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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Sensible heating as a potential mechanism for enhanced cloud formation over temperate forest
Bosman, Peter J.M. ; Heerwaarden, Chiel C. van; Teuling, Adriaan J. - \ 2019
Quarterly Journal of the Royal Meteorological Society 145 (2019)719. - ISSN 0035-9009 - p. 450 - 468.
cloud formation - flux partitioning - forest cloud cover - large-eddy simulation - sensible heat flux - sensible heating - surface heat fluxes

It has been recently shown for two forests in France (Les Landes and Sologne) that summer cloud cover over the forest is increased relative to its surroundings. This study aims to contribute to the elucidation of the physical mechanisms responsible for this increased cloud cover, focusing on surface flux partitioning. This was done by performing a case study for a heatwave day on which enhanced cloud cover over the forest of Les Landes was observed. Two numerical experiments (large-eddy simulations) with a homogeneous forest cover were performed, one in which the sensible heat flux was increased by approximately 5% of the total available energy and another one in which the same amount of energy was added to the latent heat flux. The addition of energy to the sensible heat flux led to a stronger increase in cloud cover than the same addition to the latent heat flux. The mean relative humidity at the boundary layer top showed only small differences, indicating it was not a sufficient indicator for cloud formation in this case. Important information, which immediately underlines the need for large-eddy simulations, is contained in modifications of the shape of the probability density functions of temperature and humidity. With enhanced sensible heating, the higher peak values of relative humidity contribute to an increased cloud cover. A crucial reason for the differences in cloud cover between the experiments is conjectured to be a decrease in the required amount of energy for air parcels to reach the lifting condensation level, indirectly caused by the boundary layer and near-surface warming associated with the stronger sensible heat flux. As forests in the region do have a higher sensible heat flux than their surroundings, we highlight one potential mechanism for enhanced cloud cover.

Leerlingen HPC Zetten beoordelen smaak en uiterlijk van vier nieuwe appelkruisingen
Ravesloot, M.B.M. ; Heiden, Alma van der; Bosman, Anita ; Beekhuizen, Sandra - \ 2018
Wageningen University & Research - 1 p.
Miscanthus biochar had limited effects on soil physical properties, microbial biomass, and grain yield in a four-year field experiment in Norway
O’toole, Adam ; Moni, Christophe ; Weldon, Simon ; Schols, Anne ; Carnol, Monique ; Bosman, Bernard ; Rasse, Daniel P. - \ 2018
Agriculture 8 (2018)11. - ISSN 2077-0472
Biochar - Miscanthus - Norway

The application of biochar to soils is a promising technique for increasing soil organic C and offsetting GHG emissions. However, large-scale adoption by farmers will likely require the proof of its utility to improve plant growth and soil quality. In this context, we conducted a four-year field experiment between October 2010 to October 2014 on a fertile silty clay loam Albeluvisol in Norway to assess the impact of biochar on soil physical properties, soil microbial biomass, and oat and barley yield. The following treatments were included: Control (soil), miscanthus biochar 8 t C ha−1 (BC8), miscanthus straw feedstock 8 t C ha−1 (MC8), and miscanthus biochar 25 t C ha−1 (BC25). Average volumetric water content at field capacity was significantly higher in BC25 when compared to the control due to changes in BD and total porosity. The biochar amendment had no effect on soil aggregate (2–6 mm) stability, pore size distribution, penetration resistance, soil microbial biomass C and N, and basal respiration. Biochar did not alter crop yields of oat and barley during the four growing seasons. In order to realize biochar’s climate mitigation potential, we suggest future research and development efforts should focus on improving the agronomic utility of biochar in engineered fertilizer and soil amendment products.

De Knoflookpad in Nederland: ondergang of 'slechts' een bottleneck?
Bosman, W. ; Struijk, R.P.J.H. ; Zekhuis, M. ; Ottburg, F.G.W.A. ; Crombaghs, B. ; Schut, D. ; Hoof, P. van - \ 2015
De Levende Natuur 116 (2015)1. - ISSN 0024-1520 - p. 2 - 6.
amphibia - padden - fauna - habitats - zoögeografie - oost-nederland - toads - zoogeography - east netherlands
In 2001 werd het landelijk Beschermingsplan Knoflookpad opgesteld. Wat is er sindsdien gedaan om de stand van de Knoflookpad te verbeteren en tot welke resultaten heeft dat geleid? Wat betekent dit voor de toekomst? Waar liggen de kansen voor de Knoflookpad? In een drietal artikelen komen achtereenvolgens aan bod: de historie van de Knoflookpad in Nederland, waarom en hoe in 2010 werd overgegaan tot bijplaatsing en herintroductie en tot slot welke scenario’s er zijn voor de toekomst van de Knoflookpad.
Kan de Knoflookpad op termijn van de Intensive Care af?
Ottburg, F.G.W.A. ; Crombaghs, B. ; Bosman, W. ; Zekhuis, M. ; Jansman, H.A.H. ; Snep, R.P.H. - \ 2015
De Levende Natuur 116 (2015)1. - ISSN 0024-1520 - p. 15 - 20.
amphibia - padden - fauna - habitats - beschermde soorten - natuurbeleid - toads - protected species - nature conservation policy
In 2001 werd het landelijk Beschermingsplan Knoflookpad opgesteld. Wat is er sindsdien gedaan om de stand van de Knoflookpad te verbeteren en tot welke resultaten heeft dat geleid? Wat betekent dit voor de toekomst? Waar liggen de kansen voor de Knoflookpad? In een drietal artikelen komen achtereenvolgens aan bod: de historie van de Knoflookpad in Nederland, waarom en hoe in 2010 werd overgegaan tot bijplaatsing en herintroductie en tot slot welke scenario’s er zijn voor de toekomst van de Knoflookpad.
Antimicrobial resistance in commensal Escherichia coli in veal calves is associated with antimicrobial drug use
Bosman, A.B. ; Wagenaar, J.A. ; Stegeman, J.A. ; Vernooij, J.C.M. ; Mevius, D.J. - \ 2014
Epidemiology and Infection 142 (2014)9. - ISSN 0950-2688 - p. 1893 - 1904.
to-finish farms - antibiotic-resistance - fecal samples - exposed herd - risk-factors - pigs - prevalence - coliforms - bacteria - ontario
The aim of this study was to determine the association between farm management factors, including antimicrobial drug usage, and resistance in commensal Escherichia coli isolates from the faeces of white veal calves. Ninety E. coli isolates from one pooled sample per farm (n = 48) were tested for their phenotypical resistance against amoxicillin, tetracycline, cefotaxime, ciprofloxacin and trimethoprim/sulfamethoxazole (TMP/SMX). Logistic regression analysis revealed the following risk factors (P <0·05); farmer wearing the same work clothes for several days [ciprofloxacin, odds ratio (OR) 2·6; tetracycline, OR 2·4], administration of trimethoprim-sulfonamide combinations (TMP/SMX, OR 3·0; amoxicillin, OR 3·1; tetracycline, OR 2·6), ¿0·3 animal daily dosage per production cycle (ADD/pc), quinolones (ciprofloxacin, OR 2·8), ¿1·3 ADD/pc, penicillins (ciprofloxacin, OR 3·3; tetracycline, OR 3·4), 20-40 ADD/pc, tetracyclines (tetracycline, OR 3·2) and >40 ADD/pc, tetracyclines (tetracycline, OR 13·1; amoxicillin, OR 6·5). In this study antimicrobial resistance in commensal E. coli was mainly associated with antimicrobial drug use.
Dissecting the genetic architecture of resistance to orsay virus infection in C. elegans
Sterken, M.G. ; Wang, Y. ; Snoek, L.B. ; Volkers, R.J.M. ; Riksen, J.A.G. ; Bosman, K.J. ; Pijlman, G.P. ; Kammenga, J.E. - \ 2014
In: Proceedings of Evolutionary Biology of Caenorhabditis and other Nematodes. - - p. 111 - 111.
Host-pathogen interactions play a major role in evolutionary selection and in shaping natural genetic variation. Recent identification of viral infection in C. elegans has prompted research into understanding the underlying pathways of Orsay virus (OrV) infection in natural populations. Here we report the dissection of the genetic architecture of OrV infection. We found that wild type Hawaii CB4856 strain was more resistant to OrV than the canonical Bristol N2 strain. To gain insight into the genetic architecture of resistance, 52 fully sequenced recombinant inbred lines (CB4856 x N2 RILs) were exposed to OrV using our recently developed quantitative assay. This led to the identification of two distinct loci on chromosome IV associated with OrV resistance. These loci were both associated with a lower viral load in the CB4856 genotype. Strikingly, these loci do not harbour the recently found drh-1 locus, which encodes a RIG-I like helicase that plays an important role in antiviral RNAi. To verify our results and gain additional insight into the genetic architecture, a panel of 18 introgression lines (ILs) (together covering chromosome IV entirely) was exposed to OrV. Both loci could be verified by ILs, also showing more resistance against OrV infection with the CB4856 locus. Our results provide insight in the loci underlying the higher viral resistance in CB4856. They also form an important step toward identifying polymorphic genes underlying resistance to viral infection in C. elegans.
Dissecting the genetic architecture of resistance to orsay virus infection in C. elegans
Sterken, M.G. ; Wang, Y. ; Snoek, L.B. ; Volkers, R.J.M. ; Riksen, J.A.G. ; Bosman, K.J. ; Pijlman, G.P. ; Kammenga, J.E. - \ 2014
In: Proceedings of PhD Spring School Host-Microbe Interactomics. - - p. 12 - 12.
Host-pathogen interactions play a major role in evolutionary selection and in shaping natural genetic variation. Recent identification of viral infection in C. elegans has prompted research into understanding the underlying pathways of Orsay virus (OrV) infection in natural populations. Here we report the dissection of the genetic architecture of OrV infection. We found that wild type Hawaii CB4856 strain was more resistant to OrV than the canonical Bristol N2 strain. To gain insight into the genetic architecture of resistance, 52 fully sequenced recombinant inbred lines (CB4856 x N2 RILs) were exposed to OrV using our recently developed quantitative assay. This led to the identification of two distinct loci on chromosome IV associated with OrV resistance. These loci were both associated with a lower viral load in the CB4856 genotype. Strikingly, these loci do not harbour the recently found drh-1 locus, which encodes a RIG-I like helicase that plays an important role in antiviral RNAi. To verify our results and gain additional insight into the genetic architecture, a panel of 18 introgression lines (ILs) (together covering chromosome IV entirely) was exposed to OrV. Both loci could be verified by ILs, also showing more resistance against OrV infection with the CB4856 locus. Our results provide insight in the loci underlying the higher viral resistance in CB4856. They also form an important step toward identifying polymorphic genes underlying resistance to viral infection in C. elegans.
The effects of development on gene expression in L4 Caenorhabditis elegans larvae
Riksen, J.A.G. ; Snoek, L.B. ; Sterken, M.G. ; Volkers, R.J.M. ; Klatter, M. ; Bosman, K. ; Bevers, R.P.J. ; Smant, G. ; Cossins, A.R. ; Kammenga, J.E. - \ 2014
In: Proceedings of the Berlin C. elegans Meeting. - - p. 215 - 215.
Organismal development is the most dynamic period of the life cycle yet we have only a rough understanding of the dynamics of gene expression during this period. We explore how development affects gene expression, by a detailed map of the C. elegans transcriptome. We found that over 10,000 genes display changes in expression and explored the properties of genes with different dynamics. A time series experiment was conducted on synchronized populations of C. elegans Bristol N2. The worms were grown in three batches, covering the time points from 42-64 hours post bleaching leading to a dense time series with 1 hour intervals on average. A follow up experiment was conducted using N2 and seven wild-isolates, CB4856, JU1581, JU1921, JU1930, JU1932, JU1944 and JU 1949. These were grown on two different food sources to show the applicability of the generated data as a transcriptional determinant of age. It was found that more than 10,000 genes have a dynamic expression pattern during the L4 stage. We found up- and down-regulated genes and also genes with more specific patterns. One noticeable pattern was a group of genes that is specifically up-regulated around 50 hours. Signs of purifying selection in non-coding regions of string up-regulated genes were found. This is an indication that highly up-regulated genes during development are constrained on their regulatory properties. Using the time-series we show that genotype and environment affect the development and the applicability of transcriptomics data to measure age. Our data help in understanding the transition from larvae to adult worms and can be used te eliminate experimental artefacts due to differences in developmental timing between experiments.
A heritable antiviral RNAi response limits Orsay virus infection in Caenorhabditis elegans N2
Sterken, M.G. ; Snoek, L.B. ; Bosman, K.J. ; Daamen, J. ; Riksen, J.A.G. ; Bakker, J. ; Pijlman, G.P. ; Kammenga, J.E. - \ 2014
PLoS ONE 9 (2014)2. - ISSN 1932-6203
c. elegans - gene-expression - interference - requirements - inheritance - environment - diversity - pathways - genotype - immunity
Orsay virus (OrV) is the first virus known to be able to complete a full infection cycle in the model nematode species Caenorhabditis elegans. OrV is transmitted horizontally and its infection is limited by antiviral RNA interference (RNAi). However, we have no insight into the kinetics of OrV replication in C. elegans. We developed an assay that infects worms in liquid, allowing precise monitoring of the infection. The assay revealed a dual role for the RNAi response in limiting Orsay virus infection in C. elegans. Firstly, it limits the progression of the initial infection at the step of recognition of dsRNA. Secondly, it provides an inherited protection against infection in the offspring. This establishes the heritable RNAi response as anti-viral mechanism during OrV infections in C. elegans. Our results further illustrate that the inheritance of the anti-viral response is important in controlling the infection in the canonical wild type Bristol N2. The OrV replication kinetics were established throughout the worm life-cycle, setting a standard for further quantitative assays with the OrV-C. elegans infection model.
A rapid and massive gene expression shift marking adolescent transition in C. elegans
Snoek, L.B. ; Sterken, M.G. ; Volkers, R.J.M. ; Klatter, M. ; Bosman, K.J. ; Bevers, R.P.J. ; Riksen, J.A.G. ; Smant, G. ; Cossins, A.R. ; Kammenga, J.E. - \ 2014
Scientific Reports 4 (2014). - ISSN 2045-2322
caenorhabditis-elegans - natural variation - genome - populations - robustness - diversity - profiles - genotype - project - age
Organismal development is the most dynamic period of the life cycle, yet we have only a rough understanding of the dynamics of gene expression during adolescent transition. Here we show that adolescence in Caenorhabditis elegans is characterized by a spectacular expression shift of conserved and highly polymorphic genes. Using a high resolution time series we found that in adolescent worms over 10,000 genes changed their expression. These genes were clustered according to their expression patterns. One cluster involved in chromatin remodelling showed a brief up-regulation around 50 h post-hatch. At the same time a spectacular shift in expression was observed. Sequence comparisons for this cluster across many genotypes revealed diversifying selection. Strongly up-regulated genes showed signs of purifying selection in non-coding regions, indicating that adolescence-active genes are constrained on their regulatory properties. Our findings improve our understanding of adolescent transition and help to eliminate experimental artefacts due to incorrect developmental timing.
Bulbillen: als seks niet nodig is (interview met C. Kik)
Bosman, G. ; Kik, C. - \ 2013
De Volkskrant (2013).
Vitale medewerkers in vitale organisaties: de resultaten van de sectoranalyse binnen het WO.
Vaandrager, L. ; Peeters, J.G.H. ; Bosman, A. ; Schouteten, R. ; Senden, T. - \ 2013
Vitale medewerkers in vitale organisaties: De resultaten van de sectoranalyse binnen het WO Deel 1 van de Taskforce Vitaliteit
Vaandrager, L. ; Peeters, J.G.H. ; Bosman, A. ; Schouteten, R. - \ 2013
SoFoKleS
Ontwerpdeel: Good Practice MyBalance 2.0. Deel 2 van de taskforce vitaliteit
Peeters, J.G.H. ; Vaandrager, L. ; Bosman, A. ; Schouteten, R. - \ 2013
SoFoKleS - 37 p.
An innovative team-based stop smoking competition among Maori and Pacific Island smokers: rationale and method for the study and its evaluation
Glover, M. ; Bosman, A. ; Wagemakers, A. ; Kira, A. ; Paton, C. ; Cowie, N. - \ 2013
BMC Public Health 13 (2013). - ISSN 1471-2458 - 15 p.
international quit - social support - win contest - new-zealand - cessation - intervention - community - campaign - population - efficacy
Maori and Pacific Island people have significantly higher smoking rates compared to the rest of the New Zealand population. The main aim of this paper is to describe how knowledge of Indigenous people’s practices and principles can be combined with proven effective smoking cessation support into a cessation intervention appropriate for Indigenous people.
Within-farm dynamics of ESBL/AmpC-producing Escherichia coli in veal calves: a longitudinal approach
Hordijk, J. ; Mevius, D.J. ; Kant, A. ; Bos, M.E.H. ; Graveland, H. ; Bosman, A.B. ; Hartskeerl, M. ; Heederik, D.J.J. ; Wagenaar, J.A. - \ 2013
Journal of Antimicrobial Chemotherapy 68 (2013)11. - ISSN 0305-7453 - p. 2468 - 2476.
spectrum-beta-lactamase - food-producing animals - plasmids encoding ctx-m-14 - extended-spectrum - klebsiella-pneumoniae - antimicrobial agents - companion animals - fecal carriage - young calves - resistance
OBJECTIVES: To assess the within-farm dynamics of extended-spectrum ß-lactamase (ESBL)/AmpC-producing Escherichia coli in veal calves. METHODS: Three veal-calf fattening farms were screened. Faecal samples from all calves within a compartment (109-150 per farm) were taken upon arrival on the farm (T0) and after 3, 6, 8 and 10 weeks (T3-T10). ESBL/AmpC genes were characterized by PCR and sequencing. Plasmids were characterized by transformation, PCR-based replicon typing and plasmid multilocus sequence typing (MLST). E. coli genotypes were analysed by MLST. RESULTS: At T0 the prevalence of ESBL/AmpC-producing E. coli ranged from 18% to 26%. These were predominantly isolates carrying blaCTX-M-1 and blaCTX-M-15 genes, located on various plasmids and E. coli sequence types (STs). Farm 1 was negative for ESBL/AmpC-producing E. coli after T0. Farm 2 showed an increase up to 37% at T3, which subsequently decreased gradually to 0% at T10. The presence from T3 to T10 on farm 2 was mainly caused by the clonal spread of a multiresistant E. coli ST57 harbouring blaCTX-M-14 on an IncF F2:A-:B- plasmid. Farm 3 showed a gradual decrease in prevalence to 1.4% at T10, with a relative increase of the identical clonal variant as shown for farm 2. A second clonal variant found in farm 3 was a multiresistant E. coli ST10 harbouring blaCTX-M-14 on an IncK plasmid. CONCLUSIONS: The prevalence of ESBL/AmpC-producing E. coli decreased over time. A clonal spread was observed on farm 2 and farm 3, illustrative of the complex dynamics probably associated with the use of antimicrobials.
Kweek je eigen tomaardappel
Bosman, G. ; Huigen, D.J. - \ 2013
Volkskrant (Wetenschapsbijlage) (2013). - 1 p.
Orsay Virus infection dynamics in Caenorhabditis elegans
Sterken, M.G. ; Snoek, L.B. ; Bosman, K. ; Daamen, J. ; Riksen, J.A.G. ; Bakker, J. ; Pijlman, G.P. ; Kammenga, J.E. - \ 2013
In: Proceedings of the 5th EMBO meeting 2013, 21-24 September 2013, Amsterdam, the Netherlands. - - p. 113 - 114.
The recently discovered Orsay virus (OrV) is the first virus able to complete a full infection cycle in the nematode C. elegans. This discovery creates the opportunity to study host-virus interactions in a genetically tractable host system. OrV is transmitted horizontally and antiviral RNAi was indicated to play a role during infection. Here we report a quantitative study of OrV replication and the trans-generational effects of anti-viral (RNAi) mechanisms in C. elegans. By infecting worm cohorts at different time points with OrV, progression of infection was monitored through quantification of viral RNA using qPCR. The influence of worm age and genotype on viral replication was determined. We found an age-related resistance to OrV infection and a faster replication in the wild isolate JU1580 (in which OrV was first identified) than in the canonical strain Bristol N2. In RNAi mutants in an N2 background the infection progressed considerably faster. Next, several subsequent generations exposed to virus were re-infected to determine if trans-generational effects plays a role in infections in C. elegans populations. These experiments showed that the RNAi response also plays a trans-generational role by making offspring of infected N2 less susceptible to viral replication. Consequently, N2 populations can lose the infection after a limited number of generations, whereas JU1580 populations remain infected. A dual role for the RNAi response was found. Firstly by limiting the initial infection, both in speed and viral load. Secondly by providing an inherited protection against infection. This establishes the heritable RNAi response as anti-viral mechanism during natural virus infections in C. elegans.
Minimization of the Impact of Aujeszky’s Disease Outbreaks in The Netherlands: A Conceptual Framework
Bosman, K.J. ; Mourits, M.C.M. ; Oude Lansink, A.G.J.M. ; Saatkamp, H.W. - \ 2013
Transboundary and Emerging Diseases 60 (2013)4. - ISSN 1865-1674 - p. 303 - 314.
classical swine-fever
In the Netherlands, outbreaks of Aujeszky’s Disease (AD) are controlled by vaccination and movement restriction zones (MRZ). Although this strategy avoids the socio-ethical concerns associated with pre-emptive slaughter, it can easily result in animal welfare problems and negative economic consequences. These arise because movement restrictions result in surpluses of live (vaccinated) piglets on farms. The aim is to provide insight into the development of these surpluses and its impact and to describe how measures that allow early transportation of pigs under certain conditions and to specific destinations (channelling) could reduce these problems. For the analysis, a deterministic simulation model was developed, which calculates surpluses of piglets at multiplier farms during AD outbreaks. This is performed on a weekly basis for two areas (with and without piglet surplus), three outbreak durations (minimum, moderate and long) and three strategies for movement restrictions (strict, transports within the MRZ allowed and transports outside the MRZ allowed). The results show that in case of complete movement restrictions, surpluses of piglets varying in age and vaccination status will quickly arise. These surpluses are larger for longer epidemics and can become as large as 180–340 thousand piglets (45–75% of weekly domestic production) for moderate and long epidemics, respectively. Implementation of channelling strategies that allow earlier transportation within the MRZ can reduce surpluses by about 50% to 100–150 thousand piglets maximum. Strategies that also allow transportation outside the MRZ can reduce surpluses even further to below 100 thousand piglets. It was concluded that channelling of live piglets during AD outbreaks results in a drastic reduction of problems with accommodating ready-for-transport piglets. Moreover, it reduces shortages during movement restrictions and peak supply immediately after removing the restrictions. Channelling could therefore be an important instrument to reduce the economic and animal welfare impacts of containment measures.
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