| 1. |
- Amemiya, Chris T., et al.
(författare)
-
The African coelacanth genome provides insights into tetrapod evolution
- 2013
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 496:7445, s. 311-316
-
Tidskriftsartikel (refereegranskat)abstract
- The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features. Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues show the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution.
|
|
| 2. |
- Brack, Werner, et al.
(författare)
-
Towards the review of the European Union Water Framework Directive : Recommendations for more efficient assessment and management of chemical contamination in European surface water resources
- 2017
-
Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 576, s. 720-737
-
Forskningsöversikt (refereegranskat)abstract
- Water is a vital resource for natural ecosystems and human life, and assuring a high quality of water and protecting it from chemical contamination is a major societal goal in the European Union. The Water Framework Directive (WFD) and its daughter directives are the major body of legislation for the protection and sustainable use of European freshwater resources. The practical implementation of the WFD with regard to chemical pollution has faced some challenges. In support of the upcoming WFD review in 2019 the research project SOLUTIONS and the European monitoring network NORMAN has analyzed these challenges, evaluated the state-of-the-art of the science and suggested possible solutions. We give 10 recommendations to improve monitoring and to strengthen comprehensive prioritization, to foster consistent assessment and to support solution-oriented management of surface waters. The integration of effect-based tools, the application of passive sampling for bioaccumulative chemicals and an integrated strategy for prioritization of contaminants, accounting for knowledge gaps, are seen as important approaches to advance monitoring. Including all relevant chemical contaminants in more holistic chemical status assessment, using effect-based trigger values to address priority mixtures of chemicals, to better consider historical burdens accumulated in sediments and to use models to fill data gaps are recommended for a consistent assessment of contamination. Solution-oriented management should apply a tiered approach in investigative monitoring, to identify toxicity drivers, strengthen consistent legislative frameworks and apply solutions-oriented approaches that explore risk reduction scenarios before and along with risk assessment.
|
|
| 3. |
- Eichbaum, Kathrin, et al.
(författare)
-
In vitro bioassays for detecting dioxin-like activity : Application potentials and limits of detection, a review
- 2014
-
Ingår i: Science of the Total Environment. - Amsterdam : Elsevier. - 0048-9697 .- 1879-1026. ; 487, s. 37-48
-
Tidskriftsartikel (refereegranskat)abstract
- Use of in vitro assays as screening tool to characterize contamination of a variety of environmental matrices has become an increasingly popular and powerful toolbox in the field of environmental toxicology.While bioassays cannot entirely substitute analytical methods such as gas chromatography-mass spectrometry (GC-MS), the increasing improvement of cell lines and standardization of bioassay procedures enhance their utility as bioanalytical pre-screening tests prior to more targeted chemical analytical investigations. Dioxin-receptor-based assays provide a holistic characterization of exposure to dioxin-like compounds (DLCs) by integrating their overall toxic potential, including potentials of unknown DLCs not detectable via e.g. GC-MS. Hence, they provide important additional information with respect to environmental risk assessment of DLCs.This review summarizes different in vitro bioassay applications for detection of DLCs and considers the comparability of bioassay and chemical analytically derived toxicity equivalents (TEQs) of different approaches and various matrices. These range from complex samples such as sediments through single reference to compound mixtures. A summary of bioassay derived detection limits (LODs) showed a number of current bioassays to be equally sensitive as chemical methodologies, but moreover revealed that most of the bioanalytical studies conducted to date did not report their LODs, which represents a limitation with regard to low potency samples.
|
|
| 4. |
- Eichbaum, Kathrin, et al.
(författare)
-
The dioRAMA project : assessment of dioxin-like activity in sediments and fish (Rutilus rutilus) in support of the ecotoxicological characterization of sediments
- 2013
-
Ingår i: Journal of Soils and Sediments. - : Springer. - 1439-0108 .- 1614-7480. ; 13:4, s. 770-774
-
Tidskriftsartikel (refereegranskat)abstract
- Introduction: Given the complex interactions of re-suspension processes and bioavailability of sediment-bound pollutants such as dioxin-like chemicals, there is need for a better integrative understanding of the cause-effect relationship of these pollutants. Currently, the majority of studies investigating potential risks of these chemicals only focus on characterizing sediment extracts via in vitro bioassays, thereby disregarding bioavailability, uptake, metabolism, and elimination rates of these compounds in vivo. To determine to which extent mechanism-specific effects in vitro reflect possible adverse effects in vivo, the research project dioRAMA, involving partnership between the Institute for Environmental Research of RWTH Aachen University and the Department Biochemistry/Ecotoxicology of the German Federal Institute of Hydrology, was established.Methods: Animals from an elevated trophic level-common roach (Rutilus rutilus)-will be exposed to sediments from two major German rivers. Exposure will be performed in a system that enables a concurrent monitoring of environmental parameters. In parallel, in vitro studies will be conducted to determine dioxin-like potentials of sediment and fish extracts from the in vivo exposure experiments using different cell lines with varying endpoints. Moreover, extract fractionation procedures, using the strategy of effect-directed analysis, will enable the detection of specific contaminant groups responsible for the biological activity observed.Conclusion: A closer interconnection between applied ecotoxicological science and regulatory needs will facilitate the improved assessment of dioxin-like compounds in sediment and biota. Consequently, this will enable their application in sediment management programs, which is one of the main goals of the dioRAMA project.
|
|
| 5. |
- Hinger, Gunnar, et al.
(författare)
-
Some heterocyclic aromatic compounds are Ah receptor agonists in the DR-CALUX assay and the EROD assay with RTL-W1 cells
- 2011
-
Ingår i: Environmental Science and Pollution Research. - : Springer. - 0944-1344 .- 1614-7499. ; 18:8, s. 1297-1304
-
Tidskriftsartikel (refereegranskat)abstract
- Purpose Heterocyclic aromatic compounds containing nitrogen, sulfur, or oxygen heteroatoms (NSO-HET) have been detected in air, soil, marine, and freshwater systems. However, only few publications are available investigating NSO-HET using in vitro bioassays. To support better characterization of environmental samples, selected NSO-HET were screened for dioxin-like activity in two bioassays. Methods The present study focuses on the identification and quantification of dioxin-like effects of 12 NSO-HET using the DR-CALUX assay, and the 7-ethoxyresorufin-O-deethylase (EROD) assay with the permanent fish liver cell line RTL-W1. Changes of the total medium compound concentrations during the test procedure due to, e.g., sorption or volatilization were quantified using GC/MS. Results The NSO-HET benzofuran, 2,3-dimethylbenzofuran, dibenzofuran, dibenzothiophen, acridine, xanthene, and carbazole caused a response in the DR-CALUX assay. Only benzofuran and 2,3-dimethylbenzofuran were also positive in the EROD assay. All other compounds were inactive in the EROD assay. Relative potency (REP) values ranged from (2.80 +/- 1.32) center dot 10(-8) to (3.26 A +/- 2.03) A center dot 10(-6) in the DR-CALUX and from (3.26 A +/- 0.91) A center dot 10(-7) to (4.87 A +/- 1.97) A center dot 10(-7) in the EROD assay. Conclusions The REP values were comparable to those of larger polycyclic aromatic hydrocarbons, e.g., fluoranthene and pyrene. Thus, and because of the ubiquitous distribution of heterocyclic aromatic compounds in the environment, the provided data will further facilitate the bioanalytical and analytical characterization of environmental samples towards these toxicants.
|
|
| 6. |
- Hollert, Henner, et al.
(författare)
-
Looking back - Looking forward : A novel multi-time slice weight-of-evidence approach for defining reference conditions to assess the impact of human activities on lake systems
- 2018
-
Ingår i: Science of the Total Environment. - : Elsevier. - 0048-9697 .- 1879-1026. ; 626, s. 1036-1046
-
Tidskriftsartikel (refereegranskat)abstract
- Lake ecosystems are sensitive recorders of environmental changes that provide continuous archives at annual to decadal resolution over thousands of years. The systematic investigation of land use changes and emission of pollutants archived in Holocene lake sediments as well as the reconstruction of contamination, background conditions, and sensitivity of lake systems offer an ideal opportunity to study environmental dynamics and consequences of anthropogenic impact that increasingly pose risks to human well-being. This paper discusses the use of sediment and other lines of evidence in providing a record of historical and current contamination in lake ecosystems. We present a novel approach to investigate impacts from human activities using chemical-analytical, bioanalytical, ecological, paleolimnological, paleoecotoxicological, archeological as well as modeling techniques. This multi-time slice weight-of-evidence (WOE) approach will generate knowledge on conditions prior to anthropogenic influence and provide knowledge to (i) create a better understanding of the effects of anthropogenic disturbances on biodiversity, (ii) assess water quality by using quantitative data on historical pollution and persistence of pollutants archived over thousands of years in sediments, and (iii) define environmental threshold values using modeling methods. This technique may be applied in order to gain insights into reference conditions of surface and ground waters in catchments with a long history of land use and human impact, which is still a major need that is currently not yet addressed within the context of the European Water Framework Directive.
|
|
| 7. |
- Irisarri, Iker, 1984-, et al.
(författare)
-
Phylotranscriptomic consolidation of the jawed vertebrate timetree
- 2017
-
Ingår i: Nature Ecology & Evolution. - : Nature Publishing Group. - 2397-334X. ; 1:9, s. 1370-1378
-
Tidskriftsartikel (refereegranskat)abstract
- Phylogenomics is extremely powerful but introduces new challenges as no agreement exists on ‘standards’ for data selection, curation and tree inference. We use jawed vertebrates (Gnathostomata) as a model to address these issues. Despite considerable efforts in resolving their evolutionary history and macroevolution, few studies have included a full phylogenetic diversity of gnathostomes, and some relationships remain controversial. We tested a new bioinformatic pipeline to assemble large and accu- rate phylogenomic datasets from RNA sequencing and found this phylotranscriptomic approach to be successful and highly cost- effective. Increased sequencing effort up to about 10 Gbp allows more genes to be recovered, but shallower sequencing (1.5 Gbp) is sufficient to obtain thousands of full-length orthologous transcripts. We reconstruct a robust and strongly supported timetree of jawed vertebrates using 7,189 nuclear genes from 100 taxa, including 23 new transcriptomes from previously unsampled key species. Gene jackknifing of genomic data corroborates the robustness of our tree and allows calculating genome-wide divergence times by overcoming gene sampling bias. Mitochondrial genomes prove insufficient to resolve the deepest relationships because of limited signal and among-lineage rate heterogeneity. Our analyses emphasize the importance of large, curated, nuclear datasets to increase the accuracy of phylogenomics and provide a reference framework for the evolutionary history of jawed vertebrates.
|
|
| 8. |
- Koch, Josef, et al.
(författare)
-
Temperature and food quantity effects on the harpacticoid copepod Nitocra spinipes : Combining in vivo bioassays with population modeling
- 2017
-
Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 12:3, s. 1-18
-
Tidskriftsartikel (refereegranskat)abstract
- The harpacticoid copepod Nitocra spinipes has become a popular model species for toxicity testing over the past few decades. However, the combined influence of temperature and food shortage, two climate change-related stressors, has never been assessed in this species. Consequently, effects of three temperatures (15, 20 and 25 degrees C) and six food regimes (between 0 and 5 x 10(5) algal cells/mL) on the life cycle of N. spinipes were examined in this study. Similarly to other copepod species, development times and brood sizes decreased with rising temperatures. Mortality was lowest in the 20 degrees C temperature setup, indicating a close-by temperature optimum for this species. Decreasing food concentrations led to increased development times, higher mortality and a reduction in brood size. A sex ratio shift toward more females per male was observed for increasing temperatures, while no significant relationship with food concentration was found. Temperature and food functions for each endpoint were integrated into an existing individual-based population model for N. spinipes which in the future may serve as an extrapolation tool in environmental risk assessment. The model was able to accurately reproduce the experimental data in subsequent verification simulations. We suggest that temperature, food shortage, and potentially other climate change-related stressors should be considered in environmental risk assessment of chemicals to account for non-optimal exposure conditions that may occur in the field. Furthermore, we advocate combining in vivo bioassays with population modeling as a cost effective higher tier approach to assess such considerations.
|
|
| 9. |
- Otte, Jens, et al.
(författare)
-
Contribution of Priority PAHs and POPs to Ah Receptor-Mediated Activities in Sediment Samples from the RiverElbe Estuary, Germany
- 2013
-
Ingår i: PLOS ONE. - San Francisco, USA : Public Library Service. - 1932-6203. ; 8:10
-
Tidskriftsartikel (refereegranskat)abstract
- 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.
|
|
| 10. |
- Peddinghaus, Sabrina, et al.
(författare)
-
Quantitative assessment of the embryotoxic potential of NSO-heterocyclic compounds using zebrafish (Danio rerio)
- 2012
-
Ingår i: Reproductive Toxicology. - Oxford, United Kingdom : Springer. - 0890-6238 .- 1873-1708. ; 33, s. 224-232
-
Tidskriftsartikel (refereegranskat)abstract
- Heterocyclic aromatic compounds (NSO-HET) have frequently been detected in the environment. Several studies have concluded that NSO-HET pose a threat to organisms in waters, sediments and soils. However, few publications are available assessing the ecotoxicology of NSO-HET. The present study aims toassess the embryo toxicity of heterocycles using Danio rerio. A combination of the Fish Embryo Toxicity Test and analytical quantification should aid to determine the hazard potential. Changes of the total concentrations due to sorption or volatility were quantified by GC/MS. Loss of compounds during the testwas observed primarily for volatile or hydrophobic NSO-HET. The LC50 calculated with nominal concentrations underestimates the toxicity by a factor up to 16 (2 h), demonstrating that a chemical analysis for comparing nominal and measured concentrations is essential for such investigations.
|
|
| 11. |
- Philippe, Herve, et al.
(författare)
-
Acoelomorph flatworms are deuterostomes related to Xenoturbella
- 2011
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 470:7333, s. 255-260
-
Tidskriftsartikel (refereegranskat)abstract
- Xenoturbellida and Acoelomorpha are marine worms with contentious ancestry. Both were originally associated with the flatworms (Platyhelminthes), but molecular data have revised their phylogenetic positions, generally linking Xenoturbellida to the deuterostomes(1,2) and positioning the Acoelomorpha as the most basally branching bilaterian group(s)(3-6). Recent phylogenomic data suggested that Xenoturbellida and Acoelomorpha are sister taxa and together constitute an early branch of Bilateria(7). Here we assemble three independent data sets-mitochondrial genes, a phylogenomic data set of 38,330 amino-acid positions and new microRNA (miRNA) complements-and show that the position of Acoelomorpha is strongly affected by a long-branch attraction (LBA) artefact. When we minimize LBA we find consistent support for a position of both acoelomorphs and Xenoturbella within the deuterostomes. The most likely phylogeny links Xenoturbella and Acoelomorpha in a clade we call Xenacoelomorpha. The Xenacoelomorpha is the sister group of the Ambulacraria (hemichordates and echinoderms). We show that analyses of miRNA complements(8) have been affected by character loss in the acoels and that both groups possess one miRNA and the gene Rsb66 otherwise specific to deuterostomes. In addition, Xenoturbella shares one miRNA with the ambulacrarians, and two with the acoels. This phylogeny makes sense of the shared characteristics of Xenoturbellida and Acoelomorpha, such as ciliary ultrastructure and diffuse nervous system, and implies the loss of various deuterostome characters in the Xenacoelomorpha including coelomic cavities, through gut and gill slits.
|
|
