Ron Wehrens's research while affiliated with Wageningen University & Research and other places

Publications (126)

Article
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Key message We evaluate self-organizing maps (SOM) to identify adaptation zones and visualize multi-environment genotypic responses. We apply SOM to multiple traits and crop growth model output of large-scale European sunflower data. Abstract Genotype-by-environment interactions (G × E) complicate the selection of well-adapted varieties. A possibl...
Preprint
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The biosynthesis, structure and accumulation of secondary metabolites in plants are largely controlled by genetic factors, which can vary substantially among genotypes within a species. Here we studied a global population of Arabidopsis thaliana accessions for qualitative and quantitative variation in volatile and non-volatile secondary metabolites...
Article
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A human intervention trial was conducted to study amino acid uptake of the novel Lemna protein concentrate (LPC) in comparison to whey (WPC). The study was a cross-over, double-blind, controlled trial in which 12 healthy participants received 20 grams of LPC and WPC in randomised order. The LPC consumption resulted in a significant lower postprandi...
Article
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High-throughput phenotyping is playing an increasingly important role in many areas of agriculture. Breeders will use it to obtain values for the traits of interest so that they can estimate genetic value and select promising varieties; growers may be interested in having predictions of yield well in advance of the actual harvest. In most phenotypi...
Article
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In plants, secondary metabolite profiles provide a unique opportunity to explore seasonal variation and responses to the environment. These include both abiotic and biotic factors. In field experiments, such stress factors occur in combination. This variation alters the plant metabolic profiles in yet uninvestigated ways. This data set contains tra...
Article
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The increased usage of alternative Ayurvedic treatments as potential health-beneficial therapies emphasizes the importance of studying its efficacy in sound placebo-controlled intervention trials. An example of such a traditional Ayurvedic herbal preparation is Mohana Choorna, a mixture composed of 20 different herbs and used to prevent and treat t...
Article
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Accurately detecting and counting fruits during plant growth using imaging and computer vision is of importance not only from the point of view of reducing labor intensive manual measurements of phenotypic information, but also because it is a critical step toward automating processes such as harvesting. Deep learning based methods have emerged as...
Conference Paper
In this paper we propose an image analysis method for detecting and counting tomato flowers from images taken in a greenhouse. Detecting and locating flowers is useful information for tomato growers and breeders, for phenotyping, yield prediction, and for automating procedures such as pollination and spraying. Since the tomato flowers are yellow, w...
Article
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Crop wild relatives (CWR) are wild plant taxa that are genetically related to a cultivated species and are considered rich sources of useful traits for crop improvement. CWR are generally underrepresented in genebanks, while their survival in nature is not guaranteed. Inventories and risk analyses are needed to prioritize CWR for conservation in or...
Chapter
In this paper we propose an image analysis method for detecting and counting tomato flowers from images taken in a greenhouse. Detecting and locating flowers is useful information for tomato growers and breeders, for phenotyping, yield prediction, and for automating procedures such as pollination and spraying. Since the tomato flowers are yellow, w...
Poster
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How plants respond to changing environments is commonly studied in semi-natural biodiversity experiments and analysed on a morphological trait level. On the other hand, secondary metabolites, known to play a key role in, e.g. plant defence strategies, are mainly studied under controlled conditions. However, changes in plant communities and across s...
Chapter
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Chapter
Metabolomics is a vibrant field, developing fast and attracting many scientists from adjacent disciplines. Its multidisciplinarity is one of the defining features of metabolomics: in order to describe, quantify and understand the diversity of metabolite composition of biological samples one needs chemistry, biology, mathematics and statistics, and...
Article
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The genetically encoded calcium sensor protein Cameleon YC3.6 has previously been applied for functional G protein-coupled receptor screening using receptor cell arrays. However, different types of sensors are available, with a wide range in [Ca2+] sensitivity, Hill coefficients, calcium binding domains and fluorophores, that could potentially impr...
Poster
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Plants, grown in the field, face an undefined number of stresses. How plants respond to these factors, is often studied on the level of visible traits. However, changing communities and seasons will also be reflected in the metabolic fingerprint of a plant. Understanding those dynamics will help to unravel the underlying mechanisms of ecosystem fun...
Article
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Turnip (Brassica rapa spp. rapa) is an important vegetable species, with a unique physiology. Several plant parts, including both the turnip tubers and leaves, are important for human consumption. During the development of turnip plants, the leaves function as metabolic source tissues, while the tuber first functions as a sink, while later the tube...
Data
Estimated treatment-versus-control contrasts for individual spotmixes in experiment A1. Each panel contains the result of one receptor type; dilutions are given at the y axis, with stronger dilutions towards the bottom. Significant contrasts, not containing the value of one in the confidence interval, are indicated in red. The blank injection serve...
Data
PCA loading plots for the three replicated experiments, type A. Spots of types R8 and R14 are highlighted to show the variability between spots of the same receptor type. For clarity, the largest loadings are shown with arrows, smaller ones are shown with dots only. (TIFF)
Data
Estimated treatment-versus-control contrasts for individual spotmixes in experiment A2. For explanation, see legend of S4 Fig. (TIFF)
Data
Joint analysis of type-B experiments. For explanation, see the caption of Fig 3. The reference level is given by the injection type ATP 2uM. (TIFF)
Article
Full-text available
Data analysis for flow-based in-vitro receptomics array, like a tongue-on-a-chip, is complicated by the relatively large variability within and between arrays, transfected DNA types, spots, and cells within spots. Simply averaging responses of spots of the same type would lead to high variances and low statistical power. This paper presents an appr...
Data
ExperimentB.csv: File containing data for the three experiments of type B. (CSV)
Data
Overview of bitter raste receptor genes used in the bitter-receptor array. Polymorphism variants are indicated with the aminoacid number of the receptor protein and the variable amino-acid letter code. In brackets the printed polymorphism is shown. The rightmost column contains the number of replications on the array. (PDF)
Data
PCA loading plots for the three replicated experiments, type B. Spots of types R8 and R14 are highlighted to show the variability between spots of the same receptor type. For clarity, the largest loadings are shown with arrows, smaller ones are shown with dots only. (TIFF)
Data
scripts.R: File containing R scripts for reproducing the results (including figures) in this paper. (R)
Data
ExperimentA.csv: File containing data for the three experiments of type A. (CSV)
Data
Definition of the magnitude of the spot response to an injection. The plots depict the last three injections of the data also shown in S1 Fig. The magnitude of the spot response is the ratio of the extreme point within a time window (here 30 cycles, indicated by the gray vertical lines), and the starting value, the average of the first three points...
Data
Estimated treatment-versus-control contrasts for individual spotmixes in experiment A3. For explanation, see legend of S4 Fig. (TIFF)
Article
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Introduction Lettuce (Lactuca sativa L.) is generally not specifically acknowledged for its taste and nutritional value, while its cultivation suffers from limited resistance against several pests and diseases. Such key traits are known to be largely dependent on the ability of varieties to produce specific phytochemicals. Objectives We aimed to i...
Article
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Self-organizing maps (SOMs) are popular tools for grouping and visualizing data in many areas of science. This paper describes recent changes in package kohonen, implementing several different forms of SOMs. These changes are primarily focused on making the package more useable for large data sets. Memory consumption has decreased dramatically, amo...
Article
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The aim of the study was to develop an approach to discriminate whether cheese is produced from raw or heat-treated milk. The method was based on multivariate discrimination of volatile organic compounds in the cheeses’ headspace. Although the method was developed to detect issues with food authenticity for a Dutch traditional speciality guaranteed...
Article
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Reverse-transfected cell arrays in microfluidic systems have great potential to perform large-scale parallel screening of G protein-coupled receptor (GPCR) activation. Here, we report the preparation of a novel platform using reverse transfection of HEK293 cells, imaging by stereo-fluorescence microscopy in a flowcell format, real-time monitoring o...
Article
The "Slender Spindle", one of the most used training systems for apple, was compared with the "Bi-axis", an innovative training system, to determine their effect on fruit quality and fruit distribution within the canopy on 'Gala' cultivar. Two levels of crop loads were also introduced to observe their effects through chemical and manual thinning. F...
Article
The correlation of light availability and fruit quality traits for apple fruits (Malus × domestica Borkh.) within the canopy in two training systems, Slender Spindle and Bi-axis, were tested on nine-year-old trees of 'Gala' grafted on M9 rootstock. Three trees were chosen for each training system and twelve fruits from each tree were selected in di...
Article
The Levenberg-Marquardt algorithm is a flexible iterative procedure used to solve non-linear least squares problems. In this work we study how a class of possible adaptations of this procedure can be used to solve maximum likelihood problems when the underlying distributions are in the exponential family. We formally demonstrate a local convergence...
Article
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Annotation of metabolites is an essential, yet problematic, aspect of mass spectrometry (MS)-based metabolomics assays. The current repertoire of definitive annotations of metabolite spectra in public MS databases is limited and suffers from lack of chemical and taxonomic diversity. Furthermore, the heterogeneity of the data prevents the developmen...
Article
Isotope Ratio Mass Spectrometry (IRMS), 1H Nuclear Magnetic Resonance (1H NMR), conventional chemical analysis and chemometric elaboration were used to assess quality and to define and confirm the geographical origin of 177 Italian PDO (Protected Denomination of Origin) olive oils and 86 samples imported from Tunisia. Italian olive oils were richer...
Article
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Introduction Batch effects in large untargeted metabolomics experiments are almost unavoidable, especially when sensitive detection techniques like mass spectrometry (MS) are employed. In order to obtain peak intensities that are comparable across all batches, corrections need to be performed. Since non-detects, i.e., signals with an intensity too...
Article
Alignment of peaks across samples is a difficult but unavoidable step in the data analysis for all analytical techniques containing a separation step like chromatography. Important application examples are the fields of metabolomics and proteomics. Parametric time warping (PTW) has already shown to be very useful in these fields because of the high...
Article
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Background Tracking timber is necessary in order to prevent illegal logging and protect local timber production, but there is as yet no suitable analytical traceability method. Stable isotope ratios in plants are known to reflect geographical variations. In this study we analysed four stable isotope ratios in order to develop a model able to identi...
Article
In this study, we investigated the relationship between (D/H)1, (D/H)2 and δ(13)C of ethanol and δ(18)O of water in wine, and variables describing the climate and the geography of the production area, using exploratory visualisation tools, regression analysis and linear modelling. For the first time, a large amount of data (around 4000 wine samples...
Article
Likelihood estimates of the Dirichlet distribution parameters can be obtained only through numerical algorithms. Such algorithms can provide estimates outside the correct range for the parameters and/or can require a large amount of iterations to reach convergence. These problems can be aggravated if good starting values are not provided. In this p...
Article
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Due to their sensitivity and speed, mass-spectrometry based analytical technologies are widely used to in metabolomics to characterize biological phenomena. To address issues like metadata organization, quality assessment, data processing, data storage, and, finally, submission to public repositories, bioinformatic pipelines of a non-interactive na...
Article
A comparison between the two training systems Slender Spindle and Bi-axis was performed on two main cultivars, such as ‘Galaxy Evolution’ and ‘Pink Lady’® (‘Rosy Glow’). Tree architecture description and fruit position in the canopy were monitored during the fruit maturation and ripening using a software developed to design tree architecture and fr...
Article
Full-text available
Seedless grapes are greatly appreciated for fresh and dry fruit consumption. Parthenocarpy and stenospermocarpy have been described as the main phenomena responsible for seedlessness in Vitis vinifera. However, the key genes underpinning molecular and cellular processes that play a significant role in seed development are not well characterized. To...
Article
Untargeted metabolomics is rapidly becoming an important tool for studying complex biological samples. Gas chromatography-mass spectrometry (GC-MS) is the most widely used analytical technology for metabolomic analysis of compounds that are volatile or can be chemically derivatised into volatile compounds. Unfortunately, data processing and analysi...
Article
Mass-spectrometry-based imaging approaches allow for location-specific identification of chemical components in biological samples, opening-up possibilities of much more detailed understanding of biological processes and mechanisms. Data analysis, however, is challenging, mainly because of the sheer size of such datasets. This paper presents a nove...
Article
For those chemical compounds absorbing in the UV–Vis region and not readily applicable to routine mass spectrometry ionisation methods, liquid chromatography coupled to diode array detection is a convenient platform to perform metabolite profiling. Data processing by hand is labour-intensive and error prone. In the present study a strategy based on...
Article
Estimation of mass measurement accuracy is an elementary step in the application of mass spectroscopy (MS) data towards metabolite annotations and has been addressed several times in the past. However, the reproducibility of mass measurements over a diverse set of analytes and in variable operating conditions, which are common in high-throughput me...
Article
Survey technologies, such as metabolomics and proteomics, play increasingly important roles in the investigation of complex biological systems. These methods produce data sets that typically provide a huge amount of information using relatively few samples, so that finding differences between two groups, a fairly common question in this context, ru...
Article
Canopy microclimate manipulation can have a significant effect on grapevine gene expression and can thus affect the yield of many important berry compounds. Focusing on only few targeted phenolics in the past, advanced multi-method analytical approaches are opening up much wider possibilities to fill in the gaps of missing knowledge about plant sec...
Article
Warping methods are an important class of methods that can correct for misalignments in (a.o.) chemical measurements. Their use in preprocessing of chromatographic, spectroscopic and spectrometric data has grown rapidly over the last decade. This tutorial review aims to give a critical introduction to the most important warping methods, the place o...
Article
Phenolic compounds account for the most important class of secondary metabolites in raspberries and fulfill a broad range of biological functions in plants. Due to their presence in fruits they are also considered as important bioactive compounds in human nutrition and are closely related to fruit quality. In the present study a targeted UPLC-MS/MS...
Article
Full-text available
We present automated data analysis of high-throughput high-performance liquid chromatography with diode array detection (HPLC-DAD) data using multivariate curve resolution. This technique provides spectra and elution profiles of all UV-Vis active compounds present in the mixture. The specifics of using this method in noninteractive fashion are disc...
Article
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Biomarker identification is an ever more important topic in the life sciences. With the advent of measurement methodologies based on microarrays and mass spectrometry, thousands of variables are routinely being measured on complex biological samples. Often, the question is what makes two groups of samples different. Classical hypothesis testing suf...
Article
Recently the first applications in food science and technology of the newly available volatile organic compound (VOC) detection technique proton transfer reaction‐mass spectrometry, coupled with a time of flight mass analyzer (PTR-TOF-MS), have been published. In comparison with standard techniques such as GC-MS, PTR-TOF-MS has the remarkable advan...
Article
An important prerequisite for the development and benchmarking of novel analysis methods is a well-designed comprehensive LC-MS/MS data set. Here, we present our data set consisting of 59 LC-MS/MS analyses of 50 protein samples extracted individually from Escherichia coli K12 and spiked with different concentrations of bovine carbonic anhydrase II...
Article
Biomarker selection is an important topic in the omics sciences, where holistic measurement methods routinely generate results for many variables simultaneously. Very often, only a small fraction of these variables are really associated with the phenomena of interest. Selection and identification of these biomarkers is essential for obtaining an un...
Article
In recent times we have seen the development of many "-omics" technologies. One of the youngest is undoubtedly metabolomics, which aims to define the whole chemical fingerprint unique to each specific organism. The development and optimisation of an untargeted high-throughput method capable of investigating the volatile fraction of a biological sys...
Article
The development and the validation of innovative approaches for biomarker selection are of paramount importance in many -omics technologies. Unfortunately, the actual testing of new methods on real data is difficult, because in real data sets, one can never be sure about the “true” biomarkers. In this paper, we present a publicly available metabolo...