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.

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    Initial sample extract stock concentration affects in vitro bioassay-based toxicological risk characterization
    Montano, M. ; Loffmann, L. ; Murk, A.J. ; Gutleb, A.C. - \ 2014
    Journal of Soils and Sediments 14 (2014)6. - ISSN 1439-0108 - p. 1200 - 1212.
    effect-directed analysis - suspended particulate matter - persistent organic pollutants - gene-expression calux - dioxin-like compounds - aromatic-hydrocarbons - river sediments - flood events - endocrine disruption - estrogenic activity
    Purpose Bioassays have become an alternative for sediment risk profiling, including potential compliance with sediment quality criteria (SQC). In vitro functional bioassays have evolved through standardization and validation towards a confident toxicological hazard estimate of sediments. Sample preparation is a key aspect for the improvement of bioassays. It is a standard practice to use a high single-stock concentration of extracts to further dilute test concentrations from and carry out the analysis. This study was carried out to demonstrate that high a contaminant load in a sediment extract (>20 g sediment equivalents (SEQ) ml-1) oversaturates solubility in carrier solvents and overloads the clean-up columns, potentially resulting in an under- or overestimation of the quantified dioxin-like toxic potency. Materials and methods Cleaned nonpolar sediment extracts were prepared from samples collected from various locations in Luxembourg. The influence on the quantified toxic potency of the initial stock concentration, sonication assisted dissolution and exposure period in an in vitro bioassay for dioxin-like toxic potency (Bio-TEQ) was evaluated, as well as its impact on the sediment risk characterization according to SQC. Results and discussion Stock sonication before serial dilution strongly reduced the standard variation of the outcomes. Higher initial stock concentrations (>20 g SEQ ml-1 for contaminated sediments) produced significantly lower Bio-TEQs g SEQ-1 compared to those obtained with initial stock concentrations of 2 g SEQ ml-1, probably due to solvent oversaturation. An initial stock concentration of 2 g SEQ ml-1 is low enough to prevent mis-estimation, but 20 or even 200 g SEQ ml-1 might be used when quantification of Bio-TEQ is required. The overload of extract on clean-up columns caused an overestimation of the dioxin-like potency probably due to PAH-induced false-positive responses. Conclusions Higher contaminant load in the initial extracts from sediments affects the reliability of in vitro Bio-TEQ sediment quantification. Advice is given on how to avoid underestimation because of extract oversaturation, avoid overestimation because of overload of clean-up columns and reduce variability by applying sonication in standard testing protocols for risk characterization and quantification of the sample’s toxic potency. Taking into account the new aspects revealed in this study, in addition to important issues for quality control that are already included, the in vitro bioassays based on Bio-TEQs can be applied in a comprehensive monitoring program to determine whether sediments comply with health and safety standards for humans and the environment.
    Compound-specific isotope analysis as a tool to characterize biodegradation of ethylbenzene
    Dorer, C. ; Vogt, C. ; Kleinsteuber, S. ; Stams, A.J.M. ; Richnow, H.H. - \ 2014
    Environmental Science and Technology 48 (2014)16. - ISSN 0013-936X - p. 9122 - 9132.
    sulfate-reducing conditions - aromatic-hydrocarbons - anaerobic degradation - initial reactions - aromatoleum-aromaticum - toluene dioxygenase - benzylsuccinate synthase - intrinsic bioremediation - naphthalene dioxygenase - denitrifying conditions
    This study applied one- and two-dimensional compound-specific isotope analysis (CSIA) for the elements carbon and hydrogen to assess different means of microbial ethylbenzene activation. Cultures incubated under nitrate-reducing conditions showed significant carbon and highly pronounced hydrogen isotope fractionation of comparable magnitudes, leading to nearly identical slopes in dual-isotope plots. The results imply that Georgfuchsia toluolica G5G6 and an enrichment culture dominated by an Azoarcus species activate ethylbenzene by anaerobic hydroxylation catalyzed by ethylbenzene dehydrogenase, similar to Aromatoleum aromaticum EbN1. The isotope enrichment pattern in dual plots from two strictly anaerobic enrichment cultures differed considerably from those for benzylic hydroxylation, indicating an alternative anaerobic activation step, most likely fumarate addition. Large hydrogen fractionation was quantified using a recently developed Rayleigh-based approach considering hydrogen atoms at reactive sites. Data from nine investigated microbial cultures clearly suggest that two-dimensional CSIA in combination with the magnitude of hydrogen isotope fractionation is a valuable tool to distinguish ethylbenzene degradation and may be of practical use for monitoring natural or technological remediation processes at field sites.
    Uptake, translocation and elimination in sediment-rooted macrophytes: A model-supported analysis of whole sediment toxicity test data
    Diepens, N.J. ; Arts, G.H.P. ; Focks, A. ; Koelmans, A.A. - \ 2014
    Environmental Science and Technology 48 (2014)20. - ISSN 0013-936X - p. 12344 - 12353.
    hydrophobic organic-chemicals - polychlorinated-biphenyls - myriophyllum-aquaticum - aromatic-hydrocarbons - translocation - pesticides - plants - fluxes - carbon - bioaccumulation
    Understanding bioaccumulation in sediment-rooted macrophytes is crucial for the development of sediment toxicity tests using macrophytes. Here we explore bioaccumulation in sediment-rooted macrophytes by tracking and modelling chemical flows of chlorpyrifos, linuron, and six PCBs in water-sediment-macrophyte systems. Chemical fluxes across the interfaces between pore water, overlying water, shoots, and roots were modelled using a novel multi-compartment model. The modelling yielded the first mass transfer parameter set reported for bioaccumulation by sediment-rooted macrophytes, with satisfactory narrow confidence limits for more than half of the estimated parameters. Exposure via the water column led to rapid uptake by Elodea canadensis and Myriophyllum spicatum shoots, followed by transport to the roots within 1-3 days, after which tissue concentrations gradually declined. Translocation played an important role in the exchange between shoots and roots. Exposure via spiked sediment led to gradual uptake by the roots, but subsequent transport to the shoots and overlying water remained limited for the chemicals studied. These contrasting patterns show that exposure is sensitive to test set up, chemical properties, and species traits. Although field-concentrations in water and sediment will differ from those in the tests, the model parameters can be assumed applicable for modelling exposure to macrophytes in the field.
    A European perspective on alternatives to animal testing for environmental hazard identification and risk assessment
    Scholz, S. ; Sela, E. ; Blaha, L. ; Braunbeck, T. ; Galay-Burgos, M. ; Garcia-Franco, M. ; Guinea, J. ; Kluver, N. ; Schirmer, K. ; Tanneberger, K. ; Tobor-Kaplon, M. ; Witters, H. ; Belanger, S. ; Benfenati, E. ; Creton, S. ; Cronin, M.T.D. ; Eggen, R.I.L. ; Embry, M. ; Ekman, D. ; Gourmelon, A. ; Halder, M. ; Hardy, B. ; Hartung, T. ; Hubesch, B. ; Jungmann, D. ; Lampi, M.A. ; Lee, L. van; Leonard, M. ; Kuster, E. ; Lillicrap, A. ; Luckenbach, T. ; Murk, A.J. ; Navas, J.M. ; Peijnenburg, W. ; Repetto, G. ; Salinas, E. ; Schuurmann, G. ; Spielmann, H. ; Tollefsen, K.E. ; Walter-Rohde, S. ; Whale, G. ; Wheeler, J.R. ; Winter, M.J. - \ 2013
    Regulatory Toxicology and Pharmacology 67 (2013). - ISSN 0273-2300 - p. 506 - 530.
    zebrafish danio-rerio - plant-protection products - messenger-rna expression - adverse outcome pathways - acute fish toxicity - in-vitro - toxicological concern - disrupting chemicals - aquatic toxicity - aromatic-hydrocarbons
    Tests with vertebrates are an integral part of environmental hazard identification and risk assessment of chemicals, plant protection products, pharmaceuticals, biocides, feed additives and effluents. These tests raise ethical and economic concerns and are considered as inappropriate for assessing all of the substances and effluents that require regulatory testing. Hence, there is a strong demand for replacement, reduction and refinement strategies and methods. However, until now alternative approaches have only rarely been used in regulatory settings. This review provides an overview on current regulations of chemicals and the requirements for animal tests in environmental hazard and risk assessment. It aims to highlight the potential areas for alternative approaches in environmental hazard identification and risk assessment. Perspectives and limitations of alternative approaches to animal tests using vertebrates in environmental toxicology, i.e. mainly fish and amphibians, are discussed. Free access to existing (proprietary) animal test data, availability of validated alternative methods and a practical implementation of conceptual approaches such as the Adverse Outcome Pathways and Integrated Testing Strategies were identified as major requirements towards the successful development and implementation of alternative approaches. Although this article focusses on European regulations, its considerations and conclusions are of global relevance
    Assuring safety without animal testing: the case for the human testis in vitro
    Chapin, R.E. ; Boekelheide, K. ; Cortvrindt, R. ; Duursen, M. van; Gant, T. ; Jegou, B. ; Marczylo, E. ; Pelt, A.M. van; Post, J.N. ; Roelofs, M.J. ; Schlatt, S. ; Teerds, K.J. ; Toppari, J. ; Piersma, A.H. - \ 2013
    Reproductive Toxicology 39 (2013). - ISSN 0890-6238 - p. 63 - 68.
    testicular dysgenesis syndrome - spermatogonial stem-cells - collagen gel matrix - agar-culture-system - leydig-cells - germ-cells - sertoli-cells - invitro differentiation - aromatic-hydrocarbons - 3-dimensional culture
    From 15 to 17 June 2011, a dedicated workshop was held on the subject of in vitro models for mammalian spermatogenesis and their applications in toxicological hazard and risk assessment. The workshop was sponsored by the Dutch ASAT initiative (Assuring Safety without Animal Testing), which aims at promoting innovative approaches toward toxicological hazard and risk assessment on the basis of human and in vitro data, and replacement of animal studies. Participants addressed the state of the art regarding human and animal evidence for compound mediated testicular toxicity, reviewed existing alternative assay models, and brainstormed about future approaches, specifically considering tissue engineering. The workshop recognized the specific complexity of testicular function exemplified by dedicated cell types with distinct functionalities, as well as different cell compartments in terms of microenvironment and extracellular matrix components. This complexity hampers quick results in the realm of alternative models. Nevertheless, progress has been achieved in recent years, and innovative approaches in tissue engineering may open new avenues for mimicking testicular function in vitro. Although feasible, significant investment is deemed essential to be able to bring new ideas into practice in the laboratory. For the advancement of in vitro testicular toxicity testing, one of the most sensitive end points in regulatory reproductive toxicity testing, such an investment is highly desirable.
    The genus Cladosporium
    Bench, K. ; Braun, U. ; Groenewald, J.Z. ; Crous, P.W. - \ 2012
    Studies in Mycology 72 (2012)1. - ISSN 0166-0616 - p. 1 - 401.
    leaf blotch pathogens - allii-cepae - sensu-lato - taxonomic revision - causal organism - lichenicolous fungi - sp-nov - sporotrichum-gougerotii - aromatic-hydrocarbons - molecular diagnostics
    A monographic revision of the hyphomycete genus Cladosporium s. lat. (Cladosporiaceae, Capnodiales) is presented. It includes a detailed historic overview of Cladosporium and allied genera, with notes on their phylogeny, systematics and ecology. True species of Cladosporium s. str. (anamorphs of Davidiella), are characterised by having coronate conidiogenous loci and conidial hila, i.e., with a convex central dome surrounded by a raised periclinal rim. Recognised species are treated and illustrated with line drawings and photomicrographs (light as well as scanning electron microscopy). Species known from culture are described in vivo as well as in vitro on standardised media and under controlled conditions. Details on host range/substrates and the geographic distribution are given based on published accounts, and a re-examination of numerous herbarium specimens. Various keys are provided to support the identification of Cladosporium species in vivo and in vitro. Morphological datasets are supplemented by DNA barcodes (nuclear ribosomal RNA gene operon, including the internal transcribed spacer regions ITS1 and ITS2, the 5.8S nrDNA, as well as partial actin and translation elongation factor 1-a gene sequences) diagnostic for individual species. In total 993 names assigned to Cladosporium s. lat., including Heterosporium (854 in Cladosporium and 139 in Heterosporium), are treated, of which 169 are recognized in Cladosporium s. str. The other taxa are doubtful, insufficiently known or have been excluded from Cladosporium in its current circumscription and re-allocated to other genera by the authors of this monograph or previous authors.
    Effects of mixtures of persistent organic pollutants (POPs) derived from cod liver oil on H295R steroidogenesis
    Montano, M. ; Zimmer, K.E. ; Dahl, E. ; Berge, V. ; Olsaker, I. ; Skaare, J.U. ; Murk, A.J. ; Ropstad, E. ; Verhaegen, S. - \ 2011
    Food and Chemical Toxicology 49 (2011)9. - ISSN 0278-6915 - p. 2328 - 2335.
    brominated flame retardants - polybrominated diphenyl ethers - adrenocortical carcinoma-cells - in-vitro - hormone production - gene-expression - aromatic-hydrocarbons - metabolite p,p'-dde - steroid-secretion - pbde metabolites
    Crude cod liver oil and liver oil supplements are consumed as a source of vitamin A, D and polyunsaturated fatty acids; during winter and early pregnancy. Crude cod liver oil however constitutes a considerable source of persistent organic pollutants (POPs). This paper aimed at characterizing and quantifying the influence of POP mixtures extracted from three different steps in the cod liver oil industrial process on hormone production and the expression of steroidogenesis-related genes in H295R cells. Exposure to extracts from crude cod liver oil and from its industrial waste increased progesterone (P4), cortisol (Con), testosterone (T) and estradiol (E2) production; and among others, the expression of MC2R, CYP11B1 and HSD3B2 genes. Observed effects after exposure to pharmaceutical cod liver oil extract were considerably lower. The type of effects on gene expression and hormone production were similar to those induced by forskolin and PCBs, the latter being the major contaminants within the extracts. Additional research is required to further unveil the mechanisms behind the observed steroidogenic effects and to assess whether the potential risk might outweigh the potential benefits of crude and processed cod liver oil consumption.
    Accumulation of background levels of persistent organochlorine and organobromine pollutants through the soil-earthworm-hedgehog food chain
    Vermeulen, F. ; Covaci, A. ; Havé, H. D'; Brink, N.W. van den; Blust, R. ; Coen, W. De; Bervoets, L. - \ 2010
    Environment International 36 (2010)7. - ISSN 0160-4120 - p. 721 - 727.
    brominated flame retardants - polybrominated diphenyl ethers - pollution exposure assessment - polychlorinated-biphenyls - erinaceus-europaeus - risk-assessment - aromatic-hydrocarbons - organic pollutants - sewage-sludge - hair
    The bioaccumulation of persistent organic pollutants (POPs), such as polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs) and DDT and metabolites, was investigated in the soil–earthworm–hedgehog food chain. Concentrations of selected POPs were measured in soil and earthworms collected in grassland and open woodland and in hair and blood of hedgehogs foraging in two parks containing these habitats. Despite background concentrations in soil (ranging from 1.3 to 9.3 ng/g for DDTs, 2.3 to 6.5 ng/g for PCBs and 0.08 to 0.20 ng/g for PBDEs), biota-soil accumulation factors (BSAFs) indicated that earthworms accumulated POPs (0.48–1.70 for DDTs, 1.09–2.76 for PCBs and 1.99–5.67 for PBDEs) and that animals feeding on earthworms are potentially exposed to higher concentrations of pollutants. BSAFs decreased with increasing soil concentrations for the three groups of compounds, suggesting that steady-state equilibrium was not reached in soil or earthworms. Positive, but low, log-linear relationships were found for DDT (r2 = 0.23, p <0.05 for Brasschaat and r2 = 0.63, p <0.01 for Hoboken) and PCB (r2 = 0.13, p <0.05 for both parks) concentrations between soil and earthworms. In order to relate earthworm to hedgehog POP concentrations, the foraging behavior of each individual was taken into account. The use of hair as a potential biomonitoring tissue in exposure and risk assessment of POPs was evaluated by examining the relationship between PCB and p,p'-DDE levels in hedgehogs' hair and blood. Contaminant profiles were used to gain insight into biotransformation of the studied compounds in each step of the investigated food chain and in the blood of hedgehogs, as well as the consequences thereof for their incorporation in hair. The absence of a discernable relationship between POP concentrations in earthworms and hair is possible due to variation in individual foraging behavior and POP uptake. Our results suggest that POPs in tissues should be measured from an adequate number of individuals per population instead of relying on indirect estimates from levels in soil or prey items.
    Bioassay-derived dioxin equivalent concentrations in gonads and livers of the Atlantic cod females from the Baltic Sea
    Dabrowska, H. ; Murk, A.J. ; Berg, J.H.J. van den - \ 2010
    Ecotoxicology and Environmental Safety 73 (2010)8. - ISSN 0147-6513 - p. 1829 - 1834.
    dibenzo-p-dioxins - in-vitro bioassay - calux bioassay - aromatic-hydrocarbons - dr-calux(r) bioassay - expression calux - active compounds - fish - sediments - biphenyls
    The DR-H4IIE.Luc bioassay is based on the ability of dioxin and dioxin-like contaminants to activate the AhR and its signal transduction pathway, a mechanism through which these contaminants elicit their toxic effects. The bioassay was used to examine the total dioxin-equivalent (TEQ) toxicity in gonads and livers of cod females from the southern Baltic Sea. The bioassay-derived TEQ-luc was measured after 24-h and 48-h exposure periods. Mean concentrations in the 24-h bioassay were 95 and 35 pg TEQ-luc g-1 lipid in gonads and livers, respectively, and 58 and 38 pg TEQ-luc g-1 lipid in the 48-h bioassay, respectively. The 48-h TEQ-luc levels displayed significant relationships with SPCB7 and selected PCB congeners but not with the TEQDLPCB-REP. Levels in gonads approached 10% of the LC50 for developing larvae of other marine fish, yet the impact on survival of the cod during its early life remains to be assessed in a future
    PCBs and the energy cost of migration in the European eel (Anguilla anguilla L.)
    Ginneken, V. van; Palstra, A.P. ; Leonards, P.E.G. ; Nieveen, M. ; Murk, A.J. - \ 2009
    Aquatic Toxicology 92 (2009). - ISSN 0166-445X - p. 213 - 220.
    polychlorinated-biphenyls - aromatic-hydrocarbons - sexual-maturation - silver eels - vitamin-a - exposure - metabolism - 3,3',4,4'-tetrachlorobiphenyl - netherlands - induction
    The effect of polychlorinated biphenyls (PCBs) on the energy consumption of fasting silver European eel (Anguilla anguilla L.) was studied over a 27-day period during which the animals were at rest or were swimming 800 km in Blazka swim tunnels. Three-year-old female hatchery eels (silver stage) between 73 and 80 cm long weighing around 1 kg were dosed intraperitoneally with PCBs at a nominal dosage of 10× the consumption standard as a mixture representative for planar (7 mug PCB126/kg eel), non-planar (5 mg PCB153/kg eel) and metabolizable PCBs (50 mug PCB77/kg eel) found in wild eel, or only with the vehicle (corn oil, 10 ml/kg eel). Four major observations were made: (1) PCB-exposed animals lose less weight compared to their unexposed controls; (2) PCB-concentrations on a lipid basis are 2.8-14 times higher in swimming compared to resting animals; (3) the standard metabolic rate is significantly lower in the PCB-exposed animals than in unexposed controls. In addition, PCB-exposure significantly reduces oxygen consumption during swimming, and starting at 400 km (18 days) this effect increases with time; (4) the relative spleen and liver weight significantly increased in the PCB-swim animals but not in the PCB-rest animals. The swimming animals lost about 75% more weight compared to resting animals and had about 50% lower plasma fat content. Hematocrit, haemoglobin, plasma pH, ion levels (sodium and potassium), and plasma lactate were not affected by PCB-exposure or swimming. Apparently, the current levels of PCBs and other dioxin-like compounds may seriously impair the reproduction of the European eel
    Morphological plasticity in Cladosporium sphaerospermum
    Dugan, F.M. ; Braun, U. ; Groenewald, J.Z. ; Crous, P.W. - \ 2008
    Persoonia 21 (2008). - ISSN 0031-5850 - p. 9 - 16.
    aromatic-hydrocarbons - energy-source - sole carbon
    A morphologically distinct isolate of Cladosporium sphaerospermum from a North American patent collection, referenced as Cladosporium lignicola in the patent, was examined. Generic affinity was confirmed by scanning electron microscopic examination of conidiogenous loci and conidial hila. Species identity as C. sphaerospermum was indicated by DNA sequence data derived from actin and translation elongation factor 1-¿ genes, and the internal transcribed spacer region. The isolate broadens the morphological limits of C. sphaerospermum by production of obclavate, occasionally transversely septate conidia with subrostrate conidiogenous apices (`alternarioid¿ conidia), and by production of conidia larger than those in prior standard descriptions. Type material of C. lignicola was reexamined and compared with the North American fungus, from which it is morphologically distinct. The decision to reduce C. lignicola to synonymy under C. herbarum was confirmed.
    Extraction and bioanalysis of the ecotoxicologically relevant fraction of contaminants in sediments
    Puglisi, E. ; Murk, A.J. ; Berg, J.H.J. van den; Grotenhuis, J.T.C. - \ 2007
    Environmental Toxicology and Chemistry 26 (2007)10. - ISSN 0730-7268 - p. 2122 - 2128.
    in-vitro bioassay - polychlorinated-biphenyls - aromatic-hydrocarbons - organic contaminants - pah bioavailability - beta-cyclodextrin - expression calux - techniques neets - soils - dioxin
    Assessments of the risk connected to the contamination of soils and sediments should rely on a multidisciplinary approach based on both chemical and biological techniques (i.e., the sum of exposure and effects assessment). The dioxin-responsive, chemical-activated luciferase expression (DR-CALUX) bioassay is widely applied for evaluation of the toxicity of sediments after an exhaustive extraction of the contaminants, and results are used for risk assessment purposes. Approaches based on total extraction of contaminants do not take into account the importance of bioavailability and aging processes, thus leading to possible overestimations of risk. In the present work, an approach based on nonexhaustive extraction techniques in combination with an in vitro reporter gene assay was tested on sediment samples contaminated with dioxins, polycyclic aromatic hydrocarbons, polychlorinated biphenyls (PCBs), and other xenobiotics. Tenax and hydroxypropyl-ß-cyclodextrin (HPCD) extractions over time were carried out to determine the bioavailable fractions, whereas the residual fractions were determined by means of a microwave-assisted exhaustive extraction. For both fractions, contaminant concentrations were quantified by gas chromatography¿mass spectrophotometry, and the toxic potency was determined by the DR-CALUX assay. Assessments of bioavailable fractions of PCBs by Tenax and HPCD gave comparable results and showed that after several years of aging, a considerable fraction (38¿70% of the total content for different PCBs) is still available and ecotoxicologically relevant. Coupling of nonexhaustive extraction and bioanalyses leads to a more realistic and, generally, much lower estimated risk for the toxicity of the extracts as compared to commonly adopted exhaustive techniques.
    Bioremediation of BTEX hydrocarbons: Effect of soil inoculation with the toluenegrowing fungus Cladophialophora sp strain T1
    Prenafeta, F.X. ; Ballerstedt, H. ; Gerritse, J. ; Grotenhuis, J.T.C. - \ 2004
    Biodegradation 15 (2004)1. - ISSN 0923-9820 - p. 59 - 65.
    substrate interactions - aromatic-hydrocarbons - p-xylene - degradation - benzene - biodegradation - mineralization - cometabolism - biofilters - chemicals
    The biodegradation of a mixture of benzene, toluene, ethylbenzene, xylene, (BTEX) and methyl-tert-butyl ether (MTBE) was studied in soil microcosms. Soil inoculation with the toluene-metabolising fungusCladophialophora sp. strain T1 was evaluated in sterile and non-sterile soil. Induction of biodegradation capacity following BTEX addition was faster in the soil native microflora than in axenic soil cultures of the fungus. Toluene, ethylbenzenes, and the xylenes were metabolized by the fungus but biodegradation of benzene required the activity of the indigenous soil microorganisms. MTBE was not biodegraded under the tested environmental conditions. Biodegradation profiles were also examined under two pH conditions after a long term exposure to BTEX. At neutral conditions the presence of the fungus had little effect on the intrinsic soil biodegradation capacity. At an acidic pH, however, the activity of the indigenous degraders was inhibited and the presence of Cladophialophora sp. increased significantly the biodegradation rates of toluene and ethylbenzene. Comparison of the BTEX biodegradation rates measured in soil batches combining presence and absence of indigenous degraders and the fungal inoculum indicated that no severe antagonism occurred between the indigenous bacteria and Cladophialophora sp. The presence of the fungal inoculum at the end of the experiments was confirmed by PCR-TGGE analysis of small subunits of 18S rDNA
    Paraconiothyrium, a new genus to accommodate the mycoparasite Coniothyrium minitans, anamorphs of Paraphaeosphaeria, and four new species
    Verkley, G.J.M. ; Silva, M. da; Wicklow, D.T. ; Crous, P.W. - \ 2004
    Studies in Mycology 50 (2004). - ISSN 0166-0616 - p. 323 - 335.
    ribosomal dna-sequences - microsphaeropsis-ochracea - aromatic-hydrocarbons - estuarine sediments - pcr amplification - apple scab - fungi - identification - germination - biocontrol
    Coniothyrium-like coelomycetes are drawing attention as biological control agents, potential bioremediators, and producers of antibiotics. Four genera are currently used to classify such anamorphs, namely, Coniothyrium, Microsphaeropsis, Cyclothyrium, and Cytoplea. The morphological plasticity of these fungi, however, makes it difficult to ascertain their best generic disposition in many cases. A new genus, Paraconiothyrium is here proposed to accommodate four new species, P. estuarinum, P. brasiliense, P. cyclothyrioides, and P. fungicola. Their formal descriptions are based on anamorphic characters as seen in vitro. The teleomorphs of these species are unknown, but maximum parsimony analysis of ITS and partial SSU nrDNA sequences showed that they belong in the Pleosporales and group in a clade including Paraphaeosphaeria s. str., the biocontrol agent Coniothyrium minitans, and the ubiquitous soil fungus Coniothyrium sporulosum. Coniothyrium minitans and C. sporulosum are therefore also combined into the genus Paraconiothyrium. The anamorphs of Paraphaeosphaeria michotii and Paraphaeosphaeria pilleata are regarded representative of Paraconiothyrium, but remain formally unnamed. Paraconiothyrium species are phylogenetically distant from typical members of the other coelomycete genera mentioned above
    Toxicological profiling of sediments with in vitro mechanisms-based bioassays for endocrine disruption
    Houtman, C.J. ; Cenijn, P.H. ; Hamers, T. ; Lamoree, M.H. ; Legler, J. ; Murk, A.J. ; Brouwer, A. - \ 2004
    Environmental Toxicology and Chemistry 23 (2004)1. - ISSN 0730-7268 - p. 32 - 40.
    biotesten - sediment - toxiciteit - hormonen - estuaria - rivieren - nederland - hormoonverstoorders - waterbodems - ecotoxicologie - rijn - maas - bioassays - sediment - toxicity - hormones - estuaries - rivers - netherlands - endocrine disruptors - water bottoms - ecotoxicology - river rhine - river meuse - reporter gene assays - estrogenic activity - aromatic-hydrocarbons - human transthyretin - expression assays - toxic potency - extracts - chemicals - exposure - wildlife
    In vitro bioassays are valuable tools for screening environmental samples for the presence of bioactive (e.g., endocrine-disrupting) compounds. They can be used to direct chemical analysis of active compounds in toxicity identification and evaluation (TIE) approaches. In the present study, five in vitro bioassays were used to profile toxic potencies in sediments, with emphasis on endocrine disruption. Nonpolar total and acid-treated stable extracts of sediments from 15 locations in the Rhine Meuse estuary area in The Netherlands were assessed. Dioxin-like and estrogenic activities (using dioxin-responsive chemical-activated luciferase gene expression [DR-CALUX] and estrogen-responsive chemical-activated luciferase gene expression [ER-CALUX] assays) as well as genotoxicity (UMU test) and nonspecific toxic potency (Vibrio fischeri assay) were observed in sediment extracts. For the first time, to our knowledge, in vitro displacement of thyroid hormone thyroxine (T4) from the thyroid hormone transport protein thransthyretin by sediment extracts was observed, indicating the presence of compounds potentially able to disrupt T4 plasma transport processes. Antiestrogenic activity was also observed in sediment. The present study showed the occurrence of endocrine-disrupting potencies in sediments from the Dutch delta and the suitability of the ER- and DR-CALUX bioassays to direct endocrine-disruption TIE studies.
    Toluene monooxygenase from the fungus Cladosporium sphaerospermum
    Luykx, D.M.A.M. ; Prenafeta-Boldu, F.X. ; Bont, J.A.M. de - \ 2003
    Biochemical and Biophysical Research Communications 312 (2003)2. - ISSN 0006-291X - p. 373 - 379.
    cytochrome-c reductase - cytosolic cytochrome-p450 - aromatic-hydrocarbons - liver microsomes - energy-source - sole carbon - purification - metabolism - hydroxylation - pathway
    Assimilation of toluene by Cladosporium sphaerospermum is initially catalyzed by toluene monooxygenase (TOMO). TOMO activity was induced by adding toluene to a glucose-pregrown culture of C. sphaerospermum. The corresponding microsomal enzyme needed NADPH and O2 to oxidize toluene and glycerol, EDTA, DTT, and PMSF for stabilization. TOMO activity was maximal at 35 °C and pH 7.5 and was inhibited by carbon monoxide, Metyrapone, and cytochrome c. TOMO preferred as substrates also other aromatic hydrocarbons with a short aliphatic side chain. Its reduced carbon monoxide difference spectrum showed a maximum at 451 nm. A substrate-induced Type I spectrum was observed on addition of toluene. These results indicated that TOMO is a cytochrome P450. TOMO and its corresponding reductase were eventually purified by a simultaneous purification revealing apparent molecular masses of 58 and 78 kDa, respectively.
    Recent developments in CANDECOMP/PARAFAC algorithms: a critical review
    Faber, N.M. ; Bro, R. ; Hopke, P.K. - \ 2003
    Chemometrics and Intelligent Laboratory Systems 65 (2003)1. - ISSN 0169-7439 - p. 119 - 137.
    rank annihilation method - alternating trilinear decomposition - least-squares algorithms - parafac factor-analysis - matrix fluorescence-spectra - aromatic-hydrocarbons - liquid-chromatography - multiway calibration - eigenvalue problems - 3-way arrays
    Several recently proposed algorithms for fitting the PARAFAC model are investigated and compared to more established alternatives. Alternating least squares (ALS), direct trilinear decomposition (DTLD), alternating trilinear decomposition (ATLD), self-weighted alternating trilinear decomposition (SWATLD), pseudo alternating least squares (PALS), alternating coupled vectors resolution (ACOVER), alternating slice-wise diagonalization (ASD) and alternating coupled matrices resolution (ACOMAR) are compared on both simulated and real data. For the recent algorithms, only unconstrained three-way models can be fitted. In contrast, for example, ALS allows modeling of higher-order data, as well as incorporating constraints on the parameters and handling of missing data. Nevertheless, for three-way data, the newer algorithms are interesting alternatives. It is found that the ALS estimated models are generally of a better quality than any of the alternatives even when overfactoring the model, but it is also found that ALS is significantly slower. Based on the results (in particular the poor performance of DTLD), it is advised that (a slightly modified) ASD may be a good alternative to ALS when a faster algorithm is desired.
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