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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    From Eat to trEat : Engineering the mitochondrial Eat1 enzyme for enhanced ethyl acetate production in Escherichia coli
    Kruis, Aleksander J. ; Bohnenkamp, Anna C. ; Nap, Bram ; Nielsen, Jochem ; Mars, Astrid E. ; Wijffels, Rene H. ; Oost, John Van Der; Kengen, Servé W.M. ; Weusthuis, Ruud A. - \ 2020
    Biotechnology for Biofuels 13 (2020)1. - ISSN 1754-6834
    Alcohol acetyl transferase (AAT) - Eat1 - Escherichia coli - Ethyl acetate - Mitochondria

    Background: Genetic engineering of microorganisms has become a common practice to establish microbial cell factories for a wide range of compounds. Ethyl acetate is an industrial solvent that is used in several applications, mainly as a biodegradable organic solvent with low toxicity. While ethyl acetate is produced by several natural yeast species, the main mechanism of production has remained elusive until the discovery of Eat1 in Wickerhamomyces anomalus. Unlike other yeast alcohol acetyl transferases (AATs), Eat1 is located in the yeast mitochondria, suggesting that the coding sequence contains a mitochondrial pre-sequence. For expression in prokaryotic hosts such as E. coli, expression of heterologous proteins with eukaryotic signal sequences may not be optimal. Results: Unprocessed and synthetically truncated eat1 variants of Kluyveromyces marxianus and Wickerhamomyces anomalus have been compared in vitro regarding enzyme activity and stability. While the specific activity remained unaffected, half-life improved for several truncated variants. The same variants showed better performance regarding ethyl acetate production when expressed in E. coli. Conclusion: By analysing and predicting the N-terminal pre-sequences of different Eat1 proteins and systematically trimming them, the stability of the enzymes in vitro could be improved, leading to an overall improvement of in vivo ethyl acetate production in E. coli. Truncated variants of eat1 could therefore benefit future engineering approaches towards efficient ethyl acetate production.

    Farm-scale bio-power-to-methane: Comparative analyses of economic and environmental feasibility
    Bekkering, Jan ; Zwart, Kor ; Martinus, Gerard ; Langerak, Jort ; Tideman, Jeroen ; Meij, Tineke van der; Alberts, Kees ; Steenis, Machiel van; Nap, Jan Peter - \ 2020
    International Journal of Energy Research 44 (2020)3. - ISSN 0363-907X - p. 2264 - 2277.
    bio-methanation - biogas - electrolysis - energy efficiency - greenhouse gas emission saving - supply chain optimisation

    Power-to-gas technologies are considered to be part of the future energy system, but their viability and applicability need to be assessed. Therefore, models for the viability of farm-scale bio-power-to-methane supply chains to produce green gas were analysed in terms of levelised cost of energy, energy efficiency and saving of greenhouse gas emission. In bio-power-to-methane, hydrogen from electrolysis driven by surplus renewable electricity and carbon dioxide from biogas are converted to methane by microbes in an ex situ trickle-bed reactor. Such bio-methanation could replace the current upgrading of biogas to green gas with membrane technology. Four scenarios were compared: a reference scenario without bio-methanation (A), bio-methanation (B), bio-methanation combined with membrane upgrading (C) and the latter with use of renewable energy only (all-green; D). The reference scenario (A) has the lowest costs for green gas production, but the bio-methanation scenarios (B-D) have higher energy efficiencies and environmental benefits. The higher costs of the bio-methanation scenarios are largely due to electrolysis, whereas the environmental benefits are due to the use of renewable electricity. Only the all-green scenario (D) meets the 2026 EU goal of 80% reduction of greenhouse gas emissions, but it would require a CO2 price of 200 € t−1 to achieve the levelised cost of energy of 65 €ct Nm−3 of the reference scenario. Inclusion of the intermittency of renewable energy in the scenarios substantially increases the costs. Further greening of the bio-methanation supply chain and how intermittency is best taken into account need further investigation.

    Biological treatment of gas pollutants in partitioning bioreactors
    Lebrero, Raquel ; Frutos Osvaldo, David ; Pérez, Victor ; Cantera, Sara ; Estrada, José Manuel ; Muñoz, Raúl - \ 2019
    In: Advances in Chemical Engineering / Huerta-Ochoa, Sergio, Castillo-Araiza, Carlos O., Quijano, Guillermo, Academic Press Inc. (Advances in Chemical Engineering ) - ISBN 9780128149966 - p. 239 - 274.
    Gas treatment - Gas-liquid mass transfer - Hydrophobic pollutants - NAP - Robustness

    The off-gas treatment of hydrophobic pollutants in conventional biotechnologies is typically limited by the gas-liquid mass transfer as a result of the low-concentration gradient imposed by their high partitioning coefficients. The addition of a non-aqueous-phase (NAP) with a high affinity for the gas pollutant to packed bed or suspended-growth bioreactor configurations has resulted in enhanced elimination capacities and process robustness. Despite recent research has just added more desired characteristics to the selection criteria of the optimum NAP in gas treatment applications, silicone oil continues being the most popular mass transfer vector. This technology has been successfully applied to the treatment of hexane, methane, styrene, alpha-pinene and BTEX in biofilters, biotrickling filters, stirred tank and airlift bioreactors. The maximum potential of two-phase partitioning bioreactors (TPPBs) during off-gas treatment is achieved when the microbial community is confined inside the NAP. TPPB modeling has also experienced significant advances, the most advanced platforms being able to describe the recent findings in the field. This chapter will compile and critically discuss the fundamentals and most recent breakthroughs in the field of TPPBs for gas treatment applications.

    Application of high performance compute technology in bioinformatics
    Warris, Sven - \ 2019
    Wageningen University. Promotor(en): D. de Ridder, co-promotor(en): J.P. Nap. - Wageningen : Wageningen University - ISBN 9789463951128 - 156

    Bioinformatics and computational biology are driven by growing volumes of data in biological systems that also tend to increase in complexity. The research presented in this thesis focuses on the need to analyze such data volumes in such complexity. The results show that the application of high-performance compute technologies, preferably combined with low-cost hardware, is a successful approach to generate new bioinformatics approaches that allow addressing new types of data analyses and research questions in biology.

    An overview of the technologies and recent developments in biology and computer science relevant for this thesis (Chapter 1) identifies current high-throughput sequencing platforms as a key technology. Sequencing platforms now deliver data sets up to terabytes in size for elucidating genome structure, gene content, gene activity, as well as gene variants. The concepts and technologies from computer science to handle these large amounts of data include (a) grid technologies for compute parallelization while making more efficient use of existing low-cost infrastructure; (b) graphics cards for increased compute power and (c) graph databases for large data volume storage and advanced methods for analyses. This thesis presents novel applications and added value of these three concepts for bioinformatics research.

    Small RNAs are important regulators of genome function, yet their prediction in genomes is still a major computational challenge (Chapter 2). They tend to have a minimal free energy (MFE) significantly lower than the MFE of non-small RNA sequences with the same nucleotide composition. Evaluation of many MFEs is, however, too compute-intensive for genome-wide screening. With a local grid infrastructure of desktop computers, MFE distributions of a very large collection of sequence compositions were pre-calculated and used to determine the MFE distribution for any given sequence composition by interpolation. This approach allows on-the-fly calculation for any candidate sequence composition and makes genome-wide screening with this characteristic of a pre-miRNA sequence feasible. This way, MFE evaluation can be added as a new parameter for genome-wide selection of potential small RNA candidates (Chapter 2). The concept of large-scale pre-calculation of compute-intensive parameters is one of the options for future bioinformatics analyses.

    Sequence alignment is essential in the analysis of next-generation sequencing data. The gold standard for sequence alignment is the Smith-Waterman (SW) algorithm. Existing implementations of the full SW algorithm are either not fast enough, or limited to dedicated tasks, usually to optimize for speed, whereas popular heuristic SW versions (such as BLAST) suffer from statistical issues. Graphics hardware is well-suited to speed up SW alignments, but SW on graphics cards does not report the alignment details desired by biologists for further analysis. This thesis presents the CUDA-based Parallel SW Alignment Software (PaSWAS) (Chapter 3). PaSWAS gives (a) easy access to the computational power of NVIDIA-based graphics cards for high-speed sequence alignments, (b) information such as score, number of gaps and mismatches with the accuracy of the full SW algorithm and (c) a report of multiple hits per alignment. Two use cases show the usability and versatility of the new parallel Smith-Waterman implementation for bioinformatics analyses. It demonstrates the added value of the use of low-cost graphics cards in bioinformatics software.

    To further promote the use of PaSWAS, a new implementation, pyPaSWAS, provides the SW sequence alignment code fully packed in Python and the more widely accepted OpenCL language (Chapter 4). Moreover, pyPaSWAS now supports an affine gap penalty. This way, pyPaSWAS presents an easy Python-based environment for accurate and retrievable parallel SW sequence alignments on GPUs and multi-core systems. The strategy of integrating Python with high-performance parallel compute languages to create a developer- and user-friendly environment is worth to be considered for other computationally-intensive bioinformatics algorithms.

    Thanks to the accuracy and retrieval characteristics of (py)PaSWAS, it was noted that long sequencing reads on the PacBio platform can contain many artificial palindromic sequences. These palindromes are due to errors introduced by whole-genome amplification (WGA). Next-generation sequencing requires sufficient amounts of DNA. If not available, WGA is routinely used to generate the amounts of DNA required. The introduction of artificial palindromic sequences hampers assembly and severely limits the value of long sequencing reads. Pacasus is a novel software tool to identify and resolve such artificial palindromic sequences in long sequencing reads (Chapter 5). Two use cases show that Pacasus markedly improves read mapping and assembly of WGA DNA. In comparison, the quality of mapping and assembly is similar to the quality obtained with non-amplified DNA. Therefore, with Pacasus, long-read technology becomes feasible for the sequencing of samples for which only very small amounts of DNA are available, such as single cells or single chromosomes.

    Numerous tools and databases exist to annotate and investigate the functions encoded in properly assembled genomes, such as InterProScan, KEGG, GO and many more. Comparisons of functionalities across multiple genomes is, however, not trivial. The concept of graph databases is a promising novel approach from computer science for such multi-genome comparisons. For a data set of all (> 150,000) genes of 17 fungal species functionally annotated with InterProScan, the associated KEGG, GO and annotation data are imported and interconnected in a new Neo4j graph database (Chapter 6). Relationships in this database are visualized and mined with a newly refurbished and extended Neo4j plugin for Cytoscape. Inspection of (sub)graphs of functional annotations is an attractive way to compare and group functional annotation across species. In the use case of the seventeen fungal genomes, it helped to outline, compare and explain details of the life style of groups of individual species.

    The general discussion of this thesis provides an outlook on the future of bioinformatics in the context of the results here presented (Chapter 7). A grid infrastructure is recommended as a feasible and attractive cost-effective strategy to create compute power, as is the further inclusion of graphics cards. Full implementation of graph technology is considered necessary for advancing bioinformatics. The work presented in this thesis also shows that use of grids, graphics cards and graph technology imply the redesign of existing software applications. To be able to create novel stable, predictable and user-friendly applications in bioinformatics, formal training in software engineering principles is highly recommended. Courses and other programs are necessary for the life-long learning that will be crucial for the future of bioinformatics. The main challenges for bioinformatics in the years to come are all data centered: issues with growing data volumes, with more data types and with higher data complexity. To deal with these challenges, further integration of now separate fields of science is warranted in ways we cannot even image yet.

    Development of the benthic macrofauna community after tidal restoration at Rammegors: final report
    Walles, Brenda ; Brummelhuis, Emiel ; Pool, Jesse van der; Ysebaert, Tom - \ 2019
    Yerseke : Wageningen Marine Research (Wageningen Marine Research report C042/19) - 23
    The managed realignment project Rammegors aims at re-establishing estuarine nature in a formerly freshwater wetland. For this purpose, a tidal inlet was constructed in the Krabbekreekdam to generate a reduced tidal influence that should allow the development of salt marsh area, tidal flat area and low energetic shallow sub-tidal area. A central question of the Rammegors tidal restoration project is how the flora and fauna will develop in the area. To understand the biotic and abiotic processes related to the tidal restoration in Rammegors, a monitoring programme is being executed by the Centre of Expertise Delta Technology. The monitoring focuses on the main biotic and abiotic developments in the area. This report only focuses on the early colonization of macrobenthic invertebrates in Rammegors. Benthic macrofauna and sediment sampling took place in spring and autumn 2017 and 2018 at twenty-four stations along 5 transects with varying distances from the inlet. A fast colonization of the benthic macrofauna was observed in Rammegors. Twenty-two taxa were observed in the area in spring 2017. The communities significantly differed between spring and autumn 2017. In spring densities reached high values, especially for the brackish mud shrimp Manocorophium insidiosum and mosquito larvae Chironomidae. In autumn these brackish species almost disappeared from the area. Their presence in autumn 2017 and spring 2018, even in low numbers, as well as the observation of the brackish cockle Cerastoderma glaucum indicate that a year after the tidal restoration, parts of Rammegors are still under influence of brackish water. In 2018 these species declined, indicating the transition to a marine environment. A significant relation was found between elevation and the benthic macrofauna. Total density, biomass and species richness showed a significant relation along the elevation gradient with an optimum around +0.4m NAP and lower values at both lower and higher elevations. Total density significant increases with an increase in chlorophyll-a, silt content and organic matter. A significant decrease in total density and species richness was observed with increasing bulk density, indicating that more compact sediments contain less species in lower abundances. Total density, biomass and species richness increased with increasing distance from the inlet. After two years, it is unknown if the community within the Rammegors area reached stability or develops at a slow pace. Future monitoring and a comparison to a community found in a comparable natural habitat is needed to study this.
    Determinants of successful lifestyle change during a 6-month preconception lifestyle intervention in women with obesity and infertility
    Karsten, Matty D.A. ; Oers, Anne M. van; Groen, Henk ; Mutsaerts, Meike A.Q. ; Poppel, Mireille N.M. van; Geelen, Anouk ; Beek, Cornelieke van de; Painter, Rebecca C. ; Mol, Ben W.J. ; Roseboom, Tessa J. ; Hoek, Annemieke ; Burggraaff, J.M. ; Kuchenbecker, W.K.H. ; Perquin, D.A.M. ; Koks, C.A.M. ; Golde, R. van; Kaaijk, E.M. ; Schierbeek, J.M. ; Oosterhuis, G.J.E. ; Broekmans, F.J. ; Vogel, N.E.A. ; Lambalk, C.B. ; Veen, F. van der; Klijn, N.F. ; Mercelina, P.E.A.M. ; Kasteren, Y.M. van; Nap, A.W. ; Mulder, R.J.A.B. ; Gondrie, E.T.C.M. ; Bruin, J.P. de - \ 2019
    European Journal of Nutrition 58 (2019)6. - ISSN 1436-6207 - p. 2463 - 2475.
    Determinants - Lifestyle intervention - Obesity - Preconception

    Purpose: To identify demographic, (bio)physical, behavioral, and psychological determinants of successful lifestyle change and program completion by performing a secondary analysis of the intervention arm of a randomized-controlled trial, investigating a preconception lifestyle intervention. Methods: The 6-month lifestyle intervention consisted of dietary counseling, physical activity, and behavioral modification, and was aimed at 5–10% weight loss. We operationalized successful lifestyle change as successful weight loss (≥ 5% weight/BMI ≤ 29 kg/m2), weight loss in kilograms, a reduction in energy intake, and an increase in physical activity during the intervention program. We performed logistic and mixed-effect regression analyses to identify baseline factors that were associated with successful change or program completion. Results: Women with higher external eating behavior scores had higher odds of successful weight loss (OR 1.10, 95% CI 1.05–1.16). Women with the previous dietetic support lost 0.94 kg less during the intervention period (95% CI 0.01–1.87 kg). Women with higher self-efficacy reduced energy intake more than women with lower self-efficacy (p < 0.01). Women with an older partner had an increased energy intake (6 kcal/year older, 95% CI 3–13). A high stage of change towards physical activity was associated with a higher number of daily steps (p = 0.03). A high stage of change towards weight loss was associated with completion of the intervention (p = 0.04). Conclusions: Determinants of lifestyle change and program completion were: higher external eating behavior, not having received previous dietetic support, high stage of change. This knowledge can be used to identify women likely to benefit from lifestyle interventions and develop new interventions for women requiring alternative support. Trial registration: The LIFEstyle study was registered at the Dutch trial registry (NTR 1530;

    Corrigendum: Towards recommendations for metadata and data handling in plant phenotyping
    Krajewski, Paweł ; Chen, Dijun ; Ćwiek, Hanna ; Dijk, Aalt D.J. Van; Fiorani, Fabio ; Kersey, Paul ; Klukas, Christian ; Lange, Matthias ; Markiewicz, Augustyn ; Nap, Jan Peter ; Oeveren, Jan Van; Pommier, Cyril ; Scholz, Uwe ; Schriek, Marco Van; Usadel, Björn ; Weise, Stephan - \ 2018
    Journal of Experimental Botany 69 (2018)7. - ISSN 0022-0957 - p. 1819 - 1819.
    Fate and distribution of pharmaceutically active compounds in mesocosm constructed wetlands
    He, Yujie ; Sutton, Nora B. ; Lei, Yu ; Rijnaarts, Huub H.M. ; Langenhoff, Alette A.M. - \ 2018
    Journal of Hazardous Materials 357 (2018). - ISSN 0304-3894 - p. 198 - 206.
    Effect of plants - Pharmaceuticals - Pre-photocatalysis - Removal processes - Substrate composition

    Removal of pharmaceutically active compounds (PhACs) in constructed wetlands (CWs) is a complex interplay of different processes. We studied fate and distribution of seven PhACs (caffeine, CAF; naproxen, NAP; metoprolol, MET; propranolol, PRO; ibuprofen, IBP; carbamazepine, CBZ; diclofenac, DFC) in mesocosm CWs and effects of irradiation via pre-photocatalysis, substrate composition (mainly sediment) through addition of litter (dead plant biomass), and plants. CWs showed high removal of CAF, NAP, MET, PRO, and IBP (79–99%). All seven PhACs were detected in substrate and plant tissues as well as IBP intermediates. Estimated PhAC mass balance showed that sorption dominated PRO removal in CWs while other PhACs were mainly removed by biodegradation and/or phytodegradation. Pre-photocatalysis significantly increased removal of PhACs except for CAF and IBP, and decreased accumulation of PhACs in substrate and plant tissues of the following wetland compartment. Litter addition in CW significantly enhanced removal of PRO and CBZ via biodegradation and/or phytodegradation. Plants played an essential and positive role in removing PhACs, resulting from direct phytoremediation and indirectly enhancing sorption and biodegradation. Our study provides knowledge to understand removal mechanisms of PhACs in CWs and to potentially enhance PhAC removal by developing pre-photocatalysis, adding dead plant biomass, and optimizing vegetation.

    Propagating annotations of molecular networks using in silico fragmentation
    Silva, Ricardo R. da; Wang, Mingxun ; Nothias, Louis Félix ; Hooft, Justin J.J. van der; Caraballo-Rodríguez, Andrés Mauricio ; Fox, Evan ; Balunas, Marcy J. ; Klassen, Jonathan L. ; Lopes, Norberto Peporine ; Dorrestein, Pieter C. - \ 2018
    PLoS Computational Biology 14 (2018)4. - ISSN 1553-734X

    The annotation of small molecules is one of the most challenging and important steps in untargeted mass spectrometry analysis, as most of our biological interpretations rely on structural annotations. Molecular networking has emerged as a structured way to organize and mine data from untargeted tandem mass spectrometry (MS/MS) experiments and has been widely applied to propagate annotations. However, propagation is done through manual inspection of MS/MS spectra connected in the spectral networks and is only possible when a reference library spectrum is available. One of the alternative approaches used to annotate an unknown fragmentation mass spectrum is through the use of in silico predictions. One of the challenges of in silico annotation is the uncertainty around the correct structure among the predicted candidate lists. Here we show how molecular networking can be used to improve the accuracy of in silico predictions through propagation of structural annotations, even when there is no match to a MS/MS spectrum in spectral libraries. This is accomplished through creating a network consensus of re-ranked structural candidates using the molecular network topology and structural similarity to improve in silico annotations. The Network Annotation Propagation (NAP) tool is accessible through the GNPS web-platform

    Effects of dissolved organic matter and nitrification on biodegradation of pharmaceuticals in aerobic enrichment cultures
    He, Yujie ; Langenhoff, Alette A.M. ; Comans, Rob N.J. ; Sutton, Nora B. ; Rijnaarts, Huub H.M. - \ 2018
    Science of the Total Environment 630 (2018). - ISSN 0048-9697 - p. 1335 - 1342.
    Aerobic biodegradation - Constructed wetland - DOM - Microbial degradation preference - Nitrification - Pharmaceuticals
    Natural dissolved organic matter (DOM) and nitrification can play an important role in biodegradation of pharmaceutically active compounds (PhACs) in aerobic zones of constructed wetlands (CWs). This study used an enrichment culture originating from CW sediment to study the effect of DOM and nitrification on aerobic biodegradation of seven PhACs. The enriched culture degraded caffeine (CAF), metoprolol (MET), naproxen (NAP), and ibuprofen (IBP) with a consistent biodegradability order of CAF > MET > NAP > IBP. Biodegradation of propranolol, carbamazepine, and diclofenac was insignificant (<15%). CAF biodegradation was inhibited by the easily biodegradable DOM. Conversely, DOM enhanced biodegradation of MET, NAP, and IBP, potentially by contributing more biomass capable of degrading PhACs. Nitrification enhanced biodegradation of NAP and IBP and mineralization of the PhAC mixture as well as less biodegradable DOM, which may result from co-metabolism of ammonia oxidizing bacteria or enhanced heterotrophic microbial activity under nitrification. MET biodegradation was inhibited in the presence of nitrification. DOM and nitrification effects on PhAC biodegradation in CWs gained from this study can be used in strategies to improve CW operation, namely: designing hydraulic retention times based on the biodegradability order of specific PhACs; applying DOM amendment; and introducing consistent ammonium streams to increase removal of PhACs of interest.
    pyPaSWAS : Python-based multi-core CPU and GPU sequence alignment
    Warris, Sven ; Timal, N.R.N. ; Kempenaar, Marcel ; Poortinga, Arne M. ; Geest, Henri van de; Varbanescu, Ana L. ; Nap, Jan Peter - \ 2018
    PLoS ONE 13 (2018)1. - ISSN 1932-6203
    Background Our previously published CUDA-only application PaSWAS for Smith-Waterman (SW) sequence alignment of any type of sequence on NVIDIA-based GPUs is platform-specific and therefore adopted less than could be. The OpenCL language is supported more widely and allows use on a variety of hardware platforms. Moreover, there is a need to promote the adoption of parallel computing in bioinformatics by making its use and extension more simple through more and better application of high-level languages commonly used in bioinformatics, such as Python. Results The novel application pyPaSWAS presents the parallel SW sequence alignment code fully packed in Python. It is a generic SW implementation running on several hardware platforms with multi-core systems and/or GPUs that provides accurate sequence alignments that also can be inspected for alignment details. Additionally, pyPaSWAS support the affine gap penalty. Python libraries are used for automated system configuration, I/O and logging. This way, the Python environment will stimulate further extension and use of pyPaSWAS. Conclusions pyPaSWAS presents an easy Python-based environment for accurate and retrievable parallel SW sequence alignments on GPUs and multi-core systems. The strategy of integrating Python with high-performance parallel compute languages to create a developer- and user-friendly environment should be considered for other computationally intensive bioinformatics algorithms.
    Pharmaceutical biodegradation under three anaerobic redox conditions evaluated by chemical and toxicological analyses
    He, Yujie ; Sutton, Nora ; Rijnaarts, Huub H.M. ; Langenhoff, Alette A.M. - \ 2018
    Science of the Total Environment 618 (2018). - ISSN 0048-9697 - p. 658 - 664.
    Intermediates - Nitrate reducing conditions - Pharmaceuticals - Sulfate reducing conditions, methanogenic conditions - Vibrio fischeri
    Biodegradation of pharmaceutically active compounds (PhACs) in the subsurface layer of constructed wetlands (CWs) under various anaerobic redox conditions is rarely studied. In this study, CW sediment microbial populations were enriched for PhAC biodegrading organisms. Biodegradation effectivity of a mixture of six PhACs (caffeine, CAF; naproxen, NAP; metoprolol, MET; propranolol, PRO; ibuprofen, IBP; carbamazepine, CBZ) and single compounds (CAF, NAP) was investigated under nitrate reducing, sulfate reducing, and methanogenic conditions using chemical and toxicological analyses. Biodegradation efficiencies varied strongly among the six PhACs and three redox conditions chosen. CAF and NAP were completely biodegraded under sulfate reducing and methanogenic conditions whereas biodegradation efficiencies of the other PhACs were much less (MET, PRO <. 20%; IBP, CBZ, negligible). CAF and NAP showed significantly lower biodegradation under nitrate reducing conditions than under the other two redox conditions. No difference was found in biodegradation efficiencies of CAF and NAP when present as single compound, or as a mixture with other PhACs. Different intermediates were observed, indicating different biodegradation pathways under different redox conditions and when the PhACs were present as single compound or in a mixture. From toxicological perspective, toxicity of PhACs and/or their intermediates to Vibrio fischeri was attenuated during the biodegradation process. Chemical and toxicological data showed positive correlations in principle component analysis, by which potentially toxic PhACs and intermediates are indicated for further ecotoxicological hazard assessment.
    Development of the benthic macrofauna community after tidal restoration at Rammegors : Progress report 1
    Walles, Brenda ; Brummelhuis, Emiel ; Ysebaert, Tom - \ 2017
    Yerseke : Wageningen Marine Research (Wageningen Marine Research report C110/17) - 21
    The managed realignment project Rammegors aims at re-establishing estuarine nature in a formerly freshwater wetland. For this purpose, a tidal inlet was constructed in the Krabbekreekdam to generate a reduced tidal influence that should allow the development of salt marsh area, tidal flat area and low energetic shallow sub-tidal. A central question of the Rammegors tidal restoration project is how the flora and fauna will develop in the area. To understand the biotic and abiotic processes related to the tidal restoration in Rammegors, a monitoring programme is being executed by the Centre of Expertise Delta Technology. The monitoring focuses on the main biotic and abiotic developments in the area. This progress report only focuses on the early colonization of macrobenthic invertebrates in Rammegors. Benthic macrofauna and sediment sampling took place in spring and autumn 2017 at twenty stations along 4 transects with varying distances to the outlet. A fast colonization of the benthic macrofauna was observed in Rammegors. Twenty and twenty-eight taxa were observed in the area in spring and autumn 2017 respectively. The communities significantly differed between spring and autumn. In spring densities reached high values, especially for the brackish mud shrimp Manocorophium insidiosum and mosquito larvae Chironomidae. In autumn these brackish species almost disappeared from the area. Their presence in autumn, even in low numbers, as well as the observation of the brackish cockle Cerastoderma glaucum indicate that, after the tidal restoration, parts of Rammegors are still under influence of brackish water. A relation was found between elevation and the benthic macrofauna development. Species richness showed an optimum around +0.4m NAP with lower values at both lower and higher elevations. Total density significantly increased with elevation, with highest total density at the higher elevations and a gradient in ecological richness was observed with higher richness further from the inlet. As the spring community significantly differs from the autumn community, we will continue sampling in both seasons in 2018
    Similarities between plant traits based on their connection to underlying gene functions
    Nap, Jan Peter ; Sanchez-Perez, Gabino F. ; Dijk, Aalt-Jan van - \ 2017
    PLoS ONE 12 (2017)8. - ISSN 1932-6203
    This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Understanding of phenotypes and their genetic basis is a major focus in current plant biology. Large amounts of phenotype data are being generated, both for macroscopic phenotypes such as size or yield, and for molecular phenotypes such as expression levels and metabolite levels. More insight in the underlying genetic and molecular mechanisms that influence phenotypes will enable a better understanding of how various phenotypes are related to each other. This will be a major step forward in understanding plant biology, with immediate value for plant breeding and academic plant research. Currently the genetic basis of most phenotypes remains however to be discovered, and the relatedness of different traits is unclear. We here present a novel approach to connect phenotypes to underlying biological processes and molecular functions. These connections define similarities between different types of phenotypes. The approach starts by using Quantitative Trait Locus (QTL) data, which are abundantly available for many phenotypes of interest. Overrepresentation analysis of gene functions based on Gene Ontology term enrichment across multiple QTL regions for a given phenotype, be it macroscopic or molecular, results in a small set of biological processes and molecular functions for each phenotype. Subsequently, similarity between different phenotypes can be defined in terms of these gene functions. Using publicly available rice data as example, a close relationship with defined molecular phenotypes is demonstrated for many macroscopic phenotypes. This includes for example a link between ‘leaf senescence’ and ‘aspartic acid’, as well as between ‘days to maturity’ and ‘choline’. Relationships between macroscopic and molecular phenotypes may result in more efficient marker-assisted breeding and are likely to direct future research aimed at a better understanding of plant phenotypes.
    Bronnen van nutriënten in het oppervlaktewater in het beheergebied van Wetterskip Fryslân : studie naar de herkomst en beïnvloedbaarheid van stikstof en fosfor in het oppervlaktewater voor zes polders in het beheergebied van Wetterskip Fryslân
    Boekel, E.M.P.M. van; Groenendijk, P. ; Renaud, L.V. - \ 2016
    Wageningen : Alterra, Wageningen-UR (Alterra-rapport 2727) - 50
    oppervlaktewater - voedingsstoffen - stikstof - fosfor - modellen - oppervlaktewaterkwaliteit - mestbeleid - friesland - surface water - nutrients - nitrogen - phosphorus - models - surface water quality - manure policy - friesland
    Om inzicht te krijgen in de herkomst en beïnvloedbaarheid van stikstof en fosfor in het oppervlaktewater in het beheergebied van Wetterskip Fryslân zijn met de ECHO-methodiek stofbalansen opgesteld voor een zestal polders. De beïnvloedbaarheid van bronnen is afgeleid conform de werkwijze die wordt toegepast door de Nutriëntenwerkgroep Rijn-West. Daarnaast is het effect van het mestbeleid op de nutriëntenbelasting van het oppervlaktewater in beeld gebracht op basis van uit het landelijke STONE-model afgeleide resultaten voor de uitspoeling bij gebruiksnormen van het 5e Nitraat Actieprogramma (5e NAP). Uit de resultaten blijkt dat het grootste deel (46 −74%) van de stikstof- en fosforbelasting van het oppervlaktewater afkomstig is van beïnvloedbare bronnen (actuele bemesting en nalevering bodem) met een effect op de korte en lange termijn. Bronnen met een direct effect (voornamelijk inlaatwater) dragen voor 5 − 45% bij aan de totale nutriëntenbelasting. De stikstofbelasting van het oppervlaktewater is voor 7 − 22% afkomstig van niet of moeilijk te beïnvloeden bronnen, voor fosfor ligt dit tussen 1 en 12%. Het doorrekenen van het mestbeleid (5e NAP) resulteert in een reductie van de uit- en afspoeling tussen 1,9 en 9,1%. Voor de totale nutriëntenbelasting ligt de reductie als gevolg van de maatregelen in het 5e NAP tussen 1,1 en 7,7%.
    Effect van diepe vooroeversuppletie bij Callantsoog op de benthosgemeenschap : resultaat T0-bemonstering najaar 2015
    Wijsman, J.W.M. ; Craeymeersch, J.A.M. - \ 2016
    Yerseke : IMARES (Rapport / IMARES C058/16) - 43
    zandsuppletie - oevers - zee-organismen - mariene biologie - benthos - monitoring - sand suppletion - shores - marine organisms - marine biology - benthos - monitoring
    Bij Callantsoog is er een diepe vooroeversuppletie voorzien van 1.6 miljoen m3. Doordat deze suppletie bij wijze van experiment dieper (ca -10 m NAP) wordt uitgevoerd dan reguliere vooroeversuppleties (-3 tot -8 meter NAP) is er een uitgebreid monitoringsprogramma opgesteld om het gedrag en de werking van de suppletie te volgen en ook de effecten op het bodemleven in kaart te brengen. Dit rapport beschrijft de resultaten van de eerste T0 meting van het benthos die is uitgevoerd met de schaaf en de boxcorer in september 2015.
    The Material practices of quantification: Measuring ‘deprivation’ in the Amsterdam Neighbourhood Policy
    Wilde, Mandy de; Franssen, Thomas - \ 2016
    Critical Social Policy 36 (2016)4. - ISSN 0261-0183 - p. 489 - 510.
    actor-network theory - evaluation - governmentality - quantification - social policy
    The use of indicators and indexes in social policy, as part of evidence-based policy, is understood by governmentality scholars as ‘techniques of governance’. However, we know very little about how the process of quantification is enacted in the material practices that constitute social policy itself. In this article we focus on a particular quantified object: the ‘Normal Amsterdam Level’ (NAP), used in an Amsterdam Neighbourhood Policy programme. We follow the NAP from its birth, to its life and its afterlife. We show that the qualification ‘deprived’ calls forth a whole set of problematic arrangements which are lost in a process of quantification. We understand the NAP as a generative device that actively assembles and arranges the world. These assemblages are rendered ‘hard’ through semiotic, statistical and visual techniques that produce facts about targeted neighbourhoods in relation to a city-wide average, thus serving as evidence and legitimisation for policy interventions.
    Compact tomato seedlings and plants upon overexpression of a tomato chromatin remodelling ATPase gene
    Folta, A. ; Bargsten, J.W. ; Bisseling, T. ; Nap, J.P.H. ; Mlynarova, L. - \ 2016
    Plant Biotechnology Journal 14 (2016)2. - ISSN 1467-7644 - p. 581 - 591.
    Control of plant growth is an important aspect of crop productivity and yield in agriculture. Overexpression of the AtCHR12/23 genes in Arabidopsis thaliana reduced growth habit without other morphological changes. These two genes encode Snf2 chromatin remodelling ATPases. Here, we translate this approach to the horticultural crop tomato (Solanum lycopersicum). We identified and cloned the single tomato ortholog of the two Arabidopsis Snf2 genes, designated SlCHR1. Transgenic tomato plants (cv. Micro-Tom) that constitutively overexpress the coding sequence of SlCHR1 show reduced growth in all developmental stages of tomato. This confirms that SlCHR1 combines the functions of both Arabidopsis genes in tomato. Compared to the wild type, the transgenic seedlings of tomato have significantly shorter roots, hypocotyls and reduced cotyledon size. Transgenic plants have a much more compact growth habit with markedly reduced plant height, severely compacted reproductive structures with smaller flowers and smaller fruits. The results indicate that either GMO-based or non-GMO-based approaches to modulate the expression of chromatin remodelling ATPase genes could develop into methods to control plant growth, for example to replace the use of chemical growth retardants. This approach is likely to be applicable and attractive for any crop for which growth habit reduction has added value.
    Flexible, fast and accurate sequence alignment profiling on GPGPU with PaSWAS
    Warris, S. ; Yalcin, F. ; Jackson, K.J. ; Nap, J.P.H. - \ 2015
    PLoS ONE 10 (2015)4. - ISSN 1932-6203 - 13 p.
    Motivation To obtain large-scale sequence alignments in a fast and flexible way is an important step in the analyses of next generation sequencing data. Applications based on the Smith-Waterman (SW) algorithm are often either not fast enough, limited to dedicated tasks or not sufficiently accurate due to statistical issues. Current SW implementations that run on graphics hardware do not report the alignment details necessary for further analysis. Results With the Parallel SW Alignment Software (PaSWAS) it is possible (a) to have easy access to the computational power of NVIDIA-based general purpose graphics processing units (GPGPUs) to perform high-speed sequence alignments, and (b) retrieve relevant information such as score, number of gaps and mismatches. The software reports multiple hits per alignment. The added value of the new SW implementation is demonstrated with two test cases: (1) tag recovery in next generation sequence data and (2) isotype assignment within an immunoglobulin 454 sequence data set. Both cases show the usability and versatility of the new parallel Smith-Waterman implementation. (...)
    Effect 5e Nitraat Actie Programma op de bodembelasting. Berekening bodembelasting voor berekening van de waterkwaliteit
    Koeijer, T.J. de; Luesink, H.H. - \ 2015
    Wageningen : LEI Wageningen UR (Nota / LEI Wageningen UR 2015-064) - 22
    zandgronden - mestbeleid - bodemchemie - bemesting - fosfaat - stikstof - waterkwaliteit - modellen - sandy soils - manure policy - soil chemistry - fertilizer application - phosphate - nitrogen - water quality - models
    Uit de MAMBO-berekeningen blijkt dat door invoering van het 5e NAP het gebruik van dierlijke mest op zandgrond daalt. De grootste daling treedt in het zuidelijk zandgebied op. Daarnaast treedt er een verschuiving op van de aanwending van varkensmest naar graasdiermest. Dit komt door de aanscherping van de gebruiksnormen voor fosfaat waardoor de plaatsingsruimte voor fosfaat afneemt. Door de lagere gehalten van stikstof en fosfaat in graasdiermest is het economisch aantrekkelijker om graasdiermest aan te wenden in plaats van varkensmest bij negatieve prijzen voor mestafzet. MAMBO is het Mest en Ammoniak Model voor beleidsondersteunend onderzoek.
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