|PRIMe: Platform for RIKEN Metabolomics|
Atsushi Fukushima, Miyako Kusano, Kenji Akiyama, Takeshi Obayashi, Takayuki Tohge, Masami Yokota Hirai, Shigehiko Kanaya, Masanori Arita, Yoko Shinbo, Kazuo Shinozaki, Tetsuya Sakurai and Kazuki Saito
We have developed a web-based database, "PRIMe (Platform for RIKEN Metabolomics)," which contains powerful tools for researchers to analyze gene co-expression data and mass spectral data. PRIMe has been developed with the main aim of facilitating integrated analysis for transcriptomics and metabolomics.
|Revealing Host Metabolome Reprogramming by the Economically Important Fungal Plant Pathogens Botrytis cinerea and Magnaporthe grisea|
Aileen R., Smith J., William Allwood, Amanda J. Lloyd, David I. Ellis, Royston Goodacre and Luis A.J. Mur
Metabolomic approaches including Fourier- transform infrared (FT-IR) spectroscopy and Electrospray ionisation mass spectrometry (ESI-MS) were used to elucidate changes during susceptible and resistant interactions of Magnaporthe grisea with B. distachyon. Following data mining, discriminatory analytes (m/z) were shown to be phospholipids (PL) by ESIMS-MS. We are now moving to correlate transcriptional and metabolomic changes, concentrating on PL-based regulation.
|Temporal Dynamics of Pathogenesis Related Metabolites and their Metabolic Pathways Following Inoculation of Potato Leaves with Phytophthora infestans|
Y. Abu-Nada, A. C. Kushalappa, W. D. Marshall, K. Al-Mughrabi, and A. Murphy
The resistance in potato cultivars against late blight caused by Phytophthora infestans is classified into vertical and horizontal. Several metabolites associated with resistance have been detected: phytoalexins such as rishitin, phytuberin, lubimin, solavetivone etc. Metabolite profiling is a novel technology for the discrimination of quantitative resistance in plants against pathogen stress.
|Towards Understanding of Ryegrass-Endophyte Symbiosis through Data Integration of Transcriptome and Metabolome|
Mingshu Cao, Linda Johnson, Albert Koulman, Geoff Lane and Susanne Rasmussen
Combined with extensive bioinformatics analyses, our joint analysis of transcriptomics and metabolomics data has generated interesting findings which led to further laboratory verification, such as potential genes associated with alkaloid production.
|Ethnopharmacological Evaluation of Radal (leaves of Lomatia hirsuta) through Metabolite Profiling and Isolation of 2-Methoxyjuglone.|
Henrik Toft Simonsena, Louise Berthelsenb, Anne Adsersenb, Søren Brøgger Christensenb, Alfonso Guzmánb and Per Mølgaardb
To evaluate the efficacy of the traditionally used herbal remedy Radal a metabolite profile of the original plant material was established. The EtOAc extract of the leaves and found to be active against the pathogenic fungus Candida albicans (MIC = 8 µg/ml). Cinnamic acid (2) and vanillic acid (5) were identified as the major constituents in the tea by GC-MS along with other phenolic derivatives.
|The Comparison of Lipid Extraction Methods for the Lipidomic Analysis of Human Blood Plasma|
Ali Awwad, Catharine Ortori, Dave A. Barrett and Clare A. Daykin
Although metabolomics is and should remain an integrated approach by itself, its complexity requires analogous approaches focused on its components, such as lipidomics. Lipid profiling by NMR without sample extraction, should be seen as only the first stage in lipidomic analysis. Subsequent analysis should involve extraction of the lipids from the biofluid or tissue prior to further profiling using a multi-technique metabolomic approach involving both NMR and MS.
|Profiling of Urinary Metabolites|
Vladimir V. Tolstikov, Tobias Kind, Kindra D. Brooks and Robert H. Weiss
Urine samples from healthy individuals and kidney cancer patients were used for metabolic profiling method development and for urine metabolome analysis.
|Biomarker Identification Combining Multivariate Analysis of NMR Spectra with an Innovative Spectral Data Analysis Approach in an Integrated Working Environment |
Regis Grenier, Yann Bidault, Chen Peng, Gregory M. Banik, Scott Ramos, Brian Rohrback, Tao Wang and Bin Xia,
A recently developed Metabolomics informatics solution from raw data processing to metabolite database searching, compatible with multiple instruments, has been successfully applied to the analysis of 1H NMR human serum spectra of diabetic and non-diabetic subjects. This study also highlights Overlap Density Heatmap, a novel technology that complements the use of chemometrics in biomarker identification.
|Constructing Directed Metabolic Networks from Microarray Data|
J. M. Easton, T. N. Arvanitis, A. Peet and M. Viant
Although it has been several years since metabolic networks became a commonly used analysis technique in bioinformatics, the question of how best to construct them from experimental data is still not satisfactorily resolved. Here we present a method for the construction of directed metabolic networks from microarray datasets using an enhanced version of the KEGG LIGAND database.
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