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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    Global status and conservation potential of reef sharks
    MacNeil, Aaron ; Chapman, Demian D. ; Heupel, Michelle ; Simpfendorfer, Colin A. ; Heithaus, Michael ; Meekan, Mark ; Harvey, Euan ; Goetze, Jordan ; Kiszka, Jeremy ; Bond, Mark E. ; Currey-Randall, Leanne M. ; Speed, Conrad W. ; Sherman, Samantha ; Rees, Matthew J. ; Udyawer, Vinay ; Flowers, Kathryn I. ; Clementi, Gina ; Valentin-Albanese, Jasmine ; Gorham, Taylor ; Adam, Shiham ; Khadeeja, Ali ; Pina-Amargós, Fabián ; Angulo-Valdés, Jorge A. ; Asher, Jacob ; García Barcia, Laura ; Beaufort, Océane ; Benjamin, Cecilie ; Bernard, Anthony T.F. ; Berumen, Michael L. ; Bierwagen, Stacy ; Bonnema, Erika ; Bown, Rosalind M.K. ; Bradley, Darcey ; Brooks, Edd ; Brown, Jed ; Buddo, Dayne ; Burke, Patrick ; Cáceres, Camila ; Cardeñosa, Diego ; Carrier, Jeffrey C. ; Caselle, Jennifer E. ; Charloo, Venkatesh ; Claverie, Thomas ; Clua, Eric ; Cochran, Jesse E.M. ; Cook, Neil ; Cramp, Jessica ; D’Alberto, Brooke ; Graaf, Martin de; Dornhege, Mareike ; Estep, Andy ; Fanovich, Lanya ; Farabough, Naomi F. ; Fernando, Daniel ; Flam, Anna L. ; Floros, Camilla ; Fourqurean, Virginia ; Garla, Ricardo ; Gastrich, Kirk ; George, Lachlan ; Graham, Rory ; Guttridge, Tristan ; Hardenstine, Royale S. ; Heck, Stephen ; Henderson, Aaron C. ; Hertler, Heidi ; Hueter, Robert ; Johnson, Mohini ; Jupiter, Stacy ; Kasana, Devanshi ; Kessel, Steven T. ; Kiilu, Benedict ; Kirata, Taratu ; Kuguru, Baraka ; Kyne, Fabian ; Langlois, Tim ; Lédée, Elodie J.I. ; Lindfield, Steve ; Luna-Acosta, Andrea ; Maggs, Jade ; Manjaji-Matsumoto, Mabel ; Marshall, Andrea ; Matich, Philip ; McCombs, Erin ; McLean, Dianne ; Meggs, Llewelyn ; Moore, Stephen ; Mukherji, Sushmita ; Murray, Ryan ; Kaimuddin, Muslimin ; Newman, Stephen J. ; Nogués, Josep ; Obota, Clay ; O’Shea, Owen ; Osuka, Kennedy ; Papastamatiou, Yannis P. ; Perera, Nishan ; Peterson, Bradley ; Ponzo, Alessandro ; Prasetyo, Andhika ; Quamar, Sjamsul ; Quinlan, Jessica ; Ruiz-Abierno, Alexei ; Sala, Enric ; Samoilys, Melita ; Schärer-Umpierre, Michelle ; Schlaff, Audrey ; Simpson, Nikola ; Smith, Adam N.H. ; Sparks, Lauren ; Tanna, Akshay ; Torres, Rubén ; Travers, Michael J. ; Zinnicq Bergmann, Maurits van; Vigliola, Laurent ; Ward, Juney ; Watts, Alexandra M. ; Wen, Colin ; Whitman, Elizabeth ; Wirsing, Aaron J. ; Wothke, Aljoscha ; Zarza-Gonzâlez, Esteban ; Cinner, Joshua E. - \ 2020
    Nature 583 (2020). - ISSN 0028-0836 - p. 801 - 806.

    Decades of overexploitation have devastated shark populations, leaving considerable doubt as to their ecological status1,2. Yet much of what is known about sharks has been inferred from catch records in industrial fisheries, whereas far less information is available about sharks that live in coastal habitats3. Here we address this knowledge gap using data from more than 15,000 standardized baited remote underwater video stations that were deployed on 371 reefs in 58 nations to estimate the conservation status of reef sharks globally. Our results reveal the profound impact that fishing has had on reef shark populations: we observed no sharks on almost 20% of the surveyed reefs. Reef sharks were almost completely absent from reefs in several nations, and shark depletion was strongly related to socio-economic conditions such as the size and proximity of the nearest market, poor governance and the density of the human population. However, opportunities for the conservation of reef sharks remain: shark sanctuaries, closed areas, catch limits and an absence of gillnets and longlines were associated with a substantially higher relative abundance of reef sharks. These results reveal several policy pathways for the restoration and management of reef shark populations, from direct top-down management of fishing to indirect improvement of governance conditions. Reef shark populations will only have a high chance of recovery by engaging key socio-economic aspects of tropical fisheries.

    The fungal collaboration gradient dominates the root economics space in plants
    Bergmann, Joana ; Weigelt, Alexandra ; Plas van der, Fons ; Mommer, L. ; Ruijven, J. van - \ 2020
    Science Advances 6 (2020)27. - ISSN 2375-2548 - 9 p.
    Plant economics run on carbon and nutrients instead of money. Leaf strategies aboveground span an economic spectrum from “live fast and die young” to “slow and steady,” but the economy defined by root strategies belowground remains unclear. Here, we take a holistic view of the belowground economy and show that root-mycorrhizal collaboration can short circuit a one-dimensional economic spectrum, providing an entire space of economic possibilities.Root trait data from 1810 species across the globe confirm a classical fast-slow “conservation” gradient but show that most variation is explained by an orthogonal “collaboration” gradient, ranging from “do-it-yourself”resource uptake to “outsourcing” of resource uptake to mycorrhizal fungi. This broadened “root economics space”provides a solid foundation for predictive understanding of belowground responses to changing environmental conditions.
    MEMOTE for standardized genome-scale metabolic model testing
    Lieven, Christian ; Beber, Moritz E. ; Olivier, Brett G. ; Bergmann, Frank T. ; Ataman, Meric ; Babaei, Parizad ; Bartell, Jennifer A. ; Blank, Lars M. ; Chauhan, Siddharth ; Correia, Kevin ; Diener, Christian ; Dräger, Andreas ; Ebert, Birgitta E. ; Edirisinghe, Janaka N. ; Faria, José P. ; Feist, Adam M. ; Fengos, Georgios ; Fleming, Ronan M.T. ; García-Jiménez, Beatriz ; Hatzimanikatis, Vassily ; Helvoirt, Wout van; Henry, Christopher S. ; Hermjakob, Henning ; Herrgård, Markus J. ; Kaafarani, Ali ; Kim, Hyun Uk ; King, Zachary ; Klamt, Steffen ; Klipp, Edda ; Koehorst, Jasper J. ; König, Matthias ; Lakshmanan, Meiyappan ; Lee, Dong Yup ; Lee, Sang Yup ; Lee, Sunjae ; Lewis, Nathan E. ; Liu, Filipe ; Ma, Hongwu ; Machado, Daniel ; Mahadevan, Radhakrishnan ; Maia, Paulo ; Mardinoglu, Adil ; Medlock, Gregory L. ; Monk, Jonathan M. ; Nielsen, Jens ; Nielsen, Lars Keld ; Nogales, Juan ; Nookaew, Intawat ; Palsson, Bernhard O. ; Papin, Jason A. ; Patil, Kiran R. ; Poolman, Mark ; Price, Nathan D. ; Resendis-Antonio, Osbaldo ; Richelle, Anne ; Rocha, Isabel ; Sánchez, Benjamín J. ; Schaap, Peter J. ; Malik Sheriff, Rahuman S. ; Shoaie, Saeed ; Sonnenschein, Nikolaus ; Teusink, Bas ; Vilaça, Paulo ; Vik, Jon Olav ; Wodke, Judith A.H. ; Xavier, Joana C. ; Yuan, Qianqian ; Zakhartsev, Maksim ; Zhang, Cheng - \ 2020
    Nature Biotechnology 38 (2020)4. - ISSN 1087-0156 - 1 p.

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

    MEMOTE for standardized genome-scale metabolic model testing
    Lieven, Christian ; Beber, Moritz E. ; Olivier, Brett G. ; Bergmann, Frank T. ; Ataman, Meric ; Babaei, Parizad ; Bartell, Jennifer A. ; Blank, Lars M. ; Chauhan, Siddharth ; Correia, Kevin ; Diener, Christian ; Dräger, Andreas ; Ebert, Birgitta E. ; Edirisinghe, Janaka N. ; Faria, José P. ; Feist, Adam M. ; Fengos, Georgios ; Fleming, Ronan M.T. ; García-Jiménez, Beatriz ; Hatzimanikatis, Vassily ; Helvoirt, Wout van; Henry, Christopher S. ; Hermjakob, Henning ; Herrgård, Markus J. ; Kaafarani, Ali ; Kim, Hyun Uk ; King, Zachary ; Klamt, Steffen ; Klipp, Edda ; Koehorst, Jasper J. ; König, Matthias ; Lakshmanan, Meiyappan ; Lee, Dong Yup ; Lee, Sang Yup ; Lee, Sunjae ; Lewis, Nathan E. ; Liu, Filipe ; Ma, Hongwu ; Machado, Daniel ; Mahadevan, Radhakrishnan ; Maia, Paulo ; Mardinoglu, Adil ; Medlock, Gregory L. ; Monk, Jonathan M. ; Nielsen, Jens ; Nielsen, Lars Keld ; Nogales, Juan ; Nookaew, Intawat ; Palsson, Bernhard O. ; Papin, Jason A. ; Patil, Kiran R. ; Poolman, Mark ; Price, Nathan D. ; Resendis-Antonio, Osbaldo ; Richelle, Anne ; Rocha, Isabel ; Sánchez, Benjamín J. ; Schaap, Peter J. ; Malik Sheriff, Rahuman S. ; Shoaie, Saeed ; Sonnenschein, Nikolaus ; Teusink, Bas ; Vilaça, Paulo ; Vik, Jon Olav ; Wodke, Judith A.H. ; Xavier, Joana C. ; Yuan, Qianqian ; Zakhartsev, Maksim ; Zhang, Cheng - \ 2020
    Nature Biotechnology 38 (2020)3. - ISSN 1087-0156 - p. 272 - 276.
    The physical oceanography of the transport of floating marine debris
    Sebille, Erik van; Aliani, Stefano ; Law, Kara Lavender ; Maximenko, Nikolai ; Alsina, Jose ; Bagaev, Andrei ; Bergmann, M. ; Chapron, Bertrand ; Chubarenko, Irina ; Cozar, Andres ; Delandmeter, Philippe ; Egger, Matthias ; Fox-Kemper, Baylor ; Pascal Garaba, Shungudzemwoyo ; Goddijn-Murphy, Lonneke ; Hardesty, Britta Denise ; Hoffman, M. ; Isobe, Atsuhiko ; Jongedijk, Cleo ; Kaandorp, Mikael ; Khatmullina, Liliya ; Koelmans, A.A. - \ 2020
    Environmental Research Letters 15 (2020)2. - ISSN 1748-9318
    Marine plastic debris floating on the ocean surface is a major environmental problem. However, its distribution in the ocean is poorly mapped, and most of the plastic waste estimated to have entered the ocean from land is unaccounted for. Better understanding of how plastic debris is transported from coastal and marine sources is crucial to quantify and close the global inventory of marine plastics, which in turn represents critical information for mitigation or policy strategies. At the same time, plastic is a unique tracer that provides an opportunity to learn more about the physics and dynamics of our ocean across multiple scales, from the Ekman convergence in basin-scale gyres to individual waves in the surfzone. In this review, we comprehensively discuss what is known about the different processes that govern the transport of floating marine plastic debris in both the open ocean and the coastal zones, based on the published literature and referring to insights from neighbouring fields such as oil spill dispersion, marine safety recovery, plankton connectivity, and others. We discuss how measurements of marine plastics (both in situ and in the laboratory), remote sensing, and numerical simulations can elucidate these processes and their interactions across spatio-temporal scales.
    Plasma metabolites associated with colorectal cancer stage: Findings from an international consortium
    Geijsen, Anne J.M.R. ; Roekel, Eline H. van; Duijnhoven, Fränzel J.B. van; Achaintre, David ; Bachleitner-Hofmann, Thomas ; Baierl, Andreas ; Bergmann, Michael M. ; Boehm, Jürgen ; Bours, Martijn J.L. ; Brenner, Hermann ; Breukink, Stéphanie O. ; Brezina, Stefanie ; Chang-Claude, Jenny ; Herpel, Esther ; Wilt, Johannes H.W. de; Gicquiau, Audrey ; Gigic, Biljana ; Gumpenberger, Tanja ; Hansson, Bibi M.E. ; Hoffmeister, Michael ; Holowatyj, Andreana N. ; Karner-Hanusch, Judith ; Keski-Rahkonen, Pekka ; Keulen, Eric T.P. ; Koole, Janna L. ; Leeb, Gernot ; Ose, Jennifer ; Schirmacher, Peter ; Schneider, Martin A. ; Schrotz-King, Petra ; Stift, Anton ; Ulvik, Arve ; Vogelaar, Jeroen F. ; Wesselink, Evertine ; Zutphen, Moniek van; Gsur, Andrea ; Habermann, Nina ; Kampman, Ellen ; Scalbert, Augustin ; Ueland, Per M. ; Ulrich, Alexis B. ; Ulrich, Cornelia M. ; Weijenberg, Matty P. ; Kok, Dieuwertje E. - \ 2020
    International Journal of Cancer 146 (2020)12. - ISSN 0020-7136 - p. 3256 - 3266.
    colorectal cancer - disease stage - epidemiology - metabolomics - plasma metabolites

    Colorectal cancer is the second most common cause of cancer-related death globally, with marked differences in prognosis by disease stage at diagnosis. We studied circulating metabolites in relation to disease stage to improve the understanding of metabolic pathways related to colorectal cancer progression. We investigated plasma concentrations of 130 metabolites among 744 Stages I–IV colorectal cancer patients from ongoing cohort studies. Plasma samples, collected at diagnosis, were analyzed with liquid chromatography-mass spectrometry using the Biocrates AbsoluteIDQ™ p180 kit. We assessed associations between metabolite concentrations and stage using multinomial and multivariable logistic regression models. Analyses were adjusted for potential confounders as well as multiple testing using false discovery rate (FDR) correction. Patients presented with 23, 28, 39 and 10% of Stages I–IV disease, respectively. Concentrations of sphingomyelin C26:0 were lower in Stage III patients compared to Stage I patients (pFDR < 0.05). Concentrations of sphingomyelin C18:0 and phosphatidylcholine (diacyl) C32:0 were statistically significantly higher, while citrulline, histidine, phosphatidylcholine (diacyl) C34:4, phosphatidylcholine (acyl-alkyl) C40:1 and lysophosphatidylcholines (acyl) C16:0 and C17:0 concentrations were lower in Stage IV compared to Stage I patients (pFDR < 0.05). Our results suggest that metabolic pathways involving among others citrulline and histidine, implicated previously in colorectal cancer development, may also be linked to colorectal cancer progression.

    Assessing the potential of soil carbonation and enhanced weathering through Life Cycle Assessment: A case study for Sao Paulo State, Brazil
    Lefebvre, David ; Goglio, Pietro ; Williams, Adrian ; Manning, David A.C. ; Azevedo, Antonio Carlos de; Bergmann, Magda ; Meersmans, Jeroen ; Smith, Pete - \ 2019
    Journal of Cleaner Production 233 (2019). - ISSN 0959-6526 - p. 468 - 481.
    Carbonation - Enhanced weathering - LCA - Life cycle assessment - NET - Sao paulo

    Enhanced silicate rock weathering for long-term carbon dioxide sequestration has considerable potential, but depends on the availability of suitable rocks coupled with proximity to suitable locations for field application. In this paper, we investigate the established mining industry that extracts basaltic rocks for construction from the Paraná Basin, Sao Paulo State, Brazil. Through a Life Cycle Assessment, we determine the balance of carbon dioxide emissions involved in the use of this material, the relative contribution of soil carbonation and enhanced weathering, and the potential carbon dioxide removal of Sao Paulo agricultural land through enhanced weathering of basalt rock. Our results show that enhanced weathering and carbonation respectively emit around 75 and 135 kg carbon dioxide equivalent per tonne of carbon dioxide equivalent removed (considering a quarry to field distance of 65 km). We underline transportation as the principal process negatively affecting the practice and uncover a limiting road travel distance from the quarry to the field of 540 ± 65 km for carbonation and 990 ± 116 km for enhanced weathering, above which the emissions offset the potential capture. Regarding Sao Paulo State, the application of crushed basalt at 1 t/ha to all of the State's 12 million hectares of agricultural land could capture around 1.3 to 2.4 Mt carbon dioxide equivalent through carbonation and enhanced weathering, respectively. This study suggests a lower sequestration estimate than previous studies and emphasizes the need to consider all process stages through a Life Cycle Assessment methodology, to provide more reliable estimates of the sequestration potential of greenhouse gas removal technologies.

    Plasma metabolites associated with colorectal cancer: A discovery-replication strategy
    Geijsen, Anne J.M.R. ; Brezina, Stefanie ; Keski-Rahkonen, Pekka ; Baierl, Andreas ; Bachleitner-Hofmann, Thomas ; Bergmann, Michael M. ; Boehm, Juergen ; Brenner, Hermann ; Chang-Claude, Jenny ; Duijnhoven, Fränzel J.B. van; Gigic, Biljana ; Gumpenberger, Tanja ; Hofer, Philipp ; Hoffmeister, Michael ; Holowatyj, Andreana N. ; Karner-Hanusch, Judith ; Kok, Dieuwertje E. ; Leeb, Gernot ; Ulvik, Arve ; Robinot, Nivonirina ; Ose, Jennifer ; Stift, Anton ; Schrotz-King, Petra ; Ulrich, Alexis B. ; Ueland, Per Magne ; Kampman, Ellen ; Scalbert, Augustin ; Habermann, Nina ; Gsur, Andrea ; Ulrich, Cornelia M. - \ 2019
    International Journal of Cancer 145 (2019)5. - ISSN 0020-7136 - p. 1221 - 1231.
    colorectal cancer - discovery-replication approach - metabolomics - UHPLC-QTOF-MS

    Colorectal cancer is known to arise from multiple tumorigenic pathways; however, the underlying mechanisms remain not completely understood. Metabolomics is becoming an increasingly popular tool in assessing biological processes. Previous metabolomics research focusing on colorectal cancer is limited by sample size and did not replicate findings in independent study populations to verify robustness of reported findings. Here, we performed a ultrahigh performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS) screening on EDTA plasma from 268 colorectal cancer patients and 353 controls using independent discovery and replication sets from two European cohorts (ColoCare Study: n = 180 patients/n = 153 controls; the Colorectal Cancer Study of Austria (CORSA) n = 88 patients/n = 200 controls), aiming to identify circulating plasma metabolites associated with colorectal cancer and to improve knowledge regarding colorectal cancer etiology. Multiple logistic regression models were used to test the association between disease state and metabolic features. Statistically significant associated features in the discovery set were taken forward and tested in the replication set to assure robustness of our findings. All models were adjusted for sex, age, BMI and smoking status and corrected for multiple testing using False Discovery Rate. Demographic and clinical data were abstracted from questionnaires and medical records.

    Towards valuation of biodiversity in agricultural soils : A case for earthworms
    Plaas, Elke ; Meyer-Wolfarth, Friederike ; Banse, Martin ; Bengtsson, Jan ; Bergmann, Holger ; Faber, Jack ; Potthoff, Martin ; Runge, Tania ; Schrader, Stefan ; Taylor, Astrid - \ 2019
    Ecological Economics 159 (2019). - ISSN 0921-8009 - p. 291 - 300.
    Economic value - Ecosystem engineers - Ecosystem services - Soil biodiversity - Soil management practices - Sustainability

    Soil biodiversity is deteriorating in Europe due to an on-going intensification of agriculture, climate change and food production supporting measures of the European Common Agricultural Policy (CAP). Nevertheless, the CAP tries to take biodiversity into account via proposing a range of agri-environmental measures. These ES contribute to food security, climate change mitigation, water retention and plant biomass growth. Healthy soils also help to prevent erosion, desertification, and landslides and to stabilise crop yields. The provision of ES by soil biota is a result of their impact on soil processes in interaction with soil conditions as well as soil management practices of the farmers such as tillage or crop rotations. Some taxa amongst soil biota play key roles in regulating soil processes. With respect to biocontrol of soil-borne pests, the earthworm species Lumbricus terrestris is known to play an important role in suppressing toxigenic plant pathogens, such as Fusarium culmorum and its mycotoxin deoxynivalenol (DON). We highlight the importance of earthworms for pest control to conceptualise and show how farmers’ management practices influence soil ecosystem services and outline how this can be examined in a socio-ecological context by providing a concrete example of an economical evaluation of ES provided by earthworms.

    Prediagnostic serum Vitamin D levels and the risk of Crohn's disease and ulcerative colitis in european populations : A nested case-control study
    Opstelten, Jorrit L. ; Chan, Simon S.M. ; Hart, Andrew R. ; Schaik, Fiona D.M. Van; Siersema, Peter D. ; Lentjes, Eef G.W.M. ; Khaw, Kay Tee ; Luben, Robert ; Key, Timothy J. ; Boeing, Heiner ; Bergmann, Manuela M. ; Overvad, Kim ; Palli, Domenico ; Masala, Giovanna ; Racine, Antoine ; Carbonnel, Franck ; Boutron-Ruault, Marie Christine ; Tjønneland, Anne ; Olsen, Anja ; Andersen, Vibeke ; Kaaks, Rudolf ; Kuhn, Tilman ; Tumino, Rosario ; Trichopoulou, Antonia ; Peeters, Petra H.M. ; Verschuren, W.M.M. ; Witteman, Ben J.M. ; Oldenburg, Bas - \ 2018
    Inflammatory Bowel Diseases 24 (2018)3. - ISSN 1078-0998 - p. 633 - 640.
    Crohn's disease - etiology - inflammatory bowel disease - ulcerative colitis - Vitamin D

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

    Data-Driven Modeling of Intracellular Auxin Fluxes Indicates a Dominant Role of the ER in Controlling Nuclear Auxin Uptake
    Middleton, Alistair M. ; Bosco, Cristina Dal; Chlap, Phillip ; Bensch, Robert ; Harz, Hartmann ; Ren, Fugang ; Bergmann, Stefan ; Wend, Sabrina ; Weber, Wilfried ; Hayashi, Ken Ichiro ; Zurbriggen, Matias D. ; Uhl, Rainer ; Ronneberger, Olaf ; Palme, Klaus ; Fleck, Christian ; Dovzhenko, Alexander - \ 2018
    Cell Reports 22 (2018)11. - ISSN 2211-1247 - p. 3044 - 3057.
    auxin - auxin flux - auxin sensor - endoplasmic reticulum - fluorescent aux - mathematical modeling - microscopy - nucleus - protoplasts - single cells
    In plants, the phytohormone auxin acts as a master regulator of developmental processes and environmental responses. The best characterized process in the auxin regulatory network occurs at the subcellular scale, wherein auxin mediates signal transduction into transcriptional programs by triggering the degradation of Aux/IAA transcriptional repressor proteins in the nucleus. However, whether and how auxin movement between the nucleus and the surrounding compartments is regulated remain elusive. Using a fluorescent auxin analog, we show that its diffusion into the nucleus is restricted. By combining mathematical modeling with time course assays on auxin-mediated nuclear signaling and quantitative phenotyping in single plant cell systems, we show that ER-to-nucleus auxin flux represents a major subcellular pathway to directly control nuclear auxin levels. Our findings propose that the homeostatically regulated auxin pool in the ER and ER-to-nucleus auxin fluxes underpin auxin-mediated downstream responses in plant cells. Middleton et al. study how the plant phytohormone auxin enters the nucleus by using quantitative phenotyping in single plant cell systems and bespoke mathematical models that relate controlled perturbations to experimentally measurable responses. Their findings show that auxin predominantly enters the nucleus via the endoplasmic reticulum.
    Plastic ingestion by juvenile polar cod (Boreogadus saida) in the Arctic Ocean
    Kühn, Susanne ; Schaafsma, Fokje L. ; Werven, Bernike van; Flores, Hauke ; Bergmann, Melanie ; Egelkraut-Holtus, Marion ; Tekman, Mine B. ; Franeker, Jan A. van - \ 2018
    Polar Biology 41 (2018)6. - ISSN 0722-4060 - p. 1269 - 1278.
    Airborne micro-fibre contamination - Arctic - Microplastic - Polar cod (Boreogadus saida)
    One of the recently recognised stressors in Arctic ecosystems concerns plastic litter. In this study, juvenile polar cod (Boreogadus saida) were investigated for the presence of plastics in their stomachs. Polar cod is considered a key species in the Arctic ecosystem. The fish were collected both directly from underneath the sea ice in the Eurasian Basin and in open waters around Svalbard. We analysed the stomachs of 72 individuals under a stereo microscope. Two stomachs contained non-fibrous microplastic particles. According to µFTIR analysis, the particles consisted of epoxy resin and a mix of Kaolin with polymethylmethacrylate (PMMA). Fibrous objects were excluded from this analysis to avoid bias due to contamination with airborne micro-fibres. A systematic investigation of the risk for secondary micro-fibre contamination during analytical procedures showed that precautionary measures in all procedural steps are critical. Based on the two non-fibrous objects found in polar cod stomachs, our results show that ingestion of microplastic particles by this ecologically important fish species is possible. With increasing human activity, plastic ingestion may act as an increasing stressor on polar cod in combination with ocean warming and sea-ice decline in peripheral regions of the Arctic Ocean. To fully assess the significance of this stressor and its spatial and temporal variability, future studies must apply a rigorous approach to avoid secondary pollution.
    Emergence of carp edema virus (CEV) and its significance to European common carp and koi Cyprinus carpio
    Way, K. ; Haenen, O. ; Stone, D. ; Adamek, M. ; Bergmann, S.M. ; Bigarré, L. ; Diserens, Nicolas ; El-Matbouli, M. ; Gjessing, M.C. ; Jung-Schroers, V. ; Leguay, E. ; Matras, M. ; Olesen, Niels J. ; Panzarin, Valentina ; Piačková, V. ; Toffan, A. ; Vendramin, N. ; Veselý, T. ; Waltzek, T. - \ 2017
    Diseases of Aquatic Organisms 126 (2017)2. - ISSN 0177-5103 - p. 155 - 166.
    Aquaculture - CEVD - Cyprinus carpio - Koi sleepy disease - PCR - Poxvirus
    Carp edema virus disease (CEVD), also known as koi sleepy disease, is caused by a poxvirus associated with outbreaks of clinical disease in koi and common carp Cyprinus carpio. Originally characterised in Japan in the 1970s, international trade in koi has led to the spread of CEV, although the first recognised outbreak of the disease outside of Japan was not reported until 1996 in the USA. In Europe, the disease was first recognised in 2009 and, as detection and diagnosis have improved, more EU member states have reported CEV associated with disease outbreaks. Although the structure of the CEV genome is not yet elucidated, molecular epidemiology studies have suggested distinct geographical populations of CEV infecting both koi and common carp. Detection and identification of cases of CEVD in common carp were unreliable using the original PCR primers. New primers for conventional and quantitative PCR (qPCR) have been designed that improve detection, and their sequences are provided in this paper. The qPCR primers have successfully detected CEV DNA in archive material from investigations of unexplained carp mortalities conducted >15 yr ago. Improvement in disease management and control is possible, and the principles of biosecurity, good health management and disease surveillance, applied to koi herpesvirus disease, can be equally applied to CEVD. However, further research studies are needed to fill the knowledge gaps in the disease pathogenesis and epidemiology that, currently, prevent an accurate assessment of the likely impact of CEVD on European koi and common carp aquaculture and on wild carp stocks.
    Validation of a serum neutralization test for detection of antibodies specific to cyprinid herpesvirus 3 in infected common and koi carp (Cyprinus carpio)
    Cabon, J. ; Louboutin, L. ; Castric, J. ; Bergmann, S. ; Bovo, G. ; Matras, M. ; Haenen, O. ; Olesen, N.J. ; Morin, T. - \ 2017
    Journal of Fish Diseases 40 (2017)5. - ISSN 0140-7775 - p. 687 - 701.
    common carp - CyHV-3-specific antibodies - Cyprinid herpesvirus 3 - koi - method validation - serum neutralization test
    Cyprinid herpesvirus 3 (CyHV-3) is the aetiological agent of a serious infective, notifiable disease affecting common carp and varieties. In survivors, infection is generally characterized by a subclinical latency phase with restricted viral replication. The CyHV-3 genome is difficult to detect in such carrier fish that represent a potential source of dissemination if viral reactivation occurs. In this study, the analytical and diagnostic performance of an alternative serum neutralization (SN) method based on the detection of CyHV-3-specific antibodies was assessed using 151 serum or plasma samples from healthy and naturally or experimentally CyHV-3-infected carp. French CyHV-3 isolate 07/108b was neutralized efficiently by sera from carp infected with European, American and Taiwanese CyHV-3 isolates, but no neutralization was observed using sera specific to other aquatic herpesviruses. Diagnostic sensitivity, diagnostic specificity and repeatability of 95.9%, 99.0% and 99.3%, respectively, were obtained, as well as a compliance rate of 89.9% in reproducibility testing. Neutralizing antibodies were steadily detected in infected carp subjected to restrictive or permissive temperature variations over more than 25 months post-infection. The results suggest that this non-lethal diagnostic test could be used in the future to improve the epidemiological surveillance and control of CyHV-3 disease.
    Genome-wide analysis identifies 12 loci influencing human reproductive behavior
    Barban, Nicola ; Jansen, Rick ; Vlaming, Ronald de; Vaez, Ahmad ; Mandemakers, Jornt J. ; Tropf, Felix C. ; Shen, Xia ; Wilson, James F. ; Chasman, Daniel I. ; Nolte, Ilja M. ; Tragante, Vinicius ; Laan, Sander W. van der; Perry, John R.B. ; Kong, Augustine ; Ahluwalia, Tarunveer S. ; Albrecht, Eva ; Yerges-Armstrong, Laura ; Atzmon, Gil ; Auro, Kirsi ; Ayers, Kristin ; Bakshi, Andrew ; Ben-Avraham, Danny ; Berger, Klaus ; Bergman, Aviv ; Bertram, Lars ; Bielak, Lawrence F. ; Bjornsdottir, Gyda ; Bonder, Marc Jan ; Broer, Linda ; Bui, Minh ; Barbieri, Caterina ; Cavadino, Alana ; Chavarro, Jorge E. ; Turman, Constance ; Concas, Maria Pina ; Cordell, Heather J. ; Davies, Gail ; Eibich, Peter ; Eriksson, Nicholas ; Esko, Tõnu ; Eriksson, Joel ; Falahi, Fahimeh ; Felix, Janine F. ; Fontana, Mark Alan ; Franke, Lude ; Gandin, Ilaria ; Gaskins, Audrey J. ; Gieger, Christian ; Gunderson, Erica P. ; Guo, Xiuqing ; Hayward, Caroline ; He, Chunyan ; Hofer, Edith ; Huang, Hongyan ; Joshi, Peter K. ; Kanoni, Stavroula ; Karlsson, Robert ; Kiechl, Stefan ; Kifley, Annette ; Kluttig, Alexander ; Kraft, Peter ; Lagou, Vasiliki ; Lecoeur, Cecile ; Lahti, Jari ; Li-Gao, Ruifang ; Lind, Penelope A. ; Liu, Tian ; Makalic, Enes ; Mamasoula, Crysovalanto ; Matteson, Lindsay ; Mbarek, Hamdi ; McArdle, Patrick F. ; McMahon, George ; Meddens, S.F.W. ; Mihailov, Evelin ; Miller, Mike ; Missmer, Stacey A. ; Monnereau, Claire ; Most, Peter J. van der; Myhre, Ronny ; Nalls, Mike A. ; Nutile, Teresa ; Kalafati, Ioanna Panagiota ; Porcu, Eleonora ; Prokopenko, Inga ; Rajan, Kumar B. ; Rich-Edwards, Janet ; Rietveld, Cornelius A. ; Robino, Antonietta ; Rose, Lynda M. ; Rueedi, Rico ; Ryan, Kathleen A. ; Saba, Yasaman ; Schmidt, Daniel ; Smith, Jennifer A. ; Stolk, Lisette ; Streeten, Elizabeth ; Tönjes, Anke ; Thorleifsson, Gudmar ; Ulivi, Sheila ; Wedenoja, Juho ; Wellmann, Juergen ; Willeit, Peter ; Yao, Jie ; Yengo, Loic ; Zhao, Jing Hua ; Zhao, Wei ; Zhernakova, Daria V. ; Amin, Najaf ; Andrews, Howard ; Balkau, Beverley ; Barzilai, Nir ; Bergmann, Sven ; Biino, Ginevra ; Bisgaard, Hans ; Bønnelykke, Klaus ; Boomsma, Dorret I. ; Buring, Julie E. ; Campbell, Harry ; Cappellani, Stefania ; Ciullo, Marina ; Cox, Simon R. ; Cucca, Francesco ; Toniolo, Daniela ; Davey-Smith, George ; Deary, Ian J. ; Dedoussis, George ; Deloukas, Panos ; Duijn, Cornelia M. van; Geus, Eco J.C. de; Eriksson, Johan G. ; Evans, Denis A. ; Faul, Jessica D. ; Sala, Cinzia Felicita ; Froguel, Philippe ; Gasparini, Paolo ; Girotto, Giorgia ; Grabe, Hans-Jörgen ; Greiser, Karin Halina ; Groenen, Patrick J.F. ; Haan, Hugoline G. de; Haerting, Johannes ; Harris, Tamara B. ; Heath, Andrew C. ; Heikkilä, Kauko ; Hofman, Albert ; Homuth, Georg ; Holliday, Elizabeth G. ; Hopper, John ; Hyppönen, Elina ; Jacobsson, Bo ; Jaddoe, Vincent W.V. ; Johannesson, Magnus ; Jugessur, Astanand ; Kähönen, Mika ; Kajantie, Eero ; Kardia, Sharon L.R. ; Keavney, Bernard ; Kolcic, Ivana ; Koponen, Päivikki ; Kovacs, Peter ; Kronenberg, Florian ; Kutalik, Zoltan ; Bianca, Martina la; Lachance, Genevieve ; Iacono, William G. ; Lai, Sandra ; Lehtimäki, Terho ; Liewald, David C. ; Lindgren, Cecilia M. ; Liu, Yongmei ; Luben, Robert ; Lucht, Michael ; Luoto, Riitta ; Magnus, Per ; Magnusson, Patrik K.E. ; Martin, Nicholas G. ; McGue, Matt ; McQuillan, Ruth ; Medland, Sarah E. ; Meisinger, Christa ; Mellström, Dan ; Metspalu, Andres ; Traglia, Michela ; Milani, Lili ; Mitchell, Paul ; Montgomery, Grant W. ; Mook-Kanamori, Dennis ; Mutsert, Renée de; Nohr, Ellen A. ; Ohlsson, Claes ; Olsen, Jørn ; Ong, Ken K. ; Paternoster, Lavinia ; Pattie, Alison ; Penninx, Brenda W.J.H. ; Perola, Markus ; Peyser, Patricia A. ; Pirastu, Mario ; Polasek, Ozren ; Power, Chris ; Kaprio, Jaakko ; Raffel, Leslie J. ; Räikkönen, Katri ; Raitakari, Olli ; Ridker, Paul M. ; Ring, Susan M. ; Roll, Kathryn ; Rudan, Igor ; Ruggiero, Daniela ; Rujescu, Dan ; Salomaa, Veikko ; Schlessinger, David ; Schmidt, Helena ; Schmidt, Reinhold ; Schupf, Nicole ; Smit, Johannes ; Sorice, Rossella ; Spector, Tim D. ; Starr, John M. ; Stöckl, Doris ; Strauch, Konstantin ; Stumvoll, Michael ; Swertz, Morris A. ; Thorsteinsdottir, Unnur ; Thurik, A.R. ; Timpson, Nicholas J. ; Tung, Joyce Y. ; Uitterlinden, André G. ; Vaccargiu, Simona ; Viikari, Jorma ; Vitart, Veronique ; Völzke, Henry ; Vollenweider, Peter ; Vuckovic, Dragana ; Waage, Johannes ; Wagner, Gert G. ; Wang, Jie Jin ; Wareham, Nicholas J. ; Weir, David R. ; Willemsen, Gonneke ; Willeit, Johann ; Wright, Alan F. ; Zondervan, Krina T. ; Stefansson, Kari ; Krueger, Robert F. ; Lee, James J. ; Benjamin, Daniel J. ; Cesarini, David ; Koellinger, Philipp D. ; Hoed, Marcel den; Snieder, Harold ; Mills, Melinda C. - \ 2016
    Nature Genetics 48 (2016)12. - ISSN 1061-4036 - p. 1462 - 1472.
    The genetic architecture of human reproductive behavior—age at first birth (AFB) and number of children ever born (NEB)—has a strong relationship with fitness, human development, infertility and risk of neuropsychiatric disorders. However, very few genetic loci have been identified, and the underlying mechanisms of AFB and NEB are poorly understood. We report a large genome-wide association study of both sexes including 251,151 individuals for AFB and 343,072 individuals for NEB. We identified 12 independent loci that are significantly associated with AFB and/or NEB in a SNP-based genome-wide association study and 4 additional loci associated in a gene-based effort. These loci harbor genes that are likely to have a role, either directly or by affecting non-local gene expression, in human reproduction and infertility, thereby increasing understanding of these complex traits.
    Deleterious effects of litter on marine life
    Kuhn, S. ; Bravo Rebolledo, E. ; Franeker, J.A. van - \ 2015
    In: Marine Anthropogenic Litter / Bergmann, M., Gutow, L., Klages, M., Springer International Publishing - ISBN 9783319165103 - p. 75 - 116.
    In this review we report new findings concerning interaction between marine debris and wildlife. Deleterious effects and consequences of entanglement, consumption and smothering are highlighted and discussed. The number of species known to have been affected by either entanglement or ingestion of plastic debris has doubled since 1997, from 267 to 557 species among all groups of wildlife. For marine turtles the number of affected species increased from 86 to 100 % (now 7 of 7 species), for marine mammals from 43 to 66 % (now 81 of 123 species) and for seabirds from 44 to 50 % of species (now 203 of 406 species). Strong increases in records were also listed for fish and invertebrates, groups that were previously not considered in detail. In future records of interactions between marine debris and wildlife we recommend to focus on standardized data on frequency of occurrence and quantities of debris ingested. In combination with dedicated impact studies in the wild or experiments, this will allow more detailed assessments of the deleterious effects of marine debris on individuals and populations.
    Nanoplastics in the aquatic environment
    Koelmans, A.A. ; Besseling, E. ; Shim, W.J. - \ 2015
    In: Marine Anthropogene Litter / Bergmann, M., Gutow, L., Klages, M., Berlin : Springer - ISBN 9783319165103 - p. 325 - 340.
    A growing body of literature reports on the abundance and effects of plastic debris, with an increasing focus on microplastic particles smaller than 5 mm. It has often been suggested that plastic particles in the
    Modeling the role of microplastics in Bioaccumulation of organic chemicals to marine aquatic organisms. Critical Review
    Koelmans, A.A. - \ 2015
    In: Marine Anthropogenic Litter / Bergmann M, Gutow L, Klages M (eds), M., Gutow, L., Klages, M., Berlin : Springer - ISBN 9783319165103 - p. 309 - 324.
    It has been shown that ingestion of microplastics may increase bioaccumulation of organic chemicals by aquatic organisms. This paper critically reviews the literature on the effects of plastic ingestion on the bioaccumulation of organic chemicals, emphasizing quantitative approaches and mechanistic models. It appears that the role of microplastics can be understood from chemical partitioning to microplastics and subsequent bioaccumulation by biota, with microplastic as a component of the organisms’ diet. Microplastic ingestion may either clean or contaminate the organism, depending on the chemical fugacity gradient between ingested plastic and organism tissue. To date, most laboratory studies used clean test organisms exposed to contaminated microplastic, thus favouring chemical transfer to the organism. Observed effects on bioaccumulation were either insignificant or less than a factor of two to three. In the field, where contaminants are present already, gradients can be expected to be smaller or even opposite, leading to cleaning by plastic. Furthermore, the directions of the gradients may be opposite for the different chemicals present in the chemical mixtures in microplastics and in the environment. This implies a continuous trade-off between slightly increased contamination and cleaning upon ingestion of microplastic, a trade-off that probably attenuates the overall hazard of microplastic ingestion. Simulation models have shown to be helpful in mechanistically analysing these observations and scenarios, and are discussed in detail. Still, the literature on parameterising such models is limited and further experimental work is required to better constrain the parameters in these models for the wide range of organisms and chemicals acting in the aquatic environment. Gaps in knowledge and recommendations for further research are provided.
    Evolutionary dynamics and genetic diversity from three genes of Anguilid thabdovirus
    Bellec, L. ; Cabon, J. ; Bergmann, S. ; Boisseson, C. de; Engelsma, M.Y. ; Haenen, O.L.M. ; Morin, T. ; Oleson, N.J. ; Schuetze, H. ; Toffan, A. ; Way, K. ; Bigarré, L. - \ 2014
    Journal of General Virology 95 (2014)Pt 11. - ISSN 0022-1317 - p. 2390 - 2401.
    vesicular stomatitis-virus - hemorrhagic septicemia virus - fresh-water eels - european eel - phylogenetic analysis - dna polymorphism - fish rhabdovirus - spring viremia - carp virus - p-gene
    Wild freshwater eel populations have dramatically declined in recent past decades in Europe and America, partially through the impact of several factors including the wide spread of infectious diseases. The anguillid rhabdoviruses eel virus European X (EVEX) and eel virus American (EVA) potentially play a role in this decline, even if their real contribution is still unclear. In this study, we investigate the evolutionary dynamics and genetic diversity of anguiillid rhabdoviruses by analysing sequences from the glycoprotein, nucleoprotein and phosphoprotein (P) genes of 57 viral strains collected from seven countries over 40 years using maximum-likelihood and Bayesian approaches. Phylogenetic trees from the three genes are congruent and allow two monophyletic groups, European and American, to be clearly distinguished. Results of nucleotide substitution rates per site per year indicate that the P gene is expected to evolve most rapidly. The nucleotide diversity observed is low (2–3¿%) for the three genes, with a significantly higher variability within the P gene, which encodes multiple proteins from a single genomic RNA sequence, particularly a small C protein. This putative C protein is a potential molecular marker suitable for characterization of distinct genotypes within anguillid rhabdoviruses. This study provides, to our knowledge, the first molecular characterization of EVA, brings new insights to the evolutionary dynamics of two genotypes of Anguillid rhabdovirus, and is a baseline for further investigations on the tracking of its spread.
    Irreversible fate commitment in the Arabidopsis stomatal lineage requires a Fama and Retinoblastoma-related module
    Matos, J.L. ; Lau, O.S. ; Hachez, C. ; Cruz-Ramirez, A. ; Scheres, B. ; Bergmann, D.C. - \ 2014
    eLife 3 (2014). - ISSN 2050-084X
    asymmetric cell divisions - gateway binary vectors - transcription factor - secretory peptide - guard-cells - differentiation - expression - genes - transformation - termination
    The presumed totipotency of plant cells leads to questions about how specific stem cell lineages and terminal fates could be established. In the Arabidopsis stomatal lineage, a transient self-renewing phase creates precursors that differentiate into one of two epidermal cell types, guard cells or pavement cells. We found that irreversible differentiation of guard cells involves RETINOBLASTOMA-RELATED (RBR) recruitment to regulatory regions of master regulators of stomatal initiation, facilitated through interaction with a terminal stomatal lineage transcription factor, FAMA. Disrupting physical interactions between FAMA and RBR preferentially reveals the role of RBR in enforcing fate commitment over its role in cell-cycle control in this developmental context. Analysis of the phenotypes linked to the modulation of FAMA and RBR sheds new light on the way iterative divisions and terminal differentiation are coordinately regulated in a plant stem-cell lineage. - See more at: http://elifesciences.org/content/3/e03271#sthash.f3srCCrx.dpuf
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