http://lod.bco-dmo.org/id/dataset/537359
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
2014-11-04
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
MS-based polar metabolomics on diatom response to allelopathic chemicals from red tide dinoflagellate (Karenia brevis)
2018-03-21
publication
2018-03-21
revision
BCO-DMO Linked Data URI
2018-03-21
creation
http://lod.bco-dmo.org/id/dataset/537359
Julia Kubanek
Georgia Institute of Technology
principalInvestigator
Facundo Fernandez
Georgia Institute of Technology
principalInvestigator
Brook L. Nunn
University of Washington
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., Nunn, B. L., Fernandez, F. (2018) MS-based polar metabolomics on diatom response to allelopathic chemicals from red tide dinoflagellate (Karenia brevis). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 21 March 2018) Version Date 2018-03-21 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/537359 [access date]
MS-based polar metabolomics on diatom response to allelopathic chemicals from red tide dinoflagellate (Karenia brevis) Dataset Description: <p>These mass spec data files are in Thermo-Finnigan .raw format. Vendor software can be used to view these files, and there are free viewers that can also be used (one example is&nbsp;<a href="http://compbio.cs.princeton.edu/pview/" target="_blank">PVIEW</a>). The files can also be converted to mzXML files using MSconvert.</p>
<p>Note: Data files in .raw format are also&nbsp;available from the Chorus repository (<a href="https://chorusproject.org/" target="_blank">https://chorusproject.org</a>) under project ID number 650 (project name: "Diatom response to allelopathy"), experiment ID number 848.&nbsp;See:&nbsp;<a href="https://chorusproject.org/anonymous/download/experiment/8464697144662088343" target="_blank">https://chorusproject.org/anonymous/download/experiment/8464697144662088343</a></p> Methods and Sampling: <p>Field assemblages of plankton were sampled during two cruises (EN496 and EN509), and shipboard experiments were conducted to test the community-level effects of <em>Karenia brevis</em> allelopathy on Gulf of Mexico plankton. The sampling and shipboard experiments are described fully in:<br />
Poulson-Ellestad et al. 2014. Are offshore phytoplankton susceptible to Karenia brevis allelopathy? J. Plankton Res. 36:1344-1356. doi: <a href="http://dx.doi.org/10.1093/plankt/fbu064" target="_blank">10.1093/plankt/fbu064</a></p>
<p>See related publication:<br />
Poulson-Ellestad, K.L., Jones, C.M., Roy, J., Viant, M.R., Fernandez, F.M., Kubanek, J., &amp; Nunn, B.L. 2014. Metabolomics and proteomics reveal impacts of chemically mediated competition on marine plankton. PNAS Proc Natl Acad Sci USA, 111(24): 9009-14. doi:<a href="http://dx.doi.org/10.1073/pnas.1402130111" target="_blank">10.1073/pnas.1402130111</a></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
Facundo Fernandez
Georgia Institute of Technology
404-385-4432
School of Chemistry & Biochemistry; Georgia Institute of Technology
Atlanta
GA
30332-0400
USA
Facundo.fernandez@chemistry.gatech.edu
pointOfContact
Brook L. Nunn
University of Washington
206-616-9023
Department of Genome Sciences, Foege Building S113 3720 15th Ave NE
Seattle
WA
98195
USA
brookh@uw.edu
pointOfContact
asNeeded
Dataset Version: 21 March 2018
Unknown
Xevo G2 QTOF Mass Spectrometer
theme
None, User defined
Mass Spectrometer
instrument
BCO-DMO Standard Instruments
EN496
EN509
service
Deployment Activity
Gulf of Mexico
place
Locations
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
Gulf of Mexico
2018-03-21
Gulf of Mexico
0
BCO-DMO catalogue of parameters from MS-based polar metabolomics on diatom response to allelopathic chemicals from 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
4000185972
https://datadocs.bco-dmo.org/file/KAlQAMks8WZNNm/MS-based_polar_metabolomics_on_diatom_response.zip
MS-based_polar_metabolomics_on_diatom_response.zip
download
https://osprey.bco-dmo.org/dataset/537359/data/download
download
onLine
dataset
<p>Field assemblages of plankton were sampled during two cruises (EN496 and EN509), and shipboard experiments were conducted to test the community-level effects of <em>Karenia brevis</em> allelopathy on Gulf of Mexico plankton. The sampling and shipboard experiments are described fully in:<br />
Poulson-Ellestad et al. 2014. Are offshore phytoplankton susceptible to Karenia brevis allelopathy? J. Plankton Res. 36:1344-1356. doi: <a href="http://dx.doi.org/10.1093/plankt/fbu064" target="_blank">10.1093/plankt/fbu064</a></p>
<p>See related publication:<br />
Poulson-Ellestad, K.L., Jones, C.M., Roy, J., Viant, M.R., Fernandez, F.M., Kubanek, J., &amp; Nunn, B.L. 2014. Metabolomics and proteomics reveal impacts of chemically mediated competition on marine plankton. PNAS Proc Natl Acad Sci USA, 111(24): 9009-14. doi:<a href="http://dx.doi.org/10.1073/pnas.1402130111" target="_blank">10.1073/pnas.1402130111</a></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
Xevo G2 QTOF Mass Spectrometer
Xevo G2 QTOF Mass Spectrometer
PI Supplied Instrument Name: Xevo G2 QTOF Mass Spectrometer PI Supplied Instrument Description:A Xevo G2 QTOF Mass Spectrometer was used. Instrument Name: Mass Spectrometer Instrument Short Name:Mass Spec Instrument Description: General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/
Cruise: EN496
EN496
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN496
Joseph Montoya
Georgia Institute of Technology
Cruise: EN509
EN509
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN509
Joseph Montoya
Georgia Institute of Technology
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel