Project description:Rat small intestine precision cut slices were exposed for 6 hours to in vitro digested yellow (YOd) and white onion extracts (WOd) that was followed by transcriptomics analysis. The digestion was performed to mimic the digestion that in vivo takes place in the stomach and small intestine. The transcriptomics response of the rat small intestine precision cut slices was compared to that of human Caco-2 cells and the pig in-situ small intestinal segment perfusion. The microarray data for the human Caco-2 cells (GSE83893) and the pig in-situ small intestinal segment perfusion (GSE83908) have been submitted separately from the current data on rat intestine. The goal was to obtain more insight into to which extent mode of actions depend on the experimental model. A main outcome was that each of the three models pointed to the same mode of action: induction of oxidative stress and particularly the Keap1-Nrf2 pathway. Overall design: The dataset contains results of 12 microarrays. 3 arrays for saline_digest that can be considered as the reference to which the response of the in vitro digested yellow (YOd) and white onion extracts (WOd) can be compared. 3 arrays were used for in vitro digested yellow (YOd) and 3 arrays for in vitro digested yellow (YOd). In addition, 3 arrays (called DMSO) were included for an exposure without digestion enzymes. That is informative for the effect of the enzymes in the digestion mixture.
Project description:Ethyl Acetate fraction of Streptomyces sp. CBMAI 2042 was investigated for identifying cyclodepsipeptides using electrospray ionisation tandem mass spectrometry (ESI-MS/MS). Without prior isolation, the structural determination was achieved on the basis of mass fragmentation pattern and comparison with the previously established data. The ESI-MS of the fraction in the positive ion mode gave clusters of singly and doubly charged molecular ion peaks. The ESI-MS spectrum showed peaks for the presence of the cyclodepsipeptides Valinomycin, Montanastatin and at least 5 structural analogues never reported before.
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. Overall design: The gene expression of human mesenchymal stem cells were measured after 48h exposure to organic extracts of surface water from the Hun River. Culture medium with 0.1% DMSO was used as negative control. Three independent cultures were used for control group and each treatment.
Project description:We compared the gene expression stimulated with fungal extracts from Aspergillus (A.) fumigatus, Alternaria (A.) alternata, or Penicillium (P.) notatum in NCI-H292 (a human bronchial epithelial cell line) to search Allergic bronchopulmonary mycosis (ABPM)-related genes. We identified a mucin-related MUC5AC gene, the expression of which was selectively induced by A. fumigatus. Overall design: Total RNA from NCI-H292 cells stimulated for 24 h with the A. fumigatus, A. alternata, or P. notatum fungi extracts was extracted and subjected to microarray analysis. Each experiments were perfomed once for each stimulus.
Project description:Nothapodytes nimmoniana is a natural source of camptothecin, a known anticancer drug. Stem and leaf extracts of Nothapodytes nimmoniana were studied to assess its in-vitro action on cancer progression events in a cervical cancer cell line, the HeLa. As a well-studied ideal model system, the HeLa has been chosen and the effects of extracts on cancer progression events have been traced out. HeLa cells and media samples were analyzed for differentially expressed proteins and metabolites respectively on RRLC-ESI-QTOFMS. The CBFA2T1, cysteine-rich protein 2-binding protein, Zinc finger protein 788, transcription factor RFX3 and angiomotin-like protein 1 were significantly expressed proteins while 3-Hydroxysuberic acid, Indole-3-carboxylic acid, N8-Acetylspermidine, L-Octanoylcarnitine were significantly expressed metabolites. Aminoacyl-tRNA biosynthesis, purine metabolism, and valine, leucine, arginine, proline metabolism were the most prominent pathways. The multi-omics approach has the greatest metabolites and proteins profiling potential hence was applied here to find signatures of N. nimmoniana extracts treatment of cervical cancer.
Project description:LC-MS/MS data used in a work titled "Assessing Specialized Metabolite Diversity of Alnus species by Digitized LC_MS/MS Data Analysis Workflow". Negative ion mode DDA data from 15 extracts of 4 Alnus species (barks, twigs, leaves, and fruits)
Project description:Applicability of in vitro (human Caco-2 cells) and ex vivo intestine models (rat precision cut intestine slices and the pig in-situ small intestinal segment perfusion (SISP) technique) to study the effect of food compounds. In vitro digested yellow (YOd) and white onion extracts (WOd) were used as model food compounds and transcriptomics was applied to obtain more insight into which extent mode of actions depend on the model. Overall design: Within eight male piglets (5 week-old, 8.2 kg) five paired SISP segments were prepared at 31-58% along the total length of small intestine (jejunum). At t = 0 segments were filled with 20 ml of Saline control solution (S), 20 ml onion digest (YOd or WOd), or 20 ml control digest (Sd). After 30 min, perfusion (2 ml/15 min) was started simultaneously for all segments for a period of 6 h. Perfusion was stopped and for preparation of mucosal scrapings 10 cm of the caudal part of each segment was dissected and directly frozen in liquid nitrogen and stored at -80°C. In the first 4 piglets (number 1-4), YOd and Sd samples were distributed over a pair of segments, and over the piglets according to a Latin-square design. In the second 4 piglets (number 5-8) WOd and Sd samples were distributed over segments and piglets in the same manner as in piglets 1-4. jejunum pig, host-feed interaction