| 1. |
|
|
| 2. |
- Bluhm, Kerstin, et al.
(författare)
-
Impacts of Different Exposure Scenarios on Transcript Abundances in Danio rerio Embryos when Investigating the Toxicological Burden of Riverine Sediments
- 2014
-
Ingår i: PLOS ONE. - San francisco, USA : Public Library of Science. - 1932-6203. ; 9:9
-
Tidskriftsartikel (refereegranskat)abstract
- 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.
|
|
| 3. |
- Hausen, Jonas, et al.
(författare)
-
Fishing for contaminants : identification of three mechanism specific transcriptome signatures using Danio rerio embryos
- 2018
-
Ingår i: Environmental Science and Pollution Research. - : Springer. - 0944-1344 .- 1614-7499. ; 25:5, s. 4023-4036
-
Tidskriftsartikel (refereegranskat)abstract
- In ecotoxicology, transcriptomics is an effective way to detect gene expression changes in response to environmental pollutants. Such changes can be used to identify contaminants or contaminant classes and can be applied as early warning signals for pollution. To do so, it is important to distinguish contaminant-specific transcriptomic changes from genetic alterations due to general stress. Here we present a first step in the identification of contaminant class-specific transcriptome signatures. Embryos of zebrafish (Danio rerio) were exposed to three substances (methylmercury, chlorpyrifos and Aroclor 1254, each from 24 to 48 hpf exposed) representing sediment typical contaminant classes. We analyzed the altered transcriptome to detect discriminative genes significantly regulated in reaction to the three applied contaminants. By comparison of the results of the three contaminants, we identified transcriptome signatures and biologically important pathways (using Cytoscape/ClueGO software) that react significantly to the contaminant classes. This approach increases the chance of finding genes that play an important role in contaminant class-specific pathways rather than more general processes.
|
|
| 4. |
- Hausen, Jonas, et al.
(författare)
-
Fold-change threshold screening : a robust algorithm to unmask hidden gene expression patterns in noisy aggregated transcriptome data
- 2015
-
Ingår i: Environmental Science and Pollution Research. - : Springer Berlin/Heidelberg. - 0944-1344 .- 1614-7499. ; 22:21, s. 16384-16392
-
Tidskriftsartikel (refereegranskat)abstract
- 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.
|
|
| 5. |
- Hollert, Henner, et al.
(författare)
-
Eine Weight-of-Evidence-Studie zur Bewertung der Sedimentbelastung und des Fischrückgangs in der Oberen Donau [Assessing sediments and fish health using a weight-of-evidence approach : in search for the causes of fish decline in the Danube river]
- 2009
-
Ingår i: Umweltwissenschaften und Schadstoff-Forschung. - Berlin : Springer. - 0934-3504 .- 1865-5084. ; 21:3, s. 260-263
-
Tidskriftsartikel (refereegranskat)abstract
- Background and aim Despite intensive and continuous stocking and improvement of water quality since the 1970s, fish populations, especially those of the grayling (Thymallus thymallus), have declined over the last two decades in the upper Danube River (Germany). In order to assess 1) possible links between molecular/biochemical responses and ecologically relevant effects, and 2) if ecotoxicological effects might be related to the decline in fish catches in the upper Danube river, sediment samples and fish were collected at different locations and analyzed using a weight-of-evidence (WOE) approach with several lines of evidence. The objective of the presentation is to introduce the conceptual framework and to review results of the ongoing study. As previously addressed by Chapman and Hollert (2006) a variety of lines of evidence can be used in WOE studies. Briefly, 1) a comprehensive battery of acute and mechanism-specific bioassays was used to characterize the ecotoxicological hazard potential. 2) Histopathological investigations and the micronucleus assay with erythrocytes were applied, analyzing in situ parameters. 3) Diversity and abundance of benthic macroinvertebrates and fish as well as 4) persistent organic pollutants, endocrine disrupting substances, limnochemical parameters and the concentration of heavy metals were recorded. To identify organic contaminants a spotential causes of sediment toxicity assays, 5) effect directed analysis was applied. © 2009 Springer-Verlag.
|
|
| 6. |
- Keiter, Steffen, 1971-, et al.
(författare)
-
DanTox-a novel joint research project using zebrafish (Danio rerio) to identify specific toxicity and molecular modes of action of sediment-bound pollutants
- 2010
-
Ingår i: Journal of Soils and Sediments. - Heidelberg, Germany : Springer. - 1439-0108 .- 1614-7480. ; 10:4, s. 714-717
-
Tidskriftsartikel (refereegranskat)abstract
- Introduction: The European Water Framework Directive aimsto achieve a good ecological and chemical status in surface water of European rivers by the year 2015. Since sediments and particulate matter act as secondary sources for pollutants, applied sediment toxicology is perceived to play a major rolefor obtaining new knowledge that can contribute to successful attainment of the goal. However, the existing bioassays for sediment toxicity analyses do not provide sufficient data concerning bioavailability of environmental pollutants. In this regard, there is an urgent need to combine sediment contact assays with gene expression analysis to investigate mechanism-specific sediment toxicity.Purpose: The aim of the novel joint research project is todevelop a eukaryotic test system, which can be used to investigate the ecotoxicological effects of contaminated sediments on gene expression level (DNA-array and RT-PCR).Current ecotoxicological research customarily involves a battery of bioassays to cover different toxicological endpoints (e.g., teratogenicity, genotoxicity, mutagenicity, Ah-receptor mediated toxicity, neurotoxicity). In contrast, methods that detect alterations in gene expression offer deeper insight by elucidating how chemical exposure and/or environmental challenge affect multiple metabolic pathways leading to these particular kinds of toxic response. Gene expression profiles reflect the way cells and organisms adapt or respond to a changing environment.Conclusion: The present project aspires to increase the fundamental molecular and physiological knowledge concerning the mode of action of environmental toxicants in zebrafish (Danio rerio). By working with partners from the academic and research institutions as well as from industry and waterway regulations, the success of this basic research-driven joint project in terms of development and implementation of novel sediment toxicity methods will be realized.
|
|
| 7. |
- Kosmehl, Thomas, et al.
(författare)
-
A combined DNA-microarray and mechanism-specific toxicity approach with zebrafish embryos to investigate the pollution of river sediments
- 2012
-
Ingår i: Reproductive Toxicology. - Oxford, United Kingdom : Elsevier. - 0890-6238 .- 1873-1708. ; 33:2, s. 245-253
-
Tidskriftsartikel (refereegranskat)abstract
- The zebrafish embryo has repeatedly proved to be a useful model for the analysis of effects by environmental toxicants. This proof-of-concept study was performed to investigate if an approach combining mechanism-specific bioassays with microarray techniques can obtain more in-depth insights into theecotoxicity of complex pollutant mixtures as present, e.g., in sediment extracts. For this end, altered gene expression was compared to data from established bioassays as well as to results from chemical analysis. Mechanism-specific biotests indicated a defined hazard potential of the sediment extracts, and microarray analysis revealed several classes of significantly regulated genes which could be related to the hazard potential. Results indicate that potential classes of contaminants can be assigned to sediment extracts by both classical biomarker genes and corresponding expression profile analyses of known substances. However, it is difficult to distinguish between specific responses and more universal detoxification of the organism.
|
|
| 8. |
|
|
| 9. |
- Olsman [Takner], Helena, et al.
(författare)
-
Relative differences in aryl hydrocarbon receptor-mediated response for 18 polybrominated and mixed halogenated dibenzo-p-dioxins and -furans in cell lines from four different species
- 2007
-
Ingår i: Environmental Toxicology and Chemistry. - 0730-7268 .- 1552-8618. ; 26:11, s. 2448-2454
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- As a consequence of ubiquitous use of brominated organic chemicals, there is a concern for persistent or increasing environmental levels of polybrominated dibenzo-p-dioxins/furans (PBDD/Fs) and mixed polychlorinated and polybrominated dibenzo-p-dioxins/furans (PXDD/Fs). Hence, there is a need to broaden the toxicological and environmental knowledge about these compounds, as a basis for risk assessment. In the study presented here, the relative potencies (REPs) for 18 PBDD/F and PXDD/ F congeners were determined in four dioxin-specific bioassays from different species: dioxin receptor chemically activated luciferase expression assay (DR-CALUX, rat hepatoma cells), TV101L (human hepatoma cells), and GPC.2D (guinea pig adenoma cells), as well as ethoxyresorufin-O-deethylase induction in the fish cell line RTL-W1 (rainbow trout liver cells). The bioassay specific REP factors presented here enable the assessment of the contribution from PBDD/Fs and PXDD/Fs to total 2,3,7,8-tetrachl orodibenzop-dioxin (TCDD) equivalents (TEQs: toxic equivalents), using bioassay analysis. The PBDD/Fs were found to be equally potent as their chlorinated analogues in the three mammalian assays, whereas the PXDD/Fs showed relatively higher potencies. Of special concern were the 2,3,7,8-substituted penta- and tetrahalogenated congeners, for which mean REPs were >= 1. The 2-B-1,3,7,8-CDD (2-bromo-1,3,7,8-tetrachlorodibenzo-p-dioxin) was up to three times more potent than TCDD in individual experiments (on weight basis). The RTL-W1 was less sensitive to the tested compounds with overall 10-fold lower REPs than the mammalian cell lines. Although the REP factors exhibited species-specific differences, overall resembling rank orders of dioxin-like potency were obtained.
|
|
| 10. |
- Otte, Jens C., et al.
(författare)
-
A bioassay approach to determine the dioxin-like activity in sediment extracts from the Danube River : ethoxyresorufin-O-deethylase induction in gill filaments and liver of three-spined sticklebacks (Gasterosteus aculeatus L.)
- 2008
-
Ingår i: Environment International. - Amsterdam : Elsevier. - 0160-4120 .- 1873-6750. ; 34:8, s. 1176-1184
-
Tidskriftsartikel (refereegranskat)abstract
- Sediment samples from the upper Danube River in Germany have previously been characterized as ecotoxicologically hazardous and contaminants in these sediments may contribute to the observed decline of fish populations in this river section. For the investigation of sediment toxicity there is a need for development, standardization and implementation of in vivo test systems using vertebrates. Therefore, the main objective of this study was to apply and evaluate a recently established fish gill EROD assay as a biomarker in sediment toxicity assessment by using extracts of well characterised sediment samples from the upper Danube River. This to our knowledge is the first application of this novel assay to sediment extracts. Sediments from four different sites along the upper Danube River were Soxhlet-extracted with acetone and dissolved in DMSO. Three-spined sticklebacks (Gasterosteus aculeatus L.) were exposed for 48 h to various concentrations of the extracts, to the positive control β-naphthoflavone or to the solvent. Measurements of EROD activity in gill filaments and liver microsomes followed the exposure. Concentration-dependent induction of EROD in both gill and liver was found for all sediment extracts. The highest EROD-inducing potency was determined for extracts of sediments from the sites “Öpfinger See” and “Sigmaringen” and the EROD activities in gill and liver correlated well. The results from the gill and liver assays were in accordance with in vitro results of previous investigations. The EROD activities measured in the present study corresponded with the concentrations of PAHs, PCBs and PCDD/Fs in the sediment samples derived in a previous study. The sticklebacks in this study were in the reproductive phase and a stronger EROD induction was obtained in the females than in the males. Implementation of the EROD assay in testing of sediment extracts gave highly reliable results which make this assay an ecotoxicologically relevant method for assessment of contamination with Ah receptor agonists in sediments.
|
|
