J. A. Hageman

Wageningen University & Research | WUR · Department of Mathematical and Statistical Methods

Peptides are an important group of compounds contributing to the desired, as well as the undesired taste of a food product. Their taste impressions can include aspects of sweetness, bitterness, savoury, umami and many other impressions depending on the amino acids present as well as their sequence. Identification of short peptides in foods is chall...

An autoclave treatment at 121 °C on periodate-oxidized plant polysaccharides and mixes thereof was investigated for the release of oligosaccharides to obtain a generic polysaccharide depolymerization method for polysaccharides fingerprinting. Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) analysis of the...

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Statistical modeling is an inherent part of any metabolomics study. Statistical models mainly assess the association between metabolites and the trait(s) of interest. Complicating factors are that not all metabolites are connected to the trait of interest, and modeling is hampered by the large numbers of metabolites especially in relation to the nu...

In the last decade, the field of metabolomics has developed tremendously: it is now possible to routinely measure a wide range of metabolites for many specimens at reduced costs, opening the door to many exciting experiments. To match these developments, alternative statistical methods are required. This special issue was commissioned to offer a so...

High resistance towards traditional antibiotics has urged the development of new, natural therapeutics against methicillin-resistant Staphylococcus aureus (MRSA). Prenylated (iso)flavonoids, present mainly in the Fabaceae, can serve as promising candidates. Herein, the anti-MRSA properties of 23 prenylated (iso)flavonoids were assessed in-vitro. Th...

This study aimed at determining how the degradation of cereal non-starch polysaccharides (NSP) by dietary enzymes during feed digestion can influence nutrient digestibility and NSP fermentability in broilers. Ninety-six one-day-old male broilers were assigned to 4 different treatments: control and enzyme-supplemented wheat-based (WC, WE) or maize-b...

Isothiocyanates (ITCs) derived from Brassicaceae are potential food preservatives. Their antimicrobial activity is strongly influenced by their subclass and side chain. This is the first quantitative structure-activity relationships (QSAR) study of ITCs as antibacterials. Twenty-six ITCs covering 9 subclasses were tested against Escherichia coli an...

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...

Fortification of food with iron is considered to be an effective approach to counter the global health problem caused by iron deficiency. However, reactivity of iron with the catechol moiety of food phenolics leads to discolouration and impairs bioavailability. In this study, we investigated the interplay between intrinsic and extrinsic factors on...

Assessment of the impact of variation in chloroplast and mitochondrial DNA (collectively termed the plasmotype) on plant phenotypes is challenging due to the difficulty in separating their effect from nuclear-derived variation (the nucleotype). Haploid-inducer lines can be used as efficient plasmotype donors to generate new plasmotype–nucleotype co...

Mol. Nutr. Food Res. 2019, 63, 1900189 DOI: 10.1002/mnfr.201900189 Exhaled air contains volatile organic compounds (VOCs) that are partly derived from the body's internal metabolism. Despite substantial within‐ and between‐subject variation, differences in VOC profiles among drinks could be identified, indicating that analysis of exhaled VOCs might...

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...

Scope: Exhaled volatile organic compounds (VOCs) are a possible relevant target for non-invasive assessment of metabolic responses. Using a breathomics approach, we aimed to explore whether lipid intake influences VOC profiles in exhaled air, and to obtain insight in intra- and inter-individual variations. Methods and results: Three human interv...

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...

Crop yield stability requires an attenuation of the reduction of yield losses caused by environmental stresses such as drought. Using a combination of metabolomics and high-throughput colorimetric assays, we analysed central metabolism and oxidative stress status in the flag leaf of 292 indica rice (Oryza sativa) accessions. Plants were grown in th...

To better understand the variability of the type and level of serum proteins in human milk, the milk serum proteome of Chinese mothers during lactation was investigated using proteomic techniques and compared to the milk serum proteome of Dutch mothers. This showed that total milk serum protein concentrations in Chinese human milk decreased over a...

Assessment of the impact of variation in chloroplast and mitochondrial DNA (collectively termed the plasmotype) on plant phenotypes is challenging due to the difficulty in separating their effect from nuclear-derived variation (the nucleotype). Haploid-inducer lines can be used as efficient plasmotype donors to generate new plasmotype–nucleotype co...

Assessing the impact of variation in chloroplast and mitochondrial DNA (the plasmotype) on plant phenotypes is challenging due to the difficulty in separating their effect from nuclear derived variation (the nucleotype). By using haploid inducer lines as plasmotype donors we employed an efficient and precise method to generate a panel comprising al...

Synthetic derivatives of 1,4-benzoxazin-3-ones have been shown to possess promising antimicrobial activity, whereas their natural counterparts were found lacking in this respect. In this work, quantitative structure-activity relationships (QSAR) of natural and synthetic 1,4-benzoxazin-3-ones as antimicrobials were established. Data published in lit...

In a CHO cell fed‐batch process arrest of cell proliferation and an almost threefold increase in cell size occurred, which was associated with an increase in cell specific productivity. In this study, transcriptome analysis is performed to identify the molecular mechanisms associated with this. Cell cycle analysis reveals that the cells are arreste...

Prenylated flavonoids and isoflavonoids are phytochemicals with remarkable antibacterial activity. In this study, 30 prenylated (iso)flavonoids were tested against Listeria monocytogenes and Escherichia coli (the latter in combination with an efflux pump inhibitor). Minimum inhibitory concentrations of the most active compounds ranged between 6.3-1...

To study the variability in human milk oligosaccharide (HMO) composition of Chinese human milk over a 20-wk lactation period, HMO profiles of 30 mothers were analyzed using CE-LIF. This study showed that total HMO concentrations in Chinese human milk decreased significantly over a 20-wk lactation period, independent of the mother’s SeLe status, alt...

Due to the unpredictable natural droughts that occur, causing tea farmers significant losses in tea estates, a two-day method for distinguishing between drought tolerant (DT) and drought susceptible (DS) Camellia sinensis cultivars was developed. This work was based on known cultivars developed at the Tea Research Institute in Kenya and the Tea Res...

Transcriptome and metabolism analysis were performed to evaluate the scale-down of a CHO cell fed-batch process from a 10 L bioreactor to an ambr 15® (ambr) system. Two different agitation scale-down principles were applied, resulting in two different agitation rates in the ambr system: 1300 RPM based on the agitator tip speed, and 800 rpm based on...

p>To study the variability in human milk oligosaccharide (HMO) composition of Chinese human milk over a 20-wk lactation period, HMO profiles of 30 mothers were analyzed using CE-LIF. This study showed that total HMO concentrations in Chinese human milk decreased significantly over a 20-wk lactation period, independent of the mother's SeLe status, a...

Metabolomics is a proven tool to obtain information about differences in food stuffs and to select biochemical markers for sensory quality of food products. A valuable application of untargeted metabolomics is the selection of metabolites that are (highly) predictive for sensory or phenotypical traits for use as (bio) markers. This chapter demonstr...

In this study a mapping population (F 8) of ca 200 progeny from a cross between the commercial rice varieties Apo and IR64 has been both genotyped and phenotyped. A genotyping-by-sequencing approach was first used to identify 2,681 polymorphic SNP markers which gave dense coverage of the genome with a good distribution across all 12 chromosomes. Th...

Brewing with unmalted barley can reduce the use of raw materials, thereby increasing the efficiency of the brewing process. However, unmalted barley contains several undesired components for brewing and has a low enzymatic activity. Pearling, an abrasive milling method, has been proposed as a pre-treatment for barley to remove some of its undesired...

Here we provide data from shot-gun proteomics, using filtered-aided sample preparation (FASP), dimethyl labeling and LC–MS/MS, to quantify the changes in the repertoire of human milk proteins over lactation. Milk serum proteins were analyzed at week 1, 2, 3 4, 8, 16, and 24 in milk from four individual mothers. A total of 247 proteins were identifi...

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...

Biological significance: Breast milk proteins provide nutrition, but also contribute to healthy development of infants. Despite the previously reported large number of identified breast milk proteins and their changes over lactation, less is known on the changes of these proteins in individual mothers. This study is the first to determine the qual...

The quality of rice in terms not only of its nutritional value but also in terms of its aroma and flavour is becoming increasingly important in modern rice breeding where global targets are focused on both yield stability and grain quality. In the present paper we have exploited advanced, multi-platform metabolomics approaches to determine the bioc...

Milk contains all the nutrients for the growth and development of the neonate. However, milk composition is not constant during lactation. To study the changes of the milk proteome over lactation, filter-aided sample preparation combined with dimethyl labeling followed by liquid chromatography tandem mass spectrometry was used to identify and quant...

In order to better understand the milk proteome and its changes from colostrum to mature milk, samples taken at seven time points in the first 9 days from 4 individual cows were analyzed using proteomic techniques. Both the similarity in changes from day 0 to day 9 in the quantitative milk proteome, and the differences in specific protein abundance...

Analytical fingerprinting in combination with chemometric modelling provides a powerful approach in the framework of food quality assurance. This recently emerging approach allows verifying claims regarding a whole range of food quality characteristics that were previously difficult or impossible to determine. These include claims regarding the nut...

Soy protein hydrolysates are used as the most cost effective medium supplement to enhance cell growth and recombinant protein productivity in cell cultures. Such hydrolysates contain diverse classes of compounds, such as peptides, carbohydrates and phenolic compounds. To identify if specific compounds dominate the functionality of hydrolysates in c...

In this paper, we demonstrate the use of two-mode clustering for genotype by trait and genotype by environment data. In contrast to two separate (one mode) clusterings on genotypes or traits/environments, two-mode clustering simultaneously produces homogeneous groups of genotypes and traits/environments. For two-mode clustering, we first scan all t...

The combination of the different data sources for classification purposes, also called data fusion, can be done at different levels: low-level, i.e. concatenating data matrices, medium-level, i.e. concatenating data matrices after feature selection and high-level, i.e. combining model outputs. In this paper the predictive performance of high-level...

Multiple analytical platforms are frequently used in metabolomics studies. The resulting multiple data blocks contain, in general, similar parts of information which can be disclosed by chemometric methods. The metabolites of interest, however, are usually just a minor part of the complete data block and are related to a response of interest such a...

Heat map of a simulated dataset D containing four correlated structures (variables , and ). (EPS)

Correlation pattern within hippurate peaks is shown, together with the anti-correlation between creatinine and hippurate. (EPS)

Heat map of the correlation structure of a pool X of 40 human urine NMR spectra. The statistical correlation matrix shows the highly correlated nature of NMR spectra. (EPS)

Heat map of the expected correlation pattern for the phenylalanine biosynthesis pathway for the NST 74, a phenylalanine overproducing strain and for the wild type strain. (EPS)

Detailed explanation of the mathematical and theoretical machinery underlying the reference distribution and the scaling term . (TEX)

One of the first steps in analyzing high-dimensional functional genomics data is an exploratory analysis of such data. Cluster Analysis and Principal Component Analysis are then usually the method of choice. Despite their versatility they also have a severe drawback: they do not always generate simple and interpretable solutions. On the basis of th...

The combination of the different data sources for classification purposes, also called data fusion, can be done at different levels: low-level, i.e. concatenating data matrices, medium-level, i.e. concatenating data matrices after feature selection and high-level, i.e. combining model outputs. In this paper the predictive performance of high-level...

The transcriptional responses of yeast cells to a wide variety of stress conditions have been studied extensively. In addition, deletion mutant collections have been widely used to measure the combined effect of gene loss and stress on growth (fitness). Here we present a comparative analysis of 1,095 publicly available transcription and genome-wide...

The quality of coffee is influenced by many factors such as coffee variety, agricultural and postharvest conditions, roasting parameters, and brewing. The pleasure of drinking coffee may be affected by off-notes such as burnt, green, earthy, or fermented. Their presence is related to the variety, fermentation during postharvest processing, or over-...

We present a computer-based heuristic framework for designing libraries of homogeneous catalysts. In this approach, a set of given bidentate ligand-metal complexes is disassembled into key substructures (building blocks). These include metal atoms, ligating groups, backbone groups, and residue groups. The computer then rearranges these building blo...

Metabolomics and other omics tools are generally characterized by large data sets with many variables obtained under different environmental conditions. Clustering methods and more specifically two-mode clustering methods are excellent tools for analyzing this type of data. Two-mode clustering methods allow for analysis of the behavior of subsets o...

We combined proxies traditionally used in stratigraphic research (mineral assemblages, grain size distribution, and element ratios) with soil organic carbon contents and radiocarbon dating both at a high vertical resolution, to unravel the tephra stratigraphy in volcanic ash soils. Our results show that soil profiles along an altitudinal transect i...

One of the new expanding areas in functional genomics is metabolomics: measuring the metabolome of an organism. Data being generated in metabolomics studies are very diverse in nature depending on the design underlying the experiment. Traditionally, variation in measurements is conceptually broken down in systematic variation and noise where the la...

A methodology for quantifying the diversity of homogenous catalyst libraries is introduced. Using a 'building block' approach, we assemble four catalyst libraries in silico, with sizes ranging from 86,000 to 67,000,000 Rh-ligand complexes, and analyse subsets from each library. Descriptor models, based on literature data for 39 Rh-catalysed hydrofo...

We present in this communication an alternative concept for optimising homogeneous catalysts. With this method, one extracts and screens virtual catalyst libraries, indicating regions in the catalyst space where good catalysts are likely to be found. This automated screening is done in two stages: A 'rough screening' using 2D descriptors, followed...

Clustering of metabolomics data can be hampered by noise originating from biological variation, physical sampling error and analytical error. Using data analysis methods which are not specially suited for dealing with noisy data will yield sub optimal solutions. Bootstrap aggregating (bagging) is a resampling technique that can deal with noise and...

For a detailed reconstruction of historic upper forest line (UFL) positions, new proxies in addition to traditional pollen and vegetation analyses are needed. If the straight-chain lipid composition in plant leaves and roots is specific enough to allow distinction, their records in soils and peat bogs might be used for this purpose. We tested for s...

Extractable and solvent insoluble, ester-bound lipids were analysed in an acid, sandy soil profile under Corsican pine. The n-alkanes and alkanoic acids from the soil profile showed rather poor correlations with those from the pine needles and roots, while the n-alkanol composition in the mineral horizons strongly indicated the presence of lipids d...

An alternative top-down concept for searching for homogeneous catalysts is introduced. In this approach, three multi-dimensional spaces are considered. These represent the catalysts, the descriptor values (e.g., cone angle, lipophilicity indices), and the figures of merit (e.g., turnover frequency, enantiomeric excess, or product selectivity), resp...

Multivariate calibration is a powerful tool for establishing a relationship between spectral variables and properties of interest. Usually, changes in spectral variables are ascribed to changes in the chemical composition of the sample. However, spectral intensities that are measured at varying temperatures do not only change because of changes in...

This paper introduces Tabu Search in analytical chemistry by applying it to wavelength selection. Tabu Search is a deterministic global optimization technique loosely based on concepts from artificial intelligence. Wavelength selection is a method which can be used for improving the quality of calibration models. Tabu Search uses basic, problem-spe...

Constructing multilayer optical coatings (MOCs) is a difficult large-scale optimisation problem due to the enormous size of the search space. In the present paper, a new approach for designing MOCs is presented using genetic algorithms (GAs) and tabu search (TS). In this approach, it is not necessary to specify how many layers will be present in a...

X-ray diffraction is a powerful technique for investigating the structure of crystals and crystalline powders. Unfortunately, for powders, the first step in the structure elucidation process, retrieving the unit cell parameters (indexing), is still very critical. In the present article, an improved approach to powder pattern indexing is presented....