Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1176280 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31091058_1.fastq.gz | Fastqsanger.gz | |||
| SRR31091058_2.fastq.gz | Fastqsanger.gz | |||
| SRR31091059_1.fastq.gz | Fastqsanger.gz | |||
| SRR31091059_2.fastq.gz | Fastqsanger.gz | |||
| SRR31091060_1.fastq.gz | Fastqsanger.gz |
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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.
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Project description:Purpose: The objective of this study was to evaluate the transcriptomic consequence of chronic exposure to deficient and excessive arginine supply in MIN6 pancreatic beta cells and reveal the molecular mechanisms underlying beta cell function and insulin secretion to arginine administration. Methods: After overnight adhesion, the medium was removed, and the cells were incubated in fresh DMEM medium containing low-, standard- or high-arginine concentration (LA, SA and HA) for 24 h. Following the treatment, RNA was extracted from cells for transcriptome sequencing. Results: Transcriptomics analysis allowed the detection of 23,620 and 22,939 transcripts in the LA and HA samples, among which 7,591 (3,736 up- and 3,855 down-regulated) and 197 (111 up- and 86 down-regulated) genes were expressed differently compared with the SA treatment. One hundred and forty one DEGs were overlapped between LA vs. SA and HA vs. SA comparisons, which were mainly involved in DNA replication, organic hydroxy compound metabolism and cellular response to oxidative stress. GO functional enrichment analysis demonstrated that terms related to proteasomal protein catabolic process, mRNA processing and ATP metabolic process were highly disturbed by LA administration, while DEGs induced by HA were mainly enriched to ammonium ion metabolic process, mRNA export and sterol biosynthetic process. Morever, KEGG pathway analysis revealed that DEGs between LA and SA treatments were mainly functionally classified as involved in protein processing in endoplasmic reticulum and oxidative phosphorylation, while DNA replication, steroid biosynthesis and cell cycle had more counts and reached significant difference levels according to the DEGs triggered by HA. Conclusions: These results suggested that the disturbed carbohydrate, lipid and amino acid metabolisms as well as the decreased cell proliferation, increased apoptosis and elevated oxidative stress contributed to the reduced insulin secretion in beta cells induced by LA or HA administrations.
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Project description:We provide evidence that heterosis for bacterial defense exists in hybrids crossed between some Arabidopsis accessions. Comparison of transcriptomes between hybrids exhibiting heterosis for disease resistance and their parents after inoculation with Pst DC3000 revealed that several key genes involved in salicylic acid (SA) biosynthesis were significantly up-regulated in hybrids. Consistently, in response to bacterial infection, more SA [both free SA and SA glycoside (SAG)] accumulated in hybrids compared with both parents. In addition, heterosis for bacterial defense was significantly compromised in hybrids of pad4 mutants in which the SA biosynthesis pathway was blocked. Moreover, we further revealed that increased histone H3 acetylation of the key genes involved in the SA biosynthesis pathway correlated with their up-regulated expression in hybrids.
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Project description:We provide evidence that heterosis for bacterial defense exists in hybrids crossed between some Arabidopsis accessions. Comparison of transcriptomes between hybrids exhibiting heterosis for disease resistance and their parents after inoculation with Pst DC3000 revealed that several key genes involved in salicylic acid (SA) biosynthesis were significantly up-regulated in hybrids. Consistently, in response to bacterial infection, more SA [both free SA and SA glycoside (SAG)] accumulated in hybrids compared with both parents. In addition, heterosis for bacterial defense was significantly compromised in hybrids of pad4 mutants in which the SA biosynthesis pathway was blocked. Moreover, we further revealed that increased histone H3 acetylation of the key genes involved in the SA biosynthesis pathway correlated with their up-regulated expression in hybrids. Around 30 inoculated leaves from Arabidopsis accessions Col-0 and Sei-0 as well as their reciprocal hybrids Fcs and Fsc, which showed best-parent heterosis for bacterial defense were pooled in each sample for mRNA Seq using HiSeq 2000 sequencing system (Illumina)
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