Transcription profiling of juvenile Daphnia manga following exposure to the pesticides methomyl and propanil
Ontology highlight
ABSTRACT:
ORGANISM(S): Daphnia magna
SUBMITTER: Amanda Callaghan Christopher Hill
PROVIDER: E-TABM-793 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Juvenile (<24hr old) Daphnia magna populations (n=250) were exposed (24hr) to Benzoylphenylurea growth inhibitor (14C labeled) lufenuron. Treatments were 0.15 ug/L, 0.33 ug/L, 0.65 ug/L lufenuron solvent control was 100 ul/L acetone carrier . Transcriptomic responses were screened using a D.magna cDNA microarray and the regulation of gene expression via log fold-change in transcript abundance, assessed. Genes involved in the synthesis of chitin were expected to respond to lufenuron, given the mode of action
2010-10-13 | E-TABM-798 | biostudies-arrayexpress
Project description:Juvenile (<24hr old) Daphnia magna populations (n=25) were exposed (24hr) to 0.00ug, 0.15ug, 0.33ug, 0.65ug lufenuron Benzoylphenylurea growth inhibitor. Transcriptomic responses were screened using a D.magna cDNA microarray and the regulation of gene expression via log fold-change in transcript abundance, assessed. Genes involved in the synthesis of chitin were expected to respond to lufenuron, given the mode of action. Extracted total RNA was amplified (400ng/sample) prior to hybridisation with the expectation that this would increase the abundance of significantly responding genes.
2010-10-13 | E-TABM-797 | biostudies-arrayexpress
Project description:Microarray Construction The D. magna microarray was constructed using DNA fragments from three sources: i) Stress-specific cDNAs were generated using Selective Subtractive Hybridisation (SSH) on organisms exposed to the stressors shown in Table 1. SSH was performed with forward and reverse subtraction using a PCR-Select cDNA Subtraction Kit (Clontech Laboratories Inc, USA). cDNA was prepared from mRNA extracted from batches of 100 D. magna, 48 h old, using a Straight AM-CM-"M-BM-,s mRNA Isolation Kit System (Novagen Inc., UK) (2,029 clones). ii) ESTs obtained from a cDNA library from unexposed mixed aged organisms obtained from a 3-4 week old culture (Watanabe et al. 2005) (10,272 clones). iii) cDNAs isolated following an SSH, as above, between 15 adults carrying eggs and 75 juveniles (Soetaert et al. 2006) (1,143 clones). Gene fragment annotation Sequencing of the 3,172 SSH ESTs was carried out with M13-Long primers. Blast searches were performed on specific fragments that responded significantly to the exposure treatment. Sequences were annotated according to BlastX homology search against Uniprot Swissprot (http://www.ebi.ac.uk/swissprot) and Uniprot Trembl (invertebrate section, http://www.ebi.ac.uk/trembl) March 2006. Sequences were only annotated if they were found to have a Blast hit with the expect value smaller than 0.00001 and a score above 50. GeneBank/UniProt Accession number and speciesM-CM-"M-BM-, match were recorded with each annotation. We printed PCR products generated from the above, onto glass slides. All spots have been sequenced except for (iii), only a few available and some sequencing failed for various reasons. Therefore we have the sequences for around 90% of the spots. BLAST searches revealed a large proportion (nr 60%) had no significant match with existing entries in GenBank/Uniprot/Trembl. Because of low confidence we've not considered them, otherwise this would lead to huge and erroneous assumptions. All (i and ii) sequences are available either on GenBank or on our website. All the spots that came out as significant on our experiments were reviewed and only those that have been annotated, with significant BLAST match, are being published, with respective Accession numbers, species match and E-values. Fragments were therefore described as M-CM-"M-BM-,SunnanotatedM-CM-"M-BM-,M-CM-= where no significant difference was measured or M-CM-"M-BM-,Sno significant matchM-CM-"M-BM-,M-CM-= for those that were significant but no matches were found. Significant genes were annotated respectively as described above. Dose Reponse Tests were carried out using the developed microarray on cadmium, ph, lufenuron, calcium limitation and ibuprofen; details below: Cadmium: RNA was obtained from populations of 240 D. magna, 24-48 h old, exposed for 24 h to sublethal concentrations of cadmium chloride from 0, 10, 33 to 60 M-CM-^BM-BM-5g L-1 (corresponding to 0, 6.13, 20.24 and 36.79 M-CM-^BM-BM-5g L-1 Cd2+), in quadruplicates. pH: RNA was obtained from populations of 240 D. magna, 24-48 h old, exposed for 24 h to pH ranging from 8.0 (controls), 5.5, 5.3 and 5.2, in quadruplicates. pH was maintained by adding HCl on a daily basis. Lufenuron: RNA was obtained from populations of 240 D. magna, 24-48 h old, exposed for 24 h to sublethal concentrations of C14 labelled, lufenuron ranging from 0, 0.35, 0.59 to 1.00 ug L-1, in quadruplicates. Calcium: RNA was obtained from populations of 240 D. magna, 24-48 h old, exposed for 24 h to calcium chloride limitation ranging from 195.87 (culture condition), 20, 10 and 5 mg L-1 (CaCo3), in quadruplicates. Ibuprofen: RNA was obtained from populations of 300 D. magna, 24-48 h old, exposed for 24 h to ibuprofen (IB) sodium; 0 (control), 20, 40 and 80 mg L-1, in *quadruplicates. *One replicate at 80 mg L-1 was lost, thus this treatment was done in triplicate. IB was measured as the pharmacological active ingredient. Juvenile D. magna were used in order to restrict the response to genes associated with stress responses and growth, rather than genes associated with different stages of reproduction. Following exposure, daphnids were stored in RNAlater (Ambion, UK) at -80M-CM-^BM-BM-0C.
2007-11-05 | E-MAXD-20 | biostudies-arrayexpress
Project description:Applications for silver nanomaterials in consumer products are rapidly expanding, creating an urgent need for toxicological examination of the exposure potential and ecological effects of silver nanoparticles (AgNPs). The integration of genomic techniques into environmental toxicology has presented new avenues to develop exposure biomarkers and investigate the mode of toxicity of novel chemicals. In the present study we used a 15k oligonucleotide microarray for Daphnia magna, a freshwater crustacean and common indicator species for toxicity, to differentiate between particle specific and ionic silver toxicity and to develop exposure biomarkers for citrate-coated and PVP-coated AgNPs. Gene expression profiles revealed that AgNO3 and AgNPs have distinct expression profiles suggesting different modes of toxicity. However, the gene expression profiles of the different coated AgNPs were similar revealing similarities in the cellular effects of these two particles. Major biological processes disrupted by the AgNPs include protein metabolism and signal transduction. In contrast, AgNO3 caused a downregulation of developmental processes, particularly in sensory development. Metal responsive and DNA damage repair genes were induced by the PVP AgNPs, but not the other treatments. In addition, two specific biomarkers were developed for the environmental detection of PVP AgNPs; although further verification under different environmental conditions is needed. We exposed Daphnia magna to the 1/10 LC50 and LC25 of citrate coated and PVP-coated Ag nanoparticles and Ag+ as AgNO3 for 24-h. For each exposure condition, we performed 6 replicate exposures with 5 individuals in each. All exposures were compared to a unexposed laboratory control.
2012-08-04 | E-GEOD-35150 | biostudies-arrayexpress
Project description:Zinc Oxide nanoparticles (ZnO NPs) are being rapidly developed for use in consumer products, wastewater treatment and chemotherapy providing several possible routes for ZnO NP exposure to humans and aquatic organisms. Recent studies have shown that ZnO NPs undergo rapid dissolution to Zn+2, but the relative contribution of Zn+2 to ZnO NP bioavailability and toxicity is not clear. Gene expression profiling of D. magna exposed to ZnO NPs or ZnSO4 at equitoxic concentrations demonstrated that the particles cause toxicity through a distinct mechanism compared with Zn+2. D. magna were also exposed to a SiO NPs as a particle control at equimolar concentrations. The SiO NPs resulted in few differentially expressed genes and there was very little overlap between the genes affected by the ZnO NPs and the SiO NPs, suggesting that ZnO NPs cause a distinct pattern of differentially expressed genes. In the ZnO NP exposures, effects were observed to genes involved in cytoskeletal transport, cellular respiration and reproduction. Three biomarker genes including a multi-cystatin, ferritin and a C1q containing gene were confirmed as differentially expressed in a specific pattern by ZnO NP and provide a suite of biomarkers for identifying environmental exposure to ZnO NP and differentiating between NP and ionic exposure. We exposed Daphnia magna to the 1/10 LC50 and LC25 of ZnO nanoparticles and Zn++ as ZnSO4 for 24-h. For each exposure condition, we performed 3 exposures and 2 technical replicates (as dye swap) for each exposure (6 microarrays total). All exposures were compared to a unexposed laboratory control
2010-12-31 | E-GEOD-22051 | biostudies-arrayexpress
Project description:Regulation of milk synthesis and secretion is controlled mostly through local (intra-mammary) mechanisms. To gain insight into the molecular pathways comprising this response, an analysis of mammary gene expression was conducted in 12 lactating cows shifted from twice daily to once daily milking. Tissues were sampled by biopsy from adjacent mammary quarters of these animals during the two milking frequencies, allowing changes in gene expression to be assessed within each animal. Using bovine-specific, oligonucleotide arrays representing 21,495 unique transcripts, a range of differentially expressed genes were found as a result of less frequent milk removal. A total of 12 microarrays were used in this study. Each array was hybridized with RNA derived from a mammary sample taken at each biopsy time point, such that the twice-a-day milked sample and once-a-day milked sample were contained on the same slide for each animal (12 animals). Six of the microarrays represented animals previously shown to demonstrate a âlargeâ reduction in milk yield, whereas the other six arrays represented animals that previously displayed a âsmallâ reduction in milk yield when milked once per day. Half of each yield loss group (three animals) was represented by once-a-day milked/twice-daily-milked samples for Cy5/Cy3 labelling, with the other half labelled with the opposite dye configuration. This meant that six of 12 arrays were 'dye swapped', but with biological replicates as opposed to identical replicates.
2010-05-16 | E-GEOD-16876 | biostudies-arrayexpress
Project description:Daphnia neonates (100 individuals, 24h post-hatch) and adults (20 individuals, 168h post-hatch) were exposed to DMSO carrier (0.002%), low (0.25 uM sodium dichromate, 0.01 uM benzo-a-pyrene) or high (0.75 uM soduium dichromate, 0.1 uM benzo-a-pyrene) concentrations of a genotoxicant mixture, or were untreated. Untreated controls were sampled at the initial time point, exposed Daphnia were sampled at 6h and 24h post-exposure. Transcriptional profiles were determined using an Agilent oligonucleotide microarray.
2011-03-01 | E-MTAB-551 | biostudies-arrayexpress
Project description:Flounder fish were exposed in mesocosms for seven months to a contaminated estuarine sediment made by mixing material from the Forth (high organics) and Tyne (high metals and tributyltin) estuaries (FT) or control sediment from the Ythan estuary (Y). Their gene expression profiles were compatred by cDNA microarrays.
2014-03-01 | E-MTAB-1847 | biostudies-arrayexpress
Project description:Daphnia (Daphnia pulex) is a small planktonic crustacean and a key constituent of aquatic ecosystems. It is commonly used as a model organism for studying environmental toxic challenges. In the past decade, a Daphnia genomic information and proteomic dataset has been developed. This dataset has expanded the opportunity to relate toxicological effects with “Daphnia proteomics” as it integrates proteomic knowledge in Daphnia, those approach will provide greater insights for toxicological research. In order to exploit Daphnia for ecotoxicological research, information on the post-translational modification (PTM) of proteins is necessary as this is a critical regulator of biological processes. Acetylation of lysine (Kac) is a reversible and highly regulated PTM that is associated with diverse biological functions. However, a comprehensive description of Kac in Daphnia is not yet available. Here, to understand the cellular distribution of lysine acetylation in Daphnia, we identified 98 acetylation sites in 65 proteins by immunoprecipitation using an anti-acetyllysine antibody and an liquid chromatography system supported by mass spectroscopy. We identified 28 acetylated sites connected with metabolic proteins and 6 acetylated enzymes associated with the TCA cycle in Daphnia. From GO and KEGG enrichment analyses, we showed that Kac in D. pulex is highly enriched in proteins associated with metabolic processes. Our data provide the first global analysis of lysine acetylation in D. pulex. The expanded proteomic dataset will be an important resource for the functional analysis of Kac in D. pulex and it will be nice to have a first step done using a promising future model organism.
2016-01-05 | PXD002441 | Pride
Project description:Cadmium (Cd) is a toxic metal causing sublethal and chronic effects in crustaceans. Omic technologies offer unprecedented opportunities to better understand modes of toxicity by providing a holistic view of the molecular changes underlying physiological disruption. We sought to use gene expression and metabolomic analyses to reveal the processes leading to chronic Cd toxicity in the indicator species, Daphnia magna, after a 24-h sublethal exposure (18 ug/L, corresponding to 1/10 LC50). We first confirmed that metabolites can be detected and identified in small volumes (~3-6 ul) of D. magna hemolymph using Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry and NMR spectroscopy. We then compared the altered metabolite levels from a mass spectrometry metabolomics study to differentially expressed genes identified by a D. magna 44k oligonucleotide microarray. Metabolomics identified several essential amino acids, nucleotides and fatty acids as decreased in D. magna hemolymph following Cd exposure. Transcriptional changes included decreased levels of digestive enzymes and increased expression of genes related to embryonic development. The integration of metabolomic and transcriptomic profiles, as well as incorporation of results from previous studies, has enabled construction of a conceptual model detailing how sublethal Cd disrupts energy reserves and reproduction resulting in chronic toxicity. Daphnia magna were exposed to 18 micrograms/L Cadmium sulfate for 24 hours. RNA was extracted and hybridized to a custom Daphnia magna microarray to determine genes differentially expressed by the treatment. Two treament experiment:Unexposed and Cd treatment, 6 replicates for each condition
2010-12-31 | E-GEOD-20218 | biostudies-arrayexpress