http://lod.bco-dmo.org/id/dataset/720697
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
2017-12-11
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
NMR spectral files from study of metabolomics of blue crab urine inducing fear in prey
2017-12-19
publication
2017-12-19
revision
BCO-DMO Linked Data URI
2017-12-19
creation
http://lod.bco-dmo.org/id/dataset/720697
Marc Weissburg
Georgia Institute of Technology
principalInvestigator
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: Weissburg, M., Kubanek, J. (2017) NMR spectral files from study of metabolomics of blue crab urine inducing fear in prey. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 19 December 2017) Version Date 2017-12-19 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/720697 [access date]
NMR spectral files from study of metabolomics of blue crab urine inducing fear in prey Dataset Description: <p>This dataset includes the following files, packaged in a&nbsp;.zip file:</p>
<ul>
<li>archived_pca_spectra.zip =&nbsp;unprocessed&nbsp;<sup>1</sup>H NMR spectral data files&nbsp;underlying PCA analysis&nbsp;in the publication "Chemical encoding of risk perception and predator detection among estuarine invertebrates."</li>
<li>archived_pls-r_spectra.zip =&nbsp;unprocessed <sup>1</sup>H NMR spectral data files underlying PLS-R analysis in the publication "Chemical encoding of risk perception and predator detection among estuarine invertebrates."</li>
<li>README_ArchivedSpectraDataset (1).doc = readme file describing the files.</li>
<li>spectral_labels_for_pls-r_dataset.xlsx = spreadsheet containing spectral labels.</li>
</ul>
<p>Poulin et al (2018) contains the analyses of the processed data. These NMR data files are also available from the Georgia Tech database, SMARTech at&nbsp;<a href="http://hdl.handle.net/1853/59056" target="_blank">http://hdl.handle.net/1853/59056</a></p> Methods and Sampling: <p>1H NMR spectra were processed in MATLAB, version 8.1.0.604, using NMRLab. Spectra were manually phased, baseline corrected, aligned, and the following regions excluded to remove contaminants from statistical analysis: TMSP (-0.5 to 0.5 ppm), water (4.6-5.2 ppm), residual methanol (3.2-3.4 ppm), and excess area (9.0-12.4 ppm) that contained no spectroscopic features. Spectroscopic features were clustered into 0.005 ppm bins, probabilistic quotient normalized to remove dilution bias, and generalized log (glog) transformed to avoid bias towards high concentration metabolites without affecting between-sample variation. Glog optimization values, λ, were generated from five technical replicates that consisted of equal parts from a single bulk urine sample using the methods above. For urine samples collected at Skidaway Institute of Oceanography, λ = 2.9359×10-7 and for urine samples at Georgia Tech λ = 8.2585×10-9.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1234449 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1234449
completed
Marc Weissburg
Georgia Institute of Technology
404-894-8433
School of Biological Sciences Georgia Institute of Technology
Atlanta
GA
30332-0230
USA
marc.weissburg@biology.gatech.edu
pointOfContact
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: 19 December 2017
Unknown
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.
The role of the sensory environment and predator chemical signal properties in determining NCE strength in cascading interactions on oyster reefs
https://osprey.bco-dmo.org/project/565703
The role of the sensory environment and predator chemical signal properties in determining NCE strength in cascading interactions on oyster reefs
<p><em>Extracted from the NSF award abstract:</em></p>
<p>In this project, the investigators will examine the ability of top blue crab predators to indirectly benefit the abundance of basal oyster prey by reducing the density (consumptive effects, CEs) and suppressing foraging (non-consumptive effects, NCEs) of intermediate mud crab predators. These NCEs are mediated by chemical perception of aversive cues in blue crab urine and produce a behaviorally mediated trophic cascade. Through a series of manipulative experiments, the investigators will examine how the strength of this behaviorally-mediated trophic cascade is modulated and factors that influence perceptive range such as predator diet and intake rate, and the flow environment. The investigators will also determine the chemical identity, concentration and release rate of chemical cues.</p>
<p>Identifying the quantitative and molecular aspects of aversive cues, and linking them to behavioral responses that produce trophic cascades establishes the chemical basis of risk perception by prey and how this translates into cascading ecological effects. The use of perceptive range as a framework for evaluating the effects of both chemistry and environment provides an integrated view of processes affecting chemically-mediated NCEs. The use of a water borne predator-prey signaling system to test ideas on the strength of NCEs should have broad applications.</p>
SensoryNCE
largerWorkCitation
project
eng; USA
oceans
2017-12-19
Intertidal and subtidal oyster reefs in Wassaw Sound, Georgia, US
0
BCO-DMO catalogue of parameters from NMR spectral files from study of metabolomics of blue crab urine inducing fear in prey
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
17362671
https://datadocs.bco-dmo.org/file/rgWgMrmhA9O0Lv/NMR_Data_Blue_Crab_from_GATech.zip
NMR_Data_Blue_Crab_from_GATech.zip
unprocessed NMR spectral files
download
https://osprey.bco-dmo.org/dataset/720697/data/download
download
onLine
dataset
<p>1H NMR spectra were processed in MATLAB, version 8.1.0.604, using NMRLab. Spectra were manually phased, baseline corrected, aligned, and the following regions excluded to remove contaminants from statistical analysis: TMSP (-0.5 to 0.5 ppm), water (4.6-5.2 ppm), residual methanol (3.2-3.4 ppm), and excess area (9.0-12.4 ppm) that contained no spectroscopic features. Spectroscopic features were clustered into 0.005 ppm bins, probabilistic quotient normalized to remove dilution bias, and generalized log (glog) transformed to avoid bias towards high concentration metabolites without affecting between-sample variation. Glog optimization values, λ, were generated from five technical replicates that consisted of equal parts from a single bulk urine sample using the methods above. For urine samples collected at Skidaway Institute of Oceanography, λ = 2.9359×10-7 and for urine samples at Georgia Tech λ = 8.2585×10-9.</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
PI Supplied Instrument Name: 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/