High-throughput transcriptomics of water extracts detects reductions in biological activity with water treatment processes
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PROVIDER: PRJNA1057823 | ENA |
REPOSITORIES: ENA
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Project description:The presence of numerous chemical contaminants from industrial, agricultural, and pharmaceutical sources in water supplies poses a potential risk to human and ecological health. Current chemical analyses suffer from limitations including chemical coverage and high cost, and broad-coverage in vitro assays such as transcriptomics may further improve water quality monitoring by assessing a large range of possible effects. Here, we used high-throughput transcriptomics to assess the activity induced by field-derived water extracts in MCF7 breast carcinoma cells.
2024-03-05 | GSE252117 | GEO
Project description:To assess the impact of surface water across the Hun River, several sampling sites located in the mainstream and the tributary were selected representative of pollution gradient and different pollution source. Human mesenchymal stem cells were exposed to organic extracts of surface water from six sites for 2 days. Microarrays were used to measure the gene expression. And the gene expression profiles were used to evaluate the ability of determine the potential biological effects, to differentiate different pollution source, and to identify the toxic components.
2018-06-01 | GSE110310 | GEO
Project description:we profiled the change in genome-wide gene expression of human lung cancer cells in response to treatment of water and ethanol extracts of PR and its ingredients in a dose dependent manner to investigate PR efficacy at the molecular pathway level.
2022-12-31 | GSE186218 | GEO
Project description:Gene expression profiles of human mesenchymal stem cells exposed to surface water organic extracts
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Project description:Hi-C detects novel rearrangements in HL60 and HL60/S4 cell lines
2018-12-02 | GSE120815 | GEO
Project description:In the search for sustainable drinking water, many countries are weighing up the benefits of advanced treatment technologies as a proactive measure to assist with the transformation of treated wastewater into a source of water used for the production of potable water. We investigated the biological effects along a pilot plant with an advanced water treatment process, using zebrafish embryos at different stages of development. The study took an innovative approach, comparing phenotypic observations with whole genome responses. This enabled us to keep an open mind about which chemicals might be influencing the biological activity. There was no evidence of acute toxicity at any stage of treatment, but distinctive abnormalities – skeletal, cardiovascular and pigmentation – occurred in a small proportion of embryos along the treatment process, and in a tap water, that were not detected in the aquarium water control. Reverse osmosis (RO) reduced the concentration of measured chemical contaminants in the water the most, whilst eliminating the occurrence of abnormalities detected in the fish. In contrast, advanced oxidation appeared to reverse the benefits of RO treatment by increasing the frequency of teratogenic and sub-lethal abnormalities seen in embryos. Genomic analysis found alterations to the retinoid system, which was consistent with the teratogenic abnormalities observed. In addition, we found evidence of changes to metabolic pathways, including tryptophan metabolism associated with the production of melatonin required for the control of normal circadian rhythms. Although we cannot extrapolate these preliminary findings in zebrafish embryos to human or environmental health, we show that underexplored forms of biological activity (that existing Test Guidelines are not designed to capture) occur in treated wastewater effluent, and/or may be created depending on the type of advanced treatment process used. Although the identity of the culprit chemicals are unknown at this time, our innovative approach highlights the need for more research into the effects of chemicals on the retinoid system (and metabolism).
2020-11-30 | GSE152131 | GEO
Project description:Antrodia Camphorata is well known in Taiwan as a folk medicinal fungus with anticancer and anti-inflammatory effects. In this study, we used a human acute myelogenous leukemia cell line, KG-1, as the experimental model and constructed a high-throughput gene screen integrated platform by using a combination of herbal identification, UV-VIS spectrophotometry, high performance liquid chromatography (HPLC), inductively coupled plasma mass spectrometry (ICPMS), and DNA microarray technology. Based on this science-based platform, we developed a practical quantitative method and also established an organic/inorganic chemical fingerprint for the herbal materials. In the mean while, the global gene expression patterns of the KG-1 cells treated with various A. camphorata mycelia extracts (water and methanol extracts) were compared. Furthermore, several possible biological responses and relevant marker gene would be identified by our high-throughput integrated platform. Keywords: KG-1 treated with AC extracts for 4 days, cDNA microarray, biomarker selection.
2008-11-18 | GSE3692 | GEO
Project description:Introduction Ophiocordyceps sinensis, a well-known Chinese complementary herb, is a rare and valuable therapeutic resource. Cordyceps militaris (C. militaris) is a commonly used substitute for O. sinensis. A metabolomic-based approach for exploring the similarities and differences in the metabolites of O. sinensis and C. militaris in water-boiled and 50% ethanol-soaked extracts is of great significance. Objectives To determine a vital role of extraction methodologies in influencing the metabolic composition of herbs, 1HNMR-based profiling was used to characterize the metabolic fingerprints of O. sinensis and C. militaris. Methods To make a distinction between the global metabolite profiling of O. sinensis and C. militaris extracts obtained from either the water-boiled or 50% ethanol-soaked methods, we screened the herbs samples using 1HNMR-based metabolic fingerprints combined with multivariate statistical analysis. Results This study revealed that a total of 43 (82.69% of 52) metabolites were detectable in both O. sinensis and C. militaris. According to the variable importance in projection (VIP) value and p-value from the Mann-Whitney test, 7 metabolites (alanine, aspartate, glutamate, mannitol, ornithine, serine, and trehalose) differed between O. sinensis and C. militaris. Arginine, glucose, putrescine, pyroglutamate, betaine, O-phosphocholine, and xylose differed significantly between the water-boiled and 50% ethanol-soaked methods used to prepare the herb extracts. Conclusion A total of 52 primary metabolites were identified and quantified from O. sinensis and C. militaris samples. The study suggests that a water-boiled extraction is much faster method and strongly recommended over the 50% ethanol-soaked method for both O. sinensis and C. militaris.
2019-04-28 | ST001189 | MetabolomicsWorkbench
Project description:Inflammatory Bowel Disease (IBD) is a term describing a collection of conditions characterised by chronic inflammatory disorder of the gastrointestinal tract involving an inappropriate immune response to commensal microorganisms in a genetically susceptible host. Four kiwifruit extracts, aqueous and ethyl acetate extracts of gold kiwifruit (Actinidia chinensis) or green kiwifruit (A. deliciosa), have previously demonstrated anti-inflammatory activity using in vitro models of IBD. This study examined whether these kiwifruit extracts had immune modulating effects in vivo against inflammatory processes known to be increased in patients with IBD. KFEs were used as a dietary intervention in Il10-/- mice (an in vivo model of IBD) and the C57BL/6J background strain in a 3 x 2 factorial design. While all Il10-/- mice developed significant colonic inflammation compared to the C57BL/6J mice, this was not affected by the inclusion of KFE in the diet. Whole genome gene and protein expression level profiling indicated that KFEs influenced immune signalling pathways and metabolic processes within the colonic tissue; however, the effects were subtle. In particular, adaptive immune pathways were reduced by three out of four kiwifruit extracts, with greater reduction seen in the C57BL/6J mice. This suggests that while immune-modulating activity was present in vivo, KFEs did not reduce inflammatory processes relevant to IBD. SUBMITTER_CITATION: Edmunds, Shelley Jane. The effects of kiwifruit extracts on gene and protein expression in in vitro and in vivo mouse models of inflammatory bowel disease. Diss. University of Auckland, New Zealand, 2010. http://hdl.handle.net/2292/6623
2011-03-05 | GSE27684 | GEO
Project description:Deciphering the biological processes underlying tomato biomass production and composition.
| PRJNA527463 | ENA