Summary of Study ST001056
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000709. The data can be accessed directly via it's Project DOI: 10.21228/M81M4X This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST001056 |
| Study Title | Evaluation of the short-term effects of the allelochemical umbelliferone on Triticum durum L. metabolism through GC-MS based untargeted metabolomics |
| Study Summary | Allelopathy is a plant defense mechanism by which they protect themselves from competitive species using specialized biochemicals in the form of secretion or volatiles released to the environment. Though, umbelliferone is a well-known allelochemical, its mechanism of action in a short-term treatment is far from established. We used ≈ 10–days old wheat seedlings treated with104 µM umbelliferone over a time course experiment covering 6 times points, i.e., 0h, 6h, 12h, 24h, 48h, and 96h and compared the metabolomic changes to control (mock-treated) plants. Using gas chromatography mass-spectrometry (GC-MS) based metabolomics efforts, we collectively obtained quantitative data on 177 metabolites that were derivatized (either derivatized singly or multiple times) or not representing 139 non-redundant (unique) metabolites. Out of these 139 metabolites, 118 were associated with a unique HMDB identifier, while 113 were associated with a KEGG identifier. Relative quantification of these metabolites across the time-course of umbelliferone treatment, revealed 22 compounds (sugars, fatty acids, secondary metabolites, organic acids, and amino acids) that changed significantly (repeated measures ANOVA, P-value < 0.05) with time. Using multivariate partial least squares discriminant analysis (PLS-DA) we showed the grouping of samples based on time-course across the control and umbelliferone treated plants, whereas the metabolite-metabolite Pearson correlation revealed tightly formed clusters of umbelliferone-derived metabolites, fatty acids, amino acids, and carbohydrates. Also, time-course of umbelliferone treatment revealed, that phospho-L-serine, maltose, and dehydroquinic acid were the top three metabolites showing highest importance in discrimination among the time-points. The above indicate a system-wide changes induced by umbelliferone, through dysregulation of primary as well as specialized metabolism. |
| Institute | Università Mediterranea di Reggio Calabria |
| Department | Dipartimento AGRARIA |
| Last Name | Araniti |
| First Name | Fabrizio |
| Address | Department AGRARIA, University Mediterranea of Reggio Calabria, Località Feo di Vito, SNC I-89124, Reggio Calabria RC, Italy |
| fabrizio.araniti@unirc.it | |
| Phone | +39-09651694283 |
| Submit Date | 2018-09-12 |
| Num Groups | 3 |
| Publications | In process |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | GC-MS |
| Release Date | 2020-01-13 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Sample Preparation:
| Sampleprep ID: | SP001371 |
| Sampleprep Summary: | Freshly homogenized (100 mg) plant material were obtained for each biological sample (plant) and replicates. These were transferred to a 2 ml microcentrifuge round bottom screw cap tubes (Eppendorf). Extraction was done by adding 1400 µl of methanol (at -20°C) and vortexing for 10 s after addition of 60 µl ribitol (0.2 mg/ml stock in dH2O) as an internal quantitative standard for the polar phase. Samples were transferred in a thermomixer at 70C and were shaken for 10 min (950 rpm) and were then further centrifuged for 10 min at 11000 g. The supernatants were collected and transferred to glass vials where 750 µl CHCl3 (-20°C) and 1500 µl dH2O (4°C) were sequentially added. All the samples were vortexed for 10 s and then centrifuged for another 15 min at 2200 g. Upper polar phase ((150 µl ) for each replicate were collected, transferred to a 1.5 ml tube and were dried in a vacuum concentrator without heating. Before freezing and storing at -80°C, the tubes were filled with argon and placed in a plastic bag with silica beads (for avoiding moisture and hydration during short-term storage). Before derivatization, stored samples, were placed in a vacuum concentrator for 30 minutes to eliminate any trace of humidity. Then, to the dried samples, 40 µl methoxyamine hydrochloride (20 mg/ml in pyridine) were added and incubated for 2 h in a Thermomixer (950 rpm) at 37 C. Methoxyaminated samples were then silylated by adding 70 µl of MSTFA to the aliquots. Samples were further shaken for 30 min at 37 C. |
| Sampleprep Protocol ID: | NA |
| Sampleprep Protocol Filename: | NA |
| Sampleprep Protocol Comments: | NA |
| Processing Method: | Freshly homogenized (100 mg) plant material were obtained for each biological sample (plant) and replicates. These were transferred to a 2 ml microcentrifuge round bottom screw cap tubes (Eppendorf). Extraction was done by adding 1400 µl of methanol (at -20°C) and vortexing for 10 s after addition of 60 µl ribitol (0.2 mg/ml stock in ddH2O) as an internal quantitative standard for the polar phase. Samples were transferred in a thermomixer at 70C and were shaken for 10 min (950 rpm) and were then further centrifuged for 10 min at 11000 g. The supernatants were collected and transferred to glass vials where 750 µl CHCl3 (-20°C) and 1500 µl ddH2O (4°C) were sequentially added. All the samples were vortexed for 10 s and then centrifuged for another 15 min at 2200 g. Upper polar phase (150 µl ) for each replicate were collected, transferred to a 1.5 ml tube and were dried in a vacuum concentrator without heating. Before freezing and storing at -80°C, the tubes were filled with argon and placed in a plastic bag with silica beads (for avoiding moisture and hydration during short-term storage). |
| Processing Storage Conditions: | On ice |
| Extraction Method: | Freshly homogenized (100 mg) plant material were obtained for each biological sample (plant) and replicates. These were transferred to a 2 ml microcentrifuge round bottom screw cap tubes (Eppendorf). Extraction was done by adding 1400 µl of methanol (at -20°C) and vortexing for 10 s after addition of 60 µl ribitol (0.2 mg/ml stock in ddH2O) as an internal quantitative standard for the polar phase. Samples were transferred in a thermomixer at 70C and were shaken for 10 min (950 rpm) and were then further centrifuged for 10 min at 11000 g. The supernatants were collected and transferred to glass vials where 750 µl CHCl3 (-20°C) and 1500 µl ddH2O (4°C) were sequentially added. All the samples were vortexed for 10 s and then centrifuged for another 15 min at 2200 g. Upper polar phase (150 µl ) for each replicate were collected, transferred to a 1.5 ml tube and were dried in a vacuum concentrator without heating. Before freezing and storing at -80°C, the tubes were filled with argon and placed in a plastic bag with silica beads (for avoiding moisture and hydration during short-term storage). |
| Extract Enrichment: | NA |
| Extract Cleanup: | NA |
| Extract Storage: | 4℃ |
| Sample Resuspension: | Dried for Derivatization |
| Sample Derivatization: | Methoxyaminatin + trimethylsilylation (MSTFA + 1% TMCS) |
| Sample Spiking: | 60 µl ribitol (0.2 mg/ml stock in ddH2O) |
| Subcellular Location: | NA |
