Summary of Study ST001881

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 IDST001881
Study TitleNMR Predator Cues Target Signaling Pathways in Toxic Algal Metabolome (Non-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 Date2021-07-19
Num Groups2
Total Subjects40
Study CommentsPart 2 of 3. This part includes NMR analysis of non-polar metabolites using oPLSDA. Parts 1 and 3 inlcude NMR analysis of polar 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:SU001958
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
SA174961Control 16Control
SA174962Control 14Control
SA174963Control 13Control
SA174964Control 17Control
SA174965Control 19Control
SA174966Control 1Control
SA174967Control 20Control
SA174968Control 12Control
SA174969Control 18Control
SA174970Control 15Control
SA174971Control 5Control
SA174972Control 4Control
SA174973Control 11Control
SA174974Control 2Control
SA174975Control 6Control
SA174976Control 3Control
SA174977Control 7Control
SA174978Control 10Control
SA174979Control 9Control
SA174980Control 8Control
SA174981Copepodamide 15Copepodamide
SA174982Copepodamide 14Copepodamide
SA174983Copepodamide 13Copepodamide
SA174984Copepodamide 16Copepodamide
SA174985Copepodamide 19Copepodamide
SA174986Copepodamide 12Copepodamide
SA174987Copepodamide 20Copepodamide
SA174988Copepodamide 18Copepodamide
SA174989Copepodamide 17Copepodamide
SA174990Copepodamide 1Copepodamide
SA174991Copepodamide 5Copepodamide
SA174992Copepodamide 4Copepodamide
SA174993Copepodamide 3Copepodamide
SA174994Copepodamide 2Copepodamide
SA174995Copepodamide 6Copepodamide
SA174996Copepodamide 7Copepodamide
SA174997Copepodamide 10Copepodamide
SA174998Copepodamide 9Copepodamide
SA174999Copepodamide 8Copepodamide
SA175000Copepodamide 11Copepodamide
Showing results 1 to 40 of 40

Collection:

Collection ID:CO001951
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 ID: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:TR001970
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:SP001964
Sampleprep Summary:Non-polar extracts were dissolved at a concentration equivalent to 2.27 x 10^7 A. minutum cells mL-1 in dimethyl sulfoxide d6 (99.9% atom d6-DMSO; Cambridge Isotope Labs) containing 0.1% trimethylsilane (TMS), as internal standard. The media blank extract was prepared in the smallest volume of solvent possible (175 µL). The non-polar extracts were transferred to 3 mm NMR tubes, and analyzed using a Bruker Avance IIIHD 800 MHz NMR spectrometer equipped with a 3 mm triple resonance broadband cryoprobe. Spectra of non-polar extracts were acquired using a simple 1H NMR experiment (Bruker zg30 pulse sequence) with a spectral width of 9.6 kHz centered at 4400.00 Hz over 320 scans. One treatment replicate was lost and therefore its spectrum was not acquired.
Sampleprep Protocol Filename:Predator Cues Target Signaling Pathways in Toxic Algal Metabolome_protocol.pdf
Extract Storage:-80℃

Analysis:

Analysis ID:AN003041
Analysis Type:NMR
Results File:Preprocessed_binned_nonpolar_NMRmetabolomics.txt
Units:area under the curve

NMR:

NMR ID:NM000210
Analysis ID:AN003041
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: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
Spectral Width:9.6 kHz
Baseline Correction Method:Spline
Binned Increment:0.005 ppm
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