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  • 1
    Language: German
    In: Risiko-Manager, 2012, pp. 12-15
    ISSN: 18619363
    Source: Deutsche Zentralbibliothek für Wirtschaftswissenschaften
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  • 2
    Language: English
    In: PLoS ONE, 2014, Vol. 9(9)
    Description: Purpose: Recently, a proof-of-concept study revealed the suitability of transcriptome analyses to obtain and assess changes in the abundance of transcripts in zebrafish (Danio rerio) embryos after exposure to organic sediment extracts. The present study investigated changes in the transcript abundance in zebrafish embryos exposed to whole sediment samples and corresponding organic extracts in order to identify the impact of different exposure pathways on sediment toxicity.Materials and Methods: Danio rerio embryos were exposed to sublethal concentrations of three sediment samples from the Danube River, Germany. The sediment samples were investigated both as freeze-dried samples and as organic extracts. Silica dust and a process control of the extraction procedure were used as references. After exposure, mRNA was isolated and changes in profiles of gene expression levels were examined by an oligonucleotide microarray. The microarray results were compared with bioassays, chemical analysis of the sediments and profiles of gene expression levels induced by several single substances.Results and Discussion: The microarray approach elucidated significant changes in the abundance of transcripts in exposed zebrafish embryos compared to the references. Generally, results could be related to Ah-receptor-mediated effects asconfirmed by bioassays and chemical analysis of dioxin-like contaminants, as well as to exposure to stress-inducing compounds. Furthermore, the results indicated that mixtures of chemicals, as present in sediment and extract samples, result in complex changes of gene expression level profiles difficult to compare with profiles induced by single chemical substances. Specifically, patterns of transcript abundances were less influenced by the chemical composition at the sampling site compared t the method of exposure (sediment/extract). This effect might be related to different bioavailability of chemicals.Conclusions: The apparent difference between the exposure scenarios is an important aspect that needs to be addressed when conducting analyses of alterations in the expression level of mRNA.
    Keywords: Natural Sciences ; Earth And Related Environmental Sciences ; Environmental Sciences ; Naturvetenskap ; Geovetenskap Och Miljövetenskap ; Miljövetenskap ; Enviromental Science ; Miljövetenskap
    ISSN: 1932-6203
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  • 3
  • 4
    Language: English
    In: PLoS ONE, 01 January 2014, Vol.9(2), p.e90036
    Description: Automated analysis of multi-dimensional microscopy images has become an integral part of modern research in life science. Most available algorithms that provide sufficient segmentation quality, however, are infeasible for a large amount of data due to their high complexity. In this contribution we present a fast parallelized segmentation method that is especially suited for the extraction of stained nuclei from microscopy images, e.g., of developing zebrafish embryos. The idea is to transform the input image based on gradient and normal directions in the proximity of detected seed points such that it can be handled by straightforward global thresholding like Otsu's method. We evaluate the quality of the obtained segmentation results on a set of real and simulated benchmark images in 2D and 3D and show the algorithm's superior performance compared to other state-of-the-art algorithms. We achieve an up to ten-fold decrease in processing times, allowing us to process large data sets while still providing reasonable segmentation results.
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 5
    Language: English
    In: Environmental Science and Pollution Research, 2015, Vol.22(21), pp.16247-16261
    Description: Originally designed as an alternative for the acute fish toxicity test according to, e.g., OECD TG 203, the fish embryo test (FET) with the zebrafish ( Danio rerio ) has been optimized, standardized, and validated during an OECD validation study and adopted as OECD TG 236 as a test to assess toxicity of embryonic forms of fish. Given its excellent correlation with the acute fish toxicity test and the fact that non-feeding developmental stages of fish are not categorized as protected stages according to the new European Directive 2010/63/EU on the protection of animals used for scientific purposes, the FET is ready for use not only for range-finding but also as a true alternative for the acute fish toxicity test, as required for a multitude of national and international regulations. If—for ethical reasons—not accepted as a full alternative, the FET represents at least a refinement in the sense of the 3Rs principle. Objections to the use of the FET have mainly been based on the putative lack of biotransformation capacity and the assumption that highly lipophilic and/or high molecular weight substances might not have access to the embryo due to the protective role of the chorion. With respect to bioactivation, the only substance identified so far as not being activated in the zebrafish embryo is allyl alcohol; all other biotransformation processes that have been studied in more detail so far were found to be present, albeit, in some cases, at lower levels than in adult fish. With respect to larger molecules, the extension of the test duration to 96 h (i.e., beyond hatch) has—at least for the substances tested so far—compensated for the reduced access to the embryo; however, more research is necessary to fully explore the applicability of the FET to substances with a molecular weight 〉3 kDa as well as substances with a neurotoxic mode of action. An extension of the endpoints to also cover sublethal endpoints makes the FET a powerful tool for the detection of teratogenicity, dioxin-like activity, genotoxicity and mutagenicity, neurotoxicity, as well as various forms of endocrine disruption.
    Keywords: Fish embryo test ; FET ; Validation ; Alternative test method ; OECD guideline ; Acute toxicity ; Teratogenicity ; Genotoxicity ; Endocrine disruption ; Neurotoxicity ; Biotransformation ; Cytochrome P450
    ISSN: 0944-1344
    E-ISSN: 1614-7499
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  • 6
    Language: English
    In: PLoS ONE, Sept 4, 2014, Vol.9(9)
    Description: Purpose Recently, a proof-of-concept study revealed the suitability of transcriptome analyses to obtain and assess changes in the abundance of transcripts in zebrafish (Danio rerio) embryos after exposure to organic sediment extracts. The present study investigated changes in the transcript abundance in zebrafish embryos exposed to whole sediment samples and corresponding organic extracts in order to identify the impact of different exposure pathways on sediment toxicity. Materials and Methods Danio rerio embryos were exposed to sublethal concentrations of three sediment samples from the Danube River, Germany. The sediment samples were investigated both as freeze-dried samples and as organic extracts. Silica dust and a process control of the extraction procedure were used as references. After exposure, mRNA was isolated and changes in profiles of gene expression levels were examined by an oligonucleotide microarray. The microarray results were compared with bioassays, chemical analysis of the sediments and profiles of gene expression levels induced by several single substances. Results and Discussion The microarray approach elucidated significant changes in the abundance of transcripts in exposed zebrafish embryos compared to the references. Generally, results could be related to Ah-receptor-mediated effects as confirmed by bioassays and chemical analysis of dioxin-like contaminants, as well as to exposure to stress-inducing compounds. Furthermore, the results indicated that mixtures of chemicals, as present in sediment and extract samples, result in complex changes of gene expression level profiles difficult to compare with profiles induced by single chemical substances. Specifically, patterns of transcript abundances were less influenced by the chemical composition at the sampling site compared t the method of exposure (sediment/extract). This effect might be related to different bioavailability of chemicals. Conclusions The apparent difference between the exposure scenarios is an important aspect that needs to be addressed when conducting analyses of alterations in the expression level of mRNA.
    Keywords: Dioxins – Analysis ; Dioxins – Investigations ; Embryonic Development – Analysis ; Embryonic Development – Investigations ; RNA – Analysis ; RNA – Investigations ; Gene Expression – Analysis ; Gene Expression – Investigations ; Sediments (Geology) – Analysis ; Sediments (Geology) – Investigations
    ISSN: 1932-6203
    Source: Cengage Learning, Inc.
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  • 7
    Language: English
    In: PLoS ONE, 2013, Vol. 8(10)
    Description: The estuary of the River Elbe between Hamburg and the North Sea (Germany) is a sink for contaminated sediment and suspended particulate matter (SPM). One major concern is the effect of human activities on the hydrodynamics, particularlythe intensive dredging activities in this area that may result in remobilization of sediment-bound pollutants. The aim of this study was to identify pollutants contributing to the toxicological risk associated with re-suspension of sediments in the Elbe Estuary by use of an effect-directed analysis that combines chemical and biological analyses in with specific fractionation techniques. Sediments were collected from sites along the Elbe Estuary and a site from a small harbor basin of the Elbe Estuary that is known to be polluted. The sixteen priority EPA-PAHs were quantified in organic extracts of sediments. In addition, dioxin equivalents of sediments were investigated by use of the 7-ethoxyresorufin O-deethylase assay with RTL-W1 cells and the Ah receptor-mediated luciferase transactivation assay with H4IIE-luc cells. Quantification of the 16 priorityPAHs revealed that sediments were moderately contaminated at all of the sites in the Elbe River Estuary (,0.02–0.906 mg/gdw). Sediments contained relatively small concentrations of dioxin equivalents (Bio-TEQ) with concentrations ranging from15.5 to 322 pg/g dw, which were significantly correlated with dioxin equivalents calculated based on toxicity referencevalues and concentrations of PAH. The concentration of Bio-TEQ at the reference site exceeded 200,000 pg/g dw. In apotency balance the 16 PAHs explained between 47 and 118% of the Bio-TEQ in the luciferase assay, which can be explained by the constant input of PAHs bound to SPM from the upper course of the Elbe River into its estuary. Successful identification of a significant portion of dioxin-like activity to priority PAHs in complex environmental samples such assediments has rarely been reported.
    Keywords: Natural Sciences ; Earth And Related Environmental Sciences ; Environmental Sciences ; Naturvetenskap ; Geovetenskap Och Miljövetenskap ; Miljövetenskap ; Enviromental Science ; Miljövetenskap
    ISSN: 1932-6203
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  • 8
  • 9
    Language: English
    In: Environmental Science and Pollution Research, 2015, Vol.22(21), pp.16384-16392
    Description: Transcriptomics is often used to investigate changes in an organism’s genetic response to environmental contamination. Data noise can mask the effects of contaminants making it difficult to detect responding genes. Because the number of genes which are found differentially expressed in transcriptome data is often very large, algorithms are needed to reduce the number down to a few robust discriminative genes. We present an algorithm for aggregated analysis of transcriptome data which uses multiple fold-change thresholds (threshold screening) and p values from Bayesian generalized linear model in order to assess the robustness of a gene as a potential indicator for the treatments tested. The algorithm provides a robustness indicator (ROBI) as well as a significance profile, which can be used to assess the statistical significance of a given gene for different fold-change thresholds. Using ROBI, eight discriminative genes were identified from an exemplary dataset ( Danio rerio FET treated with chlorpyrifos, methylmercury, and PCB) which could be potential indicators for a given substance. Significance profiles uncovered genetic effects and revealed appropriate fold-change thresholds for single genes or gene clusters. Fold-change threshold screening is a powerful tool for dimensionality reduction and feature selection in transcriptome data, as it effectively reduces the number of detected genes suitable for environmental monitoring. In addition, it is able to unmask patterns in altered genetic expression hidden by data noise and reduces the chance of type II errors, e.g., in environmental screening.
    Keywords: Bioinformatics ; Masked effects ; Danio rerio ; Aggregated analysis ; Ecotoxicogenomics ; Robustness indicator (ROBI) ; Bayesian generalized linear model
    ISSN: 0944-1344
    E-ISSN: 1614-7499
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  • 10
    Language: English
    In: Environmental Science and Pollution Research, 2012, Vol.19(2), pp.403-415
    Description: Byline: Bernhard Wetterauer (1), Mathias Ricking (3), Jens C. Otte (1,2), Arnold V. Hallare (6,7), Andrew Rastall (4), Lothar Erdinger (4), Jan Schwarzbauer (5), Thomas Braunbeck (1), Henner Hollert (1,6) Keywords: Cytotoxicity; DDA; DDCN; DDMS; DDT metabolites; DDMU; Dioxin-like activity; Dot blot/RNAse protection-assay; EROD; Estrogenic activity; Yeast estrogen screen Abstract: Background, aim, and scope 2,2-bis(chlorophenyl)-1,1,1-trichloroethane (DDT) metabolites, other than those routinely measured [i.e., 2,2-bis(chlorophenyl)-1,1-dichloroethylene (DDE) and 2,2-bis(chlorophenyl)-1,1-dichloroethane (DDD)], have recently been detected in elevated concentrations not only in the surface water of Teltow Canal, Berlin, but also in sediment samples from Elbe tributaries (e.g., Mulde and Havel/Spree). This was paralleled by recent reports that multiple other metabolites could emerge from the degradation of parent DDT by naturally occurring organisms or by interaction with some heavy metals. Nevertheless, only very few data on the biological activities of these metabolites are available to date. The objective of this communication is to evaluate, for the first time, the cytotoxicity, dioxin-like activity, and estrogenicity of the least-studied DDT metabolites. Methods Four DDT metabolites, p,p -2,2-bis(chlorophenyl)-1-chloroethylene (DDMU), p,p -2,2-bis(chlorophenyl)-1-chloroethane (DDMS), p,p -2,2-bis(4-ch1oropheny1)acetonitrile (DDCN), and p,p -2,2-bis(chlorophenyl)acetic acid (DDA), were selected based on their presence in environmental samples in Germany such as in sediments from the Mulde River and Teltow Canal. O,p -DDT was used as reference in all assays. Cytotoxicity was measured by neutral red retention with the permanent cell line RTG-2 of rainbow trout (Oncorhynchus mykiss). Dioxin-like activity was determined using the 7-ethoxyresorufin-O-deetylase assay. The estrogenic potential was tested in a dot blot/RNAse protection-assay with primary hepatocytes from male rainbow trout (O. mykiss) and in a yeast estrogen screen (YES) assay. Results All DDT metabolites tested revealed a clear dose--response relationship for cytotoxicity in RTG-2 cells, but no dioxin-like activities with RTL-W1 cells. The dot blot/RNAse protection-assay demonstrated that the highest non-toxic concentrations of these DDT metabolites (50 uM) had vitellogenin-induction potentials comparable to the positive control (1 nM 17[beta]-estradiol). The estrogenic activities could be ranked as o,p -DDT 〉 p,p -DDMS 〉 p,p -DDMU 〉 p,p -DDCN. In contrast, p,p -DDA showed a moderate anti-estrogenic effect. In the YES assay, besides the reference o,p -DDT, p,p -DDMS and p,p -DDMU displayed dose-dependent estrogenic potentials, whereas p,p -DDCN and p,p -DDA did not show any estrogenic potential. Discussion The reference toxicant o,p -DDT displayed a similar spectrum of estrogenic activities similar to 17[beta]-estradiol, however, with a lower potency. Both p,p -DDMS and p,p -DDMU were also shown to have dose-dependent estrogenic potentials, which were much lower than the reference o,p -DDT, in both the vitellogenin and YES bioassays. Interestingly, p,p -DDA did not show estrogenic activity but rather displayed a tendency towards anti-estrogenic activity by inhibiting the estrogenic effect of 17[beta]-estradiol. The results also showed that the p,p -metabolites DDMU, DDMS, DDCN, and DDA do not show any dioxin-like activities in RTL-W1 cells, thus resembling the major DDT metabolites DDD and DDE. Conclusions All the DDT metabolites tested did not exhibit dioxin-like activities in RTL-W1 cells, but show cytotoxic and estrogenic activities. Based on the results of the in vitro assays used in our study and on the reported concentrations of DDT metabolites in contaminated sediments, such substances could, in the future, pose interference with the normal reproductive and endocrine functions in various organisms exposed to these chemicals. Consequently, there is an urgent need to examine more comprehensively the risk of environmental concentrations of the investigated DDT metabolites using in vivo studies. However, this should be paralleled also by periodic evaluation and monitoring of the current levels of the DDT metabolites in environmental matrices. Recommendations and perspectives Our results clearly point out the need to integrate the potential ecotoxicological risks associated with the "neglected" p,p -DDT metabolites. For instance, these DDT metabolites should be integrated into sediment risk assessment initiatives in contaminated areas. One major challenge would be the identification of baseline data for such risk assessment. Further studies are also warranted to determine possible additive, synergistic, or antagonistic effects that may interfere with the fundamental cytotoxicity and endocrine activities of these metabolites. For a more conclusive assessment of the spectrum of DDT metabolites, additional bioassays are needed to identify potential anti-estrogenic, androgenic, and/or anti-androgenic effects. Author Affiliation: (1) Aquatic Ecology and Toxicology, COS-Center for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany (2) Karlsruhe Institute of Technology, Institute of Toxicology and Genetics, Forschungszentrum Karlsruhe, P.O. Box 3640, 76021, Karlsruhe, Germany (3) Department of Earth Sciences, Free University of Berlin, Malteserstr. 74-100, 12249, Berlin, Germany (4) Hygiene and Medical Microbiology, Department of Hygiene, University of Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany (5) Institute of Geology and Geochemistry of Petroleum and Coal, RWTH Aachen University, Lochnerstr. 4-20, 52056, Aachen, Germany (6) Department of Ecosystem Analysis, Institute for Environmental Research (Biology V), RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany (7) Department of Biology, CAS, University of the Philippines, Padre Faura, Manila, Philippines Article History: Registration Date: 11/07/2011 Received Date: 11/01/2010 Accepted Date: 26/05/2011 Online Date: 27/07/2011 Article note: Responsible editor: Markus Hecker
    Keywords: Cytotoxicity ; DDA ; DDCN ; DDMS ; DDT metabolites ; DDMU ; Dioxin-like activity ; Dot blot/RNAse protection-assay ; EROD ; Estrogenic activity ; Yeast estrogen screen
    ISSN: 0944-1344
    E-ISSN: 1614-7499
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