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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Above- and belowground overyielding are related at the community and species level in a grassland biodiversity experiment
Barry, Kathryn E. ; Weigelt, Alexandra ; Ruijven, Jasper van; Kroon, Hans de; Ebeling, Anne ; Eisenhauer, Nico ; Gessler, Arthur ; Ravenek, Janneke M. ; Scherer-Lorenzen, Michael ; Oram, Natalie J. ; Vogel, Anja ; Wagg, Cameron ; Mommer, Liesje - \ 2019
In: Advances in Ecological Research Academic Press Inc. (Advances in Ecological Research )
Biodiversity-ecosystem functioning - Biomass allocation - Functional diversity - Jena experiment - Light competition - Plant traits - Root biomass - Root:Shoot ratio - Shoot biomass - Species richness

Plant species richness positively affects plant productivity both above- and belowground. While this suggests that they are related at the community level, few studies have calculated above- and belowground overyielding simultaneously. It thus remains unknown whether above- and belowground overyielding are correlated. Moreover, it is unknown how belowground community level overyielding translates to the species level. We investigated above- and belowground overyielding in the Jena Trait-Based Biodiversity Experiment, at both the community and species level and across two 8-species pools. We found that above- and belowground overyielding were positively correlated at the community level and at the species level—for seven out of the 13 investigated species. Some plant species performed better in mixtures compared to monocultures and others performed worse, but the majority did so simultaneously above- and belowground. However, plants invested more in aboveground overyielding than belowground. Based on this disproportional investment in overyielding aboveground, we conclude that light was more limiting than belowground resources in the present study, which requires individual species to compete more for light than for belowground resources.

Dode vogel als waardevol onderzoeksmateriaal
Franeker, Jan Andries van - \ 2019
Determinants of successful lifestyle change during a 6-month preconception lifestyle intervention in women with obesity and infertility
Karsten, Matty D.A. ; Oers, Anne M. van; Groen, Henk ; Mutsaerts, Meike A.Q. ; Poppel, Mireille N.M. van; Geelen, Anouk ; Beek, Cornelieke van de; Painter, Rebecca C. ; Mol, Ben W.J. ; Roseboom, Tessa J. ; Hoek, Annemieke ; Burggraaff, J.M. ; Kuchenbecker, W.K.H. ; Perquin, D.A.M. ; Koks, C.A.M. ; Golde, R. van; Kaaijk, E.M. ; Schierbeek, J.M. ; Oosterhuis, G.J.E. ; Broekmans, F.J. ; Vogel, N.E.A. ; Lambalk, C.B. ; Veen, F. van der; Klijn, N.F. ; Mercelina, P.E.A.M. ; Kasteren, Y.M. van; Nap, A.W. ; Mulder, R.J.A.B. ; Gondrie, E.T.C.M. ; Bruin, J.P. de - \ 2019
European Journal of Nutrition 58 (2019)6. - ISSN 1436-6207 - p. 2463 - 2475.
Determinants - Lifestyle intervention - Obesity - Preconception

Purpose: To identify demographic, (bio)physical, behavioral, and psychological determinants of successful lifestyle change and program completion by performing a secondary analysis of the intervention arm of a randomized-controlled trial, investigating a preconception lifestyle intervention. Methods: The 6-month lifestyle intervention consisted of dietary counseling, physical activity, and behavioral modification, and was aimed at 5–10% weight loss. We operationalized successful lifestyle change as successful weight loss (≥ 5% weight/BMI ≤ 29 kg/m2), weight loss in kilograms, a reduction in energy intake, and an increase in physical activity during the intervention program. We performed logistic and mixed-effect regression analyses to identify baseline factors that were associated with successful change or program completion. Results: Women with higher external eating behavior scores had higher odds of successful weight loss (OR 1.10, 95% CI 1.05–1.16). Women with the previous dietetic support lost 0.94 kg less during the intervention period (95% CI 0.01–1.87 kg). Women with higher self-efficacy reduced energy intake more than women with lower self-efficacy (p < 0.01). Women with an older partner had an increased energy intake (6 kcal/year older, 95% CI 3–13). A high stage of change towards physical activity was associated with a higher number of daily steps (p = 0.03). A high stage of change towards weight loss was associated with completion of the intervention (p = 0.04). Conclusions: Determinants of lifestyle change and program completion were: higher external eating behavior, not having received previous dietetic support, high stage of change. This knowledge can be used to identify women likely to benefit from lifestyle interventions and develop new interventions for women requiring alternative support. Trial registration: The LIFEstyle study was registered at the Dutch trial registry (NTR 1530; http://www.trialregister.nl/trialreg/admin/rctview.asp?TC=1530).

Data from: Parasitic wasp-associated symbiont affects plant-mediated species interactions between herbivores
Cusumano, Antonino ; Zhu, F. ; Volkoff, Anne Nathalie ; Verbaarschot, P.G.H. ; Bloem, J. ; Vogel, Heiko ; Dicke, M. ; Poelman, E.H. - \ 2018
tritrophic interactions - plant-insect interactions - polydnaviruses - parasitoid - herbivore colonization - CgBV
Microbial mutualistic symbiosis is increasingly recognised as a hidden driving force in the ecology of plant–insect interactions. Although plant‐associated and herbivore‐associated symbionts clearly affect interactions between plants and herbivores, the effects of symbionts associated with higher trophic levels has been largely overlooked. At the third‐trophic level, parasitic wasps are a common group of insects that can inject symbiotic viruses (polydnaviruses) and venom into their herbivorous hosts to support parasitoid offspring development. Here, we show that such third‐trophic level symbionts act in combination with venom to affect plant‐mediated interactions by reducing colonisation of subsequent herbivore species. This ecological effect correlated with changes induced by polydnaviruses and venom in caterpillar salivary glands and in plant defence responses to herbivory. Because thousands of parasitoid species are associated with mutualistic symbiotic viruses in an intimate, specific relationship, our findings may represent a novel and widespread ecological phenomenon in plant–insect interactions
Cadmium associates with oxalate in calcium oxalate crystals and competes with calcium for translocation to stems in the cadmium bioindicator Gomphrena claussenii
Pongrac, Paula ; Serra, Tânia S. ; Castillo-Michel, Hiram ; Vogel-Mikuš, Katarina ; Arčon, Iztok ; Kelemen, Mitja ; Jenčič, Boštjan ; Kavčič, Anja ; Villafort Carvalho, Mina T. ; Aarts, Mark G.M. - \ 2018
Metallomics 10 (2018)11. - ISSN 1756-5901 - p. 1576 - 1584.

Cadmium (Cd) was shown to co-localise with calcium (Ca) in oxalate crystals in the stems and leaves of Cd tolerant Gomphrena claussenii, but Cd binding remained unresolved. Using synchrotron radiation X-ray absorption near edge spectroscopy we demonstrate that in oxalate crystals of hydroponically grown G. claussenii the vast majority of Cd is bound to oxygen ligands in oxalate crystals (>88%; Cd-O-C coordination) and the remaining Cd is bound to sulphur ligands (Cd-S-C coordination). Cadmium binding to oxalate does not depend on the amount of Ca supplied or from which organs the crystals originate (stems and mature leaves). By contrast, roots contain no oxalate crystals and therein Cd is bound predominantly by S ligands. The potential to remove Cd by extraction of Cd-rich oxalate crystals from plant material should be tested in phytoextraction or phytomining strategies.

Data from: Symbiotic polydnavirus and venom reveal parasitoid to its hyperparasitoids
Zhu, F. ; Cusumano, Antonino ; Bloem, J. ; Weldegergis, B.T. ; Nunes Villela, A. ; Fatouros, N.E. ; Loon, J.J.A. van; Dicke, M. ; Harvey, Jeffrey A. ; Vogel, Heiko ; Poelman, E.H. - \ 2018
multitrophic interactions - plant-mediated interaction network - herbivore saliva - herbivore-induced plant volatiles - parasitic wasp - Cotesia glomerata - Lysibia nana - Pieris brassicae - Brassica oleracea
Symbiotic relationships may provide organisms with key innovations that aid in the establishment of new niches. For example, during oviposition, some species of parasitoid wasps, whose larvae develop inside the bodies of other insects, inject polydnaviruses into their hosts. These symbiotic viruses disrupt host immune responses, allowing the parasitoid’s progeny to survive. Here, we show that symbiotic polydnaviruses also have a downside to the parasitoid’s progeny by initiating a multi-trophic chain of interactions that reveals the parasitoid larvae to their enemies. These enemies are hyperparasitoids that use the parasitoid progeny as host for their own offspring. We found that the virus and venom injected by the parasitoid during oviposition, but not the parasitoid progeny itself, affected hyperparasitoid attraction towards plant volatiles induced by feeding of parasitized caterpillars We identified activity of virus-related genes in the caterpillar salivary gland. Moreover, the virus affected the activity of elicitors of salivary origin that induce plant responses to caterpillar feeding. The changes in caterpillar saliva were critical in inducing plant volatiles that are used by hyperparsitoids to locate parasitized caterpillars. Our results show that symbiotic organisms may be key drivers of multi-trophic ecological interactions. We anticipate that this phenomenon is widespread in nature, because of the abundance of symbiotic microorganisms across trophic levels in ecological communities. Their role should be more prominently integrated in community ecology to understand organization of natural and managed ecosystems as well as adaptations of individual organisms that are part of these communities.
Development and analysis of the Soil Water Infiltration Global database
Rahmati, Mehdi ; Weihermüller, Lutz ; Vanderborght, Jan ; Pachepsky, Yakov A. ; Mao, Lili ; Sadeghi, Seyed Hamidreza ; Moosavi, Niloofar ; Kheirfam, Hossein ; Montzka, Carsten ; Looy, Kris Van; Toth, Brigitta ; Hazbavi, Zeinab ; Yamani, Wafa Al; Albalasmeh, Ammar A. ; Alghzawi, M.Z. ; Angulo-Jaramillo, Rafael ; Antonino, Antônio Celso Dantas ; Arampatzis, George ; Armindo, Robson André ; Asadi, Hossein ; Bamutaze, Yazidhi ; Batlle-Aguilar, Jordi ; Béchet, Béatrice ; Becker, Fabian ; Blöschl, Günter ; Bohne, Klaus ; Braud, Isabelle ; Castellano, Clara ; Cerdà, Artemi ; Chalhoub, Maha ; Cichota, Rogerio ; Císlerová, Milena ; Clothier, Brent ; Coquet, Yves ; Cornelis, Wim ; Corradini, Corrado ; Coutinho, Artur Paiva ; Oliveira, Muriel Bastista De; Macedo, José Ronaldo De; Durães, Matheus Fonseca ; Emami, Hojat ; Eskandari, Iraj ; Farajnia, Asghar ; Flammini, Alessia ; Fodor, Nándor ; Gharaibeh, Mamoun ; Ghavimipanah, Mohamad Hossein ; Ghezzehei, Teamrat A. ; Giertz, Simone ; Hatzigiannakis, Evangelos G. ; Horn, Rainer ; Jiménez, Juan José ; Jacques, Diederik ; Keesstra, Saskia Deborah ; Kelishadi, Hamid ; Kiani-Harchegani, Mahboobeh ; Kouselou, Mehdi ; Jha, Madan Kumar ; Lassabatere, Laurent ; Li, Xiaoyan ; Liebig, Mark A. ; Lichner, Lubomír ; López, María Victoria ; Machiwal, Deepesh ; Mallants, Dirk ; Mallmann, Micael Stolben ; Oliveira Marques, Jean Dalmo De; Marshall, Miles R. ; Mertens, Jan ; Meunier, Félicien ; Mohammadi, Mohammad Hossein ; Mohanty, Binayak P. ; Pulido-Moncada, Mansonia ; Montenegro, Suzana ; Morbidelli, Renato ; Moret-Fernández, David ; Moosavi, Ali Akbar ; Mosaddeghi, Mohammad Reza ; Mousavi, Seyed Bahman ; Mozaffari, Hasan ; Nabiollahi, Kamal ; Neyshabouri, Mohammad Reza ; Ottoni, Marta Vasconcelos ; Ottoni Filho, Theophilo Benedicto ; Pahlavan-Rad, Mohammad Reza ; Panagopoulos, Andreas ; Peth, Stephan ; Peyneau, Pierre Emmanuel ; Picciafuoco, Tommaso ; Poesen, Jean ; Pulido, Manuel ; Reinert, Dalvan José ; Reinsch, Sabine ; Rezaei, Meisam ; Roberts, Francis Parry ; Robinson, David ; Rodrigo-Comino, Jesüs ; Rotunno Filho, Otto Corrêa ; Saito, Tadaomi ; Suganuma, Hideki ; Saltalippi, Carla ; Sándor, Renáta ; Schütt, Brigitta ; Seeger, Manuel ; Sepehrnia, Nasrollah ; Sharifi Moghaddam, Ehsan ; Shukla, Manoj ; Shutaro, Shiraki ; Sorando, Ricardo ; Stanley, Ajayi Asishana ; Strauss, Peter ; Su, Zhongbo ; Taghizadeh-Mehrjardi, Ruhollah ; Taguas, Encarnación ; Teixeira, Wenceslau Geraldes ; Vaezi, Ali Reza ; Vafakhah, Mehdi ; Vogel, Tomas ; Vogeler, Iris ; Votrubova, Jana ; Werner, Steffen ; Winarski, Thierry ; Yilmaz, Deniz ; Young, Michael H. ; Zacharias, Steffen ; Zeng, Yijian ; Zhao, Ying ; Zhao, Hong ; Vereecken, Harry - \ 2018
Earth System Science Data 10 (2018)3. - ISSN 1866-3508 - p. 1237 - 1263.

In this paper, we present and analyze a novel global database of soil infiltration measurements, the Soil Water Infiltration Global (SWIG) database. In total, 5023 infiltration curves were collected across all continents in the SWIG database. These data were either provided and quality checked by the scientists who performed the experiments or they were digitized from published articles. Data from 54 different countries were included in the database with major contributions from Iran, China, and the USA. In addition to its extensive geographical coverage, the collected infiltration curves cover research from 1976 to late 2017. Basic information on measurement location and method, soil properties, and land use was gathered along with the infiltration data, making the database valuable for the development of pedotransfer functions (PTFs) for estimating soil hydraulic properties, for the evaluation of infiltration measurement methods, and for developing and validating infiltration models. Soil textural information (clay, silt, and sand content) is available for 3842 out of 5023 infiltration measurements (∼76%) covering nearly all soil USDA textural classes except for the sandy clay and silt classes. Information on land use is available for 76ĝ€% of the experimental sites with agricultural land use as the dominant type (∼40%). We are convinced that the SWIG database will allow for a better parameterization of the infiltration process in land surface models and for testing infiltration models. All collected data and related soil characteristics are provided online in ∗.xlsx and ∗.csv formats for reference, and we add a disclaimer that the database is for public domain use only and can be copied freely by referencing it. Supplementary data are available at https://doi.org/10.1594/PANGAEA.885492 (Rahmati et al., 2018). Data quality assessment is strongly advised prior to any use of this database. Finally, we would like to encourage scientists to extend and update the SWIG database by uploading new data to it.

Parasitic wasp-associated symbiont affects plant-mediated species interactions between herbivores
Cusumano, Antonino ; Zhu, Feng ; Volkoff, Anne Nathalie ; Verbaarschot, Patrick ; Bloem, Janneke ; Vogel, Heiko ; Dicke, Marcel ; Poelman, Erik H. - \ 2018
Ecology Letters 21 (2018)7. - ISSN 1461-023X - p. 957 - 967.
Herbivore colonisation - parasitoid - plant–insect interactions - polydnaviruses - tritrophic interactions

Microbial mutualistic symbiosis is increasingly recognised as a hidden driving force in the ecology of plant–insect interactions. Although plant-associated and herbivore-associated symbionts clearly affect interactions between plants and herbivores, the effects of symbionts associated with higher trophic levels has been largely overlooked. At the third-trophic level, parasitic wasps are a common group of insects that can inject symbiotic viruses (polydnaviruses) and venom into their herbivorous hosts to support parasitoid offspring development. Here, we show that such third-trophic level symbionts act in combination with venom to affect plant-mediated interactions by reducing colonisation of subsequent herbivore species. This ecological effect correlated with changes induced by polydnaviruses and venom in caterpillar salivary glands and in plant defence responses to herbivory. Because thousands of parasitoid species are associated with mutualistic symbiotic viruses in an intimate, specific relationship, our findings may represent a novel and widespread ecological phenomenon in plant–insect interactions.

Symbiotic polydnavirus and venom reveal parasitoid to its hyperparasitoids
Zhu, Feng ; Cusumano, Antonino ; Bloem, Janneke ; Weldegergis, Berhane T. ; Villela, Alexandre ; Fatouros, Nina E. ; Loon, Joop J.A. van; Dicke, Marcel ; Harvey, Jeffrey A. ; Vogel, Heiko ; Poelman, Erik H. - \ 2018
Proceedings of the National Academy of Sciences of the United States of America 115 (2018)20. - ISSN 0027-8424 - p. 5205 - 5210.
Herbivore - Herbivore-induced plant volatiles - Interaction network - Multitrophic interactions - Parasitic wasp - Plant-mediated - Saliva

Symbiotic relationships may provide organisms with key innovations that aid in the establishment of new niches. For example, during oviposition, some species of parasitoid wasps, whose larvae develop inside the bodies of other insects, inject polydnaviruses into their hosts. These symbiotic viruses disrupt host immune responses, allowing the parasitoid’s progeny to survive. Here we show that symbiotic polydnaviruses also have a downside to the parasitoid’s progeny by initiating a multitrophic chain of interactions that reveals the parasitoid larvae to their enemies. These enemies are hyperparasitoids that use the parasitoid progeny as host for their own offspring. We found that the virus and venom injected by the parasitoid during oviposition, but not the parasitoid progeny itself, affected hyperparasitoid attraction toward plant volatiles induced by feeding of parasitized caterpillars. We identified activity of virus-related genes in the caterpillar salivary gland. Moreover, the virus affected the activity of elicitors of salivary origin that induce plant responses to caterpillar feeding. The changes in caterpillar saliva were critical in inducing plant volatiles that are used by hyperparasitoids to locate parasitized caterpillars. Our results show that symbiotic organisms may be key drivers of multitrophic ecological interactions. We anticipate that this phenomenon is widespread in nature, because of the abundance of symbiotic microorganisms across trophic levels in ecological communities. Their role should be more prominently integrated in community ecology to understand organization of natural and managed ecosystems, as well as adaptations of individual organisms that are part of these communities.

Towards transformative social learning on the path to 1.5 degrees
Macintyre, Thomas ; Lotz-Sisitka, Heila ; Wals, A.E.J. ; Vogel, Coleen ; Tassone, V.C. - \ 2018
Current Opinion in Environmental Sustainability 31 (2018). - ISSN 1877-3435 - p. 80 - 87.
This paper provides insights into learning orientations and approaches that encourage change and transformation on the path to achieving the 1.5 degree C target. This literature review of the climate change and education/learning interface positions relevant literature in a heuristic tool, and reveals different learning approaches to addressing climate change. We highlight that although traditional lines of departure for achieving climate targets are usually technocratic in nature, especially if a zero emissions pathway is aimed for, there is an increasing realisation that climate issues are complex, deeply intertwined with unsustainable development and cultural change, and require collective engagement. Through considering the 1.5 degree C target as a metaphor for the fundamental changes needed in society, we argue that a wide range of learning orientations, including more inclusive and transformative social learning approaches, are needed to address the colossal challenges facing society.
Millennial multi-proxy reconstruction of oasis dynamics in Jordan, by the Dead Sea
Eggenberger, Sebastian ; Gobet, Erika ; Leeuwen, Jacqueline F.N. van; Schwörer, Christoph ; Knaap, Willem O. van der; Dobben, Han F. van; Vogel, Hendrik ; Tinner, Willy ; Rambeau, Claire M.C. - \ 2018
Vegetation History and Archaeobotany 27 (2018)5. - ISSN 0939-6314 - p. 649 - 664.
Fire history - Global change - Phoenix dactylifera - Pollen - Vegetation - XRF

Vegetation reconstructions in the Dead Sea region based on sediment records are potentially biased, because the vast majority of them derive from the western side of the sea, and only focus on large areas and time spans, while little is known about extra-local (< 1,000 m radius) to local (< 20 m radius) changes. To fill this gap, we compared a vegetation survey with modern pollen assemblages from the “Palm Terrace” oasis ca. 300 m b.s.l. (below sea level), at the eastern edge of the Dead Sea. This revealed how the oasis vegetation is reflected in pollen assemblages. In addition, two sediment cores were collected from the centre and the edge of a mire at the oasis to reconstruct past vegetation dynamics. We analysed sedimentary pollen and microscopic charcoal, as well as the sediment chemistry by X-ray fluorescence (XRF) and conductivity, focusing on the past ~ 1,000 years. Pollen results suggest that mesophilous Phoenix dactylifera (date palm) stands and wetland vegetation expanded there around ad 1300–1500 and 1700–1900. During the past ca. 100 years, drought-adapted Chenopodiaceae gained ground, partly replacing the palms. Results from elemental analysis, especially of elements such as chlorine, provide evidence of enhanced evaporative salinization. Increasing desertification and the associated decline of mesophilous date palm stands during the past ca. 50 years is probably related to a decrease in annual precipitation and also corresponds to decreasing water levels in the Dead Sea. These have mainly been caused by increasing extraction of fresh water from tributaries and wells, mainly for local agriculture and industry. In the future, with hotter and drier conditions as well as increased use of water, oasis vegetation along the Dead Sea might be at further risk of contraction or even extinction.

De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing
Schmidt, Maximilian H.W. ; Vogel, Alexander ; Denton, Alisandra K. ; Istace, Benjamin ; Wormit, Alexandra ; Geest, H.C. van de; Bolger, Marie E. ; Alseekh, Saleh ; Mass, Janina ; Pfaff, Christian ; Schurr, Ulrich ; Chetelat, Roger ; Maumus, Florian ; Aury, Jean-Mary ; Koren, Sergey ; Fernie, Alisdair Robert ; Zamir, Dani ; Bolger, Anthony ; Usadel, Björn - \ 2017
The Plant Cell 29 (2017)10. - ISSN 1040-4651 - p. 2336 - 2348.
Updates in nanopore technology have made it possible to obtain gigabases of sequence data. Prior to this, nanopore sequencing technology was mainly used to analyze microbial samples. Here, we describe the generation of a comprehensive nanopore sequencing data set with a median read length of 11,979 bp for a self-compatible accession of the wild tomato species Solanum pennellii. We describe the assembly of its genome to a contig N50 of 2.5 MB. The assembly pipeline comprised initial read correction with Canu and assembly with SMARTdenovo. The resulting raw nanopore-based de novo genome is structurally highly similar to that of the reference S. pennellii LA716 accession but has a high error rate and was rich in homopolymer deletions. After polishing the assembly with Illumina reads, we obtained an error rate of <0.02% when assessed versus the same Illumina data. We obtained a gene completeness of 96.53%, slightly surpassing that of the reference S. pennellii. Taken together, our data indicate that such long read sequencing data can be used to affordably sequence and assemble gigabase-sized plant genomes.
Eierraadsel opgelost: hoe meer een vogel vliegt, des te langwerpiger haar ei
Leeuwen, Johan van - \ 2017

De vorm van het ei heeft zich aangepast aan de behoeften van vogels.

Handen wassen kost maar 20 seconden, en zelfs dat lukt ons niet
Beumer, Rijkelt - \ 2017

Je hebt net nieuwe plantjes gepoot, kip klaargemaakt in de keuken of het toilet bezocht. Wat moet je daarna altijd doen? Juist: handen wassen. Maar hoe klein de moeite ook is, driekwart van de Nederlanders wast zijn handen te weinig of te kort. Microbioloog Rijkelt Beumer vertelt wat je moet weten over handhygiëne.

Juridische speelruimte N2000 voor herstel veerkracht en dynamiek in de Rijkswateren: Info-Graphic
Veraart, J.A. ; Spijkerman, A. - \ 2017
Regelgeving in het kader van de Vogel- en Habitatrichtlijn wordt soms als knelpunt ervaren bij ingrepen gericht op het herstel van de dynamiek in Rijkswateren. De afgelopen jaren is de ervaring met de regelgeving gegroeid en hebben uitspraken van het Europese gerechtshof meer duidelijkheid gegeven over de interpretatie. Nu is het tijd voor overheden en stakeholders om de uitvoering te optimaliseren en zelf de kaders in te vullen.
Biocatalytic, one-pot diterminal oxidation and esterification of n-alkanes for production of α,ω-diol and α,ω-dicarboxylic acid esters
Nuland, Youri M. van; Vogel, Fons A. de; Scott, Elinor L. ; Eggink, Gerrit ; Weusthuis, Ruud A. - \ 2017
Metabolic Engineering 44 (2017). - ISSN 1096-7176 - p. 134 - 142.
Alkanes - Monooxygenases - Whole-cell biocatalysis - α,ω-dicarboxylic acids - α,ω-diols
Direct and selective terminal oxidation of medium-chain n-alkanes is a major challenge in chemistry. Efforts to achieve this have so far resulted in low specificity and overoxidized products. Biocatalytic oxidation of medium-chain n-alkanes – with for example the alkane monooxygenase AlkB from P. putida GPo1- on the other hand is highly selective. However, it also results in overoxidation. Moreover, diterminal oxidation of medium-chain n-alkanes is inefficient. Hence, α,ω-bifunctional monomers are mostly produced from olefins using energy intensive, multi-step processes. By combining biocatalytic oxidation with esterification we drastically increased diterminal oxidation upto 92 mol% and reduced overoxidation to 3% for n-hexane. This methodology allowed us to convert medium-chain n-alkanes into α,ω-diacetoxyalkanes and esterified α,ω-dicarboxylic acids. We achieved this in a one-pot reaction with resting-cell suspensions of genetically engineered Escherichia coli. The combination of terminal oxidation and esterification constitutes a versatile toolbox to produce α,ω-bifunctional monomers from n-alkanes.
Kansen voor meer natuurlijkheid in Natura 2000-gebieden
Bijlsma, R.J. ; Jansen, A.J.M. ; Janssen, J.A.M. ; Maas, G.J. ; Pleijte, M. ; Schipper, P.C. ; Wondergem, H.E. - \ 2017
Landschap : tijdschrift voor landschapsecologie en milieukunde 34 (2017)3. - ISSN 0169-6300 - p. 144 - 153.
Aan alle Natura 2000-gebieden zijn instandhoudingsdoelstellingen toegewezen voor soorten en/of habitattypen
van de Vogel- en Habitatrichtlijn. De bezorgdheid groeit dat beheerplannen te weinig rekening
houden met noodzakelijke natuurlijke dynamiek en uitwijkmogelijkheden voor soorten. En hoe staat het
met andere natuurwaarden? Een expliciete landschapsecologische benadering biedt uitkomst en kan goed
aansluiten op het beheerplanproces en richtlijnen bieden voor vergunningverlening en handhaving.
High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice
Xiao, Liang ; Sonne, Si Brask ; Feng, Qiang ; Chen, Ning ; Xia, Zhongkui ; Li, Xiaoping ; Fang, Zhiwei ; Zhang, Dongya ; Fjære, Even ; Midtbø, Lisa Kolden ; Derrien, Muriel ; Hugenholtz, Floor ; Tang, Longqing ; Li, Junhua ; Zhang, Jianfeng ; Liu, Chuan ; Hao, Qin ; Vogel, Ulla Birgitte ; Mortensen, Alicja ; Kleerebezem, Michiel ; Licht, Tine Rask ; Yang, Huanming ; Wang, Jian ; Li, Yingrui ; Arumugam, Manimozhiyan ; Wang, Jun ; Madsen, Lise ; Kristiansen, Karsten - \ 2017
Microbiome 5 (2017). - ISSN 2049-2618 - p. 43 - 43.
129S6/Sv mice - C57BL/6J mice - High-fat feeding - Indomethacin - Microbiome - Microbiota - Obesity

BACKGROUND: It is well known that the microbiota of high-fat (HF) diet-induced obese mice differs from that of lean mice, but to what extent, this difference reflects the obese state or the diet is unclear. To dissociate changes in the gut microbiota associated with high HF feeding from those associated with obesity, we took advantage of the different susceptibility of C57BL/6JBomTac (BL6) and 129S6/SvEvTac (Sv129) mice to diet-induced obesity and of their different responses to inhibition of cyclooxygenase (COX) activity, where inhibition of COX activity in BL6 mice prevents HF diet-induced obesity, but in Sv129 mice accentuates obesity.

RESULTS: Using HiSeq-based whole genome sequencing, we identified taxonomic and functional differences in the gut microbiota of the two mouse strains fed regular low-fat or HF diets with or without supplementation with the COX-inhibitor, indomethacin. HF feeding rather than obesity development led to distinct changes in the gut microbiota. We observed a robust increase in alpha diversity, gene count, abundance of genera known to be butyrate producers, and abundance of genes involved in butyrate production in Sv129 mice compared to BL6 mice fed either a LF or a HF diet. Conversely, the abundance of genes involved in propionate metabolism, associated with increased energy harvest, was higher in BL6 mice than Sv129 mice.

CONCLUSIONS: The changes in the composition of the gut microbiota were predominantly driven by high-fat feeding rather than reflecting the obese state of the mice. Differences in the abundance of butyrate and propionate producing bacteria in the gut may at least in part contribute to the observed differences in obesity propensity in Sv129 and BL6 mice.

Local structure of Cu2+ in Cu-doped hexagonal turbostratic birnessite and Cu2+ stability under acid treatment
Qin, Zhangjie ; Xiang, Quanjun ; Liu, Fan ; Xiong, J. ; Koopal, Luuk K. ; Zheng, Lirong ; Ginder-Vogel, Matthew ; Wang, Mingxia ; Feng, Xionghan ; Tan, Wenfeng ; Yin, Hui - \ 2017
Chemical Geology 466 (2017)5. - ISSN 0009-2541 - p. 512 - 523.
Acid dissolution - Birnessite - Cu - Stability - X-ray absorption spectroscopy
Geochemical behaviors of heavy metal contaminants, such as Cu2+, are strongly controlled by natural birnessite-like minerals in both marine and terrestrial environments. However, the mechanisms of the interaction of Cu2+ with birnessite are not fully understood yet. In the present study, Cu2+ was coprecipitated with Mn2+ to produce hexagonal turbostratic birnessite, which is analogous to natural birnessite. The obtained Cu-doped birnessite was characterized by powder X-ray diffraction, field-emission scanning electron microscopy, and X-ray absorption spectroscopy (XANES+EXAFS). The stability of Cu(II) in the birnessite structure was investigated by acid treatment. Increasing the dopant content reduces the mineral crystallinity in the [001] direction and the unit cell parameter b from the hexagonal layers. It also shortens the bond length of MnO in the [MnO6] unit and the edge-sharing MnMn distance in the layers, and increases the average oxidation state (AOS) of Mn and the specific surface area. Analysis of Cu K-edge XANES and EXAFS data indicates that, only a small part of Cu(II) is inserted into the birnessite layers, while most of it is adsorbed on the vacancies. When the Cu/Mn molar ratio is increased from 0.08 to 0.23, an increasing part of Cu(II) is present as polynuclear clusters on the birnessite edge sites in the pH range of ~3.3-5.3. Reaction with H2SO4 solution is found to easily dissolve the polynuclear Cu clusters and the highly distorted Cu octahedra in innersphere complexes on the birnessite-water interface, with ~53% of the Cu2+ released into the solution. On the other hand, the reaction with HCl solution leads to reductive dissolution of the mineral matrix, the release of Mn2+ into solutions, the decrease in the first MnO and edge-sharing MnMn distances and Mn AOS, in addition to the release of Cu2+. The release rate of Cu2+ is much faster than that of Ni2+ in Ni-doped birnessites, owing to the lower stability of distorted [CuO6] octahedron upon proton attack. These results indicate the formation of multinuclear Cu complexes on birnessite surfaces under the investigated conditions. The results also suggest the lower stability of Cu2+ in these minerals and thus higher potential toxicity in acidic conditions, in comparison with other metal pollutants, such as Ni2+. This study provides new insights into the interaction mechanisms between Cu2+ and birnessite-like minerals, and help to clarify the structural stability and geochemical behaviors of Cu2+ associated with birnessite-like minerals in natural environments.
Diet-induced weight loss decreases adipose tissue oxygen tension with parallel changes in adipose tissue phenotype and insulin sensitivity in overweight humans
Vink, R.G. ; Roumans, N.J. ; Čajlaković, M. ; Cleutjens, J.P.M. ; Boekschoten, M.V. ; Fazelzadeh, P. ; Vogel, M.A.A. ; Blaak, E.E. ; Mariman, E.C. ; Baak, M.A. van; Goossens, G.H. - \ 2017
International Journal of Obesity 41 (2017)5. - ISSN 0307-0565 - p. 722 - 728.

Background/objectives: Although adipose tissue (AT) hypoxia is present in rodent models of obesity, evidence for this in humans is limited. Here, we investigated the effects of diet-induced weight loss (WL) on abdominal subcutaneous AT oxygen tension (pO 2), AT blood flow (ATBF), AT capillary density, AT morphology and transcriptome, systemic inflammatory markers and insulin sensitivity in humans. Subjects/methods: Fifteen overweight and obese individuals underwent a dietary intervention (DI), consisting of a 5-week very-low-calorie diet (VLCD, 500 kcal day -1; WL), and a subsequent 4-week weight stable diet (WS). Body composition, AT pO 2 (optochemical monitoring), ATBF (133 Xe washout), and whole-body insulin sensitivity were determined, and AT biopsies were collected at baseline, end of WL (week 5) and end of WS (week 9). Result: Body weight, body fat percentage and adipocyte size decreased significantly during the DI period. The DI markedly decreased AT pO 2 and improved insulin sensitivity, but did not alter ATBF. Finally, the DI increased AT gene expression of pathways related to mitochondrial biogenesis and non-mitochondrial oxygen consumption. Conclusions: VLCD-induced WL markedly decreases abdominal subcutaneous AT pO 2, which is paralleled by a reduction in adipocyte size, increased AT gene expression of mitochondrial biogenesis markers and non-mitochondrial oxygen consumption pathways, and improved whole-body insulin sensitivity in humans.

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