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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The effects of carbon dioxide on growth performance, welfare, and health of Atlantic salmon post-smolt (Salmo salar) in recirculating aquaculture systems
Mota, Vasco C. ; Nilsen, Tom Ole ; Gerwins, Jascha ; Gallo, Michele ; Ytteborg, Elisabeth ; Baeverfjord, Grete ; Kolarevic, Jelena ; Summerfelt, Steven T. ; Terjesen, Bendik Fyhn - \ 2019
Aquaculture 498 (2019). - ISSN 0044-8486 - p. 578 - 586.
Closed systems - CO - Hypercapnia - RAS - Salmonids

High carbon dioxide (CO2) concentrations negatively impact fish, which makes data on its tolerance especially relevant for production systems that can accumulate CO2 such as recirculating aquaculture system (RAS). The current study evaluates the effect of CO2 on the growth performance, welfare, and health of Atlantic salmon post-smolts in RAS. This study consisted of two phases. The first was a CO2 exposure phase, where eighteen tanks were used with six treatments in triplicate: 5, 12, 19, 26, 33 and 40 mg/L of CO2 during 12 weeks in a 12 ppt salinity RAS (hereafter RAS phase). In the second phase, PIT-tagged fish were transferred to a 34 ppt salinity single flow-through tank at CO2 < 5 mg/L (hereafter seawater phase) for an additional 6-week experimental period mimicking a seawater phase. Overall, mortality of fish exposed to CO2 was low and not related to treatments. The mean final body weight was significantly higher in the 5 mg/L treatment compared to CO2 treatments ≥12 mg/L at the end of RAS phase and to CO2 treatments ≥33 mg/L at the end of seawater phase. Moreover, regressions showed that growth significantly decreased linearly with increasing CO2 in the water. Eye cataracts and visible external damage on skin, operculum, and fins were inexistent and similar among CO2 treatments. Kidneys showed no signs of mineral deposits in any of the structures of the tissue. However, skin analysis showed that fish exposed to high CO2 concentrations had a significantly thinner dermis layer (both at the end of RAS and seawater phase) and a significantly thinner epidermis layer and lower mucus cells count (at the end of seawater phase). In conclusion, Atlantic salmon post-smolts cultured in brackish water RAS showed a maximum growth performance at CO2 concentrations below 12 mg/L. Except skin, no major effects of health and welfare were observed, including cataracts and nephrocalcinosis. Further studies should evaluate the molecular and physiological responses to both short-term and long-term carbon dioxide exposure.

Performance of secondary wastewater treatment methods for the removal of contaminants of emerging concern implicated in crop uptake and antibiotic resistance spread : A review
Krzeminski, Pawel ; Tomei, Maria Concetta ; Karaolia, Popi ; Langenhoff, Alette ; Almeida, C.M.R. ; Felis, Ewa ; Gritten, Fanny ; Andersen, Henrik Rasmus ; Fernandes, Telma ; Manaia, Celia M. ; Rizzo, Luigi ; Fatta-Kassinos, Despo - \ 2019
Science of the Total Environment 648 (2019). - ISSN 0048-9697 - p. 1052 - 1081.
Antibiotic resistance - Biological processes - CEC removal - Crop uptake - EU Watch list - Secondary wastewater treatment

Contaminants of emerging concern (CEC) discharged in effluents of wastewater treatment plants (WWTPs), not specifically designed for their removal, pose serious hazards to human health and ecosystems. Their impact is of particular relevance to wastewater disposal and re-use in agricultural settings due to CEC uptake and accumulation in food crops and consequent diffusion into the food-chain. This is the reason why the chemical CEC discussed in this review have been selected considering, besides recalcitrance, frequency of detection and entity of potential hazards, their relevance for crop uptake. Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) have been included as microbial CEC because of the potential of secondary wastewater treatment to offer conditions favourable to the survival and proliferation of ARB, and dissemination of ARGs. Given the adverse effects of chemical and microbial CEC, their removal is being considered as an additional design criterion, which highlights the necessity of upgrading conventional WWTPs with more effective technologies. In this review, the performance of currently applied biological treatment methods for secondary treatment is analysed. To this end, technological solutions including conventional activated sludge (CAS), membrane bioreactors (MBRs), moving bed biofilm reactors (MBBRs), and nature-based solutions such as constructed wetlands (CWs) are compared for the achievable removal efficiencies of the selected CEC and their potential of acting as reservoirs of ARB&ARGs. With the aim of giving a picture of real systems, this review focuses on data from full-scale and pilot-scale plants treating real urban wastewater. To achieve an integrated assessment, technologies are compared considering also other relevant evaluation parameters such as investment and management costs, complexity of layout and management, present scale of application and need of a post-treatment. Comparison results allow the definition of design and operation strategies for the implementation of CEC removal in WWTPs, when agricultural reuse of effluents is planned.

Representation of decision-making in European agricultural agent-based models
Huber, Robert ; Bakker, Martha ; Balmann, Alfons ; Berger, Thomas ; Bithell, Mike ; Brown, Calum ; Grêt-Regamey, Adrienne ; Xiong, Hang ; Le, Quang Bao ; Mack, Gabriele ; Meyfroidt, Patrick ; Millington, James ; Müller, Birgit ; Polhill, J.G. ; Sun, Zhanli ; Seidl, Roman ; Troost, Christian ; Finger, Robert - \ 2018
Agricultural Systems 167 (2018). - ISSN 0308-521X - p. 143 - 160.

The use of agent-based modelling approaches in ex-post and ex-ante evaluations of agricultural policies has been progressively increasing over the last few years. There are now a sufficient number of models that it is worth taking stock of the way these models have been developed. Here, we review 20 agricultural agent-based models (ABM) addressing heterogeneous decision-making processes in the context of European agriculture. The goals of this review were to i) develop a framework describing aspects of farmers’ decision-making that are relevant from a farm-systems perspective, ii) reveal the current state-of-the-art in representing farmers’ decision-making in the European agricultural sector, and iii) provide a critical reflection of underdeveloped research areas and on future opportunities in modelling decision-making. To compare different approaches in modelling farmers’ behaviour, we focused on the European agricultural sector, which presents a specific character with its family farms, its single market and the common agricultural policy (CAP). We identified several key properties of farmers’ decision-making: the multi-output nature of production; the importance of non-agricultural activities; heterogeneous household and family characteristics; and the need for concurrent short- and long-term decision-making. These properties were then used to define levels and types of decision-making mechanisms to structure a literature review. We find most models are sophisticated in the representation of farm exit and entry decisions, as well as the representation of long-term decisions and the consideration of farming styles or types using farm typologies. Considerably fewer attempts to model farmers’ emotions, values, learning, risk and uncertainty or social interactions occur in the different case studies. We conclude that there is considerable scope to improve diversity in representation of decision-making and the integration of social interactions in agricultural agent-based modelling approaches by combining existing modelling approaches and promoting model inter-comparisons. Thus, this review provides a valuable entry point for agent-based modellers, agricultural systems modellers and data driven social scientists for the re-use and sharing of model components, code and data. An intensified dialogue could fertilize more coordinated and purposeful combinations and comparisons of ABM and other modelling approaches as well as better reconciliation of empirical data and theoretical foundations, which ultimately are key to developing improved models of agricultural systems.

The Socio-Economic Impact of Extreme Precipitation and Flooding on Forest Livelihoods : Evidence from the Bolivian Amazon
Bauer, T. ; Ingram, V. ; Jong, W.D. de; Arts, B. - \ 2018
International Forestry Review 20 (2018)3. - ISSN 1465-5489 - p. 314 - 331.
climate change - extreme weather events - forest dependence - forest livelihoods - social-ecological systems

In early 2014, unprecedentedly heavy rainfall led to a flood in northern lowland Bolivia affecting the livelihoods of thousands of people relying on ecosystem services and climate sensitive sectors for their daily livelihood. Based on a case study of 50 households from indigenous forest communities living in the TCO Tacana I, ex-ante and ex-post household data were collected to obtain insights into the economic performance, livelihood strategy changes and role of forest products in the direct aftermath of the extreme weather event. A negative impact on natural resource dependent livelihood strategies was found as an immediate consequence. However, most households had recovered just one year later. There was no increase in the use of forest products to mitigate immediate income shortages. A typical high contribution of forest products to household income from before the flood continued afterwards. This article contributes to understanding of livelihood-based efforts of people living in tropical lowland forests to adapt to weather extremes.

Electrodialysis-based desalination and reuse of sea and brackish polymer-flooding produced water
Sosa-Fernandez, P.A. ; Post, J.W. ; Bruning, H. ; Leermakers, F.A.M. ; Rijnaarts, H.H.M. - \ 2018
Desalination 447 (2018). - ISSN 0011-9164 - p. 120 - 132.
Electrodialysis - Partially hydrolyzed polyacrylamide - Polymer-flooding - Produced water reuse - Viscosity

The reuse of polymer flooding produced water (PFPW) generated in oil and gas industry is limited by its salt content, making desalination by electrodialysis a promising treatment option. Therefore, this study aimed to 1) assess the technical feasibility of employing electrodialysis to desalinate PFPW generated in assorted scenarios, and 2) evaluate the reuse of the electrodialysis-desalted water to confect polymer-flooding solution. The experimental work involved desalting two kinds of synthetic PFPW solutions, one with relatively low salinity (TDS = 5000 mg/L, brackish PFPW), and another with high salinity (TDS = 32,000 mg/L, sea PFPW), at two different temperatures, and later reusing the desalted solution to prepare viscous solutions. For the electrodialysis runs, the effects of feed composition and temperature on water transport, energy consumption and current efficiency were analyzed. It was found that the presence of polymer did not significantly influence the water transport rate or the specific energy consumption for the seawater cases, but had a measurable effect when desalting brackish water at 20 °C. It was also found that some polymer remained in the stack, the loss occurring faster for the brackish PFPW. Still, both kinds of reused PFPW probed adequate to be employed as a basis for preparing n polymer solution.

Income intervention quick scan: post-harvest loss prevention measures : Farmer Income Lab Intervention Quick Scan
Beune, Renée - \ 2018
Wageningen : Wageningen Centre for Development Innovation (Report / WCDI 18-033) - 19
This quick scan, commissioned by the Farmer Income Lab, is part of a wider research effort looking at, “What are the most effective actions that lead buyers can take to enable smallholder farmers in global supply chains to meaningfully increase their incomes?”. The quick scan provides an overview of the publicly available evidence on the impact of post-harvest loss prevention measures have had on raising farmer income. Such subsidies have had little positive effect on farmer income, are not notably beneficial for women nor is this effect long-term. They have been applied at large scale. This quick scan is part of a series of 16, contributing to a synthesis report “What Works to Raise Farmer’s Income: a Landscape Review”.
Genome-wide association studies for tick resistance in Bos taurus × Bos indicus crossbred cattle : A deeper look into this intricate mechanism
Otto, Pamela I. ; Guimarães, Simone E.F. ; Verardo, Lucas L. ; Azevedo, Ana Luísa S. ; Vandenplas, Jeremie ; Soares, Aline C.C. ; Sevillano, Claudia A. ; Veroneze, Renata ; Fatima A. Pires, Maria de; Freitas, Célio de; Prata, Márcia Cristina A. ; Furlong, John ; Verneque, Rui S. ; Martins, Marta Fonseca ; Panetto, João Cláudio C. ; Carvalho, Wanessa A. ; Gobo, Diego O.R. ; Silva, Marcos Vinícius G.B. da; Machado, Marco A. - \ 2018
Journal of Dairy Science (2018). - ISSN 0022-0302
breed of origin - gene network - genetic variance - Gir × Holstein crossbred
Rhipicephalus (Boophilus) microplus is the main cattle ectoparasite in tropical areas. Gir × Holstein crossbred cows are well adapted to different production systems in Brazil. In this context, we performed genome-wide association study (GWAS) and post-GWAS analyses for R. microplus resistance in an experimental Gir × Holstein F2 population. Single nucleotide polymorphisms (SNP) identified in GWAS were used to build gene networks and to investigate the breed of origin for its alleles. Tick artificial infestations were performed during the dry and rainy seasons. Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA) and single-step BLUP procedure was used for GWAS. Post-GWAS analyses were performed by gene ontology terms enrichment and gene transcription factors networks, generated from enriched transcription factors, identified from the promoter sequences of selected gene sets. The genetic origin of marker alleles in the F2 population was assigned using the breed of origin of alleles approach. Heritability estimates for tick counts were 0.40 ± 0.11 in the rainy season and 0.54 ± 0.11 in dry season. The top ten 0.5-Mbp windows with the highest percentage of genetic variance explained by SNP markers were found in chromosomes 10 and 23 for both the dry and rainy seasons. Gene network analyses allowed the identification of genes involved with biological processes relevant to immune system functions (TREM1, TREM2, and CD83). Gene-transcription factors network allowed the identification of genes involved with immune functions (MYO5A, TREML1, and PRSS16). In resistant animals, the average proportion of animals showing significant SNPs with paternal and maternal alleles originated from Gir breed was 44.8% whereas the proportion of animals with both paternal and maternal alleles originated from Holstein breed was 11.3%. Susceptible animals showing both paternal and maternal alleles originated from Holstein breed represented 44.6% on average, whereas both paternal and maternal alleles originated from Gir breed animals represented 9.3%. This study allowed us to identify candidate genes for tick resistance in Gir × Holstein crossbreds in both rainy and dry seasons. According to the origin of alleles analysis, we found that most animals classified as resistant showed 2 alleles from Gir breed, while the susceptible ones showed alleles from Holstein. Based on these results, the identified genes may be thoroughly investigated in additional experiments aiming to validate their effects on tick resistance phenotype in cattle.
Between Soviet Legacy and Corporate Social Responsibility: Emerging Benefit Sharing Frameworks in the Irkutsk Oil Region, Russia
Tysyachnyouk, M. ; Petrov, Andrey N. ; Kuklina, Vera ; Krasnoshtanova, Natalia - \ 2018
Sustainability 10 (2018)9. - ISSN 2071-1050 - 23 p.
benefit sharing - extractive industries - natural resources - Russia - Arctic - corporate social responsibility
Benefit sharing arrangements are a central element of the interactions between oil companies and local communities in resource regions of the Arctic and sub-Arctic. This paper focused on developing a systematic understanding and typology of benefit sharing arrangements within the oil sector in the Russian Arctic and sub-Arctic, using the Irkutsk Oil Region as a case study. It provided a critical analysis of prevalent arrangements and practices (modes and mechanisms of benefit sharing), as well as examined institutional and social underpinnings of these benefit sharing frameworks. Qualitative methodology with semi-structured interviews were used. The paper demonstrated that sub-Arctic communities are not equally benefiting from oil and gas extraction. Despite a considerable variety of existing arrangements revealed by this study, no benefit sharing mode or mechanism prevalent today ensures sustainable development of local communities. This may stem from the incompatibility between post-Soviet legacies, corporate social responsibility principles, and local institutional frameworks. Although focused on a particular region, this research was indicative of general benefit sharing patterns in modern Russia and beyond.
Protection in sheep against heterologous challenge with serotype Asia-1 foot-and-mouth disease virus using high potency vaccine
Horsington, Jacquelyn ; Nfon, Charles ; Gonzales, Jose L. ; Singanallur, Nagendrakumar ; Bittner, Hilary ; Vosloo, Wilna - \ 2018
Vaccine 36 (2018)41. - ISSN 0264-410X - p. 6095 - 6102.
Foot-and-mouth disease virus - Heterologous challenge - Sheep - Vaccine efficacy

Foot-and-mouth disease virus (FMDV) serotype Asia-1 is prevalent in countries considered high risk for incursion into Australia, and has recently been responsible for a number of outbreaks in India, Bangladesh, Pakistan and Turkey. In vitro vaccine matching has shown a number of contemporary FMDV Asia-1 strains vary antigenically to the Asia-1 Shamir vaccine strain, which could result in poor protection with use of this vaccine. Therefore it was important to test the ability of the Asia-1 Shamir vaccine to protect sheep from challenge with a recent, heterologous strain at different days post-vaccination (dpv), including in an emergency vaccination scenario (challenge 4 or 7 dpv). Sheep (5 per group) were challenged with the Asia-1/PAK/19/2014 isolate by intra-nasopharyngeal instillation 21 (V21), 7 (V7) or 4 (V4) dpv with high-potency (>6 PD50) Asia-1 Shamir vaccine. An additional five sheep were mock-vaccinated with adjuvant only (antigen-free preparation) 4 days prior to challenge (A4), and five unvaccinated (UV) control sheep were also challenged. All V21, V7 and V4 sheep were protected from clinical FMD. Eighty percent of V21 sheep and 40% of V7 sheep had sterile immunity, however all V4 sheep became systemically infected. Vaccination reduced excretion of virus in nasal and oral secretions but had no effect on the development of persistent infection. All A4 sheep and UV control sheep developed clinical FMD. The high-potency Asia-1 Shamir vaccine will protect against disease should an outbreak of contemporary Asia-1 viruses occur. Intranasopharyngeal instillation is an effective challenge method for use in vaccine efficacy studies in sheep.

Testing the accuracy of feldspar single grains to date late Holocene cyclone and tsunami deposits
Brill, Dominik ; Reimann, Tony ; Wallinga, Jakob ; May, Simon Matthias ; Engel, Max ; Riedesel, Svenja ; Brückner, Helmut - \ 2018
Quaternary Geochronology 48 (2018). - ISSN 1871-1014 - p. 91 - 103.
Cyclone deposit - Feldspar dating - Post infrared infrared stimulated luminescence - Single grain dating - Transport processes - Tsunami deposit

Quartz is the preferred dosimeter for luminescence dating of Holocene sediments as optically stimulated luminescence (OSL) signals reset rapidly upon light exposure, and are stable over time. However, feldspar is required where quartz luminescence properties are inappropriate for dating, as is often the case in geologically young mountain ranges and areas with young volcanism. Here we aim to evaluate the potential of single grain feldspar luminescence dating applied to late Holocene cyclone and tsunami deposits, for which complete signal resetting can a priori not be guaranteed. To address potential problems of feldspar dating of such deposits associated with heterogeneous bleaching, remnant doses and anomalous fading, we use a low-temperature post infrared infrared stimulated luminescence protocol (pIRIR150) on single grains. For most samples, good agreement between fading corrected IR50 and non-fading corrected pIRIR150 ages is observed. Both feldspar ages generally also show good agreement with age control provided by historical data and quartz luminescence ages. pIRIR150 remnant ages in modern analogue samples are shown to be < 50 years, indicating that dating accuracy might be negatively affected by insufficient signal zeroing only for sediments younger than ∼500 years. As these minor remnant ages are interpreted as being caused by unbleachable luminescence residuals, slight age overestimation for young samples can be overcome by subtracting the remnant ages. The good agreement between pIRIR150, IR50 and quartz ages, indicates that a significant number of grains must have experienced relatively complete signal resetting during or immediately prior to transport, as the three signals are known to bleach at different rates. Since light exposure during the event is expected to be limited, we deduce that a significant portion of the grains in the cyclone and tsunami deposits was already bleached prior to the event of interest. These well-bleached grains were likely eroded at the beach, while other grains with larger remnant ages probably originate from the shallow subtidal, coastal barriers or even further inland sources. Additional signal resetting during storm and tsunami transport is indicated by slightly younger quartz than feldspar ages for grains with incomplete pre-transport resetting that were eroded at the Holocene coastal barrier.

Investigation of echosounder finger prints of Dutch pelagic freezer trawlers (SEAT II) evaluation of the SEAT II joint-industry project : evaluation of the SEAT II joint-industry project
Sakinan, Serdar ; Haan, Dick de; Burggraaf, Dirk ; Fassler, Sacha - \ 2018
IJmuiden : Wageningen Marine Research (Wageningen Marine Research rapport C020/18) - 44
The SEAT algorithm aims at classifying different fish species using relative frequency response acquired by downward looking echosounders operating at multiple frequencies. The performance of the system has been being evaluated on three Dutch freezer trawlers: Fishing Vessel (FV) SCH302 Willem van der Zwan, FV SCH6 Alida and FV SCH24 Afrika. One of these vessels (FV Alida SCH6) operates a mixture of SIMRAD EK60 & EK80 software while others operate only Simrad EK80. As reported by these vessels, the classification accuracy of the SEAT software has been reduced particularly at the later stages of the project. To investigate this problem these vessels collected acoustic data in close range of each other while targeting herring in the summer of 2017 at east of Shetland isles. Using this dataset together with calibration data, a statistical comparison was conducted. Furthermore, potential discrepancies between Simrad EK60 and EK80 systems were examined using data collected during herring assessment survey HERAS of Fishing Research Vessel (FRV) TRIDENS in July 2017. This dataset included recordings of both systems in alternating mode enabling a ping to ping comparison. It was found that two serious software bugs were likely to have influenced the calibration procedure of the EK80 software. One of these impacted the comparison of HERAS FRV Tridens records and lead to Sv gain offsets of 1.76 dB. After the correction, the measured acoustic intensities were comparable between EK60 and EK80 implying that the interchangeable application of these tools on board SCH6 should not affect species classification and measurements should be similar between vessels either using EK60 or EK80 given the instruments are calibrated correctly. The calculated relative frequency responses from the acoustic recordings of these three fishing vessels showed that FV Willem van der Zwan SCH302 and FV Alida SCH6 were found reasonably coherent, but FV Afrika SCH24 was different. These differences are associated with lower mean backscatter values of the 38 kHz channel.Similar analysis conducted in the earlier phases of this project where frequency response calculated from data collected by FV Alida SCH6 to investigate the discrepancies in the received horse mackerel frequency response and its expected fingerprints (Fassler, 2016 Annex 1). His results showed that the contribution of the 120 kHz data on the classification of varied with location and increased above latitude 52. In addition, this contribution was much lower for shoals detected in the English Channel (Fassler, 2016). Fassler (2016) also suggested that water pressure may affect the morphology of swimbladdered species and may explain the variability between shoals detected on the Atlantic Ocean and in the English Channel. The depth related effects found in different cases suggests that water depth has to be accounted for as an additional variable for each location. As suggested by Fassler (2016), these results may gain significance when the number of datasets increases.The results of the investigations presented here show that further post-processing of calibration records may improve the data quality hence the classification outputs. Particularly the unexpected reduction in the classification performance after 2016 can be improved by rolling back all the SEAT settings to an original state followed by proper calibrations settings. It is also recommended to maintain the latest software versions to ensure equipment are operating efficiently and consistent across the vessels. Regular tests with vessels fishing in close range as in the case of the summer of 2017 is a useful approach to test species recognition and to compare overall performance of the classification algorithm.
Impact and sustainability of Erasmus Mundus CASIA and TIMUR projects : Represented by individual results and achievements of grantees
Wietsma-Łącka, Ewa ; Pulatov, Alim ; Alexeyeva, Marina - \ 2018
Wageningen : Wageningen Environmental Sciences (Wageningen Environmental Sciences Report ) - ISBN 9789463433242 - 85
The aim of this publication is to summarize the main results of 8 years Erasmus Mundus Partnershipprojects leaded by Wageningen University, Department of Environmental Science. From 2010 till 2018Department of Environmental Sciences was leading CASIA and TIMUR projects within the frameworkof EU ERASMUS Mundus program involving partners form Kazakhstan, Uzbekistan, Kyrgyzstan andTajikistan - and CASIA and TIMUR projects wider objective wasthe establishment of a sustainable / operational network for academic exchange between Central Asia(CA) and European countries with a view to creating centres of excellence. Projects grantedscholarships for students at Undergraduate, Master, Doctorate, Post-Doctorate level and Academicstaff to come and study at EU partner universities. The study periods covered by scholarships varyfrom 1 month (for academic staff) up to 3 years (for Doctorates). CASIA and TIMUR Partnerships(2010-2018) offered in total 427 scholarships on different levels for which EU Erasmus Mundusprogram allocated a total budget of 8.4 million Euro. In this report, CASIA & TIMUR grantees – studentsand academic staff - are presenting their individual experiences, results and impressions achieved duringacademic mobility to Europe in the period from 2010-2018. The individual benefits of each grantee arevery important for personal development, professional career and international cooperation.
Reliability of a participant-friendly fecal collection method for microbiome analyses : A step towards large sample size investigation
Szopinska, Joanna W. ; Gresse, Raphaële ; Marel, Saskia van der; Boekhorst, Jos ; Lukovac, Sabina ; Swam, Iris van; Franke, Barbara ; Timmerman, Harro ; Belzer, Clara ; Vasquez, Alejandro Arias - \ 2018
BMC Microbiology 18 (2018)1. - ISSN 1471-2180
Bacterial DNA extraction - Fecal collection and storage method - Microbiome - Next generation sequencing - OMNIgene•GUT

Background: The effects of gut microbiota on human traits are expected to be small to moderate and adding the complexity of the human diseases, microbiome research demands big sample sizes. Fecal samples for such studies are mostly self-collected by participants at home. This imposes an extra level of complexity as sample collection and storage can be challenging. Effective, low-burden collection and storage methods allowing fecal samples to be transported properly and ensuring optimal quality and quantity of bacterial DNA for upstream analyses are necessary. Moreover, accurate assessment of the microbiome composition also depends on bacterial DNA extraction method. The aim of this study was to evaluate the reliability and efficiency of the OMNIgene•GUT kit as a participant-fecal friendly collection method (storage at room temperature for 24 h (O24h) or 7 days (O7d)) in comparison to the standard collection method (Fresh, storage at 4 °C for less than 24 h) in terms of amount of variability and information content accounting for two common DNA extraction methods. Results: Fourteen fecal samples were collected from healthy individuals (7 males, 7 females). Collection and storage methods did not differ significantly in terms of DNA concentration and Shannon diversity index. Phylum relative abundance showed significant differences for Bacteroidetes, Actinobacteria and Cyanobacteria. The differences were observed between control (Fresh) and O24h methods, but not between Fresh and O7d. These differences were not seen when performing bacterial DNA quantification based on three bacterial groups: Bacteroides spp., Bifidobacterium spp. and Clostridium cluster IV, which represent three major phyla: Bacteroidetes, Actinobacteria and Firmicutes respectively. The two DNA extraction methods differ in terms of DNA quantity, quality, bacterial diversity and bacterial relative abundance. Furthermore, principal component analysis revealed differences in microbial structure, which are driven by the DNA extraction methods more than the collection/storage methods. Conclusion: Our results have highlighted the potential of using the OMNIgene•GUT kit for collection and storage at ambient temperature, which is convenient for studies aiming to collect large samples by giving participants the possibility to send samples by post. Importantly, we revealed that the choice of DNA extraction method have an impact on the microbiome profiling.

Effector GpRpb-1 from Globodera pallida targets E3 ubiquitin ligase complexes to promote nematode infection
Diaz Granados Muñoz, Amalia - \ 2018
Endoparasitic plant-pathogenic nematodes manipulate plant cell morphology and physiology to establish sophisticated feeding structures. Modifications to plant cells are achieved through the activity of nematode secreted effectors. SPRYSECs are a remarkably expanded family of effectors identified initially in potato cyst nematodes. While SPRYSECs have been implicated in suppression of plant immunity, their intrinsic role in nematode virulence remains unexplored. GpRpb-1 is a ‘type’ SPRYSEC from Globodera pallida with virulent and avirulent variants present in field populations of the nematode. Y2H screening of a nematode-infected susceptible potato library yielded interacting candidates for a virulent GpRpb-1 that are involved in post-translational modification in the plant. We have independently confirmed that E3 ubiquitin ligase UPL3 can interact with GpRbp-1 in planta. Transcriptomic profiling of upl3 mutant plants shows that Skp-like and F-box-like E3 ubiquitin ligases are regulated upon nematode infection. Furthermore, upon silencing of the corresponding ligase genes in A. thaliana, we observed significant differences in the amount of developing females present in the roots of nematode-infected plants. The interaction of GpRbp-1 with UPL3 and the transcriptional regulation of other E3 ubiquitin ligases suggest that the intrinsic role of the effector is carried out through manipulation of the plant post-translational modification machinery. Our findings suggest that nematodes are able to use the SPRYSEC family of effectors to control different aspects of the plant cell to establish a feeding site. Therefore, our results may provide further insight into the basis of virulence of nematodes in plants.
Changes in iron metabolism during prolonged repeated walking exercise in middle-aged men and women
Terink, Rieneke ; Haaf, D. ten; Bongers, C.W.G. ; Balvers, M.G.J. ; Witkamp, R.F. ; Mensink, M. ; Eijsvogels, T.M.H. ; Klein Gunnewiek, J.M.T. ; Hopman, M.T.E. - \ 2018
European Journal of Applied Physiology (2018). - ISSN 1439-6319 - 9 p.
Fe - Hb - Hp - Repetitive exercise

Purpose: The aim of the present study was to assess the effect of prolonged and repeated exercise on iron metabolism in middle-aged adults and to compare differences between sexes. Methods: 50 male (58.9 ± 9.9 year) and 48 female (50.9 ± 11.2 year) individuals were monitored on 4 consecutive days at which they walked on average 8 h and 44 min per day at a self-determined pace. Blood samples were collected 1 or 2 days prior to the start of the exercise (baseline) and every day immediately post-exercise. Samples were analysed for iron, ferritin, haemoglobin, and haptoglobin concentrations. Results: Plasma iron decreased across days, while ferritin increased across days (both p < 0.001). Haptoglobin showed a decrease (p < 0.001) after the first day and increased over subsequent days (p < 0.001). Haemoglobin did not change after the first day, but increased during subsequent days (p < 0.05). At baseline, 8% of the participants had iron concentrations below minimum reference value (10 µmol/L), this increased to 43% at day 4. There was an interaction between sex and exercise days on iron (p = 0.028), ferritin (p < 0.001) and haemoglobin levels (p = 0.004), but not on haptoglobin levels. Conclusion: This study showed decreases in iron, increases in ferritin, a decrease followed by increases in haptoglobin and no change followed by increases in haemoglobin. This is most likely explained by (foot strike) haemolysis, inflammation, and sweat and urine losses. These processes resulted in iron levels below minimum reference value in a large number of our participants.

Retirement concerns and planning of cooperative members : a study in the Dutch healthcare sector
Apostolakis, George ; Dijk, Gert van - \ 2018
Small Business Economics (2018). - ISSN 0007-666X - 16 p.
Cooperatives - Healthcare - Retirement planning - Uncertainty

Retirement planning is a key component in achieving goals and fulfilling expectations. Although several socioeconomic and psychological factors associated with retirement planning have been reported in the literature, little is known about the influence that specific retirement-related issues have on retirement planning. We examine the influence of five concerns—the individual’s financial situation, living situation, care provision, health condition, and loneliness—on retirement planning. In addition, we investigate the influence of these concerns on individuals’ perceptions of their ideal post-retirement situations in terms of financial standards. Our dataset is derived from a 2010 web-based survey of the care and well-being sector in the Netherlands.

Tomato disease resistances in the post-genomics era
Bai, Yuling ; Yan, Zhe ; Moriones, E. ; Fernández-Muñoz, R. - \ 2018
In: Proceedings of the 5th International Symposium on Tomato Diseases. - International Society for Horticultural Science (Acta Horticulturae ) - ISBN 9789462612037 - p. 1 - 17.
CRISPR/CAS9 - Effector target - Effector-assisted R gene identification - Gene editing - Mutagenesis - Recessive resistance - Resilience to combined stresses - TILLING

Disease in tomato (Solanum lycopersicum) can be caused by many pathogenic organisms, including cellular pathogens (e.g., fungi, bacteria, phytoplasmas, oomycetes and nematodes) and non-cellular pathogens (e.g., viruses and viroids). To respond to pathogen attack, tomato plants, like other sessile organisms, have developed an immune system, where pathogen effectors and plant receptor proteins (e.g., resistance proteins) play a central role. With advances in the genomics era, our understanding of plant-pathogen interactions is evolving rapidly. For example, pathogen genomics has allowed a genome-wide study on the structure, function and evolution of effectors in pathogen genomes. So-called effectoromics offers a high-throughput functional approach to study effector-associated plant genes such as resistance (R) genes and susceptibility (S) genes. In tomato, “genome to germplasms” is facilitating a genome dimension to the exploration of plant diversity in resistance by sequencing and re-sequencing of genomes of available germplasm resources. Together with this breakthrough and powerful techniques for genome editing, novel strategies are being developed for breeding tomatoes with durable resistance to pathogens. Using examples of several tomato diseases, this review focuses on (1) layers of plant immune system, (2) the exploitation of plant S genes in resistance breeding, (3) rapid identification of R and S genes, and (4) novel routes for durable resistance to pathogens. Finally, the topic of breeding for resilience to combined biotic and abiotic stresses is discussed based on our results, which show extensive crosstalk between loci/pathways for resistance to pathogens and tolerance to abiotic stresses.

Die Auswirkungen eines Brexits auf den Agrarhandel in den Niederlanden
Berkum, Siemen van; Jongeneel, Roel ; Leeuwen, Myrna van - \ 2018
EuroChoices 17 (2018)2. - ISSN 1478-0917 - p. 38 - 46.

The UK is an important market for the Dutch agri-food sector, 10 per cent of all Dutch agricultural exports find their way to the UK. In this article the effects of two possible post-Brexit trade scenarios on Dutch agricultural trade are quantified. Model simulations indicate that Dutch exports to the UK and the rest of the world will be affected only marginally under a Free Trade Agreement between the EU and the UK. A WTO scenario will have more, yet still relatively modest, impact on Dutch exports as a result of Dutch price competitiveness in the UK market. The agricultural production value in the Netherlands will decline by around 2 per cent, mainly because of declining prices that are the result of price pressure in the EU market as a consequence of Brexit-related trade distortions. Possible impacts of non-tariff measures on trade costs are not included in the quantification. However, the UK government could request quality and/or food safety conditions on imports that are different from the current EU trade conditions. Whether the UK will do so is yet unknown, and hence provides an enormous uncertainty to businesses engaged in trade with the UK.

Perceptions of Dutch health care professionals on weight gain during chemotherapy in women with breast cancer
Kruif, J.Th.C.M. de; Scholtens, M.B. ; Rijt, J. van der; Boer, M.R. de; Berg, M.M.G.A. van den; Vries, Y.C. de; Winkels, R.M. ; Visser, M. ; Kampman, E. ; Westerman, M.J. - \ 2018
Supportive Care in Cancer (2018). - ISSN 0941-4355 - 7 p.
Breast cancer - Dietary intake - Health care professionals - Health risks - Physical activity - Weight gain

Purpose: Dutch Health care professionals (HCPs) provide little information concerning health risks associated with weight gain during chemotherapy for breast cancer. Women with breast cancer have specified the need for more information on nutrition and physical activity to deal with weight gain. The aims of this study were to assess the perceptions of Dutch HCPs on weight gain during chemotherapy and in addition evaluate whether and what kind of information on dietary intake and physical activity HCPs provide to prevent/treat weight gain during (neo)adjuvant chemotherapy. Methods: A qualitative study was conducted using semi-structured interviews with 34 HCPs involved in breast cancer care: general practitioners, oncologists, specialized nurses, and dieticians. Results: To date, little information about nutrition, physical activity, and weight gain is given during chemotherapy because it is not part of most HCPs’ training, it is not included in the guidelines and it is not the best time to bring up information in the opinion of HCPs. Weight gain was perceived as just a matter of a few kilos and not an important health issue during treatment. All HCPs felt it is better that women themselves addressed their weight gain after chemotherapy. Conclusion: More knowledge about health risks associated with chemotherapy-induced weight gain and how to combat these issues needs to be made readily available to the HCPs and should become part of their training. Existing patient guidelines should include information on how to prevent and/or reduce weight gain through self-management of nutrition intake and physical activity during and post chemotherapy.

Diaporthe diversity and pathogenicity revealed from a broad survey of grapevine diseases in europe
Guarnaccia, V. ; Groenewald, J.Z. ; Woodhall, J. ; Armengol, J. ; Cinelli, T. ; Eichmeier, A. ; Ezra, D. ; Fontaine, F. ; Gramaje, D. ; Gutierrez-Aguirregabiria, A. ; Kaliterna, J. ; Kiss, L. ; Larignon, P. ; Luque, J. ; Mugnai, L. ; Naor, V. ; Raposo, R. ; Sándor, E. ; Váczy, K.Z. ; Crous, P.W. - \ 2018
Persoonia 40 (2018). - ISSN 0031-5850 - p. 135 - 153.
Canker - Multi-locus sequence typing - Pathogenicity - Vitis

Species of Diaporthe are considered important plant pathogens, saprobes, and endophytes on a wide range of plant hosts. Several species are well-known on grapevines, either as agents of pre-or post-harvest infections, including Phomopsis cane and leaf spot, cane bleaching, swelling arm and trunk cankers. In this study we explore the occurrence, diversity and pathogenicity of Diaporthe spp. associated with Vitis vinifera in major grape production areas of Europe and Israel, focusing on nurseries and vineyards. Surveys were conducted in Croatia, Czech Republic, France, Hungary, Israel, Italy, Spain and the UK. A total of 175 Diaporthe strains were isolated from asymptomatic and symptomatic shoots, branches and trunks. A multi-locus phylogeny was established based on five genomic loci (ITS, tef1, cal, his3 and tub2), and the morphological characters of the isolates were determined. Preliminary pathogenicity tests were performed on green grapevine shoots with representative isolates. The most commonly isolated species were D. eres and D. ampelina. Four new Diaporthe species described here as D. bohemiae, D. celeris, D. hispaniae and D. hungariae were found associated with affected vines. Pathogenicity tests revealed D. baccae, D. celeris, D. hispaniae and D. hungariae as pathogens of grapevines. No symptoms were caused by D. bohemiae. This study represents the first report of D. ambigua and D. baccae on grapevines in Europe. The present study improves our understanding of the species associated with several disease symptoms on V. vinifera plants, and provides useful information for effective disease management.

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