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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Reanalyzing the Palaeoptera problem – The origin of insect flight remains obscure
Simon, Sabrina ; Blanke, Alexander ; Meusemann, Karen - \ 2018
Arthropod Structure & Development (2018). - ISSN 1467-8039
Chiastomyaria - Homologization - Metapterygota - Palaeoptera - Phylogenomics - Transcriptomics

The phylogenetic relationships of the winged insect lineages – mayflies (Ephemeroptera), damselflies and dragonflies (Odonata), and all other winged insects (Neoptera) – are still controversial with three hypotheses supported by different datasets: Palaeoptera, Metapterygota and Chiastomyaria. Here, we reanalyze available phylogenomic data with a focus on detecting confounding and alternative signal. In this context, we provide a framework to quantitatively evaluate and assess incongruent molecular phylogenetic signal inherent in phylogenomic datasets. Despite overall support for the Palaeoptera hypothesis, we also found considerable signal for Chiastomyaria, which is not easily detectable by standardized tree inference approaches. Analyses of the accumulation of signal across gene partitions showed that signal accumulates gradually. However, even in case signal only slightly supported one over the other hypothesis, topologies inferred from large datasets switch from statistically strongly supported Palaeoptera to strongly supported Chiastomyaria. From a morphological point of view, Palaeoptera currently appears to be the best-supported hypothesis; however, recent analyses were restricted to head characters. Phylogenetic approaches covering all organ systems including analyses of potential functional or developmental convergence are still pending so that the Palaeoptera problem has to be considered an open question in insect systematics.

Erratum: Assessing the impact of underwater clearance of unexploded ordnance on harbour porpoises (Phocoena phocoena) in the Southern North Sea
Benda-Beckmann, Alexander M. von; Aarts, Geert ; Sertlek, H. ; Lucke, Klaus ; Verboom, Wim C. ; Kastelein, Ronald A. ; Ketten, Darlene R. ; Bemmelen, Rob van; Lam, Frans Peter A. ; Kirkwood, Roger J. ; Ainslie, Michael A. - \ 2018
Aquatic mammals 44 (2018)3. - ISSN 0167-5427 - p. 340 - 341.
This erratum concerns Figure 9 of the original article in which the line delimiting two effect types ("Permanent hearing loss increasingly likely" and "Permanent hearing loss very likely") was misplaced. This error, which has now been corrected, affects neither the main text nor the conclusion of the study. The authors apologize for the error.
Quantifying branch architecture of tropical trees using terrestrial LiDAR and 3D modelling
Lau, Alvaro ; Bentley, Lisa Patrick ; Martius, Christopher ; Shenkin, Alexander ; Bartholomeus, Harm ; Raumonen, Pasi ; Malhi, Yadvinder ; Jackson, Tobias ; Herold, Martin - \ 2018
Trees-Structure and Function (2018). - ISSN 0931-1890 - 13 p.
Tree architecture is the three-dimensional arrangement of above ground parts of a tree. Ecologists hypothesize that the topology of tree branches represents optimized adaptations to tree’s environment. Thus, an accurate description of tree architecture leads to a better understanding of how form is driven by function. Terrestrial laser scanning (TLS) has demonstrated its potential to characterize woody tree structure. However, most current TLS methods do not describe tree architecture. Here, we examined nine trees from a Guyanese tropical rainforest to evaluate the utility of TLS for measuring tree architecture. First, we scanned the trees and extracted individual tree point clouds. TreeQSM was used to reconstruct woody structure through 3D quantitative structure models (QSMs). From these QSMs, we calculated: (1) length and diameter of branches > 10 cm diameter, (2) branching order and (3) tree volume. To validate our method, we destructively harvested the trees and manually measured all branches over 10 cm (279). TreeQSM found and reconstructed 95% of the branches thicker than 30 cm. Comparing field and QSM data, QSM overestimated branch lengths thicker than 50 cm by 1% and underestimated diameter of branches between 20 and 60 cm by 8%. TreeQSM assigned the correct branching order in 99% of all cases and reconstructed 87% of branch lengths and 97% of tree volume. Although these results are based on nine trees, they validate a method that is an important step forward towards using tree architectural traits based on TLS and open up new possibilities to use QSMs for tree architecture.
Taxonomy of the family Arenaviridae and the order Bunyavirales : update 2018
Maes, Piet ; Alkhovsky, Sergey V. ; Bào, Yīmíng ; Beer, Martin ; Birkhead, Monica ; Briese, Thomas ; Buchmeier, Michael J. ; Calisher, Charles H. ; Charrel, Rémi N. ; Choi, Il Ryong ; Clegg, Christopher S. ; Torre, Juan Carlos de la; Delwart, Eric ; DeRisi, Joseph L. ; Bello, Patrick L. Di; Serio, Francesco Di; Digiaro, Michele ; Dolja, Valerian V. ; Drosten, Christian ; Druciarek, Tobiasz Z. ; Du, Jiang ; Ebihara, Hideki ; Elbeaino, Toufic ; Gergerich, Rose C. ; Gillis, Amethyst N. ; Gonzalez, Jean Paul J. ; Haenni, Anne Lise ; Hepojoki, Jussi ; Hetzel, Udo ; Hồ, Thiện ; Hóng, Ní ; Jain, Rakesh K. ; Jansen van Vuren, Petrus ; Jin, Qi ; Jonson, Miranda Gilda ; Junglen, Sandra ; Keller, Karen E. ; Kemp, Alan ; Kipar, Anja ; Kondov, Nikola O. ; Koonin, Eugene V. ; Kormelink, Richard ; Korzyukov, Yegor ; Krupovic, Mart ; Lambert, Amy J. ; Laney, Alma G. ; LeBreton, Matthew ; Lukashevich, Igor S. ; Marklewitz, Marco ; Markotter, Wanda ; Martelli, Giovanni P. ; Martin, Robert R. ; Mielke-Ehret, Nicole ; Mühlbach, Hans Peter ; Navarro, Beatriz ; Ng, Terry Fei Fan ; Nunes, Márcio Roberto Teixeira ; Palacios, Gustavo ; Pawęska, Janusz T. ; Peters, Clarence J. ; Plyusnin, Alexander ; Radoshitzky, Sheli R. ; Romanowski, Víctor ; Salmenperä, Pertteli ; Salvato, Maria S. ; Sanfaçon, Hélène ; Sasaya, Takahide ; Schmaljohn, Connie ; Schneider, Bradley S. ; Shirako, Yukio ; Siddell, Stuart ; Sironen, Tarja A. ; Stenglein, Mark D. ; Storm, Nadia ; Sudini, Harikishan ; Tesh, Robert B. ; Tzanetakis, Ioannis E. ; Uppala, Mangala ; Vapalahti, Olli ; Vasilakis, Nikos ; Walker, Peter J. ; Wáng, Guópíng ; Wáng, Lìpíng ; Wáng, Yànxiăng ; Wèi, Tàiyún ; Wiley, Michael R. ; Wolf, Yuri I. ; Wolfe, Nathan D. ; Wú, Zhìqiáng ; Xú, Wénxìng ; Yang, Li ; Yāng, Zuòkūn ; Yeh, Shyi Dong ; Zhāng, Yǒng Zhèn ; Zhèng, Yàzhōu ; Zhou, Xueping ; Zhū, Chénxī ; Zirkel, Florian ; Kuhn, Jens H. - \ 2018
Archives of Virology (2018). - ISSN 0304-8608 - p. 1 - 16.
In 2018, the family Arenaviridae was expanded by inclusion of 1 new genus and 5 novel species. At the same time, the recently established order Bunyavirales was expanded by 3 species. This article presents the updated taxonomy of the family Arenaviridae and the order Bunyavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV) and summarizes additional taxonomic proposals that may affect the order in the near future.
Editorial : Environmental policy integration: Taking stock of policy practice in different contexts
Persson, Åsa ; Runhaar, Hens ; Karlsson-Vinkhuyzen, Sylvia ; Mullally, Gerard ; Russel, Duncan ; Widmer, Alexander - \ 2018
Environmental Science & Policy 85 (2018). - ISSN 1462-9011 - p. 113 - 115.
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.
Pesticide registration, distribution and use practices in Ghana
Onwona Kwakye, Michael ; Mengistie, Belay ; Ofosu-Anim, John ; Nuer, Alexander Tetteh K. ; Den Brink, Paul J. van - \ 2018
Environment, Development and Sustainability (2018). - ISSN 1387-585X - p. 1 - 25.
Actors - Ghana - Implementation - Pesticides - Policy - Registration

Ghana has implemented regulation on the registration, distribution and usage of pesticides in order to evaluate their environmental and human health effects. However, environmental monitoring and certified laboratories for pesticide analysis are lacking. Pesticide misuse, misapplication, contamination of the environment and human exposure still continue, and little is known to what extent pesticide registration, distribution and use is properly implemented in Ghana. This study aimed at investigating how the pesticide policy operates in Ghana, how state (policy; national/local) and non-state (importers, dealers’ and farmers) stakeholders function, what their challenges are, and to which extend the policy objectives are achieved. A conceptual framework based on the contextual interaction theory (CIT) was developed, and a review of Ghana’s pesticide policy implementation with two empirical field studies on state policy and non-state policy actors was conducted, supplemented with secondary data, and a number of interviews conducted with stakeholders and informants were used. Results indicate that pesticides are registered in compliance with the law. Non-state actors scored low with respect to their mandate which likely results in environmental and human health risks. Significant association existed between educational level attained and knowledge (χ2 = 3.614; P ≤ 0.05). Work experience or duration of farming also significantly influenced the knowledge of respondents (P < 0.001), as well as attitude (χ2 = 15.328; P < 0.05). Work experience/duration of farming also significantly influenced attitude at 95% confidence level (P < 0.001), and duration of farming was significantly associated with farm management practices at 5% level of significance (P ≤ 0.05), while state actors are not motivated and resourced. It is recommended to perform preliminary risk assessment to the aquatic environment, to derive threshold levels which are protective of communities, to screen farmers for pesticide exposure and poisoning, to develop well-targeted training programmes for pesticide retailers and farmers on pesticide use, personal protective device use, as well as pesticide management and law. Additionally, pesticide policy implementers have to be motivated and resourced to carry out their mandate, being to execute the pesticide legislation.

Recognition of microbial viability via TLR8 drives TFH cell differentiation and vaccine responses
Ugolini, Matteo ; Gerhard, Jenny ; Burkert, Sanne ; Jensen, Kristoffer Jarlov ; Georg, Philipp ; Ebner, Friederike ; Volkers, Sarah M. ; Thada, Shruthi ; Dietert, Kristina ; Bauer, Laura ; Schäfer, Alexander ; Helbig, Elisa T. ; Opitz, Bastian ; Kurth, Florian ; Sur, Saubashya ; Dittrich, Nickel ; Gaddam, Sumanlatha ; Conrad, Melanie L. ; Benn, Christine S. ; Blohm, Ulrike ; Gruber, Achim D. ; Hutloff, Andreas ; Hartmann, Susanne ; Boekschoten, Mark V. ; Müller, Michael ; Jungersen, Gregers ; Schumann, Ralf R. ; Suttorp, Norbert ; Sander, Leif E. - \ 2018
Nature Reviews. Immunology 19 (2018)4. - ISSN 1529-2908 - p. 386 - 396.
Live attenuated vaccines are generally highly efficacious and often superior to inactivated vaccines, yet the underlying mechanisms of this remain largely unclear. Here we identify recognition of microbial viability as a potent stimulus for follicular helper T cell (TFH cell) differentiation and vaccine responses. Antigen-presenting cells (APCs) distinguished viable bacteria from dead bacteria through Toll-like receptor 8 (TLR8)-dependent detection of bacterial RNA. In contrast to dead bacteria and other TLR ligands, live bacteria, bacterial RNA and synthetic TLR8 agonists induced a specific cytokine profile in human and porcine APCs, thereby promoting TFH cell differentiation. In domestic pigs, immunization with a live bacterial vaccine induced robust TFH cell and antibody responses, but immunization with its heat-killed counterpart did not. Finally, a hypermorphic TLR8 polymorphism was associated with protective immunity elicited by vaccination with bacillus Calmette-Guérin (BCG) in a human cohort. We have thus identified TLR8 as an important driver of TFH cell differentiation and a promising target for TFH cell-skewing vaccine adjuvants.
A dataset of spectral and biophysical measurements over Russian wheat fields
Wit, A.J.W. de; Roerink, G.J. ; Virchenko, Oleg ; Kleschenko, Alexander ; Bartalev, Sergey ; Savin, Igor ; Plotnikov, Dmitry ; Defourny, Pierre ; Andrimont, Raphael d' - \ 2018
wheat - Russia - remote sensing - experimental data
From 2011 to 2013 the MOCCCASIN project (MOnitoring Crops in Continental Climates through Asimillation of Satellite INformation) was carried out financed by the European Commission 7th Framework Programme. During the project, two field campaigns (2011 and 2012) were carried out at two sites (Odoyev and Plavsk) in the Tula region of Russia. During these two campaigns, observations were made at selected winter-wheat fields consisting of phenological stage, biomass samples, hemispherical photographs, spectral properties of the canopy and the soil as well as ancillary information about the field. Meteorological observations from synoptic and agrometeorological stations were collected from the stations in and surrounding the Tula region. Finally, a large trajectory throughout the whole Tula region was surveyed in order to collect fields with different crop types.
A dataset of spectral and biophysical measurements over Russian wheat fields
Wit, Allard de; Roerink, Gerbert ; Bartalev, Sergey ; Virchenko, Oleg ; Plotnikov, Dmitry ; Savin, Igor ; Kleschenko, Alexander - \ 2018
ODjAR : open data journal for agricultural research 4 (2018). - ISSN 2352-6378 - p. 22 - 27.
From 2011 to 2013 the MOCCCASIN project (MOnitoring Crops in Continental Climates through Asimillation of Satellite INformation) was carried out financed by the European Commission 7th Framework Programme. During the project, two field campaigns (2011 and 2012) were carried out at two sites (Odoyev and Plavsk) in the Tula region of Russia. During these two campaigns, observations were made at selected winter-wheat fields consisting of phenological stage, biomass samples, hemispherical photographs, spectral properties of the canopy and the soil as well as ancillary information about the field. Meteorological observations from synoptic and agrometeorological stations were collected from the stations in and surrounding the Tula region. Finally, a large trajectory throughout the whole Tula region was surveyed in order to collect fields with different crop types.
Data-Driven Modeling of Intracellular Auxin Fluxes Indicates a Dominant Role of the ER in Controlling Nuclear Auxin Uptake
Middleton, Alistair M. ; Bosco, Cristina Dal; Chlap, Phillip ; Bensch, Robert ; Harz, Hartmann ; Ren, Fugang ; Bergmann, Stefan ; Wend, Sabrina ; Weber, Wilfried ; Hayashi, Ken Ichiro ; Zurbriggen, Matias D. ; Uhl, Rainer ; Ronneberger, Olaf ; Palme, Klaus ; Fleck, Christian ; Dovzhenko, Alexander - \ 2018
Cell Reports 22 (2018)11. - ISSN 2211-1247 - p. 3044 - 3057.
auxin - auxin flux - auxin sensor - endoplasmic reticulum - fluorescent aux - mathematical modeling - microscopy - nucleus - protoplasts - single cells
In plants, the phytohormone auxin acts as a master regulator of developmental processes and environmental responses. The best characterized process in the auxin regulatory network occurs at the subcellular scale, wherein auxin mediates signal transduction into transcriptional programs by triggering the degradation of Aux/IAA transcriptional repressor proteins in the nucleus. However, whether and how auxin movement between the nucleus and the surrounding compartments is regulated remain elusive. Using a fluorescent auxin analog, we show that its diffusion into the nucleus is restricted. By combining mathematical modeling with time course assays on auxin-mediated nuclear signaling and quantitative phenotyping in single plant cell systems, we show that ER-to-nucleus auxin flux represents a major subcellular pathway to directly control nuclear auxin levels. Our findings propose that the homeostatically regulated auxin pool in the ER and ER-to-nucleus auxin fluxes underpin auxin-mediated downstream responses in plant cells. Middleton et al. study how the plant phytohormone auxin enters the nucleus by using quantitative phenotyping in single plant cell systems and bespoke mathematical models that relate controlled perturbations to experimentally measurable responses. Their findings show that auxin predominantly enters the nucleus via the endoplasmic reticulum.
Publisher Correction to : Background invertebrate herbivory on dwarf birch (Betula glandulosa-nana complex) increases with temperature and precipitation across the tundra biome
Barrio, Isabel C. ; Lindén, Elin ; Beest, Mariska Te; Olofsson, Johan ; Rocha, Adrian ; Soininen, Eeva M. ; Alatalo, Juha M. ; Andersson, Tommi ; Asmus, Ashley ; Boike, Julia ; Bråthen, Kari Anne ; Bryant, John P. ; Buchwal, Agata ; Bueno, C.G. ; Christie, Katherine S. ; Egelkraut, Dagmar ; Ehrich, Dorothee ; Fishback, Lee Ann ; Forbes, Bruce C. ; Gartzia, Maite ; Grogan, Paul ; Hallinger, Martin ; Heijmans, Monique M.P.D. ; Hik, David S. ; Hofgaard, Annika ; Holmgren, Milena ; Høye, Toke T. ; Huebner, Diane C. ; Jónsdóttir, Ingibjörg Svala ; Kaarlejärvi, Elina ; Kumpula, Timo ; Lange, Cynthia Y.M.J.G. ; Lange, Jelena ; Lévesque, Esther ; Limpens, Juul ; Macias-Fauria, Marc ; Myers-Smith, Isla ; Nieukerken, Erik J. van; Normand, Signe ; Post, Eric S. ; Schmidt, Niels Martin ; Sitters, Judith ; Skoracka, Anna ; Sokolov, Alexander ; Sokolova, Natalya ; Speed, James D.M. ; Street, Lorna E. ; Sundqvist, Maja K. ; Suominen, Otso ; Tananaev, Nikita ; Tremblay, Jean Pierre ; Urbanowicz, Christine ; Uvarov, Sergey A. ; Watts, David ; Wilmking, Martin ; Wookey, Philip A. ; Zimmermann, Heike H. ; Zverev, Vitali ; Kozlov, Mikhail V. - \ 2018
Polar Biology (2018). - ISSN 0722-4060 - p. 1 - 2.
The above mentioned article was originally scheduled for publication in the special issue on Ecology of Tundra Arthropods with guest editors Toke T. Høye . Lauren E. Culler. Erroneously, the article was published in Polar Biology, Volume 40, Issue 11, November, 2017. The publisher sincerely apologizes to the guest editors and the authors for the inconvenience caused.
New perspectives on the ecology of tree structure and tree communities through terrestrial laser scanning
Malhi, Yadvinder ; Jackson, Tobias ; Bentley, Lisa Patrick ; Lau, Alvaro ; Shenkin, Alexander ; Herold, Martin ; Calders, Kim ; Bartholomeus, Harm ; Disney, Mathias I. - \ 2018
Interface Focus 8 (2018)2. - ISSN 2042-8898
Branching - Metabolic scaling theory - Terrestrial laser scanning - Tree architecture - Tree surface area - Wind speed
Terrestrial laser scanning (TLS) opens up the possibility of describing the three-dimensional structures of trees in natural environments with unprecedented detail and accuracy. It is already being extensively applied to describe how ecosystem biomass and structure vary between sites, but can also facilitate major advances in developing and testing mechanistic theories of tree form and forest structure, thereby enabling us to understand why trees and forests have the biomass and three-dimensional structure they do. Here we focus on the ecological challenges and benefits of understanding tree form, and highlight some advances related to capturing and describing tree shape that are becoming possible with the advent of TLS. We present examples of ongoing work that applies, or could potentially apply, new TLS measurements to better understand the constraints on optimization of tree form. Theories of resource distribution networks, such as metabolic scaling theory, can be tested and further refined. TLS can also provide new approaches to the scaling of woody surface area and crown area, and thereby better quantify the metabolism of trees. Finally, we demonstrate how we can develop a more mechanistic understanding of the effects of avoidance of wind risk on tree form and maximum size. Over the next few years, TLS promises to deliver both major empirical and conceptual advances in the quantitative understanding of trees and tree-dominated ecosystems, leading to advances in understanding the ecology of why trees and ecosystems look and grow the way they do.
Responsible Research and Innovation in industry-challenges, insights and perspectives
Martinuzzi, André ; Blok, Vincent ; Brem, Alexander ; Stahl, Bernd ; Schönherr, Norma - \ 2018
Sustainability 10 (2018)3. - ISSN 2071-1050
Business ethics - Corporate social responsibility - CSR - Industry - R and D management - Responsible innovation - Responsible research and innovation - RRI - Social innovation - Sustainable innovation
The responsibility of industry towards society and the environment is a much discussed topic, both in academia and in business. Responsible Research and Innovation (RRI) has recently emerged as a new concept with the potential to advance this discourse in light of two major challenges industry is facing today. The first relates to the accelerating race to innovate in order to stay competitive in a rapidly changing world. The second concerns the need to maintain public trust in industry through innovations that generate social value in addition to economic returns. This Special Issue provides empirical and conceptual contributions that explore corporate motivations to adopt RRI, the state of implementation of concrete RRI practices, the role of stakeholders in responsible innovation processes, as well as drivers and barriers to the further diffusion of RRI in industry. Overall, these contributions highlight the relevance of RRI for firms of different sizes and sectors. They also provide insights and suggestions for managers, policymakers and researchers wishing to engage with responsibility in innovation. This editorial summarizes the most pertinent conclusions across the individual articles published in this Special Issue and concludes by outlining some fruitful avenues for future research in this space.
The Impact of Three-Dimensional Effects on the Simulation of Turbulence Kinetic Energy in a Major Alpine Valley
Goger, Brigitta ; Rotach, Mathias W. ; Gohm, Alexander ; Fuhrer, Oliver ; Stiperski, Ivana ; Holtslag, A.A.M. - \ 2018
Boundary-Layer Meteorology 168 (2018)1. - ISSN 0006-8314 - p. 1 - 27.
The correct simulation of the atmospheric boundary layer (ABL) is crucial for reliable weather forecasts in truly complex terrain. However, common assumptions for model parametrizations are only valid for horizontally homogeneous and flat terrain. Here, we evaluate the turbulence parametrization of the numerical weather prediction model COSMO with a horizontal grid spacing of Δx=1.1km
for the Inn Valley, Austria. The long-term, high-resolution turbulence measurements of the i-Box measurement sites provide a useful data pool of the ABL structure in the valley and on slopes. We focus on days and nights when ABL processes dominate and a thermally-driven circulation is present. Simulations are performed for case studies with both a one-dimensional turbulence parametrization, which only considers the vertical turbulent exchange, and a hybrid turbulence parametrization, also including horizontal shear production and advection in the budget of turbulence kinetic energy (TKE). We find a general underestimation of TKE by the model with the one-dimensional turbulence parametrization. In the simulations with the hybrid turbulence parametrization, the modelled TKE has a more realistic structure, especially in situations when the TKE production is dominated by shear related to the afternoon up-valley flow, and during nights, when a stable ABL is present. The model performance also improves for stations on the slopes. An estimation of the horizontal shear production from the observation network suggests that three-dimensional effects are a relevant part of TKE production in the valley.
Corrigendum to A genome-wide association study identifies nucleotide variants at SIGLEC5 and DEFA1A3 as risk loci for periodontitis
Munz, Matthias ; Willenborg, Christina ; Richter, Gesa M. ; Jockel-Schneider, Yvonne ; Graetz, Christian ; Staufenbiel, Ingmar ; Wellmann, Jürgen ; Berger, Klaus ; Krone, Bastian ; Hoffmann, Per ; Velde, Nathalie Van Der; Uitterlinden, André G. ; Groot, C.P.G.M. De; Sawalha, Amr H. ; Direskeneli, Haner ; Saruhan-Direskeneli, Güher ; Guzeldemir-Akcakanat, Esra ; Keceli, Huseyin Gencay ; Laudes, Matthias ; Noack, Barbara ; Teumer, Alexander ; Holtfreter, Birte ; Kocher, Thomas ; Eickholz, Peter ; Meyle, Jörg ; Doerfer, Christof ; Bruckmann, Corinna ; Lieb, Wolfgang ; Franke, Andre ; Schreiber, Stefan ; Nohutcu, Rahime M. ; Erdmann, Jeanette ; Loos, Bruno G. ; Jepsen, Soeren ; Dommisch, Henrik ; Schaefer, Arne S. - \ 2018
Human Molecular Genetics 27 (2018)5. - ISSN 0964-6906 - p. 941 - 942.
Out of the pot and into the fire : Explaining the vulnerability of an endangered small headwater stream fish to black-bass Micropterus spp. invasion
Ellender, B.R. ; Weyl, O.L.F. ; Alexander, M.E. ; Luger, A.M. ; Nagelkerke, L.A.J. ; Woodford, D.J. - \ 2018
Journal of Fish Biology 92 (2018)4. - ISSN 0022-1112 - p. 1035 - 1050.
Behaviour - Endangered fish - Evolutionary response - Micropterus - Naïveté - Pseudobarbus afer
Introduced predatory fishes have had consistently severe consequences for native fishes in stream environments around the world, although the drivers of these effects are often unclear. In the Swartkops River headwaters in South Africa, native Eastern Cape redfin Pseudobarbus afer were always absent from sites occupied by non-native black basses Micropterus salmoides and Micropterus dolomieu, but generally co-occurred with the native predators Anguilla marmorata and Anguilla mossambica. A natural experiment provided by flood-mediated recolonization of black-bass occupied sites by P. afer demonstrated depletion in black-bass invaded sites. Field behavioural observations of P. afer indicated that they foraged among benthic cover during the day, but suspended in open water at night. As the nocturnal A. marmorata and A. mossambica foraged actively within structural cover at night and M. dolomieu and M. salmoides are diurnal or crepuscular predators, P .afer is thus optimized to avoid predation by native anguillid predators and not the functionally unique predatory black basses. The integration of distributional, temporal population dynamics and behavioural data suggests that the severe effects of Micropterus spp. are probably a consequence of prey naïveté and behaviour evolved to evade native predators.
Design of triphasic poly(lactic-co-glycolic acid) nanoparticles containing a perfluorocarbon phase for biomedical applications
Swider, Edyta ; Staal, Alexander H.J. ; Riessen, N. Van; Jacobs, Linsey ; White, Paul B. ; Fokkink, Remco ; Janssen, Geert Jan ; Dinther, Eric Van; Figdor, Carl G. ; Vries, I.J.M. De; Koshkina, Olga ; Srinivas, Mangala - \ 2018
RSC Advances : An international journal to further the chemical sciences 8 (2018)12. - ISSN 2046-2069 - p. 6460 - 6470.
Poly(lactic-co-glycolic acid) (PLGA) particles are very widely used, particularly for drug delivery, including commercial clinical formulations. Adding perfluorocarbon (PFC) enables in vivo imaging and quantification of the PLGA particles through 19F NMR, MRS or MRI. PFCs are both hydrophobic and lipophobic at the same time. This property makes their encapsulation in particles challenging, as it requires the addition of a third immiscible phase during the emulsification process. Here we explore how different parameters affect the miniemulsion formation of particles loaded with perfluoro-15-crown-5-ether (PFCE). By changing the concentration of surfactant and type of solvent, we were able to control the radius of synthesized particles, between 85-200 nm. We assessed stability and release from the particles at different pH values, showing that hydrophobic agents are released from the particles by diffusion rather than degradation. With cell experiments, we show that primary human dendritic cells take up the particles without any apparent effect, including on cell migration. In summary, the control of synthesis conditions leads to particles with sufficient PFCE encapsulation, which are suitable for drug loading and cell labeling, and do not affect cell viability or functionality. Finally, these nanoparticles can be produced at GMP-grade for clinical use.
Dissipative disassembly of colloidal microgel crystals driven by a coupled cyclic reaction network
Go, Dennis ; Rommel, Dirk ; Liao, Yi ; Haraszti, Tamás ; Sprakel, Joris ; Kuehne, Alexander J.C. - \ 2018
Soft Matter 14 (2018)6. - ISSN 1744-683X - p. 910 - 915.
A plethora of natural systems rely on the consumption of chemical fuel or input of external energy to control the assembly and disassembly of functional structures on demand. While dissipative assembly has been demonstrated, the control of structural breakdown using a dissipative cycle remains almost unexplored. Here, we propose and realize a dissipative disassembly process using two coupled cyclic reactions, in which protons mediate the interaction between the cycles. We show how an ordered colloidal crystal, can cyclically transform into a disordered state by addition of energy to a chemical cycle, reversibly activating a photoacid. This cycle is coupled to the colloidal assembly cycle via the exchange of protons, which in turn trigger charging of the particles. This system is an experimental realization of a cyclic reaction-assembly network and its principle can be extended to other types of structure formation.
Modeling vegetation and carbon dynamics of managed grasslands at the global scale with LPJmL 3.6
Rolinski, Susanne ; Müller, Christoph ; Heinke, Jens ; Weindl, Isabelle ; Biewald, Anne ; Leon Bodirsky, Benjamin ; Bondeau, Alberte ; Boons-Prins, Eltje R. ; Bouwman, Alexander F. ; Leffelaar, Peter A. ; Roller, Johnny A. te; Schaphoff, Sibyll ; Thonicke, Kirsten - \ 2018
Geoscientific Model Development 11 (2018)1. - ISSN 1991-959X - p. 429 - 451.
Grassland management affects the carbon fluxes of one-third of the global land area and is thus an important factor for the global carbon budget. Nonetheless, this aspect has been largely neglected or underrepresented in global carbon cycle models. We investigate four harvesting schemes for the managed grassland implementation of the dynamic global vegetation model (DGVM) Lund-Potsdam-Jena managed Land (LPJmL) that facilitate a better representation of actual management systems globally. We describe the model implementation and analyze simulation results with respect to harvest, net primary productivity and soil carbon content and by evaluating them against reported grass yields in Europe.We demonstrate the importance of accounting for differences in grassland management by assessing potential livestock grazing densities as well as the impacts of grazing, grazing intensities and mowing systems on soil carbon stocks. Grazing leads to soil carbon losses in polar or arid regions even at moderate livestock densities ( < 0.4 livestock units per hectare-LSUha -1 ) but not in temperate regions even at much higher densities (0.4 to 1.2 LSUha -1 ). Applying LPJmL with the new grassland management options enables assessments of the global grassland production and its impact on the terrestrial biogeochemical cycles but requires a global data set on current grassland management.
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