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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Anti-inflammatory nutrition with high protein attenuates cardiac and skeletal muscle alterations in a pulmonary arterial hypertension model
Vinke, Paulien ; Bowen, T.S. ; Boekschoten, Mark V. ; Witkamp, Renger F. ; Adams, Volker ; Norren, Klaske van - \ 2019
Scientific Reports 9 (2019)1. - ISSN 2045-2322

Pulmonary arterial hypertension (PAH) is characterized by remodelling of the pulmonary arteries and right ventricle (RV), which leads to functional decline of cardiac and skeletal muscle. This study investigated the effects of a multi-targeted nutritional intervention with extra protein, leucine, fish oil and oligosaccharides on cardiac and skeletal muscle in PAH. PAH was induced in female C57BL/6 mice by weekly injections of monocrotaline (MCT) for 8 weeks. Control diet (sham and MCT group) and isocaloric nutritional intervention (MCT + NI) were administered. Compared to sham, MCT mice increased heart weight by 7%, RV thickness by 13% and fibrosis by 60% (all p < 0.05) and these were attenuated in MCT + NI mice. Microarray and qRT-PCR analysis of RV confirmed effects on fibrotic pathways. Skeletal muscle fiber atrophy was induced (P < 0.05) by 22% in MCT compared to sham mice, but prevented in MCT + NI group. Our findings show that a multi-targeted nutritional intervention attenuated detrimental alterations to both cardiac and skeletal muscle in a mouse model of PAH, which provides directions for future therapeutic strategies targeting functional decline of both tissues.

Anti-inflammatory nutrition with high protein attenuates cardiac and skeletal muscle alterations in a pulmonary arterial hypertension model
Vinke, Paulien ; Bowen, T.S. ; Boekschoten, M.V. ; Witkamp, R.F. ; Adams, V. ; Norren, K. van; Hooiveld, G.J.E.J. - \ 2019
Mus musculus - GSE125537 - PRJNA516702
Background: Pulmonary arterial hypertension (PAH) is a progressive and fatal disease predominantly affecting women and characterized by right ventricular (RV) remodeling. PAH patients experience exercise intolerance and fatigue, often associated with functional decline of their cardiac and skeletal muscle. As treatment options for these disease manifestations are very limited, there is a need for novel therapeutic strategies. The present study used a pulmonary arterial hypertension model in female mice to investigate effects of a nutritional combination (containing extra protein, leucine, fish oil and oligosaccharides) presumably targeting pathways involved in cardiac and skeletal muscle remodeling. Methods: Pulmonary arterial hypertension was induced in female mice (C57/BL6) by weekly administration of monocrotaline (MCT; s.c. 600 mg/kg) during 8 weeks, using saline injection as control. During that period, one MCT group (MCT; n=9) and the sham group (Sham; n=9) received a control diet (standard AIN-93M) while a further MCT-treated group received the nutritional intervention (NI, isocaloric) (MCT+NI; n=10). Histological analyses were performed on the RV, tibialis anterior (TA), soleus and extensor digitorum longus (EDL) muscle. Microarray and qRT-PCR analysis for gene expression were performed in RV tissue, and protein analysis by Western blot in tibialis anterior material. Results: Compared to sham mice, MCT mice showed an increase in heart weight by 7%, RV thickness by 13% and fibrosis by 60% (all p<0.05), which were attenuated in MCT+NI mice. Gene Set Enrichment Analysis (GSEA) of array data from the RV confirmed upregulation of fibrotic pathways in the MCT-compared to sham-treated mice (P<0.05), which were downregulated in MCT+NI mice. In addition, skeletal muscle fiber cross-sectional area (CSA) of the tibialis anterior was reduced (P<0.05) by 22% in MCT compared to sham mice, but preserved in the MCT+NI group (1503 vs. 1178 vs 1495 µm2, respectively), with protein expression of the key E3 ligase MuRF1 also reduced by 30% compared to MCT mice alone (p<0.05). In the EDL, CSA was also reduced (p<0.05) by 28% in MCT compared to sham mice and preserved in the group receiving nutritional intervention (764 vs. 542 Vs.742 µm2). No effect of MCT or nutritional intervention was found in the soleus. Conclusions: A multi-compound supplemented nutrition significantly attenuated changes in both cardiac and skeletal muscle in a mouse model of PAH, providing directions for future therapeutic strategies targeting functional decline of both tissues
Understanding the dissipation of continental fog by analysing the LWP budget using idealized LES and in situ observations
Wærsted, Eivind G. ; Haeffelin, Martial ; Steeneveld, Gert Jan ; Dupont, Jean Charles - \ 2018
Quarterly Journal of the Royal Meteorological Society 145 (2018)719. - ISSN 0035-9009 - p. 784 - 804.
bowen ratio - fog - Fog dissipation - fog-top entrainment - LES

Physical processes relevant for the dissipation of thick, continental fog after sunrise are studied through observations from the SIRTA observatory and idealized sensitivity studies with the large-eddy simulation model DALES. Observations of 250 fog events over 7 years show that more than half of the fog dissipations after sunrise are transitions to stratus lasting 2 hr or more. From the simulations, we quantify the contribution of each process to the liquid water path (LWP) budget of the fog. Radiative cooling is the main source of LWP, while surface turbulent heat fluxes are the most important process contributing to loss of LWP, followed by the absorption of solar radiation, the mixing with unsaturated air at the fog top and the deposition of cloud droplets. The loss of LWP by surface heat fluxes is very sensitive to the Bowen ratio, which is importantly affected by the availability of liquid water on the surface; in a run without liquid on the surface, fog dissipation occurred 85 min earlier than in the Baseline simulation. The variability of stratification and humidity above fog top is documented by 47 radiosondes and cloud radar. Using DALES, we find that the variability in stratification has an important impact on the entrainment velocity; a three times more rapid fog-top entrainment enables the cloud base to lift from the ground 90 min earlier in weak stratification than in strong stratification in the model. With relatively dry overlying air, the fog evaporates faster than if the air is near saturation, leading to 70 min earlier dissipation in our simulations. Continuous observations of the temperature and humidity profiles of the layer overlying the fog could therefore be useful for understanding and anticipating fog dissipation.

Erratum to: Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study
Hellenkamp, Björn ; Schmid, Sonja ; Doroshenko, Olga ; Opanasyuk, Oleg ; Kühnemuth, Ralf ; Adariani, Soheila Rezaei ; Ambrose, Benjamin ; Aznauryan, Mikayel ; Barth, Anders ; Birkedal, Victoria ; Bowen, Mark E. ; Chen, Hongtao ; Cordes, Thorben ; Eilert, Tobias ; Fijen, Carel ; Gebhardt, Christian ; Götz, Markus ; Gouridis, Giorgos ; Gratton, Enrico ; Ha, Taekjip ; Hao, Pengyu ; Hanke, Christian A. ; Hartmann, Andreas ; Hendrix, Jelle ; Hildebrandt, Lasse L. ; Hirschfeld, Verena ; Hohlbein, Johannes ; Hua, Boyang ; Hübner, Christian G. ; Kallis, Eleni ; Kapanidis, Achillefs N. ; Kim, Jae Yeol ; Krainer, Georg ; Lamb, Don C. ; Lee, Nam Ki ; Lemke, Edward A. ; Levesque, Brié ; Levitus, Marcia ; McCann, James J. ; Naredi-Rainer, Nikolaus ; Nettels, Daniel ; Ngo, Thuy ; Qiu, Ruoyi ; Robb, Nicole C. ; Röcker, Carlheinz ; Sanabria, Hugo ; Schlierf, Michael ; Schröder, Tim ; Schuler, Benjamin ; Seidel, Henning - \ 2018
Nature Methods : techniques for life scientists and chemists 15 (2018)11. - ISSN 1548-7091 - p. 984 - 984.
Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study
Hellenkamp, Björn ; Schmid, Sonja ; Doroshenko, Olga ; Opanasyuk, Oleg ; Kühnemuth, Ralf ; Rezaei Adariani, Soheila ; Ambrose, Benjamin ; Aznauryan, Mikayel ; Barth, Anders ; Birkedal, Victoria ; Bowen, Mark E. ; Chen, Hongtao ; Cordes, Thorben ; Eilert, Tobias ; Fijen, Carel ; Gebhardt, Christian ; Götz, Markus ; Gouridis, Giorgos ; Gratton, Enrico ; Ha, Taekjip ; Hao, Pengyu ; Hanke, Christian A. ; Hartmann, Andreas ; Hendrix, Jelle ; Hildebrandt, Lasse L. ; Hirschfeld, Verena ; Hohlbein, Johannes ; Hua, Boyang ; Hübner, Christian G. ; Kallis, Eleni ; Kapanidis, Achillefs N. ; Kim, Jae Yeol ; Krainer, Georg ; Lamb, Don C. ; Lee, Nam Ki ; Lemke, Edward A. ; Levesque, Brié ; Levitus, Marcia ; McCann, James J. ; Naredi-Rainer, Nikolaus ; Nettels, Daniel ; Ngo, Thuy ; Qiu, Ruoyi ; Robb, Nicole C. ; Röcker, Carlheinz ; Sanabria, Hugo ; Schlierf, Michael ; Schröder, Tim ; Schuler, Benjamin ; Seidel, Henning ; Streit, Lisa ; Thurn, Johann ; Tinnefeld, Philip ; Tyagi, Swati ; Vandenberk, Niels ; Vera, Andrés Manuel ; Weninger, Keith R. ; Wünsch, Bettina ; Yanez-Orozco, Inna S. ; Michaelis, Jens ; Seidel, Claus A.M. ; Craggs, Timothy D. ; Hugel, Thorsten - \ 2018
Nature Methods : techniques for life scientists and chemists 15 (2018)9. - ISSN 1548-7091 - p. 669 - 676.

Single-molecule Förster resonance energy transfer (smFRET) is increasingly being used to determine distances, structures, and dynamics of biomolecules in vitro and in vivo. However, generalized protocols and FRET standards to ensure the reproducibility and accuracy of measurements of FRET efficiencies are currently lacking. Here we report the results of a comparative blind study in which 20 labs determined the FRET efficiencies (E) of several dye-labeled DNA duplexes. Using a unified, straightforward method, we obtained FRET efficiencies with s.d. between ±0.02 and ±0.05. We suggest experimental and computational procedures for converting FRET efficiencies into accurate distances, and discuss potential uncertainties in the experiment and the modeling. Our quantitative assessment of the reproducibility of intensity-based smFRET measurements and a unified correction procedure represents an important step toward the validation of distance networks, with the ultimate aim of achieving reliable structural models of biomolecular systems by smFRET-based hybrid methods.

Data from global field experiments for potato simulations
Raymundo, Rubi ; Asseng, Senthold ; Prasad, Rishi ; Kleinwechter, Ulrich ; Condori, Bruno ; Bowen, Walter ; Wolf, J. ; Olesen, Jørgen E. ; Dong, Qiaoxue ; Zotarelli, Lincoln ; Gastelo, Manuel ; Alva, Ashok ; Travasso, Maria ; Arora, Vijay - \ 2018
potato - field experimental data - simulations
Global field experiments for potato simulations
Raymundo, Rubi ; Asseng, Senthold ; Prasad, Rishi ; Kleinwechter, Ulrich ; Condori, Bruno ; Bowen, Walter ; Wolf, Joost ; Olesen, Jørgen E. ; Dong, Qiaoxue ; Zotarelli, Lincoln ; Gastelo, Manuel ; Alva, Ashok ; Travasso, Maria ; Arora, Vijay - \ 2018
ODjAR : open data journal for agricultural research 4 (2018). - ISSN 2352-6378 - p. 35 - 44.
A large field potato experimental data set has been assembled for simulation modeling. The data are from temperate, subtropical, and tropical regions across the world and include 87 experiments with 204 treatments. Treatments include nitrogen fertilizer, irrigation, atmospheric CO2 levels, temperature, cultivars, and locations. For all experiments, measurements include tuber fresh and dry weight. For some experiments, measurements include in-season biomass, leaf area index, stem and leaf weight, N uptake, soil water, and soil N contents. Each experiment has soil characteristics and daily data for solar radiation, rainfall, and maximum and minimum temperature. The data have been quality checked and used in a previous simulation exercise. All data are in AGMIP format.
European bluetongue serotype 8 : Disease threat assessment for U.S. sheep
Drolet, Barbara S. ; Reister-Hendricks, Lindsey M. ; Podell, Brendan K. ; Breitenbach, Jonathan E. ; Mcvey, D.S. ; Rijn, Piet A. van; Bowen, Richard A. - \ 2016
Vector-Borne and Zoonotic Diseases 16 (2016)6. - ISSN 1530-3667 - p. 400 - 407.
Bluetongue virus - BTV-8 - Orbivirus - Sheep - U.S.

Bluetongue virus (BTV) is an orbivirus transmitted by biting midges (Culicoides spp.) that can result in moderate to high morbidity and mortality primarily in sheep and white-tailed deer. Although only 5 serotypes of BTV are considered endemic to the United States, as many as 11 incursive serotypes have been detected in livestock and wildlife in the past 16 years. Introductions of serotypes, with unknown virulence and disease risk, are constant threats to US agriculture. One potential incursive serotype of particular concern is the European strain of BTV-8, which was introduced into Northern Europe in 2006 and caused unprecedented livestock disease and mortality during the 2006-2007 vector seasons. To assess disease risk of BTV-8 in a common white-faced American sheep breed, eight Polled Dorset yearlings were experimentally infected and monitored for clinical signs. Viremia and viral tissue distribution were detected and quantified by real-time qRT-PCR. Overall, clinical disease was moderate with no mortality. Viremia reached as high as 9.7 log10 particles/mL and persisted at 5 logs or higher through the end of the study (28 days). Virus distribution in tissues was extensive with the highest mean titers at the peak of viremia (day 8) in the kidney (8.38 log10 particles/mg) and pancreas (8.37 log10 particles/mg). Virus persisted in tissues of some sheep at 8 logs or higher by day 28. Results of this study suggest that should BTV-8 emerge in the United States, clinical disease in this common sheep breed would likely be similar in form, duration, and severity to what is typically observed in severe outbreaks of endemic serotypes, not the extraordinary disease levels seen in Northern Europe. In addition, a majority of exposed sheep would be expected to survive and act as significant BTV-8 reservoirs with high titer viremias for subsequent transmission to other livestock and wildlife populations.

Effect of Culicoides sonorensis salivary proteins on clinical disease outcome in experimental Bleutongue virus serotype 8 infection of Dorset sheep
Drolet, B.S. ; Reister, L.M. ; Lehiy, C.J. ; Rijn, P.A. van; Bowen, R.A. - \ 2015
Veterinaria Italiana 51 (2015)4. - ISSN 0505-401X - p. 379 - 384.
The severity of Bluetongue clinical disease in ruminants varies greatly depending on the outbreak serotype/strain, animal species/breed, and immune status of the herd. To predict disease risk from any of the 26 Bluetongue virus (BTV) serotypes identified to date, experimental animal susceptibility studies are often conducted. Although sheep are the most susceptible livestock species in the US, infection of domestic breeds by injection of field isolates rarely produces the level of clinical disease observed in natural Culicoides midge‑transmitted outbreaks. Thus, outbreak risk assessments based on experimental animal infections can underestimate the severity posed by a potential outbreak with a given virus serotype or strain. The aim of this study was to determine whether secreted Culicoides salivary proteins injected simultaneously with virus, to more closely mimic midge‑delivered virus, would affect clinical disease outcome in a BTV‑8 sheep susceptibility study. Eight sheep were intradermally inoculated with BTV‑8; 4 received virus mixed with secreted Culicoides salivary proteins (BTV‑8 + Cu SP), 4 received virus alone. Clinical signs were monitored daily for type, severity and duration. In sheep receiving the BTV‑8 + Cu SP inoculum, clinical signs were more varied, more severe, and duration was three times longer compared to sheep receiving virus alone. These results suggest that Culicoides salivary proteins may play a contributing role in BTV pathology and that use of these proteins in experimental animal infections may allow development of a more robust target‑host animal model.
Characterisation of Ave1 orthologs in Venturia scab pathogens
Wheeler, J. ; Kastner, P. ; Taranto, A. ; Shiller, J. ; Boshoven, J.C. ; Mesarich, C.H. ; Thomma, B.P.H.J. ; Deng, C. ; Bowen, J. ; Plummer, K.M. - \ 2015
In: Book of Abstracts 28th Fungal Genetics Conference. - - p. 211 - 211.
Most fungal effectors are genus, species or race-specific, however a few are more broadly conserved (e.g. ECP6), and some are discontinuously distributed within the Fungi (Ave1 & AvrLm6). Single orthologs of Ave1 from Verticillium dahliae, a virulence effector that activates Ve1-mediated resistance in tomato, have been identified in unrelated fungi (Colletotrichum higginsianum, Cercospora beticola, Fusarium oxysporum f. sp. lycopersici). A subset of these activate Ve1-mediated resistance in tomato (de Jonge et al. 2012). Ave1 also shares similarity to an ortholog in the phytopathogenic bacterium Xanthomonas axonopodis pv. citri, as well as to a common family of plant natriuretic peptides and expansins, involved in plant homeostasis and plant cell wall modifications (de Jonge et al. 2012). We have identified highly expanded Ave1-like gene families (with conserved predicted cysteine patterns & 37-57% overall aa identity) in the biotrophic scab fungi, Venturia inaequalis (5 genomes) & V. pirina. The orthologs are closely associated with repeats in Venturia genomes, however only a few appear to be impacted by RIP. Like VdAve1, Venturia orthologs have a conserved intron in the 5’UTR, which causes problems for automated gene calling, especially those packages informed by transcriptome data. Several of the Venturia orthologs are up-regulated during leaf infection (RNAseq data), and some are also highly expressed during in vitro growth on cellophane (RNAseq and proteomic data, Cook et al. 2014). Synthetic peptides (36 & 39 amino acids) from two V. inaequalis Ave1 orthologs, based on conserved homeostasis-regulating domains of plant proteins, affected Arabidopsis thaliana protoplasts (swelling) and guard cells (collapse) of Tradescantia leaves in epidermal peels exposed to the peptides (0.1µM) in solution. We hypothesize that Venturia Ave1 proteins may play a role during biotrophic infection in disturbing plant homeostasis and promoting nutrient release from plant cells.
Two perspectives on the coupled carbon, water and energy exchange in the planetary boundary layer
Combe, M. ; Vilà-Guerau De Arellano, J. ; Ouwersloot, H.G. ; Jacobs, C.M.J. ; Peters, W. - \ 2015
Biogeosciences 12 (2015). - ISSN 1726-4170 - p. 103 - 123.
ensemble kalman filter - land-surface model - leaf-area index - soil-moisture - use efficiency - climate-change - crop model - stomatal conductance - data assimilation - plant geography
Understanding the interactions between the land surface and the atmosphere is key to modelling boundary-layer meteorology and cloud formation, as well as carbon cycling and crop yield. In this study we explore these interactions in the exchange of water, heat and CO2 in a cropland–atmosphere system at the diurnal and local scale. To that end, we couple an atmospheric mixed-layer model (MXL) to two land-surface schemes developed from two different perspectives: while one land-surface scheme (A-gs) simulates vegetation from an atmospheric point of view, the other (GECROS) simulates vegetation from a carbon-storage point of view. We calculate surface fluxes of heat, moisture and carbon, as well as the resulting atmospheric state and boundary-layer dynamics, over a maize field in the Netherlands, on a day for which we have a rich set of observations available. Particular emphasis is placed on understanding the role of upper-atmosphere conditions like subsidence in comparison to the role of surface forcings like soil moisture. We show that the atmospheric-oriented model (MXL-A-gs) outperforms the carbon storage-oriented model (MXL-GECROS) on this diurnal scale. We find this performance is partly due to the difference of scales at which the models were made to run. Most importantly, this performance strongly depends on the sensitivity of the modelled stomatal conductance to water stress, which is implemented differently in each model. This sensitivity also influences the magnitude of the surface fluxes of CO2, water and heat (surface control) and subsequently impacts the boundary-layer growth and entrainment fluxes (upper atmosphere control), which alter the atmospheric state. These findings suggest that observed CO2 mole fractions in the boundary layer can reflect strong influences of both the surface and upper-atmosphere conditions, and the interpretation of CO2 mole fraction variations depends on the assumed land-surface coupling. We illustrate this with a sensitivity analysis where high subsidence and soil moisture depletion, typical for periods of drought, have competing and opposite effects on the boundary-layer height h. The resulting net decrease in h induces a change of 12 ppm in the late-afternoon CO2 mole fraction. Also, the effect of such high subsidence and soil moisture depletion on the surface Bowen ratio are of the same magnitude. Thus, correctly including such two-way land-surface interactions on the diurnal scale can potentially improve our understanding and interpretation of observed variations in atmospheric CO2, as well as improve crop yield forecasts by better describing the water loss and carbon gain.
Aerosols in the convective boundary layer: Shortwave radiation effects on the coupled land-atmosphere system
Wilde Barbaro, E. ; Vilà-Guerau de Arellano, J. ; Ouwersloot, H.G. ; Schroter, J.S. ; Donovan, D.P. ; Krol, M.C. - \ 2014
Journal of Geophysical Research: Atmospheres 119 (2014)10. - ISSN 2169-897X - p. 5845 - 5863.
large-eddy-simulation - quality interactions eucaari - european integrated project - optical-properties - ammonium-nitrate - energy-balance - climate system - global scales - cloud climate - model
By combining observations and numerical simulations, we investigated the responses of the surface energy budget and the convective boundary layer (CBL) dynamics to the presence of aerosols. A detailed data set containing (thermo)dynamic observations at CESAR (Cabauw Experimental Site for Atmospheric Research) and aerosol information from the European Integrated Project on Aerosol, Cloud, Climate, and Air Quality Interactions was employed to design numerical experiments reproducing two typical clear-sky days, each characterized by contrasting thermodynamic initial profiles: (i) residual layer above a strong surface inversion and (ii) well-mixed CBL connected to the free troposphere by a capping inversion, without the residual layer in between. A large-eddy simulation (LES) model and a mixed-layer (MXL) model, coupled to a broadband radiative transfer code and a land surface model, were used to study the impacts of aerosols on shortwave radiation. Both the LES model and the MXL model results reproduced satisfactorily the observations for both days. A sensitivity analysis on a wide range of aerosol properties was conducted. Our results showed that higher loads of aerosols decreased irradiance imposing an energy restriction at the surface, delaying the morning onset of the CBL and advancing its afternoon collapse. Moderately to strongly absorbing aerosols increased the heating rate contributing positively to increase the afternoon CBL height and potential temperature and to decrease Bowen ratio. In contrast, scattering aerosols were associated with smaller heating rates and cooler and shallower CBLs. Our findings advocate the need for accounting for the aerosol influence in analyzing surface and CBL dynamics.
What drives the seasonality of photosynthesis across the Amazon basin? A cross-site analysis of eddy flux tower measurements from the Brazil flux network
Restrepo-Coupe, N. ; Rocha, H.R. da; Hutyra, L.R. ; Araujo, A.C. de; Borma, L.S. ; Christoffersen, B. ; Cabral, O.M.R. ; Camargo, P.B. de; Cardoso, F.L. ; Lola da Costa, A.C. ; Fitzjarrald, D.R. ; Kruijt, B. - \ 2013
Agricultural and Forest Meteorology 182-183 (2013). - ISSN 0168-1923 - p. 128 - 144.
net ecosystem exchange - gross primary production - rain-forest - tropical forest - leaf-area - active radiation - carbon balance - co2 flux - climate - covariance
We investigated the seasonal patterns of Amazonian forest photosynthetic activity, and the effects thereon of variations in climate and land-use, by integrating data from a network of ground-based eddy flux towers in Brazil established as part of the ‘Large-Scale Biosphere Atmosphere Experiment in Amazonia’ project. We found that degree of water limitation, as indicated by the seasonality of the ratio of sensible to latent heat flux (Bowen ratio) predicts seasonal patterns of photosynthesis. In equatorial Amazonian forests (5° N–5° S), water limitation is absent, and photosynthetic fluxes (or gross ecosystem productivity, GEP) exhibit high or increasing levels of photosynthetic activity as the dry season progresses, likely a consequence of allocation to growth of new leaves. In contrast, forests along the southern flank of the Amazon, pastures converted from forest, and mixed forest-grass savanna, exhibit dry-season declines in GEP, consistent with increasing degrees of water limitation. Although previous work showed tropical ecosystem evapotranspiration (ET) is driven by incoming radiation, GEP observations reported here surprisingly show no or negative relationships with photosynthetically active radiation (PAR). Instead, GEP fluxes largely followed the phenology of canopy photosynthetic capacity (Pc), with only deviations from this primary pattern driven by variations in PAR. Estimates of leaf flush at three non-water limited equatorial forest sites peak in the dry season, in correlation with high dry season light levels. The higher photosynthetic capacity that follows persists into the wet season, driving high GEP that is out of phase with sunlight, explaining the negative observed relationship with sunlight. Overall, these patterns suggest that at sites where water is not limiting, light interacts with adaptive mechanisms to determine photosynthetic capacity indirectly through leaf flush and litterfall seasonality. These mechanisms are poorly represented in ecosystem models, and represent an important challenge to efforts to predict tropical forest responses to climatic variations.
Evaluation of trends in high temperature extremes in north-western Europe in regional climate models
Min, E. ; Hazeleger, W. ; Oldenborgh, G.J. van; Sterl, A. - \ 2013
Environmental Research Letters 8 (2013)1. - ISSN 1748-9326
reanalysis - scale
Projections of future changes in weather extremes on the regional and local scale depend on a realistic representation of trends in extremes in regional climate models (RCMs). We have tested this assumption for moderate high temperature extremes (the annual maximum of the daily maximum 2 m temperature, T-ann.max). Linear trends in T-ann.max from historical runs of 14 RCMs driven by atmospheric reanalysis data are compared with trends in gridded station data. The ensemble of RCMs significantly underestimates the observed trends over most of the north-western European land surface. Individual models do not fare much better, with even the best performing models underestimating observed trends over large areas. We argue that the inability of RCMs to reproduce observed trends is probably not due to errors in large-scale circulation. There is also no significant correlation between the RCM T-ann.max trends and trends in radiation or Bowen ratio. We conclude that care should be taken when using RCM data for adaptation decisions.
Experimental infection of white-tailed deer with bluetongue virus serotype 8
Drolet, B.S. ; Reister, L.M. ; Mecham, J.O. ; Wilson, W.C. ; Nol, P. ; Vercauteren, K.C. ; Rijn, P.A. van; Bowen, R.A. - \ 2013
Veterinary Microbiology 166 (2013)3-4. - ISSN 0378-1135 - p. 347 - 355.
epizootic-hemorrhagic-disease - polymerase chain-reaction - wild ruminants - red deer - antilocapra-americana - pronghorn antelope - cervus-elaphus - climate-change - epidemiology - spain
Bluetongue (BT) is an insect-transmitted, economically important disease of domestic and wild ruminants. Although only five of the 26 reported bluetongue virus (BTV) serotypes are considered endemic to the USA, 10 exotic serotypes have been isolated primarily in the southeastern region of the country since 1999. For an exotic BTV serotype to become endemic there must be susceptible animal species and competent vectors. In the USA, sheep and white-tailed deer (WTD) are the primary sentinel livestock and wildlife species, respectively. In 2006, BTV-8 was introduced into Northern Europe and subsequently overwintered, causing unprecedented livestock disease and mortality during the 2006-2007 vector seasons. To assess the risk of the European strain of BTV-8 to North American WTD, and understand the role they could play after a similar introduction, eight bluetongue-seronegative WTD were inoculated with BTV-8. Body temperatures and clinical signs were recorded daily. Blood samples were analyzed for BTV RNA with quantitative real time reverse transcriptase polymerase chain reaction (qRT-PCR), serum analyzed for BTV antibodies by cELISA, and tissues taken for histopathology and qRT-PCR. All eight deer became infected and developed moderate to severe clinical disease from days 8 to 15. Peak viremia was from day 7 to 10 with detectable titers through the end of the study (28 days) in most deer. Serum antibody was detected by day 6, peaked by day 10 and continued through day 28. We conclude that North American WTD are highly susceptible to BTV-8 and would act as clinical disease sentinels and amplifying hosts during an outbreak.
Surface and atmospheric controls on the onset of moist convection over land
Gentine, P. ; Holtslag, A.A.M. ; Andrea, F. D'; Ek, M. - \ 2013
Journal of Hydrometeorology 14 (2013). - ISSN 1525-755X - p. 1443 - 1462.
large-eddy simulation - fraction diurnal behavior - probabilistic bulk model - coupled mixed-layer - boundary-layer - soil-moisture - evaporative fraction - relative-humidity - hydrologic perspective - spatial variability
The onset of moist convection over land is investigated using a conceptual approach with a slab boundary layer model. We here determine the essential factors for the onset of boundary layer clouds over land, and study their relative importance. They are: 1) the ratio of the temperature to the moisture lapse rates of the free troposphere, i.e. the inversion Bowen ratio, 2) the mean-daily surface temperature, 3) the relative humidity of the free troposphere and 4) the surface evaporative fraction. A clear transition is observed between two regimes of moistening of the boundary layer as assessed by the relative humidity at the boundary layer top. In the first so-called wet soil advantage regime, the moistening results from the increase of the mixed-layer specific humidity, which linearly depends on the surface evaporative fraction and inversion Bowen ratio through a dynamic boundary layer factor. In the second so-called dry soil advantage regime, the relative humidity tendency at the boundary layer top is controlled by the thermodynamics and changes in the moist adiabatic induced by the decreased temperature at the boundary layer top and consequent reduction in saturation water vapor pressure. This regime pertains for very deep boundary layers under weakly stratified free troposphere over hot surface conditions. In the context of the conceptual model, a rise in free-tropospheric temperature (global warming) increases the occurrence of deep convection and reduces the cloud cover over moist surfaces. This study provides new intuition and predictive capacity on the mechanism controlling the occurrence of moist convection over land
Ave1-like orthologs in Venturia: another expanded effector family emerges
Taranto, A. ; Jones, D. ; Shiller, J. ; Johnson, S. ; Hall, N. ; Cooke, I. ; Talbo, G. ; Mesarich, C.H. ; Thomma, B.P.H.J. ; Boshoven, J.C. ; Bowen, J. ; Deng, C. ; Templeton, M. ; Plummer, K.M. - \ 2013
In: Book of Abstracts 27th Fungal Genetics Conference, Asilomar, Pacific Grove, California, USA, 12-17 March 2013. - - p. 250 - 251.
Effectors are secreted by pathogens to modify plant physiology and establish disease. Plant immune receptors have evolved to recognise effectors and counter attack with defence responses. Most fungal effectors are lineage-specific, i.e. they are unique to a species, or to physiological races within a species. The availability of many whole genome sequences has revealed that some effectors are found in a discontinuous distribution within the fungal kingdom; a few phytopathogenic fungi (Colletotrichum higginsianum, Cercospora beticola, Fusarium oxysporum) possess an ortholog of Ave1 from Verticillium dahliae, an effector that activates Ve1-mediated resistance in tomato. A subset of these orthologs were shown to activate Ve1-mediated resistance in tomato. Unusually, Ave1 also shares similarity to an ortholog in the phytopathogenic bacterium Xanthomonas axonopodis, as well as to a widespread family of plant natriuretic peptides and expansins, involved in plant homeostasis and plant cell wall modification (de Jonge & van Esse et al. 2012). We have identified an expanded Ave1-like gene family in apple and pear scab fungi, Venturia inaequalis and V. pirina. These species also have expanded gene families with similarity to the Leptosphaeria maculans effector AvrLm6. V. pirina has 14 unique hits (best,1.43e-18) to VdAve1. V. inaequalis has 17 unique hits (best,1.07e-22) to VdAve1. The distribution of Ave1 orthologs is suggestive of one or more cross-kingdom gene transfer events. We are characterising Venturia Ave1-like genes to investigate the mode of gene multiplication; seek evidence of horizontal gene transfer; and determine the role of Ave1-like genes in pathogenicity. Ave1-like genes from non-Venturia fungi (and the bacterial gene) do not contain predicted introns, however, several (not all) V. inaequalis Ave1-like genes are predicted to contain introns. Codon usage bias among fungal, plant, and bacterial Ave1 orthologs, are being compared with the aim of inferring the kingdom of origin of the Venturia Ave1 orthologs. At least two ViAve1 orthologs are up-regulated during infection of apple. To determine whether the Venturia Ave1 proteins also activate a Ve1-mediated hypersensitive response, each has been co-expressed with tomato Ve1 in Nicotiana tabacum, using an Agrobacterium tumefaciens-mediated transient transformation assay.
Measuring H2O and CO2 fluxes at field scales with scintillometry: Part II-Validation and application of 1-min flux estimates
Kesteren, A.J.H. van; Hartogensis, O.K. ; Dinther, D. van; Moene, A.F. ; Bruin, H.A.R. de; Holtslag, A.A.M. - \ 2013
Agricultural and Forest Meteorology 178-179 (2013). - ISSN 0168-1923 - p. 88 - 105.
carbon-dioxide exchange - temperature-humidity correlation - energy-balance closure - surface-layer fluxes - closed c-3 wheat - structure parameters - stomatal responses - moisture fluxes - boundary-layer - solar eclipse
This paper evaluates four methods to obtain accurate averaged flux estimates under conditions of non-stationary turbulence. In Part I (Van Kesteren et al., 2012), we introduced and evaluated these four combined methods for 30-min averaging intervals, notably the flux-variance method, the Bowen-variance method, the structure-parameter method, and the energy-balance method. The aim of this paper, Part II, is to validate the accuracy of the 1-min flux estimates of the CO2 flux, FCO2, and the evapotranspiration/latent-heat flux, LvE. Furthermore, we use the 1-min fluxes to investigate flux and vegetation responses under conditions of non-stationary turbulence. Using several validation methods, we show that both the eddy-covariance method and the energy-balance method are unsuitable for estimating fluxes over 1-min averaging intervals. The three other combined methods are more successful in determining 1-min fluxes. The random error is approximately half that of the eddy-covariance method, but still some issues limit the success. The Bowen-variance method has a +0.09 systematic error and moreover, 30% of the data had to be omitted, because the method requires more stringent conditions. Furthermore, the flux-variance method has a -0.15 systematic error. The structure-parameter method performs best of all methods and accurately resolves 1-min fluxes. With this method, we do a final validation with a different data set and show that also under dry conditions the method accurately resolves FCO2, although LE was more difficult to resolve. In the last part, the structure-parameter method is successfully applied under conditions of non-stationary turbulence. We show that LvE and FCO2 have a different step response upon abrupt changes in solar radiation, because different processes drive these fluxes. Also, we observe a 2-min time lag between solar radiation and 1-min fluxes and show the relevance of taking this into account for determining light-response curves of the plants for both 1-min and 30-min averaging intervals. Furthermore, we show the relevance of 1-min fluxes for studying the light-response curves of plants for conditions with different temperature and humidity. Finally, we show that accurate estimates of 1-min averaged canopy resistances can be determined via the resistance expressions for sensible heat and LvE. As such, we show that vegetation can indeed modify its canopy resistance significantly within several minutes. (c) 2013 Elsevier B.V. All rights reserved.
A critical revision of the estimation of the latent heat flux from two-wavelength scintillometry
Ward, H.C. ; Evans, J.G. ; Hartogensis, O.K. ; Moene, A.F. ; Debruin, H.A.R. ; Grimmond, C.S.B. - \ 2013
Quarterly Journal of the Royal Meteorological Society 139 (2013)676. - ISSN 0035-9009 - p. 1912 - 1922.
large-aperture scintillometer - heterogeneous land-surface - temperature-humidity correlation - refractive-index - water-vapor - structure parameters - regional advection - eddy-covariance - scintillation - fluctuations
Simultaneous scintillometer measurements at multiple wavelengths (pairing visible or infrared with millimetre or radio waves) have the potential to provide estimates of path-averaged surface fluxes of sensible and latent heat. Traditionally, the equations to deduce fluxes from measurements of the refractive index structure parameter at the two wavelengths have been formulated in terms of absolute humidity. Here, it is shown that formulation in terms of specific humidity has several advantages. Specific humidity satisfies the requirement for a conserved variable in similarity theory and inherently accounts for density effects misapportioned through the use of absolute humidity. The validity and interpretation of both formulations are assessed and the analogy with open-path infrared gas analyser density corrections is discussed. Original derivations using absolute humidity to represent the influence of water vapour are shown to misrepresent the latent heat flux. The errors in the flux, which depend on the Bowen ratio (larger for drier conditions), may be of the order of 10%. The sensible heat flux is shown to remain unchanged. It is also verified that use of a single scintillometer at optical wavelengths is essentially unaffected by these new formulations. Where it may not be possible to reprocess two-wavelength results, a density correction to the latent heat flux is proposed for scintillometry, which can be applied retrospectively to reduce the error.
Measuring H2O and CO2 fluxes at field scales with scintillometry: Part I – Introduction and validation of four methods
Kesteren, A.J.H. van; Hartogensis, O.K. ; Dinther, D. van; Moene, A.F. ; Bruin, H.A.R. de - \ 2013
Agricultural and Forest Meteorology 178-179 (2013). - ISSN 0168-1923 - p. 75 - 87.
small aperture scintillometer - monin-obukhov similarity - temperature-humidity correlation - energy-balance closure - stable boundary-layer - surface-layer - water-vapor - sensible heat - structure parameter - heterogeneous surface
This study introduces four methods for determining turbulent water vapour and carbon dioxide flux densities, the evapotranspiration and CO2 flux respectively. These methods combine scintillometer measurements with point-sampling measurements of scalar quantities and consequently have a faster statistical convergence than the eddy-covariance method. The scintillometer measures the friction velocity and stability averaged over space, allowing the time averaging to be a minute or less in homogenous conditions. This paper aims to thoroughly test the methods by analysing their sensitivity to the variables that go into the method and validate the methods with 30-min eddy-covariance data. Introduced are: the Bowen-variance method, the flux-variance method, the structure-parameter method, and the energy-balance method. Sensitivity analysis shows that each method is sensitive to the turbulence measurements of the scalar quantities that are specific to the method, as well as to the friction velocity. This demonstrates that the accuracy of the flux results from a correct representation of the turbulence variables used by the methods. Furthermore, a 30-min flux validation shows that the methods compare well to the independent eddy-covariance fluxes. We found that the structure-parameter method performs best – a low scatter (the correlation coefficient, r = 0.99) and a 5% underestimation were observed. Also the other methods perform well, although the energy-balance did not close, because storage terms and CO2 flux were neglected. Furthermore, during the night the variance methods were influenced by non-stationarity in the measurement signal. Finally, we suggest using the correlation coefficients between temperature and scalar quantities to acquire the sign of the fluxes. Data for this study were gathered in May–June 2009 over a wheat field near Merken, Germany, in the framework of the TransRegio32 program.
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