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PROVIDER: PRJEB61072 | ENA |
REPOSITORIES: ENA
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Project description:Since the early 1980s, the population of European eels (Anguilla anguilla) has dramatically declined. Nowadays, the European eel is listed on the red list of threatened species (IUCN Red List) and is considered as critically endangered of extinction. Pollution is one of the explanations of the collapse of this species. Among their possible effects, pollutants gradually accumulated in eels during their somatic growth phase (yellow eel stage) would be remobilized during their reproductive migration leading to potential toxic events in gonads. The aim of this study was to investigate the potential effect of pollution on the gonad development of wild female silver eels. Female silver eels from two sites with differing contamination levels were artificially matured. Transcriptomic analyses by means of a 1000 candidate gene cDNA microarray were performed on gonads after 11 weeks of maturation. The results showed that the transcription levels of several genes that were associated to the gonadosomatic index (GSI) were involved in mitotic cell division but also in spermatogenesis. Genes associated to pollution were mainly involved in the mechanisms of protection against oxidative stress, in DNA repair, in the purinergic signaling pathway and in steroidogenesis, suggesting an impairment of gonad development in eels from the polluted site. This was in agreement with the fact that eels from the reference site showed a higher gonad growth in comparison to contaminated fish.
2015-01-01 | GSE64278 | GEO
Project description:This project aims to study the role played by small non-coding RNAs in the response of aquatic organisms to the presence of micropollutants in the environment. MiRNA were purified from Eels (Anguilla anguilla) sampled from two sites along the Gironde aquatic system with contrasted pollution profiles.
2019-04-09 | GSE109689 | GEO
Project description:Ecotoxicogenomic studies face the problem of the lack of gene sequence information available for toxicologically relevant non-model pollution sentinel species. In this sense, next generation sequencing technologies allow obtaining deep de novo sequence information cost-effectively. We have thus employed the platform GS-FLX of Roche technologies, in order to sequence the multitissue transcriptome of a fish species under severe population decline, the European eel (Anguilla anguilla), using normalized cDNA (Evrogen). The European eel could be successfully employed in pollution biomonitoring studies as it is a euryhaline teleost that is quite resistant to chemical exposure. We have completed a one whole plate sequencing-run using the Titanium kit of Roche from which a total of 7.8x105 reads were obtained with a length average of 303.53 bp. Annotated genes, for instance, could be further assessed as biomarkers of exposure to specific chemical compounds in marine, estuarine and river waters. Designed tool will be thus useful, in the study of: a.- the mode of action of chemical compounds in active monitoring studies using caged eels, b.- the physiological processes that are specific to freshwater eels such as the one of sexual development and reproduction, c.- reasons that could explain the disappearance of the species from European waters. In the first context, a caging experiment was performed to measure the putative effects of a paper industry effluent on eel hepatic transcription levels. For this purpose, eels were caged upstream and downstream to the SMURFFIT-KAPPA paper industry in Iurreta (Biscay, Basque Country). Thus, hepatic transcription profiles reflect the stress levels suffered by eels. The experiment contains a time serial sampling: T0 = before sampling; T1 = after 3 days of exposure; T2=after 15 days of exposure. In addition, caged eels were placed in 2 sites, Upstream (Up) and Downstream (Do) of the hotspot. 6 samples were dissected per sampling group (5 groups= ToUP; T1UP; T1Do; T2Up; T2Do), 30 samples in total
2016-07-31 | E-GEOD-53345 | biostudies-arrayexpress
Project description:Ecotoxicogenomic studies face the problem of the lack of gene sequence information available for toxicologically relevant non-model pollution sentinel species. In this sense, next generation sequencing technologies allow obtaining deep de novo sequence information cost-effectively. We have thus employed the platform GS-FLX of Roche technologies, in order to sequence the multitissue transcriptome of a fish species under severe population decline, the European eel (Anguilla anguilla), using normalized cDNA (Evrogen). The European eel could be successfully employed in pollution biomonitoring studies as it is a euryhaline teleost that is quite resistant to chemical exposure. We have completed a one whole plate sequencing-run using the Titanium kit of Roche from which a total of 7.8x105 reads were obtained with a length average of 303.53 bp. Annotated genes, for instance, could be further assessed as biomarkers of exposure to specific chemical compounds in marine, estuarine and river waters. Designed tool will be thus useful, in the study of: a.- the mode of action of chemical compounds in active monitoring studies using caged eels, b.- the physiological processes that are specific to freshwater eels such as the one of sexual development and reproduction, c.- reasons that could explain the disappearance of the species from European waters. In the first context, a caging experiment was performed to measure the putative effects of a paper industry effluent on eel hepatic transcription levels. For this purpose, eels were caged upstream and downstream to the SMURFFIT-KAPPA paper industry in Iurreta (Biscay, Basque Country). Thus, hepatic transcription profiles reflect the stress levels suffered by eels.
2016-07-31 | GSE53345 | GEO
Project description:MiSSEel - MicroRNA Sequencing in Stressed Eels
| PRJNA431726 | ENA
Project description:Many enigmas surround different aspects of freshwater eel biology and life cycle. In the same way different hypothesis about why eels are disappearing from European continental waters have been proposed. One such proposal defends that poor fat accumulation of eels, due to pollution in continental waters, might be stopping eels from reproductive migration to the Sargasso Sea. Thus, habitat deterioration could be blamed for the decline in the catchment potential of the European rivers. In this context, and with the aim to study the mode of action of environmentally relevant chemicals in eels, the multi tissue transcriptome was sequenced (454 Titanium Roche) in order to design a high density custom oligonucleotide microarray (eArray, Agilent). To validate this tool a laboratory experiment was carried to analyze the gene trasncrition profiles related to chemical compounds released from pulp and paper mills; 100 μg/L mercury and 150 μg/L β-sitosterol (only Hg data is presented here). 20 yellow European eel (Anguilla anguilla) elvers (11.7±5.35 g) obtained from a local farm (Acuivas SL, Usurbil, Gipuzkoa) were exposed for 3, 6 and 9 days. Pyrosequencing allowed the design and construction of a 60K microarray platform containing 3923 gene signatures identified through BlastN analysis and 7212 sequences annotated through BlastX coupled to Blast2Go analysis. Additional 226 sequences were incorporated from NCBI databases and 3551 from the information available in EeelBase in 2011. Two probes were generated per sequence and they were spotted twice in the array. Hepatic gene expression profiling of the exposed eels indicated that Hg significantly down-regulated (LIMMA, adj. p<0.005) only gene signatures related to selenoprotein W-1 (SeW), something typically described in mammals exposed to methyl-mercury. Increasing the adj. p value to <0.05, 116 genes were significantly regulated (38 down-regulated and 79 up-regulated). Among them, we found additional selenoproteins such as ROS metabolism related genes; glutathione peroxidases (gpx1 & gpx4b) and thioredoxine which were up-regulated. In addition, complement system genes (C3 & C4b) were also up-regulated. Studying enriched Go pathways (p<0.005) and in relation with lipid homeostasis we observed that the following pathways were enriched after exposure to Hg: fatty acids degradation and metabolism of arachidonic acid, linoleic acid, ether lipids, alpha linolenic acid, and glycerophospholipids. In addition, among the top 10 significantly enriched KEGG pathways, p53 signalling, apoptosis, and MAPK signalling were present, suggesting possible effects on cell cycle regulation. In summary, transcriptome pyrosequencing and subsequently designed microarray provided the molecular tools to successfully study the gene transcription profiles of toxic chemical compounds such as Hg in European eel tissues. In addition to study the molecular modes of action of specific chemical compounds, the developed gene expression microarray will be useful in active monitoring of the quality of freshwater environments using caged sentinel eels. This study was funded by Basque Government (SAIOTEK S-PE09UN32; Consolidated Research Groups IT810-13) and UPV/EHU (UFI 11/37). Technical and human support provided by SGIker (UPV/EHU) is acknowledged. An exposure laboratory experiment was performed in the âUr Biologia eta Experimentazio Zerbitzuaâ (UBEZ) of the University of the Basque Country (UPV/EHU) A total of 84 eels, 20.23 ± 2.84 cm in length, were acclimatized to laboratory conditions for 2 weeks in a 10 L water glass tanks under controlled conditions: 12 h light/dark cycle at 18oC, conductivity 600 μS. During this period animals were fed with commercial flakes. Ammonium, nitrites and nitrates kits (Sera GmbH) were used to systematically asses the levels of nitrogenous compounds which were maintained at 0-0.5mg/l; 0-0.5 mg/l, and 5-10 mg/l, respectively. When highest concentrations within those ranges were achieved seawater was partially replaced. A day before exposure experiment, animals were placed in 4 aquaria with 8 L of water at 600 μS. In each aquarium 21 eels were randomly distributed and exposed to: metal-mercury (Hg) (Fluka-Sigma-Aldrich) at a concentration of 100μg/L; and to a phitosterol, β-sitosterol (Sigma) at a concentration of 150 μg/ L. The last compound needed ethanol (0.01%) as vehicle. In addition to an ethanol control group, a water control (600μS) without contaminant was also prepared. Water used during the experiment was filtered at 0.5mm and treated with UV light. Toxic metabolites were measured everyday during experiment using ammonium, nitrites and nitrates test (Sera GmbH), and water was partially replaced every day. Eels were fed everyday with 10mg of commercial food per eel. After 3, 6 and 9 days exposure (T1, T2 and T3 respectively) 7 eels were anaesthetized with 3-aminobenzoate methylsulfonate salt (Sigma-Aldrich). Size and weight were measured for Fulton´s conditioning index assessments, and liver was dissected and frozen with RNA later® in liquid nitrogen for molecular studies.
2016-07-31 | E-GEOD-53344 | biostudies-arrayexpress
Project description:Many enigmas surround different aspects of freshwater eel biology and life cycle. In the same way different hypothesis about why eels are disappearing from European continental waters have been proposed. One such proposal defends that poor fat accumulation of eels, due to pollution in continental waters, might be stopping eels from reproductive migration to the Sargasso Sea. Thus, habitat deterioration could be blamed for the decline in the catchment potential of the European rivers. In this context, and with the aim to study the mode of action of environmentally relevant chemicals in eels, the multi tissue transcriptome was sequenced (454 Titanium Roche) in order to design a high density custom oligonucleotide microarray (eArray, Agilent). To validate this tool a laboratory experiment was carried to analyze the gene trasncrition profiles related to chemical compounds released from pulp and paper mills; 100 μg/L mercury and 150 μg/L β-sitosterol (only Hg data is presented here). 20 yellow European eel (Anguilla anguilla) elvers (11.7±5.35 g) obtained from a local farm (Acuivas SL, Usurbil, Gipuzkoa) were exposed for 3, 6 and 9 days. Pyrosequencing allowed the design and construction of a 60K microarray platform containing 3923 gene signatures identified through BlastN analysis and 7212 sequences annotated through BlastX coupled to Blast2Go analysis. Additional 226 sequences were incorporated from NCBI databases and 3551 from the information available in EeelBase in 2011. Two probes were generated per sequence and they were spotted twice in the array. Hepatic gene expression profiling of the exposed eels indicated that Hg significantly down-regulated (LIMMA, adj. p<0.005) only gene signatures related to selenoprotein W-1 (SeW), something typically described in mammals exposed to methyl-mercury. Increasing the adj. p value to <0.05, 116 genes were significantly regulated (38 down-regulated and 79 up-regulated). Among them, we found additional selenoproteins such as ROS metabolism related genes; glutathione peroxidases (gpx1 & gpx4b) and thioredoxine which were up-regulated. In addition, complement system genes (C3 & C4b) were also up-regulated. Studying enriched Go pathways (p<0.005) and in relation with lipid homeostasis we observed that the following pathways were enriched after exposure to Hg: fatty acids degradation and metabolism of arachidonic acid, linoleic acid, ether lipids, alpha linolenic acid, and glycerophospholipids. In addition, among the top 10 significantly enriched KEGG pathways, p53 signalling, apoptosis, and MAPK signalling were present, suggesting possible effects on cell cycle regulation. In summary, transcriptome pyrosequencing and subsequently designed microarray provided the molecular tools to successfully study the gene transcription profiles of toxic chemical compounds such as Hg in European eel tissues. In addition to study the molecular modes of action of specific chemical compounds, the developed gene expression microarray will be useful in active monitoring of the quality of freshwater environments using caged sentinel eels. This study was funded by Basque Government (SAIOTEK S-PE09UN32; Consolidated Research Groups IT810-13) and UPV/EHU (UFI 11/37). Technical and human support provided by SGIker (UPV/EHU) is acknowledged.
2016-07-31 | GSE53344 | GEO
Project description:Nanometric revolution is underway, promising technical innovations in a wide range of applications, leading to a potential boost in environmental discharges. Nanoparticle propensity to be transferred throughout trophic chains and to generate toxicity was mainly assessed in primary consumers while a lack of knowledge for higher trophic levels persists. This study focused on a predatory fish, the European eel Anguilla anguilla exposed to gold nanoparticles (AuNP, 10 nm, PEG-coated) for 21 days at three concentration levels in food: 0 (NP0), 1 (NP1) and 10 (NP10) mg Au.kg-1 . Transfer was assessed by gold quantification in eel tissues and transcriptomic responses in the liver and brain were revealed by a high-throughput RNA-sequencing approach. Eels fed at NP10 presented an erratic feeding behaviour while gold quantification only indicated transfer to intestine and kidney of NP1 exposed eels. RNA-Sequencing was performed in NP0 and NP1 eels. A total of 258 genes and 156 genes were significantly differentially transcribed in response to AuNP trophic exposure in the liver and brain, respectively. Enrichment analysis highlighted modifications in the immune system-related processes in the liver. In addition, results pointed out a shared response of both organs regarding 13 genes, most of them being involved in immune functions. This finding may shed light into the mode of action and toxicity of AuNP in fish.
2019-09-01 | GSE110011 | GEO
Project description:No studies systematically compared time-resolved and multi-tissue innate immune responses for European eels (Anguilla anguilla) with Aeromonas hydrophila infection through a high throughput method. Here, we challenged European eels with A. hydrophila (infected) or PBS (control). A low fatality rate (16.1%) was observed for infected group at 2 days post-infection (dpi). Then we examined transcriptional profiles of intestines, livers and spleens from 12 European eels with/without the infection of A. hydrophila at 6, 18 and 36 hours post-infection (hpi). The results showed that the most differentially expressed genes (DEGs) were found in the spleens at 6 hpi (7569 DEGs), followed by the intestines at 6 hpi (3129 DEGs) and the livers at 18 hpi (2722 DEGs). Only a few DEGs were found in three tissues at 36 hpi. The comparisons for DEGs numbers and KEGG enrichments suggested a consistent time-course immune responses among these three tissues. A similar enrichment of PRRs-related pathways including TLRs, NLRs and RLRs was revealed in the livers and spleens, but not in the intestines. Among immune-related DEGs, 62 paralogues pairs were found, and the expression trends of most paralogues pairs were consistent. Some paralogues of immune-related DEGs had unique domains. Furthermore, a larger clusters representing the similar tissue were revealed for the intestines and spleens. The distinct cytokine signal transduction and interaction existed between the livers and spleens. Altogether, the present study provides time-resolved and multi-tissue transcriptome characteristics of A. anguilla in response to A. hydrophila infection.
2024-11-01 | GSE188550 | GEO
Project description:Our main objectives were: 1) to test whether the caudal fin may be used to detect the effects of pollutant exposure by means of DNA microarray; 2) to test whether the fin may be used to detect the effects of pollutants in wild contaminated fish; 3) to investigate the mechanisms of toxicity for Cd metal. Detecting and unraveling specific effects of contaminants in a multi-stress field context remain a major challenge in ecotoxicology. The aim of this study was to apply a previously developed DNA microarray comprising 1000 candidate genes on caudal fin clips in order to assess the usefulness of a non-invasive method in ecotoxicogenomic studies in the European eel. Fin gene expression patterns of eels exposed in laboratory to Cd or a PCBs mixture were compared to test whether fin clips may be used to detect effects of these contaminants. Then, gene transcription profiles of wild fish from 3 sampling sites with differing contamination levels were compared to experimental exposures to test whether fin could detect and unravel the in situ effects of these contaminants. Also, transcriptomic profiles from liver and caudal fin of eels experimentally exposed to Cd were compared to test whether fins may be used to investigate the toxicity mechanisms of this metal. Our results showed distinct fin transcription profiles in response to Cd or PCBs exposure. In addition, the transcription profiles of eels from the most contaminated site clustered with the laboratory-exposed fish. Finally, gene transcription patterns from caudal fin and liver in Cd-exposed eels showed significant differences between the two organs and only 16 common genes were identified. Many of these genes were found to be involved in tissue development and in epigenetic mechanisms. This study thus demonstrates the applicability and usefulness of performing gene transcription assays on non-invasive tissue sampling in order to assess the effect of Cd and PCBs on the transcriptome of fish.
2014-12-01 | GSE62954 | GEO