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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Proficiency of WHO Global Foodborne Infections Network External Quality Assurance System Participants in Identification and Susceptibility Testing of Thermotolerant Campylobacter spp. from 2003 to 2012
Pedersen, Susanne Karlsmose ; Wagenaar, Jaap A. ; Vigre, Håkan ; Roer, Louise ; Mikoleit, Matthew ; Aidara-Kane, Awa ; Cawthorne, Amy L. ; Aarestrup, Frank M. ; Hendriksen, Rene S. - \ 2018
Journal of Clinical Microbiology 56 (2018)11. - ISSN 0095-1137
antimicrobial susceptibility testing - Campylobacter coli - Campylobacter jejuni - Global Foodborne Infections Network - identification - proficiency test - quality assurance - World Health Organization

Campylobacter spp. are foodborne and waterborne pathogens. While rather accurate estimates for these pathogens are available in industrialized countries, a lack of diagnostic capacity in developing countries limits accurate assessments of prevalence in many regions. Proficiency in the identification and susceptibility testing of these organisms is critical for surveillance and control efforts. The aim of the study was to assess performance for identification and susceptibility testing of thermotolerant Campylobacter spp. among laboratories participating in the World Health Organization (WHO) Global Foodborne Infections Network (GFN) External Quality Assurance System (EQAS) over a 9-year period. Participants (primarily national-level laboratories) were encouraged to self-evaluate their performance as part of continuous quality improvement. The ability to correctly identify Campylobacter spp. varied by year and ranged from 61.9% (2008) to 90.7% (2012), and the ability to correctly perform antimicrobial susceptibility testing (AST) for Campylobacter spp. appeared to steadily increase from 91.4% to 93.6% in the test period (2009 to 2012). The poorest performance (60.0% correct identification and 86.8% correct AST results) was observed in African laboratories. Overall, approximately 10% of laboratories reported either an incorrect identification or antibiogram. As most participants were supranational reference laboratories, these data raise significant concerns regarding capacity and proficiency at the local clinical level. Addressing these diagnostic challenges is critical for both patient-level management and broader surveillance and control efforts.

Rekenregels rundvee voor de Landbouwtelling : verantwoording van het gebruik van het Identificatie & Registratiesysteem
Os, J. van; Bartholomeus, M.G.T.M. ; Jeurissen, L.J.J. ; Reenen, C.G. van - \ 2017
Wageningen : Wettelijke Onderzoekstaken Natuur & Milieu (WOt-technical report 91) - 68
rundveehouderij - rundvee - landbouwtellingen - emissie - registratie - identificatie - bedrijfsstructuur in de landbouw - nederland - cattle husbandry - cattle - agricultural censuses - emission - registration - identification - farm structure - netherlands
Om te voldoen aan statistische verplichtingen voor veehouderij en bedrijfsstructuur en voor de registratievan emissies is informatie nodig over de rundveehouderij in Nederland. Daartoe vraagt de Rijksoverheid bijveehouders op hoeveel rundvee aanwezig is, uitgesplitst in verschillende diergroepen; dit is een onderdeelvan de jaarlijkse landbouwtelling. De Rijksoverheid streeft naar beperking van administratieve lastendruk bijondernemers. Wageningen Environmental Research heeft op verzoek van het ministerie van EconomischeZaken onderzocht in welke mate het mogelijk is om de benodigde gegevens af te leiden uit het bestaandeIdentificatie & Registratiesysteem (I&R) Rundveehouderij (een systeem voor identificatie en registratie vandieren voor dier- en volksgezondheid). Dat blijkt grotendeels goed haalbaar; voor de meeste bedrijvenkunnen alle diergroepen automatisch uit I&R bepaald worden. Voor sommige bedrijven is een aanvullendeverdeling van diergroepen over productiedoelen nodig. Deze nieuwe werkwijze leidt niet alleen tot lagereadministratieve lasten, maar ook tot een kwaliteitsverbetering van de rundveegegevens.---Information on cattle farming in the Netherlands is needed for the national statistics on beef and dairy farmsand farm structure. To obtain this information the national government asks farmers to submit informationon the number of cattle on their farms, divided into the various animal classes, as part of the annualagricultural census. The government also wants to minimise the administrative burden on farmers. At therequest of the Ministry of Economic Affairs, Wageningen Environmental Research has studied to what extentit would possible to derive the required information from the existing identification and registration system(I&R) for beef and dairy farms (a system for identifying and registering livestock for animal and humanhealth purposes). The results show that this is largely possible: for most farms all the animal classes can beautomatically derived from the I&R. For some farms it is necessary to make an additional division of animalclasses by product category. This new way of working will not only reduce the administrative burden, but itwill also lead to better quality data on beef and dairy cattle.
Comparative genomics and trait evolution in Cleomaceae, a model family for ancient polyploidy
Bergh, Erik van den - \ 2017
University. Promotor(en): Eric Schranz; Y. van de Peer. - Wageningen : Wageningen University - ISBN 9789463431705 - 106
capparaceae - genomics - polyploidy - evolution - genomes - reproductive traits - flowers - colour - glucosinolates - genetic variation - biosystematics - taxonomy - identification - genomica - polyploïdie - evolutie - genomen - voortplantingskenmerken - bloemen - kleur - glucosinolaten - genetische variatie - biosystematiek - taxonomie - identificatie

As more and more species have been sequenced, evidence has been piling up for a fascinating phenomenon that seems to occur in all plant lineages: paleopolyploidy. Polyploidy has historically been a much observed and studied trait, but until recently it was assumed that polyploids were evolutionary dead-ends due to their sterility. However, many studies since the 1990’s have challenged this notion by finding evidence for ancient genome duplications in many genomes of current species. This lead to the observation that all seed plants share at least one ancestral polyploidy event. Another polyploidy event has been proven to lie at the base of all angiosperms, further signifying the notion that ancient polyploidy is widespread and common. These findings have led to questions regarding the apparent disadvantages that can be observed in a first generation polyploid. If these disadvantages can be overcome however, duplication of a genome also presents an enormous potential for evolutionary novelty. Duplicated copies of genes are able to acquire changes that can lead to specialization of the duplicated pair into two functions (subfunctionalization) or the development of one copy towards an entirely new function (neofunctionalization).

Currently, most research towards polyploidy has focused on the economically and scientifically important Brassicaceae family containing the model plant Arabidopsis thaliana and many crops such as cabbage, rapeseed, broccoli and turnip. In this thesis, I lay the foundations for the expansion of this scope to the Cleomaceae, a widespread cosmopolitan plant family and a sister family of Brassicaceae. The species within Cleomaceae are diverse and exhibit many scientifically interesting traits. They are also in a perfect position phylogenetically to draw comparisons with the much more studied Brassicaceae. I describe the Cleomaceae and their relevance to polyploid research in more detail in the Introduction. I then describe the important first step towards setting up the genetic framework of this family with the sequencing of Tarenaya hassleriana in Chapter 1.

In Chapter 2, I have studied the effects of polyploidy on the development of C4 photosynthesis by comparing the transcriptome of C3 photosynthesis based species Tarenaya hassleriana with the C4 based Gynandropsis gynandra. C4 photosynthesis is an elaboration of the more common C3 form of photosynthesis that concentrates CO2 in specific cells leading to decreased photorespiration by the RuBisCO and higher photosynthetic efficieny in low CO2 environments. I find that polyploidy has not led to sub- or neofunctionalization towards the development of this trait, but instead find evidence for another important phenomenon in postpolyploid evolution: the dosage balance hypothesis. This hypothesis states that genes which are dependent on specific dosage levels of their products will be maintained in duplicate; any change in their function would lead to dosage imbalance which would have deleterious effects on their pathway. We show that most genes involved in photosynthesis have returned to single copy in G. gynandra and that the changes leading to C4 have mostly taken place at the expression level confirming current assumptions on the development of this trait.

In Chapter 3, I have studied the effects of polyploidy on an important class of plant defence compounds: glucosinolates. These compounds, sometimes referred to as ‘mustard oils’, play an important role in the defence against herbivores and have radiated widely in Brassicaceae to form many different ‘flavors’ to deter specific herbivores. I show that in Cleomaceae many genes responsible for these compounds have benefited from the three rounds of polyploidy that T. hassleriana has undergone and that many duplicated genes have been retained. We also show that more than 75% is actively expressed in the plant, proving that the majority of these duplications has an active function in the plant.

Finally, in Chapter 4 I investigate a simple observation made during experiments with T. hassleriana in the greenhouse regarding the variation in flower colour between different individuals: some had pink flowers and some purple. Using LC-PDA mass spectrometry we find that the two colours are caused by different levels of two anthocyanin pigments, with cyanidin dominating in the purple flowers and pelargonidin being more abundant in pink flowers. Through sequence comparison and synteny analysis between A. thaliana and T. hassleriana we find the orthologs of the genes involved in this pathway. Using a Genotyping by Sequencing method on a cross between these two flower colours, we produce a collection of SNP markers on the reference genome. With these SNPs, we find two significant binary trait loci, one of which corresponds to the location of the F3’H ortholog which performs the conversion of a pelargonidin precursor to a cyanidin precursor.

In the General Conclusion, I combine all findings of the previous chapters and explain how they establish part of a larger species framework to study ancient polyploidy in angiosperms. I then put forth what these findings can mean for possible future research and the directions that are worth to be explored further.

Elucidating the Ramularia eucalypti species complex
Videira, S.I.R. ; Groenewald, J.Z. ; Kolecka, A. ; Haren, L. van; Boekhout, T. ; Crous, P.W. - \ 2015
Persoonia 34 (2015). - ISSN 0031-5850 - p. 50 - 64.
desorption ionization-time - flight mass-spectrometry - primer sets - identification - phylogeny - pathogens - fungi - dna - epidemiology - punctiformis
The genus Ramularia includes numerous phytopathogenic species, several of which are economically important. Ramularia eucalypti is currently the only species of this genus known to infect Eucalyptus by causing severe leaf-spotting symptoms on this host. However, several isolates identified as R. eucalypti based on morphology and on nrDNA sequence data of the ITS region have recently been isolated from other plant hosts, from environmental samples and also from human clinical specimens. Identification of closely related species based on morphology is often difficult and the ITS region has previously been shown to be unreliable for species level identification in several genera. In this study we aimed to resolve this species-complex by applying a polyphasic approach involving morphology, multi-gene phylogeny and matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). Six partial genes (ITS, ACT, TEF1-a, HIS3, GAPDH and RPB2) were amplified and sequenced for a total of 44 isolates representing R. eucalypti s.lat. and closely related species. A multi-gene Bayesian phylogenetic analysis and parsimony analysis were performed, and both the resulting trees showed significant support for separation of seven species in R. eucalypti s.lat., including two previously described (R. eucalypti and R. miae), four novel species here described (R. haroldporteri, R. glennii, R. mali and R. plurivora) and one undescribed Ramularia species (sterile). Additionally, Mycosphaerella nyssicola is newly combined in Ramularia as R. nyssicola. Main mass spectra (MSPs) of several R. eucalypti s.lat. strains were generated using MALDI-TOF MS and were compared through a Principal Component Analysis (PCA) dendogram. The PCA dendrogram supported three clades containing R. plurivora, R. glenni/R. mali and R. eucalypti/R. miae. Although the dendrogram separation of species differed from the phylogenetic analysis, the clinically relevant strains were successfully identified by MALDI-TOF MS
Identifying and naming plant-pathogenic fungi: past, present, and future
Crous, P.W. ; Hawksworth, D.L. ; Wingfield, M.J. - \ 2015
Annual Review of Phytopathology 53 (2015). - ISSN 0066-4286 - p. 247 - 267.
molecular systematics - polyphyletic nature - polyphasic approach - mycorrhizal fungi - species concepts - taxonomy - genus - classification - identification - chromatography
Scientific names are crucial in communicating knowledge about fungi. In plant pathology, they link information regarding the biology, host range, distribution, and potential risk. Our understanding of fungal biodiversity and fungal systematics has undergone an exponential leap, incorporating genomics, web-based systems, and DNA data for rapid identification to link species to metadata. The impact of our ability to recognize hitherto unknown organisms on plant pathology and trade is enormous and continues to grow. Major challenges for phytomycology are intertwined with the Genera of Fungi project, which adds DNA barcodes to known biodiversity and corrects the application of old, established names via epi- or neotypification. Implementing the one fungus–one name system and linking names to validated type specimens, cultures, and reference sequences will provide the foundation on which the future of plant pathology and the communication of names of plant pathogens will rest.
A gene co-expression network predicts functional genes controlling the re-establishment of desiccation tolerance in germinated Arabidopsis thaliana seeds
Dias Costa, M.C. ; Righetti, K. ; Nijveen, H. ; Yazdanpanah, F. ; Ligterink, W. ; Buitink, J. ; Hilhorst, H.W.M. - \ 2015
Planta 242 (2015)2. - ISSN 0032-0935 - p. 435 - 449.
medicago-truncatula seeds - transcription factors - expression data - abiotic stress - dormancy - drought - identification - maturation - longevity - software
Main conclusion During re-establishment of desiccation tolerance (DT), early events promote initial protection and growth arrest, while late events promote stress adaptation and contribute to survival in the dry state. Mature seeds of Arabidopsis thaliana are desiccation tolerant, but they lose desiccation tolerance (DT) while progressing to germination. Yet, there is a small developmental window during which DT can be rescued by treatment with abscisic acid (ABA). To gain temporal resolution and identify relevant genes in this process, data from a time series of microarrays were used to build a gene co-expression network. The network has two regions, namely early response (ER) and late response (LR). Genes in the ER region are related to biological processes, such as dormancy, acquisition of DT and drought, amplification of signals, growth arrest and induction of protection mechanisms (such as LEA proteins). Genes in the LR region lead to inhibition of photosynthesis and primary metabolism, promote adaptation to stress conditions and contribute to seed longevity. Phenotyping of 12 hubs in relation to re-establishment of DT with T-DNA insertion lines indicated a significant increase in the ability to re-establish DT compared with the wild-type in the lines cbsx4, at3g53040 and at4g25580, suggesting the operation of redundant and compensatory mechanisms. Moreover, we show that re-establishment of DT by polyethylene glycol and ABA occurs through partially overlapping mechanisms. Our data confirm that co-expression network analysis is a valid approach to examine data from time series of transcriptome analysis, as it provides promising insights into biologically relevant relations that help to generate new information about the roles of certain genes for DT.
Spontaneous, non-enzymatic breakdown of peptides during enzymatic protein hydrolysis
Butre, C.I. ; Buhler, S. ; Sforza, S. ; Gruppen, H. ; Wierenga, P.A. - \ 2015
Biochimica et Biophysica Acta. Proteins & Proteomics 1854 (2015)8. - ISSN 1570-9639 - p. 987 - 994.
beta-lactoglobulin - cleavage - bond - specificity - identification - selectivity - kinetics - isolate - water
It is expected that during the hydrolysis of proteins with specific enzymes only peptides are formed that result from hydrolysis of the specific cleavage sites (i.e. specific peptides). It is, however, quite common to find a-specific peptides (i.e. resulting from a-specific cleavage), which are often ignored, or explained by impurities in the enzyme preparation. In recent work in a whey protein isolate (WPI) hydrolysate obtained with the specific Bacillus licheniformis protease (BLP), 13 peptides of 77 identified were found to be the result of a-specific cleavage. These were formed after degradation of 6 specific peptides, after 5 different types of amino acids. The fact that other peptides were not hydrolyzed after these 5 amino acids suggests that the cleavages were not the result of a contamination with a different enzyme. In other systems, certain peptide sequences have been described to degrade chemically, under relatively mild conditions. This process is referred to as spontaneous cleavage. To test if the a-specific peptides observed in the WPI hydrolysis are the results of spontaneous cleavages, the parental peptides were synthesized. Surprisingly, 4 of the 5 synthesized peptides were indeed spontaneously cleaved under the mild conditions used in this study (i.e. 40 °C and pH 8) showing that peptides are less stable than typically considered. The rate of cleavage on the a-specific bonds was found to be enhanced in the presence of BLP. This suggests that the formation of a-specific peptides is not due to side activity but rather an enhancement of intrinsic instability of the peptides.
Snooker Structure-Based Pharmacophore Model Explains Differences in Agonist and Blocker Binding to Bitter Receptor hTAS2R39
Roland, W.S.U. ; Sanders, M.P.A. ; Buren, L. van; Gouka, R.J. ; Gruppen, H. ; Vincken, J.P. ; Ritschel, T. - \ 2015
PLoS One 10 (2015)3. - ISSN 1932-6203
protein-coupled receptors - class-a gpcrs - taste receptors - activation - identification - requirements - peptides - family - assay - t2r1
The human bitter taste receptor hTAS2R39 can be activated by many dietary (iso)flavonoids. Furthermore, hTAS2R39 activity can be blocked by 6-methoxyflavanones, 4’-fluoro-6-methoxyflavanone in particular. A structure-based pharmacophore model of the hTAS2R39 binding pocket was built using Snooker software, which has been used successfully before for drug design of GPCRs of the rhodopsin subfamily. For the validation of the model, two sets of compounds, both of which contained actives and inactives, were used: (i) an (iso)flavonoid-dedicated set, and (ii) a more generic, structurally diverse set. Agonists were characterized by their linear binding geometry and the fact that they bound deeply in the hTAS2R39 pocket, mapping the hydrogen donor feature based on T5.45 and N3.36, analogues of which have been proposed to play a key role in activation of GPCRs. Blockers lack hydrogen-bond donors enabling contact to the receptor. Furthermore, they had a crooked geometry, which could sterically hinder movement of the TM domains upon receptor activation. Our results reveal characteristics of hTAS2R39 agonist and bitter blocker binding, which might facilitate the development of blockers suitable to counter the bitterness of dietary hTAS2R39 agonists in food applications.
Strategy to identify and quantify polysaccharide gums in gelled food concentrates
Grün, C.H. ; Sanders, P. ; Burg, M. van der; Schuurbiers, E. ; Adrichem, L. van; Velzen, E.J.J. van; Roo, N. de; Brunt, K. ; Westphal, Y. ; Schols, H.A. - \ 2015
Food Chemistry 166 (2015). - ISSN 0308-8146 - p. 42 - 49.
locust bean gum - polymerase-chain-reaction - guar gum - capillary-electrophoresis - enzymatic determination - starch industry - raw-materials - xanthan gum - identification - additives
A strategy for the unambiguous identification and selective quantification of xanthan gum and locust bean gum (LBG) in gelled food concentrates is presented. DNA detection by polymerase chain reaction (PCR) showed to be a fast, sensitive, and selective method that can be used as a first screening tool in intact gelled food concentrates. An efficient isolation procedure is described removing components that may interfere with subsequent analyses. NMR spectroscopy enabled the direct identification of xanthan gum and the discrimination between different galactomannans in the isolated polysaccharide fraction. An enzymatic fingerprinting method using endo-ß-mannanase, in addition to being used to differentiate between galactomannans, was developed into a selective, quantitative method for LBG, whereas monosaccharide analysis was used to quantify xanthan gum. Recoveries for xanthan gum and LBG were 87% and 70%, respectively, with in-between day relative standard deviations below 20% for xanthan gum and below 10% for LBG.
Genome-wide transcriptional profiling of Clostridium perfringens SM101 during sporulation extends the core of putative sporulation genes and genes determining spore properties and germination characteristics
Xiao, Y. ; Hijum, S.A.F.T. van; Abee, T. ; Wells-Bennik, M.H.J. - \ 2015
PLoS One 10 (2015)5. - ISSN 1932-6203 - 19 p.
bacillus-subtilis - dipicolinic acid - bacterial-spores - heat-resistance - ser/thr kinase - killing factor - identification - difficile - proteins - sequence
The formation of bacterial spores is a highly regulated process and the ultimate properties of the spores are determined during sporulation and subsequent maturation. A wide variety of genes that are expressed during sporulation determine spore properties such as resistance to heat and other adverse environmental conditions, dormancy and germination responses. In this study we characterized the sporulation phases of C. perfringens enterotoxic strain SM101 based on morphological characteristics, biomass accumulation (OD600), the total viable counts of cells plus spores, the viable count of heat resistant spores alone, the pH of the supernatant, enterotoxin production and dipicolinic acid accumulation. Subsequently, whole-genome expression profiling during key phases of the sporulation process was performed using DNA microarrays, and genes were clustered based on their time-course expression profiles during sporulation. The majority of previously characterized C. perfringens germination genes showed upregulated expression profiles in time during sporulation and belonged to two main clusters of genes. These clusters with up-regulated genes contained a large number of C. perfringens genes which are homologs of Bacillus genes with roles in sporulation and germination; this study therefore suggests that those homologs are functional in C. perfringens. A comprehensive homology search revealed that approximately half of the upregulated genes in the two clusters are conserved within a broad range of sporeforming Firmicutes. Another 30% of upregulated genes in the two clusters were found only in Clostridium species, while the remaining 20% appeared to be specific for C. perfringens. These newly identified genes may add to the repertoire of genes with roles in sporulation and determining spore properties including germination behavior. Their exact roles remain to be elucidated in future studies.
High yields of active Thermus thermophilus proline dehydrogenase are obtained using maltose-binding protein as a solubility tag.
Huijbers, M.M.E. ; Berkel, W.J.H. van - \ 2015
Biotechnology Journal 10 (2015)3. - ISSN 1860-6768 - p. 395 - 403.
multifunctional puta flavoprotein - escherichia-coli - purification - domain - stress - biosynthesis - oxidase - crystallization - overexpression - identification
Proline dehydrogenase (ProDH) catalyzes the FAD-dependent oxidation of proline to ¿1-pyrroline-5-carboxylate, the first step of proline catabolism in many organisms. Next to being involved in a number of physiological processes, ProDH is of interest for practical applications because the proline imino acid can serve as a building block for a wide range of peptides and antibiotics. ProDH is a membrane-associated protein and recombinant soluble forms of the enzyme have only been obtained in limited amounts. We here report on the heterologous production of ProDH from Thermus thermophilus (TtProDH) in Escherichia coli. Using maltose-binding protein as solubility tag, high yields of active holoenzyme are obtained. Native TtProDH can be produced from cleaving the purified fusion protein with trypsin. Size-exclusion chromatography shows that fused and clipped TtProDH form oligomers. Thermal stability and co-solvent tolerance indicate the conformational robustness of TtProDH. These properties together with the high yield make TtProDH attractive for industrial applications.
Characterisation of hydroclimatological trends and variability in the Lake Naivasha basin, Kenya
Odongo, V.O. ; Tol, C. van der; Oel, P.R. van; Meins, F.M. ; Becht, R. ; Onyando, J.O. ; Su, Z. - \ 2015
Hydrological Processes 29 (2015)15. - ISSN 0885-6087 - p. 3276 - 3293.
long-term persistence - time-series - hurst phenomenon - climatic-change - impact - identification - hydrology - ethiopia - water - precipitation
Recent hydro-climatological trends and variability characteristics were investigated for the Lake Naivasha basin with the aim of understanding the changes in water balance components and their evolution over the past 50¿years. Using a Bayesian change point analysis and modified Mann–Kendall tests, time series of annual mean, maximum, minimum, and seasonal precipitation and flow, as well as annual mean lake volumes, were analysed for the period 1960–2010 to uncover possible abrupt shifts and gradual trends. Double cumulative curve analysis was used to investigate the changes in hydrological response attributable to either human influence or climatic variability. The results indicate a significant decline in lake volumes at a mean rate of 9.35¿×¿106¿m3¿year-1. Most of the river gauging stations showed no evidence of trends in the annual mean and maximum flows as well as seasonal flows. Annual minimum flows, however, showed abrupt shifts and significant (upward/downward) trends at the main outlet stations. Precipitation in the basin showed no evidence of abrupt shifts, but a few stations showed gradual decline. The observed changes in precipitation could not explain the decline in both minimum flows and lake volumes. The findings show no evidence of any impact of climate change for the Lake Naivasha basin over the past 50¿years. This implies that other factors, such as changes in land cover and infrastructure development, have been responsible for the observed changes in streamflow and lake volumes.
Oral administration of Lactobacillus plantarum 299v modulates gene expression in the ileum of pigs: prediction of crosstalk between intestinal immune cells and sub-mucosal adipocytes
Hulst, M.M. ; Gross, G. ; Liu, Yapin ; Hoekman, A.J.W. ; Niewold, T. ; Meulen, J. van der; Smits, M.A. - \ 2015
Genes & Nutrition 10 (2015)3. - ISSN 1555-8932 - 13 p.
kappa-b - functional-analysis - in-vivo - inhibition - immunoglobulins - identification - adipogenesis - macrophages - metabolism - activation
To study host–probiotic interactions in parts of the intestine only accessible in humans by surgery (jejunum, ileum and colon), pigs were used as model for humans. Groups of eight 6-week-old pigs were repeatedly orally administered with 5 × 1012 CFU Lactobacillus plantarum 299v (L. plantarum 299v) or PBS, starting with a single dose followed by three consecutive daily dosings 10 days later. Gene expression was assessed with pooled RNA samples isolated from jejunum, ileum and colon scrapings of the eight pigs per group using Affymetrix porcine microarrays. Comparison of gene expression profiles recorded from L. plantarum 299v-treated pigs with PBS-treated pigs indicated that L. plantarum 299v affected metabolic and immunological processes, particularly in the ileum. A higher expression level of several B cell-specific transcription factors/regulators was observed, suggesting that an influx of B cells from the periphery to the ileum and/or the proliferation of progenitor B cells to IgA-committed plasma cells in the Peyer’s patches of the ileum was stimulated. Genes coding for enzymes that metabolize leukotriene B4, 1,25-dihydroxyvitamin D3 and steroids were regulated in the ileum. Bioinformatics analysis predicted that these metabolites may play a role in the crosstalk between intestinal immune cells and sub-mucosal adipocytes. Together with regulation of genes that repress NFKB- and PPARG-mediated transcription, this crosstalk may contribute to tempering of inflammatory reactions. Furthermore, the enzyme adenosine deaminase, responsible for the breakdown of the anti-inflammatory mediator adenosine, was strongly down-regulated in response to L. plantarum 299v. This suggested that L. plantarum 299v-regulated production of adenosine by immune cells like regulatory T cells may also be a mechanism that tempers inflammation in the ileum, and perhaps also in other parts of the pig’s body.
Microplastic in a macro filter feeder: humpback whale Megaptera novaeangliae
Besseling, E. ; Foekema, E.M. ; Franeker, J.A. van; Leopold, M.F. ; Bravo Rebolledo, E. ; Kuehn, S. ; Mielke, L. ; Heberle-Bors, E. ; Ijzer, J. ; Kamminga, P. ; Koelmans, A.A. - \ 2015
Marine Pollution Bulletin 95 (2015)1. - ISSN 0025-326X - p. 248 - 252.
marine-environment - plastic ingestion - balaenoptera-physalus - mediterranean sea - north-sea - debris - identification - pollutants - particles - additives
Marine filter feeders are exposed to microplastic because of their selection of small particles as food source. Baleen whales feed by filtering small particles from large water volumes. Macroplastic was found in baleen whales before. This study is the first to show the presence of microplastic in intestines of a baleen whale (Megaptera novaeangliae). Contents of its gastrointestinal tract were sieved, dissolved in 10% potassium hydroxide and washed. From the remaining dried material, potential synthetic polymer particles were selected based on density and appearance, and analysed by Fourier transform infrared (FTIR) spectroscopy. Several polymer types (polyethylene, polypropylene, polyvinylchloride, polyethylene terephthalate, nylon) were found, in varying particle shapes: sheets, fragments and threads with a size of 1 mm to 17 cm. This diversity in polymer types and particle shapes, can be interpreted as a representation of the varying characteristics of marine plastic and the unselective way of ingestion by M. novaeangliae.
Understanding the long-lasting attraction of malaria mosquitoes to odor baits
Mweresa, C.K. ; Otieno, B. ; Omusula, P. ; Weldegergis, B.T. ; Verhulst, N.O. ; Dicke, M. ; Loon, J.J.A. van; Takken, W. ; Mukabana, W.R. - \ 2015
PLoS One 10 (2015)3. - ISSN 1932-6203 - 16 p.
gambiae-sensu-stricto - human skin emanations - anopheles-gambiae - human pathogen - aedes-aegypti - human sweat - identification - culicidae - volatiles - behavior
The use of odor baits for surveillance and control of malaria mosquitoes requires robust dispensing tools. In this study, the residual activity of a synthetic mosquito attractant blend dispensed from nylon or low density polyethylene (LDPE) sachets was evaluated at weekly intervals for one year without re-impregnation. The potential role of bacteria in modulating the attraction of mosquitoes to odor-treated nylon that had been used repeatedly over the one year study period, without re-impregnation, was also investigated. Significantly higher proportions of female Anopheles gambiae sensu stricto mosquitoes were consistently attracted to treated nylon strips than the other treatments, up to one year post-treatment. Additional volatile organic compounds and various bacterial populations were found on the treated nylon strips after one year of repeated use. The most abundant bacteria were Bacillus thuringiensis and Acinetobacter baumannii. Autoclaving of treated nylon strips prior to exposure had no effect on trap collections of laboratory-reared female An. Gambiae (P = 0.17) or wild female An. Gambiae sensu lato (P = 0.26) and Mansonia spp. (P = 0.17) mosquitoes. Trap catches of wild female An. Funestus (P <0.001) and other anophelines (P <0.007) were higher when treated strips had been autoclaved prior to deployment as opposed to when the treated nylon strips were not autoclaved. By contrast, wild female Culex mosquitoes were more strongly attracted to non-autoclaved compared to autoclaved treated nylon strips (P <0.042). This study demonstrates the feasibility of using odor baits for sampling and surveillance of malaria as well as other mosquito vectors over prolonged periods of time. Preliminary evidence points towards the potential role of bacteria in sustaining prolonged use of nylon material for dispensing synthetic attractant odorants for host-seeking malaria and other mosquito vectors but further investigations are required.
Effects of beetroot (Beta vulgaris) preparations on the Maillard reaction products in milk and meat-protein model systems
Rackauskienea, I. ; Pukalskas, A. ; Rimantas Venskutonis, P. ; Fiore, A.M. ; Troise, A.D. ; Fogliano, V. - \ 2015
Food Research International 70 (2015). - ISSN 0963-9969 - p. 31 - 39.
advanced glycation endproducts - mutagenic/carcinogenic heterocyclic amines - absorbency capacity orac - antioxidant activity - beef patties - end-products - red - identification - phip - root
The effects of beetroots (Beta vulgaris) on the formation of Maillard reaction (MR) products possessing health, nutritional and sensory implications were studied. The effect of dried beetroot juice on the formation of Ne-(carboxymethyl)lysine (CML) and Ne-(2-furoylmethyl)-L-lysine (furosine) was determined in a milk model system. Beetroot juice reduced furosine formation more than CML, inferring that betalain compounds present in the juice are more effective in reducing the formation of MR products in the early stage than in the advanced stage of MR. Beetroot water extract was fractionated on Sephadex LH20 and obtained three beetroot fractions were used to assess their effect on the formation of heterocyclic amines in a meat-protein model system. Beetroot fraction possessing the highest antioxidant capacity and containing the highest betalain content reduced the amounts of 2-amino-1-methyl-6-phenylimidazo-[4,5-b]-pyridine (PhIP), 2-amino-3,8-dimethyl-imidazo-[4,5-f]-quinoxaline (MeIQx), and 2-amino-3-methylimidazo-[4,5-f]-quinoline (IQ) by approximately 60, 77 and 87%, respectively. Beetroot preparations were characterized by ultra performance liquid chromatography quadrupole time of flight mass spectrometry (UPLC–Q-TOF–MS/MS). The antioxidant activities of beetroot preparations were also evaluated by 2,2'-azinobis (3-ethylbenzothiazoline-6-sulfonic acid) radical cation (ABTSradical dot+) scavenging capacity, oxygen radical absorbance capacity (ORAC) and total phenolic compound assays. Our findings could be useful for creating novel source of functional ingredients exerting anti-carcenogenic and antiglycation activities.
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.
Hypothesis: the sound of the individual metabolic phenotype? Acoustic detection of NMR experiments
Cacciatore, S. ; Saccenti, E. ; Piccioli, M. - \ 2015
OMICS - A Journal of Integrative Biology 19 (2015)3. - ISSN 1536-2310 - p. 147 - 156.
breast-cancer - personalized medicine - disease - profiles - models - health - time - classification - identification - metabonomics
We present here an innovative hypothesis and report preliminary evidence that the sound of NMR signals could provide an alternative to the current representation of the individual metabolic fingerprint and supply equally significant information. The NMR spectra of the urine samples provided by four healthy donors were converted into audio signals that were analyzed in two audio experiments by listeners with both musical and non-musical training. The listeners were first asked to cluster the audio signals of two donors on the basis of perceived similarity and then to classify unknown samples after having listened to a set of reference signals. In the clustering experiment, the probability of obtaining the same results by pure chance was 7.04% and 0.05% for non-musicians and musicians, respectively. In the classification experiment, musicians scored 84% accuracy which compared favorably with the 100% accuracy attained by sophisticated pattern recognition methods. The results were further validated and confirmed by analyzing the NMR metabolic profiles belonging to two other different donors. These findings support our hypothesis that the uniqueness of the metabolic phenotype is preserved even when reproduced as audio signal and warrants further consideration and testing in larger study samples
Using RNA-Seq to assemble a rose transcriptome with more than 13,000 full-length expressed genes and to develop the WagRhSNP 68k Axiom SNP array for rose (Rosa L.)
Koning, C.F.S. ; Esselink, G. ; Vukosavljev, M. ; Westende, W.P.C. van 't; Gitonga, V.W. ; Krens, F.A. ; Voorrips, R.E. ; Weg, W.E. van de; Schulz, D. ; Debener, T. ; Maliepaard, C.A. ; Arens, P.F.P. ; Smulders, M.J.M. - \ 2015
Frontiers in Plant Science 6 (2015). - ISSN 1664-462X - 10 p.
powdery mildew - markers - tool - identification - resistance - genome - diversity - sequences - platform - plant
In order to develop a versatile and large SNP array for rose, we set out to mine ESTs from diverse sets of rose germplasm. For this RNA-Seq libraries containing about 700 million reads were generated from tetraploid cut and garden roses using Illumina paired-end sequencing, and from diploid Rosa multiflora using 454 sequencing. Separate de novo assemblies were performed in order to identify single nucleotide polymorphisms (SNPs) within and between rose varieties. SNPs among tetraploid roses were selected for constructing a genotyping array that can be employed for genetic mapping and marker-trait association discovery in breeding programs based on tetraploid germplasm, both from cut roses and from garden roses. In total 68,893 SNPs were included on the WagRhSNP Axiom array. Next, an orthology-guided assembly was performed for the construction of a non-redundant rose transcriptome database. A total of 21,740 transcripts had significant hits with orthologous genes in the strawberry (Fragaria vesca L.) genome. Of these 13,390 appeared to contain the full-length coding regions. This newly established transcriptome resource adds considerably to the currently available sequence resources for the Rosaceae family in general and the genus Rosa in particular.
Characterization of the bacterial community involved in the bioflocculation process of wastewater organic matter in high loaded MBRs
Faust, L. ; Szendy, M. ; Plugge, C.M. ; Brink, P.F. van den; Temmink, H. ; Rijnaarts, H.H.M. - \ 2015
Applied Microbiology and Biotechnology 99 (2015)12. - ISSN 0175-7598 - p. 5327 - 5337.
solids retention time - 16s ribosomal-rna - gradient gel-electrophoresis - improved energy recovery - in-situ hybridization - activated-sludge - microbial community - membrane bioreactor - identification - stability
High-loaded membrane bioreactors (HL-MBRs), i.e., bioreactors equipped with a membrane for biomass retention and operated at extremely short sludge and hydraulic retention times, can concentrate sewage organic matter to facilitate subsequent energy and chemical recovery from these organics. Bioflocculation, accomplished by microorganisms that produce extracellular polymers, is a very important mechanism in these reactors. Bacterial diversity of the sludge and supernatant fraction of HL-MBRs operated at very short sludge retention times (0.125, 0.5, and 1 day) were determined using a PCR-denaturing gradient gel electrophoresis (DGGE) and clone library approach and compared to the diversity in sewage. Already at a sludge retention time (SRT) of 0.125 day, a distinct bacterial community developed compared to the community in sewage. Bioflocculation, however, was low and the majority of the bacteria, especially Arcobacter, were present in the supernatant fraction. Upon increasing SRT from 0.125 to 1 day, a much stronger bioflocculation was accompanied by an increased abundance of Bacteroidetes in the (solid) sludge fraction: 27.5 % at an SRT of 0.5 day and 46.4 % at an SRT of 1 day. Furthermore, cluster analysis of DGGE profiles revealed that the bacterial community structure in the sludge was different from that in the supernatant. To localize specific bacterial classes in the sludge flocs, fluorescence in situ hybridization (FISH) was carried out with three different bacterial probes. This showed that Betaproteobacteria formed clusters in the sludge flocs whereas Alphaproteobacteria and Gammaproteobacteria were mainly present as single cells
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