Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1174387 | ENA |
REPOSITORIES: ENA
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Project description:Today, many contaminants of emerging concern can be measured in waters across the United States, including the tributaries of the Great Lakes. However, just because the chemicals can be measured does not mean that they necessarily result in harm to fish and other aquatic species. Complicating risk assessment in these waters is the fact that aquatic species are encountering the chemicals as mixtures, which may have additive or synergistic risks that cannot be calculated using single chemical hazard and concentration-response information. We developed an in vitro effects-based screening approach to help us predict potential liver toxicity and cancer in aquatic organisms using water from specific Great Lakes tributaries: St. Louis River (MN), Bad River (WI), Fox River (WI), Manitowoc River (WI), Milwaukee River (WI), Indiana Harbor Canal (IN), St. Joseph River (MI), Grand River (MI), Clinton River (MI), River Rouge (MI), Maumee River (OH), Vermilion River (OH), Cuyahoga River (OH), Genesee River (NY), and Oswego River (NY). We exposed HepG2 cells for 48hrs to medium spiked with either field collected water (final concentration of environmental samples in the exposure medium were 75% of the field-collected water samples) or purified water. Using a deep neural network we clustered our collection sites from each tributary based on water chemistry. We also performed high throughput transcriptomics on the RNA obtained from the HepG2 cells. We used the transcriptomics data with our Bayesian Inferene for Sustance and Chemical Toxicity (BISCT) Bayesian Network for Steatosis to predict the probability of the field samples yielding a gene expression pattern consistent with predicting steatosis as an outcome. Surprisingly, we found that the probability of steatosis did not correspond to the surface water chemistry clustering. Our analysis suggests that chemical signatures are not informative in predicting biological effects. Furthermore, recent reports published after we obtained our samples, suggest that chemical levels in the sediment may be more relevant for predicting potential biological effects in the fish species developing tumors in the Great Lakes basin.
2022-12-01 | GSE146903 | GEO
Project description:The copper redhorse (Moxostoma hubbsi) is an endangered fish endemic to Quebec, Canada that is only known to spawn in two locations within the Richelieu River, a waterway draining a significant area of agricultural land. Accordingly, concerns have been raised over the impacts that agricultural pesticide contamination of spawning grounds and nursery habitats within the Richelieu River may have on early life stage copper redhorse. We assessed the effects of contaminants on early life stages of copper redhorse and river redhorse (Moxostoma carinatum), a closely related fish that shares the copper redhorse’s habitat and spawning grounds but is distributed more widely and is not yet listed as endangered. Copper and river redhorse embryos (1000 each) were exposed to either Richelieu River water in an in-situ flow-through system or to laboratory water used as a control. We assessed embryos hatching time, incidence of deformities and survival in copper and river redhorses. We then performed RNA sequencing on copper redhorse larvae to better understand changes due to river water exposure. We identified 341 compounds in the river water that were absent from lab water. Pesticide concentrations in the river peaked following rainfall during the spawning season. Embryos exposed to river water hatched prematurely at 63.0 and 59.2 cumulative degree days (CDD) compared to 65.4 and 69.9 CDD in laboratory water for river and copper redhorse, respectively. Copper redhorse exposed to river water also had a significantly lower survival rate than laboratory water (73% vs. 93%). RNA sequencing of copper redhorse revealed 18 differentially expressed genes (DEGs) following river water exposure. Eight of the upregulated DEGs (cd44, il1b, lamb3, lamc2, tgm5, orm1, saa, acod1) are linked to immune function and injury response and 7 of the downregulated DEGs (cpa2, ctrb, cela2a, ctrl, cpa1, prss1, cel) are involved with digestion and nutrient absorption. This study provided valuable data on the effects of anthropogenic contaminants present in the Richelieu River and increased our knowledge on the individual and mixture effects they have on an endangered fish.
2022-06-01 | GSE185175 | GEO
Project description:This study analysed the effect of maternal hyperthyroidism on the offspring’s white adipose tissue function. Hyperthyroidism during pregnancy was induced in wild type female C57BL/6NCrl (Charles River, Germany) at the age of three to four month with 0.5 mg/L T3 (3,3’,5-Triiodo-L-thyronine, T6397, Sigma Aldrich, Germany) in drinking water with 0.01% BSA from day of positive plug check until gestational day 18 (= day before birth). Adipose tissue samples were collected at the day of sacrifice (male offspring: 5-6 months, female offspring: 6-7 months), weighted, snap frozen on dry ice, and stored at -80 °C until nucleic acid extraction. Sex-specific gene expression profiling in the gWAT samples from the offspring of maternal T3 treatment experiment was performed using GeneChip Clariom S arrays (Affymetrix, Germany).
2024-12-30 | E-MTAB-14515 | biostudies-arrayexpress
Project description:With its 2.5 Mb DNA genome packed in amphora-shaped particles of bacterium-like dimension (1.2 µm in length, 0.5 µm in diameter), the Acanthamoeba-infecting Pandoravirus salinus remained the most spectacular and intriguing virus since its description in 2013. Following its isolation from shallow marine sediment off the coast of central Chile, that of its relative Pandoravirus dulcis from a fresh water pond near Melbourne, Australia, suggested that they were the first representatives of an emerging worldwide-distributed family of giant viruses. This was further suggested when P. inopinatum discovered in Germany, was sequenced in 2015. We now report the isolation and genome sequencing of three new strains (P. quercus, P.neocaledonia, P. macleodensis) from France, New Caledonia, and Australia. Using a combination of transcriptomic, proteomic, and bioinformatic analyses, we found that these six viruses share enough distinctive features to justify their classification in a new family, the Pandoraviridae, distinct from that of other large DNA viruses.
2018-06-15 | PXD008167 | Pride
Project description:Positive-strand RNA viruses of the order Nidovirales have the largest known RNA genomes of vertebrate and invertebrate viruses with 36.7 and 41.1 kb, respectively. The acquisition of a proofreading exoribonuclease (ExoN) locus by an ancestral nidovirus enabled crossing of the 20 kb barrier. Other factors constraining genome expansions in nidoviruses remain poorly defined. Here, we assemble 76 genome sequences of invertebrate nidoviruses from >500.000 published transcriptome experiments and triple the number of known nidoviruses with >36 kb genomes, including the largest known 64 kb RNA genome. Many of the novel viral lineages acquired putative enzymatic domains that were inserted in open reading frame (ORF) 1a and ORF1b or equivalent regions and may constitute cofactors of the viral replicase or modulate infection otherwise. We classify multi-cistronic ExoN-encoding nidoviruses into seven groups and four subgroups, according to canonical and non-canonical modes of viral polymerase expression by ribosomes and genomic organization (reModes). The largest group employing the canonical reMode comprises invertebrate and vertebrate nidoviruses, including coronaviruses, with genomes ranging from 20 to 36 kb. Six groups with non-canonical reModes include giant invertebrate nidoviruses with 31 to 64 kb genomes. Among them are viruses with segmented genomes and viruses utilizing dual ribosomal frameshifting that we validate experimentally. Moreover, polyprotein length and genome size in nidoviruses show reMode- and host phylum-dependent relationships. We demonstrate that the largest polyproteins in nidoviruses may be close to an upper limit that we hypothesize to be determined by the host-inherent translation fidelity, further constraining nidovirus genome size. Thus, expansion of giant RNA virus genomes, the vertebrate/invertebrate host division, the control of viral replicase expression, and translation fidelity are interconnected.
2024-12-06 | GSE283188 | GEO
Project description:Male SHRs and normotensive Wistar-Kyoto(WKY) rats were purchased from Vital River (Vital River Laboratory Animal Technology Co., Ltd, Beijing, China). Briefly, eightteen SHRs aged seven to eight weeks old were randomly assigned to one of three groups: water group (drinking tap water), water containing 333 mg/L or 1g/L TMAO group (TMAO, product number: T1362, Tokyo Chemical Industry, Japan). Six WKY rats of the same age were used as normotensive controls. In this study, WKY rats (n=6), SHR (n=6), and SHR treated with 1g/L TMAO (n=6) were uesd for experiments.
2022-08-17 | GSE188336 | GEO
Project description:Waste water and river water samples Metagenome
| PRJNA273929 | ENA
Project description:Nontarget analysis by LC-HRMS (UHLPC Q Exactive) of seawater, river water and drinking water samples analyzed by DIA negative mode [ESI]-.
2024-04-15 | MSV000094541 | MassIVE