 2000: A comparative study of six EU member states
    Blondet, Marieke ; Koning, J. de; Borrass, L. ; Ferranti, Francesca ; Geitzenauer, M. ; Weiss, G. ; Turnhout, E. ; Winkel, G. - \ 2017
    Land Use Policy 66 (2017). - ISSN 0264-8377 - p. 346 - 355.
    The establishment of Natura 2000, the European Union’s network of protected areas, has been a challenging process and has caused a variety of conflicts. These conflicts are related to contradictory stakeholder interests and perceptions, as well as to procedural issues and feelings of exclusion, especially by concerned local land user groups. To prevent further conflict, local participation has been stressed as an important tool to increase the inclusiveness of Natura 2000 and its acceptance among land users. In this paper, we present an analysis of participation practices related to the Natura 2000 implementation processes in six EU member states. Based on material collected from semi-structured interviews and document analysis, we describe the organisational settings of the participatory processes, focusing, among other things, on the type of participants involved, the level and intensity of their involvement, and the goal of participation. In addition, we also describe the local context in which the participation processes have been embedded. Finally, we assess the outcomes of the participatory processes in terms of their impact on forest and nature conservation management practices. Our results show that local participation practices were shaped not just by the Natura 2000 policy, but also by the history of the area, including, for example, earlier conflicts among the local actors. We also show that although the participation process leads to a greater acceptance of the Natura 2000 policy, this does not relate to significant changes in management practices among local actors. These findings, however, do not suggest that participation is irrelevant. Rather, we conclude that participation involves context-dependent, localised learning processes that can only be understood by taking the historical socio-economic and institutional context in which they are situated into account.
    Agriculture and LULUCF in the 2030 Framework : Final report
    Strange Olesen, Asger ; Lesschen, J.P. ; Rayment, Matt ; Ebrahim, Naazia ; Weiss, Peter ; Arets, E.J.M.M. ; Frelih-Larsen, Ana ; Sikirica, N. ; Nabuurs, G.J. ; Schelhaas, M. - \ 2016
    Luxembourg : European Union - ISBN 9789279591235 - 121 p.
    A miniaturized optoelectronic system for rapid quantitative label-free detection of harmful species in food
    Raptis, Ioannis ; Misiakos, Konstantinos ; Makarona, Eleni ; Salapatas, Alexandros ; Petrou, Panagiota ; Kakabakos, Sotirios ; Botsialas, Athanasios ; Jobst, Gerhard ; Haasnoot, Willem ; Fernandez-Alba, Amadeo ; Lees, Michelle ; Valamontes, Evangelos - \ 2016
    In: Frontiers in Biological Detection: From Nanosensors to Systems VIII. - SPIE (Progress in Biomedical Optics and Imaging 37) - ISBN 9781628419597
    food safety - lab-on-a-chip - Mach-Zehnder interferometry - optoelectronic chip

    Optical biosensors have emerged in the past decade as the most promising candidates for portable, highly-sensitive bioanalytical systems that can be employed for in-situ measurements. In this work, a miniaturized optoelectronic system for rapid, quantitative, label-free detection of harmful species in food is presented. The proposed system has four distinctive features that can render to a powerful tool for the next generation of Point-of-Need applications, namely it accommodates the light sources and ten interferometric biosensors on a single silicon chip of a less-than-40mm2 footprint, each sensor can be individually functionalized for a specific target analyte, the encapsulation can be performed at the wafer-scale, and finally it exploits a new operation principle, Broad-band Mach-Zehnder Interferometry to ameliorate its analytical capabilities. Multi-analyte evaluation schemes for the simultaneous detection of harmful contaminants, such as mycotoxins, allergens and pesticides, proved that the proposed system is capable of detecting within short time these substances at concentrations below the limits imposed by regulatory authorities, rendering it to a novel tool for the near-future food safety applications.

    Förster resonance energy transfer and protein-induced fluorescence enhancement as synergetic multi-scale molecular rulers
    Ploetz, Evelyn ; Lerner, Eitan ; Husada, Florence ; Roelfs, Martin ; Chung, Sangyoon ; Hohlbein, Johannes ; Weiss, Shimon ; Cordes, Thorben - \ 2016
    Scientific Reports 6 (2016). - ISSN 2045-2322

    Advanced microscopy methods allow obtaining information on (dynamic) conformational changes in biomolecules via measuring a single molecular distance in the structure. It is, however, extremely challenging to capture the full depth of a three-dimensional biochemical state, binding-related structural changes or conformational cross-Talk in multi-protein complexes using one-dimensional assays. In this paper we address this fundamental problem by extending the standard molecular ruler based on Förster resonance energy transfer (FRET) into a two-dimensional assay via its combination with protein-induced fluorescence enhancement (PIFE). We show that donor brightness (via PIFE) and energy transfer efficiency (via FRET) can simultaneously report on e.g., the conformational state of double stranded DNA (dsDNA) following its interaction with unlabelled proteins (BamHI, EcoRV, and T7 DNA polymerase gp5/trx). The PIFE-FRET assay uses established labelling protocols and single molecule fluorescence detection schemes (alternating-laser excitation, ALEX). Besides quantitative studies of PIFE and FRET ruler characteristics, we outline possible applications of ALEX-based PIFE-FRET for single-molecule studies with diffusing and immobilized molecules. Finally, we study transcription initiation and scrunching of E. coli RNA-polymerase with PIFE-FRET and provide direct evidence for the physical presence and vicinity of the polymerase that causes structural changes and scrunching of the transcriptional DNA bubble.

    A Quantitative Theoretical Framework for Protein-Induced Fluorescence Enhancement-Förster-Type Resonance Energy Transfer (PIFE-FRET)
    Lerner, Eitan ; Ploetz, Evelyn ; Hohlbein, Johannes ; Cordes, Thorben ; Weiss, Shimon - \ 2016
    The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical 120 (2016)26. - ISSN 1520-6106 - p. 6401 - 6410.

    Single-molecule, protein-induced fluorescence enhancement (PIFE) serves as a molecular ruler at molecular distances inaccessible to other spectroscopic rulers such as Förster-type resonance energy transfer (FRET) or photoinduced electron transfer. In order to provide two simultaneous measurements of two distances on different molecular length scales for the analysis of macromolecular complexes, we and others recently combined measurements of PIFE and FRET (PIFE-FRET) on the single molecule level. PIFE relies on steric hindrance of the fluorophore Cy3, which is covalently attached to a biomolecule of interest, to rotate out of an excited-state trans isomer to the cis isomer through a 90° intermediate. In this work, we provide a theoretical framework that accounts for relevant photophysical and kinetic parameters of PIFE-FRET, show how this framework allows the extraction of the fold-decrease in isomerization mobility from experimental data, and show how these results provide information on changes in the accessible volume of Cy3. The utility of this model is then demonstrated for experimental results on PIFE-FRET measurement of different protein-DNA interactions. The proposed model and extracted parameters could serve as a benchmark to allow quantitative comparison of PIFE effects in different biological systems.

    Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida
    Bombarely, Aureliano ; Moser, Michel ; Amrad, Avichai ; Bao, Manzhu ; Bapaume, Laure ; Barry, Cornelius S. ; Bliek, Mattijs ; Boersma, Maaike R. ; Borghi, Lorenzo ; Bruggmann, Rémy ; Bucher, Marcel ; Agostino, Nunzio D'; Davies, Kevin ; Druege, Uwe ; Dudareva, Natalia ; Egea-Cortines, Marcos ; Delledonne, Massimo ; Fernandez-Pozo, Noe ; Franken, Philipp ; Grandont, Laurie ; Heslop-Harrison, J.S. ; Hintzsche, Jennifer ; Johns, Mitrick ; Koes, Ronald ; Lv, Xiaodan ; Lyons, Eric ; Malla, Diwa ; Martinoia, Enrico ; Mattson, Neil S. ; Morel, Patrice ; Mueller, Lukas A. ; Muhlemann, Joëlle ; Nouri, Eva ; Passeri, Valentina ; Pezzotti, Mario ; Qi, Qinzhou ; Reinhardt, Didier ; Rich, Melanie ; Richert-Pöggeler, Katja R. ; Robbins, Tim P. ; Schatz, Michael C. ; Schranz, Eric ; Schuurink, Robert C. ; Schwarzacher, Trude ; Spelt, Kees ; Tang, Haibao ; Urbanus, Susan L. ; Vandenbussche, Michiel ; Vijverberg, Kitty ; Villarino, Gonzalo H. ; Warner, Ryan M. ; Weiss, Julia ; Yue, Zhen ; Zethof, Jan ; Quattrocchio, Francesca ; Sims, Thomas L. ; Kuhlemeier, Cris - \ 2016
    Nature Plants 2 (2016). - ISSN 2055-026X

    Petunia hybrida is a popular bedding plant that has a long history as a genetic model system. We report the whole-genome sequencing and assembly of inbred derivatives of its two wild parents, P. axillaris N and P. inflata S6. The assemblies include 91.3% and 90.2% coverage of their diploid genomes (1.4 Gb; 2n = 14) containing 32,928 and 36,697 protein-coding genes, respectively. The genomes reveal that the Petunia lineage has experienced at least two rounds of hexaploidization: the older gamma event, which is shared with most Eudicots, and a more recent Solanaceae event that is shared with tomato and other solanaceous species. Transcription factors involved in the shift from bee to moth pollination reside in particularly dynamic regions of the genome, which may have been key to the remarkable diversity of floral colour patterns and pollination systems. The high-quality genome sequences will enhance the value of Petunia as a model system for research on unique biological phenomena such as small RNAs, symbiosis, self-incompatibility and circadian rhythms.

    Erratum to: Persistent aryl hydrocarbon receptor inducers increase with altitude, and estrogen-like disrupters are low in soils of the Alps
    Levy, Walkiria ; Henkelmann, Bernhard ; Bernhöft, Silke ; Bovee, Toine ; Buegger, Franz ; Jakobi, Gert ; Kirchner, Manfred ; Bassan, Rodolfo ; Kräuchi, Norbert ; Moche, Wolfgang ; Offenthaler, Ivo ; Simončič, Primoz ; Weiss, Peter ; Schramm, Karl Werner - \ 2015
    Environmental Science and Pollution Research 22 (2015)4. - ISSN 0944-1344 - p. 3180 - 3181.
    Impacts of European livestock production : Nitrogen, sulphur, phosphorus and greenhouse gas emissions, land-use, water eutrophication and biodiversity
    Leip, Adrian ; Billen, Gilles ; Garnier, Josette ; Grizzetti, Bruna ; Lassaletta, Luis ; Reis, Stefan ; Simpson, David ; Sutton, M.A. ; Vries, Wim De; Weiss, Franz ; Westhoek, Henk - \ 2015
    Environmental Research Letters 10 (2015)11. - ISSN 1748-9326
    air quality - biodiversity loss - climate change - coastal eutrophication - European Union - livestock production - soil acidification

    Livestock production systems currently occupy around 28% of the land surface of the European Union (equivalent to 65% of the agricultural land). In conjunction with other human activities, livestock production systems affect water, air and soil quality, global climate and biodiversity, altering the biogeochemical cycles of nitrogen, phosphorus and carbon. Here, we quantify the contribution of European livestock production to these major impacts. For each environmental effect, the contribution of livestock is expressed as shares of the emitted compounds and land used, as compared to the whole agricultural sector. The results show that the livestock sector contributes significantly to agricultural environmental impacts. This contribution is 78% for terrestrial biodiversity loss, 80% for soil acidification and air pollution (ammonia and nitrogen oxides emissions), 81% for global warming, and 73% for water pollution (both N and P). The agriculture sector itself is one of the major contributors to these environmental impacts, ranging between 12% for global warming and 59% for N water quality impact. Significant progress in mitigating these environmental impacts in Europe will only be possible through a combination of technological measures reducing livestock emissions, improved food choices and reduced food waste of European citizens.

    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.
    The implementation of Natura 2000 in forests: A trans- and interdisciplinary assessment of challenges and choices.
    Winkel, G. ; Blondet, M. ; Borrass, L. ; Frei, T. ; Geitzenauer, M. ; Gruppe, A. ; Jump, A. ; Koning, J. de; Sotirov, M. ; Weiss, G. ; Winter, S. ; Turnhout, E. - \ 2015
    Environmental Science & Policy 52 (2015). - ISSN 1462-9011 - p. 23 - 32.
    climate-change - biodiversity conservation - european-union - management - science - policy - network - stand
    Natura 2000 is the core of the EU's biodiversity conservation policy. 50% of the overall protected area under Natura 2000 is forest. Yet, comparatively little is known about the implementation of the policy in forests. Building on a rich set of social and natural science data, and an inter- and transdisciplinary discussion process involving scientists from different disciplines as well as EU, national and local stakeholders, this paper identifies five important challenges related to the implementation of Natura 2000 in forests: (1) the balancing of biodiversity conservation and timber production, (2) the integration of conservation (science) and local stakeholders’ demands, (3) climate change, (4) lacking and less effective funding, and (5) conflicts related to other sectoral policies. Subsequently, five possible pathways to tackle these challenges are proposed: (1) a learning approach through better communication and transparency, (2) a pathway emphasizing the role of conservation science in developing management strategies and responding to climate change, (3) an approach of better integrating Europe's citizens in the design and implementation of the policy, (4) an approach highlighting the necessity of an effective funding strategy, and (5) the vision to work towards an integrated European land use and conservation policy. In conclusion, we emphasize, on one hand, the distinct character of the five pathways but, on the other hand, underline that probably all of them need to be followed in order to make the implementation of Natura 2000 in Europe's forests a success story.
    An economics assessment of GHG mitigation policy options for EU agriculture
    Doorslaer, B. van; Witzke, P. ; Huck, I. ; Weiss, F. ; Fellmann, T. ; Salputra, G. ; Jansson, T. ; Drabik, D. ; Leip, A. - \ 2015
    Luxembourg : Publications Office of the European Union (JRC technical reports JC 3434) - ISBN 9789279454165
    europees parlement - europees fonds voor regionale ontwikkeling - landbouwbeleid - mitigatie - landbouwkundig onderzoek - emissiereductie - agrarische economie - european parliament - european regional development fund - agricultural policy - mitigation - agricultural research - emission reduction - agricultural economics
    The report presents an overview of the historical and projected development of agricultural GHG emissions in the EU. The major objective of the report is to present the improvements made in the CAPRI modelling system with respect to GHG emission accounting and especially regarding the implementation of endogenous technological mitigation options. Furthermore, the CAPRI model was applied to provide a quantitative assessment of illustrative GHG mitigation policy options in the agricultural sector, and their production and economic implications.
    Natura 2000 et les forêts de l’Europe : Comprendre et relever les defies de la mise en oeuvre
    Winkel, Georg ; Blondet, Marieke ; Borrass, Lars ; Geitzenauer, Maria ; Gruppe, Axel ; Jump, Alistair ; Koning, Jessica De; Sotirov, Metodi ; Weiss, Gerhard ; Winter, Susanne ; Turnhout, Esther - \ 2014
    Revue Forestiere Francaise 66 (2014)6. - ISSN 0035-2829 - p. 743 - 750.

    The BiodivERsA-funded BeFoFu project has investigated both ecological challenges related to management of protected forests and governance challenges related to the implementation of Natura 2000. This Policy Brief describes these socio-ecological challenges, presents key research results, and outlines policy solution pathways towards improving the effectiveness of Natura 2000 with regards to the conservation and sustainable management of Europe’s forests.

    Contribution of Dynamic Vegetation Phenology to Decadal Climate Predictability
    Weiss, M. ; Miller, P.A. ; Hurk, B.J.J.M. van den; Noije, T. van; Stefanescu, S. ; Haarsma, R. ; Ulft, L.H. van; Hazeleger, W. ; Sager, P. Le; Smith, B. ; Schurgers, G. - \ 2014
    Journal of Climate 27 (2014)22. - ISSN 0894-8755 - p. 8563 - 8577.
    leaf-area index - ensemble forecasts - data assimilation - soil-moisture - model - prediction - system - impact - skill - oscillation
    In this study, the impact of coupling and initializing the leaf area index from the dynamic vegetation model Lund-Potsdam-Jena General Ecosystem Simulator (LPJ-GUESS) is analyzed on skill of decadal predictions in the fully coupled atmosphere-land-ocean-sea ice model, the European Consortium Earth System Model (EC-Earth). Similar to the impact of initializing the model with the observed oceanic state, initializing the leaf area index (LAI) fields obtained from an offline LPJ-GUESS simulation forced by the observed atmospheric state leads to a systematic drift. A different treatment of the water and soil moisture budget in LPJ-GUESS is a likely cause of this drift. The coupled system reduces the cold bias of the reference model over land by reducing LAI (and the associated evaporative cooling), particularly outside the growing season. The coupling with the interactive vegetation module implies more degrees of freedom in the coupled model, which generates more noise that can mask a portion of the extra signal that is generated. The forecast reliability improves marginally, particularly early in the forecast. Ranked probability skill scores are also improved slightly in most areas analyzed, but the signal is not fully coherent over the forecast interval because of the relatively low number of ensemble members. Methods to remove the LAI drift and allow coupling of other variables probably need to be implemented before significant forecast skill can be expected.
    Trends in Soil, Sediment and Groundwater Quality Management
    Rijnaarts, H. ; Weiss, H. - \ 2014
    Science of the Total Environment 485-486 (2014). - ISSN 0048-9697 - p. 701 - 704.
    site - germany
    Soil, groundwater, surface water and sediment systems play an important role in quality of life. The harmful effects of chemical pollution of such systems have been a concern for politicians, the public and scientists for decades. More than half a century of experience in soil and groundwater quality management gives the opportunity to abstract some interesting trends in societal responses, and how these relate to cost effective research and management approaches.
    Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
    Schoch, C.L. ; Robbertse, B. ; Robert, V. ; Vu, D. ; Cardinali, G. ; Irinyi, L. ; Meyer, W. ; Nilsson, R.H. ; Hughes, K. ; Miller, A.N. ; Kirk, P.M. ; Abarenkov, K. ; Aime, M.C. ; Ariyawansa, H.A. ; Bidartondo, M. ; Boekhout, T. ; Buyck, B. ; Cai, Q. ; Chen, J. ; Crespo, A. ; Crous, P.W. ; Damm, U. ; Beer, Z.W. de; Dentinger, B.T.M. ; Divakar, P.K. ; Duenas, M. ; Feau, N. ; Fliegerova, K. ; Garcia, M.A. ; Ge, Z.W. ; Griffith, G.W. ; Groenewald, J.Z. ; Groenewald, M. ; Grube, M. ; Gryzenhout, M. ; Gueidan, C. ; Guo, L. ; Hambleton, S. ; Hamelin, R. ; Hansen, K. ; Hofstetter, V. ; Hong, S.B. ; Houbraken, J. ; Hyde, K.D. ; Inderbitzin, P. ; Johnston, P.A. ; Karunarathna, S.C. ; Koljalg, U. ; Kovacs, G.M. ; Kraichak, E. ; Krizsan, K. ; Kurtzman, C.P. ; Larsson, K.H. ; Leavitt, S. ; Letcher, P.M. ; Liimatainen, K. ; Liu, J.K. ; Lodge, D.J. ; Luangsa-ard, J.J. ; Lumbsch, H.T. ; Maharachchikumbura, S.S.N. ; Manamgoda, D. ; Martin, M.P. ; Minnis, A.M. ; Moncalvo, J.M. ; Mule, G. ; Nakasone, K.K. ; Niskanen, T. ; Olariaga, I. ; Papp, T. ; Petkovits, T. ; Pino-Bodas, R. ; Powell, M.J. ; Raja, H.A. ; Redecker, D. ; Sarmiento-Ramirez, J.M. ; Seifert, K.A. ; Shrestha, B. ; Stenroos, S. ; Stielow, B. ; Suh, S.O. ; Tanaka, K. ; Tedersoo, L. ; Telleria, M.T. ; Udayanga, D. ; Untereiner, W.A. ; Dieguez Uribeondo, J. ; Subbarao, K.V. ; Vagvolgyi, C. ; Visagie, C. ; Voigt, K. ; Walker, D.M. ; Weir, B.S. ; Weiss, M. ; Wijayawardene, N.N. ; Wingfield, M.J. ; Xu, J.P. ; Yang, Z.L. ; Zhang, N. ; Zhuang, W.Y. ; Federhen, S. - \ 2014
    Database : the Journal of Biological Databases and Curation 2014 (2014). - ISSN 1758-0463 - 21 p.
    internal transcribed spacer - arbuscular mycorrhizal fungi - ribosomal dna - interspecific hybridization - sequence analyses - species complex - identification - evolution - barcode - life
    DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
    Assessing the importance of technological non-CO2 GHG emission mitigation options in EU agriculture with the CAPRI model
    Witzke, P. ; Doorslaer, B. Van; Huck, I. ; Salputra, G. ; Fellmann, T. ; Drabik, D. ; Weiss, F. ; Leip, A. - \ 2014
    - p. 1 - 15.
    The European Commission started to reflect on a new policy framework on climate and energy for 2030. Identifying the best options for agriculture to contribute to future GHG emission reductions in the EU requires a comprehensive analysis of a wide range of possible policies, technological and management measures. In this context the CAPRI model has been further improved with respect to GHG emission accounting and especially regarding the endogenous implementation of technological mitigation options. In this paper we present the methodology of the new model features and highlight the importance of including endogenous technological GHG emission mitigation options in the model analysis. Results of illustrative emission mitigation scenarios show that different assumptions on the availability and uptake of technologies alter the scenario outcome significantly. The analysis indicates that possible negative impacts of mitigation policies on agricultural production and trade can drastically be reduced when technological mitigation options are available to farmers. This is a strong signal for enhanced research and development in the area of technological mitigation options, as well as policies that promote their diffusion.
    The nitrogen footprint of food products in the European Union
    Leip, A. ; Weiss, F. ; Lesschen, J.P. ; Westhoek, H. - \ 2014
    The Journal of Agricultural Science 152 (2014)S1. - ISSN 0021-8596 - p. 20 - 33.
    greenhouse-gas emissions - water footprint - agriculture - land - budgets - carbon - capri
    Nitrogen (N) is an essential element for plants and animals. Due to large inputs of mineral fertilizer, crop yields and livestock production in Europe have increased markedly over the last century, but as a consequence losses of reactive N to air, soil and water have intensified as well. Two different models (CAPRI and MITERRA) were used to quantify the N flows in agriculture in the European Union (EU27), at country-level and for EU27 agriculture as a whole, differentiated into 12 main food categories. The results showed that the N footprint, defined as the total N losses to the environment per unit of product, varies widely between different food categories, with substantially higher values for livestock products and the highest values for beef (c. 500 g N/kg beef), as compared to vegetable products. The lowest N footprint of c. 2 g N/kg product was calculated for sugar beet, fruits and vegetables, and potatoes. The losses of reactive N were dominated by N leaching and run-off, and ammonia volatilization, with 0·83 and 0·88 due to consumption of livestock products. The N investment factors, defined as the quantity of new reactive N required to produce one unit of N in the product varied between 1·2 kg N/kg N in product for pulses to 15–20 kg N for beef.
    Contribution of anthropology to the study of climate change
    Barnes, Jessica ; Dove, Michael ; Lahsen, Myanna ; Mathews, Andrew ; McElwee, Pamela ; McIntosh, Roderick ; Moore, Frances ; O'Reilly, Jessica ; Orlove, Ben ; Puri, Rajindra ; Weiss, Harvey ; Yager, Karina - \ 2013
    Nature Climate Change 3 (2013)6. - ISSN 1758-678X - p. 541 - 544.

    Understanding the challenge that climate change poses and crafting appropriate adaptation and mitigation mechanisms requires input from the breadth of the natural and social sciences. Anthropology's in-depth fieldwork methodology, long engagement in questions of society-environment interactions and broad, holistic view of society yields valuable insights into the science, impacts and policy of climate change. Yet the discipline's voice in climate change debates has remained a relatively marginal one until now. Here, we identify three key ways that anthropological research can enrich and deepen contemporary understandings of climate change.

    Metabolic Activation of Nonpolar Sediment Extracts Results in enhanced Thyroid Hormone Disrupting Potency
    Montano, M. ; Weiss, J. ; Hoffmann, L. ; Gutleb, A.C. ; Murk, A.J. - \ 2013
    Environmental Science and Technology 47 (2013)15. - ISSN 0013-936X - p. 8878 - 8886.
    persistent organic pollutants - brominated flame retardants - effect-directed analysis - halogenated aromatic-hydrocarbons - polybrominated diphenyl ethers - in-vitro - polychlorinated-biphenyls - endocrine disruption - estrogenic activity - hepatic microsomes
    Traditional sediment risk assessment predominantly considers the hazard derived from legacy contaminants that are present in nonpolar sediment extracts, such as polychlorinated biphenyls (PCBs), dioxins, furans (PCDD/Fs), and polyaromatic hydrocarbons (PAHs). Although in vivo experiments with these compounds have shown to be thyroid hormone disrupting (THD), in vitro their THD potency is not observed in nonpolar sediment extracts. This is hypothesized to be due to the absence of in vitro biotransformation which will result in bioactivation of the lipophilic compounds into THD hydroxyl metabolites. This study reveals that indeed metabolically activated nonpolar contaminants in sediments can competitively bind to thyroid hormone transport proteins. Sediment fractions were incubated with S9 rat microsomes, and the metabolites were extracted with a newly developed method that excludes most of the lipids to avoid interference in the applied nonradioactive 96-well plate TTR competitive binding assay. Metabolic activation increased the TTR binding potency of nonpolar fractions of POP-polluted sediments up to 100 times, resulting in potencies up to 240 nmol T4 equivalents/g sediment equivalent (nmol T4-Eq/g SEQ). This demonstrates that a more realistic in vitro sediment THD risk characterization should also include testing of both polar and medium polar sediment extracts for THD, as well as bioactivated nonpolar sediment fractions to prevent underestimation of its toxic potency.
    Ex vivo transcriptional profiling reveals a common set of genes important for the adaptation of Pseudomonas aeruginosa to chronically infected host sites
    Bielecki, P. ; Komor, U. ; Bielecka, A. ; Müsken, M. ; Puchalka, J. ; Pletz, M.W. ; Ballmann, M. ; Martins Dos Santos, V.A.P. ; Weiss, S. ; Häussler, S. - \ 2013
    Environmental Microbiology 15 (2013)2. - ISSN 1462-2912 - p. 570 - 587.
    burn wound infections - biofilm formation - cystic-fibrosis - therapeutic strategies - expression - motility - mutants - protein - system - identification
    The opportunistic bacterium Pseudomonas aeruginosa is a major nosocomial pathogen causing both devastating acute and chronic persistent infections. During the course of an infection, P.¿ aeruginosa rapidly adapts to the specific conditions within the host. In the present study, we aimed at the identification of genes that are highly expressed during biofilm infections such as in chronically infected lungs of patients with cystic fibrosis (CF), burn wounds and subcutaneous mouse tumours. We found a common subset of differentially regulated genes in all three in vivo habitats and evaluated whether their inactivation impacts on the bacterial capability to form biofilms in vitro and to establish biofilm-associated infections in a murine model. Additive effects on biofilm formation and host colonization were discovered by the combined inactivation of several highly expressed genes. However, even combined inactivation was not sufficient to abolish the establishment of an infection completely. These findings can be interpreted as evidence that either redundant traits encode functions that are essential for in vivo survival and chronic biofilm infections and/or bacterial adaptation is considerably achieved independently of transcription levels. Supplemental screens, will have to be applied in order to identify the minimal set of key genes essential for the establishment of chronic infectious diseases
    Developing Conceptual Framework for Ecosystem Mapping
    Banko, G. ; Weiss, M. ; Moser, D. ; Ubach, R. ; Abdul Malak, D. ; Halada, L. ; Roerink, G.J. ; Hazeu, G.W. ; Mucher, C.A. ; Hennekens, S.M. ; Schaminee, J.H.J. ; Brodsky, L. - \ 2013
    Kopenhagen : EEA - European Environment Agency
    Analytical improvements shown over four interlaboratory studies of perfluoroalkyl substances in environmental and food samples
    Weiss, J. ; Veen, I. van der; Leeuwen, S. van; Cofino, W.P. ; Crum, S.J.H. ; Boer, J. de - \ 2013
    TrAC : Trends in Analytical Chemistry 43 (2013). - ISSN 0165-9936 - p. 204 - 216.
    international harmonized protocol - population characteristics - perfluorinated compounds - mass-spectrometry - new-model - exposure - acids - uncertainties - laboratories - inference
    An increasing number of reports confirm the world-wide presence of the perfluoroalkyl substances (PFASs). As a consequence, the demand for qualitative and quantitative environmental occurrence data requires accurate risk assessments. To improve the analytical quality of the determination of PFASs in food and environmental samples, a 4th international interlaboratory study (ILS) was conducted in 2011. A total of 31 partners participated, and, depending on the sample matrix, up to 29 data sets were submitted. The ILS focused on food samples, as it was organized by the PERFOOD consortium in collaboration with QUASIMEME. The results showed that the cumulative experience of the participants has improved their analytical quality over four international ILSs. Several sources of errors were identified and methods to avoid them are suggested.
    Immunoglobulins drive terminal maturation of splenic dendritic cells
    Zietara, N. ; Lyszkiewicz, M. ; Puchalka, J. ; Gutierrez, M.G. ; Lienenklaus, S. ; Hobeika, E. ; Reth, M. ; Martins Dos Santos, V.A.P. ; Krueger, A. ; Weiss, S. - \ 2013
    Proceedings of the National Academy of Sciences of the United States of America 110 (2013)6. - ISSN 0027-8424 - p. 2282 - 2287.
    c-type lectin - cross-presentation - antigen presentation - in-vivo - functional maturation - complement receptors - immune-responses - b-lymphocytes - self-antigens - t-cells
    Nature and physiological status of antigen-presenting cells, such as dendritic cells DCs, are decisive for the immune reactions elicited. Multiple factors and cell interactions have been described that affect maturation of DCs. Here, we show that DCs arising in the absence of immunoglobulins (Ig) in vivo are impaired in cross-presentation of soluble antigen. This deficiency was due to aberrant cellular targeting of antigen to lysosomes and its rapid degradation. Function of DCs could be restored by transfer of Ig irrespective of antigen specificity and isotype. Modulation of cross-presentation by Ig was inhibited by coapplication of mannan and, thus, likely to be mediated by C-type lectin receptors. This unexpected dependency of splenic DCs on Ig to cross-present antigen provides insights into the interplay between cellular and humoral immunity and the immunomodulatory capacity of Ig
    Livestock greenhouse gas emissions and mitigation potential in Europe
    Bellarby, J. ; Tirado, R. ; Leip, A. ; Weiss, F. ; Lesschen, J.P. ; Smith, P. - \ 2013
    Global Change Biology 19 (2013)1. - ISSN 1354-1013 - p. 3 - 18.
    life-cycle assessment - ruminant production systems - carbon sequestration - soil carbon - milk-production - climate-change - meat quality - dairy-cows - food waste - land-use
    The livestock sector contributes considerably to global greenhouse gas emissions (GHG). Here, for the year 2007 we examined GHG emissions in the EU27 livestock sector and estimated GHG emissions from production and consumption of livestock products; including imports, exports and wastage. We also reviewed available mitigation options and estimated their potential. The focus of this review is on the beef and dairy sector since these contribute 60% of all livestock production emissions. Particular attention is paid to the role of land use and land use change (LULUC) and carbon sequestration in grasslands. GHG emissions of all livestock products amount to between 630 and 863 Mt CO2e, or 12–17% of total EU27 GHG emissions in 2007. The highest emissions aside from production, originate from LULUC, followed by emissions from wasted food. The total GHG mitigation potential from the livestock sector in Europe is between 101 and 377 Mt CO2e equivalent to between 12 and 61% of total EU27 livestock sector emissions in 2007. A reduction in food waste and consumption of livestock products linked with reduced production, are the most effective mitigation options, and if encouraged, would also deliver environmental and human health benefits. Production of beef and dairy on grassland, as opposed to intensive grain fed production, can be associated with a reduction in GHG emissions depending on actual LULUC emissions. This could be promoted on rough grazing land where appropriate.
    Impact of vegetation variability on potential predictability and skill of EC-Earth simulations
    Weiss, M. ; Hurk, B. van den; Haarsma, R. ; Hazeleger, W. - \ 2012
    Climate Dynamics 39 (2012)11. - ISSN 0930-7575 - p. 2733 - 2746.
    land-surface parameterization - leaf-area - soil-moisture - interannual variability - air-temperature - climate - model - sensitivity - precipitation - system
    Climate models often use a simplified and static representation of vegetation characteristics to determine fluxes of energy, momentum and water vapour between surface and lower atmosphere. In order to analyse the impact of short term variability in vegetation phenology, we use remotely-sensed leaf area index and albedo products to examine the role of vegetation in the coupled land–atmosphere system. Perfect model experiments are carried out to determine the impact of realistic temporal variability of vegetation on potential predictability of evaporation and temperature, as well as model skill of EC-Earth simulations. The length of the simulation period is hereby limited by the availability of satellite products to 2000–2010. While a realistic representation of vegetation positively influences the simulation of evaporation and its potential predictability, a positive impact on 2 m temperature is of smaller magnitude, regionally confined and more pronounced in climatically extreme years.
    Species, functional groups, and habitat preferences of birds in five agroforestry classes in Tabasco, Mexico
    Wal, J.C. van der; Peña-Álvarez, B. ; Arriaga-Weiss, S.L. ; Hernández-Daumás, S. - \ 2012
    The Wilson Journal of Ornithology 124 (2012)3. - ISSN 1559-4491 - p. 558 - 571.
    tropical forest - cacao plantations - coffee production - atlantic forest - biodiversity - diversity - landscapes - abundance - classification - conservation
    We studied species, functional groups, and habitat preferences of birds in five classes of agroforestry systems: agroforests, animal agroforestry, linear agroforestry, sequential agroforestry, and crops under tree cover in Tabasco, Mexico. Sampling sites were >2 km from natural forest fragments. Observations were made at 38 sites using 30-min point and transect counts in the morning and afternoon in the rainy season, season of northern winds, and dry season from June 2008 to May 2009. We observed 3,551 birds, which were assigned to 102 species: 72 were resident and 30 were migratory species. Overall efficiency of sampling was 82.4% and varied from 68.7% in linear agroforestry to 81.5% in animal agroforestry. Total species richness varied from 43 in sequential agroforestry to 64 in animal agroforestry. Species richness and Shannon diversity indices revealed no differences among agroforestry classes. Bird communities in animal agroforestry, linear agroforestry, and sequential agroforestry had similar species compositions, as did agroforests and crops under tree cover. Birds in all agroforestry classes were mainly forest generalists, although specialists of open areas were common, particularly in animal and sequential agroforestry. Only one individual of a forest specialist species was observed during sampling. Migrant species were mostly forest generalists, but some open area specialists occurred in animal agroforestry. Resident birds were distributed over all foraging guilds in all agroforestry classes, whereas migrants were mainly foliage-gleaning insectivores. Foraging guilds had different relative abundances among agroforestry classes. Structural diversity of agroforestry classes did not seem to influence bird species richness. Forest specialist species were virtually absent in agroforestry classes, but the avifauna in agroforestry is diverse and valuable in itself
    Farm, Land, and Soil nitrogen budgets for Agriculture in Europe calculated with CAPRI
    Leip, A. ; Britz, W. ; Weiss, F. ; Vries, W. de - \ 2011
    Environmental Pollution 159 (2011)11. - ISSN 0269-7491 - p. 3243 - 3253.
    dairy farms - nutrient balances - production systems - indicators - management - losses - netherlands - efficiency - surpluses - sweden
    We calculated farm, land, and soil N-budgets for countries in Europe and the EU27 as a whole using the agro-economic model CAPRI. For EU27, N-surplus is 55 kg N ha-1 yr-1 in a soil budget and 65 kg N2O–N ha-1 yr-1 and 67 kg N ha-1 yr-1 in land and farm budgets, respectively. NUE is 31% for the farm budget, 60% for the land budget and 63% for the soil budget. NS values are mainly related to the excretion (farm budget) and application (soil and land budget) of manure per hectare of total agricultural land. On the other hand, NUE is best explained by the specialization of the agricultural system toward animal production (farm NUE) or the share of imported feedstuff (soil NUE). Total N input, intensive farming, and the specialization to animal production are found to be the main drivers for a high NS and low NUE.
    Persistent aryl hydrocarbon receptor inducers increase with altitude, and estrogen-like disrupters are low in soils of the Alps
    Levy, W. ; Henkelmann, B. ; Bernhoft, S. ; Bovee, T.F.H. ; Buegger, F. ; Jakobi, G. ; Kirchner, M. ; Bassan, R. ; Krauchi, N. ; Moche, W. ; Offenthaler, I. ; Simoncic, P. ; Weiss, P. ; Schramm, K.W. - \ 2011
    Environmental Science and Pollution Research 18 (2011)1. - ISSN 0944-1344 - p. 99 - 110.
    green fluorescent protein - dibenzo-p-dioxin - in-vitro - polychlorinated biphenyl - toxicity equivalents - bioassay - expression - model - environment - pesticides
    analyzed for polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans and polychlorinated biphenyls by high-resolution gas chromatography/high-resolution gas spectrometry. Additionally, the EROD micro-assay and a genetically modified yeast estrogen bioassay were carried out to determine persistent aryl hydrocarbon receptors (AhR) and estrogen receptors (ER) agonists, respectively. Regarding the AhR agonists, the toxicity equivalents of analytical and EROD determined values were compared, targeting both altitude of samples and their soil organic
    Modelling the impacts of Forest Management Alternatives on recreational values in Europe
    Schelhaas, M. ; Edwards, D. ; Didion, M.P. ; Hengeveld, G.M. ; Nabuurs, G.J. ; Mason, B. ; Lindner, M. ; Moiseyev, A. ; Jay, M. ; Jensen, F. ; Lucas, B. ; Marzano, M. ; Montagne, C. ; Peace, A. ; Weiss, G. - \ 2010
    UK : Forest Research (518128 Deliverable D2.3.7)
    Retrieving crop specific green area index from remote sensing data when the spatial resolution is close to the target field size
    Duveiller, G. ; Weiss, M. ; Baret, F. ; Wit, A.J.W. de; Defourny, P. - \ 2010
    Preface : Recent advances in crop growth modelling
    Weiss, A. ; Flerchinger, G.N. ; McMaster, G.S. ; Wang, E. ; White, J.W. ; Yin, X. ; Struik, P.C. ; Wienk, J.F. - \ 2009
    NJAS Wageningen Journal of Life Sciences 57 (2009)1. - ISSN 1573-5214 - p. 3 - 3.
    Amino acid sequences directed against envelope proteins of a virus and polypeptides comprising the same for the treatment of viral diseases
    Hultberg, A. ; Maassen, C.B.M. ; Landschoot, P. ; Depla, E. ; Stortelers, C. ; Verrips, C.T. ; Gucht, S. ; Melera, J. ; Saunders, M.J. ; Haard, J.J.W. ; Weiss, R.A. ; temperton, N.J. ; Saelens, X. ; Schepens, B. ; Szyroki, A. ; Harmsen, M.M. - \ 2009
    Octrooinummer: WO2009147248, gepubliceerd: 2009-06-05.
    The present invention relates in part to amino acid sequences that are directed against and/or that can specifically bind to an envelope protein of a virus, as well as to compounds or constructs, and in particular proteins and polypeptides, that comprise or essentially consist of one or more such amino acid sequences.
    Identification of Uranyl Surface Complexes an Ferrihydrite: Advanced EXAFS Data Analysis and CD-MUSIC Modeling
    Rossberg, A. ; Ulrich, K.U. ; Weiss, S. ; Tsushima, S. ; Hiemstra, T. ; Scheinost, A.C. - \ 2009
    Environmental Science and Technology 43 (2009)5. - ISSN 0013-936X - p. 1400 - 1406.
    transformation factor-analysis - uranium(vi) sorption - adsorption - acid - hematite - spectroscopy - goethite - u(vi)
    Previous spectroscopic research suggested that uranium(VI) adsorption to iron oxides is dominated by ternary uranyl-carbonato surface complexes across an unexpectedly wide pH range. Formation of such complexes would have a significant impact on the sorption behavior and mobility of uranium in aqueous environments. We therefore reinvestigated the identity and structural coordination of uranyl sorption complexes using a combination of U LIII-edge extended X-ray absorption fine structure (EXAFS) spectroscopy and iterative transformation factor analysis, which enhances the resolution in comparison to conventional EXAFS analysis. A range of conditions (pH, CO2 partial pressure, ionic strength) made it possible to quantify the variations in surface speciation. In the resulting set of spectral data (N = 11) the variance is explained by only two components, which represent two structurally different types of surface complexes: (1) a binary uranyl surface complex with a bidentate coordination to edges of Fe(O,OH)6 octahedra and (2) a uranyl triscarbonato surface complex where one carbonate ion bridges uranyl to the surface. This ternary type B complex differs from a type A complex where uranyl is directly attached to surface atoms and carbonate is bridged by uranyl to the surface. Both surface complexes agree qualitatively and quantitatively with predictions by a charge distribution (CD) model. According to this model the edge-sharing uranyl complex has equatorial ligands (-OH2, -OH, or one -CO3 group) that point away from the surface. The monodentate uranyl triscarbonato surface complex (type B) is relevant only at high pH and elevated pCO2. At these conditions, however, it is responsible for significant uranyl sorption, whereas standard models would predict only weak sorption. This paper presents the first spectroscopic evidence of this ternary surface complex, which has significant implications for immobilization of uranyl in carbonate-rich aqueous environments
    A higher-level phylogenetic classification of the Fungi
    Hibbett, D.S. ; Binder, M. ; Bischoff, J.F. ; Blackwell, M. ; Cannon, P.F. ; Eriksson, O.E. ; Huhndorf, S. ; James, T. ; Kirk, P.M. ; Lücking, R. ; Thorsten Lumbsch, H. ; Lutzoni, F. ; Brandon Matheny, P. ; McLaughlin, D.J. ; Powell, M.J. ; Redhead, S. ; Schoch, C.L. ; Spatafora, J.W. ; Stalpers, J.A. ; Vilgalys, R. ; Aime, M.C. ; Aptroot, A. ; Bauer, R. ; Begerow, D. ; Benny, G.L. ; Castlebury, L.A. ; Crous, P.W. ; Dai, Y.C. ; Gams, W. ; Geiser, D.M. ; Griffith, G.W. ; Gueidan, C. ; Hawksworth, D.L. ; Hestmark, G. ; Hosaka, K. ; Humber, R.A. ; Hyde, K.D. ; Ironside, J.E. ; Koljalg, U. ; Kurtzman, C.P. ; Larsson, K.H. ; Lichtwardt, R. ; Longcore, J. ; Miadlikowska, J. ; Miller, A. ; Moncalvo, J.M. ; Mozley-Standridge, S. ; Oberwinkler, F. ; Parmasto, E. ; Reeb, V. ; Rogers, J.D. ; Roux, C. Le; Ryvarden, L. ; Sampaio, J.P. ; Schüssler, A. ; Sugiyama, J. ; Thorn, R.G. ; Tibell, L. ; Untereiner, W.A. ; Walker, C. ; Wang, Z. ; Weir, A. ; Weiss, M. ; White, M.M. ; Winka, K. ; Yao, Y.J. ; Zhang, N. - \ 2007
    Mycological Research 111 (2007)5. - ISSN 0953-7562 - p. 509 - 547.
    ribosomal dna-sequences - lsu rdna sequences - molecular phylogeny - ord-nov - mitochondrial sequences - natural classification - basidiomycetous yeasts - bayesian-analysis - large subunits - nuclear rdna
    A comprehensive phylogenetic classification of the kingdom Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from diverse members of the fungal taxonomic community. The classification includes 195 taxa, down to the level of order, of which 16 are described or validated here: Dikarya subkingdom nov.; Chytridiomycota, Neocallimastigomycota phyla nov.; Monoblepharidomycetes, Neocallimastigomycetes class. nov.; Eurotiomycetidae, Lecarioromycetidae, Mycocaliciomycetidae subclass. nov.; Acarosporales, Corticiales, Baeomycetales, Candelariales, Gloeophyllales, Melanosporales, Trechisporales, Umbilicariales ords. nov. The clade containing Ascomycota and Basidiomycota is classified as subkingdom Dikarya, reflecting the putative synapomorphy of dikaryotic hyphae. The most dramatic shifts in the classification relative to previous works concern the groups that have traditionally been included in the Chytridiomycota and Zygomycota. The Chytridiomycota is retained in a restricted sense, with Blastocladiomycota and Neocallimastigomycota representing segregate phyla of flagellated Fungi. Taxa traditionally placed in Zygomycota are distributed among Glomeromycota and several subphyla incertae sedis, including Mucoromycotina, Entomophthoromycotina, Kickxellomycotina, and Zoopagomycotiria. Microsporidia are included in the Fungi, but no further subdivision of the group is proposed. Several genera of 'basal' Fungi of uncertain position are not placed in any higher taxa, including Basidiobolus, Caulochytrium, Olpidium, and Rozella. (c) 2007 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.
    Corruption clubs: empirical evidence from kernel density estimates
    Herzfeld, T. ; Weiss, Ch. - \ 2007
    Applied Economics 39 (2007)12. - ISSN 0003-6846 - p. 1565 - 1572.
    A common finding of many analytical models is the existence of multiple equilibria of corruption. Countries characterized by the same economic, social and cultural background do not necessarily experience the same levels of corruption. In this article, we use Kernel Density Estimation techniques to analyse the cross-country distribution of corruption. Particular emphasis will be given to the question whether the distribution of corruption shows more than one peak. We find that most of the estimated densities exhibit twin peaks. We also provide some evidence on the intra-distribution dynamics and the persistence of corruption. We find the group of countries classified within the two 'clubs' to be very stable. Corruption is a highly persistent phenomenon. Substantial changes in the economic, political and cultural environment of countries within the 'corruption club' are required before a significant decline of corruption is to be expected.
    Relatedness of Streptococcus equi subsp. zooepidemicus strains isolated from harbour seals (Phoca vitulina) and grey seals (Halichoerus grypus) of various origins of the North Sea during 1988 - 2005
    Akineden, Oe. ; Alber, J. ; Laemmler, C. ; Weiss, R. ; Siebert, U. ; Foster, G. ; Tougaard, S. ; Brasseur, S.M.J.M. ; Reijnders, P.J.H. - \ 2007
    Veterinary Microbiology 121 (2007)1-2. - ISSN 0378-1135 - p. 158 - 162.
    molecular characterization - german north - identification
    The present study was designed to identify 15 beta-hemolytic streptococci isolated during a period between 1988 and 2005 from nine harbour seals and six grey seals from various origins of the North Sea. All isolates were identified as Streptococcus equi subsp. zooepidemicus. The bacteria were additionally investigated for relatedness by restriction fragment length polymorphism analysis of PCR amplified 16S-23S rDNA intergenic spacer region and gene szp and by macrorestriction analysis of chromosomal DNA of the strains by pulsed field gel electrophoresis. The molecular analysis yielded identical or closely related patterns within the strains of the present study and with the S. equi subsp. zooepidemicus strains isolated from harbour seals of German North Sea which were investigated previously [Akineden, O., Hassan, A.A., Alber, J., El-Sayed, A., Estoepangestie, A.T.S., Lammler, C., Weiss, R., Siebert, U., 2005. Phenotypic and genotypic properties of S. equi subsp. zooepidemicus isolated from harbor seals (Phoca vitulina) from the German North Sea during the phocine distemper outbreak in 2002. Vet. Microbiol. 110, 147-152]. This indicates that this single or closely related bacterial clone existed during both phocine distemper virus epidemics in 1988 and 2002 and that a direct transmission of the strains has occurred between two seal species and between seal populations of far distant regions possibly with grey seals as a vector.
    Korruption: Persistenz und Lock-in Effekte
    Herzfeld, T. ; Weiss, Ch. - \ 2006
    Wirtschaftspolitische Blätter 2006 (2006)4. - p. 621 - 637.
    Korruption wird häufig als Ursache fehlender Fortschritte im Entwicklungsprozess vieler Volkswirtschaften angesehen. Entsprechend steht Korruptionsbekämpfung bei der Weltbank und allen wichtigen multilateralen Organisationen der wirtschaftlichen Zusammenarbeit an vorderster Stelle der Agenda. Trotz einiger ehrlicher Anstrengungen von Regierungen und Politikern gegen Korruption vorzugehen, muss festgestellt werden, dass die Erfolge in der Bekämpfung von Korruption lediglich bescheiden sind. Korruption ist offenbar ein sehr persistentes Phänomen. Hat sich korruptes Verhalten in einer Gesellschaft einmal ausgebreitet, ist es kaum wieder zu eliminieren, die Gesellschaft ist in einer Situation mit verbreiteter Korruption ¿gefangen¿ (¿Lock-in Effekt¿). Der vorliegende Beitrag widmet sich den Ursachen von Korruption, wobei besonderes Augenmerk auf jene Erklärungen gelegt werden soll, welche für die Persistenz der Korruption bzw das Auftreten von ¿Lock-in Effekten¿ bedeutsam sind.
    Intake of micronutrients high in animal-source foods is associated with better growth in rural Kenyan school children
    Grillenberger, M. ; Neumann, C.G. ; Murphy, S.P. ; Bwibo, N.O. ; Weiss, R.E. ; Jiang, L.H. ; Hautvast, J.G.A.J. ; West, C.E. - \ 2006
    The British journal of nutrition 95 (2006)2. - ISSN 0007-1145 - p. 379 - 390.
    improve dietary quality - catch-up growth - bone - xerophthalmia - malnutrition - iron - fat - schoolchildren - childhood - toddlers
    Observational studies have shown that children in developing countries consuming diets containing high amounts of bioavailable nutrients, such as those found in animal-source foods, grow better. The present study investigated which specific nutrients from the diet of Kenyan school children predicted their growth. The children (n 544, median age 7 years) participated in a 2-year long food supplementation study with animal-source foods. Height gain during the intervention period was positively predicted by average daily intakes of energy from animal-source foods, haem Fe, preformed vitamin A, Ca and vitamin B-12. Weight gain was positively predicted by average daily intakes of energy from animal-source foods, haem Fe, preformed vitamin A, Ca and vitamin B-12. Gain in mid-upper-arm muscle area was positively predicted by average daily intakes of energy from animal-source foods and vitamin B-12. Gain in mid-upper-arm fat area was positively predicted by average daily intakes of energy from animal-source foods. Gain in subscapular skinfold thickness was not predicted by any of the nutrient intakes. Negative predictors of growth were total energy and nutrients that are contained in high amounts in plant foods. The study shows that growth was positively predicted by energy and nutrients that are provided in high amounts and in a bioavailable form in meat and milk, and their inclusion into the diets of children in developing countries should be part of all food-based programmes in order to improve micronutrient status and growth.
    Corruption and legal (in)effectiveness: an empirical investigation
    Herzfeld, T. ; Weiss, Ch. - \ 2003
    European Journal of Political Economy 19 (2003)3. - ISSN 0176-2680 - p. 621 - 632.
    Numerous studies have investigated the causes and measured the consequences of differences in corruption among countries. An effective legal system has been viewed as a key component in reducing corruption. However, estimating cross-sectional as well as panel data models, we find a significant inter-relationship between legal (in)effectiveness and various measures of corruption. This re-enforcing inter-relationship suggests that corruption is a persistent phenomenon and that strong forces tend to perpetuate corruption at fairly constant levels.
    Large-scale reconstruction of areas with intensive livestock holdings : regional challenges and prospects
    Brink, A. van den; Heinen, J. - \ 2002
    In: Les regions en face de l'aménagement du territoire, du droit et de la protection de l'environnement : 31e Symposium International FESF Strasbourg, Strasbourg, 2002 / Erich Weiss & Tanja Zangger Bern : Peter Lang - p. 271 - 284.
    Cloning and structural analysis of partial acetylcholine receptor subunit genes from the parasitic nematode Teladorsagia circumcincta
    Walker, J. ; Hoekstra, R. ; Roos, M.H. ; Wiley, L.J. ; Weiss, A.S. ; Sangster, N.C. ; Tait, A. - \ 2001
    Veterinary Parasitology 97 (2001). - ISSN 0304-4017 - p. 329 - 335.
    Microperoxidase-8 : tuning of its catalysis and reactivity
    Primus, J.L.A. - \ 2000
    Agricultural University. Promotor(en): C. Veeger; R. Weiss; I.M.C.M. Rietjens. - S.l. : S.n. - ISBN 9789058083418 - 173
    peroxidasen - katalysatoren - cytochromen - peroxidases - catalysts - cytochromes

    In this thesis, microperoxidase-8, Fe III MP-8, and the manganese variant Mn III MP-8, were studied. Insight in i) the mechanism of oxygen exchange between the oxo group of porphyrin high-valent metal-oxo species and solvent, ii) their cytochrome P450 (P450) and peroxidase catalytic reactivity and iii) the formation of their catalytic reactive intermediates is provided.

    Determinants of the peroxidase and P450 chemistry for Fe III MP-8 and Mn III MP-8 (Chapter 1)

    In the Chapter 1 of this thesis, peroxidase and P450 enzymes were compared in order to understand the major differences between both types of enzymes explaining the differences in their chemistry. It was shown that peroxidases and P450s share similar intermediates in their catalytic cycles but that both types of enzymes were structurally different. Differences in the distal environment of the heme and in the nature of the axial ligand can be regarded as having an influence on their chemistry.

    1. Differences in the heme distal environment

    A comparison of the distal heme cavity for peroxidase and P450 enzymes shows that peroxidases do not have a clearly defined hydrophobic distal pocket allowing the binding of organic substrates near the heme iron centre. With the exception of hydroperoxides which bind to the heme iron centre and are subsequently reduced by the heme group to generate catalytic reactive intermediates, the organic substrate is proposed to bind on theδ-meso heme edge thereby allowing electrons transfer to the heme prosthetic group. The fact that organic substrates cannot bind to the distal part of the peroxidase active site near the oxo group of Compound I, explains why these enzymes do not support oxygen transfer reactions. Moreover the fact that only for peroxidase mutants where some "extra space" has been created on the distal part of the active site, monooxygenases reactions are observed but catalysed at a lower rate than for heme-thiolate enzymes, corroborates the assumption that substrate binding near the heme iron favours oxygen transfer. Evolutionary speaking, peroxidases are well designed to reduce small oxygen containing molecules, hydroperoxides, and to convert them into oxidative power which may be beneficial to the cell because of the formation of useful compounds such as polymers. P450s, however, have a distal active site pocket which allows substrate binding near the heme iron center. From an evolutionary point, P450s are well designed to convert harmful xenobiotics or modifying membrane lipid components in the cell. The fact that the substrate binds close to the site where the reactive catalytic intermediates are generated favours in-situ conversion and direct oxygen transfer to the substrate. Moreover this oxygen transfer can be mediated by the various catalytic intermediates of the reaction cycle preceding the Compound I analogue and not only by the Compound I analogue. The physical proximity of the substrate and the reactive intermediates favours a reaction of the catalytic intermediates with the substrate over a transformation of a given catalytic intermediate into the following catalytic intermediate of the reaction cycle of the enzyme.

    2. Differences in the nature of the proximal axial ligand

    Peroxidases and P450s differ by the nature of their proximal axial ligand. The negative charge of the cysteinate ligand of P450s is proposed to lower the oxidation potential of the Compound I analogue intermediate thereby favouring oxygen transfer to substrate over electron abstraction from substrate . The negative charge of the sulphur atom is somewhat reinforced by the involvement of a network of hydrogen bonds from the residues of the heme proximal active site to the sulphur of the thiolate group. Theoretical MO-calculations also have shown that the sulphur orbitals of the cysteinate mix with the a 2u cationic state of the porphyrin high-valent iron-oxo intermediate along the reaction pathway. This is not observed for the proximal histidine ligand of peroxidases. In peroxidases, the neutral histidine ligand is proposed to favour electron abstraction from substrate over oxygen transfer to substrate .

    Compound I oxo exchange: implications for oxygen transfer (Chapters 2 and 3)

    In the field of heme-based catalysis, labelling studies are used to discriminate between peroxidase-type of chemistry and P450-type of chemistry. Tracing of the oxygen donor atoms in the product allows to differentiate between true oxygen transfer , where the oxygen atom inserted in the substrate originates from the primary oxygen donor, P450 chemistry, and apparent oxygen transfer where the oxygen atom inserted in the substrate originates from the solvent, peroxidase chemistry. However, heme-enzymes and the corresponding models were shown to exchange the oxo group of their Compound I intermediate, or Compound I analogue, with bulk solvent. Chapters 2 and 3 of this thesis are oriented on the mechanistic aspects of the exchangeability of the oxo group of Compound I with bulk solvent. In Chapter 2, HRP and the labelled oxygen donor are left incubating during an exchange step of variable time length before the substrate, aniline, is added. The conversion of aniline results in the insertion of one oxygen atom in the substrate by para -hydroxylation. The para -hydroxylated aniline formed during the conversion step subsequent to the exchange step was analysed by MS. This reveals an increasing percentage of the incorporation of oxygen atoms originating from the solvent when the duration of the exchange step is increased. When catalase was added between the two steps of the experiment, no product was formed. This shows that the heme catalyst induces oxygen exchange between bulk water and H 2 O 2 , to form H 2 O 2 containing oxygen atoms issued from the solvent. A mechanism explaining this oxygen exchange for an axially coordinated heme has been suggested including the reversibility of the formation of Compound I for HRP, but also for Fe III MP-8, hemin and hematin. Actually, water becomes a substrate for the porphyrin high-valent iron-oxo intermediate and competes with the organic substrate, when present, for being oxidised. In the study presented in Chapter 2, substrate oxidation and water oxidation were decoupled thereby emphasising the water oxidation step. Moreover this study indirectly suggests that oxidised heme-based systems can catalyse the formation of peroxide bonds at the (modest) apparent rate of≈1 s -1 . This is a relevant outcome of this study, since the design of molecules containing a peroxide bond is of fundamental importance for oxidation chemistry and is of particularly interest for the chemical industry.

    In Chapter 3, the same argumentation as proposed in Chapter 2 is supported by additional exchange experiments with iron and manganese water-soluble porphyrins. This chapter is an attempt to unify the views on porphyrin high-valent metal-oxo/solvent exchange processes. Direct oxygen exchange of the oxo group of Compound I, for a solvent oxygen atom is not found to account for the regeneration of H 2 O 2 during the exchange step. Also a mechanism such as oxo/hydroxo tautomerism where the transfer of two protons from the trans water axial ligand to the oxygen of the oxo group results in an exchange of the oxo oxygen cannot explain Fe III MP-8 supported oxygen exchange. The fact that Fe III MP-8 has an axial histidine ligand prevents solvent binding trans to the oxo group, which would be a prerequisite for proton transfer resulting in oxygen exchange between both axial ligands. Obviously this cannot explain oxygen exchange catalysed by axially ligated heme or metalloporphyrins like Fe III MP-8. The reversible formation of Compound I, proposed in Chapter 2, explains the results in a clear way.

    Catalytic reactivity of Fe III MP-8 and Mn III MP-8 (Chapter 4 and 5)

    The heme-peptide model, Fe III MP-8, shows peroxidase activity and can also be used as a heme-enzyme model for studying P450 chemistry based on the fact that, upon addition of ascorbate, the reactive species which are responsible for peroxidase chemistry are scavenged. As a consequence Fe III MP-8 can be active in two modes: the peroxidase mode where the catalysis is dominated by porphyrin high-valent iron-oxo intermediates and the P450 mode where the porphyrin high-valent iron-oxo intermediates are (partially) scavenged and catalysis is mainly performed by intermediates appearing prior to Compound I in the reaction cycle. The switch between the two modes is provided by the addition of ascorbate to the system in the case of P450 chemistry, which acts as scavenger for porphyrin high-valent iron-oxo intermediates.

    In Chapter 4 the reactivity of Fe III MP-8 for H 2 O 2 supported O- and N-dealkylation, a peroxidase/P450 type of reaction, has been investigated. In the peroxidase mode, i.e. without ascorbate addition, the rate of conversion of the substrates is correlated with their quantum mechanically calculated first ionisation potential. This indicates that their conversion proceeds via an initial electron abstraction from the substrate. This is corroborated by the observation of a large amount of polymerisation products together with the formation of small amounts of N-dealkylated products. In contrast however O-dealkylation was not observed. This observation that O-alkylated substrates are not dealkylated in the peroxidase mode can be related to the fact that their first ionisation potential is too low. In the P450 mode, i.e. in the presence of ascorbate, O- and N-alkylated substrates are both converted and a correlation with the calculated first ionisation potential of the substrates no longer exists. This suggests that O- and N-dealkylations in the P450 mode proceed via a non-radical type of mechanism and thus through other intermediates than Compound I and Compound II, since ascorbate is a scavenger of Compound I and II. As an alternative reactive species the non-radical type PorFe III -(hydro)peroxo intermediate, may be the species involved in the P450 mode of Fe III MP-8 supported O- and N-dealkylation. The PorFe III (hydro)peroxo intermediate is known as Compound 0 and appears before Compound I in the catalytic cycle. Mechanisms for Compound 0 supported O- and N-dealkylations are discussed in detail.

    The aim of the investigations described in Chapter 5 was to gain information on the nature of the different reactive species involved in MP-8 supported catalysis comparing again peroxidase and P450 reactions. For this purpose the manganese variant of Fe(III)MP-8, Mn(III)MP-8 was synthesised. Iron and manganese porphyrin complexes have a similar chemistry but differ in their reaction kinetics providing information concerning which type of intermediate is involved in catalysis. The conversion of guaiacol (2-methoxyphenol), ortho -dianisidine (3,3'-dimethoxybenzidine) and aniline catalysed by Fe III MP-8 and Mn III MP-8 was studied. The first two substrates are models for the peroxidase reactivity of heme-enzymes and the third one is a model for the P450 reactivity of heme-enzymes. The pH-dependence of the rate of conversion, k cat , of each substrate was studied for Fe III MP-8 and Mn III MP-8 supported conversions, using H 2 O 2 as oxygen donor. For the peroxidase mode it was shown that the optimal pH for Mn III MP-8 supported conversions is pH 11, about 2 units higher than for Fe III MP-8 which has an optimal pH of 9. This can be correlated to the lower reduction potential of the Mn III MP-8/Mn II MP-8 transition when compared to the iron complex. The iron atom is proposed to better stabilise the deprotonated coordinated hydroperoxide molecule than the manganese centre due to its higher electron withdrawing effect on the proximal oxygen of the (hydro)peroxo group. For the cytochrome P450 mode, i.e. in the presence of ascorbate, it was found that Mn III MP-8 was not able to catalyse the para -hydroxylation of aniline whereas it was possible for Fe III MP-8 under the same conditions. These results are in line with the conclusions of Chapter 4 and indicate that the MP-8 supported cytochrome P450 chemistry proceeds via a PorFe III -hydroperoxo intermediate. This also explains the absence of aniline hydroxylation activity for Mn III MP-8 based catalysis because the Mn III -(hydro)peroxo intermediate is much less reactive toward electrophilic hydroxylation than the corresponding iron intermediate. As a consequence the hydroxylation of aniline by Fe III MP-8 may be performed by Compound 0. However, as stressed also in Chapter 4, Compound I and II, typical of the peroxidase mode, may also play a role in the P450 mode since ascorbate competes with aniline for oxidation by Compound I and II.

    Characterisation of peroxidase and P450 intermediates (Chapter 6 and 7)

    One of the major drawbacks of MP-8 is the high inactivation rate observed for the catalyst under operational conditions in both the P450 and the peroxidase mode. In an effort aiming at understanding the reasons for the fast inactivation of Fe III MP-8, the fate of the catalyst was studied under turnover conditions in the absence of substrate. Chapter 6 presents the characterisation of a modified Fe III MP-8 with a hydroxylated His18. The modified catalyst was isolated under operational conditions in the presence of H 2 O 2 . The structure of the native and the modified Fe III MP-8 were compared by HPLC, UV/visible, ESI-MS 2 and 1 H-NMR. Analysis showed the formation of a product more hydrophilic than Fe III MP-8, with an intact heme ring and having an extra oxygen inserted on the peptide. ESI-MS 2 and 1 H-NMR suggest the extra oxygen atom to be inserted on the Nδ1 of the imidazole ring of the His18. The formation of the modified intermediate is inhibited by ascorbate and labelling studies have shown that the inserted oxygen originates from the solvent. This suggests the modified Fe III MP-8 to derive from a Compound I analogue of Fe III MP-8. The fact that the solvent-assisted hydroxylation occurs on the proximal histidine ligand suggests the second oxidation equivalent of the analogue of Fe III MP-8 Compound I to be majorly delocalised on the His18 axial ligand by mesomerism.

    The characterisation and the analysis of the kinetics of formation of the heme-intermediates competent in MP-8-supported peroxidase and P450 catalysis is the subject of Chapter 7. The kinetics for the formation of Compound 0, Compound I analogue and Compound II were compared for Fe III MP-8 and Mn III MP-8. Analysis reveals a one order of magnitude higher rate of formation of PorFe III -OOH (k = 1.3×10 6 M -1 .s -1 ) when compared to the rate of formation of PorMn III -OOH (k = 1.1×10 5 M -1 .s -1 ). The overall rate of the reaction for both complexes with H 2 O 2 , increases with higher pH-values. The corresponding pK a values which were found to explain this pH-dependency are in complete agreement with the optimal values for Fe III MP-8 (pH 9.2) and Mn III MP-8 (pH 11.0) supported catalysis (Chapter 5) and were found to correspond to the deprotonation of metal-bound water for Fe III MP-8. This explains how heme-peptide models which lack a distal histidine, acting as an acid/base catalyst for the deprotonation of H 2 O 2 and for the subsequent cleavage of the O-O peroxide bond, facilitate the deprotonation of H 2 O 2 . For MP-8, the peroxide deprotonation may proceeds through a concerted mechanism which results in the replacement of the hydroxyl ligand by a hydroperoxo ligand. It is not sure, however, how MP-8 catalyses the cleavage of the O-O peroxide bond, since no residue or group able to deliver protons to the distal oxygen in order to facilitate bond cleavage are present on the distal site. An eventual participation of the Nδ1 of the imidazole ring of the His18 of a second molecule of MP-8 as proton donor cannot be excluded. The manganese Compound 0 is proposed to be heterolytically cleaved into a Compound I type of intermediate, Mn IV MP-8=O(R ·+ ), where the second oxidation equivalent seems to be localised on the peptide part of the molecule. This is suggested by the analysis of the transient UV/visible and EPR spectra of oxidised Mn III MP-8. Based on the kinetic analysis and on the results of Chapter 6, iron Compound 0 is also proposed to be heterolytically cleaved into a similar Compound I type of intermediate, Fe IV MP-8=O(R ·+ ), with a cleavage rate analogue to the one of the manganese complex (k≈150 s -1 ).

    To summarise, in peroxidases, the hydroperoxo intermediate is rapidly converted, during the reaction cycle, into Compound I catalysed by the residues of the distal heme pocket. In P450s the corresponding hydroperoxo or peroxo intermediates may react with the substrate bound in the active site before they are converted into a Compound I analogue. In other words, P450 chemistry is not only based on the catalytic reactivity of Compound I but also on the reactivity of Compound 0 and the deprotonated form of Compound 0 respectively the PorFe III -hydroperoxo and the PorFe III -peroxo intermediates. Whereas the isoelectronic analogue of Compound I can be seen as an intermediate in electrophilic reactions such as Compound 0, the deprotonated Compound 0 is proposed to be active in both electrophilic and nucleophilic reactions.

    As a consequence, one might conclude that designing a biomimic for the P450 chemistry requires two majors conditions: i) the presence of an open active site and ii) the stabilisation of the catalytic reactive intermediates preceding the formation of the porphyrin high-valent iron-oxo intermediate in the reaction cycle. Fe III MP-8 and Mn III MP-8 resemble an open peroxidase active site having no distal environment. It has been shown that for both MP-8 models the co-ordination of a molecule of hydrogen peroxide on the metal is facilitated by bound water, providing the pH in the medium is high (Chapter 7). This questions the role played by the distal histidine ligand in peroxidases. Generally the hydroperoxide substrate is proposed to be deprotonated by the distal histidine ligand before it displaces metal bound water. But the preliminary deprotonation of the bound water by the distal histidine, followed by concerted deprotonation of the hydroperoxide and displacement of the hydroxyl ligand might be considered as a relevant alternative mechanism. In order to mimic P450 catalysis, the porphyrin iron-hydroperoxo and the porphyrin iron-peroxo intermediates should be stabilised with respect to the porphyrin high-valent metal-oxo intermediate. This is rendered possible by partially scavenging the porphyrin high-valent metal-oxo intermediates species analogue of Compound I using ascorbate, regenerating the native MP-8. The reductant competes with the substrate for the oxidation by the porphyrin high-valent metal-oxo intermediate and does almost not affect porphyrin iron-(hydro)peroxo-based intermediates. Therefore in the presence of ascorbate, i.e. in the P450 mode, MP-8 can be considered as a model for P450 chemistry and without ascorbate, i.e. in the peroxidase mode, MP-8 can be considered as a model for peroxidase chemistry.

    As a conclusion, the present work has contributed to the better understanding of the chemistry of metalloporphyrin hydroperoxo and metalloporphyrin peroxo intermediates both relevant active species of the P450 chemistry. Furthermore the peroxidase mimic, MP-8, can efficiently be used as a model for the P450 chemistry.

    Modelling of a storage process for product quality control purposes
    Verdijck, G.J.C. ; Hertog, M.L.A.T.M. ; Weiss, M. ; Preisig, H.A. - \ 1999
    Computers and Chemical Engineering (1999)Supplement. - ISSN 0098-1354 - p. 911 - 914.
    Model based product quality control for a potato storage facility
    Verdijck, G.J.C. ; Weiss, M. ; Preisig, H.A. - \ 1999
    In: 1999 American Control Conference, 2-4 June, at San Diego (USA)
    Incorporation and characterization of iron(III)tetramesitylporphirin and microperoxidase-8 in the molecular sieve MCM-41
    Schünemann, V. ; Trautwein, A.X. ; Rietjens, I.M.C.M. ; Boersma, M.G. ; Veeger, C. ; Mandon, D. ; Weiss, R. ; Mahl, K. ; Colapietro, C. ; Piech, M. ; Austin, R.N. - \ 1999
    Inorganic Chemistry 38 (1999). - ISSN 0020-1669 - p. 4901 - 4905.
    The effect of iron to manganese substitution on microperoxidase-8 catalysed peroxidase and cytochrome P450 type of catalysis
    Primus, J.L. ; Boersma, M.G. ; Mandon, D. ; Boeren, S. ; Veeger, C. ; Weiss, R. ; Rietjens, I.M.C.M. - \ 1999
    Journal of Biological Inorganic Chemistry 4 (1999). - ISSN 0949-8257 - p. 274 - 283.
    This study describes the catalytic properties of manganese microperoxidase 8 [Mn(III)MP8] compared to iron microperoxidase 8 [Fe(III)MP8]. The mini-enzymes were tested for pH-dependent activity and operational stability in peroxidase-type conversions, using 2-methoxyphenol and 3,3'-dimethoxybenzidine, and in a cytochrome P450-like oxygen transfer reaction converting aniline to para-aminophenol. For the peroxidase type of conversions the Fe to Mn replacement resulted in a less than 10-fold decrease in the activity at optimal pH, whereas the aniline para-hydroxylation is reduced at least 30-fold. In addition it was observed that the peroxidase type of conversions are all fully blocked by ascorbate and that aniline para-hydroxylation by Fe(III)MP8 is increased by ascorbate whereas aniline para-hydroxylation by Mn(III)MP8 is inhibited by ascorbate. Altogether these results indicate that different types of reactive metal oxygen intermediates are involved in the various conversions. Compound I/II, scavenged by ascorbate, may be the reactive species responsible for the peroxidase reactions, the polymerization of aniline and (part of) the oxygen transfer to aniline in the absence of ascorbate. The para-hydroxylation of aniline by Fe(III)MP8, in the presence of ascorbate, must be mediated by another reactive iron-oxo species which could be the electrophilic metal(III) hydroperoxide anion of microperoxidase 8 [M(III)OOH MP8]. The lower oxidative potential of Mn, compared to Fe, may affect the reactivity of both compound I/II and the metal(III) hydroperoxide anion intermediate, explaining the differential effect of the Fe to Mn substitution on the pH-dependent behavior, the rate of catalysis and the operational stability of MP8.
    Dynamic model development for an industrial potato starch drier
    Verdijck, G.J.C. ; Weiss, M. ; Preisig, H.A. - \ 1998
    Modelling of a Pneumatic Dryer for Potato Starch
    Verdijck, G.J.C. ; Weiss, M. ; Preisig, H.A. - \ 1998
    Journal of Food Engineering 37 (1998)3. - ISSN 0260-8774 - p. 243 - 258.
    Dehalobacter restrictus gen. nov. and sp. nov.: a strictly anaerobic bacterium that reductively dechlorinates tetra- and trichloroethene in an anaerobic respiration.
    Holliger, C. ; Hahn, D. ; Harmsen, H. ; Ludwig, W. ; Schumacher, W. ; Tindal, B. ; Vasquez, F. ; Weiss, N. ; Zehnder, A.J.B. - \ 1998
    Archives of Microbiology 169 (1998). - ISSN 0302-8933 - p. 313 - 321.
    Book review: Essential oil crops, E.A. Weiss (ed.).
    Pol, P.A. van de - \ 1998
    Scientia Horticulturae 76 (1998)3-4. - ISSN 0304-4238 - p. 231 - 233.
    Characterisation of an acetylcholine receptor gene of Haemonchus contortus in relation to levamisole resistance
    Hoekstra, R. ; Visser, A. ; Wiley, L. ; Weiss, A.S. ; Sangster, N.C. ; Roos, M.H. - \ 1997
    Molecular and biochemical parasitology 84 (1997)2. - ISSN 0166-6851 - p. 179 - 187.
    The anthelmintic drug levamisole is thought to bind to nicotinic acetylcholine receptors of nematodes. It is possible that resistance to this drug is associated with either a change in binding characteristics or a reduction in the number of nicotinic acetylcholine receptors. Therefore, the molecular mechanism of levamisole resistance in the parasitic nematode Haemonchus contortus was studied by isolating and characterising cDNA clones encoding a putative ligand binding nicotinic acetylcholine receptor subunit, HCA1, of two susceptible and one levamisole resistant population. HcA1 is related to unc-38, a nicotinic acetylcholine receptor subunit gene associated with levamisole resistance in Caenorhabditis elegans. Although extensive sequence analyses of hca1 sequences revealed poly-morphism at amino acid level, no association with levamisole resistance could be detected. Restriction fragment length polymorphism analyses confirmed that, although polymorphism was detected, no selection of a specific allele of heal has taken place during selection for levamisole resistance in various levamisole resistant populations.
    Changing forest functions in NW Europe: from alienation to involvement
    Vos, W. - \ 1996
    In: Forestry in the context of rural development: future research needs. EFI Proceedings 15:127-139 / Glück, P., Weiss, G.,
    Styles of forest management by small forest owners, characteristics and scope for rural development.
    Ploeg, J.D. van der; Wiersum, K.F. - \ 1996
    In: COST Seminar on Forestry in the context of rural development: future research needs, Vienna, Austria, P. Glück, G. Weiss (eds.). European Forest Institute Proc. no. 15, Joensuu, Finland - p. 45 - 57.
    Interaction between the substrate and the high-valent-iron-oxo porphyrin cofactor as a possible factor influencing the regioselectivity of cytochrome P450 catalysed aromatic ring hydroxylation of 3-fluoro(methyl)anilines.
    Koerts, J. ; Boeren, S. ; Vervoort, J. ; Weiss, R. ; Veeger, C. ; Rietjens, I.M.C.M. - \ 1996
    Chemico-Biological Interactions 99 (1996). - ISSN 0009-2797 - p. 129 - 146.
    Co-suppression of the petunia homeotic gene fbp2 affects the identity of the generative meristem
    Angenent, G.C. ; Franken, J. ; Busscher, M. ; Weiss, D. ; Tunen, A.J. van - \ 1995
    The Plant Journal 5 (1995). - ISSN 0960-7412 - p. 33 - 44.
    Identification of endogenous gibberellins in Petunia flowers. Identification of anthocyanin biosynthetic gene expression and antagonistic effect of abscisic acid.
    Weiss, D. ; Luit, A. van der; Knegt, E. ; Vermeer, E. ; Mol, J.N.M. ; Kooter, J.M. - \ 1995
    Plant Physiology 107 (1995). - ISSN 0032-0889 - p. 695 - 702.
    A new index of abdominal adiposity as an indicator of risk for cardiovascular disease. A cross-population study.
    Valdez, R. ; Seidell, J.C. ; Ahn, Y.I. ; Weiss, K.M. - \ 1993
    International Journal of Obesity 17 (1993). - ISSN 0307-0565 - p. 77 - 82.
    In quest of tropical micrometeorology for on-farm weather advisories. A guest editorial.
    Stigter, C.J. ; Weiss, A. - \ 1986
    Agricultural and Forest Meteorology 36 (1986)4. - ISSN 0168-1923 - p. 289 - 296.
    Influence of polymerization initiation rate on permeability of aqueous polyacrylamide gels
    Weiss, N. ; Vliet, T. van; Silberberg, A. - \ 1981
    Journal of polymer science. Polymer physics edition 19 (1981). - ISSN 0098-1273 - p. 1505 - 1512.
    Permeability of heterogeneous gels
    Weiss, N. ; Vliet, T. van; Silberberg, A. - \ 1979
    Journal of polymer science. Polymer physics edition 17 (1979). - ISSN 0098-1273 - p. 2229 - 2240.
    Suitability of hen eggs for incubation in the fresh state and after storage : Review based on the study of 198 references
    Rol'nik, V.V. ; Weiss - Vladimirov, L. - \ 1977
    Wageningen : Pudoc (Literature survey. Centre for Agricultural Publishing and Documentation no. 38) - ISBN 9789022006092 - 58
    eierproducten - eieren - kippen - pluimvee - zoölogie - egg products - eggs - fowls - poultry - zoology
    Check title to add to marked list

    Show 20 50 100 records per page

    Please log in to use this service. Login as Wageningen University & Research user or guest user in upper right hand corner of this page.