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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New robust weighted averaging- and model-based methods for assessing trait–environment relationships
Braak, Cajo J.F. ter - \ 2019
Methods in Ecology and Evolution 10 (2019)11. - ISSN 2041-210X - p. 1962 - 1971.
community assembly - community-weighted means - fourth-corner approach - generalized linear mixed models - species niche centroid - trait-based ecology - weighted averaging - Whittaker Siskiyou Mountains data

Statistical analysis of trait–environment association is challenging owing to the lack of a common observation unit: Community-weighted mean regression (CWMr) uses site points, multilevel models focus on species points, and the fourth-corner correlation uses all species-site combinations. This situation invites the development of new methods capable of using all observation levels. To this end, new multilevel and weighted averaging-based regression methods are proposed. Compared to existing methods, the new multilevel method, called MLM3, has additional site-related random effects; they represent the unknowns in the environment that interact with the trait. The new weighted averaging method combines site-level CWMr with a species-level regression of Species Niche Centroids on to the trait. Because species can vary enormously in frequency and abundance giving diversity variation among sites, the regressions are weighted by Hill's effective number (N2) of occurrences of each species and the N2-diversity of a site, and are subsequently combined in a sequential test procedure known as the max test. Using the test statistics of these new methods, the permutation-based max test provides strong statistical evidence for trait–environment association in a plant community dataset, where existing methods show weak evidence. In simulations, the existing multilevel model showed bias and type I error inflation, whereas MLM3 did not. Out of the weighted averaging-based regression methods, the N2-weighted version best controlled the type I error rate. MLM3 was superior to the weighted averaging-based methods with up to 30% more power. Both methods can be extended (a) to account for phylogeny and spatial autocorrelation and (b) to select functional traits and environmental variables from a greater set of variables.

Safety and efficacy of ChAdOx1 RVF vaccine against Rift Valley fever in pregnant sheep and goats
Stedman, Anna ; Wright, Daniel ; Wichgers Schreur, Paul J. ; Clark, Madeleine H.A. ; Hill, Adrian V.S. ; Gilbert, Sarah C. ; Francis, Michael J. ; Keulen, Lucien van; Kortekaas, Jeroen ; Charleston, Bryan ; Warimwe, George M. - \ 2019
Vaccines 4 (2019)1. - ISSN 2076-393X

Rift Valley fever virus (RVFV) is a zoonotic mosquito-borne virus that was first discovered in Kenya in 1930 and has since spread to become endemic in much of Africa and the Arabian Peninsula. Rift Valley fever (RVF) causes recurrent outbreaks of febrile illness associated with high levels of mortality and poor outcomes during pregnancy—including foetal malformations, spontaneous abortion and stillbirths—in livestock, and associated with miscarriage in humans. No vaccines are available for human use and those licensed for veterinary use have potential drawbacks, including residual virulence that may contraindicate their use in pregnancy. To address this gap, we previously developed a simian adenovirus vectored vaccine, ChAdOx1 RVF, that encodes RVFV envelope glycoproteins. ChAdOx1 RVF is fully protective against RVF in non-pregnant livestock and is also under development for human use. Here, we now demonstrate that when administered to pregnant sheep and goats, ChAdOx1 RVF is safe, elicits high titre RVFV neutralizing antibody, and provides protection against viraemia and foetal loss, although this protection is not as robust for the goats. In addition, we provide a description of RVFV challenge in pregnant goats and contrast this to the pathology observed in pregnant sheep. Together, our data further support the ongoing development of ChAdOx1 RVF vaccine for use in livestock and humans.

The Effect of Calcium Buffering and Calcium Sensor Type on the Sensitivity of an Array-Based Bitter Receptor Screening Assay.
Roelse, M. ; Wehrens, H.R.M.J. ; Henquet, M.G.L. ; Witkamp, R.F. ; Hall, R.D. ; Jongsma, M.A. - \ 2019
Chemical Senses 44 (2019)7. - ISSN 0379-864X - p. 497 - 505.
The genetically encoded calcium sensor protein Cameleon YC3.6 has previously been applied for functional G protein–coupled receptor screening using receptor cell arrays. However, different types of sensors are available, with a wide range in [Ca2+] sensitivity, Hill coefficients, calcium binding domains, and fluorophores, which could potentially improve the performance of the assay. Here, we compared the responses of 3 structurally different calcium sensor proteins (Cameleon YC3.6, Nano140, and Twitch2B) simultaneously, on a single chip, at different cytosolic expression levels and in combination with 2 different bitter receptors, TAS2R8 and TAS2R14. Sensor concentrations were modified by varying the amount of calcium sensor DNA that was printed on the DNA arrays prior to reverse transfection. We found that ~2-fold lower concentrations of calcium sensor protein, by transfecting 4 times less sensor-coding DNA, resulted in more sensitive bitter responses. The best results were obtained with Twitch2B, where, relative to YC3.6 at the default DNA concentration, a 4-fold lower DNA concentration increased sensitivity 60-fold and signal strength 5- to 10-fold. Next, we compared the performance of YC3.6 and Twitch2B against an array with 11 different bitter taste receptors. We observed a 2- to 8-fold increase in sensitivity using Twitch2B compared with YC3.6. The bitter receptor arrays contained 300 spots and could be exposed to a series of 18 injections within 1 h resulting in 5400 measurements. These optimized sensor conditions provide a basis for enhancing receptomics calcium assays for receptors with poor Ca2+ signaling and will benefit future high-throughput receptomics experiments.
Electrochemically Gated Long-Distance Charge Transport in Photosystem I
López-Martínez, Montse ; López-Ortiz, Manuel ; Antinori, Maria Elena ; Wientjes, Emilie ; Nin-Hill, Alba ; Rovira, Carme ; Croce, Roberta ; Díez-Pérez, Ismael ; Gorostiza, Pau - \ 2019
Angewandte Chemie-International Edition 58 (2019)38. - ISSN 1433-7851 - p. 13280 - 13284.
current decay - electrochemical gating - electron transfer - photosynthesis - scanning tunneling microscopy

The transport of electrons along photosynthetic and respiratory chains involves a series of enzymatic reactions that are coupled through redox mediators, including proteins and small molecules. The use of native and synthetic redox probes is key to understanding charge transport mechanisms and to the design of bioelectronic sensors and solar energy conversion devices. However, redox probes have limited tunability to exchange charge at the desired electrochemical potentials (energy levels) and at different protein sites. Herein, we take advantage of electrochemical scanning tunneling microscopy (ECSTM) to control the Fermi level and nanometric position of the ECSTM probe in order to study electron transport in individual photosystem I (PSI) complexes. Current–distance measurements at different potentiostatic conditions indicate that PSI supports long-distance transport that is electrochemically gated near the redox potential of P700, with current extending farther under hole injection conditions.

Introductory overview of identifiability analysis: A guide to evaluating whether you have the right type of data for your modeling purpose
Guillaume, Joseph H.A. ; Jakeman, John D. ; Marsili-Libelli, Stefano ; Asher, Michael ; Brunner, Philip ; Croke, B. ; Hill, Mary C. ; Jakeman, Anthony J. ; Keesman, Karel J. ; Razavi, S. ; Stigter, Johannes D. - \ 2019
Environmental Modelling & Software 119 (2019). - ISSN 1364-8152 - p. 418 - 432.
Derivative based methods - Emulation - Hessian - Identifiability - Non-uniqueness - Response surface - Uncertainty

Identifiability is a fundamental concept in parameter estimation, and therefore key to the large majority of environmental modeling applications. Parameter identifiability analysis assesses whether it is theoretically possible to estimate unique parameter values from data, given the quantities measured, conditions present in the forcing data, model structure (and objective function), and properties of errors in the model and observations. In other words, it tackles the problem of whether the right type of data is available to estimate the desired parameter values. Identifiability analysis is therefore an essential technique that should be adopted more routinely in practice, alongside complementary methods such as uncertainty analysis and evaluation of model performance. This article provides an introductory overview to the topic. We recommend that any modeling study should document whether a model is non-identifiable, the source of potential non-identifiability, and how this affects intended project outcomes.

Students’, colleagues’ and research partners’ experience about work and accomplishments from collaborating with Robin Thompson
Hickey, John ; Hill, William G. ; Blasco, Agustin ; Cameron, Neil ; Cullis, Brian ; McGuirk, Brian ; Mäntysaari, Esa ; Ruane, John ; Simm, Geoff ; Veerkamp, Roel ; Visscher, Peter M. ; Wray, Naomi R. - \ 2019
Journal of Animal Breeding and Genetics 136 (2019)4. - ISSN 0931-2668 - p. 301 - 309.
Bioturbation and erosion rates along the soil-hillslope conveyor belt, part 1: Insights from single-grain feldspar luminescence
Román-Sánchez, Andrea ; Reimann, Tony ; Wallinga, Jakob ; Vanwalleghem, Tom - \ 2019
Earth Surface Processes and Landforms 44 (2019)10. - ISSN 0197-9337 - p. 2051 - 2065.
bioturbation - Critical Zone - erosion - feldspar luminescence - soil formation

The interplay of bioturbation, soil production and long-term erosion–deposition in soil and landscape co-evolution is poorly understood. Single-grain post-infrared infrared stimulated luminescence (post-IR IRSL) measurements on sand-sized grains of feldspar from the soil matrix can provide direct information on all three processes. To explore the potential of this novel method, we propose a conceptual model of how post-IR IRSL-derived burial age and fraction of surface-visiting grains change with soil depth and along a hillslope catena. We then tested this conceptual model by comparison with post-IR IRSL results for 15 samples taken at different depths within four soil profiles along a hillslope catena in the Santa Clotilde Critical Zone Observatory (southern Spain). In our work, we observed clear differences in apparent post-IR IRSL burial age distributions with depth along the catena, with younger ages and more linear age–depth structure for the hill-base profile, indicating the influence of lateral deposition processes. We noted shallower soils and truncated burial age–depth functions for the two erosional mid-slope profiles, and an exponential decline of burial age with depth for the hill-top profile. We suggest that the downslope increase in the fraction of surface-visiting grains at intermediate depths (20 cm) indicates creep to be the dominant erosion process. Our study demonstrates that single-grain feldspar luminescence signature-depth profiles provide a new way of tracing vertical and lateral soil mixing and transport processes. In addition, we propose a new objective luminescence-based criterion for mapping the soil-bedrock boundary, thus producing soil depths in better agreement with geomorphological process considerations. Our work highlights the possibilities of feldspar single grain techniques to provide quantitative insights into soil production, bioturbation and erosion–deposition.

Bioturbation and erosion rates along the soil-hillslope conveyor belt, part 2: Quantification using an analytical solution of the diffusion–advection equation
Román-Sánchez, Andrea ; Laguna, Ana ; Reimann, Tony ; Giráldez, Juan Vicente ; Peña, Adolfo ; Vanwalleghem, Tom - \ 2019
Earth Surface Processes and Landforms 44 (2019)10. - ISSN 0197-9337 - p. 2066 - 2080.
bioturbation - critical zone - deposition - diffusivity - erosion - feldspar luminescence dating - sensitivity and uncertainty - soil formation

Particles on soil-mantled hillslopes are subject to downslope transport by erosion processes and vertical mixing by bioturbation. Both are key processes for understanding landscape evolution and soil formation, and affect the functioning of the critical zone. We show here how the depth–age information, derived from feldspar-based single grain post-infrared infrared stimulated luminescence (pIRIR), can be used to simultaneously quantify erosion and bioturbation processes along a hillslope. In this study, we propose, for the first time, an analytical solution for the diffusion–advection equation to calculate the diffusivity constant and erosion–deposition rates. We have fitted this model to age–depth data derived from 15 soil samples from four soil profiles along a catena located under natural grassland in the Santa Clotilde Critical Zone Observatory, in the south of Spain. A global sensitivity analysis was used to assess the relative importance of each model parameter in the output. Finally, the posterior probability density functions were calculated to evaluate the uncertainty in the model parameter estimates. The results show that the diffusivity constant at the surface varies from 11.4 to 81.9 mm2 a-1 for the hilltop and hill-base profile, respectively, and between 7.4 and 64.8 mm2 a-1 at 50 cm depth. The uncertainty in the estimation of the erosion–deposition rates was found to be too high to make a reliable estimate, probably because erosion–deposition processes are much slower than bioturbation processes in this environment. This is confirmed by a global sensitivity analysis that shows how the most important parameters controlling the age–depth structure in this environment are the diffusivity constant and regolith depth. Finally, we have found a good agreement between the soil reworking rates proposed by earlier studies, considering only particle age and depth, and the estimated diffusivity constants. The soil reworking rates are effective rates, corrected for the proportion of particles actually participating in the process.

Portraying primary fraction teaching: A variety of mathematical richness, pedagogic strategies, and use of curriculum materials
Thurlings, Marieke ; Koopman, Maaike ; Brok, Perry den; Pepin, Birgit - \ 2019
International Journal of Education in Mathematics, Science and Technology 7 (2019)2. - p. 170 - 185.
Cluster analysis - Explorative study - Fraction lessons - Instruction - Mathematical quality of

In this study, the variety in quality of instruction in fraction lessons at Grade 5 in Dutch primary schools was investigated. Twenty-four teachers participated in the study. To examine the quality of instruction of fraction lessons, Hill‟s mathematical quality of instruction framework and general pedagogical instruction strategies (seen to contribute to effective teaching) were combined into an observational scheme. In particular, it was investigated if profiles based on lesson observations could be identified using cluster analysis, and how these profiles could be characterized. The cluster analysis was validated by comparing different types of cluster analyses, discriminant analysis as well as via expert consultation sessions. Results showed six profiles of fraction lessons, which differed in terms of the extent to whether teaching was connectivist or transmissionist in nature, and the extent to which teaching was student-focused or content-focused. The study contributes to existing studies by developing the Quality of Instruction for Fraction Lessons (QIFL) framework, and by showing a more nuanced and richer picture of the teaching of fractions than previous studies. In terms of practical implications, the study showed that it is the combination of organizing a lesson well, a good pedagogical climate, and a focus on understanding the subject matter that contributes to good teaching.

Co-current crossflow microfiltration in a microchannel
Amar, Levy I. ; Hill, Michael I. ; Faria, Monica ; Guisado, Daniela ; Rijn, Cees J.M. van; Leonard, Edward F. - \ 2019
Biomedical Microdevices 21 (2019)1. - ISSN 1387-2176 - 1 p.
Blood - Constant transmembrane pressure - Cross-flow - Erythrocytes - Microfiltration model - Microfluidics - Microsieve - Nanopores - Plasma - Sieve

Steady state crossflow microfiltration (CMF) is an important and often necessary means of particle separation and concentration for both industrial and biomedical processes. The factors controlling the performance of CMF have been extensively reviewed. A major factor is transmembrane pressure (TMP). Because microchannels have small height, they tend to have high pressure gradients in the feed-flow direction. In the extreme, these gradients may even reverse the pressure across the membrane (inciting backflow). It is therefore desirable to compensate for the effect of feed-flow on the TMP, aiming at constant transmembrane pressure (cTMP) at a value which maximizes filtrate flux. This is especially critical during filtration of deformable particles (e.g. erythrocytes) through low intrinsic resistance membranes. Filtration flux is generally taken to be directly proportional to TMP, with pressure drop along the channel decreasing in the flow direction. A co-current flow of filtrate in a suitably designed filtrate collecting channel is shown to allow the TMP to remain constant and permit the sieving surface to perform optimally, permitting up to twice as much filtration over that of a naïve configuration. Manipulation of the filtrate channel may be even more beneficial if it prevents backflow that might otherwise occur at the end of a sufficiently long channel. Experiments with erythrocyte suspensions, reported here, validate these concepts.

Unexpected role of canonical aerobic methanotrophs in upland agricultural soils
Ho, Adrian ; Lee, Hyo Jung ; Reumer, Max ; Meima-Franke, Marion ; Raaijmakers, Ciska ; Zweers, Hans ; Boer, Wietse de; Putten, Wim H. Van der; Bodelier, Paul L.E. - \ 2019
Soil Biology and Biochemistry 131 (2019). - ISSN 0038-0717 - p. 1 - 8.
C labelling - High-affinity methane oxidation - Methylocystaceae - PLFA analysis/ land-use change - pmoA

Aerobic oxidation of methane at (circum-)atmospheric concentrations (<40 ppmv) has long been assumed to be catalyzed by the as-yet-uncultured high-affinity methanotrophs in well-aerated, non-wetland (upland) soils, the only known biological methane sink globally. Although the low-affinity canonical methanotrophs with cultured representatives have been detected along with the high-affinity ones, their role as a methane sink in upland soils remains enigmatic. Here, we show that canonical methanotrophs can contribute to (circum-)atmospheric methane uptake in agricultural soils. We performed a stable-isotope 13C–CH4 labelling incubation in the presence and absence of bio-based residues that were added to the soil to track the flow of methane. Residue amendment transiently stimulated methane uptake rate (<50 days). Soil methane uptake was sustained throughout the incubation (130 days), concomitant to the enrichment of 13C–CO2. The 13C-enriched phospholipid fatty acids (PLFAs) were distinct in both soils, irrespective of amendments, and were unambiguously assigned almost exclusively to canonical alphaproteobacterial methanotrophs with cultured representatives. 16S rRNA and pmoA gene sequence analyses revealed that the as-yet-uncultured high-affinity methanotrophs were virtually absent in these soils. The stable-isotope labelling approach allowed to attribute soil methane uptake to canonical methanotrophs, whereas these were not expected to consume (circum-)atmospheric methane. Our findings thus revealed an overlooked reservoir of high-affinity methane-oxidizers represented by the canonical methanotrophs in agriculture-impacted upland soils. Given that upland agricultural soils have been thought to marginally or do not contribute to atmospheric methane consumption due to the vulnerability of the high-affinity methanotrophs, our findings suggest a thorough revisiting of the contribution of agricultural soils, and the role of agricultural management to mitigation of climate change.

Understanding mode of action can drive the translational pipeline towards more reliable health benefits for probiotics
Kleerebezem, Michiel ; Binda, Sylvie ; Bron, Peter A. ; Gross, Gabriele ; Hill, Colin ; Hylckama Vlieg, Johan E.T. van; Lebeer, Sarah ; Satokari, Reetta ; Ouwehand, Arthur C. - \ 2019
Current Opinion in Biotechnology 56 (2019). - ISSN 0958-1669 - p. 55 - 60.

The different levels of knowledge described in a translational pipeline (the connection of molecular mechanisms with pre-clinical physiological and human health effects) are not complete for many probiotics. At present, we are not in a position to fully understand the mechanistic basis of many well established probiotic health benefits which, in turn, limits our ability to use mechanisms to predict which probiotics are likely to be effective in any given population. Here we suggest that this concept of a translation pipeline connecting mechanistic insights to probiotic efficacy can support the selection and production of improved probiotic products. Such a conceptual pipeline would also provide a framework for the design of clinical trials to convincingly demonstrate the benefit of probiotics to human health in well-defined subpopulations.

First records of Hyalomma rufipes and Ixodes neitzi (Acari : Ixodidae) found on large carnivores in South Africa
Baauw, Anna H. ; Heyne, Heloise ; Williams, Kathryn S. ; Hill, Russell A. ; Heitkönig, Ignas M.A. ; Williams, Samual T. - \ 2019
Ticks and Tick-borne Diseases 10 (2019)1. - ISSN 1877-959X - p. 128 - 131.
Brown hyena - Hyalomma rufipes - Ixodes neitzi - Leopard

Ixodid ticks (Acari: Ixodidae) are important disease vectors for large carnivores, but the composition of the tick communities that parasitize carnivores is poorly understood. We collected ticks from leopards (Panthera pardus) and brown hyenas (Hyaena brunnea) in the Soutpansberg Mountains, South Africa, to determine which species feed on these carnivores. We identified a total of eight tick species belonging to six genera, and recorded Ixodes neitzi and Hyalomma rufipes on P. pardus for the first time.

Erratum to: The sponge microbiome project
Moitinho-Silva, Lucas ; Nielsen, Shaun ; Amir, Amnon ; Gonzalez, Antonio ; Ackermann, Gail L. ; Cerrano, Carlo ; Astudillo-Garcia, Carmen ; Easson, Cole ; Sipkema, Detmer ; Liu, Fang ; Steinert, Georg ; Kotoulas, Giorgos ; McCormack, Grace P. ; Feng, Guofang ; Bell, James J. ; Vicente, Jan ; Björk, Johannes R. ; Montoya, Jose M. ; Olson, Julie B. ; Reveillaud, Julie ; Steindler, Laura ; Pineda, Mari Carmen ; Marra, Maria V. ; Ilan, Micha ; Taylor, Michael W. ; Polymenakou, Paraskevi ; Erwin, Patrick M. ; Schupp, Peter J. ; Simister, Rachel L. ; Knight, Rob ; Thacker, Robert W. ; Costa, Rodrigo ; Hill, Russell T. ; Lopez-Legentil, Susanna ; Dailianis, Thanos ; Ravasi, Timothy ; Hentschel, Ute ; Li, Zhiyong ; Webster, Nicole S. ; Thomas, Torsten - \ 2018
GigaScience 7 (2018)12. - ISSN 2047-217X
Root branching toward water involves posttranslational modification of transcription factor ARF7
Orosa-Puente, Beatriz ; Leftley, Nicola ; Wangenheim, Daniel von; Banda, Jason ; Srivastava, Anjil K. ; Hill, Kristine ; Truskina, Jekaterina ; Bhosale, Rahul ; Morris, Emily ; Srivastava, Moumita ; Kümpers, Britta ; Goh, Tatsuaki ; Fukaki, Hidehiro ; Vermeer, Joop E.M. ; Vernoux, Teva ; Dinneny, José R. ; French, Andrew P. ; Bishopp, Anthony ; Sadanandom, Ari ; Bennett, Malcolm J. - \ 2018
Science 362 (2018)6421. - ISSN 0036-8075 - p. 1407 - 1410.

Plants adapt to heterogeneous soil conditions by altering their root architecture. For example, roots branch when in contact with water by using the hydropatterning response. We report that hydropatterning is dependent on auxin response factor ARF7. This transcription factor induces asymmetric expression of its target gene LBD16 in lateral root founder cells. This differential expression pattern is regulated by posttranslational modification of ARF7 with the small ubiquitin-like modifier (SUMO) protein. SUMOylation negatively regulates ARF7 DNA binding activity. ARF7 SUMOylation is required to recruit the Aux/IAA (indole-3-acetic acid) repressor protein IAA3. Blocking ARF7 SUMOylation disrupts IAA3 recruitment and hydropatterning. We conclude that SUMO-dependent regulation of auxin response controls root branching pattern in response to water availability.

A protocol for an intercomparison of biodiversity and ecosystem services models using harmonized land-use and climate scenarios
Kim, Hyejin ; Rosa, Isabel M.D. ; Alkemade, Rob ; Leadley, Paul ; Hurtt, George ; Popp, Alexander ; Vuuren, Detlef P. van; Anthoni, Peter ; Arneth, Almut ; Baisero, Daniele ; Caton, Emma ; Chaplin-Kramer, Rebecca ; Chini, Louise ; Palma, Adriana De; Fulvio, Fulvio Di; Marco, Moreno Di; Espinoza, Felipe ; Ferrier, Simon ; Fujimori, Shinichiro ; Gonzalez, Ricardo E. ; Gueguen, Maya ; Guerra, Carlos ; Harfoot, Mike ; Harwood, Thomas D. ; Hasegawa, Tomoko ; Haverd, Vanessa ; Havlík, Petr ; Hellweg, Stefanie ; Hill, Samantha L.L. ; Hirata, Akiko ; Hoskins, Andrew J. ; Janse, Jan H. ; Jetz, Walter ; Johnson, Justin A. ; Krause, Andreas ; Leclère, David ; Martins, Ines S. ; Matsui, Tetsuya ; Merow, Cory ; Obersteiner, Michael ; Ohashi, Haruka ; Poulter, Benjamin ; Purvis, Andy ; Quesada, Benjamin ; Rondinini, Carlo ; Schipper, Aafke M. ; Sharp, Richard ; Takahashi, Kiyoshi ; Thuiller, Wilfried ; Titeux, Nicolas - \ 2018
Geoscientific Model Development 11 (2018)11. - ISSN 1991-959X - p. 4537 - 4562.

To support the assessments of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES), the IPBES Expert Group on Scenarios and Models is carrying out an intercomparison of biodiversity and ecosystem services models using harmonized scenarios (BES-SIM). The goals of BES-SIM are (1) to project the global impacts of land-use and climate change on biodiversity and ecosystem services (i.e., nature's contributions to people) over the coming decades, compared to the 20th century, using a set of common metrics at multiple scales, and (2) to identify model uncertainties and research gaps through the comparisons of projected biodiversity and ecosystem services across models. BES-SIM uses three scenarios combining specific Shared Socio-economic Pathways (SSPs) and Representative Concentration Pathways (RCPs)-SSP1xRCP2.6, SSP3xRCP6.0, SSP5xRCP8.6-to explore a wide range of land-use change and climate change futures. This paper describes the rationale for scenario selection, the process of harmonizing input data for land use, based on the second phase of the Land Use Harmonization Project (LUH2), and climate, the biodiversity and ecosystem services models used, the core simulations carried out, the harmonization of the model output metrics, and the treatment of uncertainty. The results of this collaborative modeling project will support the ongoing global assessment of IPBES, strengthen ties between IPBES and the Intergovernmental Panel on Climate Change (IPCC) scenarios and modeling processes, advise the Convention on Biological Diversity (CBD) on its development of a post-2020 strategic plans and conservation goals, and inform the development of a new generation of nature-centred scenarios.

Erythrocyte fouling on micro-engineered membranes
Amar, Levy I. ; Guisado, Daniela ; Faria, Monica ; Jones, James P. ; Rijn, Cees J.M. van; Hill, Michael I. ; Leonard, Edward F. - \ 2018
Biomedical Microdevices 20 (2018)3. - ISSN 1387-2176
Blood - Cross-flow - Erythrocytes - Fouling - Microfiltration model - Microfluidics - Microsieve - Nanopores - Photolithography - Sieve

Crossflow microfiltration of plasma from blood through microsieves in a microchannel is potentially useful in many biomedical applications, including clinically as a wearable water removal device under development by the authors. We report experiments that correlate filtration rates, transmembrane pressures (TMP) and shear rates during filtration through a microscopically high channel bounded by a low intrinsic resistance photolithographically-produced porous semiconductor membrane. These experiments allowed observation of erythrocyte behavior at the filtering surface and showed how their unique deformability properties dominated filtration resistance. At low filtration rates (corresponding to low TMP), they rolled along the filter surface, but at higher filtration rates (corresponding to higher TMP), they anchored themselves to the filter membrane, forming a self-assembled, incomplete monolayer. The incompleteness of the layer was an essential feature of the monolayer’s ability to support sustainable filtration. Maximum steady-state filtration flux was a function of wall shear rate, as predicted by conventional crossflow filtration theory, but, contrary to theories based on convective diffusion, showed weak dependence of filtration on erythrocyte concentration. Post-filtration scanning electron micrographs revealed significant capture and deformation of erythrocytes in all filter pores in the range 0.25 to 2 μm diameter. We report filtration rates through these filters and describe a largely unrecognized mechanism that allows stable filtration in the presence of substantial cell layers.

High spatial variation in population size and symbiotic performance of Rhizobium leguminosarum bv. trifolii with white clover in New Zealand pasture soils
Wakelin, Steven ; Tillard, Guyléne ; Ham, Robert van; Ballard, Ross ; Farquharson, Elizabeth ; Gerard, Emily ; Geurts, Rene ; Brown, Matthew ; Ridgway, Hayley ; O’Callaghan, Maureen - \ 2018
PLoS ONE 13 (2018)2. - ISSN 1932-6203
Biological nitrogen fixation through the legume-rhizobia symbiosis is important for sustainable pastoral production. In New Zealand, the most widespread and valuable symbiosis occurs between white clover (Trifolium repens L.) and Rhizobium leguminosarum bv. trifolii (Rlt). As variation in the population size (determined by most probable number assays; MPN) and effectiveness of N-fixation (symbiotic potential; SP) of Rlt in soils may affect white clover performance, the extent in variation in these properties was examined at three different spatial scales: (1) From 26 sites across New Zealand, (2) at farm-wide scale, and (3) within single fields. Overall, Rlt populations ranged from 95 to >1 x 108 per g soil, with variation similar at the three spatial scales assessed. For almost all samples, there was no relationship between rhizobia population size and ability of the population to fix N during legume symbiosis (SP). When compared with the commercial inoculant strain, the SP of soils ranged between 14 to 143% efficacy. The N-fixing ability of rhizobia populations varied more between samples collected from within a single hill country field (0.8 ha) than between 26 samples collected from diverse locations across New Zealand. Correlations between SP and calcium and aluminium content were found in all sites, except within a dairy farm field. Given the general lack of association between SP and MPN, and high spatial variability of SP at single field scale, provision of advice for treating legume seed with rhizobia based on field-average MPN counts needs to be carefully considered.
Feeding the world while reducing farmer poverty? Analysis of rice relative yield and labour productivity gaps in two Beninese villages
Paresys, Lise ; Saito, Kazuki ; Dogliotti, Santiago ; Malézieux, Eric ; Huat, Joël ; Kropff, Martin J. ; Rossing, Walter A.H. - \ 2018
European Journal of Agronomy 93 (2018). - ISSN 1161-0301 - p. 95 - 112.
Labour productivity gap - Labour-saving technologies - Management practices - Rice - Yield gap
Improvements in agricultural land and labour productivity are needed to meet the growing food demand and reduce farmer poverty in sub-Saharan Africa. The objectives of this study were to (i) quantify variation in labour inputs, yield and labour productivity among rice fields; (ii) elicit factors associated with this variation; and (iii) identify opportunities for improving yield and labour productivity. The study was carried out in two contrasting Beninese villages: Zonmon in the south and Pelebina in the north-west. In Zonmon 82 irrigated rice fields were surveyed during the 2013 and 2014 dry seasons. In Pelebina 50 rainfed lowland rice fields were surveyed over three rainy seasons (2012–2014). Data on farmer field management practices and field conditions were recorded through interviews with farmers, on-farm observations and measurements. Stepwise regression analyses were used to identify variables associated with variation in yield, labour inputs and labour productivity. Average yields were 4.8 ± 2.0 t ha−1 in Zonmon and 2.3 ± 1.2 t ha−1 in Pelebina. Average labour productivity, however, was larger in Pelebina (17 kg of paddy rice person-day−1) than in Zonmon (8 kg of paddy rice person-day−1). Relative yield gaps (43–48%) and labour productivity gaps (59–63%) were similar in the villages. There was no trade-off between yield and labour or labour productivity within the villages, suggesting that in many cases rice yields can be increased without additional labour inputs. The major labour-demanding farming operations were bird scaring in Zonmon and harvesting and threshing in Pelebina. We identified opportunities to improve rice yield and labour productivity, given current farmer knowledge and resource endowment. Based on the statistical models fitted per village, increasing the average hill density would result in up to 1.2 t ha−1 more yield, and up to 4 kg person-day−1 greater labour productivity for Zonmon. Increasing the average field size and avoiding rice shading would result in up to 0.8 t ha−1 more yield, and up to 17.1 kg person-day−1 greater labour productivity for Pelebina. Further enhancing yield and labour productivity will require (i) introducing small-scale mechanisation and other labour-saving innovations, in particular for labour-demanding farming operations such as bird scaring in Zonmon and harvesting and threshing in Pelebina; and (ii) combining analyses of yields and labour productivities at field level with detailed analyses of labour use and labour productivity at farm level. We found that, on average, one hectare in Zonmon contributed twice as much to Beninese rice production than one hectare in Pelebina but with a two times smaller reward for farmer labour. This paradox of higher yields but lower labour productivity in such different rice growing environments and farming systems should be addressed in elaborating development policies.
Culex quinquefasciatus quinquefasciatus strain:Thai Transcriptome or Gene expression
Taparia, T. ; Ignell, Rickard ; Hill, Sharon Rose - \ 2017
PRJNA385151 - Culex quinquefasciatus quinquefasciatus
This study used quantitative RNA-Sequencing analyses to explore blood meal induced regulation of chemosensory gene families in the antennae of 6 days post-emergence C. quinquefasciatus females, 24 hours post blood feeding.
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