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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    Risks to biodiversity from cocoa suitability shifts under a changing climate
    Arnell, A.P. ; Sassen, M. ; Hill, S.J. ; Soesbergen, A. van - \ 2020
    Unfolding Dilemmas of Urban Public Spaces : Recommendations by JPI Urban Europe’s AGORA
    Riegler, Johannes ; Bylund, Jonas ; Ersoy, Aksel ; Wrangsten, Caroline ; Odbert, Chelina ; Gollner, Christoph ; Lee, Dahae ; Hill, Emma ; Lorenz, Florian ; Mulligan, Joe ; Peters, Karin - \ 2020
    JPI Urban Europe - 81 p.
    Bending the curve of terrestrial biodiversity needs an integrated strategy
    Leclère, David ; Obersteiner, Michael ; Barrett, Mike ; Butchart, Stuart H.M. ; Chaudhary, Abhishek ; Palma, Adriana De; DeClerck, Fabrice A.J. ; Marco, Moreno Di; Doelman, Jonathan C. ; Dürauer, Martina ; Freeman, Robin ; Harfoot, Michael ; Hasegawa, Tomoko ; Hellweg, Stefanie ; Hilbers, Jelle P. ; Hill, Samantha L.L. ; Humpenöder, Florian ; Jennings, Nancy ; Krisztin, Tamás ; Mace, Georgina M. ; Ohashi, Haruka ; Popp, Alexander ; Purvis, Andy ; Schipper, Aafke M. ; Tabeau, Andrzej ; Valin, Hugo ; Meijl, Hans van; Zeist, Willem Jan van; Visconti, Piero ; Alkemade, Rob ; Almond, Rosamunde ; Bunting, Gill ; Burgess, Neil D. ; Cornell, Sarah E. ; Fulvio, Fulvio Di; Ferrier, Simon ; Fritz, Steffen ; Fujimori, Shinichiro ; Grooten, Monique ; Harwood, Thomas ; Havlík, Petr ; Herrero, Mario ; Hoskins, Andrew J. ; Jung, Martin ; Kram, Tom ; Lotze-Campen, Hermann ; Matsui, Tetsuya ; Meyer, Carsten ; Nel, Deon ; Newbold, Tim ; Schmidt-Traub, Guido ; Stehfest, Elke ; Strassburg, Bernardo B.N. ; Vuuren, Detlef P. van; Ware, Chris ; Watson, James E.M. ; Wu, Wenchao ; Young, Lucy - \ 2020
    Nature 585 (2020). - ISSN 0028-0836 - p. 551 - 556.

    Increased efforts are required to prevent further losses to terrestrial biodiversity and the ecosystem services that it provides1,2. Ambitious targets have been proposed, such as reversing the declining trends in biodiversity3; however, just feeding the growing human population will make this a challenge4. Here we use an ensemble of land-use and biodiversity models to assess whether—and how—humanity can reverse the declines in terrestrial biodiversity caused by habitat conversion, which is a major threat to biodiversity5. We show that immediate efforts, consistent with the broader sustainability agenda but of unprecedented ambition and coordination, could enable the provision of food for the growing human population while reversing the global terrestrial biodiversity trends caused by habitat conversion. If we decide to increase the extent of land under conservation management, restore degraded land and generalize landscape-level conservation planning, biodiversity trends from habitat conversion could become positive by the mid-twenty-first century on average across models (confidence interval, 2042–2061), but this was not the case for all models. Food prices could increase and, on average across models, almost half (confidence interval, 34–50%) of the future biodiversity losses could not be avoided. However, additionally tackling the drivers of land-use change could avoid conflict with affordable food provision and reduces the environmental effects of the food-provision system. Through further sustainable intensification and trade, reduced food waste and more plant-based human diets, more than two thirds of future biodiversity losses are avoided and the biodiversity trends from habitat conversion are reversed by 2050 for almost all of the models. Although limiting further loss will remain challenging in several biodiversity-rich regions, and other threats—such as climate change—must be addressed to truly reverse the declines in biodiversity, our results show that ambitious conservation efforts and food system transformation are central to an effective post-2020 biodiversity strategy.

    Regional Mapping and Spatial Distribution Analysis of Canopy Palms in an Amazon Forest Using Deep Learning and VHR Images
    Wagner, Fabien H. ; Dalagnol, Ricardo ; Tagle Casapia, Ximena ; Streher, Annia S. ; Phillips, Oliver L. ; Gloor, Emanuel ; Aragão, Luiz E.O.C. - \ 2020
    Remote Sensing 12 (2020)14. - ISSN 2072-4292
    Mapping plant species at the regional scale to provide information for ecologists and forest managers is a challenge for the remote sensing community. Here, we use a deep learning algorithm called U-net and very high-resolution multispectral images (0.5 m) from GeoEye satellite to identify, segment and map canopy palms over ∼3000 km 2 of Amazonian forest. The map was used to analyse the spatial distribution of canopy palm trees and its relation to human disturbance and edaphic conditions. The overall accuracy of the map was 95.5% and the F1-score was 0.7. Canopy palm trees covered 6.4% of the forest canopy and were distributed in more than two million patches that can represent one or more individuals. The density of canopy palms is affected by human disturbance. The post-disturbance density in secondary forests seems to be related to the type of disturbance, being higher in abandoned pasture areas and lower in forests that have been cut once and abandoned. Additionally, analysis of palm trees’ distribution shows that their abundance is controlled naturally by local soil water content, avoiding both flooded and waterlogged areas near rivers and dry areas on the top of the hills. They show two preferential habitats, in the low elevation above the large rivers, and in the slope directly below the hill tops. Overall, their distribution over the region indicates a relatively pristine landscape, albeit within a forest that is critically endangered because of its location between two deforestation fronts and because of illegal cutting. New tree species distribution data, such as the map of all adult canopy palms produced in this work, are urgently needed to support Amazon species inventory and to understand their distribution and diversity.
    Tutorial and R-package TraitEnvMLMWA for new robust weighted averaging- and model-based methods for assessing trait-environment relationships
    Braak, C.J.F. ter - \ 2019
    Wageningen : Wageningen University & Research
    This material with R-code and R package TraitEnvMLMWA is part of the paper "ter Braak (2019) New robust weighted averaging- and model-based methods for assessing trait-environment relationships. Methods in Ecology and Evolution https://doi.org/10.1111/2041-210X.13278 ". This is the version 8, a minor update. See readme.txt. The abstract of the paper is:

    1. 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.

    2. 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.

    3. 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.
    Potential impacts of agricultural development on freshwater biodiversity in the Lake Victoria basin
    Soesbergen, Arnout van; Sassen, Marieke ; Kimsey, Samuel ; Hill, Samantha - \ 2019
    Aquatic conservation: marine and freshwater ecosystems 29 (2019)7. - ISSN 1052-7613 - p. 1052 - 1062.
    agricultural development - freshwater biodiversity - Lake Victoria - land-use change - modelling - rivers - scenarios

    The Lake Victoria basin (LVB) and its tributary rivers are a major biodiversity hot spot, containing at least 234 native fish species, 135 native aquatic plant species, and 50 native freshwater mollusc species. Lake Victoria itself is home to around 500 fish species, most of which are haplochromine cichlids. The LVB is increasingly under threat from unsustainable land conversion and the intensification of agriculture. High population growth is driving the expansion of agriculture, urbanization, and freshwater abstractions, which have a profound impact on freshwater biodiversity. In addition, increased demand for agricultural crops from domestic and international markets are likely to lead to larger agricultural operations, further threatening freshwater biodiversity. This study explores these potential future impacts on the biodiversity found in freshwater rivers in the LVB as a result of projected future changes in land use. A newly developed database of land-use impacts on freshwater biodiversity is introduced, with a focus on ecological community composition data from freshwater habitats under human pressures. Impacts on freshwater biodiversity are then projected under four different scenarios of land-use change. Results show that land use has a significant impact on freshwater biodiversity. Freshwater biodiversity is projected to be at most risk in sub-basins in the Tanzanian, Rwandan, and Burundian part of the LVB, such as the Kagera and Magoga/Isonga sub-basins. Local species richness levels are particularly affected in the Magoga/Isonga sub-basin in Tanzania, with an average loss of 10.8% across all scenarios. Model results show the potential to identify broad spatial patterns of likely threats and pressures on freshwater ecosystems under different socio-economic futures. The analysis of these patterns, where they are consistent and where they differ, can support the production of policy that strives to find the optimal balance between development and conservation in an uncertain future.

    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. - ISSN 2147-611X - 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
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