Summary of Study ST001296
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 PR000877. The data can be accessed directly via it's Project DOI: 10.21228/M8B382 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST001296 |
| Study Title | Metabolomics and Hormonomics to Crack the Code of Filbert Growth |
| Study Summary | Introduction: Plants respond to changes in their environments through hormonal activation of a physiological cascade that redirects metabolic resources and growth. In filberts (Corylus sp.), chelated iron promotes the growth of new shoots but the mechanism(s) are not understood. Objectives: To use untargeted metabolomics and hormonomics approaches to generate novel hypotheses for the morphoregulatory role of ferric ethylenediamine-N,N'-di-(ortho-hydroxyphenyl) acetic acid (Fe-EDDHA) in filbert shoot organogenesis in vitro. Methods: Data were generated using previously optimized standardized untargeted metabolomics protocols with time of flight mass spectrometry. Multivariate statistical tools (principal component and partial least squares discriminant analysis) did not detect significant differences. Discovery tools Significance Analysis of Microarrays (SAM), multiple linear regression analysis, Bayesian analysis, logical algorithms, machine learning, synthetic biotransformations, targeted hormonomics, and online resources including MetaboAnalyst were used. Results: Starch/sucrose metabolism and shikimate pathway metabolites were increased. Dose dependent decreases were found in polyphenol metabolism, specifically ellagic acid and its methylated derivative 3,4,3'-tri-O-methylellagic acid. Hormonomics analysis revealed significant differences in phytohormones and their conjugates. FeEDDHA treatment reduced indole-3-acetic acid, abscisic acid, salicylic acid, jasmonic acid conjugates (JA-Trp, JA-Ile, OH-JA) and dihydrozeatinglucoside in regenerating explants. Serotonin (5HT) was decreased in FeEDDHA-treated regenerating tissues while the related metabolite melatonin was increased. Eight phenolic conjugates of 5HT and eight catabolites were affected by FeEDDHA indicating that metabolism to sequester, deactivate and metabolize 5HT was induced by Fe(III). Tryptophan was metabolized through kynurenine but not anthranilate. Conclusion: Seven novel hypotheses were generated to guide future studies to understand the regulatory control(s) of shoot organogenesis. |
| Institute | University of British Columbia |
| Department | Chemistry |
| Laboratory | PlantSMART |
| Last Name | Murch |
| First Name | Susan |
| Address | 3247 University Way |
| susan.murch@ubc.ca | |
| Phone | 250-807-9566 |
| Submit Date | 2019-12-20 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Waters) |
| Analysis Type Detail | LC-MS |
| Release Date | 2020-06-20 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000877 |
| Project DOI: | doi: 10.21228/M8B382 |
| Project Title: | Metabolomics and Hormonomics to Crack the Code of Filbert Growth |
| Project Type: | Plant Untargeted MS Metabolomics |
| Project Summary: | Introduction: Plants respond to changes in their environments through hormonal activation of a physiological cascade that redirects metabolic resources and growth. In filberts (Corylus sp.), chelated iron promotes the growth of new shoots but the mechanism(s) are not understood. Objectives: To use untargeted metabolomics and hormonomics approaches to generate novel hypotheses for the morphoregulatory role of ferric ethylenediamine-N,N'-di-(ortho-hydroxyphenyl) acetic acid (Fe-EDDHA) in filbert shoot organogenesis in vitro. Methods: Data were generated using previously optimized standardized untargeted metabolomics protocols with time of flight mass spectrometry. Multivariate statistical tools (principal component and partial least squares discriminant analysis) did not detect significant differences. Discovery tools Significance Analysis of Microarrays (SAM), multiple linear regression analysis, Bayesian analysis, logical algorithms, machine learning, synthetic biotransformations, targeted hormonomics, and online resources including MetaboAnalyst were used. Results: Starch/sucrose metabolism and shikimate pathway metabolites were increased. Dose dependent decreases were found in polyphenol metabolism, specifically ellagic acid and its methylated derivative 3,4,3'-tri-O-methylellagic acid. Hormonomics analysis revealed significant differences in phytohormones and their conjugates. FeEDDHA treatment reduced indole-3-acetic acid, abscisic acid, salicylic acid, jasmonic acid conjugates (JA-Trp, JA-Ile, OH-JA) and dihydrozeatinglucoside in regenerating explants. Serotonin (5HT) was decreased in FeEDDHA-treated regenerating tissues while the related metabolite melatonin was increased. Eight phenolic conjugates of 5HT and eight catabolites were affected by FeEDDHA indicating that metabolism to sequester, deactivate and metabolize 5HT was induced by Fe(III). Tryptophan was metabolized through kynurenine but not anthranilate. Conclusion: Seven novel hypotheses were generated to guide future studies to understand the regulatory control(s) of shoot organogenesis. |
| Institute: | University of British Columbia |
| Department: | Chemistry |
| Laboratory: | PlantSMART |
| Last Name: | Murch |
| First Name: | Susan |
| Address: | 3247 University Way |
| Email: | susan.murch@ubc.ca |
| Phone: | 250-807-9566 |
| Contributors: | Lauren A E Erland, Christina E Turi, Praveen K Saxena, Susan J Murch |
Subject:
| Subject ID: | SU001370 |
| Subject Type: | Plant |
| Subject Species: | Corylus avellana;Corylus americana |
| Taxonomy ID: | 13451;78632 |
| Genotype Strain: | Corylus avellana;Corylus americana(cv Geneva) |
Factors:
Subject type: Plant; Subject species: Corylus avellana;Corylus americana (Factor headings shown in green)
| mb_sample_id | local_sample_id | FeEDDHA (µM) |
|---|---|---|
| SA094156 | 10_18_2011 M1C | - |
| SA094157 | 10_18_2011 M1B | - |
| SA094158 | 10_18_2011 M1A | - |
| SA094159 | 10_18_2011 M2C | 230 |
| SA094160 | 10_18_2011 M2A | 230 |
| SA094161 | 10_18_2011 M2B | 230 |
| SA094162 | 10_18_2011 M3B | 460 |
| SA094163 | 10_18_2011 M3A | 460 |
| SA094164 | 10_18_2011 M3C | 460 |
| SA094165 | 10_18_2011 M4C | 690 |
| SA094166 | 10_18_2011 M4A | 690 |
| SA094167 | 10_18_2011 M4B | 690 |
| Showing results 1 to 12 of 12 |
Collection:
| Collection ID: | CO001365 |
| Collection Summary: | Cultures were sampled in triplicate on day 35 of the culture period, |
| Sample Type: | Plant |
Treatment:
| Treatment ID: | TR001385 |
| Treatment Summary: | Filbert (C. avellana L. × C. americana Marshall cv. Geneva; Grimo Nut Nursery, Niagara-on-the-Lake, ON, Canada) shoot cultures were provided from germplasm maintained at the Gosling Research Institute for Plant Preservation (GRIPP; University of Guelph, Guelph, ON). Plantlets were grown in GA-7 vessels according to methods previously described (Garrison et al. 2013; Latawa et al. 2016). In brief, cultures were grown on semi-solid modified NCGR-COR medium (Yu and Reed 1995) supplemented with 10 g L-1 myo-inositol, 200 mg L-1 glycine, 100 mg L-1 nicotinic acid, 100 mg L-1 thiamine (PhytoTechnology Laboratories), 17.6 µM benzylaminopurine (BAP; Sigma-Aldrich), 0.014 µM indole-3-butyric acid (IBA; Sigma-Aldrich), 0.29 µM gibberellic acid (GA3; PhytoTechnology Laboratories), and 30 g L-1 glucose with 0, 230, 460 and 690 µM Fe-EDDHA (Sigma, St. Louis, MO) and the pH of the medium was adjusted to 5.7 before autoclaving at 121 ºC for 20 min. Cultures were maintained in a growth room at 23 ± 2oC with a 16 h photoperiod of 40 µmol m-2 s-1 provided by cool-white fluorescent lamps (Osram Sylvania Ltd., Mississauga, ON, Canada). |
Sample Preparation:
| Sampleprep ID: | SP001378 |
| Sampleprep Summary: | Cultures were sampled in triplicate on day 35 of the culture period, accurately weighed (50 mg), and homogenized in 1 mL of 70% ethanol for 30 s (Kontes Pellet Pestle, Fisher Scientific). Samples were centrifuged (16,000 x g) for 3 min to settle particulate matter and the supernatant was filtered (0.1 µm, Ultrafree-MC filtered centrifuge tubes; Millipore, MS, USA) prior to chromatography. |
Combined analysis:
| Analysis ID | AN002157 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Waters Acquity |
| Column | Waters BEH Acquity C18 (150 x 2.1mm,1.7um) |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | Waters Micromass QTOF Premier |
| Ion Mode | POSITIVE |
| Units | Peak Intensity |
Chromatography:
| Chromatography ID: | CH001575 |
| Chromatography Summary: | Extracts and 70% ethanol blanks (n=3 for each treatment) were separated using a Waters BEH Acquity C18 (2.1 X 150 mm, 1.7 µm) column with the following gradient: 0.1% aqueous formic acid:acetonitrile (0.0-25 min, 95:5-5:95 v/v, 25.01-30.0 min, 95:5 v/v). The flow rate was set to 0.25 mL min-1 for 30 mins at 30 ◦C (Waters Acquity UPLC). |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters BEH Acquity C18 (150 x 2.1mm,1.7um) |
| Column Temperature: | 30 |
| Flow Gradient: | 0.0 - 10.0 min, : 95:5-5:95 v/v, 10.0-15.0 min, 5:95 v/v, 15.0-20.0min, 5:95-95:5 v/v, 20.0-25.0min, 95:5 v/v) |
| Flow Rate: | 0.25 ml/min |
| Solvent A: | 100% water; 1% formic acid |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002006 |
| Analysis ID: | AN002157 |
| Instrument Name: | Waters Micromass QTOF Premier |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | A steady flow of leucine enkephalin (Waters 1525 HPLC binary solvent manager, 2 ng mL-1) was used as the internal standard for calibration of the Micromass LCT Premier series ToF-MS (Waters Inc.). Time of flight mass spectrometry was used with previously published optimized conditions (Brown, Murch, et al. 2012; Brown et al. 2012) including: electrospray ionization and positive ion detection in W mode, mass range of 100-1000 amu and a scan time of 0.1s. Data were collected with MassLynx V4.1 and exported via MarkerLynx. Data were processed in Excel™ to align retention times and remove multiply charged ions as described previously (Brown et al. 2012; Brown et al. 2012; Turi and Murch 2013; Turi et al. 2014). |
| Ion Mode: | POSITIVE |
