GNPS - Authentic chemical standards_Steroids and bile acids
Ontology highlight
ABSTRACT:
INSTRUMENT(S): maXis
ORGANISM(S): Chemical Standards
SUBMITTER: 
Pieter Dorrestein
PROVIDER: MSV000081583 | GNPS | Wed Oct 04 12:57:00 BST 2017
REPOSITORIES: GNPS
Similar Datasets
Project description:LC-MS data of pooled chemical standards. Data were collected using DDA and full-scan (0eV, 10eV and 20 eV isCID).
Bile acid pool: glycocholic acid (GCA), glycochenodeoxycholic acid (GCDCA), taurodeoxycholic acid (TDCA), taurocholic acid (TCA), taurolithocholic acid (TLCA), and tauro-3alphahydroxy-12ketocholanoic acid.
Drug pool: sertraline, venlafaxine, ritonavir, darunavir, losartan, quetiapine, sulfasalazine, and abacavir.
| MSV000095789 | GNPS
Project description:data from the analysis of chemical standards analyzed in positive and negative ionization mode. data collected using data-dependent acquisition.
2019-01-04 | MSV000083297 | GNPS
Project description:To characterize the adaptation processes of C. jejuni to sublethal concentrations of bile acids, that are a crucial component of the intestinal antimicrobial defense, including cholic- , chenodeoxycholic-, taurocholic-, glycocholic-, deoxycholic-, lithocholic-, and ursodeoxycholic acid, we used proteome profiling by label-free mass spectrometry (SWATH-MS). The most toxic bile acids, deoxycholic- and chenodeoxycholic acid induced the most significant changes in protein expression. In detail we found a significant down-regulation of in principle all basic biosynthetic pathways and a general decrease of the transcription machinery. Concurrently, an induction of factors involved in detoxification of reactive oxygen species, protein folding, and bile acid exporting efflux pumps was detected. The metabolism was optimized in such a way that the more energy-efficient aerobic respiration pathway was increased, while the energy-inefficient anaerobic branches of the electron transport chain were down-regulated. Uptake of amino acids in order to catabolize them was also increased. These results show that C. jejuni has a well-built, differentiated system of adaptation to bile acids stress. The findings of this study will enhance the understanding of the biology on the interaction of C. jejuni with the human intestine, and may provide clues to future medical treatment and prevention of C. jejuni infections.
2018-10-01 | PXD009088 | Pride
Project description:MS/MS fragmentation data on bile acid standards were acquired on the QE - with a gradient developed to separate between isomeric pairs on a Polar C18 column and a fragmentation energy of NCE 45.
2023-05-22 | MSV000092003 | MassIVE
Project description:Analysis of wild type genome expression profile altered by albino chemicals. Results uncovered a several groups of genes that were significant responsive to these chemicals which may contribute to the albino phenotype. WT (Col-0) sown on 0.5x MS agar medium and stratified in the dark at 4 °C for 3 days and then germinated in the light condition (16 h light/8 h dark) for 5 days at 22 °C, and then transfer to the 0.5x MS solution one day for adapt the treatment condition. In the DAG 6 (day after germination), final concentration 50 μM chemicals (7606596 and 5929745) were supplemented into the medium for chemical treatment. Approximately 2,000 seedlings were used to collect tissues before the chemicals treatment as the time zero samples. Seedlings were collected after the chemical treatment for 3 hours and 12 hours. Total RNA extracted from the collected samples was applied in each microarray experiment with Arabidopsis ATH1 GeneChip (Affymetrix). Qiagen RNAeasy mini kit (Qiagen) was used for RNA preparation. cDNA labeling, array hybridization, and scanning followed by standard Affymetrix expression array protocol. Two independent sets of microarray analyses were performed in this assay.
2012-03-27 | E-GEOD-36887 | biostudies-arrayexpress
Project description:Clostridioides difficile is a Gram-positive anaerobic bacterium that is the leading cause of hospital-acquired gastroenteritis in the US. In the gut milieu, C. difficile encounters microbiota-derived bile acids capable of inhibiting its growth, which are thought to be a mechanism of colonization resistance. While the levels of certain bile acids in the gut correlate with susceptibility to C. difficile infection, their molecular targets in C. difficile remain unknown. In this study, we sought to use chemical proteomics to identify bile acid-interacting proteins in C. difficile. Using photoaffinity bile acid probes and chemical proteomics, we identified a previously uncharacterized MerR family protein, CD3583 (now BapR), as a putative bile acid-sensing transcription regulator. Our data indicate that BapR binds and is stabilized by lithocholic acid (LCA) in C. difficile. Although loss of BapR did not affect C. difficile's sensitivity to LCA, bapR mutant cells elongated more in the presence of LCA than wild-type cells. Transcriptomics revealed that BapR regulates the expression of the gene clusters mdeA-cd3573 and cd0618-cd0616, and cwpV, with the expression of the mdeA-cd3573 locus being specifically de-repressed in the presence of LCA in a BapR-dependent manner. Electrophoretic mobility shift assays revealed that BapR directly binds to the mdeA promoter region. Since mdeA is involved in amino acid-related sulfur metabolism and the mdeA-cd3573 locus encodes putative transporters, we propose that BapR senses a gastrointestinal tract-specific small molecule, LCA, as an environmental cue for metabolic adaptation.
2022-06-03 | GSE205226 | GEO
Project description:Microbiome-encoded bile acid metabolism modulates colonic transit times
| PRJEB38547 | ENA
Project description:Bile acid diarrhoea is a chronic condition caused by increased delivery of bile acids to the colon. The underlying mechanisms remain to be elucidated. To investigate genes involved in bile acid diarrhoea, systems-level analyses were employed on a rat bile acid diarrhoea model. Twelve male Wistar Munich rats, housed in metabolic cages, were fed either control or bile acid-mixed (1% w/w) diets for ten days. Food intake, water intake, urine volume, bodyweight and faecal output were monitored daily. After euthanasia, colonic epithelial cells were isolated using calcium-chelation and processed for systems-level analyses, i.e. RNA-sequencing transcriptomics and mass spectrometry proteomics. Bile acid-fed rats suffered diarrhoea, indicated by increased drinking, faeces weight and faecal water content compared with control rats. Urine output was unchanged. With bile acid-feeding, RNA-sequencing revealed 204 increased and 401 decreased mRNAs; mass spectrometry 183 increased and 111 decreased proteins. Among the altered genes were genes associated with electrolyte and water transport (including Slc12a7, Clca4 and Aqp3) and genes associated with bile acid transport (Slc2b1, Abcg2, Slc51a, Slc51b and Fabps). Correlation analysis showed a significant positive correlation (Pearson’s r=0.28) between changes in mRNA-expression and changes in protein-expression. However, caution must be exercised in making a direct correlation between experimentally determined transcriptomes and proteomes. Genes associated with bile acid transport responded to bile acid-feeding, suggesting that colonic bile acid transport occur by regulated protein facilitated mechanisms rather than passive diffusion. In addition, the study provides annotated rat colonic epithelial cell transcriptome and proteome with response to bile acid-feeding.
2024-05-10 | GSE174249 | GEO
Project description:Identification of a bile acid-binding transcription factor in Clostridioides difficile using chemical proteomics
| PRJNA844117 | ENA
Project description:The gut microbiome can impact brain health and is altered in Parkinson’s disease (PD) patients. The vermiform appendix is a lymphoid tissue implicated in the storage and regulation of the gut microbiome. Here, we investigate changes in the functional microbiome in the appendix of PD patients relative to controls by metatranscriptomic analysis. In the PD appendix, we find microbial dysbiosis affecting lipid metabolism, particularly an upregulation of bacteria responsible for secondary bile acid synthesis. Likewise, proteomic and transcript analysis in the PD gut corroborates a disruption in cholesterol homeostasis and lipid catabolism. Bile acid analysis in the PD appendix reveals an increase in the microbially-derived, toxic secondary bile acids deoxycholic acid (DCA) and lithocholic acid (LCA). Synucleinopathy in mice induces similar microbiome alterations to those of PD patients and heightens microbial changes to gut inflammation. As observed in PD, the mouse model of synucleinopathy has elevated DCA and LCA. Raised levels of DCA and LCA can lead to liver injury, and an analysis of blood markers of liver dysfunction shows evidence of biliary abnormalities in PD patients, including elevated alkaline phosphatase and bilirubin. Increased bilirubin levels are also evident before PD diagnosis, in individuals at-risk of developing PD. In sum, microbially-derived toxic bile acids are heightened in PD and biliary changes may even precede the onset of overt motor symptoms.
2021-08-01 | GSE156647 | GEO