Highly specific enrichment of rare nucleic acid fractions using Thermus thermophilus argonaute with applications in cancer diagnostics
Song, Jinzhao ; Hegge, Jorrit W. ; Mauk, Michael G. ; Chen, Junman ; Till, Jacob E. ; Bhagwat, Neha ; Azink, Lotte T. ; Peng, Jing ; Sen, Moen ; Mays, Jazmine ; Carpenter, Erica L. ; Oost, John van der; Bau, Haim H. - \ 2020
Nucleic acids research 48 (2020)4. - ISSN 0305-1048 - p. e19 - e19.
Detection of disease-associated, cell-free nucleic acids in body fluids enables early diagnostics, genotyping and personalized therapy, but is challenged by the low concentrations of clinically significant nucleic acids and their sequence homology with abundant wild-type nucleic acids. We describe a novel approach, dubbed NAVIGATER, for increasing the fractions of Nucleic Acids of clinical interest Via DNA-Guided Argonaute from Thermus thermophilus (TtAgo). TtAgo cleaves specifically guide-complementary DNA and RNA with single nucleotide precision, greatly increasing the fractions of rare alleles and, enhancing the sensitivity of downstream detection methods such as ddPCR, sequencing, and clamped enzymatic amplification. We demonstrated 60-fold enrichment of the cancer biomarker KRAS G12D and ∼100-fold increased sensitivity of Peptide Nucleic Acid (PNA) and Xenonucleic Acid (XNA) clamp PCR, enabling detection of low-frequency (<0.01%) mutant alleles (∼1 copy) in blood samples of pancreatic cancer patients. NAVIGATER surpasses Cas9-based assays (e.g. DASH, Depletion of Abundant Sequences by Hybridization), identifying more mutation-positive samples when combined with XNA-PCR. Moreover, TtAgo does not require targets to contain any specific protospacer-adjacent motifs (PAM); is a multi-turnover enzyme; cleaves ssDNA, dsDNA and RNA targets in a single assay; and operates at elevated temperatures, providing high selectivity and compatibility with polymerases.
The peatland map of Europe
Tanneberger, Franziska ; Tegetmeyer, C. ; Busse, S. ; Barthelmes, A. ; Shumka, S. ; Mariné, A.M. ; Jenderedjian, K. ; Steiner, G.M. ; Essl, F. ; Etzold, J. ; Mendes, C. ; Kozulin, A. ; Frankard, P. ; Milanović, ; Ganeva, A. ; Apostolova, I. ; Alegro, A. ; Delipetrou, P. ; Navrátilová, J. ; Risager, M. ; Leivits, A. ; Fosaa, A.M. ; Tuominen, S. ; Muller, F. ; Bakuradze, T. ; Sommer, M. ; Christanis, K. ; Szurdoki, E. ; Oskarsson, H. ; Brink, S.H. ; Connolly, J. ; Bragazza, L. ; Martinelli, G. ; Aleksāns, O. ; Priede, A. ; Sungaila, D. ; Melovski, L. ; Belous, T. ; Saveljić, D. ; Vries, F. De; Moen, A. ; Dembek, W. ; Mateus, J. ; Hanganu, J. ; Sirin, A. ; Markina, A. ; Napreenko, M. ; Lazarević, P. ; Stanová, V.Š. ; Skoberne, P. ; Pérez, P.H. ; Pontevedra-Pombal, X. ; Lonnstad, J. ; Küchler, M. ; Wüst-Galley, C. ; Kirca, S. ; Mykytiuk, O. ; Lindsay, R. ; Joosten, H. - \ 2017
Mires and Peat 19 (2017). - ISSN 1819-754X
Drained peatland - GIS - Histosol - Mire - Organic soil - Peat
Based on the ‘European Mires Book’ of the International Mire Conservation Group (IMCG), this article provides a composite map of national datasets as the first comprehensive peatland map for the whole of Europe. We also present estimates of the extent of peatlands and mires in each European country individually and for the entire continent. A minimum peat thickness criterion has not been strictly applied, to allow for (often historically determined) country-specific definitions. Our ‘peatland’ concept includes all ‘mires’, which are peatlands where peat is being formed. The map was constructed by merging national datasets in GIS while maintaining the mapping scales of the original input data. This ‘bottom-up’ approach indicates that the overall area of peatland in Europe is 593,727 km2. Mires were found to cover more than 320,000 km2 (around 54 % of the total peatland area). If shallow-peat lands (< 30 cm peat) in European Russia are also taken into account, the total peatland area in Europe is more than 1,000,000 km2 which is almost 10 % of the total surface area. Composite inventories of national peatland information, as presented here for Europe, may serve to identify gaps and priority areas for field survey, and help to cross-check and calibrate remote sensing based mapping approaches.
Formalized classification of European fen vegetation at the alliance level
Peterka, Tomáš ; Hájek, Michal ; Jiroušek, Martin ; Jiménez-Alfaro, Borja ; Aunina, Liene ; Bergamini, Ariel ; Dítě, Daniel ; Felbaba-Klushyna, Ljuba ; Graf, Ulrich ; Hájková, Petra ; Hettenbergerová, Eva ; Ivchenko, Tatiana G. ; Jansen, Florian ; Koroleva, Natalia E. ; Lapshina, Elena D. ; Lazarević, Predrag M. ; Moen, Asbjørn ; Napreenko, Maxim G. ; Pawlikowski, Paweł ; Plesková, Zuzana ; Sekulová, Lucia ; Smagin, Viktor A. ; Tahvanainen, Teemu ; Thiele, Annett ; Biţǎ-Nicolae, Claudia ; Biurrun, Idoia ; Brisse, Henry ; Ćušterevska, Renata ; Bie, Els De; Ewald, Jörg ; FitzPatrick, Úna ; Font, Xavier ; Jandt, Ute ; Kącki, Zygmunt ; Kuzemko, Anna ; Landucci, Flavia ; Moeslund, Jesper E. ; Pérez-Haase, Aaron ; Rašomavičius, Valerijus ; Rodwell, John S. ; Schaminée, Joop H.J. ; Šilc, Urban ; Stančić, Zvjezdana ; Chytrý, Milan ; Schwabe-Kratochwil, Angelika - \ 2017
Applied Vegetation Science 20 (2017)1. - ISSN 1402-2001 - p. 124 - 142.
Biogeography - Ecological gradients - Endangered habitats - Mires - Relevés - Supervised vegetation classification - Unsupervised vegetation classification - Vegetation plots - Wetlands
Aims: Phytosociological classification of fen vegetation (Scheuchzerio palustris-Caricetea fuscae class) differs among European countries. Here we propose a unified vegetation classification of European fens at the alliance level, provide unequivocal assignment rules for individual vegetation plots, identify diagnostic species of fen alliances, and map their distribution. Location: Europe, western Siberia and SE Greenland. Methods: 29 049 vegetation-plot records of fens were selected from databases using a list of specialist fen species. Formal definitions of alliances were created using the presence, absence and abundance of Cocktail-based species groups and indicator species. DCA visualized the similarities among the alliances in an ordination space. The ISOPAM classification algorithm was applied to regional subsets with homogeneous plot size to check whether the classification based on formal definitions matches the results of unsupervised classifications. Results: The following alliances were defined: Caricion viridulo-trinervis (sub-halophytic Atlantic dune-slack fens), Caricion davallianae (temperate calcareous fens), Caricion atrofusco-saxatilis (arcto-alpine calcareous fens), Stygio-Caricion limosae (boreal topogenic brown-moss fens), Sphagno warnstorfii-Tomentypnion nitentis (Sphagnum-brown-moss rich fens), Saxifrago-Tomentypnion (continental to boreo-continental nitrogen-limited brown-moss rich fens), Narthecion scardici (alpine fens with Balkan endemics), Caricion stantis (arctic brown-moss rich fens), Anagallido tenellae-Juncion bulbosi (Ibero-Atlantic moderately rich fens), Drepanocladion exannulati (arcto-boreal-alpine non-calcareous fens), Caricion fuscae (temperate moderately rich fens), Sphagno-Caricion canescentis (poor fens) and Scheuchzerion palustris (dystrophic hollows). The main variation in the species composition of European fens reflected site chemistry (pH, mineral richness) and sorted the plots from calcareous and extremely rich fens, through rich and moderately rich fens, to poor fens and dystrophic hollows. ISOPAM classified regional subsets according to this gradient, supporting the ecological meaningfulness of this classification concept on both the regional and continental scale. Geographic/macroclimatic variation was reflected in the second most important gradient. Conclusions: The pan-European classification of fen vegetation was proposed and supported by the data for the first time. Formal definitions developed here allow consistent and unequivocal assignment of individual vegetation plots to fen alliances at the continental scale.
Data from: The evolutionary legacy of diversification predicts ecosystem function
Yguel, Benjamin ; Jactel, H. ; Pearse, Ian S. ; Moen, Daniel ; Winter, M. de; Hortal, J. ; Helmus, Matthew R. ; Kühn, I. ; Pavoine, S. ; Purschke, Oliver ; Weiher, Evan ; Violle, C. ; Ozinga, W.A. ; Brändle, Martin ; Bartish, I. ; Prinzing, Andreas - \ 2016
Wageningen University & Research
community ecology - evolutionary history - lineage-through-time plots - phylogenetic diversity - productivity - species coexistence
The Rdata files are simulated phylogenies and lineage through time plot of these simulated phylogenies, used in Yguel et al. 2016 AmNat. The code to extract the LTT plot from the phylogenies is given in the Appendices of the article as well as the method used to make these simulations.The name of the Rdata file indicates which simulation the file is refering to. The Excel files contain measures of phylogenetic structure of these simulated phylogenies (Measure phylogenetic structure parameters on simulated phylogenies.xlsx) and phylogenies of the experimental communities used in the article (Measure phylogenetic structure parameters on Cadotte Zanne phylog.xlsx). The code to calculate a1, a2, a3, and to measure S1 and S2 are given in the method of the article. In all excel files, a1 a2 a3 are the polynomial parameters fitted on the LTT plots. S1 and S2 are respectively ES1 and ES2, the "elderness surface" presented in the article. MPD, MNTD, gamma, and Colless are the common phylogenetic structure measurement (see also method), and invNRI and invNTI the standardized version of MPD and MNTD. RichSpe or Sps correspond to the species richness. PlotID corresponds to the identification of the plot. Mean19962007 corresponds to the mean productivity from 1996 to 2007.
The evolutionary legacy of diversification predicts ecosystem function
Yguel, Benjamin ; Jactel, Hervé ; Pearse, Ian S. ; Moen, Daniel ; Winter, Marten ; Hortal, Joaquin ; Helmus, Matthew R. ; Kühn, Ingolf ; Pavoine, Sandrine ; Purschke, Oliver ; Weiher, Evan ; Violle, Cyrille ; Ozinga, Wim ; Brändle, Martin ; Bartish, Igor ; Prinzing, Andreas - \ 2016
American Naturalist 188 (2016)4. - ISSN 0003-0147 - p. 398 - 410.
Community ecology - Evolutionary history - Lineage-throughtime plots - Phylogenetic diversity - Productivity - Species coexistence
Theory suggests that the structure of evolutionary history represented in a species community may affect its functioning, but phylogenetic diversity metrics do not allow for the identification of major differences in this structure. Here we propose a new metric, ELDERness (for Evolutionary Legacy of DivERsity) to estimate evolutionary branching patterns within communities by fitting a polynomial function to lineage-through-time (LTT) plots. We illustrate how real and simulated community branching patterns can be more correctly described by ELDERness and can successfully predict ecosystem functioning. In particular, the evolutionary history of branching patterns can be encapsulated by the parameters of third-order polynomial functions and further measured through only two parameters, the “ELDERness surfaces.” These parameters captured variation in productivity of a grassland community better than existing phylogenetic diversity or diversification metrics and independent of species richness or presence of nitrogen fixers. Specifically, communitieswith small ELDERness surfaces (constant accumulation of lineages through time in LTT plots) were more productive, consistent with increased productivity resulting from complementary lineages combined with niche filling within lineages. Overall, while existing phylogenetic diversity metrics remain useful in many contexts, we suggest that our ELDERness approach better enables testing hypotheses that relate complex patterns of macroevolutionary history represented in local communities to ecosystem functioning.
The major autolysin Acm2 from Lactobacillus plantarum undergoes cytoplasmic O-glycosylation
Fredriksen, L. ; Mathiesen, G. ; Moen, A. ; Bron, P.A. ; Kleerebezem, M. ; Eijsink, V.G.H. ; Egge-Jacobsen, W. - \ 2012
Journal of Bacteriology 194 (2012)2. - ISSN 0021-9193 - p. 325 - 333.
binding-protein gspb - n-acetylglucosaminidase - signal peptides - gene-expression - system - peptidoglycan - endopeptidase - glycoprotein - specificity - diversity
The major autolysin Acm2 from the probiotic strain Lactobacillus plantarum WCFS1 contains high proportions of alanine, serine, and threonine in its N-terminal so-called AST domain. It has been suggested that this extracellular protein might be glycosylated, but this has not been experimentally verified. We used high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS) to study the possible occurrence of glycans on peptides generated from lactobacillary surface proteins by protease treatment. This approach yielded five glycopeptides in various glycoforms, all derived from the AST domain of Acm2. All five glycopeptides contained the hydroxy-amino acids serine and threonine, suggesting that Acm2 is O-glycosylated. By using lectin blotting with succinylated wheat germ agglutinin, and by comparing the wild-type strain with an Acm2-negative derivative (NZ3557), we found that the attached N-acetylhexosamines are most likely N-acetylglucosamines (GlcNAc). NZ3557 was further used as a genetic background to express an Acm2 variant lacking its secretion signal, resulting in intracellular expression of Acm2. We show that this intracellular version of Acm2 is also glycosylated, indicating that the GlcNAc modification is an intracellular process.
Genome sequence of the pea aphid Acyrthosiphon pisum
Richards, Stephen ; Gibbs, Richard A. ; Gerardo, Nicole M. ; Moran, Nancy ; Nakabachi, Atsushi ; Stern, David ; Tagu, Denis ; Wilson, Alex C.C. ; Muzny, Donna ; Kovar, Christie ; Cree, Andy ; Chacko, Joseph ; Chandrabose, Mimi N. ; Dao, Marvin Diep ; Dinh, Huyen H. ; Gabisi, Ramatu Ayiesha ; Hines, Sandra ; Hume, Jennifer ; Jhangian, Shalini N. ; Joshi, Vandita ; Lewis, Lora R. ; Liu, Yih Shin ; Lopez, John ; Morgan, Margaret B. ; Nguyen, Ngoc Bich ; Okwuonu, Geoffrey O. ; Ruiz, San Juana ; Santibanez, Jireh ; Wright, Rita A. ; Fowler, Gerald R. ; Hitchens, Matthew E. ; Lozado, Ryan J. ; Moen, Charles ; Steffen, David ; Warren, James T. ; Zhang, Jingkun ; Nazareth, Lynne V. ; Chavez, Dean ; Davis, Clay ; Lee, Sandra L. ; Patel, Bella Mayurkumar ; Pu, Ling Ling ; Bell, Stephanie N. ; Johnson, Angela Jolivet ; Vattathil, Selina ; Williams, Rex L. ; Shigenobu, Shuji ; Dang, Phat M. ; Morioka, Mizue ; Fukatsu, Takema ; Kudo, Toshiaki ; Miyagishima, Shin Ya ; Jiang, Huaiyang ; Worley, Kim C. ; Legeai, Fabrice ; Gauthier, Jean Pierre ; Collin, Olivier ; Zhang, Lan ; Chen, Hsiu Chuan ; Ermolaeva, Olga ; Hlavina, Wratko ; Kapustin, Yuri ; Kiryutin, Boris ; Kitts, Paul ; Maglott, Donna ; Murphy, Terence ; Pruitt, Kim ; Sapojnikov, Victor ; Souvorov, Alexandre ; Thibaud-Nissen, Françoise ; Câmara, Francisco ; Guigó, Roderic ; Stanke, Mario ; Solovyev, Victor ; Kosarev, Peter ; Gilbert, Don ; Gabaldón, Toni ; Huerta-Cepas, Jaime ; Marcet-Houben, Marina ; Pignatelli, Miguel ; Moya, Andrés ; Rispe, Claude ; Ollivier, Morgane ; Quesneville, Hadi ; Permal, Emmanuelle ; Llorens, Carlos ; Futami, Ricardo ; Hedges, Dale ; Robertson, Hugh M. ; Alioto, Tyler ; Mariotti, Marco ; Nikoh, Naruo ; McCutcheon, John P. ; Burke, Gaelen ; Kamins, Alexandra ; Latorre, Amparo ; Ashton, Peter ; Calevro, Federica ; Charles, Hubert ; Colella, Stefano ; Douglas, Angela E. ; Jander, Georg ; Jones, Derek H. ; Febvay, Gérard ; Kamphuis, Lars G. ; Kushlan, Philip F. ; Macdonald, Sandy ; Ramsey, John ; Schwartz, Julia ; Seah, Stuart ; Thomas, Gavin ; Vellozo, Augusto ; Cass, Bodil ; Degnan, Patrick ; Hurwitz, Bonnie ; Leonardo, Teresa ; Koga, Ryuichi ; Altincicek, Boran ; Anselme, Caroline ; Atamian, Hagop ; Barribeau, Seth M. ; Vos, Martin De; Duncan, Elizabeth ; Evans, Jay ; Ghanim, Murad ; Heddi, Abdelaziz ; Kaloshian, Isgouhi ; Vincent-Monegat, Carole ; Parker, Ben J. ; Pérez-Brocal, Vicente ; Rahbé, Yvan ; Spragg, Chelsea J. ; Tamames, Javier ; Tamarit, Daniel ; Tamborindeguy, Cecilia ; Vilcinskas, Andreas ; Bickel, Ryan D. ; Brisson, Jennifer A. ; Butts, Thomas ; Chang, Chun Che ; Christiaens, Olivier ; Davis, Gregory K. ; Duncan, Elizabeth ; Ferrier, David ; Iga, Masatoshi ; Janssen, Ralf ; Lu, Hsiao Ling ; McGregor, Alistair ; Miura, Toru ; Smagghe, Guy ; Smith, James ; Zee, Maurijn Van Der; Velarde, Rodrigo ; Wilson, Megan ; Dearden, Peter ; Edwards, Owain R. ; Gordon, Karl ; Hilgarth, Roland S. ; Rider, Stanley Dean ; Srinivasan, Dayalan ; Walsh, Thomas K. ; Ishikawa, Asano ; Jaubert-Possamai, Stéphanie ; Fenton, Brian ; Huang, Wenting ; Rizk, Guillaume ; Lavenier, Dominique ; Nicolas, Jacques ; Smadja, Carole ; Zhou, Jing Jiang ; Vieira, Filipe G. ; He, Xiao Li ; Liu, Renhu ; Rozas, Julio ; Field, Linda M. ; Campbell, Peter ; Carolan, James C. ; Fitzroy, Carol I.J. ; Reardon, Karen T. ; Reeck, Gerald R. ; Singh, Karam ; Wilkinson, Thomas L. ; Huybrechts, Jurgen ; Abdel-Latief, Mohatmed ; Robichon, Alain ; Veenstra, Jan A. ; Hauser, Frank ; Cazzamali, Giuseppe ; Schneider, Martina ; Williamson, Michael ; Stafflinger, Elisabeth ; Hansen, Karina K. ; Grimmelikhuijzen, Cornelis J.P. ; Price, Daniel R.G. ; Caillaud, Marina ; Fleet, Eric Van; Ren, Qinghu ; Gatehouse, John A. ; Brault, Véronique ; Monsion, Baptiste ; Diaz, Jason ; Hunnicutt, Laura ; Ju, Ho Jong ; Pechuan, Ximo ; Aguilar, José ; Cortés, Teresa ; Ortiz-Rivas, Benjamín ; Martínez-Torres, David ; Dombrovsky, Aviv ; Dale, Richard P. ; Davies, T.G.E. ; Williamson, Martin S. ; Jones, Andrew ; Sattelle, David ; Williamson, Sally ; Wolstenholme, Adrian ; Cottret, Ludovic ; Sagot, Marie France ; Heckel, David G. ; Hunter, Wayne - \ 2010
PloS Biology 8 (2010)2. - ISSN 1544-9173
Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.
Variations in mountain vegetation use by reindeer (Rangifer tarandus) affects dry heath but not grass heath
Moen, J. ; Boogerd, C. ; Skarin, A. - \ 2009
Journal of Vegetation Science 20 (2009)5. - ISSN 1100-9233 - p. 805 - 813.
semi-domesticated reindeer - plant community - tundra - productivity - herbivores - impacts - growth
Question: Are differences in landscape use of semi-domesticated reindeer reflected in the vegetation of summer grazing grounds? Location: Alpine heaths, central east Sweden. Methods: Dry heath and grass heath vegetation plots with inferred grazing intensities (high, intermediate and low) were selected a priori from an interpolated pellet count map compiled in 2002. In each plot, faecal pellets were counted, environmental variables measured and vegetation sampled by listing presence and absence. Species composition was compared with a detrended correspondence analysis, and a canonical correspondence analysis was used to infer relations between species composition and environmental variables. Plots were also clustered to provide groupings for an indicator species analysis. Results: Significant differences in faecal pellet count were present between the highest and lowest grazing intensities for both vegetation types, showing that the pattern in the interpolated pellet maps was robust. Differences in species composition between grazing intensities were found for the dry heath only. Here, there was an apparent grazing gradient, with lichens and mosses in the low-use plots and grasses and herbs in the high-use plots. No such gradient was found for the grass heath. Conclusions: Within the dry heath vegetation type, grazing levels had a subtle effect on the vegetation, while no effects were seen in the grass heath, probably as a result of the dominance of more grazing-tolerant graminoids. Even in the dry heath, species richness did not differ between grazing levels, but the relative abundances of species differed.
Financial-economic analysis of Bovine Viral Diarrhoea Virus control in Dutch dairy herds
Saatkamp, H.W. ; Beek, P.M.J.C. ; Moen, A.R. ; Groenendaal, H. - \ 2009
|Measurement of trace elements in liver biopsy samples from cattle
Ouweltjes, W. ; Zeeuw, A.C. de; Moen, A. ; Counotte, G.H.M. - \ 2007
Tijdschrift voor Diergeneeskunde 132 (2007)3. - ISSN 0040-7453 - p. 76 - 83.
urine-analyse - diagnostische technieken - biopsie - diagnose - sporenelementen - rundvee - sporenelementtekorten - diervoeding - mineralenvoeding - lever - urine analysis - diagnostic techniques - biopsy - diagnosis - trace elements - cattle - trace element deficiencies - animal nutrition - mineral nutrition - liver - mineral status - beef-cattle - copper - zinc - supplementation - manganese - calves - iron
Serum, plasma, or urine samples are usually used for the measurement of the trace elements copper, zinc, iron, selenium, because these samples are easy to obtain; however, these samples are not always appropriate. For example, it is not possible to measure molybdenum, the major antagonist of copper, in blood or urine. Therefore measurement of trace elements in liver tissue is considered the gold standard. For the assessment of selenium the method of choice remains determination of glutathion peroxidase in erythrocytes and for the assessment of magnesium determination of magnesium in urine. We determined the accuracy and repeatability of measuring trace elements in liver biopsies and whole liver homogenates. The levels of trace elements measured were similar in both preparations (92% agreement). Liver biopsy in live animals is a relatively simple procedure but not common in the Netherlands. Reference levels of trace elements, classified as too low, low, adequate, high, and too high, were established on the basis of our research and information in the literature. In a second study we investigated the practical aspects of obtaining liver tissue samples and their use. Samples were collected from cattle on a commercial dairy farm. Liver biopsy provided additional information to that obtained from serum and urine samples. We prepared a biopsy protocol and a test package, which we tested on 14 farms where an imbalance of trace minerals was suspected. Biopsy samples taken from 4 to 6 animals revealed extreme levels of trace elements
The Cholesterol-Raising Factor from Coffee Beans, Cafestol, as an Agonist Ligand for the Farnesoid and Pregnane X Receptors
Ricketts, M.L. ; Boekschoten, M.V. ; Kreeft, A.J. ; Hooiveld, G.J.E.J. ; Moen, C.J.A. ; Müller, M.R. ; Frants, R.R. ; Kasanmoentalib, S. ; Post, S.M. ; Princen, H.M.G. ; Porter, J.G. ; Katan, M.B. ; Hofker, M.H. ; Moore, D.D. - \ 2007
Molecular endocrinology 21 (2007)7. - ISSN 0888-8809 - p. 1603 - 1616.
bile-acid synthesis - e-asterisk-3-leiden transgenic mice - glutathione-s-transferase - negative feedback-regulation - salt export pump - nuclear receptor - gene-expression - triglyceride levels - serum-cholesterol - boiled coffee
Cafestol, a diterpene present in unfiltered coffee brews such as Scandinavian boiled, Turkish, and cafetière coffee, is the most potent cholesterol-elevating compound known in the human diet. Several genes involved in cholesterol homeostasis have previously been shown to be targets of cafestol, including cholesterol 7-hydroxylase (CYP7A1), the rate-limiting enzyme in bile acid biosynthesis. We have examined the mechanism by which cafestol elevates serum lipid levels. Changes in several lipid parameters were observed in cafestol-treated APOE3Leiden mice, including a significant increase in serum triglyceride levels. Microarray analysis of these mice identified alterations in hepatic expression of genes involved in lipid metabolism and detoxification, many of which are regulated by the nuclear hormone receptors farnesoid X receptor (FXR) and pregnane X receptor (PXR). Further studies demonstrate that cafestol is an agonist ligand for FXR and PXR, and that cafestol down-regulates expression of the bile acid homeostatic genes CYP7A1, sterol 12-hydroxylase, and Na+-taurocholate cotransporting polypeptide in the liver of wild-type but not FXR null mice. Cafestol did not affect genes known to be up-regulated by FXR in the liver of wild-type mice, but did increase expression of the positive FXR-target genes intestinal bile acid-binding protein and fibroblast growth factor 15 (FGF15) in the intestine. Because FGF15 has recently been shown to function in an enterohepatic regulatory pathway to repress liver expression of bile acid homeostatic genes, its direct induction in the gut may account for indirect effects of cafestol on liver gene expression. PXR-dependent gene regulation of cytochrome P450 3A11 and other targets by cafestol was also only seen in the intestine. Using a double FXR/PXR knockout mouse model, we found that both receptors contribute to the cafestol-dependent induction of intestinal FGF15 gene expression. In conclusion, cafestol acts as an agonist ligand for both FXR and PXR, and this may contribute to its impact on cholesterol homeostasis.
|Predicting the occurrence of intermittent turbulence in the stable boundary layer
Wiel, B.J.H. van de; Hartogensis, O.K. ; Ronda, R.J. ; Moen, A. ; DeBruin, H.A.R. ; Holtslag, A.A.M. - \ 2002
In: Proceedings European Geophysical Society, XCVII General Assembly, Nice, France, April 2002 E.G.S.
Polycyclic aromatic hydrocarbon degradation by the white rot fungus Bjerkandera sp. strain BOS55
Kotterman, M. - \ 1998
Agricultural University. Promotor(en): J.A.M. de Bont; J.A. Field. - S.l. : S.n. - ISBN 9789054859055 - 104
bodemdegradatie - biodegradatie - polycyclische koolwaterstoffen - bjerkandera - soil degradation - biodegradation - polycyclic hydrocarbons - bjerkandera
Outline of this thesis
Summary and concluding remarks
First, this chapter will show the evidence that PAHs are oxidized extracellularly by the ligninolytic enzymes of the white rot fungus Bjerkandera sp. strain BOS55. The parameters which influence the PAH degrading capacity of the white rot fungus are then discussed. The results concerning the degradation of PAHs with respect to mineralization, accumulation of metabolites and effect on mutagenicity are summarized. Finally, the future prospects of white rot fungal bioremediation of PAH polluted soils are discussed briefly.
PAH DEGRADATION BY WHITE ROT FUNGI
In this study, further evidence was obtained demonstrating that extracellular oxidation by peroxidases is the main mechanism of PAH metabolism in white rot fungi (Chapter 2, 3, 4 and 5). The rate of PAH oxidation was similar in extracellular culture fluids as in the whole cultures. Furthermore, the same metabolite of anthracene oxidation, anthraquinone, was observed in similar yields in both extracellular culture fluids and whole cultures. Anthraquinone is a well-known metabolite of anthracene oxidation by ligninolytic enzymes (Haemmerli 1988; Hammel et al., 1991, Field et al., 1996b; Sack et al., 1997). Additionally, the oxidation of the ligninolytic indicator dye Poly R-478 was found to be correlated to PAH oxidation. The aromatic polymer Poly R-478 is a substrate of peroxidases and can only be oxidized extracellularly due to its excessive size. The involvement of peroxidases was also indicated by the stimulation of PAH and Poly R-478 oxidation by increasing the hydrogen peroxide production rate.
Oxidation of PAH by non-ligninolytic cultures of white rot fungi has also been reported (Sutherland et al., 1991). The PAH metabolites observed, trans-dihydrodiols, suggested intracellular oxidation by P450 monooxygenases. White rot fungi have cytochrome P450 monooxygenases, which are capable of oxidizing PAH under physiological conditions when ligninolytic enzymes were not expressed (Masaphy et al. 1996; Bezalel et al., 1997). In this study, no significant participation of intracellular monooxygenases in the oxidation of PAH by ligninolytic cultures of Bjerkandera sp. strain BOS55 could be demonstrated.
ENHANCEMENT OF THE PAH OXIDATION BY WHITE ROT FUNGI
Physiological Parameters Limiting PAH Oxidation Biomass.
Addition of Mn to 6-day-old Mn-deficient cultures simultaneously with anthracene decreased the anthracene oxidation as well as the anthraquinone accumulation (Chapter 3), suggesting Mn, in some way, also affected the activity of the existing ligninolytic enzymes. Mn can scavenge reduced oxygen radicals like superoxide (Rotschild et al., 1998), which might be disadvantageous for the oxidation of anthracene.
H 2 O 2 production rate.
The results of our study clearly show that of the physiological parameters that improve PAH oxidation by Bjerkandera sp. strain BOS55, the hydrogen peroxide production rate is the most important parameter.
Non-physiological Parameters Limiting PAH Oxidation
The hypothesis that the oxidation rate of PAHs by the ligninolytic enzymes was limited by the low bioavailability was confirmed by the 5-fold increase in the PAH oxidation rate when the bioavailability of the PAH was increased by the addition of surfactants to adequately aerated high-N cultures. The surfactants had no positive effect on the ligninolytic activity, instead, toxicity was observed. However, the partial loss of biocatalytic activity was clearly overcompensated by the increased bioavailability of PAH (Chapter 4).
The role of surfactants in increasing the bioavailability was shown to be due to their effect on decreasing the particle size of the PAH precipitates and on increasing the apparent aqueous solubility of the PAHs. Both factors are shown to increase PAH bioavailability (Tiehm, 1994; Volkering et al., 1992; Rouse et al., 1994; Volkering et al., 1995; Field et al., 1996b). The addition of surfacants often fails to stimulate bacterial degradation of PAH, since many surfactants can have toxic effects above the CMC (Rouse et al., 1994) or preferential degradation of the surfactant occurs (Grimberg et al., 1996; Tiehm, 1994). Tween 80, a commonly used surfactant that showed both high PAH solubilizing activity as well as low toxicity towards Bjerkandera sp. strain BOS55, was degraded rapidly by the fungus. The stimulatory effect of Tween 80 on the benzo[ a ]pyrene oxidation rate, however, was still observed after degradation of the surfactant. Apparently, the reduction in benzo[ a ]pyrene particle size by Tween 80 accounted for the increased bioavailability and hence the oxidation rate (Chapter 4).
The large effect of the two PAH oxidation rate limiting factors identified in this study, the hydrogen peroxide production rate and the PAH bioavailability, was demonstrated in extracellular culture fluids of high-N cultures of Bjerkandera sp. strain BOS55. By enhancing the hydrogen peroxide production rate with exogenous glucose oxidase and by enhancing the PAH bioavailability with surfactants, the anthracene oxidation rate could be increased 4- and 5-fold, respectively. The combination of both effects led to a 14-fold increase to a very high rate of anthracene oxidation of 1450 mg liter -1day -1. Under these conditions, the 5-ring PAH benzo[ a ]pyrene was oxidized at a rate of 450 mg liter -1day -1.
FATE AND ENVIRONMENTAL IMPACT OF PAH DEGRADATION BY WHITE ROT FUNGI
In this study, the addition of natural occurring microflora in soils, sediment sludge and activated sludge to cultures of Bjerkandera sp. strain BOS55 with oxidized [ 14C]-radiolabeled benzo[ a ]pyrene resulted in a rapid increase in mineralization. A 21% higher recovery of 14CO 2 was observed upon addition of the natural occurring microflora, confirming that some of the metabolites had high bioavailability and biodegradability. These results also showed that the benzo[ a ]pyrene metabolites were mineralized faster and to a higher level by the added microflora than by the fungal culture itself. Table 1 summarizes the main findings of this study together with other studies in the literature concerning the combined action of white rot fungi and indigenous microflora.
The results taken as a whole clearly show that the white rot fungal oxidized PAH metabolites are mineralized faster by indigenous microflora of different sources than their parent PAH. The metabolites of fungal oxidation are also better substrates for bacteria than for the white rot fungi themselves. The highest stimulatory effect of fungal "pre-oxidation" on the mineralization of PAHs is observed with benzo[ a ]pyrene, which also has the lowest bioavailability and degradability of the PAHs tested. Consequently, a faster and higher level of PAH mineralization is obtained by sequential treatment than by bacteria or fungi alone and the observed accumulation of white rot fungal PAH metabolites in pure cultures is therefore not likely to occur under non-sterile conditions, e.g. creosote contaminated soils.
FUTURE PROSPECT OF WHITE ROT FUNGI IN THE BIOREMEDIATION OF PAH CONTAMINATED SOILS
The large difference between the PAH bioavailability in artificially contaminated and aged industrially contaminated soils is probably mainly caused by the method of soil contamination. In artificially contaminated soils, PAHs are added to the soil dissolved in solvents. After evaporation of the solvent, PAH are likely to be present as precipitated particles. The degradation rate of this artificially added benzo[ a ]pyrene by Bjerkandera sp. strain BOS55 appeared to be influenced mainly by the particle size of these precipitates and not by the presence or absence of organic matter (non published results). Generally, the recalcitrance of PAH in soil systems is attributed partly to adsorption of PAH to adsorbents such as organic matter (Pignatello and Xing, 1996; Luthy et al., 1997). In contaminated soils at gasification sites and creosote-facilities, the PAH spills are associated with non-aqueous phase liquids (NAPLs) such as coal tar and mineral oils. Due to the high hydrophobicity, PAHs are sequestered by the NAPLs, resulting in lower aqueous concentrations than in the absence of NAPLs (Efroymson and Alexander, 1995). Only very low mass transfer of PAH out of NAPLs has been observed (Efroymson and Alexander, 1994; Yeom et al., 1996), which can be decreased even more by weathering and hardening (Luthy et al., 1997), severely decreasing the bioavailability.
Whether PAH polluted soils can be bioremediated successfully in the near future strongly depends on the bioavailability of PAH in the specific soil, and therefore on methods that can possibly increase this bioavailability. The use of surfactants, which have been successfully applied in liquid cultures (Chapter 4), also resulted in higher PAH degradation by Bjerkandera sp. strain BOS55 in both artificially contaminated as aged industrially contaminated soils (non published results). The use of non-toxic, relatively persistent surfactants could therefore increase the potential of biological remediation of PAH contaminated soils.
Increased risk of abortion following neosporoa caninum abortion outbreak: a retrospective and prospective cohort study in four dairy herds.
Moen, A.R. ; Wouda, W. ; Mul, M.F. ; Graat, E.A.M. ; Werven, T. van - \ 1998
Theriogenology 49 (1998). - ISSN 0093-691X - p. 1301 - 1309.
|Development of expertise in teaching: Do we really know what we are talking about?
Beijaard, D. ; Driel, J. van; Meijer, P. ; Kwo, O. ; Gudmundsdottir, S. ; Moen, T. ; Verloop, N. ; Vries, Y. de - \ 1997
In: ISATT (1997) Program of the 8th biennial Conference of the International Study Association on Teacher Thinking. Kiel / Lang, M., - p. 40 - 40.
Een nieuwe kijk op hei : verslag van de heideworkshop gehouden op 25 mei 1993 te Wageningen
Beije, H.M. ; Moen, P. ; Wijnhoven, A.L.J. - \ 1994
Wageningen : IBN-DLO (IBN - rapport 073) - 64
heidegebieden - landschap - landschapsbescherming - landschapsecologie - natuurbescherming - nederland - plantengemeenschappen - heathlands - landscape - landscape conservation - landscape ecology - nature conservation - netherlands - plant communities
|Relations between acrotelm depth, phreatic levels and their seasonal fluctuations, surface slope and drainage effects in a raised bog in the Irish Midlands.
Schaaf, S. van der - \ 1994
In: Univ. Trondheim Vitensk. mus. Rapp. Bot. Ser. 1: Regional variation and conservation of mire ecosystems / Moen, A., Binns, R., - p. 54 - 54.
The sequence of appearance of leghaemoglobin and nitrogenase components I and II in root nodules of Pisum Sativum
Bisseling, T. ; Moen, A.A. ; Bos, R.C. van den; Kammen, A. van - \ 1980
Journal of general microbiology 118 (1980)2. - ISSN 0022-1287 - p. 377 - 381.
|Sequence of appearance of leghaemoglobin and the two nitrogenase components in rot nodules op Pisum sativum as studied by radioimmonoassay
Bisseling, T. ; Bos, R.C. van den; Moen, A.A. ; Hontelez, J.G.J. ; Kammen, A. van - \ 1979
In: Proc. Int. Symp. on Nitrogen Fixation Brighton, G35 (1979)
|Literature study on the potential irrigated acreage in the world : in the framework of the project on population doubling and food supply, of the Free University Amsterdam
Moen, H.J. ; Beek, K.J. - \ 1974
Wageningen : ILRI - 14
bibliografieën - irrigatie - grondvermogen - landevaluatie - bodemgeschiktheid - wereld - bibliographies - irrigation - land capability - land evaluation - soil suitability - world