Summary of Study ST001896
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 PR001188. The data can be accessed directly via it's Project DOI: 10.21228/M84X4Z 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 | ST001896 |
| Study Title | NMR Differentiating toxic and nontoxic congeneric harmful algae using the non-polar metabolome (Experiment 2) |
| Study Type | 1H NMR Metabolomics to compare toxic and non-toxic species |
| Study Summary | Metabolomics comparison of toxic and non-toxic species of phytoplankton from the genus Alexandrium.This study was carried out using 2 pairwise experiments, A. catenella compared to A. tamarense (Experiment 1) and A. pacificum compared to A. tamarense (Experiment 2). This study includes the NMR data from Experiment 2. |
| Institute | Georgia Institute of Technology |
| Department | School of Biological Sciences, School of Chemistry and Biochemistry, Center for Microbial Dynamics and Infection, Parker H. Petit Institute for Bioengineering and Bioscience |
| Laboratory | Kubanek Lab |
| Last Name | Brown |
| First Name | Emily |
| Address | 950 Atlantic Dr Atlanta, Georgia USA 30332 |
| julia.kubanek@biosci.gatech.edu | |
| Phone | 404-894-8424 |
| Submit Date | 2021-07-20 |
| Num Groups | 2 |
| Total Subjects | 30 |
| Study Comments | Part 2 of 3. This part includes NMR analysis of non-polar metabolites from Experiment 2 using oPLSDA. Parts 1 and 3 inlcude NMR analysis of non-polar metabolites from Experiment 1 and the corresponding mass spectrometry metabolomics for both Experiments 1 and 2. |
| Raw Data Available | Yes |
| Raw Data File Type(s) | fid |
| Analysis Type Detail | NMR |
| Release Date | 2021-08-09 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001188 |
| Project DOI: | doi: 10.21228/M84X4Z |
| Project Title: | Differentiating toxic and nontoxic congeneric harmful algae using the non-polar metabolome |
| Project Summary: | Recognition and rejection of chemically defended prey is critical to maximizing fitness for predators. Paralytic shellfish toxins (PSTs) which strongly inhibit voltage-gated sodium channels in diverse animal taxa are produced by several species of the bloom-forming algal genus Alexandrium where they appear to function as chemical defenses against grazing copepods. Despite PSTs being produced and localized within phytoplankton cells, some copepods distinguish toxic from non-toxic prey, selectively ingesting less toxic cells, in ways that suggest cell surface recognition perhaps associated with non-polar metabolites. In this study LC/MS and NMR-based metabolomics revealed that the non-polar metabolomes of two toxic species (Alexandrium catenella and Alexandrium pacificum) vary considerably from their non-toxic congener Alexandrium tamarense despite all three being very closely related. Toxic and non-toxic Alexandrium spp. were distinguished from each other by metabolites belonging to seven lipid classes. Of these, 17 specific metabolites were significantly more abundant in both toxic A. catenella and A. pacificum compared to non-toxic A. tamarense suggesting that just a small portion of the observed metabolic variability is associated with toxicity. Future experiments aimed at deciphering chemoreception mechanisms of copepod perception of Alexandrium toxicity should consider these metabolites, and the broader lipid classes phosphatidylcholines and sterols, as potential candidate cues. |
| Institute: | Georgia Institute of Technology |
| Last Name: | Brown |
| First Name: | Emily |
| Address: | 950 Atlantic Dr Atlanta GA 30332, USA |
| Email: | julia.kubanek@biosci.gatech.edu |
| Phone: | 404-894-8424 |
Subject:
| Subject ID: | SU001974 |
| Subject Type: | Other organism |
| Subject Species: | Alexandrium pacificum; Alexandrium tamarense |
| Taxonomy ID: | 1565494; 2926 |
| Genotype Strain: | CCMP 1493; CCMP 2023 |
| Gender: | Not applicable |
Factors:
Subject type: Other organism; Subject species: Alexandrium pacificum; Alexandrium tamarense (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA176028 | Apacificum 11 | Alexandrium_pacificum |
| SA176029 | Apacificum 10 | Alexandrium_pacificum |
| SA176030 | Apacificum 13 | Alexandrium_pacificum |
| SA176031 | Apacificum 15 | Alexandrium_pacificum |
| SA176032 | Apacificum 1 | Alexandrium_pacificum |
| SA176033 | Apacificum 9 | Alexandrium_pacificum |
| SA176034 | Apacificum 14 | Alexandrium_pacificum |
| SA176035 | Apacificum 12 | Alexandrium_pacificum |
| SA176036 | Apacificum 4 | Alexandrium_pacificum |
| SA176037 | Apacificum 8 | Alexandrium_pacificum |
| SA176038 | Apacificum 2 | Alexandrium_pacificum |
| SA176039 | Apacificum 5 | Alexandrium_pacificum |
| SA176040 | Apacificum 3 | Alexandrium_pacificum |
| SA176041 | Apacificum 6 | Alexandrium_pacificum |
| SA176042 | Apacificum 7 | Alexandrium_pacificum |
| SA176043 | Atamarense 10 | Alexandrium_tamarense |
| SA176044 | Atamarense 11 | Alexandrium_tamarense |
| SA176045 | Atamarense 12 | Alexandrium_tamarense |
| SA176046 | Atamarense 14 | Alexandrium_tamarense |
| SA176047 | Atamarense 9 | Alexandrium_tamarense |
| SA176048 | Atamarense 15 | Alexandrium_tamarense |
| SA176049 | Atamarense 13 | Alexandrium_tamarense |
| SA176050 | Atamarense 1 | Alexandrium_tamarense |
| SA176051 | Atamarense 3 | Alexandrium_tamarense |
| SA176052 | Atamarense 2 | Alexandrium_tamarense |
| SA176053 | Atamarense 4 | Alexandrium_tamarense |
| SA176054 | Atamarense 5 | Alexandrium_tamarense |
| SA176055 | Atamarense 7 | Alexandrium_tamarense |
| SA176056 | Atamarense 6 | Alexandrium_tamarense |
| SA176057 | Atamarense 8 | Alexandrium_tamarense |
| Showing results 1 to 30 of 30 |
Collection:
| Collection ID: | CO001967 |
| Collection Summary: | Alexandrium cells were collected by vacuum filtration onto GF/F filters and quenched with liquid nitrogen. Frozen cells with filters were stored in foil (previously muffled for 3 h at 450 °C) at -80 °C until extraction. |
| Collection Protocol Filename: | Differentiating_toxic_and_nontoxic_congeneric_harmful_algae_using_the_non-polar_metabolome_protocol.pdf |
| Sample Type: | Algae |
| Collection Method: | Filtration and Freeze |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001986 |
| Treatment Summary: | Metabolomes of toxic versus non-toxic species were compared using the following experimental pairings: A. tamarense (n=15) with A. catenella (n=15) (Experiment 1) and A. tamarense (n=15) with A. pacificum (n=15) (Experiment 2). The same non-toxic strain of A. tamarense was used in both experiments but the two experiments were conducted separately, in different months, to make the experiment manageable based on availability of batches grown from stock cultures. For both experiments, Alexandrium spp. cultures at a cell density of 12,000 to 13,000 cells mL-1 were split into fifteen 300 mL subcultures of each species which grew for two days. At the end of each experiment, during harvesting, a 1.0 mL aliquot from each culture was preserved with Lugol’s solution to measure cell concentrations |
| Treatment Protocol Filename: | Differentiating_toxic_and_nontoxic_congeneric_harmful_algae_using_the_non-polar_metabolome_protocol.pdf |
| Treatment: | Species comparison |
Sample Preparation:
| Sampleprep ID: | SP001980 |
| Sampleprep Summary: | Non polar extracts were dissolved with volumes calculated to account for different cell densities at the time of harvesting, to a concentration equivalent to 1.62 x 10^7 Alexandrium cells mL-1 in dimethyl sulfoxide d6 (99.9% atom d6-DMSO; Cambridge Isotope Labs) containing 0.1% trimethylsilane (TMS) as internal standard for 1H nuclear magnetic resonance (NMR) spectroscopy analysis. The extracts were transferred to 3 mm NMR tubes. Extracts from Experiment 2 (A. tamarense-A. pacificum) were analyzed using a Bruker Avance IIIHD 700 MHz NMR spectrometer equipped with a 5 mm indirect broadband cryoprobe, because the 800 MHz instrument was unavailable at the time of data acquisition. Spectra of non-polar extracts from both experiments were acquired using a Bruker zg30 pulse sequence 1H NMR experiment compiled from 320 scans. Due to poor NMR spectral quality two A. pacificum and four A. tamarense replicate spectra were removed for Experiment 2. |
| Sampleprep Protocol Filename: | Differentiating toxic and nontoxic congeneric harmful algae using the non-polar metabolome_protocol.pdf |
| Extract Storage: | -80℃ |
Analysis:
| Analysis ID: | AN003077 |
| Analysis Type: | NMR |
| Results File: | Preprocessed_binned_Experiment2_ApvAt_NMRmetabolomics.txt |
| Units: | area under the curve |
NMR:
| NMR ID: | NM000213 |
| Analysis ID: | AN003077 |
| Instrument Name: | Bruker Avance IIIHD |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 1D-1H |
| Spectrometer Frequency: | 700 MHz |
| NMR Probe: | 5 mm indirect broadband cryoprobe |
| NMR Solvent: | Dimethyl sulfoxide d6 (99.9% atom d6-DMSO; Cambridge Isotope Labs) containing 0.1% trimethylsilane |
| NMR Tube Size: | 3 mm |
| Pulse Sequence: | zg30 |
| Number Of Scans: | 320 |
| Baseline Correction Method: | Spline |
| Binned Increment: | 0.005 ppm |
