http://lod.bco-dmo.org/id/dataset/640505
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
2016-03-14
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Inhibition data for 3 peptidases at Bogue Sound NC and Tennessee River at Knoxville (SEDpep project)
2016-03-14
publication
2016-03-14
revision
BCO-DMO Linked Data URI
2016-03-14
creation
http://lod.bco-dmo.org/id/dataset/640505
Andrew Steen
University of Tennessee Knoxville
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: Steen, A. (2016) Inhibition data for 3 peptidases at Bogue Sound NC and Tennessee River at Knoxville (SEDpep project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 14 March 2016) Version Date 2016-03-14 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/640505 [access date]
Inhibition data for 3 peptidases at Bogue Sound NC and Tennessee River at Knoxville. Dataset Description: <p>Inhibition data for 3 peptidases at Bogue Sound NC and Tennessee River at Knoxville.</p> Methods and Sampling: <p>Inhibition parameters were measured from vo of Arg-AMC, Leu-AMC, and Pro-AMC, as a function of the concentration of various pNA inhibitors, as described in Steen et al (2015) (doi:<a href="http://dx.doi.org/10.3354/ame01755" target="_blank">10.3354/ame01755</a>)</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0939564 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0939564
onGoing
Andrew Steen
University of Tennessee Knoxville
865-456 0851
Department of Earth and Planetary Sciences 1412 Circle Drive
Knoxville
TN
37996-1410
USA
asteen1@utk.edu
pointOfContact
asNeeded
Dataset Version: 14 March 2016
Unknown
amino_acid
AA_abbrev
delta_Gr
pNA_subs
polarity
hydrophobicity
MW
Dauwe_score1
Dauwe_score2
location
substrate
inhib_slope
inhib_slope_SE
rsq
pval
is_homologous
rel_Ki
rel_Ki_SE
low_err
high_err
theme
None, User defined
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
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.
Center for Dark Energy Biosphere Investigations
http://www.darkenergybiosphere.org
Center for Dark Energy Biosphere Investigations
The mission of the Center for Dark Energy Biosphere Investigations (C-DEBI) is to explore life beneath the seafloor and make transformative discoveries that advance science, benefit society, and inspire people of all ages and origins.
C-DEBI provides a framework for a large, multi-disciplinary group of scientists to pursue fundamental questions about life deep in the sub-surface environment of Earth. The fundamental science questions of C-DEBI involve exploration and discovery, uncovering the processes that constrain the sub-surface biosphere below the oceans, and implications to the Earth system. What type of life exists in this deep biosphere, how much, and how is it distributed and dispersed? What are the physical-chemical conditions that promote or limit life? What are the important oxidation-reduction processes and are they unique or important to humankind? How does this biosphere influence global energy and material cycles, particularly the carbon cycle? Finally, can we discern how such life evolved in geological settings beneath the ocean floor, and how this might relate to ideas about the origin of life on our planet?
C-DEBI's scientific goals are pursued with a combination of approaches:
(1) coordinate, integrate, support, and extend the research associated with four major programs—Juan de Fuca Ridge flank (JdF), South Pacific Gyre (SPG), North Pond (NP), and Dorado Outcrop (DO)—and other field sites;
(2) make substantial investments of resources to support field, laboratory, analytical, and modeling studies of the deep subseafloor ecosystems;
(3) facilitate and encourage synthesis and thematic understanding of submarine microbiological processes, through funding of scientific and technical activities, coordination and hosting of meetings and workshops, and support of (mostly junior) researchers and graduate students; and
(4) entrain, educate, inspire, and mentor an interdisciplinary community of researchers and educators, with an emphasis on undergraduate and graduate students and early-career scientists.
Note: Katrina Edwards was a former PI of C-DEBI; James Cowen is a former co-PI.
Data Management:
C-DEBI is committed to ensuring all the data generated are publically available and deposited in a data repository for long-term storage as stated in their Data Management Plan (PDF) and in compliance with the NSF Ocean Sciences Sample and Data Policy. The data types and products resulting from C-DEBI-supported research include a wide variety of geophysical, geological, geochemical, and biological information, in addition to education and outreach materials, technical documents, and samples. All data and information generated by C-DEBI-supported research projects are required to be made publically available either following publication of research results or within two (2) years of data generation.
To ensure preservation and dissemination of the diverse data-types generated, C-DEBI researchers are working with BCO-DMO Data Managers make data publicly available online. The partnership with BCO-DMO helps ensure that the C-DEBI data are discoverable and available for reuse. Some C-DEBI data is better served by specialized repositories (NCBI's GenBank for sequence data, for example) and, in those cases, BCO-DMO provides dataset documentation (metadata) that includes links to those external repositories.
C-DEBI
largerWorkCitation
program
Novel peptidases in subsurface sediments: Activities and substrate specificities
https://osprey.bco-dmo.org/project/636401
Novel peptidases in subsurface sediments: Activities and substrate specificities
<p><em>Description from <a href="http://www.darkenergybiosphere.org/research/proposalsFunded.html" target="_blank">C-DEBI</a>:</em><br />
The goal of this project was to explore the mechanisms of subsurface organoheterotrophy by identifying the range of extracellular peptidases present in sediments of the White Oak River, NC, consistent with C-DEBI Research Theme 1, Activity in the Deep Subseafloor Biosphere: function & rates of global biogeochemical processes. This grant funded two sampling expeditions to the White Oak River as well as extensive laboratory work with a purified peptidase that was supplied by collaborators Andrzej Joachimiak and Karolina Michalska of Argonne National Laboratory and preparatory work on peptidases of the Tennessee River. So far this dataset has led to the submission of two manuscripts, with one more manuscript in preparation. The White Oak River work showed that a wide range of peptidases are present in depths up to 80 cm in the White Oak River, which is deeper than the zone of methanogenesis. Although absolute peptidase activities declined with depth, activities normalized to cell abundance were roughly constant, and activities normalized to organic carbon oxidation rates increased nearly two orders of magnitude relative to the surface, indicating that extracellular peptidases were important to the subsurface ecosystem. Biochemical analysis of a purified peptidase that was expressed by the Argonne group showed it to be a novel aminopeptidase with specificity for N-terminal cysteine, a function not previously observed in peptidses. In summary, <em>in situ</em> and <em>in vitro</em> studies of subsurface peptidases revealed that they are ecologically important and may contain novel properties.</p>
SEDpep
largerWorkCitation
project
eng; USA
oceans
2016-03-14
White Oak River Station H, (34 44.490'N, 77 07.44W); Tennessee River at Knoxville TN (Volunteer Landing Dock), and Bogue Sound at the Institute of Marine Sciences dock, Morehead City, NC.
0
BCO-DMO catalogue of parameters from Inhibition data for 3 peptidases at Bogue Sound NC and Tennessee River at Knoxville (SEDpep 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
http://lod.bco-dmo.org/id/dataset-parameter/640587.rdf
Name: amino_acid
Units: dimensionless
Description: <p>Amino acid.</p>
http://lod.bco-dmo.org/id/dataset-parameter/640588.rdf
Name: AA_abbrev
Units: dimensionless
Description: <p>Single-letter amino acid abbreviation.</p>
http://lod.bco-dmo.org/id/dataset-parameter/640589.rdf
Name: delta_Gr
Units: ?
Description: <p>?</p>
http://lod.bco-dmo.org/id/dataset-parameter/640590.rdf
Name: pNA_subs
Units: ?
Description: <p>?</p>
http://lod.bco-dmo.org/id/dataset-parameter/640591.rdf
Name: polarity
Units: dimensionless
Description: <p>Description of polarity.</p>
http://lod.bco-dmo.org/id/dataset-parameter/640592.rdf
Name: hydrophobicity
Units: ?
Description: <p>Hydrophobicity.</p>
http://lod.bco-dmo.org/id/dataset-parameter/640593.rdf
Name: MW
Units: grams per mole
Description: <p>Molecular weight of the amino acid.</p>
http://lod.bco-dmo.org/id/dataset-parameter/640594.rdf
Name: Dauwe_score1
Units: ?
Description: <p>?</p>
http://lod.bco-dmo.org/id/dataset-parameter/640595.rdf
Name: Dauwe_score2
Units: ?
Description: <p>?</p>
http://lod.bco-dmo.org/id/dataset-parameter/640596.rdf
Name: location
Units: dimensionless
Description: <p>Sampling location.</p>
http://lod.bco-dmo.org/id/dataset-parameter/640597.rdf
Name: substrate
Units: dimensionless
Description: <p>Substrate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/640598.rdf
Name: inhib_slope
Units: ?
Description: <p>Inhibition slope.</p>
http://lod.bco-dmo.org/id/dataset-parameter/640599.rdf
Name: inhib_slope_SE
Units: ?
Description: <p>Standard error of inhibition slope.</p>
http://lod.bco-dmo.org/id/dataset-parameter/640600.rdf
Name: rsq
Units: ?
Description: <p>?</p>
http://lod.bco-dmo.org/id/dataset-parameter/640601.rdf
Name: pval
Units: ?
Description: <p>?</p>
http://lod.bco-dmo.org/id/dataset-parameter/640602.rdf
Name: is_homologous
Units: dimensionless
Description: <p>?</p>
http://lod.bco-dmo.org/id/dataset-parameter/640603.rdf
Name: rel_Ki
Units: ?
Description: <p>Inhibition binding constant, Ki. Given relative to the homologous pNA substrate, as described in Steen et al. (2015).</p>
http://lod.bco-dmo.org/id/dataset-parameter/640604.rdf
Name: rel_Ki_SE
Units: ?
Description: <p>Standard error of inhibition binding constant, Ki. Given relative to the homologous pNA substrate, as described in Steen et al. (2015).</p>
http://lod.bco-dmo.org/id/dataset-parameter/640605.rdf
Name: low_err
Units: ?
Description: <p>?</p>
http://lod.bco-dmo.org/id/dataset-parameter/640606.rdf
Name: high_err
Units: ?
Description: <p>?</p>
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
13968
https://datadocs.bco-dmo.org/file/0AAMnlrfY24APL/TN-BS_water_inhibition.csv
TN-BS_water_inhibition.csv
Primary data file for dataset ID 640505
download
https://osprey.bco-dmo.org/dataset/640505/data/download
download
onLine
dataset
<p>Inhibition parameters were measured from vo of Arg-AMC, Leu-AMC, and Pro-AMC, as a function of the concentration of various pNA inhibitors, as described in Steen et al (2015) (doi:<a href="http://dx.doi.org/10.3354/ame01755" target="_blank">10.3354/ame01755</a>)</p>
Specified by the Principal Investigator(s)
<p>Data processing is described in more detail in the Steen et al. (2015) paper (doi:<a href="http://dx.doi.org/10.3354/ame01755" target="_blank">10.3354/ame01755</a>). Full R code and all raw data is given at <a href="http://github.com/adsteen/subspec" target="_blank">http://github.com/adsteen/subspec</a>.</p>
<p>BCO-DMO processing:<br />
- modified parameter names to conform with BCO-DMO naming conventions;<br />
- replaced "NA" with "nd" (no data).</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