http://lod.bco-dmo.org/id/dataset/731159
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2018-03-20
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
NMR-based polar metabolomics on diatom response to allelopathic chemicals from the red tide dinoflagellate (Karenia brevis)
2017-03-20
publication
2017-03-20
revision
BCO-DMO Linked Data URI
2017-03-20
creation
http://lod.bco-dmo.org/id/dataset/731159
Julia Kubanek
Georgia Institute of Technology
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Kubanek, J. (2017) NMR-based polar metabolomics on diatom response to allelopathic chemicals from the red tide dinoflagellate (Karenia brevis). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2017-03-20 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/731159 [access date]
NMR-based polar metabolomics on diatom response to allelopathic chemicals from the red tide dinoflagellate (Karenia brevis) Dataset Description: <p>NMR-based polar metabolomics on diatom response to allelopathic chemicals from the red tide dinoflagellate (Karenia brevis).</p>
<p>The raw NMR spectral data are also available at:&nbsp;<a href="https://smartech.gatech.edu/handle/1853/59097" target="_blank">https://smartech.gatech.edu/handle/1853/59097</a></p> Methods and Sampling: <p>Please see supporting information file associated with publication:<br />
Poulson-Ellestad, Jones, Roy, Viant, Fernandez, Kubanek, Nunn (2014) Metabolomics and proteomics reveal impacts of chemically mediated competition on marine plankton. Proc. Natl. Acad. Sci. USA 111:9009-9014. doi:<a href="http://dx.doi.org/10.1073/pnas.1402130111" target="_blank">10.1073/pnas.1402130111</a></p>
<p>Spectra were collected on a Bruker Avance 500-MHz DRX NMR spectrometer equipped with a 5-mm broadband direct probe, with an excitation-sculpting gradient pulse program for water suppression as follows: 11-μs (90°) pulse, 22-μs (180°) pulse, and 2-ms (108°) shaped pulse (5). The spectral width was 5.5 kHz, with a relaxation delay of 1 s. For each sample, 256 scans were compiled to gather adequate signal for analysis.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1060300 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1060300
completed
Julia Kubanek
Georgia Institute of Technology
404-894-8424
School of Biological Sciences Georgia Institute of Technology
Atlanta
GA
30332-0230
USA
julia.kubanek@biosci.gatech.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Bruker Avance 500-MHz DRX NMR spectrometer
theme
None, User defined
Nuclear Magnetic Resonance Spectrometers
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Waterborne chemical cues in the plankton: a systems biology approach
http://devwp.kubanek.biology.gatech.edu/red-tide-competition-and-metabolomics/
Waterborne chemical cues in the plankton: a systems biology approach
<p><em>Description from NSF award abstract:</em><br />
Competition is a major force structuring communities, including the marine plankton. The release of compounds that inhibit competitors, a process known as allelopathy, is hypothesized to be important among phytoplankton, especially for species that compete poorly for resources yet form dense blooms. Ecological interactions involving the toxic red tide dinoflagellate <em>Karenia brevis</em> present an ideal system for understanding chemically mediated interactions. Blooms of this species occur frequently in accessible coastal areas of the Gulf of Mexico, causing massive fish kills and contaminating shellfish. The dramatic consequences of these blooms motivate the following questions. What strategies does this harmful alga use in competition with other phytoplankton? What lethal and sub-lethal effects are experienced by competitors? How do phytoplankton respond, resist, and detoxify their surroundings? What roles do chemical cues play in these interactions? How are different phytoplankton communities affected by allelopathy?</p>
<p>Previous studies have shown that <em>K. brevis</em> is allelopathic to several naturally co-occurring phytoplankton species, but compounds other than the known neurotoxic brevetoxins produced by <em>K. brevis</em> generally were responsible. This species produces allelopathic mixtures of unstable, 500-1000 Da organic compounds which cause reduced photosystem II activity and disrupt cell membranes of sensitive species, whereas some other competitors remain unaffected. Moreover, natural blooms of <em>K. brevis </em>were allelopathic to the competing diatom <em>Skeletonema grethae</em>. This species, in turn, appeared to influence the chemistry of <em>K. brevis</em>, reducing its allelopathic effects. Death is a rare outcome of <em>K. brevis </em>allelopathy; more subtle, non-lethal responses have predominated. Overall, environmental context may be critical for predicting what ecologically important chemical mediators are released into marine systems and the consequences of these compounds to plankton communities.</p>
<p>The project will:<br />
1) Characterize the exudate metabolome among <em>K. brevis </em>samples of varying allelopathic potency. Exudates of <em>K. brevis </em>strains and natural bloom samples will be studied by mass spectrometry (MS) and nuclear magnetic resonance (NMR) metabolomics to pinpoint candidate chemical cues involved in competition. <em>Karenia brevis</em> protein expression will be examined by MS proteomics to test whether <em>K. brevis</em> up- or down-regulates key proteins involved in pathway networks in response to challenges by competitors.</p>
<p> 2) Seek to understand sub-lethal metabolic impacts of exposure to allelopathy on target phytoplankton, by studying responses of phytoplankton to <em>K. brevis </em>allelopathy by MS-based metabolomics and proteomics. This work will provide an unbiased approach to determining molecular targets of allelopathy and allow testing of whether sub-lethal responses to allelopathy include suppressed fundamental cellular functioning and up-regulated pathways related to stress and detoxification.</p>
<p> 3) Relate allelopathic sensitivity to metabolic responses in target phytoplankton, by comparing metabolomic and proteomic changes of sensitive versus resistant competitors to <em>K. brevis </em>allelopathy. The expectation is that more resistant species experience enhancement of detoxification pathways and more robust, unaffected cellular function relative to competitors most sensitive to allelopathy.</p>
<p> 4) Determine how estuarine and off-shore phytoplankton differ in their physiological responses to allelopathy, because allelopathy may be more important for maintaining dense blooms in near-shore waters than in the initiation of blooms off-shore.</p>
<p>Phytoplankton blooms can be devastating to local economies and pose human health risks. The discovery of new chemically mediated interactions and metabolic responses in the marine plankton could eventually lead to prediction and control strategies to alleviate the harmful consequences of these blooms. Continued effort to characterize mixtures of allelopathic compounds and determine their effects on competing species could lead to biodegradable treatments for reducing phytoplankton or microbial growth in aquatic and terrestrial environments. This study builds on past successes, applying lessons learned from chemistry about ecological processes and using ecological insights to discover unique natural products with important biological functions.</p>
Plankton Chemical Cues
largerWorkCitation
project
eng; USA
biota
oceans
2017-03-20
Gulf of Mexico
0
BCO-DMO catalogue of parameters from NMR-based polar metabolomics on diatom response to allelopathic chemicals from the red tide dinoflagellate (Karenia brevis)
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
37597368
https://datadocs.bco-dmo.org/file/qAW8RpPi1jPQ0W/archived_spectra_0.zip
archived_spectra_0.zip
download
2283
https://datadocs.bco-dmo.org/file/N7o1DKPhM14BAV/readme_archivedspectra.txt
readme_archivedspectra.txt
download
https://osprey.bco-dmo.org/dataset/731159/data/download
download
onLine
dataset
<p>Please see supporting information file associated with publication:<br />
Poulson-Ellestad, Jones, Roy, Viant, Fernandez, Kubanek, Nunn (2014) Metabolomics and proteomics reveal impacts of chemically mediated competition on marine plankton. Proc. Natl. Acad. Sci. USA 111:9009-9014. doi:<a href="http://dx.doi.org/10.1073/pnas.1402130111" target="_blank">10.1073/pnas.1402130111</a></p>
<p>Spectra were collected on a Bruker Avance 500-MHz DRX NMR spectrometer equipped with a 5-mm broadband direct probe, with an excitation-sculpting gradient pulse program for water suppression as follows: 11-μs (90°) pulse, 22-μs (180°) pulse, and 2-ms (108°) shaped pulse (5). The spectral width was 5.5 kHz, with a relaxation delay of 1 s. For each sample, 256 scans were compiled to gather adequate signal for analysis.</p>
Specified by the Principal Investigator(s)
<p>Spectra were imported into MATLAB, version 7.12.0, and preprocessing was performed in NMRLab (6) and ProMetab 3.3 (7). Spectra were aligned to the chemical shift of the internal standard (TMSP) at 0.00 ppm, manually phased, and baseline corrected. Spectral regions around TMSP (−0.5 to 0.5 ppm), water (4.6–5.0 ppm for A. glacialis; 4.0–4.9 ppm for T. pseudonana), and residual methanol (3.3–3.5 ppm) were removed before noise filtering. For the A. glacialis experiment only in which a small number of K. brevis cells escaped from the dialysis tubing, we removed signals caused by K. brevis cell contamination (identified by their presence in K. brevis blank culture extracts), to not confound intracellular K. brevis and T. pseudonana metabolites. These regions included the following: 1.41–1.42, 2.65– 2.67, 2.93–2.95, 2.98–3.02, and 4.15–4.40 ppm. Spectra were then binned (0.005 ppm), probabilistic quotient normalized (8) to account for slight differential dilution among samples, generalized log (glog) transformed to account for variance among signals within each sample reducing bias toward highly concentrated metabolites, and mean centered. The lambda values for glog optimization were obtained using a set of five quality control extracts generated with the above methods from a single large batch culture of each diatom species (9). The λ value for T. pseudonana was 9.8068 × 10−8, whereas a λ value of 5.7289 × 10−9 was used for A. glacialis samples.</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Bruker Avance 500-MHz DRX NMR spectrometer
Bruker Avance 500-MHz DRX NMR spectrometer
PI Supplied Instrument Name: Bruker Avance 500-MHz DRX NMR spectrometer Instrument Name: Nuclear Magnetic Resonance Spectrometers Instrument Short Name:NMR Instrument Description: Instruments that identify and quantify magnetically active chemical entities by subjecting a sample to orthogonal magnetic and electrical fields. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB18/