Project description:Staphylococcus aureus (S. aureus) is a gram-positive bacterium that causes a wide range of diseases. Terpinen-4-ol is a monoterpene component contained in most plant essential oils with good antibacterial activity. In this study, terpinen-4-ol effectively inhibited 13 strains of S. aureus, and effectively inhibited the biofilm of MRSA. Metabolomics and transcriptomics were used to elucidate changes in MRSA cells exposed to terpinen-4-ol. Terpinen-4-ol significantly changed (greater than a 2- or less than a 2-fold change) the expression of 304 genes and the level of 847 metabolites (greater than a 1.5- or less than a 0.67-fold change) in MRSA. The levels of genes and metabolites related to the valine, leucine and isoleucine biosynthesis metabolism pathway, the purine and pyrimidine metabolism pathway, energy metabolism and β-lactam resistance were dramatically changed in biofilms exposed to terpinen-4-ol. To the best of our knowledge, this research is the first to report the metabolite and expression profiles of MRSA exposed to terpinen-4-ol.
Project description:The interplay between pathogens and hosts has been studied for decades using targeted approaches such as the analysis of mutants and host immunological responses. Although much has been learned from such studies, they focus on individual pathways and fail to reveal the global effects of infection on the host. To alleviate this issue, high-throughput methods such as transcriptomics and proteomics have been used to study host-pathogen interactions. Recently, metabolomics was established as a new method to study changes in the biochemical composition of host tissues. We report a metabolomics study of Salmonella enterica serovar Typhimurium infection. We used Fourier Transform Ion Cyclotron Resonance Mass Spectrometry with Direct Infusion to reveal that dozens of host metabolic pathways are affected by Salmonella in a murine infection model. In particular, multiple host hormone pathways are disrupted. Our results identify unappreciated effects of infection on host metabolism and shed light on mechanisms used by Salmonella to cause disease, and by the host to counter infection. Female C57BL/6 mice were infected with Salmonella enterica serovar Typhimurium SL1344 cells by oral gavage. Feces and livers were collected and metabolites extracted using acetonitrile. For experiments with feces, samples were collected from 4 mice before and after infection. For liver experiments, 11 uninfected and 11 infected mice were used. Samples were combined into 3 groups of 3-4 mice each, resulting in the analysis of 3 group samples of uninfected and 3 of infected mice. Extracts were infused into a 12-T Apex-Qe hybrid quadrupole-FT-ICR mass spectrometer equipped with an Apollo II electrospray ionization source, a quadrupole mass filter and a hexapole collision cell. Raw mass spectrometry data were processed as described elsewhere (Han et al. 2008. Metabolomics. 4:128-140 [PMID 19081807]). To identify differences in metabolite composition between uninfected and infected samples, we filtered the list of masses for metabolites which were present on one set of samples but not the other. Additionally, we calculated the ratios between averaged intensities of metabolites from uninfected and infected mice. To assign possible metabolite identities, monoisotopic neutral masses of interest were queried against MassTrix (http://masstrix.org). Masses were searched against the Mus musculus database within a mass error of 3 ppm. Data were analyzed by unpaired t tests with 95% confidence intervals.
Project description:We have employed whole genome microarray expression to distinguish the effect of diversely functionalized magnetic silica nanoparticles on human HepaRG cells. Cells were exposed in vitro, and datasets of differentially expressed genes were identified for NPs versus control samples.
2017-09-23 | GSE98236 | GEO
Project description:Transcriptome sequencing of golden mussel foot exposed to magnetic nanoparticles
Project description:This is a prospective, multi-centered study to assess whether urine metabolomics can play a role in the screening of colorectal cancer (CRC). Urine samples will be collected from 1000 patients going through an established CRC screening program, and from a further 500 patients who already have a diagnosis of CRC. Using nuclear magnetic resonance (NMR) spectroscopy, the 1H NMR spectrum of urine samples will be analyzed for specific metabolites, and establish the metabolomic signature of colorectal cancer. The results from metabolomic urinalysis of this screening cohort will be compared with results from colonoscopy, histological descriptions, fecal occult blood testing (FOBT), and fecal immune testing (FIT) to assess the accuracy of urine metabolomics in identifying patients with polyps and malignancies. The urine metabolomic results from the colorectal cancer group will be correlated with operative, histological and clinical staging to define the role of urine metabolomics in assessing colorectal cancer type, location and stage. Additionally approximately 300 urine samples from breast cancer patients and 300 from prostate cancer patients will be collected to validate that the colorectal cancer signature is unique.
Project description:Untargeted metabolomic study of Vibrio cholerae using HR-LC-MS/MS in positive mode. Four groups were established based on growth mode (planktonic or biofilm) and Ag nanoparticle exposition (exposed or non-exposed).
Project description:Mussels (Mytilus galloprovincialis) were exposed during 24 hours to a waterborne infection with 10E8 CFU/ml Vibrio splendidus (reference strain LGP32) in the tank water. Five biological replicates were used for each infected and control conditions.
Project description:From the result of the gene expression analyses of human hepatoma cell line, HepG2, a number of genes associated with cell proliferation and DNA repair were distinctively up-regulated by Ag-nanoparticle exposure, suggesting that Ag-nanoparticles might stimulate cell proliferation and DNA damage, which are considered to be mechanisms playing an important role for carcinogenesis and tumor progression. The inductions of these genes involved in cell proliferation were also observed in PS-nanoparticles and Ag2CO3-exposed cells. In addition, the inductions of DNA repair-associated genes were also observed in Ag2CO3-exposure. These results suggest that both “nanoshape” and “silver” can cause the inductions of these gene expression patterns. Furthermore, cysteine, a strong ionic silver ligand partially abolished these gene expressions induced by silver nanoparticles. Ionic silver sourced from Ag-nanoparticles could not fully explain these gene expressions.
Project description:This dataset contains LC-MS raw files of Hs578T cell extracts exposed to doxorubicin and controls for untargeted metabolomics as part of:
A novel hybrid zwitterionic hydrophilic interaction liquid chromatography for untargeted metabolomics using rigorous metabolite identification approach reveals metabolic perturbations in doxorubicin-treated breast cancer cells