Summary of Study ST001880

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 PR001186. The data can be accessed directly via it's Project DOI: 10.21228/M8DD61 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.

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Study IDST001880
Study TitleNMR Predator Cues Target Signaling Pathways in Toxic Algal Metabolome (Polar metabolites)
Study Type1H NMR Metabolomics to elucidate signaling pathway
Study SummaryMetabolomics investigation of the phytoplankton Alexandrium minutum with and without copepod cues in order to explore cell signaling involved in toxin induction.
Institute
Georgia Institute of Technology
DepartmentSchool of Biological Sciences, School of Chemistry and Biochemistry, Center for Microbial Dynamics and Infection, Parker H. Petit Institute for Bioengineering and Bioscience
LaboratoryKubanek Lab
Last NameBrown
First NameEmily
Address950 Atlantic Dr Atlanta, Georgia USA 30332
Emailjulia.kubanek@biosci.gatech.edu
Phone404-894-8424
Submit Date2021-07-15
Num Groups2
Total Subjects40
Study CommentsPart 1 of 3. This part includes NMR analysis of polar metabolites using oPLSDA. Parts 2 and 3 inlcude NMR analysis of nonpolar metabolites and the corresponding mass spectrometry metabolomics for both polar and non-polar metabolites.
Raw Data AvailableYes
Raw Data File Type(s)fid
Analysis Type DetailNMR
Release Date2021-07-27
Release Version1
Emily Brown Emily Brown
https://dx.doi.org/10.21228/M8DD61
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001186
Project DOI:doi: 10.21228/M8DD61
Project Title:Predator Cues Target Signaling Pathways in Toxic Algal Metabolome
Project Type:Metabolomics to elucidate signaling pathway
Project Summary:Early detection of predators is critical to the survival of all living organisms. For phytoplankton, recognition and response to chemical cues from predators, as evidence of predation risk, is particularly crucial. The phytoplankton Alexandrium minutum upregulates its toxicity when exposed to copepodamides, a suite of compounds released by copepod predators. However, how A. minutum perceives these predatory cues and what metabolic pathways are involved in initiating toxin induction remains unknown. In this study LC/MS and NMR-based metabolomics uncovered subtle physiological responses of A. minutum to copepodamides, including dysregulation of valine biosynthesis and enhancement of butanoate metabolism and arginine biosynthesis. While we have yet to identify a chemoreceptor directly activated by copepod cues, based on the results of inhibition experiments detection of copepodamides appears to disrupt the activity of serine/threonine phosphatases leading to increased jasmonic acid biosynthesis and signaling, which leads to amplified gonyautoxin biosynthesis in A. minutum. This study is an important step toward a better understanding of chemosensory ecology of predator-prey interactions in phytoplankton.
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, GA, 30332, USA
Email:julia.kubanek@biosci.gatech.edu
Phone:404-894-8424
Project Comments:This study has 3 parts: 2 NMR (polar and non-polar metabolites) and MS
Contributors:Emily R. Brown, Sam G. Moore, David A. Gaul, and Julia Kubanek

Subject:

Subject ID:SU001960
Subject Type:Other organism
Subject Species:Alexandrium minutum
Taxonomy ID:39455
Genotype Strain:CCMP 113
Gender:Not applicable

Factors:

Subject type: Other organism; Subject species: Alexandrium minutum (Factor headings shown in green)

mb_sample_id local_sample_id Treatment
SA175050Control 16Control
SA175051Control 14Control
SA175052Control 13Control
SA175053Control 17Control
SA175054Control 19Control
SA175055Control 1Control
SA175056Control 20Control
SA175057Control 12Control
SA175058Control 18Control
SA175059Control 15Control
SA175060Control 5Control
SA175061Control 4Control
SA175062Control 11Control
SA175063Control 2Control
SA175064Control 6Control
SA175065Control 3Control
SA175066Control 7Control
SA175067Control 10Control
SA175068Control 9Control
SA175069Control 8Control
SA175070Copepodamide 15Copepodamide
SA175071Copepodamide 14Copepodamide
SA175072Copepodamide 13Copepodamide
SA175073Copepodamide 16Copepodamide
SA175074Copepodamide 19Copepodamide
SA175075Copepodamide 12Copepodamide
SA175076Copepodamide 20Copepodamide
SA175077Copepodamide 18Copepodamide
SA175078Copepodamide 17Copepodamide
SA175079Copepodamide 1Copepodamide
SA175080Copepodamide 5Copepodamide
SA175081Copepodamide 4Copepodamide
SA175082Copepodamide 3Copepodamide
SA175083Copepodamide 2Copepodamide
SA175084Copepodamide 6Copepodamide
SA175085Copepodamide 7Copepodamide
SA175086Copepodamide 10Copepodamide
SA175087Copepodamide 9Copepodamide
SA175088Copepodamide 8Copepodamide
SA175089Copepodamide 11Copepodamide
Showing results 1 to 40 of 40

Collection:

Collection ID:CO001953
Collection Summary:Alexandrium minutum 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:Predator_Cues_Target_Signaling_Pathways_in_Toxic_Algal_Metabolome_protocol.pdf
Sample Type:Algae
Collection Method:Filtration and Freeze
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001972
Treatment Summary:Twice, first at the start of the experiment and again 24 h later, 1.5 mL of either 0.2 µM copepodamides (copepod cue) in DMSO (treatment, n=20) or DMSO alone (control, n=20) were added aseptically to 300 mL cultures of Alexandrium minutum resulting in a final concentration of 1 nM copepodamides.
Treatment Protocol Filename:Predator_Cues_Target_Signaling_Pathways_in_Toxic_Algal_Metabolome_protocol.pdf

Sample Preparation:

Sampleprep ID:SP001966
Sampleprep Summary:Polar extracts were dissolved at a concentration equivalent to 1.70 x 10^7 A. minutum cells mL-1 in 90:10 H2O/D2O (99.96% atom D2O; Cambridge Isotope Labs) with 0.2 mM phosphate buffer (pH 7.4) and 0.25 mM 3 (trimethylsilyl)propionic 2,2,3,3d 4 acid (TMSP), as internal standard, for 1H NMR spectroscopy analysis. The media blank extract was prepared in the smallest volume of solvent possible (175 µL). Particulates were excluded by briefly centrifuging the samples and then carefully transferring the extracts into 3 mm NMR tubes. The extracts were analyzed using a Bruker Avance IIIHD 800 MHz NMR spectrometer equipped with a 3 mm triple resonance broadband cryoprobe. Spectra for the polar extracts were acquired using a 1D water presaturation (Bruker zgpr pulse sequence) with a spectral width of 12 kHz centered at 3758.36 Hz, with a relaxation delay 3 s, over 480 scans.
Sampleprep Protocol Filename:Predator Cues Target Signaling Pathways in Toxic Algal Metabolome_protocol.pdf
Extract Storage:-80℃

Analysis:

Analysis ID:AN003046
Analysis Type:NMR
Results File:Preprocessed_binned_polar_NMRmetabolomics.txt
Units:area under the curve

NMR:

NMR ID:NM000211
Analysis ID:AN003046
Instrument Name:Bruker Avance IIIHD
Instrument Type:FT-NMR
NMR Experiment Type:1D-1H
Spectrometer Frequency:800 MHz
NMR Probe:3 mm triple resonance broadband cryoprobe
NMR Solvent:90:10 H2O/D2O (99.96% atom D2O; Cambridge Isotope Labs) with 0.2 mM phosphate buffer (pH 7.4) and 0.25 mM 3-(trimethylsilyl)propionic-2,2,3,3d4-acid
NMR Tube Size:3 mm
Pulse Sequence:zgpr
Number Of Scans:480
Relaxation Delay:3s
Spectral Width:12 kHz
Baseline Correction Method:Spline
Binned Increment:0.005 ppm
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