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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    Effect of the DGAT1 K232A genotype of dairy cows on the milk metabolome and proteome
    Lu, J. ; Boeren, S. ; Hooijdonk, A.C.M. van; Vervoort, J.J.M. ; Hettinga, K.A. - \ 2015
    Journal of Dairy Science 98 (2015)5. - ISSN 0022-0302 - p. 3460 - 3469.
    h-1-nmr spectroscopy - sample preparation - identification - stomatin - membrane - proteins - gene - cattle - yield
    Diglyceride O-acyltransferase 1 (DGAT1) is the enzyme that catalyzes the synthesis of triglycerides from diglycerides and acyl-coenzyme A. The DGAT1 K232A polymorphism was previously shown to have a significant influence on bovine milk production characteristics (milk yield, protein content, fat content, and fatty acid composition). The mechanism of this influence has, however, not been elucidated. In this study, metabolomics (1H-nuclear magnetic resonance) and proteomics (laser chromatography-tandem mass spectrometry) were applied to determine the serum and lipid metabolite composition and milk fat globule membrane proteome of milk samples from cows with the DGAT1 KK and AA genotypes. The milk samples from cows with the DGAT1 KK genotype contained more stomatin, sphingomyelin, choline, and carnitine, and less citrate, creatine or phosphocreatine, glycerol-phosphocholine, mannose-like sugar, acetyl sugar phosphate, uridine diphosphate (UDP)-related sugar, and orotic acid compared with milk samples from cows with the DGAT1 AA genotype. Based on these results, we propose that the differences between the DGAT1 genotypes may be related to stomatin-sphingomyelin lipid rafts as well as structural (cell membrane) differences in epithelial cells of the mammary gland. In conclusion, our study shows that, in addition to previously described changes in triglyceride composition, cows differing in DGAT1 polymorphism differ in their milk proteome and metabolome, which may help in further understanding the effect of the DGAT1 K232A polymorphism on milk production characteristics.
    Rapid detection of pesticides not amenable to multi-residue methods by flow injection-tandem mass spectrometry
    Mol, J.G.J. ; Dam, R.C.J. van - \ 2014
    Analytical and Bioanalytical Chemistry 406 (2014)27. - ISSN 1618-2642 - p. 6817 - 6825.
    liquid-chromatography - aminomethylphosphonic acid - quantitative-analysis - sample preparation - maleic hydrazide - lc-ms/ms - glyphosate - cereals - vegetables - dilution
    Flow injection combined with tandem mass spectrometry (MS/MS) was investigated for the rapid detection of highly polar pesticides that are not amenable to multi-residue methods because they do not partition into organic solvents and require dedicated chromatographic conditions. The pesticides included in this study were amitrole, chlormequat, cyromazine, daminozide, diquat, ethephon, fosetyl-Al, glufosinate, glyphosate and its metabolite aminomethylphosphonic acid, maleic hydrazide, mepiquat and paraquat. The composition of the flow-injection solvent was optimized to achieve maximum MS/MS sensitivity. Instrumental limits of detection varied between
    Polyelectrolyte coatings prevent interferences from charged nanoparticles in SPME speciation analysis
    Zielinska, K. ; Leeuwen, H.P. van - \ 2014
    Analytica Chimica Acta 844 (2014). - ISSN 0003-2670 - p. 44 - 47.
    solid-phase microextraction - performance liquid-chromatography - surface modification - sample preparation - triclosan - fibers
    In this work we present a new approach for protection of the fiber in solid phase microextraction (SPME) from interfering charged particles present in the sample medium. It involves coating of commercial poly(dimethylsiloxane) extraction phase with polyelectrolyte layer composed of poly(diallyldimethylammonium chloride), and poly(sodium 4-styrenesulfonate). The modified fiber provides reproducible, convenient and fast extraction capabilities toward the model analyte, triclosan (TCS). A negatively charged polyelectrolyte coating prevents sorbing oxidic nanoparticles from both partitioning into the PDMS phase and aggregation at its surface. The results for the TCS/nanoparticle sample show that the polyelectrolyte layer-modified solid phase extracts just the free form of the organic compound and enables dynamic speciation analysis of the nanoparticulate target analyte complex.
    Proteomics Analysis of the Zebrafish Skeletal Extracellular Matrix
    Kessels, M.Y. ; Huitema, L.F.A. ; Boeren, S. ; Kranenbarg, S. ; Schulte-Merker, S. ; Leeuwen, J.L. van; Vries, S.C. de - \ 2014
    PLoS ONE 9 (2014)3. - ISSN 1932-6203
    gene-expression - bone-development - serine-protease - in-vivo - endochondral ossification - sample preparation - binding protein-5 - axial skeleton - cartilage - differentiation
    The extracellular matrix of the immature and mature skeleton is key to the development and function of the skeletal system. Notwithstanding its importance, it has been technically challenging to obtain a comprehensive picture of the changes in skeletal composition throughout the development of bone and cartilage. In this study, we analyzed the extracellular protein composition of the zebrafish skeleton using a mass spectrometry-based approach, resulting in the identification of 262 extracellular proteins, including most of the bone and cartilage specific proteins previously reported in mammalian species. By comparing these extracellular proteins at larval, juvenile, and adult developmental stages, 123 proteins were found that differed significantly in abundance during development. Proteins with a reported function in bone formation increased in abundance during zebrafish development, while analysis of the cartilage matrix revealed major compositional changes during development. The protein list includes ligands and inhibitors of various signaling pathways implicated in skeletogenesis such as the Int/Wingless as well as the insulin-like growth factor signaling pathways. This first proteomic analysis of zebrafish skeletal development reveals that the zebrafish skeleton is comparable with the skeleton of other vertebrate species including mammals. In addition, our study reveals 6 novel proteins that have never been related to vertebrate skeletogenesis and shows a surprisingly large number of differences in the cartilage and bone proteome between the head, axis and caudal fin regions. Our study provides the first systematic assessment of bone and cartilage protein composition in an entire vertebrate at different stages of development.
    Molecular characterization and functional analyses of ZtWor1, a transcriptional regulator of the fungal wheat pathogen Zymoseptoria tritici
    Mirzadi Gohari, A. ; Mehrabi, R. ; Robert, O. ; Ince, I.A. ; Boeren, J.A. ; Schuster, M. ; Steinberg, G. ; Wit, P.J.G.M. de; Kema, G.H.J. - \ 2014
    Molecular Plant Pathology 15 (2014)4. - ISSN 1464-6722 - p. 394 - 405.
    phytopathogen mycosphaerella-graminicola - candida-albicans - sample preparation - septoria-tritici - azole fungicides - master regulator - gene - protein - resistance - cultivars
    Zymoseptoria tritici causes the major fungal wheat disease septoria tritici blotch, and is increasingly being used as a model for transmission and population genetics, as well as host–pathogen interactions. Here, we study the biological function of ZtWor1, the orthologue of Wor1 in the fungal human pathogen Candida albicans, as a representative of a superfamily of regulatory proteins involved in dimorphic switching. In Z.¿tritici, this gene is pivotal for pathogenesis, as ZtWor1 mutants were nonpathogenic and complementation restored the wild-type phenotypes. In¿planta expression analyses showed that ZtWor1 is up-regulated during the initiation of colonization and fructification, and regulates candidate effector genes, including one that was discovered after comparative proteome analysis of the Z.¿tritici wild-type strain and the ZtWor1 mutant, which was particularly expressed in¿planta. Cell fusion and anastomosis occur frequently in ZtWor1 mutants, reminiscent of mutants of MgGpb1, the ß-subunit of the heterotrimeric G protein. Comparative expression of ZtWor1 in knock-out strains of MgGpb1 and MgTpk2, the catalytic subunit of protein kinase A, suggests that ZtWor1 is downstream of the cyclic adenosine monophosphate (cAMP) pathway that is crucial for pathogenesis in many fungal plant pathogens
    Identification of proteomic biomarkers in M. Longissimus dorsi as potential predictors of pork quality
    Pas, M.F.W. te; Kruijt, L. ; Pierzchala, M. ; Crump, R.E. ; Boeren, S. ; Keuning, E. ; Hoving-Bolink, A.H. ; Hortós, M. ; Gispert, M. ; Arnau, J. ; Diestre, A. ; Mulder, H.A. - \ 2013
    Meat Science 95 (2013)3. - ISSN 0309-1740 - p. 679 - 687.
    meat quality - sample preparation - muscles - values - performance - expression - slaughter - traits - system - breeds
    Meat quality traits have low heritability and large environmental influences. To predict, improve and manage meat quality, proteomic biomarkers are superior to genetic markers. The objectives of this research were (1) to find associations between proteome profiles of longissimus muscle at slaughter and meat quality SELDI-TOF proteome profiles of 142 LargeWhite × Duroc cross pigs showed relationships among peaks or combinations of peaks and meat quality traits with highest significance for drip loss and ultimate pH. Calculated accuracies of prediction of traits ranged from 20 up to 80%. Differentially expressed proteins related to drip loss and ultimate pH were identified by NanoLC-FTMSMS. The proteins highlight biological mechanisms that may explain how these traits develop biologically and how they are related to each other
    Plant Metabolomics and Its Potential for Systems Biology Research: Background Concepts, Technology, and Methodology
    Allwood, J.W. ; Vos, C.H. de; Moing, A. ; Deborde, C. ; Erban, A. ; Kopka, J. ; Goodacre, R. ; Hall, R.D. - \ 2011
    In: Methods in Systems Biology / Jameson, D., Verma, M., Westerhoff, H. V., - p. 299 - 336.
    chromatography-mass-spectrometry - minimum reporting standards - arabidopsis-thaliana - gas-chromatography - liquid-chromatography - functional genomics - tomato fruit - metabolite profiles - magnetic-resonance - sample preparation
    The "metabolome" comprises the entire complement of small molecules in a plant or any other organism. It represents the ultimate phenotype of cells, deduced from the perturbation of gene expression and the modulation of protein function, as well as environmental cues. Extensive advances over the past decade, regarding the high-throughput (HTP) nature of "omics" research, have given birth to the expectation that a type of "systems level" overview may soon be possible. Having such a global overview of the molecular organization of a plant in the context of a particular set of genetic or environmental conditions, be it at cell, organ, or whole plant level, would clearly be very powerful. Currently, we are far from achieving this goal; however, within our hands, plant metabolomics is an HTP and informative "omics" approach to both sample generation and data generation, as well as raw data preprocessing, statistical analysis, and biological interpretation. Within this chapter, we aim to describe the great attention given to experimental design to ensure that the correct sample set and control are included and to, thereby, enable reliable statistical analysis of the data. For as comprehensive metabolite coverage as possible, we advocate the use of multiparallel approaches; thus, we describe a step-by-step standardized method for Nuclear magnetic resonance spectroscopy, as well as discussing with reference to standardized methodologies the techniques of gas chromatography-time of flight/mass spectrometry, and liquid chromatography mass spectrometry.
    Selenium speciation in different organs of African catfish (Clarias gariepinus) enriched through a selenium-enriched garlic based diet
    Pedrero, Z. ; Murillo, S. ; Camara, C. ; Schram, E. ; Luten, J.B. ; Feldmann, I. ; Jakubowski, N. ; Madrid, Y. - \ 2011
    Journal of Analytical Atomic Spectrometry 26 (2011)1. - ISSN 0267-9477 - p. 116 - 125.
    hplc-icp-ms - enzymatic probe sonication - isotope-dilution analysis - plasma-mass spectrometry - food-chain selenium - se-speciation - sample preparation - brassica-juncea - human health - brazil nuts
    Speciation of Se in fish is needed to elucidate the metabolism of this element in living organisms in the marine environment. In this paper, selenium concentration and its species distribution in several organs and tissues (liver, gills, kidney, muscle and gastrointestinal tract) of African catfish fed with a selenium-enriched garlic based diet was studied. The intention of this paper is focused on both the investigation of selenium distribution in the soluble protein fraction and the detection of selenoaminoacids. Thus, two different procedures have been developed. In the first procedure, screening of selenium in proteins in the Tris-buffer soluble fraction of different tissues was carried out by size exclusion chromatography-inductively coupled plasma-mass spectrometry (SEC-ICP-MS) and by laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) after sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) separation and electroblotting onto membranes. For the amino acid analysis, several sample treatments for Se-species extraction, based on enzymatic hydrolysis, were compared. The best results were obtained for incubation at controlled temperature. Application of several sample treatments in conjunction with different chromatographic techniques (reverse phase, anion exchange and ion exchange/size exclusion) was crucial to unambiguous Se-species identification. In Se-enriched African catfish a noticeable increase in the content of selenium in different organs was observed, except for the liver, where the Se level remained unaltered. The kidney was the Se-target organ in animals fed with enriched Se food. Selenomethionine (SeMet) was the main Se species identified in fillet extracts, whereas the presence of selenocysteine (SeCys) was detected in the liver and both SeMet and SeCys were present in the kidney.
    Genotype and planting density effects on rooting traits and yield in cotton (Gossypium hirsutum L.)
    Zhang, L.Z. ; Li, B.G. ; Yan, G.T. ; Werf, W. van der; Spiertz, J.H.J. ; Zhang, S.P. - \ 2006
    Journal of Integrative Plant Biology 48 (2006)11. - ISSN 1672-9072 - p. 1287 - 1293.
    water-uptake - length density - sample preparation - small-diameter - soil-water - growth - maize - systems - shoot - model
    Root density distribution of plants is a major indicator of competition between plants and determines resource capture from the soil. This experiment was conducted in 2005 at Anyang, located in the Yellow River region, Henan Province, China. Three cotton (Gossypium hirsutum L.) cultivars were chosen: hybrid Bt-cultivar CRI46, conventional Bt-cultivars CRI44 and CRI45. Six planting densities were designed, ranging from 1.5 to 12.0 plants/m2Root parameters such as surface area, diameter and length were analyzed by using the DT-SCAN image analysis method. The root length density (RLD), root average diameter and root area index (RAI), root surface area per unit land area, were studied. The results showed that RLD and RAI differed between genotypes; hybrid CRI46 had significantly higher (P <0.05) RLD and RAI values than conventional cultivars, especially under low planting densities, less than 3.0 plants/m2The root area index (RAI) of hybrid CRI46 was 61% higher than of CRI44 and CRI45 at the flowering stage. The RLD and RAI were also significantly different (P = 0.000) between planting densities. The depth distribution of RAI showed that at increasing planting densities RAI was increasingly distributed in the soil layers below 50 cm. The RAI of hybrid CRI46 was for all planting densities, obviously higher than other cultivars during the flowering and boll stages. It was concluded that the hybrid had a strong advantage in root maintenance preventing premature senescence of roots. The root diameter of hybrid CRI46 had a genetically higher root diameter at planting densities lower than 6.0 plants/m2Good associations were found between yield and RAI in different stages. The optimum planting density ranged from 4.50 plants/m2 to 6.75 plants/m2 for conventional cultivars and around 4.0¿5.0 plants/m2 for hybrids.
    Ginkgolides and bilobalide: Their physical, chromatographic and spectroscopic properties
    Beek, T.A. van - \ 2005
    Bioorganic and Medicinal Chemistry 13 (2005)17. - ISSN 0968-0896 - p. 5001 - 5012.
    evaporative light-scattering - liquid-chromatography - mass-spectrometry - terpene trilactones - sample preparation - extract egb-761 - leaf extracts - leaves - phytopharmaceuticals - products
    Ginkgolides A, B, C, J, K, L and M and bilobalide are rare terpene trilactones that have been isolated from leaves and root bark of the Chinese tree Ginkgo biloba. The structures of the highly oxidized ginkgolides were independently elucidated in the 1960s by the groups of Nakanishi and Sakabe. Later these compounds were found to be potent and selective antagonists of platelet activating factor, which fact triggered much new research. During the past 40 years, much physical, chromatographic and spectroscopic data have been published on these compounds in various, sometimes inaccessible, sources. The published melting points, solubility in different solvents, ionization constants, chromatographic behaviour, specific optical rotations, UV, IR, MS and NMR data, and X-ray studies are summarized and, where necessary, discussed. The literature until April 2005 has been reviewed
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