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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    Developing multiscale and integrative nature–people scenarios using the Nature Futures Framework
    Pereira, Laura M. ; Davies, Kathryn K. ; Belder, Eefje ; Ferrier, Simon ; Karlsson‐vinkhuyzen, Sylvia ; Kim, Hyejin ; Kuiper, Jan J. ; Okayasu, Sana ; Palomo, Maria G. ; Pereira, Henrique M. ; Peterson, Garry ; Sathyapalan, Jyothis ; Schoolenberg, Machteld ; Alkemade, Rob ; Carvalho Ribeiro, Sonja ; Greenaway, Alison ; Hauck, Jennifer ; King, Nicholas ; Lazarova, Tanya ; Ravera, Federica ; Chettri, Nakul ; Cheung, W.W.L. ; Hendriks, Rob J.J. ; Kolomytsev, Grygoriy O. ; Leadley, Paul ; Metzger, Jean Paul ; Ninan, Karachepone N. ; Pichs, Ramon ; Popp, Alexander ; Rondinini, Carlo ; Isabel, Rosa ; Vuuren, Detlef P. van; Lundquist, Carolyn J. - \ 2020
    People and Nature (2020). - ISSN 2575-8314 - 24 p.
    Scientists have repeatedly argued that transformative, multiscale global scenarios are needed as tools in the quest to halt the decline of biodiversity and achieve sustainability goals.
    As a first step towards achieving this, the researchers who participated in the scenarios and models expert group of the Intergovernmental Science‐Policy Platform on Biodiversity and Ecosystem Services (IPBES) entered into an iterative, participatory process that led to the development of the Nature Futures Framework (NFF).
    The NFF is a heuristic tool that captures diverse, positive relationships of humans with nature in the form of a triangle. It can be used both as a boundary object for continuously opening up more plural perspectives in the creation of desirable nature scenarios and as an actionable framework for developing consistent nature scenarios across multiple scales.
    Here we describe the methods employed to develop the NFF and how it fits into a longer term process to create transformative, multiscale scenarios for nature. We argue that the contribution of the NFF is twofold: (a) its ability to hold a plurality of perspectives on what is desirable, which enables the development of joint goals and visions and recognizes the possible convergence and synergies of measures to achieve these visions and (b), its multiscale functionality for elaborating scenarios and models that can inform decision‐making at relevant levels, making it applicable across specific places and perspectives on nature.
    If humanity is to achieve its goal of a more sustainable and prosperous future rooted in a flourishing nature, it is critical to open up a space for more plural perspectives of human–nature relationships. As the global community sets out to develop new goals for biodiversity, the NFF can be used as a navigation tool helping to make diverse, desirable futures possible
    “Customer is king”: Staging consumer culture in a food aid organization
    Andriessen, Thirza ; Horst, Hilje Van der; Morrow, Oona - \ 2020
    Journal of Consumer Culture (2020). - ISSN 1469-5405 - 20 p.
    Belgium - charity - consumer culture - ethnography - food aid receiver - food assistance - Food insecurity - market exchange - social supermarkets

    This paper intervenes in critical debates on the role of charitable food aid in meeting the material, social, emotional, and cultural needs of the people who depend on this aid. It offers a detailed case study of a social grocery in Belgium that attempts to circumvent the power inequalities and negative social and emotional impacts of charitable giving through staging consumer culture, and treating clients as customers. This is accomplished with supporting performances of consumption norms around product choice, the act of paying, and the selection of appropriate foods – which improves the ability of participants to meet their personal needs as well as the broader standards of consumer society that they are otherwise excluded from. These other ways of doing food aid are theorized through the lens of consumer culture, to explain what is at stake in performing the norms of market exchange in a consumer society.

    Publisher Correction: 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.

    Metabolomics profiling of visceral and abdominal subcutaneous adipose tissue in colorectal cancer patients : results from the ColoCare study
    Ose, Jennifer ; Holowatyj, Andreana N. ; Nattenmüller, Johanna ; Gigic, Biljana ; Lin, Tengda ; Himbert, Caroline ; Habermann, Nina ; Achaintre, David ; Scalbert, Augustin ; Keski-Rahkonen, Pekka ; Böhm, Jürgen ; Schrotz-King, Petra ; Schneider, Martin ; Ulrich, Alexis ; Kampman, Ellen ; Weijenberg, Matty ; Gsur, Andrea ; Ueland, Per Magne ; Kauczor, Hans Ulrich ; Ulrich, Cornelia M. - \ 2020
    Cancer Causes and Control 31 (2020). - ISSN 0957-5243 - p. 723 - 735.
    Adipose tissue - Colorectal cancer - Glycerophospholipids - Survival

    Purpose: Underlying mechanisms of the relationship between body fatness and colorectal cancer remain unclear. This study investigated associations of circulating metabolites with visceral (VFA), abdominal subcutaneous (SFA), and total fat area (TFA) in colorectal cancer patients. Methods: Pre-surgery plasma samples from 212 patients (stage I–IV) from the ColoCare Study were used to perform targeted metabolomics. VFA, SFA, and TFA were quantified by computed tomography scans. Partial correlation and linear regression analyses of VFA, SFA, and TFA with metabolites were computed and corrected for multiple testing. Cox proportional hazards were used to assess 2-year survival. Results: In patients with metastatic tumors, SFA and TFA were statistically significantly inversely associated with 16 glycerophospholipids (SFA: pFDR range 0.017–0.049; TFA: pFDR range 0.029–0.048), while VFA was not. Doubling of ten of the aforementioned glycerophospholipids was associated with increased risk of death in patients with metastatic tumors, but not in patients with non-metastatic tumors (phet range: 0.00044–0.049). Doubling of PC ae C34:0 was associated with ninefold increased risk of death in metastatic tumors (Hazard Ratio [HR], 9.05; 95% confidence interval [CI] 2.17–37.80); an inverse association was observed in non-metastatic tumors (HR 0.17; 95% CI 0.04–0.87; phet = 0.00044). Conclusion: These data provide initial evidence that glycerophospholipids in metastatic colorectal cancer are uniquely associated with subcutaneous adiposity, and may impact overall survival.

    Enabling reusability of plant phenomic datasets with MIAPPE 1.1
    Papoutsoglou, Evangelia A. ; Faria, Daniel ; Arend, Daniel ; Arnaud, Elizabeth ; Athanasiadis, Ioannis N. ; Chaves, Inês ; Coppens, Frederik ; Cornut, Guillaume ; Costa, Bruno V. ; Ćwiek-Kupczyńska, Hanna ; Droesbeke, Bert ; Finkers, Richard ; Gruden, Kristina ; Junker, Astrid ; King, Graham J. ; Krajewski, Paweł ; Lange, Matthias ; Laporte, Marie Angélique ; Michotey, Célia ; Oppermann, Markus ; Ostler, Richard ; Poorter, Hendrik ; Ramı́rez-Gonzalez, Ricardo ; Ramšak, Živa ; Reif, Jochen C. ; Rocca-Serra, Philippe ; Sansone, Susanna Assunta ; Scholz, Uwe ; Tardieu, François ; Uauy, Cristobal ; Usadel, Björn ; Visser, Richard G.F. ; Weise, Stephan ; Kersey, Paul J. ; Miguel, Célia M. ; Adam-Blondon, Anne Françoise ; Pommier, Cyril - \ 2020
    New Phytologist 227 (2020)1. - ISSN 0028-646X - p. 260 - 273.
    findability - interoperability - metadata - phenomics - plant phenotyping - reusability - standards

    Enabling data reuse and knowledge discovery is increasingly critical in modern science, and requires an effort towards standardising data publication practices. This is particularly challenging in the plant phenotyping domain, due to its complexity and heterogeneity. We have produced the MIAPPE 1.1 release, which enhances the existing MIAPPE standard in coverage, to support perennial plants, in structure, through an explicit data model, and in clarity, through definitions and examples. We evaluated MIAPPE 1.1 by using it to express several heterogeneous phenotyping experiments in a range of different formats, to demonstrate its applicability and the interoperability between the various implementations. Furthermore, the extended coverage is demonstrated by the fact that one of the datasets could not have been described under MIAPPE 1.0. MIAPPE 1.1 marks a major step towards enabling plant phenotyping data reusability, thanks to its extended coverage, and especially the formalisation of its data model, which facilitates its implementation in different formats. Community feedback has been critical to this development, and will be a key part of ensuring adoption of the standard.

    Comparative Greenhouse Gas Footprinting of Online versus Traditional Shopping for Fast-Moving Consumer Goods : A Stochastic Approach
    Shahmohammadi, Sadegh ; Steinmann, Zoran J.N. ; Tambjerg, Lau ; Loon, Patricia van; King, J.M.H. ; Huijbregts, Mark A.J. - \ 2020
    Environmental Science and Technology 54 (2020)6. - ISSN 0013-936X - p. 3499 - 3509.

    Variability in consumer practices and choices is typically not addressed in comparisons of environmental impacts of traditional shopping and e-commerce. Here, we developed a stochastic model to quantify the variability in the greenhouse gas (GHG) footprints of product distribution and purchase of fast-moving consumer goods (FMCGs) via three prevalent retail channels in the United Kingdom (U.K.). We found that shopping via bricks and clicks (click and fulfillment via physical store delivery) most likely decreases the GHG footprints when substituting traditional shopping, while FMCGs purchased through pure players with parcel delivery often have higher GHG footprints compared to those purchased via traditional retail. The number of items purchased and the last-mile travel distance are the dominant contributors to the variability in the GHG footprints of all three retail channels. We further showed that substituting delivery vans with electric cargo bikes can lead to a GHG emission reduction of 26% via parcel delivery. Finally, we showed the differences in the "last mile" GHG footprint of traditional shopping in the U.K. compared to three other countries (China, Netherlands, and the United States), which are primarily caused by the different shares of modes of transport (walking and by car, bus, and bike).

    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.
    Mayflies in Ecotoxicity Testing: Methodological Needs and Knowledge Gaps
    Sibley, Paul ; Lagadic, Laurent ; McCoole, Matt ; Norberg-King, Teresa ; Roessink, Ivo ; Soucek, David ; Watson-Leung, Trudy ; Wirtz, Jeff - \ 2020
    Integrated Environmental Assessment and Management 16 (2020)2. - ISSN 1551-3793 - p. 292 - 293.
    One-carbon metabolites, B-vitamins and associations with systemic inflammation and angiogenesis biomarkers among colorectal cancer patients: Results from the ColoCare Study
    Kiblawi, Rama ; Holowatyj, Andreana N. ; Gigic, Biljana ; Brezina, Stefanie ; Geijsen, Anne J.M.R. ; Ose, Jennifer ; Lin, Tengda ; Hardikar, Sheetal ; Himbert, Caroline ; Warby, Christy A. ; Böhm, Jürgen ; Bours, Martijn J.L. ; Duijnhoven, Fränzel J.B. Van; Gumpenberger, Tanja ; Kok, Dieuwertje E. ; Koole, Janna L. ; Roekel, Eline H. Van; Schrotz-King, Petra ; Ulvik, Arve ; Gsur, Andrea ; Habermann, Nina ; Weijenberg, Matty P. ; Ueland, Per Magne ; Schneider, Martin ; Ulrich, Alexis ; Ulrich, Cornelia M. ; Playdon, Mary - \ 2020
    The British journal of nutrition 123 (2020)10. - ISSN 0007-1145 - p. 1187 - 1200.
    B-vitamins - colorectal cancer - CRPangiogenesis - folate - folic acid - inflammation - One-carbon metabolism - Vitamin B

    B-vitamins involved in one-carbon metabolism have been implicated in the development of inflammation- A nd angiogenesis-related chronic diseases, such as colorectal cancer. Yet, the role of one-carbon metabolism in inflammation and angiogenesis among colorectal cancer patients remains unclear.The objective of this study was to investigate associations of components of one-carbon metabolism with inflammation and angiogenesis biomarkers among newly diagnosed colorectal cancer patients (n=238) in the prospective ColoCare Study, Heidelberg.We cross-sectionally analyzed associations between 12 B-vitamins and one-carbon metabolites and 10 inflammation and angiogenesis biomarkers from pre-surgery serum samples using multivariable linear regression models. We further explored associations among novel biomarkers in these pathways with Spearman partial correlation analyses. We hypothesized that pyridoxal-5'-phosphate (PLP) is inversely associated with inflammatory biomarkers.We observed that PLP was inversely associated with CRP (r=-0.33, plinear<0.0001), SAA (r=-0.23, plinear=0.003), IL-6 (r=-0.39, plinear <0.0001), IL-8 (r=-0.20, plinear=0.02) and TNFα (r=-0.12, plinear=0.045). Similar findings were observed for 5-methyl-tetrahydrofolate and CRP (r=-0.14), SAA (r=-0.14) and TNFα (r=-0.15) among colorectal cancer patients. Folate catabolite apABG was positively correlated with IL-6 (r= 0.27, plinear<0.0001) and pABG was positively correlated with IL-8 (r= 0.21, plinear<0.0001), indicating higher folate utilization during inflammation.Our data support the hypothesis of inverse associations between PLP and inflammatory biomarkers among colorectal cancer patients. A better understanding of the role and inter-relation of PLP and other one-carbon metabolites with inflammatory processes among colorectal carcinogenesis and prognosis could identify targets for future dietary guidance for colorectal cancer patients.

    Cross-protection induced by a A/MAY/97 emergency vaccine against intra-serotype heterologous challenge with a foot-and-mouth disease virus from the A/ASIA/G-VII lineage
    Dekker, Aldo ; Sanz-Bernardo, Beatriz ; Singanallur, Nagendrakumar Balasubramanian ; Ludi, Anna B. ; Horsington, Jacquelyn ; Eblé, Phaedra L. ; King, Donald P. ; Vosloo, Wilna - \ 2020
    Vaccines 8 (2020)1. - ISSN 2076-393X
    Cross-protection - FMD - Foot-and-mouth disease - Heterologous protection - Potency test - Vaccine

    Since 2015, outbreaks of foot-and-mouth disease (FMD) in the Middle East have been caused by a new emerging viral lineage, A/ASIA/G-VII. Invitro vaccine matching data indicated that this virus poorly matched (low r1-value) with vaccines that were being used in the region as well as most other commercially available vaccines. The aim of this study was to assess the performance of two candidate vaccines against challenge with a representative field virus from the A/ASIA/G-VII lineage. The results from an initial full dose protection study provided encouraging data for the A/MAY/97 vaccine, while the A22 /IRQ/64 vaccine only protected 2/7 vaccinated animals. In view of these promising results, this vaccine was tested in a potency test (PD50) experiment in which 5 cattle were vaccinated with a full dose, 5 cattle with a 1/3 dose and 5 cattle with a 1/9 dose of vaccine. At 21 days post vaccination these vaccinated cattle and 3 control cattle were challenged intradermolingually with a field isolate from the A/ASIA/G-VII lineage. The intra-serotype heterologous potency test resulted in an intra-serotype heterologous potency of 6.5 PD50 /dose. These data support previous studies showing that a high potency emergency vaccine can protect against clinical disease when challenged with a heterologous strain of the same serotype, indicating that not only the r1-value of the vaccine, but also the homologous potency of a vaccine should be taken into account when advising vaccines to control an outbreak.

    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.

    In the land of the blind the speculative eye is king
    Duineveld, Martijn - \ 2019
    The possibilities and limitations of observing silent risks and dangers in evolving governance
    Strategieën precisiebemesting op gras
    Lokhorst, C. ; Oenema, J. - \ 2019
    V-focus 16 (2019)3. - ISSN 1574-1575 - p. 18 - 20.
    In het project Grass4Farming is de afgelopen twee jaar op Dairy Campus en bij maatschap Kroes gewerkt aan een proof of concept voor strategieën (King John en Robin Hood) voor precisiebemesting binnen percelen voor grasland op basis van met sensoren gemeten plaats- en tijdspecifieke bodem- en gewasinformatie.Variabele bemesting in de akkerbouw op basis van bodem- en gewasinformatie wordt gezien als een belangrijke toepassing en het gebruik ervan bij granen en aardappels wordt gestimuleerd. De laatste paar jaar is er steeds meer aandacht voor het gewas gras, om ook daar principes uit de precisielandbouw toe te passen. Bemesting van grasland is complex omdat een melkveehouder binnen een jaar te maken heeft met meerdere oogsten, meerdere percelen, verschillende soorten mest, met en zonder beweiding en een beperkte plaatsingsruimte. De ontwikkelde PerceelVerdeler (http://webapplicaties.wur.nl/software/perceelverdeler) is een handig hulpmiddel om meststoffen zo goed mogelijk te verdelen.
    Enzyme promiscuity shapes adaptation to novel growth substrates
    Guzmán, Gabriela I. ; Sandberg, Troy E. ; LaCroix, Ryan A. ; Nyerges, Ákos ; Papp, Henrietta ; Raad, Markus de; King, Zachary A. ; Hefner, Ying ; Northen, Trent R. ; Notebaart, Richard A. ; Pál, Csaba ; Palsson, Bernhard O. ; Papp, Balázs ; Feist, Adam M. - \ 2019
    Molecular Systems Biology 15 (2019)4. - ISSN 1744-4292 - p. e8462 - e8462.
    adaptive evolution - enzyme promiscuity - genome‐scale modeling - systems biology

    Evidence suggests that novel enzyme functions evolved from low-level promiscuous activities in ancestral enzymes. Yet, the evolutionary dynamics and physiological mechanisms of how such side activities contribute to systems-level adaptations are not well characterized. Furthermore, it remains untested whether knowledge of an organism's promiscuous reaction set, or underground metabolism, can aid in forecasting the genetic basis of metabolic adaptations. Here, we employ a computational model of underground metabolism and laboratory evolution experiments to examine the role of enzyme promiscuity in the acquisition and optimization of growth on predicted non-native substrates in Escherichia coli K-12 MG1655. After as few as approximately 20 generations, evolved populations repeatedly acquired the capacity to grow on five predicted non-native substrates-D-lyxose, D-2-deoxyribose, D-arabinose, m-tartrate, and monomethyl succinate. Altered promiscuous activities were shown to be directly involved in establishing high-efficiency pathways. Structural mutations shifted enzyme substrate turnover rates toward the new substrate while retaining a preference for the primary substrate. Finally, genes underlying the phenotypic innovations were accurately predicted by genome-scale model simulations of metabolism with enzyme promiscuity.

    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.

    Navigating shades of social capital and trust to leverage opportunities for rural innovation
    King, Barbara ; Fielke, Simon ; Bayne, Karen ; Klerkx, Laurens ; Nettle, Ruth - \ 2019
    Journal of Rural Studies 68 (2019). - ISSN 0743-0167 - p. 123 - 134.
    Agricultural knowledge and innovation systems - Companion - Competence and commitment trust - Innovation network composition - Rural innovation projects

    This paper makes a contribution to understanding the impact of relational trust, as embodied within bonding, bridging and linking social capital, on rural innovation. Using cases of multi-stakeholder groups who work together on shared problems it explores how social capital and different forms of trust (companion, competence and commitment) influence rural innovation processes. Looking at both the ‘bright’ and ‘dark’ side of social capital, our focus is on how social capital and trust constrain and enable the process of innovation. The study highlights both positive and negative effects of social capital in the context of three fixed term projects that were part of New Zealand's Primary Innovation programme (2012–2017). Our findings show that there was a unique composition of social capital and trust at the outset of each project and that dark social capital was a critical constraint in each case. Enabling innovation processes required committed and dedicated brokers who provided bridging social capital and embodied competence trust to enable participants' confidence. Such brokers are capable of recognising and managing different 'shades’ of social capital and trust in pursuing desired project outcomes. A main theoretical implication of this study is that a better understanding of social capital and trust is needed to enable innovation facilitators and project managers to design and undertake fixed term rural innovation projects effectively. This is because social capital determines whether the composition of relationships within networks of actors involved in innovation projects enables innovation, or to the contrary constrains innovation. Specifically the implications and implementation of bridging social capital and competence trust are key determinants of successful innovation processes.

    The transnational dimension of international organizations' duty of care towards their civilian personnel : Lessons from the case law on states' extraterritorial human rights obligations
    Macchi, Chiara - \ 2018
    In: The Duty of Care of International Organizations Towards Their Civilian Personnel / de Guttry, A., Frulli, M., Greppi, E., Macchi, C., The Hague : T.M.C. Asser Press - ISBN 9789462652576 - p. 433 - 456.
    Due diligence - Duty of care - European court of human rights - Extraterritorial human rights obligations - Functional protection - International organizations

    The purpose of this chapter is to establish under which conditions the civilian personnel sent on mission fall within the human rights jurisdiction of the sending international organization, and the extent of the positive human rights obligations that the latter, consequently, owes to the former. Section 17.2 reviews the existing jurisprudence on the extraterritorial human rights obligations (ETOs) of States with a view to assessing whether the so-called 'spatial' model and 'personal' model of jurisdiction can provide adequate conceptual bases for the grounding of international organizations' human rights obligations towards their civilian personnel sent on mission. Section 17.3, building upon the tripartite definition of jurisdiction elaborated by King and taking stock of the available ETO jurisprudence, distills the principles that ground the human rights jurisdiction of an international organization and delimit the extent of its positive human rights obligations towards its personnel. The conclusions of this analysis support the existence of a duty of care anchored in international human rights law that places on the sending international organization positive obligations towards its civilian personnel wherever the latter carries out its tasks, the existence of which does not depend on the formal nature of the employment relationship between the international organization and the individual.

    Evidence for selection pressure from resistant potato genotypes but not from fungicide application within a clonal Phytophthora infestans population
    Stellingwerf, J.S. ; Phelan, S. ; Doohan, F.M. ; Ortiz, V. ; Griffin, D. ; Bourke, A. ; Hutten, R.C.B. ; Cooke, D.E.L. ; Kildea, S. ; Mullins, E. - \ 2018
    Plant Pathology 67 (2018)7. - ISSN 0032-0862 - p. 1528 - 1538.
    Host resistance - Phytophthora infestans - Population genetics - Potato - SSR genotyping
    Insight into pathogen population dynamics provides a key input for effective disease management of the potato late blight pathogen Phytophthora infestans. Phytophthora infestans populations vary from genetically complex to more simple with a few clonal lineages. The presence or absence of certain strains of P. infestans may impact the efficacy of fungicides or host resistance. Current evidence indicates that genetically, the Irish populations of P. infestans are relatively simple with a few clonal lineages. In this study, P. infestans populations were genetically characterized based on samples collected at the national centre for potato breeding during the period 2012-16. The dominance of clonal lineages within this P. infestans population was confirmed and the potential selection pressure of fungicide treatment (2013-15) and host resistance (2016) on this clonal P. infestans population was then investigated. It was found that fungicide products did not notably affect the genetic structure of sampled populations relative to samples from untreated control plants. In contrast, samples taken from several resistant potato genotypes were found to be more often of the EU_13_A2 lineage than those taken from control King Edward plants or potato genotypes with low resistance ratings. Resistant potato varieties Sarpo Mira and Bionica, containing characterized R genes, were found to strongly select for EU_13_A2 strains.
    A Pressure Test to Make 10 Molecules in 90 Days : External Evaluation of Methods to Engineer Biology
    Casini, Arturo ; Chang, Fang Yuan ; Eluere, Raissa ; King, Andrew M. ; Young, Eric M. ; Dudley, Quentin M. ; Karim, Ashty ; Pratt, Katelin ; Bristol, Cassandra ; Forget, Anthony ; Ghodasara, Amar ; Warden-Rothman, Robert ; Gan, Rui ; Cristofaro, Alexander ; Borujeni, Amin Espah ; Ryu, Min Hyung ; Li, Jian ; Kwon, Yong Chan ; Wang, He ; Tatsis, Evangelos ; Rodriguez-Lopez, Carlos ; O'Connor, Sarah ; Medema, Marnix H. ; Fischbach, Michael A. ; Jewett, Michael C. ; Voigt, Christopher ; Gordon, D.B. - \ 2018
    Journal of the American Chemical Society 140 (2018)12. - ISSN 0002-7863 - p. 4302 - 4316.
    Centralized facilities for genetic engineering, or "biofoundries", offer the potential to design organisms to address emerging needs in medicine, agriculture, industry, and defense. The field has seen rapid advances in technology, but it is difficult to gauge current capabilities or identify gaps across projects. To this end, our foundry was assessed via a timed "pressure test", in which 3 months were given to build organisms to produce 10 molecules unknown to us in advance. By applying a diversity of new approaches, we produced the desired molecule or a closely related one for six out of 10 targets during the performance period and made advances toward production of the others as well. Specifically, we increased the titers of 1-hexadecanol, pyrrolnitrin, and pacidamycin D, found novel routes to the enediyne warhead underlying powerful antimicrobials, established a cell-free system for monoterpene production, produced an intermediate toward vincristine biosynthesis, and encoded 7802 individually retrievable pathways to 540 bisindoles in a DNA pool. Pathways to tetrahydrofuran and barbamide were designed and constructed, but toxicity or analytical tools inhibited further progress. In sum, we constructed 1.2 Mb DNA, built 215 strains spanning five species (Saccharomyces cerevisiae, Escherichia coli, Streptomyces albidoflavus, Streptomyces coelicolor, and Streptomyces albovinaceus), established two cell-free systems, and performed 690 assays developed in-house for the molecules.
    MAPK-triggered chromatin reprogramming by histone deacetylase in plant innate immunity
    Latrasse, David ; Jégu, Teddy ; Li, H. ; Zelicourt, Axel de; Raynaud, Cécile ; Legras, Stéphanie ; Gust, Andrea ; Samajova, Olga ; Veluchamy, Alaguraj ; Rayapuram, Naganand ; Ramirez-Prado, Juan Sebastian ; Kulikova, O. ; Colcombet, Jean ; Genot, Baptiste ; Bisseling, A.H.J. ; Benhamed, Moussa ; Hirt, Heribert - \ 2017
    King Abdullah University of Science and Technology
    GSE99936 - Arabidopsis thaliana - PRJNA390146
    Microbial-associated molecular patterns (MAMPs) activate several MAP Kinases (MAPKs), which are major regulators of the innate immune response in Arabidopsis that induce large-scale changes in gene expression. Here, we determined whether MAMP-triggered gene expression involves chromatin modifications at the chromosomal level. Our results show that histone acetylation and deacetylation are major regulators of MAMP-triggered gene expression and implicate the histone deacetylase HD2B in the reprogramming of defense gene expression and innate immunity. The MAPK MPK3 directly interacts with and phosphorylates HD2B, thereby regulating the intra-nuclear compartmentalization and function of the histone deacetylase. By studying a number of gene loci that undergo MAMP-dependent activation or repression, our data reveal a mechanistic model for how protein kinase signaling directly impacts chromatin reprogramming in plant defense.
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