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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Indicators of resilience during the transition period in dairy cows : A case study
Dixhoorn, I.D.E. van; Mol, R.M. de; Werf, J.T.N. van der; Mourik, S. van; Reenen, C.G. van - \ 2018
Journal of Dairy Science (2018). - ISSN 0022-0302 - 12 p.
behavior - dairy cow - dynamic indicator - resilience - transition period
The transition period is a demanding phase in the life of dairy cows. Metabolic and infectious disorders frequently occur in the first weeks after calving. To identify cows that are less able to cope with the transition period, physiologic or behavioral signals acquired with sensors might be useful. However, it is not yet clear which signals or combination of signals and which signal properties are most informative with respect to disease severity after calving. Sensor data on activity and behavior measurements as well as rumen and ear temperature data from 22 dairy cows were collected during a period starting 2 wk before expected parturition until 6 wk after parturition. During this period, the health status of each cow was clinically scored daily. A total deficit score (TDS) was calculated based on the clinical assessment, summarizing disease length and intensity for each cow. Different sensor data properties recorded during the period before calving as well as the period after calving were tested as a predictor for TDS using univariate analysis of covariance. To select the model with the best combination of signals and signal properties, we quantified the prediction accuracy for TDS in a multivariate model. Prediction accuracy for TDS increased when sensors were combined, using static and dynamic signal properties. Statistically, the most optimal linear combination of predictors consisted of average eating time, variance of daily ear temperature, and regularity of daily behavior patterns in the dry period. Our research indicates that a combination of static and dynamic sensor data properties could be used as indicators of cow resilience.
Big data navigeren telers over paar jaar naar hun doelstellingen: 'Sla na 300 meter linksaf'
Mourik, Simon van - \ 2018
Comparative analysis of binding patterns of MADS-domain proteins in Arabidopsis thaliana
Aerts, Niels ; Bruijn, Suzanne de; Mourik, Hilda van; Angenent, Gerco C. ; Dijk, Aalt D.J. van - \ 2018
BMC Plant Biology 18 (2018)1. - ISSN 1471-2229
CArG-box - ChIP-seq - MADS-domain proteins - Sequence conservation - Transcription factor binding specificity

Background: Correct flower formation requires highly specific temporal and spatial regulation of gene expression. In Arabidopsis thaliana the majority of the master regulators that determine flower organ identity belong to the MADS-domain transcription factor family. The canonical DNA binding motif for this transcription factor family is the CArG-box, which has the consensus CC(A/T)6GG. However, so far, a comprehensive analysis of MADS-domain binding patterns has not yet been performed. Results: Eight publicly available ChIP-seq datasets of MADS-domain proteins that regulate the floral transition and flower formation were analyzed. Surprisingly, the preferred DNA binding motif of each protein was a CArG-box with an NAA extension. Furthermore, motifs of other transcription factors were found in the vicinity of binding sites of MADS-domain transcription factors, suggesting that interaction of MADS-domain proteins with other transcription factors is important for target gene regulation. Finally, conservation of CArG-boxes between Arabidopsis ecotypes was assessed to obtain information about their evolutionary importance. CArG-boxes that fully matched the consensus were more conserved than other CArG-boxes, suggesting that the perfect CArG-box is evolutionary more important than other CArG-box variants. Conclusion: Our analysis provides detailed insight into MADS-domain protein binding patterns. The results underline the importance of an extended version of the CArG-box and provide a first view on evolutionary conservation of MADS-domain protein binding sites in Arabidopsis ecotypes.

Brasseur, Sophie Marie Jacqueline Michele - \ 2018
Automated body weight prediction of dairy cows using 3-dimensional vision
Song, X. ; Bokkers, E.A.M. ; Tol, P.P.J. van der; Groot Koerkamp, P.W.G. ; Mourik, S. van - \ 2018
Journal of Dairy Science 101 (2018)5. - ISSN 0022-0302 - p. 4448 - 4459.
automation - dairy cattle - morphological trait - three-dimensional vision - uncertainty
The objectives of this study were to quantify the error of body weight prediction using automatically measured morphological traits in a 3-dimensional (3-D) vision system and to assess the influence of various sources of uncertainty on body weight prediction. In this case study, an image acquisition setup was created in a cow selection box equipped with a top-view 3-D camera. Morphological traits of hip height, hip width, and rump length were automatically extracted from the raw 3-D images taken of the rump area of dairy cows (n = 30). These traits combined with days in milk, age, and parity were used in multiple linear regression models to predict body weight. To find the best prediction model, an exhaustive feature selection algorithm was used to build intermediate models (n = 63). Each model was validated by leave-one-out cross-validation, giving the root mean square error and mean absolute percentage error. The model consisting of hip width (measurement variability of 0.006 m), days in milk, and parity was the best model, with the lowest errors of 41.2 kg of root mean square error and 5.2% mean absolute percentage error. Our integrated system, including the image acquisition setup, image analysis, and the best prediction model, predicted the body weights with a performance similar to that achieved using semi-automated or manual methods. Moreover, the variability of our simplified morphological trait measurement showed a negligible contribution to the uncertainty of body weight prediction. We suggest that dairy cow body weight prediction can be improved by incorporating more predictive morphological traits and by improving the prediction model structure.
Developments and interlaboratory study of the analysis of short-chain chlorinated paraffins
Mourik, L.M. van; Veen, I. van der; Crum, S. ; Boer, J. de - \ 2018
TrAC : Trends in Analytical Chemistry 102 (2018). - ISSN 0165-9936 - p. 32 - 40.
Analysis - Interlaboratory studies - Laboratory agreement - Short polychlorinated n-alkanes (sPCAs) - Short-chain chlorinated paraffins (SCCPs)
To survey the conformity and quality of the results between laboratories for short-chain chlorinated paraffins (SCCPs) determination, we reviewed current and novel analytical methods and organized four worldwide laboratory exercises between 2011 and 2017. Participants were requested to analyse test solutions and extracts of various matrices with their method of choice. Thirty-three laboratories participated (9–22 per round), of which 55–81% were able to submit data. Large differences in results between laboratories were found (CVs 23–137%) but results improved over time, while the levels in the test materials decreased. In the last round acceptable CV values (<25%) were obtained for the test solution. In the last round, results obtained by the GC–ECNI-LRMS technique varied most, which is disconcerting as this technique is most commonly applied. We strongly suggest to continue monitoring comparability of laboratories to assess consensus in SCCP analysis, with a focus on quantification procedures applied.
Regulation of intercellular target of monopteros 7 protein transport in the arabidopsis root
Lu, Kuan Ju ; Rybel, Bert De; Mourik, Hilda Van; Weijers, Dolf - \ 2018
Development 145 (2018)2. - ISSN 0950-1991
Cell-cell communication - Embryogenesis - Plasmodesmata - Protein transport - RAM - TMO7
Intercellular communication coordinates hypophysis establishment in the Arabidopsis embryo. Previously, TARGET OF MONOPTEROS 7 (TMO7) was reported to be transported to the hypophysis, the founder cell of the root cap, and RNA suppression experiments implicated its function in embryonic root development. However, the protein properties and mechanisms mediating TMO7 protein transport, and the role the movement plays in development remained unclear. Here, we report that in the post-embryonic root, TMO7 and its close relatives are transported into the root cap through plasmodesmata in a sequence-dependent manner. We also show that nuclear residence is crucial for TMO7 transport, and postulate that modification, potentially phosphorylation, labels TMO7 for transport. Additionally, three novel CRISPR/Cas9-induced tmo7 alleles confirmed a role in hypophysis division, but suggest complex redundancies with close relatives in root formation. Finally, we demonstrate that TMO7 transport is biologically meaningful, as local expression partially restores hypophysis division in a plasmodesmal protein transport mutant. Our study identifies motifs and amino acids that are pivotal for TMO7 protein transport, and establishes the importance of TMO7 in hypophysis and root development.
Data from: The origin of floral organ identity quartets
Ruelens, Philip ; Zhang, Zhicheng ; Mourik, H. van; Maere, Steven ; Kaufmann, K. ; Geuten, Koen - \ 2017
evolution - angiosperms - flower development - MADS-domain - ancestral sequence rteconstruction
The origin of flowers has puzzled plant biologists ever since Darwin referred to their sudden appearance in the fossil record as an abominable mystery. Flowers are considered to be an assembly of protective, attractive and reproductive male and female leaf-like organs. Their origin cannot be understood by a morphological comparison to gymnosperms, their closest relatives, which develop separate male or female cones. Despite these morphological differences, gymnosperms and angiosperms possess a similar genetic toolbox consisting of phylogenetically related MADS-domain proteins. Using ancestral MADS-domain protein reconstruction, we trace the evolution of organ identity quartets along the stem lineage of crown angiosperms. We provide evidence that current floral quartets specifying male organ identity, which consist of four types of subunits, evolved from ancestral complexes of two types of subunits through gene duplication and integration of SEPALLATA proteins just before the origin of flowering plants. Our results suggest that protein interaction changes underlying this compositional shift were the result of a gradual and reversible evolutionary trajectory. Modelling shows that such compositional changes may have facilitated the evolution of the perfect, bisexual flower.
Natriumgevoeligheid en recirculatie bij Cymbidium in 3 teeltjaren : Behoud plantgezondheid en voorkomen groeiremming bij hergebruik drainwater
Kromwijk, Arca ; Voogt, Wim ; Steenhuizen, Johan ; Winkel, Aat van; Mourik, Nico van - \ 2017
Bleiswijk : Wageningen University & Research, BU Glastuinbouw (Rapport WPR 735) - 54
In the Netherlands, the government and horticultural industry have agreed to lower the emission of nutrients to the environment. Until recently no drain water was reused in the cultivation of Cymbidium orchids as growers were allowed to discharge the drain water when a sodium level of more than 0 mmol/l was reached. As reusing drain water is a new phenomenon for Cymbidium, growers were faced with a lack of knowledge on the effects of drain water reuse. Therefore a trial was started to investigate the effect of sodium accumulation on crop growth and flowering in two varieties of Cymbidium. Different sodium concentrations are given while maintaining the EC at 0.8. These sodium treatments have a lower “nutritional EC” than the control treatment without sodium. In the first year of cultivation unusual symptoms in the leaves emerged at the two highest levels of sodium resulting in dead leaf tips / leaves. This is potassium deficiency, induced by the lower potassium concentration in the nutritional solution and by inhibition of the potassium uptake by a high sodium concentration. In the first year of cultivation, sodium accumulation had no effect on production as the flower stalks were already induced before or just after the start of the treatments. In the second and third year of cultivation, sodium accumulation reduced production and quality of Cymbidium. This research is funded by the Cymbidium growers in the Netherlands, Product Board for Horticulture, Top Sector Horticulture & Propagation Materials and Foundation Program Fund Greenhouse Horticulture.
Comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects
Buelow, Elena ; Bello González, Teresita D.J. ; Fuentes, Susana ; Steenhuijsen Piters, Wouter A.A. de; Lahti, Leo ; Bayjanov, Jumamurat R. ; Majoor, Eline A.M. ; Braat, Johanna C. ; Mourik, Maaike S.M. van; Oostdijk, Evelien A.N. ; Willems, Rob J.L. ; Bonten, Marc J.M. ; Passel, Mark W.J. van; Smidt, Hauke ; Schaik, Willem van - \ 2017
Microbiome 5 (2017)1. - ISSN 2049-2618 - p. 88 - 88.
Anti-bacterial agents - Antibiotic prophylaxis - Drug resistance - Intensive care - Microbial - Microbiome
BACKGROUND: The gut microbiota is a reservoir of opportunistic pathogens that can cause life-threatening infections in critically ill patients during their stay in an intensive care unit (ICU). To suppress gut colonization with opportunistic pathogens, a prophylactic antibiotic regimen, termed "selective decontamination of the digestive tract" (SDD), is used in some countries where it improves clinical outcome in ICU patients. Yet, the impact of ICU hospitalization and SDD on the gut microbiota remains largely unknown. Here, we characterize the composition of the gut microbiota and its antimicrobial resistance genes ("the resistome") of ICU patients during SDD and of healthy subjects.RESULTS: From ten patients that were acutely admitted to the ICU, 30 fecal samples were collected during ICU stay. Additionally, feces were collected from five of these patients after transfer to a medium-care ward and cessation of SDD. Feces from ten healthy subjects were collected twice, with a 1-year interval. Gut microbiota and resistome composition were determined using 16S rRNA gene phylogenetic profiling and nanolitre-scale quantitative PCRs. The microbiota of the ICU patients differed from the microbiota of healthy subjects and was characterized by lower microbial diversity, decreased levels of Escherichia coli and of anaerobic Gram-positive, butyrate-producing bacteria of the Clostridium clusters IV and XIVa, and an increased abundance of Bacteroidetes and enterococci. Four resistance genes (aac(6')-Ii, ermC, qacA, tetQ), providing resistance to aminoglycosides, macrolides, disinfectants, and tetracyclines, respectively, were significantly more abundant among ICU patients than in healthy subjects, while a chloramphenicol resistance gene (catA) and a tetracycline resistance gene (tetW) were more abundant in healthy subjects.CONCLUSIONS: The gut microbiota of SDD-treated ICU patients deviated strongly from the gut microbiota of healthy subjects. The negative effects on the resistome were limited to selection for four resistance genes. While it was not possible to disentangle the effects of SDD from confounding variables in the patient cohort, our data suggest that the risks associated with ICU hospitalization and SDD on selection for antibiotic resistance are limited. However, we found evidence indicating that recolonization of the gut by antibiotic-resistant bacteria may occur upon ICU discharge and cessation of SDD.
Divergent regulation of Arabidopsis SAUR genes : A focus on the SAUR10-clade
Mourik, Hilda van; Dijk, Aalt D.J. van; Stortenbeker, Niek ; Angenent, Gerco C. ; Bemer, Marian - \ 2017
BMC Plant Biology 17 (2017). - ISSN 1471-2229
ABA - Auxin - Brassinosteroids - Cell elongation - Growth - Hormones - Regulatory region - SAUR - Shade response

Background: Small Auxin-Upregulated RNA (SAUR) genes encode growth regulators that induce cell elongation. Arabidopsis contains more than 70 SAUR genes, of which the growth-promoting function has been unveiled in seedlings, while their role in other tissues remained largely unknown. Here, we focus on the regulatory regions of Arabidopsis SAUR genes, to predict the processes in which they play a role, and understand the dynamics of plant growth. Results: In this study, we characterized in detail the entire SAUR10-clade: SAUR8, SAUR9, SAUR10, SAUR12, SAUR16, SAUR50, SAUR51 and SAUR54. Overexpression analysis revealed that the different proteins fulfil similar functions, while the SAUR expression patterns were highly diverse, showing expression throughout plant development in a variety of tissues. In addition, the response to application of different hormones largely varied between the different genes. These tissue-specific and hormone-specific responses could be linked to transcription factor binding sites using in silico analyses. These analyses also supported the existence of two groups of SAURs in Arabidopsis: Class I genes can be induced by combinatorial action of ARF-BZR-PIF transcription factors, while Class II genes are not regulated by auxin. Conclusions:SAUR10-clade genes generally induce cell-elongation, but exhibit diverse expression patterns and responses to hormones. Our experimental and in silico analyses suggest that transcription factors involved in plant development determine the tissue specific expression of the different SAUR genes, whereas the amplitude of this expression can often be controlled by hormone response transcription factors. This allows the plant to fine tune growth in a variety of tissues in response to internal and external signals.

Targets of FRUITFULL in the pistil/silique [ChIP-Seq]
Bemer, M. ; Mourik, H. van; Angenent, G.C. - \ 2017
Arabidopsis thaliana - GSE79554 - PRJNA316152
To learn more about the role of FRUITFULL (FUL), in pistil/silique development, we performed a ChIP-seq experiment to identify direct targets of FUL in the pistil/silique.
FRUITFULL controls SAUR10 expression and regulates Arabidopsis growth and architecture
Bemer, Marian ; Mourik, Hilda van; Muiño, Jose M. ; Ferrándiz, Cristina ; Kaufmann, Kerstin ; Angenent, Gerco C. - \ 2017
Journal of Experimental Botany 68 (2017)13. - ISSN 0022-0957 - p. 3391 - 3403.
MADS-domain transcription factors are well known for their roles in plant development and regulate sets of downstream genes that have been uncovered by high-throughput analyses. A considerable number of these targets are predicted to function in hormone responses or responses to environmental stimuli, suggesting that there is a close link between developmental and environmental regulators of plant growth and development. Here, we show that the Arabidopsis MADS-domain factor FRUITFULL (FUL) executes several functions in addition to its noted role in fruit development. Among the direct targets of FUL, we identified SMALL AUXIN UPREGULATED RNA 10 (SAUR10), a growth regulator that is highly induced by a combination of auxin and brassinosteroids and in response to reduced R:FR light. Interestingly, we discovered that SAUR10 is repressed by FUL in stems and inflorescence branches. SAUR10 is specifically expressed at the abaxial side of these branches and this localized activity is influenced by hormones, light conditions and by FUL, which has an effect on branch angle. Furthermore, we identified a number of other genes involved in hormone pathways and light signalling as direct targets of FUL in the stem, demonstrating a connection between developmentally and environmentally regulated growth programs.
The use of sensor data before parturition as an indicator of resilience of dairy cows in early lactation
Mol, R.M. de; Dixhoorn, I.D.E. van; Werf, J.T.N. van der; Reenen, C.G. van; Mourik, S. van - \ 2017
In: Precision Livestock Farming '17. - - p. 399 - 415.
dairy cows - transition - sensors - circadian rhythm - early warning
The transition period is a critical phase in the life of dairy cows. Metabolic and
infectious disorders occur mostly in the first weeks after calving. These disorders
can be considered as critical transitions for which early-warning indicators might
be available following the theory of resilience of biological systems. Sensor data
might be useful to notice early-warning signals like slower recovery from
perturbations, increased autocorrelations and increased variance. Sensor data
(measuring activity and behaviour) and extensive reference data were collected
for a group of 22 dairy cows during a period from 2 weeks prior to expected
parturition until 6 weeks after parturition. During this period the cows were
scored daily for health status. The number of days of diminished health (DDH)
were used a health measure of a cow. The correlations of the log-transformed
DDH with several sensor quantities were determined. Correlations with average
values were significant (*) for inactive time and eating time. Correlations with
variances were significant (*) for ear temperature and number of steps.
Correlations with autocorrelations were not significant. Correlations with
nonperiodicity were significant for eating time (*), number of steps (**), motion
index (**) and lying time (***); where nonperiodicity was defined as the mean
squared error of the correlogram with a sinusoid with a 24h cycle and an
amplitude of 0.25. The high correlations before parturition of some sensor data
with nonperiodicity might be used as indicator for critical transitions after
parturition. Further research is needed to validate whether a regular life may
prevent disorders in dairy cows.
MADS specificity : Unravelling the dual function of the MADS domain protein FRUITFULL
Mourik, Hilda van - \ 2017
University. Promotor(en): Gerco Angenent, co-promotor(en): Kerstin Kaufmann. - Wageningen : Wageningen University - ISBN 9789463436724 - 199
transcription factors - dna binding proteins - arabidopsis thaliana - mads-box proteins - protein-protein interactions - gene regulation - transcriptiefactoren - dna-bindende eiwitten - mads-box eiwitten - eiwit-eiwit interacties - genregulatie

Encrypted in the DNA lays most information needed for the development of an organism. The transcription of this information into precise patterns of gene activity results in the development of different cell types, organs, and developmental structures. Moreover, transcriptional regulation enables an organism to respond to changing environmental conditions. Essential for the regulation of transcription are DNA-binding transcription factors (TFs). TFs bind the DNA in a sequence-specific fashion. Upon binding of a TF to its DNA binding site, TFs typically activate or repress the transcription of nearby genes. To better understand transcriptional regulation it is essential to study DNA binding specificity of TFs.

In the last decades, technological advances allowed the development of high-throughput methods to study protein-DNA interactions. Traditional in vitro methods study one or a few interactions, while new high-throughput methods can determine TF specificity by measuring relative DNA-binding affinities against a large collection or even all possible binding sites. Several high-throughput techniques to study TF-DNA interactions are discussed in Chapter 1 of this thesis. These new technologies and methods resulted in a fast growing number of studies on DNA binding specificities of TFs, expanding the knowledge about TF specificity. A review on the current knowledge of TF DNA binding specificity is described in Chapter 1.

One aspect that influences DNA binding of TFs are differences in ability to form protein-protein interactions. The aim of this thesis was to study the role of protein-protein interactions in determining DNA binding specificity of a developmental regulatory MADS domain TF in Arabidopsis thaliana. While the members of the MADS-box protein family have many, diverse in vivo functions, all members bind in vitro to a 10-bp motif called the CArG-box. Moreover, studies demonstrated that closely related MADS proteins are expressed in the same cells, therefore encountering the same DNA accessibility and DNA methylation patterns, but bind different in vivo targets. Interestingly, MADS domain proteins bind DNA obligatorily as homo- and heterodimers and the interactions between MADS domain proteins are highly protein specific. Hence, MADS domain proteins are a perfect model system to study the influence of intra-family protein interactions on DNA binding specificity.

To study the influence of protein-protein interactions on DNA-binding specificity this work focusses on one specific MADS domain protein, FRUITFULL (FUL). FUL is expressed at two stages during flower development and, in both stages FUL has highly diverse functions. In Chapter 2 we demonstrate using RNA-seq that FUL regulates different sets of target genes in the two stages. Moreover, using ChIP-seq we show that FUL genomic DNA binding is partly tissue-specific. These tissue-specifically bound and regulated genes are in line with the known dual functions of FUL during development. Interestingly, using protein complex immunoprecipitation for the two studied tissues/stages we show that the interactions of FUL with other MADS domain proteins are also tissue-specific. To determine whether the tissue-specific in vivo binding pattern are due to differences in DNA binding specificity of the FUL-MADS dimers, we studied the DNA binding specificities of the different protein complexes using SELEX-seq. The SELEX-seq results show that although all tested dimers preferably bind the canonical binding motif of MADS domain proteins, different dimers have different preferences for nucleotides within and surrounding the canonical binding site. Hence, different MADS domain dimers have different in vitro DNA binding specificities. By mapping the SELEX-seq affinities to the genome we were able to compare these results with in vivo tissue-specific ChIP-seq data. This analysis revealed a strong correlation between tissue-specific dimer affinities and tissue-specific genomic binding sites of FUL. Hence, we show that the choice of MADS dimerization partner influences DNA binding specificity, highlighting the role of intra-family protein interactions in defining DNA binding specificity.

To allow other researchers to determine genome-wide DNA binding of TFs Chapter 3 provides a step-by-step guide for ChIP-seq experiments and computational analysis. The protocol is designed for wet-lab biologists to perform ChIP-seq experiments and analyse their own ChIP-seq data.

Using the genome-wide DNA binding patterns determined by ChIP-seq, Chapter 4 and Chapter 5 take a more detailed look at some of the genes directly bound by FUL. In Chapter 4, we demonstrate a connection between developmentally and environmentally regulated growth programs. We studied a gene directly bound by FUL in pistil tissue, SMALL AUXIN UPREGULATED RNA 10 (SAUR10). SAUR10 expression is regulated by FUL in multiple tissues, among others cauline leaves, stems, and branches. The results show that the expression of SAUR10 at the abaxial side of branches is influenced by a combination of environmental and developmental regulated growth programs: hormones, light conditions, and FUL binding. This spatial regulation possibly affects the angle between the side branches and the main inflorescence stem. Additionally, we discuss several other FUL target genes involved in hormone pathways and light conditions.

Chapter 5 focusses on the putative direct targets of FUL in IM tissue. Among the putative direct targets two genes involved in flavonoid synthesis were identified, FLAVONOID SYNTHESE 1 (FLS1) and UDP-GLUCOSYL TRANSFERASE 78D3 (UGT78D3). Interestingly, similar to the ful-7 mutant, the fls1 mutant is late flowering. Moreover, expression data exposed an increased gene expression for both FLS1 and UGT78D3 in developing meristems and showed FLS1 expression to be influenced by light conditions. We report the first link between the MADS domain protein FUL and flavonoid synthesis in Arabidopsis. Moreover, our results indicate a possible link between flavonoids and flowering time.

In Chapter 6 I discuss the findings of this thesis and make suggestions for further research. Taken together, the work in this thesis shows that intra-family protein interactions can influence DNA-binding specificity of a protein. Thereby these protein-protein interactions can influence genome-wide binding patterns and, as a result, the function of a protein. Moreover, by studying several putative direct targets of FUL in more detail, we demonstrated a connection between development and environment in growth-regulated programs. Interestingly, the FUL target SAUR10 is repressed by FUL in several tissues, including cauline leaves, inflorescence stems, and branches. However, no influence of FUL on SAUR10 expression could be detected in the pistil. So, despite the binding of FUL to the promotor of SAUR10 in the pistil, this binding does not result in gene regulation. This finding reflects the complex relation between TF occupancy and gene regulation, further research is needed to better understand this relation. Moreover, besides MADS domain protein interactions, we found FUL to interact with several proteins of other families. The role of these cross-family protein interactions in cooperative gene regulation is not fully understood and will be an important research topic in the coming years.

Performance of extended and unscented Kalman filters for state and parameter estimation of a greenhouse climate model
López-Cruz, I.L. ; Beveren, P.J.M. Van; Mourik, S. Van; Henten, E.J. Van - \ 2017
In: International Symposium on New Technologies and Management for Greenhouses - GreenSys2015 International Society for Horticultural Science (Acta Horticulturae ) - ISBN 9789462611665 - p. 175 - 181.
Data assimilation - Dynamic model - Greenhouse environment - Model calibration - Uncertainty
In dynamic modeling of the greenhouse climate, prediction errors are a significant issue due to uncertainties in initial state values, input variables, model parameters and model structure, all propagating in time in a nonlinear way. We investigated a data assimilation approach using two non-linear Kalman filters in light of prediction uncertainty. An extended (EKF) and an unscented (UKF) Kalman filters were designed to estimate climate states, and also both the states and model parameters. The states to be estimated were air temperature, absolute humidity and carbon dioxide concentration inside a greenhouse. Year round measurements from a Dutch greenhouse with a rose crop were used. The dynamic model was first calibrated manually by estimating ten of its parameters. Uncertainties of the measurements needed for designing EKF and UKF were specified via literature sources whereas the uncertainties related to the process were tuned. Both filters increased the model predictive power several orders of magnitude with respect to mean squared error (MSE) statistics and one order of magnitude with respect to mean absolute error (MAE) analyzed during autumn-winter and spring-summer seasons when only the model states were estimated. However, no improvement on the one step ahead state predictions were achieved when both states and model parameters were estimated by both nonlinear filters. Results showed that data assimilation based on nonlinear Kalman filters is advantageous over data assimilation that uses only model calibration. Therefore, improved model of the greenhouse climate by data assimilation can be used in controlling and optimizing more efficiently the greenhouse system.
The effects of model reduction and data assimilation on greenhouse climate predictions
Mourik, S. Van; Beveren, P.J.M. Van; López-Cruz, I.L. ; Henten, E.J. Van - \ 2017
In: International Symposium on New Technologies and Management for Greenhouses - GreenSys2015 International Society for Horticultural Science (Acta Horticulturae ) - ISBN 9789462611665 - p. 235 - 241.
Black box models - Control - First principle models - Modelling - Uncertainty analysis
We investigated the effect of model reduction and data assimilation on prediction accuracy of greenhouse climate. For this, a first-principle model was reduced, and calibrated with measurement data. Calibration data consisted of a time series of temperature, humidity, and carbon-dioxide concentration in a rose greenhouse, together with 15 variables related to outside climate and control actions. The results indicate that model reduction does not produce a crucial loss of prediction accuracy. In contrast, data assimilation decreases the size and variance of prediction errors drastically, making predictions much more reliable. A static linear model seems to predict the most essential input-output response for temperature and humidity, but the predictive power for carbon-dioxide concentration is limited. The prediction errors have standard deviations of typically 2°C, for temperature, 5-10% for relative humidity, and 200-300 ppm for CO2. The prediction errors have biases of the same order, which differ per period for which the predictions are made. We believe these results are promising for modelling climate via a static black box approach, in combination with data assimilation. The relatively low computational demand for uncertainty analysis and easy model building provide a suitable starting point for investigating augmented systems, such as plant development based on controlled climate.
Development of a model forecasting Dermanyssus gallinae's population dynamics for advancing Integrated Pest Management in laying hen facilities
Mul, Monique F. ; Riel, Johannes van; Roy, Lise ; Zoons, Johan ; Andre, Geert ; George, David R. ; Meerburg, Bastiaan G. ; Dicke, Marcel ; Mourik, Simon van; Groot Koerkamp, Peter W.G. - \ 2017
Veterinary Parasitology 245 (2017). - ISSN 0304-4017 - p. 128 - 140.
Dermanyssus gallinae - Integrated Pest Management (IPM) - Population model - Poultry Gallus gallus - Treatment effect

The poultry red mite, Dermanyssus gallinae, is the most significant pest of egg laying hens in many parts of the world. Control of D. gallinae could be greatly improved with advanced Integrated Pest Management (IPM) for D. gallinae in laying hen facilities. The development of a model forecasting the pests’ population dynamics in laying hen facilities without and post-treatment will contribute to this advanced IPM and could consequently improve implementation of IPM by farmers. The current work describes the development and demonstration of a model which can follow and forecast the population dynamics of D. gallinae in laying hen facilities given the variation of the population growth of D. gallinae within and between flocks. This high variation could partly be explained by house temperature, flock age, treatment, and hen house. The total population growth variation within and between flocks, however, was in part explained by temporal variation. For a substantial part this variation was unexplained. A dynamic adaptive model (DAP) was consequently developed, as models of this type are able to handle such temporal variations. The developed DAP model can forecast the population dynamics of D. gallinae, requiring only current flock population monitoring data, temperature data and information of the dates of any D. gallinae treatment. Importantly, the DAP model forecasted treatment effects, while compensating for location and time specific interactions, handling the variability of these parameters. The characteristics of this DAP model, and its compatibility with different mite monitoring methods, represent progression from existing approaches for forecasting D. gallinae that could contribute to advancing improved Integrated Pest Management (IPM) for D. gallinae in laying hen facilities.

Effect of nickel and cobalt on methanogenic enrichment cultures and role of biogenic sulfide in metal toxicity attenuation
Luz Ferreira Martins Paulo, Lara da; Ramiro-Garcia, Javier ; Mourik, Simon van; Stams, Alfons J.M. ; Machado de Sousa, Diana - \ 2017
Frontiers in Microbiology 8 (2017)JUL. - ISSN 1664-302X
Anaerobic sludge - Heavy metals - Inhibition - Stimulation - Sulfate - Sulfide
Metals play an important role in microbial metabolism by acting as cofactors for many enzymes. Supplementation of biological processes with metals may result in improved performance, but high metal concentrations are often toxic to microorganisms. In this work, methanogenic enrichment cultures growing on H2/CO2 or acetate were supplemented with trace concentrations of nickel (Ni) and cobalt (Co), but no significant increase in methane production was observed in most of the tested conditions. However, high concentrations of these metals were detrimental to methanogenic activity of the cultures. Cumulative methane production (after 6 days of incubation) from H2/CO2 was 40% lower in the presence of 8 mM of Ni or 30 mM of Co, compared to controls without metal supplementation. When acetate was used as substrate, cumulative methane production was also reduced: by 18% with 8 mM of Ni and by 53% with 30 mM of Co (after 6 days of incubation). Metal precipitation with sulfide was further tested as a possible method to alleviate metal toxicity. Anaerobic sludge was incubated with Co (30 mM) and Ni (8 mM) in the presence of sulfate or sulfide. The addition of sulfide helped to mitigate the toxic effect of the metals. Methane production from H2/CO2 was negatively affected in the presence of sulfate, possibly due to competition of hydrogenotrophic methanogens by sulfate-reducing bacteria. However, in the enrichment cultures growing on acetate, biogenically produced sulfide had a positive effect and more methane was produced in these incubations than in similar assays without sulfate addition. The outcome of competition between methanogens and sulfate-reducing bacteria is a determinant factor for the success of using biogenic sulfide as detoxification method.
Co-learning cycles to support the design of innovative farm systems in southern Mali
Falconnier, Gatien N. ; Descheemaeker, Katrien ; Mourik, Thomas A. Van; Adam, Myriam ; Sogoba, Bougouna ; Giller, Ken E. - \ 2017
European Journal of Agronomy 89 (2017). - ISSN 1161-0301 - p. 61 - 74.
Ex ante trade-off analysis - Food self-sufficiency - Income - Participatory research

Farm systems were re-designed together with farmers during three years (2013–2015) in Southern Mali with the aim to improve income without compromising food self-sufficiency. A cyclical learning model with three steps was used: Step 1 was the co-design of a set of crop/livestock technical options, Step 2 the on-farm testing and appraisal of these options and Step 3 a participatory ex-ante analysis of re-designed farm systems incorporating the tested options. Two iterations of the cycle were performed, in order to incorporate farmers’ point of view and researchers’ learning. We worked together with 132 farmers representing four farm types: High Resource Endowed with Large Herd (HRE-LH); High Resource Endowed (HRE); Medium Resource Endowed (MRE) and Low Resource Endowed (LRE) farms. In the first cycle of 2012–2014 farmers re-designed their farms and the reconfigurations were assessed ex ante using the average yields and gross margins obtained in the 2013 on-farm trials. HRE-LH farmers experienced a disappointing decrease in food self-sufficiency and MRE farmers were disappointed by the marginal improvement in gross margin. In a second cycle in 2014–2015, farmer insights gathered during field days and statistical analysis of trial results allowed a better understanding of the variability of option performance and the link with farm context: niches were identified within the farms (soil type/previous crop combinations) where options performed better. The farm systems were re-designed using this niche-specific information on yield and gross margin, which solved the concerns voiced by farmers during the first cycle. Without compromising food self-sufficiency, maize/cowpea intercropping in the right niche combined with stall feeding increased HRE-LH and HRE farm gross margin by 20–26% respectively (i.e. 690 and 545 US$ year−1) with respect to the current farm system. Replacement of sorghum by soyabean (or cowpea) increased MRE and LRE farm gross margin by 29 and 9% respectively (i.e. 545 and 32 US$ year−1). Farmers highlighted the saliency of the niches and the re-designed farm system, and indicated that the extra income could be re-invested in the farm. Our study demonstrates the feasibility and the usefulness of a cyclical and adaptive combination of participatory approaches, on-farm trials and ex-ante analysis to foster learning by farmers and researchers, allowing an agile reorientation of project actions and the generation of innovative farm systems that improve farm income without compromising food self-sufficiency. The re-designed farm systems based on simple, reproducible guidelines such as farm type, previous crop and soil type can be scaled-out by extension workers and guide priority setting in (agricultural) policies and institutional development.

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