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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    Sel1L-Hrd1 ER-associated degradation maintains β cell identity via TGF-β signaling
    Shrestha, Neha ; Liu, Tongyu ; Ji, Yewei ; Reinert, Rachel B. ; Torres, Mauricio ; Li, Xin ; Zhang, Maria ; Tang, Chih-Hang Anthony ; Hu, Chih-Chi Andrew ; Liu, Chengyang ; Naji, Ali ; Liu, Ming ; Lin, Jiandie D. ; Kersten, Sander ; Arvan, Peter ; Qi, Ling - \ 2020
    The Journal of Clinical Investigation 130 (2020)7. - ISSN 0021-9738 - p. 3499 - 3510.
    β Cell apoptosis and dedifferentiation are 2 hotly debated mechanisms underlying β cell loss in type 2 diabetes; however, the molecular drivers underlying such events remain largely unclear. Here, we performed a side-by-side comparison of mice carrying β cell-specific deletion of ER-associated degradation (ERAD) and autophagy. We reported that, while autophagy was necessary for β cell survival, the highly conserved Sel1L-Hrd1 ERAD protein complex was required for the maintenance of β cell maturation and identity. Using single-cell RNA-Seq, we demonstrated that Sel1L deficiency was not associated with β cell loss, but rather loss of β cell identity. Sel1L-Hrd1 ERAD controlled β cell identity via TGF-β signaling, in part by mediating the degradation of TGF-β receptor 1. Inhibition of TGF-β signaling in Sel1L-deficient β cells augmented the expression of β cell maturation markers and increased the total insulin content. Our data revealed distinct pathogenic effects of 2 major proteolytic pathways in β cells, providing a framework for therapies targeting distinct mechanisms of protein quality control
    ER-associated degradation is required for the maintenance of β cell identity via TGFβ signaling
    Shrestha, Neha ; Liu, T. ; Ji, Yewei ; Reinert, Rachel B. ; Torres, Mauricio ; Zhang, M. ; Tang, C.A. ; Hu, C.A. ; Liu, Chengyang ; Naji, Ali ; Lin, Jiandie D. ; Kersten, Sander ; Arvan, Peter ; Qi, Ling ; Hooiveld, Guido - \ 2020
    Wageningen University & Research
    Mus musculus - GSE143757 - PRJNA601502
    β cell apoptosis and dedifferentiation are two hotly-debated mechanisms underlying β cell loss in type 2 diabetes (T2D); however, the molecular drivers underlying such events remain largely unclear. Here, by performing a side-by-side comparison of mice carrying β cell-specific deletion of endoplasmic reticulum (ER)-associated degradation (ERAD) and autophagy, we report that while autophagy appears necessary for β cell survival, the highly conserved Sel1L-Hrd1 ERAD protein complex is required for the maintenance of β cell maturation and identity. Notably, SEL1L expression is significantly reduced in human T2D islets compared to healthy human islets. At the single cell level, we demonstrate that Sel1L deficiency is not associated with β cell loss, but rather loss of β cell identity. Mechanistically, we find that Sel1L-Hrd1 ERAD controls β cell identity via TGFβ signaling, in part by mediating the degradation of TGF-β receptor 1 (TGFβRI). Inhibition of TGFβ signaling in Sel1L-deficient β cells augments the expression of β cell maturation markers and increases the total insulin content. Our data reveal profound but distinct pathogenic effects of two major proteolytic pathways in β cells, providing a new framework for therapies targeting distinct mechanisms of protein quality control
    Synthesis and characterization of a supported Pd complex on carbon nanofibers for the selective decarbonylation of stearic acid to 1-heptadecene : The importance of subnanometric Pd dispersion
    Ochoa, Elba ; Henao, Wilson ; Fuertes, Sara ; Torres, Daniel ; Haasterecht, Tomas Van; Scott, Elinor ; Bitter, Harry ; Suelves, Isabel ; Pinilla, Jose Luis - \ 2020
    Catalysis Science & Technology 10 (2020)9. - ISSN 2044-4753 - p. 2970 - 2985.

    Production of linear α-olefins from renewable sources is gaining increasing attention because it allows the transition from the current petrochemical synthesis route to a more sustainable scenario. In this work, we describe the synthesis and characterization of an innovative catalyst based on a di-μ-chloro-bis[palladium(ii) anthranilate] complex highly dispersed by incipient wetness impregnation over acyl chlorinated carbon nanofibers. The subnanometric dispersion of the metal complex allowed higher catalytic efficiency for the selective decarbonylation of stearic acid to 1-heptadecene as compared to the reference homogenous catalyst. The best catalytic performance (90 mol% selectivity, 71 mol% conversion, and TON = 484) was achieved under mild reaction conditions (atmospheric pressure, 140 °C) with a Pd loading in solution of 0.14 mol%. The post-mortem catalyst characterization and the recyclability tests evidenced the high stability of the catalyst. The highly dispersed catalyst developed in this work provides new opportunities in the rational design of more efficient catalytic systems for the sustainable transformation of fatty acids.

    Samenvattingen Fusarium
    Nijs, W.C.M. de; Torres Sanchez, David ; Ordonez Roman, N.I. ; Maryani Martawi, N. ; Meijer, H.J.G. ; Seidl, M.F. ; Kema, G.H.J. - \ 2020
    Gewasbescherming 51 (2020)2. - ISSN 0166-6495 - p. 67 - 71.
    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.

    Connectivity and plasticity determine collagen network fracture
    Burla, Federica ; Dussi, Simone ; Martinez-Torres, Cristina ; Tauber, Justin ; Gucht, Jasper van der; Koenderink, Gijsje H. - \ 2020
    Proceedings of the National Academy of Sciences of the United States of America 117 (2020)15. - ISSN 0027-8424 - p. 8326 - 8334.
    Collagen - Connectivity - Fracture - Network

    Collagen forms the structural scaffold of connective tissues in all mammals. Tissues are remarkably resistant against mechanical deformations because collagen molecules hierarchically self-assemble in fibrous networks that stiffen with increasing strain. Nevertheless, collagen networks do fracture when tissues are overloaded or subject to pathological conditions such as aneurysms. Prior studies of the role of collagen in tissue fracture have mainly focused on tendons, which contain highly aligned bundles of collagen. By contrast, little is known about fracture of the orientationally more disordered collagen networks present in many other tissues such as skin and cartilage. Here, we combine shear rheology of reconstituted collagen networks with computer simulations to investigate the primary determinants of fracture in disordered collagen networks. We show that the fracture strain is controlled by the coordination number of the network junctions, with less connected networks fracturing at larger strains. The hierarchical structure of collagen fine-tunes the fracture strain by providing structural plasticity at the network and fiber level. Our findings imply that low connectivity and plasticity provide protective mechanisms against network fracture that can optimize the strength of biological tissues.

    Regulation of endoplasmic reticulum-mitochondria contacts and mitochondrial dynamics by Sel1L-Hrd1 ERAD during thermogenesis
    Zhou, Zhangsen ; Torres, Mauricio ; Sha, Haibo ; Halbrook, Christopher J. ; Bergh, Françoise van den; Reinert, Rachel B. ; Yamada, Tatsuya ; Wang, Siwen ; Luo, Yingying ; Hunter, Allen H. ; Wang, Chunqing ; Sanderson, Thomas H. ; Liu, Meilian ; Taylor, Aaron ; Sesaki, Hiromi ; Lyssiotis, Costas A. ; Wu, Jun ; Kersten, Sander ; Beard, Daniel A. ; Qi, Ling - \ 2020
    Wageningen University
    GSE145895 - PRJNA608688 - Mus musculus
    Organelles such as endoplasmic reticulum (ER) and mitochondria interact with each other at specialized domains on the ER known as mitochondria-associated membranes (MAMs). Here, using three-dimensional high-resolution imaging techniques, we show that the Sel1LHrd1 protein complex, the most conserved branch of ER-associated protein degradation (ERAD), exerts a profound impact on ER-mitochondria contacts and mitochondrial dynamics, at least in part, by regulating the turnover and hence the abundance of the MAM protein sigma receptor 1 (SigmaR1). Sel1L or Hrd1 deficiency in brown adipocytes impairs dynamic interaction between ER and mitochondria, leading to the formation of pleomorphic “megamitochondria” and, in some cases with penetrating ER tubule(s), in response to acute cold challenge. Mice with ERAD deficiency are cold sensitive and exhibit mitochondrial dysfunction in brown adipocytes. Mechanistically, endogenous SigmaR1 is targeted for proteasomal degradation by Sel1L-Hrd1 ERAD, whose accumulation in ERAD-deficient cells leads to mitofusin 2 (Mfn2) oligomerization, thereby linking ERAD to mitochondrial dynamics. Our study identifies Sel1L-Hrd1 ERAD as a critical determinant of ER-mitochondria contacts, thereby regulating mitochondrial dynamics and thermogenesis.
    Endoplasmic reticulum-associated degradation regulates mitochondrial dynamics in brown adipocytes
    Zhou, Zhangsen ; Torres, Mauricio ; Sha, Haibo ; Halbrook, Christopher J. ; Bergh, Françoise van den; Reinert, Rachel B. ; Yamada, Tatsuya ; Wang, Siwen ; Luo, Yingying ; Hunter, Allen H. ; Wang, Chunqing ; Sanderson, Thomas H. ; Liu, Meilian ; Taylor, Aaron ; Sesaki, Hiromi ; Lyssiotis, Costas A. ; Wu, Jun ; Kersten, Sander ; Beard, Daniel A. ; Qi, Ling - \ 2020
    Science 368 (2020)6486. - ISSN 0036-8075 - p. 54 - 60.

    The endoplasmic reticulum (ER) engages mitochondria at specialized ER domains known as mitochondria-associated membranes (MAMs). Here, we used three-dimensional high-resolution imaging to investigate the formation of pleomorphic “megamitochondria” with altered MAMs in brown adipocytes lacking the Sel1L-Hrd1 protein complex of ER-associated protein degradation (ERAD). Mice with ERAD deficiency in brown adipocytes were cold sensitive and exhibited mitochondrial dysfunction. ERAD deficiency affected ER-mitochondria contacts and mitochondrial dynamics, at least in part, by regulating the turnover of the MAM protein, sigma receptor 1 (SigmaR1). Thus, our study provides molecular insights into ER-mitochondrial cross-talk and expands our understanding of the physiological importance of Sel1L-Hrd1 ERAD.

    Circulating Levels of Insulin-like Growth Factor 1 and Insulin-like Growth Factor Binding Protein 3 Associate With Risk of Colorectal Cancer Based on Serologic and Mendelian Randomization Analyses
    Murphy, Neil ; Carreras-Torres, Robert ; Song, Mingyang ; Chan, Andrew T. ; Martin, Richard M. ; Papadimitriou, Nikos ; Dimou, Niki ; Tsilidis, Konstantinos K. ; Banbury, Barbara ; Bradbury, Kathryn E. ; Besevic, Jelena ; Rinaldi, Sabina ; Riboli, Elio ; Cross, Amanda J. ; Travis, Ruth C. ; Agnoli, Claudia ; Albanes, Demetrius ; Berndt, Sonja I. ; Bézieau, Stéphane ; Bishop, D.T. ; Brenner, Hermann ; Buchanan, Daniel D. ; Onland-Moret, N.C. ; Burnett-Hartman, Andrea ; Campbell, Peter T. ; Casey, Graham ; Castellví-Bel, Sergi ; Chang-Claude, Jenny ; Chirlaque, María Dolores ; Chapelle, Albert de la; English, Dallas ; Figueiredo, Jane C. ; Gallinger, Steven J. ; Giles, Graham G. ; Gruber, Stephen B. ; Gsur, Andrea ; Hampe, Jochen ; Hampel, Heather ; Harrison, Tabitha A. ; Hoffmeister, Michael ; Hsu, Li ; Huang, Wen Yi ; Huyghe, Jeroen R. ; Jenkins, Mark A. ; Keku, Temitope O. ; Kühn, Tilman ; Kweon, Sun Seog ; Marchand, Loic Le; Li, Christopher I. ; Li, Li ; Lindblom, Annika ; Martín, Vicente ; Milne, Roger L. ; Moreno, Victor ; Newcomb, Polly A. ; Offit, Kenneth ; Ogino, Shuji ; Ose, Jennifer ; Perduca, Vittorio ; Phipps, Amanda I. ; Platz, Elizabeth A. ; Potter, John D. ; Qu, Conghui ; Rennert, Gad ; Sakoda, Lori C. ; Schafmayer, Clemens ; Schoen, Robert E. ; Slattery, Martha L. ; Tangen, Catherine M. ; Ulrich, Cornelia M. ; Duijnhoven, Franzel J.B. van; Guelpen, Bethany Van; Visvanathan, Kala ; Vodicka, Pavel ; Vodickova, Ludmila ; Vymetalkova, Veronika ; Wang, Hansong ; White, Emily ; Wolk, Alicja ; Woods, Michael O. ; Wu, Anna H. ; Zheng, Wei ; Peters, Ulrike ; Gunter, Marc J. - \ 2020
    Gastroenterology 158 (2020)5. - ISSN 0016-5085 - p. 1300 - 1312.e20.
    CRC - GWAS - Risk Factors - Signal Transduction

    Background & Aims: Human studies examining associations between circulating levels of insulin-like growth factor 1 (IGF1) and insulin-like growth factor binding protein 3 (IGFBP3) and colorectal cancer risk have reported inconsistent results. We conducted complementary serologic and Mendelian randomization (MR) analyses to determine whether alterations in circulating levels of IGF1 or IGFBP3 are associated with colorectal cancer development. Methods: Serum levels of IGF1 were measured in blood samples collected from 397,380 participants from the UK Biobank, from 2006 through 2010. Incident cancer cases and cancer cases recorded first in death certificates were identified through linkage to national cancer and death registries. Complete follow-up was available through March 31, 2016. For the MR analyses, we identified genetic variants associated with circulating levels of IGF1 and IGFBP3. The association of these genetic variants with colorectal cancer was examined with 2-sample MR methods using genome-wide association study consortia data (52,865 cases with colorectal cancer and 46,287 individuals without [controls]) Results: After a median follow-up period of 7.1 years, 2665 cases of colorectal cancer were recorded. In a multivariable-adjusted model, circulating level of IGF1 associated with colorectal cancer risk (hazard ratio per 1 standard deviation increment of IGF1, 1.11; 95% confidence interval [CI] 1.05–1.17). Similar associations were found by sex, follow-up time, and tumor subsite. In the MR analyses, a 1 standard deviation increment in IGF1 level, predicted based on genetic factors, was associated with a higher risk of colorectal cancer risk (odds ratio 1.08; 95% CI 1.03–1.12; P = 3.3 × 10–4). Level of IGFBP3, predicted based on genetic factors, was associated with colorectal cancer risk (odds ratio per 1 standard deviation increment, 1.12; 95% CI 1.06–1.18; P = 4.2 × 10–5). Colorectal cancer risk was associated with only 1 variant in the IGFBP3 gene region (rs11977526), which also associated with anthropometric traits and circulating level of IGF2. Conclusions: In an analysis of blood samples from almost 400,000 participants in the UK Biobank, we found an association between circulating level of IGF1 and colorectal cancer. Using genetic data from 52,865 cases with colorectal cancer and 46,287 controls, a higher level of IGF1, determined by genetic factors, was associated with colorectal cancer. Further studies are needed to determine how this signaling pathway might contribute to colorectal carcinogenesis.

    Time delay evaluation on thewater-leaving irradiance retrieved from empirical models and satellite imagery
    Otto, Peter ; Vallejo-Rodríguez, Ramiro ; Keesstra, Saskia ; León-Becerril, Elizabeth ; Anda, José de; Hernández-Mena, Leonel ; Real-Olvera, Jorge del; Jesús Díaz-Torres, José de - \ 2020
    Remote Sensing 12 (2020)1. - ISSN 2072-4292
    Empirical model - Lake Chapala - Landsat-8 - NIR reflectance - Shallow lake - Spatial randomness - Subtropical zone - Temporal delay - Turbidity

    Temporal delays and spatial randomness between ground-based data and satellite overpass involve important deviations between the empirical model output and real data; these are factors poorly considered in the model calibration. The inorganic matter-generated turbidity in Lake Chapala (Mexico) was taken as a study case to expose the influence of such factors. Ground-based data from this study and historical records were used as references. We take advantage of the at-surface reflectance from Landsat-8, sun-glint corrections, a reduced NIR-band range, and null organic matter incidence in these wavelengths to diminish the physical phenomena-related radiometric artifacts; leaving the spatio-temporal relationships as the principal factor inducing the model uncertainty. Non-linear correlations were assessed to calibrate the best empirical model; none of them presented a strong relationship (<73%), including that based on hourly delays. This last model had the best predictability only for the summer-fall season, explaining 71% of the turbidity variation in 2016, and 59% in 2017, with RMSEs < 24%. The instantaneous turbidity maps depicted the hydrodynamic complexity of the lake, highlighting a strong component of spatial randomness associated with the temporal delays. Reasonably, robust empirical models will be developed if several dates and sampling-sites are synchronized with more satellite overpasses.

    The TIR-NB-LRR pair DSC1 and WRKY19 contributes to basal immunity of Arabidopsis to the root-knot nematode Meloidogyne incognita
    Warmerdam, Sonja ; Sterken, Mark G. ; Sukarta, Octavina C.A. ; Schaik, Casper C. Van; Oortwijn, Marian E.P. ; Lozano-Torres, Jose L. ; Bakker, Jaap ; Smant, Geert ; Goverse, Aska - \ 2020
    BMC Plant Biology 20 (2020)1. - ISSN 1471-2229
    Background
    Root-knot nematodes transform vascular host cells into permanent feeding structures to withdraw nutrients from the host plant. Ecotypes of Arabidopsis thaliana can display large quantitative variation in susceptibility to the root-knot nematode Meloidogyne incognita, which is thought to be independent of dominant major resistance genes. However, in an earlier genome-wide association study of the interaction between Arabidopsis and M. incognita we identified a quantitative trait locus harboring homologs of dominant resistance genes but with minor effect on susceptibility to the M. incognita population tested.
    Results
    Here, we report on the characterization of two of these genes encoding the TIR-NB-LRR immune receptor DSC1 (DOMINANT SUPPRESSOR OF Camta 3 NUMBER 1) and the TIR-NB-LRR-WRKY-MAPx protein WRKY19 in nematode-infected Arabidopsis roots. Nematode infection studies and whole transcriptome analyses using the Arabidopsis mutants showed that DSC1 and WRKY19 co-regulate susceptibility of Arabidopsis to M. incognita.
    Conclusion
    Given the head-to-head orientation of DSC1 and WRKY19 in the Arabidopsis genome our data suggests that both genes may function as a TIR-NB-LRR immune receptor pair. Unlike other TIR-NB-LRR pairs involved in dominant disease resistance in plants, DSC1 and WRKY19 most likely regulate basal levels of immunity to root-knot nematodes.
    Characterization of goat prions demonstrates geographical variation of scrapie strains in Europe and reveals the composite nature of prion strains
    Nonno, Romolo ; Marina Moreno, Alberto ; Espinosa, J.C. ; Fast, C. ; Keulen, L.J.M. van; Spiropoulos, J. ; Lantier, Isabelle ; Andrèoletti, Olivier ; Pirisinu, L. ; Bari, M.A. Di; Aguilar-Calvo, Patricia ; Sklaviadis, Theodoros ; Papasavva-Stylianou, P. ; Acutis, Pier Luigi ; Acin, C. ; Bossers, A. ; Jacobs, Jorge G. ; Vaccari, G. ; Agostino, C. D'; Chiappini, B. ; Lantier, F. ; Groschup, Martin H. ; Agrimi, U. ; Torres, Juan Maria ; Langeveld, J.P.M. - \ 2020
    Scientific Reports 10 (2020)1. - ISSN 2045-2322
    Bovine Spongiform Encephalopathy (BSE) is the only animal prion which has been recognized as a zoonotic agent so far. The identification of BSE in two goats raised the need to reliably identify BSE in small ruminants. However, our understanding of scrapie strain diversity in small ruminants remains ill-defined, thus limiting the accuracy of BSE surveillance and spreading fear that BSE might lurk unrecognized in goats. We investigated prion strain diversity in a large panel of European goats by a novel experimental approach that, instead of assessing the neuropathological profile after serial transmissions in a single animal model, was based on the direct interaction of prion isolates with several recipient rodent models expressing small ruminants or heterologous prion proteins. The findings show that the biological properties of scrapie isolates display different patterns of geographical distribution in Europe and suggest that goat BSE could be reliably discriminated from a wide range of biologically and geographically diverse goat prion isolates. Finally, most field prion isolates showed composite strain features, with discrete strain components or sub-strains being present in different proportions in individual goats or tissues. This has important implications for understanding the nature and evolution of scrapie strains and their transmissibility to other species, including humans.
    The Influence of Larval Stage and Density on Oviposition Site-Selection Behavior of the Afrotropical Malaria Mosquito Anopheles coluzzii (Diptera: Culicidae)
    Mwingira, Victor ; Spitzen, Jeroen ; Mboera, Leonard E.G. ; Torres-Estrada, José ; Takken, Willem ; Reisen, William - \ 2020
    Journal of Medical Entomology 57 (2020)3. - ISSN 0022-2585 - p. 657 - 666.
    In the selection of oviposition sites female mosquitoes use various cues to assess site quality to optimize survival of progeny. The presence of conspecific larvae influences this process. Interactive effects of oviposition site selection were studied in the malaria mosquito Anopheles coluzzii Coetzee & Wilkerson in dual- and no-choice assays, by exposing single gravid mosquitoes to oviposition cups containing 1) larvae of different developmental stages, 2) larvae-conditioned water (LCW), and 3) cups where visual cues of conspecific larvae were absent. Early-stage conspecific larvae had a positive effect on the oviposition response. By contrast, late stages of conspecific larvae had a negative effect. Oviposition choice was dependent on larval density. Moreover, in oviposition cups where larvae were hidden from view, late-stage larvae had a significant negative effect on oviposition suggesting the involvement of olfactory cues. LCW had no effect on oviposition response, indicating involvement of chemicals produced by larvae in vivo. It is concluded that the presence of larvae in a breeding site affects the oviposition response depending on the development stage of the larvae. These responses appear to be mediated by olfactory cues emitted by the larval habitat containing live larvae, resulting in the enhanced reproductive fitness of the females.
    Molecular characterization of Ecuadorian quinoa (Chenopodium quinoa Willd.) diversity : implications for conservation and breeding
    Salazar, Juan ; Jaramillo Roman, Viviana ; Gutierrez, Bernardo ; Loo, E.N. van; Lourdes Torres, María de; Torres, Andrés Francisco - \ 2019
    Euphytica 215 (2019)3. - ISSN 0014-2336
    Breeding - Ecuador - Genetic diversity - Population structure - Quinoa - SSR

    Quinoa (Chenopodium quinoa Willd.) is recognized as an important crop to improve global food security. It has gained international recognition because of the nutritional value of its seeds and its broad agronomic resilience. Although several studies have attempted to characterize the genetic diversity of quinoa, none have focused on evaluating germplasm from Ecuador; the latter considered a relevant subcenter of diversity for the species. In this study, 84 accessions representing the species’ cultivated range in the Ecuadorian Andes were characterized using 15 species-specific SSR markers. The extent of allelic richness (196 alleles) and genetic heterozygosity (H E = 0.71) detected for these accessions demonstrate that Ecuadorian quinoa is highly diverse. Phenetic analyzes structured Ecuadorian germplasm into 3 subgroups; each containing genotypes from all surveyed provinces. Average expected heterozygosity was high for all 3 subgroups (0.53 ≤ H E ≤ 0.72), and Nei-pairwise comparisons showed significant genetic divergence among them (0.31 ≤ Nei DST ≤ 0.84). The lack of a clear geographic pattern in the genetic structure of Ecuadorian quinoa led us to believe that the 3 reported subgroups constitute independent genetic lineages representing ancestral landrace populations which have been disseminated throughout Ecuador via informal seed networks. Nevertheless, a Wilcoxon test showed that at least one subgroup had been subject to intensive inbreeding and selection; and possibly corresponds to the local commercial variety INIAP-Tunkahuan. Our results show that ancestral quinoa diversity in Ecuador has prevailed despite the introduction of commercial varieties, and should be preserved for future use in breeding programs.

    Correction to: Molecular characterization of Ecuadorian quinoa (Chenopodium quinoa Willd.) diversity: implications for conservation and breeding
    Salazar, Juan ; Roman, Viviana Jaramillo ; Gutierrez, Bernardo ; Loo, Eibertus Nicolaas van; Lourdes Torres, María de; Torres, Andrés Francisco - \ 2019
    Euphytica 215 (2019)12. - ISSN 0014-2336

    Due to an unfortunate error of miscommunication, two of the co-authors of this manuscript were omitted from the original publication. The correct representation of the authors and their affiliations are listed here and should be treated as definitive. Juan Salazar1, Viviana Jaramillo Roman2, Bernardo Gutierrez1,3, Eibertus Nicolaas van Loo2, Mari´a de Lourdes Torres1, Andre´s Francisco Torres1,2 1. Laboratorio de Biotecnologi´a Vegetal, Colegio de Ciencias Biolo´gicas y Ambientales, Universidad San Francisco de Quito USFQ, Diego de Robles y Vi´a Interocea´nica, Cumbaya´, Ecuador 2. Wageningen UR Plant Breeding, Wageningen University and Research, PO Box 386, 6700 AJ Wageningen, The Netherlands 3. Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK Furthermore, the acknowledgments section has been adapted to match the changes in authorship. The corrected acknowledgements, presented below, are definitive: This research was funded with a Chancellor’s Grant (2015) from Universidad San Francisco de Quito USFQ (Quito-Ecuador). Germplasm access and research permit were granted by the Ministry of Environment of Ecuador (MAE-DNB-CM-2016- 0044). The authors would like to acknowledge the technical assistance offered by researchers at the Plant Biotechnology Laboratory (COCIBA, USFQ), as well as Dr. Leonardo Zurita for his assistance with georeferenced mapping. The authors would also like to acknowledge Dr. Gerard van der Linden (Wageningen University and Research) for supporting our efforts to search and collect quinoa germplasm throughout the Andes of Ecuador.

    Key knowledge gaps to achieve global sustainability goals
    Mastrángelo, Matías E. ; Pérez-Harguindeguy, Natalia ; Enrico, Lucas ; Bennett, Elena ; Lavorel, Sandra ; Cumming, Graeme S. ; Abeygunawardane, Dilini ; Amarilla, Leonardo D. ; Burkhard, Benjamin ; Egoh, Benis N. ; Frishkoff, Luke ; Galetto, Leonardo ; Huber, Sibyl ; Karp, Daniel S. ; Ke, Alison ; Kowaljow, Esteban ; Kronenburg-García, Angela ; Locatelli, Bruno ; Martín-López, Berta ; Meyfroidt, Patrick ; Mwampamba, Tuyeni H. ; Nel, Jeanne ; Nicholas, Kimberly A. ; Nicholson, Charles ; Oteros-Rozas, Elisa ; Rahlao, Sebataolo J. ; Raudsepp-Hearne, Ciara ; Ricketts, Taylor ; Shrestha, Uttam B. ; Torres, Carolina ; Winkler, Klara J. ; Zoeller, Kim - \ 2019
    Nature Sustainability 2 (2019). - ISSN 2398-9629 - p. 1115 - 1121.

    Regional and global assessments periodically update what we know, and highlight what remains to be known, about the linkages between people and nature that both define and depend upon the state of the environment. To guide research that better informs policy and practice, we systematically synthesize knowledge gaps from recent assessments of four regions of the globe and three key themes by the Intergovernmental Science-Policy Platform for Biodiversity and Ecosystem Services. We assess their relevance to global sustainability goals and trace their evolution relative to those identified in the Millennium Ecosystem Assessment. We found that global sustainability goals cannot be achieved without improved knowledge on feedbacks between social and ecological systems, effectiveness of governance systems and the influence of institutions on the social distribution of ecosystem services. These top research priorities have persisted for the 14 years since the Millennium Ecosystem Assessment. Our analysis also reveals limited understanding of the role of indigenous and local knowledge in sustaining nature’s benefits to people. Our findings contribute to a policy-relevant and solution-oriented agenda for global, long-term social-ecological research.

    Rarity of monodominance in hyperdiverse Amazonian forests
    Steege, Hans Ter; Henkel, Terry W. ; Helal, Nora ; Marimon, Beatriz S. ; Marimon-Junior, Ben Hur ; Huth, Andreas ; Groeneveld, Jürgen ; Sabatier, Daniel ; Souza Coelho, Luiz de; Andrade Lima Filho, Diogenes de; Salomão, Rafael P. ; Amaral, Iêda Leão ; Almeida Matos, Francisca Dionízia de; Castilho, Carolina V. ; Phillips, Oliver L. ; Guevara, Juan Ernesto ; Jesus Veiga Carim, Marcelo de; Cárdenas López, Dairon ; Magnusson, William E. ; Wittmann, Florian ; Irume, Mariana Victória ; Martins, Maria Pires ; Silva Guimarães, José Renan da; Molino, Jean François ; Bánki, Olaf S. ; Piedade, Maria Teresa Fernandez ; Pitman, Nigel C.A. ; Mendoza, Abel Monteagudo ; Ramos, José Ferreira ; Luize, Bruno Garcia ; Moraes de Leão Novo, Evlyn Márcia ; Núñez Vargas, Percy ; Silva, Thiago Sanna Freire ; Venticinque, Eduardo Martins ; Manzatto, Angelo Gilberto ; Reis, Neidiane Farias Costa ; Terborgh, John ; Casula, Katia Regina ; Honorio Coronado, Euridice N. ; Montero, Juan Carlos ; Feldpausch, Ted R. ; Duque, Alvaro ; Costa, Flávia R.C. ; Arboleda, Nicolás Castaño ; Schöngart, Jochen ; Killeen, Timothy J. ; Vasquez, Rodolfo ; Mostacedo, Bonifacio ; Demarchi, Layon O. ; Assis, Rafael L. ; Baraloto, Chris ; Engel, Julien ; Petronelli, Pascal ; Castellanos, Hernán ; Medeiros, Marcelo Brilhante de; Quaresma, Adriano ; Simon, Marcelo Fragomeni ; Andrade, Ana ; Camargo, José Luís ; Laurance, Susan G.W. ; Laurance, William F. ; Rincón, Lorena M. ; Schietti, Juliana ; Sousa, Thaiane R. ; Sousa Farias, Emanuelle de; Lopes, Maria Aparecida ; Magalhães, José Leonardo Lima ; Mendonça Nascimento, Henrique Eduardo ; Lima de Queiroz, Helder ; Aymard C, Gerardo A. ; Brienen, Roel ; Revilla, Juan David Cardenas ; Vieira, Ima Célia Guimarães ; Cintra, Bruno Barçante Ladvocat ; Stevenson, Pablo R. ; Feitosa, Yuri Oliveira ; Duivenvoorden, Joost F. ; Mogollón, Hugo F. ; Araujo-Murakami, Alejandro ; Ferreira, Leandro Valle ; Lozada, José Rafael ; Comiskey, James A. ; Toledo, José Julio de; Damasco, Gabriel ; Dávila, Nállarett ; Draper, Freddie ; García-Villacorta, Roosevelt ; Lopes, Aline ; Vicentini, Alberto ; Alonso, Alfonso ; Dallmeier, Francisco ; Gomes, Vitor H.F. ; Lloyd, Jon ; Neill, David ; Aguiar, Daniel Praia Portela de; Arroyo, Luzmila ; Carvalho, Fernanda Antunes ; Souza, Fernanda Coelho de; Amaral, Dário Dantas do; Feeley, Kenneth J. ; Gribel, Rogerio ; Pansonato, Marcelo Petratti ; Barlow, Jos ; Berenguer, Erika ; Ferreira, Joice ; Fine, Paul V.A. ; Guedes, Marcelino Carneiro ; Jimenez, Eliana M. ; Licona, Juan Carlos ; Peñuela Mora, Maria Cristina ; Villa, Boris ; Cerón, Carlos ; Maas, Paul ; Silveira, Marcos ; Stropp, Juliana ; Thomas, Raquel ; Baker, Tim R. ; Daly, Doug ; Dexter, Kyle G. ; Huamantupa-Chuquimaco, Isau ; Milliken, William ; Pennington, Toby ; Ríos Paredes, Marcos ; Fuentes, Alfredo ; Klitgaard, Bente ; Pena, José Luis Marcelo ; Peres, Carlos A. ; Silman, Miles R. ; Tello, J.S. ; Chave, Jerome ; Cornejo Valverde, Fernando ; Fiore, Anthony Di; Hilário, Renato Richard ; Phillips, Juan Fernando ; Rivas-Torres, Gonzalo ; Andel, Tinde R. van; Hildebrand, Patricio von; Noronha, Janaína Costa ; Barbosa, Edelcilio Marques ; Barbosa, Flávia Rodrigues ; Matos Bonates, Luiz Carlos de; Sá Carpanedo, Rainiellen de; Dávila Doza, Hilda Paulette ; Fonty, Émile ; GómeZárate Z, Ricardo ; Gonzales, Therany ; Gallardo Gonzales, George Pepe ; Hoffman, Bruce ; Junqueira, André Braga ; Malhi, Yadvinder ; Andrade Miranda, Ires Paula de; Pinto, Linder Felipe Mozombite ; Prieto, Adriana ; Jesus Rodrigues, Domingos de; Rudas, Agustín ; Ruschel, Ademir R. ; Silva, Natalino ; Vela, César I.A. ; Vos, Vincent Antoine ; Zent, Egleé L. ; Zent, Stanford ; Weiss Albuquerque, Bianca ; Cano, Angela ; Carrero Márquez, Yrma Andreina ; Correa, Diego F. ; Costa, Janaina Barbosa Pedrosa ; Flores, Bernardo Monteiro ; Galbraith, David ; Holmgren, Milena ; Kalamandeen, Michelle ; Nascimento, Marcelo Trindade ; Oliveira, Alexandre A. ; Ramirez-Angulo, Hirma ; Rocha, Maira ; Scudeller, Veridiana Vizoni ; Sierra, Rodrigo ; Tirado, Milton ; Umaña Medina, Maria Natalia ; Heijden, Geertje van der; Vilanova Torre, Emilio ; Vriesendorp, Corine ; Wang, Ophelia ; Young, Kenneth R. ; Ahuite Reategui, Manuel Augusto ; Baider, Cláudia ; Balslev, Henrik ; Cárdenas, Sasha ; Casas, Luisa Fernanda ; Farfan-Rios, William ; Ferreira, Cid ; Linares-Palomino, Reynaldo ; Mendoza, Casimiro ; Mesones, Italo ; Torres-Lezama, Armando ; Giraldo, Ligia Estela Urrego ; Villarroel, Daniel ; Zagt, Roderick ; Alexiades, Miguel N. ; Oliveira, Edmar Almeida de; Garcia-Cabrera, Karina ; Hernandez, Lionel ; Palacios Cuenca, Walter ; Pansini, Susamar ; Pauletto, Daniela ; Ramirez Arevalo, Freddy ; Sampaio, Adeilza Felipe ; Valderrama Sandoval, Elvis H. ; Valenzuela Gamarra, Luis ; Levesley, Aurora ; Pickavance, Georgia ; Melgaço, Karina - \ 2019
    Scientific Reports 9 (2019). - ISSN 2045-2322

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

    Tucumã: A toolbox for spatiotemporal remote sensing image analysis [Software and Data Sets]
    Menini, Nathalia ; Almeida, Alexandre E. ; Lamparelli, Rubens ; Maire, Guerric Le; Oliveira, Rafael S. ; Verbesselt, Jan ; Hirota, Marina ; S. Torres, Ricardo Da - \ 2019
    In: IEEE Geoscience and Remote Sensing Magazine / Bruzzone, L., IEEE Geoscience and Remote Sensing Magazine 7 (2019)3. - ISSN 2168-6831IEEE (IEEE Geoscience and Remote Sensing Magazine 3) - p. 110 - 122.
    Remote sensing images have been broadly employed over the past decades to detect and investigate temporal changes on Earth's surface. Appropriate tools are needed to support complex analyses of temporal data in various domains, ranging from purely scientific to educational. There are many existing tools, but it is often necessary to switch among them several times. Typical inter operability issues include system mismatch and the variety of user profiles and data types.
    Emulation of a Detailed Urban Drainage Simulator to Be Applied for Short-Term Predictions
    Mahmoodian, Mahmood ; Torres-Matallana, J.A. ; Leopold, Ulrich ; Schutz, Georges ; Clemens, Francois - \ 2019
    In: New Trends in Urban Drainage Modelling - UDM 2018. - Springer Verlag (Green Energy and Technology ) - ISBN 9783319998664 - p. 592 - 596.
    Emulator - Gaussian process - InfoWorks® ICM - Surrogate model - Urban drainage

    The challenge of this study is to investigate on applicability of a data-driven Gaussian Process Emulator (GPE) technique to develop a surrogate model for a computationally expensive and detailed urban drainage simulator. The novelty is the consideration of (short) time series for the simulation inputs and outputs. Such simulation setup is interesting in applications such as Model Predictive Control (MPC) in which numerous, fast and frequent simulation results are required. Here, an emulator is developed to predict a storage tank’s volume in a small case study in Luxembourg. Three main inputs are considered as the GPE’s parameters: Initial volume in the tank, the level in which the outlet pump of the tank must start to work, and the time series of expected rainfall in the upcoming 2 h. The output of interest is the total volume of the storage tank for the next 24 h. A dataset of 2000 input-output scenarios were produced using different possible combinations of the inputs and running the detailed simulator (InfoWorks® ICM). 80% of the dataset were applied to train the emulator and 20% to validate the results. Distributions of Nash-Sutcliffe efficiency and Volumetric Efficiency are presented as indicators for quantification of the emulation error. Based on the preliminary results, it can be concluded that the introduced technique is able to reduce the simulations runtime significantly while imposing some inevitable accuracy cost. More investigation is required to validate the more generic applicability of this technique for multiple outputs and interactions between different urban drainage components.

    Micropropagation of Solanum quitoense var. quitoense by apical bud, petiole and hypocotyl culture
    Gutirrez, Bernardo ; Cobo, María Mercedes ; Orellana, Miguel ; Vega, Joely ; Arahana, Venancio ; Jaramillo, Viviana ; Lourdes Torres, María de - \ 2019
    Plant Biotechnology Reports 36 (2019)2. - ISSN 1342-4580 - p. 91 - 97.
    1-naphtaleneacetic acid (NAA) - 6-benzylaminopurine (BAP) - Andean crop - gibberellic acid (GA3) - in vitro culture - Solanum quitoense

    The development of in vitro propagation methods can improve the current commercial use and conservation of plants like naranjilla (Solanum quitoense), a distinctive Andean crop and key emerging agricultural product. In the present study, we report in vitro culture protocols for naranjilla apical buds, hypocotyls and petioles. In apical bud culture, MS medium supplemented with 0.10 mg l−1 1-naphtaleneacetic acid (NAA) produced longer plantlets with greater number of leaves. Hypocotyl culture yielded higher number of shoots when using older explants in MS medium supplemented with different combinations of NAA, 6-benzylaminopurine (BAP) and gibberellic acid (GA3). Petiole culture produced a significantly higher number of shoots per explant, with more abundant and bigger leaves, when using MS medium supplemented with 0.02 mg l−1 NAA, 4.50 mg l−1 BAP and 1.00 mg l−1 GA3. A factorial analysis reveals that the interaction between GA3 and NAA/BAP plays an important role in shoot regeneration. These results provide new tools for the in vitro regeneration of naranjilla plants, improving on previously reported protocols for this species by using alternative explant types and regeneration protocols.

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