Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    The global abundance of tree palms
    Muscarella, Robert ; Emilio, Thaise ; Phillips, Oliver L. ; Lewis, Simon L. ; Slik, Ferry ; Baker, William J. ; Couvreur, Thomas L.P. ; Eiserhardt, Wolf L. ; Svenning, Jens Christian ; Affum-Baffoe, Kofi ; Aiba, Shin Ichiro ; Almeida, Everton C. de; Almeida, Samuel S. de; Oliveira, Edmar Almeida de; Álvarez-Dávila, Esteban ; Alves, Luciana F. ; Alvez-Valles, Carlos Mariano ; Carvalho, Fabrício Alvim ; Guarin, Fernando Alzate ; Andrade, Ana ; Aragão, Luis E.O.C. ; Murakami, Alejandro Araujo ; Arroyo, Luzmila ; Ashton, Peter S. ; Corredor, Gerardo A.A. ; Baker, Timothy R. ; Camargo, Plinio Barbosa de; Barlow, Jos ; Bastin, Jean François ; Bengone, Natacha Nssi ; Berenguer, Erika ; Berry, Nicholas ; Blanc, Lilian ; Böhning-Gaese, Katrin ; Bonal, Damien ; Bongers, Frans ; Bradford, Matt ; Brambach, Fabian ; Brearley, Francis Q. ; Brewer, Steven W. ; Camargo, Jose L.C. ; Campbell, David G. ; Castilho, Carolina V. ; Castro, Wendeson ; Catchpole, Damien ; Cerón Martínez, Carlos E. ; Chen, Shengbin ; Chhang, Phourin ; Cho, Percival ; Chutipong, Wanlop ; Clark, Connie ; Collins, Murray ; Comiskey, James A. ; Medina, Massiel Nataly Corrales ; Costa, Flávia R.C. ; Culmsee, Heike ; David-Higuita, Heriberto ; Davidar, Priya ; Aguila-Pasquel, Jhon del; Derroire, Géraldine ; Fiore, Anthony Di; Do, Tran Van; Doucet, Jean Louis ; Dourdain, Aurélie ; Drake, Donald R. ; Ensslin, Andreas ; Erwin, Terry ; Ewango, Corneille E.N. ; Ewers, Robert M. ; Fauset, Sophie ; Feldpausch, Ted R. ; Ferreira, Joice ; Ferreira, Leandro Valle ; Fischer, Markus ; Franklin, Janet ; Fredriksson, Gabriella M. ; Gillespie, Thomas W. ; Gilpin, Martin ; Gonmadje, Christelle ; Gunatilleke, Arachchige Upali Nimal ; Hakeem, Khalid Rehman ; Hall, Jefferson S. ; Hamer, Keith C. ; Harris, David J. ; Harrison, Rhett D. ; Hector, Andrew ; Hemp, Andreas ; Herault, Bruno ; Pizango, Carlos Gabriel Hidalgo ; Honorio Coronado, Eurídice N. ; Hubau, Wannes ; Hussain, Mohammad Shah ; Ibrahim, Faridah Hanum ; Imai, Nobuo ; Joly, Carlos A. ; Joseph, Shijo ; Anitha, K. ; Kartawinata, Kuswata ; Kassi, Justin ; Killeen, Timothy J. ; Kitayama, Kanehiro ; Klitgård, Bente Bang ; Kooyman, Robert ; Labrière, Nicolas ; Larney, Eileen ; Laumonier, Yves ; Laurance, Susan G. ; Laurance, William F. ; Lawes, Michael J. ; Levesley, Aurora ; Lisingo, Janvier ; Lovejoy, Thomas ; Lovett, Jon C. ; Lu, Xinghui ; Lykke, Anne Mette ; Magnusson, William E. ; Mahayani, Ni Putu Diana ; Malhi, Yadvinder ; Mansor, Asyraf ; Peña, Jose Luis Marcelo ; Marimon-Junior, Ben H. ; Marshall, Andrew R. ; Melgaco, Karina ; Bautista, Casimiro Mendoza ; Mihindou, Vianet ; Millet, Jérôme ; Milliken, William ; Mohandass, D. ; Mendoza, Abel Lorenzo Monteagudo ; Mugerwa, Badru ; Nagamasu, Hidetoshi ; Nagy, Laszlo ; Seuaturien, Naret ; Nascimento, Marcelo T. ; Neill, David A. ; Neto, Luiz Menini ; Nilus, Rueben ; Vargas, Mario Percy Núñez ; Nurtjahya, Eddy ; Araújo, R.N.O. de; Onrizal, Onrizal ; Palacios, Walter A. ; Palacios-Ramos, Sonia ; Parren, Marc ; Paudel, Ekananda ; Morandi, Paulo S. ; Pennington, R.T. ; Pickavance, Georgia ; Pipoly, John J. ; Pitman, Nigel C.A. ; Poedjirahajoe, Erny ; Poorter, Lourens ; Poulsen, John R. ; Prasad, P.R.C. ; Prieto, Adriana ; Puyravaud, Jean Philippe ; Qie, Lan ; Quesada, Carlos A. ; Ramírez-Angulo, Hirma ; Razafimahaimodison, Jean Claude ; Reitsma, Jan Meindert ; Requena-Rojas, Edilson J. ; Correa, Zorayda Restrepo ; Rodriguez, Carlos Reynel ; Roopsind, Anand ; Rovero, Francesco ; Rozak, Andes ; Lleras, Agustín Rudas ; Rutishauser, Ervan ; Rutten, Gemma ; Punchi-Manage, Ruwan ; Salomão, Rafael P. ; Sam, Hoang Van; Sarker, Swapan Kumar ; Satdichanh, Manichanh ; Schietti, Juliana ; Schmitt, Christine B. ; Marimon, Beatriz Schwantes ; Senbeta, Feyera ; Nath Sharma, Lila ; Sheil, Douglas ; Sierra, Rodrigo ; Silva-Espejo, Javier E. ; Silveira, Marcos ; Sonké, Bonaventure ; Steininger, Marc K. ; Steinmetz, Robert ; Stévart, Tariq ; Sukumar, Raman ; Sultana, Aisha ; Sunderland, Terry C.H. ; Suresh, Hebbalalu Satyanarayana ; Tang, Jianwei ; Tanner, Edmund ; Steege, Hans ter; Terborgh, John W. ; Theilade, Ida ; Timberlake, Jonathan ; Torres-Lezama, Armando ; Umunay, Peter ; Uriarte, María ; Gamarra, Luis Valenzuela ; Bult, Martin van de; Hout, Peter van der; Martinez, Rodolfo Vasquez ; Vieira, Ima Célia Guimarães ; Vieira, Simone A. ; Vilanova, Emilio ; Cayo, Jeanneth Villalobos ; Wang, Ophelia ; Webb, Campbell O. ; Webb, Edward L. ; White, Lee ; Whitfeld, Timothy J.S. ; Wich, Serge ; Willcock, Simon ; Wiser, Susan K. ; Young, Kenneth R. ; Zakaria, Rahmad ; Zang, Runguo ; Zartman, Charles E. ; Zo-Bi, Irié Casimir ; Balslev, Henrik - \ 2020
    Global Ecology and Biogeography (2020). - ISSN 1466-822X
    above-ground biomass - abundance patterns - Arecaceae - local abiotic conditions - Neotropics - pantropical biogeography - tropical rainforest - wood density

    Aim: Palms are an iconic, diverse and often abundant component of tropical ecosystems that provide many ecosystem services. Being monocots, tree palms are evolutionarily, morphologically and physiologically distinct from other trees, and these differences have important consequences for ecosystem services (e.g., carbon sequestration and storage) and in terms of responses to climate change. We quantified global patterns of tree palm relative abundance to help improve understanding of tropical forests and reduce uncertainty about these ecosystems under climate change. Location: Tropical and subtropical moist forests. Time period: Current. Major taxa studied: Palms (Arecaceae). Methods: We assembled a pantropical dataset of 2,548 forest plots (covering 1,191 ha) and quantified tree palm (i.e., ≥10 cm diameter at breast height) abundance relative to co-occurring non-palm trees. We compared the relative abundance of tree palms across biogeographical realms and tested for associations with palaeoclimate stability, current climate, edaphic conditions and metrics of forest structure. Results: On average, the relative abundance of tree palms was more than five times larger between Neotropical locations and other biogeographical realms. Tree palms were absent in most locations outside the Neotropics but present in >80% of Neotropical locations. The relative abundance of tree palms was more strongly associated with local conditions (e.g., higher mean annual precipitation, lower soil fertility, shallower water table and lower plot mean wood density) than metrics of long-term climate stability. Life-form diversity also influenced the patterns; palm assemblages outside the Neotropics comprise many non-tree (e.g., climbing) palms. Finally, we show that tree palms can influence estimates of above-ground biomass, but the magnitude and direction of the effect require additional work. Conclusions: Tree palms are not only quintessentially tropical, but they are also overwhelmingly Neotropical. Future work to understand the contributions of tree palms to biomass estimates and carbon cycling will be particularly crucial in Neotropical forests.

    Comparison of volatile trapping techniques for the comprehensive analysis of food flavourings by Gas Chromatography-Mass Spectrometry
    Diez-Simon, Carmen ; Ammerlaan, Brenda ; Berg, Marco van den; Duynhoven, John van; Jacobs, Doris ; Mumm, Roland ; Hall, Robert D. - \ 2020
    Journal of Chromatography. A, Including electrophoresis and other separation methods 1624 (2020). - ISSN 0021-9673
    Gas chromatography-mass spectrometry (GC-MS) - Headspace techniques - Maillard reaction - Process flavors - Stir bar sorptive extraction (SBSE) - Volatiles

    Trapping volatiles is a convenient way to study aroma compounds but it is important to determine which volatile trapping method is most comprehensive in extracting the most relevant aroma components when investigating complex food products. Awareness of their limitations is also crucial. (Un)targeted metabolomic approaches were used to determine the volatile profiles of two commercial flavourings. Four trapping techniques were tested as was the addition of salt to the mixture. Comprehensiveness and repeatability were compared and SBSE proved particularly suitable for extracting components such as polysulfides, pyrazines and terpene alcohols, and provided an overall broader chemical spectrum. SPME proved to be more suitable in extracting sesquiterpenes and DHS in extracting monoterpenes. Adding salt to the sample had only quantitative effects on volatiles as detected by SPME. These results help clarify the advantages and limitations of different trapping techniques and hence deliver a valuable decision tool for food matrix analysis.

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

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

    Resilience in coastal dune grasslands: pH and soil organic matter effects on P nutrition, plant strategies, and soil communities
    Kooijman, Annemieke ; Morriën, Elly ; Jagers Op Akkerhuis, Gerard ; Missong, Anna ; Bol, Roland ; Klumpp, Erwin ; Hall, Rutger ; Til, Mark van; Kalbitz, Karsten ; Bloem, Jaap - \ 2020
    Ecosphere 11 (2020)5. - ISSN 2150-8925
    Soil organic matter (SOM) and pH are key ecosystem drivers, influencing resilience to environmental change. We tested the separate effects of pH and SOM on nutrient availability, plant strategies, and soil community composition in calcareous and acidic Grey dunes (H2130) with low, intermediate, and/or high SOM, which differ in sensitivity to high atmospheric N deposition. Soil organic matter was mainly important for biomass parameters of plants, microbes, and soil animals, and for microarthropod diversity and network complexity. However, differences in pH led to fundamental differences in P availability and plant strategies, which overruled the normal soil community patterns, and influenced resilience to N deposition. In calcareous dunes with low grass‐encroachment, P availability was low despite high amounts of inorganic P, due to low solubility of calcium phosphates and strong P sorption to Fe oxides at high pH. Calcareous dunes were dominated by low‐competitive arbuscular mycorrhizal (AM) plants, which profit from mycorrhiza especially at low P. In acidic dunes with high grass‐encroachment, P availability increased as calcium phosphates dissolved and P sorption weakened with the shift from Fe oxides to Fe‐OM complexes. Weakly sorbed and colloidal P increased, and at least part of the sorbed P was organic. Acidic dunes were dominated by nonmycorrhizal (NM) plants, which increase P uptake through exudation of carboxylates and phosphatase enzymes, which release weakly sorbed P, and disintegrate labile organic P. The shifts in P availability and plant strategies also changed the soil community. Contrary to expectations, the bacterial pathway was more important in acidic than in calcareous dunes, possibly due to exudation of carboxylates and phosphatases by NM plants, which serve as bacterial food resource. Also, the fungal AM pathway was enhanced in calcareous dunes, and fungal feeders more abundant, due to the presence of AM fungi. The changes in soil communities in turn reduced expected differences in N cycling between calcareous and acidic dunes. Our results show that SOM and pH are important, but separate ecosystem drivers in Grey dunes. Differences in resilience to N deposition are mainly due to pH effects on P availability and plant strategies, which in turn overruled soil community patterns.
    Framework species approach proves robust in restoring forest on fire prone invasive grass : A case study from Panama
    Boeschoten, Laura E. ; Breugel, Michiel van; Bailon, Mario ; Balbuena, Johana ; Nuñez, Miguel ; Cerezo, Arturo ; Hall, Jefferson S. - \ 2020
    Journal of Sustainable Forestry (2020). - ISSN 1054-9811
    Ecosystem rehabilitation - framework species approach - grass elimination - invasive species - reforestation - Saccharum spontaneum

    Grasses and fire pose a major challenge for forest restoration. Here we evaluate a case study of reforestation in an area invaded by the tall invasive grass Saccharum spontaneum in the Panama Canal Watershed. The project objectives were to (1) replace Saccharum with a forest, (2) restore a stratified mixed species forest and (3) sequester carbon. We aimed to compare the practice of forest restoration with a treatment grounded in theory. Therefore, the first species selection method followed business-as-usual: contractors planted any combination of 130 prescribed species. The second method followed the framework species approach, a mixture of 22 species was planted to ensure early shade, create a stratified forest over time, attract seed dispersers, and for their potential to fix N2. Both treatments showed successful restoration trajectories 8.5 years after planting, they did not differ in structural characteristics (stem density, basal area, aboveground biomass, height, and amount of Saccharum). However, based on the species present, the framework approach shows more potential to become a stratified forest. As the framework approach also withstood fires much better than the business-as-usual approach, we conclude that it improves restoration success in this human-dominated landscape.

    Species and sex-specific chemosensory gene expression in Anopheles coluzzii and An. quadriannulatus antennae
    Athrey, Giridhar ; Popkin-Hall, Zachary ; Cosme, Luciano Veiga ; Takken, Willem ; Slotman, Michel Andre - \ 2020
    Parasites & Vectors 13 (2020)1. - ISSN 1756-3305
    Anopheles - Chemosensation - Host seeking - Mating - Olfaction

    Background: Olfactory cues drive mosquito behaviors such as host-seeking, locating sugar sources and oviposition. These behaviors can vary between sexes and closely related species. For example, the malaria vector Anopheles coluzzii is highly anthropophilic, whereas An. quadriannulatus is not. These behavioral differences may be reflected in chemosensory gene expression. Methods: The expression of chemosensory genes in the antennae of both sexes of An. coluzzii and An. quadriannulatus was compared using RNA-seq. The sex-biased expression of several genes in An. coluzzii was also compared using qPCR. Results: The chemosensory expression is mostly similar in the male antennae of An. coluzzii and An. quadriannulatus, with only a few modest differences in expression. A handful of chemosensory genes are male-biased in both species; the highly expressed gustatory receptor AgGr33, odorant binding proteins AgObp25, AgObp26 and possibly AgObp10. Although the chemosensory gene repertoire is mostly shared between the sexes, several highly female-biased AgOrs, AgIrs, and one AgObp were identified, including several whose expression is biased towards the anthropophilic An. coluzzii. Additionally, the expression of several chemosensory genes is biased towards An. coluzzii in both sexes. Conclusions: Chemosensory gene expression is broadly similar between species and sexes, but several sex- biased/specific genes were identified. These may modulate sex- and species-specific behaviors. Although the male behavior of these species remains poorly studied, the identification of sex- and species-specific chemosensory genes may provide fertile ground for future work.[Figure not available: see fulltext.]

    The invasive Asian bush mosquito Aedes japonicus found in the Netherlands can experimentally transmit Zika virus and Usutu virus
    Abbo, Sandra R. ; Visser, Tessa M. ; Wang, Haidong ; Göertz, Giel P. ; Fros, Jelke J. ; Abma-henkens, Marleen H.C. ; Geertsema, Corinne ; Vogels, Chantal B.F. ; Koopmans, Marion P.G. ; Reusken, Chantal B.E.M. ; Hall-Mendelin, Sonja ; Hall, Roy A. ; Oers, Monique M. Van; Koenraadt, C.J.M. ; Pijlman, Gorben P. - \ 2020
    PLoS Neglected Tropical Diseases 14 (2020)4. - ISSN 1935-2727 - 22 p.
    Background - The Asian bush mosquito Aedes japonicus is invading Europe and was first discovered in Lelystad, the Netherlands in 2013, where it has established a permanent population. In this study, we investigated the vector competence of Ae. japonicus from the Netherlands for the emerging Zika virus (ZIKV) and zoonotic Usutu virus (USUV). ZIKV causes severe congenital microcephaly and Guillain-Barré syndrome in humans. USUV is closely related to West Nile virus, has recently spread throughout Europe and is causing mass mortality of birds. USUV infection in humans can result in clinical manifestations ranging from mild disease to severe neurological impairments.
    Methodology/Principal findings - In our study, field-collected Ae. japonicus females received an infectious blood meal with ZIKV or USUV by droplet feeding. After 14 days at 28°C, 3% of the ZIKV-blood fed mosquitoes and 13% of the USUV-blood fed mosquitoes showed virus-positive saliva, indicating that Ae. japonicus can transmit both viruses. To investigate the effect of the mosquito midgut barrier on virus transmission, female mosquitoes were intrathoracically injected with ZIKV or USUV. Of the injected mosquitoes, 96% (ZIKV) and 88% (USUV) showed virus-positive saliva after 14 days at 28°C. This indicates that ZIKV and USUV can efficiently replicate in Ae. japonicus but that a strong midgut barrier is normally restricting virus dissemination. Small RNA deep sequencing of orally infected mosquitoes confirmed active replication of ZIKV and USUV, as demonstrated by potent small interfering RNA responses against both viruses. Additionally, de novo small RNA assembly revealed the presence of a novel narnavirus in Ae. japonicus.
    Conclusions/Significance - Given that Ae. japonicus can experimentally transmit arthropod-borne viruses (arboviruses) like ZIKV and USUV and is currently expanding its territories, we should consider this mosquito as a potential vector for arboviral diseases in Europe
    Designing future dairy systems for New Zealand using reflexive interactive design
    Romera, A.J. ; Bos, A.P. ; Neal, M. ; Eastwood, C.R. ; Chapman, D. ; McWilliam, W. ; Royds, D. ; O'Connor, C. ; Brookes, R. ; Connolly, J. ; Hall, P. ; Clinton, P.W. - \ 2020
    Agricultural Systems 181 (2020). - ISSN 0308-521X
    Dairy - Design - Integral sustainability - Reflexion - Stakeholder - Territory

    Globally, agricultural systems are facing unprecedented challenges. The problems are of systemic nature and will require transformational changes and systemic redesign. In this study, we investigated the redesign of dairy systems in New Zealand, due to their large economic, social and environmental influence nationally. We did not set the boundaries of the ‘dairy systems’ from the outset, letting this definition be part of the design process. We applied ‘Reflexive Interactive Design’ (RIO), an approach aimed at structurally addressing complex trade-offs and contributing, by process and design, to change towards sustainable development and integral sustainability (i.e. in all relevant dimensions of sustainability). A detailed system analysis was conducted, followed by two rounds of structured design focused on four main stakeholders (‘actors') identified as part of the RIO process: the farmers, the citizens, the consumers, and the dairy cows. Our study established design goals related to enhancing the wellbeing of humans and animals, enhancing environmental performance, economics and resilience of dairy systems and reconnecting dairy farming with the rest of society. The process took us beyond the boundaries of a dairy farm and identified the territorial level as the object of design, arriving at a design concept we have called the ‘Agro-ecological Park’. The name was chosen to convey an analogy with ‘Eco-industrial Parks’. Operating as a multifunctional network, the Park has the goal of delivering multiple benefits for its members, and multiple goods and services for the rest of society. The coordinated network articulates linkages between farmers and many other businesses and people in the territory. The individual dairy farm is redesigned to be a node in that network rather than operating as an isolated entity. That way, much of the weight for the increased complexity and multifunctionality now demanded of farming can be carried by the network instead of the individual farmer. These preliminary design ideas, and the reasoning behind them, should encourage new perspectives on the complex problems facing NZ dairy farming, and agriculture globally, in the upcoming decades.

    Comparative Metabolomics and Molecular Phylogenetics of Melon (Cucumis melo, Cucurbitaceae) Biodiversity
    Moing, Annick ; Allwood, J.W. ; Aharoni, Asaph ; Baker, John ; Beale, M.H. ; Ben-Dor, Shifra ; Biais, B. ; Brigante, Federico ; Burger, Yosef ; Deborde, C. ; Erban, A. ; Doron-Faigenboim, Adi ; Gur, Amit ; Goodacre, R. ; Hansen, T. ; Jacob, Daniel ; Katzir, Nurit ; Kopka, Joachim ; Lewinsohn, Efraim ; Maucourt, Mickael ; Meir, Sagit ; Miller, Sonia ; Mumm, R. ; Oren, Elad ; Paris, Harry S. ; Rogachev, Ilana ; Rollin, Dominique ; Saar, Uzi ; Schjoerring, Jan K. ; Tadmor, Y. ; Tzuri, Galil ; Vos, C.H. de; Ward, J. ; Yeselson, Elena ; Hall, R.D. ; Schaffer, A. - \ 2020
    Metabolites 10 (2020)3. - ISSN 2218-1989 - 26 p.
    The broad variability of Cucumis melo (melon, Cucurbitaceae) presents a challenge to conventional classification and organization within the species. To shed further light on the infraspecific relationships within C. melo, we compared genotypic and metabolomic similarities among 44 accessions representative of most of the cultivar-groups. Genotyping-by-sequencing (GBS) provided
    over 20,000 single-nucleotide polymorphisms (SNPs). Metabolomics data of the mature fruit flesh and rind provided over 80,000 metabolomic and elemental features via an orchestra of six complementary metabolomic platforms. These technologies probed polar, semi-polar, and non-polar metabolite
    fractions as well as a set of mineral elements and included both flavor- and taste-relevant volatile and non-volatile metabolites. Together these results enabled an estimate of “metabolomic/elemental distance” and its correlation with the genetic GBS distance of melon accessions. This study indicates
    that extensive and non-targeted metabolomics/elemental characterization produced classifications that strongly, but not completely, reflect the current and extensive genetic classification. Certain melon Groups, such as Inodorous, clustered in parallel with the genetic classifications while other genome
    to metabolome/element associations proved less clear. We suggest that the combined genomic, metabolic, and element data reflect the extensive sexual compatibility among melon accessions and the breeding history that has, for example, targeted metabolic quality traits, such as taste and flavor.
    Ultra-Processing or Oral Processing? A Role for Energy Density and Eating Rate in Moderating Energy Intake from Processed Foods
    Forde, Ciarán G. ; Mars, Monica ; Graaf, Kees De - \ 2020
    Current Developments in Nutrition 4 (2020)3. - ISSN 2475-2991
    eating rate - energy density - energy intake rate - food texture - metabolic disease - obesity - ultra-processed foods - unprocessed foods

    Background: Recent observational data and a controlled in-patient crossover feeding trial show that consumption of "ultra-processed foods" (UPFs), as defined by the NOVA classification system, is associated with higher energy intake, adiposity, and at a population level, higher prevalence of obesity. A drawback of the NOVA classification is the lack of evidence supporting a causal mechanism for why UPFs lead to overconsumption of energy. In a recent study by Hall the energy intake rate in the UPF condition (48 kcal/min) was >50% higher than in the unprocessed condition (31 kcal/min). Extensive empirical evidence has shown the impact that higher energy density has on increasing ad libitum energy intake and body weight. A significant body of research has shown that consuming foods at higher eating rates is related to higher energy intake and a higher prevalence of obesity. Energy density can be combined with eating rate to create a measure of energy intake rate (kcal/min), providing an index of a food's potential to promote increased energy intake. Objective: The current paper compared the association between measured energy intake rate and level of processing as defined by the NOVA classification. Methods: Data were pooled from 5 published studies that measured energy intake rates across a total sample of 327 foods. Results: We show that going from unprocessed, to processed, to UPFs that the average energy intake rate increases from 35.5 ± 4.4, to 53.7 ± 4.3, to 69.4 ± 3.1 kcal/min (P < 0.05). However, within each processing category there is wide variability in the energy intake rate. Conclusions: We conclude that reported relations between UPF consumption and obesity should account for differences in energy intake rates when comparing unprocessed and ultra-processed diets. Future research requires well-controlled human feeding trials to establish the causal mechanisms for why certain UPFs can promote higher energy intake.

    Metabolomics should be deployed in the identification and characterization of gene-edited crops
    Fraser, Paul D. ; Aharoni, Asaph ; Hall, Robert D. ; Huang, Sanwen ; Giovannoni, James J. ; Sonnewald, Uwe ; Fernie, Alisdair R. - \ 2020
    The Plant Journal 102 (2020)5. - ISSN 0960-7412 - p. 897 - 902.
    crop regulation - food system - genome-editing - metabolomics - substantial equivalence

    Gene-editing techniques are currently revolutionizing biology, allowing far greater precision than previous mutagenic and transgenic approaches. They are becoming applicable to a wide range of plant species and biological processes. Gene editing can rapidly improve a range of crop traits, including disease resistance, abiotic stress tolerance, yield, nutritional quality and additional consumer traits. Unlike transgenic approaches, however, it is not facile to forensically detect gene-editing events at the molecular level, as no foreign DNA exists in the elite line. These limitations in molecular detection approaches are likely to focus more attention on the products generated from the technology than on the process in itself. Rapid advances in sequencing and genome assembly increasingly facilitate genome sequencing as a means of characterizing new varieties generated by gene-editing techniques. Nevertheless, subtle edits such as single base changes or small deletions may be difficult to distinguish from normal variation within a genotype. Given these emerging scenarios, downstream ‘omics’ technologies reflective of edited affects, such as metabolomics, need to be used in a more prominent manner to fully assess compositional changes in novel foodstuffs. To achieve this goal, metabolomics or ‘non-targeted metabolite analysis’ needs to make significant advances to deliver greater representation across the metabolome. With the emergence of new edited crop varieties, we advocate: (i) concerted efforts in the advancement of ‘omics’ technologies, such as metabolomics, and (ii) an effort to redress the use of the technology in the regulatory assessment for metabolically engineered biotech crops.

    Variation in secondary metabolites in a unique set of tomato accessions collected in Turkey
    Bakir, Sena ; Capanoglu, Esra ; Hall, Robert D. ; Vos, Ric C.H. de - \ 2020
    Food Chemistry 317 (2020). - ISSN 0308-8146
    Acetonitrile (Pubchem CID: 6342) - Formic acid (Pubchem CID: 284) provided by Merck (Frankfurter, Germany) - LC-MS grade methanol (Pubchem CID: 887) - Metabolomics - Multivariate analysis - Semi-polar phytochemicals - Tomato

    In this study, 50 tomato landraces grown in Turkey were investigated in terms of their secondary metabolite profiles. Each accession was planted in 2016 and 2017 in 3 replicates in an open field. In this study, color, pH and brix of the fruit samples were measured and an unbiased LCMS-based metabolomics approach was applied. Based on Principal Components Analysis (PCA) and Hierarchical Cluster Analysis (HCA) of the relative abundance levels of >250 metabolites, it could be concluded that fruit size was the most influential to the biochemical composition, rather than the geographical origin of accessions. Results indicated substantial biodiversity in various metabolites generally regarded as key to fruit quality aspects, including sugars; phenolic compounds like phenylpropanoids and flavonoids; alkaloids and glycosides of flavour-related volatile compounds. The phytochemical data provides insight into which Turkish accessions might be most promising as starting materials for the tomato processing and breeding industries.

    Identification of bioactive phytochemicals in mulberries
    D’urso, Gilda ; Mes, Jurriaan J. ; Montoro, Paola ; Hall, Robert D. ; Vos, Ric C.H. de - \ 2020
    Metabolites 10 (2020)1. - ISSN 2218-1989
    Antioxidant activity - High resolution mass spectrometry - In vitro gastrointestinal digestion - Mulberry - α-glucosidase inhibitory activity

    Mulberries are consumed either freshly or as processed fruits and are traditionally used to tackle several diseases, especially type II diabetes. Here, we investigated the metabolite compositions of ripe fruits of both white (Morus alba) and black (Morus nigra) mulberries, using reversed-phase HPLC coupled to high resolution mass spectrometry (LC-MS), and related these to their in vitro antioxidant and α-glucosidase inhibitory activities. Based on accurate masses, fragmentation data, UV/Vis light absorbance spectra and retention times, 35 metabolites, mainly comprising phenolic compounds and amino sugar acids, were identified. While the antioxidant activity was highest in M. nigra, the α-glucosidase inhibitory activities were similar between species. Both bioactivities were mostly resistant to in vitro gastrointestinal digestion. To identify the bioactive compounds, we combined LC-MS with 96-well-format fractionation followed by testing the individual fractions for α-glucosidase inhibition, while compounds responsible for the antioxidant activity were identified using HPLC with an online antioxidant detection system. We thus determined iminosugars and phenolic compounds in both M. alba and M. nigra, and anthocyanins in M. nigra as being the key α-glucosidase inhibitors, while anthocyanins in M. nigra and both phenylpropanoids and flavonols in M. alba were identified as key antioxidants in their ripe berries.

    Green and White Asparagus (Asparagus officinalis): A Source of Developmental, Chemical and Urinary Intrigue
    Pegiou, Irini ; Mumm, R. ; Acharya, Parag ; Vos, C.H. de; Hall, R.D. - \ 2020
    Metabolites 10 (2020)1. - ISSN 2218-1989
    asparagus; secondary metabolites; asparagus aroma; flavour; phytonutrients; plant metabolomics
    Asparagus (Asparagus officinalis) is one of the world’s top 20 vegetable crops. Both green and white shoots (spears) are produced; the latter being harvested before becoming exposed to light. The crop is grown in nearly all areas of the world, with the largest production regions being China, Western Europe, North America and Peru. Successful production demands high farmer input and specific environmental conditions and cultivation practices. Asparagus materials have also been used for centuries as herbal medicine. Despite this widespread cultivation and consumption, we still know relatively little about the biochemistry of this crop and how this relates to the nutritional, flavour, and neutra-pharmaceutical properties of the materials used. To date, no-one has directly compared the contrasting compositions of the green and white crops. In this short review, we have summarised most of the literature to illustrate the chemical richness of the crop and how this might relate to key quality parameters. Asparagus has excellent nutritional properties and its flavour/fragrance is attributed to a set of volatile components including pyrazines and sulphur-containing compounds. More detailed research, however, is needed and we propose that (untargeted) metabolomics should have a more prominent role to play in these investigations.
    Mass Spectrometry Data Processing
    Neumann, Steffen ; Yanes, Oscar ; Mumm, Roland ; Franceschi, Pietro - \ 2019
    In: Metabolomics / Wehrens, Ron, Salek, Reza, Chapman and Hall/CRC - ISBN 9781315370583 - p. 73 - 99.
    Data from: Rapid plastic breeding response to rain matches peak prey abundance in a tropical savannah bird
    Hidalgo Aranzamendi, Nataly ; Hall, Michelle L. ; Kingma, Sjouke ; Pol, Martijn van de; Peters, Anne - \ 2019
    Dryad
    trophic interactions - annual cycle - tropics - phenology - Timing of reproduction - Phenotypic Plasticity - avian life-history - unpredictable environment - Malurus coronatus
    1. Changes in climate are shifting the timing of life cycle events in the natural world. Compared to northern-temperate areas, these effects are relatively poorly understood in tropical and southern regions, where there is limited information on how timing of breeding and food availability are affected by climatic factors, and where patterns of breeding activity are more unpredictable within and between years. 2. Combining a new statistical modelling approach with 5 years of continuous individual-based monitoring of a monsoonal tropical insectivorous bird, we quantified (i) the proximate climatic drivers at two trophic levels: timing of breeding and abundance of arthropod prey; (ii) the effect of climate variation on reproductive output and (iii) the role of individual plasticity. 3. Rainfall was identified as the main determinant of phenology at both trophic levels. Throughout the year, likelihood of egg laying increased very rapidly in response to even small amounts of rain during the preceding 0-3 weeks. Adult body mass and male sperm storage also increased rapidly after rain, suggesting high breeding preparedness. Additionally, females were flexible, since they were more likely to nest if their previous attempt was longer ago and unsuccessful. Arthropod abundance also increased after rainfall, but more slowly, with a peak around 10 weeks. Therefore, the peak food availability coincided with the presence of dependent fledglings. 4. Fitness benefits of nesting after more rain appeared to be linked to offspring quantity rather than quality: nest attempts following higher rainfall produced larger clutches, but showed no improvement in nestling mass or relative fledging success. The response of clutch size to rainfall was plastic, since repeated sampling showed that individual females laid larger clutches after more rain, possibly mediated by improved body mass. 5. Rapid, individually flexible breeding in response to rainfall and slower increase in arthropod abundance also as a response to rainfall, might buffer insectivorous species living in tropical seasonal environments from climate-change induced phenological trophic mismatches.
    HIP-BB1.5 ‘Metabolomics of seed potatoes during storage’
    Hall, Robert ; Struik, Paul - \ 2019
    Receptomics, design of a microfluidic receptor screening technology
    Roelse, Margriet - \ 2019
    Wageningen University. Promotor(en): R.D. Hall; R.F. Witkamp, co-promotor(en): M.A. Jongsma. - Wageningen : Wageningen University - ISBN 9789463950817 - 193

    This thesis describes the development of a G Protein-Coupled Receptor (GPCR) screening technology that combines a receptor cell array (~300 spots) with microfluidics. This technology was developed for the purpose of sensing the taste of, or active components in complex samples. GPCR activation was monitored using a genetically encoded calcium indicator (GECI) which was based on a change in Förster Resonance Energy Transfer (FRET) between two fluorescent proteins linked by a calcium binding domain which, upon binding of calcium, induces a conformational change between the fluorophores. The receptor cell arrays were created by reverse transfection of printed plasmid DNA. The arrays were assembled in a flowcell, connected to a microfluidic system, and mounted on a stereo fluorescence microscope. This setup allowed for controlled and importantly, repeated sample exposure while monitoring the changes in intracellular calcium in real-time.

    GPCRs play an important role in many physiological or disease-related processes. These membrane proteins have evolved to sense a wide range of molecules that can be of either exogenous or endogenous origin. Their sensing mechanisms are complex and potentially involve many cellular signalling events depending the cell type. The introductory chapter of this thesis presents a brief overview of the GPCR types and their signalling pathways with a focus on taste signalling. This chapter also places the microfluidic receptomics technology within the framework of existing receptor screening technologies.

    The second chapter explores the general principles, setup and characterization of the microfluidic biosensor to measure GPCR activation via imaging of [Ca2+] changes in recombinant human HEK293 cells. These cells expressed a combination of the Neurokinin 1-receptor and Cameleon YC3.6 protein as calcium indicator. Here, a stable cell line was employed for robust expression with little variation

    Next to GPCRs, the system was also used for the detection of transient receptor potential channel Vanilloid 1 (TRPV1) ion channel activation by means of the Cameleon YC3.6 calcium sensor as is reported in Chapter 3. This assay was performed with LCMS fractions and whole extracts of chilli pepper fruits which led to the identification of new ion channel agonists. This chapter also discusses the possibility of coupling the receptomics assay directly to an LCMS as an additional on-line bioactivity detector. The general discussion of this thesis (Chapter 7) elaborates on this topic with additional perspectives on the feasibility of coupling the two systems.

    Chapter 4 provides an extensive technical characterization of the preparation and measurement of reverse transfected cell arrays using fluorescent proteins. The response of the Neurokinin 1-receptor in relation to its gene dose in reverse transfection was studied, as well as response reproducibility during repeated activations.

    These results led to a study of bitter taste receptors in relation to sensitivity-determining parameters such as sensor type and calcium buffering (Chapter 5). This chapter aimed to enhance the sensitivity and robustness of the receptor assay and showed proof of concept with bitter receptor arrays that performed in the same range as existing state-of-the-art platforms. Such bitter taste receptor arrays may be employed for future screenings of new bitter taste agonists or modulators and the identification of bitter principles in foods.

    Development of software and statistical models -the linear mixed model, as presented in Chapter 6- to analyse this new type of data showed that a spot-based comparison of sequentially-tested samples yielded the most reliable data and largely eliminated inter-spot differences in signal strength. The method could also visualize receptor specific differences between samples in the presence of a simulated host cell response. A host cell response, induced by ATP, was used to show that specific bitter receptor responses from compound spikes were cumulative to the host cell response and can be retrieved from a host cell response signal by means of comparative analysis.

    The general discussion (Chapter 7) critically discusses the advantages and limitations of this new micro-fluidics approach and details which additional developments are needed to advance the technology further. The receptomics technology as described in this thesis is argued to be complementary to microplate screening technologies and represents a new analytical paradigm. The microfluidics aspect and overall assay size reduction are more cost efficient and allow both a high content dynamics analysis as well as the development of novel applications such as direct identification of bioactive compounds by coupling of LCMS to receptomics.

    All in all, this thesis presents an enabling receptor screening technology that is based on new design principles. This receptomics technology offers novel applications and has potential in the bioactivity screening of crude extracts.

    Statistics: The Essentials
    Wehrens, H.R.M.J. ; Franceschi, Pietro - \ 2019
    In: Metabolomics: Practical Guide to Design and Analysis / Wehrens, Ron, Salek, Reza, New York : Chapman and Hall - ISBN 9781315370583 - 28 p.
    A basic understanding of statistics is essential in analyzing metabolomics data. In particular, the reasons behind common assumptions made in statistical inference, such as normally distributed data, should be understood. Because of the highly multivariate nature of metabolomics data, multiple-testing issues arise and should be dealt with appropriately. Multivariate analysis and visualization methods are easily applied now that they are commonly available in many software packages, but the interpretation of the results, and in particular the choices of data pretreatment and model selection, are less easily understood. This chapter discusses the basics of these and some other approaches.
    Conclusion
    Wehrens, H.R.M.J. ; Salek, Reza - \ 2019
    In: Metabolomics: Practical Guide to Design and Analysis / Wehrens, Ron, Salek, Reza, New York : Chapman and Hall - ISBN 9781315370583 - 6 p.
    Metabolomics is a vibrant field, developing fast and attracting many scientists from adjacent disciplines. Its multi-disciplinarity bases are one of the defining features of metabolomics. In order to quantify and understand the diversity of the metabolite composition of biological samples one needs chemistry, biology, mathematics and statistics, and computer science (to name just the most central disciplines). Such multi-disciplinarity has been reflected in the programs of many metabolomics conferences. Metabolomics conferences often contain parallel or breakout sessions on topics that may be entirely different from one another (e.g., mass-spectrometry-based or NMR-based metabolomics, computational metabolomics, medical applications, environmental applications, etcetera). Such diversity makes it difficult to obtain a bird’s eye view, especially for scientists new to the field. Whatever one’s background, one needs to know the basics of many of these fields, and this is where we had set the primary function of this work. We aim to provide a concise yet global overview of the field of metabolomics. If this book can contribute to a better understanding of each other’s viewpoints and vocabulary used, the most important goal has been achieved.
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