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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CRISPR-Cas genome engineering of esterase activity in Saccharomyces cerevisiae steers aroma formation
Dank, Alexander ; Smid, Eddy J. ; Notebaart, Richard A. - \ 2018
BMC Research Notes 11 (2018)1. - ISSN 1756-0500 - 1 p.
Aroma - CRISRP-Cas9 - Esterase - Saccharomyces cerevisiae

OBJECTIVE: Saccharomyces cerevisiae is used worldwide for the production of ale-type beers. This yeast is responsible for the production of the characteristic fruity aroma compounds. Esters constitute an important group of aroma active secondary metabolites produced by S. cerevisiae. Previous work suggests that esterase activity, which results in ester degradation, may be the key factor determining the abundance of fruity aroma compounds. Here, we test this hypothesis by deletion of two S. cerevisiae esterases, IAH1 and TIP1, using CRISPR-Cas9 genome editing and by studying the effect of these deletions on esterase activity and extracellular ester pools.

RESULTS: Saccharomyces cerevisiae mutants were constructed lacking esterase IAH1 and/or TIP1 using CRISPR-Cas9 genome editing. Esterase activity using 5-(6)-carboxyfluorescein diacetate (cFDA) as substrate was found to be significantly lower for ΔIAH1 and ΔIAH1ΔTIP1 mutants compared to wild type (WT) activity (P < 0.05 and P < 0.001, respectively). As expected, we observed an increase in relative abundance of acetate and ethyl esters and an increase in ethyl esters in ΔIAH1 and ΔTIP1, respectively. Interestingly, the double gene disruption mutant ΔIAH1ΔTIP1 showed an aroma profile comparable to WT levels, suggesting the existence and activation of a complex regulatory mechanism to compensate multiple genomic alterations in aroma metabolism.

Plant functional trait change across a warming tundra biome
Bjorkman, Anne D. ; Myers-Smith, Isla H. ; Elmendorf, Sarah C. ; Normand, Signe ; Rüger, Nadja ; Beck, Pieter S.A. ; Blach-Overgaard, Anne ; Blok, Daan ; Cornelissen, J.H.C. ; Forbes, Bruce C. ; Georges, Damien ; Goetz, Scott J. ; Guay, Kevin C. ; Henry, Gregory H.R. ; Hillerislambers, Janneke ; Hollister, Robert D. ; Karger, Dirk N. ; Kattge, Jens ; Manning, Peter ; Prevéy, Janet S. ; Rixen, Christian ; Schaepman-Strub, Gabriela ; Thomas, Haydn J.D. ; Vellend, Mark ; Wilmking, Martin ; Wipf, Sonja ; Carbognani, Michele ; Hermanutz, Luise ; Lévesque, Esther ; Molau, Ulf ; Petraglia, Alessandro ; Soudzilovskaia, Nadejda A. ; Spasojevic, Marko J. ; Tomaselli, Marcello ; Vowles, Tage ; Alatalo, Juha M. ; Alexander, Heather D. ; Anadon-Rosell, Alba ; Angers-Blondin, Sandra ; Beest, Mariska te; Berner, Logan ; Björk, Robert G. ; Buchwal, Agata ; Buras, Allan ; Christie, Katherine ; Heijmans, Monique M.P.D. ; Ozinga, Wim A. - \ 2018
Nature 526 (2018). - ISSN 0028-0836 - p. 57 - 62.
The tundra is warming more rapidly than any other biome on Earth, and the potential ramifications are far-reaching because of global feedback effects between vegetation and climate. A better understanding of how environmental factors shape plant structure and function is crucial for predicting the consequences of environmental change for ecosystem functioning. Here we explore the biome-wide relationships between temperature, moisture and seven key plant functional traits both across space and over three decades of warming at 117 tundra locations. Spatial temperature–trait relationships were generally strong but soil moisture had a marked influence on the strength and direction of these relationships, highlighting the potentially important influence of changes in water availability on future trait shifts in tundra plant communities. Community height increased with warming across all sites over the past three decades, but other traits lagged far behind predicted rates of change. Our findings highlight the challenge of using space-for-time substitution to predict the functional consequences of future warming and suggest that functions that are tied closely to plant height will experience the most rapid change. They also reveal the strength with which environmental factors shape biotic communities at the coldest extremes of the planet and will help to improve projections of functional changes in tundra ecosystems with climate warming.
Monitoreo climático: herramienta al servicio de la caficultura Colombiana
Sarmiento, Ninibeth ; Ramírez, Carolina ; Jaramillo, Álvaro ; Restrepo, Alexander ; García López, Juan Carlos ; Wolters, W. ; Miguel Ayala, L. - \ 2018
Bogota : APC Columbia - ISBN 9789588490298 - 110
Meta-analysis of genome-wide association studies of aggressive and chronic periodontitis identifies two novel risk loci
Munz, Matthias ; Richter, Gesa M. ; Loos, Bruno G. ; Jepsen, Søren ; Divaris, Kimon ; Offenbacher, Steven ; Teumer, Alexander ; Holtfreter, Birte ; Kocher, Thomas ; Bruckmann, Corinna ; Jockel-Schneider, Yvonne ; Graetz, Christian ; Ahmad, Ilyas ; Staufenbiel, Ingmar ; Velde, Nathalie Van Der; Uitterlinden, André G. ; Groot, Lisette C.P.G.M. De; Wellmann, Jürgen ; Berger, Klaus ; Krone, Bastian ; Hoffmann, Per ; Laudes, Matthias ; Lieb, Wolfgang ; Franke, Andre ; Erdmann, Jeanette ; Dommisch, Henrik ; Schaefer, Arne S. - \ 2018
European Journal of Human Genetics (2018). - ISSN 1018-4813
Periodontitis is one of the most common inflammatory diseases, with a prevalence of 11% worldwide for the severe forms and an estimated heritability of 50%. It is classified into the widespread moderate form chronic periodontitis (CP) and the rare early-onset and severe phenotype aggressive periodontitis (AgP). These different disease manifestations are thought to share risk alleles and predisposing environmental factors. To obtain novel insights into the shared genetic etiology and the underlying molecular mechanisms of both forms, we performed a two step-wise meta-analysis approach using genome-wide association studies of both phenotypes. Genotypes from imputed genome-wide association studies (GWAS) of AgP and CP comprising 5,095 cases and 9,908 controls of North-West European genetic background were included. Two loci were associated with periodontitis at a genome-wide significance level. They located within the pseudogene MTND1P5 on chromosome 8 (rs16870060-G, P = 3.69 × 10−9, OR = 1.36, 95% CI = [1.23–1.51]) and intronic of the long intergenic non-coding RNA LOC107984137 on chromosome 16, downstream of the gene SHISA9 (rs729876-T, P = 9.77 × 10−9, OR = 1.24, 95% CI = [1.15–1.34]). This study identified novel risk loci of periodontitis, adding to the genetic basis of AgP and CP.
Genome-wide association meta-analysis of coronary artery disease and periodontitis reveals a novel shared risk locus
Munz, Matthias ; Richter, Gesa M. ; Loos, Bruno G. ; Jepsen, Søren ; Divaris, Kimon ; Offenbacher, Steven ; Teumer, Alexander ; Holtfreter, Birte ; Kocher, Thomas ; Bruckmann, Corinna ; Jockel-Schneider, Yvonne ; Graetz, Christian ; Munoz, Loreto ; Bhandari, Anita ; Tennstedt, Stephanie ; Staufenbiel, Ingmar ; Velde, Nathalie Van Der; Uitterlinden, André G. ; Groot, Lisette C.P.G.M. De; Wellmann, Jürgen ; Berger, Klaus ; Krone, Bastian ; Hoffmann, Per ; Laudes, Matthias ; Lieb, Wolfgang ; Franke, Andre ; Dommisch, Henrik ; Erdmann, Jeanette ; Schaefer, Arne S. - \ 2018
Scientific Reports 8 (2018)1. - ISSN 2045-2322
Evidence for a shared genetic basis of association between coronary artery disease (CAD) and periodontitis (PD) exists. To explore the joint genetic basis, we performed a GWAS meta-analysis. In the discovery stage, we used a German aggressive periodontitis sample (AgP-Ger; 680 cases vs 3,973 controls) and the CARDIoGRAMplusC4D CAD meta-analysis dataset (60,801 cases vs 123,504 controls). Two SNPs at the known CAD risk loci ADAMTS7 (rs11634042) and VAMP8 (rs1561198) passed the pre-assigned selection criteria (PAgP-Ger < 0.05; PCAD < 5 × 10−8; concordant effect direction) and were replicated in an independent GWAS meta-analysis dataset of PD (4,415 cases vs 5,935 controls). SNP rs1561198 showed significant association (PD[Replication]: P = 0.008 OR = 1.09, 95% CI = [1.02–1.16]; PD [Discovery + Replication]: P = 0.0002, OR = 1.11, 95% CI = [1.05–1.17]). For the associated haplotype block, allele specific cis-effects on VAMP8 expression were reported. Our data adds to the shared genetic basis of CAD and PD and indicate that the observed association of the two disease conditions cannot be solely explained by shared environmental risk factors. We conclude that the molecular pathway shared by CAD and PD involves VAMP8 function, which has a role in membrane vesicular trafficking, and is manipulated by pathogens to corrupt host immune defense.
Data from: Reanalyzing the Palaeoptera problem - the origin of insect flight remains obscure
Simon, S. ; Blanke, Alexander ; Meusemann, Karen - \ 2018
transcriptomics - phylogenomics - homologization - odonata - ephemeroptera - neoptera - palaeoptera - chiastomyaria - metapterygota
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.
Controlling the Hierarchical Assembly of π-Conjugated Oligoelectrolytes
Zheng, Tingting ; Feng, Huanhuan ; Broek, Johanna M. van den; Rahimi, Khosrow ; Kuehne, Alexander J.C. ; Vries, Renko de; Sprakel, Joris - \ 2018
Macromolecular Rapid Communications 39 (2018)16. - ISSN 1022-1336
conjugated polyelectrolytes - hierarchical materials - pathway control - self-assembly

Here, a means of controlling the assembly pathways of p-conjugated oligoelectrolytes into supramolecular fibers and microtubes is presented, and it is shown how the addition of small end-caps to well-defined and pH-responsive conjugated oligomers can alter the balance between repulsive and attractive supramolecular forces and enables control of the morphology of the hierarchical assembly process. The assembly stages from nuclei to protofibers are evidenced and a hypothesis on the mechanism of microtubes formation using a combination of analytical methods is provided, revealing different degrees of order at different scales along the structural hierarchy.

Quality assurance framework development based on six new ECV data products to enhance user confidence for climate applications
Nightingale, Joanne ; Boersma, Klaas Folkert ; Muller, Jan Peter ; Compernolle, Steven ; Lambert, Jean Christopher ; Blessing, Simon ; Giering, Ralf ; Gobron, Nadine ; Smedt, Isabelle De ; Coheur, Pierre ; George, Maya ; Schulz, Jörg ; Wood, Alexander - \ 2018
Remote Sensing 10 (2018)8. - ISSN 2072-4292
Climate applications - Climate data records - CO - Earth observation satellites - Essential climate variables - FAPAR - HCHO - LAI - NO2 - Quality assurance - Surface albedo - Traceability - User requirements

Data from Earth observation (EO) satellites are increasingly used to monitor the environment, understand variability and change, inform evaluations of climate model forecasts, and manage natural resources. Policymakers are progressively relying on the information derived from these datasets to make decisions on mitigating and adapting to climate change. These decisions should be evidence based, which requires confidence in derived products, as well as the reference measurements used to calibrate, validate, or inform product development. In support of the European Union's Earth Observation Programmes Copernicus Climate Change Service (C3S), the Quality Assurance for Essential Climate Variables (QA4ECV) project fulfilled a gap in the delivery of climate quality satellite-derived datasets, by prototyping a generic system for the implementation and evaluation of quality assurance (QA) measures for satellite-derived ECV climate data record products. The project demonstrated the QA system on six new long-term, climate quality ECV data records for surface albedo, leaf area index (LAI), fraction of absorbed photosynthetically active radiation (FAPAR), nitrogen dioxide (NO2), formaldehyde (HCHO), and carbon monoxide (CO). The provision of standardised QA information provides data users with evidence-based confidence in the products and enables judgement on the fitness-for-purpose of various ECV data products and their specific applications.

The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization
Nishiyama, Tomoaki ; Sakayama, Hidetoshi ; Vries, Jan de; Buschmann, Henrik ; Saint-Marcoux, Denis ; Ullrich, Kristian K. ; Haas, Fabian B. ; Vanderstraeten, Lisa ; Becker, Dirk ; Lang, Daniel ; Vosolsobě, Stanislav ; Rombauts, Stephane ; Wilhelmsson, Per K.I. ; Janitza, Philipp ; Kern, Ramona ; Heyl, Alexander ; Rümpler, Florian ; Villalobos, L.I.A.C. ; Clay, John M. ; Skokan, Roman ; Toyoda, Atsushi ; Suzuki, Yutaka ; Kagoshima, Hiroshi ; Schijlen, Elio ; Tajeshwar, Navindra ; Catarino, Bruno ; Hetherington, Alexander J. ; Saltykova, Assia ; Bonnot, Clemence ; Breuninger, Holger ; Symeonidi, Aikaterini ; Radhakrishnan, Guru V. ; Nieuwerburgh, Filip Van; Deforce, Dieter ; Chang, Caren ; Karol, Kenneth G. ; Hedrich, Rainer ; Ulvskov, Peter ; Glöckner, Gernot ; Delwiche, Charles F. ; Petrášek, Jan ; Peer, Yves Van de; Friml, Jiri ; Beilby, Mary ; Dolan, Liam ; Kohara, Yuji ; Sugano, Sumio ; Fujiyama, Asao ; Delaux, Pierre Marc ; Quint, Marcel ; Theißen, Günter ; Hagemann, Martin ; Harholt, Jesper ; Dunand, Christophe ; Zachgo, Sabine ; Langdale, Jane ; Maumus, Florian ; Straeten, Dominique Van Der; Gould, Sven B. ; Rensing, Stefan A. - \ 2018
Cell 174 (2018)2. - ISSN 0092-8674 - p. 448 - 464.e24.
Chara - charophyte - phragmoplast - Phragmoplastophyta - phytohormones - plant evolution - reactive oxygen species - streptophyte - transcriptional regulation
Land plants evolved from charophytic algae, among which Charophyceae
possess the most complex body plans. We present the genome of Chara braunii;
comparison of the genome to those of land plants identified
evolutionary novelties for plant terrestrialization and land plant
heritage genes. C. braunii employs unique xylan synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism similar to that of land plants, and many phytohormones. C. braunii plastids
are controlled via land-plant-like retrograde signaling, and
transcriptional regulation is more elaborate than in other algae. The
morphological complexity of this organism may result from expanded gene
families, with three cases of particular note: genes effecting tolerance
to reactive oxygen species (ROS), LysM receptor-like kinases, and transcription factors (TFs). Transcriptomic analysis of sexual reproductive structures reveals intricate control by TFs, activity of the ROS gene network, and the ancestral use of plant-like storage and stress protection proteins in the zygote.
Comparing impacts of climate change and mitigation on global agriculture by 2050
Meijl, Hans Van; Havlik, Petr ; Lotze-Campen, Hermann ; Stehfest, Elke ; Witzke, Peter ; Domínguez, Ignacio P. ; Bodirsky, Benjamin L. ; Dijk, Michiel van; Doelman, Jonathan ; Fellmann, Thomas ; Humpenöder, Florian ; Koopman, Jason F.L. ; Müller, Christoph ; Popp, Alexander ; Tabeau, Andrzej ; Valin, Hugo ; Zeist, Willem J. van - \ 2018
Environmental Research Letters 13 (2018)6. - ISSN 1748-9318
adaptation - agriculture - climate change - economic models - mitigation - shared socioeconomic pathways

Systematic model inter-comparison helps to narrow discrepancies in the analysis of the future impact of climate change on agricultural production. This paper presents a set of alternative scenarios by five global climate and agro-economic models. Covering integrated assessment (IMAGE), partial equilibrium (CAPRI, GLOBIOM, MAgPIE) and computable general equilibrium (MAGNET) models ensures a good coverage of biophysical and economic agricultural features. These models are harmonized with respect to basic model drivers, to assess the range of potential impacts of climate change on the agricultural sector by 2050. Moreover, they quantify the economic consequences of stringent global emission mitigation efforts, such as non-CO2 emission taxes and land-based mitigation options, to stabilize global warming at 2 °C by the end of the century under different Shared Socioeconomic Pathways. A key contribution of the paper is a vis-à-vis comparison of climate change impacts relative to the impact of mitigation measures. In addition, our scenario design allows assessing the impact of the residual climate change on the mitigation challenge. From a global perspective, the impact of climate change on agricultural production by mid-century is negative but small. A larger negative effect on agricultural production, most pronounced for ruminant meat production, is observed when emission mitigation measures compliant with a 2 °C target are put in place. Our results indicate that a mitigation strategy that embeds residual climate change effects (RCP2.6) has a negative impact on global agricultural production relative to a no-mitigation strategy with stronger climate impacts (RCP6.0). However, this is partially due to the limited impact of the climate change scenarios by 2050. The magnitude of price changes is different amongst models due to methodological differences. Further research to achieve a better harmonization is needed, especially regarding endogenous food and feed demand, including substitution across individual commodities, and endogenous technological change.

Innovative Strategies for Observations in the Arctic Atmospheric Boundary Layer (ISOBAR)-the Hailuoto 2017 campaign
Kral, Stephan T. ; Reuder, Joachim ; Vihma, Timo ; Suomi, Irene ; O'Connor, Ewan ; Kouznetsov, Rostislav ; Wrenger, Burkhard ; Rautenberg, Alexander ; Urbancic, Gabin ; Jonassen, Marius O. ; Båserud, Line ; Maronga, Björn ; Mayer, Stephanie ; Lorenz, Torge ; Holtslag, Albert A.M. ; Steeneveld, Gert J. ; Seidl, Andrew ; Müller, Martin ; Lindenberg, Christian ; Langohr, Carsten ; Voss, Hendrik ; Bange, Jens ; Hundhausen, Marie ; Hilsheimer, Philipp ; Schygulla, Markus - \ 2018
Atmosphere 9 (2018)7. - ISSN 2073-4433
Arctic - Boundary layer remote sensing - Ground-based in-situ observations - Polar - Remotely piloted aircraft systems (RPAS) - Sea ice - Stable atmospheric boundary layer - Turbulence - Unmanned aerial vehicles (UAV)

The aim of the research project "Innovative Strategies for Observations in the Arctic Atmospheric Boundary Layer (ISOBAR)" is to substantially increase the understanding of the stable atmospheric boundary layer (SBL) through a combination of well-established and innovative observation methods as well as by models of different complexity. During three weeks in February 2017, a first field campaign was carried out over the sea ice of the Bothnian Bay in the vicinity of the Finnish island of Hailuoto. Observations were based on ground-based eddy-covariance (EC), automatic weather stations (AWS) and remote-sensing instrumentation as well as more than 150 flight missions by several different Unmanned Aerial Vehicles (UAVs) during mostly stable and very stable boundary layer conditions. The structure of the atmospheric boundary layer (ABL) and above could be resolved at a very high vertical resolution, especially close to the ground, by combining surface-based measurements with UAV observations, i.e., multicopter and fixed-wing profiles up to 200magl and 1800magl, respectively. Repeated multicopter profiles provided detailed information on the evolution of the SBL, in addition to the continuous SODAR and LIDAR wind measurements. The paper describes the campaign and the potential of the collected data set for future SBL research and focuses on both the UAV operations and the benefits of complementing established measurement methods by UAV measurements to enable SBL observations at an unprecedented spatial and temporal resolution.

Decoupling Livestock from Land Use through Industrial Feed Production Pathways
Pikaar, Ilje ; Matassa, Silvio ; Bodirsky, Benjamin L. ; Weindl, Isabelle ; Humpenöder, Florian ; Rabaey, Korneel ; Boon, Nico ; Bruschi, Michele ; Yuan, Zhiguo ; Zanten, Hannah van; Herrero, Mario ; Verstraete, Willy ; Popp, Alexander - \ 2018
Environmental Science and Technology 52 (2018)13. - ISSN 0013-936X - p. 7351 - 7359.

One of the main challenges for the 21st century is to balance the increasing demand for high-quality proteins while mitigating environmental impacts. In particular, cropland-based production of protein-rich animal feed for livestock rearing results in large-scale agricultural land-expansion, nitrogen pollution, and greenhouse gas emissions. Here we propose and analyze the long-term potential of alternative animal feed supply routes based on industrial production of microbial proteins (MP). Our analysis reveals that by 2050, MP can replace, depending on socio-economic development and MP production pathways, between 10-19% of conventional crop-based animal feed protein demand. As a result, global cropland area, global nitrogen losses from croplands and agricultural greenhouse gas emissions can be decreased by 6% (0-13%), 8% (-3-8%), and 7% (-6-9%), respectively. Interestingly, the technology to industrially produce MP at competitive costs is directly accessible for implementation and has the potential to cause a major structural change in the agro-food system.

Prediction of enteric methane production, yield, and intensity in dairy cattle using an intercontinental database
Niu, Mutian ; Kebreab, Ermias ; Hristov, Alexander N. ; Oh, Joonpyo ; Arndt, Claudia ; Bannink, André ; Bayat, Ali R. ; Brito, André F. ; Boland, Tommy ; Casper, David ; Crompton, Les A. ; Dijkstra, Jan ; Eugène, Maguy A. ; Garnsworthy, Phil C. ; Haque, Md Najmul ; Hellwing, Anne L.F. ; Huhtanen, Pekka ; Kreuzer, Michael ; Kuhla, Bjoern ; Lund, Peter ; Madsen, Jørgen ; Martin, Cécile ; Mcclelland, Shelby C. ; Mcgee, Mark ; Moate, Peter J. ; Muetzel, Stefan ; Muñoz, Camila ; O'Kiely, Padraig ; Peiren, Nico ; Reynolds, Christopher K. ; Schwarm, Angela ; Shingfield, Kevin J. ; Storlien, Tonje M. ; Weisbjerg, Martin R. ; Yáñez-Ruiz, David R. ; Yu, Zhongtang - \ 2018
Global Change Biology (2018). - ISSN 1354-1013 - p. 3368 - 3389.
Dairy cows - Dry matter intake - Enteric methane emissions - Methane intensity - Methane yield - Prediction models
Enteric methane (CH4) production from cattle contributes to global greenhouse gas emissions. Measurement of enteric CH4 is complex, expensive, and impractical at large scales; therefore, models are commonly used to predict CH4 production. However, building robust prediction models requires extensive data from animals under different management systems worldwide. The objectives of this study were to (1) collate a global database of enteric CH4 production from individual lactating dairy cattle; (2) determine the availability of key variables for predicting enteric CH4 production (g/day per cow), yield [g/kg dry matter intake (DMI)], and intensity (g/kg energy corrected milk) and their respective relationships; (3) develop intercontinental and regional models and cross-validate their performance; and (4) assess the trade-off between availability of on-farm inputs and CH4 prediction accuracy. The intercontinental database covered Europe (EU), the United States (US), and Australia (AU). A sequential approach was taken by incrementally adding key variables to develop models with increasing complexity. Methane emissions were predicted by fitting linear mixed models. Within model categories, an intercontinental model with the most available independent variables performed best with root mean square prediction error (RMSPE) as a percentage of mean observed value of 16.6%, 14.7%, and 19.8% for intercontinental, EU, and United States regions, respectively. Less complex models requiring only DMI had predictive ability comparable to complex models. Enteric CH4 production, yield, and intensity prediction models developed on an intercontinental basis had similar performance across regions, however, intercepts and slopes were different with implications for prediction. Revised CH4 emission conversion factors for specific regions are required to improve CH4 production estimates in national inventories. In conclusion, information on DMI is required for good prediction, and other factors such as dietary neutral detergent fiber (NDF) concentration, improve the prediction. For enteric CH4 yield and intensity prediction, information on milk yield and composition is required for better estimation.
Plant Structure-Function Relationships and Woody Tissue Respiration: Upscaling to Forests from Laser-Derived Measurements
Meir, Patrick ; Shenkin, Alexander ; Disney, Mathias ; Rowland, Lucy ; Malhi, Yadvinder ; Herold, Martin ; Costa, Antonio C.L. da - \ 2018
In: Plant Respiration: Metabolic Fluxes and Carbon Balance / Tcherkez, G., Ghashghaie, J., Cham : Springer (Advances in Photosynthesis and Respiration ) - ISBN 9783319687018 - p. 89 - 105.
Land surface processes dominate the observed global signal of large inter-annual variability in the global carbon cycle , and this signal is itself dominated by responses of tropical forests to climatic variation and extremes. However, our understanding of the functioning of these forests is poorly constrained, not least in terms of the size and climate-sensitivity of gross ecosystem respiratory CO2 emission. Woody tissue CO2 effluxes contribute substantially to gross ecosystem CO2 emissions, thereby influencing the net ecosystem exchange of carbon. Our ability to estimate this component of the forest respiration budget has been limited by our technical capacity to measure vegetation size and structure in sufficient detail and at sufficient scale. The outcome has been to leave large uncertainties in land-surface model performance and prediction. A key challenge in estimating woody tissue CO2 efflux for the ecosystem has been the scaling of measurements made with chambers from the level of an organ to the stand. Appropriate scalars such as woody tissue mass, surface area and volume all require accurate structural information on both size and pattern. For individual trees, pattern is dominated by branching structure and this fundamentally determines how trees partition resources to address the trade-offs inherent in the simultaneous maintenance of structural integrity and metabolism. The detailed structural information needed to address this challenge has until recently been extremely scarce because of the difficulty of acquiring it, even for a single large tree. Recent developments in terrestrial light detection and ranging (LiDAR) technology have made possible a step change in our ability to quantify and describe tree form for continuous forest, for example describing hundreds of adjacent trees at the hectare scale. Connecting this new capability with tree physiology and fundamental theories of plant structure and metabolism offers to change the way we understand plant functional biology and its variation with environment, biogeography and phylogeny.
Reanalyzing the Palaeoptera problem – The origin of insect flight remains obscure
Simon, Sabrina ; Blanke, Alexander ; Meusemann, Karen - \ 2018
Arthropod Structure & Development 47 (2018)4. - ISSN 1467-8039 - p. 328 - 338.
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 32 (2018)5. - ISSN 0931-1890 - p. 1219 - 1231.
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 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.
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.
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