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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Priorities and opportunities in the application of the ecosystem services concept in risk assessment for chemicals in the environment
Faber, J.H. ; Marshall, Stuart ; Brink, P.J. van den; Maltby, Lorraine - \ 2019
Science of the Total Environment 651 (2019). - ISSN 0048-9697 - p. 1067 - 1077.
The ecosystem services approach has gained broad interest in regulatory and policy circles for use in ecological risk assessment. Whilst identifying several challenges, scientific experts from European regulatory authorities,
the chemical industry and academia considered the approach applicable to all chemical sectors and potentially contributing to greater ecological relevance for setting and assessing environmental protection goals compared to current European regulatory frameworks for chemicals. These challengeswere addressed in workshops to develop a common understanding across stakeholders on how the ecosystem services concept might be used in chemical risk assessment and what would need to be done to implement it. This paper describes the consensus
outcome of those discussions. Knowledge gaps and research needs were identified and prioritised, exploring the use of novel approaches from ecology, ecotoxicology and ecological modelling. Where applicable, distinction is
made between prospective and retrospective ecological risk assessment. For prospective risk assessment the development of environmental scenarios accounting for chemical exposure and ecological conditions was designated
as a top priority. For retrospective risk assessment the top priority research need was development of reference conditions for key ecosystem services and guidance for their derivation. Both prospective and retrospective
risk assessment would benefit from guidance on the taxa and measurement endpoints relevant to specific ecosystem services and from improved understanding of the relationships between measurement endpoints
fromstandard toxicity tests and the ecosystemservices of interest (i.e. assessment endpoints). The development of mechanistic models, which could serve as ecological production functions, was identified as a priority.
A conceptual framework for future chemical risk assessment based on an ecosystem services approach is presented.
presented.
©
Addressing global ruminant agricultural challenges through understanding the rumen microbiome : Past, present, and future
Huws, Sharon A. ; Creevey, Christopher J. ; Oyama, Linda B. ; Mizrahi, Itzhak ; Denman, Stuart E. ; Popova, Milka ; Muñoz-Tamayo, Rafael ; Forano, Evelyne ; Waters, Sinead M. ; Hess, Matthias ; Tapio, Ilma ; Smidt, Hauke ; Krizsan, Sophie J. ; Yáñez-Ruiz, David R. ; Belanche, Alejandro ; Guan, Leluo ; Gruninger, Robert J. ; McAllister, Tim A. ; Newbold, C.J. ; Roehe, Rainer ; Dewhurst, Richard J. ; Snelling, Tim J. ; Watson, Mick ; Suen, Garret ; Hart, Elizabeth H. ; Kingston-Smith, Alison H. ; Scollan, Nigel D. ; Prado, Rodolpho M. Do; Pilau, Eduardo J. ; Mantovani, Hilario C. ; Attwood, Graeme T. ; Edwards, Joan E. ; McEwan, Neil R. ; Morrisson, Steven ; Mayorga, Olga L. ; Elliott, Christopher ; Morgavi, Diego P. - \ 2018
Frontiers in Microbiology 9 (2018)SEP. - ISSN 1664-302X
Diet - Host - Methane - Microbiome - Omics - Production - Rumen

The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi, methanogenic archaea and phages. These microbes interact closely to breakdown plant material that cannot be digested by humans, whilst providing metabolic energy to the host and, in the case of archaea, producing methane. Consequently, ruminants produce meat and milk, which are rich in high-quality protein, vitamins and minerals, and therefore contribute to food security. As the world population is predicted to reach approximately 9.7 billion by 2050, an increase in ruminant production to satisfy global protein demand is necessary, despite limited land availability, and whilst ensuring environmental impact is minimized. Although challenging, these goals can be met, but depend on our understanding of the rumen microbiome. Attempts to manipulate the rumen microbiome to benefit global agricultural challenges have been ongoing for decades with limited success, mostly due to the lack of a detailed understanding of this microbiome and our limited ability to culture most of these microbes outside the rumen. The potential to manipulate the rumen microbiome and meet global livestock challenges through animal breeding and introduction of dietary interventions during early life have recently emerged as promising new technologies. Our inability to phenotype ruminants in a high-throughput manner has also hampered progress, although the recent increase in "omic" data may allow further development of mathematical models and rumen microbial gene biomarkers as proxies. Advances in computational tools, high-throughput sequencing technologies and cultivation-independent "omics" approaches continue to revolutionize our understanding of the rumen microbiome. This will ultimately provide the knowledge framework needed to solve current and future ruminant livestock challenges.

Chimeric O1K foot-and-mouth disease virus with SAT2 outer capsid as an FMD vaccine candidate
Kotecha, Abhay ; Perez-Martin, Eva ; Harvey, Yongjie ; Zhang, Fuquan ; Ilca, Serban L. ; Fry, Elizabeth E. ; Jackson, Ben ; Maree, Francois ; Scott, Katherine ; Hecksel, Corey W. ; Harmsen, Michiel M. ; Mioulet, Valérie ; Wood, Britta ; Juleff, Nick ; Stuart, David I. ; Charleston, Bryan ; Seago, Julian - \ 2018
Scientific Reports 8 (2018)1. - ISSN 2045-2322

Foot-and-mouth disease virus (FMDV) is highly contagious and infects cloven-hoofed domestic livestock leading to foot-and-mouth disease (FMD). FMD outbreaks have severe economic impact due to production losses and associated control measures. FMDV is found as seven distinct serotypes, but there are numerous subtypes within each serotype, and effective vaccines must match the subtypes circulating in the field. In addition, the O and Southern African Territories (SAT) serotypes, are relatively more thermolabile and their viral capsids readily dissociate into non-immunogenic pentameric subunits, which can compromise the effectiveness of FMD vaccines. Here we report the construction of a chimeric clone between the SAT2 and O serotypes, designed to have SAT2 antigenicity. Characterisation of the chimeric virus showed growth kinetics equal to that of the wild type SAT2 virus with better thermostability, attributable to changes in the VP4 structural protein. Sequence and structural analyses confirmed that no changes from SAT2 were present elsewhere in the capsid as a consequence of the VP4 changes. Following exposure to an elevated temperature the thermostable SAT2-O1K chimera induced higher neutralizing-antibody titres in comparison to wild type SAT2 virus.

ICTV virus taxonomy profile : Baculoviridae
Harrison, Robert L. ; Herniou, Elisabeth A. ; Jehle, Johannes A. ; Theilmann, David A. ; Burand, John P. ; Becnel, James J. ; Krell, Peter J. ; Oers, Monique M. van; Mowery, Joseph D. ; Bauchan, Gary R. ; Lefkowitz, Elliot J. ; Davison, Andrew J. ; Siddell, Stuart G. ; Simmonds, Peter ; Sabanadzovic, Sead ; Smith, Donald B. ; Orton, Richard J. ; Harrach, Balázs - \ 2018
Journal of General Virology 99 (2018)9. - ISSN 0022-1317 - p. 1185 - 1186.
Baculoviridae - ICTV Report - Taxonomy

The family Baculoviridae comprises large viruses with circular dsDNA genomes ranging from 80 to 180 kbp. The virions consist of enveloped, rod-shaped nucleocapsids and are embedded in distinctive occlusion bodies measuring 0.15–5 µm. The occlusion bodies consist of a matrix composed of a single viral protein expressed at high levels during infection. Members of this family infect exclusively larvae of the insect orders Lepidoptera, Hymenoptera and Diptera. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Baculoviridae, which is available at www.ictv.global/report/baculoviridae.

Toward sustainable environmental quality : Priority research questions for Europe
Brink, Paul J. Van den; Boxall, Alistair B.A. ; Maltby, Lorraine ; Brooks, Bryan W. ; Rudd, Murray A. ; Backhaus, Thomas ; Spurgeon, David ; Verougstraete, Violaine ; Ajao, Charmaine ; Ankley, Gerald T. ; Apitz, Sabine E. ; Arnold, Kathryn ; Brodin, Tomas ; Cañedo-Argüelles, Miguel ; Chapman, Jennifer ; Corrales, Jone ; Coutellec, Marie Agnès ; Fernandes, Teresa F. ; Fick, Jerker ; Ford, Alex T. ; Giménez Papiol, Gemma ; Groh, Ksenia J. ; Hutchinson, Thomas H. ; Kruger, Hank ; Kukkonen, Jussi V.K. ; Loutseti, Stefania ; Marshall, Stuart ; Muir, Derek ; Ortiz-Santaliestra, Manuel E. ; Paul, Kai B. ; Rico, Andreu ; Rodea-Palomares, Ismael ; Römbke, Jörg ; Rydberg, Tomas ; Segner, Helmut ; Smit, Mathijs ; Gestel, Cornelis A.M. van; Vighi, Marco ; Werner, Inge ; Zimmer, Elke I. ; Wensem, Joke van - \ 2018
Environmental Toxicology and Chemistry 37 (2018)9. - ISSN 0730-7268 - p. 2281 - 2295.
Chemical management - Environmental risk assessment - Global megatrends - Key questions exercise - Sustainability

The United Nations' Sustainable Development Goals have been established to end poverty, protect the planet, and ensure prosperity for all. Delivery of the Sustainable Development Goals will require a healthy and productive environment. An understanding of the impacts of chemicals which can negatively impact environmental health is therefore essential to the delivery of the Sustainable Development Goals. However, current research on and regulation of chemicals in the environment tend to take a simplistic view and do not account for the complexity of the real world, which inhibits the way we manage chemicals. There is therefore an urgent need for a step change in the way we study and communicate the impacts and control of chemicals in the natural environment. To do this requires the major research questions to be identified so that resources are focused on questions that really matter. We present the findings of a horizon-scanning exercise to identify research priorities of the European environmental science community around chemicals in the environment. Using the key questions approach, we identified 22 questions of priority. These questions covered overarching questions about which chemicals we should be most concerned about and where, impacts of global megatrends, protection goals, and sustainability of chemicals; the development and parameterization of assessment and management frameworks; and mechanisms to maximize the impact of the research. The research questions identified provide a first-step in the path forward for the research, regulatory, and business communities to better assess and manage chemicals in the natural environment.

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 163 (2018)8. - ISSN 0304-8608 - p. 2295 - 2310.
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.
Electrostatic stiffening and induced persistence length for coassembled molecular bottlebrushes
Storm, Ingeborg M. ; Stuart, Martien A.C. ; Vries, Renko de; Leermakers, Frans A.M. - \ 2018
Physical Review. E, Statistical nonlinear, and soft matter physics 97 (2018)3. - ISSN 2470-0045
A self-consistent field analysis for tunable contributions to the persistence length of isolated semiflexible polymer chains including electrostatically driven coassembled deoxyribonucleic acid (DNA) bottlebrushes is presented. When a chain is charged, i.e., for polyelectrolytes, there is, in addition to an intrinsic rigidity, an electrostatic stiffening effect, because the electric double layer resists bending. For molecular bottlebrushes, there is an induced contribution due to the grafts. We explore cases beyond the classical phantom main-chain approximation and elaborate molecularly more realistic models where the backbone has a finite volume, which is necessary for treating coassembled bottlebrushes. We find that the way in which the linear charge density or the grafting density is regulated is important. Typically, the stiffening effect is reduced when there is freedom for these quantities to adapt to the curvature stresses. Electrostatically driven coassembled bottlebrushes, however, are relatively stiff because the chains have a low tendency to escape from the compressed regions and the electrostatic binding force is largest in the convex part. For coassembled bottlebrushes, the induced persistence length is a nonmonotonic function of the polymer concentration: For low polymer concentrations, the stiffening grows quadratically with coverage; for semidilute polymer concentrations, the brush chains retract and regain their Gaussian size. When doing so, they lose their induced persistence length contribution. Our results correlate well with observed physical characteristics of electrostatically driven coassembled DNA-bioengineered protein-polymer bottlebrushes.
Force and Scale Dependence of the Elasticity of Self-Assembled DNA Bottle Brushes
Rocha, Márcio Santos ; Storm, Ingeborg M. ; Bazoni, Raniella Falchetto ; Ramos, Ésio Bessa ; Hernandez-Garcia, Armando ; Cohen Stuart, Martien A. ; Leermakers, Frans ; Vries, Renko De - \ 2018
Macromolecules 51 (2018)1. - ISSN 0024-9297 - p. 204 - 212.
As a model system to study the elasticity of bottle-brush polymers, we here introduce self-assembled DNA bottle brushes, consisting of a DNA main chain that can be very long and still of precisely defined length, and precisely monodisperse polypeptide side chains that are physically bound to the DNA main chains. Polypeptide side chains have a diblock architecture, where one block is a small archaeal nucleoid protein Sso7d that strongly binds to DNA. The other block is a net neutral, hydrophilic random coil polypeptide with a length of exactly 798 amino acids. Light scattering shows that for saturated brushes the grafting density is one side chain per 5.6 nm of DNA main chain. According to small-angle X-ray scattering, the brush diameter is D = 17 nm. By analyzing configurations of adsorbed DNA bottle brushes using AFM, we find that the effective persistence of the saturated DNA bottle brushes is Peff = 95 nm, but from force-extension curves of single DNA bottle brushes measured using optical tweezers we find Peff = 15 nm. The latter is equal to the value expected for DNA coated by the Sso7d binding block alone. The apparent discrepancy between the two measurements is rationalized in terms of the scale dependence of the bottle-brush elasticity using theory previously developed to analyze the scale-dependent electrostatic stiffening of DNA at low ionic strengths.
Advantages and challenges associated with implementing an ecosystem services approach to ecological risk assessment for chemicals
Maltby, Lorraine ; Brink, Paul J. van den; Faber, Jack H. ; Marshall, Stuart - \ 2018
Science of the Total Environment 621 (2018). - ISSN 0048-9697 - p. 1342 - 1351.
Ecological indicators - Ecotoxicity tests - Landscape-scale risk assessment
The ecosystem services (ES) approach is gaining broad interest in regulatory and policy arenas for use in landscape management and ecological risk assessment. It has the potential to bring greater ecological relevance to the setting of environmental protection goals and to the assessment of the ecological risk posed by chemicals. A workshop, organised under the auspices of the Society of Environmental Toxicology and Chemistry Europe, brought together scientific experts from European regulatory authorities, the chemical industry and academia to discuss and evaluate the challenges associated with implementing an ES approach to chemical ecological risk assessment (ERA).Clear advantages of using an ES approach in prospective and retrospective ERA were identified, including: making ERA spatially explicit and of relevance to management decisions (i.e. indicating what ES to protect and where); improving transparency in communicating risks and trade-offs; integrating across multiple stressors, scales, habitats and policies. A number of challenges were also identified including: the potential for increased complexity in assessments; greater data requirements; limitations in linking endpoints derived from current ecotoxicity tests to impacts on ES.In principle, the approach was applicable to all chemical sectors, but the scale of the challenge of applying an ES approach to general chemicals with widespread and dispersive uses leading to broad environmental exposure, was highlighted. There was agreement that ES-based risk assessment should be based on the magnitude of impact rather than on toxicity thresholds. The need for more bioassays/tests with functional endpoints was recognized, as was the role of modelling and the need for ecological production functions to link measurement endpoints to assessment endpoints. Finally, the value of developing environmental scenarios that can be combined with spatial information on exposure, ES delivery and service provider vulnerability was recognized.
Supplementary material from "Increased SBPase activity improves photosynthesis and grain yield in wheat grown in greenhouse conditions"
Driever, S.M. ; Simkin, Andrew J. ; Alotaibi, Saqer ; Fisk, Stuart J. ; Madgwick, Pippa J. ; Sparks, Caroline A. ; Jones, Huw D. ; Lawson, Tracy ; Parry, Martin A.J. ; Raines, Christine A. - \ 2017
sedoheptulose-1 - 7-biphosphatase - Calvin-Benson cycle - transgenic - biomass - yield
To meet the growing demand for food, substantial improvements in yields are needed. This is particularly the case for wheat, where global yield has stagnated in recent years. Increasing photosynthesis has been identified as a primary target to achieve yield improvements. To increase leaf photosynthesis in wheat, the level of the Calvin–Benson cycle enzyme sedoheptulose-1,7-biphosphatase (SBPase) has been increased through transformation and expression of a Brachypodium distachyon SBPase gene construct. Transgenic lines with increased SBPase protein levels and activity were grown under greenhouse conditions and showed enhanced leaf photosynthesis and increased total biomass and dry seed yield. This showed the potential of improving yield potential by increasing leaf photosynthesis in a crop species such as wheat. The results are discussed with regards to future strategies for further improvement of photosynthesis in wheat.This article is part of the themed issue ‘Enhancing photosynthesis in crop plants: targets for improvement’.
Templated co-assembly into nanorods of polyanions and artificial virus capsid proteins
Hernandez-Garcia, A. ; Cohen Stuart, M.A. ; Vries, R. De - \ 2017
Soft Matter 14 (2017)1. - ISSN 1744-683X - p. 132 - 139.
Recombinant triblock polypeptides C-Sn-B, where C is a 400 amino acid long hydrophilic random coil block, Sn is a multimer of the silk-like octapeptide S = (GAGAGAGQ), and B = K12 is an oligolysine, have previously been shown to encapsulate double stranded DNA into rod-shaped, virus-like particles. In order to gain insight of the co-assembly process, and in order to be able to use these proteins for templating other types of nanorods, we here explore their co-assembly with a range of polyanionic templates: poly(acrylic acids) (PAA) of a wide range of lengths, poly(styrene sulphonate) (PSS) and the stiff anionic polysaccharide xanthan. The formation of the complexes was characterized using Dynamic Light Scattering (DLS), cryogenic Transmission Electronic Microscopy (Cryo-TEM) and Atomic Force Microscopy (AFM). Except at very high molar masses, we find that flexible anionic PAA and PSS lead to co-assembly of proteins with single polyanion chains into nanorods, with a packing factor as expected on the basis of charge stochiometry. Only for very long PAA templates (8 × 105 Da) we find evidence for heterogeneous complexes with thin and thick sections. For the very stiff xanthan chains, we find that its stiffness precludes co-assembly with the artificial viral capsid proteins into condensed and regular nanorods. Given the simple and robust formation of rod-like structures with a range of polyanionic templates, we anticipate that the artificial virus proteins will be useful for preparing high-aspect ratio nanoparticles and scaffolds of precise size and find applications in nanotechnology and materials science for which currently natural rod-like viruses are being explored.
ICTV virus taxonomy profile : Hepeviridae
Purdy, Michael A. ; Harrison, Tim J. ; Jameel, S. ; Meng, X.J. ; Okamoto, H. ; Poel, W.H.M. Van Der; Smith, Donald B. ; Lefkowitz, Elliot J. ; Davison, Andrew J. ; Siddell, Stuart G. ; Simmonds, Peter ; Adams, Michael J. ; Smith, Donald B. ; Orton, Richard J. ; Knowles, Nick J. - \ 2017
Journal of General Virology 98 (2017)11. - ISSN 0022-1317 - p. 2645 - 2646.
Avian hepatitis E virus - Hepatitis E virus - Hepeviridae - ICTV - Piscihepevirus - Swine hepatitis E virus - Taxonomy
The family Hepeviridae includes enterically transmitted small non-enveloped positive-sense RNA viruses. It includes the genera Piscihepevirus, whose members infect fish, and Orthohepevirus, whose members infect mammals and birds. Members of the genus Orthohepevirus include hepatitis E virus, which is responsible for self-limiting acute hepatitis in humans and several mammalian species; the infection may become chronic in immunocompromised individuals. Extrahepatic manifestations of Guillain–Barré syndrome, neuralgic amyotrophy, glomerulonephritis and pancreatitis have been described in humans. Avian hepatitis E virus causes hepatitis–splenomegaly syndrome in chickens. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Hepeviridae, which is available at www.ictv.global/report/hepeviridae.
Dimensions of biodiversity loss : Spatial mismatch in land-use impacts on species, functional and phylogenetic diversity of European bees
Palma, Adriana De; Kuhlmann, Michael ; Bugter, Rob ; Ferrier, Simon ; Hoskins, Andrew J. ; Potts, Simon G. ; Roberts, Stuart P.M. ; Schweiger, Oliver ; Purvis, Andy - \ 2017
Diversity and Distributions 23 (2017)12. - ISSN 1366-9516 - p. 1435 - 1446.
agricultural intensification - land-use conversion - non-random species loss - pollinator diversity
Aim: Agricultural intensification and urbanization are important drivers of biodiversity change in Europe. Different aspects of bee community diversity vary in their sensitivity to these pressures, as well as independently influencing ecosystem service provision (pollination). To obtain a more comprehensive understanding of human impacts on bee diversity across Europe, we assess multiple, complementary indices of diversity. Location: One Thousand four hundred and forty six sites across Europe. Methods: We collated data on bee occurrence and abundance from the published literature and supplemented them with the PREDICTS database. Using Rao's Quadratic Entropy, we assessed how species, functional and phylogenetic diversity of 1,446 bee communities respond to land-use characteristics including land-use class, cropland intensity, human population density and distance to roads. We combined these models with statistically downscaled estimates of land use in 2005 to estimate and map—at a scale of approximately 1 km2—the losses in diversity relative to semi-natural/natural baseline (the predicted diversity of an uninhabited grid square, consisting only of semi-natural/natural vegetation). Results: We show that—relative to the predicted local diversity in uninhabited semi-natural/natural habitat—half of all EU27 countries have lost over 10% of their average local species diversity and two-thirds of countries have lost over 5% of their average local functional and phylogenetic diversity. All diversity measures were generally lower in pasture and higher-intensity cropland than in semi-natural/natural vegetation, but facets of diversity showed less consistent responses to human population density. These differences have led to marked spatial mismatches in losses: losses in phylogenetic diversity were in some areas almost 20 percentage points (pp.) more severe than losses in species diversity, but in other areas losses were almost 40 pp. less severe. Main conclusions: These results highlight the importance of exploring multiple measures of diversity when prioritizing and evaluating conservation actions, as species-diverse assemblages may be phylogenetically and functionally impoverished, potentially threatening pollination service provision.
Towards ecosystem-based management : identifying operational food-web indicators for marine ecosystems
Tam, Jamie C. ; Link, Jason S. ; Rossberg, Axel G. ; Rogers, Stuart I. ; Levin, Philip S. ; Rochet, Marie-Joelle ; Bundy, Alida ; Belgrano, Andrea ; Libralato, Simone ; Tomczak, Maciej ; Wolfshaar, K.E. van de; Pranovi, Fabio ; Gorokhova, Elena ; Large, Scott I. ; Niquil, Nathalie ; Greenstreet, Simon P.R. ; Druon, Jean-Noel ; Lesutiene, Jurate ; Johansen, Marie ; Preciado, Izaskun ; Patricio, Joana ; Palialexis, Andreas ; Tett, Paul ; Johansen, Geir O. ; Houle, Jennifer ; Rindorf, Anna - \ 2017
ICES Journal of Marine Science 74 (2017)7. - ISSN 1054-3139 - p. 2040 - 2052.
ecoystem-based management - Good environmental status - Indicator selection - integrated ecosystem assessment - marine strategy framework directive
Modern approaches to Ecosystem-Based Management and sustainable use of marine resources must account for the myriad of pressures (interspecies, human and environmental) affecting marine ecosystems. The network of feeding interactions between co-existing species and populations (food webs) are an important aspect of all marine ecosystems and biodiversity. Here we describe and discuss a process to evaluate the selection of operational food-web indicators for use in evaluating marine ecosystem status. This process brought together experts in food-web ecology, marine ecology, and resource management, to identify available indicators that can be used to inform marine management. Standard evaluation criteria (availability and quality of data, conceptual basis, communicability, relevancy to management) were implemented
to identify practical food-web indicators ready for operational use and indicators that hold promise for future use in policy and management. The major attributes of the final suite of operational food-web indicators were structure and functioning. Indicators that represent resilience of the marine ecosystem were less developed. Over 60 potential food-web indicators were evaluated and the final selection of operational food-web indicators includes: the primary production required to sustain a fishery, the productivity of seabirds (or charismatic megafauna), zooplankton indicators, primary productivity, integrated trophic indicators, and the biomass of trophic guilds. More efforts
should be made to develop thresholds-based reference points for achieving Good Environmental Status. There is also a need for international
collaborations to develop indicators that will facilitate management in marine ecosystems used by multiple countries.
Production of protein‐based polymers in Pichia pastoris
Werten, Marc W.T. - \ 2017
University. Promotor(en): Martien Cohen Stuart; Gerrit Eggink, co-promotor(en): Frits de Wolf. - Wageningen : Wageningen University - ISBN 9789463436069 - 241
proteins - polymers - pichia pastoris - gelatin - proteolysis - biosynthesis - eiwitten - polymeren - gelatine - proteolyse - biosynthese

From a chemistry perspective, proteins can be thought of as polymers of amino acids, linked by amide bonds. They feature unsurpassed control over monomer sequence and molecular size. The amino acid sequence of proteins determines their three-dimensional folded structure, resulting in unique properties. Proteins such as collagen, elastin, and silk play a crucial structure-forming role in various tissues and animal architecture such as spider webs. These proteins are characterized by highly repetitive amino acid sequences, and can reversibly self-assemble into supramolecular structures through the formation of noncovalent bonds. These unique properties have sparked the interest of material scientists, and mimics of these proteins have been designed and produced as heterologous proteins in suitable expression systems.

The most commonly employed host for these so-called protein-based polymers, or protein polymers for short, is the bacterium Escherichia coli. In this thesis, we explored the use of an alternative platform, namely the methylotrophic yeast Pichia pastoris (Komagataella phafii). This organism is well-known for its often relatively high yields, and offers a choice between intracellular and secretory production. Secretion of the polymer into the medium provides a highly effective first purification step, and precludes the need for cell disruption procedures that are cost-prohibitive at an industrial scale.

We evaluated the secretory production in P. pastoris of various protein polymers: murine collagen fragments (gelatins), a de novo-designed highly hydrophilic gelatin, silk-like proteins, hydrogel-forming triblock copolymers with collagen-inspired end blocks, block copolymers with heterodimer-forming modules, and silk-inspired triblock copolymers that feature integrin-binding or proteoglycan-binding cell-adhesive motifs. All of these protein polymers were produced at g/L levels, and various bioprocessing and strain engineering strategies were employed to address problems such as proteolytic degradation and other undesired posttranslational modifications. The basic physicochemical properties of the polymers produced were studied, which revealed interesting characteristics. Some of these polymers show promise for further development towards biomedical applications such as tissue engineering and controlled drug release.

Increased sbpase activity improves photosynthesis and grain yield in wheat grown in greenhouse conditions
Driever, Steven M. ; Simkin, Andrew J. ; Alotaibi, Saqer ; Fisk, Stuart J. ; Madgwick, Pippa J. ; Sparks, Caroline A. ; Jones, Huw D. ; Lawson, Tracy ; Parry, Martin A.J. ; Raines, Christine A. - \ 2017
Philosophical Transactions of the Royal Society B. Biological sciences 372 (2017)1730. - ISSN 0962-8436
Biomass - Calvin-Benson cycle - Sedoheptulose-1,7-biphosphatase - Transgenic - Yield
To meet the growing demand for food, substantial improvements in yields are needed. This is particularly the case for wheat, where global yield has stagnated in recent years. Increasing photosynthesis has been identified as a primary target to achieve yield improvements. To increase leaf photosynthesis in wheat, the level of the Calvin–Benson cycle enzyme sedoheptulose-1,7-biphosphatase (SBPase) has been increased through transformation and expression of a Brachypodium distachyon SBPase gene construct. Transgenic lines with increased SBPase protein levels and activity were grown under greenhouse conditions and showed enhanced leaf photosynthesis and increased total biomass and dry seed yield. This showed the potential of improving yield potential by increasing leaf photosynthesis in a crop species such as wheat. The results are discussed with regard to future strategies for further improvement of photosynthesis in wheat. This article is part of the themed issue ‘Enhancing photosynthesis in crop plants: targets for improvement’.
Large meta-analysis of genome-wide association studies identifies five loci for lean body mass
Zillikens, M.C. ; Demissie, Serkalem ; Hsu, Yi Hsiang ; Yerges-Armstrong, Laura M. ; Chou, Wen Chi ; Stolk, Lisette ; Livshits, Gregory ; Broer, Linda ; Johnson, Toby ; Koller, Daniel L. ; Kutalik, Zoltán ; Luan, J.A. ; Malkin, Ida ; Ried, Janina S. ; Smith, Albert V. ; Thorleifsson, Gudmar ; Vandenput, Liesbeth ; Hua Zhao, Jing ; Zhang, Weihua ; Aghdassi, Ali ; Åkesson, Kristina ; Amin, Najaf ; Baier, Leslie J. ; Barroso, Inês ; Bennett, David A. ; Bertram, Lars ; Biffar, Rainer ; Bochud, Murielle ; Boehnke, Michael ; Borecki, Ingrid B. ; Buchman, Aron S. ; Byberg, Liisa ; Campbell, Harry ; Campos Obanda, Natalia ; Cauley, Jane A. ; Cawthon, Peggy M. ; Cederberg, Henna ; Chen, Zhao ; Cho, Nam H. ; Jin Choi, Hyung ; Claussnitzer, Melina ; Collins, Francis ; Cummings, Steven R. ; Jager, Philip L. De; Demuth, Ilja ; Dhonukshe-Rutten, Rosalie A.M. ; DIatchenko, Luda ; Eiriksdottir, Gudny ; Enneman, Anke W. ; Erdos, Mike ; Eriksson, Johan G. ; Eriksson, Joel ; Estrada, Karol ; Evans, Daniel S. ; Feitosa, Mary F. ; Fu, Mao ; Garcia, Melissa ; Gieger, Christian ; Girke, Thomas ; Glazer, Nicole L. ; Grallert, Harald ; Grewal, Jagvir ; Han, Bok Ghee ; Hanson, Robert L. ; Hayward, Caroline ; Hofman, Albert ; Hoffman, Eric P. ; Homuth, Georg ; Hsueh, Wen Chi ; Hubal, Monica J. ; Hubbard, Alan ; Huffman, Kim M. ; Husted, Lise B. ; Illig, Thomas ; Ingelsson, Erik ; Ittermann, Till ; Jansson, John Olov ; Jordan, Joanne M. ; Jula, Antti ; Karlsson, Magnus ; Khaw, Kay Tee ; Kilpelaïnen, Tuomas O. ; Klopp, Norman ; Kloth, Jacqueline S.L. ; Koistinen, Heikki A. ; Kraus, William E. ; Kritchevsky, Stephen ; Kuulasmaa, Teemu ; Kuusisto, Johanna ; Laakso, Markku ; Lahti, Jari ; Lang, Thomas ; Langdahl, Bente L. ; Launer, Lenore J. ; Lee, Jong Young ; Lerch, Markus M. ; Lewis, Joshua R. ; Lind, Lars ; Lindgren, Cecilia M. ; Liu, Yongmei ; Liu, Tian ; Liu, Youfang ; Ljunggren, Östen ; Lorentzon, Mattias ; Luben, Robert N. ; Maixner, William ; McGuigan, Fiona E. ; Medina-Gomez, Carolina ; Meitinger, Thomas ; Melhus, Håkan ; Mellström, Dan ; Melov, Simon ; Michaëlsson, Karl ; Mitchell, Braxton D. ; Morris, Andrew P. ; Mosekilde, Leif ; Newman, Anne ; Nielson, Carrie M. ; O'Connell, Jeffrey R. ; Oostra, Ben A. ; Orwoll, Eric S. ; Palotie, Aarno ; Parker, Stephan ; Peacock, Munro ; Perola, Markus ; Peters, Annette ; Polasek, Ozren ; Prince, Richard L. ; Raïkkönen, Katri ; Ralston, Stuart H. ; Ripatti, Samuli ; Robbins, John A. ; Rotter, Jerome I. ; Rudan, Igor ; Salomaa, Veikko ; Satterfield, Suzanne ; Schadt, Eric E. ; Schipf, Sabine ; Scott, Laura ; Sehmi, Joban ; Shen, Jian ; Soo Shin, Chan ; Sigurdsson, Gunnar ; Smith, Shad ; Soranzo, Nicole ; Stančáková, Alena ; Steinhagen-Thiessen, Elisabeth ; Streeten, Elizabeth A. ; Styrkarsdottir, Unnur ; Swart, Karin M.A. ; Tan, Sian Tsung ; Tarnopolsky, Mark A. ; Thompson, Patricia ; Thomson, Cynthia A. ; Thorsteinsdottir, Unnur ; Tikkanen, Emmi ; Tranah, Gregory J. ; Tuomilehto, Jaakko ; Schoor, Natasja M. van; Verma, Arjun ; Vollenweider, Peter ; Völzke, Henry ; Wactawski-Wende, Jean ; Walker, Mark ; Weedon, Michael N. ; Welch, Ryan ; Wichman, H.E. ; Widen, Elisabeth ; Williams, Frances M.K. ; Wilson, James F. ; Wright, Nicole C. ; Xie, Weijia ; Yu, Lei ; Zhou, Yanhua ; Chambers, John C. ; Döring, Angela ; Duijn, Cornelia M. Van; Econs, Michael J. ; Gudnason, Vilmundur ; Kooner, Jaspal S. ; Psaty, Bruce M. ; Spector, Timothy D. ; Stefansson, Kari ; Rivadeneira, Fernando ; Uitterlinden, André G. ; Wareham, Nicholas J. ; Ossowski, Vicky ; Waterworth, Dawn M. ; Loos, Ruth J.F. ; Karasik, David ; Harris, Tamara B. ; Ohlsson, Claes ; Kiel, Douglas P. - \ 2017
Nature Communications 8 (2017)1. - ISSN 2041-1723
Lean body mass, consisting mostly of skeletal muscle, is important for healthy aging. We performed a genome-wide association study for whole body (20 cohorts of European ancestry with n = 38,292) and appendicular (arms and legs) lean body mass (n = 28,330) measured using dual energy X-ray absorptiometry or bioelectrical impedance analysis, adjusted for sex, age, height, and fat mass. Twenty-one single-nucleotide polymorphisms were significantly associated with lean body mass either genome wide (p < 5 × 10-8) or suggestively genome wide (p < 2.3 × 10-6). Replication in 63,475 (47,227 of European ancestry) individuals from 33 cohorts for whole body lean body mass and in 45,090 (42,360 of European ancestry) subjects from 25 cohorts for appendicular lean body mass was successful for five single-nucleotide polymorphisms in/near HSD17B11, VCAN, ADAMTSL3, IRS1, and FTO for total lean body mass and for three single-nucleotide polymorphisms in/near VCAN, ADAMTSL3, and IRS1 for appendicular lean body mass. Our findings provide new insight into the genetics of lean body mass.
ICTV virus taxonomy profile : Ophioviridae
García, María Laura ; Bó, Elena Dal; Graça, John V. da; Gago-Zachert, Selma ; Hammond, John ; Moreno, Pedro ; Natsuaki, Tomohide ; Pallás, Vicente ; Navarro, Jose A. ; Reyes, Carina A. ; Luna, Gabriel Robles ; Sasaya, Takahide ; Tzanetakis, Ioannis E. ; Vaira, Anna María ; Verbeek, Martin ; Lefkowitz, Elliot J. ; Davison, Andrew J. ; Siddell, Stuart G. ; Simmonds, Peter ; Adams, Michael J. ; Smith, Donald B. ; Orton, Richard J. ; Sanfaçon, Hélène - \ 2017
Journal of General Virology 98 (2017)6. - ISSN 0022-1317 - p. 1161 - 1162.
Blueberry mosaic associated virus - Citrus psorosis virus - ICTV - Lettuce ring necrosis virus - Mirafiori lettuce big-vein virus - Ophioviridae - Taxonomy
The Ophioviridae is a family of filamentous plant viruses, with single-stranded negative, and possibly ambisense, RNA genomes of 11.3-12.5 kb divided into 3-4 segments, each encapsidated separately. Virions are naked filamentous nucleocapsids, forming kinked circles of at least two different contour lengths. The sole genus, Ophiovirus, includes seven species. Four ophioviruses are soil-transmitted and their natural hosts include trees, shrubs, vegetables and bulbous or corm-forming ornamentals, both monocots and dicots. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Ophioviridae, which is available at http://www.ictv.global/report/ophioviridae.
Illuminating the Reaction Pathways of Viromimetic Assembly
Cingil, Hande E. ; Boz, Emre B. ; Biondaro, Giovanni ; Vries, Renko De; Cohen Stuart, Martien A. ; Kraft, Daniela J. ; Schoot, Paul Van der; Sprakel, Joris - \ 2017
Journal of the American Chemical Society 139 (2017)13. - ISSN 0002-7863 - p. 4962 - 4968.
The coassembly of well-defined biological nanostructures relies on a delicate balance between attractive and repulsive interactions between biomolecular building blocks. Viral capsids are a prototypical example, where coat proteins exhibit not only self-interactions but also interact with the cargo they encapsulate. In nature, the balance between antagonistic and synergistic interactions has evolved to avoid kinetic trapping and polymorphism. To date, it has remained a major challenge to experimentally disentangle the complex kinetic reaction pathways that underlie successful coassembly of biomolecular building blocks in a noninvasive approach with high temporal resolution. Here we show how macromolecular force sensors, acting as a genome proxy, allow us to probe the pathways through which a viromimetic protein forms capsids. We uncover the complex multistage process of capsid assembly, which involves recruitment and complexation, followed by allosteric growth of the proteinaceous coat. Under certain conditions, the single-genome particles condense into capsids containing multiple copies of the template. Finally, we derive a theoretical model that quantitatively describes the kinetics of recruitment and growth. These results shed new light on the origins of the pathway complexity in biomolecular coassembly.
Navigating in Foldonia: Using Accelerated Molecular Dynamics to Explore Stability, Unfolding and Self-healing of the β-Solenoid Structure Formed by a Silk-like Polypeptide
Cohen Stuart, M.A. ; Hall, Carol K. - \ 2017
PLoS Computational Biology 13 (2017)3. - ISSN 1553-734X
The β roll molecules with sequence (GAGAGAGQ)10 stack via hydrogen bonding to form fibrils which have been themselves been used to make viral capsids of DNA strands, supramolecular nanotapes and pH-responsive gels. Accelerated molecular dynamics (aMD) simulations are used to investigate the unfolding of a stack of two β roll molecules, (GAGAGAGQ)10, to shed light on the folding mechanism by which silk-inspired polypeptides form fibrils and to identify the dominant forces that keep the silk-inspired polypeptide in a β roll configuration. Our study shows that a molecule in a stack of two β roll molecules unfolds in a step-wise fashion mainly from the C terminal. The bottom template is found to play an important role in stabilizing the β roll structure of the molecule on top by strengthening the hydrogen bonds in the layer that it contacts. Vertical hydrogen bonds within the β roll structure are considerably weaker than lateral hydrogen bonds, signifying the importance of lateral hydrogen bonds in stabilizing the β roll structure. Finally, an intermediate structure was found containing a β hairpin and an anti-parallel β sheet consisting of strands from the top and bottom molecules, revealing the self-healing ability of the β roll stack.
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